Use of slow filtration columns to assess oxygen respiration, consumption of dissolved organic carbon, nitrogen transformations, and microbial parameters in hyporheic sediments.

PubMed

Mermillod-Blondin, F; Mauclaire, L; Montuelle, B

2005-05-01

Biogeochemical processes mediated by microorganisms in river sediments (hyporheic sediments) play a key role in river metabolism. Because biogeochemical reactions in the hyporheic zone are often limited to the top few decimetres of sediments below the water-sediment interface, slow filtration columns were used in the present study to quantify biogeochemical processes (uptakes of O2, DOC, and nitrate) and the associated microbial compartment (biomass, respiratory activity, and hydrolytic activity) at a centimetre scale in heterogeneous (gravel and sand) sediments. The results indicated that slow filtration columns recreated properly the aerobic-anaerobic gradient classically observed in the hyporheic zone. O2 and NO3- consumptions (256 +/- 13 microg of O2 per hour and 14.6 +/- 6.1 microg of N-NO3- per hour) measured in columns were in the range of values measured in different river sediments. Slow filtration columns also reproduced the high heterogeneity of the hyporheic zone with the presence of anaerobic pockets in sediments where denitrification and fermentation processes occurred. The respiratory and hydrolytic activities of bacteria were strongly linked with the O2 consumption in the experimental system, highlighting the dominance of aerobic processes in our river sediments. In comparison with these activities, the bacterial biomass (protein content) integrated both aerobic and anaerobic processes and could be used as a global microbial indicator in our system. Finally, slow filtration columns are an appropriate tool to quantify in situ rates of biogeochemical processes and to determine the relationship between the microbial compartment and the physico-chemical environment in coarse river sediments.

Microbial transformations of arsenic: Mobilization from glauconitic sediments to water

USGS Publications Warehouse

Mumford, Adam C.; Barringer, Julia L.; Benzel, William M.; Reilly, Pamela A.; Young, L.Y.

2012-01-01

In the Inner Coastal Plain of New Jersey, arsenic (As) is released from glauconitic sediment to carbon- and nutrient-rich shallow groundwater. This As-rich groundwater discharges to a major area stream. We hypothesize that microbes play an active role in the mobilization of As from glauconitic subsurface sediments into groundwater in the Inner Coastal Plain of New Jersey. We have examined the potential impact of microbial activity on the mobilization of arsenic from subsurface sediments into the groundwater at a site on Crosswicks Creek in southern New Jersey. The As contents of sediments 33–90 cm below the streambed were found to range from 15 to 26.4 mg/kg, with siderite forming at depth. Groundwater beneath the streambed contains As at concentrations up to 89 μg/L. Microcosms developed from site sediments released 23 μg/L of As, and active microbial reduction of As(V) was observed in microcosms developed from site groundwater. DNA extracted from site sediments was amplified with primers for the 16S rRNA gene and the arsenate respiratory reductase gene, arrA, and indicated the presence of a diverse anaerobic microbial community, as well as the presence of potential arsenic-reducing bacteria. In addition, high iron (Fe) concentrations in groundwater and the presence of iron-reducing microbial genera suggests that Fe reduction in minerals may provide an additional mechanism for release of associated As, while arsenic-reducing microorganisms may serve to enhance the mobility of As in groundwater at this site.

Succession in a microbial mat community: A gaian perspective

NASA Astrophysics Data System (ADS)

Stolz, J. F.

The Gaia hypothesis originally proposed by James E. Lovelock states that the composition, oxidation-reduction state and temperature of the troposphere are actively regulated by the activities of the biota. The gaian concept has been extrapolated to include the composition of surface sediments through the process of biomineralization. The stratified microbial community dominated by the cyanobacterium Microcoleus chthonoplastes is actively involved in the deposition of laminated sediments at Laguna Figueroa, Baja California, Mexico. Unusually heavy rains in the winters of 1979 and 1980 flooded the evaporite flat with up to 3 meters of meteoric water and deposited 5 - 10 cm of allocthonous sediment. The composition of the microbial community changed as a succession of dominating microbial species ensued, ultimately leading to the recolonization of the surface sediment by the original Microcoleus-dominated community. The resiliency of bacterial communities is suggested to be an important mechanism of gaian control systems. Present address: Control and Energy Conversion Division, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, U.S.A.

Effect of nutrient amendments on indigenous hydrocarbon biodegradation in oil-contaminated beach sediments.

PubMed

Xu, Ran; Obbard, Jeffrey P

2003-01-01

Nutrient amendment to oil-contaminated beach sediments is a critical factor for the enhancement of indigenous microbial activity and biodegradation of petroleum hydrocarbons in the intertidal marine environment. In this study, we investigated the stimulatory effect of the slow-release fertilizers Osmocote (Os; Scotts, Marysville, OH) and Inipol EAP-22 (Ip; ATOFINA Chemicals, Philadelphia, PA) combined with inorganic nutrients on the bioremediation of oil-spiked beach sediments using an open irrigation system with artificial seawater over a 45-d period. Osmocote is comprised of a semipermeable membrane surrounding water-soluble inorganic N, P, and K. Inipol, which contains organic N and P, has been used for oil cleanup on beach substrate. Nutrient concentrations and microbial activity in sediments were monitored by analyzing sediment leachates and metabolic dehydrogenase activity of the microbial biomass, respectively. Loss of aliphatics (n-C12 to n-C33, pristane, and phytane) was significantly greater (total loss between 95 and 97%) in oil-spiked sediments treated with Os alone or in combination with other nutrient amendments, compared with an unamended oil-spiked control (26% loss) or sediments treated with the other nutrient amendments (28-65% loss). A combination of Os and soluble nutrients (SN) was favorable for the rapid metabolic stimulation of the indigenous microbial biomass, the sustained release of nutrients, and the enhanced biodegradation of petroleum hydrocarbons in leached, oil-contaminated sediments.

Archaeal populations in hypersaline sediments underlying orange microbial mats in the Napoli mud volcano.

PubMed

Lazar, Cassandre Sara; L'haridon, Stéphane; Pignet, Patricia; Toffin, Laurent

2011-05-01

Microbial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. Hence, they could be visible indicators of anaerobic oxidation of methane (AOM) and methane cycling processes in underlying sediments. The Napoli mud volcano is situated in the Olimpi Area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor. Sediments associated with a brine pool and microbial orange mats of the Napoli mud volcano were recovered during the Medeco cruise. Based on analysis of RNA-derived sequences, the "active" archaeal community was composed of many uncultured lineages, such as rice cluster V or marine benthic group D. Function methyl coenzyme M reductase (mcrA) genes were affiliated with the anaerobic methanotrophic Archaea (ANME) of the ANME-1, ANME-2a, and ANME-2c groups, suggesting that AOM occurred in these sediment layers. Enrichment cultures showed the presence of viable marine methylotrophic Methanococcoides in shallow sediment layers. Thus, the archaeal community diversity seems to show that active methane cycling took place in the hypersaline microbial mat-associated sediments of the Napoli mud volcano.

Microbial respiration and extracellular enzyme activity in sediments from the Gulf of Mexico hypoxic zone

EPA Science Inventory

This study explores the relationship between sediment chemistry (TC, TN, TP) and microbial respiration (DHA) and extracellular enzyme activity (EEA) across the Gulf of Mexico (GOM) hypoxic zone. TC, TN, and TP were all positively correlated with each other (r=0.19-0.68). DHA was ...

Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes

PubMed Central

Yanagawa, Katsunori; Morono, Yuki; de Beer, Dirk; Haeckel, Matthias; Sunamura, Michinari; Futagami, Taiki; Hoshino, Tatsuhiko; Terada, Takeshi; Nakamura, Ko-ichi; Urabe, Tetsuro; Rehder, Gregor; Boetius, Antje; Inagaki, Fumio

2013-01-01

Sediment-hosting hydrothermal systems in the Okinawa Trough maintain a large amount of liquid, supercritical and hydrate phases of CO2 in the seabed. The emission of CO2 may critically impact the geochemical, geophysical and ecological characteristics of the deep-sea sedimentary environment. So far it remains unclear whether microbial communities that have been detected in such high-CO2 and low-pH habitats are metabolically active, and if so, what the biogeochemical and ecological consequences for the environment are. In this study, RNA-based molecular approaches and radioactive tracer-based respiration rate assays were combined to study the density, diversity and metabolic activity of microbial communities in CO2-seep sediment at the Yonaguni Knoll IV hydrothermal field of the southern Okinawa Trough. In general, the number of microbes decreased sharply with increasing sediment depth and CO2 concentration. Phylogenetic analyses of community structure using reverse-transcribed 16S ribosomal RNA showed that the active microbial community became less diverse with increasing sediment depth and CO2 concentration, indicating that microbial activity and community structure are sensitive to CO2 venting. Analyses of RNA-based pyrosequences and catalyzed reporter deposition-fluorescence in situ hybridization data revealed that members of the SEEP-SRB2 group within the Deltaproteobacteria and anaerobic methanotrophic archaea (ANME-2a and -2c) were confined to the top seafloor, and active archaea were not detected in deeper sediments (13–30 cm in depth) characterized by high CO2. Measurement of the potential sulfate reduction rate at pH conditions of 3–9 with and without methane in the headspace indicated that acidophilic sulfate reduction possibly occurs in the presence of methane, even at very low pH of 3. These results suggest that some members of the anaerobic methanotrophs and sulfate reducers can adapt to the CO2-seep sedimentary environment; however, CO2 and pH in the deep-sea sediment were found to severely impact the activity and structure of the microbial community. PMID:23096400

Deep sea microbial fuel cell output as a proxy for microbial activity

NASA Astrophysics Data System (ADS)

Richter, K.; George, R.; Hardy, K. R.

2016-02-01

Abstract: Microbial fuel cells (MFCs) work by providing bacteria in anaerobic sediments with an electron acceptor (anode) that stimulates metabolism of organic matter. The buried anode is connected via control circuitry to a cathode exposed to oxygen in the overlying water. During metabolism, bacteria release hydrogen ions into the sediment and transfer electrons extra-cellularly to the anode, which eventually reduce dissolved oxygen at the cathode, forming water. The current is chiefly limited by the rate of microbial metabolism at the anode and serves as a proxy for microbial activity. The Office of Naval Research has encouraged development of microbial fuel cells in the marine environment at a number of academic and naval institutions and studies of important environmental parameters that affect fuel cell performance. Earlier work in shallow sediments of San Diego Bay showed that the most important environmental parameters that control fuel cell power output in San Diego Bay were total organic carbon in the sediment and seasonal water temperature. Current MFC work at SPAWAR includes extension of microbial fuel cell tests to the deep sea environment (>4000 m) and, in parallel, testing microbial fuel cells in the laboratory under deep sea conditions. We are pursuing a field efforts to deploy a microbial fuel cell in progressively deeper water, record in situ power and temperature over several weeks, and retrieve the fuel cell along with sediment samples for analysis. We are also pursuing a laboratory effort to build a matching microbial fuel cell in a pressure vessel capable of matching the pressure and temperature of deep water, and stocking the pressure vessel with deep water sediment in order to take measurements analogous to those in the field. We also hope to determine whether bacteria growing on the anode are different from bacteria growing in the bulk sediment via DNA analysis. The current progress and results from this work at SPAWAR will be presented.

Microbial Breakdown of Organic Carbon in the Diverse Sediments of Guaymas Basin

NASA Astrophysics Data System (ADS)

Hoarfrost, A.; Snider, R.; Arnosti, C.

2015-12-01

Guaymas Basin is characterized by sediments under conditions ranging from hemipelagic to hydrothermal. This wide range in geochemical contexts results in diverse microbial communities that may have varying abilities to access organic matter. We can address these functional differences by comparing enzyme activities initializing the breakdown of organic matter across these sediment types; however, previous direct measurements of the extracellular hydrolysis of complex organic carbon in sediments are sparse. We measured this first step of heterotrophic processing of organic matter in sediments at 5-10cm and 55-60cm depth from a wide range of environmental settings in Guaymas Basin. Sediment sources included sulfidic seeps on the Sonora Margin, hemipelagic ridge flank sediments, and hydrothermically altered Sonora Margin sediments bordering a methane seep site. Hydrolysis of organic substrates varied by depth and by sediment source, but despite high energy potential and organic carbon load in sulfidic sediments, activity was not highest where hydrothermal influence was highest. These results suggest that heterotrophic breakdown of organic carbon in Guaymas Basin sediments may be sensitive to factors including varying composition of organic carbon available in different sediment types, or differences in microbial community capacities to access specific organic substrates.

Sediment Enzyme Activities and Microbial Community Diversity in an Oligotrophic Drinking Water Reservoir, Eastern China

PubMed Central

Zhang, Haihan; Huang, Tinglin; Liu, Tingting

2013-01-01

Drinking water reservoir plays a vital role in the security of urban water supply, yet little is known about microbial community diversity harbored in the sediment of this oligotrophic freshwater environmental ecosystem. In the present study, integrating community level physiological profiles (CLPPs), nested polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and clone sequence technologies, we examined the sediment urease and protease activities, bacterial community functional diversity, genetic diversity of bacterial and fungal communities in sediments from six sampling sites of Zhou cun drinking water reservoir, eastern China. The results showed that sediment urease activity was markedly distinct along the sites, ranged from 2.48 to 11.81 mg NH3-N/(g·24h). The highest average well color development (AWCD) was found in site C, indicating the highest metabolic activity of heterotrophic bacterial community. Principal component analysis (PCA) revealed tremendous differences in the functional (metabolic) diversity patterns of the sediment bacterial communities from different sites. Meanwhile, DGGE fingerprints also indicated spatial changes of genetic diversity of sediment bacterial and fungal communities. The sequence BLAST analysis of all the sediment samples found that Comamonas sp. was the dominant bacterial species harbored in site A. Alternaria alternate, Allomyces macrogynus and Rhizophydium sp. were most commonly detected fungal species in sediments of the Zhou cun drinking water reservoir. The results from this work provide new insights about the heterogeneity of sediment microbial community metabolic activity and genetic diversity in the oligotrophic drinking water reservoir. PMID:24205265

15N indicates an active N-cycling microbial community in low carbon, freshwater sediments.

NASA Astrophysics Data System (ADS)

Sheik, C.

2017-12-01

Earth's large lakes are unique aquatic ecosystems, but we know little of the microbial life driving sedimentary biogeochemical cycles and ultimately the isotopic record. In several of these large lakes, water column productivity is constrained by element limitation, such as phosphorus and iron, creating oligotrophic water column conditions that drive low organic matter content in sediments. Yet, these sediments are biogeochemically active and have been shown to have oxygen consumption rates akin to pelagic ocean sediments and complex sulfur cycling dynamics. Thus, large oligotrophic lakes provide unique and interesting biogeochemical contrast to highly productive freshwater and coastal marine systems. Using Lake Superior as our study site, we found microbial community structure followed patterns in bulk sediment carbon and nitrogen concentrations. These observed patterns were loosely driven by land proximity, as some stations are more coastal and have higher rates of sedimentation, allochthonous carbon inputs and productivity than pelagic sites. Interestingly, upper sediment carbon and nitrogen stable isotopes were quite different from water column. Sediment carbon and nitrogen isotopes correlated significantly with microbial community structure. However, 15N showed much stronger correlation than 13C, and became heavier with core depth. Coinciding with the increase in 15N values, we see evidence of both denitrification and anammox processes in 16S rRNA gene libraries and metagenome assembled genomes. Given that microorganisms prefer light isotopes and that these N-cycling processes both contribute to N2 production and efflux from the sediment, the increase in 15N with sediment depth suggests microbial turnover. Abundance of these genomes also varies with depth suggesting these novel microorganisms are partitioning into specific sediment geochemical zones. Additionally, several of these genomes contain genes involved in sulphur cycling, suggesting a dual biogeochemical role and potential for a cryptic sulfur cycle. Together, Lake Superior sediments offer a glimpse into microbial metabolism in carbon limited environments. Further the pervasiveness of co-metabolic pathways suggests interpretation of isotopic records may be messier than previously thought.

Periodic sediment shift in migrating ripples influences benthic microbial activity

NASA Astrophysics Data System (ADS)

Zlatanović, Sanja; Fabian, Jenny; Mendoza-Lera, Clara; Woodward, K. Benjamin; Premke, Katrin; Mutz, Michael

2017-06-01

Migrating bedforms have high levels of particulate organic matter and high rates of pore water exchange, causing them to be proposed as hot spots of carbon turnover in rivers. Yet, the shifting of sediments and associated mechanical disturbance within migrating bedforms, such as ripples, may stress and abrade microbial communities, reducing their activity. In a microcosm experiment, we replicated the mechanical disturbances caused by the periodic sediment shift within ripples under oligotrophic conditions. We assessed the effects on fungal and bacterial biomass ratio (F:B), microbial community respiration (CR), and bacterial production (BCP) and compared with stable undisturbed sediments. Interactions between periodic mechanical disturbance and sediment-associated particulate organic matter (POM) were tested by enriching sediments collected from migrating ripples with different qualities of POM (fish feces, leaf litter fragments and no addition treatments). F:B and BCP were affected by an interaction between mechanical disturbance and POM quality. Fish feces enriched sediments showed increased F:B and BCP compared to sediments with lower POM quality and responded with a decrease of F:B and BCP to sediment disturbance. In the other POM treatments F:B and BCP were not affected by disturbance. Microbial respiration was however reduced by mechanical disturbance to similar low activity levels regardless of POM qualities added, whereas fish feces enriched sediment showed short temporary boost of CR. With the worldwide proliferation of migrating sand ripples due to massive catchment erosion, suppressed mineralization of POM will increasingly affect stream metabolism, downstream transport of POM and carbon cycling from reach to catchment scale.

Spatial Structure and Activity of Sedimentary Microbial Communities Underlying a Beggiatoa spp. Mat in a Gulf of Mexico Hydrocarbon Seep

PubMed Central

Lloyd, Karen G.; Albert, Daniel B.; Biddle, Jennifer F.; Chanton, Jeffrey P.; Pizarro, Oscar; Teske, Andreas

2010-01-01

Background Subsurface fluids from deep-sea hydrocarbon seeps undergo methane- and sulfur-cycling microbial transformations near the sediment surface. Hydrocarbon seep habitats are naturally patchy, with a mosaic of active seep sediments and non-seep sediments. Microbial community shifts and changing activity patterns on small spatial scales from seep to non-seep sediment remain to be examined in a comprehensive habitat study. Methodology/Principal Findings We conducted a transect of biogeochemical measurements and gene expression related to methane- and sulfur-cycling at different sediment depths across a broad Beggiatoa spp. mat at Mississippi Canyon 118 (MC118) in the Gulf of Mexico. High process rates within the mat (∼400 cm and ∼10 cm from the mat's edge) contrasted with sharply diminished activity at ∼50 cm outside the mat, as shown by sulfate and methane concentration profiles, radiotracer rates of sulfate reduction and methane oxidation, and stable carbon isotopes. Likewise, 16S ribosomal rRNA, dsrAB (dissimilatory sulfite reductase) and mcrA (methyl coenzyme M reductase) mRNA transcripts of sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae) and methane-cycling archaea (ANME-1 and ANME-2) were prevalent at the sediment surface under the mat and at its edge. Outside the mat at the surface, 16S rRNA sequences indicated mostly aerobes commonly found in seawater. The seep-related communities persisted at 12–20 cm depth inside and outside the mat. 16S rRNA transcripts and V6-tags reveal that bacterial and archaeal diversity underneath the mat are similar to each other, in contrast to oxic or microoxic habitats that have higher bacterial diversity. Conclusions/Significance The visual patchiness of microbial mats reflects sharp discontinuities in microbial community structure and activity over sub-meter spatial scales; these discontinuities have to be taken into account in geochemical and microbiological inventories of seep environments. In contrast, 12–20 cm deep in the sediments microbial communities performing methane-cycling and sulfate reduction persist at lower metabolic rates regardless of mat cover, and may increase activity rapidly when subsurface flow changes. PMID:20090951

North Pond: a natural observatory for sub-seafloor oxidant supply and metabolic reactions

NASA Astrophysics Data System (ADS)

Ziebis, Wiebke; Ferdelman, Timothy; McManus, James; Muratli, Jesse; Picard, Aude; Schmidt-Schierhorn, Friederike; Stephan, Sebastian; Villinger, Heinrich; Edwards, Katrina J.

2010-05-01

Evidence of upward transport of oxidants from basaltic aquifers to deeply buried sediments has raised questions on microbial respiration and energy cycling within the deep biosphere. Sediment ponds that occur over a vast area of sea floor on the flank of the Mid-Atlantic Ridge maybe ideal observatories to study the role of unsuspected sources of oxidants for sub-seafloor microbial life. The western flank of the Mid-Atlantic Ridge, at 22°45'N is characterized by depressions filled with sediment and surrounded by high relief topography of 7 Ma old basement. The largest depressions are 5 km to 20 km wide and sediment thickness varies but can reach 400 m (Langseth et al. 1992). They are believed to overly recharge zones for the venting of fluids that takes place locally through unsedimented young ocean crust. If we consider the sediments as boundaries overlying the hydrologically active crustal environment, then using profiles of bioactive compounds measured through the sediment layer with the goal to extract information on transport and reactions is an obvious approach to understanding the implications of subsurface transport of oxidants on metabolic activity. Recently obtained deep oxygen profiles obtained during a site survey expedition in February/March of 2009 onboard RV Maria S. Merian to North Pond, one of the larger (70 square km) and best studied sediment ponds, provided proof of this principal. North Pond is the site of the proposed IODP Expedition "677 Mid-Atlantic Microbiology". Investigations included heat-flow, single-channel seismic and bathymetry surveys, as well as gravity coring. Oxygen measurements and pore water sampling (25 cm depth intervals) were performed directly on intact sediment cores, which were subsequently sampled for microbiological analyses, as well as for incubation experiments to test for autotrophic and heterotrophic microbial activity. The entire sediment column down to > 8 m sediment depth contained oxygen. In the central part of the sediment pond oxygen decreased continuously with depth, indicating an active aerobic microbial community, while nitrate concentrations increased. In contrast, along the northern and western rims of North Pond, oxygen concentrations remained surprisingly constant with depth at values around 170 µM. In addition, at 3 locations along the north shore oxygen profiles indicated an upward supply of oxygen from the underlying basaltic basement. Pore water nutrient profiles and incubation experiments confirmed active microbial communities throughout the sediment layer, as well as the influence of upward transport of oxidants on microbial processes in deeply buried sediments. Langseth, M.G., K. Becker, R.P. Von Herzen, and P. Schultheiss. 1992. Heat and fluid flow through sediments on the western flank of the Mid-Atlantic Ridge: A hydrogeological study of North Pond. Geophys. Res. Lett. 19: 517-520.

Hydrothermal activity lowers trophic diversity in Antarctic hydrothermal sediments

NASA Astrophysics Data System (ADS)

Bell, James B.; Reid, William D. K.; Pearce, David A.; Glover, Adrian G.; Sweeting, Christopher J.; Newton, Jason; Woulds, Clare

2017-12-01

Hydrothermal sediments are those in which hydrothermal fluid is discharged through sediments and are one of the least studied deep-sea ecosystems. We present a combination of microbial and biochemical data to assess trophodynamics between and within hydrothermal and background areas of the Bransfield Strait (1050-1647 m of depth). Microbial composition, biomass, and fatty acid signatures varied widely between and within hydrothermally active and background sites, providing evidence of diverse metabolic activity. Several species had different feeding strategies and trophic positions between hydrothermally active and inactive areas, and the stable isotope values of consumers were not consistent with feeding morphology. Niche area and the diversity of microbial fatty acids was lowest at the most hydrothermally active site, reflecting trends in species diversity. Faunal uptake of chemosynthetically produced organics was relatively limited but was detected at both hydrothermal and non-hydrothermal sites, potentially suggesting that hydrothermal activity can affect trophodynamics over a much wider area than previously thought.

Impact of protists on a hydrocarbon-degrading bacterial community from deep-sea Gulf of Mexico sediments: A microcosm study

NASA Astrophysics Data System (ADS)

Beaudoin, David J.; Carmichael, Catherine A.; Nelson, Robert K.; Reddy, Christopher M.; Teske, Andreas P.; Edgcomb, Virginia P.

2016-07-01

In spite of significant advancements towards understanding the dynamics of petroleum hydrocarbon degrading microbial consortia, the impacts (direct or indirect via grazing activities) of bacterivorous protists remain largely unknown. Microcosm experiments were used to examine whether protistan grazing affects the petroleum hydrocarbon degradation capacity of a deep-sea sediment microbial community from an active Gulf of Mexico cold seep. Differences in n-alkane content between native sediment microcosms and those treated with inhibitors of eukaryotes were assessed by comprehensive two-dimensional gas chromatography following 30-90 day incubations and analysis of shifts in microbial community composition using small subunit ribosomal RNA gene clone libraries. More biodegradation was observed in microcosms supplemented with eukaryotic inhibitors. SSU rRNA gene clone libraries from oil-amended treatments revealed an increase in the number of proteobacterial clones (particularly γ-proteobacteria) after spiking sediments with diesel oil. Bacterial community composition shifted, and degradation rates increased, in treatments where protists were inhibited, suggesting protists affect the hydrocarbon degrading capacity of microbial communities in sediments collected at this Gulf of Mexico site.

Marine coastal sediments microbial hydrocarbon degradation processes: contribution of experimental ecology in the omics’era

PubMed Central

Cravo-Laureau, Cristiana; Duran, Robert

2014-01-01

Coastal marine sediments, where important biological processes take place, supply essential ecosystem services. By their location, such ecosystems are particularly exposed to human activities as evidenced by the recent Deepwater Horizon disaster. This catastrophe revealed the importance to better understand the microbial processes involved on hydrocarbon degradation in marine sediments raising strong interests of the scientific community. During the last decade, several studies have shown the key role played by microorganisms in determining the fate of hydrocarbons in oil-polluted sediments but only few have taken into consideration the whole sediment’s complexity. Marine coastal sediment ecosystems are characterized by remarkable heterogeneity, owning high biodiversity and are subjected to fluctuations in environmental conditions, especially to important oxygen oscillations due to tides. Thus, for understanding the fate of hydrocarbons in such environments, it is crucial to study microbial activities, taking into account sediment characteristics, physical-chemical factors (electron acceptors, temperature), nutrients, co-metabolites availability as well as sediment’s reworking due to bioturbation activities. Key information could be collected from in situ studies, which provide an overview of microbial processes, but it is difficult to integrate all parameters involved. Microcosm experiments allow to dissect in-depth some mechanisms involved in hydrocarbon degradation but exclude environmental complexity. To overcome these lacks, strategies have been developed, by creating experiments as close as possible to environmental conditions, for studying natural microbial communities subjected to oil pollution. We present here a review of these approaches, their results and limitation, as well as the promising future of applying “omics” approaches to characterize in-depth microbial communities and metabolic networks involved in hydrocarbon degradation. In addition, we present the main conclusions of our studies in this field. PMID:24575083

Improved measurement of extracellular enzymatic activities in subsurface sediments using competitive desorption treatment

NASA Astrophysics Data System (ADS)

Hoarfrost, Adrienne; Snider, Rachel; Arnosti, Carol

2017-02-01

Extracellular enzymatic activities initiate microbially-driven heterotrophic carbon cycling in subsurface sediments. While measurement of hydrolytic activities in sediments is fundamental to our understanding of carbon cycling, these measurements are often technically difficult due to sorption of organic substrates to the sediment matrix. Most methods that measure hydrolysis of organic substrates in sediments rely on recovery of a fluorophore or fluorescently-labeled target substrate from a sediment incubation. The tendency for substrates to sorb to sediments results in lower recovery of an added substrate, and can result in data that are unusable or difficult to interpret. We developed a treatment using competitive desorption of a fluorescently-labeled, high molecular weight organic substrate that improves recovery of the labeled substrate from sediment subsamples. Competitive desorption treatment improved recovery of the fluorescent substrate by a median of 66%, expanded the range of sediments for which activity measurements could be made, and was effective in sediments from a broad range of geochemical contexts. More reliable measurements of hydrolytic activities in sediments will yield usable and more easily interpretable data from a wider range of sedimentary environments, enabling better understanding of microbially-catalyzed carbon cycling in subsurface environments.

Experimental removal of wetland emergent vegetation leads to decreased methylmercury production in surface sediment

USGS Publications Warehouse

Windham-Myers, L.; Marvin-DiPasquale, M.; Krabbenhoft, D.P.; Agee, J.L.; Cox, M.H.; Heredia-Middleton, P.; Coates, C.; Kakouros, E.

2009-01-01

We performed plant removal (devegetation) experiments across a suite of ecologically diverse wetland settings (tidal salt marshes, river floodplain, rotational rice fields, and freshwater wetlands with permanent or seasonal flooding) to determine the extent to which the presence (or absence) of actively growing plants influences the activity of the Hg(II)-methylating microbial community and the availability of Hg(II) to those microbes. Vegetated control plots were paired with neighboring devegetated plots in which photosynthetic input was terminated 4-8 months prior to measurements, through clipping aboveground biomass, severing belowground connections, and shading the sediment surface to prevent regrowth. Across all wetlands, devegetation decreased the activity of the Hg(II)-methylating microbial community (kmeth) by 38%, calculated MeHg production potential (MP) rates by 36%, and pore water acetate concentration by 78%. Decreases in MP were associated with decreases in microbial sulfate reduction in salt marsh settings. In freshwater agricultural wetlands, decreases in MP were related to indices of microbial iron reduction. Sediment MeHg concentrations were also significantly lower in devegetated than in vegetated plots in most wetland settings studied. Devegetation effects were correlated with live root density (percent volume) and were most profound in vegetated sites with higher initial pore water acetate concentrations. Densely rooted wetlands had the highest rates of microbial Hg(II)-methylation activity but often the lowest concentrations of bioavailable reactive Hg(II). We conclude that the exudation of labile organic carbon (e.g., acetate) by plants leads to enhanced microbial sulfate and iron reduction activity in the rhizosphere, which results in high rates of microbial Hg(II)-methyation and high MeHg concentrations in wetland sediment.

Experimental removal of wetland emergent vegetation leads to decreased methylmercury production in surface sediment

USGS Publications Warehouse

Windham-Myers, Lisamarie; Marvin-DiPasquale, Mark; Krabbenhoft, David P.; Agee, Jennifer L.; Cox, Marisa H.; Heredia-Middleton, Pilar; Coates, Carolyn; Kakouros, Evangelos

2009-01-01

We performed plant removal (devegetation) experiments across a suite of ecologically diverse wetland settings (tidal salt marshes, river floodplain, rotational rice fields, and freshwater wetlands with permanent or seasonal flooding) to determine the extent to which the presence (or absence) of actively growing plants influences the activity of the Hg(II)-methylating microbial community and the availability of Hg(II) to those microbes. Vegetated control plots were paired with neighboring devegetated plots in which photosynthetic input was terminated 4–8 months prior to measurements, through clipping aboveground biomass, severing belowground connections, and shading the sediment surface to prevent regrowth. Across all wetlands, devegetation decreased the activity of the Hg(II)-methylating microbial community (kmeth) by 38%, calculated MeHg production potential (MP) rates by 36%, and pore water acetate concentration by 78%. Decreases in MP were associated with decreases in microbial sulfate reduction in salt marsh settings. In freshwater agricultural wetlands, decreases in MP were related to indices of microbial iron reduction. Sediment MeHg concentrations were also significantly lower in devegetated than in vegetated plots in most wetland settings studied. Devegetation effects were correlated with live root density (percent volume) and were most profound in vegetated sites with higher initial pore water acetate concentrations. Densely rooted wetlands had the highest rates of microbial Hg(II)-methylation activity but often the lowest concentrations of bioavailable reactive Hg(II). We conclude that the exudation of labile organic carbon (e.g., acetate) by plants leads to enhanced microbial sulfate and iron reduction activity in the rhizosphere, which results in high rates of microbial Hg(II)-methyation and high MeHg concentrations in wetland sediment.

Response of sediment microbial community structure in a freshwater reservoir to manipulations in oxygen availability.

PubMed

Bryant, Lee D; Little, John C; Bürgmann, Helmut

2012-04-01

Hypolimnetic oxygenation systems (HOx) are being increasingly used in freshwater reservoirs to elevate dissolved oxygen levels in the hypolimnion and suppress sediment-water fluxes of soluble metals (e.g. Fe and Mn) which are often microbially mediated. We assessed changes in sediment microbial community structure and corresponding biogeochemical cycling on a reservoir-wide scale as a function of HOx operations. Sediment microbial biomass as quantified by DNA concentration was increased in regions most influenced by the HOx. Following an initial decrease in biomass in the upper sediment while oxygen concentrations were low, biomass typically increased at all depths as the 4-month-long oxygenation season progressed. A distinct shift in microbial community structure was only observed at the end of the season in the upper sediment near the HOx. While this shift was correlated to HOx-enhanced oxygen availability, increased TOC levels and precipitation of Fe- and Mn-oxides, abiotic controls on Fe and Mn cycling, and/or the adaptability of many bacteria to variations in prevailing electron acceptors may explain the delayed response and the comparatively limited changes at other locations. While the sediment microbial community proved remarkably resistant to relatively short-term changes in HOx operations, HOx-induced variation in microbial structure, biomass, and activity was observed after a full season of oxygenation. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Microbial Community Structure in Lake and Wetland Sediments from a High Arctic Polar Desert Revealed by Targeted Transcriptomics

PubMed Central

Stoeva, Magdalena K.; Aris-Brosou, Stéphane; Chételat, John; Hintelmann, Holger; Pelletier, Philip; Poulain, Alexandre J.

2014-01-01

While microbial communities play a key role in the geochemical cycling of nutrients and contaminants in anaerobic freshwater sediments, their structure and activity in polar desert ecosystems are still poorly understood, both across heterogeneous freshwater environments such as lakes and wetlands, and across sediment depths. To address this question, we performed targeted environmental transcriptomics analyses and characterized microbial diversity across three depths from sediment cores collected in a lake and a wetland, located on Cornwallis Island, NU, Canada. Microbial communities were characterized based on 16S rRNA and two functional gene transcripts: mcrA, involved in archaeal methane cycling and glnA, a bacterial housekeeping gene implicated in nitrogen metabolism. We show that methane cycling and overall bacterial metabolic activity are the highest at the surface of lake sediments but deeper within wetland sediments. Bacterial communities are highly diverse and structured as a function of both environment and depth, being more diverse in the wetland and near the surface. Archaea are mostly methanogens, structured by environment and more diverse in the wetland. McrA transcript analyses show that active methane cycling in the lake and wetland corresponds to distinct communities with a higher potential for methane cycling in the wetland. Methanosarcina spp., Methanosaeta spp. and a group of uncultured Archaea are the dominant methanogens in the wetland while Methanoregula spp. predominate in the lake. PMID:24594936

Microbial Community Composition, Functions, and Activities in the Gulf of Mexico 1 Year after the Deepwater Horizon Accident

PubMed Central

Yergeau, Etienne; Maynard, Christine; Sanschagrin, Sylvie; Champagne, Julie; Juck, David; Lee, Kenneth

2015-01-01

Several studies have assessed the effects of the released oil on microbes, either during or immediately after the Deepwater Horizon accident. However, little is known about the potential longer-term persistent effects on microbial communities and their functions. In this study, one water column station near the wellhead (3.78 km southwest of the wellhead), one water column reference station outside the affected area (37.77 km southeast of the wellhead), and deep-sea sediments near the wellhead (3.66 km southeast of the wellhead) were sampled 1 year after the capping of the well. In order to analyze microbial community composition, function, and activity, we used metagenomics, metatranscriptomics, and mineralization assays. Mineralization of hexadecane was significantly higher at the wellhead station at a depth of ∼1,200 m than at the reference station. Community composition based on taxonomical or functional data showed that the samples taken at a depth of ∼1,200 m were significantly more dissimilar between the stations than at other depths (surface, 100 m, 750 m, and >1,500 m). Both Bacteria and Archaea showed reduced activity at depths of ∼1,200 m when the wellhead station was compared to the reference station, and their activity was significantly higher in surficial sediments than in 10-cm sediments. Surficial sediments also harbored significantly different active genera than did 5- and 10-cm sediments. For the remaining microbial parameters assessed, no significant differences could be observed between the wellhead and reference stations and between surface and 5- to 10-cm-deep sediments. PMID:26092461

Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin

PubMed Central

Vigneron, Adrien; Cruaud, Perrine; Roussel, Erwan G.; Pignet, Patricia; Caprais, Jean-Claude; Callac, Nolwenn; Ciobanu, Maria-Cristina; Godfroy, Anne; Cragg, Barry A.; Parkes, John R.; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Toffin, Laurent

2014-01-01

Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments. PMID:25099369

Consumption of freons CFC-11 and CFC-12 by anaerobic sediments and soils

USGS Publications Warehouse

Lovley, D.R.; Woodward, J.C.

1992-01-01

A variety of anaerobic sediments and soils consumed CFC-11 (CFCl3) and CFC-12 (CF2Cl2). An aerobic soil did not. Active microbial metabolism was required for CFC-12 uptake in all of the sediments examined. CFC-11 uptake was faster in the presence of microbial activity, but reduced components in the sediments also resulted in nonenzymatic CFC-11 consumption in most instances. CFC-12 uptake in a culture of Clostridium pasteurianum provided a model for the sediment uptake of CFC-11 and CFC-12 that required active microbial metabolism. Consumption of CFC-11 in the presence of reduced hematin demonstrated a potential mechanism for nonenzymatic CFC-11 consumption. These findings demonstrate that CFC-11 and CFC-12 are not biochemically inert under anaerobic conditions. This suggests that anaerobic degradation of CFC-11 and CFC-12 in anaerobic landfills might prevent some disposed CFC-11 and CFC-12 from entering the atmosphere. The results also suggest that CFC-11 and CFC-12 cannot be used as stable tracers in anaerobic environments. Furthermore, although the microbial sink for atmospheric CFC-11 and CFC-12 is much less than current anthropogenic release, this sink could have a significant long-term effect on the amount of CFC-11 and CFC-12 reaching the stratosphere.

Alteration of extracellular enzyme activity and microbial abundance by biochar addition: Implication for carbon sequestration in subtropical mangrove sediment.

PubMed

Luo, Ling; Gu, Ji-Dong

2016-11-01

Biochar has attracted more and more attention due to its essential role in adsorbing pollutants, improving soil fertility, and modifying greenhouse gas emission. However, the influences of biochar on extracellular enzyme activity and microbial abundance are still lack and debatable. Currently, there is no information about the impact of biochar on the function of mangrove ecosystems. Therefore, we explored the effects of biochar on extracellular enzyme activity and microbial abundance in subtropical mangrove sediment, and further estimated the contribution of biochar to C sequestration. In this study, sediments were amended with 0 (control), 0.5, 1.0 and 2.0% of biochar and incubated at 25 °C for 90 days. After incubation, enzyme activities, microbial abundance and the increased percentage of sediment organic C content were determined. Both increase (phenol oxidase and β-glucosidase) and decrease (peroxidase, N-acetyl-glucosaminidase and acid phosphatase) of enzyme activities were observed in biochar treatments, but only peroxidase activity showed statistical significance (at least p < 0.01) compared to the control. Moreover, the activities of all enzymes tested were significantly related to the content of biochar addition (at least p < 0.05). On the other hand, bacterial and fungal abundance in biochar treatments were remarkably lower than control (p < 0.001), and the significantly negative relationship (p < 0.05) between bacterial abundance and the content of biochar was found. Additionally, the increased percentage of organic C gradually increased with biochar addition rate, which provided evidence for applying biochar to mitigate climate change. Given the importance of microorganisms and enzyme activities in sediment organic matter decomposition, the increased C sequestration might be explained by the large decrease of microbial abundance and enzyme activity after biochar intervention. Copyright © 2016 Elsevier Ltd. All rights reserved.

Influence of diesel contamination on the benthic microbial/meiofaunal food web of a Louisiana salt marsh

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carman, K.R.; Fleeger, J.W.; Pomarico, S.

The authors studied the influence of diesel-contaminated sediments on the benthic microbial/meiofaunal food web from a Louisiana salt marsh. Diesel-contaminated sediment was added to microcosms (intact cores of marsh mud) in a range of doses, and a suite of microbial and meiofaunal responses were measured over a 28-day period. The authors measured bacterial and microalgal (Chl a) abundance, bacterial and microalgal activity using radiotracers ({sup 14}C-acetate and {sup 14}CO{sub 2}, respectively), meiofaunal grazing on microalgae, meiofaunal community structure, and meiofaunal physiological condition. Preliminary results indicate that diesel-contaminated sediments influence microalgal biomass and activity, as well as the life histories ofmore » benthic copepod species.« less

Molecular phylogenetic and chemical analyses of the microbial mats in deep-sea cold seep sediments at the northeastern Japan Sea.

PubMed

Arakawa, Shizuka; Sato, Takako; Sato, Rumi; Zhang, Jing; Gamo, Toshitaka; Tsunogai, Urumu; Hirota, Akinari; Yoshida, Yasuhiko; Usami, Ron; Inagaki, Fumio; Kato, Chiaki

2006-08-01

Microbial communities inhabiting deep-sea cold seep sediments at the northeastern Japan Sea were characterized by molecular phylogenetic and chemical analyses. White patchy microbial mats were observed along the fault offshore the Hokkaido Island and sediment samples were collected from two stations at the southern foot of the Shiribeshi seamount (M1 site at a depth of 2,961 m on the active fault) and off the Motta Cape site (M2 site at a depth of 3,064 m off the active fault). The phylogenetic and terminal-restriction fragment polymorphism analyses of PCR-amplified 16S rRNA genes revealed that microbial community structures were different between two sampling stations. The members of ANME-2 archaea and diverse bacterial components including sulfate reducers within Deltaproteobacteria were detected from M1 site, indicating the occurrence of biologically mediated anaerobic oxidation of methane, while microbial community at M2 site was predominantly composed of members of Marine Crenarchaeota group I, sulfate reducers of Deltaproteobacteria, and sulfur oxidizers of Epsilonproteobacteria. Chemical analyses of seawater above microbial mats suggested that concentrations of sulfate and methane at M1 site were largely decreased relative to those at M2 site and carbon isotopic composition of methane at M1 site shifted heavier ((13)C-enriched), the results of which are consistent with molecular analyses. These results suggest that the mat microbial communities in deep-sea cold seep sediments at the northeastern Japan Sea are significantly responsible for sulfur and carbon circulations and the geological activity associated with plate movements serves unique microbial habitats in deep-sea environments.

Evidence of synsedimentary microbial activity and iron deposition in ferruginous crusts of the Late Cenomanian Utrillas Formation (Iberian Basin, central Spain)

NASA Astrophysics Data System (ADS)

García-Hidalgo, José F.; Elorza, Javier; Gil-Gil, Javier; Herrero, José M.; Segura, Manuel

2018-02-01

Ferruginous sandstones and crusts are prominent sedimentary features throughout the continental (braided)-coastal siliciclastic (estuarine-tidal) wedges of the Late Cenomanian Utrillas Formation in the Iberian Basin. Crust types recognized are: Ferruginous sandy crusts (Fsc) with oxides-oxyhydroxides (hematite and goethite) concentrated on sandstone tops presenting a fibro-radial internal structure reminding organic structures that penetrate different mineral phases, suggesting the existence of bacterial activity in crust development; Ferruginous muddy crusts (Fmc) consisting of wavy, laminated, microbial mats, being composed mainly of hematite. On the other hand, a more dispersed and broader mineralization included as Ferruginous sandstones with iron oxides and oxyhydroxides (hematite and goethite) representing a limited cement phase on these sediments. The presence of microbial remains, ferruginous minerals, Microbially-induced sedimentary structures, microbial laminites and vertebrate tracks preserved due to the presence of biofilms suggest firstly a direct evidence of syn-depositional microbial activity in these sediments; and, secondly, that iron accumulation and ferruginous crusts development occurred immediately after deposition of the host, still soft sediments. Ferruginous crusts cap sedimentary cycles and they represent the gradual development of hard substrate conditions, and the development of a discontinuity surface at the top of the parasequence sets, related to very low sedimentary rates; the overlying sediments record subsequent flooding of underlying shallower environments; crusts are, consequently, interpreted as boundaries for these higher-order cycles in the Iberian Basin.

The stratified microbial community at Laguna Figueroa, Baja California, Mexico: A possible model for prephanerozoic laminated microbial communities preserved in cherts

NASA Astrophysics Data System (ADS)

Stolz, John F.; Margulis, Lynn

1984-12-01

The microbial mat community of the evaporite flat at North Pond, Laguna Figueroa (Baja California, Mexico) was actively involved in the production of laminated sediments prior to 1978. Heavy rains in 1979 and 1980 flooded the mat with 1 and 3 meters of meteoric water respectively. The flooding deposited up to 10 cm of silicoclastic sediment over theMicrocoleus-dominated mat and resulted in the cessation of laminated sediment deposition. In 1982, the surface had been recolonized by species of cyanobacteria (Spirulina, Oscillatoria) and purple photosynthetic bacteria (Chromatium, Thiocapsa). The silicoclastic sediments and residual evaporites, which overlaid the laminated sediment, had been reworked into an anaerobic, sulfide-rich mud and contained well preserved sheaths of filamentous and coccoid bacteria.

Microbial Community Composition, Functions, and Activities in the Gulf of Mexico 1 Year after the Deepwater Horizon Accident.

PubMed

Yergeau, Etienne; Maynard, Christine; Sanschagrin, Sylvie; Champagne, Julie; Juck, David; Lee, Kenneth; Greer, Charles W

2015-09-01

Several studies have assessed the effects of the released oil on microbes, either during or immediately after the Deepwater Horizon accident. However, little is known about the potential longer-term persistent effects on microbial communities and their functions. In this study, one water column station near the wellhead (3.78 km southwest of the wellhead), one water column reference station outside the affected area (37.77 km southeast of the wellhead), and deep-sea sediments near the wellhead (3.66 km southeast of the wellhead) were sampled 1 year after the capping of the well. In order to analyze microbial community composition, function, and activity, we used metagenomics, metatranscriptomics, and mineralization assays. Mineralization of hexadecane was significantly higher at the wellhead station at a depth of ∼1,200 m than at the reference station. Community composition based on taxonomical or functional data showed that the samples taken at a depth of ∼1,200 m were significantly more dissimilar between the stations than at other depths (surface, 100 m, 750 m, and >1,500 m). Both Bacteria and Archaea showed reduced activity at depths of ∼1,200 m when the wellhead station was compared to the reference station, and their activity was significantly higher in surficial sediments than in 10-cm sediments. Surficial sediments also harbored significantly different active genera than did 5- and 10-cm sediments. For the remaining microbial parameters assessed, no significant differences could be observed between the wellhead and reference stations and between surface and 5- to 10-cm-deep sediments. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Is DOM driver of the microbial carrying capacity in pristine porous groundwater ecosystems? - lab-scale experiments in 2D sediment flow-through microcosms

NASA Astrophysics Data System (ADS)

Hofmann, Roland; Griebler, Christian

2017-04-01

Groundwater ecosystems are an essential resource for drinking water and at the same time constitute fascinating habitats subject to increasing (anthropogenic) disturbances. In our research, we look for ways to qualitatively and quantitatively access, and predict the resistance and resilience (potential) of groundwater ecosystems in consequence of selected disturbances. As a central goal we hope to identify and quantify the underlying biological and ecological key drivers of the microbial Carrying Capacity (mCC) - an ecological concept established in macro-ecology - we assume directly connected to the ecosystem's productivity and the resistance and resilience of aquifers. We further hypothesize, that the ecosystems' mCC is a result of available energy and constitutes a promising proxy for the potential of groundwater ecosystems to withstand impacts and recover from it. In a first approach we studied the dynamics of the microbial standing stock (biomass) and growth (productivity) productivity of a natural groundwater microbial community in parallel 2-D sediment flow-through systems. Selected zones of the model aquifers were disturbed by elevated DOM concentrations. Both the 'mobile' (free floating) and 'sessile' (sediment attached) microbial components were followed over time in terms of biomass, growth, and specific activities (ATP, carbon use efficiency) and taxonomic composition. Sediment regions supplied with elevated concentrations of natural DOM showed increased biomass, activities and taxonomic richness with the sediment community, while differences in the mobile microbial were marginal. Specifically, the carbon use efficiency was significantly increased in the DOM amended sediment zones. In contrast, the microbial community that received the mainly refractory natural background DOM was able to metabolize polymers more efficiently in substrate use tests (ECOLOG), seen as an adaptation to the energy-poor subsurface. Quasi-stationary conditions were reached in the model aquifers only after several weeks. The quantitative link between microbial productivity and mCC is currently evaluated.

Applicability of API ZYM to capture seasonal and spatial variabilities in lake and river sediments.

PubMed

Patel, Drashti; Gismondi, Renee; Alsaffar, Ali; Tiquia-Arashiro, Sonia M

2018-05-02

Waters draining into a lake carry with them much of the suspended sediment that is transported by rivers and streams from the local drainage basin. The organic matter processing in the sediments is executed by heterotrophic microbial communities, whose activities may vary spatially and temporally. Thus, to capture and evaluate some of these variabilities in the sediments, we sampled six sites: three from the St. Clair River and three from Lake St. Clair in spring, summer, fall, and winter of 2016. At all sites and dates, we investigated the spatial and temporal variations in 19 extracellular enzyme activities using API ZYM. Our results indicated that a broad range of enzymes were found to be active in the sediments. Phosphatases, lipases, and esterases were synthesized most intensively by the sediment microbial communities. No consistent difference was found between the lake and sediment samples. Differences were more obvious between sites and seasons. Sites with the highest metabolic (enzyme) diversity reflected the capacity of the sediment microbial communities to breakdown a broader range of substrates and may be linked to differences in river and lake water quality. The seasonal variability of the enzymes activities was governed by the variations of environmental factors caused by anthropogenic and terrestrial inputs, and provides information for a better understanding of the dynamics of sediment organic matter of the river and lake ecosystems. The experimental results suggest that API ZYM is a simple and rapid enzyme assay procedure to evaluate natural processes in ecosystems and their changes.

The pH and pCO2 dependence of sulfate reduction in shallow-sea hydrothermal CO2 – venting sediments (Milos Island, Greece)

PubMed Central

Bayraktarov, Elisa; Price, Roy E.; Ferdelman, Timothy G.; Finster, Kai

2013-01-01

Microbial sulfate reduction (SR) is a dominant process of organic matter mineralization in sulfate-rich anoxic environments at neutral pH. Recent studies have demonstrated SR in low pH environments, but investigations on the microbial activity at variable pH and CO2 partial pressure are still lacking. In this study, the effect of pH and pCO2 on microbial activity was investigated by incubation experiments with radioactive 35S targeting SR in sediments from the shallow-sea hydrothermal vent system of Milos, Greece, where pH is naturally decreased by CO2 release. Sediments differed in their physicochemical characteristics with distance from the main site of fluid discharge. Adjacent to the vent site (T ~40–75°C, pH ~5), maximal sulfate reduction rates (SRR) were observed between pH 5 and 6. SR in hydrothermally influenced sediments decreased at neutral pH. Sediments unaffected by hydrothermal venting (T ~26°C, pH ~8) expressed the highest SRR between pH 6 and 7. Further experiments investigating the effect of pCO2 on SR revealed a steep decrease in activity when the partial pressure increased from 2 to 3 bar. Findings suggest that sulfate reducing microbial communities associated with hydrothermal vent system are adapted to low pH and high CO2, while communities at control sites required a higher pH for optimal activity. PMID:23658555

The pH and pCO2 dependence of sulfate reduction in shallow-sea hydrothermal CO2 - venting sediments (Milos Island, Greece).

PubMed

Bayraktarov, Elisa; Price, Roy E; Ferdelman, Timothy G; Finster, Kai

2013-01-01

Microbial sulfate reduction (SR) is a dominant process of organic matter mineralization in sulfate-rich anoxic environments at neutral pH. Recent studies have demonstrated SR in low pH environments, but investigations on the microbial activity at variable pH and CO2 partial pressure are still lacking. In this study, the effect of pH and pCO2 on microbial activity was investigated by incubation experiments with radioactive (35)S targeting SR in sediments from the shallow-sea hydrothermal vent system of Milos, Greece, where pH is naturally decreased by CO2 release. Sediments differed in their physicochemical characteristics with distance from the main site of fluid discharge. Adjacent to the vent site (T ~40-75°C, pH ~5), maximal sulfate reduction rates (SRR) were observed between pH 5 and 6. SR in hydrothermally influenced sediments decreased at neutral pH. Sediments unaffected by hydrothermal venting (T ~26°C, pH ~8) expressed the highest SRR between pH 6 and 7. Further experiments investigating the effect of pCO2 on SR revealed a steep decrease in activity when the partial pressure increased from 2 to 3 bar. Findings suggest that sulfate reducing microbial communities associated with hydrothermal vent system are adapted to low pH and high CO2, while communities at control sites required a higher pH for optimal activity.

Metabolic activity of subseafloor microbes in the South Pacific Gyre

NASA Astrophysics Data System (ADS)

Morono, Y.; Ito, M.; Terada, T.; Inagaki, F.

2013-12-01

The South Pacific Gyre (SPG) is characterized as the most oligotrophic open ocean environment. The sediment is rich in oxygen but poor in energy-sources such as reduced organic matter, and hence harbors very low numbers of microbial cells in relatively shallow subseafloor sediment (D'Hondt et al., 2009; Kallmeyer et al., 2012). In such an energy-limited sedimentary habitat, a small size of microbial community persists living functions with extraordinary low oxygen-consumption rate (Røy et al., 2012). During IODP Expedition 329, a series of sediment samples were successfully recovered from 7 drill sites (U1365-1371) from the seafloor to basement in the SPG, providing an unprecedented opportunity to study metabolic activity of the aerobic subseafloor microbial communities. We initiated incubation onboard by adding stable isotope-labeled substrates to the freshly collected sediment sample, such as 13C and/or 15N-labeled bicarbonate, glucose, amino acids, acetate, and ammonium under the (micro-) aerobic condition. One of the technological challenges in this study is to harvest microbial cells from very low-biomass sediment samples for the analysis using nano-scale secondary ion mass spectrometry (NanoSIMS). To address the technical issue, we improved existing cell separation technique for the SPG sediment samples with small inorganic zeolitic grains. By monitoring cell recovery rates through an image-based cell enumeration technique (Morono et al., 2009), we found that cell recovery rates in the SPG sediment samples are generally lower than those in other oceanographic settings (i.e., organic-rich ocean margin sediments). To gain higher cell recovery ratio, we applied multiple density gradient layers, resulting in the cell recovery ratio up to around 80-95% (Morono et al., in press). Then, using the newly developed cell separation technique, we successfully sorted enough number of microbial cells in small spots on the membrane (i.e., 103 to 105 cells per spot). NanoSIMS analysis showed incorporation of the supplemented stable isotope-labeled substrates after 1.5 year-incubation. The substrate incorporation rates of individual microbial cell ranged in average from 1/10 to 1/2 of those values previously observed in an organic-rich ocean margin sediment (Morono et al., 2011). References S. D'Hondt et al., Subseafloor sedimentary life in the South Pacific Gyre. Proc Natl Acad Sci USA 106, 11651 (2009) J. Kallmeyeret al., Global distribution of microbial abundance and biomass in subseafloor sediment. Proc Natl Acad Sci USA 109, 16213 (2012) H. Røy et al., Aerobic microbial respiration in 86-million-year-old deep-sea red clay. Science 336, 922 (2012) Y. Morono et al. Discriminative detection and enumeration of microbial life in marine subsurface sediments. ISME J 3, 503 (2009) Y. Morono et al., An Improved Cell Separation Technique for Marine Subsurface Sediments: Applications for High-throughput Analysis Using Flow Cytometry and Cell Sorting. Environ Microbiol, (2013) Y. Morono et al., Carbon and nitrogen assimilation in deep subseafloor microbial cells. Proc Natl Acad Sci USA 108, 18295 (2011)

Effects of Resource Chemistry on the Composition and Function of Stream Hyporheic Biofilms

PubMed Central

Hall, E. K.; Besemer, K.; Kohl, L.; Preiler, C.; Riedel, K.; Schneider, T.; Wanek, W.; Battin, T. J.

2012-01-01

Fluvial ecosystems process large quantities of dissolved organic matter as it moves from the headwater streams to the sea. In particular, hyporheic sediments are centers of high biogeochemical reactivity due to their elevated residence time and high microbial biomass and activity. However, the interaction between organic matter and microbial dynamics in the hyporheic zone remains poorly understood. We evaluated how variance in resource chemistry affected the microbial community and its associated activity in experimentally grown hyporheic biofilms. To do this we fed beech leaf leachates that differed in chemical composition to a series of bioreactors filled with sediment from a sub-alpine stream. Differences in resource chemistry resulted in differences in diversity and phylogenetic origin of microbial proteins, enzyme activity, and microbial biomass stoichiometry. Specifically, increased lignin, phenolics, and manganese in a single leachate resulted in increased phenoloxidase and peroxidase activity, elevated microbial biomass carbon:nitrogen ratio, and a greater proportion of proteins of Betaproteobacteria origin. We used this model system to attempt to link microbial form (community composition and metaproteome) with function (enzyme activity) in order to better understand the mechanisms that link resource heterogeneity to ecosystem function in stream ecosystems. PMID:22347877

Effects of resource chemistry on the composition and function of stream hyporheic biofilms.

USGS Publications Warehouse

Hall, E.K.; Besemer, K.; Kohl, L.; Preiler, C.; Reidel, K.; Schneider, T.; Wanek, W.; Battin, T.J.

2012-01-01

Fluvial ecosystems process large quantities of dissolved organic matter as it moves from the headwater streams to the sea. In particular, hyporheic sediments are centers of high biogeochemical reactivity due to their elevated residence time and high microbial biomass and activity. However, the interaction between organic matter and microbial dynamics in the hyporheic zone remains poorly understood. We evaluated how variance in resource chemistry affected the microbial community and its associated activity in experimentally grown hyporheic biofilms. To do this we fed beech leaf leachates that differed in chemical composition to a series of bioreactors filled with sediment from a sub-alpine stream. Differences in resource chemistry resulted in differences in diversity and phylogenetic origin of microbial proteins, enzyme activity, and microbial biomass stoichiometry. Specifically, increased lignin, phenolics, and manganese in a single leachate resulted in increased phenoloxidase and peroxidase activity, elevated microbial biomass carbon:nitrogen ratio, and a greater proportion of proteins of Betaproteobacteria origin. We used this model system to attempt to link microbial form (community composition and metaproteome) with function (enzyme activity) in order to better understand the mechanisms that link resource heterogeneity to ecosystem function in stream ecosystems.

Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada.

PubMed

Ruuskanen, Matti O; St Pierre, Kyra A; St Louis, Vincent L; Aris-Brosou, Stéphane; Poulain, Alexandre J

2018-01-01

The Arctic is undergoing rapid environmental change, potentially affecting the physicochemical constraints of microbial communities that play a large role in both carbon and nutrient cycling in lacustrine environments. However, the microbial communities in such Arctic environments have seldom been studied, and the drivers of their composition are poorly characterized. To address these gaps, we surveyed the biologically active surface sediments in Lake Hazen, the largest lake by volume north of the Arctic Circle, and a small lake and shoreline pond in its watershed. High-throughput amplicon sequencing of the 16S rRNA gene uncovered a community dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, similar to those found in other cold and oligotrophic lake sediments. We also show that the microbial community structure in this Arctic polar desert is shaped by pH and redox gradients. This study lays the groundwork for predicting how sediment microbial communities in the Arctic could respond as climate change proceeds to alter their physicochemical constraints.

[Cloning, expression and characterization of a novel esterase from marine sediment microbial metagenomic library].

PubMed

Xu, Shiqing; Hu, Yongfei; Yuan, Aihua; Zhu, Baoli

2010-07-01

To clone, express and characterize a novel esterase from marine sediment microbial metagenomic library. Using esterase segregation agar containing tributyrin, we obtained esterase positive fosmid clone FL10 from marine sediment microbial metagenomic library. This fosmid was partially digested with Sau3A I to construct the sublibrary, from which the esterase positive subclone pFLS10 was obtained. The full length of the esterase gene was amplified and cloned into the expressing vector pET28a, and the recombinant plasmid was transformed into E. coli BL21 cells. We analyse the enzyme activity and study the characterization of the esterase after its expression and purification. An ORF (Open Reading Frame) of 924 bp was identified from the subclone pFLS10. Sequence analysis indicated that it showed 71% amino acid identity to esterase (ADA70030) from a marine sediment metagenomic library. The esterase is a novel low-temperature-active esterase and had highest lipolytic activity to the substrate of 4-nitrophenyl butyrate (C4). The optimum temperature of the esterase was 20 degrees C, the optimum pH was 7.5. The esterase in this study had good thermostability at 20 degrees C and good pH stability at pH8 -10. Significant increase in lipolytic activity was observed with addition of K+ and Mg2+, while decrease with Mn2+ etc. We obtained the novel esterase gene fls10 from the marine sediment microbial metagenomic library. The esterase had good thermostability and high lipolytic activity at low temperature and under basic conditions, which laid a basis for industrial application.

Diversity and Distribution of Prokaryotes within a Shallow-Water Pockmark Field.

PubMed

Giovannelli, Donato; d'Errico, Giuseppe; Fiorentino, Federica; Fattorini, Daniele; Regoli, Francesco; Angeletti, Lorenzo; Bakran-Petricioli, Tatjana; Vetriani, Costantino; Yücel, Mustafa; Taviani, Marco; Manini, Elena

2016-01-01

Pockmarks are crater-like depression on the seafloor associated with hydrocarbon ascent through muddy sediments in continental shelves around the world. In this study, we examine the diversity and distribution of benthic microbial communities at shallow-water pockmarks adjacent to the Middle Adriatic Ridge. We integrate microbial diversity data with characterization of local hydrocarbons concentrations and sediment geochemistry. Our results suggest these pockmarks are enriched in sedimentary hydrocarbons, and host a microbial community dominated by Bacteria, even in deeper sediment layers. Pockmark sediments showed higher prokaryotic abundance and biomass than surrounding sediments, potentially due to the increased availability of organic matter and higher concentrations of hydrocarbons linked to pockmark activity. Prokaryotic diversity analyses showed that the microbial communities of these shallow-water pockmarks are unique, and comprised phylotypes associated with the cycling of sulfur and nitrate compounds, as well as numerous know hydrocarbon degraders. Altogether, this study suggests that shallow-water pockmark habitats enhance the diversity of the benthic prokaryotic biosphere by providing specialized environmental niches.

Linking microbial assemblages to paleoenvironmental conditions from the Holocene and Last Glacial Maximum times in Laguna Potrok Aike sediments, Argentina

NASA Astrophysics Data System (ADS)

Vuillemin, Aurele; Ariztegui, Daniel; Leavitt, Peter R.; Bunting, Lynda

2014-05-01

Laguna Potrok Aike is a closed basin located in the southern hemisphere's mid-latitudes (52°S) where paleoenvironmental conditions were recorded as temporal sedimentary sequences resulting from variations in the regional hydrological regime and geology of the catchment. The interpretation of the limnogeological multiproxy record developed during the ICDP-PASADO project allowed the identification of contrasting time windows associated with the fluctuations of Southern Westerly Winds. In the framework of this project, a 100-m-long core was also dedicated to a detailed geomicrobiological study which aimed at a thorough investigation of the lacustrine subsurface biosphere. Indeed, aquatic sediments do not only record past climatic conditions, but also provide a wide range of ecological niches for microbes. In this context, the influence of environmental features upon microbial development and survival remained still unexplored for the deep lacustrine realm. Therefore, we investigated living microbes throughout the sedimentary sequence using in situ ATP assays and DAPI cell count. These results, compiled with pore water analysis, SEM microscopy of authigenic concretions and methane and fatty acid biogeochemistry, provided evidence for a sustained microbial activity in deep sediments and pinpointed the substantial role of microbial processes in modifying initial organic and mineral fractions. Finally, because the genetic material associated with microorganisms can be preserved in sediments over millennia, we extracted environmental DNA from Laguna Potrok Aike sediments and established 16S rRNA bacterial and archaeal clone libraries to better define the use of DNA-based techniques in reconstructing past environments. We focused on two sedimentary horizons both displaying in situ microbial activity, respectively corresponding to the Holocene and Last Glacial Maximum periods. Sequences recovered from the productive Holocene record revealed a microbial community adapted to subsaline conditions producing methane with a high potential of organic matter degradation. In contrast, sediments rich in volcanic detritus from the Last Glacial Maximum showed a substantial presence of lithotrophic microorganisms and sulphate-reducing bacteria mediating authigenic minerals. Together, these features suggested that microbial communities developed in response to climatic control of lake and catchment productivity at the time of sediment deposition. Prevailing climatic conditions exerted a hierarchical control on the microbial composition of lake sediments by regulating the influx of organic and inorganic material to the lake basin, which in turn determined water column chemistry, production and sedimentation of particulate material, resulting in the different niches sheltering these microbial assemblages. Moreover, it demonstrated that environmental DNA can constitute sedimentary archives of phylogenetic diversity and diagenetic processes over tens of millennia.

The nature and function of microbial enzymes in subsurface marine sediments

NASA Astrophysics Data System (ADS)

Steen, A. D.; Schmidt, J.

2016-02-01

Isotopic and genomic evidence indicates that marine sediments contain populations of active heterotrophic microorganisms which appear to metabolize old, detrital, apparently recalcitrant organic matter. In surface communities, heterotrophs use extracellular enzymes to access complex organic matter. In subsurface sediments, in which microbial doubling times can be on the order of hundreds or thousands of years, it is not clear whether extracellular enzymes could remain stable and active long enough to constitute a 'profitable' stragtegy for accessing complex organic carbon. Here we present evidence that a wide range of extracellular enzyme are active in subsurface sediments from two different environments: the White Oak River, NC, and deep (up to 80 m) sediments of the Baltic Sea Basin recovered from IODP Expedition 347. In the White Oak River, enzymes from deeper sediments appear to be better-adapted to highly-degraded organic matter than enzymes from surface sediments. In the Baltic Sea, preliminary data suggest that enzymes related to nitrogen acquisition are preferentially expressed. By characterizing the extracellular enzymes present in marine sediments, we hope to achieve a better understanding of the mechanisms that control sedimentary organic matter remineralization and preservation.

Distinct Microbial Assemblage Structure and Archaeal Diversity in Sediments of Arctic Thermokarst Lakes Differing in Methane Sources.

PubMed

Matheus Carnevali, Paula B; Herbold, Craig W; Hand, Kevin P; Priscu, John C; Murray, Alison E

2018-01-01

Developing a microbial ecological understanding of Arctic thermokarst lake sediments in a geochemical context is an essential first step toward comprehending the contributions of these systems to greenhouse gas emissions, and understanding how they may shift as a result of long term changes in climate. In light of this, we set out to study microbial diversity and structure in sediments from four shallow thermokarst lakes in the Arctic Coastal Plain of Alaska. Sediments from one of these lakes (Sukok) emit methane (CH 4 ) of thermogenic origin, as expected for an area with natural gas reserves. However, sediments from a lake 10 km to the North West (Siqlukaq) produce CH 4 of biogenic origin. Sukok and Siqlukaq were chosen among the four lakes surveyed to test the hypothesis that active CH 4 -producing organisms (methanogens) would reflect the distribution of CH 4 gas levels in the sediments. We first examined the structure of the little known microbial community inhabiting the thaw bulb of arctic thermokarst lakes near Barrow, AK. Molecular approaches (PCR-DGGE and iTag sequencing) targeting the SSU rRNA gene and rRNA molecule were used to profile diversity, assemblage structure, and identify potentially active members of the microbial assemblages. Overall, the potentially active (rRNA dominant) fraction included taxa that have also been detected in other permafrost environments (e.g., Bacteroidetes, Actinobacteria, Nitrospirae, Chloroflexi, and others). In addition, Siqlukaq sediments were unique compared to the other sites, in that they harbored CH 4 -cycling organisms (i.e., methanogenic Archaea and methanotrophic Bacteria), as well as bacteria potentially involved in N cycling (e.g., Nitrospirae) whereas Sukok sediments were dominated by taxa typically involved in photosynthesis and biogeochemical sulfur (S) transformations. This study revealed a high degree of archaeal phylogenetic diversity in addition to CH 4 -producing archaea, which spanned nearly the phylogenetic extent of currently recognized Archaea phyla (e.g., Euryarchaeota, Bathyarchaeota, Thaumarchaeota, Woesearchaeota, Pacearchaeota, and others). Together these results shed light on expansive bacterial and archaeal diversity in Arctic thermokarst lakes and suggest important differences in biogeochemical potential in contrasting Arctic thermokarst lake sediment ecosystems.

Cellular content of biomolecules in sub-seafloor microbial communities

NASA Astrophysics Data System (ADS)

Braun, Stefan; Morono, Yuki; Becker, Kevin W.; Hinrichs, Kai-Uwe; Kjeldsen, Kasper U.; Jørgensen, Bo B.; Lomstein, Bente Aa.

2016-09-01

Microbial biomolecules, typically from the cell envelope, can provide crucial information about distribution, activity, and adaptations of sub-seafloor microbial communities. However, when cells die these molecules can be preserved in the sediment on timescales that are likely longer than the lifetime of their microbial sources. Here we provide for the first time measurements of the cellular content of biomolecules in sedimentary microbial cells. We separated intact cells from sediment matrices in samples from surficial, deeply buried, organic-rich, and organic-lean marine sediments by density centrifugation. Amino acids, amino sugars, muramic acid, and intact polar lipids were analyzed in both whole sediment and cell extract, and cell separation was optimized and evaluated in terms of purity, separation efficiency, taxonomic resemblance, and compatibility to high-performance liquid chromatography and mass spectrometry for biomolecule analyses. Because cell extracts from density centrifugation still contained considerable amounts of detrital particles and non-cellular biomolecules, we further purified cells from two samples by fluorescence-activated cell sorting (FACS). Cells from these highly purified cell extracts had an average content of amino acids and lipids of 23-28 fg cell-1 and 2.3 fg cell-1, respectively, with an estimated carbon content of 19-24 fg cell-1. In the sediment, the amount of biomolecules associated with vegetative cells was up to 70-fold lower than the total biomolecule content. We find that the cellular content of biomolecules in the marine subsurface is up to four times lower than previous estimates. Our approach will facilitate and improve the use of biomolecules as proxies for microbial abundance in environmental samples and ultimately provide better global estimates of microbial biomass.

Laboratory studies to characterize the efficacy of sand capping a coal tar-contaminated sediment.

PubMed

Hyun, Seunghun; Jafvert, Chad T; Lee, Linda S; Rao, P Suresh C

2006-06-01

Placement of a microbial active sand cap on a coal tar-contaminated river sediment has been suggested as a cost effective remediation strategy. This approach assumes that the flux of contaminants from the sediment is sufficiently balanced by oxygen and nutrient fluxes into the sand layer such that microbial activity will reduce contaminant concentrations within the new benthic zone and reduce the contaminant flux to the water column. The dynamics of such a system were evaluated using batch and column studies with microbial communities from tar-contaminated sediment under different aeration and nutrient inputs. In a 30-d batch degradation study on aqueous extracts of coal tar sediment, oxygen and nutrient concentrations were found to be key parameters controlling the degradation rates of polycyclic aromatic hydrocarbons (PAHs). For the five PAHs monitored (naphthalene, fluorene, phenanthrene, anthracene, and pyrene), degradation rates were inversely proportional to molecular size. For the column studies, where three columns were packed with a 20-cm sand layer on the top of a 5 cm of sediment layer, flow was established to sand layers with (1) aerated water, (2) N(2) sparged water, or (3) HgCl(2)-sterilized N(2) sparged water. After steady-state conditions, PAH concentrations in effluents were the lowest in the aerated column, except for pyrene, whose concentration was invariant with all effluents. These laboratory scale studies support that if sufficient aeration can be achieved in the field through either active and passive means, the resulting microbially active sand layer can improve the water quality of the benthic zone and reduce the flux of many, but not all, PAHs to the water column.

Microbial processes at the beds of glaciers and ice sheets: a look at life below the Whillans Ice Stream

NASA Astrophysics Data System (ADS)

Mikucki, J.; Campen, R.; Vancleave, S.; Scherer, R. P.; Coenen, J. J.; Powell, R. D.; Tulaczyk, S. M.

2017-12-01

Groundwater, saturated sediments and hundreds of subglacial lakes exist below the ice sheets of Antarctica. The few Antarctic subglacial environments sampled to date all contain viable microorganisms. This is a significant finding because microbes are known to be key in mediating biogeochemical cycles. In sediments, microbial metabolic activity can also result in byproducts or direct interactions with sediment particles that influence the physical and geochemical characteristics of the matrix they inhabit. Subglacial Lake Whillans (SLW), a fresh water lake under the Whillans Ice Stream that drains into the Ross Sea at its grounding zone, was recently sampled as part of the NSF-funded Whillans Ice Stream Subglacial Access Research Drilling (WISSARD) project. Sediments from both SLW and its grounding zone contain microbial taxa related to iron, sulfur, nitrogen and methane oxidizers. In addition to molecular data, biogeochemical measurements and culture based experiments on Whillans sediments support the notion that the system is chemosynthetic with energy derived in part by cycling inorganic compounds. Etch pitting and mineral precipitates on fossil sponge spicules suggest that spicules may also provide microbial nutrients in these environments. Perhaps the most widespread microbial process that affects sediment structure and mineral weathering is the production of extra polymeric substances (EPS). Several phylogenetic groups detected in Whillans sediments are known to produce EPS and we have observed its production in pure cultures enriched directly from these sediments. Our data sheds light on how microbial life persists below the Antarctic Ice Sheet despite extended isolation in icy darkness, and how these microbes may be shaping their environment.

Distributions of microbial activities in deep subseafloor sediments

NASA Technical Reports Server (NTRS)

D'Hondt, Steven; Jorgensen, Bo Barker; Miller, D. Jay; Batzke, Anja; Blake, Ruth; Cragg, Barry A.; Cypionka, Heribert; Dickens, Gerald R.; Ferdelman, Timothy; Hinrichs, Kai-Uwe;

[Characterization of microbial activities in marine mudflat sediment using FDA hydrolase analysis].

PubMed

Liu, Ye; Zou, Li; Liu, Lu; Gao, Dong-Mei

2013-10-01

A method based on fluorescence spectrometry was developed to detect the microbial activities in marine mudflat sediment, where is characterized by high salinity, complex organic compounds and low microbial biomass. This paper optimized the sample extracts, the detection equipment for reaction products, the pretreatment methods, and the experimental conditions. The optimal procedure is described as following. Fresh sediment was first extracted with sterilized and aged seawater, followed by the addition of Tween-80 solution, then uniformly dispersed by thorough oscillating, and kept steady for precipitation. After filtration through a sterilized membrane (1. 2 microm, sterilized in boiling water repeatedly) , the supernatant was supplemented with an appropriate amount of FDA solution and allowed to react in dark for 180 min at temperature ranged 25-30 degrees C . The reaction was terminated by the addition of acetone, and the fluorescence intensity of the reaction mixture was measured within 25 min using a molecular fluorescence photometer at an excitation wavelength of 488 nm and an emission wavelength of 530 nm, and the detection range of this method (dry weight) was 3.0 x10(3)-1. 1 x 10(5) ind.g-1. The microbial activity was reported as fluorescence content in per unit sediment mass (microg.g-1, dry weight).

The microbial community structure in petroleum-contaminated sediments corresponds to geophysical signatures

USGS Publications Warehouse

Allen, J.P.; Atekwana, E.A.; Duris, J.W.; Werkema, D.D.; Rossbach, S.

2007-01-01

The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueousphase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes. Copyright ?? 2007, American Society for Microbiology. All Rights Reserved.

The influence of permanently submerged macrophytes on sediment mercury distribution, mobility and methylation potential in a brackish Norwegian fjord.

PubMed

Olsen, Marianne; Schaanning, Morten Thorne; Braaten, Hans Fredrik Veiteberg; Eek, Espen; Moy, Frithjof E; Lydersen, Espen

2018-01-01

Macrophytes are shown to affect the microbial activity in different aqueous environments, with an altering of the sediment cycling of mercury (Hg) as a potential effect. Here, we investigated how a meadow with permanently submerged macrophytes in a contaminated brackish fjord in southern Norway influenced the conditions for sulfate reducing microbial activity, the methyl-Hg (MeHg) production and the availability of MeHg. Historically discharged Hg from a chlor-alkali plant (60-80tons, 1947-1987) was evident through high Hg concentrations (491mgTot-Hgkg -1 , 268μgMeHgkg -1 ) in intermediate sediment depths (10-20cm) outside of the meadow, with reduced concentrations within the meadow. Natural recovery of the fjord was revealed by lower sediment surface concentrations (1.9-15.5mgTot-Hgkg -1 , 1.3-3.2μgMeHgkg -1 ). Within the meadow, vertical gradients of sediment hydrogen sulfide (H 2 S) E h and pH suggested microbial sulfate reduction in 2-5cm depths, coinciding with peak values of relative MeHg levels (0.5% MeHg). We assume that MeHg production rates was stimulated by the supply and availability of organic carbon, microbial activity and a sulfide oxidizing agent (e.g. O 2 ) within the rhizosphere. Following this, % MeHg in sediment (0-5cm) within the meadow was approximately 10× higher compared to outside the meadow. Further, enhanced availability of MeHg within the meadow was demonstrated by significantly higher fluxes (p<0.01) from sediment to overlying water (0.1-0.6ngm -2 d -1 ) compared to sediment without macrophytes (0.02-0.2ngm -2 d -1 ). Considering the productivity and species richness typical for such habitats, submerged macrophyte meadows located within legacy Hg contaminated sediment sites may constitute important entry points for MeHg into food webs. Copyright © 2017 Elsevier B.V. All rights reserved.

Bacterial Diversity Across a Turbidite-Stranded Sediment-Water Interface, La Jolla Canyon, CA

NASA Astrophysics Data System (ADS)

Harrison, B. K.; Flood, B.; Myrbo, A.; Bailey, J.

2016-12-01

The emplacement of gravity-driven sediment flows imposes a significant physical and geochemical impact on underlying sediment and microbial communities. Although previous studies have established lasting mineralogical (e.g., McKay and Pederson, 2014) and biological signatures (e.g., Anschutz et al., 2002) of turbidite deposition, the response of prokaryotes within and beneath debris flows remains poorly constrained. Both bacterial cells associated with the underlying sediment and allocthonous material must respond to substantially altered selective pressures. As a consequence, turbidites and underlying sediments provide an exceptional opportunity to examine 1) microbial community response to sedimentation 2) preservation and identification of microbial dispersal mechanisms. We collected Illumina MiSeq sequence libraries across an intact marine turbidite boundary at 25cm sediment depth in La Jolla canyon off the coast of California. 16S rRNA gene signatures of relict and active bacterial populations exhibit persistent differences attributable to turbidite deposition. In particular, the sedimentary boundary is sharply demarcated at the cm scale by the diversity and abundance of Chloroflexi, Planctomycetes, and Actinobacteria. Variations in the abundance of putative dissimilatory sulfate-reducing Deltaproteobacteria across the stranded sediment-water interface reflect persistent turbidite-induced changes to the geochemical environment. This work raises the possibility that abrupt sedimentological events may alter the microbial community in a manner that persists with burial.

Morphological signatures of microbial activity across sediment and light microenvironments of Lake Vanda, Antarctica

NASA Astrophysics Data System (ADS)

Mackey, Tyler J.; Sumner, Dawn Y.; Hawes, Ian; Jungblut, Anne D.

2017-11-01

Cyanobacteria-dominated microbial mats in Lake Vanda grow with pinnacles and ridges separated by prostrate mat. Rocks protrude over microbial mats on the lake bottom to create localized, dm-scale gradients in sedimentation and irradiance. The effects of sedimentation on pinnacle and ridge growth were isolated from photosynthetic activity by contrasting growth across microenvironmental gradients. Sedimentation rate was measured as the mass of sand and mud sized sediment in mat that accumulated over 11 years, and the incident light was modeled near and under rocks by reconstructing topography using Structure from Motion techniques. Morphologically diverse pinnacles and ridges were documented in both exposed and sheltered mat microenvironments, in addition to growing downward from the underside of overhanging rocks. Mat that grew with > 40% irradiance under overhangs did not have consistent differences in pinnacle density or ridge abundance as a function of sedimentation rates or irradiance when compared to exposed mat. However, their morphology did change significantly with changes in the direction of incident irradiance. Where irradiance was < 40% ambient or light intersected the mat at very low angles, few pinnacles were present and ridges were preferentially aligned parallel to incident light direction. These observations indicate that pinnacle nucleation and spacing were not strongly influenced by sedimentation but pinnacle and ridge morphology varied in response to directional irradiance.

Microbial physiology-based model of ethanol metabolism in subsurface sediments

NASA Astrophysics Data System (ADS)

Jin, Qusheng; Roden, Eric E.

2011-07-01

A biogeochemical reaction model was developed based on microbial physiology to simulate ethanol metabolism and its influence on the chemistry of anoxic subsurface environments. The model accounts for potential microbial metabolisms that degrade ethanol, including those that oxidize ethanol directly or syntrophically by reducing different electron acceptors. Out of the potential metabolisms, those that are active in the environment can be inferred by fitting the model to experimental observations. This approach was applied to a batch sediment slurry experiment that examined ethanol metabolism in uranium-contaminated aquifer sediments from Area 2 at the U.S. Department of Energy Field Research Center in Oak Ridge, TN. According to the simulation results, complete ethanol oxidation by denitrification, incomplete ethanol oxidation by ferric iron reduction, ethanol fermentation to acetate and H 2, hydrogenotrophic sulfate reduction, and acetoclastic methanogenesis: all contributed significantly to the degradation of ethanol in the aquifer sediments. The assemblage of the active metabolisms provides a frame work to explore how ethanol amendment impacts the chemistry of the environment, including the occurrence and levels of uranium. The results can also be applied to explore how diverse microbial metabolisms impact the progress and efficacy of bioremediation strategies.

Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes.

PubMed

Kumar, Amit; Ng, Daphne H P; Wu, Yichao; Cao, Bin

2018-05-28

Re-naturalized quarry lakes are important ecosystems, which support complex communities of flora and fauna. Microorganisms associated with sediment and water form the lowest trophic level in these ecosystems and drive biogeochemical cycles. A direct comparison of microbial taxa in water and sediment microbial communities is lacking, which limits our understanding of the dominant functions that are carried out by the water and sediment microbial communities in quarry lakes. In this study, using the 16S rDNA amplicon sequencing approach, we compared microbial communities in the water and sediment in two re-naturalized quarry lakes in Singapore and elucidated putative functions of the sediment and water microbial communities in driving major biogeochemical processes. The richness and diversity of microbial communities in sediments of the quarry lakes were higher than those in the water. The composition of the microbial communities in the sediments from the two quarries was highly similar to one another, while those in the water differed greatly. Although the microbial communities of the sediment and water samples shared some common members, a large number of microbial taxa (at the phylum and genus levels) were prevalent either in sediment or water alone. Our results provide valuable insights into the prevalent biogeochemical processes carried out by water and sediment microbial communities in tropical granite quarry lakes, highlighting distinct microbial processes in water and sediment that contribute to the natural purification of the resident water.

Rapid assay for microbially reducible ferric iron in aquatic sediments

USGS Publications Warehouse

Lovely, Derek R.; Philips , Elizabeth J.P.

1987-01-01

The availability of ferric iron for microbial reduction as directly determined by the activity of iron-reducing organisms was compared with its availability as determined by a newly developed chemical assay for microbially reducible iron. The chemical assay was based on the reduction of poorly crystalline ferric iron by hydroxylamine under acidic conditions. There was a strong correlation between the extent to which hydroxylamine could reduce various synthetic ferric iron forms and the susceptibility of the iron to microbial reduction in an enrichment culture of iron-reducing organisms. When sediments that contained hydroxylamine-reducible ferric iron were incubated under anaerobic conditions, ferrous iron accumulated as the concentration of hydroxylamine-reducible ferric iron declined over time. Ferrous iron production stopped as soon as the hydroxylamine-reducible ferric iron was depleted. In anaerobic incubations of reduced sediments that did not contain hydroxylamine-reducible ferric iron, there was no microbial iron reduction, even though the sediments contained high concentrations of oxalate-extractable ferric iron. A correspondence between the presence of hydroxylamine-reducible ferric iron and the extent of ferric iron reduction in anaerobic incubations was observed in sediments from an aquifer and in fresh- and brackish-water sediments from the Potomac River estuary. The assay is a significant improvement over previously described procedures for the determination of hydroxylamine-reducible ferric iron because it provides a correction for the high concentrations of solid ferrous iron which may also be extracted from sediments with acid. This is a rapid, simple technique to determine whether ferric iron is available for microbial reduction.

Archaeal Populations in Hypersaline Sediments Underlying Orange Microbial Mats in the Napoli Mud Volcano▿†

PubMed Central

Lazar, Cassandre Sara; L'Haridon, Stéphane; Pignet, Patricia; Toffin, Laurent

2011-01-01

Microbial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. Hence, they could be visible indicators of anaerobic oxidation of methane (AOM) and methane cycling processes in underlying sediments. The Napoli mud volcano is situated in the Olimpi Area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor. Sediments associated with a brine pool and microbial orange mats of the Napoli mud volcano were recovered during the Medeco cruise. Based on analysis of RNA-derived sequences, the “active” archaeal community was composed of many uncultured lineages, such as rice cluster V or marine benthic group D. Function methyl coenzyme M reductase (mcrA) genes were affiliated with the anaerobic methanotrophic Archaea (ANME) of the ANME-1, ANME-2a, and ANME-2c groups, suggesting that AOM occurred in these sediment layers. Enrichment cultures showed the presence of viable marine methylotrophic Methanococcoides in shallow sediment layers. Thus, the archaeal community diversity seems to show that active methane cycling took place in the hypersaline microbial mat-associated sediments of the Napoli mud volcano. PMID:21335391

Gene expression in the deep biosphere.

PubMed

Orsi, William D; Edgcomb, Virginia P; Christman, Glenn D; Biddle, Jennifer F

2013-07-11

Scientific ocean drilling has revealed a deep biosphere of widespread microbial life in sub-seafloor sediment. Microbial metabolism in the marine subsurface probably has an important role in global biogeochemical cycles, but deep biosphere activities are not well understood. Here we describe and analyse the first sub-seafloor metatranscriptomes from anaerobic Peru Margin sediment up to 159 metres below the sea floor, represented by over 1 billion complementary DNA (cDNA) sequence reads. Anaerobic metabolism of amino acids, carbohydrates and lipids seem to be the dominant metabolic processes, and profiles of dissimilatory sulfite reductase (dsr) transcripts are consistent with pore-water sulphate concentration profiles. Moreover, transcripts involved in cell division increase as a function of microbial cell concentration, indicating that increases in sub-seafloor microbial abundance are a function of cell division across all three domains of life. These data support calculations and models of sub-seafloor microbial metabolism and represent the first holistic picture of deep biosphere activities.

Effects of nutrient load on microbial activities within a seagrass-dominated ecosystem: Implications of changes in seagrass blue carbon.

PubMed

Liu, Songlin; Jiang, Zhijian; Wu, Yunchao; Zhang, Jingping; Arbi, Iman; Ye, Feng; Huang, Xiaoping; Macreadie, Peter Ian

2017-04-15

Nutrient loading is a leading cause of global seagrass decline, triggering shifts from seagrass- to macroalgal-dominance. Within seagrass meadows of Xincun Bay (South China Sea), we found that nutrient loading (due to fish farming) increased sediment microbial biomass and extracellular enzyme activity associated with carbon cycling (polyphenol oxidase, invertase and cellulase), with a corresponding decrease in percent sediment organic carbon (SOC), suggesting that nutrients primed microorganism and stimulated SOC remineralization. Surpisingly, however, the relative contribution of seagrass-derived carbon to bacteria (δ 13 C bacteria ) increased with nutrient loading, despite popular theory being that microbes switch to consuming macroalgae which are assumed to provide a more labile carbon source. Organic carbon sources of fungi were unaffected by nutrient loading. Overall, this study suggests that nutrient loading changes the relative contribution of seagrass and algal sources to SOC pools, boosting sediment microbial biomass and extracellular enzyme activity, thereby possibly changing seagrass blue carbon. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany

PubMed Central

Gründger, Friederike; Jiménez, Núria; Thielemann, Thomas; Straaten, Nontje; Lüders, Tillmann; Richnow, Hans-Hermann; Krüger, Martin

2015-01-01

Coal-bearing sediments are major reservoirs of organic matter potentially available for methanogenic subsurface microbial communities. In this study the specific microbial community inside lignite-bearing sedimentary basin in Germany and its contribution to methanogenic hydrocarbon degradation processes was investigated. The stable isotope signature of methane measured in groundwater and coal-rich sediment samples indicated methanogenic activity. Analysis of 16S rRNA gene sequences showed the presence of methanogenic Archaea, predominantly belonging to the orders Methanosarcinales and Methanomicrobiales, capable of acetoclastic or hydrogenotrophic methanogenesis. Furthermore, we identified fermenting, sulfate-, nitrate-, and metal-reducing, or acetogenic Bacteria clustering within the phyla Proteobacteria, complemented by members of the classes Actinobacteria, and Clostridia. The indigenous microbial communities found in the groundwater as well as in the coal-rich sediments are able to degrade coal-derived organic components and to produce methane as the final product. Lignite-bearing sediments may be an important nutrient and energy source influencing larger compartments via groundwater transport. PMID:25852663

Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole.

PubMed

Kinsman-Costello, L E; Sheik, C S; Sheldon, N D; Allen Burton, G; Costello, D M; Marcus, D; Uyl, P A Den; Dick, G J

2017-03-01

For a large part of earth's history, cyanobacterial mats thrived in low-oxygen conditions, yet our understanding of their ecological functioning is limited. Extant cyanobacterial mats provide windows into the putative functioning of ancient ecosystems, and they continue to mediate biogeochemical transformations and nutrient transport across the sediment-water interface in modern ecosystems. The structure and function of benthic mats are shaped by biogeochemical processes in underlying sediments. A modern cyanobacterial mat system in a submerged sinkhole of Lake Huron (LH) provides a unique opportunity to explore such sediment-mat interactions. In the Middle Island Sinkhole (MIS), seeping groundwater establishes a low-oxygen, sulfidic environment in which a microbial mat dominated by Phormidium and Planktothrix that is capable of both anoxygenic and oxygenic photosynthesis, as well as chemosynthesis, thrives. We explored the coupled microbial community composition and biogeochemical functioning of organic-rich, sulfidic sediments underlying the surface mat. Microbial communities were diverse and vertically stratified to 12 cm sediment depth. In contrast to previous studies, which used low-throughput or shotgun metagenomic approaches, our high-throughput 16S rRNA gene sequencing approach revealed extensive diversity. This diversity was present within microbial groups, including putative sulfate-reducing taxa of Deltaproteobacteria, some of which exhibited differential abundance patterns in the mats and with depth in the underlying sediments. The biological and geochemical conditions in the MIS were distinctly different from those in typical LH sediments of comparable depth. We found evidence for active cycling of sulfur, methane, and nutrients leading to high concentrations of sulfide, ammonium, and phosphorus in sediments underlying cyanobacterial mats. Indicators of nutrient availability were significantly related to MIS microbial community composition, while LH communities were also shaped by indicators of subsurface groundwater influence. These results show that interactions between the mats and sediments are crucial for sustaining this hot spot of biological diversity and biogeochemical cycling. © 2016 John Wiley & Sons Ltd.

Rates and extent of microbial debromination in the deep subseafloor biosphere

NASA Astrophysics Data System (ADS)

Berg, R. D.; Solomon, E. A.; Morris, R. M.

2013-12-01

Recent genomic and porewater geochemical data suggest that reductive dehalogenation of a wide range of halogenated organic compounds could represent an important energy source for deep subseafloor microbial communities. At continental slope sites worldwide, there is a remarkably linear relationship between porewater profiles of ammonium and bromide, indicating that the factors controlling the distribution and rates of dehalogenation have the potential to influence carbon and nitrogen cycling in the deep subsurface biosphere. Though this metabolic pathway could play an important role in the cycling of otherwise refractory pools of carbon and nitrogen in marine sediments and provide energy to microbial communities in the deep subsurface biosphere, the rates and extent of dehalogenation in marine sediments are poorly constrained. Here we report net reaction rate profiles of debromination activity in continental slope sediments, calculated from numerical modeling of porewater bromide profiles from several margins worldwide. The reaction rate profiles indicate three common zones of debromination activity in slope sediments: 1) low rates of debromination, and a potential bromine sink, in the upper sediment column correlating to the sulfate reduction zone, with net bromide removal rates from -3.6 x 10^-2 to -4.85 x 10^-1 μmol m^-2 yr^-1, 2) high rates of debromination from the sulfate-methane transition zone to ~40-100 mbsf, with net bromide release rates between 7.1 x 10^-2 to 3.9 x 10^-1 μmol m^-2 yr^-1, and 3) an inflection point at ~40-100 mbsf, below which net rates of debromination decrease by an order of magnitude and at several sites are indistinguishable from zero. These results indicate that dehalogenating activity is widely distributed in marine sediments, providing energy to fuel deep subseafloor microbial communities, with potentially important consequences for the global bromine and nitrogen cycles.

Human and Environmental Impacts on River Sediment Microbial Communities

DOE PAGES

Gibbons, Sean M.; Jones, Edwin; Bearquiver, Angelita; ...

2014-05-19

Sediment microbial communities are responsible for a majority of the metabolic activity in river and stream ecosystems. Understanding the dynamics in community structure and function across freshwater environments will help us to predict how these ecosystems will change in response to human land-use practices. Here we present a spatiotemporal study of sediments in the Tongue River (Montana, USA), comprising six sites along 134 km of river sampled in both spring and fall for two years. Sequencing of 16S rRNA amplicons and shotgun metagenomes revealed that these sediments are the richest (~65,000 microbial ‘species’ identified) and most novel (93% of OTUsmore » do not match known microbial diversity) ecosystems analyzed by the Earth Microbiome Project to date, and display more functional diversity than was detected in a recent review of global soil metagenomes. Community structure and functional potential have been significantly altered by anthropogenic drivers, including increased pathogenicity and antibiotic metabolism markers near towns and metabolic signatures of coal and coalbed methane extraction byproducts. The core (OTUs shared across all samples) and the overall microbial community exhibited highly similar structure, and phylogeny was weakly coupled with functional potential. Together, these results suggest that microbial community structure is shaped by environmental drivers and niche filtering, though stochastic assembly processes likely play a role as well. These results indicate that sediment microbial communities are highly complex and sensitive to changes in land use practices.« less

Short-chain alkane cycling in deep Gulf of Mexico cold-seep sediments

NASA Astrophysics Data System (ADS)

Sibert, R.; Joye, S. B.; Hunter, K.

2015-12-01

Mixtures of light hydrocarbon gases are common in deep Gulf of Mexico cold-seep sediments, and are typically dissolved in pore fluids, adsorbed to sediment particles, trapped in methane ice, or as free gas. The dominant component in these natural gas mixtures is usually methane (>80% C1), but ethane (C2) and propane (C3) are nearly always present in trace amounts (<1% total). The processes that control the concentration and isotopic signature of these gases in sediments are well explained for methane, but the controls for C2/C3 cycling are still a relative mystery. Methane production proceeds in deep anoxic sediments by either 1) thermocatalytic cracking of fossil organic matter, or 2) as a direct product of microbial metabolism, i.e. methanogenesis. In surface sediments, it appears that both microbial consumption and chemical deposition of methane (i.e. as methane clathrate) ensures that >95% of the methane produced at depth never reaches the water column. Production of C1 and C2 in deep-sea sediments has been historically attributed only to thermocatalytic processes, though limited data suggests production of C2/C3 compounds through the activity of archaea at depth. Furthermore, carbon isotopic data on ethane and propane from deep cores of Gulf of Mexico sediments suggest alkanogenesis at >3 m depth in the sediment column and alkane oxidation in uppermost oxidant-rich sediments. Additional studies have also isolated microorganisms capable of oxidizing ethane and propane in the laboratory, but field studies of microbial-driven dynamics of C2/C3 gases in cold-seep sediments are rare. Here, we present the results of a series of incubation experiments using sediment slurries culled from surface sediments from one of the most prolific natural oil and gas seeps in the Gulf of Mexico. Rates of alkane oxidation were measured under a variety of conditions to assess the surface-driven microbial controls on C2/C3 cycling in cold-seep environments. Such microbial processes are important in terms of the possible 'oxidative overprinting' of alkane isotopic signatures produced at depth, possibly obscuring typical microbial isotopic signals.

Colonization of overlaying water by bacteria from dry river sediments.

PubMed

Fazi, Stefano; Amalfitano, Stefano; Piccini, Claudia; Zoppini, Annamaria; Puddu, Alberto; Pernthaler, Jakob

2008-10-01

We studied the diversity, community composition and activity of the primary microbial colonizers of the water above freshly re-wetted sediments from a temporary river. Dried sediments, collected from Mulargia River (Sardinia, Italy), were covered with sterile freshwater in triplicate microcosms, and changes of the planktonic microbial assemblage were monitored over a 48 h period. During the first 9 h bacterial abundance was low (1.5 x 10(4) cells ml(-1)); it increased to 3.4 x 10(6) cells ml(-1) after 28 h and did not change thereafter. Approximately 20% of bacteria exhibited DNA de novo synthesis already after 9 h of incubation. Changes of the ratios of (3)H-leucine to (3)H-thymidine incorporation rates indicated a shift of growth patterns during the experiment. Extracellular enzyme activity showed a maximum at 48 h with aminopeptidase activity (430.8 +/- 22.6 nmol MCA l(-1) h(-1)) significantly higher than alkaline phosphatase (98.6 +/- 4.3 nmol MUF l(-1) h(-1)). The primary microbial colonizers of the overlaying water - as determined by 16S rRNA gene sequence analysis - were related to at least six different phylogenetic lineages of Bacilli and to Alphaproteobacteria (Brevundimonas spp. and Caulobacter spp.). Large bacterial cells affiliated to one clade of Bacillus sp. were rare in the dried sediments, but constituted the majority of the planktonic microbial assemblage and of cells with detectable DNA-synthesis until 28 h after re-wetting. Their community contribution decreased in parallel with a rise of flagellated and ciliated protists. Estimates based on cell production rates suggested that the rapidly enriched Bacillus sp. suffered disproportionally high loss rates from selective predation, thus favouring the establishment of a more heterogenic assemblage of microbes (consisting of Proteobacteria, Actinobacteria and Cytophaga-Flavobacteria). Our results suggest that the primary microbial colonizers of the water above dried sediments are passively released into the plankton and that their high growth potential is counteracted by the activity of bacterivorous protists.

Active subsurface cellular function in the Baltic Sea Basin, IODP Exp 347

NASA Astrophysics Data System (ADS)

Reese, B. K.; Zinke, L. A.; Bird, J. T.; Lloyd, K. G.; Marshall, I.; Amend, J.; Jørgensen, B. B.

2016-12-01

The Baltic Sea Basin is a unique depositional setting that has experienced periods of glaciation and deglaciation as a result of global temperature fluctuations over the course of several hundred thousand years. This has resulted in laminated sediments formed during periods with strong permanent salinity stratification. The high sedimentation rates (100-500 cm/1000 y) make this an ideal setting to understand the microbial structure of a deep biosphere community in a high-organic matter environment. The responses of deep sediment microbial communities to variations in conditions during and after deposition are poorly understood. Samples were collected through scientific drilling during the International Ocean Discovery Program (IODP) Expedition 347 on board the Greatship Manisha, September-November 2013. We examined the active microbial community structure using the 16S rRNA gene transcript and active functional genes through metatranscriptome sequencing. Major biogeochemical shifts have been observed in response to the depositional history between the limnic, brackish, and marine phases. The microbial community structure in the BSB is diverse and reflective of the unique changes in the geochemical profile. These data further define the existence life in the deep subsurface and the survival mechanisms required for this extreme environment.

13C-DEPLETED MICROBIAL LIPIDS INDICATE SEASONAL METHANOTROPHIC ACTIVITY IN SHALLOW ESTUARINE SEDIMENTS

EPA Science Inventory

Compound specific isotope analysis was combined with phospholipid fatty acid (PLFA) analysis to identify methanotrophic activity in members of the sedimentary microbial community in the Altamaha and Savannah River estuaries in Georgia. 13C-depleted PLFAs indicate methane utilizat...

Anthropogenic impact on mangrove sediments triggers differential responses in the heavy metals and antibiotic resistomes of microbial communities.

PubMed

Cabral, Lucélia; Júnior, Gileno Vieira Lacerda; Pereira de Sousa, Sanderson Tarciso; Dias, Armando Cavalcante Franco; Lira Cadete, Luana; Andreote, Fernando Dini; Hess, Matthias; de Oliveira, Valéria Maia

2016-09-01

Mangroves are complex and dynamic ecosystems highly dependent on diverse microbial activities. In the last decades, these ecosystems have been exposed to and affected by diverse human activities, such as waste disposal and accidental oil spills. Complex microbial communities inhabiting the soil and sediment of mangroves comprise microorganisms that have developed mechanisms to adapt to organic and inorganic contaminants. The resistance of these microbes to contaminants is an attractive property and also the reason why soil and sediment living microorganisms and their enzymes have been considered promising for environmental detoxification. The aim of the present study was to identify active microbial genes in heavy metals, i.e., Cu, Zn, Cd, Pb and Hg, and antibiotic resistomes of polluted and pristine mangrove sediments through the comparative analysis of metatranscriptome data. The concentration of the heavy metals Zn, Cr, Pb, Cu, Ni, Cd, and Hg and abundance of genes and transcripts involved in resistance to toxic compounds (the cobalt-zinc-cadmium resistance protein complex; the cobalt-zinc-cadmium resistance protein CzcA and the cation efflux system protein CusA) have been closely associated with sites impacted with petroleum, sludge and other urban waste. The taxonomic profiling of metatranscriptome sequences suggests that members of Gammaproteobacteria and Deltaproteobacteria classes contribute to the detoxification of the polluted soil. Desulfobacterium autotrophicum was the most abundant microorganism in the oil-impacted site and displayed specific functions related to heavy metal resistance, potentially playing a key role in the successful persistence of the microbial community of this site. Copyright © 2016 Elsevier Ltd. All rights reserved.

Energetic constraints on life in deep marine sediments

NASA Astrophysics Data System (ADS)

Amend, J.; LaRowe, D.

2013-12-01

Microorganisms are abundant in deep-sea sediments, but what percentage of cells is active, how fast do they grow, and what factors control their diversity and population size? Geochemical modelling of redox reaction energetics can help in answering these questions. Calculations of Gibbs energies reveal which reactions are thermodynamically possible, but they also highlight which geochemical variables (e.g., temperature, pressure, pH, composition) may control microbial activity and how the amount and type of biomass are affected by energy limitations. We will discuss recent results from sediment cores collected at the Peru Margin (active continental shelf with high primary productivity and significant organic matter accumulation), the South Pacific Gyre (ultra-slow sedimentation rate and low organic carbon content), and the Juan de Fuca Ridge flank (high rate of sedimentation influenced by hydrothermal circulation). However, this approach to evaluating bioenergetic potential and predicting microbial activity can be applied to any environment where the geochemistry is well characterized, even if microbiology data have not been collected. When Gibbs energies are calculated on a basis of per mole of electrons transferred (as is commonly done), aerobic oxidation of hydrogen and organic matter in South Pacific Gyre sediments is the most exergonic. Based on this, one might posit that the fastest catabolic rates and the largest biomass would be found there. However, cell counts at Juan de Fuca and the Peru Margin are several orders of magnitude higher. When recast as energy densities (in J per cm3 of sediment), we observe far more energy available in sediments at Juan de Fuca and the Peru Margin than at those in the South Pacific Gyre. We also note that the identity of the most exergonic reaction changes with depth, suggesting corresponding changes in the microbial community structure. The thermodynamic approach used here for energy supply can also be used for energy demand, including the often-considered minimum or threshold energy, also referred to as the biological energy quantum. Based on this energetic minimum theory, many reactions cannot support microbial communities because their energy yield is apparently too low. However, we show that when evaluated as energy densities, some energetically ';impossible' catabolisms become ';possible' and vice versa.

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation

PubMed Central

Yazdani Foshtomi, Maryam; Braeckman, Ulrike; Derycke, Sofie; Sapp, Melanie; Van Gansbeke, Dirk; Sabbe, Koen; Willems, Anne; Vincx, Magda; Vanaverbeke, Jan

2015-01-01

Objectives The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea. Spatio-Temporal Patterns of the Microbial Communities Our results indicated that bacteria (total and β-AOB) showed more spatio-temporal variation than archaea (total and AOA) as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices. Macrofauna, Microbes and the Benthic N-Cycle Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal activity. We hypothesized that the latter effect can be explained by their bioturbating and bio-irrigating activities, increasing the spatial complexity of the biogeochemical environment. PMID:26102286

Effect of redox conditions on MTBE biodegradation in surface water Sediments

USGS Publications Warehouse

Bradley, P.M.; Chapelle, F.H.; Landmeyer, J.E.

2001-01-01

Microbial degradation of methyl tert-butyl ether (MTBE) was observed in surface water-sediment microcosms under anaerobic conditions. The efficiency and products of anaerobic MTBE biodegradation were dependent on the predominant terminal electron-accepting conditions. In the presence of substantial methanogenic activity, MTBE biodegradation was nominal and involved reduction of MTBE to the toxic product, tert-butyl alcohol (TBA). In the absence of significant methanogenic activity, accumulation of [14C]TBA generally decreased, and mineralization of [U-14C]MTBE to 14CO2 generally increased as the oxidative potential of the predominant terminal electron acceptor increased in the order of SO4, Fe(III), Mn(IV) < NO3 < O2. Microbial mineralization of MTBE to CO2 under Mn(IV)or SO4-reducing conditions has not been reported previously. The results of this study indicate that microorganisms inhabiting the sediments of streams and lakes can degrade MTBE effectively under a range of anaerobic terminal electron-accepting conditions. Thus, anaerobic bed sediment microbial processes may provide a significant environmental sink for MTBE in surface water systems throughout the United States.

Phylogenetic and enzymatic diversity of deep subseafloor aerobic microorganisms in organics- and methane-rich sediments off Shimokita Peninsula.

PubMed

Kobayashi, Tohru; Koide, Osamu; Mori, Kozue; Shimamura, Shigeru; Matsuura, Takae; Miura, Takeshi; Takaki, Yoshihiro; Morono, Yuki; Nunoura, Takuro; Imachi, Hiroyuki; Inagaki, Fumio; Takai, Ken; Horikoshi, Koki

2008-07-01

"A meta-enzyme approach" is proposed as an ecological enzymatic method to explore the potential functions of microbial communities in extreme environments such as the deep marine subsurface. We evaluated a variety of extra-cellular enzyme activities of sediment slurries and isolates from a deep subseafloor sediment core. Using the new deep-sea drilling vessel "Chikyu", we obtained 365 m of core sediments that contained approximately 2% organic matter and considerable amounts of methane from offshore the Shimokita Peninsula in Japan at a water depth of 1,180 m. In the extra-sediment fraction of the slurry samples, phosphatase, esterase, and catalase activities were detected consistently throughout the core sediments down to the deepest slurry sample from 342.5 m below seafloor (mbsf). Detectable enzyme activities predicted the existence of a sizable population of viable aerobic microorganisms even in deep subseafloor habitats. The subsequent quantitative cultivation using solid media represented remarkably high numbers of aerobic, heterotrophic microbial populations (e.g., maximally 4.4x10(7) cells cm(-3) at 342.5 mbsf). Analysis of 16S rRNA gene sequences revealed that the predominant cultivated microbial components were affiliated with the genera Bacillus, Shewanella, Pseudoalteromonas, Halomonas, Pseudomonas, Paracoccus, Rhodococcus, Microbacterium, and Flexibacteracea. Many of the predominant and scarce isolates produced a variety of extra-cellular enzymes such as proteases, amylases, lipases, chitinases, phosphatases, and deoxyribonucleases. Our results indicate that microbes in the deep subseafloor environment off Shimokita are metabolically active and that the cultivable populations may have a great potential in biotechnology.

Identification of Members of the Metabolically Active Microbial Populations Associated with Beggiatoa Species Mat Communities from Gulf of Mexico Cold-Seep Sediments

PubMed Central

Mills, Heath J.; Martinez, Robert J.; Story, Sandra; Sobecky, Patricia A.

2004-01-01

In this study, the composition of the metabolically active fraction of the microbial community occurring in Gulf of Mexico marine sediments (water depth, 550 to 575 m) with overlying filamentous bacterial mats was determined. The mats were mainly composed of either orange- or white-pigmented Beggiatoa spp. Complementary 16S ribosomal DNA (crDNA) was obtained from rRNA extracted from three different sediment depths (0 to 2, 6 to 8, and 10 to 12 cm) that had been subjected to reverse transcription-PCR amplification. Domain-specific 16S PCR primers were used to construct 12 different 16S crDNA libraries containing 333 Archaea and 329 Bacteria clones. Analysis of the Archaea clones indicated that all sediment depths associated with overlying orange- and white-pigmented microbial mats were almost exclusively dominated by ANME-2 (95% of total Archaea clones), a lineage related to the methanogenic order Methanosarcinales. In contrast, bacterial diversity was considerably higher, with the dominant phylotype varying by sediment depth. An equivalent number of clones detected at 0 to 2 cm, representing a total of 93%, were related to the γ and δ classes of Proteobacteria, whereas clones related to δ-Proteobacteria dominated the metabolically active fraction of the bacterial community occurring at 6 to 8 cm (79%) and 10 to 12 cm (85%). This is the first phylogenetics-based evaluation of the presumptive metabolically active fraction of the Bacteria and Archaea community structure investigated along a sediment depth profile in the northern Gulf of Mexico, a hydrocarbon-rich cold-seep region. PMID:15345432

Effects of organic carbon supply rates on uranium mobility in a previously bioreduced contaminated sediment.

PubMed

Wan, Jiamin; Tokunaga, Tetsu K; Kim, Yongman; Brodie, Eoin; Daly, Rebecca; Hazen, Terry C; Firestone, Mary K

2008-10-15

Bioreduction-based strategies for remediating uranium (U)-contaminated sediments face the challenge of maintaining the reduced status of U for long times. Because groundwater influxes continuously bring in oxidizing terminal electron acceptors (O2, NO3(-)), it is necessary to continue supplying organic carbon (OC) to maintain the reducing environment after U bioreduction is achieved. We tested the influence of OC supply rates on mobility of previously microbial reduced uranium U(IV) in contaminated sediments. We found that high degrees of U mobilization occurred when OC supply rates were high, and when the sediment still contained abundant Fe(III). Although 900 days with low levels of OC supply minimized U mobilization, the sediment redox potential increased with time as did extractable U(VI) fractions. Molecular analyses of total microbial activity demonstrated a positive correlation with OC supply and analyses of Geobacteraceae activity (RT-qPCR of 16S rRNA) indicated continued activity even when the effluent Fe(II) became undetectable. These data support our hypothesis on the mechanisms responsible for remobilization of U under reducing conditions; that microbial respiration caused increased (bi)carbonate concentration and formation of stable uranyl carbonate complexes, thereby shifted U(IV)/U(VI) equilibrium to more reducing potentials. The data also suggested that low OC concentrations could not sustain the reducing condition of the sediment for much longer time. Bioreduced U(IV) is not sustainable in an oxidizing environment for a very long time.

Enumeration of viruses and prokaryotes in deep-sea sediments and cold seeps of the Gulf of Mexico

USGS Publications Warehouse

Kellogg, Christina A.

2010-01-01

Little is known about the distribution and abundance of viruses in deep-sea cold-seep environments. Like hydrothermal vents, seeps support communities of macrofauna that are sustained by chemosynthetic bacteria. Sediments close to these communities are hypothesized to be more microbiologically active and therefore to host higher numbers of viruses than non-seep areas. Push cores were taken at five types of Gulf of Mexico habitats at water depths below 1000 m using a remotely operated vehicle (ROV). The habitats included non-seep reference sediment, brine seeps, a microbial mat, an urchin field, and a pogonophoran worm community. Samples were processed immediately for enumeration of viruses and prokaryotes without the addition of a preservative. Prokaryote counts were an order of magnitude lower in sediments directly in contact with macrofauna (urchins, pogonophorans) compared to all other samples (107 vs. 108 cells g-1 dry weight) and were highest in areas of elevated salinity (brine seeps). Viral-Like Particle (VLP) counts were lowest in the reference sediments and pogonophoran cores (108 VLP g-1 dry wt), higher in brine seeps (109 VLP g-1 dry wt), and highest in the microbial mats (1010 VLP g-1 dry wt). Virus-prokaryote ratios (VPR) ranged from <5 in the reference sediment to >30 in the microbial mats and >60 in the urchin field. VLP counts and VPR were all significantly greater than those reported from sediments in the deep Mediterranean Sea and in most cases were higher than recent data from a cold-seep site near Japan. The high VPR suggest that greater microbial activity in or near cold-seep environments results in greater viral production and therefore higher numbers of viruses.

Enumeration of viruses and prokaryotes in deep-sea sediments and cold seeps of the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Kellogg, Christina A.

2010-11-01

Little is known about the distribution and abundance of viruses in deep-sea cold-seep environments. Like hydrothermal vents, seeps support communities of macrofauna that are sustained by chemosynthetic bacteria. Sediments close to these communities are hypothesized to be more microbiologically active and therefore to host higher numbers of viruses than non-seep areas. Push cores were taken at five types of Gulf of Mexico habitats at water depths below 1000 m using a remotely operated vehicle (ROV). The habitats included non-seep reference sediment, brine seeps, a microbial mat, an urchin field, and a pogonophoran worm community. Samples were processed immediately for enumeration of viruses and prokaryotes without the addition of a preservative. Prokaryote counts were an order of magnitude lower in sediments directly in contact with macrofauna (urchins, pogonophorans) compared to all other samples (107 vs. 108 cells g-1 dry weight) and were highest in areas of elevated salinity (brine seeps). Viral-Like Particle (VLP) counts were lowest in the reference sediments and pogonophoran cores (108 VLP g-1 dry wt), higher in brine seeps (109 VLP g-1 dry wt), and highest in the microbial mats (1010 VLP g-1 dry wt). Virus-prokaryote ratios (VPR) ranged from <5 in the reference sediment to >30 in the microbial mats and >60 in the urchin field. VLP counts and VPR were all significantly greater than those reported from sediments in the deep Mediterranean Sea and in most cases were higher than recent data from a cold-seep site near Japan. The high VPR suggest that greater microbial activity in or near cold-seep environments results in greater viral production and therefore higher numbers of viruses.

Effects of elevated sulfate concentration on the mobility of arsenic in the sediment-water interface.

PubMed

Li, Shiyu; Yang, Changliang; Peng, Changhui; Li, Haixia; Liu, Bin; Chen, Chuan; Chen, Bingyu; Bai, Jinyue; Lin, Chen

2018-06-15

The adsorption/desorption of arsenic (As) at the sediment-water interface in lakes is the key to understanding whether As can enter the ecosystem and participate in material circulation. In this study, the concentrations of As(III), total arsenic [As(T)], sulfide, iron (Fe), and dissolved organic carbon (DOC) in overlying water were observed after the initial sulfate (SO 4 2- ) concentrations were increased by four gradients in the presence and absence of microbial systems. The results indicate that increased SO 4 2- concentrations in overlying water triggered As desorption from sediments. Approximately 10% of the desorbed As was desorbed directly as arsenite or arsenate by competitive adsorption sites on the iron salt surface; 21% was due to the reduction of iron (hydr)oxides; and 69% was due to microbial activity, as compared with a system with no microbial activity. The intensity of microbial activity was controlled by the SO 4 2- and DOC concentrations in the overlying water. In anaerobic systems, which had SO 4 2- and DOC concentrations higher than 47 and 7 mg/L, respectively, microbial activity was promoted by SO 4 2- and DOC; As(III) was desorbed under these indoor simulation conditions. When either the SO 4 2- or DOC concentration was lower than its respective threshold of 47 or 7 mg/L, or when either of these indices was below its concentration limit, it was difficult for microorganisms to use SO 4 2- and DOC to enhance their own activities. Therefore, conditions were insufficient for As desorption. The migration of As in lake sediments was dominated by microbial activity, which was co-limited by SO 4 2- and DOC. The concentrations of SO 4 2- and DOC in the overlying water are thus important for the prevention and control of As pollution in lakes. We recommend controlling SO 4 2- and DOC concentrations as a method for controlling As inner-source pollution in lake water. Copyright © 2018 Elsevier Inc. All rights reserved.

Anoxia stimulates microbially catalyzed metal release from Animas River sediments.

PubMed

Saup, Casey M; Williams, Kenneth H; Rodríguez-Freire, Lucía; Cerrato, José M; Johnston, Michael D; Wilkins, Michael J

2017-04-19

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amended with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2- -reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.

Energy and power limits for microbial activity

NASA Astrophysics Data System (ADS)

LaRowe, D.; Amend, J.

2014-12-01

The goal of this presentation is to describe a quantitative framework for determining how energy limits microbial activity, biomass and, ultimately, biogeochemical processes. Although this model can be applied to any environment, its utility is demonstrated in marine sediments, which are an attractive test habitat because they encompass a broad spectrum of energy levels, varying amounts of biomass and are ubiquitous. The potential number of active microbial cells in Arkonas Basin (Baltic Sea) sediments are estimated as a function of depth by quantifying the amount of energy that is available to them and the rate at which it is supplied: power. The amount of power supplied per cubic centimeter of sediment is determined by calculating the Gibbs energy of fermentation and sulfate reduction in combination with the rate of particulate organic carbon, POC, degradation. The Reactive Continuum Model (Boudreau and Ruddick, 1991), RCM, is used to determine the rate at which POC is made available for microbial consumption. The RCM represents POC as containing a range of different types of organic compounds whose ability to be consumed by microorganisms varies as a function of the age of the sediment and on the distribution of compound types that were initially deposited. The sediment age model and RCM parameters determined by (Mogollon et al., 2012) are used. The power available for fermentation and sulfate reduction coupled to H2 and acetate oxidation varies from 10-8 W cm-3 at the sediment water interface to between 10-11 - 10-12 W cm-3 at 3.5 meters below the seafloor, mbsf. Using values of maintenance powers for each of these catabolic activities taken from the literature, the total number of active cells in these sediments similarly decreases from just less than 108 cell cm-3 at the SWI to 4.6 x 104 cells cm-3 at 3.5 mbsf. The number of moles of POC decreases from 2.6 x 10-5 to 9.5 x 10-6, also becoming more recalcitrant with depth. Boudreau, B. P. and Ruddick, B. R. (1991) On a reactive continuum representation of organic matter diagenesis. Amer. J. Sci. 291, 507-538. Mogollon, J. M., Dale, A. W., Fossing, H. and Regnier, P. (2012) Timescales for the development of methanogenesis and free gas layers in recently-deposited sediments of Arkona Bason (Baltic Sea). Biogeosciences 9, 1915-1933.

Depth-dependent geochemical and microbiological gradients in Fe(III) deposits resulting from coal mine-derived acid mine drainage

PubMed Central

Brantner, Justin S.; Haake, Zachary J.; Burwick, John E.; Menge, Christopher M.; Hotchkiss, Shane T.; Senko, John M.

2014-01-01

We evaluated the depth-dependent geochemistry and microbiology of sediments that have developed via the microbially-mediated oxidation of Fe(II) dissolved in acid mine drainage (AMD), giving rise to a 8–10 cm deep “iron mound” that is composed primarily of Fe(III) (hydr)oxide phases. Chemical analyses of iron mound sediments indicated a zone of maximal Fe(III) reducing bacterial activity at a depth of approximately 2.5 cm despite the availability of dissolved O2 at this depth. Subsequently, Fe(II) was depleted at depths within the iron mound sediments that did not contain abundant O2. Evaluations of microbial communities at 1 cm depth intervals within the iron mound sediments using “next generation” nucleic acid sequencing approaches revealed an abundance of phylotypes attributable to acidophilic Fe(II) oxidizing Betaproteobacteria and the chloroplasts of photosynthetic microeukaryotic organisms in the upper 4 cm of the iron mound sediments. While we observed a depth-dependent transition in microbial community structure within the iron mound sediments, phylotypes attributable to Gammaproteobacterial lineages capable of both Fe(II) oxidation and Fe(III) reduction were abundant in sequence libraries (comprising ≥20% of sequences) from all depths. Similarly, abundances of total cells and culturable Fe(II) oxidizing bacteria were uniform throughout the iron mound sediments. Our results indicate that O2 and Fe(III) reduction co-occur in AMD-induced iron mound sediments, but that Fe(II)-oxidizing activity may be sustained in regions of the sediments that are depleted in O2. PMID:24860562

Next-Generation Sequencing of Microbial Communities in the Athabasca River and Its Tributaries in Relation to Oil Sands Mining Activities

PubMed Central

Yergeau, Etienne; Lawrence, John R.; Sanschagrin, Sylvie; Waiser, Marley J.; Korber, Darren R.

2012-01-01

The Athabasca oil sands deposit is the largest reservoir of crude bitumen in the world. Recently, the soaring demand for oil and the availability of modern bitumen extraction technology have heightened exploitation of this reservoir and the potential unintended consequences of pollution in the Athabasca River. The main objective of the present study was to evaluate the potential impacts of oil sands mining on neighboring aquatic microbial community structure. Microbial communities were sampled from sediments in the Athabasca River and its tributaries as well as in oil sands tailings ponds. Bacterial and archaeal 16S rRNA genes were amplified and sequenced using next-generation sequencing technology (454 and Ion Torrent). Sediments were also analyzed for a variety of chemical and physical characteristics. Microbial communities in the fine tailings of the tailings ponds were strikingly distinct from those in the Athabasca River and tributary sediments. Microbial communities in sediments taken close to tailings ponds were more similar to those in the fine tailings of the tailings ponds than to the ones from sediments further away. Additionally, bacterial diversity was significantly lower in tailings pond sediments. Several taxonomic groups of Bacteria and Archaea showed significant correlations with the concentrations of different contaminants, highlighting their potential as bioindicators. We also extensively validated Ion Torrent sequencing in the context of environmental studies by comparing Ion Torrent and 454 data sets and by analyzing control samples. PMID:22923391

Deep-biosphere methane production stimulated by geofluids in the Nankai accretionary complex

PubMed Central

Kubo, Yusuke; Hoshino, Tatsuhiko; Sakai, Sanae; Arnold, Gail L.; Case, David H.; Lever, Mark A.; Morita, Sumito; Nakamura, Ko-ichi

2018-01-01

Microbial life inhabiting subseafloor sediments plays an important role in Earth’s carbon cycle. However, the impact of geodynamic processes on the distributions and carbon-cycling activities of subseafloor life remains poorly constrained. We explore a submarine mud volcano of the Nankai accretionary complex by drilling down to 200 m below the summit. Stable isotopic compositions of water and carbon compounds, including clumped methane isotopologues, suggest that ~90% of methane is microbially produced at 16° to 30°C and 300 to 900 m below seafloor, corresponding to the basin bottom, where fluids in the accretionary prism are supplied via megasplay faults. Radiotracer experiments showed that relatively small microbial populations in deep mud volcano sediments (102 to 103 cells cm−3) include highly active hydrogenotrophic methanogens and acetogens. Our findings indicate that subduction-associated fluid migration has stimulated microbial activity in the mud reservoir and that mud volcanoes may contribute more substantially to the methane budget than previously estimated. PMID:29928689

Size and Carbon Content of Sub-seafloor Microbial Cells at Landsort Deep, Baltic Sea

PubMed Central

Braun, Stefan; Morono, Yuki; Littmann, Sten; Kuypers, Marcel; Aslan, Hüsnü; Dong, Mingdong; Jørgensen, Bo B.; Lomstein, Bente Aa.

2016-01-01

The discovery of a microbial ecosystem in ocean sediments has evoked interest in life under extreme energy limitation and its role in global element cycling. However, fundamental parameters such as the size and the amount of biomass of sub-seafloor microbial cells are poorly constrained. Here we determined the volume and the carbon content of microbial cells from a marine sediment drill core retrieved by the Integrated Ocean Drilling Program (IODP), Expedition 347, at Landsort Deep, Baltic Sea. To determine their shape and volume, cells were separated from the sediment matrix by multi-layer density centrifugation and visualized via epifluorescence microscopy (FM) and scanning electron microscopy (SEM). Total cell-carbon was calculated from amino acid-carbon, which was analyzed by high-performance liquid chromatography (HPLC) after cells had been purified by fluorescence-activated cell sorting (FACS). The majority of microbial cells in the sediment have coccoid or slightly elongated morphology. From the sediment surface to the deepest investigated sample (~60 m below the seafloor), the cell volume of both coccoid and elongated cells decreased by an order of magnitude from ~0.05 to 0.005 μm3. The cell-specific carbon content was 19–31 fg C cell−1, which is at the lower end of previous estimates that were used for global estimates of microbial biomass. The cell-specific carbon density increased with sediment depth from about 200 to 1000 fg C μm−3, suggesting that cells decrease their water content and grow small cell sizes as adaptation to the long-term subsistence at very low energy availability in the deep biosphere. We present for the first time depth-related data on the cell volume and carbon content of sedimentary microbial cells buried down to 60 m below the seafloor. Our data enable estimates of volume- and biomass-specific cellular rates of energy metabolism in the deep biosphere and will improve global estimates of microbial biomass. PMID:27630628

Evolution of Mudstone Porosity, Permeability, and Microstructure in the Presence of Microorganisms During Vertical Compression

NASA Astrophysics Data System (ADS)

Mills, T.; Reece, J. S.

2016-12-01

Here we investigate the influence of microbial activity on the mechanical and transport properties of mudstones during early diagenesis. Despite the proven presence of microbial communities in marine sediments to depths of >500 meters below sea floor (mbsf), little is known about the interactions between microorganisms and sediments, especially during the early stages of burial and compression. To characterize and quantify the impact of microbial activity on mudstone properties, we compare natural mudstone samples treated with iron reducing bacteria Shewanella Oneidensis MR-1 and those without bacteria. Two bulk mudstones are experimentally prepared using sediments from Integrated Ocean Drilling Program Sites U1319 and U1324 in the Gulf of Mexico. The sediments originated from 4-13 mbsf in the Brazos-Trinity Basin and from three depth intervals (3-14 mbsf, 23-32 mbsf, and 493-502 mbsf) in the Ursa Basin. The sediments are dried and ground to clay- and silt-sized particles and homogenized into two natural mudstone powders. These powders are then used to make reproducible mudstone samples through a process called resedimentation, which replicates natural deposition and burial. Changes in microstructure, porosity, compressibility, and permeability are measured while the biotic (with bacteria) and abiotic (without bacteria) mudstones are being uniaxially compressed over several weeks to a maximum stress of 100 kPa. We anticipate that biofilm growth in pore spaces will decrease porosity, compressibility, and permeability, and the resultant microstructural changes created by microorganisms will be evident in high-resolution scanning electron microscope (SEM) images. Recognition of the micro-scale processes that take place during the early stages of mudstone diagenesis, especially those mediated by microbial activity, and their long-term effects on mudstone properties can lead to better identification and more effective production of unconventional hydrocarbon reservoirs.

Mangrove succession enriches the sediment microbial community in South China

PubMed Central

Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai

2016-01-01

Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession. PMID:27265262

Mangrove succession enriches the sediment microbial community in South China.

PubMed

Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai

2016-06-06

Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession.

Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis

PubMed Central

Won, Nam-Il; Kim, Ki-Hwan; Kang, Ji Hyoun; Park, Sang Rul; Lee, Hyuk Je

2017-01-01

The coastal ecosystems are considered as one of the most dynamic and vulnerable environments under various anthropogenic developments and the effects of climate change. Variations in the composition and diversity of microbial communities may be a good indicator for determining whether the marine ecosystems are affected by complex forcing stressors. DNA sequence-based metagenomics has recently emerged as a promising tool for analyzing the structure and diversity of microbial communities based on environmental DNA (eDNA). However, few studies have so far been performed using this approach to assess the impacts of human activities on the microbial communities in marine systems. In this study, using metagenomic DNA sequencing (16S ribosomal RNA gene), we analyzed and compared seawater and sediment communities between sand mining and control (natural) sites in southern coastal waters of Korea to assess whether anthropogenic activities have significantly affected the microbial communities. The sand mining sites harbored considerably lower levels of microbial diversities in the surface seawater community during spring compared with control sites. Moreover, the sand mining areas had distinct microbial taxonomic group compositions, particularly during spring season. The microbial groups detected solely in the sediment load/dredging areas (e.g., Marinobacter, Alcanivorax, Novosphingobium) are known to be involved in degradation of toxic chemicals such as hydrocarbon, oil, and aromatic compounds, and they also contain potential pathogens. This study highlights the versatility of metagenomics in monitoring and diagnosing the impacts of human disturbance on the environmental health of marine ecosystems from eDNA. PMID:28134828

Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis.

PubMed

Won, Nam-Il; Kim, Ki-Hwan; Kang, Ji Hyoun; Park, Sang Rul; Lee, Hyuk Je

2017-01-27

The coastal ecosystems are considered as one of the most dynamic and vulnerable environments under various anthropogenic developments and the effects of climate change. Variations in the composition and diversity of microbial communities may be a good indicator for determining whether the marine ecosystems are affected by complex forcing stressors. DNA sequence-based metagenomics has recently emerged as a promising tool for analyzing the structure and diversity of microbial communities based on environmental DNA (eDNA). However, few studies have so far been performed using this approach to assess the impacts of human activities on the microbial communities in marine systems. In this study, using metagenomic DNA sequencing (16S ribosomal RNA gene), we analyzed and compared seawater and sediment communities between sand mining and control (natural) sites in southern coastal waters of Korea to assess whether anthropogenic activities have significantly affected the microbial communities. The sand mining sites harbored considerably lower levels of microbial diversities in the surface seawater community during spring compared with control sites. Moreover, the sand mining areas had distinct microbial taxonomic group compositions, particularly during spring season. The microbial groups detected solely in the sediment load/dredging areas (e.g., Marinobacter, Alcanivorax, Novosphingobium) are known to be involved in degradation of toxic chemicals such as hydrocarbon, oil, and aromatic compounds, and they also contain potential pathogens. This study highlights the versatility of metagenomics in monitoring and diagnosing the impacts of human disturbance on the environmental health of marine ecosystems from eDNA.

Influence of silver nanoparticles on benthic oxygen consumption of microbial communities in freshwater sediments determined by microelectrodes.

PubMed

Miao, Lingzhan; Wang, Chao; Hou, Jun; Wang, Peifang; Ao, Yanhui; Li, Yi; Yao, Yu; Lv, Bowen; Yang, Yangyang; You, Guoxiang; Xu, Yi

2017-05-01

The increased use of silver nanoparticles (AgNPs) will inevitably result in the release of these particles into aquatic environments, with sediments as a substantial sink. However, we do not know whether AgNPs present potential impacts in sediment functioning. In this study, a microcosm approach was constructed, and the potential impacts of AgNPs and PVP-coated AgNPs on oxygen consumption in freshwater sediments (collected from Taihu Lake) were determined using oxygen microelectrodes. To our knowledge, this is the first time that microelectrodes have been used to estimate the impacts of AgNPs in sediments. The steady-state oxygen microprofiles showed that environmental relevant concentration (1 mg/L nano-Ag) did not lead to an apparent change in the oxygen consumption rates of benthic microbial communities in sediment. The addition of 10 mg/L uncoated AgNPs resulted in remarkable differences in the oxygen concentration profiles within 4-5 h and significantly inhibited the oxygen consumption of benthic microbial communities in the upper sediment layer (∼1 mm) after 100 h. Simultaneously, an increase of oxygen consumption in sediment lower zones was observed. These results may suggest that aerobic microorganisms in the upper layer of the sediment reduced metabolic activity to avoid the toxic stress from AgNPs. Concomitantly, facultative aerobes below the metabolically active upper layer switched from fermentation or anaerobic respiration to aerobic respiration as oxygen bioavailability increased in the lower zones of the sediment. In addition, PVP coating reduced the nanotoxicity of AgNPs in benthic microorganisms due to the decreased dissolution of AgNPs in the filtered overlying water, a phenomenon that merits further investigation. Copyright © 2017 Elsevier Ltd. All rights reserved.

NATURAL ATTENUATION FOR ECOSYSTEM RESTORATION IN NY/NJ HARBOR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van der Lelie, D.; Reid-Green, J. D.; Stern, E. A.

2003-12-31

We have investigated the feasibility of using natural attenuation methods for ecosystem restoration in New York/New Jersey Harbor. Measurements were made of the most probable number of sulfate-reducing bacteria (SRB) in native sediments and in samples, which had been supplemented with an appropriate electron donor and electron acceptor. The results showed that the activity of the endogenous microbial population in the native sediment was high enough to make possible adequate chemical transformation rates. The bioavailability of the zinc in the sediments was measured using the BIOMET biosensor technique. The bioavailability of the zinc was effectively eliminated following the microbial activities.more » We concluded that natural attenuation could be used effectively in treating sediments from Newark Bay and surrounding waters and that the resultant materials could likely be used in environmental restoration projects of the type proposed for construction in South Kearny, NJ.« less

In situ microbiota distinguished primary anthropogenic stressor in freshwater sediments.

PubMed

Xie, Yuwei; Floehr, Tilman; Zhang, Xiaowei; Xiao, Hongxia; Yang, Jianghua; Xia, Pu; Burton, G Allen; Hollert, Henner

2018-08-01

Conventional assessment and evaluation of sediment quality are based on laboratory-based ecotoxicological and chemical measurements with lack of concern for ecological relevance. Microbiotas in sediment are responsive to pollutants and can be used as alternative ecological indicators of sediment pollutants; however, the linkage between the microbial ecology and ecotoxicological endpoints in response to sediment contamination has been poorly evaluated. Here, in situ microbiotas from the Three Gorges Reservoir (TGR) area of the Yangtze River were characterized by DNA metabarcoding approaches, and then, changes of in situ microbiotas were compared with the ecotoxicological endpoint, aryl hydrocarbon receptor (AhR) mediated activity, and level of polycyclic aromatic hydrocarbons (PAHs) in sediments. PAHs and organic pollutant mixtures mediating AhR activity had different effects on the structures of microbiotas. Specifically, Shannon indices of protistan communities were negatively correlated with the levels of AhR mediated activity and PAHs. The sediment AhR activity was positively correlated with the relative abundance of prokaryotic Acetobacteraceae, but had a negative correlation with protistan Oxytrichidae. Furthermore, a quantitative classification model was built to predict the level of AhR activity based on the relative abundances of Acetobacteraceae and Oxytrichidae. These results suggested that in situ Protista communities could provide a useful tool for monitoring and assessing ecological stressors. The observed responses of microbial community provided supplementary evidence to support that the AhR-active pollutants, such as PAHs, were the primary stressors of the aquatic community in TGR area. Copyright © 2018 Elsevier Ltd. All rights reserved.

Viral activities and life cycles in deep subseafloor sediments.

PubMed

Engelhardt, Tim; Orsi, William D; Jørgensen, Bo Barker

2015-12-01

Viruses are highly abundant in marine subsurface sediments and can even exceed the number of prokaryotes. However, their activity and quantitative impact on microbial populations are still poorly understood. Here, we use gene expression data from published continental margin subseafloor metatranscriptomes to qualitatively assess viral diversity and activity in sediments up to 159 metres below seafloor (mbsf). Mining of the metatranscriptomic data revealed 4651 representative viral homologues (RVHs), representing 2.2% of all metatranscriptome sequence reads, which have close translated homology (average 77%, range 60-97% amino acid identity) to viral proteins. Archaea-infecting RVHs are exclusively detected in the upper 30 mbsf, whereas RVHs for filamentous inoviruses predominate in the deepest sediment layers. RVHs indicative of lysogenic phage-host interactions and lytic activity, notably cell lysis, are detected at all analysed depths and suggest a dynamic virus-host association in the marine deep biosphere studied here. Ongoing lytic viral activity is further indicated by the expression of clustered, regularly interspaced, short palindromic repeat-associated cascade genes involved in cellular defence against viral attacks. The data indicate the activity of viruses in subsurface sediment of the Peruvian margin and suggest that viruses indeed cause cell mortality and may play an important role in the turnover of subseafloor microbial biomass. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation.

PubMed

Yazdani Foshtomi, Maryam; Braeckman, Ulrike; Derycke, Sofie; Sapp, Melanie; Van Gansbeke, Dirk; Sabbe, Koen; Willems, Anne; Vincx, Magda; Vanaverbeke, Jan

2015-01-01

The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea. Our results indicated that bacteria (total and β-AOB) showed more spatio-temporal variation than archaea (total and AOA) as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices. Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal activity. We hypothesized that the latter effect can be explained by their bioturbating and bio-irrigating activities, increasing the spatial complexity of the biogeochemical environment.

Organic priority substances and microbial processes in river sediments subject to contrasting hydrological conditions.

PubMed

Zoppini, Annamaria; Ademollo, Nicoletta; Amalfitano, Stefano; Casella, Patrizia; Patrolecco, Luisa; Polesello, Stefano

2014-06-15

Flood and drought events of higher intensity and frequency are expected to increase in arid and semi-arid regions, in which temporary rivers represent both a water resource and an aquatic ecosystem to be preserved. In this study, we explored the variation of two classes of hazardous substances (Polycyclic Aromatic Hydrocarbons and Nonylphenols) and the functioning of the microbial community in river sediments subject to hydrological fluctuations (Candelaro river basin, Italy). Overall, the concentration of pollutants (∑PAHs range 8-275ngg(-1); ∑NPs range 299-4858ngg(-1)) suggests a moderate degree of contamination. The conditions in which the sediments were tested, flow (high/low) and no flow (wet/dry/arid), were associated to significant differences in the chemical and microbial properties. The total organic carbon contribution decreased together with the stream flow reduction, while the contribution of C-PAHs and C-NPs tended to increase. NPs were relatively more concentrated in sediments under high flow, while the more hydrophobic PAHs accumulated under low and no flow conditions. Passing from high to no flow conditions, a gradual reduction of microbial processes was observed, to reach the lowest specific bacterial carbon production rates (0.06fmolCh(-1)cell(-1)), extracellular enzyme activities, and the highest doubling time (40h) in arid sediments. In conclusion, different scenarios for the mobilization of pollutants and microbial processes can be identified under contrasting hydrological conditions: (i) the mobilization of pollutants under high flow and a relatively higher probability for biodegradation; (ii) the accumulation of pollutants during low flow and lower probability for biodegradation; (iii) the drastic reduction of pollutant concentrations under dry and arid conditions, probably independently from the microbial activity (abiotic processes). Our findings let us infer that a multiple approach has to be considered for an appropriate water resource exploitation and a more realistic prevision of the impact of pollutants in temporary waters. Copyright © 2014 Elsevier B.V. All rights reserved.

Interactive effects of multiple stressors revealed by sequencing total (DNA) and active (RNA) components of experimental sediment microbial communities.

PubMed

Birrer, Simone C; Dafforn, Katherine A; Simpson, Stuart L; Kelaher, Brendan P; Potts, Jaimie; Scanes, Peter; Johnston, Emma L

2018-05-15

Coastal waterways are increasingly exposed to multiple stressors, e.g. contaminants that can be delivered via pulse or press exposures. Therefore, it is crucial that ecological impacts can be differentiated among stressors to manage ecosystem threats. We investigated microbial community development in sediments exposed to press and pulse stressors. Press exposures were created with in situ mesocosm sediments containing a range of 'metal' concentrations (sediment contaminated with multiple metal(loid)s) and organic enrichment (fertiliser), while the pulse exposure was simulated by a single dose of organic fertiliser. All treatments and exposure concentrations were crossed in a fully factorial field experiment. We used amplicon sequencing to compare the sensitivity of the 1) total (DNA) and active (RNA) component of 2) bacterial (16S rRNA) and eukaryotic (18S rRNA) communities to contaminant exposures. Overall microbial community change was greater when exposed to press than pulse stressors, with the bacterial community responding more strongly than the eukaryotes. The total bacterial community represents a more time-integrated measure of change and proved to be more sensitive to multiple stressors than the active community. Metals and organic enrichment treatments interacted such that the effect of metals was weaker when the sediment was organically enriched. Taxa-level analyses revealed that press enrichment resulted in potential functional changes, mainly involving nitrogen cycling. Furthermore, enrichment generally reduced the abundance of active eukaryotes in the sediment. As well as demonstrating interactive impacts of metals and organic enrichment, this study highlights the sensitivity of next-generation sequencing for ecosystem biomonitoring of interacting stressors and identifies opportunities for more targeted application. Copyright © 2018 Elsevier B.V. All rights reserved.

Microbial community structure and methane-cycling activity of subsurface sediments at Mississippi Canyon 118 before the Deepwater Horizon disaster

NASA Astrophysics Data System (ADS)

Underwood, Sarah; Lapham, Laura; Teske, Andreas; Lloyd, Karen G.

2016-07-01

The Deepwater Horizon disaster caused a shift in microbial communities in Gulf of Mexico seawater, but less is known about the baseline for microbial communities in the underlying sediments. We compared 16S rRNA and functional gene sequences deriving from DNA and RNA with geochemical profiles (sulfate and methane concentrations, δ13C of methane and carbon dioxide, and chloride concentrations) of a sediment gravity core from the upper continental slope of the northwestern Gulf of Mexico (MC118) in 2008, 15 km from the spill site. The highest number of archaeal sequences were ANME-1 and ANME-2 archaea in the sulfate-reducing upper core segments (12 and 42 cmbsf), ANME-1 and Methanomicrobiales in the middle methanogenic depths (200 and 235 cmbsf), and ANME-1 at the deepest depths (309, 400, and 424 cmbsf). The presence of mcrA gene transcripts showed that members of the ANME-1 group are active throughout the core and transcribe the mcrA gene, a key gene of methanogenesis and anaerobic methane oxidation. The bacterial community consists mostly of members of the Deltaproteobacteria, Chloroflexi, Cytophaga, Epsilonproteobacteria, and the Japan Sea Group 1 throughout the core. The commonly detected genera of gammaproteobacterial hydrocarbon-degrading bacteria in the water column are not found in this sediment survey, indicating that the benthic sediment is an unlikely reservoir for these aerobes. However, the sediments contain members of the sulfate-reducing families Desulfobulbaceae and Desulfobacteraceae, some members of which degrade and completely oxidize aromatic hydrocarbons and alkanes, and the Desulfobacterium anilini lineage of obligately aromatics-degrading sulfate reducers. Thus, the benthic sediments are the most likely reservoir for the active deltaproteobacterial populations that were observed repeatedly after the Deepwater Horizon spill in the fall of 2010.

Linking Specific Heterotrophic Bacterial Populations to Bioreduction of Uranium and Nitrate in Contaminated Subsurface Sediments by Using Stable Isotope Probing▿†

PubMed Central

Akob, Denise M.; Kerkhof, Lee; Küsel, Kirsten; Watson, David B.; Palumbo, Anthony V.; Kostka, Joel E.

2011-01-01

Shifts in terminal electron-accepting processes during biostimulation of uranium-contaminated sediments were linked to the composition of stimulated microbial populations using DNA-based stable isotope probing. Nitrate reduction preceded U(VI) and Fe(III) reduction in [13C]ethanol-amended microcosms. The predominant, active denitrifying microbial groups were identified as members of the Betaproteobacteria, whereas Actinobacteria dominated under metal-reducing conditions. PMID:21948831

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments.

PubMed

Hernsdorf, Alex W; Amano, Yuki; Miyakawa, Kazuya; Ise, Kotaro; Suzuki, Yohey; Anantharaman, Karthik; Probst, Alexander; Burstein, David; Thomas, Brian C; Banfield, Jillian F

2017-08-01

Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H 2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H 2 , often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H 2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H 2 consumption and retardation of radionuclide migration.

Methane related changes in prokaryotic activity along geochemical profiles in sediments of Lake Kinneret (Israel)

NASA Astrophysics Data System (ADS)

Bar Or, I.; Ben-Dov, E.; Kushmaro, A.; Eckert, W.; Sivan, O.

2014-06-01

Microbial methane oxidation process (methanotrophy) is the primary control on the emission of the greenhouse gas methane (CH4) to the atmosphere. In terrestrial environments, aerobic methanotrophic bacteria are mainly responsible for oxidizing the methane. In marine sediments the coupling of the anaerobic oxidation of methane (AOM) with sulfate reduction, often by a consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria, was found to consume almost all the upward diffusing methane. Recently, we showed geochemical evidence for AOM driven by iron reduction in Lake Kinneret (LK) (Israel) deep sediments and suggested that this process can be an important global methane sink. The goal of the present study was to link the geochemical gradients found in the porewater (chemical and isotope profiles) with possible changes in microbial community structure. Specifically, we examined the possible shift in the microbial community in the deep iron-driven AOM zone and its similarity to known sulfate driven AOM populations. Screening of archaeal 16S rRNA gene sequences revealed Thaumarchaeota and Euryarchaeota as the dominant phyla in the sediment. Thaumarchaeota, which belongs to the family of copper containing membrane-bound monooxgenases, increased with depth while Euryarchaeota decreased. This may indicate the involvement of Thaumarchaeota, which were discovered to be ammonia oxidizers but whose activity could also be linked to methane, in AOM in the deep sediment. ANMEs sequences were not found in the clone libraries, suggesting that iron-driven AOM is not through sulfate. Bacterial 16S rRNA sequences displayed shifts in community diversity with depth. Proteobacteria and Chloroflexi increased with depth, which could be connected with their different dissimilatory anaerobic processes. The observed changes in microbial community structure suggest possible direct and indirect mechanisms for iron-driven AOM in deep sediments.

Biofilm-induced bioclogging produces sharp interfaces in hyporheic flow, redox conditions, and microbial community structure

NASA Astrophysics Data System (ADS)

Caruso, Alice; Boano, Fulvio; Ridolfi, Luca; Chopp, David L.; Packman, Aaron

2017-05-01

Riverbed sediments host important biogeochemical processes that play a key role in nutrient dynamics. Sedimentary nutrient transformations are mediated by bacteria in the form of attached biofilms. The influence of microbial metabolic activity on the hydrochemical conditions within the hyporheic zone is poorly understood. We present a hydrobiogeochemical model to assess how the growth of heterotrophic and autotrophic biomass affects the transport and transformation of dissolved nitrogen compounds in bed form-induced hyporheic zones. Coupling between hyporheic exchange, nitrogen metabolism, and biomass growth leads to an equilibrium between permeability reduction and microbial metabolism that yields shallow hyporheic flows in a region with low permeability and high rates of microbial metabolism near the stream-sediment interface. The results show that the bioclogging caused by microbial growth can constrain rates and patterns of hyporheic fluxes and microbial transformation rate in many streams.

Benthic microbial abundance and activities in an intensively trawled ecosystem (Thermaikos Gulf, Aegean Sea)

NASA Astrophysics Data System (ADS)

Polymenakou, Paraskevi N.; Pusceddu, Antonio; Tselepides, Anastasios; Polychronaki, Thalia; Giannakourou, Antonia; Fiordelmondo, Carla; Hatziyanni, Eleni; Danovaro, Roberto

2005-12-01

Abundance of benthic bacteria, heterotrophic nanoflagellates and ciliates, extracellular enzymatic activities, bacterial C production, C mineralisation and sediment community oxygen consumption rates were measured in the Thermaikos Gulf (Northeastern Mediterranean), before (September 2001), and during intense trawling activities (October 2001 and February 2002). The biochemical composition of sedimentary organic matter has revealed that bottom trawling had an effect on the trophic state of Thermaikos Gulf. Changes on the benthic microbial food web were also recorded, during the three sampling seasons. Even though trawling-induced sediment resuspension did not alter significantly the abundance of the microbial components, with the exception of the most impacted station, it determined changes regarding their relative importance. Thus, the ratios of bacterium to nanoflagellates and ciliate to nanoflagellates abundance increased in the trawled stations, causing a sudden increase in bacterial C production, in comparison to the non-trawled station. Four months later, the effects of trawling on the microbial food web were less evident, masked possibly by the drastic decrease in the water temperature. The results of the present work suggest that bottom trawling induces alteration of the sedimentological variables and can be considered as a factor affecting the function of the microbial food web in marine coastal ecosystems. These alterations cause faster mobilisation of organic C buried in the sediment and increase nutrient concentrations and availability in the system, thus inducing an effect that could lead to coastal eutrophication.

Soil Microbial Community Contribution to Small Headwater Stream Metabolism.

NASA Astrophysics Data System (ADS)

Clapcott, J. E.; Gooderham, J. P.; Barmuta, L. A.; Davies, P. E.

2005-05-01

The temporal dynamics of sediment respiration were examined in seven small headwater streams in forested catchments in 2004. A strong seasonal response was observed with higher respiration rates in depositional zones than in gravel runs. The data were also examined in the context of proportional habitat distributions that highlighted the importance of high flow events in shaping whole stream metabolic budgets. This study specifically examines the question of terrestrial soil respiration contribution to whole stream metabolism by the controlled inundation of terrestrial soils. The experiment included six experimentally inundated terrestrial zones, six terrestrial controls, and six in-stream depositional zones. Sediment bacterial respiration was measured using 14C leucine incorporation and cotton strip bioassays were also employed to provide an indicative measure of sediment microbial activity. Despite high variability and exhibiting significantly lower bacterial activity than in-stream sediments, modelling using flow data and habitat mapping illustrated the important contribution of terrestrial soil respiration to the whole stream metabolic budgets of small headwater streams. In addition, microbial community composition examined using phospholipid fatty acid analysis clearly differentiated between terrestrial and aquatic communities. Freshly inundated terrestrial communities remained similar to un-inundated controls after 28 days.

Stimulation of Microbially Mediated Arsenic Release in Bangladesh Aquifers by Young Carbon Indicated by Radiocarbon Analysis of Sedimentary Bacterial Lipids.

PubMed

Whaley-Martin, K J; Mailloux, B J; van Geen, A; Bostick, B C; Silvern, R F; Kim, C; Ahmed, K M; Choudhury, I; Slater, G F

2016-07-19

The sources of reduced carbon driving the microbially mediated release of arsenic to shallow groundwater in Bangladesh remain poorly understood. Using radiocarbon analysis of phospholipid fatty acids (PLFAs) and potential carbon pools, the abundance and carbon sources of the active, sediment-associated, in situ bacterial communities inhabiting shallow aquifers (<30 m) at two sites in Araihazar, Bangladesh, were investigated. At both sites, sedimentary organic carbon (SOC) Δ(14)C signatures of -631 ± 54‰ (n = 12) were significantly depleted relative to dissolved inorganic carbon (DIC) of +24 ± 30‰ and dissolved organic carbon (DOC) of -230 ± 100‰. Sediment-associated PLFA Δ(14)C signatures (n = 10) at Site F (-167‰ to +20‰) and Site B (-163‰ to +21‰) were highly consistent and indicated utilization of carbon sources younger than the SOC, likely from the DOC pool. Sediment-associated PLFA Δ(14)C signatures were consistent with previously determined Δ(14)C signatures of microbial DNA sampled from groundwater at Site F indicating that the carbon source for these two components of the subsurface microbial community is consistent and is temporally stable over the two years between studies. These results demonstrate that the utilization of relatively young carbon sources by the subsurface microbial community occurs at sites with varying hydrology. Further they indicate that these young carbon sources drive the metabolism of the more abundant sediment-associated microbial communities that are presumably more capable of Fe reduction and associated release of As. This implies that an introduction of younger carbon to as of yet unaffected sediments (such as those comprising the deeper Pleistocene aquifer) could stimulate microbial communities and result in arsenic release.

Harnessing a methane-fueled, sediment-free mixed microbial community for utilization of distributed sources of natural gas.

PubMed

Marlow, Jeffrey J; Kumar, Amit; Enalls, Brandon C; Reynard, Linda M; Tuross, Noreen; Stephanopoulos, Gregory; Girguis, Peter

2018-06-01

Harnessing the metabolic potential of uncultured microbial communities is a compelling opportunity for the biotechnology industry, an approach that would vastly expand the portfolio of usable feedstocks. Methane is particularly promising because it is abundant and energy-rich, yet the most efficient methane-activating metabolic pathways involve mixed communities of anaerobic methanotrophic archaea and sulfate reducing bacteria. These communities oxidize methane at high catabolic efficiency and produce chemically reduced by-products at a comparable rate and in near-stoichiometric proportion to methane consumption. These reduced compounds can be used for feedstock and downstream chemical production, and at the production rates observed in situ they are an appealing, cost-effective prospect. Notably, the microbial constituents responsible for this bioconversion are most prominent in select deep-sea sediments, and while they can be kept active at surface pressures, they have not yet been cultured in the lab. In an industrial capacity, deep-sea sediments could be periodically recovered and replenished, but the associated technical challenges and substantial costs make this an untenable approach for full-scale operations. In this study, we present a novel method for incorporating methanotrophic communities into bioindustrial processes through abstraction onto low mass, easily transportable carbon cloth artificial substrates. Using Gulf of Mexico methane seep sediment as inoculum, optimal physicochemical parameters were established for methane-oxidizing, sulfide-generating mesocosm incubations. Metabolic activity required >∼40% seawater salinity, peaking at 100% salinity and 35 °C. Microbial communities were successfully transferred to a carbon cloth substrate, and rates of methane-dependent sulfide production increased more than threefold per unit volume. Phylogenetic analyses indicated that carbon cloth-based communities were substantially streamlined and were dominated by Desulfotomaculum geothermicum. Fluorescence in situ hybridization microscopy with carbon cloth fibers revealed a novel spatial arrangement of anaerobic methanotrophs and sulfate reducing bacteria suggestive of an electronic coupling enabled by the artificial substrate. This system: 1) enables a more targeted manipulation of methane-activating microbial communities using a low-mass and sediment-free substrate; 2) holds promise for the simultaneous consumption of a strong greenhouse gas and the generation of usable downstream products; and 3) furthers the broader adoption of uncultured, mixed microbial communities for biotechnological use. © 2018 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals Inc.

Use of phytoremediated sediments dredged in maritime port as plant nursery growing media.

PubMed

Mattei, Paola; D'Acqui, Luigi P; Nicese, Francesco P; Lazzerini, Giulio; Masciandaro, Grazia; Macci, Cristina; Doni, Serena; Sarteschi, Francesco; Giagnoni, Laura; Renella, Giancarlo

2017-01-15

We evaluated the potential of a phytoremediated sediment (TR) dredged from maritime port as peat-free growth substrate for seven ornamental plants, in comparison with an untreated sediment (NT), in a greenhouse experiment. The studied plants were Quercus ilex, Photinia x fraseri, Viburnum tinus, Cistus albidus, Raphiolepis indica, Westringia fruticosa and Teucrium fruticans. Plant growth was monitored for ten months, and the changes in the physico-chemical properties, toxicity, microbial biomass and enzyme activities involved in the C, P and N cycles were also monitored during the plant growth period. The results showed that the studied ornamental plants could grow on both NT and TR sediments, but that the growth was higher on TR sediment. The plant growth induced changes in the sediment chemical functional groups, with clear separation between NT and TR sediments for each of the studied plant. Microbial biomass and enzyme activities significantly increased during the plant growth, more in TR than in NT sediment. Toxicity was detected in NT sediments during the plant growth whereas it was not observed in NT sediments during the whole growth period. We concluded that phytoremediation converted the dredged maritime sediments into suitable substrates for growing ornamental plants, and that the re-use by plant nursery industry can be a sustainable management and valorization for remediated sediments. Copyright © 2016 Elsevier Ltd. All rights reserved.

Response of a salt marsh microbial community to metal contamination

NASA Astrophysics Data System (ADS)

Mucha, Ana P.; Teixeira, Catarina; Reis, Izabela; Magalhães, Catarina; Bordalo, Adriano A.; Almeida, C. Marisa R.

2013-09-01

Salt marshes are important sinks for contaminants, namely metals that tend to accumulate around plant roots and could eventually be taken up in a process known as phytoremediation. On the other hand, microbial communities display important roles in the salt marsh ecosystems, such as recycling of nutrients and/or degradation of organic contaminants. Thus, plants can benefit from the microbial activity in the phytoremediation process. Nevertheless, above certain levels, metals are known to be toxic to microorganisms, fact that can eventually compromise their ecological functions. In this vein, the aim of present study was to investigate, in the laboratory, the effect of selected metals (Cd, Cu and Pb) on the microbial communities associated to the roots of two salt marsh plants. Sediments colonized by Juncus maritimus and Phragmites australis were collected in the River Lima estuary (NW Portugal), and spiked with each of the metals at three different Effects Range-Median (ERM) concentrations (1, 10×, 50×), being ERM the sediment quality guideline that indicates the concentration above which adverse biological effects may frequently occur. Spiked sediments were incubated with a nutritive saline solution, being left in the dark under constant agitation for 7 days. The results showed that, despite the initial sediments colonized by J. maritimus and P. australis displayed significant (p < 0.05) differences in terms of microbial community structure (evaluated by ARISA), they presented similar microbial abundances (estimated by DAPI). Also, in terms of microbial abundance, both sediments showed a similar response to metal addition, with a decrease in number of cells only observed for the higher addition of Cu. Nevertheless, both Cu and Pb, at intermediate metals levels promote a shift in the microbial community structure, with possibly effect on the ecological function of these microbial communities in salt marshes. These changes may affect plants phytoremediation potential and further work on this subject is in need.

Distinctive Sediment and Adjacent Groundwater Microbial Communities in Bangladesh Aquifers Suggested Through Microbial Lipid Distribution and δ13C Analysis

NASA Astrophysics Data System (ADS)

Martin, K. J. W.; van Geen, A.; Bostick, B. C.; Mailloux, B. J.; Ahmed, K. M.; Choudhury, I.; Slater, G.

2016-12-01

Arsenic groundwater contamination throughout shallow aquifer sediments in Southern Asia has resulted in a large-scale human health crisis. There is a strong consensus that microbial iron reduction coupled to organic carbon oxidation is the predominant mechanism driving this arsenic release. However, limited research has examined the composition and functioning of the indigenous microbial communities. Further, such research has varied between studies targeting microbial communities associated with groundwater versus those associated with sediments. The overall aim of this research study was to use microbial lipid biomarkers of bacterial and micro-eukaryal (phospholipid fatty acids (PLFA)) and archaea (di- and tetra- bound ether lipids) distributions and δ13C analysis to compare the indigenous sedimentary-associated microbial communities with the groundwater-associated microbial communities in Bangladesh aquifers. Field sampling was carried out at four locations (Site B, F, SAM and CAT) in the Araihazar Upazila, Bangladesh in 2013 and 2015. A significant difference (p<0.00001) was found between the cell abundances in the groundwater-associated (2.8 x 101 to 3.0 x 102 cells/mL) (n=9) and the sediment-associated communities (averaging 1.1 x 107 cells/gram (n=19). Long-chain fatty acid methyl esters (FAME's) (C22-C29) derived from micro-eukaryotes were present in the sediments of both Site B and F comprising up to 17 % and 7% (mole %) of the total FAME distribution respectively but not detected in any of the groundwater filters. Shallow Site B sedimentary PLFA showed a progressive depletion in δ13C with depth from -24 to -31 ‰, whereas Site F sedimentary PLFA from similar depths did not show the same trend. Groundwater PLFA from Site B (14 m) contained FAME 18:1 with an average δ13C of -41‰, possibly indicating methanogenic activity (methanogen lipid analysis is ongoing). The results of this study highly suggests that Bangaldesh aquifer sediment and groundwater microbial communties are distinctive and cannot be used interchangably within future research studies investigating microbal arsenic release in these systems.

Saturated CO2 inhibits microbial processes in CO2-vented deep-sea sediments

NASA Astrophysics Data System (ADS)

de Beer, D.; Haeckel, M.; Neumann, J.; Wegener, G.; Inagaki, F.; Boetius, A.

2013-02-01

This study focused on biogeochemical processes and microbial activity in sediments of a natural deep-sea CO2 seepage area (Yonaguni Knoll IV hydrothermal system, Japan). The aim was to assess the influence of the geochemical conditions occurring in highly acidic and CO2 saturated sediments on sulphate reduction (SR) and anaerobic methane oxidation (AOM). Porewater chemistry was investigated from retrieved sediment cores and in situ by microsensor profiling. The sites sampled around a sediment-hosted hydrothermal CO2 vent were very heterogeneous in porewater chemistry, indicating a complex leakage pattern. Near the vents, droplets of liquid CO2 were observed to emanate from the sediments, and the pH reached approximately 4.5 in a sediment depth >6 cm, as determined in situ by microsensors. Methane and sulphate co-occurred in most sediment samples from the vicinity of the vents down to a depth of at least 3 m. However, SR and AOM were restricted to the upper 7-15 cm below seafloor, although neither temperature, low pH, nor the availability of methane and sulphate could be limiting microbial activity. We argue that the extremely high subsurface concentrations of dissolved CO2 (1000-1700 mM), through the ensuing high H2CO3 levels (approx. 1-2 mM) uncouples the proton-motive-force (PMF) and thus inhibits biological energy conservation by ATPase-driven phosphorylation. This limits life to the surface sediment horizons above the liquid CO2 phase, where less extreme conditions prevail. Our results may have to be taken into consideration in assessing the consequences of deep-sea CO2 sequestration on benthic element cycling and on the local ecosystem state.

Effect of Water Chemistry and Hydrodynamics on Nitrogen Transformation Activity and Microbial Community Functional Potential in Hyporheic Zone Sediment Columns

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Yuanyuan; Liu, Chongxuan; Nelson, William C.

Nitrogen (N) transformation in hyporheic zone (HZ) is an important component in N-cycling in ecosystems. A column study was conducted to investigate N transformation in a HZ sediment with a focus on how characteristic HZ properties including water chemistry, fluid residence time, and dynamic groundwater and surface water exchange affect on N transformation. Metagenomic and quantitative polymerase chain reaction (qPCR) analyses were performed to evaluate the dynamic changes in microbial community structure and its function in response to N transformation. The results indicated that N transformation in the HZ sediment was collectively controlled by microbial community functions including: denitrification, dissimilatorymore » nitrate reduction to ammonium (DNRA), nitrification, and anaerobic ammonium oxidation (anammox). However, the spatial distribution of the microbial community functions and associated biogeochemical reaction rates and products changed quickly in response to experimental perturbation, and was influenced by various factors including water chemistry (dissolved O2 and N species), desorption of sediment associated organic carbon, ion exchange reactions of NH4+, and fluid residence time. The results of this study implied that the microbial community in the HZ would exhibit strong function zonation along N and O gradients, which in turn would control the rates and products of N transformation.« less

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

PubMed Central

Imachi, Hiroyuki; Aoi, Ken; Tasumi, Eiji; Saito, Yumi; Yamanaka, Yuko; Saito, Yayoi; Yamaguchi, Takashi; Tomaru, Hitoshi; Takeuchi, Rika; Morono, Yuki; Inagaki, Fumio; Takai, Ken

2011-01-01

Microbial methanogenesis in subseafloor sediments is a key process in the carbon cycle on the Earth. However, the cultivation-dependent evidences have been poorly demonstrated. Here we report the cultivation of a methanogenic microbial consortium from subseafloor sediments using a continuous-flow-type bioreactor with polyurethane sponges as microbial habitats, called down-flow hanging sponge (DHS) reactor. We anaerobically incubated methane-rich core sediments collected from off Shimokita Peninsula, Japan, for 826 days in the reactor at 10 °C. Synthetic seawater supplemented with glucose, yeast extract, acetate and propionate as potential energy sources was provided into the reactor. After 289 days of operation, microbiological methane production became evident. Fluorescence in situ hybridization analysis revealed the presence of metabolically active microbial cells with various morphologies in the reactor. DNA- and RNA-based phylogenetic analyses targeting 16S rRNA indicated the successful growth of phylogenetically diverse microbial components during cultivation in the reactor. Most of the phylotypes in the reactor, once it made methane, were more closely related to culture sequences than to the subsurface environmental sequence. Potentially methanogenic phylotypes related to the genera Methanobacterium, Methanococcoides and Methanosarcina were predominantly detected concomitantly with methane production, while uncultured archaeal phylotypes were also detected. Using the methanogenic community enrichment as subsequent inocula, traditional batch-type cultivations led to the successful isolation of several anaerobic microbes including those methanogens. Our results substantiate that the DHS bioreactor is a useful system for the enrichment of numerous fastidious microbes from subseafloor sediments and will enable the physiological and ecological characterization of pure cultures of previously uncultivated subseafloor microbial life. PMID:21654849

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor.

PubMed

Imachi, Hiroyuki; Aoi, Ken; Tasumi, Eiji; Saito, Yumi; Yamanaka, Yuko; Saito, Yayoi; Yamaguchi, Takashi; Tomaru, Hitoshi; Takeuchi, Rika; Morono, Yuki; Inagaki, Fumio; Takai, Ken

2011-12-01

Microbial methanogenesis in subseafloor sediments is a key process in the carbon cycle on the Earth. However, the cultivation-dependent evidences have been poorly demonstrated. Here we report the cultivation of a methanogenic microbial consortium from subseafloor sediments using a continuous-flow-type bioreactor with polyurethane sponges as microbial habitats, called down-flow hanging sponge (DHS) reactor. We anaerobically incubated methane-rich core sediments collected from off Shimokita Peninsula, Japan, for 826 days in the reactor at 10 °C. Synthetic seawater supplemented with glucose, yeast extract, acetate and propionate as potential energy sources was provided into the reactor. After 289 days of operation, microbiological methane production became evident. Fluorescence in situ hybridization analysis revealed the presence of metabolically active microbial cells with various morphologies in the reactor. DNA- and RNA-based phylogenetic analyses targeting 16S rRNA indicated the successful growth of phylogenetically diverse microbial components during cultivation in the reactor. Most of the phylotypes in the reactor, once it made methane, were more closely related to culture sequences than to the subsurface environmental sequence. Potentially methanogenic phylotypes related to the genera Methanobacterium, Methanococcoides and Methanosarcina were predominantly detected concomitantly with methane production, while uncultured archaeal phylotypes were also detected. Using the methanogenic community enrichment as subsequent inocula, traditional batch-type cultivations led to the successful isolation of several anaerobic microbes including those methanogens. Our results substantiate that the DHS bioreactor is a useful system for the enrichment of numerous fastidious microbes from subseafloor sediments and will enable the physiological and ecological characterization of pure cultures of previously uncultivated subseafloor microbial life.

Shifts in microbial community structure and function in stream sediments during experimentally simulated riparian succession.

PubMed

Frossard, Aline; Gerull, Linda; Mutz, Michael; Gessner, Mark O

2013-05-01

Successional changes of terrestrial vegetation can profoundly influence stream ecosystem structure and function. We hypothesized that microbial enzyme production and community structure in stream beds depend on terrestrial litter inputs that reflect different stages of riparian succession. Outdoor experimental channels were supplied with leaf-litter of varying quantities and qualities to mimic litter supply during five successional stages: (1) an initial biofilm stage; (2) an open-land stage with grass litter; (3) a transitional stage with mixed grass and birch litter; (4) an early forest stage with birch litter; and (5) an advanced forest stage with 2.5 × the amount of birch litter. Mean potential activities of nitrogen- and phosphorus-acquiring enzymes in sediments (20.7 and 67.3 μmol g(-1) dry mass) were 12-70 times greater than those of carbon-acquiring enzymes (0.96-1.71 μmol g(-1) dry mass), with the former reduced 1.3-8.3-fold in channels with tree litter. These patterns could suggest gradually diminishing nutrient limitation of microbial activity during riparian succession, potentially linked both to an increasing supply by the added litter and to a lower nutrient demand as algal biomass and labile carbon supply by photosynthetic exudates declined. As the observed shifts in nutrient-acquiring enzymes were reflected in changes of sediment microbial communities, these results indicate that both the type and density of terrestrial vegetation control microbial community structure and function in stream sediments, particularly enzyme production related to nutrient cycling. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Anoxia stimulates microbially catalyzed metal release from Animas River sediments

DOE PAGES

Saup, Casey M.; Williams, Kenneth H.; Rodríguez-Freire, Lucía; ...

2017-03-06

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amendedmore » with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2-reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.« less

Anoxia stimulates microbially catalyzed metal release from Animas River sediments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saup, Casey M.; Williams, Kenneth H.; Rodríguez-Freire, Lucía

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amendedmore » with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2-reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.« less

Structural and functional diversity of microbial communities from a lake sediment contaminated with trenbolone, an endocrine-disrupting chemical.

PubMed

Radl, Viviane; Pritsch, Karin; Munch, Jean Charles; Schloter, Michael

2005-09-01

Effects of trenbolone (TBOH), a hormone used in cattle production, on the structure and function of microbial communities in a fresh water sediment from a lake in Southern Germany were studied in a microcosm experiment. The microbial community structure and the total gene pool of the sediment, assessed by 16S rRNA/rDNA and RAPD fingerprint analysis, respectively, were not significantly affected by TBOH. In contrast, the N-acetyl-glucosaminidase activity was almost 50% lower in TBOH treated samples (P<0.05). Also, the substrate utilization potential, measured using the BIOLOG system, was reduced after TBOH treatment. Interestingly, this potential did not recover at the end of the experiment, i.e. 19 days after the addition of the chemical. Repeated application of TBOH did not lead to an additional reduction in the substrate utilization potential. Overall results indicate that microbial community function was more sensitive to TBOH treatment than the community structure and the total gene pool.

Role of environmental factors and microorganisms in determining the fate of polycyclic aromatic hydrocarbons in the marine environment

PubMed Central

Duran, Robert; Cravo-Laureau, Cristiana

2016-01-01

Polycyclic aromatic hydrocarbons (PAHs) are widespread in marine ecosystems and originate from natural sources and anthropogenic activities. PAHs enter the marine environment in two main ways, corresponding to chronic pollution or acute pollution by oil spills. The global PAH fluxes in marine environments are controlled by the microbial degradation and the biological pump, which plays a role in particle settling and in sequestration through bioaccumulation. Due to their low water solubility and hydrophobic nature, PAHs tightly adhere to sediments leading to accumulation in coastal and deep sediments. Microbial assemblages play an important role in determining the fate of PAHs in water and sediments, supporting the functioning of biogeochemical cycles and the microbial loop. This review summarises the knowledge recently acquired in terms of both chronic and acute PAH pollution. The importance of the microbial ecology in PAH-polluted marine ecosystems is highlighted as well as the importance of gaining further in-depth knowledge of the environmental services provided by microorganisms. PMID:28201512

Development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium.

PubMed

Teixeira, Catarina; Almeida, C Marisa R; Nunes da Silva, Marta; Bordalo, Adriano A; Mucha, Ana P

2014-09-15

Microbial assisted phytoremediation is a promising, though yet poorly explored, new remediation technique. The aim of this study was to develop autochthonous microbial consortia resistant to cadmium that could enhance phytoremediation of salt-marsh sediments contaminated with this metal. The microbial consortia were selectively enriched from rhizosediments colonized by Juncus maritimus and Phragmites australis. The obtained consortia presented similar microbial abundance but a fairly different community structure, showing that the microbial community was a function of the sediment from which the consortia were enriched. The effect of the bioaugmentation with the developed consortia on cadmium uptake, and the microbial community structure associated to the different sediments were assessed using a microcosm experiment. Our results showed that the addition of the cadmium resistant microbial consortia increased J. maritimus metal phytostabilization capacity. On the other hand, in P. australis, microbial consortia amendment promoted metal phytoextraction. The addition of the consortia did not alter the bacterial structure present in the sediments at the end of the experiments. This study provides new evidences that the development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium might be a simple, efficient, and environmental friendly remediation procedure. Development of autochthonous microbial consortia resistant to cadmium that enhanced phytoremediation by salt-marsh plants, without a long term effect on sediment bacterial diversity. Copyright © 2014 Elsevier B.V. All rights reserved.

Electricity generation by anaerobic bacteria and anoxic sediments from hypersaline soda lakes

USGS Publications Warehouse

Miller, L.G.; Oremland, R.S.

2008-01-01

Anaerobic bacteria and anoxic sediments from soda lakes produced electricity in microbial fuel cells (MFCs). No electricity was generated in the absence of bacterial metabolism. Arsenate respiring bacteria isolated from moderately hypersaline Mono Lake (Bacillus selenitireducens), and salt-saturated Searles Lake, CA (strain SLAS-1) oxidized lactate using arsenate as the electron acceptor. However, these cultures grew equally well without added arsenate using the MFC anode as their electron acceptor, and in the process oxidized lactate more efficiently. The decrease in electricity generation by consumption of added alternative electron acceptors (i.e. arsenate) which competed with the anode for available electrons proved to be a useful indicator of microbial activity and hence life in the fuel cells. Shaken sediment slurries from these two lakes also generated electricity, with or without added lactate. Hydrogen added to sediment slurries was consumed but did not stimulate electricity production. Finally, electricity was generated in statically incubated "intact" sediment cores from these lakes. More power was produced in sediment from Mono Lake than from Searles Lake, however microbial fuel cells could detect low levels of metabolism operating under moderate and extreme conditions of salt stress. ?? 2008 US Government.

Elucidating Microbial Species-Specific Effects on Organic Matter Transformation in Marine Sediments

NASA Astrophysics Data System (ADS)

Mahmoudi, N.; Enke, T. N.; Beaupre, S. R.; Teske, A.; Cordero, O. X.; Pearson, A.

2017-12-01

Microbial transformation and decomposition of organic matter in sediments constitutes one of the largest fluxes of carbon in marine environments. Mineralization of sedimentary organic matter by microorganisms results in selective degradation such that bioavailable or accessible compounds are rapidly metabolized while more recalcitrant, complex compounds are preserved and buried in sediment. Recent studies have found that the ability to use different carbon sources appears to vary among microorganisms, suggesting that the availability of certain pools of carbon can be specific to the taxa that utilize the pool. This implies that organic matter mineralization in marine environments may depend on the metabolic potential of the microbial populations that are present and active. The goal of our study was to investigate the extent to which organic matter availability and transformation may be species-specific using sediment from Guaymas Basin (Gulf of California). We carried out time-series incubations using bacterial isolates and sterilized sediment in the IsoCaRB system which allowed us to measure the production rates and natural isotopic signatures (δ13C and Δ14C) of microbially-respired CO2. Separate incubations using two different marine bacterial isolates (Vibrio sp. and Pseudoalteromonas sp.) and sterilized Guaymas Basin sediment under oxic conditions showed that the rate and total quantity of organic matter metabolized by these two species differs. Approximately twice as much CO2 was collected during the Vibrio sp. incubation compared to the Pseudoalteromonas sp. incubation. Moreover, the rate at which organic matter was metabolized by the Vibrio sp. was much higher than the Pseudoalteromonas sp. indicating the intrinsic availability of organic matter in sediments may depend on the species that is present and active. Isotopic analyses of microbially respired CO2 will be used to constrain the type and age of organic matter that is accessible to each species. Moreover, molecular analysis of subsamples collected from each incubation will link carbon utilization with the underlying gene expression. Our study sheds light on the degree to which the metabolic capacities of microorganisms affect carbon transformation in sedimentary environments.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system.

PubMed

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; Van Nostrand, J D; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-10-04

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S 0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S 0 and Fe 2+ , which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

NASA Astrophysics Data System (ADS)

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-10-01

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

PubMed Central

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; Van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-01-01

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system. PMID:27698381

SULFATE-REDUCING BACTERIA IN THE SEAGRASS RHIZOSPHERE

EPA Science Inventory

Seagrasses are rooted in anoxic sediments that support high levels of microbial activity including utilization of sulfate as a terminal electron acceptor which is reduced to sulfide. Sulfate reduction in seagrass bed sediments is stimulated by input of organic carbon through the ...

Milankovitch-scale correlations between deeply buried microbial populations and biogenic ooze lithology

USGS Publications Warehouse

Aiello, I.W.; Bekins, B.A.

2010-01-01

The recent discoveries of large, active populations of microbes in the subseafloor of the world's oceans supports the impact of the deep biosphere biota on global biogeochemical cycles and raises important questions concerning the functioning of these extreme environments for life. These investigations demonstrated that subseafloor microbes are unevenly distributed and that cell abundances and metabolic activities are often independent from sediment depths, with increased prokaryotic activity at geochemical and/or sedimentary interfaces. In this study we demonstrate that microbial populations vary at the scale of individual beds in the biogenic oozes of a drill site in the eastern equatorial Pacific (Ocean Drilling Program Leg 201, Site 1226). We relate bedding-scale changes in biogenic ooze sediment composition to organic carbon (OC) and microbial cell concentrations using high-resolution color reflectance data as proxy for lithology. Our analyses demonstrate that microbial concentrations are an order of magnitude higher in the more organic-rich diatom oozes than in the nannofossil oozes. The variations mimic small-scale variations in diatom abundance and OC, indicating that the modern distribution of microbial biomass is ultimately controlled by Milankovitch-frequency variations in past oceanographic conditions. ?? 2010 Geological Society of America.

Impact of silver nanoparticles on benthic prokaryotes in heavy metal-contaminated estuarine sediments in a tropical environment.

PubMed

Antizar-Ladislao, B; Bhattacharya, B D; Ray Chaudhuri, S; Sarkar, S K

2015-10-15

Little knowledge is available about the potential impact of commercial silver nanoparticles (Ag-NPs) on estuarine microbial communities. The Hugli river estuary, India, is susceptible to heavy metals pollution through boat traffic, and there is the potential for Ag-NP exposure via effluent discharged from ongoing municipal and industrial activities located in close proximity. This study investigated the effects of commercial Ag-NPs on native microbial communities in estuarine sediments collected from five stations, using terminal restriction fragment length polymorphism (T-RFLP) technique. An increase in the number of bacteria in consortium in sediments was observed following exposure to Ag-NPs. In general microbial communities may be resistant in estuarine systems to the antimicrobial effects of commercial Ag-NPs, but key microorganisms, such as Pelobacter propionicus, disappeared following exposure to Ag-NPs. In conclusion, the T-RFLP analysis indicated that Ag-NPs have the potential to shape estuarine sediment bacterial community structure. Copyright © 2015 Elsevier Ltd. All rights reserved.

Opportunistic Pathogens and Microbial Communities and Their Associations with Sediment Physical Parameters in Drinking Water Storage Tank Sediments.

PubMed

Qin, Ke; Struewing, Ian; Domingo, Jorge Santo; Lytle, Darren; Lu, Jingrang

2017-10-26

The occurrence and densities of opportunistic pathogens (OPs), the microbial community structure, and their associations with sediment elements from eight water storage tanks in Ohio, West Virginia, and Texas were investigated. The elemental composition of sediments was measured through X-ray fluorescence (XRF) spectra. The occurrence and densities of OPs and amoeba hosts (i.e., Legionella spp. and L . pneumophila , Mycobacterium spp., P. aeruginosa , V. vermiformis, Acanthamoeba spp.) were determined using genus- or species-specific qPCR assays. Microbial community analysis was performed using next generation sequencing on the Illumina Miseq platform. Mycobacterium spp. were most frequently detected in the sediments and water samples (88% and 88%), followed by Legionella spp. (50% and 50%), Acanthamoeba spp. (63% and 13%), V. vermiformis (50% and 25%), and P. aeruginosa (0 and 50%) by qPCR method. Comamonadaceae (22.8%), Sphingomonadaceae (10.3%), and Oxalobacteraceae (10.1%) were the most dominant families by sequencing method. Microbial communities in water samples were mostly separated with those in sediment samples, suggesting differences of communities between two matrices even in the same location. There were associations of OPs with microbial communities. Both OPs and microbial community structures were positively associated with some elements (Al and K) in sediments mainly from pipe material corrosions. Opportunistic pathogens presented in both water and sediments, and the latter could act as a reservoir of microbial contamination. There appears to be an association between potential opportunistic pathogens and microbial community structures. These microbial communities may be influenced by constituents within storage tank sediments. The results imply that compositions of microbial community and elements may influence and indicate microbial water quality and pipeline corrosion, and that these constituents may be important for optimal storage tank management within a distribution system.

Opportunistic Pathogens and Microbial Communities and Their Associations with Sediment Physical Parameters in Drinking Water Storage Tank Sediments

PubMed Central

Qin, Ke; Struewing, Ian; Domingo, Jorge Santo; Lytle, Darren

2017-01-01

The occurrence and densities of opportunistic pathogens (OPs), the microbial community structure, and their associations with sediment elements from eight water storage tanks in Ohio, West Virginia, and Texas were investigated. The elemental composition of sediments was measured through X-ray fluorescence (XRF) spectra. The occurrence and densities of OPs and amoeba hosts (i.e., Legionella spp. and L. pneumophila, Mycobacterium spp., P. aeruginosa, V. vermiformis, Acanthamoeba spp.) were determined using genus- or species-specific qPCR assays. Microbial community analysis was performed using next generation sequencing on the Illumina Miseq platform. Mycobacterium spp. were most frequently detected in the sediments and water samples (88% and 88%), followed by Legionella spp. (50% and 50%), Acanthamoeba spp. (63% and 13%), V. vermiformis (50% and 25%), and P. aeruginosa (0 and 50%) by qPCR method. Comamonadaceae (22.8%), Sphingomonadaceae (10.3%), and Oxalobacteraceae (10.1%) were the most dominant families by sequencing method. Microbial communities in water samples were mostly separated with those in sediment samples, suggesting differences of communities between two matrices even in the same location. There were associations of OPs with microbial communities. Both OPs and microbial community structures were positively associated with some elements (Al and K) in sediments mainly from pipe material corrosions. Opportunistic pathogens presented in both water and sediments, and the latter could act as a reservoir of microbial contamination. There appears to be an association between potential opportunistic pathogens and microbial community structures. These microbial communities may be influenced by constituents within storage tank sediments. The results imply that compositions of microbial community and elements may influence and indicate microbial water quality and pipeline corrosion, and that these constituents may be important for optimal storage tank management within a distribution system. PMID:29072631

Establishment of a Polychlorinated Biphenyl-Dechlorinating Microbial Consortium, Specific for Doubly Flanked Chlorines, in a Defined, Sediment-Free Medium

PubMed Central

Wu, Qingzhong; Sowers, Kevin R.; May, Harold D.

2000-01-01

Estuarine sediment from Charleston Harbor, South Carolina, was used as inoculum for the development of an anaerobic enrichment culture that specifically dechlorinates doubly flanked chlorines (i.e., chlorines bound to carbon that are flanked on both sides by other chlorine-carbon bonds) of polychlorinated biphenyls (PCBs). Dechlorination was restricted to the para chlorine in cultures enriched with 10 mM fumarate, 50 ppm (173 μM) 2,3,4,5-tetrachlorobiphenyl, and no sediment. Initially the rate of dechlorination decreased upon the removal of sediment from the medium. However, the dechlorinating activity was sustainable, and following sequential transfer in a defined, sediment-free estuarine medium, the activity increased to levels near that observed with sediment. The culture was nonmethanogenic, and molybdate, ampicillin, chloramphenicol, neomycin, and streptomycin inhibited dechlorination activity; bromoethanesulfonate and vancomycin did not. Addition of 17 PCB congeners indicated that the culture specifically removes double flanked chlorines, preferably in the para position, and does not attack ortho chlorines. This is the first microbial consortium shown to para or meta dechlorinate a PCB congener in a defined sediment-free medium. It is the second PCB-dechlorinating enrichment culture to be sustained in the absence of sediment, but its dechlorinating capabilities are entirely different from those of the other sediment-free PCB-dechlorinating culture, an ortho-dechlorinating consortium, and do not match any previously published Aroclor-dechlorinating patterns. PMID:10618202

Diffusivity in surficial sediments and benthic mats determined by use of a combined N 2O-O 2 microsensor

NASA Astrophysics Data System (ADS)

Glud, Ronnie Nøhr; Jensen, Kim; Revsbech, Niels Peter

1995-01-01

Diffusional characteristics of two biologically active surface sediments were determined by use of a combined N 2O-O 2 microsensor. By analyzing changes in the N2O-gradients in these sediments, it was possible to determine the product ( φDs) for this species with submillimetre depth resolution, where φ is the porosity and Ds the substrate diffusion coefficient. The ( φDs)-value for O 2 could be calculated then from ( φDs)-value for N 2O, because the diffusivity of the two molecules were modified in the same way within the sediment. Both sediments exhibited fine-scale horizontal and vertical variability in diffusion characteristics, and this must be accounted for when analyzing microprofile data. The average ( φDs)-value for N 2O at 20°C for an estuarine surface sediment was 0.93 × 10 -5 cm2 s -1 (at 0-4 mm depth), while the value for the upper 2 mm of a stream sediment covered by a microbial mat was 1.42 × 10 -5 cm 2 s -1. Biological inactivation and oxidation by exposure to an O 2 atmosphere had no effect on the measured ( φDs) for the estuarine sediment; however, the value for the sediment covered by a microbial mat, with dense populations of meiofauna, decreased by 20%. The method presented is ideal for measurements of diffusivity at a high spatial resolution in surficial sediments and densely packed microbial communities.

Deep subsurface microbial processes

USGS Publications Warehouse

Lovley, D.R.; Chapelle, F.H.

1995-01-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of other habitats, the study of deep subsurface microbiology is still in its infancy.

Differences in Hyporheic-Zone Microbial Community Structure along a Heavy-Metal Contamination Gradient

PubMed Central

Feris, Kevin; Ramsey, Philip; Frazar, Chris; Moore, Johnnie N.; Gannon, James E.; Holben, William E.

2003-01-01

The hyporheic zone of a river is nonphotic, has steep chemical and redox gradients, and has a heterotrophic food web based on the consumption of organic carbon entrained from downwelling surface water or from upwelling groundwater. The microbial communities in the hyporheic zone are an important component of these heterotrophic food webs and perform essential functions in lotic ecosystems. Using a suite of methods (denaturing gradient gel electrophoresis, 16S rRNA phylogeny, phospholipid fatty acid analysis, direct microscopic enumeration, and quantitative PCR), we compared the microbial communities inhabiting the hyporheic zone of six different river sites that encompass a wide range of sediment metal loads resulting from large base-metal mining activity in the region. There was no correlation between sediment metal content and the total hyporheic microbial biomass present within each site. However, microbial community structure showed a significant linear relationship with the sediment metal loads. The abundances of four phylogenetic groups (groups I, II, III, and IV) most closely related to α-, β-, and γ-proteobacteria and the cyanobacteria, respectively, were determined. The sediment metal content gradient was positively correlated with group III abundance and negatively correlated with group II abundance. No correlation was apparent with regard to group I or IV abundance. This is the first documentation of a relationship between fluvially deposited heavy-metal contamination and hyporheic microbial community structure. The information presented here may be useful in predicting long-term effects of heavy-metal contamination in streams and provides a basis for further studies of metal effects on hyporheic microbial communities. PMID:12957946

Changing bacterial profile of Sundarbans, the world heritage mangrove: impact of anthropogenic interventions.

PubMed

Chakraborty, Arpita; Bera, Amit; Mukherjee, Arghya; Basak, Pijush; Khan, Imroze; Mondal, Arindam; Roy, Arunava; Bhattacharyya, Anish; SenGupta, Sohan; Roy, Debojyoti; Nag, Sudip; Ghosh, Abhrajyoti; Chattopadhyay, Dhrubajyoti; Bhattacharyya, Maitree

2015-04-01

Mangrove microbial communities and their associated activities have profound impact on biogeochemical cycles. Although microbial composition and structure are known to be influenced by biotic and abiotic factors in the mangrove sediments, finding direct correlations between them remains a challenge. In this study we have explored sediment bacterial diversity of the Sundarbans, a world heritage site using a culture-independent molecular approach. Bacterial diversity was analyzed from three different locations with a history of exposure to differential anthropogenic activities. 16S rRNA gene libraries were constructed and partial sequencing of the clones was performed to identify the microbial strains. We identified bacterial strains known to be involved in a variety of biodegradation/biotransformation processes including hydrocarbon degradation, and heavy metal resistance. Canonical Correspondence Analysis of the environmental and exploratory datasets revealed correlations between the ecological indices associated with pollutant levels and bacterial diversity across the sites. Our results indicate that sites with similar exposure of anthropogenic intervention reflect similar patterns of microbial diversity besides spatial commonalities.

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments

PubMed Central

Kearns, Patrick J.; Angell, John H.; Howard, Evan M.; Deegan, Linda A.; Stanley, Rachel H. R.; Bowen, Jennifer L.

2016-01-01

Microorganisms control key biogeochemical pathways, thus changes in microbial diversity, community structure and activity can affect ecosystem response to environmental drivers. Understanding factors that control the proportion of active microbes in the environment and how they vary when perturbed is critical to anticipating ecosystem response to global change. Increasing supplies of anthropogenic nitrogen to ecosystems globally makes it imperative that we understand how nutrient supply alters active microbial communities. Here we show that nitrogen additions to salt marshes cause a shift in the active microbial community despite no change in the total community. The active community shift causes the proportion of dormant microbial taxa to double, from 45 to 90%, and induces diversity loss in the active portion of the community. Our results suggest that perturbations to salt marshes can drastically alter active microbial communities, however these communities may remain resilient by protecting total diversity through increased dormancy. PMID:27666199

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments.

PubMed

Kearns, Patrick J; Angell, John H; Howard, Evan M; Deegan, Linda A; Stanley, Rachel H R; Bowen, Jennifer L

2016-09-26

Microorganisms control key biogeochemical pathways, thus changes in microbial diversity, community structure and activity can affect ecosystem response to environmental drivers. Understanding factors that control the proportion of active microbes in the environment and how they vary when perturbed is critical to anticipating ecosystem response to global change. Increasing supplies of anthropogenic nitrogen to ecosystems globally makes it imperative that we understand how nutrient supply alters active microbial communities. Here we show that nitrogen additions to salt marshes cause a shift in the active microbial community despite no change in the total community. The active community shift causes the proportion of dormant microbial taxa to double, from 45 to 90%, and induces diversity loss in the active portion of the community. Our results suggest that perturbations to salt marshes can drastically alter active microbial communities, however these communities may remain resilient by protecting total diversity through increased dormancy.

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments

NASA Astrophysics Data System (ADS)

Kearns, Patrick J.; Angell, John H.; Howard, Evan M.; Deegan, Linda A.; Stanley, Rachel H. R.; Bowen, Jennifer L.

2016-09-01

Microorganisms control key biogeochemical pathways, thus changes in microbial diversity, community structure and activity can affect ecosystem response to environmental drivers. Understanding factors that control the proportion of active microbes in the environment and how they vary when perturbed is critical to anticipating ecosystem response to global change. Increasing supplies of anthropogenic nitrogen to ecosystems globally makes it imperative that we understand how nutrient supply alters active microbial communities. Here we show that nitrogen additions to salt marshes cause a shift in the active microbial community despite no change in the total community. The active community shift causes the proportion of dormant microbial taxa to double, from 45 to 90%, and induces diversity loss in the active portion of the community. Our results suggest that perturbations to salt marshes can drastically alter active microbial communities, however these communities may remain resilient by protecting total diversity through increased dormancy.

Freezing and hungry? Hydrocarbon degrading microbial communities in Barents Sea sediments around Svalbard

NASA Astrophysics Data System (ADS)

Krueger, Martin; Straaten, Nontje

2017-04-01

The Polar Regions are characterised by varying temperatures and changing ice coverage, so most of the primary production take place in the warmer season. Consequently, sedimentation rates and nutrient input are low. The diversity and metabolic potentials of the microbial communities inhabiting these sediments in the Northern Barents Sea are largely unknown. Recent reports on natural methane seeps as well as the increase in hydrocarbon exploration activities in the Arctic initiated our studies on the potential of indigenous microbial communities to degrade methane and higher hydrocarbons under in situ pressure and temperature conditions. Furthermore, the subseafloor geochemistry in these areas was studied, together with important microbial groups, like methanotrophs, methanogens, metal and sulfate reducers, which may drive seafloor ecosystems in the Northern Barents Sea. Sediment samples were collected in several areas around Svalbard in the years 2013-2016 ranging from shallow (200m) areas on the Svalbard shelf to deep sea areas on the eastern Yermak Plateau (3200m water depths). Shelf sediments showed the highest organic carbon content which decreased with increasing depths. Iron and manganese as potential electron acceptors were found in the porewater especially in the top 50 cm of the cores, while sulfate was always present in substantial amounts in porewater samples down to the end of the up to two metre long cores. Concentrations of dissolved methane and carbon dioxide were low. The potential of the indigenous microorganisms to degrade methane and higher hydrocarbons as well as different oils under in situ temperatures and pressures was widespread in surface sediments. Degradation rates were higher under aerobic than under anaerobic conditions, and decreased with increasing sediment as well as water depths. Similar pattern were found for other metabolic processes, including sulfate, Fe and Mn reduction as well as carbon dioxide and methane production rates. Ongoing molecular biological analyses of original sediments and enrichment cultures indicate the presence of diverse and varying microbial communities.

Carbon and nitrogen assimilation in deep subseafloor microbial cells.

PubMed

Morono, Yuki; Terada, Takeshi; Nishizawa, Manabu; Ito, Motoo; Hillion, François; Takahata, Naoto; Sano, Yuji; Inagaki, Fumio

2011-11-08

Remarkable numbers of microbial cells have been observed in global shallow to deep subseafloor sediments. Accumulating evidence indicates that deep and ancient sediments harbor living microbial life, where the flux of nutrients and energy are extremely low. However, their physiology and energy requirements remain largely unknown. We used stable isotope tracer incubation and nanometer-scale secondary ion MS to investigate the dynamics of carbon and nitrogen assimilation activities in individual microbial cells from 219-m-deep lower Pleistocene (460,000 y old) sediments from the northwestern Pacific off the Shimokita Peninsula of Japan. Sediment samples were incubated in vitro with (13)C- and/or (15)N-labeled glucose, pyruvate, acetate, bicarbonate, methane, ammonium, and amino acids. Significant incorporation of (13)C and/or (15)N and growth occurred in response to glucose, pyruvate, and amino acids (∼76% of total cells), whereas acetate and bicarbonate were incorporated without fostering growth. Among those substrates, a maximum substrate assimilation rate was observed at 67 × 10(-18) mol/cell per d with bicarbonate. Neither carbon assimilation nor growth was evident in response to methane. The atomic ratios between nitrogen incorporated from ammonium and the total cellular nitrogen consistently exceeded the ratios of carbon, suggesting that subseafloor microbes preferentially require nitrogen assimilation for the recovery in vitro. Our results showed that the most deeply buried subseafloor sedimentary microbes maintain potentials for metabolic activities and that growth is generally limited by energy but not by the availability of C and N compounds.

Carbon and nitrogen assimilation in deep subseafloor microbial cells

PubMed Central

Morono, Yuki; Terada, Takeshi; Nishizawa, Manabu; Ito, Motoo; Hillion, François; Takahata, Naoto; Sano, Yuji; Inagaki, Fumio

2011-01-01

Remarkable numbers of microbial cells have been observed in global shallow to deep subseafloor sediments. Accumulating evidence indicates that deep and ancient sediments harbor living microbial life, where the flux of nutrients and energy are extremely low. However, their physiology and energy requirements remain largely unknown. We used stable isotope tracer incubation and nanometer-scale secondary ion MS to investigate the dynamics of carbon and nitrogen assimilation activities in individual microbial cells from 219-m-deep lower Pleistocene (460,000 y old) sediments from the northwestern Pacific off the Shimokita Peninsula of Japan. Sediment samples were incubated in vitro with 13C- and/or 15N-labeled glucose, pyruvate, acetate, bicarbonate, methane, ammonium, and amino acids. Significant incorporation of 13C and/or 15N and growth occurred in response to glucose, pyruvate, and amino acids (∼76% of total cells), whereas acetate and bicarbonate were incorporated without fostering growth. Among those substrates, a maximum substrate assimilation rate was observed at 67 × 10−18 mol/cell per d with bicarbonate. Neither carbon assimilation nor growth was evident in response to methane. The atomic ratios between nitrogen incorporated from ammonium and the total cellular nitrogen consistently exceeded the ratios of carbon, suggesting that subseafloor microbes preferentially require nitrogen assimilation for the recovery in vitro. Our results showed that the most deeply buried subseafloor sedimentary microbes maintain potentials for metabolic activities and that growth is generally limited by energy but not by the availability of C and N compounds. PMID:21987801

Analyses of outcrop and sediment grains observed and collected from the Sirena Deep and Middle Pond of the Mariana Trench

NASA Astrophysics Data System (ADS)

Hand, K. P.; Bartlett, D. H.; Fryer, P.

2012-12-01

During a March 2012 expedition we recovered sediments from two locales within the Marina Trench - Middle Pond and Sirena Deep. Samples were recovered from a Niskin bottle deployed on a passive lander platform that released an arm after touching down on the seafloor. The impact of the arm holding the Niskin bottle caused sediments to enter the bottle; this process was seen in images and on video captured by the lander. The combination of imagery and preliminary analyses of the sediments indicates that the Sirena Deep locale is a region of serpentinization and active microbial communities. Images show several outcrops consistent with serpentinization, some of which are coated with filamentous microbial mats. Results and analyses of these samples will be presented.

Characterization of Metabolically Active Bacterial Populations in Subseafloor Nankai Trough Sediments above, within, and below the Sulfate–Methane Transition Zone

PubMed Central

Mills, Heath J.; Reese, Brandi Kiel; Shepard, Alicia K.; Riedinger, Natascha; Dowd, Scot E.; Morono, Yuki; Inagaki, Fumio

2012-01-01

A remarkable number of microbial cells have been enumerated within subseafloor sediments, suggesting a biological impact on geochemical processes in the subseafloor habitat. However, the metabolically active fraction of these populations is largely uncharacterized. In this study, an RNA-based molecular approach was used to determine the diversity and community structure of metabolically active bacterial populations in the upper sedimentary formation of the Nankai Trough seismogenic zone. Samples used in this study were collected from the slope apron sediment overlying the accretionary prism at Site C0004 during the Integrated Ocean Drilling Program Expedition 316. The sediments represented microbial habitats above, within, and below the sulfate–methane transition zone (SMTZ), which was observed approximately 20 m below the seafloor (mbsf). Small subunit ribosomal RNA were extracted, quantified, amplified, and sequenced using high-throughput 454 pyrosequencing, indicating the occurrence of metabolically active bacterial populations to a depth of 57 mbsf. Transcript abundance and bacterial diversity decreased with increasing depth. The two communities below the SMTZ were similar at the phylum level, however only a 24% overlap was observed at the genus level. Active bacterial community composition was not confined to geochemically predicted redox stratification despite the deepest sample being more than 50 m below the oxic/anoxic interface. Genus-level classification suggested that the metabolically active subseafloor bacterial populations had similarities to previously cultured organisms. This allowed predictions of physiological potential, expanding understanding of the subseafloor microbial ecosystem. Unique community structures suggest very diverse active populations compared to previous DNA-based diversity estimates, providing more support for enhancing community characterizations using more advanced sequencing techniques. PMID:22485111

Shifts in microbial community composition following surface application of dredged river sediments.

PubMed

Baniulyte, Dovile; Favila, Emmanuel; Kelly, John J

2009-01-01

Sediment input to the Illinois River has drastically decreased river depth and reduced habitats for aquatic organisms. Dredging is being used to remove sediment from the Illinois River, and the dredged sediment is being applied to the surface of a brownfield site in Chicago with the goal of revegetating the site. In order to determine the effects of this drastic habitat change on sediment microbial communities, we examined sediment physical, chemical, and microbial characteristics at the time of sediment application to the soil surface as well as 1 and 2 years after application. Microbial community biomass was determined by measurement of lipid phosphate. Microbial community composition was assessed using phospholipid fatty acid (PLFA) analysis, terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes, and clone library sequencing of 16S rRNA genes. Results indicated that the moisture content, organic carbon, and total nitrogen content of the sediment all decreased over time. Total microbial biomass did not change over the course of the study, but there were significant changes in the composition of the microbial communities. PLFA analysis revealed relative increases in fungi, actinomycetes, and Gram positive bacteria. T-RFLP analysis indicated a significant shift in bacterial community composition within 1 year of application, and clone library analysis revealed relative increases in Proteobacteria, Gemmatimonadetes, and Bacteriodetes and relative decreases in Acidobacteria, Spirochaetes, and Planctomycetes. These results provide insight into microbial community shifts following land application of dredged sediment.

Organic content influences sediment microbial fuel cell performance and community structure.

PubMed

Zhao, Qing; Li, Ruying; Ji, Min; Ren, Zhiyong Jason

2016-11-01

This study constructed sediment microbial fuel cells (SMFCs) with different organic loadings without the amendment of external substrates, and it investigated how such variation affects electricity generation and microbial community structure. Results found sediment characteristics significantly influenced SMFC performance and appropriate organic content is important to maintain stable power outputs. SMFCs with loss of ignition (LOI) of 5% showed the most reliable performance in this study, while high organic content (LOI 10-16%) led to higher but very unstable voltage output because of biogas accumulation and worm activities. SMFCs with low organic content (1-3%) showed low power output. Different bacterial communities were found in SMFCs shown various power generation performance even those with similar organic contents. Thermodesulfovibrionaceae was found closely related to the system startup and Desulfobulbaceae showed great abundance in SMFCs with high power production. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evidence of active methanogen communities in shallow sediments of the sonora margin cold seeps.

PubMed

Vigneron, Adrien; L'Haridon, Stéphane; Godfroy, Anne; Roussel, Erwan G; Cragg, Barry A; Parkes, R John; Toffin, Laurent

2015-05-15

In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic Archaea were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic Methanococcoides burtonii relatives and several new autotrophic Methanogenium lineages, confirming the cooccurrence of Methanosarcinales and Methanomicrobiales methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments

PubMed Central

Hernsdorf, Alex W; Amano, Yuki; Miyakawa, Kazuya; Ise, Kotaro; Suzuki, Yohey; Anantharaman, Karthik; Probst, Alexander; Burstein, David; Thomas, Brian C; Banfield, Jillian F

2017-01-01

Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H2, often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H2 consumption and retardation of radionuclide migration. PMID:28350393

Arsenic release from shallow aquifers of the Hetao basin, Inner Mongolia: evidence from bacterial community in aquifer sediments and groundwater.

PubMed

Li, Yuan; Guo, Huaming; Hao, Chunbo

2014-12-01

Indigenous microbes play crucial roles in arsenic mobilization in high arsenic groundwater systems. Databases concerning the presence and the activity of microbial communities are very useful in evaluating the potential of microbe-mediated arsenic mobilization in shallow aquifers hosting high arsenic groundwater. This study characterized microbial communities in groundwaters at different depths with different arsenic concentrations by DGGE and one sediment by 16S rRNA gene clone library, and evaluated arsenic mobilization in microcosm batches with the presence of indigenous bacteria. DGGE fingerprints revealed that the community structure changed substantially with depth at the same location. It indicated that a relatively higher bacterial diversity was present in the groundwater sample with lower arsenic concentration. Sequence analysis of 16S rRNA gene demonstrated that the sediment bacteria mainly belonged to Pseudomonas, Dietzia and Rhodococcus, which have been widely found in aquifer systems. Additionally, NO3(-)-reducing bacteria Pseudomonas sp. was the largest group, followed by Fe(III)-reducing, SO4(2-)-reducing and As(V)-reducing bacteria in the sediment sample. These anaerobic bacteria used the specific oxyanions as electron acceptor and played a significant role in reductive dissolution of Fe oxide minerals, reduction of As(V), and release of arsenic from sediments into groundwater. Microcosm experiments, using intact aquifer sediments, showed that arsenic release and Fe(III) reduction were microbially mediated in the presence of indigenous bacteria. High arsenic concentration was also observed in the batch without amendment of organic carbon, demonstrating that the natural organic matter in sediments was the potential electron donor for microbially mediated arsenic release from these aquifer sediments.

Quantifying Enhanced Microbial Dehalogenation Impacting the Fate and Transport of Organohalide Mixtures in Contaminated Sediments

DTIC Science & Technology

2012-02-01

supplying Anacostia River sediment, Dr. Matti Verta, Finnish Environment Institute, for providing Kymijoki River sediment, and the Meadowlands...dehalogenating activity; 2) Characterize the effect of sedimentary conditions on the ( bio )transformation rates of organohalide mixtures and their...the fate and transport of organohalide contaminants, co-amendments and ( bio )transformation products under various bioremediation scenarios. The

Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea

PubMed Central

Graw, Michael F.; D'Angelo, Grace; Borchers, Matthew; Thurber, Andrew R.; Johnson, Joel E.; Zhang, Chuanlun; Liu, Haodong; Colwell, Frederick S.

2018-01-01

The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics. PMID:29696012

Spatial heterogeneity in sulfur isotopes: implications for modern environments and paleoenvironmental reconstructions

NASA Astrophysics Data System (ADS)

Fike, D. A.; Jones, D. S.; Fischer, W. W.

2011-12-01

Sulfur isotope ratio data have been used to provide significant insights into global biogeochemical cycling over Earth history. In addition to providing a framework for the construction of global redox budgets, these observations also provide the primary constraints on the advent and environmental importance of particular microbial metabolisms. As the chemostratigraphic record has become better resolved in space and time, however, reports of coeval discordant data are increasingly common - both within and between individual sedimentary basins. If accurate, this variability challenges our understanding of the first order behavior of the 'global' sulfur biogeochemical cycle. Some of this discordance may be due to spatial gradients in important oceanographic parameters; however, we think that a more likely culprit is ongoing microbial metabolic activity (that impacts the isotopic composition recorded by geological samples) during both syndepositional sediment reworking and early diagenetic lithification. Modern studies have recently highlighted the efficacy with which microbial activity during sediment remobilization can dramatically alter isotopic profiles. Further, the magnitude of local, microbially driven variations in S isotopes in modern sediments is sufficiently large that uneven incorporation of these signatures during deposition and lithification can explain much of the observed discordance in chemostratigraphic reconstructions of sulfur cycling. Here we attempt to link spatial variability in the sedimentary rock record with understanding of modern microbial systems operating in marine sediments. To that end we examine chemostratigraphic records of sulfur isotope (δ34S) data spanning the terminal Neoproterozoic to early Paleozoic eras and assess their scales of spatial reproducibility. We can gain insight into interpreting the observed patterns in these records by examining modern (bio)sedimentary environments. This understanding also allows us to reflect on and refine time series isotope ratio data that constrain the behavior of the sulfur cycle over long timescales.

Microbial Enzyme Stoichiometry and Nutrient Limitation in US Streams and Rivers

EPA Science Inventory

We analyzed water and sediment chemistry, catchment land cover, and extracellular enzymes (ecoenzymes) activities related to microbial C, N, and P acquisition in more than 2100 1st- 10th order streams. Streams were selected from a probability design to represent the entire popula...

Microbial production of organic acids in aquitard sediments and its role in aquifer geochemistry

USGS Publications Warehouse

McMahon, P.B.; Chapelle, F.H.

1991-01-01

MICROBIAL activity in aquifers plays an important part in the chemical evolution of ground water1-5. The most important terminal electron-accepting microbial processes in deeply buried anaerobic aquifers are iron reduction, sulphate reduction and methanogenesis5-8, each of which requires simple organic compounds or hydrogen (H2) as electron donors. Until now, the source of these compounds was unknown because the concentrations of dissolved organic carbon and sedimentary organic carbon in aquifers are extremely low9-11. Here we show that rates of microbial fermentation exceed rates of respiration in organic-rich aquitards (low-permeability sediments stratigraphically adjacent to higher-permeability aquifer sediments), resulting in a net accumulation of simple organic acids in pore waters. In aquifers, however, respiration outpaces fermentation, resulting in a net consumption of organic acids. The concentration gradient that develops in response to these two processes drives a net diffusive flux of organic acids from aquitards to aquifers. Diffusion calculations demonstrate that rates of organic acid transport are sufficient to account for observed rates of microbial respiration in aquifers. This overall process effectively links the large pool of sedimentary organic carbon in aquitards to microbial respiration in aquifers, and is a principal mechanism driving groundwater chemistry changes in aquifers.

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities

PubMed Central

Marlow, Jeffrey J.; Skennerton, Connor T.; Li, Zhou; Chourey, Karuna; Hettich, Robert L.; Pan, Chongle; Orphan, Victoria J.

2016-01-01

Marine methane seep habitats represent an important control on the global flux of methane. Nucleotide-based meta-omics studies outline community-wide metabolic potential, but expression patterns of environmentally relevant proteins are poorly characterized. Proteomic stable isotope probing (proteomic SIP) provides additional information by characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities, offering enhanced detection through system-wide product integration. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 unique proteins were identified, 11% of which were 15N-labeled. Consistent with the dominant anaerobic oxidation of methane (AOM) activity commonly observed in anoxic seep sediments, proteins associated with sulfate reduction and reverse methanogenesis—including the ANME-2 associated methylenetetrahydromethanopterin reductase (Mer)—were all observed to be actively synthesized (15N-enriched). Conversely, proteins affiliated with putative aerobic sulfur-oxidizing epsilon- and gammaproteobacteria showed a marked decrease over time in our anoxic sediment incubations. The abundance and phylogenetic range of 15N-enriched methyl-coenzyme M reductase (Mcr) orthologs, many of which exhibited novel post-translational modifications, suggests that seep sediments provide niches for multiple organisms performing analogous metabolisms. In addition, 26 proteins of unknown function were consistently detected and actively expressed under conditions supporting AOM, suggesting that they play important roles in methane seep ecosystems. Stable isotope probing in environmental proteomics experiments provides a mechanism to determine protein durability and evaluate lineage-specific responses in complex microbial communities placed under environmentally relevant conditions. Our work here demonstrates the active synthesis of a metabolically specific minority of enzymes, revealing the surprising longevity of most proteins over the course of an extended incubation experiment in an established, slow-growing, methane-impacted environmental system. PMID:27199908

Biogeochemistry of the coupled manganese-iron-sulfur cycles of intertidal surface sediments

NASA Astrophysics Data System (ADS)

Bosselmann, K.; Boettcher, M. E.; Billerbeck, M.; Walpersdorf, E.; Debeer, D.; Brumsack, H.-J.; Huettel, M.; Joergensen, B. B.

2003-04-01

The biogeochemistry of the coupled iron-manganese-sulfur-carbon cycles was studied in temperate intertidal surface sediments of the German Wadden Sea (North Sea). Coastal sampling sites include sand, mixed and mud flats with different organic matter and metal contents and permeability reflecting different hydrodynamic regimes. The field study focusses on the influence of temperature, organic matter load, and sediment types on the dynamics of biogeochemical reactions on different time scales (season, day-night, tidal cycles). One of the main interests was related to the cycling of metals (Mn, Fe) in relation to the activity of sulfate-reducing bacteria. Pore water profiles were investigated by sediment sectioning and high resolution gel sampling techniques. Microbial sulfate reduction rates were measured using radiolabeled sulfate with the whole core incubation technique and the spatial distribution of bacterial activity was visualised by using "2D-photoemulsion-monitoring technique". The biogeochemical sulfur cycle was additionally characterised by the stable isotope ratios (S,O) of different sulfur species (e.g., SO_4, AVS, pyrite). Element transfers (metals, nutrients) across the sediment-water interface were additionally quantified by the application of benthic flux chambers. Microbial sulfate reduction was generally highest in the suboxic zone of the surface sediments indicating its potential importance for the mobilization of iron and manganese. In organic matter poor permeable sediments tidal effects additionally influence the spatial and temporal distribution of dissolved redox-sensitive metals. In organic matter-rich silty and muddy sediments, temperature controlled the microbial sulfate reduction rates. Depth-integrated sulfate reduction rates in sandy sediments were much lower and controlled by both temperature and organic matter. Formation of anoxic sediment surfaces due to local enhanced organic matter load (so-called "black spots") may create windows of an increase flux of metals, nutrients and hydrogen sulfide. Acknowledgements: The study was supported by German Science Foundation within the DFG-research group "BioGeoChemistry of the Waddensea" and Max Planck Society.

Molecular fossils of prokaryotes in ancient authigenic minerals: archives of microbial activity in reefs and mounds?

NASA Astrophysics Data System (ADS)

Heindel, Katrin; Birgel, Daniel; Richoz, Sylvain; Westphal, Hildegard; Peckmann, Jörn

2016-04-01

Molecular fossils (lipid biomarkers) are commonly used as proxies in organic-rich sediments of various sources, including eukaryotes and prokaryotes. Usually, molecular fossils of organisms transferred from the water column to the sediment are studied to monitor environmental changes (e.g., temperature, pH). Apart from these 'allochthonous' molecular fossils, prokaryotes are active in sediments and mats on the seafloor and leave behind 'autochthonous' molecular fossils in situ. In contrast to many phototrophic organisms, most benthic sedimentary prokaryotes are obtaining their energy from oxidation or reduction of organic or inorganic substrates. A peculiarity of some of the sediment-thriving prokaryotes is their ability to trigger in situ mineral precipitation, often but not only due to metabolic activity, resulting in authigenic rocks (microbialites). During that process, prokaryotes are rapidly entombed in the mineral matrix, where the molecular fossils are protected from early (bio)degradation. In contrast to other organic compounds (DNA, proteins etc.), molecular fossils can be preserved over very long time periods (millions of years). Thus, molecular fossils in authigenic mineral phases are perfectly suitable to trace microbial activity back in time. Among the best examples of molecular fossils, which are preserved in authigenic rocks are various microbialites, forming e.g. in phototrophic microbial mats and at cold seeps. Microbialite formation is reported throughout earth history. We here will focus on reefal microbialites form the Early Triassic and the Holocene. After the End-Permian mass extinction, microbialites covered wide areas on the ocean margins. In microbialites from the Griesbachian in Iran and Turkey (both Neotethys), molecular fossils of cyanobacteria, archaea, anoxygenic phototrophs, and sulphate-reducing bacteria indicate the presence of layered microbial mats on the seafloor, in which carbonate precipitation was induced. In association with metazoans other than corals (sponges, bivalves, gastropods, ostracods) and foraminifera, first metazoan-microbialite reefs developed on the Early Triassic seafloor. After the last glacial maximum, microbialites formed in coral reefs. Our evidence shows that sulphate-reducing bacteria played an intrinsic role in the precipitation of these microbialites during the Holocene sea-level rise. With more nutrients and organic matter distributed in the reef ecosystem, anoxic microenvironments preferentially developed. Such conditions favored heterotrophic bacteria, particularly, sulphate-reducing bacteria. It is suggested that matrix-solute interaction related to the activity of sulphate reducers induced carbonate precipitation in extracellular polymeric substances. Overall, authigenic mineral phases from various environments can be used as excellent archives to describe former microbial activity in sediments. The early entombment of the lipids in the mineral matrix avoids the loss of specific and important information, which may have been lost in soft sediments rather quick.

Shifts in identity and activity of methanotrophs in arctic lake sediments in response to temperature changes

USGS Publications Warehouse

He, Ruo; Wooller, Matthew J.; Pohlman, John W.; Quensen, John; Tiedje, James M.; Leigh, Mary Beth

2012-01-01

Methane (CH4) flux to the atmosphere is mitigated via microbial CH4 oxidation in sediments and water. As arctic temperaturesincrease, understanding the effects of temperature on the activity and identity of methanotrophs in arctic lake sediments is importantto predicting future CH4 emissions. We used DNA-based stable-isotope probing (SIP), quantitative PCR (Q-PCR), andpyrosequencing analyses to identify and characterize methanotrophic communities active at a range of temperatures (4°C, 10°C,and 21°C) in sediments (to a depth of 25 cm) sampled from Lake Qalluuraq on the North Slope of Alaska. CH4 oxidation activitywas measured in microcosm incubations containing sediments at all temperatures, with the highest CH4 oxidation potential of37.5 mol g1 day1 in the uppermost (depth, 0 to 1 cm) sediment at 21°C after 2 to 5 days of incubation. Q-PCR of pmoA and ofthe 16S rRNA genes of type I and type II methanotrophs, and pyrosequencing of 16S rRNA genes in 13C-labeled DNA obtained bySIP demonstrated that the type I methanotrophs Methylobacter, Methylomonas, and Methylosoma dominated carbon acquisitionfrom CH4 in the sediments. The identity and relative abundance of active methanotrophs differed with the incubation temperature.Methylotrophs were also abundant in the microbial community that derived carbon from CH4, especially in the deeper sediments(depth, 15 to 20 cm) at low temperatures (4°C and 10°C), and showed a good linear relationship (R0.82) with the relativeabundances of methanotrophs in pyrosequencing reads. This study describes for the first time how methanotrophiccommunities in arctic lake sediments respond to temperature variations.

Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor

PubMed Central

Yanagawa, Katsunori; Ijiri, Akira; Breuker, Anja; Sakai, Sanae; Miyoshi, Youko; Kawagucci, Shinsuke; Noguchi, Takuroh; Hirai, Miho; Schippers, Axel; Ishibashi, Jun-ichiro; Takaki, Yoshihiro; Sunamura, Michinari; Urabe, Tetsuro; Nunoura, Takuro; Takai, Ken

2017-01-01

Subseafloor microbes beneath active hydrothermal vents are thought to live near the upper temperature limit for life on Earth. We drilled and cored the Iheya North hydrothermal field in the Mid-Okinawa Trough, and examined the phylogenetic compositions and the products of metabolic functions of sub-vent microbial communities. We detected microbial cells, metabolic activities and molecular signatures only in the shallow sediments down to 15.8 m below the seafloor at a moderately distant drilling site from the active hydrothermal vents (450 m). At the drilling site, the profiles of methane and sulfate concentrations and the δ13C and δD isotopic compositions of methane suggested the laterally flowing hydrothermal fluids and the in situ microbial anaerobic methane oxidation. In situ measurements during the drilling constrain the current bottom temperature of the microbially habitable zone to ~45 °C. However, in the past, higher temperatures of 106–198 °C were possible at the depth, as estimated from geochemical thermometry on hydrothermally altered clay minerals. The 16S rRNA gene phylotypes found in the deepest habitable zone are related to those of thermophiles, although sequences typical of known hyperthermophilic microbes were absent from the entire core. Overall our results shed new light on the distribution and composition of the boundary microbial community close to the high-temperature limit for habitability in the subseafloor environment of a hydrothermal field. PMID:27754478

Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor.

PubMed

Yanagawa, Katsunori; Ijiri, Akira; Breuker, Anja; Sakai, Sanae; Miyoshi, Youko; Kawagucci, Shinsuke; Noguchi, Takuroh; Hirai, Miho; Schippers, Axel; Ishibashi, Jun-Ichiro; Takaki, Yoshihiro; Sunamura, Michinari; Urabe, Tetsuro; Nunoura, Takuro; Takai, Ken

2017-02-01

Subseafloor microbes beneath active hydrothermal vents are thought to live near the upper temperature limit for life on Earth. We drilled and cored the Iheya North hydrothermal field in the Mid-Okinawa Trough, and examined the phylogenetic compositions and the products of metabolic functions of sub-vent microbial communities. We detected microbial cells, metabolic activities and molecular signatures only in the shallow sediments down to 15.8 m below the seafloor at a moderately distant drilling site from the active hydrothermal vents (450 m). At the drilling site, the profiles of methane and sulfate concentrations and the δ 13 C and δD isotopic compositions of methane suggested the laterally flowing hydrothermal fluids and the in situ microbial anaerobic methane oxidation. In situ measurements during the drilling constrain the current bottom temperature of the microbially habitable zone to ~45 °C. However, in the past, higher temperatures of 106-198 °C were possible at the depth, as estimated from geochemical thermometry on hydrothermally altered clay minerals. The 16S rRNA gene phylotypes found in the deepest habitable zone are related to those of thermophiles, although sequences typical of known hyperthermophilic microbes were absent from the entire core. Overall our results shed new light on the distribution and composition of the boundary microbial community close to the high-temperature limit for habitability in the subseafloor environment of a hydrothermal field.

Diversity and survivability of microbial community in ancient permafrost sediment of northeast Siberia

NASA Astrophysics Data System (ADS)

Liang, R.; Lau, M.; Vishnivetskaya, T. A.; Lloyd, K. G.; Pfiffner, S. M.; Rivkina, E.; Onstott, T. C.

2017-12-01

The prevalence of microorganisms in frozen permafrost has been well documented in ancient sediment up to several million years old. However, the long term survivability and metabolic activity of microbes over geological timespans remain underexplored. Siberian permafrost sediment was collected at various depths (1.4m, 11.8 m and 24.8m) to represent a wide range of geological time from thousands to millions of years. Extracellular (eDNA) and intracellular DNA (iDNA) was simultaneously recovered for sequencing to characterize the potentially extinct and extant microbial community. Additionally, aspartic acid racemization assay (D/L Asp) was used to infer the metabolic activity of microbes in ancient permafrost. As compared with the young sample (1.4m), DNA yield and content of aspartic acid dramatically decreased in old samples (11.8m and 24.8m). However, D/L Asp and eDNA/iDNA significantly increased with the geological age. Such findings suggested that ancient microbiomes might be subjected to racemization or even DNA/proteins degradation at subzero temperature over the wide geological time scale. Preliminary characterization of microbial community indicated that the majority of sequences in old samples were identified as bacteria and only a small fraction was identified as archaea from the iDNA pool. While the eDNA and iDNA fractions shared similar dominant taxa at phylum level, the relative abundance of Proteobacteria in eDNA library was much higher than iDNA. By contrast, the phylum affiliated with Firmicutes was more numerically abundant in the iDNA fraction. More dramatic differences were observed between eDNA and iDNA library at lower taxonomic levels. Particularly, the microbial lineages affiliated with the genera Methanoregula, Desulfosporosinus and Syntrophomonas were only detected in the iDNA library. Such taxonomic difference between the relic eDNA and iDNA suggested that numerous species become locally "extinct" whereas many other taxa might survive in ancient sediment. Ultimately, when coupling our current findings to the D/L Asp in cellular proteins and metaproteomics, a better understanding will be achieved about the microbial activity of the extant microbial community and their roles in biogeochemical cycling in ancient permafrost.

Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur cycling and unexpected aerobic metabolism

PubMed Central

Elshahed, Mostafa S.; Najar, Fares Z.; Krumholz, Lee R.

2015-01-01

Zodletone spring is a sulfide-rich spring in southwestern Oklahoma characterized by shallow, microoxic, light-exposed spring water overlaying anoxic sediments. Previously, culture-independent 16S rRNA gene based diversity surveys have revealed that Zodletone spring source sediments harbor a highly diverse microbial community, with multiple lineages putatively involved in various sulfur-cycling processes. Here, we conducted a metatranscriptomic survey of microbial populations in Zodletone spring source sediments to characterize the relative prevalence and importance of putative phototrophic, chemolithotrophic, and heterotrophic microorganisms in the sulfur cycle, the identity of lineages actively involved in various sulfur cycling processes, and the interaction between sulfur cycling and other geochemical processes at the spring source. Sediment samples at the spring’s source were taken at three different times within a 24-h period for geochemical analyses and RNA sequencing. In depth mining of datasets for sulfur cycling transcripts revealed major sulfur cycling pathways and taxa involved, including an unexpected potential role of Actinobacteria in sulfide oxidation and thiosulfate transformation. Surprisingly, transcripts coding for the cyanobacterial Photosystem II D1 protein, methane monooxygenase, and terminal cytochrome oxidases were encountered, indicating that genes for oxygen production and aerobic modes of metabolism are actively being transcribed, despite below-detectable levels (<1 µM) of oxygen in source sediment. Results highlight transcripts involved in sulfur, methane, and oxygen cycles, propose that oxygenic photosynthesis could support aerobic methane and sulfide oxidation in anoxic sediments exposed to sunlight, and provide a viewpoint of microbial metabolic lifestyles under conditions similar to those seen during late Archaean and Proterozoic eons. PMID:26417542

Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur cycling and unexpected aerobic metabolism.

PubMed

Spain, Anne M; Elshahed, Mostafa S; Najar, Fares Z; Krumholz, Lee R

2015-01-01

Zodletone spring is a sulfide-rich spring in southwestern Oklahoma characterized by shallow, microoxic, light-exposed spring water overlaying anoxic sediments. Previously, culture-independent 16S rRNA gene based diversity surveys have revealed that Zodletone spring source sediments harbor a highly diverse microbial community, with multiple lineages putatively involved in various sulfur-cycling processes. Here, we conducted a metatranscriptomic survey of microbial populations in Zodletone spring source sediments to characterize the relative prevalence and importance of putative phototrophic, chemolithotrophic, and heterotrophic microorganisms in the sulfur cycle, the identity of lineages actively involved in various sulfur cycling processes, and the interaction between sulfur cycling and other geochemical processes at the spring source. Sediment samples at the spring's source were taken at three different times within a 24-h period for geochemical analyses and RNA sequencing. In depth mining of datasets for sulfur cycling transcripts revealed major sulfur cycling pathways and taxa involved, including an unexpected potential role of Actinobacteria in sulfide oxidation and thiosulfate transformation. Surprisingly, transcripts coding for the cyanobacterial Photosystem II D1 protein, methane monooxygenase, and terminal cytochrome oxidases were encountered, indicating that genes for oxygen production and aerobic modes of metabolism are actively being transcribed, despite below-detectable levels (<1 µM) of oxygen in source sediment. Results highlight transcripts involved in sulfur, methane, and oxygen cycles, propose that oxygenic photosynthesis could support aerobic methane and sulfide oxidation in anoxic sediments exposed to sunlight, and provide a viewpoint of microbial metabolic lifestyles under conditions similar to those seen during late Archaean and Proterozoic eons.

Microbial responses to polycyclic aromatic hydrocarbon contamination in temporary river sediments: Experimental insights.

PubMed

Zoppini, Annamaria; Ademollo, Nicoletta; Amalfitano, Stefano; Capri, Silvio; Casella, Patrizia; Fazi, Stefano; Marxsen, Juergen; Patrolecco, Luisa

2016-01-15

Temporary rivers are characterized by dry-wet phases and represent an important water resource in semi-arid regions worldwide. The fate and effect of contaminants have not been firmly established in temporary rivers such as in other aquatic environments. In this study, we assessed the effects of sediment amendment with Polycyclic Aromatic Hydrocarbons (PAHs) on benthic microbial communities. Experimental microcosms containing natural (Control) and amended sediments (2 and 20 mg PAHs kg(-1) were incubated for 28 days. The PAH concentrations in sediments were monitored weekly together with microbial community structural (biomass and phylogenetic composition by TGGE and CARD-FISH) and functional parameters (ATP concentration, community respiration rate, bacterial carbon production rate, extracellular enzyme activities). The concentration of the PAH isomers did not change significantly with the exception of phenanthrene. No changes were observed in the TGGE profiles, whereas the occurrence of Alpha- and Beta-Proteobacteria was significantly affected by the treatments. In the amended sediments, the rates of carbon production were stimulated together with aminopeptidase enzyme activity. The community respiration rates showed values significantly lower than the Control after 1 day from the amendment then recovering the Control values during the incubation. A negative trend between the respiration rates and ATP concentration was observed only in the amended sediments. This result indicates a potential toxic effect on the oxidative phosphorylation processes. The impoverishment of the energetic resources that follows the PAH impact may act as a domino on the flux of energy from prokaryotes to the upper level of the trophic chain, with the potential to alter the temporary river functioning.

Quantification of microbial activity in subsurface environments using a hydrogenase enzyme assay

NASA Astrophysics Data System (ADS)

Adhikari, R. R.; Nickel, J.; Kallmeyer, J.

2012-04-01

The subsurface biosphere is the largest microbial ecosystem on Earth. Despite its large size and extensive industrial exploitation, very little is known about the role of microbial activity in the subsurface. Subsurface microbial activity plays a fundamental role in geochemical cycles of carbon and other biologically important elements. How the indigenous microbial communities are supplied with energy is one of the most fundamental questions in subsurface research. It is still an enigma how these communities can survive with such recalcitrant carbon over geological time scales. Despite its usually very low concentration, hydrogen is an important element in subsurface environments. Heterotrophic and chemoautotrophic microorganisms use hydrogen in their metabolic pathways; they either obtain protons from the radiolysis of water and/or cleavage of hydrogen generated by the alteration of basaltic crust, or they dispose of protons by formation of water. Hydrogenase (H2ase) is a ubiquitous intracellular enzyme that catalyzes the interconversion of molecular hydrogen and/or water into protons and electrons. The protons are used for the synthesis of ATP, thereby coupling energy-generating metabolic processes to electron acceptors such as carbon dioxide or sulfate. H2ase activity can therefore be used as a measure for total microbial activity as it targets a key metabolic compound rather than a specific turnover process. Using a highly sensitive tritium assay we measured H2ase enzyme activity in the organic-rich sediments of Lake Van, a saline, alkaline lake in eastern Turkey and in marine subsurface sediments of the Barents Sea. Additionally, sulfate reduction rates (SRRs) were measured to compare the results of the H2ase enzyme assay with the quantitatively most important electron acceptor process. H2ase activity was found at all sites, measured values and distribution of activity varied widely with depth and between sites. At the Lake Van sites H2ase activity ranged from ca. 20 mmol H2 cm-3 d-1 close to the sediment-water interface to 0.5 mmol H2 cm-3 d-1 at a depth of 0.8 m. In samples from the Barents Sea H2ase activity ranged between 0.1 to 2.5 mmol H2 cm-3 d-1 down to a depth of 1.60 m. At all sites the SRR profile followed the H2ase activity profile until SRR declined to values close to the minimum detection limit (~10 pmol cm-3 d-1). H2ase activity increased again after SRR declined, indicating that other microbial processes are becoming quantitatively more important. The H2ase and SRR data show that our assay has a potential to become a valuable tool to measure total subsurface microbial activity.

Deep subsurface life in Bengal Fan sediments (IODP Exp. 354)

NASA Astrophysics Data System (ADS)

Adhikari, R. R.; Heuer, V. B.; Elvert, M.; Kallmeyer, J.; Kitte, J. A.; Wörmer, L.; Hinrichs, K. U.

2017-12-01

We collected Bengal Fan sediment samples along a 8°N transect during International Ocean Discovery Program Expedition 354 (February - March 2015, Singapore - Colombo, Sri Lanka) to study subseafloor life in this, as yet unstudied, area. Among other biogeochemical parameters, we quantified microbial biomass by analyzing prokaryotic cells using epifluorescence microscopy after detaching cells from the sediment, and bacterial endospores by analyzing the diagnostic biomarker dipicolinic acid (DPA) by detection of fluorescence of the terbium-DPA complex. To gain understanding of total microbial activity, we quantified hydrogen utilization potential of hydrogenase enzymes, which are ubiquitous in subsurface microorganisms, by using a tritium assay. We measured highest cell concentrations of ca. 108 cells g-1 in shallow sediments close to the seafloor. These concentrations are one to two orders of magnitude lower than in most marine continental margin settings [1]. Similar to the global trend [1], cell concentrations decreased with depth according to a power-law function. Endospore concentrations scattered between ca. 105 and 107 cells g-1 sediment at all sites and depths. We could not observe a clear relationship of endospore concentration and sediment depth; instead, it appears to be linked to lithology and total organic carbon content. Bulk Hydrogenase enzyme activity ranged from nmolar to μmolar range of H2 g-1d-1. Similar to previous observations [2], per-cell hydrogen utilization depends on vertical biogeochemical zones, which could be due to the differences in hydrogen utilization requirements/efficiency of the respective metabolic processes such as sulfate reduction, methanogenesis, fermentation etc. Bengal fan is highly dynamic due to channel and levee systems and the sediments are dominated by turbidites, thick sand layers and hemipelagic deposits, which may control biogeochemical zonation. Based on our microbial biomass and activity data, we suggest that the nature, quality and origin of sedimentary material influence the deep subsurface life. [1] Kallmeyer et al., (2012) PNAS 109(40), 16213-16216 [2] Adhikari et al., (2016) Frontiers in Microbiology 7:8

Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands.

PubMed

Böer, Simone I; Hedtkamp, Stefanie I C; van Beusekom, Justus E E; Fuhrman, Jed A; Boetius, Antje; Ramette, Alban

2009-07-01

Bacterial community structure and microbial activity were determined together with a large number of contextual environmental parameters over 2 years in subtidal sands of the German Wadden Sea in order to identify the main factors shaping microbial community structure and activity in this habitat. Seasonal changes in temperature were directly reflected in bacterial activities and total community respiration, but could not explain variations in the community structure. Strong sediment depth-related patterns were observed for bacterial abundances, carbon production rates and extracellular enzymatic activities. Bacterial community structure also showed a clear vertical variation with higher operational taxonomic unit (OTU) numbers at 10-15 cm depth than in the top 10 cm, probably because of the decreasing disturbance by hydrodynamic forces with sediment depth. The depth-related variations in bacterial community structure could be attributed to vertical changes in bacterial abundances, chlorophyll a and NO(3)(-), indicating that spatial patterns of microbes are partially environmentally controlled. Time was the most important single factor affecting microbial community structure with an OTU replacement of up to 47% over 2 years and a contribution of 34% to the total variation. A large part of this variation was not related to any environmental parameters, suggesting that temporal variations in bacterial community structure are caused by yet unknown environmental drivers and/or by stochastic events in coastal sand habitats. Principal ecosystem functions such as benthic oxygen consumption and extracellular hydrolysis of organic matter were, however, at a high level at all times, indicating functional redundancy in the microbial communities.

Potential contribution of microbial degradation to natural attenuation of MTBE in surface water systems

USGS Publications Warehouse

Bradley, P.M.; Chapelle, F.H.; Landmeyer, J.E.

2001-01-01

The potential contribution of in situ biodegradation as a mechanism for natural attenuation of MTBE in surface water was studied. Surface water sediments from streams and lakes at 11 sites throughout the US. Microbial degradation of [U-14C] MTBE was observed in surface-water-sediment microcosms under anaerobic conditions, but the efficiency and products of anaerobic MTBE biodegradation were strongly dependent on the predominant terminal electron accepting conditions. In the presence of substantial methanogenic activity, MTBE biodegradation was nominal and involved reduction of MTBE to t-butanol (TBA). Under more oxidizing conditions, minimal accumulation of 14C-TBA and significant mineralization of [U-14C] MTBE to 14CO2 were observed. Microorganisms inhabiting the bed sediments of streams and lakes could degrade MTBE effectively under a range of anaerobic terminal electron accepting conditions. Thus, anaerobic bed sediment microbial processes also might contribute to natural attenuation of MTBE in surface water systems throughout the US. This is an abstract of a paper presented at the 222nd ACS National Meting (Chicago, IL 8/26-30/2001).

Origin of dolomite in Miocene Monterey Shale and related formations in the Temblor Range, California

USGS Publications Warehouse

Friedman, I.; Murata, K.J.

1979-01-01

Dolomites in thick sections of Miocene Monterey Shale and related formations in the Temblor Range of California acquired their isotopic compositions as they formed at shallow depth in the original sediment rich in organic matter, and retained the composition against the vicissitudes of burial diagenesis. The oxygen isotopes of dolomites of successive beds record changes in temperature of bottom water while the carbon isotopes of the same samples indicate changes in the kind of microbial activity (sulfate reduction vs carbohydrate fermentation) that prevailed at shallow depths in the sediment. In an auxiliary study, two samples of dolomite from sediments of Cariaco Basin off Venezuela (DSDP site 147) were found to have ??5C13 of -14.1 and -9.8 per ml PDB, although they occur in a heavy-carbon zone containing bicarbonate as heavy as +8.4 per ml. These dolomites probably originated at shallow depth in the light-carbon zone of microbial sulfate reducers and were buried under later sediments down into the heavy-carbon zone of microbial fermenters of carbohydrates without losing their original light-carbon composition. ?? 1979.

Geochemical Evidence for Recent Hydrothermal Alteration of Marine Sediments in Mid-Okinawa Trough, Southwest Japan

NASA Astrophysics Data System (ADS)

Tanaka, A.; Abe, G.; Yamaguchi, K. E.

2014-12-01

Recent studies have shown that submarine hydrothermal system supports diverse microbial life. Bio-essential metals supporting such microbial communities were released from basalts by high-temperature water-rock interaction in deeper part of the oceanic crust and carried by submarine fluid flow. Its total quantity in global hydrothermal settings has been estimated to be on the order of ~1019 g/yr, which is surprisingly on the same order of the total river flows (Urabe et al., 2011). Therefore, it is important to explore how submarine river system works, i.e., to understand mechanism and extent of elemental transport, which should lead to understanding of the roles of hydrothermal circulation in oceanic crust in controlling elemental budget in the global ocean and geochemical conditions to support deep hot biosphere. 　We performed REE analysis of marine sediments influenced by submarine hydrothermal activity in Mid-Okinawa Trough. The sediment samples used in this study are from IODP site at Iheya North region and JADE site at Izena region. The samples show alternation between volcanic and clastic sediments. Hydrothermal fluids of this area contain elevated concentrations of volatile components such as H2, CO2, CH4, NH4+, and H2S, supporting diverse chemoautotrophic microbial community (Nakagawa et al., 2005). The purpose of this study is to examine the effect of hydrothermal activity on the REE signature of the sediments. Chondrite-normalized REE patterns of the samples show relative enrichment of light over heavy REEs, weak positive Ce anomalies, and variable degrees of negative Eu anomalies. The REE patterns suggest the sediments source was mainly basalt, suggesting insignificant input of continental materials. Negative Eu anomalies found in the IODP site become more pronounced with increasing depth, suggesting progressive increase of hydrothermal alteration where Eu was reductively dissolved into fluids by decomposition of feldspars. Contrary, at the JADE site, magnitude of negative Eu anomalies was variable independent of the sediment depth. This suggests changes in the redox conditions, most likely due to occasional invasions of O2-bearing seawater into sediments. Different regimes of hydrothermal fluid flows govern the chemical environments of marine sediments in active hydrothermal areas.

Microbial ecology of arsenic-mobilizing Cambodian sediments: lithological controls uncovered by stable-isotope probing.

PubMed

Héry, Marina; Rizoulis, Athanasios; Sanguin, Hervé; Cooke, David A; Pancost, Richard D; Polya, David A; Lloyd, Jonathan R

2015-06-01

Microbially mediated arsenic release from Holocene and Pleistocene Cambodian aquifer sediments was investigated using microcosm experiments and substrate amendments. In the Holocene sediment, the metabolically active bacteria, including arsenate-respiring bacteria, were determined by DNA stable-isotope probing. After incubation with (13) C-acetate and (13) C-lactate, active bacterial community in the Holocene sediment was dominated by different Geobacter spp.-related 16S rRNA sequences. Substrate addition also resulted in the enrichment of sequences related to the arsenate-respiring Sulfurospirillum spp. (13) C-acetate selected for ArrA related to Geobacter spp. whereas (13) C-lactate selected for ArrA which were not closely related to any cultivated organism. Incubation of the Pleistocene sediment with lactate favoured a 16S rRNA-phylotype related to the sulphate-reducing Desulfovibrio oxamicus DSM1925, whereas the ArrA sequences clustered with environmental sequences distinct from those identified in the Holocene sediment. Whereas limited As(III) release was observed in Pleistocene sediment after lactate addition, no arsenic mobilization occurred from Holocene sediments, probably because of the initial reduced state of As, as determined by X-ray Absorption Near Edge Structure. Our findings demonstrate that in the presence of reactive organic carbon, As(III) mobilization can occur in Pleistocene sediments, having implications for future strategies that aim to reduce arsenic contamination in drinking waters by using aquifers containing Pleistocene sediments. © 2014 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Interconnection of Key Microbial Functional Genes for Enhanced Benzo[a]pyrene Biodegradation in Sediments by Microbial Electrochemistry.

PubMed

Yan, Zaisheng; He, Yuhong; Cai, Haiyuan; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Krumholz, Lee R; Jiang, He-Long

2017-08-01

Sediment microbial fuel cells (SMFCs) can stimulate the degradation of polycyclic aromatic hydrocarbons in sediments, but the mechanism of this process is poorly understood at the microbial functional gene level. Here, the use of SMFC resulted in 92% benzo[a]pyrene (BaP) removal over 970 days relative to 54% in the controls. Sediment functions, microbial community structure, and network interactions were dramatically altered by the SMFC employment. Functional gene analysis showed that c-type cytochrome genes for electron transfer, aromatic degradation genes, and extracellular ligninolytic enzymes involved in lignin degradation were significantly enriched in bulk sediments during SMFC operation. Correspondingly, chemical analysis of the system showed that these genetic changes resulted in increases in the levels of easily oxidizable organic carbon and humic acids which may have resulted in increased BaP bioavailability and increased degradation rates. Tracking microbial functional genes and corresponding organic matter responses should aid mechanistic understanding of BaP enhanced biodegradation by microbial electrochemistry and development of sustainable bioremediation strategies.

Biodegradation of organic compounds in vadose zone and aquifer sediments.

PubMed Central

Konopka, A; Turco, R

1991-01-01

The microbial processes that occur in the subsurface under a typical Midwest agricultural soil were studied. A 26-m bore was installed in November of 1988 at a site of the Purdue University Agronomy Research Center. Aseptic collections of soil materials were made at 17 different depths. Physical analysis indicated that the site contained up to 14 different strata. The site materials were primarily glacial tills with a high carbonate content. The N, P, and organic C contents of sediments tended to decrease with depth. Ambient water content was generally less than the water content, which corresponds to a -0.3-bar equivalent. No pesticides were detected in the samples, and degradation of added 14C-labeled pesticides (atrazine and metolachlor) was not detected in slurry incubations of up to 128 days. The sorption of atrazine and metolachlor was correlated with the clay content of the sediments. Microbial biomass (determined by direct microscopic count, viable count, and phospholipid assay) in the tills was lower than in either the surface materials or the aquifer located at 25 m. The biodegradation of glucose and phenol occurred rapidly and without a lag in samples from the aquifer capillary fringe, saturated zone, and surface soils. In contrast, lag periods and smaller biodegradation rates were found in the till samples. Subsurface sediments are rich in microbial numbers and activity. The most active strata appear to be transmissive layers in the saturated zone. This implies that the availability of water may limit activity in the profile. PMID:1768098

Phospholipids fatty acids of drinking water reservoir sedimentary microbial community: Structure and function responses to hydrostatic pressure and other physico-chemical properties.

PubMed

Chai, Bei-Bei; Huang, Ting-Lin; Zhao, Xiao-Guang; Li, Ya-Jiao

2015-07-01

Microbial communities in three drinking water reservoirs, with different depth in Xi'an city, were quantified by phospholipids fatty acids analysis and multivariate statistical analysis was employed to interpret their response to different hydrostatic pressure and other physico-chemical properties of sediment and overlying water. Principle component analyses of sediment characteristics parameters showed that hydrostatic pressure was the most important effect factor to differentiate the overlying water quality from three drinking water reservoirs from each other. NH4+ content in overlying water was positive by related to hydrostatic pressure, while DO in water-sediment interface and sediment OC in sediment were negative by related with it. Three drinking water reservoir sediments were characterized by microbial communities dominated by common and facultative anaerobic Gram-positive bacteria, as well as, by sulfur oxidizing bacteria. Hydrostatic pressure and physico-chemical properties of sediments (such as sediment OC, sediment TN and sediment TP) were important effect factors to microbial community structure, especially hydrostatic pressure. It is also suggested that high hydrostatic pressure and low dissolved oxygen concentration stimulated Gram-positive and sulfate-reducing bacteria (SRB) bacterial population in drinking water reservoir sediment. This research supplied a successful application of phospholipids fatty acids and multivariate analysis to investigate microbial community composition response to different environmental factors. Thus, few physico-chemical factors can be used to estimate composition microbial of community as reflected by phospholipids fatty acids, which is difficult to detect.

Hourly and daily variation of sediment redox potential in tidal wetland sediments

USGS Publications Warehouse

Catallo, W. James

1999-01-01

Variation of electrochemical oxidation-reduction (redox) potential was examined in surface salt march sediments under conditions of flooding and tidal simulation in mesocosms and field sites. Time series were generated of redox potential measured in sediment profiles at 2-10 cm depth using combination Pt-Ag/AgCl (ORP) electrodes. Redox potential data were acquired at rapid rates (1-55 samples/h) over extended periods (3-104 days) along with similar times series of temperature (water, air, soil) and pH. It was found that redox potential vaired as a result of water level changes and was unrelated to diurnal changes in temperature or pH, the latter of which changed by 370 mV redox potential decrease in under 48 hours). Attenuatoin of microbial activity by [gamma] y-radiation and toxic chemicals elimintated this response. In tidal salt marsh mesocosms where the sediment-plant assemblages were exposed to a simulated diurnal tide, redox potenial oscillations of 40-300 mV amplitude were recoded that has the same periodicity as the flood-drain cycle. Periodic redoc potential time series were observed repeatedly in sediments receiving tidal pulsing but not in those sediments exposed to static hydrological conditions. Data collected over 12 days from a coastal marsh site experiencing diurnal tides showed similar fluctuations in redox potential. Data from the experimentents indicated that (a) redox potential can be a dynamic, nonlinear variable in coastal and estuarine wetland sediments over hourly and daily scales, and the designs of biogeochemical experiments should reflect this, (b) redox potential can change rapidly and signigicantly in coastal wetland sediments in response of flooding and draining, (c) microbial community processes are primarily determinants of the time course of redox potential in wetland sediments, and elimination of inhibition of microbial activity (e.g. by pollutants) can significantly alter that behavior, and (d) fast redox potential dynamics appear to be characteristic of sediments that experience changes in hydrology. The rapid redox potential changes observed in these systems indicated dynamic metabolic and biogeochemical conditions in the field, and confirmed that hourly and daily redox potential variations should be resolved in studies of sediment functioning.

Interactions between metals and microbial communities in New Bedford Harbor, Massachusetts.

PubMed Central

Ford, T; Sorci, J; Ika, R; Shine, J

1998-01-01

The fate of toxic metals in marine sediments depends on a combination of the physical, chemical, and biologic conditions encountered in any given environment. These conditions may vary dramatically, both spatially and temporally, in response to factors ranging from seasonal changes and storm events to human activities such as dredging or remediation efforts. This paper describes a program designed to evaluate the interrelationships between the microbial community and pollutants in the New Bedford Harbor, Massachusetts, area, a U.S. Environmental Protection Agency designated Superfund site. Research has focused on establishing distributional relationships between contaminant metals, fluxes of metals between sediments and the overlying water, changes in microbial diversity in response to metals, and potential use of the microbial community as a biomarker of contaminant availability. This research has shown that a significant flux of metals to the water column is mediated by benthic biologic activity, and that microbial communities may be a responsive marker of contaminant stress. A combination of biogeochemical studies and the use of molecular tools can be used to improve our understanding of the fate and effect of heavy metals released to aquatic systems. Images Figure 1 Figure 3 Figure 4 PMID:9703489

Physical Factors Correlate to Microbial Community Structure and Nitrogen Cycling Gene Abundance in a Nitrate Fed Eutrophic Lagoon.

PubMed

Highton, Matthew P; Roosa, Stéphanie; Crawshaw, Josie; Schallenberg, Marc; Morales, Sergio E

2016-01-01

Nitrogenous run-off from farmed pastures contributes to the eutrophication of Lake Ellesmere, a large shallow lagoon/lake on the east coast of New Zealand. Tributaries periodically deliver high loads of nitrate to the lake which likely affect microbial communities therein. We hypothesized that a nutrient gradient would form from the potential sources (tributaries) creating a disturbance resulting in changes in microbial community structure. To test this we first determined the existence of such a gradient but found only a weak nitrogen (TN) and phosphorous gradient (DRP). Changes in microbial communities were determined by measuring functional potential (quantification of nitrogen cycling genes via nifH , nirS , nosZI , and nosZII using qPCR), potential activity (via denitrification enzyme activity), as well as using changes in total community (via 16S rRNA gene amplicon sequencing). Our results demonstrated that changes in microbial communities at a phylogenetic (relative abundance) and functional level (proportion of the microbial community carrying nifH and nosZI genes) were most strongly associated with physical gradients (e.g., lake depth, sediment grain size, sediment porosity) and not nutrient concentrations. Low nitrate influx at the time of sampling is proposed as a factor contributing to the observed patterns.

Cambrian rivers and floodplains: the significance of microbial cementation, groundwater and aeolian sediment transport

NASA Astrophysics Data System (ADS)

Reesink, A. J. H.; Best, J.; Freiburg, J. T.; Nathan, W.

2016-12-01

Rivers that existed before land plants colonized the Earth are commonly considered to be unaffected by microbial activity on their floodplains, because the limited cementation produced by microbial activity is insufficient to stabilize the river banks. Although this assumption is likely correct, such emphasis on channel dynamics ignores the potential role of floodplain dynamics as an integral component of the river system. Detailed analysis of cores from the Cambrian Mount Simon Sandstone, Illinois, suggests that a significant proportion of the terrestrial sequence is composed of flat-bedded `crinkly' structures that provide evidence of cementation by soil crusts and microbial biofilms, and that promoted the adhesion of sediment to sticky surfaces. Wind ripples and local desert pavements were abundant. These findings highlight that sediment deposition on Cambrian floodplains was often dominated by wind in locations where the ground water table reached the surface, and was thus likely independent of sediment transport within the river channel. Erosion by wind would thus have been hindered by surface cementation and the formation of desert pavements. Such ground water control on deposition, and resistance to erosion by floodplain surface hardening, appear to have been the primary controls on Cambrian floodplain topography. Because floodplain topography poses a key control on channel and floodplain flow, these processes may have affected patterns of erosion and deposition, as well as reach-scale dynamics such as channel avulsions. The autonomous operation of wind-and-groundwater controlled floodplains makes pre-vegetated river systems more sensitive to climatic conditions such as precipitation and evaporation, and strikingly different from those that occurred after the development of land plants.

[Development of Sediment Micro-Interface Under Physical and Chironomus plumosus Combination Disturbance].

PubMed

Wang, Ren; Li, Da-peng; Huang, Yong; Liu, Yan-jian; Chen, Jun

2015-11-01

Synergistic effect of physical and Chironomus plumosus combination disturbance on the characteristics of the micro-environment and micro-interface was investigated by the Rhizon samplers and Unisense micro sensor system. The results showed that the oxygen penetration depth (OPD), total oxygen exchange (TOE), water content and total microbial activity increased under the combination disturbance and bioturbation and were kept at the higher level, compared with the control. These parameters increased with the physical intensity under combination disturbance. However, the content of Fe2+ decreased under the combination disturbance and bioturbation and the decrease was more obvious than that in the control. The changes of the Fe2+, the water content and the total microbial activity were large at 0-4 cm depth in the sediments. Therefore, the area might be the active area for the transformation of internal sedimentary phosphorus forms. The curve fitting was used for the OPD, TOE, the content of Fe2+, the water content and the total microbial activity with the physical intensity under combination disturbance. It was observed that the second-order polynomial equation was suitable for the curve fitting. In addition, jump type synergistic effect was presented in the above mentioned parameters under combination disturbance when the physical intensity was higher than 34 r x min(-1). The remodeling on the sediment micro-interface and micro-environment might be the main inducing mechanism for the transformation of internal phosphorus.

Evidence of in situ microbial activity and sulphidogenesis in perennially sub-0 °C and hypersaline sediments of a high Arctic permafrost spring.

PubMed

Lamarche-Gagnon, Guillaume; Comery, Raven; Greer, Charles W; Whyte, Lyle G

2015-01-01

The lost hammer (LH) spring perennially discharges subzero hypersaline reducing brines through thick layers of permafrost and is the only known terrestrial methane seep in frozen settings on Earth. The present study aimed to identify active microbial communities that populate the sediments of the spring outlet, and verify whether such communities vary seasonally and spatially. Microcosm experiments revealed that the biological reduction of sulfur compounds (SR) with hydrogen (e.g., sulfate reduction) was potentially carried out under combined hypersaline and subzero conditions, down to -20 °C, the coldest temperature ever recorded for SR. Pyrosequencing analyses of both 16S rRNA (i.e., cDNA) and 16S rRNA genes (i.e., DNA) of sediments retrieved in late winter and summer indicated fairly stable bacterial and archaeal communities at the phylum level. Potentially active bacterial and archaeal communities were dominated by clades related to the T78 Chloroflexi group and Halobacteria species, respectively. The present study indicated that SR, hydrogenotrophy (possibly coupled to autotrophy), and short-chain alkane degradation (other than methane), most likely represent important, previously unaccounted for, metabolic processes carried out by LH microbial communities. Overall, the obtained findings provided additional evidence that the LH system hosts active communities of anaerobic, halophilic, and cryophilic microorganisms despite the extreme conditions in situ.

Active Marine Subsurface Bacterial Population Composition in Low Organic Carbon Environments from IODP Expedition 320

NASA Astrophysics Data System (ADS)

Shepard, A.; Reese, B. K.; Mills, H. J.; IODP Expedition 320 Shipboard Science Party

2011-12-01

The marine subsurface environment contains abundant and active microorganisms. These microbial populations are considered integral players in the marine subsurface biogeochemical system with significance in global geochemical cycles and reservoirs. However, variations in microbial community structure, activity and function associated with the wide-ranging sedimentary and geochemical environments found globally have not been fully resolved. Integrated Ocean Drilling Program Expedition 320 recovered sediments from site U1332. Two sampling depths were selected for analysis that spanned differing lithological units in the sediment core. Sediments were composed of mostly clay with zeolite minerals at 8 meters below sea floor (mbsf). At 27 mbsf, sediments were composed of alternating clayey radiolarian ooze and nannofossil ooze. The concentration of SO42- had little variability throughout the core and the concentration of Fe2+ remained close to, or below, detection limits (0.4 μM). Total organic carbon content ranged from a low of 0.03 wt% to a high of 0.07 wt% between 6 and 30 mbsf providing an opportunity to evaluate marine subsurface microbial communities under extreme electron donor limiting conditions. The metabolically active fraction of the bacterial population was isolated by the extraction and amplification of 16S ribosomal RNA. Pyrosequencing of 16S rRNA transcripts and subsequent bioinformatic analyses provided a robust data set (15,931 total classified sequences) to characterize the community at a high resolution. As observed in other subsurface environments, the overall diversity of active bacterial populations decreased with depth. The population shifted from a diverse but evenly distributed community at approximately 8 mbsf to a Firmicutes dominated population at 27 mbsf (80% of sequences). A total of 95% of the sequences at 27 mbsf were grouped into three genera: Lactobacillus (phylum Firmicutes) at 80% of the total sequences, Marinobacter (phylum Proteobacteria) at 8%, and Formosa (phylum Bacteroidetes) at 7%. These lineages support a paradigm suggesting the importance of fermentation in the subsurface. However, this study extends the predicted range for fermentation below the shallow subsurface and into organic carbon limited marine sediments. Other previously characterized subsurface active populations from environments with higher organic carbon concentrations do not show similar levels of reduced diversity or predominance of fermentative populations. This study further emphasizes the spatial variability of microbial populations in the deep subsurface and highlights the need for continued exploration.

Fungal and Prokaryotic Activities in the Marine Subsurface Biosphere at Peru Margin and Canterbury Basin Inferred from RNA-Based Analyses and Microscopy

PubMed Central

Pachiadaki, Maria G.; Rédou, Vanessa; Beaudoin, David J.; Burgaud, Gaëtan; Edgcomb, Virginia P.

2016-01-01

The deep sedimentary biosphere, extending 100s of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea, and microbial eukaryotes. Far less is known about microbial eukaryotes in subsurface habitats, albeit several studies have indicated that fungi dominate microbial eukaryotic communities and fungal molecular signatures (of both yeasts and filamentous forms) have been detected in samples as deep as 1740 mbsf. Here, we compare and contrast fungal ribosomal RNA gene signatures and whole community metatranscriptomes present in sediment core samples from 6 and 95 mbsf from Peru Margin site 1229A and from samples from 12 and 345 mbsf from Canterbury Basin site U1352. The metatranscriptome analyses reveal higher relative expression of amino acid and peptide transporters in the less nutrient rich Canterbury Basin sediments compared to the nutrient rich Peru Margin, and higher expression of motility genes in the Peru Margin samples. Higher expression of genes associated with metals transporters and antibiotic resistance and production was detected in Canterbury Basin sediments. A poly-A focused metatranscriptome produced for the Canterbury Basin sample from 345 mbsf provides further evidence for active fungal communities in the subsurface in the form of fungal-associated transcripts for metabolic and cellular processes, cell and membrane functions, and catalytic activities. Fungal communities at comparable depths at the two geographically separated locations appear dominated by distinct taxa. Differences in taxonomic composition and expression of genes associated with particular metabolic activities may be a function of sediment organic content as well as oceanic province. Microscopic analysis of Canterbury Basin sediment samples from 4 and 403 mbsf produced visualizations of septate fungal filaments, branching fungi, conidiogenesis, and spores. These images provide another important line of evidence supporting the occurrence and activity of fungi in the deep subseafloor biosphere. PMID:27375571

Fungal and Prokaryotic Activities in the Marine Subsurface Biosphere at Peru Margin and Canterbury Basin Inferred from RNA-Based Analyses and Microscopy.

PubMed

Pachiadaki, Maria G; Rédou, Vanessa; Beaudoin, David J; Burgaud, Gaëtan; Edgcomb, Virginia P

2016-01-01

The deep sedimentary biosphere, extending 100s of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea, and microbial eukaryotes. Far less is known about microbial eukaryotes in subsurface habitats, albeit several studies have indicated that fungi dominate microbial eukaryotic communities and fungal molecular signatures (of both yeasts and filamentous forms) have been detected in samples as deep as 1740 mbsf. Here, we compare and contrast fungal ribosomal RNA gene signatures and whole community metatranscriptomes present in sediment core samples from 6 and 95 mbsf from Peru Margin site 1229A and from samples from 12 and 345 mbsf from Canterbury Basin site U1352. The metatranscriptome analyses reveal higher relative expression of amino acid and peptide transporters in the less nutrient rich Canterbury Basin sediments compared to the nutrient rich Peru Margin, and higher expression of motility genes in the Peru Margin samples. Higher expression of genes associated with metals transporters and antibiotic resistance and production was detected in Canterbury Basin sediments. A poly-A focused metatranscriptome produced for the Canterbury Basin sample from 345 mbsf provides further evidence for active fungal communities in the subsurface in the form of fungal-associated transcripts for metabolic and cellular processes, cell and membrane functions, and catalytic activities. Fungal communities at comparable depths at the two geographically separated locations appear dominated by distinct taxa. Differences in taxonomic composition and expression of genes associated with particular metabolic activities may be a function of sediment organic content as well as oceanic province. Microscopic analysis of Canterbury Basin sediment samples from 4 and 403 mbsf produced visualizations of septate fungal filaments, branching fungi, conidiogenesis, and spores. These images provide another important line of evidence supporting the occurrence and activity of fungi in the deep subseafloor biosphere.

Controls of Sediment Nitrogen Dynamics in Tropical Coastal Lagoons

PubMed Central

Enrich-Prast, Alex; Figueiredo, Viviane; Esteves, Francisco de Assis; Nielsen, Lars Peter

2016-01-01

Sediment denitrification rates seem to be lower in tropical environments than in temperate environments. Using the isotope pairing technique, we measured actual denitrification rates in the sediment of tropical coastal lagoons. To explain the low denitrification rates observed at all study sites (<5 μmol N2 m-2 h-1), we also evaluated potential oxygen (O2) consumption, potential nitrification, potential denitrification, potential anammox, and estimated dissimilatory nitrate (NO3-) reduction to ammonium (NH4+; DNRA) in the sediment. 15NO3- and 15NH4+ conversion was measured in oxic and anoxic slurries from the sediment surface. Sediment potential O2 consumption was used as a proxy for overall mineralization activity. Actual denitrification rates and different potential nitrogen (N) oxidation and reduction processes were significantly correlated with potential O2 consumption. The contribution of potential nitrification to total O2 consumption decreased from contributing 9% at sites with the lowest sediment mineralization rates to less than 0.1% at sites with the highest rates. NO3- reduction switched completely from potential denitrification to estimated DNRA. Ammonium oxidation and nitrite (NO2-) reduction by potential anammox contributed up to 3% in sediments with the lowest sediment mineralization rates. The majority of these patterns could be explained by variations in the microbial environments from stable and largely oxic conditions at low sediment mineralization sites to more variable conditions and the prevalences of anaerobic microorganisms at high sediment mineralization sites. Furthermore, the presence of algal and microbial mats on the sediment had a significant effect on all studied processes. We propose a theoretical model based on low and high sediment mineralization rates to explain the growth, activity, and distribution of microorganisms carrying out denitrification and DNRA in sediments that can explain the dominance or coexistence of DNRA and denitrification processes. The results presented here show that the potential activity of anaerobic nitrate-reducing organisms is not dependent on the availability of environmental NO3-. PMID:27175907

Controls of Sediment Nitrogen Dynamics in Tropical Coastal Lagoons.

PubMed

Enrich-Prast, Alex; Figueiredo, Viviane; Esteves, Francisco de Assis; Nielsen, Lars Peter

2016-01-01

Sediment denitrification rates seem to be lower in tropical environments than in temperate environments. Using the isotope pairing technique, we measured actual denitrification rates in the sediment of tropical coastal lagoons. To explain the low denitrification rates observed at all study sites (<5 μmol N2 m-2 h-1), we also evaluated potential oxygen (O2) consumption, potential nitrification, potential denitrification, potential anammox, and estimated dissimilatory nitrate (NO3-) reduction to ammonium (NH4+; DNRA) in the sediment. 15NO3- and 15NH4+ conversion was measured in oxic and anoxic slurries from the sediment surface. Sediment potential O2 consumption was used as a proxy for overall mineralization activity. Actual denitrification rates and different potential nitrogen (N) oxidation and reduction processes were significantly correlated with potential O2 consumption. The contribution of potential nitrification to total O2 consumption decreased from contributing 9% at sites with the lowest sediment mineralization rates to less than 0.1% at sites with the highest rates. NO3- reduction switched completely from potential denitrification to estimated DNRA. Ammonium oxidation and nitrite (NO2-) reduction by potential anammox contributed up to 3% in sediments with the lowest sediment mineralization rates. The majority of these patterns could be explained by variations in the microbial environments from stable and largely oxic conditions at low sediment mineralization sites to more variable conditions and the prevalences of anaerobic microorganisms at high sediment mineralization sites. Furthermore, the presence of algal and microbial mats on the sediment had a significant effect on all studied processes. We propose a theoretical model based on low and high sediment mineralization rates to explain the growth, activity, and distribution of microorganisms carrying out denitrification and DNRA in sediments that can explain the dominance or coexistence of DNRA and denitrification processes. The results presented here show that the potential activity of anaerobic nitrate-reducing organisms is not dependent on the availability of environmental NO3-.

Potential sources of hydrocarbons and their microbial degradation in sediments from the deep geothermal Lusi site, Indonesia

NASA Astrophysics Data System (ADS)

Krueger, Martin; Mazzini, Adriano; Scheeder, Georg; Blumenberg, Martin

2017-04-01

The Lusi eruption represents one of the largest ongoing sedimentary hosted geothermal systems, which started in 2006 following an earthquake on Java Island. Since then it has been continuously producing hot and hydrocarbon rich mud from a central crater with peaks reaching 180.000 m3 per day. Numerous investigations focused on the study of microbial communities which thrive at offshore methane and oil seeps and mud volcanoes, however very little has been done on onshore seeping structures. Lusi represents a unique opportunity to complete a comprehensive study of onshore microbial communities fed by the seepage of CH4 as well as of liquid hydrocarbons originating from one or more km below the surface. While the source of the methane at Lusi is unambiuous, the origin of the seeping oil is still discussed. Both, source and maturity estimates from biomarkers, are in favor of a type II/III organic matter source. Likely the oils were formed from the studied black shales (deeper Ngimbang Fm.) which contained a Type III component in the Type II predominated organic matter. In all samples large numbers of active microorganisms were present. Rates for aerobic methane oxidation were high, as was the potential of the microbial communities to degrade different hydrocarbons. The data suggests a transition of microbial populations from an anaerobic, hydrocarbon-driven metabolism in fresher samples from center or from small seeps to more generalistic, aerobic microbial communities in older, more consolidated sediments. Ongoing microbial activity in crater sediment samples under high temperatures (80-95C) indicate a deep origin of the involved microorganisms. First results of molecular analyses of the microbial community compositions confirm the above findings. This study represents an initial step to better understand onshore seepage systems and provides an ideal analogue for comparison with the better investigated offshore structures.

Biomarkers and Metabolic Patterns in the Sediments of Evolving Glacial Lakes as a Proxy for Planetary Lake Exploration.

PubMed

Parro, Víctor; Blanco, Yolanda; Puente-Sánchez, Fernando; Rivas, Luis A; Moreno-Paz, Mercedes; Echeverría, Alex; Chong-Díaz, Guillermo; Demergasso, Cecilia; Cabrol, Nathalie A

2018-05-01

Oligotrophic glacial lakes in the Andes Mountains serve as models to study the effects of climate change on natural biological systems. The persistent high UV regime and evolution of the lake biota due to deglaciation make Andean lake ecosystems potential analogues in the search for life on other planetary bodies. Our objective was to identify microbial biomarkers and metabolic patterns that represent time points in the evolutionary history of Andean glacial lakes, as these may be used in long-term studies as microscale indicators of climate change processes. We investigated a variety of microbial markers in shallow sediments from Laguna Negra and Lo Encañado lakes (Región Metropolitana, Chile). An on-site immunoassay-based Life Detector Chip (LDChip) revealed the presence of sulfate-reducing bacteria, methanogenic archaea, and exopolymeric substances from Gammaproteobacteria. Bacterial and archaeal 16S rRNA gene sequences obtained from field samples confirmed the results from the immunoassays and also revealed the presence of Alpha-, Beta-, Gamma-, and Deltaproteobacteria, as well as cyanobacteria and methanogenic archaea. The complementary immunoassay and phylogenetic results indicate a rich microbial diversity with active sulfate reduction and methanogenic activities along the shoreline and in shallow sediments. Sulfate inputs from the surrounding volcanic terrains during deglaciation may explain the observed microbial biomarker and metabolic patterns, which differ with depth and between the two lakes. A switch from aerobic and heterotrophic metabolisms to anaerobic ones such as sulfate reduction and methanogenesis in the shallow shores likely reflects the natural evolution of the lake sediments due to deglaciation. Hydrodynamic deposition of sediments creates compartmentalization (e.g., sediments with different structure and composition surrounded by oligotrophic water) that favors metabolic transitions. Similar phenomena would be expected to occur on other planetary lakes, such as those of Titan, where watery niches fed by depositional events would be surrounded by a "sea" of hydrocarbons. Key Words: Glacier lakes-Sedimentation-Prokaryotic metabolisms and biomarkers-Deglaciation-Life detection-Planetary exploration. Astrobiology 18, 586-606.

Seasonal hyporheic dynamics control coupled microbiology and geochemistry in Colorado River sediments

DOE PAGES

Danczak, Robert E.; Sawyer, Audrey H.; Williams, Kenneth H.; ...

2016-12-03

Riverbed microbial communities play an oversized role in many watershed ecosystem functions, including the processing of organic carbon, cycling of nitrogen, and alterations to metal mobility. The structure and activity of microbial assemblages depend in part on geochemical conditions set by river-groundwater exchange or hyporheic exchange. In order to assess how seasonal changes in river-groundwater mixing affect these populations in a snowmelt-dominated fluvial system, vertical sediment and pore water profiles were sampled at three time points at one location in the hyporheic zone of the Colorado River and analyzed by using geochemical measurements, 16S rRNA gene sequencing, and ecological modeling.more » Oxic river water penetrated deepest into the subsurface during peak river discharge, while under base flow conditions, anoxic groundwater dominated shallower depths. Over a 70 cm thick interval, riverbed sediments were therefore exposed to seasonally fluctuating redox conditions and hosted microbial populations statistically different from those at both shallower and deeper locations. Additionally, microbial populations within this zone were shown to be the most dynamic across sampling time points, underlining the critical role that hyporheic mixing plays in constraining microbial abundances. Given such mixing effects, we anticipate that future changes in river discharge in mountainous, semiarid western U.S. watersheds may affect microbial community structure and function in riverbed environments, with potential implications for biogeochemical processes in riparian regions.« less

Seasonal hyporheic dynamics control coupled microbiology and geochemistry in Colorado River sediments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Danczak, Robert E.; Sawyer, Audrey H.; Williams, Kenneth H.

Riverbed microbial communities play an oversized role in many watershed ecosystem functions, including the processing of organic carbon, cycling of nitrogen, and alterations to metal mobility. The structure and activity of microbial assemblages depend in part on geochemical conditions set by river-groundwater exchange or hyporheic exchange. In order to assess how seasonal changes in river-groundwater mixing affect these populations in a snowmelt-dominated fluvial system, vertical sediment and pore water profiles were sampled at three time points at one location in the hyporheic zone of the Colorado River and analyzed by using geochemical measurements, 16S rRNA gene sequencing, and ecological modeling.more » Oxic river water penetrated deepest into the subsurface during peak river discharge, while under base flow conditions, anoxic groundwater dominated shallower depths. Over a 70 cm thick interval, riverbed sediments were therefore exposed to seasonally fluctuating redox conditions and hosted microbial populations statistically different from those at both shallower and deeper locations. Additionally, microbial populations within this zone were shown to be the most dynamic across sampling time points, underlining the critical role that hyporheic mixing plays in constraining microbial abundances. Given such mixing effects, we anticipate that future changes in river discharge in mountainous, semiarid western U.S. watersheds may affect microbial community structure and function in riverbed environments, with potential implications for biogeochemical processes in riparian regions.« less

Seasonal hyporheic dynamics control coupled microbiology and geochemistry in Colorado River sediments

NASA Astrophysics Data System (ADS)

Danczak, Robert E.; Sawyer, Audrey H.; Williams, Kenneth H.; Stegen, James C.; Hobson, Chad; Wilkins, Michael J.

2016-12-01

Riverbed microbial communities play an oversized role in many watershed ecosystem functions, including the processing of organic carbon, cycling of nitrogen, and alterations to metal mobility. The structure and activity of microbial assemblages depend in part on geochemical conditions set by river-groundwater exchange or hyporheic exchange. To assess how seasonal changes in river-groundwater mixing affect these populations in a snowmelt-dominated fluvial system, vertical sediment and pore water profiles were sampled at three time points at one location in the hyporheic zone of the Colorado River and analyzed by using geochemical measurements, 16S rRNA gene sequencing, and ecological modeling. Oxic river water penetrated deepest into the subsurface during peak river discharge, while under base flow conditions, anoxic groundwater dominated shallower depths. Over a 70 cm thick interval, riverbed sediments were therefore exposed to seasonally fluctuating redox conditions and hosted microbial populations statistically different from those at both shallower and deeper locations. Additionally, microbial populations within this zone were shown to be the most dynamic across sampling time points, underlining the critical role that hyporheic mixing plays in constraining microbial abundances. Given such mixing effects, we anticipate that future changes in river discharge in mountainous, semiarid western U.S. watersheds may affect microbial community structure and function in riverbed environments, with potential implications for biogeochemical processes in riparian regions.

Functional structure of laminated microbial sediments from a supratidal sandy beach of the German Wadden Sea (St. Peter-Ording)

NASA Astrophysics Data System (ADS)

Bühring, Solveig I.; Kamp, Anja; Wörmer, Lars; Ho, Stephanie; Hinrichs, Kai-Uwe

2014-01-01

Hidden for the untrained eye through a thin layer of sand, laminated microbial sediments occur in supratidal beaches along the North Sea coast. The inhabiting microbial communities organize themselves in response to vertical gradients of light, oxygen or sulfur compounds. We performed a fine-scale investigation on the vertical zonation of the microbial communities using a lipid biomarker approach, and assessed the biogeochemical processes using a combination of microsensor measurements and a 13C-labeling experiment. Lipid biomarker fingerprinting showed the overarching importance of cyanobacteria and diatoms in these systems, and heterocyst glycolipids revealed the presence of diazotrophic cyanobacteria even in 9 to 20 mm depth. High abundance of ornithine lipids (OL) throughout the system may derive from sulfate reducing bacteria, while a characteristic OL profile between 5 and 8 mm may indicate presence of purple non-sulfur bacteria. The fate of 13C-labeled bicarbonate was followed by experimentally investigating the uptake into microbial lipids, revealing an overarching importance of cyanobacteria for carbon fixation. However, in deeper layers, uptake into purple sulfur bacteria was evident, and a close microbial coupling could be shown by uptake of label into lipids of sulfate reducing bacteria in the deepest layer. Microsensor measurements in sediment cores collected at a later time point revealed the same general pattern as the biomarker analysis and the labeling experiments. Oxygen and pH-microsensor profiles showed active photosynthesis in the top layer. The sulfide that diffuses from deeper down and decreases just below the layer of active oxygenic photosynthesis indicates the presence of sulfur bacteria, like anoxygenic phototrophs that use sulfide instead of water for photosynthesis.

Cultivation-dependent analysis of the microbial diversity associated with the seagrass meadows in Xincun Bay, South China Sea.

PubMed

Jiang, Yu-Feng; Ling, Juan; Wang, You-Shao; Chen, Biao; Zhang, Yan-Ying; Dong, Jun-De

2015-10-01

Microbial communities have largely existed in the seagrass meadows. A total of 496 strains of the bacteria in the seagrass meadows, which belonged to 50 genera, were obtained by the plate cultivation method from three sites of Xincun Bay, South China Sea. The results showed that Bacillales and Vibrionales accounted for the highest proportions of organisms in all communities. The diversity of the bacteria in the sediment was higher than that associated with seagrass. Thalassia hemperichii possessed the highest abundance of bacteria, followed by Enhalus acoroides and Cymodocea rotundata. Robust seasonal dynamics in microbial community composition were also observed. It was found that microbial activities were closely tied to the growth stage of the seagrass. The microbial distribution was the lowest in site 3. The abundance of the bacteria was linked to the interactions between bacteria and plants, the condition of plant and even the coastal water quality and the nutrition level in the sediment.

Effects of Environmental Toxicants on Metabolic Activity of Natural Microbial Communities

PubMed Central

Barnhart, Carole L. H.; Vestal, J. Robie

1983-01-01

Two methods of measuring microbial activity were used to study the effects of toxicants on natural microbial communities. The methods were compared for suitability for toxicity testing, sensitivity, and adaptability to field applications. This study included measurements of the incorporation of 14C-labeled acetate into microbial lipids and microbial glucosidase activity. Activities were measured per unit biomass, determined as lipid phosphate. The effects of various organic and inorganic toxicants on various natural microbial communities were studied. Both methods were useful in detecting toxicity, and their comparative sensitivities varied with the system studied. In one system, the methods showed approximately the same sensitivities in testing the effects of metals, but the acetate incorporation method was more sensitive in detecting the toxicity of organic compounds. The incorporation method was used to study the effects of a point source of pollution on the microbiota of a receiving stream. Toxic doses were found to be two orders of magnitude higher in sediments than in water taken from the same site, indicating chelation or adsorption of the toxicant by the sediment. The microbiota taken from below a point source outfall was 2 to 100 times more resistant to the toxicants tested than was that taken from above the outfall. Downstream filtrates in most cases had an inhibitory effect on the natural microbiota taken from above the pollution source. The microbial methods were compared with commonly used bioassay methods, using higher organisms, and were found to be similar in ability to detect comparative toxicities of compounds, but were less sensitive than methods which use standard media because of the influences of environmental factors. PMID:16346432

Long-term impact of hydrological regime on structure and functions of microbial communities in riverine wetland sediments.

PubMed

Foulquier, Arnaud; Volat, Bernadette; Neyra, Marc; Bornette, Gudrun; Montuelle, Bernard

2013-08-01

In a context of global change, alterations in the water cycle may impact the structure and function of terrestrial and aquatic ecosystems. Wetlands are particularly at risk because hydrological regime has a major influence on microbially mediated biogeochemical processes in sediments. While the influence of water availability on wetland biogeochemical processes has been comprehensively studied, the influence of hydrological regime on microbial community structure has been overlooked. We tested for the effect of hydrological regime on the structure and functions of microbial communities by comparing sediments collected at multiple sites in the Ain département (Eastern France). Each site consisted of two plots, one permanently and one seasonally inundated. At the time of sampling, all plots were continuously inundated for more than 6 months but still harboured distinct bacterial communities. This change in community structure was not associated with marked modifications in the rates of microbial activities involved in the C and N cycles. These results suggest that the observed structural change could be related to bacterial taxa responding to the environmental variations associated with different hydrological regimes, but not strongly associated with the biogeochemical processes monitored here. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Bacterial abundance and activity in deep-sea sediments from the eastern North Atlantic

NASA Astrophysics Data System (ADS)

Eardly, D. F.; Carton, M. W.; Gallagher, J. M.; Patching, J. W.

Results are presented from four cruises to the Porcupine Abyssal Plain (PAP site) that took place during the BENGAL project from September 1996 to March 1998, and two cruises to the PAP and an oligotrophic site (EUMELI) that took place during the DEEPSEAS project between September 1993 and March 1994. Bacterial abundances in sediment and sediment contact water were measured by epifluorescence microscopy. Bacterial activity was determined by 3H-thymidine incorporation as a measure of DNA synthesis, and by 3H-leucine incorporation as a measure of protein synthesis. Activities were measured under atmospheric and in situ pressures and temperatures. Bacterial activity was usually higher in samples incubated at in situ pressure than those incubated at atmospheric pressure indicating that a barophilic community was dominant. Inter-cruise comparisons of abundance and activity during the BENGAL project showed no firm evidence of there being a seasonal response in the benthic microbial community to any episodic phytodetritus event. This was probably because of inter-annual variations in the quality and quantity of phytodetritus deposition at the PAP site, the rapid remineralization of fresh organic material by the microbial communities and the timing of cruises to the study area. 3H-thymidine and 3H-leucine incorporation in sediments was higher during the BENGAL period than the DEEPSEAS programme. A methodological change in the 3H-thymidine incorporation technique for sediments may explain the differences in DNA synthesis observed between the two projects, whereas the lower levels of protein synthesis observed during the DEEPSEAS programme probably reflected both inter-annual variations in activity at the PAP site and the lower productivity that prevailed at surface at the EUMELI oligotrophic site. Rates of 3H-thymidine incorporation in sediment contact water were similar during both projects.

Microbial Life in Ridge Flank Crustal Fluids at Baby Bare Seamount, Juan de Fuca Ridge

NASA Astrophysics Data System (ADS)

Huber, J. A.; Johnson, H. P.; Butterfield, D. A.; Baross, J. A.

2005-12-01

To determine the microbial community diversity within old oceanic crust, a novel sampling strategy was used to collect crustal fluids at Baby Bare Seamount, a 3.5 Ma old outcrop located in the northeast Pacific Ocean on the eastern flank of the Juan de Fuca Ridge. Stainless steel probes were driven directly into the igneous ocean crust to obtain samples of ridge flank crustal fluids. Genetic signatures and enrichment cultures of microorganisms demonstrate that these crustal fluids host a microbial community composed of species indigenous to the subseafloor, including anaerobic thermophiles, and species from other deep-sea habitats, such as seawater and sediments. Evidence using molecular techniques indicates the presence of a relatively small but active microbial population, dominated by bacteria. The microbial community diversity found in the crustal fluids may indicate habitat variability in old oceanic crust, with inputs of nutrients from seawater, sediment pore-water fluids and possibly hydrothermal sources. This report further supports the presence of an indigenous microbial community in ridge flank crustal fluids and advances our understanding of the potential physiological and phylogenetic diversity of this community.

Prokaryotic diversity, composition structure, and phylogenetic analysis of microbial communities in leachate sediment ecosystems.

PubMed

Liu, Jingjing; Wu, Weixiang; Chen, Chongjun; Sun, Faqian; Chen, Yingxu

2011-09-01

In order to obtain insight into the prokaryotic diversity and community in leachate sediment, a culture-independent DNA-based molecular phylogenetic approach was performed with archaeal and bacterial 16S rRNA gene clone libraries derived from leachate sediment of an aged landfill. A total of 59 archaeal and 283 bacterial rDNA phylotypes were identified in 425 archaeal and 375 bacterial analyzed clones. All archaeal clones distributed within two archaeal phyla of the Euryarchaeota and Crenarchaeota, and well-defined methanogen lineages, especially Methanosaeta spp., are the most numerically dominant species of the archaeal community. Phylogenetic analysis of the bacterial library revealed a variety of pollutant-degrading and biotransforming microorganisms, including 18 distinct phyla. A substantial fraction of bacterial clones showed low levels of similarity with any previously documented sequences and thus might be taxonomically new. Chemical characteristics and phylogenetic inferences indicated that (1) ammonium-utilizing bacteria might form consortia to alleviate or avoid the negative influence of high ammonium concentration on other microorganisms, and (2) members of the Crenarchaeota found in the sediment might be involved in ammonium oxidation. This study is the first to report the composition of the microbial assemblages and phylogenetic characteristics of prokaryotic populations extant in leachate sediment. Additional work on microbial activity and contaminant biodegradation remains to be explored.

Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hou, Zhangshuan; Nelson, William C.; Stegen, James C.

The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of water, nutrients, and organic matter occur in response to variations in discharge and riverbed properties. Within this region, a confluence of surface-derived organic carbon and subsurface nitrogen (in the form of nitrate) has been shown to stimulate microbial activity and transformations of carbon and nitrogen species. For example, production of gases such as CO 2, N 2 and N 2O indicate hyporheic zones might have a significant effect on energy and nutrient flows between the atmosphere and the subsurface. Managed and seasonal rivermore » stage changes and geomorphology-controlled sediment texture drive water flow within the HZ of the Columbia River. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the HZ, the grain size distributions for sediment samples taken across 320 m of shoreline were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of carbon and nitrogen oxidizers were found to explain the variability in many biogeochemical attributes. Microbial community analysis revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae, together comprising ~20% of the total community across all samples, but scant ammonia-oxidizing Bacteria. Network analysis of operational taxonomic units and the measured geophysical, chemical, and functional parameters showed negative relationships between abundance-based modules of organisms and sand and mud contents, and positive relationships with total organic carbon. The relationships identified in this work indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Some member populations of these sub-communities appear to respond directly to environmental conditions, while others may be dependent on the function of the first group. For example, nitrification is a strong primary response to the observed conditions, and this activity appears to support a larger heterotrophic community. Relationships between facies and hydrobiogeochemical properties enables facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.« less

Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies

DOE PAGES

Hou, Zhangshuan; Nelson, William C.; Stegen, James C.; ...

2017-09-20

The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of water, nutrients, and organic matter occur in response to variations in discharge and riverbed properties. Within this region, a confluence of surface-derived organic carbon and subsurface nitrogen (in the form of nitrate) has been shown to stimulate microbial activity and transformations of carbon and nitrogen species. For example, production of gases such as CO 2, N 2 and N 2O indicate hyporheic zones might have a significant effect on energy and nutrient flows between the atmosphere and the subsurface. Managed and seasonal rivermore » stage changes and geomorphology-controlled sediment texture drive water flow within the HZ of the Columbia River. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the HZ, the grain size distributions for sediment samples taken across 320 m of shoreline were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of carbon and nitrogen oxidizers were found to explain the variability in many biogeochemical attributes. Microbial community analysis revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae, together comprising ~20% of the total community across all samples, but scant ammonia-oxidizing Bacteria. Network analysis of operational taxonomic units and the measured geophysical, chemical, and functional parameters showed negative relationships between abundance-based modules of organisms and sand and mud contents, and positive relationships with total organic carbon. The relationships identified in this work indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Some member populations of these sub-communities appear to respond directly to environmental conditions, while others may be dependent on the function of the first group. For example, nitrification is a strong primary response to the observed conditions, and this activity appears to support a larger heterotrophic community. Relationships between facies and hydrobiogeochemical properties enables facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.« less

Microbial processes and organic priority substances in marine coastal sediments (Adriatic Sea, Italy)

NASA Astrophysics Data System (ADS)

Zoppini, Annamaria; Ademollo, Nicoletta; Amalfitano, Stefano; Dellisanti, Walter; Lungarini, Silvia; Miserocchi, Stefano; Patrolecco, Luisa; Langone, Leonardo

2015-04-01

PERSEUS EU FP7 Project aims to identify the interacting patterns of natural and human-derived pressures to assess their impact on marine ecosystems and, using the objectives and principles of the Marine Strategy Framework Directive (MSFD) as a vehicle, to design an effective and innovative research governance framework based on sound scientific knowledge. In the frame of this Project (subtask 1.3.3 ADREX: Adriatic and Ionian Seas Experiment), monitoring surveys were conducted in the Adriatic Sea (Italy) in order to study the variation of structural and functional characteristics of native bacterial communities and the occurrence of selected classes of organic priority substances in sediments. The study area represents a good natural laboratory sensitive to climate variability and human pressure, owing to the semi-enclosed nature of the Adriatic Sea and to the increasing trend of human activities in the coastal regions. During the cruise ADRI-13 (November 2013) and ADRI-14 (October 2014) we sampled several coastal sites from the mouth of the Po River to the Otranto strait. Surface sediments were collected in all areas, while sediment cores were sampled in selected sites. Microbes associated with marine sediments play an important role in the C-flux being responsible for the transformation of organic detritus (autochthonous and allochthonous) into biomass. The sediment bacterial abundance was determined by epifluorescence microscopy and the rate of bacterial carbon production by measuring the 3H-leucine uptake rates. The community respiration rate was estimated by the measurement of the electron transport system (ETS) activity. The sediment contamination level was determined by measuring the concentration of contaminants included in the list of organic priority substances: PAHs, bisphenol A (BPA), alkylphenols (APs). The extraction/clean-up of PAHs, BPA and APs was performed by ultrasonic bath with the appropriate solvents, followed by analytical determination with LC-MS or HPLC UV-fluorescence. The joint analysis of the microbial properties and the concentration of the organic pollutants reflects the impact of anthropic pressure on the selected coastal areas. At the surface layers, the microbial carbon assimilation and mineralization rates were affected by the increasing concentration of pollutants. The highest concentrations of organic pollutants were detected in the deeper sediment layers (20 cm) where a significant reduction of microbial metabolic activities was observed. The results of this study can contribute to acquire information to improve the MSFD and to reach the good environmental status.

Investigating Microbial Activity in Diazotrophic Methane Seep Sediment via Transcript Analysis and Single-Cell FISH-NanoSIMS

NASA Astrophysics Data System (ADS)

Dekas, A. E.; Connon, S. A.; Chadwick, G.; Orphan, V. J.

2012-12-01

Methane seep microbial ecosystems are phylogenetically diverse and physiologically complex, and require culture-independent techniques to accurately investigate metabolic activity. In the present study we combine an RNA analysis of four key microbial genes with FISH-NanoSIMS analysis of single cells to determine the diversity of nitrogen fixing microorganisms (diazotrophs) present at a deep-sea methane-seeping site, as well as investigate the methane-dependency of a variety of community members. Recently, methane-dependent nitrogen fixation was observed in Mound 12 Costa Rica sediments, and was spatially correlated with the abundance of aggregates of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacterial symbionts (SRB). Combined with the detection of 15N uptake from 15N2 in these aggregates, this suggested that the ANME-SRB aggregates are the primary diazotrophs in seep sediment. However, the diversity of dinitrogenase reductase (nifH) sequences recovered from several deep-sea locales, including Mound 12, suggests a greater diversity of diazotrophs in marine sediment. To investigate the activity of these potential diazotrophs in Mound 12 sediment, we investigated a suite of RNA transcripts in 15N2 incubations in both the presence and absence of methane: nifH, bacterial 16S rRNA, methyl coenzyme M reductase A (mcrA), and adenosine-5'-phosposulfate reductase alpha subunit (aprA). No nifH transcripts were recovered in incubations without methane, consistent with previous measurements lacking 15N2 uptake in the same sediments. The activity of the bacterial community in general, assessed by variable transcription, was also greatly affected by the presence or absence of methane. Single-cell fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS) was employed to confirm diazotrophic activity (15N2 uptake) and protein synthesis (15NH4+ uptake) of particular species implicated as ecologically important by the pattern of transcripts recovered in the mesocosm experiments. This analysis revealed 15N enrichment in free-living (i.e. non-ANME associated) members of the Desulfobulbaceae in 15N2 incubations with methane, while free-living Desulfosarcina/Desulfococcus cells, as well as nearly 40 unidentified DAPI-stained cells, were not 15N enriched. However, further NanoSIMS analyses of DSB in a variety of incubation conditions suggests that this enrichment may be due to N sharing between the ANME and DSB while in tight physical association, and then subsequent dissociation, rather than nitrogen fixation by the DSB. If true, this is an excellent example of the potential pitfalls of single cell stable isotope labeling experiments, and potential false positives due to the recycling of labeled material between (even transiently) closely associated symbionts. This work highlights both the utility of transcript analysis as a hypothesis-generator for direct analyses of microbial activity via stable isotope labeling, as well as the need to contextualize labeling experiments with investigations of microbial community structure.

Anaerobic Oxidation of Methane at a Marine Methane Seep in a Forearc Sediment Basin off Sumatra, Indian Ocean

PubMed Central

Siegert, Michael; Krüger, Martin; Teichert, Barbara; Wiedicke, Michael; Schippers, Axel

2011-01-01

A cold methane seep was discovered in a forearc sediment basin off the island Sumatra, exhibiting a methane-seep adapted microbial community. A defined seep center of activity, like in mud volcanoes, was not discovered. The seep area was rather characterized by a patchy distribution of active spots. The relevance of anaerobic oxidation of methane (AOM) was reflected by 13C-depleted isotopic signatures of dissolved inorganic carbon. The anaerobic conversion of methane to CO2 was confirmed in a 13C-labeling experiment. Methane fueled a vital microbial community with cell numbers of up to 4 × 109 cells cm−3 sediment. The microbial community was analyzed by total cell counting, catalyzed reporter deposition–fluorescence in situ hybridization (CARD–FISH), quantitative real-time PCR (qPCR), and denaturing gradient gel electrophoresis (DGGE). CARD–FISH cell counts and qPCR measurements showed the presence of Bacteria and Archaea, but only small numbers of Eukarya. The archaeal community comprised largely members of ANME-1 and ANME-2. Furthermore, members of the Crenarchaeota were frequently detected in the DGGE analysis. Three major bacterial phylogenetic groups (δ-Proteobacteria, candidate division OP9, and Anaerolineaceae) were abundant across the study area. Several of these sequences were closely related to the genus Desulfococcus of the family Desulfobacteraceae, which is in good agreement with previously described AOM sites. In conclusion, the majority of the microbial community at the seep consisted of AOM-related microorganisms, while the relevance of higher hydrocarbons as microbial substrates was negligible. PMID:22207865

Effects of Non-Indigenous Oysters on Microbial Diversity and Ecosystem Functioning

PubMed Central

Green, Dannielle S.; Boots, Bas; Crowe, Tasman P.

2012-01-01

Invasive ecosystem engineers can physically and chemically alter the receiving environment, thereby affecting biodiversity and ecosystem functioning. The Pacific oyster, Crassostrea gigas, invasive throughout much of the world, can establish dense populations monopolising shorelines and possibly altering ecosystem processes including decomposition and nutrient cycling. The effects of increasing cover of invasive C. gigas on ecosystem processes and associated microbial assemblages in mud-flats were tested experimentally in the field. Pore-water nutrients (NH4 + and total oxidised nitrogen), sediment chlorophyll content, microbial activity, total carbon and nitrogen, and community respiration (CO2 and CH4) were measured to assess changes in ecosystem functioning. Assemblages of bacteria and functionally important microbes, including methanogens, methylotrophs and ammonia-oxidisers were assessed in the oxic and anoxic layers of sediment using terminal restriction length polymorphism of the bacterial 16S rRNA, mxaF, amoA and archaeal mcrA genes respectively. At higher covers (40 and 80%) of oysters there was significantly greater microbial activity, increased chlorophyll content, CO2 (13 fold greater) and CH4 (6 fold greater) emission from the sediment compared to mud-flats without C. gigas. At 10% cover, C. gigas increased the concentration of total oxidised nitrogen and altered the assemblage structure of ammonia-oxidisers and methanogens. Concentrations of pore-water NH4 + were increased by C. gigas regardless of cover. Invasive species can alter ecosystem functioning not only directly, but also indirectly, by affecting microbial communities vital for the maintenance of ecosystem processes, but the nature and magnitude of these effects can be non-linear, depending on invader abundance. PMID:23144762

Anaerobic Oxidation of Methane at a Marine Methane Seep in a Forearc Sediment Basin off Sumatra, Indian Ocean.

PubMed

Siegert, Michael; Krüger, Martin; Teichert, Barbara; Wiedicke, Michael; Schippers, Axel

2011-01-01

A cold methane seep was discovered in a forearc sediment basin off the island Sumatra, exhibiting a methane-seep adapted microbial community. A defined seep center of activity, like in mud volcanoes, was not discovered. The seep area was rather characterized by a patchy distribution of active spots. The relevance of anaerobic oxidation of methane (AOM) was reflected by (13)C-depleted isotopic signatures of dissolved inorganic carbon. The anaerobic conversion of methane to CO(2) was confirmed in a (13)C-labeling experiment. Methane fueled a vital microbial community with cell numbers of up to 4 × 10(9) cells cm(-3) sediment. The microbial community was analyzed by total cell counting, catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH), quantitative real-time PCR (qPCR), and denaturing gradient gel electrophoresis (DGGE). CARD-FISH cell counts and qPCR measurements showed the presence of Bacteria and Archaea, but only small numbers of Eukarya. The archaeal community comprised largely members of ANME-1 and ANME-2. Furthermore, members of the Crenarchaeota were frequently detected in the DGGE analysis. Three major bacterial phylogenetic groups (δ-Proteobacteria, candidate division OP9, and Anaerolineaceae) were abundant across the study area. Several of these sequences were closely related to the genus Desulfococcus of the family Desulfobacteraceae, which is in good agreement with previously described AOM sites. In conclusion, the majority of the microbial community at the seep consisted of AOM-related microorganisms, while the relevance of higher hydrocarbons as microbial substrates was negligible.

Role of microbial Fe(III) reduction and solution chemistry in aggregation and settling of suspended particles in the Mississippi River Delta plain, Louisiana, USA

USGS Publications Warehouse

Jaisi, Deb P.; Ji, Shanshan; Dong, Hailiang; Blake, Ruth E.; Eberl, Dennis D.; Kim, Jinwook

2008-01-01

River-dominated delta areas are primary sites of active biogeochemical cycling, with productivity enhanced by terrestrial inputs of nutrients. Particle aggregation in these areas primarily controls the deposition of suspended particles, yet factors that control particle aggregation and resulting sedimentation in these environments are poorly understood. This study was designed to investigate the role of microbial Fe(III) reduction and solution chemistry in aggregation of suspended particles in the Mississippi Delta. Three representative sites along the salinity gradient were selected and sediments were collected from the sediment-water interface. Based on quantitative mineralogical analyses 88–89 wt.% of all minerals in the sediments are clays, mainly smectite and illite. Consumption of SO42− and the formation of H2S and pyrite during microbial Fe(III) reduction of the non-sterile sediments by Shewanella putrefaciens CN32 in artificial pore water (APW) media suggest simultaneous sulfate and Fe(III) reduction activity. The pHPZNPC of the sediments was ≤3.5 and their zeta potentials at the sediment-water interface pH (6.9–7.3) varied from −35 to −45 mV, suggesting that both edges and faces of clay particles have negative surface charge. Therefore, high concentrations of cations in pore water are expected to be a predominant factor in particle aggregation consistent with the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. Experiments on aggregation of different types of sediments in the same APW composition revealed that the sediment with low zeta potential had a high rate of aggregation. Similarly, addition of external Fe(II) (i.e. not derived from sediments) was normally found to enhance particle aggregation and deposition in all sediments, probably resulting from a decrease in surface potential of particles due to specific Fe(II) sorption. Scanning and transmission electron microscopy (SEM, TEM) images showed predominant face-to-face clay aggregation in native sediments and composite mixtures of biopolymer, bacteria, and clay minerals in the bioreduced sediments. However, a clear need remains for additional information on the conditions, if any, that favor the development of anoxia in deep- and bottom-water bodies supporting Fe(III) reduction and resulting in particle aggregation and sedimentation.

Deep aquifer as driver for mineral authigenesis in Gulf of Alaska sediments (IODP Expedition 341, Site U1417)

NASA Astrophysics Data System (ADS)

Zindorf, Mark; März, Christian; Wagner, Thomas; Strauss, Harald; Gulick, Sean P. S.; Jaeger, John M.; LeVay, Leah J.

2016-04-01

Bacterial sulphate reduction plays a key role in authigenic mineral formation in marine sediments. Usually, decomposition of organic matter follows a sequence of microbial metabolic pathways, where microbial sulphate reduction leads to sulphate depletion deeper in the sediment. When sulphate is consumed completely from the pore waters, methanogenesis commences. The contact of sulphate- and methane-containing pore waters is a well-defined biogeochemical boundary (the sulphate-methane transition zone, SMTZ). Here authigenic pyrite, barite and carbonates form. Pyrite formation is directly driven by bacterial sulphate reduction since pyrite precipitates from produced hydrogen sulphide. Barite and carbonate formation are secondary effects resulting from changes of the chemical milieu due to microbial activity. However, this mineral authigenesis is ultimately linked to abiotic processes that determine the living conditions for microorganisms. At IODP Site U1417 in the Gulf of Alaska, a remarkable diagenetic pattern has been observed: Between sulphate depletion and methane enrichment, a ~250 m wide gap exists. Consequently, no SMTZ can be found under present conditions, but enrichments of pyrite indicate that such zones have existed in the past. Solid layers consisting of authigenic carbonate-cemented sand were partly recovered right above the methane production zone, likely preventing continued upward methane diffusion. At the bottom of the sediment succession, the lower boundary of the methanogenic zone is constrained by sulphate-rich pore waters that appear to originate from a deeper source. Here, a well-established SMTZ exists, but in reversed order (sulphate diffusing up, methane diffusing down). Sulphur isotopes of pyrite reveal that sulphate reduction here does not occur under closed system conditions. This indicates that a deep aquifer is actively recharging the deep sulphate pool. Similar deep SMTZs have been found at other sites, yet mostly in geologically active environments such as ridge flanks or above subduction zones. Therefore Site U1417, in a relatively inactive intraplate environment, represents a so far under-sampled geochemical setting. Calculated accumulation times for authigenic minerals in the deep SMTZ are on the same order of magnitude as the onset of subduction-related bending of the Pacific Plate, suggesting that both processes are linked. Plate bending could create fractures in the overlying sediments allowing seawater to penetrate and recharge a deep aquifer. Our study provides insights into a newly discovered geological process suitable for delivering sulphate-rich water deep into the sediments and installing diagenetically active environments where microbial activity would otherwise be very limited.

Environmental Microbial Community Proteomics: Status, Challenges and Perspectives.

PubMed

Wang, Da-Zhi; Kong, Ling-Fen; Li, Yuan-Yuan; Xie, Zhang-Xian

2016-08-05

Microbial community proteomics, also termed metaproteomics, is an emerging field within the area of microbiology, which studies the entire protein complement recovered directly from a complex environmental microbial community at a given point in time. Although it is still in its infancy, microbial community proteomics has shown its powerful potential in exploring microbial diversity, metabolic potential, ecological function and microbe-environment interactions. In this paper, we review recent advances achieved in microbial community proteomics conducted in diverse environments, such as marine and freshwater, sediment and soil, activated sludge, acid mine drainage biofilms and symbiotic communities. The challenges facing microbial community proteomics are also discussed, and we believe that microbial community proteomics will greatly enhance our understanding of the microbial world and its interactions with the environment.

Chloroethene Biodegradation Potential, ADOT/PF Peger Road Maintenance Facility, Fairbanks, Alaska

USGS Publications Warehouse

Bradley, Paul M.; Chapelle, Frances H.

2004-01-01

A series of 14C-radiotracer-based microcosm experiments were conducted to assess: 1) the extent, rate and products of microbial dechlorination of trichloroethene (TCE), cis-dichloroethene (cis-DCE) and vinyl chloride (VC) in sediments at the Peger Road site; 2) the effect of three electron donor amendments (molasses, shrimp and crab chitin, and 'Hydrogen Release Compound' (HRC)) on microbial degradation of TCE in three Peger Road sediments; and 3) the potential significance at the site of chloroethene biodegradation processes other than reductive dechlorination. In these experiments, TCE biodegradation yielded the reduced products, DCE and VC, and the oxidation product CO 2. Biodegradation of DCE and VC involved stoichiometric oxidation to CO 2. Both laboratory microcosm study and field redox assessment results indicated that the predominant terminal electron accepting process in Peger Road plume sediments under anoxic conditions was Mn/Fe-reduction. The rates of chloroethene biodegradation observed in Peger Road sediment microcosms under low temperature conditions (4?C) were within the range of those observed in sediments from temperate (20?C) aquifer systems. This result confirmed that biodegradation can be a significant mechanism for in situ contaminant remediation even in cold temperature aquifers. The fact that CO2 was the sole product of cis-DCE and VC biodegradation detected in Peger Road sediments indicated that a natural attenuation assessment based on reduced daughter product accumulation may significantly underestimate the potential for DCE and VC biodegradation at the Peger Road. Neither HRC nor molasses addition stimulated TCE reductive dechlorination. The fact that molasses and HRC amendment did stimulate Mn/Fe-reduction suggests that addition of these electron donors favored microbial Mn/Fe-reduction to the detriment of microbial TCE dechlorinating activity. In contrast, amendment of sediment microcosms with shrimp and crab chitin resulted in the establishment of mixed Mn/Fe-reducing, SO42--reducing and methanogenic conditions and enhanced TCE biodegradation in two of three Peger Road sediment treatments.

Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities.

PubMed

Patin, Nastassia V; Schorn, Michelle; Aguinaldo, Kristen; Lincecum, Tommie; Moore, Bradley S; Jensen, Paul R

2017-02-15

Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments. Copyright © 2017 American Society for Microbiology.

Application of Biofilm Covered Activated Carbon Particles as a Microbial Inoculum Delivery System for Enhanced Bioaugmentation of PCBs in Contaminated Sediment

DTIC Science & Technology

2013-09-01

after anaerobic digestion at thermophilic conditions (60- 70C). Application of biofilm covered activated carbon particles as a microbial inoculum...Sludge Thickener; Sludge = Sludge after anaerobic digestion at thermophilic conditions (60- 70C). C3. Microscopic evaluation of dechlorinating...associated enzymes are capable of opening the biphenyl ring structure and transform the molecule into a linear structure, this changed structure was not

Microbial community composition along a 50 000-year lacustrine sediment sequence

PubMed Central

Ariztegui, Daniel; Horn, Fabian; Kallmeyer, Jens; Orsi, William D

2018-01-01

Abstract For decades, microbial community composition in subseafloor sediments has been the focus of extensive studies. In deep lacustrine sediments, however, the taxonomic composition of microbial communities remains undercharacterized. Greater knowledge on microbial diversity in lacustrine sediments would improve our understanding of how environmental factors, and resulting selective pressures, shape subsurface biospheres in marine and freshwater sediments. Using high-throughput sequencing of 16S rRNA genes across high-resolution climate intervals covering the last 50 000 years in Laguna Potrok Aike, Argentina, we identified changes in microbial populations in response to both past environmental conditions and geochemical changes of the sediment during burial. Microbial communities in Holocene sediments were most diverse, reflecting a layering of taxa linked to electron acceptors availability. In deeper intervals, the data show that salinity, organic matter and the depositional conditions over the Last Glacial-interglacial cycle were all selective pressures in the deep lacustrine assemblage resulting in a genetically distinct biosphere from the surface dominated primarily by Bathyarchaeota and Atribacteria groups. However, similar to marine sediments, some dominant taxa in the shallow subsurface persisted into the subsurface as minor fraction of the community. The subsequent establishment of a deep subsurface community likely results from a combination of paleoenvironmental factors that have shaped the pool of available substrates, together with substrate depletion and/or reworking of organic matter with depth. PMID:29471361

Multiwall carbon nanotubes increase the microbial community in crude oil contaminated fresh water sediments.

PubMed

Abbasian, Firouz; Lockington, Robin; Palanisami, Thavamani; Megharaj, Mallavarapu; Naidu, Ravi

2016-01-01

Since crude oil contamination is one of the biggest environmental concerns, its removal from contaminated sites is of interest for both researchers and industries. In situ bioremediation is a promising technique for decreasing or even eliminating crude oil and hydrocarbon contamination. However, since these compounds are potentially toxic for many microorganisms, high loads of contamination can inhibit the microbial community and therefore reduce the removal rate. Therefore, any strategy with the ability to increase the microbial population in such circumstances can be of promise in improving the remediation process. In this study, multiwall carbon nanotubes were employed to support microbial growth in sediments contaminated with crude oil. Following spiking of fresh water sediments with different concentrations of crude oil alone and in a mixture with carbon nanotubes for 30days, the microbial profiles in these sediments were obtained using FLX-pyrosequencing. Next, the ratios of each member of the microbial population in these sediments were compared with those values in the untreated control sediment. This study showed that combination of crude oil and carbon nanotubes can increase the diversity of the total microbial population. Furthermore, these treatments could increase the ratios of several microorganisms that are known to be effective in the degradation of hydrocarbons. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches.

PubMed

Hassenrück, Christiane; Fink, Artur; Lichtschlag, Anna; Tegetmeyer, Halina E; de Beer, Dirk; Ramette, Alban

2016-05-01

To understand how ocean acidification (OA) influences sediment microbial communities, naturally CO2-rich sites are increasingly being used as OA analogues. However, the characterization of these naturally CO2-rich sites is often limited to OA-related variables, neglecting additional environmental variables that may confound OA effects. Here, we used an extensive array of sediment and bottom water parameters to evaluate pH effects on sediment microbial communities at hydrothermal CO2 seeps in Papua New Guinea. The geochemical composition of the sediment pore water showed variations in the hydrothermal signature at seep sites with comparable pH, allowing the identification of sites that may better represent future OA scenarios. At these sites, we detected a 60% shift in the microbial community composition compared with reference sites, mostly related to increases in Chloroflexi sequences. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. pH variation may therefore often not be the primary cause of microbial changes when sampling is done along complex environmental gradients. Thus, we recommend an ecosystem approach when assessing OA effects on sediment microbial communities under natural conditions. This will enable a more reliable quantification of OA effects via a reduction of potential confounding effects. © FEMS 2016.

How To Live with Phosphorus Scarcity in Soil and Sediment: Lessons from Bacteria

PubMed Central

Tapia-Torres, Yunuen; Rodríguez-Torres, Maria Dolores; Islas, Africa; Souza, Valeria; García-Oliva, Felipe

2016-01-01

ABSTRACT Phosphorus (P) plays a fundamental role in the physiology and biochemistry of all living things. Recent evidence indicates that organisms in the oceans can break down and use P forms in different oxidation states (e.g., +5, +3, +1, and −3); however, information is lacking for organisms from soil and sediment. The Cuatro Ciénegas Basin (CCB), Mexico, is an oligotrophic ecosystem with acute P limitation, providing a great opportunity to assess the various strategies that bacteria from soil and sediment use to obtain P. We measured the activities in sediment and soil of different exoenzymes involved in P recycling and evaluated 1,163 bacterial isolates (mainly Bacillus spp.) for their ability to use six different P substrates. DNA turned out to be a preferred substrate, comparable to a more bioavailable P source, potassium phosphate. Phosphodiesterase activity, required for DNA degradation, was observed consistently in the sampled-soil and sediment communities. A capability to use phosphite (PO33−) and calcium phosphate was observed mainly in sediment isolates. Phosphonates were used at a lower frequency by both soil and sediment isolates, and phosphonatase activity was detected only in soil communities. Our results revealed that soil and sediment bacteria are able to break down and use P forms in different oxidation states and contribute to ecosystem P cycling. Different strategies for P utilization were distributed between and within the different taxonomic lineages analyzed, suggesting a dynamic movement of P utilization traits among bacteria in microbial communities. IMPORTANCE Phosphorus (P) is an essential element for life found in molecules, such as DNA, cell walls, and in molecules for energy transfer, such as ATP. The Valley of Cuatro Ciénegas, Coahuila (Mexico), is a unique desert characterized by an extreme limitation of P and a great diversity of microbial life. How do bacteria in this valley manage to obtain P? We measured the availability of P and the enzymatic activity associated with P release in soil and sediment. Our results revealed that soil and sediment bacteria can break down and use P forms in different oxidation states and contribute to ecosystem P cycling. Even genetically related bacterial isolates exhibited different preferences for molecules, such as DNA, calcium phosphate, phosphite, and phosphonates, as substrates to obtain P, evidencing a distribution of roles for P utilization and suggesting a dynamic movement of P utilization traits among bacteria in microbial communities. PMID:27235437

How To Live with Phosphorus Scarcity in Soil and Sediment: Lessons from Bacteria.

PubMed

Tapia-Torres, Yunuen; Rodríguez-Torres, Maria Dolores; Elser, James J; Islas, Africa; Souza, Valeria; García-Oliva, Felipe; Olmedo-Álvarez, Gabriela

2016-08-01

Phosphorus (P) plays a fundamental role in the physiology and biochemistry of all living things. Recent evidence indicates that organisms in the oceans can break down and use P forms in different oxidation states (e.g., +5, +3, +1, and -3); however, information is lacking for organisms from soil and sediment. The Cuatro Ciénegas Basin (CCB), Mexico, is an oligotrophic ecosystem with acute P limitation, providing a great opportunity to assess the various strategies that bacteria from soil and sediment use to obtain P. We measured the activities in sediment and soil of different exoenzymes involved in P recycling and evaluated 1,163 bacterial isolates (mainly Bacillus spp.) for their ability to use six different P substrates. DNA turned out to be a preferred substrate, comparable to a more bioavailable P source, potassium phosphate. Phosphodiesterase activity, required for DNA degradation, was observed consistently in the sampled-soil and sediment communities. A capability to use phosphite (PO3 (3-)) and calcium phosphate was observed mainly in sediment isolates. Phosphonates were used at a lower frequency by both soil and sediment isolates, and phosphonatase activity was detected only in soil communities. Our results revealed that soil and sediment bacteria are able to break down and use P forms in different oxidation states and contribute to ecosystem P cycling. Different strategies for P utilization were distributed between and within the different taxonomic lineages analyzed, suggesting a dynamic movement of P utilization traits among bacteria in microbial communities. Phosphorus (P) is an essential element for life found in molecules, such as DNA, cell walls, and in molecules for energy transfer, such as ATP. The Valley of Cuatro Ciénegas, Coahuila (Mexico), is a unique desert characterized by an extreme limitation of P and a great diversity of microbial life. How do bacteria in this valley manage to obtain P? We measured the availability of P and the enzymatic activity associated with P release in soil and sediment. Our results revealed that soil and sediment bacteria can break down and use P forms in different oxidation states and contribute to ecosystem P cycling. Even genetically related bacterial isolates exhibited different preferences for molecules, such as DNA, calcium phosphate, phosphite, and phosphonates, as substrates to obtain P, evidencing a distribution of roles for P utilization and suggesting a dynamic movement of P utilization traits among bacteria in microbial communities. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Ecosystem-level studies of terrestrial carbon reveal contrasting bacterial metabolism in different aquatic habitats.

PubMed

Attermeyer, Katrin; Premke, Katrin; Hornick, Thomas; Hilt, Sabine; Grossart, Hans-Peter

2013-12-01

In aquatic systems, terrestrial dissolved organic matter (t-DOM) is known to stimulate bacterial activities in the water column, but simultaneous effects of autumnal leaf input on water column and sediment microbial dynamics in littoral zones of lakes remain largely unknown. The study's objective was to determine the effects of leaf litter on bacterial metabolism in the littoral water and sediment, and subsequently, the consequences for carbon cycling and food web dynamics. Therefore, in late fall, we simultaneously measured water and sediment bacterial metabolism in the littoral zone of a temperate shallow lake after adding terrestrial particulate organic matter (t-POM), namely, maize leaves. To better evaluate bacterial production (BP) and community respiration (CR) in sediments, we incubated sediment cores with maize leaves of different quality (nonleached and leached) under controlled laboratory conditions. Additionally, to quantify the incorporated leaf carbon into microbial biomass, we determined carbon isotopic ratios of fatty acids from sediment and leaf-associated microbes from a laboratory experiment using 13C-enriched beech leaves. The concentrations of dissolved organic carbon (DOC) increased significantly in the lake after the addition of maize leaves, accompanied by a significant increase in water BP. In contrast, sediment BP declined after an initial peak, showing no positive response to t-POM addition. Sediment BP and CR were also not stimulated by t-POM in the laboratory experiment, either in short-term or in long-term incubations, except for a short increase in CR after 18 hours. However, this increase might have reflected the metabolism of leaf-associated microorganisms. We conclude that the leached t-DOM is actively incorporated into microbial biomass in the water column but that the settling leached t-POM (t-POML) does not enter the food web via sediment bacteria. Consequently, t-POML is either buried in the sediment or introduced into the aquatic food web via microorganisms (bacteria and fungi) directly associated with t-POM(L) and via benthic macroinvertebrates by shredding of t-POM(L). The latter pathway represents a "benthic shortcut" which efficiently transfers t-POM(L) to higher trophic levels.

Microbial acetogenesis as a source of organic acids in ancient Atlantic Coastal Plain sediments

USGS Publications Warehouse

Chapelle, F.H.; Bradley, P.M.

1996-01-01

Field and laboratory evidence shows that deeply buried (90-888 m) fine-grained sediments of the Atlantic Coastal Plain contain viable acetogenic microorganisms, and that these microorganisms actively produce organic acids. Concentrations of formate, acetate, and propionate in pore waters extracted from fine-grained sediments ranged from 50 ??M to 5 mM and were much higher than in adjacent pore waters associated with sandy sediments (<2 ??M). Laboratory studies showed that asceptically cored fine-grained sediments incubated under a H2 atmosphere produced formate and acetate, and that H14CO-3 was converted to 14C-acetate and 14C-formate over time. An enrichment culture of these acetogenic microorganisms was recovered from one long-term incubation that showed the presence of several morphologically distinct gram-positive, rod-shaped bacteria. These microorganisms were capable of growth under autotrophic (H2 + CO2), heterotrophic (syringate), and mixotrophic (H2 + CO2 + syringate) conditions. These results suggest that microbial acetogenesis, rather than abiotic processes, is the most important organic acid-producing mechanism during low-temperature (???30 ??C) diagenesis of Atlantic Coastal Plain sediments.

A New Sensitive GC-MS-based Method for Analysis of Dipicolinic Acid and Quantifying Bacterial Endospores in Deep Marine Subsurface Sediment

NASA Astrophysics Data System (ADS)

Fang, J.

2015-12-01

Marine sediments cover more than two-thirds of the Earth's surface and represent a major part of the deep biosphere. Microbial cells and microbial activity appear to be widespread in these sediments. Recently, we reported the isolation of gram-positive anaerobic spore-forming piezophilic bacteria and detection of bacterial endospores in marine subsurface sediment from the Shimokita coalbed, Japan. However, the modern molecular microbiological methods (e.g., DNA-based microbial detection techniques) cannot detect bacterial endospore, because endospores are impermeable and are not stained by fluorescence DNA dyes or by ribosomal RNA staining techniques such as catalysed reporter deposition fluorescence in situ hybridization. Thus, the total microbial cell abundance in the deep biosphere may has been globally underestimated. This emphasizes the need for a new cultivation independent approach for the quantification of bacterial endospores in the deep subsurface. Dipicolinic acid (DPA, pyridine-2,6-dicarboxylic acid) is a universal and specific component of bacterial endospores, representing 5-15wt% of the dry spore, and therefore is a useful indicator and quantifier of bacterial endospores and permits to estimate total spore numbers in the subsurface biosphere. We developed a sensitive analytical method to quantify DPA content in environmental samples using gas chromatography-mass spectrometry. The method is sensitive and more convenient in use than other traditional methods. We applied this method to analyzing sediment samples from the South China Sea (obtained from IODP Exp. 349) to determine the abundance of spore-forming bacteria in the deep marine subsurface sediment. Our results suggest that gram-positive, endospore-forming bacteria may be the "unseen majority" in the deep biosphere.

Methylmercury production in sediment from agricultural and non-agricultural wetlands in the Yolo Bypass, California, USA

USGS Publications Warehouse

Marvin-DiPasquale, Mark; Windham-Myers, Lisamarie; Agee, Jennifer L.; Kakouros, Evangelos; Kieu, Le H.; Fleck, Jacob A.; Alpers, Charles N.; Stricker, Craig A.

2014-01-01

As part of a larger study of mercury (Hg) biogeochemistry and bioaccumulation in agricultural (rice growing) and non-agricultural wetlands in California's Central Valley, USA, seasonal and spatial controls on methylmercury (MeHg) production were examined in surface sediment. Three types of shallowly-flooded agricultural wetlands (white rice, wild rice, and fallow fields) and two types of managed (non-agricultural) wetlands (permanently and seasonally flooded) were sampled monthly-to-seasonally. Dynamic seasonal changes in readily reducible ‘reactive’ mercury (Hg(II)R), Hg(II)-methylation rate constants (kmeth), and concentrations of electron acceptors (sulfate and ferric iron) and donors (acetate), were all observed in response to field management hydrology, whereas seasonal changes in these parameters were more muted in non-agricultural managed wetlands. Agricultural wetlands exhibited higher sediment MeHg concentrations than did non-agricultural wetlands, particularly during the fall through late-winter (post-harvest) period. Both sulfate- and iron-reducing bacteria have been implicated in MeHg production, and both were demonstrably active in all wetlands studied. Stoichiometric calculations suggest that iron-reducing bacteria dominated carbon flow in agricultural wetlands during the growing season. Sulfate-reducing bacteria were not stimulated by the addition of sulfate-based fertilizer to agricultural wetlands during the growing season, suggesting that labile organic matter, rather than sulfate, limited their activity in these wetlands. Along the continuum of sediment geochemical conditions observed, values of kmeth increased approximately 10,000-fold, whereas Hg(II)R decreased 100-fold. This suggests that, with respect to the often opposing trends of Hg(II)-methylating microbial activity and Hg(II) availability for methylation, microbial activity dominated the Hg(II)-methylation process, and that along this biogeochemical continuum, conditions that favored microbial sulfate reduction resulted in the highest calculated MeHg production potential rates. Rice straw management options aimed at limiting labile carbon supplies to surface sediment during the post-harvest fall–winter period may be effective in limiting MeHg production within agricultural wetlands.

Methylmercury production in sediment from agricultural and non-agricultural wetlands in the Yolo Bypass, California, USA.

PubMed

Marvin-DiPasquale, Mark; Windham-Myers, Lisamarie; Agee, Jennifer L; Kakouros, Evangelos; Kieu, Le H; Fleck, Jacob A; Alpers, Charles N; Stricker, Craig A

2014-06-15

As part of a larger study of mercury (Hg) biogeochemistry and bioaccumulation in agricultural (rice growing) and non-agricultural wetlands in California's Central Valley, USA, seasonal and spatial controls on methylmercury (MeHg) production were examined in surface sediment. Three types of shallowly-flooded agricultural wetlands (white rice, wild rice, and fallow fields) and two types of managed (non-agricultural) wetlands (permanently and seasonally flooded) were sampled monthly-to-seasonally. Dynamic seasonal changes in readily reducible 'reactive' mercury (Hg(II)R), Hg(II)-methylation rate constants (kmeth), and concentrations of electron acceptors (sulfate and ferric iron) and donors (acetate), were all observed in response to field management hydrology, whereas seasonal changes in these parameters were more muted in non-agricultural managed wetlands. Agricultural wetlands exhibited higher sediment MeHg concentrations than did non-agricultural wetlands, particularly during the fall through late-winter (post-harvest) period. Both sulfate- and iron-reducing bacteria have been implicated in MeHg production, and both were demonstrably active in all wetlands studied. Stoichiometric calculations suggest that iron-reducing bacteria dominated carbon flow in agricultural wetlands during the growing season. Sulfate-reducing bacteria were not stimulated by the addition of sulfate-based fertilizer to agricultural wetlands during the growing season, suggesting that labile organic matter, rather than sulfate, limited their activity in these wetlands. Along the continuum of sediment geochemical conditions observed, values of kmeth increased approximately 10,000-fold, whereas Hg(II)R decreased 100-fold. This suggests that, with respect to the often opposing trends of Hg(II)-methylating microbial activity and Hg(II) availability for methylation, microbial activity dominated the Hg(II)-methylation process, and that along this biogeochemical continuum, conditions that favored microbial sulfate reduction resulted in the highest calculated MeHg production potential rates. Rice straw management options aimed at limiting labile carbon supplies to surface sediment during the post-harvest fall-winter period may be effective in limiting MeHg production within agricultural wetlands. © 2013.

Microbial dehalogenation of organohalides in marine and estuarine environments.

PubMed

Zanaroli, Giulio; Negroni, Andrea; Häggblom, Max M; Fava, Fabio

2015-06-01

Marine sediments are the ultimate sink and a major entry way into the food chain for many highly halogenated and strongly hydrophobic organic pollutants, such as polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins (PCDDs), polybrominated diphenylethers (PBDEs) and 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT). Microbial reductive dehalogenation in anaerobic sediments can transform these contaminants into less toxic and more easily biodegradable products. Although little is still known about the diversity of respiratory dehalogenating bacteria and their catabolic genes in marine habitats, the occurrence of dehalogenation under actual site conditions has been reported. This suggests that the activity of dehalogenating microbes may contribute, if properly stimulated, to the in situ bioremediation of marine and estuarine contaminated sediments. Copyright © 2015 Elsevier Ltd. All rights reserved.

Sulfur reduction in sediments of marine and evaporite environments

NASA Technical Reports Server (NTRS)

Klug, M. J.; Boston, P.; Francois, R.; Gyure, R. A.; Javor, B.; Tribble, G.; Vairavamurthy, A.

1985-01-01

Transformations of sulfur in sediments of ponds ranging in salinities from that of normal seawater to those of brines saturated with sodium chloride were examined. The chemistry of the sediment and pore waters were focused on with emphasis on the fate of sulfate reduction. The effects of increasing salinity on both forms of sulfur and microbial activity were determined. A unique set of chemical profiles and sulfate-reducing activity was found for the sediments of each of the sites examined. The quantity of organic matter in the salt pond sediments was significantly greater than that occurring in the adjacent intertidal site. The total quantitative and qualitative distribution of volatile fatty acids was also greater in the salt ponds. Volatile fatty acids increased with salinity.

Mercury cycling in agricultural and managed wetlands of California: experimental evidence of vegetation-driven changes in sediment biogeochemistry and methylmercury production

USGS Publications Warehouse

Windham-Myers, Lisamarie; Marvin-DiPasquale, Mark; Stricker, Craig A.; Agee, Jennifer L.; Kieu, Le H.; Kakouros, Evangelos

2014-01-01

The role of live vegetation in sediment methylmercury (MeHg) production and associated biogeochemistry was examined in three types of agricultural wetlands (domesticated or white rice, wild rice, and fallow fields) and adjacent managed natural wetlands (cattail- and bulrush or tule-dominated) in the Yolo Bypass region of California's Central Valley, USA. During the active growing season for each wetland, a vegetated:de-vegetated paired plot experiment demonstrated that the presence of live plants enhanced microbial rates of mercury methylation by 20 to 669% (median = 280%) compared to de-vegetated plots. Labile carbon exudation by roots appeared to be the primary mechanism by which microbial methylation was enhanced in the presence of vegetation. Pore-water acetate (pw[Ac]) decreased significantly with de-vegetation (63 to 99%) among all wetland types, and within cropped fields, pw[Ac] was correlated with both root density (r = 0.92) and microbial Hg(II) methylation (kmeth. r = 0.65). Sediment biogeochemical responses to de-vegetation were inconsistent between treatments for “reactive Hg” (Hg(II)R), as were reduced sulfur and sulfate reduction rates. Sediment MeHg concentrations in vegetated plots were double those of de-vegetated plots (median = 205%), due in part to enhanced microbial MeHg production in the rhizosphere, and in part to rhizoconcentration via transpiration-driven pore-water transport. Pore-water concentrations of chloride, a conservative tracer, were elevated (median = 22%) in vegetated plots, suggesting that the higher concentrations of other constituents around roots may also be a function of rhizoconcentration rather than microbial activity alone. Elevated pools of amorphous iron (Fe) in vegetated plots indicate that downward redistribution of oxic surface waters through transpiration acts as a stimulant to Fe(III)-reduction through oxidation of Fe(II)pools. These data suggest that vegetation significantly affected rhizosphere biogeochemistry through organic exudation and transpiration-driven concentration of pore-water constituents and oxidation of reduced compounds. While the relative role of vegetation varied among wetland types, macrophyte activity enhanced MeHg production.

Sequencing Insights into Microbial Communities in the Water and Sediments of Fenghe River, China.

PubMed

Lu, Sidan; Sun, Yujiao; Zhao, Xuan; Wang, Lei; Ding, Aizhong; Zhao, Xiaohui

2016-07-01

The connection between microbial community structure and spatial variation and pollution in river waters has been widely investigated. However, water and sediments together have rarely been explored. In this study, Illumina high-throughput sequencing was performed to analyze microbes in 24 water and sediment samples from natural to anthropogenic sources and from headstream to downstream areas. These data were used to assess variability in microbial community structure and diversity along in the Fenghe River, China. The relationship between bacterial diversity and environmental parameters was statistically analyzed. An average of 1682 operational taxonomic units was obtained. Microbial diversity increased from the headstream to downstream and tended to be greater in sediment compared with water. The water samples near the headstream endured relatively low Shannon and Chao1 indices. These diversity indices and the number of observed species in the water and sediment samples increase downstream. The parameters also differ in the two river tributaries. Community structures shift based on the extent of nitrogen pollution variation in the sediment and water samples. The four most dominant genera in the water community were Escherichia, Acinetobacter, Comamonadaceae, and Pseudomonas. In the sediments, the most dominant genera were Stramenopiles, Flavobacterium, Pseudomonas, and Comamonadaceae. The number of ammonia-oxidizing archaea in the headstream water slightly differed from that in the sediment but varied considerably in the downstream sediments. Statistical analysis showed that community variation is correlated with changes in ammonia nitrogen, total nitrogen, and nitrate nitrogen. This study identified different microbial community structures in river water and sediments. Overall this study emphasized the need to elucidate spatial variations in bacterial diversity in water and sediments associated with physicochemical gradients and to show the effects of such variation on waterborne microbial community structures.

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments

PubMed Central

Heidelberg, John F.

2016-01-01

ABSTRACT The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching Alphaproteobacteria, two novel organisms within the Proteobacteria, and new members of the Nitrospirae, Nitrospinae, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry. IMPORTANCE This research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1 Thaumarchaeota, Nitrospinae, and Nitrospirae and neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium. PMID:27208118

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments.

PubMed

Tully, Benjamin J; Heidelberg, John F

2016-07-15

The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching Alphaproteobacteria, two novel organisms within the Proteobacteria, and new members of the Nitrospirae, Nitrospinae, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry. This research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1 Thaumarchaeota, Nitrospinae, and Nitrospirae and neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium. Copyright © 2016 Tully and Heidelberg.

Microbial processes and communities in sediment samples along a transect across the Lusi mud volcano, Indonesia

NASA Astrophysics Data System (ADS)

Krueger, Martin; Straaten, Nontje; Mazzini, Adriano

2015-04-01

The Lusi eruption represents one of the largest ongoing sedimentary hosted geothermal systems. This eruption started in 2006 following to a 6.3 M earthquake that stroke Java Island. Since then it has been spewing boiling mud from a central crater with peaks reaching 180.000 m3 per day. Today an area of about 8 km2 is covered by locally dried mud breccia where a network of hundreds of satellite seeping pools is active. Numerous investigations focused on the study of offshore microbial colonies that commonly thrive at offshore methane seeps and mud volcanoes, however very little has been done for onshore seeping structures. Lusi represents a unique opportunity to complete a comprehensive study of onshore microbial communities fed by the seepage of CH4 and CO2 as well as of heavier liquid hydrocarbons originating from several km below the surface. We conducted a sampling campaign at the Lusi site collecting samples of fresh mud close to the erupting crater using a remote controlled drone. In addition we completed a transect towards outer parts of the crater to collect older, weathered samples for comparison. In all samples active microorganisms were present. The highest activities for CO2 and CH4 production as well as for CH4 oxidation and hydrocarbon degradation were observed in medium-age mud samples collected roughly in the middle of the transect. Rates for aerobic methane oxidation were high, as was the potential of the microbial communities to degrade hydrocarbons (oils, alkanes, BTEX tested). The data suggests a transition of microbial populations from an anaerobic, hydrocarbon-driven metabolism in fresher samples from center or from small seeps to more generalistic, aerobic microbial communities in older, more consolidated sediments. Currently, the microbial communities in the different sediment samples are analyzed using quantitative PCR and T-RFLP combined with MiSeq sequencing. This study represents an initial step to better understand onshore seepage systems and provides an ideal analogue for comparison with the better investigated offshore structures.

Environment-Dependent Distribution of the Sediment nifH-Harboring Microbiota in the Northern South China Sea

PubMed Central

Yang, Jinying; Li, Jing; Luan, Xiwu; Zhang, Yunbo; Gu, Guizhou; Xue, Rongrong; Zong, Mingyue; Klotz, Martin G.

2013-01-01

The South China Sea (SCS), the largest marginal sea in the Western Pacific Ocean, is a huge oligotrophic water body with very limited influx of nitrogenous nutrients. This suggests that sediment microbial N2 fixation plays an important role in the production of bioavailable nitrogen. To test the molecular underpinning of this hypothesis, the diversity, abundance, biogeographical distribution, and community structure of the sediment diazotrophic microbiota were investigated at 12 sampling sites, including estuarine, coastal, offshore, deep-sea, and methane hydrate reservoirs or their prospective areas by targeting nifH and some other functional biomarker genes. Diverse and novel nifH sequences were obtained, significantly extending the evolutionary complexity of extant nifH genes. Statistical analyses indicate that sediment in situ temperature is the most significant environmental factor influencing the abundance, community structure, and spatial distribution of the sediment nifH-harboring microbial assemblages in the northern SCS (nSCS). The significantly positive correlation of the sediment pore water NH4+ concentration with the nifH gene abundance suggests that the nSCS sediment nifH-harboring microbiota is active in N2 fixation and NH4+ production. Several other environmental factors, including sediment pore water PO43− concentration, sediment organic carbon, nitrogen and phosphorus levels, etc., are also important in influencing the community structure, spatial distribution, or abundance of the nifH-harboring microbial assemblages. We also confirmed that the nifH genes encoded by archaeal diazotrophs in the ANME-2c subgroup occur exclusively in the deep-sea methane seep areas, providing for the possibility to develop ANME-2c nifH genes as a diagnostic tool for deep-sea methane hydrate reservoir discovery. PMID:23064334

Restoration and Purification of Dissolved Organic Nitrogen by Bacteria and Phytoremediation in Shallow Eutrophic Lakes Sediments

NASA Astrophysics Data System (ADS)

Li, Xin; Yue, Yi

2018-06-01

Endogenous organic nitrogen loadings in lake sediments have increased with human activity in recent decades. A 6-month field study from two disparate shallow eutrophic lakes could partly reveal these issues by analysing seasonal variations of biodegradation and phytoremediation in the sediment. This paper describes the relationship between oxidation reduction potential, temperature, microbial activity and phytoremediation in nitrogen cycling by calculation degradative index of dissolved organic nitrogen and amino acid decomposition. The index was being positive in winter and negative in summer while closely positive correlated with biodegradation. Our analysis revealed that rather than anoxic condition, biomass is the primary factor to dissolved organic nitrogen distribution and decomposition. Some major amino acids statistics also confirm the above view. The comparisons of organic nitrogen and amino acid in abundance and seasons in situ provides that demonstrated plants cue important for nitrogen removal by their roots adsorption and immobilization. In conclusion, enhanced microbial activity and phytoremediation with the seasons will reduce the endogenous nitrogen loadings by the coupled mineralization and diagenetic process.

Microbial Life of North Pacific Oceanic Crust

NASA Astrophysics Data System (ADS)

Schumann, G.; Koos, R.; Manz, W.; Reitner, J.

2003-12-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed reactions that influence the geophysical properties of these environments. Drilling into 45-Ma oceanic basaltic crust in a deepwater environment during ODP Leg 200 provided a promising opportunity to explore the abundance, diversity and activity of micro-organisms. The combined use of culture-independent molecular phylogenetic analyses and enrichment culture techniques is an advantageous approach in investigating subsurface microbial ecosystems. Enrichment culture methods allow the evaluation of potential activities and functions. Microbiological investigations revealed few aerobic cultivable, in part hitherto unknown, micro-organisms in deep submarine sediments and basaltic lava flows. 16S rDNA sequencing of isolates from sediment revealed the next relatives to be members of the genera Halomonas, Pseudomonas, and Lactobacillus. Within the Pseudomonadaceae the closest relative is Acinetobacter sp., which was isolated from a deep subsurface environment. The next phylogenetical relatives within the Halomonadaceae are bacteria typically isolated from Soda lakes, which are considered as model of early life conditions. Interestingly, not only sediment bacteria could be obtained in pure culture. Aerobic strains could also be successfully isolated from the massive tholeiitic basalt layer at a depth of 76.16 mbsf (46 m below the sediment/basement contact). These particular isolates are gram-positive with low G+C content of DNA, phylogenetically affiliated to the phylum Firmicutes. The closest neighbors are e.g. a marine Bacillus isolated from the Gulf of Mexico and a low G+C gram-positive bacterium, which belongs to the microbial flora in the deepest sea mud of the Mariana Trench, isolated from a depth of 10,897 m. Based on the similarity values, the isolates represent hitherto undescribed species of the deep biosphere. Molecular microbial diversity is currently determined by cloning und comparative 16S rRNA gene analyses. The first results will also be presented. In summary, the low number of isolates, cultivated under aerobic conditions, is in good agreement with the common opinion that most of the bacteria within the deep biosphere are anaerobic. Thus, studies of microbial community structure in solid geological materials are feasible and constitute further evidence that continuing microbiological activity in the challenging exploration of the deep sub-seafloor biosphere environment is absolutely promising.

Alkalinity production in intertidal sands intensified by lugworm bioirrigation.

PubMed

Rao, Alexandra M F; Malkin, Sairah Y; Montserrat, Francesc; Meysman, Filip J R

2014-07-05

Porewater profiles and sediment-water fluxes of oxygen, nutrients, pH, calcium, alkalinity, and sulfide were measured in intertidal sandflat sediments from the Oosterschelde mesotidal lagoon (The Netherlands). The influence of bioturbation and bioirrigation by the deep-burrowing polychaete Arenicola marina on the rates and sources of benthic alkalinity generation was examined by comparing measurements in intact and defaunated sediment cores before and after the addition of A. marina in summer and fall 2011. Higher organic matter remineralization rates, shallower O 2 penetration, and greater sediment-water solute fluxes were observed in summer, consistent with higher sediment community metabolic rates at a higher temperature. Lugworm activity stimulated porewater exchange (5.1 × in summer, 1.9 × in fall), organic matter remineralization (6.2 × in summer, 1.9 × in fall), aerobic respiration (2.4 × in summer, 2.1 × in fall), alkalinity release (4.7 × in summer, 4.0 × in fall), nutrient regeneration, and iron cycling. The effects of lugworm activity on net sediment-water fluxes were similar but more pronounced in summer than in fall. Alkalinity release in fall was entirely driven by metabolic carbonate dissolution, while this process explained between 22 and 69% of total alkalinity production in summer, indicating the importance of other processes in this season. By enhancing organic matter remineralization and the reoxidation of reduced metabolites by the sediment microbial community, lugworm activity stimulated the production of dissolved inorganic carbon and metabolic acidity, which in turn enhanced metabolic CaCO 3 dissolution efficiency. In summer, evidence of microbial long distance electron transport (LDET) was observed in defaunated sediment. Thus, alkalinity production by net carbonate dissolution was likely supplemented by anaerobic respiration and LDET in summer.

Adaption of the microbial community to continuous exposures of multiple residual antibiotics in sediments from a salt-water aquacultural farm.

PubMed

Xi, Xiuping; Wang, Min; Chen, Yongshan; Yu, Shen; Hong, Youwei; Ma, Jun; Wu, Qian; Lin, Qiaoyin; Xu, Xiangrong

2015-06-15

Residual antibiotics from aquacultural farming may alter microbial community structure in aquatic environments in ways that may adversely or positively impact microbially-mediated ecological functions. This study investigated 26 ponds (26 composited samples) used to produce fish, razor clam and shrimp (farming and drying) and 2 channels (10 samples) in a saltwater aquacultural farm in southern China to characterize microbial community structure (represented by phospholipid fatty acids) in surface sediments (0-10 cm) with long-term exposure to residual antibiotics. 11 out of 14 widely-used antibiotics were quantifiable at μg kg(-1) levels in sediments but their concentrations did not statistically differ among ponds and channels, except norfloxacin in drying shrimp ponds and thiamphenicol in razor clam ponds. Concentrations of protozoan PLFAs were significantly increased in sediments from razor clam ponds while other microbial groups were similar among ponds and channels. Both canonical-correlation and stepwise-multiple-regression analyses on microbial community and residual antibiotics suggested that roxithromycin residuals were significantly related to shifts in microbial community structure in sediments. This study provided field evidence that multiple residual antibiotics at low environmental levels from aquacultural farming do not produce fundamental shifts in microbial community structure. Copyright © 2015 Elsevier B.V. All rights reserved.

Occurrence of microbial acetate-oxidation in ~2 km-deep coal-bearing sediments off the Shimokita Peninsula, Japan (IODP Expedition 337)

NASA Astrophysics Data System (ADS)

Ijiri, A.; Inagaki, F.

2015-12-01

During the Integrated Ocean Drilling Program (IODP) Expedition 337 in 2012, the riser-drilling vessel Chikyu extended the previous world depth record of scientific ocean drilling and made one of the deepest scientific borehole down to 2466 m below the seafloor (mbsf) at Site C0020 Hole A off the Shimokita Peninsula, Japan. The sedimentary sequence consists of 17 lignite layers below 1.5 km bellow the seafloor. Microbiological and geochemical data consistently showed evidence for the existence of microbial communities associated with lignite coal beds in the coal-bearing sediments (Inagaki and Hinrichs et al., Science, 2015). Since lignite coals produce substantial dissolved organic compounds during the burial alternation process, volatile fatty acids may play important roles for microbial life and its activity in the deep sedimentary environment. To address this hypothesis, we measured methanogenic and acetate-oxidation activities by radiotracer incubation experiments using 14C-labelled substrate ([2-14C]-acetate) immediately after core recovery. Activity of aceticlastic methanogenesis was observed in the sediment above the coal-baring layers (>1990 mbsf), ranging from 0.2 to 1.2 pmol cm-3 d-1. The highest activity was observed in a coal-bed horizon at 1990 mbsf. However, aceticlastic methanogenesis was below the detection limit in sediment samples below the 2 km-coal layers. Activity of acetate oxidation to CO2 was measured by 14CO2 production rate from [2-14C]-acetate. Interestingly, the acetate-oxidation activity was observed in sediments above the coal beds, which values were generally higher than those of methanogenesis with the maximum value of 33 pmol cm-3 d-1 at 1800 mbsf. The rates gradually decreased with increasing depth from 1800 mbsf and reached below the detection limit (i.e., 0.05 pmol cm-3 d-1) in 2 km-deep coal-bed samples. The occurrence of relatively high acetate oxidation at ~1800 mbsf above the coal formation suggests that microbes respire acetate with available electron acceptors such as glauconitic iron oxides in the deep sedimentary environment.

The succession of microbial community in the organic rich fish-farm sediment during bioremediation by introducing artificially mass-cultured colonies of a small polychaete, Capitella sp. I.

PubMed

Kunihiro, Tadao; Miyazaki, Tomoaki; Uramoto, Yuuta; Kinoshita, Kyoko; Inoue, Akihiro; Tamaki, Sayaka; Hama, Daigo; Tsutsumi, Hiroaki; Ohwada, Kouichi

2008-01-01

We monitored seasonal changes of the abundance and composition of microorganisms in the fish-farm sediment in Kusuura Bay, Amakusa, Japan, using the quinone profiling technique, during bioremediation by introducing cultured colonies of polychaete, Capitella sp. I. In November 2004, approximately 9.2 million cultured worms were transferred to the fish-farm sediment, which increased rapidly, and reached 458.5 gWW/m(2) (528,000 indiv./m(2)) in March 2005. During this fast-increasing period of Capitella, the microbial quinone content of the surface sediment (0-2 cm) also increased markedly, and reached 237 micromol/m(2) in January 2005, although the water temperature decreased to the lowest levels in the year. Particularly, the mole fraction of ubiquinone-10 in total quinones in the sediment, indicating the presence of alpha subclass of Proteobacteria, increased by 9.3%. These facts suggest that the bacterial growth was enhanced markedly by the biological activities of worms in the sediment, and the bacteria played an important role in the decomposition of the organic matter in the sediment.

Temperature-driven decoupling of key phases of organic matter degradation in marine sediments.

PubMed

Weston, Nathaniel B; Joye, Samantha B

2005-11-22

The long-term burial of organic carbon in sediments results in the net accumulation of oxygen in the atmosphere, thereby mediating the redox state of the Earth's biosphere and atmosphere. Sediment microbial activity plays a major role in determining whether particulate organic carbon is recycled or buried. A diverse consortium of microorganisms that hydrolyze, ferment, and terminally oxidize organic compounds mediates anaerobic organic matter mineralization in anoxic sediments. Variable temperature regulation of the sequential processes, leading from the breakdown of complex particulate organic carbon to the production and subsequent consumption of labile, low-molecular weight, dissolved intermediates, could play a key role in controlling rates of overall organic carbon mineralization. We examined sediment organic carbon cycling in a sediment slurry and in flow through bioreactor experiments. The data show a variable temperature response of the microbial functional groups mediating organic matter mineralization in anoxic marine sediments, resulting in the temperature-driven decoupling of the production and consumption of organic intermediates. This temperature-driven decoupling leads to the accumulation of labile, low-molecular weight, dissolved organic carbon at low temperatures and low-molecular weight dissolved organic carbon limitation of terminal metabolism at higher temperatures.

Microbiology: A microbial arsenic cycle in a salt-saturated, extreme environment

USGS Publications Warehouse

Oremland, R.S.; Kulp, T.R.; Blum, J.S.; Hoeft, S.E.; Baesman, S.; Miller, L.G.; Stolz, J.F.

2005-01-01

Searles Lake is a salt-saturated, alkaline brine unusually rich in the toxic element arsenic. Arsenic speciation changed from arsenate [As(V)] to arsenite [As(III)] with sediment depth. Incubated anoxic sediment slurries displayed dissimilatory As(V)-reductase activity that was markedly stimulated by H2 or sulfide, whereas aerobic slurries had rapid As(III)-oxidase activity. An anaerobic, extremely haloalkaliphilic bacterium was isolated from the sediment that grew via As(V) respiration, using either lactate or sulfide as its electron donor. Hence, a full biogeochemical cycle of arsenic occurs in Searles Lake, driven in part by inorganic electron donors.

Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment.

PubMed

Lomstein, Bente Aa; Langerhuus, Alice T; D'Hondt, Steven; Jørgensen, Bo B; Spivack, Arthur J

2012-03-18

Two decades of scientific ocean drilling have demonstrated widespread microbial life in deep sub-seafloor sediment, and surprisingly high microbial-cell numbers. Despite the ubiquity of life in the deep biosphere, the large community sizes and the low energy fluxes in this vast buried ecosystem are not yet understood. It is not known whether organisms of the deep biosphere are specifically adapted to extremely low energy fluxes or whether most of the observed cells are in a dormant, spore-like state. Here we apply a new approach--the D:L-amino-acid model--to quantify the distributions and turnover times of living microbial biomass, endospores and microbial necromass, as well as to determine their role in the sub-seafloor carbon budget. The approach combines sensitive analyses of unique bacterial markers (muramic acid and D-amino acids) and the bacterial endospore marker, dipicolinic acid, with racemization dynamics of stereo-isomeric amino acids. Endospores are as abundant as vegetative cells and microbial activity is extremely low, leading to microbial biomass turnover times of hundreds to thousands of years. We infer from model calculations that biomass production is sustained by organic carbon deposited from the surface photosynthetic world millions of years ago and that microbial necromass is recycled over timescales of hundreds of thousands of years.

Microbial Sulfate Reduction Potential in Coal-Bearing Sediments Down to ~2.5 km below the Seafloor off Shimokita Peninsula, Japan

PubMed Central

Glombitza, Clemens; Adhikari, Rishi R.; Riedinger, Natascha; Gilhooly, William P.; Hinrichs, Kai-Uwe; Inagaki, Fumio

2016-01-01

Sulfate reduction is the predominant anaerobic microbial process of organic matter mineralization in marine sediments, with recent studies revealing that sulfate reduction not only occurs in sulfate-rich sediments, but even extends to deeper, methanogenic sediments at very low background concentrations of sulfate. Using samples retrieved off the Shimokita Peninsula, Japan, during the Integrated Ocean Drilling Program (IODP) Expedition 337, we measured potential sulfate reduction rates by slurry incubations with 35S-labeled sulfate in deep methanogenic sediments between 1276.75 and 2456.75 meters below the seafloor. Potential sulfate reduction rates were generally extremely low (mostly below 0.1 pmol cm−3 d−1) but showed elevated values (up to 1.8 pmol cm−3 d−1) in a coal-bearing interval (Unit III). A measured increase in hydrogenase activity in the coal-bearing horizons coincided with this local increase in potential sulfate reduction rates. This paired enzymatic response suggests that hydrogen is a potentially important electron donor for sulfate reduction in the deep coalbed biosphere. By contrast, no stimulation of sulfate reduction rates was observed in treatments where methane was added as an electron donor. In the deep coalbeds, small amounts of sulfate might be provided by a cryptic sulfur cycle. The isotopically very heavy pyrites (δ34S = +43‰) found in this horizon is consistent with its formation via microbial sulfate reduction that has been continuously utilizing a small, increasingly 34S-enriched sulfate reservoir over geologic time scales. Although our results do not represent in-situ activity, and the sulfate reducers might only have persisted in a dormant, spore-like state, our findings show that organisms capable of sulfate reduction have survived in deep methanogenic sediments over more than 20 Ma. This highlights the ability of sulfate-reducers to persist over geological timespans even in sulfate-depleted environments. Our study moreover represents the deepest evidence of a potential for sulfate reduction in marine sediments to date. PMID:27761134

Microbial Sulfate Reduction Potential in Coal-Bearing Sediments Down to ~2.5 km below the Seafloor off Shimokita Peninsula, Japan.

PubMed

Glombitza, Clemens; Adhikari, Rishi R; Riedinger, Natascha; Gilhooly, William P; Hinrichs, Kai-Uwe; Inagaki, Fumio

2016-01-01

Sulfate reduction is the predominant anaerobic microbial process of organic matter mineralization in marine sediments, with recent studies revealing that sulfate reduction not only occurs in sulfate-rich sediments, but even extends to deeper, methanogenic sediments at very low background concentrations of sulfate. Using samples retrieved off the Shimokita Peninsula, Japan, during the Integrated Ocean Drilling Program (IODP) Expedition 337, we measured potential sulfate reduction rates by slurry incubations with 35 S-labeled sulfate in deep methanogenic sediments between 1276.75 and 2456.75 meters below the seafloor. Potential sulfate reduction rates were generally extremely low (mostly below 0.1 pmol cm -3 d -1 ) but showed elevated values (up to 1.8 pmol cm -3 d -1 ) in a coal-bearing interval (Unit III). A measured increase in hydrogenase activity in the coal-bearing horizons coincided with this local increase in potential sulfate reduction rates. This paired enzymatic response suggests that hydrogen is a potentially important electron donor for sulfate reduction in the deep coalbed biosphere. By contrast, no stimulation of sulfate reduction rates was observed in treatments where methane was added as an electron donor. In the deep coalbeds, small amounts of sulfate might be provided by a cryptic sulfur cycle. The isotopically very heavy pyrites (δ 34 S = +43‰) found in this horizon is consistent with its formation via microbial sulfate reduction that has been continuously utilizing a small, increasingly 34 S-enriched sulfate reservoir over geologic time scales. Although our results do not represent in-situ activity, and the sulfate reducers might only have persisted in a dormant, spore-like state, our findings show that organisms capable of sulfate reduction have survived in deep methanogenic sediments over more than 20 Ma. This highlights the ability of sulfate-reducers to persist over geological timespans even in sulfate-depleted environments. Our study moreover represents the deepest evidence of a potential for sulfate reduction in marine sediments to date.

Final Report Real Time Monitoring of Rates of Subsurface Microbial Activity Associated with Natural Attenuation and Electron Donor Availability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lovley, Derek R.

The project was successful in developing new sensing technologies for monitoring rates of microbial activity in soils and sediments and also developed a novel proof-of-concept for monitoring the presence of bioavailable concentrations of a diversity of metabolites and toxic components in sedimentary environments. These studies led not only to publications in the peer-reviewed literature, but also two patent applications and a start-up company.

EVIDENCE FOR MICROBIAL ENHANCED ELECTRICAL CONDUCTIVITY IN HYDROCARBON-CONTAMINATED SEDIMENTS

EPA Science Inventory

Electrical conductivity of sediments during microbial mineralization of diesel was investigated in a mesoscale column experiment consisting of biotic contaminated and uncontaminated columns. Microbial population numbers increased with a clear pattern of depth zonation within the ...

Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors.

PubMed

Frossard, Aline; Gerull, Linda; Mutz, Michael; Gessner, Mark O

2012-03-01

A fundamental issue in microbial and general ecology is the question to what extent environmental conditions dictate the structure of communities and the linkages with functional properties of ecosystems (that is, ecosystem function). We approached this question by taking advantage of environmental gradients established in soil and sediments of small stream corridors in a recently created, early successional catchment. Specifically, we determined spatial and temporal patterns of bacterial community structure and their linkages with potential microbial enzyme activities along the hydrological flow paths of the catchment. Soil and sediments were sampled in a total of 15 sites on four occasions spread throughout a year. Denaturing gradient gel electrophoresis (DGGE) was used to characterize bacterial communities, and substrate analogs linked to fluorescent molecules served to track 10 different enzymes as specific measures of ecosystem function. Potential enzyme activities varied little among sites, despite contrasting environmental conditions, especially in terms of water availability. Temporal changes, in contrast, were pronounced and remarkably variable among the enzymes tested. This suggests much greater importance of temporal dynamics than spatial heterogeneity in affecting specific ecosystem functions. Most strikingly, bacterial community structure revealed neither temporal nor spatial patterns. The resulting disconnect between bacterial community structure and potential enzyme activities indicates high functional redundancy within microbial communities even in the physically and biologically simplified stream corridors of early successional landscapes.

Microbial Interactions with Natural Organic Matter Extracted from the Oak Ridge FRC

NASA Astrophysics Data System (ADS)

Wu, X.; Jagadamma, S.; Lancaster, A.; Adams, M. W. W.; Hazen, T.; Justice, N.; Chakraborty, R.

2015-12-01

Natural organic matter (NOM) is central to microbial food webs; however, little is known about the interplay between the physical and chemical characteristics of NOM and its turnover by microbial communities based upon biotic and abiotic parameters (e.g., biogenic precursors, redox state, bioavailability). Microbial activity changes the structures and properties that influence further bioavailability of NOM. To date, our understanding of these interactions is insufficient, and indigenous microbial activities that regulate NOM turnover are poorly resolved. It is critical to identify NOM characteristics to the structure and composition of microbial communities and to the metabolic potential of that community. Towards that end, sediment samples collected from the background area well FW305 (Oak Ridge Field Research Center, Oak Ridge, TN) were tested for NOM extraction methods that used three mild solvents, e.g., phosphate buffered saline (PBS), pyrophosphate, and MilliQ-water. MilliQ-water was finally chosen for extracting sediment samples via shaking and sonication. Groundwater from well FW301 was used as an inoculum to which the extracted NOM was added as carbon sources to feed native microbes. To identify the specific functional groups of extracted NOM that are bioavailable to indigenous microbes, several techniques, including FTIR, LC-MS, EEM, were applied to characterize the extracted NOM as well as the transformed NOM metabolites. 16S rDNA amplicon sequencing was also performed to identify the specific microbial diversity that was enriched and microbial isolates that preferentially grew with these NOM was also cultivated in the lab for future detailed studies.

Evaluating the performance of water purification in a vegetated groundwater recharge basin maintained by short-term pulsed infiltration events.

PubMed

Mindl, Birgit; Hofer, Julia; Kellermann, Claudia; Stichler, Willibald; Teichmann, Günter; Psenner, Roland; Danielopol, Dan L; Neudorfer, Wolfgang; Griebler, Christian

2015-01-01

Infiltration of surface water constitutes an important pillar in artificial groundwater recharge. However, insufficient transformation of organic carbon and nutrients, as well as clogging of sediments often cause major problems. The attenuation efficiency of dissolved organic carbon (DOC), nutrients and pathogens versus the risk of bioclogging for intermittent recharge were studied in an infiltration basin covered with different kinds of macrovegetation. The quality and concentration of organic carbon, major nutrients, as well as bacterial biomass, activity and diversity in the surface water, the porewater, and the sediment matrix were monitored over one recharge period. Additionally, the numbers of viral particles and Escherichia coli were assessed. Our study showed a fast establishment of high microbial activity. DOC and nutrients have sustainably been reduced within 1.2 m of sediment passage. Numbers of E. coli, which were high in the topmost centimetres of sediment porewater, dropped below the detection limit. Reed cover was found to be advantageous over bushes and trees, since it supported higher microbial activities along with a good infiltration and purification performance. Short-term infiltration periods of several days followed by a break of similar time were found suitable for providing high recharge rates, and good water purification without the risk of bioclogging.

H2 cycling and microbial bioenergetics in anoxic sediments

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; DeVincenzi, Donald (Technical Monitor)

2001-01-01

The simple biochemistry of H2 is central to a large number of microbial processes, affecting the interaction of organisms with each other and with the environment. In anoxic sediments, the great majority of microbial redox processes involve H2 as a reactant, product, or potential by-product, and the thermodynamics of these processes are thus highly sensitive to fluctuations in environmental H2 concentrations. In turn, H2 concentrations are controlled by the activity of H2-consuming microorganisms, which efficiently utilize this substrate down to levels which correspond to their bioenergetic limitations. Consequently, any environmental change which impacts the thermodynamics of H2-consuming organisms is mirrored by a corresponding change in H2 concentrations. This phenomenon is illustrated in anoxic sediments from Cape Lookout Bight, NC, USA: H2 concentrations are controlled by a suite of environmental parameters (e.g., temperature, sulfate concentrations) in a fashion which can be quantitatively described by a simple thermodynamic model. These findings allow us to calculate the apparent minimum quantity of biologically useful energy in situ. We find that sulfate reducing bacteria are not active at energy yields below -18 kJ per mole sulfate, while methanogenic archaea exhibit a minimum close to -10 kJ per mole methane.

Microbial diversity and stratification of South Pacific abyssal marine sediments.

PubMed

Durbin, Alan M; Teske, Andreas

2011-12-01

Abyssal marine sediments cover a large proportion of the ocean floor, but linkages between their microbial community structure and redox stratification have remained poorly constrained. This study compares the downcore gradients in microbial community composition to porewater oxygen and nitrate concentration profiles in an abyssal marine sediment column in the South Pacific Ocean. Archaeal 16S rRNA clone libraries showed a stratified archaeal community that changed from Marine Group I Archaea in the aerobic and nitrate-reducing upper sediment column towards deeply branching, uncultured crenarchaeotal and euryarchaeotal lineages in nitrate-depleted, anaerobic sediment horizons. Bacterial 16S rRNA clone libraries revealed a similar shift on the phylum and subphylum level within the bacteria, from a complex community of Alpha-, Gamma- and Deltaproteobacteria, Actinobacteria and Gemmatimonadetes in oxic surface sediments towards uncultured Chloroflexi and Planctomycetes in the anaerobic sediment column. The distinct stratification of largely uncultured bacterial and archaeal groups within the oxic and nitrate-reducing marine sediment column provides initial constraints for their microbial habitat preferences. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing.

PubMed

Mhuantong, Wuttichai; Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Eurwilaichitr, Lily; Tangphatsornruang, Sithichoke; Boonchayaanant, Benjaporn; Limpiyakorn, Tawan; Pattaragulwanit, Kobchai; Punmatharith, Thantip; McEvoy, John; Khan, Eakalak; Rachakornkij, Manaskorn; Champreda, Verawat

2015-01-01

The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas.

Anaerobic biodegradation of PAHs in mangrove sediment with amendment of NaHCO3.

PubMed

Li, Chun-Hua; Wong, Yuk-Shan; Wang, Hong-Yuan; Tam, Nora Fung-Yee

2015-04-01

Mangrove sediment is unique in chemical and biological properties. Many of them suffer polycyclic aromatic hydrocarbon (PAH) contamination. However, the study on PAH biological remediation for mangrove sediment is deficient. Enriched PAH-degrading microbial consortium and electron acceptor amendment are considered as two effective measures. Compared to other electron acceptors, the study on CO2, which is used by methanogens, is still seldom. This study investigated the effect of NaHCO3 amendment on the anaerobic biodegradation of four mixed PAHs, namely fluorene (Fl), phenanthrene (Phe), fluoranthene (Flua) and pyrene (Pyr), with or without enriched PAH-degrading microbial consortium in mangrove sediment slurry. The trends of various parameters, including PAH concentrations, microbial population size, electron-transport system activities, electron acceptor and anaerobic gas production were monitored. The results revealed that the inoculation of enriched PAH-degrading consortium had a significant effect with half lives shortened by 7-13 days for 3-ring PAHs and 11-24 days for 4-ring PAHs. While NaHCO3 amendment did not have a significant effect on the biodegradation of PAHs and other parameters, except that CO2 gas in the headspace of experimental flasks was increased. One of the possible reasons is that mangrove sediment contains high concentrations of other electron acceptors which are easier to be utilized by anaerobic bacteria, the other one is that the anaerobes in mangrove sediment can produce enough CO2 gas even without adding NaHCO3. Copyright © 2015. Published by Elsevier B.V.

Desiccation of sediments affects assimilate transport within aquatic plants and carbon transfer to microorganisms.

PubMed

von Rein, I; Kayler, Z E; Premke, K; Gessler, A

2016-11-01

With the projected increase in drought duration and intensity in future, small water bodies, and especially the terrestrial-aquatic interfaces, will be subjected to longer dry periods with desiccation of the sediment. Drought effects on the plant-sediment microorganism carbon continuum may disrupt the tight linkage between plants and microbes which governs sediment carbon and nutrient cycling, thus having a potential negative impact on carbon sequestration of small freshwater ecosystems. However, research on drought effects on the plant-sediment carbon transfer in aquatic ecosystems is scarce. We therefore exposed two emergent aquatic macrophytes, Phragmites australis and Typha latifolia, to a month-long summer drought in a mesocosm experiment. We followed the fate of carbon from leaves to sediment microbial communities with 13 CO 2 pulse labelling and microbial phospholipid-derived fatty acid (PLFA) analysis. We found that drought reduced the total amount of carbon allocated to stem tissues but did not delay the transport. We also observed an increase in accumulation of 13 C-labelled sugars in roots and found a reduced incorporation of 13 C into the PLFAs of sediment microorganisms. Drought induced a switch in plant carbon allocation priorities, where stems received less new assimilates leading to reduced starch reserves whilst roots were prioritised with new assimilates, suggesting their use for osmoregulation. There were indications that the reduced carbon transfer from roots to microorganisms was due to the reduction of microbial activity via direct drought effects rather than to a decrease in root exudation or exudate availability. © 2016 German Botanical Society and The Royal Botanical Society of the Netherlands.

Impact of seasonal variation on Escherichia coli concentrations in the riverbed sediments in the Apies River, South Africa.

PubMed

Abia, Akebe Luther King; Ubomba-Jaswa, Eunice; Momba, Maggy Ndombo Benteke

2015-12-15

Many South Africans living in resource-poor settings with little or no access to pipe-borne water still rely on rivers as alternative water sources for drinking and other purposes. The poor microbial quality of such water bodies calls for appropriate monitoring. However, routine monitoring only takes into consideration the microbial quality of the water column, and does not include monitoring of the riverbed sediments for microbial pollution. This study sought to investigate the microbial quality of riverbed sediments in the Apies River, Gauteng Province, South Africa, using Escherichia coli as a faecal indicator organism and to investigate the impact of seasonal variation on its abundance. Weekly samples were collected at 10 sampling sites on the Apies River between May and August 2013 (dry season) and between January and February 2014 (wet season). E. coli was enumerated using the Colilert®-18 Quanti-Tray® 2000 system. All sites tested positive for E. coli. Wastewater treatment work effluents had the highest negative impact on the river water quality. Seasonal variations had an impact on the concentration of E. coli both in water and sediments with concentrations increasing during the wet season. A strong positive correlation was observed between temperature and the E. coli concentrations. We therefore conclude that the sediments of the Apies River are heavily polluted with faecal indicator bacteria and could also harbour other microorganisms including pathogens. The release of such pathogens into the water column as a result of the resuspension of sediments due to extreme events like floods or human activities could increase the health risk of the populations using the untreated river water for recreation and other household purposes. There is therefore an urgent need to reconsider and review the current South African guidelines for water quality monitoring to include sediments, so as to protect human health and other aquatic lives. Copyright © 2015 Elsevier B.V. All rights reserved.

Diversity of microbial communities correlated to physiochemical parameters in a digestion basin of a zero-discharge mariculture system.

PubMed

Cytryn, Eddie; Gelfand, Ilya; Barak, Yoram; van Rijn, Jaap; Minz, Dror

2003-01-01

Bacterial community structure and physiochemical parameters were examined in a sedimentation basin of a zero-discharge mariculture system. The system consisted of an intensively stocked fish basin from which water was recirculated through two separate treatment loops. Surface water from the basin was pumped over a trickling filter in one loop while bottom-water was recirculated through a sedimentation basin followed by a fluidized bed reactor in the other. Ammonia oxidation to nitrate in the trickling filter and organic matter digestion together with nitrate reduction in the sedimentation basin and fluidized bed reactor, allowed zero-discharge operation of the system. Relatively high concentrations of oxygen, nitrate, sulphate and organic matter detected simultaneously in the digestion basin suggested the potential for a wide range of microbially-mediated transformation processes. In this study, physiochemical parameters were correlated to bacterial diversity and distribution in horizontal and vertical profiles within this basin in an effort to obtain a basic understanding of the chemical and microbial processes in this system. Chemical activity and microbial diversity, the latter measured by denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction (PCR) amplified 16S rDNA fragments, were higher in the sludge layer than in the overlying aqueous layer of the basin. Chemical parameters in sludge samples close to the basin inlet suggested enhanced microbial activity relative to other sampling areas with evidence of both nitrate and sulphate reduction. Four of the nine DGGE bands identified in this zone were affiliated with the Bacteroidetes phylum. Detected sequences closely related to sequences of organisms involved in the sulphur cycle included Desulfovibrio, Dethiosulfovibrio and apparent sulphur oxidizers from the gamma-proteobacteria. In addition, a number of sequences from the beta and alpha-proteobacteria were identified.

Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution.

PubMed

Coelho, Francisco J R C; Cleary, Daniel F R; Costa, Rodrigo; Ferreira, Marina; Polónia, Ana R M; Silva, Artur M S; Simões, Mário M Q; Oliveira, Vanessa; Gomes, Newton C M

2016-09-01

There is growing concern that predicted changes to global ocean chemistry will interact with anthropogenic pollution to significantly alter marine microbial composition and function. However, knowledge of the compounding effects of climate change stressors and anthropogenic pollution is limited. Here, we used 16S and 18S rRNA (cDNA)-based activity profiling to investigate the differential responses of selected microbial taxa to ocean acidification and oil hydrocarbon contamination under controlled laboratory conditions. Our results revealed that a lower relative abundance of sulphate-reducing bacteria (Desulfosarcina/Desulfococcus clade) due to an adverse effect of seawater acidification and oil hydrocarbon contamination (reduced pH-oil treatment) may be coupled to changes in sediment archaeal communities. In particular, we observed a pronounced compositional shift and marked reduction in the prevalence of otherwise abundant operational taxonomic units (OTUs) belonging to the archaeal Marine Benthic Group B and Marine Hydrothermal Vent Group (MHVG) in the reduced pH-oil treatment. Conversely, the abundance of several putative hydrocarbonoclastic fungal OTUs was higher in the reduced pH-oil treatment. Sediment hydrocarbon profiling, furthermore, revealed higher concentrations of several alkanes in the reduced pH-oil treatment, corroborating the functional implications of the structural changes to microbial community composition. Collectively, our results advance the understanding of the response of a complex microbial community to the interaction between reduced pH and anthropogenic pollution. In future acidified marine environments, oil hydrocarbon contamination may alter the typical mixotrophic and k-/r-strategist composition of surface sediment microbiomes towards a more heterotrophic state with lower doubling rates, thereby impairing the ability of the ecosystem to recover from acute oil contamination events. © 2016 John Wiley & Sons Ltd.

Microbial Community Analysis in Water Storage Tank Sediment Exposed to Monochloramine - Portland

EPA Science Inventory

Sediment accumulation in water storage facilities causes water quality degradation, including enhanced biological growth and more rapid disinfectant decay. The current research evaluated the microbial community composition after a drinking water storage facility’s sediment was e...

Microbial Community Analysis in Water Storage Tank Sediment Exposed to Monochloramine

EPA Science Inventory

Sediment accumulation in water storage facilities causes water quality degradation, including enhanced biological growth and more rapid disinfectant decay. The current research evaluated the microbial community composition after a drinking water storage facility’s sediment was e...

Community Composition of Nitrous Oxide-Related Genes in Salt Marsh Sediments Exposed to Nitrogen Enrichment.

PubMed

Angell, John H; Peng, Xuefeng; Ji, Qixing; Craick, Ian; Jayakumar, Amal; Kearns, Patrick J; Ward, Bess B; Bowen, Jennifer L

2018-01-01

Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated profiles of microbial communities and communities of micro-organisms containing specific nitrogen cycling genes that encode several enzymes ( amoA, norB, nosZ) related to nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms involved in the production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that previously measured rates of nitrous oxide production and consumption are likely the result of changes in community structure, not simply changes in microbial activity.

CoBOP: Microbial Biofilms: A Parameter Altering the Apparent Optical Properties of Sediments, Seagrasses and Surfaces

DTIC Science & Technology

2002-09-30

CoBOP: Microbial Biofilms: A Parameter Altering the Apparent Optical Properties of Sediments, Seagrasses and Surfaces Alan W. Decho Department...TITLE AND SUBTITLE CoBOP: Microbial Biofilms: A Parameter Altering the Apparent Optical Properties of Sediments, Seagrasses and Surfaces 5a. CONTRACT...structures produced by bacteria. Their growth appears to depend on biofilm processes and light distributions ( photosynthesis ). Therefore, the data acquired

CoBOP: Microbial Biofilms: A Parameter Altering the Apparent Optical Properties of Sediments, Seagrasses and Surfaces

DTIC Science & Technology

2003-09-30

CoBOP: MICROBIAL BIOFILMS: A PARAMETER ALTERING THE APPARENT OPTICAL PROPERTIES OF SEDIMENTS, SEAGRASSES AND SURFACES. Alan W. Decho Department...AND SUBTITLE CoBOP: Microbial Biofilms: A Parameter Altering The Apparent Optical Properties Of Sediments, Seagrasses And Surfaces 5a. CONTRACT...biofilm processes and light distributions ( photosynthesis ). Therefore, the data acquired from this project will be closely paired with results of

Early diagenesis in the sediments of the Congo deep-sea fan dominated by massive terrigenous deposits: Part III - Sulfate- and methane- based microbial processes

NASA Astrophysics Data System (ADS)

Pastor, L.; Toffin, L.; Decker, C.; Olu, K.; Cathalot, C.; Lesongeur, F.; Caprais, J.-C.; Bessette, S.; Brandily, C.; Taillefert, M.; Rabouille, C.

2017-08-01

Geochemical profiles (SO42-, H2S, CH4, δ13CH4) and phylogenetic diversity of Archaea and Bacteria from two oceanographic cruises dedicated to the lobes sediments of the Congo deep-sea fan are presented in this paper. In this area, organic-rich turbidites reach 5000 m and allow the establishment of patchy cold-seep-like habitats including microbial mats, reduced sediments, and vesicomyid bivalves assemblages. These bivalves live in endosymbiosis with sulfur-oxidizing bacteria and use sulfides to perform chemosynthesis. In these habitats, unlike classical abyssal sediments, anoxic processes are dominant. Total oxygen uptake fluxes and methane fluxes measured with benthic chambers are in the same range as those of active cold-seep environments, and oxygen is mainly used for reoxidation of reduced compounds, especially in bacterial mats and reduced sediments. High concentrations of methane and sulfate co-exist in the upper 20 cm of sediments, and evidence indicates that sulfate-reducing microorganisms and methanogens co-occur in the shallow layers of these sediments. Simultaneously, anaerobic oxidation of methane (AOM) with sulfate as the electron acceptor is evidenced by the presence of ANMEs (ANaerobic MEthanotroph). Dissolved sulfide produced through the reduction of sulfate is reoxidized through several pathways depending on the habitat. These pathways include vesicomyid bivalves uptake (adults or juveniles in the bacterial mats habitats), reoxidation by oxygen or iron phases within the reduced sediment, or reoxidation by microbial mats. Sulfide uptake rates by vesicomyids measured in sulfide-rich sea water (90±18 mmol S m-2 d-1) were similar to sulfide production rates obtained by modelling the sulfate profile with different bioirrigation constants, highlighting the major control of vesicomyids on sulfur cycle in their habitats.

INTERACTIONS AMONG PHOSPHATE AMENDMENTS, MICROBES AND URANIUM MOBILITY IN CONTAMINATED SEDIMENTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knox, A

2007-08-30

The use of sequestering agents for the transformation of radionuclides in low concentrations in contaminated soils/sediments offers considerable potential for long-term environmental cleanup. This study evaluated the influence of four phosphate amendments and two microbial amendments on U availability. The synchrotron X-ray fluorescence mapping of the untreated U-contaminated sediment showed that U was closely associated with Mn. All tested phosphate amendments reduced aqueous U concentration more than 90%, likely due to formation of insoluble phosphate precipitates. The addition of A. piechaudii and P. putida alone were found to reduce U concentrations 63% and 31% respectively. Uranium sorption in phosphate treatmentsmore » was significantly reduced in the presence of microbes. However, increased microbial activity in the treated sediment led to reduction of phosphate effectiveness. The average U concentration in 1 M MgCl{sub 2} extract from U amended sediment was 437 {micro}g/kg, but in the same sediment without microbes (autoclaved sediment), the extractable U concentration was only 103 {micro}g/kg. When the autoclaved amended sediment was treated with autoclaved biological apatite, U concentration in the 1 M MgCl{sub 2} extract was {approx}0 {micro}g/kg. Together these tests suggest that microbes may enhance U leaching and reduce phosphate amendment remedial effectiveness.« less

Mercury cycling in stream ecosystems. 2. Benthic methylmercury production and bed sediment-pore water partitioning.

PubMed

Marvin-Dipasquale, Mark; Lutz, Michelle A; Brigham, Mark E; Krabbenhoft, David P; Aiken, George R; Orem, William H; Hall, Britt D

2009-04-15

Mercury speciation, controls on methylmercury (MeHg) production, and bed sediment-pore water partitioning of total Hg (THg) and MeHg were examined in bed sediment from eight geochemically diverse streams where atmospheric deposition was the predominant Hg input. Across all streams, sediment THg concentrations were best described as a combined function of sediment percent fines (%fines; particles < 63 microm) and organic content. MeHg concentrations were best described as a combined function of organic content and the activity of the Hg(II)-methylating microbial community and were comparable to MeHg concentrations in streams with Hg inputs from industrial and mining sources. Whole sediment tin-reducible inorganic reactive Hg (Hg(II)R) was used as a proxy measure for the Hg(II) pool available for microbial methylation. In conjunction with radiotracer-derived rate constants of 203Hg(II) methylation, Hg(II)R was used to calculate MeHg production potential rates and to explain the spatial variability in MeHg concentration. The %Hg(II)R (of THg) was low (2.1 +/- 5.7%) and was inversely related to both microbial sulfate reduction rates and sediment total reduced sulfur concentration. While sediment THg concentrations were higher in urban streams, %MeHg and %Hg(II)R were higher in nonurban streams. Sediment pore water distribution coefficients (log Kd's) for both THg and MeHg were inversely related to the log-transformed ratio of pore water dissolved organic carbon (DOC) to bed sediment %fines. The stream with the highest drainage basin wetland density also had the highest pore water DOC concentration and the lowest log Kd's for both THg and MeHg. No significant relationship existed between overlying water MeHg concentrations and those in bed sediment or pore water, suggesting upstream sources of MeHg production may be more important than local streambed production as a driver of water column MeHg concentration in drainage basins that receive Hg inputs primarily from atmospheric sources.

Enhanced biodegradation by hydraulic heterogeneities in petroleum hydrocarbon plumes.

PubMed

Bauer, Robert D; Rolle, Massimo; Bauer, Sebastian; Eberhardt, Christina; Grathwohl, Peter; Kolditz, Olaf; Meckenstock, Rainer U; Griebler, Christian

2009-02-27

In case of dissolved electron donors and acceptors, natural attenuation of organic contaminant plumes in aquifers is governed by hydrodynamic mixing and microbial activity. Main objectives of this work were (i) to determine whether aerobic and anaerobic biodegradation in porous sediments is controlled by transverse dispersion, (ii) to elucidate the effect of sediment heterogeneity on mixing and biodegradation, and (iii) to search for degradation-limiting factors. Comparative experiments were conducted in two-dimensional sediment microcosms. Aerobic toluene and later ethylbenzene degradation by Pseudomonas putida strain F1 was initially followed in a plume developing from oxic to anoxic conditions and later under steady-state mixing-controlled conditions. Competitive anaerobic degradation was then initiated by introduction of the denitrifying strain Aromatoleum aromaticum EbN1. In homogeneous sand, aerobic toluene degradation was clearly controlled by dispersive mixing. Similarly, under denitrifying conditions, microbial activity was located at the plume's fringes. Sediment heterogeneity caused flow focusing and improved the mixing of reactants. Independent from the electron accepting process, net biodegradation was always higher in the heterogeneous setting with a calculated efficiency plus of 23-100% as compared to the homogeneous setup. Flow and reactive transport model simulations were performed in order to interpret and evaluate the experimental results.

A Long-Term Cultivation of an Anaerobic Methane-Oxidizing Microbial Community from Deep-Sea Methane-Seep Sediment Using a Continuous-Flow Bioreactor

PubMed Central

Aoki, Masataka; Ehara, Masayuki; Saito, Yumi; Yoshioka, Hideyoshi; Miyazaki, Masayuki; Saito, Yayoi; Miyashita, Ai; Kawakami, Shuji; Yamaguchi, Takashi; Ohashi, Akiyoshi; Nunoura, Takuro; Takai, Ken; Imachi, Hiroyuki

2014-01-01

Anaerobic oxidation of methane (AOM) in marine sediments is an important global methane sink, but the physiological characteristics of AOM-associated microorganisms remain poorly understood. Here we report the cultivation of an AOM microbial community from deep-sea methane-seep sediment using a continuous-flow bioreactor with polyurethane sponges, called the down-flow hanging sponge (DHS) bioreactor. We anaerobically incubated deep-sea methane-seep sediment collected from the Nankai Trough, Japan, for 2,013 days in the bioreactor at 10°C. Following incubation, an active AOM activity was confirmed by a tracer experiment using 13C-labeled methane. Phylogenetic analyses demonstrated that phylogenetically diverse Archaea and Bacteria grew in the bioreactor. After 2,013 days of incubation, the predominant archaeal components were anaerobic methanotroph (ANME)-2a, Deep-Sea Archaeal Group, and Marine Benthic Group-D, and Gammaproteobacteria was the dominant bacterial lineage. Fluorescence in situ hybridization analysis showed that ANME-1 and -2a, and most ANME-2c cells occurred without close physical interaction with potential bacterial partners. Our data demonstrate that the DHS bioreactor system is a useful system for cultivating fastidious methane-seep-associated sedimentary microorganisms. PMID:25141130

Macrobenthos community structure and trophic relationships within active and inactive Pacific hydrothermal sediments

NASA Astrophysics Data System (ADS)

Levin, Lisa A.; Mendoza, Guillermo F.; Konotchick, Talina; Lee, Raymond

2009-09-01

Hydrothermal fluids passing through sediments create a habitat hypothesized to influence the community structure of infaunal macrobenthos. Here we characterize the density, biomass, species composition, diversity, distributions, lifestyle, and nutritional sources of macroinfauna in hydrothermal sediments in NE and SW Pacific settings, and draw comparisons in search of faunal attributes characteristic of this habitat. There is increasing likelihood that seafloor massive sulfide deposits, associated with active and inactive hydrothermal venting, will be mined commercially. This creates a growing imperative for a more thorough understanding of the structure, dynamics, and resilience of the associated sediment faunas, and has stimulated the research presented here. Macrobenthic assemblages were studied at Manus Basin (1430-1634 m, Papua New Guinea [PNG]) as a function of location (South Su vs. Solwara 1), and hydrothermal activity (active vs. inactive), and at Middle Valley (2406-2411 m, near Juan de Fuca Ridge) as a function of habitat (active clam bed, microbial mat, hot mud, inactive background sediment). The studies conducted in PNG formed part of the environmental impact assessment work for the Solwara 1 Project of Nautilus Minerals Niugini Limited. We hypothesized that hydrothermally active sites should support (a) higher densities and biomass, (b) greater dominance and lower diversity, (c) a higher fraction of deposit feeders, and (d) greater isotopic evidence for chemosynthetic food sources than inactive sites. Manus Basin macrofauna generally had low density (<1000 ind. m -2) and low biomass (0.1-1.07 g m -2), except for the South Su active site, which had higher density (3494 ind. m -2) and biomass (11.94 g m -2), greater dominance (R1D=76%), lower diversity and more spatial (between-core) homogeneity than the Solwara 1 and South Su inactive sites. Dominant taxa at Manus Basin were Spionidae ( Prionospio sp.) in active sediments, and tanaids and deposit-feeding nuculanoid bivalves in active and inactive sediments. At Middle Valley, hot mud sediments supported few animals (1011 ind m -2) and low biomass (1.34 g m -2), while active clam bed sediments supported a high-density (19,984 ind m -2), high-biomass (4.46 g m -2), low-diversity assemblage comprised of largely orbiniid and syllid polychaetes. Microbial mat sediments had the most diverse assemblage (mainly orbiniid, syllid, dorvilleid, and ampharetid polychaetes) with intermediate densities (8191 ind m -2) and high biomass (4.23 g m -2). Fauna at both Manus Basin active sites had heavy δ 13C signatures (-17‰ to -13‰) indicative of chemosynthetic, TCA-cycle microbes at the base of the food chain. In contrast, photosynthesis and sulfide oxidation appear to fuel most of the fauna at Manus Basin inactive sites (δ 13C=-29‰ to -20‰) and Middle Valley active clam beds and microbial mats (δ 13C=-36‰ to -20‰). The two hydrothermal regions, located at opposite ends of the Pacific Ocean, supported different habitats, sharing few taxa at the generic or family level, but both exhibited elevated infaunal density and high dominance at selected sites. Subsurface-deposit feeding and bacterivory were prevalent feeding modes. Both the Manus Basin and Middle Valley assemblages exhibit significant within-region heterogeneity, apparently conferred by variations in hydrothermal activity and associated biogenic habitats.

Permeability structure and its influence on microbial activity at off-Shimokita basin, Japan

NASA Astrophysics Data System (ADS)

Tanikawa, W.; Yamada, Y.; Sanada, Y.; Kubo, Y.; Inagaki, F.

2016-12-01

The microbial populations and the limit of microbial life are probably limited by chemical, physical, and geological conditions, such as temperature, pore water chemistry, pH, and water activity; however, the key parameters affecting growth in deep subseafloor sediments remain unclarified (Hinrichs and Inagaki 2012). IODP expedition 337 was conducted near a continental margin basin off Shimokita Peninsula, Japan to investigate the microbial activity under deep marine coalbed sediments down to 2500 mbsf. Inagaki et al. (2015) discovered that microbial abundance decreased markedly with depth (the lowest cell density of <1 cell/cm3 was recorded below 2000 mbsf), and that the coal bed layers had relatively higher cell densities. In this study, permeability was measured on core samples from IODP Expedition 337 and Expedition CK06-06 in the D/V Chikyu shakedown cruise. Permeability was measured at in-situ effective pressure condition. Permeability was calculated by the steady state flow method by keeping differential pore pressure from 0.1 to 0.8 MPa.Our results show that the permeability for core samples decreases with depth from 10-16 m2 on the seafloor to 10-20 m2 at the bottom of hole. However, permeability is highly scattered within the coal bed unit (1900 to 2000 mbsf). Permeabilities for sandstone and coal is higher than those for siltstone and shale, therefore the scatter of the permeabilities at the same unit is due to the high variation of lithology. The highest permeability was observed in coal samples and this is probably due to formation of micro cracks (cleats). Permeability estimated from the NMR logging using the empirical parameters is around two orders of magnitude higher than permeability of core samples, even though the relative permeability variation at vertical direction is quite similar between core and logging data.The higher cell density is observed in the relatively permeable formation. On the other hand, the correlation between cell density, water activity, and porosity is not clear. On the assumption that pressure gradient is constant through the depth, flow rate can be proportional to permeability of sediments. Flow rate probably restricts the availability of energy and nutrient for microorganism, therefore permeability might have influenced on the microbial activity in the coalbed basin.

Pathways for arsenic from sediments to groundwater to streams: Biogeochemical processes in the Inner Coastal Plain, New Jersey, USA

USGS Publications Warehouse

Barringer, Julia L.; Mumford, Adam; Young, Lily Y.; Reilly, Pamela A.; Bonin, Jennifer L.; Rosman, Robert

2010-01-01

The Cretaceous and Tertiary sediments that underlie the Inner Coastal Plain of New Jersey contain the arsenic-rich mineral glauconite. Streambed sediments in two Inner Coastal Plain streams (Crosswicks and Raccoon Creeks) that traverse these glauconitic deposits are enriched in arsenic (15–25 mg/kg), and groundwater discharging to the streams contains elevated levels of arsenic (>80 μg/L at a site on Crosswicks Creek) with arsenite generally the dominant species. Low dissolved oxygen, low or undetectable levels of nitrate and sulfate, detectable sulfide concentrations, and high concentrations of iron and dissolved organic carbon (DOC) in the groundwater indicate that reducing environments are present beneath the streambeds and that microbial activity, fueled by the DOC, is involved in releasing arsenic and iron from the geologic materials. In groundwater with the highest arsenic concentrations at Crosswicks Creek, arsenic respiratory reductase gene (arrA) indicated the presence of arsenic-reducing microbes. From extracted DNA, 16s rRNA gene sequences indicate the microbial community may include arsenic-reducing bacteria that have not yet been described. Once in the stream, iron is oxidized and precipitates as hydroxide coatings on the sediments. Arsenite also is oxidized and co-precipitates with or is sorbed to the iron hydroxides. Consequently, dissolved arsenic concentrations are lower in streamwater than in the groundwater, but the arsenic contributed by groundwater becomes part of the arsenic load in the stream when sediments are suspended during high flow. A strong positive relation between concentrations of arsenic and DOC in the groundwater samples indicates that any process—natural or anthropogenic—that increases the organic carbon concentration in the groundwater could stimulate microbial activity and thus increase the amount of arsenic that is released from the geologic materials.

Identifying the Linkages Between Microbial Activity and Gas Flux of Subaerial Volcanic Environments: A Guide to Exploring Magmatic Planets and Moons

NASA Astrophysics Data System (ADS)

Miller, H. A.; Lopez, T. M.; Fischer, T. P.; Schrenk, M. O.

2017-11-01

Promising contemporary analogs of habitable environments are fumaroles associated with active volcanism. Experimental studies linking sediments, microbes, and volatile outgassing may lead to new bio- or geosignatures of habitability.

Energetic Constraints of Subseafloor Life

NASA Astrophysics Data System (ADS)

D'Hondt, S.; Spivack, A. J.; Wang, G.

2014-12-01

Mean per-cell rates of catabolic activity, energy flux, and biomass turnover are orders of magnitude slower in subseafloor sediment than in the surface world. Despite extreme scarcity of electron donors, competing metabolic pathways co-occur for hundreds of meters deep in subseafloor sediment deposited over millions of years. Our study of an example site (ODP Site 1226) indicates that the energy yields of these competing reactions are pinned to a thermodynamic minimum (Wang et al., 2010). The simplest explanation of this long-term co-existence is thermodynamic cooperation, where microorganisms utilize different but co-existing pathways that remove each other's reaction products. Our Site 1226 results indicate that the energy flux to subseafloor sedimentary microbes is extremely low. Comparison to biomass turnover rates at other sites suggests that most of this flux may be used for building biomolecules from existing components (e.g., amino acids in the surrounding sediment), rather than for de novo biosynthesis from inorganic chemicals. Given these discoveries, ocean drilling provides a tremendous opportunity to address several mysteries of microbial survival and natural selection under extreme energy limitation. Some of these mysteries are centered on microbial communities. To what extent do counted cells in subseafloor sediment constitute a deep microbial necrosphere? How do different kinds of microbes interact to sustain their mean activity at low average rates for millions of years? Other mysteries relate to individual cells. How slowly can a cell metabolize? How long can a cell survive at such low rates of activity? What properties allow microbes to be sustained by low fluxes of energy? In what ways do subseafloor organisms balance the benefit(s) of maximizing energy recovery with the need to minimize biochemical cost(s) of energy recovery? References Wang, G., et al., 2010. Geochimica et Cosmochimica Acta 74, 3938-3947.

Microbial diversity in methane hydrate-bearing deep marine sediments core preserved in the original pressure.

NASA Astrophysics Data System (ADS)

Takahashi, Y.; Hata, T.; Nishida, H.

2017-12-01

In normal coring of deep marine sediments, the sampled cores are exposed to the pressure of the atmosphere, which results in dissociation of gas-hydrates and might change microbial diversity. In this study, we analyzed microbial composition in methane hydrate-bearing sediment core sampled and preserved by Hybrid-PCS (Pressure Coring System). We sliced core into three layers; (i) outside layer, which were most affected by drilling fluids, (ii) middle layer, and (iii) inner layer, which were expected to be most preserved as the original state. From each layer, we directly extracted DNA, and amplified V3-V4 region of 16S rRNA gene. We determined at least 5000 of nucleotide sequences of the partial 16S rDNA from each layer by Miseq (Illumina). In the all layers, facultative anaerobes, which can grow with or without oxygen because they can metabolize energy aerobically or anaerobically, were detected as majority. However, the genera which are often detected anaerobic environment is abundant in the inner layer compared to the outside layer, indicating that condition of drilling and preservation affect the microbial composition in the deep marine sediment core. This study was conducted as a part of the activity of the Research Consortium for Methane Hydrate Resources in Japan [MH21 consortium], and supported by JOGMEC (Japan Oil, Gas and Metals National Corporation). The sample was provided by AIST (National Institute of Advanced Industrial Science and Technology).

Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams.

PubMed

Wilhelm, Linda; Besemer, Katharina; Fasching, Christina; Urich, Tim; Singer, Gabriel A; Quince, Christopher; Battin, Tom J

2014-08-01

Glaciers harbour diverse microorganisms, which upon ice melt can be released downstream. In glacier-fed streams microorganisms can attach to stones or sediments to form benthic biofilms. We used 454-pyrosequencing to explore the bulk (16S rDNA) and putatively active (16S rRNA) microbial communities of stone and sediment biofilms across 26 glacier-fed streams. We found differences in community composition between bulk and active communities among streams and a stronger congruence between biofilm types. Relative abundances of rRNA and rDNA were positively correlated across different taxa and taxonomic levels, but at lower taxonomic levels, the higher abundance in either the active or the bulk communities became more apparent. Here, environmental variables played a minor role in structuring active communities. However, we found a large number of rare taxa with higher relative abundances in rRNA compared with rDNA. This suggests that rare taxa contribute disproportionately to microbial community dynamics in glacier-fed streams. Our findings propose that high community turnover, where taxa repeatedly enter and leave the 'seed bank', contributes to the maintenance of microbial biodiversity in harsh ecosystems with continuous environmental perturbations, such as glacier-fed streams. © 2014 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Bioelectric production from sediment of pond fishing and molasses using microbial fuel cell (MFC) technology-base with the influence of substrate concentration variety

NASA Astrophysics Data System (ADS)

Syafitri, L. M.; Saputro, Y. A.; Hana, P. N.; Hardiani, D.; Raharjo, B.

2018-03-01

Indonesia is currently faced the problem of the need for electrical energy. MFC is a technology that can be used to generate electricity by utilizing microbial activity. The aims of this study is to manage the molasses waste and sediment of fishery as a substrate in the MFC system. The research method was performed by preparing anode and cathode connected by a salt bridge forming the system of MFC Double Chamber. The result of bacteriology test using Total Plate Count (TPC) method showed that the number of bacterial colonies on the sediment substrate was 4.1 × 106 cfu/gr, while the molasses substrate was 7,1 × 104 cfu/gr. The measurement result of electricity showed that 25% sediment and 75% molasses substrate variation resulted in the highest average voltage and power density that are 0.372 V and 813.191 mW/m2. The conclusion of this research is that the mixture of sediment with molasses substrate can increase the production of electricity produced by MFC system.

Change of microbial community structure and functional gene abundance in nonylphenol-degrading sediment.

PubMed

Wang, Zhao; Yang, Yuyin; He, Tao; Xie, Shuguang

2015-04-01

Biodegradation by autochthonous microbial community is an important way to clean up nonylphenol (NP) from contaminated river sediment. Knowledge of sediment microbial community can aid in our understanding of biological processes related to NP degradation. However, the change in sediment microbial community associated with NP biodegradation remains unclear. The present study investigated the shift in bacterial community structure and NP-degrading gene abundance in response to NP attenuation in river sediment. Sediment microcosms with different levels of 4-NP (0, 100, or 300 μg/g) were constructed. A nearly complete attenuation of NP occurred in the microcosm with 100 μg/g NP after 9 days' incubation, while a residual NP rate of 8.1 % was observed in the microcosm with 300 μg/g NP after 22 days' incubation. Illumina MiSeq sequencing analysis indicated that Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes predominated in NP-degrading river sediment. Sediment bacterial community structure varied significantly during NP biodegradation and subsequent incubation, which was affected by the level of added NP. The n-alkane biodegradation (alkB) gene abundance showed a significant variation in each NP-amended microcosm (100 or 300 μg/g), while a significant increase in the single component monooxygenase (sMO) gene abundance only occurred in the microcosm spiked with 300 μg/g NP. This study can provide some new insights toward NP-degrading microbial ecology in the environment.

Effect of salinity on mercury methylating benthic microbes and their activities in Great Salt Lake, Utah

USGS Publications Warehouse

Boyd, Eric S.; Yu, Ri-Qing; Barkay, Tamar; Hamilton, Trinity L.; Baxter, Bonnie K.; Naftz, David L.; Marvin-DiPasquale, Mark

2017-01-01

Surface water and biota from Great Salt Lake (GSL) contain some of the highest documented concentrations of total mercury (THg) and methylmercury (MeHg) in the United States. In order to identify potential biological sources of MeHg and controls on its production in this ecosystem, THg and MeHg concentrations, rates of Hg(II)-methylation and MeHg degradation, and abundances and compositions of archaeal and bacterial 16 rRNA gene transcripts were determined in sediment along a salinity gradient in GSL. Rates of Hg(II)-methylation were inversely correlated with salinity and were at or below the limits of detection in sediment sampled from areas with hypersaline surface water. The highest rates of Hg(II)-methylation were measured in sediment with low porewater salinity, suggesting that benthic microbial communities inhabiting less saline environments are supplying the majority of MeHg in the GSL ecosystem. The abundance of 16S rRNA gene transcripts affiliated with the sulfate reducer Desulfobacterium sp. was positively correlated with MeHg concentrations and Hg(II)-methylation rates in sediment, indicating a potential role for this taxon in Hg(II)-methylation in low salinity areas of GSL. Reactive inorganic Hg(II) (a proxy used for Hg(II) available for methylation) and MeHg concentrations were inversely correlated with salinity. Thus, constraints imposed by salinity on Hg(II)-methylating populations and the availability of Hg(II) for methylation are inferred to result in higher MeHg production potentials in lower salinity environments. Benthic microbial MeHg degradation was also most active in lower salinity environments. Collectively, these results suggest an important role for sediment anoxia and microbial sulfate reducers in the production of MeHg in low salinity GSL sub-habitats and may indicate a role for salinity in constraining Hg(II)-methylation and MeHg degradation activities by influencing the availability of Hg(II) for methylation.

The role of subglacial microbes in carbon cycling and methane release in the past and present

NASA Astrophysics Data System (ADS)

Stibal, M.; Bech Mikkelsen, A.; Wadham, J. L.; Telling, J.; Hawkings, J.; Lis, G. P.; Lawson, E. C.; Hasan, F.; Dubnick, A.; Elberling, B.; Jacobsen, C. S.

2012-12-01

Subglacial environments are largely anoxic, contain organic carbon (OC) overridden by glacier ice during periods of advance, and harbour active microbial communities. This creates favourable conditions for a variety of microbial metabolisms, including methanogenesis. Yet little is known of the past and present potentials of subglacial microbes to take part in carbon cycling including methane production. Here we present data on the abundance and diversity of prokaryotic microbes, the activity of methanogenic archaea and the amount and character of OC in subglacial sediment and runoff from the Greenland Ice Sheet and compare them to those from other Arctic glaciers. The investigated Greenland subglacial sediment was of Holocene-aged soil origin and contained less bioavailable OC compared to subglacial sediments of lacustrine origin. The total microbial abundance and diversity was relatively low and the community was dominated by Proteobacteria. The identified clones were related to bacteria with both aerobic and anaerobic metabolisms, indicating the presence of both oxic and anoxic conditions in the sediments. Significant numbers of methanogens (up to 7×104 cells g-1) were detected and clones of Methanomicrobiales were identified in the clone library. Long lag periods (up to >200 days) were observed before significant methane concentrations (~0.2 pmol g-1 day-1 at 1C) were measured in long-term incubation experiments. These rates were lower than those measured in subglacial sediments containing more bioavailable OC. We use the measured rates of methanogenesis to estimate the potential for methane production beneath the Laurentide/Inuitian/Cordilleran and Fennoscandian Ice Sheets during a typical 85 ka Quaternary glacial/interglacial cycle. We predict that contrasting rates of methane production are likely to occur beneath glaciers that overran different types of substrate. Methane production from overridden soils such as those in Greenland is likely to be lower than that from lacustrine-derived sediments, possibly due to a difference in organic substrate lability. This finding highlights the importance of considering the character of different OC pools when calculating present and predicting future subglacial CH4 production rates. We also examine the modern potential of subglacial microbes, including methanogens, to be exported to downstream ecosystems in an active state, and suggest that due to the accelerated melting of glaciers and ice sheets worldwide large amounts of active microbes are transported to downstream ecosystems where they can resume their activity.

Enrichment of arsenic transforming and resistant heterotrophic bacteria from sediments of two salt lakes in Northern Chile.

PubMed

Lara, José; Escudero González, Lorena; Ferrero, Marcela; Chong Díaz, Guillermo; Pedrós-Alió, Carlos; Demergasso, Cecilia

2012-05-01

Microbial populations are involved in the arsenic biogeochemical cycle in catalyzing arsenic transformations and playing indirect roles. To investigate which ecotypes among the diverse microbial communities could have a role in cycling arsenic in salt lakes in Northern Chile and to obtain clues to facilitate their isolation in pure culture, sediment samples from Salar de Ascotán and Salar de Atacama were cultured in diluted LB medium amended with NaCl and arsenic, at different incubation conditions. The samples and the cultures were analyzed by nucleic acid extraction, fingerprinting analysis, and sequencing. Microbial reduction of As was evidenced in all the enrichments carried out in anaerobiosis. The results revealed that the incubation factors were more important for determining the microbial community structure than arsenic species and concentrations. The predominant microorganisms in enrichments from both sediments belonged to the Firmicutes and Proteobacteria phyla, but most of the bacterial ecotypes were confined to only one system. The occurrence of an active arsenic biogeochemical cycle was suggested in the system with the highest arsenic content that included populations compatible with microorganisms able to transform arsenic for energy conservation, accumulate arsenic, produce H(2), H(2)S and acetic acid (potential sources of electrons for arsenic reduction) and tolerate high arsenic levels.

MICROBIAL DIVERSITY IN SURFACE SEDIMENTS: A COMPARISON OF TWO ESTUARINE CONTINUUMS

EPA Science Inventory

The microbial diversity in estuarine sediments of the Altamaha and Savannah Rivers in Georgia were compared temporally and spatially using phospholipid fatty acid (PLFA) analysis. Surface sediment samples collected along a salinity gradient were also analyzed for ATP, TOC, and C ...

Dynamics of bacterial assemblages and removal of polycyclic aromatic hydrocarbons in oil-contaminated coastal marine sediments subjected to contrasted oxygen regimes.

PubMed

Militon, Cécile; Jézéquel, Ronan; Gilbert, Franck; Corsellis, Yannick; Sylvi, Léa; Cravo-Laureau, Cristiana; Duran, Robert; Cuny, Philippe

2015-10-01

To study the impact of oxygen regimes on the removal of polycylic aromatic hydrocarbons (PAHs) in oil-spill-affected coastal marine sediments, we used a thin-layer incubation method to ensure that the incubated sediment was fully oxic, anoxic, or was influenced by oxic-anoxic switches without sediment stirring. Hydrocarbon content and microbial assemblages were followed during 60 days to determine PAH degradation kinetics and microbial community dynamics according to the oxygenation regimes. The highest PAH removal, with 69 % reduction, was obtained at the end of the experiment under oxic conditions, whereas weaker removals were obtained under oscillating and anoxic conditions (18 and 12 %, respectively). Bacterial community structure during the experiment was determined using a dual 16S rRNA genes/16S rRNA transcripts approach, allowing the characterization of metabolically active bacteria responsible for the functioning of the bacterial community in the contaminated sediment. The shift of the metabolically active bacterial communities showed that the selection of first responders belonged to Pseudomonas spp. and Labrenzia sp. and included an unidentified Deltaproteobacteria-irrespective of the oxygen regime-followed by the selection of late responders adapted to the oxygen regime. A novel unaffiliated phylotype (B38) was highly active during the last stage of the experiment, at which time, the low-molecular-weight (LMW) PAH biodegradation rates were significant for permanent oxic- and oxygen-oscillating conditions, suggesting that this novel phylotype plays an active role during the restoration phase of the studied ecosystem.

Mechanisms for chelator stimulation of microbial Fe(III) -oxide reduction

USGS Publications Warehouse

Lovley, D.R.; Woodward, J.C.

1996-01-01

The mechanisms by which nitrilotriacetic acid (NTA) stimulated Fe(III) reduction in sediments from a petroleum-contaminated aquifer were investigated in order to gain insight into how added Fe(III) chelators stimulate the activity of hydrocarbon-degrading, Fe(III)-reducing microorganisms in these sediments, and how naturally occurring Fe(III) chelators might promote Fe(III) reduction in aquatic sediments. NTA solubilized Fe(III) from the aquifer sediments. NTA stimulation of microbial Fe(III) reduction did not appear to be the result of making calcium, magnesium, potassium, or trace metals more available to the microorganisms. Stimulation of Fe(III) reduction could not be attributed to NTA serving as a source of carbon or fixed nitrogen for Fe(III)-reducing bacteria as NTA was not degraded in the sediments. Studies with the Fe(III)-reducing microorganism, Geobacter metallireducens, and pure Fe(III)-oxide forms, demonstrated that NTA stimulated the reduction of a variety of Fe(III) forms, including highly crystalline Fe(III)-oxides such as goethite and hematite. The results suggest that NTA solubilization of insoluble Fe(III)-oxide is an important mechanism for the stimulation of Fe(III) reduction by NTA in aquifer sediments.

DEEP BIOSPHERE. Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor.

PubMed

Inagaki, F; Hinrichs, K-U; Kubo, Y; Bowles, M W; Heuer, V B; Hong, W-L; Hoshino, T; Ijiri, A; Imachi, H; Ito, M; Kaneko, M; Lever, M A; Lin, Y-S; Methé, B A; Morita, S; Morono, Y; Tanikawa, W; Bihan, M; Bowden, S A; Elvert, M; Glombitza, C; Gross, D; Harrington, G J; Hori, T; Li, K; Limmer, D; Liu, C-H; Murayama, M; Ohkouchi, N; Ono, S; Park, Y-S; Phillips, S C; Prieto-Mollar, X; Purkey, M; Riedinger, N; Sanada, Y; Sauvage, J; Snyder, G; Susilawati, R; Takano, Y; Tasumi, E; Terada, T; Tomaru, H; Trembath-Reichert, E; Wang, D T; Yamada, Y

2015-07-24

Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ~40° to 60°C sediment associated with lignite coal beds at ~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers, cultivation data, and gas compositions. Concentrations of indigenous microbial cells below 1.5 km ranged from <10 to ~10(4) cells cm(-3). Peak concentrations occurred in lignite layers, where communities differed markedly from shallower subseafloor communities and instead resembled organotrophic communities in forest soils. This suggests that terrigenous sediments retain indigenous community members tens of millions of years after burial in the seabed. Copyright © 2015, American Association for the Advancement of Science.

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea).

PubMed

Wang, Yong; Li, Jiang Tao; He, Li Sheng; Yang, Bo; Gao, Zhao Ming; Cao, Hui Luo; Batang, Zenon; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

2015-01-01

In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin.

The life sulfuric: microbial ecology of sulfur cycling in marine sediments

PubMed Central

Wasmund, Kenneth; Mußmann, Marc

2017-01-01

Summary Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular‐ and ecosystem‐level processes. Sulfur‐transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate‐rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep‐subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. PMID:28419734

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea)

PubMed Central

Wang, Yong; Li, Jiang Tao; He, Li Sheng; Yang, Bo; Gao, Zhao Ming; Cao, Hui Luo; Batang, Zenon; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

2015-01-01

In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin. PMID:26485717

Potential for Ureolytically Driven Calcite Precipitation to Remediate Strontium-90 at the Hanford 100-N Area

NASA Astrophysics Data System (ADS)

Fujita, Y.; Taylor, J. L.; Wendt, L.; Reed, D.; Smith, R. W.

2009-12-01

A groundwater plume of Strontium-90 at the 100-N Springs Area of the U. S. Department of Energy’s Hanford Reservation in Washington is discharging into the Columbia River. Previous pump and treat activities to remove the 90Sr were ineffective and consequently discontinued; immobilization of the contaminant in situ is preferable, but no proven methods to accomplish this objective currently exist. This study was a preliminary assessment of the feasibility at the 100-N Area of a novel in situ remediation approach for 90Sr, where microbial urea hydrolysis is used to drive the precipitation of calcite and the co-precipitation of strontium in the calcite. Water quality data from the 100-N site indicated that geochemical conditions at the site were conducive to stable calcite precipitation, and groundwater and sediment samples from the site were examined to assess the urea hydrolyzing capabilities of the native microbial populations. Estimated average numbers of ureolytic organisms in the groundwater, determined using cultivation-based tests (Most Probable Number) for urease activity, ranged from 72 to 1,100 cells mL-1. Estimated numbers of ureC gene targets in the water samples, as determined by quantitative polymerase chain reaction (qPCR) assays, ranged from 850 to 17,600 copies mL-1; the ureC gene codes for the catalytic subunit of urease. In the sediment samples, ureC gene targets ranged from non-detectable to 925,000 copies g-1 of sediment. For both water and sediment, the number of ureolytic cells (estimated by qPCR) generally amounted to < 5% of the total microbial cell numbers. Nevertheless, estimates of in situ ureolysis rates using trace levels of 14C-labeled urea added to the groundwater and sediment samples in the laboratory indicate that significant urea hydrolyzing activity exists in the 100-N subsurface. Normalizing the measured urea hydrolysis rates to 1 L of in situ pore space resulted in hydrolysis rates on the order of 9.5 nmol L-1 hr-1 and 170 to 2,500 nmol L-1 hr-1 for groundwater and sediments, respectively. The results suggest that the majority (99%) of the in situ urea hydrolyzing potential is associated with organisms attached to the sediments. A mixed kinetic-equilibrium model for ureolytically driven calcite precipitation was developed and parameterized using available characterization data for the 100-N site. The model was used to simulate the effects of urea treatment on the 100-N subsurface, and predict the quantities of calcite precipitated and Sr removed as a co-precipitate. Together, the microbial characterization data and geochemical modeling suggest that the Hanford 100-N area has the requisite microbial geochemical characteristics for application of the ureolytically driven calcite precipitation remediation approach for 90Sr.

Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability.

PubMed

Brannen-Donnelly, Kathleen; Engel, Annette S

2015-01-01

Unchanging physicochemical conditions and nutrient sources over long periods of time in cave and karst subsurface habitats, particularly aquifers, can support stable ecosystems, termed autochthonous microbial endokarst communities (AMEC). AMEC existence is unknown for other karst settings, such as epigenic cave streams. Conceptually, AMEC should not form in streams due to faster turnover rates and seasonal disturbances that have the capacity to transport large quantities of water and sediment and to change allochthonous nutrient and organic matter sources. Our goal was to investigate whether AMEC could form and persist in hydrologically active, epigenic cave streams. We analyzed bacterial diversity from cave water, sediments, and artificial substrates (Bio-Traps®) placed in the cave at upstream and downstream locations. Distinct communities existed for the water, sediments, and Bio-Trap® samplers. Throughout the study period, a subset of community members persisted in the water, regardless of hydrological disturbances. Stable habitat conditions based on flow regimes resulted in more than one contemporaneous, stable community throughout the epigenic cave stream. However, evidence for AMEC was insufficient for the cave water or sediments. Community succession, specifically as predictable exogenous heterotrophic microbial community succession, was evident from decreases in community richness from the Bio-Traps®, a peak in Bio-Trap® community biomass, and from changes in the composition of Bio-Trap® communities. The planktonic community was compositionally similar to Bio-Trap® initial colonizers, but the downstream Bio-Trap® community became more similar to the sediment community at the same location. These results can help in understanding the diversity of planktonic and attached microbial communities from karst, as well as microbial community dynamics, stability, and succession during disturbance or contamination responses over time.

Nitrogen cycling processes and microbial community composition in bed sediments in the Yukon River at Pilot Station

USGS Publications Warehouse

Repert, Deborah A.; Underwood, Jennifer C.; Smith, Richard L.; Song, Bongkeun

2014-01-01

Information on the contribution of nitrogen (N)-cycling processes in bed sediments to river nutrient fluxes in large northern latitude river systems is limited. This study examined the relationship between N-cycling processes in bed sediments and N speciation and loading in the Yukon River near its mouth at the Bering Sea. We conducted laboratory bioassays to measure N-cycling processes in sediment samples collected over distinct water cycle seasons. In conjunction, the microbial community composition in the bed sediments using genes involved in N-cycling (narG, napA, nosZ, and amoA) and 16S rRNA gene pyrosequences was examined. Temporal variation was observed in net N mineralization, nitrate uptake, and denitrification rate potentials and correlated strongly with sediment carbon (C) and extractable N content and microbial community composition rather than with river water nutrient concentrations. The C content of the bed sediment was notably impacted by the spring flood, ranging from 1.1% in the midst of an ice-jam to 0.1% immediately after ice-out, suggesting a buildup of organic material (OM) prior to scouring of the bed sediments during ice break up. The dominant members of the microbial community that explained differences in N-processing rates belonged to the genera Crenothrix,Flavobacterium, and the family of Comamonadaceae. Our results suggest that biogeochemical processing rates in the bed sediments appear to be more coupled to hydrology, nutrient availability in the sediments, and microbial community composition rather than river nutrient concentrations at Pilot Station.

Morphology and ultrastructure of epilithic versus cryptic, microbial growth in lower Cambrian phosphorites from the Montagne Noire, France.

PubMed

Alvaro, J J; Clausen, S

2010-03-01

The lower Cambrian grainy phosphorites of the northern Montagne Noire occur interbedded with grey to black, laminated to massive shales and limestones deposited along the edge of a continental shelf, associated with slope-related facies and unstable substrates. The concentration of phosphate took place by repeated alternations of low sedimentation rates and condensation (hardgrounds), in situ early-diagenetic precipitation of fluorapatite, winnowing and polyphase reworking of previously phosphatized skeletons and hardground-derived clasts. The succession of repeated cycles of sedimentation, phosphate concentration, and reworking led to multi-event phosphate deposits rich in allochthonous particles. Phosphogenesis was primarily mediated by microbial activity, which is evidenced by the abundance of phosphatized putative microbial remains. These occur as smooth and segmented filaments, sheaths, and ovoid-shaped coccoids. These simple morphologies commonly form composite frameworks as a result of their aggregation and entanglement, leading to the record of biofilms, microbial mats, and complex networks. These infested the calcitic skeletonized microfossils that littered the substrate. Microbial activity evidences epilithic (anisotropic coatings on skeletons), euendolithic (perforating skeletal walls), and cryptoendolithic (lining inter- and intraparticulate pores) strategies, the latter dominated by bundles of filaments and globular clusters that grew along the cavities of helcionellids and hyoliths. According to their epilithic versus cryptic strategies, microbial populations that penetrated and dwelled inside hard skeletal substrates show different network and colonial morphologies. These early Cambrian shell concentrations were the loci of a stepwise colonization made by saprophytic to mutualistic, cyanobacterial-fungal consortia. Their euendolithic and cryptoendolithic ecological niches provided microbial refugia to manage the grazing impact mainly led by metazoans.

The role of certain infauna and vascular plants in the mediation of redox reactions in marine sediments

NASA Technical Reports Server (NTRS)

Hines, Mark E.

1992-01-01

The mechanisms by which certain animals and plants affect redox processes in sediments was examined by studying three environments: (1) subtidal sediments dominated by the deposit-feeding polychaete Heteromastus filiformis; (2) a saltmarsh inhabited by the tall form of Spartina alterniflora; and (3) tropical carbonate sediments inhabited by three species of seagrasses. S-35-sulfide production rates were compared to pool sizes of dissolved sulfide and dissolved iron. In all of the sediments studied, rates of sulfide reduction were enhanced by macroorganisms while the rate of turnover of dissolved sulfide increased. The polychaete enhanced microbial activity and redox cycling primarily by subducting particles of organic matter and oxidized iron during sediment reworking. The Spartina species enhanced anaerobic activity by transporting primarily dissolved organic matter and oxidants. Although the final result of both animal and plant activities was the enhancement of sub-surface cycling of sulfur and iron, decreased dissolved sulfide and increased dissolved iron concentrations, the mechanisms which produced these results differed dramatically.

Effect of biostimulation on the microbial community in PCB-contaminated sediments through periodic amendment of sediment with iron.

PubMed

Srinivasa Varadhan, A; Khodadoust, Amid P; Brenner, Richard C

2011-10-01

Reductive dehalogenation of polychlorinated biphenyls (PCBs) by indigenous dehalorespiring microorganisms in contaminated sediments may be enhanced via biostimulation by supplying hydrogen generated through the anaerobic corrosion of elemental iron added to the sediment. In this study, the effect of periodic amendment of sediment with various dosages of iron on the microbial community present in sediment was investigated using phospholipid fatty acid analysis (PLFA) over a period of 18 months. Three PCB-contaminated sediments (two freshwater lake sediments and one marine sediment) were used. Signature biomarker analysis of the microbial community present in all three sediments revealed the enrichment of Dehalococcoides species, the population of which was sustained for a longer period of time when the sediment microcosms were amended with the lower dosage of iron (0.01 g iron per g dry sediment) every 6 months as compared to the blank system (without iron). Lower microbial stress levels were reported for the system periodically amended with 0.01 g of iron per g dry sediment every 6 months, thus reducing the competition from other hydrogen-utilizing microorganisms like methanogens, iron reducers, and sulfate reducers. The concentration of hydrogen in the system was found to be an important factor influencing the shift in microbial communities in all sediments with time. Periodic amendment of sediment with larger dosages of iron every 3 months resulted in the early prevalence of Geobacteraceae and sulfate-reducing bacteria followed by methanogens. An average pH of 8.4 (range of 8.2-8.6) and an average hydrogen concentration of 0.75% (range of 0.3-1.2%) observed between 6 and 15 months of the study were found to be conducive to sustaining the population of Dehalococcoides species in the three sediments amended with 0.01 g iron per g dry sediment. Biostimulation of indigenous PCB dechlorinators by the periodic amendment of contaminated sediments with low dosages of iron metal may therefore be an effective technology for remediation of PCB-contaminated sediments.

A bench-scale assessment for phosphorus release control of sediment by an oxygen-releasing compound (ORC).

PubMed

Yang, Jie; Lin, Feng K; Yang, Lei; Hua, Dan Y

2015-01-01

The effects of oxygen-releasing compound (ORC) on the control of phosphorus (P) release as well as the spatial and temporal distribution of P fractions in sediment were studied through a bench-scale test. An ORC with an extended oxygen-releasing capacity was prepared. The results of the oxygen-releasing test showed that the ORC provided a prolonged period of oxygen release with a highly effective oxygen content of 60.6% when compared with powdery CaO2. In the bench-scale test, an ORC dose of 180 g·m(-2) provided a higher inhibition efficiency for P release within 50 days. With the application of the ORC, the dissolved oxygen (DO) concentration and redox potential (ORP) of the overlying water were notably improved, and the dissolved total phosphorus (DTP) was maintained below 0.689 mg·L(-1) compared to 2.906 mg·L(-1) without the ORC treatment. According to the P fractions distribution, the summation of all detectable P fractions in each sediment layer exhibited an enhanced accumulation tendency with the application of ORC. Higher phosphorus retention efficiencies were observed in the second and third layers of sediment from days 10 to 20 with the ORC. Phosphorus was trapped mainly in the form of iron bound P (Fe-P) and organically bound P (O-P) in sediment with the ORC, whereas the effects of the ORC on exchangeable P (EX-P), apatite-associated P (A-P) and detrital P (De-P) in the sediment sample were not significant. The microbial activities of the sediment samples demonstrated that both the dehydrogenase activity (DHA) and alkaline phosphatase activity (APA) in the upper sediment layer increased with the ORC treatment, which indicated that the mineralization of P was accelerated and the microbial biomass was increased. As the accumulation of P suppressed the release of P, the sediment exhibited an increased P retention efficiency with the application of the ORC.

Investigating the Differences in the Total and Active Microbial Community of Mid-Atlantic Ridge Sediments

NASA Astrophysics Data System (ADS)

Sobol, M. S.; Zinke, L. A.; Orcutt, B.; Mills, H. J.; Edwards, K. J.; Girguis, P. R.; Reese, B. K.

2016-02-01

Microbes in the marine deep subsurface are key mediators of many geochemical cycles. It is important to understand how microbial communities and the diversity of those communities impacts geochemical cycling. Sediment cores were collected from IODP (Integrated Ocean Drilling Program) Expedition 336 to the western flank of the mid-Atlantic ridge also referred to as North Pond. The dissolved oxygen concentration decreased with depth for 60-70 mbsf, followed by a sharp increase in oxygen until it terminated at the basement. The 16S rRNA genes (DNA) and transcripts (RNA) were extracted simultaneously using a method designed by Reese et al. (2013) to differentiate between the total and active microbial community structures, respectively, as well as correlate the putative metabolism with the geochemistry. We observed many differences between the active and total communities. Sequences most closely related to Cyanobacteria were found to dominate the total community at both sites, but were found in small numbers in the active community. The most abundant phyla in the active community were Alphaproteobacteria, which suggests that they may have high activity even though the abundance was not as great in the total community. This suggests that, even in small numbers, bacteria are capable of contributing greatly to their environment. Principal Component Analysis (PCA) and Singular Value Decomposition (SVD) showed that iron-reducing bacteria in the active (RNA) community correlated strongly with solid phase iron oxides. SVD also showed that the putative nitrate reducers in the active community were found in greater abundance where porewater NO3- and NO2- total concentrations were elevated. Overall, the active (RNA) community correlated significantly with the geochemistry whereas the total (DNA) community did not. Therefore, RNA analysis yields a more accurate representation of how microbial communities impact geochemical cycling.

PAH effects on meio- and microbial benthic communities strongly depend on bioavailability.

PubMed

Lindgren, J Fredrik; Hassellöv, Ida-Maja; Dahllöf, Ingela

2014-01-01

The effects of anthropogenic pollutants in dissimilar habitats can vary depending on differences in bioavailability. The factors determining bioavailability are not yet fully understood. This study was performed to evaluate whether analysis of total PAH concentrations in sediments is a satisfactory measurement to indicate environmental effects or if bioavailability is needed to be taken into account. We have here performed a 60-day experiment, where nominal PAH concentrations of 1,300 μg/kg sediment were added to three different marine sediments. Meiofaunal and microbial communities were analyzed for alterations in community response at 30 and 60 days. Results showed that bioavailability of PAHs varied between the three different sediments. Nonetheless, the petroleum addition gave rise to significant negative effects on all three sediments at both time points. The two direct measurements of toxicity on the microbial community, potential nitrification and denitrification, displayed a lower effect of the PAH addition in the muddy sediment at both time points, compared to the other two sediment types. No effects were seen in the analysis of meiofaunal community structure. Measurements of PAH bioavailability in the three sediment types concurred with the results from the microbial community, revealing a lower bioavailability in the muddy sediment compared to the other two sediment types, 34% compared to sandy and 18% compared to organic at day 0. At day 60 it was 61% lower compared to sandy and 20% lower compared to organic. The negative effects of the PAH addition on the microbial nitrogen cycle were in six out of eight cases best correlated to the amount of alkylated bioavailable PAH in the sediments, and thus microbial nitrogen cycle is a possible good indicator for assessing PAH-induced stress. The results presented here have implications for risk analysis studies of petroleum-contaminated marine sediments; consequently, sediment characteristics and its effects on bioavailability are important to include. In addition, these results add to the understanding that bioavailability measurements of PAHs are a more correct assessment compared to measurements of total PAH concentrations, and need to be included when estimating effects of PAHs in marine benthic communities. Copyright © 2013 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Tao; Kukkadapu, Ravi K.; Griffin, Aron M.

Fe(III)-oxides and Fe(III)-bearing phyllosilicates are the two major iron sources utilized as electron acceptors by dissimilatory iron-reducing bacteria (DIRB) in anoxic soils and sediments. Although there have been many studies of microbial Fe(III)-oxide and Fe(III)-phyllosilicate reduction with both natural and specimen materials, no controlled experimental information is available on the interaction between these two phases when both are available for microbial reduction. In this study, the model DIRB Geobacter sulfurreducens was used to examine the pathways of Fe(III) reduction in Fe(III)-oxide stripped subsurface sediment that was coated with different amounts of synthetic high surface area goethite. Cryogenic (12K) 57Fe Mössbauermore » spectroscopy was used to determine changes in the relative abundances of Fe(III)-oxide, Fe(III)-phyllosilicate, and phyllosilicate-associated Fe(II) (Fe(II)-phyllosilicate) in bioreduced samples. Analogous Mössbauer analyses were performed on samples from abiotic Fe(II) sorption experiments in which sediments were exposed to a quantity of exogenous soluble Fe(II) (FeCl22H2O) comparable to the amount of Fe(II) produced during microbial reduction. A Fe partitioning model was developed to analyze the fate of Fe(II) and assess the potential for abiotic Fe(II)-catalyzed reduction of Fe(III)-phyllosilicatesilicates. The microbial reduction experiments indicated that although reduction of Fe(III)-oxide accounted for virtually all of the observed bulk Fe(III) reduction activity, there was no significant abiotic electron transfer between oxide-derived Fe(II) and Fe(III)-phyllosilicatesilicates, with 26-87% of biogenic Fe(II) appearing as sorbed Fe(II) in the Fe(II)-phyllosilicate pool. In contrast, the abiotic Fe(II) sorption experiments showed that 41 and 24% of the added Fe(II) engaged in electron transfer to Fe(III)-phyllosilicate surfaces in synthetic goethite-coated and uncoated sediment. Differences in the rate of Fe(II) addition and system redox potential may account for the microbial and abiotic reaction systems. Our experiments provide new insight into pathways for Fe(III) reduction in mixed Fe(III)-oxide/Fe(III)-phyllosilicate assemblages, and provide key mechanistic insight for interpreting microbial reduction experiments and field data from complex natural soils and sediments.« less

Correlating microbial community profiles with geochemical conditions in a watershed heavily contaminated by an antimony tailing pond.

PubMed

Xiao, Enzong; Krumins, Valdis; Tang, Song; Xiao, Tangfu; Ning, Zengping; Lan, Xiaolong; Sun, Weimin

2016-08-01

Mining activities have introduced various pollutants to surrounding aquatic and terrestrial environments, causing adverse impacts to the environment. Indigenous microbial communities are responsible for the biogeochemical cycling of pollutants in diverse environments, indicating the potential for bioremediation of such pollutants. Antimony (Sb) has been extensively mined in China and Sb contamination in mining areas has been frequently encountered. To date, however, the microbial composition and structure in response to Sb contamination has remained overlooked. Sb and As frequently co-occur in sulfide-rich ores, and co-contamination of Sb and As is observed in some mining areas. We characterized, for the first time, the microbial community profiles and their responses to Sb and As pollution from a watershed heavily contaminated by Sb tailing pond in Southwest China. The indigenous microbial communities were profiled by high-throughput sequencing from 16 sediment samples (535,390 valid reads). The comprehensive geochemical data (specifically, physical-chemical properties and different Sb and As extraction fractions) were obtained from river water and sediments at different depths as well. Canonical correspondence analysis (CCA) demonstrated that a suite of in situ geochemical and physical factors significantly structured the overall microbial community compositions. Further, we found significant correlations between individual phylotypes (bacterial genera) and the geochemical fractions of Sb and As by Spearman rank correlation. A number of taxonomic groups were positively correlated with the Sb and As extractable fractions and various Sb and As species in sediment, suggesting potential roles of these phylotypes in Sb biogeochemical cycling. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbial community stratification controlled by the subseafloor fluid flow and geothermal gradient at the Iheya North hydrothermal field in the Mid-Okinawa Trough (Integrated Ocean Drilling Program Expedition 331).

PubMed

Yanagawa, Katsunori; Breuker, Anja; Schippers, Axel; Nishizawa, Manabu; Ijiri, Akira; Hirai, Miho; Takaki, Yoshihiro; Sunamura, Michinari; Urabe, Tetsuro; Nunoura, Takuro; Takai, Ken

2014-10-01

The impacts of lithologic structure and geothermal gradient on subseafloor microbial communities were investigated at a marginal site of the Iheya North hydrothermal field in the Mid-Okinawa Trough. Subsurface marine sediments composed of hemipelagic muds and volcaniclastic deposits were recovered through a depth of 151 m below the seafloor at site C0017 during Integrated Ocean Drilling Program Expedition 331. Microbial communities inferred from 16S rRNA gene clone sequencing in low-temperature hemipelagic sediments were mainly composed of members of the Chloroflexi and deep-sea archaeal group. In contrast, 16S rRNA gene sequences of marine group I Thaumarchaeota dominated the microbial phylotype communities in the coarse-grained pumiceous gravels interbedded between the hemipelagic sediments. Based on the physical properties of sediments such as temperature and permeability, the porewater chemistry, and the microbial phylotype compositions, the shift in the physical properties of the sediments is suggested to induce a potential subseafloor recharging flow of oxygenated seawater in the permeable zone, leading to the generation of variable chemical environments and microbial communities in the subseafloor habitats. In addition, the deepest section of sediments under high-temperature conditions (∼90°C) harbored the sequences of an uncultivated archaeal lineage of hot water crenarchaeotic group IV that may be associated with the high-temperature hydrothermal fluid flow. These results indicate that the subseafloor microbial community compositions and functions at the marginal site of the hydrothermal field are highly affected by the complex fluid flow structure, such as recharging seawater and underlying hydrothermal fluids, coupled with the lithologic transition of sediments. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments.

PubMed

Currie, Ashleigh R; Tait, Karen; Parry, Helen; de Francisco-Mora, Beatriz; Hicks, Natalie; Osborn, A Mark; Widdicombe, Steve; Stahl, Henrik

2017-01-01

Marine ecosystems are exposed to a range of human-induced climate stressors, in particular changing carbonate chemistry and elevated sea surface temperatures as a consequence of climate change. More research effort is needed to reduce uncertainties about the effects of global-scale warming and acidification for benthic microbial communities, which drive sedimentary biogeochemical cycles. In this research, mesocosm experiments were set up using muddy and sandy coastal sediments to investigate the independent and interactive effects of elevated carbon dioxide concentrations (750 ppm CO 2 ) and elevated temperature (ambient +4°C) on the abundance of taxonomic and functional microbial genes. Specific quantitative PCR primers were used to target archaeal, bacterial, and cyanobacterial/chloroplast 16S rRNA in both sediment types. Nitrogen cycling genes archaeal and bacterial ammonia monooxygenase ( amoA ) and bacterial nitrite reductase ( nirS ) were specifically targeted to identify changes in microbial gene abundance and potential impacts on nitrogen cycling. In muddy sediment, microbial gene abundance, including amoA and nirS genes, increased under elevated temperature and reduced under elevated CO 2 after 28 days, accompanied by shifts in community composition. In contrast, the combined stressor treatment showed a non-additive effect with lower microbial gene abundance throughout the experiment. The response of microbial communities in the sandy sediment was less pronounced, with the most noticeable response seen in the archaeal gene abundances in response to environmental stressors over time. 16S rRNA genes ( amoA and nirS ) were lower in abundance in the combined stressor treatments in sandy sediments. Our results indicated that marine benthic microorganisms, especially in muddy sediments, are susceptible to changes in ocean carbonate chemistry and seawater temperature, which ultimately may have an impact upon key benthic biogeochemical cycles.

Microbial Community Stratification Controlled by the Subseafloor Fluid Flow and Geothermal Gradient at the Iheya North Hydrothermal Field in the Mid-Okinawa Trough (Integrated Ocean Drilling Program Expedition 331)

PubMed Central

Breuker, Anja; Schippers, Axel; Nishizawa, Manabu; Ijiri, Akira; Hirai, Miho; Takaki, Yoshihiro; Sunamura, Michinari; Urabe, Tetsuro; Nunoura, Takuro; Takai, Ken

2014-01-01

The impacts of lithologic structure and geothermal gradient on subseafloor microbial communities were investigated at a marginal site of the Iheya North hydrothermal field in the Mid-Okinawa Trough. Subsurface marine sediments composed of hemipelagic muds and volcaniclastic deposits were recovered through a depth of 151 m below the seafloor at site C0017 during Integrated Ocean Drilling Program Expedition 331. Microbial communities inferred from 16S rRNA gene clone sequencing in low-temperature hemipelagic sediments were mainly composed of members of the Chloroflexi and deep-sea archaeal group. In contrast, 16S rRNA gene sequences of marine group I Thaumarchaeota dominated the microbial phylotype communities in the coarse-grained pumiceous gravels interbedded between the hemipelagic sediments. Based on the physical properties of sediments such as temperature and permeability, the porewater chemistry, and the microbial phylotype compositions, the shift in the physical properties of the sediments is suggested to induce a potential subseafloor recharging flow of oxygenated seawater in the permeable zone, leading to the generation of variable chemical environments and microbial communities in the subseafloor habitats. In addition, the deepest section of sediments under high-temperature conditions (∼90°C) harbored the sequences of an uncultivated archaeal lineage of hot water crenarchaeotic group IV that may be associated with the high-temperature hydrothermal fluid flow. These results indicate that the subseafloor microbial community compositions and functions at the marginal site of the hydrothermal field are highly affected by the complex fluid flow structure, such as recharging seawater and underlying hydrothermal fluids, coupled with the lithologic transition of sediments. PMID:25063666

Identification of active dehalorespiring microbial populations in anoxic river sediment by RNA-based stable isotope probing

NASA Astrophysics Data System (ADS)

Kittelmann, S.; Friedrich, M. W.

2005-12-01

Tetrachloroethene (perchloroethylene, PCE), a persistent contaminant in aquifers, soils and sediments, can be reductively dechlorinated by anaerobic microorganisms in a process referred to as dehalorespiration. However, the biodiversity of dehalorespiring microorganisms and their distribution especially in pristine environments is largely unexplored. Therefore, the aim of this study was to detect potentially novel PCE-dehalorespiring microorganisms by using stable isotope probing (SIP), a technique that allows to directly identify the function of uncultivated microbial populations. We simulated a PCE contamination by incubating pristine river sediment in the presence of PCE at a steady, low aqueous concentration (20 μM). Dehalogenation activity in microcosms (20 nmol cis-dichloroethene per ml slurry per day formed) was detected already after 4 weeks at 20°C with sediment indigenous electron donors. The microbial community in sediment incubations was probed with 13C-labelled acetate (0.5 mM) as electron donor and carbon source at 15°C for 3 days. After RNA extraction, "heavy" 13C-rRNA and light 12C-rRNA were separated by isopycnic centrifugation, and Bacteria-related populations in gradient fractions were characterised by terminal restriction fragment length polymorphism analysis and cloning. In heavy gradient fractions from the microcosm with PCE, we detected a prominent 506-bp terminal restriction fragment (T-RF) and a few minor T-RFs only. In contrast, in the control without PCE, Bacteria-specific rRNA was restricted to light gradient fractions, and the prominent T-RFs found in the PCE-dechlorinating microcosm were of minor importance. Apparently, 13C-acetate was incorporated into bacterial rRNA more effectively in PCE-respiring microcosms. Thus, rRNA-SIP provides strong evidence for the presence of PCE-dehalorespiring, 13C-acetate-utilising populations in river sediment microcosms. Cloning/sequencing analysis identified the prominent members of the heavy gradient fractions as members of the phylum Chloroflexi only distantly related to cultivated dechlorinating Dehalococcides spp.

[Effects of outbreak and extinction of algal blooms on the microbial community structure in sediments of Chaohu Lake].

PubMed

Diao, Xiao-jun; Li, Yi-wei; Wang, Shu-guang

2015-01-01

Although impacts of algal bloom on the physicochemical and biological properties of water and sediment in many lakes have been largely studied, less attention is paid to the impact of outbreak and extinction of algal blooms on the microbial community structure in sediment. In this study, outbreak and extinction of algal blooms and their effects on the microbial community structure in sediment of Chaohu Lake were studied by PCR-DGGE method. The results showed that algal blooms formed between May 15 and June 20, sustained from June 20 to September 5, and then went into extinction. In the region without algal blooms, PCR-DGGE analysis showed that microbial species, Shannon-Wiener diversity index and Simpson dominance index changed slightly over time; moreover, the microbial community structure had high similarity during the whole study. Temperature may be the main factor affecting the fluctuation of the microbial community structure in this region. In the region with algal blooms, however, microbial species and Shannon-Wiener diversity index were higher during the formation and extinction of algal blooms and lower in the sustaining blooms stage than those in the region without algal blooms. But the Simpson dominance index showed the opposite trend over time. In addition, the microbial community structure had low similarity during the whole study. The results suggested that outbreak and extinction of algal blooms produced different effects on the microbial community structure and the dominant microbial species, which may be related to the variation of water properties caused by temperature and algal blooms. This study showed that outbreak and extinction of algal blooms caused different effects on microbes in lake sediment, and this is significantly important to deeply evaluate the effects of algal bloom on the aquatic ecosystem of the lake and effectively control algal blooms using sediment microbes.

Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China.

PubMed

Liu, Jun; Chen, Xi; Shu, Hao-Yue; Lin, Xue-Rui; Zhou, Qi-Xing; Bramryd, Torleif; Shu, Wen-Sheng; Huang, Li-Nan

2018-04-01

The release of toxic organic pollutants and heavy metals by primitive electronic waste (e-waste) processing to waterways has raised significant concerns, but little is known about their potential ecological effects on aquatic biota especially microorganisms. We characterized the microbial community composition and diversity in sediments sampled along two rivers consistently polluted by e-waste, and explored how community functions may respond to the complex combined pollution. High-throughput 16S rRNA gene sequencing showed that Proteobacteria (particularly Deltaproteobacteria) dominated the sediment microbial assemblages followed by Bacteroidetes, Acidobacteria, Chloroflexi and Firmicutes. PICRUSt metagenome inference provided an initial insight into the metabolic potentials of these e-waste affected communities, speculating that organic pollutants degradation in the sediment might be mainly performed by some of the dominant genera (such as Sulfuricurvum, Thiobacillus and Burkholderia) detected in situ. Statistical analyses revealed that toxic organic compounds contributed more to the observed variations in sediment microbial community structure and predicted functions (24.68% and 8.89%, respectively) than heavy metals (12.18% and 4.68%), and Benzo(a)pyrene, bioavailable lead and electrical conductivity were the key contributors. These results have shed light on the microbial assemblages in e-waste contaminated river sediments, indicating a potential influence of e-waste pollution on the microbial community structure and function in aquatic ecosystems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water.

PubMed

Lu, Xiao-Ming; Chen, Chang; Zheng, Tian-Ling

2017-05-01

Pyrosequencing and metagenomic profiling were used to assess the phylogenetic and functional characteristics of microbial communities residing in sediments collected from the estuaries of Rivers Oujiang (OS) and Jiaojiang (JS) in the western region of the East China Sea. Another sediment sample was obtained from near the shore far from estuaries, used for contrast (CS). Characterization of estuary sediment bacterial communities showed that toxic chemicals potentially reduced the natural variability in microbial communities, while they increased the microbial metabolic enzymes and pathways. Polycyclic aromatic hydrocarbons (PAHs) and nitrobenzene were negatively correlated with the bacterial community variation. The dominant class in the sediments was Gammaproteobacteria. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) enzyme profiles, dominant enzymes were found in estuarine sediments, which increased greatly, such as 2-oxoglutarate synthase, acetolactate synthase, inorganic diphosphatase, and aconitate hydratase. In KEGG pathway profiles, most of the pathways were also dominated by specific metabolism in these sediments and showed a marked increase, for instance alanine, aspartate, and glutamate metabolism, carbon fixation pathways in prokaryotes, and aminoacyl-tRNA biosynthesis. The estuarine sediment bacterial diversity varied with the polluted river water inputs. In the estuary receiving river water from the more seriously polluted River Oujiang, the sediment bacterial community function was more severely affected.

Bacterial dominance in subseafloor sediments characterized by methane hydrates

USGS Publications Warehouse

Briggs, Brandon R.; Inagaki, Fumio; Morono, Yuki; Futagami, Taiki; Huguet, Carme; Rosell-Mele, Antoni; Lorenson, T.D.; Colwell, Frederick S.

2015-01-01

The degradation of organic carbon in subseafloor sediments on continental margins contributes to the largest reservoir of methane on Earth. Sediments in the Andaman Sea are composed of ~ 1% marine-derived organic carbon and biogenic methane is present. Our objective was to determine microbial abundance and diversity in sediments that transition the gas hydrate occurrence zone (GHOZ) in the Andaman Sea. Microscopic cell enumeration revealed that most sediment layers harbored relatively low microbial abundance (103–105 cells cm−3). Archaea were never detected despite the use of both DNA- and lipid-based methods. Statistical analysis of terminal restriction fragment length polymorphisms revealed distinct microbial communities from above, within, and below the GHOZ, and GHOZ samples were correlated with a decrease in organic carbon. Primer-tagged pyrosequences of bacterial 16S rRNA genes showed that members of the phylum Firmicutes are predominant in all zones. Compared with other seafloor settings that contain biogenic methane, this deep subseafloor habitat has a unique microbial community and the low cell abundance detected can help to refine global subseafloor microbial abundance.

[Influence of Submerged Plants on Microbial Community Structure in Sediment of Hongze Lake].

PubMed

Zhang, Ding-yu; Zhang, Ting-xi; Dong, Dan-ping; Li, De-fang; Wang, Guo-xiang

2016-05-15

Phospholipid fatty acids (PLFAs) method was applied to analyze the influence of submerged plants on sediment microbial community structure, in order to investigate the changes of sediment microbial community structure for different kinds of the submerged plants in different growth periods. Particularly, Potamogeton crispus L., Potamogeton pectinatus L and the mixed group were chosen as the typical submerged plants in Hongze Lake for investigation in this paper. The results indicated that the change of total PLFAs in different periods was significant, on the contrary, the PLFA change for different groups in the same period was insignificant. The values of G⁺ PLFA/G⁻ PLFA in the submerged plant group were also highly related to the different growth periods, which demonstrated that the root function of the submerged plant had a severe impact on the microbial community in sediment. Furthermore, some environmental factors, such as Temperature, pH, TOC and DO, were correlated to characteristic phospholipid of PLFAs in sediment, which means the environmental factors could also affect the microbial community structure.

Desulfofrigus sp. prevails in sulfate-reducing dilution cultures from sediments of the Benguela upwelling area.

PubMed

Kraft, Beate; Engelen, Bert; Goldhammer, Tobias; Lin, Yu-Shih; Cypionka, Heribert; Könneke, Martin

2013-04-01

Sediments of coastal upwelling areas are generally characterized by a high content of organic carbon that is mainly degraded via anaerobic microbial processes including sulfate reduction as a major terminal oxidation step. Despite the high importance of sulfate reduction in these sediments, the identity of sulfate-reducing bacteria (SRB) has remained almost unknown. Here, we applied a cultivation-based approach using selective enrichment conditions to study the diversity and distribution of active SRB in sediments along a transect perpendicular to the continental slope off the coast of Namibia (Meteor-cruise M76/1). To promote growth of the most abundant SRB, dilution series were prepared and amended with hydrogen, acetate, or a mixture of monomers representing typical substrates for SRB. Growth of SRB could be detected in the presence of all electron donors and from sediment down to 4 m depth. 16S rRNA gene-based DGGE analysis and sequencing revealed the predominance of SRB related to psychrophiles in particular to the genus Desulfofrigus, which made up 1 % of the total microbial community, accounting for an absolute abundance of up to 4.8 × 10(7)  cells mL(-1) . In general, the abundance of cultured SRB changed with depth and between the different sampling sites and correlated with the content of organic carbon as previously reported. Growth of chemolithotrophic SRB in relatively high dilution steps and the enrichment of methanogens as well as acetogens from deeper sediment point to a competition between hydrogen-utilizing microbial processes and their biogeochemical significance in deep sediment layers of the Benguela upwelling area. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Anaerobic Methane-Oxidizing Microbial Community in a Coastal Marine Sediment: Anaerobic Methanotrophy Dominated by ANME-3.

PubMed

Bhattarai, Susma; Cassarini, Chiara; Gonzalez-Gil, Graciela; Egger, Matthias; Slomp, Caroline P; Zhang, Yu; Esposito, Giovanni; Lens, Piet N L

2017-10-01

The microbial community inhabiting the shallow sulfate-methane transition zone in coastal sediments from marine Lake Grevelingen (The Netherlands) was characterized, and the ability of the microorganisms to carry out anaerobic oxidation of methane coupled to sulfate reduction was assessed in activity tests. In vitro activity tests of the sediment with methane and sulfate demonstrated sulfide production coupled to the simultaneous consumption of sulfate and methane at approximately equimolar ratios over a period of 150 days. The maximum sulfate reduction rate was 5 μmol sulfate per gram dry weight per day during the incubation period. Diverse archaeal and bacterial clades were retrieved from the sediment with the majority of them clustered with Euryarchaeota, Thaumarcheota, Bacteroidetes, and Proteobacteria. The 16S rRNA gene sequence analysis showed that the sediment from marine Lake Grevelingen contained anaerobic methanotrophic Archaea (ANME) and methanogens as archaeal clades with a role in the methane cycling. ANME at the studied site mainly belong to the ANME-3 clade. This study provides one of the few reports for the presence of ANME-3 in a shallow coastal sediment. Sulfate-reducing bacteria from Desulfobulbus clades were found among the sulfate reducers, however, with very low relative abundance. Desulfobulbus has previously been commonly found associated with ANME, whereas in our study, ANME-3 and Desulfobulbus were not observed simultaneously in clusters, suggesting the possibility of independent AOM by ANME-3.

Biogeochemical and microbiological characteristic of the pockmark sediments, the Gdansk Deep, The Baltic Sea

NASA Astrophysics Data System (ADS)

Pimenov, Nikolay; Kanapatskiy, Timur; Sivkov, Vadim; Toshchakov, Stepan; Korzhenkov, Aleksei; Ulyanova, Marina

2016-04-01

Comparison of the biogeochemical and microbial features was done for the gas-bearing and background sediments as well as near-bottom water of the Gdansk Deep, The Baltic Sea. Data were received in October, 2015 during 64th cruise of the R/V Akademik Mstislav Keldysh. Gas-bearing sediments were sampled within the known pockmark (Gas-Point, depth 94 m). Background sediments area (BG-Point, depth 86 m) was located several km off the pockmark area. The sulphate concentration in the pore water of the surface sediment layer (0-5 cm) of Gas-Point was 9,7 mmol/l, and sharply decreased with depth (did not exceed 1 mmol/l deeper than 50 cm). The sulphate concentration decrease at BG-Point also took place but was not so considerable. Sulphate concentration decrease is typical for the organic rich sediments of the high productive areas, both as for the methane seep areas. Fast sulphate depletion occurs due to active processes of its microbial reduction by consortium of the sulphate-reduction bacteria, which may use low-molecular organic compounds or hydrogen, formed at the different stages of the organic matter destruction; as well as within the process of the anaerobic methane oxidation by consortium of the methane-trophic archaea and sulphate-reduction bacteria. Together with sulphate concentration decrease the methane content increase, typical for the marine sediments, occurred. At the Gas-Point the methane concentration varied within 10 μmol/dm3 in the surface layer till its maximum at sediment horizon of 65 cm (5 mmol/dm3), and decreased to 1.5 mmol/dm3 at depth of 300 cm. The BG-Point maximum values were defined at sediment horizon 6 cm (2,6 μmol/dm3). Methane sulfate transition zone at the Gas-Point sediments was at 25-35 cm depth; whereas it was not defined at the BG-Point mud. High methane concentration in the gas-bearing sediments results in the formation of the methane seep from the sediments to the near-bottom water. So the Gas-Point near-bottom waters were characterized by high methane concentration (0.36-0.50 μmol/l) even in the water 2-5 m above the bottom (0.08-0.28 μmol/l), whereas at the BG-Point sediments methane concentration in the near-bottom water was 0.06-0.08 μmol/l. In order to get insights into the structure of microbial community responsible for realization of these redox processes we performed microbial community profiling using high-throughput 16S amplicon sequencing. DNA was extracted from sediments and water column in pockmark and background zones. NGS libraries were prepared with fusion primers for V4 variable region (Caporaso et al., 2012) and sequenced on the MiSeq system. Results well correlated with new data obtained from the analysis of the intensity of microbial processes. The study was financed by the Russian Scientific Fund (grant 14-37-00047). Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012 Aug;6(8):1621-4

Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing

PubMed Central

Mhuantong, Wuttichai; Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Eurwilaichitr, Lily; Tangphatsornruang, Sithichoke; Boonchayaanant, Benjaporn; Limpiyakorn, Tawan; Pattaragulwanit, Kobchai; Punmatharith, Thantip; McEvoy, John; Khan, Eakalak; Rachakornkij, Manaskorn; Champreda, Verawat

2015-01-01

The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas. PMID:26020967

Microbial ecological associations in the surface sediments of Bohai strait

NASA Astrophysics Data System (ADS)

Wang, Bin; Liu, Hongmei; Tang, Haitian; Hu, Xiaoke

2017-09-01

Microbial communities play key roles in the marine ecosystem. Despite a few studies on marine microbial communities in deep straits, ecological associations among microbial communities in the sediments of shallow straits have not been fully investigated. The Bohai Strait in northern China (average depth less than 20 m) separates the Bohai Sea from the Yellow Sea and has organic-rich sediments. In this study, in the summer of 2014, six stations across the strait were selected to explore the taxonomic composition of microbial communities and their ecological associations. The four most abundant classes were Gammaproteobacteria, Deltaproteobacteria, Bacilli and Flavobacteriia. Temperature, total carbon, depth, nitrate, fishery breeding and cold water masses influenced the microbial communities, as suggested by representational difference and composition analyses. Network analysis of microbial associations revealed that key families included Flavobacteriaceae, Pirellulaceae and Piscirickettsiaceae. Our findings suggest that the families with high phylogenetic diversity are key populations in the microbial association network that ensure the stability of microbial ecosystems. Our study contributes to a better understanding of microbial ecology in complex hydrological environments.

Deep Subseafloor Fungi as an Untapped Reservoir of Amphipathic Antimicrobial Compounds.

PubMed

Navarri, Marion; Jégou, Camille; Meslet-Cladière, Laurence; Brillet, Benjamin; Barbier, Georges; Burgaud, Gaëtan; Fleury, Yannick

2016-03-10

The evolving global threat of antimicrobial resistance requires a deep renewal of the antibiotic arsenal including the isolation and characterization of new drugs. Underexplored marine ecosystems may represent an untapped reservoir of novel bioactive molecules. Deep-sea fungi isolated from a record-depth sediment core of almost 2000 m below the seafloor were investigated for antimicrobial activities. This antimicrobial screening, using 16 microbial targets, revealed 33% of filamentous fungi synthesizing bioactive compounds with activities against pathogenic bacteria and fungi. Interestingly, occurrence of antimicrobial producing isolates was well correlated with the complexity of the habitat (in term of microbial richness), as higher antimicrobial activities were obtained at specific layers of the sediment core. It clearly highlights complex deep-sea habitats as chemical battlefields where synthesis of numerous bioactive compounds appears critical for microbial competition. The six most promising deep subseafloor fungal isolates were selected for the production and extraction of bioactive compounds. Depending on the fungal isolates, antimicrobial compounds were only biosynthesized in semi-liquid or solid-state conditions as no antimicrobial activities were ever detected using liquid fermentation. An exception was made for one fungal isolate, and the extraction procedure designed to extract amphipathic compounds was successful and highlighted the amphiphilic profile of the bioactive metabolites.

Possible roles of uncultured archaea in carbon cycling in methane-seep sediments

NASA Astrophysics Data System (ADS)

Yoshinaga, Marcos Y.; Lazar, Cassandre S.; Elvert, Marcus; Lin, Yu-Shih; Zhu, Chun; Heuer, Verena B.; Teske, Andreas; Hinrichs, Kai-Uwe

2015-09-01

Studies on microbial carbon cycling uniformly confirm that anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria represent the dominant and most active fraction of the sedimentary microbial community in methane-seep sediments. However, little is known about other frequently observed and abundant microbial taxa, their role in carbon cycling and association with the anaerobic oxidation of methane (AOM). Here, we provide a comprehensive characterization of stable carbon isotopes (δ13C) from several intact polar lipid (IPL) classes and metabolite pools in a downcore profile at a cold seep within the oxygen minimum zone off Pakistan. We aimed to evaluate microbial carbon metabolism using IPLs in relation to redox conditions, metabolites and 16S rRNA gene libraries. The 13C-depleted signature of carbon pools and microbial metabolites in pore waters (e.g., dissolved inorganic carbon, lactate and acetate) demonstrated high accumulation of AOM-associated biomass and subsequent turnover thereof. ANMEs accounted for a small fraction of the archaeal 16S rRNA gene survey, whereas sequences of other uncultured benthic archaea dominated the clone libraries, particularly the Marine Benthic Group D. On the basis of lipid diversity and carbon isotope information, we suggest that structurally diverse phospho- and glycolipids, including the recently identified unsaturated tetraethers that are particularly abundant in this setting, are likely derived from archaea other than ANMEs. Through the evaluation of δ13C values of individual IPL, our results indicate heterotrophy as a possible metabolic pathway of archaea in these AOM-dominated sediments.

Dredging effects on selected nutrient concentrations and ecoenzymatic activity in two drainage ditch sediments in the lower Mississippi River Valley

USDA-ARS?s Scientific Manuscript database

Agricultural drainage ditches are conduits between production acreage and receiving aquatic systems. Often overlooked for their mitigation capabilities, agricultural drainage ditches provide an important role for nutrient transformation via microbial metabolism. Variations in ecoenzyme activities ...

Harnessing a methane‐fueled, sediment‐free mixed microbial community for utilization of distributed sources of natural gas

PubMed Central

Marlow, Jeffrey J.; Kumar, Amit; Enalls, Brandon C.; Reynard, Linda M.; Tuross, Noreen

2018-01-01

Abstract Harnessing the metabolic potential of uncultured microbial communities is a compelling opportunity for the biotechnology industry, an approach that would vastly expand the portfolio of usable feedstocks. Methane is particularly promising because it is abundant and energy‐rich, yet the most efficient methane‐activating metabolic pathways involve mixed communities of anaerobic methanotrophic archaea and sulfate reducing bacteria. These communities oxidize methane at high catabolic efficiency and produce chemically reduced by‐products at a comparable rate and in near‐stoichiometric proportion to methane consumption. These reduced compounds can be used for feedstock and downstream chemical production, and at the production rates observed in situ they are an appealing, cost‐effective prospect. Notably, the microbial constituents responsible for this bioconversion are most prominent in select deep‐sea sediments, and while they can be kept active at surface pressures, they have not yet been cultured in the lab. In an industrial capacity, deep‐sea sediments could be periodically recovered and replenished, but the associated technical challenges and substantial costs make this an untenable approach for full‐scale operations. In this study, we present a novel method for incorporating methanotrophic communities into bioindustrial processes through abstraction onto low mass, easily transportable carbon cloth artificial substrates. Using Gulf of Mexico methane seep sediment as inoculum, optimal physicochemical parameters were established for methane‐oxidizing, sulfide‐generating mesocosm incubations. Metabolic activity required >∼40% seawater salinity, peaking at 100% salinity and 35 °C. Microbial communities were successfully transferred to a carbon cloth substrate, and rates of methane‐dependent sulfide production increased more than threefold per unit volume. Phylogenetic analyses indicated that carbon cloth‐based communities were substantially streamlined and were dominated by Desulfotomaculum geothermicum. Fluorescence in situ hybridization microscopy with carbon cloth fibers revealed a novel spatial arrangement of anaerobic methanotrophs and sulfate reducing bacteria suggestive of an electronic coupling enabled by the artificial substrate. This system: 1) enables a more targeted manipulation of methane‐activating microbial communities using a low‐mass and sediment‐free substrate; 2) holds promise for the simultaneous consumption of a strong greenhouse gas and the generation of usable downstream products; and 3) furthers the broader adoption of uncultured, mixed microbial communities for biotechnological use. PMID:29460958

Anaerobic Methane Oxidation Driven by Microbial Reduction of Natural Organic Matter in a Tropical Wetland

PubMed Central

Valenzuela, Edgardo I.; Prieto-Davó, Alejandra; López-Lozano, Nguyen E.; Hernández-Eligio, Alberto; Vega-Alvarado, Leticia; Juárez, Katy; García-González, Ana Sarahí; López, Mercedes G.

2017-01-01

ABSTRACT Wetlands constitute the main natural source of methane on Earth due to their high content of natural organic matter (NOM), but key drivers, such as electron acceptors, supporting methanotrophic activities in these habitats are poorly understood. We performed anoxic incubations using freshly collected sediment, along with water samples harvested from a tropical wetland, amended with 13C-methane (0.67 atm) to test the capacity of its microbial community to perform anaerobic oxidation of methane (AOM) linked to the reduction of the humic fraction of its NOM. Collected evidence demonstrates that electron-accepting functional groups (e.g., quinones) present in NOM fueled AOM by serving as a terminal electron acceptor. Indeed, while sulfate reduction was the predominant process, accounting for up to 42.5% of the AOM activities, the microbial reduction of NOM concomitantly occurred. Furthermore, enrichment of wetland sediment with external NOM provided a complementary electron-accepting capacity, of which reduction accounted for ∼100 nmol 13CH4 oxidized · cm−3 · day−1. Spectroscopic evidence showed that quinone moieties were heterogeneously distributed in the wetland sediment, and their reduction occurred during the course of AOM. Moreover, an enrichment derived from wetland sediments performing AOM linked to NOM reduction stoichiometrically oxidized methane coupled to the reduction of the humic analogue anthraquinone-2,6-disulfonate. Microbial populations potentially involved in AOM coupled to microbial reduction of NOM were dominated by divergent biota from putative AOM-associated archaea. We estimate that this microbial process potentially contributes to the suppression of up to 114 teragrams (Tg) of CH4 · year−1 in coastal wetlands and more than 1,300 Tg · year−1, considering the global wetland area. IMPORTANCE The identification of key processes governing methane emissions from natural systems is of major importance considering the global warming effects triggered by this greenhouse gas. Anaerobic oxidation of methane (AOM) coupled to the microbial reduction of distinct electron acceptors plays a pivotal role in mitigating methane emissions from ecosystems. Given their high organic content, wetlands constitute the largest natural source of atmospheric methane. Nevertheless, processes controlling methane emissions in these environments are poorly understood. Here, we provide tracer analysis with 13CH4 and spectroscopic evidence revealing that AOM linked to the microbial reduction of redox functional groups in natural organic matter (NOM) prevails in a tropical wetland. We suggest that microbial reduction of NOM may largely contribute to the suppression of methane emissions from tropical wetlands. This is a novel avenue within the carbon cycle in which slowly decaying NOM (e.g., humic fraction) in organotrophic environments fuels AOM by serving as a terminal electron acceptor. PMID:28341676

Anaerobic Methane Oxidation Driven by Microbial Reduction of Natural Organic Matter in a Tropical Wetland.

PubMed

Valenzuela, Edgardo I; Prieto-Davó, Alejandra; López-Lozano, Nguyen E; Hernández-Eligio, Alberto; Vega-Alvarado, Leticia; Juárez, Katy; García-González, Ana Sarahí; López, Mercedes G; Cervantes, Francisco J

2017-06-01

Wetlands constitute the main natural source of methane on Earth due to their high content of natural organic matter (NOM), but key drivers, such as electron acceptors, supporting methanotrophic activities in these habitats are poorly understood. We performed anoxic incubations using freshly collected sediment, along with water samples harvested from a tropical wetland, amended with 13 C-methane (0.67 atm) to test the capacity of its microbial community to perform anaerobic oxidation of methane (AOM) linked to the reduction of the humic fraction of its NOM. Collected evidence demonstrates that electron-accepting functional groups (e.g., quinones) present in NOM fueled AOM by serving as a terminal electron acceptor. Indeed, while sulfate reduction was the predominant process, accounting for up to 42.5% of the AOM activities, the microbial reduction of NOM concomitantly occurred. Furthermore, enrichment of wetland sediment with external NOM provided a complementary electron-accepting capacity, of which reduction accounted for ∼100 nmol 13 CH 4 oxidized · cm -3 · day -1 Spectroscopic evidence showed that quinone moieties were heterogeneously distributed in the wetland sediment, and their reduction occurred during the course of AOM. Moreover, an enrichment derived from wetland sediments performing AOM linked to NOM reduction stoichiometrically oxidized methane coupled to the reduction of the humic analogue anthraquinone-2,6-disulfonate. Microbial populations potentially involved in AOM coupled to microbial reduction of NOM were dominated by divergent biota from putative AOM-associated archaea. We estimate that this microbial process potentially contributes to the suppression of up to 114 teragrams (Tg) of CH 4 · year -1 in coastal wetlands and more than 1,300 Tg · year -1 , considering the global wetland area. IMPORTANCE The identification of key processes governing methane emissions from natural systems is of major importance considering the global warming effects triggered by this greenhouse gas. Anaerobic oxidation of methane (AOM) coupled to the microbial reduction of distinct electron acceptors plays a pivotal role in mitigating methane emissions from ecosystems. Given their high organic content, wetlands constitute the largest natural source of atmospheric methane. Nevertheless, processes controlling methane emissions in these environments are poorly understood. Here, we provide tracer analysis with 13 CH 4 and spectroscopic evidence revealing that AOM linked to the microbial reduction of redox functional groups in natural organic matter (NOM) prevails in a tropical wetland. We suggest that microbial reduction of NOM may largely contribute to the suppression of methane emissions from tropical wetlands. This is a novel avenue within the carbon cycle in which slowly decaying NOM (e.g., humic fraction) in organotrophic environments fuels AOM by serving as a terminal electron acceptor. Copyright © 2017 American Society for Microbiology.

Arsenic release by indigenous bacteria Bacillus cereus from aquifer sediments at Datong Basin, northern China

NASA Astrophysics Data System (ADS)

Xie, Zuoming; Wang, Yanxin; Duan, Mengyu; Xie, Xianjun; Su, Chunli

2011-03-01

Endemic arsenic poisoning due to long-term drinking of high arsenic groundwater has been reported in Datong Basin, northern China. To investigate the effects of microbial activities on arsenic mobilization in contaminated aquifers, Bacillus cereus ( B. cereus) isolated from high arsenic aquifer sediments of the basin was used in our microcosm experiments. The arsenic concentration in the treatment with both bacteria and sodium citrate or glucose had a rapid increase in the first 18 d, and then, it declined. Supplemented with bacteria only, the concentration could increase on the second day. By contrast, the arsenic concentration in the treatment supplemented with sodium citrate or glucose was kept very low. These results indicate that bacterial activities promoted the release of arsenic in the sediments. Bacterial activities also influenced other geochemical parameters of the aqueous phase, such as pH, Eh, and the concentrations of dissolved Fe, Mn, and Al that are important controls on arsenic release. The removal of Fe, Mn, and Al from sediment samples was observed with the presence of B. cereus. The effects of microbial activities on Fe, Mn, and Al release were nearly the same as those on As mobilization. The pH values of the treatments inoculated with bacteria were lower than those without bacteria, still at alkaline levels. With the decrease of Eh values in treatments inoculated with bacteria, the microcosms became more reducing and are thus favorable for arsenic release.

Microbial communities associated with ferromanganese nodules and the surrounding sediments

PubMed Central

Tully, Benjamin J.; Heidelberg, John F.

2013-01-01

The formation and maintenance of deep-sea ferromanganese/polymetallic nodules still remains a mystery 140 years after their discovery. The wealth of rare metals concentrated in these nodules has spurred global interest in exploring the mining potential of these resources. The prevailing theory of abiotic formation has been called into question and the role of microbial metabolisms in nodule development is now an area of active research. To understand the community structure of microbes associated with nodules and their surrounding sediment, we performed targeted sequencing of the V4 hypervariable region of the 16S rRNA gene from three nodules collected from the central South Pacific. Results have shown that the microbial communities of the nodules are significantly distinct from the communities in the surrounding sediments, and that the interiors of the nodules harbor communities different from the exterior. This suggests not only differences in potential metabolisms between the nodule and sediment communities, but also differences in the dominant metabolisms of interior and exterior communities. We identified several operational taxonomic units (OTUs) unique to both the nodule and sediment environments. The identified OTUs were assigned putative taxonomic identifications, including two OTUs only found associated with the nodules, which were assigned to the α-Proteobacteria. Finally, we explored the diversity of the most assigned taxonomic group, the Thaumarchaea MG-1, which revealed novel OTUs compared to previous research from the region and suggests a potential role as a source of fixed carbon for ammonia oxidizing archaea in the environment. PMID:23805131

Actinobacterial diversity across a marine transgression in the deep subsurface off Shimokita Peninsula, Japan

NASA Astrophysics Data System (ADS)

Harrison, B. K.; Bailey, J. V.

2013-12-01

Sediment horizons represent a significant - but not permanent - barrier to microbial transport. Cells commonly attach to mineral surfaces in unconsolidated sediments. However, by taxis, growth, or passive migration under advecting fluids, some portion of the microbial community may transgress sedimentary boundaries. Few studies have attempted to constrain such transport of community signatures in the marine subsurface and its potential impact on biogeography. Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula recovered sediments over a greater than 1km interval representing a gradual decrease of terrestrial influence, from tidal to continental shelf depositional settings. This sequence represents a key opportunity to link subsurface microbial communities to lithological variability and investigate the permanence of community signatures characteristic of distinct depositional regimes. The phylogenetic connectivity between marine and terrestrially-influenced deposits may demonstrate to what degree sediments offer a substantial barrier to cell transport in the subsurface. Previous work has demonstrated that the Actinobacterial phylum is broadly distributed in marine sediments (Maldonado et al., 2005), present and active in the deep subsurface (Orsi et al., 2013), and that marine and terrestrial lineages may potentially be distinguished by 16S rRNA gene sequencing (e.g. Prieto-Davó et al., 2013). We report on Actinobacteria-specific 16S rRNA gene diversity recovered between 1370 and 2642 mbsf with high-throughput sequencing using the Illumina MiSeq platform, as well as selective assembly and analysis of environmental clone libraries.

Impact of volcanic ash on anammox communities in deep sea sediments.

PubMed

Song, Bongkeun; Buckner, Caroline T; Hembury, Deborah J; Mills, Rachel A; Palmer, Martin R

2014-04-01

Subaerial explosive volcanism contributes substantial amounts of material to the oceans, but little is known about the impact of volcanic ash on sedimentary microbial activity. We have studied anammox communities in deep sea sediments near the volcanically active island of Montserrat, Lesser Antilles. The rates of anammox and denitrification in the sediments were measured using (15)N isotope pairing incubation experiments, while 16S rRNA genes were used to examine anammox community structures. The higher anammox rates were measured in sediment containing the lower accumulation of volcanic ash in the surface sediments, while the lowest activities were found in sediments with the highest ash deposit. 16S rRNA gene analysis revealed the presence of 'Candidatus Scalindua spp.' in the sediments. The lowest diversity of anammox bacteria was observed in the sediments with the highest ash deposit. Overall, this study demonstrates that the deposition of volcanic material in deep sea sediments has negative impacts on activity and diversity of the anammox community. Since anammox may account for up to 79% of N2 production in marine ecosystems, periods of extensive explosive volcanism in Earth history may have had a hitherto unrecognized negative impact on the sedimentary nitrogen removal processes. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Drivers of Microbial Metabolic Activity, Biogeochemical Cycling and Associated Greenhouse Gas Production in Streambed Sediments

NASA Astrophysics Data System (ADS)

Comer-Warner, S.; Krause, S.; Gooddy, D.; Blaen, P.; Brekenfeld, N.; Wexler, S.; Kaiser, J.

2017-12-01

Hotspots of enhanced biogeochemical reactivity are produced where groundwater and surface water mixes in streambed sediments. This enhanced reactivity is due to elevated residence times and nutrient concentrations found in these areas, leading to increased rates of microbial metabolic activity. Streambed sediments, therefore, may be important in reducing catchment-wide nutrient concentrations through increased cycling. However, they also have the potential to produce high concentrations of greenhouse gases (CO2, CH4 and N2O), as end-products of respiration and intermediate products of denitrification. The hydrological and biogeochemical drivers of streambed C and N cycling, are still insufficiently understood. Here we present results from biogeochemical sampling and tracer experiments in an agricultural sandstone stream in the UK. Nutrient, DOC and greenhouse gas concentrations, as well as d13CCO2, were measured in the streambed sediment in multilevel piezometers, and nutrient concentrations, as well as d15NNO3 and d18ONO3, were measured in Diffusive Equilibrium in Thin-film Gels. Tracer experiments using both conservative (Fluorescein and NaCl) and smart (Resazurin-Resorufin) tracers were performed to determine in-stream metabolism, transient storage and solute transport times in sub-reaches of the stream. Our results show large differences in nutrient and greenhouse gas concentrations between sub-reaches dominated by gravel sediments and those dominated by sandy sediments, as well as seasonally. This suggests temperature, sediment type and residence time are key controls on streambed nutrient cycling and greenhouse gas production. The results of this study have important implications for future greenhouse gas estimates from streams and rivers, particularly as the contribution of sediment greenhouse gas production is recognised as increasingly significant.

Hydrogen Biogeochemistry in Anaerobic and Photosynthetic Ecosystems

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; DeVincenzi, Donald L. (Technical Monitor)

2000-01-01

The simple biochemistry of molecular hydrogen is central to a large number of microbial processes, affecting the interaction of organisms with each other and with the environment. In anoxic sediments, a great majority of microbial redox processes involve hydrogen as a reactant, product or potential by-product. Accordingly, the energetics (thermodynamics) of each of these processes is affected by variations in local H2 concentrations. It has long been established that this effect is important in governing microbe-microbe interactions and there are multiple demonstrations that "interspecies hydrogen transfer" can alter the products of, inhibit/stimulate, or even reverse microbial metabolic reactions. In anoxic sediments, H2 concentrations themselves are thought to be controlled by the thermodynamics of the predominant H2-consuming microbial process. In sediments from Cape Lookout Bight, this relationship quantitatively describes the co-variation of H2 concentrations with temperature (for methanogens and sulfate reducers) and with sulfate concentration (for sulfate reducers). The quantitative aspect is import= for two reasons: 1) it permits the modeling of H2-sensitive biogeochemistry, such as anaerobic methane oxidation or pathways of organic matter remineralization, as a function of environmental controls; 2) for such a relationship to be observed requires that intracellular biochemistry and bioenergetics are being directly expressed in a component of the extracellular medium. H2 could therefore be utilized a non-invasive probe of cellular energetic function in intact microbial ecosystems. Based on the latter principle we have measured down-core profiles of H2 and other relevant physico-chemical parameters in order to calculate the metabolic energy yields (DG) that support microbial metabolism in Cape Lookout Bight sediments. Methanogens in this system apparently function with energy yields significantly smaller than the minimum requirements suggested by pure culture studies. Our recent work has extended the study of hydrogen to cyanobacterial mat communities. The large amounts of reducing power generated during photosynthetic activity carry the potential to contribute a swamping term to the H2 economy of the anaerobic microbial populations within the mat - and thereby to alter the population structure and biogeochemical function of the mat as a whole. In hypersaline microbial mats, we observe a distinct diel cycle in H2 production and a substantial corresponding flux. On an early Earth dominated by microbial mats, this transmission of photosynthetic reducing power may have carried important implications for both biospheric and atmospheric evolution.

Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China

PubMed Central

Wang, Shang; Dong, Hailiang; Hou, Weiguo; Jiang, Hongchen; Huang, Qiuyuan; Briggs, Brandon R.; Huang, Liuqin

2014-01-01

Temporal variation in geochemistry can cause changes in microbial community structure and diversity. Here we studied temporal changes of microbial communities in Tengchong hot springs of Yunnan Province, China in response to geochemical variations by using microbial and geochemical data collected in January, June and August of 2011. Greater temporal variations were observed in individual taxa than at the whole community structure level. Water and sediment communities exhibited different temporal variation patterns. Water communities were largely stable across three sampling times and dominated by similar microbial lineages: Hydrogenobaculum in moderate-temperature acidic springs, Sulfolobus in high-temperature acidic springs, and Hydrogenobacter in high-temperature circumneutral to alkaline springs. Sediment communities were more diverse and responsive to changing physicochemical conditions. Most of the sediment communities in January and June were similar to those in waters. However, the August sediment community was more diverse and contained more anaerobic heterotrophs than the January and June: Desulfurella and Acidicaldus in moderate-temperature acidic springs, Ignisphaera and Desulfurococcus in high-temperature acidic springs, the candidate division OP1 and Fervidobacterium in alkaline springs, and Thermus and GAL35 in neutral springs. Temporal variations in physicochemical parameters including temperature, pH, and dissolved organic carbon may have triggered the observed microbial community shifts. PMID:25524763

Light-Dependant Biostabilisation of Sediments by Stromatolite Assemblages

PubMed Central

Paterson, David M.; Aspden, Rebecca J.; Visscher, Pieter T.; Consalvey, Mireille; Andres, Miriam S.; Decho, Alan W.; Stolz, John; Reid, R. Pamela

2008-01-01

For the first time we have investigated the natural ecosystem engineering capacity of stromatolitic microbial assemblages. Stromatolites are laminated sedimentary structures formed by microbial activity and are considered to have dominated the shallows of the Precambrian oceans. Their fossilised remains are the most ancient unambiguous record of early life on earth. Stromatolites can therefore be considered as the first recognisable ecosystems on the planet. However, while many discussions have taken place over their structure and form, we have very little information on their functional ecology and how such assemblages persisted despite strong eternal forcing from wind and waves. The capture and binding of sediment is clearly a critical feature for the formation and persistence of stromatolite assemblages. Here, we investigated the ecosystem engineering capacity of stromatolitic microbial assemblages with respect to their ability to stabilise sediment using material from one of the few remaining living stromatolite systems (Highborne Cay, Bahamas). It was shown that the most effective assemblages could produce a rapid (12–24 h) and significant increase in sediment stability that continued in a linear fashion over the period of the experimentation (228 h). Importantly, it was also found that light was required for the assemblages to produce this stabilisation effect and that removal of assemblage into darkness could lead to a partial reversal of the stabilisation. This was attributed to the breakdown of extracellular polymeric substances under anaerobic conditions. These data were supported by microelectrode profiling of oxygen and calcium. The structure of the assemblages as they formed was visualised by low-temperature scanning electron microscopy and confocal laser microscopy. These results have implications for the understanding of early stromatolite development and highlight the potential importance of the evolution of photosynthesis in the mat forming process. The evolution of photosynthesis may have provided an important advance for the niche construction activity of microbial systems and the formation and persistence of the stromatolites which came to dominate shallow coastal environments for 80% of the biotic history of the earth. PMID:18781202

Light-dependant biostabilisation of sediments by stromatolite assemblages.

PubMed

Paterson, David M; Aspden, Rebecca J; Visscher, Pieter T; Consalvey, Mireille; Andres, Miriam S; Decho, Alan W; Stolz, John; Reid, R Pamela

2008-09-10

For the first time we have investigated the natural ecosystem engineering capacity of stromatolitic microbial assemblages. Stromatolites are laminated sedimentary structures formed by microbial activity and are considered to have dominated the shallows of the Precambrian oceans. Their fossilised remains are the most ancient unambiguous record of early life on earth. Stromatolites can therefore be considered as the first recognisable ecosystems on the planet. However, while many discussions have taken place over their structure and form, we have very little information on their functional ecology and how such assemblages persisted despite strong eternal forcing from wind and waves. The capture and binding of sediment is clearly a critical feature for the formation and persistence of stromatolite assemblages. Here, we investigated the ecosystem engineering capacity of stromatolitic microbial assemblages with respect to their ability to stabilise sediment using material from one of the few remaining living stromatolite systems (Highborne Cay, Bahamas). It was shown that the most effective assemblages could produce a rapid (12-24 h) and significant increase in sediment stability that continued in a linear fashion over the period of the experimentation (228 h). Importantly, it was also found that light was required for the assemblages to produce this stabilisation effect and that removal of assemblage into darkness could lead to a partial reversal of the stabilisation. This was attributed to the breakdown of extracellular polymeric substances under anaerobic conditions. These data were supported by microelectrode profiling of oxygen and calcium. The structure of the assemblages as they formed was visualised by low-temperature scanning electron microscopy and confocal laser microscopy. These results have implications for the understanding of early stromatolite development and highlight the potential importance of the evolution of photosynthesis in the mat forming process. The evolution of photosynthesis may have provided an important advance for the niche construction activity of microbial systems and the formation and persistence of the stromatolites which came to dominate shallow coastal environments for 80% of the biotic history of the earth.

Biogeochemical Cycle of Methanol in Anoxic Deep-Sea Sediments

PubMed Central

Yanagawa, Katsunori; Tani, Atsushi; Yamamoto, Naoya; Hachikubo, Akihiro; Kano, Akihiro; Matsumoto, Ryo; Suzuki, Yohey

2016-01-01

The biological flux and lifetime of methanol in anoxic marine sediments are largely unknown. We herein reported, for the first time, quantitative methanol removal rates in subsurface sediments. Anaerobic incubation experiments with radiotracers showed high rates of microbial methanol consumption. Notably, methanol oxidation to CO2 surpassed methanol assimilation and methanogenesis from CO2/H2 and methanol. Nevertheless, a significant decrease in methanol was not observed after the incubation, and this was attributed to the microbial production of methanol in parallel with its consumption. These results suggest that microbial reactions play an important role in the sources and sinks of methanol in subseafloor sediments. PMID:27301420

Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River

PubMed Central

Smith, Maria W.; Davis, Richard E.; Youngblut, Nicholas D.; Kärnä, Tuomas; Herfort, Lydie; Whitaker, Rachel J.; Metcalf, William W.; Tebo, Bradley M.; Baptista, António M.; Simon, Holly M.

2015-01-01

Lateral bays of the lower Columbia River estuary are areas of enhanced water retention that influence net ecosystem metabolism through activities of their diverse microbial communities. Metagenomic characterization of sediment microbiota from three disparate sites in two brackish lateral bays (Baker and Youngs) produced ∼100 Gbp of DNA sequence data analyzed subsequently for predicted SSU rRNA and peptide-coding genes. The metagenomes were dominated by Bacteria. A large component of Eukaryota was present in Youngs Bay samples, i.e., the inner bay sediment was enriched with the invasive New Zealand mudsnail, Potamopyrgus antipodarum, known for high ammonia production. The metagenome was also highly enriched with an archaeal ammonia oxidizer closely related to Nitrosoarchaeum limnia. Combined analysis of sequences and continuous, high-resolution time series of biogeochemical data from fixed and mobile platforms revealed the importance of large-scale reciprocal particle exchanges between the mainstem estuarine water column and lateral bay sediments. Deposition of marine diatom particles in sediments near Youngs Bay mouth was associated with a dramatic enrichment of Bacteroidetes (58% of total Bacteria) and corresponding genes involved in phytoplankton polysaccharide degradation. The Baker Bay sediment metagenome contained abundant Archaea, including diverse methanogens, as well as functional genes for methylotrophy and taxonomic markers for syntrophic bacteria, suggesting that active methane cycling occurs at this location. Our previous work showed enrichments of similar anaerobic taxa in particulate matter of the mainstem estuarine water column. In total, our results identify the lateral bays as both sources and sinks of biogenic particles significantly impacting microbial community composition and biogeochemical activities in the estuary. PMID:26483785

The life sulfuric: microbial ecology of sulfur cycling in marine sediments.

PubMed

Wasmund, Kenneth; Mußmann, Marc; Loy, Alexander

2017-08-01

Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

CHANGES IN ENANTIOMERIC FRACTIONS DURING MICROBIAL REDUCTIVE DECHLORINATION OF PCB132, PCB149, AND AROCLOR 1254 IN LAKE HARTWELL SEDIMENT MICROCOSMS

EPA Science Inventory

Enantioselectivity of microbial reductive dechlorination of chiral PCBs in sediments from Lake Hartwell, SC, was determined by microcosm studies and enantiomer-specific GC analysis. Sediments from two locations in the vicinity of the highest levels of PCB contamination were used...

Anaerobic degradation of 1,1,2,2-tetrachloroethane and association with microbial communities in a freshwater tidal wetland, Aberdeen Proving Ground, Maryland : laboratory experiments and comparisons to field data

USGS Publications Warehouse

Lorah, Michelle M.; Voytek, Mary A.; Kirshtein, Julie D.; Jones, Elizabeth J.

2003-01-01

Defining biodegradation rates and processes is a critical part of assessing the feasibility of monitored natural attenuation as a remediation method for ground water containing organic contaminants. During 1998?2001, the U.S. Geological Survey conducted a microbial study at a freshwater tidal wetland along the West Branch Canal Creek, Aberdeen Proving Ground, Maryland, as part of an investigation of natural attenuation of chlorinated volatile organic compounds (VOCs) in the wetland sediments. Geochemical analyses and molecular biology techniques were used to investigate factors controlling anaerobic degradation of 1,1,2,2-tetrachloroethane (TeCA), and to characterize the microbial communities that potentially are important in its degradation. Rapid TeCA and daughter product degradation observed in laboratory experiments and estimated with field data confirm that natural attenuation is a feasible remediation method at this site. The diverse microbial community that seems to be involved in TeCA degradation in the wetland sediments varies with changing spatial and seasonal conditions, allowing continued effective natural attenuation throughout the year. Rates of TeCA degradation in anaerobic microcosm experiments conducted with wetland sediment collected from two different sites (WB23 and WB30) and during three different seasons (March?April 1999, July?August 1999, and October?November 2000) showed little spatial variability but high seasonal variability. Initial first-order degradation rate constants for TeCA ranged from 0.10?0.01 to 0.16?0.05 per day (half-lives of 4.3 to 6.9 days) for March?April 1999 and October?November 2000 microcosms incubated at 19 degrees Celsius, whereas lower rate constants of 0 ? 0.03 and 0.06 ? 0.03 per day were obtained in July?August 1999 microcosms incubated at 19 degrees Celsius. Microbial community profiles showed that low microbial biomass and microbial diversity in the summer, possibly due to competition for nutrients by the wetland vegetation, could account for these unexpectedly low degradation rates. In microcosms incubated at 5 degrees Celsius, about 50 percent of the initial TeCA in solution was converted to daughter products within a 35-day incubation period, indicating that biodegradation in the wetland sediments can continue during cold winter temperatures. Initial pathways of TeCA degradation were the same in the wetland sediment microcosms regardless of the season or sediment collection site, the reduction-oxidation conditions, and the previous exposure of the sediment to contamination. Immediate and simultaneous dichloroelimination and hydrogenolysis, producing 1,2-dichloro-ethene (12DCE) and 1,1,2-trichloroethane (112TCA), respectively, were the initial TeCA degradation pathways in all live microcosm experiments. The production and degradation of vinyl chloride (VC), which is the most toxic of the TeCA daughter compounds, was affected by spatial and seasonal variability, reduction-oxidation condition, and pre-exposure of the wetland sediment. TeCA-amended microcosms constructed with WB30 sediment showed approximately twice as much VC production as those constructed with WB23 sediment. Results of 112TCA-amended microcosms indicated that the greater production of VC in the WB30 sediment resulted from a greater predominance of the 112TCA dichloro-elimination pathway in these sediments. VC degradation also was substantially higher in microcosms constructed with WB30 sediment than those constructed with WB23 sediment, resulting in lower VC concentrations at the end of WB30 microcosms. Enrichment experiments in which microcosm slurry was amended with high initial VC concentrations showed that the spatial difference in VC degradation was negligible after prolonged incubation under methanogenic conditions. Inhibition of methanogenic activity in microcosms by addition of sulfate or of 2-bromoethanesulfonic acid inhibited production and degradation of VC. Inhibition of methanogenesis b

Compositional Characteristics of Dissolved Organic Matter released from the sediment of Han river in Korea.

NASA Astrophysics Data System (ADS)

Oh, H.; Choi, J. H.

2017-12-01

The dissolved organic matter (DOM) has variable characteristics depending on the sources. The DOM of a river is affected by rain water, windborne material, surface and groundwater flow, and sediments. In particular, sediments are sources and sinks of nutrients and pollutants in aquatic ecosystems by supplying large amounts of organic matter. The DOM which absorbs ultraviolet and visible light is called colored dissolved organic matter (CDOM). CDOM is responsible for the optical properties of natural waters in several biogeochemical and photochemical processes and absorbs UV-A (315-400 nm) and UV-B (280-315), which are harmful to aquatic ecosystems (Helms et al., 2008). In this study, we investigated the quantity and quality of DOM and CDOM released from the sediments of Han river which was impacted by anthropogenic activities and hydrologic alternation of 4 Major River Restoration Project. The target area of this study is Gangchenbo (GC), Yeojubo (YJ), and Ipobo(IP) of the Han River, Korea. Sediments and water samples were taken on July and August of 2016 and were incubated at 20° up to 7 days. Absorbance was measured with UV-visible spectrophotometer (Libra S32 PC, Biochrom). Fluorescence intensity determined with Fluorescence EEMs (F-7000, Hitachi). Absorbance and fluorescence intensity were used to calculate Specific Ultraviolet Absorbance (SUVA254), Humification index (HIX), Biological index (BIX), Spectral slope (SR) and component analysis. The DOC concentration increased after 3 days of incubation. According to the SUVA254 analysis, the microbial activity is highest in the initial overlying water of IP. HIX have range of 1.35-4.08, and decrease poly aromatic structures of organic matter during incubation. From the results of the BIX, autochthonous organic matter was released from the sediments. In all sites, Humic-like DOM, Microbial humic-like DOM and Protein-like DOM increased significantly between Day 0 and 3(except Humic-like, Microbial humic-like DOM in IP). Spectral slope ratio of all sites increased according to incubation, which means that the amount of CDOM increased from the sediment to overlying water.

Dehalogenation activities and distribution of reductive dehalogenase homologous genes in marine subsurface sediments.

PubMed

Futagami, Taiki; Morono, Yuki; Terada, Takeshi; Kaksonen, Anna H; Inagaki, Fumio

2009-11-01

Halogenated organic compounds serve as terminal electron acceptors for anaerobic respiration in a diverse range of microorganisms. Here, we report on the widespread distribution and diversity of reductive dehalogenase homologous (rdhA) genes in marine subsurface sediments. A total of 32 putative rdhA phylotypes were detected in sediments from the southeast Pacific off Peru, the eastern equatorial Pacific, the Juan de Fuca Ridge flank off Oregon, and the northwest Pacific off Japan, collected at a maximum depth of 358 m below the seafloor. In addition, significant dehalogenation activity involving 2,4,6-tribromophenol and trichloroethene was observed in sediment slurry from the Nankai Trough Forearc Basin. These results suggest that dehalorespiration is an important energy-yielding pathway in the subseafloor microbial ecosystem.

Quantitative microbial risk assessment (QMRA) shows increased public health risk associated with exposure to river water under conditions of riverbed sediment resuspension.

PubMed

Abia, Akebe Luther King; Ubomba-Jaswa, Eunice; Genthe, Bettina; Momba, Maggy Ndombo Benteke

2016-10-01

Although higher microbial concentrations have been reported in sediments than in the overlying water column, most quantitative microbial risk assessment (QMRA) studies have not clearly indicated the contribution of sediment-borne pathogens to estimated risks. Thus, the present study aimed at determining the public health risk associated with exposure to pathogenic bacteria in polluted river water under undisturbed conditions and conditions of sediment resuspension in the Apies River, Gauteng, South Africa. Microbial pathogens were isolated and identified using culture and molecular methods. The beta-Poisson dose-response model was used to estimate the probability of infection (Pi) with the various pathogens, following accidental/intentional ingestion of 1mL or 100mL (or 50mL) of untreated river water. Mean wet season Escherichia coli counts ranged between 5.8E+01 and 8.8E+04MPN/100mL (water column) and between 2.40E+03 and 1.28E+05MPN/100mL (sediments). Mean dry season E. coli counts ranged between 5.11E+00 and 3.40E+03MPN/100mL (water column) and between 5.09E+00 and 6.30E+03MPN/100mL (sediments). Overall (water and sediments) Vibrio cholerae was the most detected pathogen (58.8%) followed by Salmonella spp. (23.9%) and Shigella (10.1%). Ingestion of 1mL of river water could lead to 0%-4% and 1%-74% Pi with E. coli during the dry and wet season, respectively. During the dry season, the Pi with V. cholerae, Salmonella spp. and Shigella spp. were 0%-1.39%, 0%-4.11% and 0%-0.16% respectively, depending on volume of water ingested. The risks of infections with all microorganisms increased during the wet season. A 2-log increase in water E. coli count following sediments disturbance led to approximately 10 times higher Pi with E. coli than when sediments were undisturbed. Therefore, the use of the untreated water from the Apies River for drinking, household purposes or recreational activities poses a potential health risk to the users of the river. Copyright © 2016 Elsevier B.V. All rights reserved.

Influence of deglaciation on microbial communities in marine sediments off the coast of Svalbard, Arctic Circle.

PubMed

Park, Soo-Je; Park, Byoung-Joon; Jung, Man-Young; Kim, So-Jeong; Chae, Jong-Chan; Roh, Yul; Forwick, Matthias; Yoon, Ho-Il; Rhee, Sung-Keun

2011-10-01

Increases in global temperatures have been shown to enhance glacier melting in the Arctic region. Here, we have evaluated the effects of meltwater runoff on the microbial communities of coastal marine sediment located along a transect of Temelfjorden, in Svalbard. As close to the glacier front, the sediment properties were clearly influenced by deglaciation. Denaturing gradient gel electrophoresis profiles showed that the sediment microbial communities of the stations of glacier front (stations 188-178) were distinguishable from that of outer fjord region (station 176). Canonical correspondence analysis indicated that total carbon and calcium carbonate in sediment and chlorophyll a in bottom water were key factors driving the change of microbial communities. Analysis of 16S rRNA gene clone libraries suggested that microbial diversity was higher within the glacier-proximal zone (station 188) directly affected by the runoffs than in the outer fjord region. While the crenarchaeotal group I.1a dominated at station 176 (62%), Marine Benthic Group-B and other Crenarchaeota groups were proportionally abundant. With regard to the bacterial community, alpha-Proteobacteria and Flavobacteria lineages prevailed (60%) at station 188, whereas delta-Proteobacteria (largely sulfate-reducers) predominated (32%) at station 176. Considering no clone sequences related to sulfate-reducers, station 188 may be more oxic compared to station 176. The distance-wise compositional variation in the microbial communities is attributable to their adaptations to the sediment environments which are differentially affected by melting glaciers.

[Effects of Perfluoroalkyl Substances on the Microbial Community Structure in Surface Sediments of Typical River, China].

PubMed

Sun, Ya-jun; Wang, Tie-yu; Peng, Xia-wei; Wang, Pei

2015-07-01

In order to reveal the relationship between Perfluoroalkyl substances (PFASs) contamination and the bacterial community composition, surface sediment samples were collected along the Xiaoqing River in Shandong Province in April and July 2014 (XQ1-XQ10), where many PFASs manufacturers were located. PFASs were quantified by HPLC/MS-MS, related environmental factors affecting the microbial community structure were measured, and the microbial community structure in surface sediments was measured by the second-generation sequencing technology Illumina MiSeq. The results not only revealed the degree of PFASs pollution in the sediments of Xiaoqing River, but also illustrated the relationship between PFASs pollution and the microbial community structure. Among the twelve kinds of PFASs detected in this study, PFOA was the predominant compound, and the highest PFOA concentrations were detected in the sample of XQ5 (April: 456. 2 ng. g-1; July: 748.7 ng . g-1) located at the downstream of Xiaoqing River with many fluoropolymer producing facilities. PFOA contamination was the main factor affecting the microbial community structure in April, accordingly community richness and evenness were significantly negatively correlated with PFOA levels. The abundance of Thiobacillus increased with the increasing PFOA concentration in the sediment PFOA. This suggested that Thiobacillus was sensitive to PFOA pollution and might be the potential indicator to reveal the degree of PFOA pollution in sediment. When the concentrations of PFOA were below 100 ng . g-1, no significant effects on the microbial community structure were observed.

In-Well Sediment Incubators to Evaluate Microbial Community Stability and Dynamics following Bioimmobilization of Uranium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baldwin, Brett R.; Peacock, Aaron D.; Gan, M.

2009-09-23

An in-situ incubation device (ISI) was developed in order to investigate the stability and dynamics of sediment associated microbial communities to prevailing subsurface oxidizing or reducing conditions. Here we describe the use of these devices at the Old Rifle Uranium Mill Tailings Remedial Action (UMTRA) site. During the 7 month deployment oxidized Rifle aquifer background sediments (RABS) were deployed in previously biostimulated wells under iron reducing conditions, cell densities of known iron reducing bacteria including Geobacteraceae increased significantly showing the microbial community response to local subsurface conditions. PLFA profiles of RABS following in situ deployment were strikingly similar to thosemore » of adjacent sediment cores suggesting ISI results could be extrapolated to the native material of the test plots. Results for ISI deployed reduced sediments showed only slight changes in community composition and pointed toward the ability of the ISIs to monitor microbial community stability and response to subsurface conditions.« less

Life under ice: Investigating microbial-related biogeochemical cycles in the seasonally-covered Great Lake Onego, Russia

NASA Astrophysics Data System (ADS)

Thomas, Camille; Ariztegui, Daniel; Victor, Frossard; Emilie, Lyautey; Marie-Elodie, Perga; Life Under Ice Scientific Team

2016-04-01

The Great European lakes Ladoga and Onego are important resources for Russia in terms of drinking water, energy, fishing and leisure. Because their northern location (North of Saint Petersburgh), these lakes are usually ice-covered during winter. Due to logistical reasons, their study has thus been limited to the ice-free periods, and very few data are available for the winter season. As a matter of fact, comprehension of large lakes behaviour in winter is very limited as compared to the knowledge available from small subpolar lakes or perennially ice-covered polar lakes. To tackle this issue, an international consortium of scientists has gathered around the « life under ice » project to investigate physical, chemical and biogeochemical changes during winter in Lake Onego. Our team has mainly focused on the characterization and quantification of biological processes, from the water column to the sediment, with a special focus on methane cycling and trophic interactions. A first « on-ice » campaign in March 2015 allowed the sampling of a 120 cm sedimentary core and the collection of water samples at multiple depths. The data resulting from this expedition will be correlated to physical and chemical parameters collected simultaneously. A rapid biological activity test was applied immediately after coring in order to test for microbial activity in the sediments. In situ adenosine-5'-triphosphate (ATP) measurements were carried out in the core and taken as an indication of living organisms within the sediments. The presence of ATP is a marker molecule for metabolically active cells, since it is not known to form abiotically. Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) were extracted from these samples, and quantified. Quantitative polymerase chain reactions (PCR) were performed on archaeal and bacterial 16S rRNA genes used to reconstruct phylogenies, as well as on their transcripts. Moreover, functional genes involved in the methane and nitrogen cycles were also quantified in both sediment and water column. Preliminary results show that in the sediment, methanogenesis occurs below 7 cm. Above this redox boundary, methanotrophs are abundant but there activity remains enigmatic (10000 times less transcript than gene copies). Based on 16S rRNA transcripts, Bacteria and Archaea seem to have their maximum activity within the first 7 cm. These data are validated by ATP measurements. The principal peaks of activity actually lie at the water sediment interface, and at the redox boundary (7cm). High-throughput sequencing of 16S rRNA genes (both from DNA and RNA) are currently being performed to gain further understanding on the main actors of these microbial processes in the sediment. Diversity analysis are also being prepared and will allow to characterize the relationship between planktonic and benthic communities in the ice-covered lake.

Thalassic biogas production from sea wrack biomass using different microbial seeds: cow manure, marine sediment and sea wrack-associated microflora.

PubMed

Marquez, Gian Powell B; Reichardt, Wolfgang T; Azanza, Rhodora V; Klocke, Michael; Montaño, Marco Nemesio E

2013-04-01

Sea wrack (dislodged sea grasses and seaweeds) was used in biogas production. Fresh water scarcity in island communities where sea wrack could accumulate led to seawater utilization as liquid substrate. Three microbial seeds cow manure (CM), marine sediment (MS), and sea wrack-associated microflora (SWA) were explored for biogas production. The average biogas produced were 2172±156 mL (MS), 1223±308 mL (SWA) and 551±126 mL (CM). Though methane potential (396.9 mL(CH4) g(-1) volatile solid) computed from sea wrack proximate values was comparable to other feedstocks, highest methane yield was low (MS=94.33 mL(CH4) g(-1) VS). Among the microbial seeds, MS proved the best microbial source in utilizing sea wrack biomass and seawater. However, salinity (MS=42‰) observed exceeded average seawater salinity (34‰). Hence, methanogenic activity could have been inhibited. This is the first report on sea wrack biomass utilization for thalassic biogas production. Copyright © 2013 Elsevier Ltd. All rights reserved.

Exploring frontiers of the deep biosphere through scientific ocean drilling

NASA Astrophysics Data System (ADS)

Inagaki, F.; D'Hondt, S.; Hinrichs, K. U.

2015-12-01

Since the first deep biosphere-dedicated Ocean Drilling Program (ODP) Leg 201 using the US drill ship JOIDES Resolution in 2002, scientific ocean drilling has offered unique opportunities to expand our knowledge of the nature and extent of the deep biosphere. The latest estimate of the global subseafloor microbial biomass is ~1029cells, accounting for 4 Gt of carbon and ~1% of the Earth's total living biomass. The subseafloor microbial communities are evolutionarily diverse and their metabolic rates are extraordinarily slow. Nevertheless, accumulating activity most likely plays a significant role in elemental cycles over geological time. In 2010, during Integrated Ocean Drilling Program (IODP) Expedition 329, the JOIDES Resolutionexplored the deep biosphere in the open-ocean South Pacific Gyre—the largest oligotrophic province on our planet. During Expedition 329, relatively high concentrations of dissolved oxygen and significantly low biomass of microbial populations were observed in the entire sediment column, indicating that (i) there is no limit to life in open-ocean sediment and (ii) a significant amount of oxygen reaches through the sediment to the upper oceanic crust. This "deep aerobic biosphere" inhabits the sediment throughout up to ~37 percent of the world's oceans. The remaining ~63 percent of the oceans is comprised of higher productivity areas that contain the "deep anaerobic biosphere". In 2012, during IODP Expedition 337, the Japanese drill ship Chikyu explored coal-bearing sediments down to 2,466 meters below the seafloor off the Shimokita Peninsula, Japan. Geochemical and microbiological analyses consistently showed the occurrence of methane-producing communities associated with the coal beds. Cell concentrations in deep sediments were notably lower than those expected from the global regression line, implying that the bottom of the deep biosphere is approached in these beds. Taxonomic composition of the deep coal-bearing communities profoundly differs from those in shallower marine sediments and instead resembles organotrophic communities in forest soils. These findings suggest that the terrigenous microbial ecosystem has been partly retained from the original depositional setting over 20 million years and contributed to deep carbon cycling ever since.

Identity and abundance of active sulfate-reducing bacteria in deep tidal flat sediments determined by directed cultivation and CARD-FISH analysis.

PubMed

Gittel, Antje; Mussmann, Marc; Sass, Henrik; Cypionka, Heribert; Könneke, Martin

2008-10-01

The identity and abundance of potentially active sulfate-reducing bacteria (SRB) in several metre deep sediments of a tidal sand flat in the German Wadden Sea were assessed by directed cultivation and cultivation-independent CARD-FISH analysis (catalysed reporter deposition fluorescence in situ hybridization). Presumably abundant SRB from different sediment layers between 0.5 and 4 m depth were selectively enriched in up to million-fold diluted cultures supplemented with lactate, acetate or hydrogen. Partial 16S rRNA gene sequences obtained from highest dilution steps showing sulfide formation indicated growth of deltaproteobacterial SRB belonging to the Desulfobulbaceae and the Desulfobacteraceae as well as of members of the Firmicutes. Subsequent isolation resulted in 10 novel phylotypes of both litho- and organotrophic sulfate-reducing Deltaproteobacteria. Molecular pre-screening identified six isolates as members of the Desulfobulbaceae, sharing highest identities with either candidatus 'Desulfobacterium corrodens' (95-97%) or Desulfobacterium catecholicum (98%), and four isolates as members of Desulfobacteraceae, being related to either Desulfobacter psychrotolerans (98%) or Desulfobacula phenolica (95-97%). Relatives of D. phenolica were exlusively isolated from 50 and 100 cm deep sediments with 10 and 2 mM of pore water sulfate respectively. In contrast, relatives of D. corrodens, D. psychrotolerans and D. catecholicum were also obtained from layers deeper than 100 cm and with less than 2 mM sulfate. The high in situ abundance of members of both families in sediment layers beneath 50 cm could be confirmed via CARD-FISH analysis performed with a set of six SRB-specific oligonucleotide probes. Moreover, SRB represented a numerically significant fraction of the microbial community throughout the sediment (up to 7%) and reached even higher cell numbers in deep, sulfate-poor layers than in the sulfate-rich surface sediment. This relatively large community size of potentially active SRB in deep sandy sediments might on the one hand be a result of their syntrophic association with other anaerobes. Our results furthermore support the hypothesis that enhanced advective pore water transport might supply nutrients to microbial communities in deep sandy sediments and point to their so far unrecognized contribution to biogeochemical processes in Wadden Sea sediments.

Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics.

PubMed

Urich, Tim; Lanzén, Anders; Stokke, Runar; Pedersen, Rolf B; Bayer, Christoph; Thorseth, Ingunn H; Schleper, Christa; Steen, Ida H; Ovreas, Lise

2014-09-01

Deep-sea hydrothermal vents are unique environments on Earth, as they host chemosynthetic ecosystems fuelled by geochemical energy with chemolithoautotrophic microorganisms at the basis of the food webs. Whereas discrete high-temperature venting systems have been studied extensively, the microbiotas associated with low-temperature diffuse venting are not well understood. We analysed the structure and functioning of microbial communities in two diffuse venting sediments from the Jan Mayen vent fields in the Norwegian-Greenland Sea, applying an integrated 'omics' approach combining metatranscriptomics, metaproteomics and metagenomics. Polymerase chain reaction-independent three-domain community profiling showed that the two sediments hosted highly similar communities dominated by Epsilonproteobacteria, Deltaproteobacteria and Gammaproteobacteria, besides ciliates, nematodes and various archaeal taxa. Active metabolic pathways were identified through transcripts and peptides, with genes of sulphur and methane oxidation, and carbon fixation pathways highly expressed, in addition to genes of aerobic and anaerobic (nitrate and sulphate) respiratory chains. High expression of chemotaxis and flagella genes reflected a lifestyle in a dynamic habitat rich in physico-chemical gradients. The major metabolic pathways could be assigned to distinct taxonomic groups, thus enabling hypotheses about the function of the different prokaryotic and eukaryotic taxa. This study advances our understanding of the functioning of microbial communities in diffuse hydrothermal venting sediments. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Water level changes affect carbon turnover and microbial community composition in lake sediments.

PubMed

Weise, Lukas; Ulrich, Andreas; Moreano, Matilde; Gessler, Arthur; Kayler, Zachary E; Steger, Kristin; Zeller, Bernd; Rudolph, Kristin; Knezevic-Jaric, Jelena; Premke, Katrin

2016-05-01

Due to climate change, many lakes in Europe will be subject to higher variability of hydrological characteristics in their littoral zones. These different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. We used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover. (13)C-labelled particulate organic carbon was used to trace and estimate carbon uptake into bacterial biomass (via phospholipid fatty acids) and respiration. Microbial community changes were monitored by combining DNA- and RNA-based real-time PCR quantification and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA. The shifting hydrological regimes in the sediment primarily caused two linked microbial effects: changes in the use of available organic carbon and community composition changes. Drying sediments yielded the highest CO2 emission rates, whereas hydrological shifts increased the uptake of allochthonous organic carbon for respiration. T-RFLP patterns demonstrated that only the most extreme hydrological changes induced a significant shift in the active and total bacterial communities. As current scenarios of climate change predict an increase of drought events, frequent variations of the hydrological regimes of many lake littoral zones in central Europe are anticipated. Based on the results of our study, this phenomenon may increase the intensity and amplitude in rates of allochthonous organic carbon uptake and CO2 emissions. © FEMS 2016.

Water level changes affect carbon turnover and microbial community composition in lake sediments

PubMed Central

Weise, Lukas; Ulrich, Andreas; Moreano, Matilde; Gessler, Arthur; E. Kayler, Zachary; Steger, Kristin; Zeller, Bernd; Rudolph, Kristin; Knezevic-Jaric, Jelena; Premke, Katrin

2016-01-01

Due to climate change, many lakes in Europe will be subject to higher variability of hydrological characteristics in their littoral zones. These different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. We used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover. 13C-labelled particulate organic carbon was used to trace and estimate carbon uptake into bacterial biomass (via phospholipid fatty acids) and respiration. Microbial community changes were monitored by combining DNA- and RNA-based real-time PCR quantification and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA. The shifting hydrological regimes in the sediment primarily caused two linked microbial effects: changes in the use of available organic carbon and community composition changes. Drying sediments yielded the highest CO2 emission rates, whereas hydrological shifts increased the uptake of allochthonous organic carbon for respiration. T-RFLP patterns demonstrated that only the most extreme hydrological changes induced a significant shift in the active and total bacterial communities. As current scenarios of climate change predict an increase of drought events, frequent variations of the hydrological regimes of many lake littoral zones in central Europe are anticipated. Based on the results of our study, this phenomenon may increase the intensity and amplitude in rates of allochthonous organic carbon uptake and CO2 emissions. PMID:26902802

Microbial Community in High Arsenic Shallow Groundwater Aquifers in Hetao Basin of Inner Mongolia, China

PubMed Central

Li, Ping; Wang, Yanhong; Dai, Xinyue; Zhang, Rui; Jiang, Zhou; Jiang, Dawei; Wang, Shang; Jiang, Hongchen; Wang, Yanxin; Dong, Hailiang

2015-01-01

A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12–267 operational taxonomic units (OTUs). Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO4 2-, SO4 2-/total sulfur ratio, and Fe2+ were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia. PMID:25970606

Microbial community in high arsenic shallow groundwater aquifers in Hetao Basin of Inner Mongolia, China.

PubMed

Li, Ping; Wang, Yanhong; Dai, Xinyue; Zhang, Rui; Jiang, Zhou; Jiang, Dawei; Wang, Shang; Jiang, Hongchen; Wang, Yanxin; Dong, Hailiang

2015-01-01

A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12-267 operational taxonomic units (OTUs). Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO4(2-), SO4(2-)/total sulfur ratio, and Fe(2+) were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia.

Salt marsh sediment bacteria: their distribution and response to external nutrient inputs.

PubMed

Bowen, Jennifer L; Crump, Byron C; Deegan, Linda A; Hobbie, John E

2009-08-01

A primary focus among microbial ecologists in recent years has been to understand controls on the distribution of microorganisms in various habitats. Much less attention has been paid to the way that environmental disturbance interacts with processes that regulate bacterial community composition. We determined how human disturbance affected the distribution and community structure of salt marsh sediment bacteria by using denaturing gradient gel electrophoresis of 16S rRNA in five different habitats in each of four salt marshes located in northeastern Massachusetts, USA. Two of the four marsh creeks were experimentally enriched 15 x above background by the addition of nitrogen and phosphorus fertilizers for two or more growing seasons. Our results indicate that extrinsic factors acting at broad scales do not influence the distribution of salt marsh sediment bacteria. Intrinsic factors, controlled by local-scale environmental heterogeneity, do play a role in structuring these sediment microbial communities, although nutrient enrichment did not have a consequential effect on the microbial community in most marsh habitats. Only in one habitat, a region of the marsh creek wall that is heavily colonized by filamentous algae, did we see any effect of fertilization on the microbial community structure. When similar habitats were compared among marshes, there was considerable convergence in the microbial community composition during the growing season. Environmental factors that correlated best with microbial community composition varied with habitat, suggesting that habitat-specific intrinsic forces are primarily responsible for maintaining microbial diversity in salt marsh sediments.

Linking benthic microbial community dynamics to diel redox variations in a near shore costal environment, Héeia Fishpond

NASA Astrophysics Data System (ADS)

Frank, K. L.; Rogers, K. L.; Wheat, C. G.; Alegado, R.

2016-12-01

Microbes play crucial roles in mediating biogeochemical cycling in coastal marine habitats. In shallow coastal ecosystems, excess primary productivity and respiration of pelagic phototrophic organisms generate striking diel variations in dissolved oxygen concentrations, leading to substantial vertical migration of redox transition zones in the sediment. However, the relationship between microbial community dynamics and the establishment of these geochemical gradients, especially over a diel time frame, remains poorly constrained. Here we examine the biogeochemical drivers of diel redox dynamics by integrating comprehensive geochemical, taxonomic, functional gene abundance, and thermodynamic datasets from Héeia Fishpond (HFP) sediment cores. HFP, an 88-acre tidally-influenced, shallow Hawaiian coastal estuarine system, is analogous to a large mesocosm embedded in a natural coastal environment, making it an ideal site for coastal biogeochemical studies. Taxonomic assessments of bacterial diversity via 16S rRNA genes revealed centimeter- scale variability with depth, with similar taxa present in all samples, but their relative abundances varied substantially among horizons. There were significant correlation between changes in geochemical composition and changes in community structure. Additionally, functional gene abundance was correlated with energy potential and aligned with activity. The taxanomic data and porewater geochemistry from HFP sediments suggest that redox variations observed in iron and sulfur speciation result from depth-related changes in microbial activity and community structure over a diel period. By linking community diversity to metabolic activity in the context of the geochemical environment, this research provides valuable insight into the connectivity of iron and sulfur metabolic modes.

Microbial Communities Associated with Phosphorite-bearing Sediments

NASA Astrophysics Data System (ADS)

Zoss, R.; Bailey, J.; Flood, B.; Jones, D. S.

2016-12-01

Phosphorus is a limiting nutrient in the environment and is an important component of many biological molecules. Calcium phosphate mineral deposits known as phosphorites, are also the primary source of P for agriculture. Understanding phosphorite formation may improve management of P resources. However, the processes that mediate calcium phosphate mineral precipitation in certain marine pore waters remain poorly understood. Phosphogenesis occurs in sediments beneath some oceanic upwelling zones that harbor polyphosphate-accumulating giant sulfur bacteria (GSB). These bacteria may concentrate phosphate in sediment pore waters - creating supersaturated conditions with respect to apatite. However, the relationship between microbes and phosphogenesis is not fully resolved. To further study this relationship, we examined microbial communities from two sources: sediment cores recovered from the shelf of the Benguela region, and DNA extracted from washed phosphorites recovered from those same sediments. We used itag and clone library sequencing of the 16S rRNA gene to examine the microbial communities and their relationship with the environment. We found that many of our sediments shared large numbers of phylotypes with one another, and that the same metabolic guilds were represented at localities across the shelf. Sulfur-reducing bacteria and sulfur-oxidizing bacteria were abundant in our datasets. Phylotypes that are known to carry out nitrification and/or anammox (anaerobic ammonia oxidation) were also well-represented. Our phosphorite extraction, however, contained a distinct microbial community from those observed in the modern sediments. We observed both an enrichment of certain common microbial classes and a complete absence of others. These results could represent an ancient microbial assemblage that was present when the apatite precipitated. While these taxa may or may not have contributed to apatite precipitation, several groups represented in the phosphorite dataset have the genetic potential, as determined through the analysis of published genomes, to synthesize, and perhaps accumulate, polyphosphate.

A comparison of microbial communities in deep-sea polymetallic nodules and the surrounding sediments in the Pacific Ocean

NASA Astrophysics Data System (ADS)

Wu, Yue-Hong; Liao, Li; Wang, Chun-Sheng; Ma, Wei-Lin; Meng, Fan-Xu; Wu, Min; Xu, Xue-Wei

2013-09-01

Deep-sea polymetallic nodules, rich in metals such as Fe, Mn, and Ni, are potential resources for future exploitation. Early culturing and microscopy studies suggest that polymetallic nodules are at least partially biogenic. To understand the microbial communities in this environment, we compared microbial community composition and diversity inside nodules and in the surrounding sediments. Three sampling sites in the Pacific Ocean containing polymetallic nodules were used for culture-independent investigations of microbial diversity. A total of 1013 near full-length bacterial 16S rRNA gene sequences and 640 archaeal 16S rRNA gene sequences with ~650 bp from nodules and the surrounding sediments were analyzed. Bacteria showed higher diversity than archaea. Interestingly, sediments contained more diverse bacterial communities than nodules, while the opposite was detected for archaea. Bacterial communities tend to be mostly unique to sediments or nodules, with only 13.3% of sequences shared. The most abundant bacterial groups detected only in nodules were Pseudoalteromonas and Alteromonas, which were predicted to play a role in building matrix outside cells to induce or control mineralization. However, archaeal communities were mostly shared between sediments and nodules, including the most abundant OTU containing 290 sequences from marine group I Thaumarchaeota. PcoA analysis indicated that microhabitat (i.e., nodule or sediment) seemed to be a major factor influencing microbial community composition, rather than sampling locations or distances between locations.

Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities

PubMed Central

Cole, Jessica K; Peacock, Joseph P; Dodsworth, Jeremy A; Williams, Amanda J; Thompson, Daniel B; Dong, Hailiang; Wu, Geng; Hedlund, Brian P

2013-01-01

Great Boiling Spring is a large, circumneutral, geothermal spring in the US Great Basin. Twelve samples were collected from water and four different sediment sites on four different dates. Microbial community composition and diversity were assessed by PCR amplification of a portion of the small subunit rRNA gene using a universal primer set followed by pyrosequencing of the V8 region. Analysis of 164 178 quality-filtered pyrotags clearly distinguished sediment and water microbial communities. Water communities were extremely uneven and dominated by the bacterium Thermocrinis. Sediment microbial communities grouped according to temperature and sampling location, with a strong, negative, linear relationship between temperature and richness at all taxonomic levels. Two sediment locations, Site A (87–80 °C) and Site B (79 °C), were predominantly composed of single phylotypes of the bacterial lineage GAL35 (p̂=36.1%), Aeropyrum (p̂=16.6%), the archaeal lineage pSL4 (p̂=15.9%), the archaeal lineage NAG1 (p̂=10.6%) and Thermocrinis (p̂=7.6%). The ammonia-oxidizing archaeon ‘Candidatus Nitrosocaldus' was relatively abundant in all sediment samples <82 °C (p̂=9.51%), delineating the upper temperature limit for chemolithotrophic ammonia oxidation in this spring. This study underscores the distinctness of water and sediment communities in GBS and the importance of temperature in driving microbial diversity, composition and, ultimately, the functioning of biogeochemical cycles. PMID:23235293

Heterotrophic and Autotrophic Microbial Populations in Cold Perennial Springs of the High Arctic ▿ †

PubMed Central

Perreault, Nancy N.; Greer, Charles W.; Andersen, Dale T.; Tille, Stefanie; Lacrampe-Couloume, Georges; Lollar, Barbara Sherwood; Whyte, Lyle G.

2008-01-01

The saline springs of Gypsum Hill in the Canadian high Arctic are a rare example of cold springs originating from deep groundwater and rising to the surface through thick permafrost. The heterotrophic bacteria and autotrophic sulfur-oxidizing bacteria (up to 40% of the total microbial community) isolated from the spring waters and sediments were classified into four phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) based on 16S rRNA gene analysis; heterotrophic isolates were primarily psychrotolerant, salt-tolerant, facultative anaerobes. Some of the isolates contained genes for thiosulfate oxidation (soxB) and anoxygenic photosynthesis (pufM), possibly enabling the strains to better compete in these sulfur-rich environments subject to long periods of illumination in the Arctic summer. Although leucine uptake by the spring water microbial community was low, CO2 uptake was relatively high under dark incubation, reinforcing the idea that primary production by chemoautotrophs is an important process in the springs. The small amounts of hydrocarbons in gases exsolving from the springs (0.38 to 0.51% CH4) were compositionally and isotopically consistent with microbial methanogenesis and possible methanotrophy. Anaerobic heterotrophic sulfur oxidation and aerobic autotrophic sulfur oxidation activities were demonstrated in sediment slurries. Overall, our results describe an active microbial community capable of sustainability in an extreme environment that experiences prolonged periods of continuous light or darkness, low temperatures, and moderate salinity, where life seems to rely on chemolithoautotrophy. PMID:18805995

Biogeochemistry of a submerged groundwater seep ecosystem in Lake Huron near karst region of Alpena, MI

NASA Astrophysics Data System (ADS)

Kinsman-Costello, L. E.; Dick, G.; Sheik, C.; Burton, G. A.; Sheldon, N. D.

2015-12-01

Submerged groundwater seeps in Lake Huron establish ecosystems with distinctive geochemical conditions. In the Middle Island Sinkhole (MIS), a 23-m deep seep, groundwater seepage establishes low O2 (< 4 mg L-1), high sulfate (6 mM) conditions, in which a purple cyanobacteria-dominated mat thrives. The mat is capable of anoxygenic photosynthesis, oxygenic photosynthesis, and chemosynthesis. Within the top 3 cm of the mat-water interface, hydrogen sulfide concentrations increase to 1-7 mM. Little is known about the structure and function of microbes within organic-rich, high-sulfide sediments beneath the mat. Using pore water and sediment geochemical characterization along with microbial community analysis, we elucidated relationships between microbial community structure and ecosystem function along vertical gradients. In sediment pore waters, biologically reactive solutes (SO42-, NH4+, PO43-, and CH4) displayed steep vertical gradients, reflecting biological and geochemical functioning. In contrast, more conservative ions (Ca+2, Mg+2, Na+, and Cl-), did not change significantly with depth in MIS sediments, indicating groundwater influence in the sediment profile. MIS sediments contained more organic matter than typical Lake Huron sediments, and were generally higher in nutrients, metals, and sulfur (acid volatile sulfide). Using the Illumina MiSeq platform we detected 14,127 unique operational taxonomic units across sediment and surface mat samples. Microbial community composition in the MIS was distinctly different from non-groundwater affected areas at similar depth nearby in Lake Huron (ANOSIM, R= 0.74, p=0.002). MIS sediment communities were more diverse that MIS surface mat communities and changed with depth into sediments. MIS sediment community composition was related to several geochemical variables, including organic matter and multiple indicators of phosphorus availability. Elucidating the structure and function of microbial consortia in MIS, a highly unique and environmentally vulnerable ecosystem, provides a rare opportunity to understand relationships between microbial species and their environment and may provide insights into the evolution of life under ancient low-oxygen, high-sulfur conditions.

New microbes as causative agents of Ibuprofen degradation capabilities in the hyporheic zone of a lowland stream

NASA Astrophysics Data System (ADS)

Njeru, Cyrus; Posselt, Malte; Horn, Marcus A.

2017-04-01

Ibuprofen is a non-steroidal anti-inflammatory pain reliever and among pharmaceutical residues detected in aquatic environments. Widespread use of the drug and incomplete removal during waste water treatment results in its persistence in effluents and receiving waters. Potential total removal by microbial activity in the hyporheic zone (HZ) of rivers downstream of wastewater treatment plant discharge sites has been hypothesized. Ibuprofen degradation associated microbial communities in are essentially unknown. To address this hypothesis, two sets of oxic HZ sediment microcosms spiked with ibuprofen only (5, 40, 200 and 400 µM), or ibuprofen and 1 mM acetate were set up under laboratory conditions. Ibuprofen degradation in non-sterile relative to autoclaved sediments indicated removal by microbial degradation. Ibuprofen was completely consumed in the absence and presence of supplemental acetate after approximately 11 and 16 days, respectively. Refeeding of ibuprofen and acetate after the first depletion resulted in complete degradation within 24 hours in all treatments. Metabolites of ibuprofen included 1-, 2-, 3-hydroxy- and carboxyibuprofen. Quantitative real-time PCR revealed no pronounced differences in copy numbers of 16S rRNA gene or transcripts between non-spiked controls and treatments. Time resolved triplicate amplicon Illumina MiSeq sequencing targeting the 16S rRNA genes and transcripts revealed increased relative abundances of Proteobacteria, Acidobacteria, Actinobacteria and Firmicutes in treatments with compared to those without ibuprofen. Alpha-, Beta- and Deltaproteobacteria were most active as indicated by RNA based analyses. Enrichment and isolation yielded new Alphaproteobacteria utilizing ibuprofen as sole carbon and energy source. The collective results indicated that (i) HZ sediments sustain efficient biotic (micro-)pollutant removal and (ii) are a reservoir of hitherto unknown microbial diversity associated with such ecosystem services, including the genera Fodinicola, Hyphobacterium, and subgroup 6 Acidobacteria.

Interactions between microbial iron reduction and metal geochemistry: effect of redox cycling on transition metal speciation in iron bearing sediments.

PubMed

Cooper, D Craig; Picardal, Flynn F; Coby, Aaron J

2006-03-15

Microbial iron reduction is an important biogeochemical process that can affect metal geochemistry in sediments through direct and indirect mechanisms. With respectto Fe(III) (hydr)oxides bearing sorbed divalent metals, recent reports have indicated that (1) microbial reduction of goethite/ferrihydrite mixtures preferentially removes ferrihydrite, (2) this process can incorporate previously sorbed Zn(II) into an authigenic crystalline phase that is insoluble in 0.5 M HCl, (3) this new phase is probably goethite, and (4) the presence of nonreducible minerals can inhibit this transformation. This study demonstrates that a range of sorbed transition metals can be selectively sequestered into a 0.5 M HCl insoluble phase and that the process can be stimulated through sequential steps of microbial iron reduction and air oxidation. Microbial reduction experiments with divalent Cd, Co, Mn, Ni, Pb, and Zn indicate that all metals save Mn experienced some sequestration, with the degree of metal incorporation into the 0.5 M HCl insoluble phase correlating positively with crystalline ionic radius at coordination number = 6. Redox cycling experiments with Zn adsorbed to synthetic goethite/ferrihydrite or iron-bearing natural sediments indicate that redox cycling from iron reducing to iron oxidizing conditions sequesters more Zn within authigenic minerals than microbial iron reduction alone. In addition, the process is more effective in goethite/ferrihydrite mixtures than in iron-bearing natural sediments. Microbial reduction alone resulted in a -3x increase in 0.5 M HCl insoluble Zn and increased aqueous Zn (Zn-aq) in goethite/ferrihydrite, but did not significantly affect Zn speciation in natural sediments. Redox cycling enhanced the Zn sequestration by approximately 12% in both goethite/ferrihydrite and natural sediments and reduced Zn-aq to levels equal to the uninoculated control in goethite/ferrihydrite and less than the uninoculated control in natural sediments. These data suggest that in situ redox cycling may serve as an effective method for

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

PubMed Central

Mason, Olivia U; Scott, Nicole M; Gonzalez, Antonio; Robbins-Pianka, Adam; Bælum, Jacob; Kimbrel, Jeffrey; Bouskill, Nicholas J; Prestat, Emmanuel; Borglin, Sharon; Joyner, Dominique C; Fortney, Julian L; Jurelevicius, Diogo; Stringfellow, William T; Alvarez-Cohen, Lisa; Hazen, Terry C; Knight, Rob; Gilbert, Jack A; Jansson, Janet K

2014-01-01

The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of ∼4.1 million barrels of oil to the Gulf of Mexico; >22% of this oil is unaccounted for, with unknown environmental consequences. Here we investigated the impact of oil deposition on microbial communities in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using 14C-labeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant hydrocarbon degradation pathway encoded genes involved in degrading aliphatic and simple aromatics via butane monooxygenase. The activity of key hydrocarbon degradation pathways by sediment microbes was confirmed by determining the mineralization of 14C-labeled model substrates in the following order: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)'s benchmarks for polycyclic aromatic hydrocarbons (PAHs) compared with those that did not. Importantly, these data demonstrate that the indigenous sediment microbiota contributed an important ecosystem service for remediation of oil in the Gulf. However, PAHs were more recalcitrant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem. PMID:24451203

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mason, Olivia U.; Scott, Nicole M.; Gonzalez, Antonio

The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of ~4.1 million barrels of oil to the Gulf of Mexico; >22% of this oil is unaccounted for, with unknown environmental consequences. Here we investigated the impact of oil deposition on microbial communities in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using 14C-labeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, bothmore » of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant hydrocarbon degradation pathway encoded genes involved in degrading aliphatic and simple aromatics via butane monooxygenase. The activity of key hydrocarbon degradation pathways by sediment microbes was confirmed by determining the mineralization of 14C-labeled model substrates in the following order: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)’s benchmarks for polycyclic aromatic hydrocarbons (PAHs) compared with those that did not. Importantly, these data demonstrate that the indigenous sediment microbiota contributed an important ecosystem service for remediation of oil in the Gulf. However, PAHs were more recalcitrant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem.« less

Microbially catalyzed nitrate-dependent metal/radionuclide oxidation in shallow subsurface sediments

NASA Astrophysics Data System (ADS)

Weber, K.; Healy, O.; Spanbauer, T. L.; Snow, D. D.

2011-12-01

Anaerobic, microbially catalyzed nitrate-dependent metal/radionuclide oxidation has been demonstrated in a variety of sediments, soils, and groundwater. To date, studies evaluating U bio-oxidation and mobilization have primarily focused on anthropogenically U contaminated sites. In the Platte River Basin U originating from weathering of uranium-rich igneous rocks in the Rocky Mountains was deposited in shallow alluvial sediments as insoluble reduced uranium minerals. These reduced U minerals are subject to reoxidation by available oxidants, such nitrate, in situ. Soluble uranium (U) from natural sources is a recognized contaminant in public water supplies throughout the state of Nebraska and Colorado. Here we evaluate the potential of anaerobic, nitrate-dependent microbially catalyzed metal/radionuclide oxidation in subsurface sediments near Alda, NE. Subsurface sediments and groundwater (20-64ft.) were collected from a shallow aquifer containing nitrate (from fertilizer) and natural iron and uranium. The reduction potential revealed a reduced environment and was confirmed by the presence of Fe(II) and U(IV) in sediments. Although sediments were reduced, nitrate persisted in the groundwater. Nitrate concentrations decreased, 38 mg/L to 30 mg/L, with increasing concentrations of Fe(II) and U(IV). Dissolved U, primarily as U(VI), increased with depth, 30.3 μg/L to 302 μg/L. Analysis of sequentially extracted U(VI) and U(IV) revealed that virtually all U in sediments existed as U(IV). The presence of U(IV) is consistent with reduced Fe (Fe(II)) and low reduction potential. The increase in aqueous U concentrations with depth suggests active U cycling may occur at this site. Tetravalent U (U(IV)) phases are stable in reduced environments, however the input of an oxidant such as oxygen or nitrate into these systems would result in oxidation. Thus co-occurrence of nitrate suggests that nitrate could be used by bacteria as a U(IV) oxidant. Most probable number enumeration of nitrate-dependent U(IV) oxidizing microorganisms demonstrated an abundant community ranging from 1.61x104 to 2.74x104 cells g-1 sediment. Enrichments initiated verified microbial U reduction and U oxidation coupled to nitrate reduction. Sediment slurries were serially diluted and incubated over a period of eight weeks and compared to uninoculated controls. Oxidation (0-4,554 μg/L) and reduction (0-55 μg/L) of U exceeded uninoculated controls further providing evidence of a U biogeochemical cycling in these subsurface sediments. The oxidation of U(IV) could contribute to U mobilization in the groundwater and result in decreased water quality. Not only could nitrate serve as an oxidant, but Fe(III) could also contribute to U mobilization. Nitrate-dependent Fe(II) oxidation is an environmentally ubiquitous process facilitated by a diversity of microorganisms. Additional research is necessary in order to establish a role of biogenic Fe(III) oxides in U geochemical cycling at this site. These microbially mediated processes could also have a confounding effect on uranium mobility in subsurface environments.

Characterization of a Highly Enriched Microbial Consortium Reductively Dechlorinating 2,3-Dichlorophenol and 2,4,6-Trichlorophenol and the Corresponding cprA Genes from River Sediment.

PubMed

El-Sayed, Wael S

2016-08-26

Anaerobic reductive dechlorination of 2,3-dichlorophenol (2,3DCP) and 2,4,6-trichlorophenol (2,4,6TCP) was investigated in microcosms from River Nile sediment. A stable sediment-free anaerobic microbial consortium reductively dechlorinating 2,3DCP and 2,4,6TCP was established. Defined sediment-free cultures showing stable dechlorination were restricted to ortho chlorine when enriched with hydrogen as the electron donor, acetate as the carbon source, and either 2,3-DCP or 2,4,6-TCP as electron acceptors. When acetate, formate, or pyruvate were used as electron donors, dechlorination activity was lost. Only lactate can replace dihydrogen as an electron donor. However, the dechlorination potential was decreased after successive transfers. To reveal chlororespiring species, the microbial community structure of chlorophenol-reductive dechlorinating enrichment cultures was analyzed by PCR-denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Eight dominant bacteria were detected in the dechlorinating microcosms including members of the genera Citrobacter, Geobacter, Pseudomonas, Desulfitobacterium, Desulfovibrio and Clostridium. Highly enriched dechlorinating cultures were dominated by four bacterial species belonging to the genera Pseudomonas, Desulfitobacterium, and Clostridium. Desulfitobacterium represented the major fraction in DGGE profiles indicating its importance in dechlorination activity, which was further confirmed by its absence resulting in complete loss of dechlorination. Reductive dechlorination was confirmed by the stoichiometric dechlorination of 2,3DCP and 2,4,6TCP to metabolites with less chloride groups and by the detection of chlorophenol RD cprA gene fragments in dechlorinating cultures. PCR amplified cprA gene fragments were cloned and sequenced and found to cluster with the cprA/pceA type genes of Dehalobacter restrictus.

The Primary Results of Analyses on The Archaeal and Bacterial Diversity of Active Cave Environments Settled in Limestones at Southern Turkey

NASA Astrophysics Data System (ADS)

Tok, Ezgi; Kurt, Halil; Tunga Akarsubasi, A.

2016-04-01

The microbial diversity of cave sediments which are obtained from three different caves named Insuyu, Balatini and Altınbeşik located at Southern Turkey has been investigated using molecular methods for biomineralization . The total number of 22 samples were taken in duplicates from the critical zones of the caves at where the water activity is observed all year round. Microbial communities were monitored by 16S rRNA gene based PCR-DGGE (Polymerase Chain Reaction - Denaturating Gradient Gel Electrophoresis) methodology. DNA were extracted from the samples by The PowerSoil® DNA Isolation Kit (MO BIO Laboratories inc., CA) with the modifications on the producer's protocol. The synthetic DNA molecule poly-dIdC was used to increase the yield of PCR amplification via blocking the reaction between CaCO3 and DNA molecules. Thereafter samples were amplified by using both Archaeal and Bacterial universal primers (ref). Subsequently, archaeal and bacterial diversities in cave sediments, were investigated to be able to compare with respect to their similarities by using DGGE. DGGE patterns were analysed with BioNumerics software 5.1. Similarity matrix and dendograms of the DGGE profiles were generated based on the Dice correlation coefficient (band-based) and unweighted pair-group method with arithmetic mean (UPGMA). The structural diversity of the microbial community was examined by the Shannon index of general diversity (H). Similtaneously, geochemical analyses of the sediment samples were performed within the scope of this study. Total organic carbon (TOC), x-ray diffraction spectroscopy (XRD) and x-ray fluorescence spectroscopy (XRF) analysis of sediments were also implemented. The extensive results will be obtained at the next stages of the study currently carried on.

Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill

PubMed Central

Beazley, Melanie J.; Martinez, Robert J.; Rajan, Suja; Powell, Jessica; Piceno, Yvette M.; Tom, Lauren M.; Andersen, Gary L.; Hazen, Terry C.; Van Nostrand, Joy D.; Zhou, Jizhong; Mortazavi, Behzad; Sobecky, Patricia A.

2012-01-01

Coastal salt marshes are highly sensitive wetland ecosystems that can sustain long-term impacts from anthropogenic events such as oil spills. In this study, we examined the microbial communities of a Gulf of Mexico coastal salt marsh during and after the influx of petroleum hydrocarbons following the Deepwater Horizon oil spill. Total hydrocarbon concentrations in salt marsh sediments were highest in June and July 2010 and decreased in September 2010. Coupled PhyloChip and GeoChip microarray analyses demonstrated that the microbial community structure and function of the extant salt marsh hydrocarbon-degrading microbial populations changed significantly during the study. The relative richness and abundance of phyla containing previously described hydrocarbon-degrading bacteria (Proteobacteria, Bacteroidetes, and Actinobacteria) increased in hydrocarbon-contaminated sediments and then decreased once hydrocarbons were below detection. Firmicutes, however, continued to increase in relative richness and abundance after hydrocarbon concentrations were below detection. Functional genes involved in hydrocarbon degradation were enriched in hydrocarbon-contaminated sediments then declined significantly (p<0.05) once hydrocarbon concentrations decreased. A greater decrease in hydrocarbon concentrations among marsh grass sediments compared to inlet sediments (lacking marsh grass) suggests that the marsh rhizosphere microbial communities could also be contributing to hydrocarbon degradation. The results of this study provide a comprehensive view of microbial community structural and functional dynamics within perturbed salt marsh ecosystems. PMID:22815990

Connectivity of microbial populations in coral reef environments: microbiomes of sediment, fish and water

NASA Astrophysics Data System (ADS)

Biddle, J.; Leon, Z. R.; McCargar, M.; Drew, J.

2016-12-01

The benthic environments of coral reefs are heavily shaped by physiochemical factors, but also the ecological interactions of the animals and plants in the reef ecosystem. Microbial populations may be shared between the ecosystem of sediments, seagrasses and reef fish, however it is unknown to what degree. We investigated the potential connections between the microbiomes of sediments, seagrass blades and roots (Syringodium isoetifolium), Surgeonfish (A. nigricauda, Acanthurinae sp. unknown, C. striatus) and Parrotfish (C. spinidens) guts in reef areas of Fiji. We contrasted these with sediment samples from the Florida Keys and ocean water microbiomes from the Atlantic, Pacific and Indian Oceans. In general, we see a higher diversity of sediment microbial communities in Fiji compared to the Florida Keys. However, many of the same taxa are shared in these chemically similar environments, whereas the ocean water environments are completely distinct with few overlapping groups. We were able to show connectivity of a core microbiome between seagrass, fish and sediments in Fiji, including identifying a potential environmental reservoir of a surgeonfish symbiont, Epulopiscum. Finally, we show that fish guts have different microbial populations from crop to hindgut, and that microbial populations differ based on food source. The connection of these ecosystems suggest that the total microbiome of these environments may vary as their animal inhabitants shift in a changing ocean.

Microbial eukaryotic distributions and diversity patterns in a deep-sea methane seep ecosystem.

PubMed

Pasulka, Alexis L; Levin, Lisa A; Steele, Josh A; Case, David H; Landry, Michael R; Orphan, Victoria J

2016-09-01

Although chemosynthetic ecosystems are known to support diverse assemblages of microorganisms, the ecological and environmental factors that structure microbial eukaryotes (heterotrophic protists and fungi) are poorly characterized. In this study, we examined the geographic, geochemical and ecological factors that influence microbial eukaryotic composition and distribution patterns within Hydrate Ridge, a methane seep ecosystem off the coast of Oregon using a combination of high-throughput 18S rRNA tag sequencing, terminal restriction fragment length polymorphism fingerprinting, and cloning and sequencing of full-length 18S rRNA genes. Microbial eukaryotic composition and diversity varied as a function of substrate (carbonate versus sediment), activity (low activity versus active seep sites), sulfide concentration, and region (North versus South Hydrate Ridge). Sulfide concentration was correlated with changes in microbial eukaryotic composition and richness. This work also revealed the influence of oxygen content in the overlying water column and water depth on microbial eukaryotic composition and diversity, and identified distinct patterns from those previously observed for bacteria, archaea and macrofauna in methane seep ecosystems. Characterizing the structure of microbial eukaryotic communities in response to environmental variability is a key step towards understanding if and how microbial eukaryotes influence seep ecosystem structure and function. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Trace fossils of microbial colonization on Mars: Criteria for search and for sample return

NASA Technical Reports Server (NTRS)

Friedmann, E. I.

1988-01-01

The recent discovery of microbial trace-fossil formation in the frigid Ross Desert of Antarctica suggests that early primitive life on Mars may have left behind similar signatures. These trace fossils are apparent as chemical or physical changes in rock (or sediment) structure (or chemistry) caused by the activity of organisms. Life on Mars, if it ever existed, almost certainly did not evolve above the level of microorganisms, and this should be considered in search for fossil life. For the reasons detailed here, microbial trace fossils seem to be a better and more realistic target for search than would be true microbial fossils (remnants of cellular structures).

Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile.

PubMed

Zhu, Renbin; Shi, Yu; Ma, Dawei; Wang, Can; Xu, Hua; Chu, Haiyan

2015-11-25

Current penguin activity in Antarctica affects the geochemistry of sediments and their microbial communities; the effects of historical penguin activity are less well understood. Here, bacterial diversity in ornithogenic sediment was investigated using high-throughput pyrosequencing. The relative abundances of dominant phyla were controlled by the amount of historical penguin guano deposition. Significant positive correlations were found between both the bacterial richness and diversity, and the relative penguin number (p < 0.01); this indicated that historical penguin activity drove the vertical distribution of the bacterial communities. The lowest relative abundances of individual phyla corresponded to lowest number of penguin population at 1,800-2,300 yr BP during a drier and colder period; the opposite was observed during a moister and warmer climate (1,400-1,800 yr BP). This study shows that changes in the climate over millennia affected penguin populations and the outcomes of these changes affect the sediment bacterial community today.

Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile

PubMed Central

Zhu, Renbin; Shi, Yu; Ma, Dawei; Wang, Can; Xu, Hua; Chu, Haiyan

2015-01-01

Current penguin activity in Antarctica affects the geochemistry of sediments and their microbial communities; the effects of historical penguin activity are less well understood. Here, bacterial diversity in ornithogenic sediment was investigated using high-throughput pyrosequencing. The relative abundances of dominant phyla were controlled by the amount of historical penguin guano deposition. Significant positive correlations were found between both the bacterial richness and diversity, and the relative penguin number (p < 0.01); this indicated that historical penguin activity drove the vertical distribution of the bacterial communities. The lowest relative abundances of individual phyla corresponded to lowest number of penguin population at 1,800–2,300 yr BP during a drier and colder period; the opposite was observed during a moister and warmer climate (1,400–1,800 yr BP). This study shows that changes in the climate over millennia affected penguin populations and the outcomes of these changes affect the sediment bacterial community today. PMID:26601753

Exploration of Microbial Diversity and Community Structure of Lonar Lake: The Only Hypersaline Meteorite Crater Lake within Basalt Rock

PubMed Central

Paul, Dhiraj; Kumbhare, Shreyas V.; Mhatre, Snehit S.; Chowdhury, Somak P.; Shetty, Sudarshan A.; Marathe, Nachiket P.; Bhute, Shrikant; Shouche, Yogesh S.

2016-01-01

Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21–47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments. PMID:26834712

Salinity is a key factor driving the nitrogen cycling in the mangrove sediment.

PubMed

Wang, Haitao; Gilbert, Jack A; Zhu, Yongguan; Yang, Xiaoru

2018-08-01

Coastal ecosystems are hotspots for nitrogen cycling, and specifically for nitrogen removal from water and sediment through the coupled nitrification-denitrification process. Salinity is globally important in structuring bacterial and archaeal communities, but the association between salinity and microbially-mediated nitrification and denitrification remains unclear. The denitrification activity and composition and structure of microbial nitrifiers and denitrifiers were characterized across a gradient of manipulated salinity (0, 10, 20 and 30ppt) in a mangrove sediment. Salinity negatively correlated with both denitrifying activity and the abundance of nirK and nosZ denitrifying genes. Ammonia-oxidizing bacteria (AOB), which dominated nitrification, had significantly greater abundance at intermediate salinity (10 and 20ppt). However, a positive correlation between ammonia concentration and salinity suggested that nitrifying activity might also be inhibited at higher salinity. The community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nirK, nirS and nosZ denitrifying communities, were all significantly correlated with salinity. These changes were also associated with structural shifts in phylogeny. These findings provide a strong evidence that salinity is a key factor that influences the nitrogen transformations in coastal wetlands, indicating that salinity intrusion caused by climate change might have a broader impact on the coastal biospheres. Copyright © 2018 Elsevier B.V. All rights reserved.

Impact of natural oil and higher hydrocarbons on microbial diversity, distribution, and activity in Gulf of Mexico cold-seep sediments

NASA Astrophysics Data System (ADS)

Orcutt, Beth N.; Joye, Samantha B.; Kleindienst, Sara; Knittel, Katrin; Ramette, Alban; Reitz, Anja; Samarkin, Vladimir; Treude, Tina; Boetius, Antje

2010-11-01

Gulf of Mexico cold seeps characterized by variable compositions and magnitudes of hydrocarbon seepage were sampled in order to investigate the effects of natural oils, methane, and non-methane hydrocarbons on microbial activity, diversity, and distribution in seafloor sediments. Though some sediments were characterized by relatively high quantities of oil, which may be toxic to some microorganisms, high rates of sulfate reduction (SR, 27.9±14.7 mmol m-2 d-1), anaerobic oxidation of methane (AOM, 16.2±6.7 mmol m-2 d-1), and acetate oxidation (2.74±0.76 mmol m-2 d-1) were observed in radiotracer measurements. In many instances, the SR rate was higher than the AOM rate, indicating that non-methane hydrocarbons fueled SR. Analysis of 16S rRNA gene clone libraries revealed phylogenetically diverse communities that were dominated by phylotypes of sulfate-reducing bacteria (SRB) and anaerobic methanotrophs of the ANME-1 and ANME-2 varieties. Another group of archaea form a Gulf of Mexico-specific clade (GOM ARC2) that may be important in brine-influenced, oil-impacted sediments from deeper water. Additionally, species grouping within the uncultivated Deltaproteobacteria clades SEEP-SRB3 and -SRB4, as well as relatives of Desulfobacterium anilini, were observed in relatively higher abundance in the oil-impacted sediments, suggesting that these groups of SRB may be involved in or influenced by degradation of higher hydrocarbons or petroleum byproducts.

Microbial Community Response to Carbon Substrate Amendment in Mercury Impacted Sediments: Implications on Microbial Methylation of Mercury.

NASA Astrophysics Data System (ADS)

Elias, D. A.; Somenahally, A. C.; Moberly, J. G.; Hurt, R. A., Jr.; Brown, S. D.; Podar, M.; Palumbo, A. V.; Gilmour, C. C.

2015-12-01

Methylmercury (MeHg) is a neurotoxic and bio-accumulative product of the microbial methylation of inorganic mercury (Hg(II)). Methylating organisms are now known to exist in almost all anaerobic niches including fermentation, Fe(III)- and sulfate- reduction as well as methanogenesis. The study objective was to determine the effect of different carbon sources on the microbial community and methylating populations in particular along a Hg contaminated creek. Sediment cores from upstream and downstream at the Hg contaminated East Fork Poplar Creek (EFPC), Oak Ridge TN, and a background site were sectioned by depth, and Hg-methylation potential (HgMP) assays were performed using stable isotope spikes. Sediments from the lowest depth possessed the highest in-situ activity. Replicate samples were amended with different carbon substrates (cellulose, acetate, propionate, lactate, ethanol and methanol), spiked with stable isotopes for HgMP assays and incubated for 24hrs. Sequencing of the 16S rRNA gene was performed to determine alterations in Bacterial and Archaeal population dynamics. Additionally, bioinformatics and our new qualitative and quantitative hgcAB primers were utilized to determine microbial community structure alterations and correlate organism and gene abundance with altered MeHg generation. HgMP was significantly reduced in cellulose amended sediments while acetate and propionate slightly decreased HgMP in both sites. Methanol, ethanol and lactate increased the HgMP in EFPC downstream while cellulose amendment significantly decreased the Proteobacteria, and the Firmicutes increased but none are currently known to produce MeHg. Geobacter bemidjiensis in particular significantly decreased in cellulose amended sediments in all three sites from being predominant in-situ. This suggests that in EFPC downstream and background sites, the prevalent Hg-methyaltors might be Deltaprotebacteria, since upstream, cellulose amendment did not reduce HgMP even though relative composition of Deltaproteobacteria decreased significantly. Hence the phylogenetic distribution of Hg-methylating bacteria upstream may be much broader. Most Archaea belonged to either Euryarchaeota or Crenarchaeota, but there were no consistent trends with specific groups among the treatments.

Geomicrobiology of basal ice in a temperate glacier: implications for primary microbial production and export, elemental cycling and soil formation

NASA Astrophysics Data System (ADS)

Toubes-Rodrigo, Mario; Potgieter-Vermaak, Sanja; Sen, Robin; Elliott, David R.; Cook, Simon J.

2017-04-01

Basal ice is a significant sub-glacial component of glaciers and ice sheets that arises from ice-bedrock/substrate interaction. As a result, basal ice of a glacier retains a distinctive physical and chemical signature characterised by a high sediment- and low bubble-content and selective ionic enrichment. Previous research concluded that sediment entrapped in the basal ice matrix originates from the bedrock/substrate, and harbours an active microbial community. However, the nature and significance of the microbial community inhabiting basal ice facies remains poorly characterised. This paper reports on an integrated chemical, mineralogical, and microbial community analysis of basal ice in the subglacial environment at Svínafellsjökull, in south-east Iceland. Basal ice sediment supported 10E7 cells g^-1 and, based on glacier velocity and sediment flux, an estimated 10E17 cells a^-1 are exported to the glacier foreland. Furthermore, 16S rRNA gene analysis highlighted a glacier basal ice bacterial community dominated by Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi. Sequences ascribed to chemolithotrophic-related species (Thiobacillus, Syderoxidans) were highly abundant. Minerological analyses of basal ice sediment confirmed dominant silicates and iron-containing minerals that represent susceptible substrates open to oxidation by the aforementioned chemolithotrophs. Previous studies have suggested that basal ice could constitute a good analogue for astrobiology. Svínafellsjökull and Mars geology are similar - volcanically derived rocks with a high abundance of silicates and iron-rich minerals, reinforcing this idea. Understanding where the limits of life in extreme environments, such as debris-rich basal ice, could help to unravel how life on other planets could succeed, and could help to identify which markers to use in order to find it. In dark and isolated basal ice niches, the dominating chemolithotrophic bacterial community are likely to act as primary producers, fixing carbon while weathering minerals and thus providing a plausible mechanism to explain how a basal ice microbial ecosystem can be sustained.

Autonomous, Retrievable, Deep Sea Microbial Fuel Cell

NASA Astrophysics Data System (ADS)

Richter, K.

2014-12-01

Microbial fuel cells (MFCs) work by providing bacteria in anaerobic sediments with an electron acceptor (anode) that stimulates metabolism of organic matter. The buried anode is connected via control circuitry to a cathode exposed to oxygen in the overlying water. During metabolism, bacteria release hydrogen ions into the sediment and transfer electrons extra-cellularly to the anode, which eventually reduce dissolved oxygen at the cathode, forming water. The open circuit voltage is approximately 0.8 v. The voltage between electrodes is operationally kept at 0.4 v with a potentiastat. The current is chiefly limited by the rate of microbial metabolism at the anode. The Office of Naval Research has encouraged development of microbial fuel cells in the marine environment at a number of academic and naval institutions. Earlier work in shallow sediments of San Diego Bay showed that the most important environmental parameters that control fuel cell power output in San Diego Bay were total organic carbon in the sediment and seasonal water temperature. Current MFC work at SPAWAR includes extension of microbial fuel cell tests to the deep sea environment (>1000 m) and, in parallel, testing microbial fuel cells in the laboratory under deep sea conditions. One question we are asking is whether MFC power output from deep water sediments repressurized and chilled in the laboratory comparable to those measured in situ. If yes, mapping the power potential of deep sea sediments may be made much easier, requiring sediment grabs and lab tests rather than deployment and retrieval of fuel cells. Another question we are asking is whether in situ temperature and total organic carbon in the deep sea sediment can predict MFC power. If yes, then we can make use of the large collection of publicly available, deep sea oceanographic measurements to make these predictions, foregoing expensive work at sea. These regressions will be compared to those derived from shallow water measurements.

Mercury cycling in stream ecosystems. 2. Benthic methylmercury production and bed sediment - Pore water partitioning

USGS Publications Warehouse

Marvin-DiPasquale, Mark; Lutz, Michelle A; Brigham, Mark E.; Krabbenhoft, David P.; Aiken, George R.; Orem, William H.; Hall, Britt D.

2009-01-01

Mercury speciation, controls on methylmercury (MeHg) production, and bed sediment−pore water partitioning of total Hg (THg) and MeHg were examined in bed sediment from eight geochemically diverse streams where atmospheric deposition was the predominant Hg input. Across all streams, sediment THg concentrations were best described as a combined function of sediment percent fines (%fines; particles < 63 μm) and organic content. MeHg concentrations were best described as a combined function of organic content and the activity of the Hg(II)-methylating microbial community and were comparable to MeHg concentrations in streams with Hg inputs from industrial and mining sources. Whole sediment tin-reducible inorganic reactive Hg (Hg(II)R) was used as a proxy measure for the Hg(II) pool available for microbial methylation. In conjunction with radiotracer-derived rate constants of 203Hg(II) methylation, Hg(II)R was used to calculate MeHg production potential rates and to explain the spatial variability in MeHg concentration. The %Hg(II)R (of THg) was low (2.1 ± 5.7%) and was inversely related to both microbial sulfate reduction rates and sediment total reduced sulfur concentration. While sediment THg concentrations were higher in urban streams, %MeHg and %Hg(II)R were higher in nonurban streams. Sediment pore water distribution coefficients (log Kd’s) for both THg and MeHg were inversely related to the log-transformed ratio of pore water dissolved organic carbon (DOC) to bed sediment %fines. The stream with the highest drainage basin wetland density also had the highest pore water DOC concentration and the lowest log Kd’s for both THg and MeHg. No significant relationship existed between overlying water MeHg concentrations and those in bed sediment or pore water, suggesting upstream sources of MeHg production may be more important than local streambed production as a driver of water column MeHg concentration in drainage basins that receive Hg inputs primarily from atmospheric sources.

Structures of benthic prokaryotic communities and their hydrolytic enzyme activities resuspended from samples of intertidal mudflats: An experimental approach

NASA Astrophysics Data System (ADS)

Mallet, Clarisse; Agogué, Hélène; Bonnemoy, Frédérique; Guizien, Katell; Orvain, Francis; Dupuy, Christine

2014-09-01

Resuspended sediment can increase plankton biomass and the growth of bacteria, thus influencing the coastal planktonic microbial food web. But little is known about resuspension itself: is it a single massive change or a whole series of events and how does it affect the quantity and quality of resuspended prokaryotic cells? We simulated the sequential erosion of mud cores to better understand the fate and role of benthic prokaryotes resuspended in the water column. We analyzed the total, attached and free-living prokaryotic cells resuspended, their structure and the activities of their hydrolytic enzymes in terms of the biotic and abiotic factors that affect the composition of microphytobenthic biofilm. Free living prokaryotes were resuspended during the fluff layer erosion phase (for shear velocities below 5 cm · s- 1) regardless of the bed sediment composition. At the higher shear velocities, resuspended prokaryotes were attached to particulate matter. Free and attached cells are thus unevenly distributed, scattered throughout the organic matter (OM) in the uppermost mm of the sediment. Only 10-27% of the total cells initially resuspended were living and most of the Bacteria were Cyanobacteria and Gamma-proteobacteria; their numbers increased to over 30% in parallel with the hydrolytic enzyme activity at highest shear velocity. These conditions released prokaryotic cells having different functions that lie deep in the sediment; the most important of them are Archaea. Finally, composition of resuspended bacterial populations varied with resuspension intensity, and intense resuspension events boosted the microbial dynamics and enzyme activities in the bottom layers of sea water.

Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments.

PubMed

Li, Dong; Sharp, Jonathan O; Drewes, Jörg E

2016-01-01

To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction-modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants.

Uranium Biomineralization by Natural Microbial Phosphatase Activities in the Subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sobecky, Patricia A.

2015-04-06

In this project, inter-disciplinary research activities were conducted in collaboration among investigators at The University of Alabama (UA), Georgia Institute of Technology (GT), Lawrence Berkeley National Laboratory (LBNL), Brookhaven National Laboratory (BNL), the DOE Joint Genome Institute (JGI), and the Stanford Synchrotron Radiation Light source (SSRL) to: (i) confirm that phosphatase activities of subsurface bacteria in Area 2 and 3 from the Oak Ridge Field Research Center result in solid U-phosphate precipitation in aerobic and anaerobic conditions; (ii) investigate the eventual competition between uranium biomineralization via U-phosphate precipitation and uranium bioreduction; (iii) determine subsurface microbial community structure changes of Areamore » 2 soils following organophosphate amendments; (iv) obtain the complete genome sequences of the Rahnella sp. Y9-602 and the type-strain Rahnella aquatilis ATCC 33071 isolated from these soils; (v) determine if polyphosphate accumulation and phytate hydrolysis can be used to promote U(VI) biomineralization in subsurface sediments; (vi) characterize the effect of uranium on phytate hydrolysis by a new microorganism isolated from uranium-contaminated sediments; (vii) utilize positron-emission tomography to label and track metabolically-active bacteria in soil columns, and (viii) study the stability of the uranium phosphate mineral product. Microarray analyses and mineral precipitation characterizations were conducted in collaboration with DOE SBR-funded investigators at LBNL. Thus, microbial phosphorus metabolism has been shown to have a contributing role to uranium immobilization in the subsurface.« less

Characterization of anaerobic heterotrophic bacteria isolated from freshwater lake sediments.

PubMed Central

Molongoski, J J; Klug, M J

1976-01-01

Strict anaerobic culture techniques were used to quantitatively and qualitatively evaluate the anaerobic heterotrophic bacteria present at the sediment-water interface of hyperutrophic Wintergreen Lake (Augusta, Mich.). Anaerobic plate counts remained constant from March through December, 1973, ranging from 2.4 X 10(6) to 5.7 X 10(6) organisms/g (dry weight) of sediment. The isolatable bacteria represented a small percentage of the total microbial community, which was shown by direct microscopic counts to be 2.0 X 10'' organisms/g (dry weight) of sediment during June and July. Bacteria of the genus Clostridium dominated the isolates obtained, accounting for 71.8% of the 960 isolates examined. A single species, Clostridium bifermentens, comprised 47.7% of the total. Additional bacterial groups and the percentage in which they were isolated included: Streptococcus sp. (10.8%), unidentified curved rods (9.5%y, gram-positive nonsporing rods (5.6%), and motile gram-negative rods (1.9%). Temperature growth studies demonstrated the ability of all the isolates to grow at in situ sediment temperatures. Gas-liqid radiochromatography was used to determine the soluble metabolic end products from [U-14C]glucose and a U-14C-labeled amino acid mixture by representative sedimentary clostridial isolates and by natural sediment microbial communities. At in situ temperatures the natural sediment microflora produced soluble fermentative end products characteristic of those elaborated by the clostridial isolates tested. These results are considered strong presumptive evidence that clostridia are actively metabolizing in the sediments of Wintergreen Lake. PMID:942211

Isoprenoid quinones resolve the stratification of microbial redox processes in a biogeochemical continuum from the photic zone to deep anoxic sediments of the Black Sea.

PubMed

Becker, Kevin W; Elling, Felix J; Schröder, Jan M; Lipp, Julius S; Goldhammer, Tobias; Zabel, Matthias; Elvert, Marcus; Overmann, Jörg; Hinrichs, Kai-Uwe

2018-03-09

The stratified water column of the Black Sea serves as a model ecosystem for studying the interactions of microorganisms with major biogeochemical cycles. Here we provide detailed analysis of isoprenoid quinones to study microbial redox processes in the ocean. In a continuum from the photic zone through the chemocline into deep anoxic sediments of the southern Black Sea, diagnostic quinones and inorganic geochemical parameters indicate niche segregation between redox processes and corresponding shifts in microbial community composition. Quinones specific for oxygenic photosynthesis and aerobic respiration dominate oxic waters, while quinones associated with thaumarchaeal ammonia-oxidation and bacterial methanotrophy, respectively, dominate a narrow interval in suboxic waters. Quinone distributions indicate highest metabolic diversity within the anoxic zone, with anoxygenic photosynthesis being a major process in its photic layer. In the dark anoxic layer, quinone profiles indicate occurrence of bacterial sulfur and nitrogen cycling, archaeal methanogenesis, and archaeal methanotrophy. Multiple novel ubiquinone isomers, possibly originating from unidentified intra-aerobic anaerobes, occur in this zone. The respiration modes found in the anoxic zone continue into shallow subsurface sediments, but quinone abundances rapidly decrease within the upper 50 cm below sea floor, reflecting the transition to lower energy availability. In the deep subseafloor sediments, quinone distributions and geochemical profiles indicate archaeal methanogenesis/methanotrophy and potentially bacterial fermentative metabolisms. We observed that sedimentary quinone distributions track lithology, which supports prior hypotheses that deep biosphere community composition and metabolisms are determined by environmental conditions during sediment deposition. Importance Microorganisms play crucial roles in global biogeochemical cycles. Yet, we have only a fragmentary understanding of the diversity of microorganisms and their metabolisms, as the majority remains uncultured. Thus, culture-independent approaches are critical for determining microbial diversity and active metabolic processes. In order to resolve the stratification of microbial communities in the Black Sea, we comprehensively analyzed redox process-specific isoprenoid quinone biomarkers in a unique continuous record from the photic zone through the chemocline into anoxic subsurface sediments. We describe an unprecedented quinone diversity that allowed us to detect distinct biogeochemical processes including oxygenic photosynthesis, archaeal ammonia oxidation, aerobic methanotrophy and anoxygenic photosynthesis in defined geochemical zones. Copyright © 2018 American Society for Microbiology.

Methanogenesis in the sediment of the acidic Lake Caviahue in Argentina

NASA Astrophysics Data System (ADS)

Koschorreck, Matthias; Wendt-Potthoff, Katrin; Scharf, Burkhard; Richnow, Hans H.

2008-12-01

The biogeochemistry of methane in the sediments of Lake Caviahue was examined by geochemical analysis, microbial activity assays and isotopic analysis. The pH in the water column was 2.6 and increased up to a pH of 6 in the deeper sediment pore waters. The carbon isotope composition of CH 4 was between - 65 and - 70‰ which is indicative for the biological origin of the methane. The enrichment factor ɛ increased from - 46‰ in the upper sediment column to more than - 80 in the deeper sediment section suggesting a transition from acetoclastic methanogenesis to CO 2 reduction with depth. In the most acidic surface layer of the sediment (pH < 4) methanogenesis is inhibited as suggested by a linear CH 4 concentration profile, activity assays and MPN analysis. The CH 4 activity assays and the CH 4 profile indicate that methanogenesis in the sediment of Lake Caviahue was active below 40 cm depth. At that depth the pH was above 4 and sulfate reduction was sulfate limited. Methane was diffusing with a flux of 0.9 mmol m - 2 d - 1 to the sediment surface where it was probably oxidized. Methanogenesis contributed little to the sediments carbon budget and had no significant impact on lake water quality. The high biomass content of the sediment, which was probably caused by the last eruption of Copahue Volcano, supported high rates of sulfate reduction which probably raised the pH and created favorable conditions for methanogens in deeper sediment layers.

Geophysical Monitoring of Coupled Microbial and Geochemical Processes During Stimulated Subsurface Bioremediation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Kenneth H.; Kemna, Andreas; Wilkins, Michael J.

2009-08-05

Understanding how microorganisms alter their physical and chemical environment during bioremediation is hindered by our inability to resolve subsurface microbial activity with high spatial resolution. Here we demonstrate the use of a minimally invasive geophysical technique to monitor stimulated microbial activity during acetate amendment in an aquifer near Rifle, Colorado. During electrical induced polarization (IP) measurements, spatiotemporal variations in the phase response between imposed electric current and the resultant electric field correlated with changes in groundwater geochemistry accompanying stimulated iron and sulfate reduction and sulfide mineral precipitation. The magnitude of the phase response varied with measurement frequency (0.125 and 1more » Hz) andwasdependent upon the dominant metabolic process. The spectral effect was corroborated using a biostimulated column experiment containing Rifle sediments and groundwater. Fluids and sediments recovered from regions exhibiting an anomalous phase response were enriched in Fe(II), dissolved sulfide, and cell-associated FeS nanoparticles. The accumulation of mineral precipitates and electroactive ions altered the ability of pore fluids to conduct electrical charge, accounting for the anomalous IP response and revealing the usefulness of multifrequency IP measurements for monitoring mineralogical and geochemical changes accompanying stimulated subsurface bioremediation.« less

Characteristics of environmental correlations between iron (oxyhydr)oxide nanoparticles and microbial activity

NASA Astrophysics Data System (ADS)

Tamura, T.; Kyono, A.; Muratani, M.

2014-12-01

Nanoparticulate iron oxides and oxyhydroxides with large surface area and high chemical reactivity cause the immobilization of heavy metals and the provision of essential nutrients to organisms. Environmental correlations between microbial activity and nanomorphology of iron (oxyhydr)oxides are significantly important for earth surface processes. In this study, we characterize iron (oxyhydr)oxide nanoparticles and microorganisms in natural lake sediments and describe their association observed between particle nanostructures and microbial species. About 40 cm depth of boring core sample was collected from Lake Kasumigaura, Lake Ushiku, Kokai River and Lake Tega, Japan. To distinguish both iron nanoparticles and growing bacterial colonies with depths, boring core samples were divided into three to five pieces. Particle morphologies, size, aggregation states, mineral species, and microorganisms were observed by transmission electron microscopy (TEM), X-ray diffraction (XRD), and rRNA gene sequences. Redox potential and pH of the lake sediments were also measured. The core sample from top is mainly composed of quartz of coarse-grained materials, while that from bottom is of ferrihydrite of fine grained materials. The authors will show the results of experiments and discuss the interrelation between iron nanoparticles and microorganisms.

Microbial Biogeography on the Legacies of Historical Events in the Arctic Subsurface Sediments

NASA Astrophysics Data System (ADS)

Han, Dukki; Nam, Seung-Il; Hur, Hor-Gil

2017-04-01

The Arctic marine environment consists of various microbial habitats. The niche preference of microbial assemblages in the Arctic Ocean has been surveyed with the modern environmental change by oceanographic traits such as sea-ice dynamics, current circulation, and sedimentation. The North Pacific inflow from the shallow and narrow Bering Strait is highly susceptible to sea-level fluctuations, and thus the water mass exchange mediated by the history of sea-ice between the North Pacific and the Chukchi Sea in the Arctic Ocean. Over geological timescale, the climate change may provide putative evidences for ecological niche for the Arctic microbial assemblages as well as geological records in response to the paleoclimate change. In the present study, the multidisciplinary approach, based on microbiology, geology, and geochemistry, was applied to survey the microbial assemblages in the Arctic subsurface sediments and help further integrate the microbial biogeography and biogeochemical patterns in the Arctic subsurface biosphere. Our results describe microbial assemblages with high-resolution paleoceanographic records in the Chukchi Sea sediment core (ARA02B/01A-GC; 5.4 mbsf) to show the processes that drive microbial biogeographic patterns in the Arctic subsurface sediments. We found microbial habitat preferences closely linked to Holocene paleoclimate records as well as geological, geochemical, and microbiological evidence for the inference of the sulphate-methane transition zone (SMTZ) in the Chukchi Sea. Especially, the vertically distributed predominant populations of Gammaproteobacteria and Marine Group II Euryarchaeota in the ARA02B/01A-GC consistent with the patterns of the known global SMTZs and Holocene sedimentary records, suggesting that in-depth microbiological profiles integrated with geological records may be indirectly useful for reconstructing Arctic paleoclimate changes. In the earliest phase of Mid Holocene in the ARA02B/01A-GC with concentrated crenarchaeol (a unique biomarker for Marine Group I Thaumarchaea), the most abundant archaeal population was Marine Group II Euryarchaeota rather than Marine Group I Thaumarchaea, suggesting that the interpretation of archaeal tetraether lipids in subsurface sediments needs careful consideration for paleoceanography. In conclusion, our findings have important implications for the availability of microbial biogeography in the sedimentary record. The present study offers a deeper understanding of the legacies of historical events during the Holocene and implies that the survey of microbial biogeography may be an appropriate tool to monitor potential effects from the climate change in the Arctic Ocean.

D:L-Amino Acid Modeling Reveals Fast Microbial Turnover of Days to Months in the Subsurface Hydrothermal Sediment of Guaymas Basin.

PubMed

Møller, Mikkel H; Glombitza, Clemens; Lever, Mark A; Deng, Longhui; Morono, Yuki; Inagaki, Fumio; Doll, Mechthild; Su, Chin-Chia; Lomstein, Bente A

2018-01-01

We investigated the impact of temperature on the microbial turnover of organic matter (OM) in a hydrothermal vent system in Guaymas Basin, by calculating microbial bio- and necromass turnover times based on the culture-independent D:L-amino acid model. Sediments were recovered from two stations near hydrothermal mounds (<74°C) and from one cold station (<9°C). Cell abundance at the two hydrothermal stations dropped from 10 8 to 10 6 cells cm -3 within ∼5 m of sediment depth resulting in a 100-fold lower cell number at this depth than at the cold site where numbers remained constant at 10 8 cells cm -3 throughout the recovered sediment. There were strong indications that the drop in cell abundance was controlled by decreasing OM quality. The quality of the sedimentary OM was determined by the diagenetic indicators %T AA C (percentage of total organic carbon present as amino acid carbon), %T AA N (percentage of total nitrogen present as amino acid nitrogen), aspartic acid:β-alanine ratios, and glutamic acid:γ-amino butyric acid ratios. All parameters indicated that the OM became progressively degraded with increasing sediment depth, and the OM in the hydrothermal sediment was more degraded than in the uniformly cold sediment. Nonetheless, the small community of microorganisms in the hydrothermal sediment demonstrated short turnover times. The modeled turnover times of microbial bio- and necromass in the hydrothermal sediments were notably faster (biomass: days to months; necromass: up to a few hundred years) than in the cold sediments (biomass: tens of years; necromass: thousands of years), suggesting that temperature has a significant influence on the microbial turnover rates. We suggest that short biomass turnover times are necessary for maintance of essential cell funtions and to overcome potential damage caused by the increased temperature.The reduced OM quality at the hyrothemal sites might thus only allow for a small population size of microorganisms.

Microbial Community Responses to Organophosphate Substrate Additions in Contaminated Subsurface Sediments

PubMed Central

Martinez, Robert J.; Wu, Cindy H.; Beazley, Melanie J.; Andersen, Gary L.; Conrad, Mark E.; Hazen, Terry C.; Taillefert, Martial; Sobecky, Patricia A.

2014-01-01

Background Radionuclide- and heavy metal-contaminated subsurface sediments remain a legacy of Cold War nuclear weapons research and recent nuclear power plant failures. Within such contaminated sediments, remediation activities are necessary to mitigate groundwater contamination. A promising approach makes use of extant microbial communities capable of hydrolyzing organophosphate substrates to promote mineralization of soluble contaminants within deep subsurface environments. Methodology/Principal Findings Uranium-contaminated sediments from the U.S. Department of Energy Oak Ridge Field Research Center (ORFRC) Area 2 site were used in slurry experiments to identify microbial communities involved in hydrolysis of 10 mM organophosphate amendments [i.e., glycerol-2-phosphate (G2P) or glycerol-3-phosphate (G3P)] in synthetic groundwater at pH 5.5 and pH 6.8. Following 36 day (G2P) and 20 day (G3P) amended treatments, maximum phosphate (PO4 3−) concentrations of 4.8 mM and 8.9 mM were measured, respectively. Use of the PhyloChip 16S rRNA microarray identified 2,120 archaeal and bacterial taxa representing 46 phyla, 66 classes, 110 orders, and 186 families among all treatments. Measures of archaeal and bacterial richness were lowest under G2P (pH 5.5) treatments and greatest with G3P (pH 6.8) treatments. Members of the phyla Crenarchaeota, Euryarchaeota, Bacteroidetes, and Proteobacteria demonstrated the greatest enrichment in response to organophosphate amendments and the OTUs that increased in relative abundance by 2-fold or greater accounted for 9%–50% and 3%–17% of total detected Archaea and Bacteria, respectively. Conclusions/Significance This work provided a characterization of the distinct ORFRC subsurface microbial communities that contributed to increased concentrations of extracellular phosphate via hydrolysis of organophosphate substrate amendments. Within subsurface environments that are not ideal for reductive precipitation of uranium, strategies that harness microbial phosphate metabolism to promote uranium phosphate precipitation could offer an alternative approach for in situ sequestration. PMID:24950228

Final Scientific/Technical Report, DE-FG02-06ER64171, Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity – Subproject to Co-PI Eric E. Roden

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eric E. Roden

2009-07-08

This report summarizes research conducted in conjunction with a project entitled “Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity”, which was funded through the Integrative Studies Element of the former NABIR Program (now the Environmental Remediation Sciences Program) within the Office of Biological and Environmental Research. Dr. Darrell Chandler (originally at Argonne National Laboratory, now with Akonni Biosystems) was the overall PI/PD for the project. The overall project goals were to (1) apply a model iron-reducer and sulfate-reducer microarray and instrumentation systems to sediment and groundwater samples from the Scheibe et al. FRC Areamore » 2 field site, UMTRA sediments, and other DOE contaminated sites; (2) continue development and expansion of a 16S rRNA/rDNA¬-targeted probe suite for microbial community dynamics as new sequences are obtained from DOE-relevant sites; and (3) address the fundamental molecular biology and analytical chemistry associated with the extraction, purification and analysis of functional genes and mRNA in environmental samples. Work on the UW subproject focused on conducting detailed batch and semicontinuous culture reactor experiments with uranium-contaminated FRC Area 2 sediment. The reactor experiments were designed to provide coherent geochemical and microbiological data in support of microarray analyses of microbial communities in Area 2 sediments undergoing biostimulation with ethanol. A total of four major experiments were conducted (one batch and three semicontinuous culture), three of which (the batch and two semicontinuous culture) provided samples for DNA microarray analysis. A variety of other molecular analyses (clone libraries, 16S PhyloChip, RT-PCR, and T-RFLP) were conducted on parallel samples from the various experiments in order to provide independent information on microbial community response to biostimulation.« less

Biomineralization of U(VI) phosphate promoted by microbially-mediated phytate hydrolysis in contaminated soils

NASA Astrophysics Data System (ADS)

Salome, Kathleen R.; Beazley, Melanie J.; Webb, Samuel M.; Sobecky, Patricia A.; Taillefert, Martial

2017-01-01

The bioreduction of uranium may immobilize a significant fraction of this toxic contaminant in reduced environments at circumneutral pH. In oxic and low pH environments, however, the low solubility of U(VI)-phosphate minerals also makes them good candidates for the immobilization of U(VI) in the solid phase. As inorganic phosphate is generally scarce in soils, the biomineralization of U(VI)-phosphate minerals via microbially-mediated organophosphate hydrolysis may represent the main immobilization process of uranium in these environments. In this study, contaminated sediments were incubated aerobically in two pH conditions to examine whether phytate, a naturally-occurring and abundant organophosphate in soils, could represent a potential phosphorous source to promote U(VI)-phosphate biomineralization by natural microbial communities. While phytate hydrolysis was not evident at pH 7.0, nearly complete hydrolysis was observed both with and without electron donor at pH 5.5, suggesting indigenous microorganisms express acidic phytases in these sediments. While the rate of hydrolysis of phytate generally increased in the presence of uranium, the net rate of inorganic phosphate production in solution was decreased and inositol phosphate intermediates were generated in contrast to similar incubations conducted without uranium. These findings suggest uranium stress enhanced the phytate-metabolism of the microbial community, while simultaneously inhibiting phosphatase production and/or activity by the indigenous population. Finally, phytate hydrolysis drastically decreased uranium solubility, likely due to formation of ternary sorption complexes, U(VI)-phytate precipitates, and U(VI)-phosphate minerals. Overall, the results of this study provide evidence for the ability of natural microbial communities to liberate phosphate from phytate in acidic sediments, possibly as a detoxification mechanism, and demonstrate the potential utility of phytate-promoted uranium immobilization in subsurface environments. These processes should be investigated in more detail with pure cultures isolated from these sediments.

Chemoautotrophic carbon fixation rates and active bacterial communities in intertidal marine sediments.

PubMed

Boschker, Henricus T S; Vasquez-Cardenas, Diana; Bolhuis, Henk; Moerdijk-Poortvliet, Tanja W C; Moodley, Leon

2014-01-01

Chemoautotrophy has been little studied in typical coastal marine sediments, but may be an important component of carbon recycling as intense anaerobic mineralization processes in these sediments lead to accumulation of high amounts of reduced compounds, such as sulfides and ammonium. We studied chemoautotrophy by measuring dark-fixation of 13C-bicarbonate into phospholipid derived fatty acid (PLFA) biomarkers at two coastal sediment sites with contrasting sulfur chemistry in the Eastern Scheldt estuary, The Netherlands. At one site where free sulfide accumulated in the pore water right to the top of the sediment, PLFA labeling was restricted to compounds typically found in sulfur and ammonium oxidizing bacteria. At the other site, with no detectable free sulfide in the pore water, a very different PLFA labeling pattern was found with high amounts of label in branched i- and a-PLFA besides the typical compounds for sulfur and ammonium oxidizing bacteria. This suggests that other types of chemoautotrophic bacteria were also active, most likely Deltaproteobacteria related to sulfate reducers. Maximum rates of chemoautotrophy were detected in first 1 to 2 centimeters of both sediments and chemosynthetic biomass production was high ranging from 3 to 36 mmol C m(-2) d(-1). Average dark carbon fixation to sediment oxygen uptake ratios were 0.22±0.07 mol C (mol O2)(-1), which is in the range of the maximum growth yields reported for sulfur oxidizing bacteria indicating highly efficient growth. Chemoautotrophic biomass production was similar to carbon mineralization rates in the top of the free sulfide site, suggesting that chemoautotrophic bacteria could play a crucial role in the microbial food web and labeling in eukaryotic poly-unsaturated PLFA was indeed detectable. Our study shows that dark carbon fixation by chemoautotrophic bacteria is a major process in the carbon cycle of coastal sediments, and should therefore receive more attention in future studies on sediment biogeochemistry and microbial ecology.

Relationships between microbial communities and environmental parameters at sites impacted by mining of volcanogenic massive sulfide deposits, Prince William Sound, Alaska

USGS Publications Warehouse

Foster, A.L.; Munk, L.; Koski, R.A.; Shanks, Wayne C.; Stillings, L.L.

2008-01-01

The relations among geochemical parameters and sediment microbial communities were examined at three shoreline sites in the Prince William Sound, Alaska, which display varying degrees of impact by acid-rock drainage (ARD) associated with historic mining of volcanogenic massive sulfide deposits. Microbial communities were examined using total fatty acid methyl esters (FAMEs), a class of compounds derived from lipids produced by eukaryotes and prokaryotes (bacteria and Archaea); standard extraction techniques detect FAMEs from both living (viable) and dead (non-viable) biomass, but do not detect Archaeal FAMEs. Biomass and diversity (as estimated by FAMEs) varied strongly as a function of position in the tidal zone, not by study site; subtidal muds, Fe oxyhydroxide undergoing biogenic reductive dissolution, and peat-rich intertidal sediment had the highest values. These estimates were lowest in acid-generating, intertidal zone sediment; if valid, the estimates suggest that only one or two bacterial species predominate in these communities, and/or that Archeal species are important members of the microbial community in this sediment. All samples were dominated by bacterial FAMEs (median value >90%). Samples with the highest absolute abundance of eukaryotic FAMEs were biogenic Fe oxyhydroxides from shallow freshwater pools (fungi) and subtidal muds (diatoms). Eukaryotic FAMEs were practically absent from low-pH, sulfide-rich intertidal zone sediments. The relative abundance of general microbial functional groups such as aerobes/anaerobes and gram(+)/gram(-) was not estimated due to severe inconsistency among the results obtained using several metrics reported in the literature. Principal component analyses (PCAs) were performed to investigate the relationship among samples as separate functions of water, sediment, and FAMEs data. PCAs based on water chemistry and FAMEs data resulted in similar relations among samples, whereas the PCA based on sediment chemistry produced a very different sample arrangement. Specifically, the sediment parameter PCA grouped samples with high bulk trace metal concentration regardless of whether the metals were incorporated into secondary precipitates or primary sulfides. The water chemistry PCA and FAMEs PCA appear to be less prone to this type of artifact. Signature lipids in sulfide-rich sediments could indicate the presence of acid-tolerant and/or acidophilic members of the genus Thiobacillus or they could indicate the presence of SO4-reducing bacteria. The microbial community documented in subtidal and offshore sediments is rich in SRB and/or facultative anaerobes of the Cytophaga-Flavobacterium group; both could reasonably be expected in PWS coastal environments. The results of this study provide evidence for substantial feedback between local (meter to centimeter-scale) geochemical variations, and sediment microbial community composition, and show that microbial community signatures in the intertidal zone are significantly altered at sites where ARD drainage is present relative to sites where it is not, even if the sediment geochemistry indicates net accumulation of ARD-generated trace metals in the intertidal zone. ?? 2007 Elsevier Ltd. All rights reserved.

Chemotrophic Microbial Mats and Their Potential for Preservation in the Rock Record

NASA Astrophysics Data System (ADS)

Bailey, Jake V.; Orphan, Victoria J.; Joye, Samantha B.; Corsetti, Frank A.

2009-11-01

Putative microbialites are commonly regarded to have formed in association with photosynthetic microorganisms, such as cyanobacteria. However, many modern microbial mat ecosystems are dominated by chemotrophic bacteria and archaea. Like phototrophs, filamentous sulfur-oxidizing bacteria form large mats at the sediment/water interface that can act to stabilize sediments, and their metabolic activities may mediate the formation of marine phosphorites. Similarly, bacteria and archaea associated with the anaerobic oxidation of methane (AOM) catalyze the precipitation of seafloor authigenic carbonates. When preserved, lipid biomarkers, isotopic signatures, body fossils, and lithological indicators of the local depositional environment may be used to identify chemotrophic mats in the rock record. The recognition of chemotrophic communities in the rock record has the potential to transform our understanding of ancient microbial ecologies, evolution, and geochemical conditions. Chemotrophic microbes on Earth occupy naturally occurring interfaces between oxidized and reduced chemical species and thus may provide a new set of search criteria to target life-detection efforts on other planets.

Discriminative detection and enumeration of microbial life in marine subsurface sediments.

PubMed

Morono, Yuki; Terada, Takeshi; Masui, Noriaki; Inagaki, Fumio

2009-05-01

Detection and enumeration of microbial life in natural environments provide fundamental information about the extent of the biosphere on Earth. However, it has long been difficult to evaluate the abundance of microbial cells in sedimentary habitats because non-specific binding of fluorescent dye and/or auto-fluorescence from sediment particles strongly hampers the recognition of cell-derived signals. Here, we show a highly efficient and discriminative detection and enumeration technique for microbial cells in sediments using hydrofluoric acid (HF) treatment and automated fluorescent image analysis. Washing of sediment slurries with HF significantly reduced non-biological fluorescent signals such as amorphous silica and enhanced the efficiency of cell detachment from the particles. We found that cell-derived SYBR Green I signals can be distinguished from non-biological backgrounds by dividing green fluorescence (band-pass filter: 528/38 nm (center-wavelength/bandwidth)) by red (617/73 nm) per image. A newly developed automated microscope system could take a wide range of high-resolution image in a short time, and subsequently enumerate the accurate number of cell-derived signals by the calculation of green to red fluorescence signals per image. Using our technique, we evaluated the microbial population in deep marine sediments offshore Peru and Japan down to 365 m below the seafloor, which provided objective digital images as evidence for the quantification of the prevailing microbial life. Our method is hence useful to explore the extent of sub-seafloor life in the future scientific drilling, and moreover widely applicable in the study of microbial ecology.

Subarctic Lake Sediment Microbial Community Contributions to Methane Emission Patterns

NASA Astrophysics Data System (ADS)

Emerson, J. B.; Varner, R. K.; Parks, D.; Wik, M.; Neumann, R.; Johnson, J. E.; Singleton, C. M.; Woodcroft, B. J.; Tollerson, R., II; Owusu-Dommey, A.; Binder, M.; Freitas, N. L.; Crill, P. M.; Saleska, S. R.; Tyson, G. W.; Rich, V. I.

2017-12-01

Northern post-glacial lakes have recently been identified as a significant and increasing source of carbon to the atmosphere, largely through ebullition (bubbling) of microbially produced methane from the sediments. Ebullitive methane flux has been shown to correlate significantly with sediment surface temperatures, suggesting that solar radiation is the primary driver of methane emissions from these lakes. However, the slope of this relationship (i.e., the extent to which increasing temperature increases ebullitive methane emissions) differs spatially, both within and among lakes. As microbes are responsible for both methane generation and removal in lakes, we hypothesized that microbial communities—previously uncharacterized in post-glacial lake sediments—could be contributing to spatiotemporal differences in methane emission responses to temperature. We compared methane emission data with sediment microbial (metagenomic and amplicon), isotopic, and geochemical characterizations across two post-glacial lakes in Northern Sweden. With increasing temperatures, the increase in methane emissions was greater in lake middles (deeper water) than lake edges (shallower water), consistent with higher abundances of methanogens in sediments from lake middles than edges, along with significant differences in microbial community composition between these regions. Using sparse partial least squares statistical modeling, microbial abundances (including the abundances of methane-cycling microorganisms and of reconstructed population genomes, e.g., from Planctomycetes, Thermoplasmatales, and Candidate Phylum Aminicenantes) were better predictors of porewater methane concentrations than abiotic variables. These results suggest that, although temperature controls methane emissions, microbial community composition and function may drive the rate and magnitude of this temperature response in subarctic post-glacial lakes.

Seasonal changes in microbial community structure and activity imply winter production is linked to summer hypoxia in a large lake.

PubMed

Wilhelm, Steven W; LeCleir, Gary R; Bullerjahn, George S; McKay, Robert M; Saxton, Matthew A; Twiss, Michael R; Bourbonniere, Richard A

2014-02-01

Carbon and nutrient cycles in large temperate lakes such as Lake Erie are primarily driven by phototrophic and heterotrophic microorganisms, although our understanding of these is often constrained to late spring through summer due to logistical constraints. During periods of > 90% ice cover in February of 2008, 2009, and 2010, we collected samples from an icebreaker for an examination of bacterial production as well as microbial community structure. In comparison with summer months (August 2002 and 2010), we tested hypotheses concerning seasonal changes in microbial community diversity and production. Bacterial production estimates were c. 2 orders of magnitude higher (volume normalized) in summer relative to winter. Our observations further demonstrate that the microbial community, including single-celled phototrophs, varied in composition between August and February. Sediment traps deployed and collected over a 3 year period (2008-2011) confirmed that carbon export was ongoing and not limiting winter production. The results support the notion that active primary producers in winter months export carbon to the sediments that is not consumed until the warmer seasons. The establishment of this linkage is a critical observation in efforts to understand the extent and severity of annual summertime formations of a zone of regional hypoxia in Lake Erie. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Insight from Genomics on Biogeochemical Cycles in a Shallow-Sea Hydrothermal System

NASA Astrophysics Data System (ADS)

Lu, G. S.; Amend, J.

2015-12-01

Shallow-sea hydrothermal ecosystems are dynamic, high-energy systems influenced by sunlight and geothermal activity. They provide accessible opportunities for investigating thermophilic microbial biogeochemical cycles. In this study, we report biogeochemical data from a shallow-sea hydrothermal system offshore Paleochori Bay, Milos, Greece, which is characterized by a central vent covered by white microbial mats with hydrothermally influenced sediments extending into nearby sea grass area. Geochemical analysis and deep sequencing provide high-resolution information on the geochemical patterns, microbial diversity and metabolic potential in a two-meter transect. The venting fluid is elevated in temperature (~70oC), low in pH (~4), and enriched in reduced species. The geochemical pattern shows that the profile is affected by not only seawater dilution but also microbial regulation. The microbial community in the deepest section of vent core (10-12 cm) is largely dominated by thermophilic archaea, including a methanogen and a recently described Crenarcheon. Mid-core (6-8 cm), the microbial community in the venting area switches to the hydrogen utilizer Aquificae. Near the sediment-water interface, anaerobic Firmicutes and Actinobacteria dominate, both of which are commonly associated with subsurface and hydrothermal sites. All other samples are dominated by diverse Proteobacteria. The sulfate profile is strongly correlated with the population size of delta- and episilon-proteobactia. The dramatic decrease in concentrations of As and Mn in pore fluids as a function of distance from the vent suggests that in addition to seawater dilution, microorganisms are likely transforming these and other ions through a combination of detoxification and catabolism. In addition, high concentrations of dissolved Fe are only measurable in the shallow sea grass area, suggesting that iron-transforming microorganisms are controlling Fe mobility, and promoting biomineralization. Taken together, these samples represent the effects of submarine venting on sediment microbial communities both vertically and horizontally in the predicted fluid flow path, and will provide a detailed investigation of genetic potential for biogeochemical cycling at Paleochori Bay.

LABORATORY AND FIELD RESULTS LINKING HIGH CONDUCTIVITIES TO THE MICROBIAL DEGRADATION OF PETROLEUM HYDROCARBONS

EPA Science Inventory

The results of a field and laboratory investigation of unconsolidated sediments contaminated by petroleum hydrocarbons and undergoing natural biodegradation are presented. Fundamental to geophysical investigations of hydrocarbon impacted sediments is the assessment of how microbi...

A thiotrophic microbial community in an acidic brine lake in Northern Chile.

PubMed

Escudero, Lorena; Oetiker, Nia; Gallardo, Karem; Tebes-Cayo, Cinthya; Guajardo, Mariela; Nuñez, Claudia; Davis-Belmar, Carol; Pueyo, J J; Chong Díaz, Guillermo; Demergasso, Cecilia

2018-05-10

The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies. Besides, a comparison between similar systems in Australia highlights key microbial components and specific ones associated with geological settings and environmental conditions. Sediment and water samples from the Salar de Gorbea were collected, physicochemical parameters measured and geochemical and molecular biological analyses performed. A low diversity microbial community was observed in brines and sediments dominated by Actinobacteria, Algae, Firmicutes and Proteobacteria. Most of the constituent genera have been reported to be either sulfur oxidizing microorganisms or ones having the potential for sulfur oxidation given available genomic data and information drawn from the literature on cultured relatives. In addition, a link between sulfur oxidation and carbon fixation was observed. In contrast, to acid mine drainage communities, Gorbea microbial diversity is mainly supported by chemolithoheterotrophic, facultative chemolithoautotrophic and oligotrophic sulfur oxidizing populations indicating that microbial activity should also be considered as a causative agent of local acidity.

Microbial diversity in Brazilian mangrove sediments – a mini review

PubMed Central

Ghizelini, Angela Michelato; Mendonça-Hagler, Leda Cristina Santana; Macrae, Andrew

2012-01-01

The importance and protection of mangrove ecosystems has been recognized in Brazilian Federal law since 1965. Being protected in law, however, has not always guaranteed their protection in practice. Mangroves are found in coastal and estuarine locations, which are prime real estate for the growth of cities, ports and other economic activities important for Brazilian development. In this mini-review we introduce what mangroves are and why they are so important. We give a brief overview of the microbial diversity found in mangrove sediments and then focus on diversity studies from Brazilian mangroves. We highlight the breadth and depth of knowledge about mangrove microbial communities gained from studying Brazilian mangroves. We report on the exciting findings of molecular microbial ecology methods that have been very successfully applied to study bacterial communities. We note that there have been fewer studies that focus on fungal communities and that fungal diversity studies deserve more attention. The review ends with a look at how a combination of new molecular biology methods and isolation studies are being developed to monitor and conserve mangrove ecosystems and their associated microbial communities. These recent studies are having a global impact and we hope they will help to protect and re-establish mangrove ecosystems. PMID:24031949

Effects of inorganic electron acceptors on methanogenesis and methanotrophy and on the community structure of bacteria and archaea in sediments of a boreal lake

NASA Astrophysics Data System (ADS)

Rissanen, Antti J.; Karvinen, Anu; Nykänen, Hannu; Peura, Sari; Tiirola, Marja; Mäki, Anita; Kankaala, Paula

2016-04-01

Lake sediments are globally significant sources of CH4 to the atmosphere, but the factors controlling the production and consumption of CH4 in these systems are understudied. Increasing availability of electron acceptors (EA) (other than CO2) in sediments can decrease or even suppress CH4 production by diverting the electron flow (from H2 and organic substances) from methanogenic to other anaerobic respiration pathways. However, whether these changes in microbial function extend down to changes in the structure of microbial communities is not known. Also anaerobic oxidation of methane (AOM) could be enhanced by increased availability of EAs (SO42-, NO3-, Fe3+ and Mn4+), but information on the role of this process in lake sediments is scarce. We studied the effects of inorganic EAs on the potential for CH4 production and consumption and on the structure of microbial communities in sediments of a boreal lake. Anoxic slurries of sediment samples collected from two depths (0 - 10 cm; 10 - 30 cm) of the profundal zone of a boreal, mesotrophic Lake Ätäskö, were amended with 1) CH4 or with CH4 and either 2) 10 mM Mn4+, 3) 10 mM Fe3+, 4) O2 or 5) CH2F2 (inhibitor of aerobic methane oxidation) and incubated at +10° C for up to 4 months. Furthermore, slurries from the 10 - 30 cm layer were amended with CH4 and either 6) 2 mM NO3- or 7) 2 mM SO42- and incubated at +4 ° C for up to 14 months. The processes were measured using 13C-labelling and by concentration measurements of CH4 and CO2. Effects of treatments 1-3 on microbial communities were also analysed by next-generation sequencing of 16S rRNA, as well as methyl coenzyme-M reductase gene amplicons and mRNA transcripts. CH4 production (max. 83 nmol gdw-1d-1) took place in the anaerobic treatments but was generally decreased by the addition of NO3-, SO42-, Fe3+ and Mn4+. Although the structure of sediment archaeal community was resistant to Fe3+/Mn4+ - additions, slight changes in the structure of bacterial community occurred. Besides decreasing the availability of methanogenic substrates, the Mn4+/Fe3+ - induced changes in the bacterial community also probably decreased the H2:acetate - ratio in the substrate pool. This led to increase in the relative activity (mRNA level) of some operational taxonomic units assigned to aceticlastic Methanosaetaceae and decrease in the relative activity of hydrogenotrophic Methanoregulaceae in the sediment. CH4 oxidation (0.02 - 0.30 nmol gdw-1d-1 in anaerobic and 18 - 73 nmol gdw-1d-1in aerobic treatments) took place without EA additions and was enhanced only by O2. This suggests decoupling of the process from the reduction of other inorganic EAs. The results also indicate that Fe3+/Mn4+ - reduction did not increase CH4 oxidation via increased availability of SO42- by cryptic sulfur cycle or via increased availability of organic EAs. Furthermore, ANME - archaea were only ≤ 3% of sediment archaeal community and their relative activity was decreased during incubations. Thus, EA driving CH4 oxidation in the anoxic sediments of the lake remains unknown or the process was methanogen-driven via trace methane oxidation.

Marine Microbial Community Response to Inorganic and Organic Sediment Amendments in Laboratory Mesocosms

DTIC Science & Technology

2011-07-23

organoclay in geotextile mats), acetate, and chitin on environmental microbial communities in overlying water and sediment profiles are reported here...Significant changes in both bacterial cell densities and populations were observed in response to amendments of apatiteþorganoclay, chitin , and acetate... chitin treatment led to a dominance of Bacteroidetes and Alphaproteobacteria. In amended sediments, Firmicutes, Bacteroidetes, and Deltaproteobacteria

Diversity of Bacillus-like organisms isolated from deep-sea hypersaline anoxic sediments

PubMed Central

Sass, Andrea M; McKew, Boyd A; Sass, Henrik; Fichtel, Jörg; Timmis, Kenneth N; McGenity, Terry J

2008-01-01

Background The deep-sea, hypersaline anoxic brine lakes in the Mediterranean are among the most extreme environments on earth, and in one of them, the MgCl2-rich Discovery basin, the presence of active microbes is equivocal. However, thriving microbial communities have been detected especially in the chemocline between deep seawater and three NaCl-rich brine lakes, l'Atalante, Bannock and Urania. By contrast, the microbiota of these brine-lake sediments remains largely unexplored. Results Eighty nine isolates were obtained from the sediments of four deep-sea, hypersaline anoxic brine lakes in the Eastern Mediterranean Sea: l'Atalante, Bannock, Discovery and Urania basins. This culture collection was dominated by representatives of the genus Bacillus and close relatives (90% of all isolates) that were investigated further. Physiological characterization of representative strains revealed large versatility with respect to enzyme activities or substrate utilization. Two third of the isolates did not grow at in-situ salinities and were presumably present as endospores. This is supported by high numbers of endospores in Bannock, Discovery and Urania basins ranging from 3.8 × 105 to 1.2 × 106 g-1 dw sediment. However, the remaining isolates were highly halotolerant growing at salinities of up to 30% NaCl. Some of the novel isolates affiliating with the genus Pontibacillus grew well under anoxic conditions in sulfidic medium by fermentation or anaerobic respiration using dimethylsulfoxide or trimethylamine N-oxide as electron acceptor. Conclusion Some of the halophilic, facultatively anaerobic relatives of Bacillus appear well adapted to life in this hostile environment and suggest the presence of actively growing microbial communities in the NaCl-rich, deep-sea brine-lake sediments. PMID:18541011

The giant cold-water coral mound as a nested microbial/metazoan system: physical, chemical, biological and geological picture (ESF EuroDiversity MiCROSYSTEMS)

NASA Astrophysics Data System (ADS)

Henriet, J. P.; Microsystems Team

2009-04-01

The MiCROSYSTEMS project under the ESF EUROCORES EuroDiversity scheme is a holistic and multi-scale approach in studying microbial diversity and functionality in a nested microbial/metazoan system, which thrives in deep waters: the giant cold-water coral mound. Studies on prolific cold-water coral sites have been carried out from the canyons of the Bay of Biscay to the fjords of the Norwegian margin, while the Pen Duick carbonate mound province off Morocco developed into a joint natural lab for studying in particular the impact of biogeochemical and microbial processes on modern sedimentary diagenesis within the reef sediments, in complement to the studies on I0DP Exp. 307 cores (Challenger Mound, off Ireland). Major outcomes of this research can be summarized as follows. • IODP Exp. 307 on Challenger Mound had revealed a significant prokaryotic community both within and beneath the carbonate mound. MiCROSYSTEMS unveils a remarkable degree of compartmentalization in such community from the seawater, the coral skeleton surface and mucus to the reef sediments. The occurrence of such multiple and distinct microbial compartments associated with cold-water coral ecosystems promotes opportunities for microbial diversity in the deep ocean. • New cases of co-habitation of cold-water corals and giant deep-water oysters were discovered in the Bay of Biscay, which add a new facet of macrofaunal diversity to cold-water coral reef systems. • The discovery of giant, ancient coral graveyards on the Moroccan mounds not only fuels the debate about natural versus anthropogenic mass extinction, but these open frameworks simultaneously invite for the study of bio-erosion and early diagenesis, in particular organo-mineralization, and of the possible role and significance of these thick, solid rubble patches in 3D mound-building and consolidation. • The assessment of the carbonate budget of a modern cold-water coral mound (Challenger Mound) reveals that only 33 to 40 wt % of carbonate is derived from corals and suggests a selective enrichment of the hemipelagic carbonate fraction, compared to adjacent sediment drift deposits. • The detection of allochthonous fluids, in particular brines, in the pore space of the surficial mound sediments on the Pen Duick Escarpment hints towards the presence of salt deposits deep underneath, and simultaneously provides the first direct evidence of advective fluid transfer from the deep, throughout the mound substrate and the full mound height. Potential stratigraphic pathways leading from the deeper basinal realms directly to the mound setting have been imaged in a spectacular way through high-resolution pseudo-3D seismic imaging. Geophysical signatures of free gas accumulations have been detected a few hundreds of meters below the mound base, but low concentrations of methane and the absence of lipid biomarkers from methane-dependent prokaryotes suggest low fluxes of methane-derived carbon and thus very small rates of anaerobic oxidation of methane (AOM) in the immediate mound subsurface. Local changes in the sediment biogeochemistry are most likely dictated by slow diffusive fluid transfer, operating in a heterogeneous way in the subsurface. • Cultivation experiments with sediments from microbially active mound zones have allowed to study microbially induced carbonate precipitation and provide a tool for the interpretation of carbonate mineralogy. The development and operation of a continuous high-pressure bioreactor (100 bars) allows to simulate in an ex situ mode the impact of environmental parameter changes onto the functioning of relevant microbial communities. • The detected influx of sulfate in mound sediments implies that bacterial sulfate reduction can be the dominant anaerobic carbon mineralization process. Groundwater flow modeling suggests that currents impinging on the escarpment and the flanks of an exposed mound can account for a significant influx and transport of sulfate through convective fluid transfer within the mound sediments. Oceanic currents consequently provide not only a major control on the external flux of nutrients to the mound-building communities, but they also potentially drive internal flow in the mound. The extant hydrodynamic climate of the mound setting is documented through long-term lander deployments and CTD stations: the current records reveal a significant tidal and seasonal variability. The past environmental record over the last 400 ka is documented in a most comprehensive sedimentary archive, sampled with long cores at the foot of the Pen Duick Escarpment during the MD169 ‘MiCROSYSTEMS' cruise in July 2008. • MiCROSYSTEMS has significantly contributed to the successful submission of IODP proposal 673-Full, which should (i) document the whole-mound architecture and the mound setting on Pen Duick Escarpment as well as a most comprehensive stratigraphic record on a reference site at the foot of the escarpment, (ii) reveal the full spatial pattern in microbial diversity, activity and functionality throughout the mound and underneath, and (iii) unravel the plumbing system of a mound and the dynamic interaction between advective, convective and diffusive transfers of organic and inorganic compounds, which impact on biogeochemical equilibria, microbial activity and early diagenetic processes.

Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments.

PubMed

Dyksma, Stefan; Bischof, Kerstin; Fuchs, Bernhard M; Hoffmann, Katy; Meier, Dimitri; Meyerdierks, Anke; Pjevac, Petra; Probandt, David; Richter, Michael; Stepanauskas, Ramunas; Mußmann, Marc

2016-08-01

Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine carbon and sulfur cycles.

Characterization of microbes carried in dust

USDA-ARS?s Scientific Manuscript database

There is still a lack of understanding of how soil microbial community distribution is controlled by wind erosion. This information is of international concern as eroded sediments can potentially carry away the active labile organic soil particulates containing key microorganisms involved in soil bi...

A deep oxic ecosystem in the subseafloor South Pacific Gyre

NASA Astrophysics Data System (ADS)

D'Hondt, S. L.; Inagaki, F.; Alvarez Zarikian, C. A.; Integrated Ocean Drilling Program Expedition 329 Shipboard Scientific Party

2011-12-01

Scientific ocean drilling has demonstrated the occurrence of rich microbial communities, abundant active cells and diverse anaerobic activities in anoxic subseafloor sediment. Buried organic matter from the surface photosynthetic world sustains anaerobic heterotrophs in anoxic sediment as deeply buried as 1.6 km below the seafloor. However, these studies have been mostly restricted to the organic-rich sediment of continental margins and biologically productive regions. IODP Expedition 329 discovered that subseafloor habitat and life are fundamentally different in the vast expanse of organic-poor sediment that underlies Earth's largest oceanic province, the South Pacific Gyre (SPG). Dissolved O2 and dissolved major nutrients (C, N, P) are present throughout the entire sediment sequence and the upper basaltic basement of the SPG. The drilled sediment is up to 75 m thick. Although heterotrophic O2 reduction (aerobic respiration) persists for millions of years in SPG sediment (which accumulates very slowly), it falls below minimum detection just a few meters to tens of meters beneath the SPG seafloor. Cell concentrations approach minimum detection at similar depths, but are intermittently detectable throughout the entire sediment sequence. In situ radiolysis of water may be a significant source of energy for the microbes that inhabit the deepest (oldest) sediment.

INTERREGIONAL COMPARISONS OF SEDIMENT MICROBIAL RESPIRATION IN STREAMS

EPA Science Inventory

The rate of microbial respiration on fine-grained stream sediments was measured at 369 first to fourth-order streams in the Central Appalachians, Colorado's Southern Rockies, and California's Central Valley in 1994 and 1995. Study streams were randomly selected from the USEPA's ...

Microbial activity in the marine deep biosphere: progress and prospects.

PubMed

Orcutt, Beth N; Larowe, Douglas E; Biddle, Jennifer F; Colwell, Frederick S; Glazer, Brian T; Reese, Brandi Kiel; Kirkpatrick, John B; Lapham, Laura L; Mills, Heath J; Sylvan, Jason B; Wankel, Scott D; Wheat, C Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists-all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these "extreme" environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) "theme team" on microbial activity (www.darkenergybiosphere.org).

Microbial activity in the marine deep biosphere: progress and prospects

PubMed Central

Orcutt, Beth N.; LaRowe, Douglas E.; Biddle, Jennifer F.; Colwell, Frederick S.; Glazer, Brian T.; Reese, Brandi Kiel; Kirkpatrick, John B.; Lapham, Laura L.; Mills, Heath J.; Sylvan, Jason B.; Wankel, Scott D.; Wheat, C. Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org). PMID:23874326

Isotopic identification of the source of methane in subsurface sediments of an area surrounded by waste disposal facilities

USGS Publications Warehouse

Hackley, Keith C.; Liu, Chao-Li; Trainor, D.

1999-01-01

The major source of methane (CH4) in subsurface sediments on the property of a former hazardous waste treatment facility was determined using isotopic analyses measured on CH4 and associated groundwater. The site, located on an earthen pier built into a shallow wetland lake, has had a history of waste disposal practices and is surrounded by landfills and other waste management facilities. Concentrations of CH4 up to 70% were found in the headspace gases of several piezometers screened at 3 different depths (ranging from 8 to 17 m) in lacustrine and glacial till deposits. Possible sources of the CH4 included a nearby landfill, organic wastes from previous impoundments and microbial gas derived from natural organic matter in the sediments. Isotopic analyses included ??13C, ??D, 14C, and 3H on select CH4 samples and ??D and ??18O on groundwater samples. Methane from the deepest glacial till and intermediate lacustrine deposits had ??13C values from -79 to -82???, typical of natural 'drift gas' generated by microbial CO2-reduction. The CH4 from the shallow lacustrine deposits had ??13C values from -63 to -76???, interpreted as a mixture between CH4 generated by microbial fermentation and the CO2-reduction processes within the subsurface sediments. The ??D values of all the CH4 samples were quite negative ranging from -272 to -299???. Groundwater sampled from the deeper zones also showed quite negative ??D values that explained the light ??D observed for the CH4. Radiocarbon analyses of the CH4 showed decreasing 14C activity with depth, from a high of 58 pMC in the shallow sediments to 2 pMC in the deeper glacial till. The isotopic data indicated the majority of CH4 detected in the fill deposits of this site was microbial CH4 generated from naturally buried organic matter within the subsurface sediments. However, the isotopic data of CH4 from the shallow piezometers was more variable and the possibility of some mixing with oxidized landfill CH4 could not be completely ruled out.

The Influence of Chitosan Substrate and Its Nanometric Form Toward the Green Power Generation in Sediment Microbial Fuel Cell.

PubMed

Karthikeyan, C; Sathishkumar, Y; Lee, Yang Soo; Kim, Ae Rhan; Yoo, Dong Jin; Kumar, G Gnana

2017-01-01

A simple, environmental friendly and biologically important sediment interfaced fuel cell was developed for the green energy generation. The soil sediment used for the study is enriched of rich anthropogenic free organic carbon, sufficient manganese and high level potassium contents as evidenced from the geochemical characterizations. The saccharides produced by the catalytic reaction of substrate chitosan were utilized for the growth of microorganisms and electron shuttling processes. Chitosan substrate influenced sediment microbial fuel cells exhibited the nearly two fold power increment over the substrate free fuel cells. The fuel cell efficiencies were further increased by bringing the substrate chitosan at nanometric level, which is nearly three and two fold higher than that of substrate free and chitosan influenced sediment microbial fuel cells, respectively, and the influential parameters involved in the power and longevity issues were addressed with different perspectives.

Efficiency of fluorescence in situ hybridization for bacterial cell identification in temporary river sediments with contrasting water content.

PubMed

Fazi, Stefano; Amalfitano, Stefano; Pizzetti, Ilaria; Pernthaler, Jakob

2007-09-01

We studied the efficiency of two hybridization techniques for the analysis of benthic bacterial community composition under varying sediment water content. Microcosms were set up with sediments from four European temporary rivers. Wet sediments were dried, and dry sediments were artificially rewetted. The percentage of bacterial cells detected by fluorescence in situ hybridization with fluorescently monolabeled probes (FISH) significantly increased from dry to wet sediments, showing a positive correlation with the community activity measured via incorporation of (3)H leucine. FISH and signal amplification by catalyzed reporter deposition (CARD-FISH) could significantly better detect cells with low activity in dried sediments. Through the application of an optimized cell permeabilization protocol, the percentage of hybridized cells by CARD-FISH showed comparable values in dry and wet conditions. This approach was unrelated to (3)H leucine incorporation rates. Moreover, the optimized protocol allowed a significantly better visualization of Gram-positive Actinobacteria in the studied samples. CARD-FISH is, therefore, proposed as an effective technique to compare bacterial communities residing in sediments with contrasting water content, irrespective of differences in the activity state of target cells. Considering the increasing frequencies of flood and drought cycles in European temporary rivers, our approach may help to better understand the dynamics of microbial communities in such systems.

Geochemical Tracers and Rates of Short-Chain Alkane Production in Gulf of Mexico Cold Seep Sediments

NASA Astrophysics Data System (ADS)

Sibert, R.; Bernard, B. B.; Brooks, J. M.; Hunter, K.; Joye, S. B.

2014-12-01

The organic-rich cold seep sediments in the deep Gulf of Mexico commonly contain mixtures of light hydrocarbon gases either dissolved in pore fluids, adsorbed to sediment particles, trapped in methane ice, or as free gas. The dominant component in these natural gas mixtures is typically methane (C1), but ethane (C2) and propane (C3) are nearly always present in trace or major amounts. The ratio of C1:C2:C3 varies but C2 and C3 are typically present at single digit percent levels, whereas methane usually dominates at >80%. Methane production proceeds by at least two well-studied mechanisms: either 1) by thermocatalytic cracking of fossil organic matter, or 2) as a direct product of microbial metabolism, methanogenesis. In contrast, ethane and propane production in deep-sea sediments has been historically attributed only to thermocatalytic processes. However, limited data suggests production of C2/C3 compounds through the activity of archaea. Such studies of microbial- driven dynamics of C2/C3 gases (i.e. 'alkanogenesis') in cold seep sediments are rare. Furthermore, the identities of potential substrates are poorly constrained and no attempt has been made to quantify production rates of C2/C3 gases. However, carbon isotopic data on ethane and propane from deep cores from the Gulf of Mexico suggest alkanogenesis at depth in the sediment column and alkane oxidation in uppermost oxidant-rich sediments. Here, we present the results of a series of incubation experiments using sediment slurries culled from GC600, one of the most prolific natural oil and gas seeps in the Gulf of Mexico. Rates of both alkane production and oxidation were measured under a variety of conditions to assess the net rates of alkane production and elucidate the driving microbiological mechanisms and controls on the central processes of >C1 alkane cycling in cold seep sediments. Microbial processes are important both in terms of alkane production and oxidation, raising many questions as to the biological production of these gases across the biosphere.

Microbial distributions detected by an oligonucleotide microarray across geochemical zones associated with methane in marine sediments from the Ulleung Basin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Briggs, Brandon R; Graw, Michael; Brodie, Eoin L

2013-11-01

The biogeochemical processes that occur in marine sediments on continental margins are complex; however, from one perspective they can be considered with respect to three geochemical zones based on the presence and form of methane: sulfate–methane transition (SMTZ), gas hydrate stability zone (GHSZ), and free gas zone (FGZ). These geochemical zones may harbor distinct microbial communities that are important in biogeochemical carbon cycles. The objective of this study was to describe the microbial communities in sediments from the SMTZ, GHSZ, and FGZ using molecular ecology methods (i.e. PhyloChip microarray analysis and terminal restriction fragment length polymorphism (T-RFLP)) and examining themore » results in the context of non-biological parameters in the sediments. Non-metric multidimensional scaling and multi-response permutation procedures were used to determine whether microbial community compositions were significantly different in the three geochemical zones and to correlate samples with abiotic characteristics of the sediments. This analysis indicated that microbial communities from all three zones were distinct from one another and that variables such as sulfate concentration, hydrate saturation of the nearest gas hydrate layer, and depth (or unmeasured variables associated with depth e.g. temperature, pressure) were correlated to differences between the three zones. The archaeal anaerobic methanotrophs typically attributed to performing anaerobic oxidation of methane were not detected in the SMTZ; however, the marine benthic group-B, which is often found in SMTZ, was detected. Within the GHSZ, samples that were typically closer to layers that contained higher hydrate saturation had indicator sequences related to Vibrio-type taxa. These results suggest that the biogeographic patterns of microbial communities in marine sediments are distinct based on geochemical zones defined by methane.« less

Multilevel samplers as microcosms to assess microbial response to biostimulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baldwin, Brett R.; Peacock, Aaron D.; Park, Melora M.

Passive multilevel samplers (MLS) containing a solid matrix for microbial colonization were used in conjunction with a push-pull biostimulation experiment designed to promote biological U(VI) and Tc(VII) reduction. MLS were deployed at 24 elevations in the injection well and two down gradient wells to investigate the spatial variability in microbial community composition and growth prior to and following biostimulation. The microbial community was characterized by real-time PCR (Q-PCR) quantification of Bacteria, NO3- reducing bacteria (nirS and nirK), δ-proteobacteria, Geobacter sp., and methanogens (mcrA). Pretest cell densities were low overall but varied substantially with significantly greater Bacterial populations detected at circumneutralmore » pH (T-test, α=0.05) suggesting carbon substrate and low pH limitations of microbial activity. Although pretest cell densities were low, denitrifying bacteria were dominant members of the microbial community. Biostimulation with an ethanol amended groundwater resulted in concurrent NO3- and Tc(VII) reduction followed by U(VI) reduction. Q-PCR analysis of MLS revealed significant (1-2 orders of magnitude, T-test, α=0.05) increases in cell densities of Bacteria, denitrifiers, δ-proteobacteria, Geobacter sp., and methanogens in response to biostimulation. Traditionally characterization of sediment samples has been used to investigate the microbial community response to biostimulation, however, collection of sediment samples is expensive and not conducive to deep aquifers or temporal studies. The results presented demonstrate that push-pull tests with passive MLS provide an inexpensive approach to determine the effect of biostimulation on contaminant concentrations, geochemical conditions, and the microbial community composition and function.« less

Long-term preservation of microbial ecosystems in permafrost

NASA Astrophysics Data System (ADS)

Gilichinsky, D. A.; Vorobyova, E. A.; Erokhina, L. G.; Fyordorov-Dayvdov, D. G.; Chaikovskaya, N. R.

It has been established that significant numbers (up to 10 million cells per gram of sample) of living microorganisms of various ecological and morphological groups have been preserved under permafrost conditions, at temperatures ranging from -9 to -13°C and depths of up to 100 m, for thousands and sometimes millions of years. Preserved since the formation of permafrost in sand-clay sediments of the Pliocene-Quaternary period and in paleosols and peats buried among them, these cells are the only living organisms that have survived for a geologically significant period of time. The complexity of the microbial community preserved varies with the age of the permafrost. Eukaryotes are found only in Holocene sediments; while prokaryotes are found to greater ages, i.e., Pliocene and Pleistocene. The diversity of microorganisms decreases with increasing age of sediments, and as a result cocci and corynebacteria are predominant. Enzyme activity (catalase and hydrolytic enzymes) and photosynthetic pigments (chlorophyll and pheophytin have also been detected in permafrost sediments. These results permit us to outline some approaches to the search for traces of life in the permafrost of Martian sediments by borehole core sampling. It is in the deep horizons (and not on the planet surface), isolated by permafrost from the external conditions, that results similar to those obtained on Earth can be expected.

Availability of ferric iron for microbial reduction in bottom sediments of the freshwater tidal potomac river.

PubMed

Lovley, D R; Phillips, E J

1986-10-01

The distribution of Fe(III), its availability for microbial reduction, and factors controlling Fe(III) availability were investigated in sediments from a freshwater site in the Potomac River Estuary. Fe(III) reduction in sediments incubated under anaerobic conditions and depth profiles of oxalate-extractable Fe(III) indicated that Fe(III) reduction was limited to depths of 4 cm or less, with the most intense Fe(III) reduction in the top 1 cm. In incubations of the upper 4 cm of the sediments, Fe(III) reduction was as important as methane production as a pathway for anaerobic electron flow because of the high rates of Fe(III) reduction in the 0- to 0.5-cm interval. Most of the oxalate-extractable Fe(III) in the sediments was not reduced and persisted to a depth of at least 20 cm. The incomplete reduction was not the result of a lack of suitable electron donors. The oxalate-extractable Fe(III) that was preserved in the sediments was considered to be in a form other than amorphous Fe(III) oxyhydroxide, since synthetic amorphous Fe(III) oxyhydroxide, amorphous Fe(III) oxyhydroxide adsorbed onto clay, and amorphous Fe(III) oxyhydroxide saturated with adsorbed phosphate or fulvic acids were all readily reduced. Fe(3)O(4) and the mixed Fe(III)-Fe(II) compound(s) that were produced during the reduction of amorphous Fe(III) oxyhydroxide in an enrichment culture were oxalate extractable but were not reduced, suggesting that mixed Fe(III)-Fe(II) compounds might account for the persistence of oxalate-extractable Fe(III) in the sediments. The availability of microbially reducible Fe(III) in surficial sediments demonstrates that microbial Fe(III) reduction can be important to organic matter decomposition and iron geochemistry. However, the overall extent of microbial Fe(III) reduction is governed by the inability of microorganisms to reduce most of the Fe(III) in the sediment.

Benthic Community Structure and Sediment Geochemical Properties at Hydrocarbon Seeps Along the Continental Slope of the Western North Atlantic

NASA Astrophysics Data System (ADS)

Demopoulos, A. W.; Bourque, J. R.; Brooke, S.

2015-12-01

Hydrocarbon seeps support distinct benthic communities capable of utilizing reduced chemical compounds for nutrition. In recent years, methane seepage has been increasingly documented along the continental slope of the U.S. Atlantic margin. In 2012 and 2013, two seeps were investigated in this region: a shallow site near Baltimore Canyon (410-450 m) and a deep site near Norfolk Canyon (1600 m). Both sites contain extensive mussel beds and microbial mats. Sediment cores and grab samples were collected to quantify the abundance, diversity, and community structure of benthic macrofauna (>300 mm) in relationship to the associated sediment environment (organic carbon and nitrogen, stable isotopes 13C and 15N, grain size, and depth) of mussel beds, mats, and slope habitats. Macrofaunal densities in microbial mats were four times greater than those present in mussel beds and slope sediments. Macrofaunal communities were distinctly different both between depths and among habitat types. Specifically, microbial mat sediments were dominated by the annelid families Dorvilleidae, Capitellidae, and Tubificidae, while mussel habitats had higher proportions of crustaceans. Diversity was lower in Baltimore microbial mat habitats, but higher in mussel and slope sediments compared to Norfolk seep habitats found at deeper depths. Multivariate statistical analysis identified sediment carbon:nitrogen (C:N) ratios and 13C values as important variables for structuring the macrofaunal communities. Higher C:N ratios were present within microbial mat habitats and depleted 13C values occurred in sediments adjacent to mussel beds found in Norfolk Canyon seeps. Differences in the quality and source of organic matter present in the seep habitats are known to be important drivers in macrofaunal community structure and associated food webs. The multivariate analysis provides new insight into the relative importance of the seep sediment quality in supporting dense macrofaunal communities compared to other seeps found throughout the region.

Temporal and spatial changes of microbial community in an industrial effluent receiving area in Hangzhou Bay.

PubMed

Zhang, Yan; Chen, Lujun; Sun, Renhua; Dai, Tianjiao; Tian, Jinping; Zheng, Wei; Wen, Donghui

2016-06-01

Anthropogenic activities usually contaminate water environments, and have led to the eutrophication of many estuaries and shifts in microbial communities. In this study, the temporal and spatial changes of the microbial community in an industrial effluent receiving area in Hangzhou Bay were investigated by 454 pyrosequencing. The bacterial community showed higher richness and biodiversity than the archaeal community in all sediments. Proteobacteria dominated in the bacterial communities of all the samples; Marine_Group_I and Methanomicrobia were the two dominant archaeal classes in the effluent receiving area. PCoA and AMOVA revealed strong seasonal but minor spatial changes in both bacterial and archaeal communities in the sediments. The seasonal changes of the bacterial community were less significant than those of the archaeal community, which mainly consisted of fluctuations in abundance of a large proportion of longstanding species rather than the appearance and disappearance of major archaeal species. Temperature was found to positively correlate with the dominant bacteria, Betaproteobacteria, and negatively correlate with the dominant archaea, Marine_Group_I; and might be the primary driving force for the seasonal variation of the microbial community. Copyright © 2016. Published by Elsevier B.V.

Seasonal and spatial variations in microbial activity at various phylogenetic resolutions at a groundwater - surface water interface.

PubMed

Yu, Ran; Smets, Barth F; Gan, Ping; MacKay, Allison A; Graf, Joerg

2014-05-01

We investigated the seasonal and spatial variation in activity and density of the metabolically active in situ microbial community (AIMC) at a landfill leachate-impacted groundwater - surface water interface (GSI). A series of AIMC traps were designed and implemented for AIMC sampling and microbial activity and density examinations. Measurements were made not only at the level of bacterial domain but also at the levels of alphaproteobacterial Rhizobiales order and gammaproteobacterial Pseudomonas genus, both of which included a large number of iron-oxidizing bacteria as revealed from previous analysis. Consistently higher microbial activities with less variation in depth were measured in the AIMC traps than in the ambient sediments. Flood disturbance appeared to control AIMC activity distributions at the gradually elevated GSI. The highest AIMC activities were generally obtained from locations closest to the free surface water boundary except during the dry season when microbial activities were similar across the entire GSI. A clone library of AIMC 16S rRNA genes was constructed, and it confirmed the predominant role of the targeted alphaproteobacterial group in AIMC activity and composition. This taxon constituted 2%-14% of all bacteria with similar activity distribution profiles. The Pseudomonas group occupied only 0.1‰-0.5‰ of the total bacterial density, but its activity was 27 times higher than the bacterial average. Of the 16S rRNA sequences in the AIMC clone library, 7.5% were phylogenetically related to putative IOB, supporting the occurrence and persistence of active microbial iron oxidation across the studied iron-rich GSI ecosystem.

Leakage of CO2 from sub-seafloor CO2 storage sites to the seabed; Impacts on sediment microorganisms and geochemical parameters during in situ and laboratory leakage experiments

NASA Astrophysics Data System (ADS)

Reigstad, L. J.; Hannisdal, B.; Hoffmann, F. U.; Sweetman, A. K.; Baumberger, T.; Eickmann, B.; Røy, H.; Thorseth, I. H.; Pedersen, R. B.

2013-12-01

Since 1996, 14 million tons of CO2 extracted from natural gas have been injected into the Utsira Formation, a saline aquifer at ~1000 m depth in the North Sea. The injected CO2 covers today an area of 4 x 2 km2. At present, there are three international treaties protecting the oceans, and all three allow CO2 storage in sub-seabed geological formations. One of these, the EU Directive 2009/31, states that monitoring must take place before, during and after CO2 storage in order to detect leakage of CO2 and significant adverse effects on the surrounding environment. However, few environmental studies have investigated the potential impacts of a CO2 leakage on the microbial life and geochemical conditions in seafloor sediment. To remedy this, we performed two experiments with abrupt CO2 acidification on the top 10 cm of the seafloor close to the North Sea storage site: 1) One laboratory CO2 acidification experiment on undisturbed sediment cores from the seafloor overlying the CO2 storage site (80 m water depth). The continuous flow of CO2 acidified seawater (pH 6.4) with 20 000 μatm pCO2 over the cores lasted for 1.5 months with sediment core terminations at regular intervals. 2) In situ CO2 acidification experiments carried out on the seafloor at 350 m water depth, with life span of 40 hours and exposure to 20 000 μatm pCO2. Both experiments showed increased O2 consumption in the water overlying the CO2 acidified sediment relative to the control sediment, indicating a rise in metabolic activity due to the treatment. After about 12 hours of acidification and throughout the laboratory experimental period, an increase in macrofauna burial activity could be seen, with dead/dying macrofauna appearing on the sediment surface. The pyrosequencing amplicon dataset obtained after bacterial and archaeal 16S rRNA amplification (RNA level) was subjected to multivariate analyses (PCA, NMDS), revealing changes in the active community on phylum, class and OTU levels. Changes were detected on all three levels in all depths investigated, but the response to acidification appeared among less-abundant prokaryotic groups in the sediment, rather than the numerically dominant groups. Quantification of the 16S rRNA genes (DNA level) indicated no increase in cell numbers in response to the treatment. However, an increase in the in situ microbial sulfate reduction rates and/or expression of marker genes for sulfate reduction (RNA level) was discovered. Analyses of marker gene expression for other prokaryotic metabolisms will be presented as well as correlations between specific organisms and geochemical parameters. Within the limitations of the experimental set up, our studies indicate that a leakage of CO2 from a sub-seafloor storage site may not dramatically change the composition of the active microbial community in the seabed sediment though we did register activity changes in some metabolisms.

Assessment of the physicochemical conditions sediments in a polluted tidal flat colonized by microbial mats in Bahía Blanca Estuary (Argentina).

PubMed

Spetter, C V; Buzzi, N S; Fernández, E M; Cuadrado, D G; Marcovecchio, J E

2015-02-28

The aim of this work is to assess the physicochemical conditions of the supratidal sediments colonized by microbial mats at two sites from Rosales Harbor (Bahía Blanca Estuary, Argentina) close to sewage discharge. Both sites differed in the size grain. No differences in pH, Eh and temperature were observed. Moisture retention and chlorophyll a concentration were significantly different between sites and sediment layers. Heavy metals and organic matter content were significantly higher in SII. No statistical differences were found in porewater nutrients concentration, being higher in SI (except DSi). The presence of Escherichia coli in water and sediment (1000 CFU/100 mL - uncountable and 35-40 CFU g(-1) dw, respectively) evidenced microbial contamination in the study area. The relationships between the physicochemical parameters evaluated and the influence of the sewage discharge allow defining two different areas in the Rosales Harbor despite the proximity and the presence of microbial mats.

A survey of alterations in microbial community diversity in marine sediments in response to oil from the Deepwater Horizon spill: Northern Gulf of Mexico shoreline, Texas to Florida

USGS Publications Warehouse

Lisle, John T.

2011-01-01

Microbial community genomic DNA was extracted from sediment samples collected from the northern Gulf of Mexico (NGOM) coast. These samples had a high probability of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon (DWH) drilling site. The hypothesis for this project was that presence of M-1 oil in coastal sediments would significantly alter the diversity within the microbial communities associated with the impacted sediments. To determine if community-level changes did or did not occur following exposure to M-1 oil, microbial community-diversity fingerprints were generated and compared. Specific sequences within the community's genomic DNA were first amplified using the polymerase chain reaction (PCR) using a primer set that provides possible resolution to the species level. A second nested PCR that was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. These nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Sediment samples with similar fingerprints were grouped and compared to oil-fingerprint data from Rosenbauer and others (2010). The microbial community fingerprints grouped closely when identifying those sites that had been impacted by M-1 oil (N=12) and/or some mixture of M-1 and other oil (N=4), based upon the oil fingerprints. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the NGOM coast. These communities contain microbes capable of degrading oil and related hydrocarbons, making this information relevant to response and recovery of the NGOM from the DWH incident.

Anaerobic degradation of benzene in diverse anoxic environments

USGS Publications Warehouse

Kazumi, J.; Caldwell, M.E.; Suflita, J.M.; Lovely, D.R.; Young, L.Y.

1997-01-01

Benzene has often been observed to be resistant to microbial degradation under anoxic conditions. A number of recent studies, however, have demonstrated that anaerobic benzene utilization can occur. This study extends the previous reports of anaerobic benzene degradation to sediments that varied with respect to contamination input, predominant redox condition, and salinity. In spite of differences in methodology, microbial degradation of benzene was noted in slurries constructed with sediments from various geographical locations and range from aquifer sands to fine-grained estuarine muds, under methanogenic, sulfate-reducing, and iron-reducing conditions. In aquifer sediments under methanogenic conditions, benzene loss was concomitant with methane production, and microbial utilization of [14C]benzene yielded 14CO2 and 14CH4. In slurries with estuarine and aquifer sediments under sulfate-reducing conditions, the loss of sulfate in amounts consistent with the stoichiometric degradation of benzene or the conversion of [14C]benzene to 14CO2 indicates that benzene was mineralized. Benzene loss also occurred in the presence of Fe(III) in sediments from freshwater environments. Microbial benzene utilization, however, was not observed under denitrifying conditions. These results indicate that the potential for the anaerobic degradation of benzene, which was once thought to be resistant to non-oxygenase attack, exists in a variety of aquatic sediments from widely distributed locations.

Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes.

PubMed

Yang, Jian; Ma, Li'an; Jiang, Hongchen; Wu, Geng; Dong, Hailiang

2016-04-26

Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P < 0.001) with lake salinity instead of geographic distance. This suggests that lake salinity is more important than geographic distance in shaping the microbial diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions.

Bacterial abundance and composition in marine sediments beneath the Ross Ice Shelf, Antarctica.

PubMed

Carr, S A; Vogel, S W; Dunbar, R B; Brandes, J; Spear, J R; Levy, R; Naish, T R; Powell, R D; Wakeham, S G; Mandernack, K W

2013-07-01

Marine sediments of the Ross Sea, Antarctica, harbor microbial communities that play a significant role in the decomposition, mineralization, and recycling of organic carbon (OC). In this study, the cell densities within a 153-cm sediment core from the Ross Sea were estimated based on microbial phospholipid fatty acid (PLFA) concentrations and acridine orange direct cell counts. The resulting densities were as high as 1.7 × 10⁷ cells mL⁻¹ in the top ten centimeters of sediments. These densities are lower than those calculated for most near-shore sites but consistent with deep-sea locations with comparable sedimentation rates. The δ¹³C measurements of PLFAs and sedimentary and dissolved carbon sources, in combination with ribosomal RNA (SSU rRNA) gene pyrosequencing, were used to infer microbial metabolic pathways. The δ¹³C values of dissolved inorganic carbon (DIC) in porewaters ranged downcore from -2.5‰ to -3.7‰, while δ¹³C values for the corresponding sedimentary particulate OC (POC) varied from -26.2‰ to -23.1‰. The δ¹³C values of PLFAs ranged between -29‰ and -35‰ throughout the sediment core, consistent with a microbial community dominated by heterotrophs. The SSU rRNA gene pyrosequencing revealed that members of this microbial community were dominated by β-, δ-, and γ-Proteobacteria, Actinobacteria, Chloroflexi and Bacteroidetes. Among the sequenced organisms, many appear to be related to known heterotrophs that utilize OC sources such as amino acids, oligosaccharides, and lactose, consistent with our interpretation from δ¹³CPLFA analysis. Integrating phospholipids analyses with porewater chemistry, δ¹³CDIC and δ¹³CPOC values and SSU rRNA gene sequences provides a more comprehensive understanding of microbial communities and carbon cycling in marine sediments, including those of this unique ice shelf environment. © 2013 John Wiley & Sons Ltd.

Microbial fuel cells for biosensor applications.

PubMed

Yang, Huijia; Zhou, Minghua; Liu, Mengmeng; Yang, Weilu; Gu, Tingyue

2015-12-01

Microbial fuel cells (MFCs) face major hurdles for real-world applications as power generators with the exception of powering small sensor devices. Despite tremendous improvements made in the last two decades, MFCs are still too expensive to build and operate and their power output is still too small. In view of this, in recently years, intensive researches have been carried out to expand the applications into other areas such as acid and alkali production, bioremediation of aquatic sediments, desalination and biosensors. Unlike power applications, MFC sensors have the immediate prospect to be practical. This review covers the latest developments in various proposed biosensor applications using MFCs including monitoring microbial activity, testing biochemical oxygen demand, detection of toxicants and detection of microbial biofilms that cause biocorrosion.

Cultivation and diversity of fungi buried in the Baltic Sea sediments

NASA Astrophysics Data System (ADS)

Xiao, N.

2015-12-01

@font-face { "ＭＳ 明朝"; }@font-face { "Century"; }@font-face { "Century"; }@font-face { "@ＭＳ 明朝"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0mm 0mm 0.0001pt; text-align: justify; font-size: 12pt; ; }.MsoChpDefault { ; }div.WordSection1 { page: WordSection1; } Studies on molecular biological and cultivation have been done for the prokaryotic microbial community in the deep biosphere. Compare to the prokaryotic community, few attempts have been done for eukaryotic microbial community. Here we report the study on fungi buried in deep-subsurface sediments by approaches of both cultivation and molecular diversity survey. Cultivation targeting fungi has been done using a sequential sediment samples obtained from the Baltic Sea, Landsort Deep site during the IODP expedition 347. 6 culture media with different nutrition and salt concentration have been tried for the fungi cultivation. 50 isolates of fungi were obtained from the sediment samples. The surface sediments showed richness of fungi strains but not for the deep sediments. Internal Transcribed Spacer (ITS) regions of RNA genes were amplified and for the identification of the isolates. The isolates were classified to 11 different genera. Pseudeurotium bakeri was the dominant strain throughout the glacial and interglacial sediments. We also found different representative fungal strains from glacial and interglacial sediments, suggesting the cultivated strains are buried from different sources. The survey of fungal diversity was done by sequencing the 18S RNA genes in the total DNA extracted from selected sediment samples. Fungi community showed different cluster in the glacial and interglacial sediments.Our results revealed the presence and activity of fungi in the deep biosphere of the Baltic sea and provided evidence of fungal community response to the climate change.

Microbial community and nitrogen cycling shift with snowmelt in high-elevation barren soils of Mount Rainier National Park

NASA Astrophysics Data System (ADS)

Simpson, A.; Zabowski, D.

2015-12-01

Climate change and nutrient deposition have the potential to accelerate soil formation in high-elevation sediments recently exposed by glacier or snow melt. This process has implications not only for ecosystem formation on Earth but for the formation of Earth-like ecosystems on other planets and icy moons. Research into microbial communities shifting from subnival to mesotrophic conditions has mainly focused on changes on respiration and biomass, and is generally limited to one or two well-studied geographical locations. In particular, more information is needed on microbial shifts in snow-covered volcanic sediments, which may prove the closest analog to the most 'habitable' non-terrestrial environments for Earth microorganisms. We sampled in volcanic soil and sediment along gradients of elevation and snowmelt - dry soil, moist soil next to snowpack, and soil underneath snowpack - at the Muir Snowfields at Mount Rainier National Park, in order to investigate changes in carbon and nitrogen compounds, microbial diversity and gene expression. Initial results show a decrease in available ammonium and increase in microbial biomass carbon in exposed sediment with increasing soil moisture, and a sharp decrease in microbial C:N ratios after snowmelt and drying. Available/labile organic carbon and organic nitrogen decrease strongly with elevation, while microbial biomass carbon and nitrogen and mineral nitrogen compounds show no change with elevation. Though gene expression data is needed for confirmation, we hypothesize that these snowfields receive strong wind-borne deposits of carbon and nitrogen but that chemoautotrophic communities under semi-permanent snowpack do not shift to more mesotrophic communities until after exposed sediment has already begun to desiccate, limiting soil formation.

Magnetic Susceptibility as a Proxy for Investigating Microbial Mediated Iron Reduction

EPA Science Inventory

We investigated magnetic susceptibility (MS) variations in hydrocarbon contaminated sediments. Our objective was to determine if MS can be used as an intrinsic bioremediation indicator due to the activity of iron-reducing bacteria. A contaminated and an uncontaminated core were r...

Microbes of deep marine sediments as viewed by metagenomics

NASA Astrophysics Data System (ADS)

Biddle, J.

2015-12-01

Ten years after the first deep marine sediment metagenome was produced, questions still exist about the nucleic acid sequences we have retrieved. Current data sets, including the Peru Margin, Costa Rica Margin and Iberian Margin show that consistently, data forms larger assemblies at depth due to the reduced complexity of the microbial community. But are these organisms active or preserved? At SMTZs, a change in the assembly statistics is noted, as well as an increase in cell counts, suggesting that cells are truly active. As depth increases, genome sizes are consistently large, suggesting that much like soil microbes, sedimentary microbes may maintain a larger reportorie of genomic potential. Functional changes are seen with depth, but at many sites are not correlated to specific geochemistries. Individual genomes show changes with depth, which raises interesting questions on how the subsurface is settled and maintained. The subsurface does have a distinct genomic signature, including unusual microbial groups, which we are now able to analyze for total genomic content.

Interactions between Natural Organic Matter and Native Microbes in the Oak Ridge FRC Groundwater

NASA Astrophysics Data System (ADS)

Wu, X.; Hazen, T.; Fox, P. M.; Nico, P. S.; Li, Q.; Yang, W.; Liu, Y.; Hess, N. J.; Zhang, P.; Qin, Y.; Zhou, J.; Chakraborty, R.

2016-12-01

Natural organic matter (NOM) is central to microbial food webs; however, little is known about the interplay between the physical and chemical characteristics of the carbon in NOM and its turnover by microbial communities. Microbial activity changes NOM's structure and properties, which may further influence the bioavailability of NOM. The change of NOM may reversely affect the microbial community structure as well. To date, our understanding of these interactions is insufficient, and it is critical to identify the role of NOM to carbon turnover, structure of microbial community and to the metabolic potential of that community. In this study, we aimed to study the interactions between NOM and native microbial communities present in groundwater at a background site (FW305 well) at Oak Ridge Field Research Center, TN. The total organic carbon and inorganic carbon in FW305 deep sediment samples were 0.071% and 0.011%, respectively. Water-soluble NOM was extracted from these sediment samples, the extraction efficiencies were 3.2% for organic carbon and 1.6% for inorganic carbon. The extracted NOM was then provided as the sole carbon source to native microbes present in groundwater. Subsamples were harvested several times from these incubations during a 50-day study. 16S rRNA gene amplicon sequencing and Geochip were used to identify the changes of microbial communities and expression of functional genes during transformation of the NOM. Several advanced chemical techniques including FTICR-MS and NEXAFS were used to characterize the C pool (i.e., NOM metabolites and microbial byproducts). Preliminary data clearly showed that microbial community responded to NOM, and shifted as functional groups in NOM transformed. Further detailed metabolite and gene-based analysis to elucidate these changes is currently being conducted.

Geoelectrical Evidence of Microbial Degradation of Diesel Contaminated Sediments

NASA Astrophysics Data System (ADS)

Werkema, D. D.; Atekwana, E. A.; Rossbach, S.; Sauck, W. A.

2003-12-01

The alteration of physical properties by microbial activity in petroleum contaminated sediments was investigated using geophysical techniques in laboratory column experiments. Microbial population growth was determined by the Most Probable Number technique (MPN), community dynamics were determined by the rDNA intergenic spacer analysis (RISA), microbial mineralization of diesel fuel was assessed using dissolved inorganic carbon (DIC), enhanced mineral dissolution was determined by dissolved calcium, and the vertical geoelectrical profile was measured using DC resistivity (converted to conductivity). The columns simulated a saturation profile and contained sanitized, uniform sand with the following experimental treatments: diesel + microbes, diesel, microbes, and no treatment. After 16 months, two important conclusions were drawn. First, the relative increase in magnitude of the parameters measured was highest in the diesel + microbe column (showing at least 110% increase), lower in the diesel column and lowest (actually showing a decrease) in the column with no treatment. Further, the diesel + microbe column showed the greatest increase in oil degrading microbial populations (135%) compared to the column with no treatment, which showed no changes. Secondly, the depth at which the conductivity reached the maximum occurred within and slightly above the diesel layer (which represents a depth that was originally water wet). It was further observed that the relative change in bulk conductivity below the saturated zone is of a lower magnitude than above (<10%). These results suggest the diesel layer, and the zone slightly above, were the most biologically active. Additionally, the diesel + microbe column showed RISA fragments attributed to microbial succession typically observed in organic contaminant plumes. A simple Archie's Law analysis was used to estimate the pore water conductivities necessary to reproduce the bulk conductivity measured. This analysis shows that relative to the column with only microbes (selected as the control to be most representative of field conditions), the diesel column revealed a 2.3 fold increase and the diesel + microbe column showed a 3 fold increase in pore water conductivity. This increase was located within the diesel layer above the water saturated zone. Within the saturated zone, the no treatment column showed a 0.81 fold increase, the diesel column a 1.28, and the diesel + microbe column 1.45. We conclude from this study that microbial activity and the resultant biogeochemical changes played an important role in modifying the geoelectrical properties of aquifers and sediments rich in organic carbon and mineralized by bacteria by increasing the bulk conductivity. This conductive zone occurred within and immediately above the free-phase petroleum layer. In natural environments with high concentrations of organic compounds available as electron donors, geophysical techniques may potentially be used as indicators of microbial activity. Notice: This is an abstract of a proposed presentation and does not necessarily reflect the United States Environmental Protection Agency (EPA) policy. The actual presentation has not been peer reviewed by EPA. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

Biogeochemistry and geomicrobiology of cold-water coral carbonate mounds - lessons learned from IODP Expedition 307

NASA Astrophysics Data System (ADS)

Ferdelman, Timothy; Wehrmann, Laura; Mangelsdorf, Kai; Kano, Akihiro; Williams, Trevor; Jean-Pierre, Henriet

2010-05-01

Large mound structures associated with cold-water coral ecosystems commonly occur on the slopes of continental margins, for instance, west of Ireland in the Porcupine Seabight, the Gulf of Cadiz or the Straits of Florida. In the Porcupine Seabight over 1500 mounds of up to 5 km in diameter and 250 m height lie at water depths of 600 to 900 m. The cold-water coral reef ecosystems associated with these structures are considered to be "hotspots" of organic carbon mineralization and microbial systems. To establish a depositional and biogeochemical/diagenetic model for cold-water carbonate mounds, Challenger Mound and adjacent continental slope sites were drilled in May 2005 during IODP Expedition 307. One major objective was to test whether deep sub-surface hydrocarbon flow and enhanced microbial activity within the mound structure was important in producing and stabilizing these sedimentary structures. Drilling results showed that the Challenger mound succession (IODP Site U1317) is 130 to 150 meters thick, and mainly consists of floatstone and rudstone facies formed of fine sediments and cold-water branching corals. Pronounced recurring cycles on the scales of several meters are recognized in carbonate content (up to 70% carbonate) and color reflectance, and are probably associated with Pleistocene glacial-interglacial cycles. A role for methane seepage and subsequent anaerobic oxidation was discounted both as a hard-round substrate for mound initiation and as a principal source of carbonate within the mound succession. A broad sulfate-methane transition (approximately 50 m thick)within the Miocene sediments suggested that the zone of anaerobic oxidation of methane principally occurs below the moundbase. In the mound sediments, interstitial water profiles of sulfate, alkalinity, Mg, and Sr suggested a tight coupling between carbonate diagenesis and low rates of microbial sulfate reduction. Overall organic carbon mineralization within cold-water coral mound appeared to be dominated by low rates of iron- and sulfate-reduction that occur in discrete layers within the mound. This was consistent with distributions of total cell-counts, acetate turnover (Webster et al. 2009) and hydrogenase activity (Soffiento et al. 2009). However, biomarker lipid distributions suggested that the Miocene sediments underlying the mound, into which sulfate is diffusing, as well as the sediments from the non-cold water coral reference site (U1318) contain higher abundances of living microbes. The results obtained from Expedition 307 are consistent with a picture emerging from other biogeochemical studies of cold-water coral mound and reef sites. Unless impacted by some external forcing (e.g. fluid flow or erosion event), the microbial activity in the underlying cold-water coral mound sediments is largely decoupled from the highly diverse, active surface ecosystem. References: Soffiento B, Spivack AJ, Smith DC, and D'Hondt S (2009) Hydrogenase activity in deeply buried sediments of the Arctic and North Atlantic Oceans. Geomicro. J. 26: 537-545. Webster, G, Blazejak A, Cragg BA, Schippers A, Sass H, Rinna J, Tang X, Mathes F, Ferdelman TG., Fry JC, Weightman AJ, and Parkes RJ. 2009. Subsurface microbiology and biogeochemistry of a deep, cold-water carbonate mound from the Porcupine Seabight (IODP Expediton 307). Env. Microbiol., 11, 239-257, doi:10.1111/j.1462-2920.01759.x.

Distribution, activity and function of short-chain alkane degrading phylotypes in hydrothermal vent sediments

NASA Astrophysics Data System (ADS)

Adams, M. M.; Joye, S. B.; Hoarfrost, A.; Girguis, P. R.

2012-12-01

Global geochemical analyses suggest that C2-C4 short chain alkanes are a common component of the utilizable carbon pool in deep-sea sediments worldwide and have been found in diverse ecosystems. From a thermodynamic standpoint, the anaerobic microbial oxidation of these aliphatic hydrocarbons is more energetically yielding than the anaerobic oxidation of methane (AOM). Therefore, the preferential degradation of these hydrocarbons may compete with AOM for the use of oxidants such as sulfate, or other potential oxidants. Such processes could influence the fate of methane in the deep-sea. Sulfate-reducing bacteria (SRB) from hydrocarbon seep sediments of the Gulf of Mexico and Guaymas Basin have previously been enriched that anaerobically oxidize short chain alkanes to generate CO2 with the preferential utilization of 12C-enriched alkanes (Kniemeyer et al. 2007). Different temperature regimens along with multiple substrates were tested and a pure culture (deemed BuS5) was isolated from mesophilic enrichments with propane or n-butane as the sole carbon source. Through comparative sequence analysis, strain BuS5 was determined to cluster with the metabolically diverse Desulfosarcina / Desulfococcus cluster, which also contains the SRB found in consortia with anaerobic, methane-oxidizing archaea in seep sediments. Enrichments from a terrestrial, low temperature sulfidic hydrocarbon seep also corroborated that propane degradation occurred with most bacterial phylotypes surveyed belonging to the Deltaproteobacteria, particularly Desulfobacteraceae (Savage et al. 2011). To date, no microbes capable of ethane oxidation or anaerobic C2-C4 alkane oxidation at thermophilic temperature have been isolated. The sediment-covered, hydrothermal vent systems found at Middle Valley (Juan de Fuca Ridge, eastern Pacific Ocean) are a prime environment for investigating mesophilic to thermophilic anaerobic oxidation of short-chain alkanes, given the elevated temperatures and dissolved hydrocarbon species characteristic of these metalliferous sediments. These systems are also characterized by sharp physicochemical gradients that have been shown to have a pronounced effect on microbial ecology and activity. Sediments were collected from a Middle Valley field with relatively high concentrations of short-chain alkanes and incubated in anaerobic batch reactors with each individual alkane (C1, C2, C3 and C4, respectively) at a range of temperatures (25, 55 and 75 °C) to mimic environmental physico-chemical conditions in a closed system. Stable carbon isotope ratios and radiotracer incubations provide clear evidence for C2-C4 alkane oxidation in the sediments over time. Upon identifying sediments with anaerobic alkane oxidation activity, microbial communities were screened via 16S rRNA pyrosequencing, and key phylotypes were then quantified using both molecular and microscopic methods. There were shifts in overall community composition and putative alkane-oxidizing phylotypes after the incubation period with the alkane substrates. These are the first evidence to date indicating that anaerobic C2-C4 alkane oxidation occurs across a broad range of temperatures in metalliferous sediments.

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities

DOE PAGES

Marlow, Jeffery; Skennerton, Connor T.; Li, Zhou; ...

2016-04-29

Marine methane seep habitats represent an important control on the global flux of methane between the subsurface and water column reservoirs. Meta-omics studies have begun to outline community-wide metabolic potential, but expression patterns of proteins that enact sulfate-mediated anaerobic methane oxidation in seeps are poorly characterized. Proteomic stable isotope probing (proteomic SIP) offers an additional layer of information for characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track the protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 proteinsmore » were identified, 21% of which were 15N-labeled. We observed active synthesis (15N enrichment) of all proteins believed to be involved in sulfate reduction and reverse methanogenesis including methylenetetrahydromethanopterin reductase (Mer). The abundance and phylogenetic range of methyl-coenzyme M reductase (Mcr) orthologs produced during incubation experiments suggests that seeps provide sufficient niches for multiple organisms performing analogous metabolisms. Twenty-eight previously unreported post-translational modifications of McrA were measured, indicating dynamic enzymatic machinery and offering a dimension of functional diversity beyond gene-dictated sequence. RNA polymerase associated with putative sulfur-oxidizing Epsilonproteobacteria and aerobic Gammaproteobacteria were more abundant among pre-incubation proteins, suggesting diminished metabolic activity in long-term anoxic, sulfidic experimental incubations. Twenty-six proteins of unknown function were detected in all proteomic experiments and actively expressed in labeled experiments, suggesting that they play important roles in methane seep ecosystems. The addition of stable isotope probing to environmental proteomics experiments provides a mechanism to begin to assess the degree to which diagnostic meatbolic proteins are long-lived or acively synthesized in complex, slow-growing microbial communities. Our work here demonstrates that sediment-hosted microbial assemblages in marine methane seeps are dynamic, heterogeneous systems with broad functional diversity.« less

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marlow, Jeffery; Skennerton, Connor T.; Li, Zhou

Marine methane seep habitats represent an important control on the global flux of methane between the subsurface and water column reservoirs. Meta-omics studies have begun to outline community-wide metabolic potential, but expression patterns of proteins that enact sulfate-mediated anaerobic methane oxidation in seeps are poorly characterized. Proteomic stable isotope probing (proteomic SIP) offers an additional layer of information for characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track the protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 proteinsmore » were identified, 21% of which were 15N-labeled. We observed active synthesis (15N enrichment) of all proteins believed to be involved in sulfate reduction and reverse methanogenesis including methylenetetrahydromethanopterin reductase (Mer). The abundance and phylogenetic range of methyl-coenzyme M reductase (Mcr) orthologs produced during incubation experiments suggests that seeps provide sufficient niches for multiple organisms performing analogous metabolisms. Twenty-eight previously unreported post-translational modifications of McrA were measured, indicating dynamic enzymatic machinery and offering a dimension of functional diversity beyond gene-dictated sequence. RNA polymerase associated with putative sulfur-oxidizing Epsilonproteobacteria and aerobic Gammaproteobacteria were more abundant among pre-incubation proteins, suggesting diminished metabolic activity in long-term anoxic, sulfidic experimental incubations. Twenty-six proteins of unknown function were detected in all proteomic experiments and actively expressed in labeled experiments, suggesting that they play important roles in methane seep ecosystems. The addition of stable isotope probing to environmental proteomics experiments provides a mechanism to begin to assess the degree to which diagnostic meatbolic proteins are long-lived or acively synthesized in complex, slow-growing microbial communities. Our work here demonstrates that sediment-hosted microbial assemblages in marine methane seeps are dynamic, heterogeneous systems with broad functional diversity.« less

Modeling the Formation of Hydrate-Filled Veins in Fine-Grained Sediments from in Situ Microbial Methane

NASA Astrophysics Data System (ADS)

Malinverno, A.; Cook, A.; Daigle, H.

2016-12-01

Continental margin sediments are dominantly fine-grained silt and clay, and methane hydrates in these sediments are often found in semi-vertical veins and fractures. In several instances, these hydrate veins occupy discrete depth intervals that are a few tens of meters thick and are surrounded by hydrate-free sediments. As they are not connected with gas sources beneath the base of the gas hydrate stability zone (GHSZ), these isolated hydrate-bearing intervals have been interpreted as formed by in situ microbial methane. To investigate the formation of these hydrate deposits, we applied a time-dependent advection-diffusion-reaction model that includes the effects of sedimentation, compaction, solute diffusion, and microbial methane generation. Microbial methane generation depends on the amount of metabolizable organic carbon deposited at the seafloor, whose progressive degradation produces methane beneath the sulfate reduction zone. If the amount of organic carbon entering the methanogenic zone is kept constant in time, we found that the computed amounts of hydrate formed in discrete intervals within the GHSZ are well below those estimated from observations. On the other hand, if the deposition of organic carbon is higher in a given time interval, methane generation during burial is more intense in the corresponding sediment interval, resulting in enhanced hydrate formation. With variations in organic carbon deposition comparable to those generally observed in continental margins, our model was able to reproduce the methane hydrate contents that were estimated from drilling. These results support the suggestion that in situ microbial generation associated with transient organic carbon deposition is the source of methane that forms isolated intervals of hydrate-filled veins in fine-grained sediments.

Modeling the Formation of Hydrate-Filled Veins in Fine-Grained Sediments from in Situ Microbial Methane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malinverno, Alberto; Cook, Ann; Daigle, Hugh

Continental margin sediments are dominantly fine-grained silt and clay, and methane hydrates in these sediments are often found in semi-vertical veins and fractures. In several instances, these hydrate veins occupy discrete depth intervals that are a few tens of meters thick and are surrounded by hydrate-free sediments. As they are not connected with gas sources beneath the base of the gas hydrate stability zone (GHSZ), these isolated hydrate-bearing intervals have been interpreted as formed by in situ microbial methane. To investigate the formation of these hydrate deposits, we applied a time-dependent advection-diffusion-reaction model that includes the effects of sedimentation, compaction,more » solute diffusion, and microbial methane generation. Microbial methane generation depends on the amount of metabolizable organic carbon deposited at the seafloor, whose progressive degradation produces methane beneath the sulfate reduction zone. If the amount of organic carbon entering the methanogenic zone is kept constant in time, we found that the computed amounts of hydrate formed in discrete intervals within the GHSZ are well below those estimated from observations. On the other hand, if the deposition of organic carbon is higher in a given time interval, methane generation during burial is more intense in the corresponding sediment interval, resulting in enhanced hydrate formation. With variations in organic carbon deposition comparable to those generally observed in continental margins, our model was able to reproduce the methane hydrate contents that were estimated from drilling. These results support the suggestion that in situ microbial generation associated with transient organic carbon deposition is the source of methane that forms isolated intervals of hydrate-filled veins in fine-grained sediments.« less

Methane Metabolizing Microbial Communities in the Cold Seep Areas in the Northern Continental Shelf of South China Sea

NASA Astrophysics Data System (ADS)

Wang, F.; Liang, Q.

2016-12-01

Marine sediment contains large amount of methane, estimated approximately 500-2500 gigatonnes of dissolved and hydrated methane carbon stored therein, mainly in continental margins. In localized specific areas named cold seeps, hydrocarbon (mainly methane) containing fluids rise to the seafloor, and support oases of ecosystem composed of various microorganisms and faunal assemblages. South China Sea (SCS) is surrounded by passive continental margins in the west and north and convergent margins in the south and east. Thick organic-rich sediments have accumulated in the SCS since the late Mesozoic, which are continuing sources to form gas hydrates in the sediments of SCS. Here, Microbial ecosystems, particularly those involved in methane transformations were investigated in the cold seep areas (Qiongdongnan, Shenhu, and Dongsha) in the northern continental shelf of SCS. Multiple interdisciplinary analytic tools such as stable isotope probing, geochemical analysis, and molecular ecology, were applied for a comprehensive understanding of the microbe mediated methane transformation in this project. A variety of sediments cores have been collected, the geochemical profiles and the associated microbial distribution along the sediment cores were recorded. The major microbial groups involved in the methane transformation in these sediment cores were revealed, known methane producing and oxidizing archaea including Methanosarcinales, anaerobic methane oxidizing groups ANME-1, ANME-2 and their niche preference in the SCS sediments were found. In-depth comparative analysis revealed the presence of SCS-specific archaeal subtypes which probably reflected the evolution and adaptation of these methane metabolizing microbes to the SCS environmental conditions. Our work represents the first comprehensive analysis of the methane metabolizing microbial communities in the cold seep areas along the northern continental shelf of South China Sea, would provide new insight into the mechanisms of methane biotransformation.

Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes.

PubMed

Coolen, Marco J L; Cypionka, Heribert; Sass, Andrea M; Sass, Henrik; Overmann, Jörg

2002-06-28

Late Pleistocene organic-rich sediments (sapropels) from the eastern Mediterranean Sea harbor unknown, metabolically active chemoorganotrophic prokaryotes. As compared to the carbon-lean intermediate layers, sapropels exhibit elevated cell numbers, increased activities of hydrolytic exoenzymes, and increased anaerobic glucose degradation rates, suggesting that microbial carbon substrates originate from sapropel layers up to 217,000 years old. 16S ribosomal RNA gene analyses revealed that as-yet-uncultured green nonsulfur bacteria constitute up to 70% of the total microbial biomass. Crenarchaeota constitute a smaller fraction (on average, 16%). A slow but significant turnover of glucose could be detected. Apparently, sapropels are still altered by the metabolic activity of green nonsulfur bacteria and crenarchaeota.

Mineralization Of PAHs In Coal-Tar Impacted Aquifer Sediments And Associated Microbial Community Structure Investigated With FISH

EPA Science Inventory

The microbial community structure and mineralization of polycyclic aromatic hydrocarbons (PAHs) in a coal-tar contaminated aquifer were investigated spatially using fluorescence in situ hybridization (FISH) and in laboratory-scale incubations of the aquifer sediments. DAPI-detect...

Biogeography and Biodiversity in Sulfide Structures of Active and Inactive Vents at Deep-Sea Hydrothermal Fields of the Southern Mariana Trough▿ †

PubMed Central

Kato, Shingo; Takano, Yoshinori; Kakegawa, Takeshi; Oba, Hironori; Inoue, Kazuhiko; Kobayashi, Chiyori; Utsumi, Motoo; Marumo, Katsumi; Kobayashi, Kensei; Ito, Yuki; Ishibashi, Jun-ichiro; Yamagishi, Akihiko

2010-01-01

The abundance, diversity, activity, and composition of microbial communities in sulfide structures both of active and inactive vents were investigated by culture-independent methods. These sulfide structures were collected at four hydrothermal fields, both on- and off-axis of the back-arc spreading center of the Southern Mariana Trough. The microbial abundance and activity in the samples were determined by analyzing total organic content, enzymatic activity, and copy number of the 16S rRNA gene. To assess the diversity and composition of the microbial communities, 16S rRNA gene clone libraries including bacterial and archaeal phylotypes were constructed from the sulfide structures. Despite the differences in the geological settings among the sampling points, phylotypes related to the Epsilonproteobacteria and cultured hyperthermophilic archaea were abundant in the libraries from the samples of active vents. In contrast, the relative abundance of these phylotypes was extremely low in the libraries from the samples of inactive vents. These results suggest that the composition of microbial communities within sulfide structures dramatically changes depending on the degree of hydrothermal activity, which was supported by statistical analyses. Comparative analyses suggest that the abundance, activity and diversity of microbial communities within sulfide structures of inactive vents are likely to be comparable to or higher than those in active vent structures, even though the microbial community composition is different between these two types of vents. The microbial community compositions in the sulfide structures of inactive vents were similar to those in seafloor basaltic rocks rather than those in marine sediments or the sulfide structures of active vents, suggesting that the microbial community compositions on the seafloor may be constrained by the available energy sources. Our findings provide helpful information for understanding the biogeography, biodiversity and microbial ecosystems in marine environments. PMID:20228114

Comparison among the microbial communities in the lake, lake wetland, and estuary sediments of a plain river network.

PubMed

Huang, Wei; Chen, Xing; Wang, Kun; Chen, Junyi; Zheng, Binghui; Jiang, Xia

2018-06-10

Sediment microbial communities from plain river networks exert different effects on pollutant transformation and migration in lake basins. In this study, we examined millions of Illumina reads (16S rRNA gene amplicons) to compare lake, lake wetland, and estuary bacterial communities through a technically consistent approach. Results showed that bacterial communities in the sampled lake sediments had the highest alpha-diversity (Group B), than in sampled lake wetland sediments and estuary sediments. Proteobacteria was the most abundant (more than 30%) phyla in all the sediments. The lake sediments had more Nitrospirae (1.63%-11.75%) and Acidobacteria (3.46%-10.21%) than the lake wetland and estuary sediments, and estuary sediments had a greater abundance of the phylum Firmicutes (mean of 22.30%). Statistical analysis (LEfSe) revealed that lake wetland sediments contained greater abundances of the class Anaerolineaceae, orders Xanthomonadales, Pseudomonadales, and genera Flavobacterium, Acinetobacter. The lake sediments had a distinct community of diverse primary producers, such as phylum Acidobacteria, order Ignavibacteriales, and families Nitrospiraceae, Hydrogenophilaceae. Total phosphorus and organic matter were the main factors influencing the bacterial communities in sediments from several parts of the lake wetland and river estuary (p < .05). The novel insights into basin pollution control in plain river networks may be obtained from microbial distribution in sediments from different basin regions. © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Evidence and biogeochemical implications for glacially-derived sediments in an active margin cold seep

USGS Publications Warehouse

Pohlman, John W.; Riedel, Michael; Novosel, Ivana; Bauer, James E.; Canuel, Elizabeth A.; Paull, Charles K.; Coffin, Richard B.; Grabowski, Kenneth S.; Knies, David L.; Hyndman, Roy D.; Spence, George D.

2011-01-01

Delineating sediment organic matter origins and sediment accumulation rates at gas hydratebearing and hydrocarbon seeps is complicated by the microbial transfer of 13C-depleted and 14Cdepleted methane carbon into sedimentary pools. Sediment 13C and 14C measurements from four cores recovered at Bullseye vent on the northern Cascadia margin are used to identify methane carbon assimilation into different carbon pools. While the total organic carbon (TOC) is mostly unaltered and primarily terrigenous in origin, planktonic foraminifera and the bulk carbonate display evidence of methane overprinting. Mass balance models are applied to determine the extent to which methane overprinting increased the radiocarbon ages of the biogenic foraminifera. The corrected and calibrated foraminifera ages between sediment depths of 70 and 573 cm are from 14.9 to 15.9 ka BP, which coincides with the retreat of the late Quaternary Cordilleran Ice Sheet from Vancouver Island. Uniform TOC _13C values of -24.5 ± 0.5‰ from the upper 8 meters of sediment at Bullseye vent suggest all cored material is Pleistocene-derived glacimarine material deposited as the ice edge retreated landward. Bullseye vent is located within an uplifted sediment block isolated from turbidite deposition and has been a site of non-deposition since the ice sheet retreated from the shelf. Biogeochemical implications of seep sediments being dominated by aged, organic-poor (<0.4 wt% TOC) material are that methane is the primary energy source, and microbes directly and indirectly associated with the anaerobic oxidation of methane (AOM) will dominate the seep microbial community.

In situ remediation of contaminated marinesediment: an overview.

PubMed

Lofrano, G; Libralato, G; Minetto, D; De Gisi, S; Todaro, F; Conte, B; Calabrò, D; Quatraro, L; Notarnicola, M

2017-02-01

Sediment tends to accumulate inorganic and persistent hydrophobic organic contaminants representing one of the main sinks and sources of pollution. Generally, contaminated sediment poses medium- and long-term risks to humans and ecosystem health; dredging activities or natural resuspension phenomena (i.e., strongly adverse weather conditions) can remobilize pollution releasing it into the water column. Thus, ex situ traditional remediation activities (i.e., dredging) can be hazardous compared to in situ techniques that try to keep to a minimum sediment mobilization, unless dredging is compulsory to reach a desired bathymetric level. We reviewed in situ physico-chemical (i.e., active mixing and thin capping, solidification/stabilization, chemical oxidation, dechlorination, electrokinetic separation, and sediment flushing) and bio-assisted treatments, including hybrid solutions (i.e., nanocomposite reactive capping, bioreactive capping, microbial electrochemical technologies). We found that significant gaps still remain into the knowledge about the application of in situ contaminated sediment remediation techniques from the technical and the practical viewpoint. Only activated carbon-based technologies are well developed and currently applied with several available case studies. The environmental implication of in situ remediation technologies was only shortly investigated on a long-term basis after its application, so it is not clear how they can really perform.

The Seagrass Holobiont and Its Microbiome

PubMed Central

Ugarelli, Kelly; Chakrabarti, Seemanti; Laas, Peeter; Stingl, Ulrich

2017-01-01

Seagrass meadows are ecologically and economically important components of many coastal areas worldwide. Ecosystem services provided by seagrasses include reducing the number of microbial pathogens in the water, providing food, shelter and nurseries for many species, and decreasing the impact of waves on the shorelines. A global assessment reported that 29% of the known areal extent of seagrasses has disappeared since seagrass areas were initially recorded in 1879. Several factors such as direct and indirect human activity contribute to the demise of seagrasses. One of the main reasons for seagrass die-offs all over the world is increased sulfide concentrations in the sediment that result from the activity of sulfate-reducing prokaryotes, which perform the last step of the anaerobic food chain in marine sediments and reduce sulfate to H2S. Recent seagrass die-offs, e.g., in the Florida and Biscayne Bays, were caused by an increase in pore-water sulfide concentrations in the sediment, which were the combined result of unfavorable environmental conditions and the activities of various groups of heterotrophic bacteria in the sulfate-rich water-column and sediment that are stimulated through increased nutrient concentrations. Under normal circumstances, seagrasses are able to withstand low levels of sulfide, probably partly due to microbial symbionts, which detoxify sulfide by oxidizing it to sulfur or sulfate. Novel studies are beginning to give greater insights into the interactions of microbes and seagrasses, not only in the sulfur cycle. Here, we review the literature on the basic ecology and biology of seagrasses and focus on studies describing their microbiome. PMID:29244764

Living microbial ecosystems within the active zone of catagenesis: Implications for feeding the deep biosphere

NASA Astrophysics Data System (ADS)

Horsfield, B.; Schenk, H. J.; Zink, K.; Ondrak, R.; Dieckmann, V.; Kallmeyer, J.; Mangelsdorf, K.; di Primio, R.; Wilkes, H.; Parkes, R. J.; Fry, J.; Cragg, B.

2006-06-01

Earth's largest reactive carbon pool, marine sedimentary organic matter, becomes increasingly recalcitrant during burial, making it almost inaccessible as a substrate for microorganisms, and thereby limiting metabolic activity in the deep biosphere. Because elevated temperature acting over geological time leads to the massive thermal breakdown of the organic matter into volatiles, including petroleum, the question arises whether microorganisms can directly utilize these maturation products as a substrate. While migrated thermogenic fluids are known to sustain microbial consortia in shallow sediments, an in situ coupling of abiotic generation and microbial utilization has not been demonstrated. Here we show, using a combination of basin modelling, kinetic modelling, geomicrobiology and biogeochemistry, that microorganisms inhabit the active generation zone in the Nankai Trough, offshore Japan. Three sites from ODP Leg 190 have been evaluated, namely 1173, 1174 and 1177, drilled in nearly undeformed Quaternary and Tertiary sedimentary sequences seaward of the Nankai Trough itself. Paleotemperatures were reconstructed based on subsidence profiles, compaction modelling, present-day heat flow, downhole temperature measurements and organic maturity parameters. Today's heat flow distribution can be considered mainly conductive, and is extremely high in places, reaching 180 mW/m 2. The kinetic parameters describing total hydrocarbon generation, determined by laboratory pyrolysis experiments, were utilized by the model in order to predict the timing of generation in time and space. The model predicts that the onset of present day generation lies between 300 and 500 m below sea floor (5100-5300 m below mean sea level), depending on well location. In the case of Site 1174, 5-10% conversion has taken place by a present day temperature of ca. 85 °C. Predictions were largely validated by on-site hydrocarbon gas measurements. Viable organisms in the same depth range have been proven using 14C-radiolabelled substrates for methanogenesis, bacterial cell counts and intact phospholipids. Altogether, these results point to an overlap of abiotic thermal degradation reactions going on in the same part of the sedimentary column as where a deep biosphere exists. The organic matter preserved in Nankai Trough sediments is of the type that generates putative feedstocks for microbial activity, namely oxygenated compounds and hydrocarbons. Furthermore, the rates of thermal degradation calculated from the kinetic model closely resemble rates of respiration and electron donor consumption independently measured in other deep biosphere environments. We deduce that abiotically driven degradation reactions have provided substrates for microbial activity in deep sediments at this convergent continental margin.

Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages

PubMed Central

Pasulka, Alexis L.; Marlow, Jeffrey J.; Grupe, Benjamin M.; Levin, Lisa A.

2015-01-01

ABSTRACT Marine methane seeps are globally distributed geologic features in which reduced fluids, including methane, are advected upward from the subsurface. As a result of alkalinity generation during sulfate-coupled methane oxidation, authigenic carbonates form slabs, nodules, and extensive pavements. These carbonates shape the landscape within methane seeps, persist long after methane flux is diminished, and in some cases are incorporated into the geologic record. In this study, microbial assemblages from 134 native and experimental samples across 5,500 km, representing a range of habitat substrates (carbonate nodules and slabs, sediment, bottom water, and wood) and seepage conditions (active and low activity), were analyzed to address two fundamental questions of seep microbial ecology: (i) whether carbonates host distinct microbial assemblages and (ii) how sensitive microbial assemblages are to habitat substrate type and temporal shifts in methane seepage flux. Through massively parallel 16S rRNA gene sequencing and statistical analysis, native carbonates are shown to be reservoirs of distinct and highly diverse seep microbial assemblages. Unique coupled transplantation and colonization experiments on the seafloor demonstrated that carbonate-associated microbial assemblages are resilient to seep quiescence and reactive to seep activation over 13 months. Various rates of response to simulated seep quiescence and activation are observed among similar phylogenies (e.g., Chloroflexi operational taxonomic units) and similar metabolisms (e.g., putative S oxidizers), demonstrating the wide range of microbial sensitivity to changes in seepage flux. These results imply that carbonates do not passively record a time-integrated history of seep microorganisms but rather host distinct, diverse, and dynamic microbial assemblages. PMID:26695630

Dehalogenation Activities and Distribution of Reductive Dehalogenase Homologous Genes in Marine Subsurface Sediments▿ †

PubMed Central

Futagami, Taiki; Morono, Yuki; Terada, Takeshi; Kaksonen, Anna H.; Inagaki, Fumio

2009-01-01

Halogenated organic compounds serve as terminal electron acceptors for anaerobic respiration in a diverse range of microorganisms. Here, we report on the widespread distribution and diversity of reductive dehalogenase homologous (rdhA) genes in marine subsurface sediments. A total of 32 putative rdhA phylotypes were detected in sediments from the southeast Pacific off Peru, the eastern equatorial Pacific, the Juan de Fuca Ridge flank off Oregon, and the northwest Pacific off Japan, collected at a maximum depth of 358 m below the seafloor. In addition, significant dehalogenation activity involving 2,4,6-tribromophenol and trichloroethene was observed in sediment slurry from the Nankai Trough Forearc Basin. These results suggest that dehalorespiration is an important energy-yielding pathway in the subseafloor microbial ecosystem. PMID:19749069

Carbon fixation in sediments of Sino-Pacific seas-differential contributions of bacterial and archaeal domains

NASA Astrophysics Data System (ADS)

Das, Anindita; Cao, Wenrui; Zhang, Hongjie; Saren, Gaowa; Jiang, Mingyu; Yu, Xinke

2017-11-01

Oceanic stretches experiencing perpetual darkness and extreme limitation of utilizable organic matter often rely on chemosynthetic carbon (C)-fixation. However, C-fixation is not limited to carbon-deplete environments alone but might also occur in varying degrees in carbon-replete locales depending on the nature and concentration of utilizable carbon, electron donors and acceptors. Quantification of microbial C-fixation and relative contribution of domains bacteria and archaea are therefore crucial. The present experiment estimates the differential rates of C-fixation by archaea and bacteria along with the effects of different electron donors. Four Sino-Pacific marine sediments from Bashi strait (Western Pacific Warm Pool), East China Sea, South China Sea and Okinawa Trough were examined. Total microbial C-uptake was estimated by doping of aqueous NaH14CO3. Total bacterial C-uptake was measured by blocking archaeal metabolism using inhibitor GC7. Archaeal contribution was estimated by subtracting total bacterial from total microbial C-uptake. Effect of electron donor addition was analyzed by spiking with ammonium, sulfide, and reduced metals. Results suggested that C-fixation in marine sediments was not the function of archaea alone, which was in contrast to results from several recent publications. C-fixing bacteria are also equally active. Often in spite of great effort of one domain to fix carbon, the system does not become net C-fixing due to equal and opposite C-releasing activity of the other domain. Thus a C-releasing bacterial or archaeal community can become C-fixing with the change of nature and concentration of electron donors.

Phototrophs in high-iron-concentration microbial mats: physiological ecology of phototrophs in an iron-depositing hot spring

NASA Technical Reports Server (NTRS)

Pierson, B. K.; Parenteau, M. N.; Griffin, B. M.

1999-01-01

At Chocolate Pots Hot Springs in Yellowstone National Park the source waters have a pH near neutral, contain high concentrations of reduced iron, and lack sulfide. An iron formation that is associated with cyanobacterial mats is actively deposited. The uptake of [(14)C]bicarbonate was used to assess the impact of ferrous iron on photosynthesis in this environment. Photoautotrophy in some of the mats was stimulated by ferrous iron (1.0 mM). Microelectrodes were used to determine the impact of photosynthetic activity on the oxygen content and the pH in the mat and sediment microenvironments. Photosynthesis increased the oxygen concentration to 200% of air saturation levels in the top millimeter of the mats. The oxygen concentration decreased with depth and in the dark. Light-dependent increases in pH were observed. The penetration of light in the mats and in the sediments was determined. Visible radiation was rapidly attenuated in the top 2 mm of the iron-rich mats. Near-infrared radiation penetrated deeper. Iron was totally oxidized in the top few millimeters, but reduced iron was detected at greater depths. By increasing the pH and the oxygen concentration in the surface sediments, the cyanobacteria could potentially increase the rate of iron oxidation in situ. This high-iron-content hot spring provides a suitable model for studying the interactions of microbial photosynthesis and iron deposition and the role of photosynthesis in microbial iron cycling. This model may help clarify the potential role of photosynthesis in the deposition of Precambrian banded iron formations.

Microbial carbon metabolism associated with electrogenic sulphur oxidation in coastal sediments.

PubMed

Vasquez-Cardenas, Diana; van de Vossenberg, Jack; Polerecky, Lubos; Malkin, Sairah Y; Schauer, Regina; Hidalgo-Martinez, Silvia; Confurius, Veronique; Middelburg, Jack J; Meysman, Filip J R; Boschker, Henricus T S

2015-09-01

Recently, a novel electrogenic type of sulphur oxidation was documented in marine sediments, whereby filamentous cable bacteria (Desulfobulbaceae) are mediating electron transport over cm-scale distances. These cable bacteria are capable of developing an extensive network within days, implying a highly efficient carbon acquisition strategy. Presently, the carbon metabolism of cable bacteria is unknown, and hence we adopted a multidisciplinary approach to study the carbon substrate utilization of both cable bacteria and associated microbial community in sediment incubations. Fluorescence in situ hybridization showed rapid downward growth of cable bacteria, concomitant with high rates of electrogenic sulphur oxidation, as quantified by microelectrode profiling. We studied heterotrophy and autotrophy by following (13)C-propionate and -bicarbonate incorporation into bacterial fatty acids. This biomarker analysis showed that propionate uptake was limited to fatty acid signatures typical for the genus Desulfobulbus. The nanoscale secondary ion mass spectrometry analysis confirmed heterotrophic rather than autotrophic growth of cable bacteria. Still, high bicarbonate uptake was observed in concert with the development of cable bacteria. Clone libraries of 16S complementary DNA showed numerous sequences associated to chemoautotrophic sulphur-oxidizing Epsilon- and Gammaproteobacteria, whereas (13)C-bicarbonate biomarker labelling suggested that these sulphur-oxidizing bacteria were active far below the oxygen penetration. A targeted manipulation experiment demonstrated that chemoautotrophic carbon fixation was tightly linked to the heterotrophic activity of the cable bacteria down to cm depth. Overall, the results suggest that electrogenic sulphur oxidation is performed by a microbial consortium, consisting of chemoorganotrophic cable bacteria and chemolithoautotrophic Epsilon- and Gammaproteobacteria. The metabolic linkage between these two groups is presently unknown and needs further study.

Microbiome succession during ammonification in eelgrass bed sediments.

PubMed

Ettinger, Cassandra L; Williams, Susan L; Abbott, Jessica M; Stachowicz, John J; Eisen, Jonathan A

2017-01-01

Eelgrass ( Zostera marina ) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, also known as diagenesis, from plots at a field site in Bodega Bay, CA. Sediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples ( n  = 4 per plot) under a N 2 atmosphere, incubated them at in situ temperatures (15 °C) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at seven, 13 and 19 days to characterize changes in the relative abundances of microbial taxa throughout ammonification. Within-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in predicted sulfur reducers ( Desulfobacterales ) and corresponding increases in predicted sulfide oxidizers ( Thiotrichales ). None of these changes in composition or richness were associated with variation in ammonification rates. Our results showed that the microbiome of sediment from different plots followed similar successional patterns, which we infer to be due to changes related to sulfur metabolism. These large changes likely overwhelmed any potential changes in sediment microbiome related to ammonification rate. We found no relationship between eelgrass presence or genetic composition and the microbiome. This was likely due to our sampling of bulk sediments to measure ammonification rates rather than sampling microbes in sediment directly in contact with the plants and suggests that eelgrass influence on the sediment microbiome may be limited in spatial extent. More in-depth functional studies associated with eelgrass microbiome will be required in order to fully understand the implications of these microbial communities in broader host-plant and ecosystem functions (e.g., elemental cycling and eelgrass-microbe interactions).

Metabolic Potential of Microbial Genomes Reconstructed from a Deep-Sea Oligotrophic Sediment Metagenome

NASA Astrophysics Data System (ADS)

Tully, B. J.; Huber, J. A.; Heidelberg, J. F.

2016-02-01

The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration and primary productivity in the global oceans, making it one of the most oligotrophic environments on earth. As a direct result of the low-standing biomass in surface waters, deep-sea sediments are thin and contain small amount of labile organic carbon. It was recently shown that the sediment column within the SPG is fully oxic through to the underlying basalt basement and may be representative of 9-37% of the global marine environment. In addition, it appears that approximately 50% of the total organic carbon is removed from the oligotrophic sediments within the first 20 centimeters beneath the sea floor (cmbsf). To understand the microbial processes that contribute to the removal of the labile organic matter, metagenomic sequencing and analysis was carried out on a sample of sediment collected from 0-5 cmbsf from SPG site 10 (U1369). Analysis of 9 partially reconstructed environmental genomes revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper ocean organisms, with deep branches within the Alpha- and Gammaproteobacteria, Nitrospirae, Nitrospina, the phylum NC10, and several unique phylogenetic groups. Within these partially complete genomes there is evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to the nitrification. Additionally, despite low sedimentation and hypothesized energy-limitation, members of the SPG microbial community had motility and chemotactic genes and possessed mechanisms for the utilization of high molecular weight organic matter, including exoproteases and peptide specific membrane transporters. Simultaneously, the SPG genomes showed a limited potential for the degradation of recalcitrant carbon compounds. Finally, the presence of putative genes with functions involved with denitrification and the consumption of C1 compounds suggest that there may be microenvironments in the surface sediments were microbes can deplete oxygen concentrations to hypoxic/anoxic levels. This study represents an important first analysis in understanding how microorganisms in oligotrophic sediments impact deep-sea carbon transformations.

Changes in the Functional Potential of Diverse and Active Bacterial Communities in Arctic Deep-Sea Sediments along a Water Depth Gradient

NASA Astrophysics Data System (ADS)

Rapp, J. Z.; Bienhold, C.; Offre, P.; Boetius, A.

2016-02-01

The deep sea covers approximately 70% of the Earth's surface and the majority of its seafloor is composed of fine-grained sediments. Bacteria are the dominant organisms in these sediments, accounting for up to 90% of total benthic biomass. Although benthic bacterial communities are assumed to play a central role in biogeochemical cycling at the seafloor, we still have very limited knowledge of their diversity, activity and ecological functions. We sampled Arctic deep-sea surface sediments from seven stations along a gradient from 1000 m to 5500 m water depth at the long-term ecological research station HAUSGARTEN in Fram Strait. Bacterial cell numbers decreased with depth from 3.8*108 to 1.3*108 cells per ml sediment. Illumina 16S rRNA gene surveys based on DNA and cDNA revealed substantial shifts in the structure of the total and active bacterial community along this gradient, which could be linked to environmental parameters, especially organic matter availability. The functional potential and actual activity of microbial communities was investigated using meta-genomic and -transcriptomic sequencing of four representative samples. Reconstruction of 16S rRNA genes from metagenomic data indicated a stronger contribution of certain groups at 1200-2500 m depth (e.g. OM190, Planctomycetacia, Betaproteobacteria) as compared to 3500-5500 m depth (e.g. SAR202 clade, Subgroup 22, Cytophagia). Analysis of orthologous gene clusters and protein families suggested that the genetic potential of microbial communities at the deepest station varied from that of communities at shallower depth, with higher representation of genes involved in the TCA cycle and in the biosynthesis of fatty acids, amino acids and vitamin biosynthesis at the deepest station. The observed variations may result from the accumulation of organic matter at the deepest station caused by the funnel-like topography at this site. The research contributes to European Research Council Advanced Investigator grant no. 294757.

Microbial Communities and Organic Matter Composition in Surface and Subsurface Sediments of the Helgoland Mud Area, North Sea

PubMed Central

Oni, Oluwatobi E.; Schmidt, Frauke; Miyatake, Tetsuro; Kasten, Sabine; Witt, Matthias; Hinrichs, Kai-Uwe; Friedrich, Michael W.

2015-01-01

The role of microorganisms in the cycling of sedimentary organic carbon is a crucial one. To better understand relationships between molecular composition of a potentially bioavailable fraction of organic matter and microbial populations, bacterial and archaeal communities were characterized using pyrosequencing-based 16S rRNA gene analysis in surface (top 30 cm) and subsurface/deeper sediments (30–530 cm) of the Helgoland mud area, North Sea. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) was used to characterize a potentially bioavailable organic matter fraction (hot-water extractable organic matter, WE-OM). Algal polymer-associated microbial populations such as members of the Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia were dominant in surface sediments while members of the Chloroflexi (Dehalococcoidales and candidate order GIF9) and Miscellaneous Crenarchaeota Groups (MCG), both of which are linked to degradation of more recalcitrant, aromatic compounds and detrital proteins, were dominant in subsurface sediments. Microbial populations dominant in subsurface sediments (Chloroflexi, members of MCG, and Thermoplasmata) showed strong correlations to total organic carbon (TOC) content. Changes of WE-OM with sediment depth reveal molecular transformations from oxygen-rich [high oxygen to carbon (O/C), low hydrogen to carbon (H/C) ratios] aromatic compounds and highly unsaturated compounds toward compounds with lower O/C and higher H/C ratios. The observed molecular changes were most pronounced in organic compounds containing only CHO atoms. Our data thus, highlights classes of sedimentary organic compounds that may serve as microbial energy sources in methanic marine subsurface environments. PMID:26635758

MICROBIAL ACTIVITY: AN INDICATOR OF WATERSHED IMPACTRS ON RIVERINE COASTAL WETLANDS OF LAKE MICHIGAN

EPA Science Inventory

The loss of watershed storage and/or forest cover due to land use, is expected to increase nutrient levels and sedimentation in the riverine coastal wetlands. Watershed indicators should be able to distinguish between degradation gradients, separating reference, transitional, and...

Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types.

PubMed

Ji, Yang; Angel, Roey; Klose, Melanie; Claus, Peter; Marotta, Humberto; Pinho, Luana; Enrich-Prast, Alex; Conrad, Ralf

2016-12-01

Tropical lake sediments are a significant source for the greenhouse gas methane. We studied function (pathway, rate) and structure (abundance, taxonomic composition) of the microbial communities (Bacteria, Archaea) leading to methane formation together with the main physicochemical characteristics in the sediments of four clear water, six white water and three black water lakes of the Amazon River system. Concentrations of sulfate and ferric iron, pH and δ 13 C of organic carbon were usually higher, while concentrations of carbon, nitrogen and rates of CH 4 production were generally lower in white water versus clear water or black water sediments. Copy numbers of bacterial and especially archaeal ribosomal RNA genes also tended to be relatively lower in white water sediments. Hydrogenotrophic methanogenesis contributed 58 ± 16% to total CH 4 production in all systems. Network analysis identified six communities, of which four were comprised mostly of bacteria found in all sediment types, while two were mostly in clear water sediment. Terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing showed that the compositions of the communities differed between the different sediment systems, statistically related to the particular physicochemical conditions and to CH 4 production rates. Among the archaea, clear water, white water, and black water sediments contained relatively more Methanomicrobiales, Methanosarcinaceae and Methanocellales, respectively, while Methanosaetaceae were common in all systems. Proteobacteria, Deltaproteobacteria (Myxococcales, Syntrophobacterales, sulfate reducers) in particular, Acidobacteria and Firmicutes were the most abundant bacterial phyla in all sediment systems. Among the other important bacterial phyla, clear water sediments contained relatively more Alphaproteobacteria and Planctomycetes, whereas white water sediments contained relatively more Betaproteobacteria, Firmicutes, Actinobacteria, and Chloroflexi than the respective other sediment systems. The data showed communities of bacteria common to all sediment types, but also revealed microbial groups that were significantly different between the sediment types, which also differed in physicochemical conditions. Our study showed that function of the microbial communities may be understood on the basis of their structures, which in turn are determined by environmental heterogeneity. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial Community Response to Simulated Petroleum Seepage in Caspian Sea Sediments

PubMed Central

Stagars, Marion H.; Mishra, Sonakshi; Treude, Tina; Amann, Rudolf; Knittel, Katrin

2017-01-01

Anaerobic microbial hydrocarbon degradation is a major biogeochemical process at marine seeps. Here we studied the response of the microbial community to petroleum seepage simulated for 190 days in a sediment core from the Caspian Sea using a sediment-oil-flow-through (SOFT) system. Untreated (without simulated petroleum seepage) and SOFT sediment microbial communities shared 43% bacterial genus-level 16S rRNA-based operational taxonomic units (OTU0.945) but shared only 23% archaeal OTU0.945. The community differed significantly between sediment layers. The detection of fourfold higher deltaproteobacterial cell numbers in SOFT than in untreated sediment at depths characterized by highest sulfate reduction rates and strongest decrease of gaseous and mid-chain alkane concentrations indicated a specific response of hydrocarbon-degrading Deltaproteobacteria. Based on an increase in specific CARD-FISH cell numbers, we suggest the following groups of sulfate-reducing bacteria to be likely responsible for the observed decrease in aliphatic and aromatic hydrocarbon concentration in SOFT sediments: clade SCA1 for propane and butane degradation, clade LCA2 for mid- to long-chain alkane degradation, clade Cyhx for cycloalkanes, pentane and hexane degradation, and relatives of Desulfobacula for toluene degradation. Highest numbers of archaea of the genus Methanosarcina were found in the methanogenic zone of the SOFT core where we detected preferential degradation of long-chain hydrocarbons. Sequencing of masD, a marker gene for alkane degradation encoding (1-methylalkyl)succinate synthase, revealed a low diversity in SOFT sediment with two abundant species-level MasD OTU0.96. PMID:28503173

Field Evidence for Magnetite Formation by a Methanogenic Microbial Community

NASA Astrophysics Data System (ADS)

Rossbach, S.; Beaver, C. L.; Williams, A.; Atekwana, E. A.; Slater, L. D.; Ntarlagiannis, D.; Lund, A.

2015-12-01

The aged, subsurface petroleum spill in Bemidji, Minnesota, has been surveyed with magnetic susceptibility (MS) measurements. High MS values were found in the free-product phase around the fluctuating water table. Although we had hypothesized that high MS values are related to the occurrence of the mineral magnetite resulting from the activity of iron-reducing bacteria, our microbial analysis pointed to the presence of a methanogenic microbial community at the locations and depths of the highest MS values. Here, we report on a more detailed microbial analysis based on high-throughput sequencing of the 16S rRNA gene of sediment samples from four consecutive years. In addition, we provide geochemical data (FeII/FeIII concentrations) to refine our conceptual model of methanogenic hydrocarbon degradation at aged petroleum spills and demonstrate that the microbial induced changes of sediment properties can be monitored with MS. The methanogenic microbial community at the Bemidji site consisted mainly of the syntrophic, hydrocarbon-degrading Smithella and the hydrogenotrophic, methane-generating Methanoregula. There is growing evidence in the literature that not only Bacteria, but also some methanogenic Archaea are able to reduce iron. In fact, a recent study reported that the methanogen Methanosarcina thermophila produced magnetite during the reduction of ferrihydrite in a laboratory experiment when hydrogen was present. Therefore, our finding of high MS values and the presence of magnetite in the methanogenic zone of an aged, subsurface petroleum spill could very well be the first field evidence for magnetite formation during methanogenic hydrocarbon degradation.

Anaerobic decomposition of cellulose by alkaliphilic microbial community of Owens Lake, California

NASA Astrophysics Data System (ADS)

Pikuta, Elena V.; Itoh, Takashi; Hoover, Richard B.

2005-09-01

The study of alkaliphilic microbial communities from anaerobic sediments of Owens and Mono Lakes in California has established the presence of active microbial cellulolytic processes in both studied lakes. The prior study of the microbial diversity of anaerobes in Mono Lake showed that the trophic chain of organic decomposition includes secondary anaerobes that previously were found to be unknown species (Spirochaeta americana, Tindallia californiensis, and Desulfonatronum thiodismutans). As we published earlier, the secondary anaerobes of Owens Lake morphologically were found to be very similar to those of Mono Lake. However, detailed comparison of the physiology and genetics has led to the conclusion that some links of organic decomposition in the trophic chain of the Owens Lake community are represented by a different unknown species. A new isolate of a sugarlytics free-living spirochete from Owens Lake ASpC2, which morphologically was similar to S. americana AspG1T isolated from Mono Lake, was found to have a different metabolic capacity such as the lack of capability to produce hydrogen during the fermentation of sugars. Furthermore, from the same microbial community of Owens Lake, another sugarlytics spore-forming alkaliphilic strain SCA was isolated in pure culture and described. Here we discuss the universal structure of the microbial community, types of microbial communities, review some hypothesis about Earth's Primordial Ocean and relevant new discoveries about water on Mars. This paper also presents some of the characteristics of novel isolates from anaerobic sediments of Owens Lake as a unique relic ecosystem of Astrobiological significance, and describes the participation of these strains in the process of cellulose degradation.

Use of enzymatic tools for biomonitoring inorganic pollution in aquatic sediments: a case study (Bor, Serbia)

PubMed Central

2013-01-01

Background Sediment bacterial communities are key players in biogeochemical cycling of elements in the aquatic environment. Copper mining, smelting, and processing operations located in Bor area (Serbia) are major environmental hot spots in the lower Danube Basin and Western Balkans. In the present study, we evaluate the influence of trace element (TE) concentration in sediments and physico-chemical properties of water on sediment microbial communities in water streams adjacent to the Copper Smelter Complex Bor (RTB Bor, Serbia). The degree to which metabolic activities of bacterial biota inhabiting differently polluted sites is inhibited by inorganic pollution were compared using selected enzymatic bioindicators. Results Cu, Zn, Pb, and As concentrations systematically exceeded the target values for metal loadings in aquatic sediments. Water electrical conductivity (WEC) followed the same pattern of spatial variation, irrespective of season. Interestingly, the most intense enzymatic activity occurred at the reference site although this site showed the greatest TE levels in aquatic sediments. Catalase activity (CA), potential dehydrogenase activity (PDA), actual dehydrogenase activity (ADA), urease activity (UA), and phosphatase activity (PA) in aquatic sediments displayed heterogeneous patterns of spatio-temporal variation. Inorganic pollution greatly affected CA, ADA, and PDA, but much less so UA and PA. Canonical correlation analysis showed that pH and WEC were the strongest determinants of enzymatic activity in bacterial biota, with the latter variable being reversely correlated with the enzymatic indicator of sediment quality (EISQ). The median values of EISQ increased with distance from the major sources of pollution. In addition, it was found that sites with different degrees of inorganic pollution can be appropriately classified by applying cluster analysis to EISQ, TE levels in sediments, and physico-chemical properties of water. Conclusions Because EISQ can precisely identify changes in overall enzymatic activity of sediment bacterial communities, this enzymatic bioindicator has a great potential for biomonitoring the current status of inorganic pollution in aquatic ecosystems. PMID:23536970

Diversity and composition of sediment bacteria in subtropical coastal wetlands of North Stradbroke Island, Queensland, Australia

NASA Astrophysics Data System (ADS)

Chuvochina, Maria; Sampayo, Eugenia; Welti, Nina; Hayes, Matthew; Lu, Yang; Lovelock, Catherine; Lockington, David

2013-04-01

Coastal wetlands provide a wide variety of important ecosystem services but continue to suffer disturbance, degradation and deforestation. Sediment bacteria are responsible for major nutrient transformation and recycling in these ecosystems. Insight into microbial community composition and the factors that determine them may improve our understanding of biogeochemical processes, food web dynamics, biodegradation processes and, thus, help to develop the management strategies for preserving the ecosystem health and services. Characterizing shifts in community taxa along environmental gradients has been shown to provide a useful tool for determining the major drivers affecting community structure and function. North Stradbroke Island (NSI) in Southern Queensland presents considerable habitat diversity including variety of groundwater dependent ecosystems such as lakes, swamps, sedge-like salt marshes and mangroves. Ecological responses of continuous groundwater extraction for municipal purposes and sand mining operations on NSI are still need to be assessed in order to protect its unique environment. Changes in coastal hydrology due to either climate change or human activity may directly affect microbial populations and, thus, biogeochemical cycles of nutrients. These may result in altering/losing some ecosystem services provided by coastal wetlands. In this study we examine microbial diversity and determine environmental controls on bacterial community structure along a natural transition from freshwater forested wetland (melaleuca woodland), sedge-like salt marsh and into mangroves located at NSI. The study area is characterized by significant groundwater flow, nutrient limitation and sharp transition from one ecosystem type to another. Sediment cores (0-5 cm and 20-25 cm depth) were collected from three representative sites of each zone (mangroves - salt marsh - freshwater wetland) along the salinity gradient in August 2012. Subsamples were set aside for use in chemical analyses, microbiological analysis and for porewater extraction. Microbial community structure and diversity are assessed using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments and barcoded pyrosequencing. To evaluate the relationships between microbial communities and environmental variables we use bioinformatical and statistical tools. Physico-chemical parameters included measurements of sediment pH, temperature, salinity and nutrients composition. Background information regarding hydrology and vegetation is incorporated in the study. Sediment bacteria play a vital role in wetland ecological function, and they are very sensitive to environmental changes. Considering coastal wetlands of NSI as a model area, our study may contribute to the knowledge of factors shaping microbial diversity in tropical wetlands, help to gain insight into the microbe-nutrient-plant relationships, and also serve as background for conservation plans to safeguard these ecosystems.

Use of slow-release fertilizer and biopolymers for stimulating hydrocarbon biodegradation in oil-contaminated beach sediments.

PubMed

Xu, Ran; Yong, Li Ching; Lim, Yong Giak; Obbard, Jeffrey Philip

2005-01-01

Nutrient concentration and hydrocarbon bioavailability are key factors affecting biodegradation rates of oil in contaminated beach sediments. The effect of a slow-release fertilizer, Osmocote, as well as two biopolymers, chitin and chitosan, on the bioremediation of oil-spiked beach sediments was investigated using an open irrigation system over a 56-day period under laboratory conditions. Osmocote was effective in sustaining a high level of nutrients in leached sediments, as well as elevated levels of microbial activity and rates of hydrocarbon biodegradation. Chitin was more biodegradable than chitosan and gradually released nitrogen into the sediment. The addition of chitin or chitosan to the Osmocote amended sediments enhanced biodegradation rates of the alkanes relative to the presence of Osmocote alone, where chitosan was more effective than chitin due to its greater oil sorption capacity. Furthermore, chitosan significantly enhanced the biodegradation rates of all target polycyclic aromatic hydrocarbons.

Profiling microbial community in a watershed heavily contaminated by an active antimony (Sb) mine in Southwest China.

PubMed

Sun, Weimin; Xiao, Enzong; Dong, Yiran; Tang, Song; Krumins, Valdis; Ning, Zengping; Sun, Min; Zhao, Yanlong; Wu, Shiliang; Xiao, Tangfu

2016-04-15

Located in Southwest China, the Chahe watershed has been severely contaminated by upstream active antimony (Sb) mines. The extremely high concentrations of Sb make the Chahe watershed an excellent model to elucidate the response of indigenous microbial activities within a severe Sb-contaminated environment. In this study, water and surface sediments from six locations in the Chahe watershed with different levels of Sb contamination were analyzed. Illumina sequencing of 16S rRNA amplicons revealed more than 40 phyla from the domain Bacteria and 2 phyla from the domain Archaea. Sequences assigned to the genera Flavobacterium, Sulfuricurvum, Halomonas, Shewanella, Lactobacillus, Acinetobacter, and Geobacter demonstrated high relative abundances in all sequencing libraries. Spearman's rank correlations indicated that a number of microbial phylotypes were positively correlated with different speciation of Sb, suggesting potential roles of these phylotypes in microbial Sb cycling. Canonical correspondence analysis further demonstrated that geochemical parameters, including water temperature, pH, total Fe, sulfate, aqueous Sb, and Eh, significantly structured the overall microbial community in Chahe watershed samples. Our findings offer a direct and reliable reference to the diversity of microbial communities in the presence of extremely high Sb concentrations, and may have potential implications for in situ bioremediation strategies of Sb contaminated sites. Copyright © 2016 Elsevier B.V. All rights reserved.

Biodegradation of petroleum hydrocarbons in estuarine sediments: metal influence.

PubMed

Almeida, Raquel; Mucha, Ana P; Teixeira, Catarina; Bordalo, Adriano A; Almeida, C Marisa R

2013-02-01

In this work, the potential effect of metals, such as Cd, Cu and Pb, on the biodegradation of petroleum hydrocarbons in estuarine sediments was investigated under laboratory conditions. Sandy and muddy non-vegetated sediments were collected in the Lima River estuary (NW Portugal) and spiked with crude oil and each of the metals. Spiked sediments were left in the dark under constant shaking for 15 days, after which crude oil biodegradation was evaluated. To estimate microbial abundance, total cell counts were obtained by DAPI staining and microbial community structure was characterized by ARISA. Culturable hydrocarbon degraders were determined using a modified most probable number protocol. Total petroleum hydrocarbons concentrations were analysed by Fourier Transform Infrared Spectroscopy after their extraction by sonication, and metal contents were determined by atomic absorption spectrometry. The results obtained showed that microbial communities had the potential to degrade petroleum hydrocarbons, with a maximum of 32 % degradation obtained for sandy sediments. Both crude oil and metals changed the microbial community structure, being the higher effect observed for Cu. Also, among the studied metals, only Cu displayed measurable deleterious effect on the hydrocarbons degradation process, as shown by a decrease in the hydrocarbon degrading microorganisms abundance and in the hydrocarbon degradation rates. Both degradation potential and metal influence varied with sediment characteristics probably due to differences in contaminant bioavailability, a feature that should be taken into account in developing bioremediation strategies for co-contaminated estuarine sites.

Denitrification in a large river: consideration of geomorphic controls on microbial activity and community structure.

PubMed

Tatariw, Corianne; Chapman, Elise L; Sponseller, Ryan A; Mortazavi, Behzad; Edmonds, Jennifer W

2013-10-01

Ecological theory argues that the controls over ecosystem processes are structured hierarchically, with broader-scale drivers acting as constraints over the interactions and dynamics at nested levels of organization. In river ecosystems, these interactions may arise from broadscale variation in channel form that directly shapes benthic habitat structure and indirectly constrains resource supply and biological activity within individual reaches. To evaluate these interactions, we identified sediment characteristics, water chemistry, and denitrifier community structure as factors influencing benthic denitrification rates in a sixth-order river that flows through two physiographic provinces and the transitional zone between them, each with distinct geomorphological properties. We found that denitrification rates tracked spatial changes in sediment characteristics and varied seasonally with expected trends in stream primary production. Highest rates were observed during the spring and summer seasons in the physiographic province dominated by fine-grained sediments, illustrating how large-scale changes in river structure can constrain the location of denitrification hotspots. In addition, nirS and nirK community structure each responded differently to variation in channel form, possibly due to changes in dissolved oxygen and organic matter supply. This shift in denitrifier community structure coincident with higher rates of N removal via denitrification suggests that microbial community structure may influence biogeochemical processes.

Modelling sediment-microbial dynamics in the South Nation River, Ontario, Canada: Towards the prediction of aquatic and human health risk.

PubMed

Droppo, I G; Krishnappan, B G; Liss, S N; Marvin, C; Biberhofer, J

2011-06-01

Runoff from agricultural watersheds can carry a number of agricultural pollutants and pathogens; often associated with the sediment fraction. Deposition of this sediment can impact water quality and the ecology of the river, and the re-suspension of such sediment can become sources of contamination for reaches downstream. In this paper a modelling framework to predict sediment and associated microbial erosion, transport and deposition is proposed for the South Nation River, Ontario, Canada. The modelling framework is based on empirical relationships (deposition and re-suspension fluxes), derived from laboratory experiments in a rotating circular flume using sediment collected from the river bed. The bed shear stress governing the deposition and re-suspension processes in the stream was predicted using a one dimensional mobile boundary flow model called MOBED. Counts of live bacteria associated with the suspended and bed sediments were used in conjunction with measured suspended sediment concentration at an upstream section to allow for the estimation of sediment associated microbial erosion, transport and deposition within the modelled river reach. Results suggest that the South Nation River is dominated by deposition periods with erosion only occurring at flows above approximately 250 m(3) s(-1) (above this threshold, all sediment (suspended and eroded) with associated bacteria are transported through the modelled reach). As microbes are often associated with sediments, and can survive for extended periods of time, the river bed is shown to be a possible source of pathogenic organisms for erosion and transport downstream during large storm events. It is clear that, shear levels, bacteria concentrations and suspended sediment are interrelated requiring that these parameters be studied together in order to understand aquatic microbial dynamics. It is important that any management strategies and operational assessments for the protection of human and aquatic health incorporate the sediment compartments (suspended and bed sediment) and the energy dynamics within the system in order to better predict the concentration of indicator organism. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

Exploring Microbial Life in Oxic Sediments Underlying Oligotrophic Ocean Gyres

NASA Astrophysics Data System (ADS)

Ziebis, W.; Orcutt, B.; Wankel, S. D.; D'Hondt, S.; Szubin, R.; Kim, J. N.; Zengler, K.

2015-12-01

Oxygen, carbon and nutrient availability are defining parameters for microbial life. In contrast to organic-rich sediments of the continental margins, where high respiration rates lead to a depletion of O2 within a thin layer at the sediment surface, it was discovered that O2 penetrates several tens of meters into organic-poor sediments underlying oligotrophic ocean gyres. In addition, nitrate, another important oxidant, which usually disappears rapidly with depth in anoxic sediments, tends to accumulate above seawater concentrations in the oxic subsurface, reflecting the importance of nitrogen cycling processes, including both nitrification and denitrification. Two IODP drilling expeditions were vital for exploring the nature of the deep subsurface beneath oligotrophic ocean gyres, expedition 329 to the South Pacific Gyre (SPG) and expedition 336 to North Pond, located on the western flank of the Mid-Atlantic ridge beneath the North Atlantic Gyre. Within the ultra-oligotrophic SPG O2 penetrates the entire sediment column from the sediment-water interface to the underlying basement to depths of > 75 m. At North Pond, a topographic depression filled with sediment and surrounded by steep basaltic outcrops, O2 penetrates deeply into the sediment (~ 30 m) until it eventually becomes depleted. O2 also diffuses upward into the sediment from seawater circulating within the young crust underlying the sediment, resulting in a deep oxic layer several meters above the basalt. Despite low organic carbon contents microbial cells persist throughout the entire sediment column within the SPG (> 75 m) and at North Pond, albeit at low abundances. We explored the nature of the subsurface microbial communities by extracting intact cells from large volumes of sediment obtained from drill cores of the two expeditions. By using CARD-FiSH, amplicon (16s rRNA) and metagenome sequencing we shed light on the phylogenetic and functional diversity of the elusive communities residing in the deep oxic sediments of these two different areas. Given the global extent of this oxic subsurface studies of the diversity and metabolic potential of its biome, together with the analyses of porewater geochemical and isotopic composition, are beginning to reveal its role in global biogeochemical cycles.

Characterization of Ichthyocidal Activity of Pfiesteria piscicida: Dependence on the Dinospore Cell Density

PubMed Central

Drgon, Tomás; Saito, Keiko; Gillevet, Patrick M.; Sikaroodi, Masoumeh; Whitaker, Brent; Krupatkina, Danara N.; Argemi, Federico; Vasta, Gerardo R.

2005-01-01

The ichthyocidal activity of Pfiesteria piscicida dinospores was examined in an aquarium bioassay format by exposing fish to either Pfiesteria-containing environmental sediments or clonal P. piscicida. The presence of Pfiesteria spp. and the complexity of the microbial assemblage in the bioassay were assessed by molecular approaches. Cell-free water from bioassays that yielded significant fish mortality failed to show ichthyocidal activity. Histopathological examination of moribund and dead fish failed to reveal the skin lesions reported elsewhere. Fish larvae within “cages” of variable mesh sizes were killed in those where the pore size exceeded that of Pfiesteria dinospores. In vitro exposure of fish larvae to clonal P. piscicida indicated that fish mortality was directly proportional to the dinospore cell density. Dinospores clustered around the mouth, eyes, and operculi, suggesting that fish health may be affected by their direct interaction with skin, gill epithelia, or mucous surfaces. Molecular fingerprinting revealed the presence of a very diverse microbial community of bacteria, protists, and fungi within bioassay aquaria containing environmental sediments. Some components of the microbial community were identified as potential fish pathogens, preventing the rigorous identification of Pfiesteria spp. as the only cause of fish death. In summary, our results strongly suggest (i) that this aquarium bioassay format, which has been extensively reported in the literature, is unsuitable to accurately assess the ichthyocidal activity of Pfiesteria spp. and (ii) that the ichthyocidal activity of Pfiesteria spp. is mostly due to direct interactions of the zoospores with fish skin and gill epithelia rather than to soluble factors. PMID:15640229

Development and evaluation of the bacterial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model.

PubMed

Hong, Eun-Mi; Park, Yongeun; Muirhead, Richard; Jeong, Jaehak; Pachepsky, Yakov A

2018-02-15

The Agricultural Policy/Environmental eXtender (APEX) is a watershed-scale water quality model that includes detailed representation of agricultural management. The objective of this work was to develop a process-based model for simulating the fate and transport of manure-borne bacteria on land and in streams with the APEX model. The bacteria model utilizes manure erosion rates to estimate the amount of edge-of-field bacteria export. Bacteria survival in manure is simulated as a two-stage process separately for each manure application event. In-stream microbial fate and transport processes include bacteria release from streambeds due to sediment resuspension during high flow events, active release from the streambed sediment during low flow periods, bacteria settling with sediment, and survival. Default parameter values were selected from published databases and evaluated based on field observations. The APEX model with the newly developed microbial fate and transport module was applied to simulate fate and transport of the fecal indicator bacterium Escherichia coli in the Toenepi watershed, New Zealand that was monitored for seven years. The stream network of the watershed ran through grazing lands with daily bovine waste deposition. Results show that the APEX with the bacteria module reproduced well the monitored pattern of E. coli concentrations at the watershed outlet. The APEX with the microbial fate and transport module will be utilized for predicting microbial quality of water as affected by various agricultural practices, evaluating monitoring protocols, and supporting the selection of management practices based on regulations that rely on fecal indicator bacteria concentrations. Published by Elsevier B.V.

Fatty Acid and Carbon Isotopic Evidence for type I Methanotrophs in Microbial Mats from a Shallow Marine Gas Seep, Coal Oil Point, CA.

NASA Astrophysics Data System (ADS)

Ding, H.; Valentine, D.

2005-12-01

To study the microbial community in a Southern California seep field, sediment and bacterial mat samples were collected from natural gas-bearing and gas-free surfaces at two distinct seeps in the Coal Oil Point seep field, offshore Santa Barbara. Fatty acids in these samples were extracted, analyzed and identified. Using gas chromatography (GC), more than 30 different fatty acids were separated. Generally, fatty acid concentrations in natural gas-bearing samples were about 5-fold higher compared to gas-free samples. Using gas chromatography mass sepctrometry (GC-MS), all separated fatty acids were identified in each sample. The major constituents included saturated 14:0, 16:0, 18:0, branched i-15, a-15 and unsaturated 16:1 and 18:1 series fatty acids. GC-IRMS (isotope ratio mass spectrometry) analysis provided the 13C of all major fatty acids and some 16:1 series fatty acids were found to be more depleted than -40% in samples associated with gas seepage. After treatment with dimethyl disufide (DMDS), the 16:1 series fatty acids were resolved into five distinct components, including common composition 16:1(7), bacterial specific i-16:1(7) and typical biomarkers of type I methnotrophs 16:1(8), 16(6) and 16:1(5), suggesting an important role for methnotrophs in seep sediments and microbial mats. These results provide evidence for the activity of type I methanotrophic bacteria in microbial mats and surficial sediments at the Coal Oil Point seep field, and have implications for methane cycling in this and other seep

Fungi from Admiralty Bay (King George Island, Antarctica) Soils and Marine Sediments.

PubMed

Wentzel, Lia Costa Pinto; Inforsato, Fábio José; Montoya, Quimi Vidaurre; Rossin, Bruna Gomes; Nascimento, Nadia Regina; Rodrigues, André; Sette, Lara Durães

2018-06-19

Extreme environments such as the Antarctic can lead to the discovery of new microbial taxa, as well as to new microbial-derived natural products. Considering that little is known yet about the diversity and the genetic resources present in these habitats, the main objective of this study was to evaluate the fungal communities from extreme environments collected at Aldmiralty Bay (Antarctica). A total of 891 and 226 isolates was obtained from soil and marine sediment samples, respectively. The most abundant isolates from soil samples were representatives of the genera Leucosporidium, Pseudogymnoascus, and a non-identified Ascomycota NIA6. Metschnikowia sp. was the most abundant taxon from marine samples, followed by isolates from the genera Penicillium and Pseudogymnoascus. Many of the genera were exclusive in marine sediment or terrestrial samples. However, representatives of eight genera were found in both types of samples. Data from non-metric multidimensional scaling showed that each sampling site is unique in their physical-chemical composition and fungal community. Biotechnological potential in relation to enzymatic production at low/moderate temperatures was also investigated. Ligninolytic enzymes were produced by few isolates from root-associated soil. Among the fungi isolated from marine sediments, 16 yeasts and nine fungi showed lipase activity and three yeasts and six filamentous fungi protease activity. The present study permitted increasing our knowledge on the diversity of fungi that inhabit the Antarctic, finding genera that have never been reported in this environment before and discovering putative new species of fungi.

Microbial Remobilisation on Riverbed Sediment Disturbance in Experimental Flumes and a Human-Impacted River: Implication for Water Resource Management and Public Health in Developing Sub-Saharan African Countries

PubMed Central

Abia, Akebe Luther King; James, Chris; Ubomba-Jaswa, Eunice; Benteke Momba, Maggy Ndombo

2017-01-01

Resuspension of sediment-borne microorganisms (including pathogens) into the water column could increase the health risk for those using river water for different purposes. In the present work, we (1) investigated the effect of sediment disturbance on microbial resuspension from riverbed sediments in laboratory flow-chambers and in the Apies River, Gauteng, South Africa; and (2) estimated flow conditions for sediment-borne microorganism entrainment/resuspension in the river. For mechanical disturbance, the top 2 cm of the sediment in flow-chambers was manually stirred. Simulating sudden discharge into the river, water (3 L) was poured within 30 s into the chambers at a 45° angle to the chamber width. In the field, sediment was disturbed by raking the riverbed and by cows crossing in the river. Water samples before and after sediment disturbance were analysed for Escherichia coli. Sediment disturbance caused an increase in water E. coli counts by up to 7.9–35.8 times original values. Using Shields criterion, river-flow of 0.15–0.69 m3/s could cause bed particle entrainment; while ~1.57–7.23 m3/s would cause resuspension. Thus, sediment disturbance in the Apies River would resuspend E. coli (and pathogens), with possible negative health implications for communities using such water. Therefore, monitoring surface water bodies should include microbial sediment quality. PMID:28295001

Microbial Remobilisation on Riverbed Sediment Disturbance in Experimental Flumes and a Human-Impacted River: Implication for Water Resource Management and Public Health in Developing Sub-Saharan African Countries.

PubMed

Abia, Akebe Luther King; James, Chris; Ubomba-Jaswa, Eunice; Benteke Momba, Maggy Ndombo

2017-03-15

Resuspension of sediment-borne microorganisms (including pathogens) into the water column could increase the health risk for those using river water for different purposes. In the present work, we (1) investigated the effect of sediment disturbance on microbial resuspension from riverbed sediments in laboratory flow-chambers and in the Apies River, Gauteng, South Africa; and (2) estimated flow conditions for sediment-borne microorganism entrainment/resuspension in the river. For mechanical disturbance, the top 2 cm of the sediment in flow-chambers was manually stirred. Simulating sudden discharge into the river, water (3 L) was poured within 30 s into the chambers at a 45° angle to the chamber width. In the field, sediment was disturbed by raking the riverbed and by cows crossing in the river. Water samples before and after sediment disturbance were analysed for Escherichia coli. Sediment disturbance caused an increase in water E. coli counts by up to 7.9-35.8 times original values. Using Shields criterion, river-flow of 0.15-0.69 m³/s could cause bed particle entrainment; while ~1.57-7.23 m³/s would cause resuspension. Thus, sediment disturbance in the Apies River would resuspend E. coli (and pathogens), with possible negative health implications for communities using such water. Therefore, monitoring surface water bodies should include microbial sediment quality.

Kinetic and microbial community analysis of methyl ethyl ketone biodegradation in aquifer sediments.

PubMed

Fahrenfeld, N; Pruden, A; Widdowson, M

2017-02-01

Methyl ethyl ketone (MEK) is a common groundwater contaminant often present with more toxic compounds of primary interest. Because of this, few studies have been performed to determine the effect of microbial community structure on MEK biodegradation rates in aquifer sediments. Here, microcosms were prepared with aquifer sediments containing MEK following a massive spill event and compared to laboratory-spiked sediments, with MEK biodegradation rates quantified under mixed aerobic/anaerobic conditions. Biodegradation was achieved in MEK-contaminated site sediment microcosms at about half of the solubility (356 mg/L) with largely Firmicutes population under iron-reducing conditions. MEK was biodegraded at a higher rate [4.0 ± 0.74 mg/(L days)] in previously exposed site samples compared to previously uncontaminated sediments [0.51 ± 0.14 mg/(L days)]. Amplicon sequencing and denaturing gradient gel electrophoresis of 16S rRNA genes were combined to understand the relationship between contamination levels, biodegradation, and community structure across the plume. More heavily contaminated sediments collected from an MEK-contaminated field site had the most similar communities than less contaminated sediments from the same site despite differences in sediment texture. The more diverse microbial community observed in the laboratory-spiked sediments reduced MEK concentration 47 % over 92 days. Results of this study suggest lower rates of MEK biodegradation in iron-reducing aquifer sediments than previously reported for methanogenic conditions and biodegradation rates comparable to previously reported nitrate- and sulfate-reducing conditions.

Transport of a conservative and "smart" tracers' in a first-order creek: role of transient storage type

USDA-ARS?s Scientific Manuscript database

Quantification of microbial fate and transport in streams has become one of most important topics in studying biogeochemical properties and behavior of stream ecosystems. Using "smart" tracer such as resazurin (Raz) allows assessment of sediment-water interactions and associated biological activity ...

Biogeochemical factors influencing net mercury methylation in contaminated freshwater sediments from the St. Lawrence River in Cornwall, Ontario, Canada.

PubMed

Avramescu, Mary-Luyza; Yumvihoze, Emmanuel; Hintelmann, Holger; Ridal, Jeff; Fortin, Danielle; Lean, David R S

2011-02-01

The activity of various anaerobic microbes, including sulfate reducers (SRB), iron reducers (FeRP) and methanogens (MPA) has been linked to mercury methylation in aquatic systems, although the relative importance of each microbial group in the overall process is poorly understood in natural sediments. The present study focused on the biogeochemical factors (i.e. the relative importance of various groups of anaerobic microbes (FeRP, SRB, and MPA) that affect net monomethylmercury (MMHg) formation in contaminated sediments of the St. Lawrence River (SRL) near Cornwall (Zone 1), Ontario, Canada. Methylation and demethylation potentials were measured separately by using isotope-enriched mercury species ((200)Hg(2+) and MM(199)Hg(+)) in sediment microcosms treated with specific microbial inhibitors. Sediments were sampled and incubated in the dark at room temperature in an anaerobic chamber for 96h. The potential methylation rate constants (K(m)) and demethylation rates (K(d)) were found to differ significantly between microcosms. The MPA-inhibited microcosm had the highest potential methylation rate constant (0.016d(-1)), whereas the two SRB-inhibited microcosms had comparable potential methylation rate constants (0.003d(-1) and 0.002d(-1), respectively). The inhibition of methanogens stimulated net methylation by inhibiting demethylationand by stimulating methylation along with SRB activity. The inhibition of both methanogens and SRB was found to enhance the iron reduction rates but did not completely stop MMHg production. The strong positive correlation between K(m) and Sulfate Reduction Rates (SRR) and between K(d) and Methane Production Rates (MPR) supports the involvement of SRB in Hg methylation and MPA in MMHg demethylation in the sediments. In contrast, the strong negative correlation between K(d) and Iron Reduction Rates (FeRR) shows that the increase in FeRR corresponds to a decrease in demethylation, indicating that iron reduction may influence net methylation in the SLR sediments by decreasing demethylation rather than favouring methylation. Copyright © 2010 Elsevier B.V. All rights reserved.

The Abundance and Activity of Nitrate-Reducing Microbial Populations in Estuarine Sediments

NASA Astrophysics Data System (ADS)

Cardarelli, E.; Francis, C. A.

2014-12-01

Estuaries are productive ecosystems that ameliorate nutrient and metal contaminants from surficial water supplies. At the intersection of terrestrial and aquatic environments, estuarine sediments host major microbially-mediated geochemical transformations. These include denitrification (the conversion of nitrate to nitrous oxide and/or dinitrogen) and dissimilatory nitrate reduction to ammonium (DNRA). Denitrification has historically been seen as the predominant nitrate attenuation process and functions as an effective sink for nitrate. DNRA has previously been believed to be a minor nitrate reduction process and transforms nitrate within the ecosystem to ammonium, a more biologically available N species. Recent studies have compared the two processes in coastal environments and determined fluctuating environmental conditions may suppress denitrification, supporting an increased role for DNRA in the N cycle. Nitrate availability and salinity are factors thought to influence the membership of the microbial communities present, and the nitrate reduction process that predominates. The aim of this study is to investigate how nitrate concentration and salinity alter the transcript abundances of N cycling functional gene markers for denitrification (nirK, nirS) and DNRA (nrfA) in estuarine sediments at the mouth of the hypernutrified Old Salinas River, CA. Short-term whole core incubations amended with artificial freshwater/artificial seawater (2 psu, 35 psu) and with varying NO3- concentrations (200mM, 2000mM) were conducted to assess the activity as well as the abundance of the nitrate-reducing microbial populations present. Gene expression of nirK, nirS, and nrfA at the conclusion of the incubations was quantified using reverse transcription quantitative polymerase chain reaction (RT-qPCR). High abundances of nirK, nirS, and nrfA under particular conditions coupled with the resulting geochemical data ultimately provides insight onto how the aforementioned factors influence N cycling related gene expression and rates of nitrate reduction.

The geomicrobiology of the Greenland Ice Sheet: impact on DOC export (Invited)

NASA Astrophysics Data System (ADS)

Wadham, J. L.; Stibal, M.; Lawson, E. C.; Barnett, M. J.; Hasan, F.; Telling, J.; Anesio, A.; Lis, G.; Cullen, D.; Butler, C.; Tranter, M.; Nienow, P. W.

2010-12-01

The Greenland Ice Sheet (GrIS) is the largest mass of ice in the northern hemisphere, and contributes ~370 km3 in runoff annually to the Arctic Ocean. While recent work has highlighted runoff increases of up to 100% from the GrIS over the next century, very little is known about the associated impacts upon rates of sediment-bound and dissolved organic carbon export from the ice sheet to the coastal ocean. This is relevant given recent work that has suggested that the high proportion of labile dissolved organic carbon (DOC) present in glacial runoff may be important in sustaining the productivity of ecosystems downstream. Here we report the phylogenetic and functional diversity of micro-organisms inhabiting the surface and basal regions of the Greenland Ice Sheet (at Leverett Glacier, SW Greenland), and whose activity influences the biogeochemical composition of runoff. Real time PCR data on runoff, together with 16S-rRNA bacterial clone libraries on sediments, demonstrate a subglacial microbial community that contrasts phylogenetically and functionally with the ice sheet surface ecosystem. We envisage that large sectors of the subglacial environment are microbially active, with overridden paleosols and in-washed surface organic matter providing a carbon substrate for a range of metabolic pathways. This includes methanogenesis which proceeds at rates similar to deep ocean sediments and via a CO2/H2 pathway. These subglacial microbial communities serve to chemically modify the DOC composition of meltwater inputs from the ice sheet surface and modulate the reactivity of bulk DOC exported in runoff. Evidence for subglacial microbial influences on DOC in runoff includes elevated concentrations of dissolved carbohydrates (e.g. glucose and fructose of up to 1 μmol/L), which are preferentially exported during subglacial outburst events. We examine the temporal changes in DOC export in runoff from the ice sheet over a full melt season, and consider how changes in total runoff over the coming century may perturb this contribution.

SEDIMENT MICROBIAL RESPIRATION IN A SYNOPTIC SURVEY OF MID-ATLANTIC REGION STREAMS

EPA Science Inventory

l. The rate of microbial respiration on fine-grained stream sediments was measured at 196 first-to third-order sites in the mid-Atlantic region of the United States.2. Sample collection took place between April and July in 1993, 1994 and 1995.3. Study streams were randomly sele...

Biodegradation of organic matter and anodic microbial communities analysis in sediment microbial fuel cells with/without Fe(III) oxide addition.

PubMed

Xu, Xun; Zhao, Qingliang; Wu, Mingsong; Ding, Jing; Zhang, Weixian

2017-02-01

To enhance the biodegradation of organic matter in sediment microbial fuel cell (SMFC), Fe(III) oxide, as an alternative electron acceptor, was added into the sediment. Results showed that the SMFC with Fe(III) oxide addition obtained higher removal efficiencies for organics than the SMFC without Fe(III) oxide addition and open circuit bioreactor, and produced a maximum power density (P max ) of 87.85mW/m 2 with a corresponding maximum voltage (V max ) of 0.664V. The alteration of UV-254 and specific ultraviolet absorbance (SUVA) also demonstrated the organic matter in sediments can be effectively removed. High-throughput sequencing of anodic microbial communities indicated that bacteria from the genus Geobacter were predominantly detected (21.23%) in the biofilm formed on the anode of SMFCs, while Pseudomonas was the most predominant genus (18.12%) in the presence of Fe(III) oxide. Additionally, compared with the open circuit bioreactor, more electrogenic bacteria attached to the biofilm of anode in SMFCs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Geomorphic and geochemical controls on leaf wax biomarker transport and preservation in alluvial river systems: Rio Bermejo, Argentina

NASA Astrophysics Data System (ADS)

Repasch, M. N.; Sachse, D.; Hovius, N.; Scheingross, J. S.; Szupiany, R. N.

2017-12-01

Rivers are the primary conduits for organic carbon (OC) transfer from vegetation-rich uplands to long-term sinks, and thus are responsible for significant fluxes among different reservoirs of the carbon cycle. Fluxes of terrestrial OC out of river systems are generally less than fluxes into the systems, indicating loss of OC either during active fluvial transport, during residence in the active channel belt, or in older deposits outside of the active channel belt. Sedimentary biomarkers can be used to elucidate the mechanisms of transport, preservation, and/or transformation of OC during its passage from source to sink. In this study we evaluate the influence of fluvial sediment transport on preservation of terrestrial leaf wax n-alkanes. Our natural laboratory is the Rio Bermejo in northern Argentina, which transports sediment and organic matter from the central Andes over 700 km across the foreland basin without input of foreign material from tributaries. Rapid channel migration rates in a region of flexural foreland basin uplift (the forebulge) are responsible for remobilization of floodplain sediment and terrestrial OC. By sampling suspended sediment, river bank sediment, and soil from several locations along the length of the Rio Bermejo, and analyzing the dissolved chemistry, biomarker composition, and compound-specific stable isotopes, we can evaluate the geomorphic and geochemical processes that act to influence the preservation of terrestrial biomarkers through the river system. Data suggest that concentrations of long-chain terrestrial (C25-C33) alkanes decrease downstream, while concentrations of short-chain (C15-C19) alkanes increase. This trend is corroborated by a downstream increase in suspended sediment δ13C values, suggesting a replacement of terrestrial OC by microbial OC. It is likely that microbial degradation is responsible for loss of terrestrial biomarkers as their residence time in the river system increases. Controlled laboratory experiments and analysis of modern and aged river bank sediment samples will determine where and over what timescales leaf wax alkanes are oxidized by microorganisms. With these data, we will be able to quantify the loss of OC during fluvial transit and determine the mechanisms responsible, enabling carbon cycle models to account for these losses.

Iron oxides stimulate sulfate-driven anaerobic methane oxidation in seeps

DOE PAGES

Sivan, Orit; Antler, Gilad; Turchyn, Alexandra V.; ...

2014-09-22

Seep sediments are dominated by intensive microbial sulfate reduction coupled to the anaerobic oxidation of methane (AOM). Through geochemical measurements of incubation experiments with methane seep sediments collected from Hydrate Ridge, we provide insight into the role of iron oxides in sulfate-driven AOM. Seep sediments incubated with 13C-labeled methane showed co-occurring sulfate reduction, AOM, and methanogenesis. The isotope fractionation factors for sulfur and oxygen isotopes in sulfate were about 40‰ and 22‰, respectively, reinforcing the difference between microbial sulfate reduction in methane seeps versus other sedimentary environments (for example, sulfur isotope fractionation above 60‰ in sulfate reduction coupled to organicmore » carbon oxidation or in diffusive sedimentary sulfate–methane transition zone). The addition of hematite to these microcosm experiments resulted in significant microbial iron reduction as well as enhancing sulfate-driven AOM. The magnitude of the isotope fractionation of sulfur and oxygen isotopes in sulfate from these incubations was lowered by about 50%, indicating the involvement of iron oxides during sulfate reduction in methane seeps. The similar relative change between the oxygen versus sulfur isotopes of sulfate in all experiments (with and without hematite addition) suggests that oxidized forms of iron, naturally present in the sediment incubations, were involved in sulfate reduction, with hematite addition increasing the sulfate recycling or the activity of sulfur-cycling microorganisms by about 40%. Furthermore, these results highlight a role for natural iron oxides during bacterial sulfate reduction in methane seeps not only as nutrient but also as stimulator of sulfur recycling.« less

A survey of microbial community diversity in marine sediments impacted by petroleum hydrocarbons from the Gulf of Mexico and Atlantic shorelines, Texas to Florida

USGS Publications Warehouse

Lisle, John T.; Stellick, Sarah H.

2011-01-01

Microbial community genomic DNA was extracted from sediment samples collected along the Gulf of Mexico and Atlantic coasts from Texas to Florida. Sample sites were identified as being ecologically sensitive and (or) as having high potential of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon blowout. The diversity within the microbial communities associated with the collected sediments provides a baseline dataset to which microbial community-diversity data from impacted sites could be compared. To determine the microbial community diversity in the samples, genetic fingerprints were generated and compared. Specific sequences within the community genomic DNA were first amplified using the polymerase chain reaction (PCR) with a primer set that provides possible resolution to the species level. A second nested PCR was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. The nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Samples with similar fingerprints were grouped and compared to oil-fingerprint data from the same sites (Rosenbauer and others, 2011). The microbial community fingerprints were generally grouped into sites that had been shown to contain background concentrations of non-Deepwater Horizon oil. However, these groupings also included sites where no oil signature was detected. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the Gulf of Mexico and Atlantic coasts from Texas to Florida.

Environmental characteristics and changes of sediment pore water dissolved organic matter in four Chinese lakes.

PubMed

Mostofa, Khan M G; Li, Wen; Wu, Fengchang; Liu, Cong-Qiang; Liao, Haiqing; Zeng, Li; Xiao, Min

2018-01-01

Sediment pore waters were examined in four Chinese lakes (Bosten, Qinghai, Chenghai and Dianchi) to characterise the sources of dissolved organic matter (DOM) and their microbial changes in the sediment depth profiles. Parallel factor (PARAFAC) modelling on the sample fluorescence spectra confirmed that the pore water DOM was mostly composed of two components with a mixture of both allochthonous and autochthonous fulvic acid-like substances in three lakes, except Lake Dianchi, and protein-like components in Lake Bosten. However, DOM in Lake Dianchi was composed of three components, including a fulvic acid-like, and two unidentified components, which could originate from mixed sources of either sewerage-impacted allochthonous or autochthonous organic matter (OM). Dissolved organic carbon (DOC) concentrations were typically high (583-7410 μM C) and fluctuated and increased vertically in the depth profile. The fluorescence intensity of the fulvic acid-like substance and absorbance at 254 nm increased vertically in the sediment pore waters of three lakes. A significant relationship between DOC and the fluorescence intensity of the fulvic acid-like component in the sediment pore waters of three lakes, except Lake Dianchi, suggested that the fulvic acid-like component could significantly contribute to total DOM and could originate via complex microbial processes in early diagenesis on OM (ca. phytoplankton, terrestrial plant material) in these lakes. Pore water DOM components could therefore be a useful indicator to assess the DOM sources of the lake sediment during sedimentation over the past several decades, which have been heavily affected by ambient terrestrial vegetation and human activities.

Manganese(II)-oxidizing Bacillus spores in Guaymas Basin hydrothermal sediments and plumes.

PubMed

Dick, Gregory J; Lee, Yifan E; Tebo, Bradley M

2006-05-01

Microbial oxidation and precipitation of manganese at deep-sea hydrothermal vents are important oceanic biogeochemical processes, yet nothing is known about the types of microorganisms or mechanisms involved. Here we report isolation of a number of diverse spore-forming Mn(II)-oxidizing Bacillus species from Guaymas Basin, a deep-sea hydrothermal vent environment in the Gulf of California, where rapid microbially mediated Mn(II) oxidation was previously observed. mnxG multicopper oxidase genes involved in Mn(II) oxidation were amplified from all Mn(II)-oxidizing Bacillus spores isolated, suggesting that a copper-mediated mechanism of Mn(II) oxidation could be important at deep-sea hydrothermal vents. Phylogenetic analysis of 16S rRNA and mnxG genes revealed that while many of the deep-sea Mn(II)-oxidizing Bacillus species are very closely related to previously recognized isolates from coastal sediments, other organisms represent novel strains and clusters. The growth and Mn(II) oxidation properties of these Bacillus species suggest that in hydrothermal sediments they are likely present as spores that are active in oxidizing Mn(II) as it emerges from the seafloor.

Genomic insights into the metabolic potential and interactions between marine methanotrophic ANME archaea and associated bacteria

NASA Astrophysics Data System (ADS)

Orphan, V. J.; Skennerton, C.; Chadwick, G.; Haroon, F.; Tyson, G. W.; Leu, A.; Hatzenpichler, R.; Woyke, T.; Malmstrom, R.; Yu, H.; Scheller, S.

2015-12-01

Cooperative metabolic interactions between multiple groups of methanotrophic 'ANME' archaea and sulfate-reducing bacteria represent the primary sink for methane within continental margin sediments. These syntrophic associations are frequently observed as structured multi-celled consortia in methane seeps, often comprising a substantial proportion of the microbial biomass within near seafloor seep sediments. Since their discovery nearly 15 years ago, a number of distinct ANME groups and multiple sulfate-reducing bacterial partners have been described from seep environments worldwide. Attempts to reconstruct the genomes of some ANME organisms have been reported, however the ecological physiology and metabolic interactions of distinct ANME lineages and their bacterial partners remains poorly understood. Here, we used a fluorescence azide-alkyne click chemistry technique known as BONCAT combined with FAC sorting to examine patterns in microbial membership and the genomes of single, metabolically active ANME-bacterial consortia recovered from methane seep sediments. This targeted consortia-level sequencing approach revealed significant diversity in the ANME-bacterial associations in situ as well as insights into the potential syntrophic mechanisms underpinning these enigmatic methane-fueled partnerships.

Electricity generation through a photo sediment microbial fuel cell using algae at the cathode.

PubMed

Neethu, B; Ghangrekar, M M

2017-12-01

Sediment microbial fuel cells (SMFCs) are bio-electrochemical devices generating electricity from redox gradients occurring across the sediment-water interface. Sediment microbial carbon-capture cell (SMCC), a modified SMFC, uses algae grown in the overlying water of sediment and is considered as a promising system for power generation along with algal cultivation. In this study, the performance of SMCC and SMFC was evaluated in terms of power generation, dissolved oxygen variations, sediment organic matter removal and algal growth. SMCC gave a maximum power density of 22.19 mW/m 2 , which was 3.65 times higher than the SMFC operated under similar conditions. Sediment organic matter removal efficiencies of 77.6 ± 2.1% and 61.0 ± 1.3% were obtained in SMCC and SMFC, respectively. With presence of algae at the cathode, a maximum chemical oxygen demand and total nitrogen removal efficiencies of 63.3 ± 2.3% (8th day) and 81.6 ± 1.2% (10th day), respectively, were observed. The system appears to be favorable from a resources utilization perspective as it does not depend on external aeration or membranes and utilizes algae and organic matter present in sediment for power generation. Thus, SMCC has proven its applicability for installation in an existing oxidation pond for sediment remediation, algae growth, carbon conversion and power generation, simultaneously.

High Prevalence of Gammaproteobacteria in the Sediments of Admiralty Bay and North Bransfield Basin, Northwestern Antarctic Peninsula.

PubMed

Franco, Diego C; Signori, Camila N; Duarte, Rubens T D; Nakayama, Cristina R; Campos, Lúcia S; Pellizari, Vivian H

2017-01-01

Microorganisms dominate most Antarctic marine ecosystems, in terms of biomass and taxonomic diversity, and play crucial role in ecosystem functioning due to their high metabolic plasticity. Admiralty Bay is the largest bay on King George Island (South Shetland Islands, Antarctic Peninsula) and a combination of hydro-oceanographic characteristics (bathymetry, sea ice and glacier melting, seasonal entrance of water masses, turbidity, vertical fluxes) create conditions favoring organic carbon deposition on the seafloor and microbial activities. We sampled surface sediments from 15 sites across Admiralty Bay (100-502 m total depth) and the adjacent North Bransfield Basin (693-1147 m), and used the amplicon 454-sequencing of 16S rRNA gene tags to compare the bacterial composition, diversity, and microbial community structure across environmental parameters (sediment grain size, pigments and organic nutrients) between the two areas. Marine sediments had a high abundance of heterotrophic Gammaproteobacteria (92.4% and 83.8% inside and outside the bay, respectively), followed by Alphaproteobacteria (2.5 and 5.5%), Firmicutes (1.5 and 1.6%), Bacteroidetes (1.1 and 1.7%), Deltaproteobacteria (0.8 and 2.5%) and Actinobacteria (0.7 and 1.3%). Differences in alpha-diversity and bacterial community structure were found between the two areas, reflecting the physical and chemical differences in the sediments, and the organic matter input.

Optimizing sample pretreatment for compound-specific stable carbon isotopic analysis of amino sugars in marine sediment

NASA Astrophysics Data System (ADS)

Zhu, R.; Lin, Y.-S.; Lipp, J. S.; Meador, T. B.; Hinrichs, K.-U.

2014-01-01

Amino sugars are quantitatively significant constituents of soil and marine sediment, but their sources and turnover in environmental samples remain poorly understood. The stable carbon isotopic composition of amino sugars can provide information on the lifestyles of their source organisms and can be monitored during incubations with labeled substrates to estimate the turnover rates of microbial populations. However, until now, such investigation has been carried out only with soil samples, partly because of the much lower abundance of amino sugars in marine environments. We therefore optimized a procedure for compound-specific isotopic analysis of amino sugars in marine sediment employing gas chromatography-isotope ratio mass spectrometry. The whole procedure consisted of hydrolysis, neutralization, enrichment, and derivatization of amino sugars. Except for the derivatization step, the protocol introduced negligible isotopic fractionation, and the minimum requirement of amino sugar for isotopic analysis was 20 ng, i.e. equivalent to ~ 8 ng of amino sugar carbon. Our results obtained from δ13C analysis of amino sugars in selected marine sediment samples showed that muramic acid had isotopic imprints from indigenous bacterial activities, whereas glucosamine and galactosamine were mainly derived from organic detritus. The analysis of stable carbon isotopic compositions of amino sugars opens a promising window for the investigation of microbial metabolisms in marine sediments and the deep marine biosphere.