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.

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.

Microbial incorporation of nitrogen in stream detritus

Treesearch

Diane M. Sanzone; Jennifer L. Tank; Judy L. Meyer; Patrick J. Mulholland; Stuart E.G. Findlay

2001-01-01

We adapted the chloroform fumigation method to determine microbial nitrogen (N) and microbial incorporation of 15N on three common substrates [leaves, wood and fine benthic organic matter (FBOM)] in three forest streams. We compared microbial N and 15 content of samples collected during a 6-week15N-NH...

Effects of labile carbon addition on a headwater stream food web

Treesearch

Heidi S. Wilcox; J. Bruce Wallace; Judy L. Meyer; Jonathan P. Benstead

2005-01-01

We added dextrose for two 8-week periods (summer and autumn) to a highly heterotrophic headwater stream in North Carolina, U.S.A., to examine the responses of its benthic food web to increased labile carbon. We hypothesized that addition of labile carbon would elevate microbial abundance and activity, resulting in greater resource availability and higher...

Biological control of trace metal and organometal benthic fluxes in a eutrophic lagoon (Thau Lagoon, Mediterranean Sea, France)

NASA Astrophysics Data System (ADS)

Point, D.; Monperrus, M.; Tessier, E.; Amouroux, D.; Chauvaud, L.; Thouzeau, G.; Jean, F.; Amice, E.; Grall, J.; Leynaert, A.; Clavier, J.; Donard, O. F. X.

2007-04-01

In situ benthic chamber experiments were conducted in the Thau Lagoon that allowed the simultaneous determination of the benthic exchanges of trace metals (Cd, Co, Cu, Mn, Pb and U) and mercury species (iHg and MMHg). Fluxes of organotin compounds (MBT, DBT and TBT) were also investigated for the first time. The benthic incubations were performed during two campaigns at four stations that presented different macrobenthic and macrophytic species distribution and abundance (see [Thouzeau, G., Grall, J., Clavier, J., Chauvaud, L., Jean, F., Leynaert, A., Longpuirt, S., Amice, E., Amouroux, D., 2007. Spatial and temporal variability of benthic biogeochemical fluxes associated with macrophytic and macrofaunal distributions in the Thau lagoon (France). Estuarine, Coastal and Shelf Science 72 (3), 432 446.]). The results indicate that most of the flux intensity as well as the temporal and spatial variability can be explained by the combined influence of microscale and macroscale processes. Microscale changes were identified using Mn flux as a good indicator of the redox conditions at the sediment water interface, and by extension, as an accurate proxy of benthic fluxes for most trace metals and mercury species. We also observed that the redox gradient at the interface is promoted by both microbial and macrobenthic species activity that governs O2 budgets. Macroscale processes have been investigated considering macrobenthic organisms activity (macrofauna and macroalgal cover). The density of such macroorganisms is able to explain most of the spatial and temporal variability of the benthic metal fluxes within a specific site. A tentative estimation of the flux of metals and organometals associated with deposit feeder and suspension feeder activity was found to be in the range of the flux determined within the chambers for most considered elements. Furthermore, a light/dark incubation investigating a dense macroalgal cover present at the sediment surface illustrates the role of photosynthetic activity in controlling benthic exchanges. Significant changes in benthic flux intensity and/or direction were reported for all redox sensitive elements (Cd, Co, Cu, Mn, Pb, U, and iHg). For MMHg and organotin species, other complimentary processes such as photodegradation/uptake and hydrophobic absorption/desorption need to be considered. This work demonstrates that the processes governing benthic exchanges are complex and that benthic organisms play a major role in the significant seasonal, diurnal and spatial variability of trace metals and organometals benthic fluxes in the lagoon.

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.

Effects of Atrazine, Metolachlor, Carbaryl and Chlorothalonil on Benthic Microbes and Their Nutrient Dynamics

PubMed Central

Elias, Daniel; Bernot, Melody J.

2014-01-01

Atrazine, metolachlor, carbaryl, and chlorothalonil are detected in streams throughout the U.S. at concentrations that may have adverse effects on benthic microbes. Sediment samples were exposed to these pesticides to quantify responses of ammonium, nitrate, and phosphate uptake by the benthic microbial community. Control uptake rates of sediments had net remineralization of nitrate (−1.58 NO3 µg gdm−1 h−1), and net assimilation of phosphate (1.34 PO4 µg gdm−1 h−1) and ammonium (0.03 NH4 µg gdm−1 h−1). Metolachlor decreased ammonium and phosphate uptake. Chlorothalonil decreased nitrate remineralization and phosphate uptake. Nitrate, ammonium, and phosphate uptake rates are more pronounced in the presence of these pesticides due to microbial adaptations to toxicants. Our interpretation of pesticide availability based on their water/solid affinities supports no effects for atrazine and carbaryl, decreasing nitrate remineralization, and phosphate assimilation in response to chlorothalonil. Further, decreased ammonium and phosphate uptake in response to metolachlor is likely due to affinity. Because atrazine target autotrophs, and carbaryl synaptic activity, effects on benthic microbes were not hypothesized, consistent with results. Metolachlor and chlorothalonil (non-specific modes of action) had significant effects on sediment microbial nutrient dynamics. Thus, pesticides with a higher affinity to sediments and/or broad modes of action are likely to affect sediment microbes' nutrient dynamics than pesticides dissolved in water or specific modes of action. Predicted nutrient uptake rates were calculated at mean and peak concentrations of metolachlor and chlorothalonil in freshwaters using polynomial equations generated in this experiment. We concluded that in natural ecosystems, peak chlorothalonil and metolachlor concentrations could affect phosphate and ammonium by decreasing net assimilation, and nitrate uptake rates by decreasing remineralization, relative to mean concentrations of metolachlor and chlorothalonil. Our regression equations can complement models of nitrogen and phosphorus availability in streams to predict potential changes in nutrient dynamics in response to pesticides in freshwaters. PMID:25275369

Microbial ecology of deep-water mid-Atlantic canyons

USGS Publications Warehouse

Kellogg, Christina A.

2011-01-01

The research described in this fact sheet will be conducted from 2012 to 2014 as part of the U.S. Geological Survey's DISCOVRE (DIversity, Systematics, and COnnectivity of Vulnerable Reef Ecosystems) Program. This integrated, multidisciplinary effort will be investigating a variety of topics related to unique and fragile deep-sea ecosystems from the microscopic level to the ecosystem level. One goal is to improve understanding, at the microbiological scale, of the benthic communities (including corals) that reside in and around mid-Atlantic canyon habitats and their associated environments. Specific objectives include identifying and characterizing the microbial associates of deep-sea corals, characterizing the microbial biofilms on hard substrates to better determine their role in engineering the ecosystem, and adding a microbial dimension to benthic community structure and function assessments by characterizing micro-eukaryotes, bacteria, and archaea in deep-sea sediments.

Microbially induced and microbially catalysed precipitation: two different carbonate factories

NASA Astrophysics Data System (ADS)

Meister, Patrick

2016-04-01

The landmark paper by Schlager (2003) has revealed three types of benthic carbonate production referred to as "carbonate factories", operative at different locations at different times in Earth history. The tropical or T-factory comprises the classical platforms and fringing reefs and is dominated by carbonate precipitation by autotrophic calcifying metazoans ("biotically controlled" precipitation). The cool or C-factory is also biotically controlled but via heterotrophic, calcifying metazoans in cold and deep waters at the continental margins. A further type is the mud-mound or M-factory, where carbonate precipitation is supported by microorganisms but not controlled by a specific enzymatic pathway ("biotically induced" precipitation). How exactly the microbes influence precipitation is still poorly understood. Based on recent experimental and field studies, the microbial influence on modern mud mound and microbialite growth includes two fundamentally different processes: (1) Metabolic activity of microbes may increase the saturation state with respect to a particular mineral phase, thereby indirectly driving the precipitation of the mineral phase: microbially induced precipitation. (2) In a situation, where a solution is already supersaturated but precipitation of the mineral is inhibited by a kinetic barrier, microbes may act as a catalyser, i.e. they lower the kinetic barrier: microbially catalysed precipitation. Such a catalytic effect can occur e.g. via secreted polymeric substances or specific chemical groups on the cell surface, at which the minerals nucleate or which facilitate mechanistically the bonding of new ions to the mineral surface. Based on these latest developments in microbialite formation, I propose to extend the scheme of benthic carbonate factories of Schlager et al. (2003) by introducing an additional branch distinguishing microbially induced from microbially catalysed precipitation. Although both mechanisms could be operative in a M-factory, and it is difficult to distinguish their products, their cause is very different. A Mi-factory ("i" for induced) is predominant under low carbonate saturation in normal seawater; a Mc-factory ("c" for catalysed) is operative in higher-alkalinity waters. The latter conditions may not only occur in shallow seas restricted from open sea water but may also have occurred in the aftermath of catastrophic events (e.g. P/T boundary) or during the Precambrian, before the onset of metazoan calcifiers. Thus, adding the additional distinction between microbially induced and microbially catalysed precipitation would allow the application of Schlager's concept of benthic carbonate factories beyond the Phanerozoic and probably over the entire Earth history.

Stimulation of microbial nitrogen cycling in aquatic ecosystems by benthic macrofauna: mechanisms and environmental implications

NASA Astrophysics Data System (ADS)

Stief, P.

2013-12-01

Invertebrate animals that live at the bottom of aquatic ecosystems (i.e., benthic macrofauna) are important mediators between nutrients in the water column and microbes in the benthos. The presence of benthic macrofauna stimulates microbial nutrient dynamics through different types of animal-microbe interactions, which potentially affect the trophic status of aquatic ecosystems. This review contrasts three types of animal-microbe interactions in the benthos of aquatic ecosystems: (i) ecosystem engineering, (ii) grazing, and (iii) symbiosis. Their specific contributions to the turnover of fixed nitrogen (mainly nitrate and ammonium) and the emission of the greenhouse gas nitrous oxide are evaluated. Published data indicate that ecosystem engineering by sediment-burrowing macrofauna stimulates benthic nitrification and denitrification, which together allows fixed nitrogen removal. However, the release of ammonium from sediments is enhanced more strongly than the sedimentary uptake of nitrate. Ecosystem engineering by reef-building macrofauna increases nitrogen retention and ammonium concentrations in shallow aquatic ecosystems, but allows organic nitrogen removal through harvesting. Grazing by macrofauna on benthic microbes apparently has small or neutral effects on nitrogen cycling. Animal-microbe symbioses provide abundant and distinct benthic compartments for a multitude of nitrogen-cycle pathways. Recent studies reveal that ecosystem engineering, grazing, and symbioses of benthic macrofauna significantly enhance nitrous oxide emission from shallow aquatic ecosystems. The beneficial effect of benthic macrofauna on fixed nitrogen removal through coupled nitrification-denitrification can thus be offset by the concurrent release of (i) ammonium that stimulates aquatic primary production and (ii) nitrous oxide that contributes to global warming. Overall, benthic macrofauna intensifies the coupling between benthos, pelagial, and atmosphere through enhanced turnover and transport of nitrogen.

Stimulation of microbial nitrogen cycling in aquatic ecosystems by benthic macrofauna: mechanisms and environmental implications

NASA Astrophysics Data System (ADS)

Stief, P.

2013-07-01

Invertebrate animals that live at the bottom of aquatic ecosystems (i.e., benthic macrofauna) are important mediators between nutrients in the water column and microbes in the benthos. The presence of benthic macrofauna stimulates microbial nutrient dynamics through different types of animal-microbe interactions, which potentially affect the trophic status of aquatic ecosystems. This review contrasts three types of animal-microbe interactions in the benthos of aquatic ecosystems: (i) ecosystem engineering, (ii) grazing, and (iii) symbiosis. Their specific contributions to the turnover of fixed nitrogen (mainly nitrate and ammonium) and the emission of the greenhouse gas nitrous oxide are evaluated. Published data indicate that ecosystem engineering by sediment-burrowing macrofauna stimulates benthic nitrification and denitrification, which together allows fixed nitrogen removal. However, the release of ammonium from sediments often is enhanced even more than the sedimentary uptake of nitrate. Ecosystem engineering by reef-building macrofauna increases nitrogen retention and ammonium concentrations in shallow aquatic ecosystems, but allows organic nitrogen removal through harvesting. Grazing by macrofauna on benthic microbes apparently has small or neutral effects on nitrogen cycling. Animal-microbe symbioses provide abundant and distinct benthic compartments for a multitude of nitrogen-cycle pathways. Recent studies revealed that ecosystem engineering, grazing, and symbioses of benthic macrofauna significantly enhance nitrous oxide emission from shallow aquatic ecosystems. The beneficial effect of benthic macrofauna on fixed nitrogen removal through coupled nitrification-denitrification can thus be offset by the concurrent release of (i) ammonium that stimulates aquatic primary production and (ii) nitrous oxide that contributes to global warming. Overall, benthic macrofauna intensifies the coupling between benthos, pelagial, and atmosphere through enhanced turnover and transport of nitrogen.

The gut microbial community of Midas cichlid fish in repeatedly evolved limnetic-benthic species pairs.

PubMed

Franchini, Paolo; Fruciano, Carmelo; Frickey, Tancred; Jones, Julia C; Meyer, Axel

2014-01-01

Gut bacterial communities are now known to influence a range of fitness related aspects of organisms. But how different the microbial community is in closely related species, and if these differences can be interpreted as adaptive is still unclear. In this study we compared microbial communities in two sets of closely related sympatric crater lake cichlid fish species pairs that show similar adaptations along the limnetic-benthic axis. The gut microbial community composition differs in the species pair inhabiting the older of two crater lakes. One major difference, relative to other fish, is that in these cichlids that live in hypersaline crater lakes, the microbial community is largely made up of Oceanospirillales (52.28%) which are halotolerant or halophilic bacteria. This analysis opens up further avenues to identify candidate symbiotic or co-evolved bacteria playing a role in adaptation to similar diets and life-styles or even have a role in speciation. Future functional and phylosymbiotic analyses might help to address these issues.

Terminal proterozoic mid-shelf Benthic microbial mats in the Centralian Superbasin and their environmental significance

NASA Astrophysics Data System (ADS)

Logan, Graham A.; Calver, Clive R.; Gorjan, Paul; Summons, Roger E.; Hayes, John M.; Walter, Malcolm R.

1999-05-01

A combined sedimentological and biogeochemical study has been conducted on several Terminal Proterozoic mid-shelf microbial mat facies from the Centralian Super-basin. Isotopic and organic geochemical analysis of the bitumen and kerogen indicated that two sources of organic matter from 'planktonic' and 'benthic microbial-mat' populations contributed to the sediment. The 'planktonic' source provided a suite of n-alkanes with C 20, whereas, the 'benthic' source contributed an overlay of n-alkanes >C 20 with a strong even preference, together with mid-chain methyl alkanes. Kerogen and biomarkers derived from the microbial mat were found to be depleted in 13C relative to planktonic material. Pyrite in the micorbial mats was also found to be depleted in 34S compared to surrounding facies. The combination of these observations suggested that the mats may have been at least partly composed of sulfide oxidising bacteria. These organisms have specific environmental tolerances that set limits on palaeo-environment. Their requirement for oxygen indicates that the water column above the mid-shelf could not have been anoxic. Accordingly, from the results and age determinations reported here, it would appear that mid-shelf environments of the Centralian Superbasin of Australia were seeing significant levels of oxygen through the Ediacarian.

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.

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

Impact of CO2 leakage from sub-seabed carbon dioxide capture and storage (CCS) reservoirs on benthic virus-prokaryote interactions and functions.

PubMed

Rastelli, Eugenio; Corinaldesi, Cinzia; Dell'Anno, Antonio; Amaro, Teresa; Queirós, Ana M; Widdicombe, Stephen; Danovaro, Roberto

2015-01-01

Atmospheric CO2 emissions are a global concern due to their predicted impact on biodiversity, ecosystems functioning, and human life. Among the proposed mitigation strategies, CO2 capture and storage, primarily the injection of CO2 into marine deep geological formations has been suggested as a technically practical option for reducing emissions. However, concerns have been raised that possible leakage from such storage sites, and the associated elevated levels of pCO2 could locally impact the biodiversity and biogeochemical processes in the sediments above these reservoirs. Whilst a number of impact assessment studies have been conducted, no information is available on the specific responses of viruses and virus-host interactions. In the present study, we tested the impact of a simulated CO2 leakage on the benthic microbial assemblages, with specific focus on microbial activity and virus-induced prokaryotic mortality (VIPM). We found that exposure to levels of CO2 in the overlying seawater from 1,000 to 20,000 ppm for a period up to 140 days, resulted in a marked decrease in heterotrophic carbon production and organic matter degradation rates in the sediments, associated with lower rates of VIPM, and a progressive accumulation of sedimentary organic matter with increasing CO2 concentrations. These results suggest that the increase in seawater pCO2 levels that may result from CO2 leakage, can severely reduce the rates of microbial-mediated recycling of the sedimentary organic matter and viral infections, with major consequences on C cycling and nutrient regeneration, and hence on the functioning of benthic ecosystems.

Biogeochemical and Microbial Variation across 5500 km of Antarctic Surface Sediment Implicates Organic Matter as a Driver of Benthic Community Structure

PubMed Central

Learman, Deric R.; Henson, Michael W.; Thrash, J. Cameron; Temperton, Ben; Brannock, Pamela M.; Santos, Scott R.; Mahon, Andrew R.; Halanych, Kenneth M.

2016-01-01

Western Antarctica, one of the fastest warming locations on Earth, is a unique environment that is underexplored with regards to biodiversity. Although pelagic microbial communities in the Southern Ocean and coastal Antarctic waters have been well-studied, there are fewer investigations of benthic communities and most have a focused geographic range. We sampled surface sediment from 24 sites across a 5500 km region of Western Antarctica (covering the Ross Sea to the Weddell Sea) to examine relationships between microbial communities and sediment geochemistry. Sequencing of the 16S and 18S rRNA genes showed microbial communities in sediments from the Antarctic Peninsula (AP) and Western Antarctica (WA), including the Ross, Amundsen, and Bellingshausen Seas, could be distinguished by correlations with organic matter concentrations and stable isotope fractionation (total organic carbon; TOC, total nitrogen; TN, and δ13C). Overall, samples from the AP were higher in nutrient content (TOC, TN, and NH4+) and communities in these samples had higher relative abundances of operational taxonomic units (OTUs) classified as the diatom, Chaetoceros, a marine cercozoan, and four OTUs classified as Flammeovirgaceae or Flavobacteria. As these OTUs were strongly correlated with TOC, the data suggests the diatoms could be a source of organic matter and the Bacteroidetes and cercozoan are grazers that consume the organic matter. Additionally, samples from WA have lower nutrients and were dominated by Thaumarchaeota, which could be related to their known ability to thrive as lithotrophs. This study documents the largest analysis of benthic microbial communities to date in the Southern Ocean, representing almost half the continental shoreline of Antarctica, and documents trophic interactions and coupling of pelagic and benthic communities. Our results indicate potential modifications in carbon sequestration processes related to change in community composition, identifying a prospective mechanism that links climate change to carbon availability. PMID:27047451

Microbial-meiofaunal interrelationships in coastal sediments of the Red Sea.

PubMed

El-Serehy, Hamed A; Al-Rasheid, Khaled A; Al-Misned, Fahad A; Al-Talasat, Abdul Allah R; Gewik, Mohamed M

2016-05-01

Population density and biomass of bacteria and meiofauna were investigated seasonally in the sediments of the north-western bank of Red Sea. Samples of sediments were collected seasonally from three different stations to determine microphytobenthic biomass (chlorophyll a), protein, lipid, carbohydrate, and total organic matter concentrations. These investigations revealed that microbial components tended to increase their dominancy, whereas sensitive meiofauna were extremely reduced during the entire study period. Thus a very low density of the total meiofauna (with an annual average of 109 ± 26 ind./10 cm(2)) was recorded whilst the benthic microbial population densities exhibited higher values (ranging from 0.31 ± 0.02 × 10(8) to 43.67 ± 18.62 × 10(8)/g dry sediment). These changes in the relative importance analysis of benthic microbial components versus meiofaunal ones seem to be based on the impact of organic matter accumulation on the function and structure of these benthic communities. Proteins, lipids and carbohydrates showed very low concentration values, and the organic matter mostly consisted of carbohydrates, reflecting lower nutritional values for benthic fauna in general and meiofauna in particular. The distribution of microbial and meiofaunal communities seems to be dependent on the quality of the organic matter rather than on its quantity. Total organic matter concentrations varied between 5.8 and 7.6 mg/g, with organic carbon accounting for only 32% of the total organic matter. Chlorophyll a attained very low values, fluctuating between 0.11 and 0.56 μg/g, indicating the oligotrophy of the studied area. The very low concentration of chlorophyll a in the Red Sea sediment suggests that the sedimentary organic matter, heterotrophic bacteria and/or protozoa constitute an alternative resource that is consumed by meiofauna when algae are less abundant. Protozoa, therefore, represent the "missing link in bacteria-meiofauna interaction in the Red Sea marine sediment ecosystem.

Metagenomic analysis of sediments under seaports influence in the Equatorial Atlantic Ocean.

PubMed

Tavares, Tallita Cruz Lopes; Normando, Leonardo Ribeiro Oliveira; de Vasconcelos, Ana Tereza Ribeiro; Gerber, Alexandra Lehmkuhl; Agnez-Lima, Lucymara Fassarella; Melo, Vânia Maria Maciel

2016-07-01

Maritime ports are anthropogenic interventions capable of causing serious alterations in coastal ecosystems. In this study, we examined the benthic microbial diversity and community structure under the influence of two maritime ports, Mucuripe (MUC) and Pecém (PEC), at Equatorial Atlantic Ocean in Northeast Brazil. Those seaports differ in architecture, time of functioning, cargo handling and contamination. The microbiomes from MUC and PEC were also compared in silico to 11 other globally distributed marine microbiomes. The comparative analysis of operational taxonomic units (OTUs) retrieved by PCR-DGGE showed that MUC presents greater richness and β diversity of Bacteria and Archaea than PEC. In line with these results, metagenomic analysis showed that MUC and PEC benthic microbial communities share the main common bacterial phyla found in coastal environments, although can be distinguish by greater abundance of Cyanobacteria in MUC and Deltaproteobacteria in PEC. Both ports differed in Archaea composition, being PEC port sediments dominated by Thaumarchaeota. The microbiomes showed little divergence in their potential metabolic pathways, although shifts on the microbial taxonomic signatures involved in nitrogen and sulphur metabolic pathways were observed. The comparative analysis of different benthic marine metagenomes from Brazil, Australia and Mexico grouped them by the geographic location rather than by the type of ecosystem, although at phylum level seaport sediments share a core microbiome constituted by Proteobacteria, Cyanobacteria, Actinobacteria, Tenericuteres, Firmicutes, Bacteriodetes and Euryarchaeota. Our results suggest that multiple physical and chemical factors acting on sediments as a result of at least 60years of port operation play a role in shaping the benthic microbial communities at taxonomic level, but not at functional level. Copyright © 2016 Elsevier B.V. All rights reserved.

Benthic communities in the deep Mediterranean Sea: exploring microbial and meiofaunal patterns in slope and basin ecosystems

NASA Astrophysics Data System (ADS)

Sevastou, K.; Lampadariou, N.; Polymenakou, P. N.; Tselepides, A.

2013-07-01

The long-held perception of the deep sea consisting of monotonous slopes and uniform oceanic basins has over the decades given way to the idea of a complex system with wide habitat heterogeneity. Under the prism of a highly diverse environment, a large dataset was used to describe and compare spatial patterns of the dominant small-size components of deep-sea benthos, metazoan meiofauna and microbes, from Mediterranean basins and slopes. A grid of 73 stations sampled at five geographical areas along the central-eastern Mediterranean Basin (central Mediterranean, northern Aegean Sea, Cretan Sea, Libyan Sea, eastern Levantine) spanning over 4 km in depth revealed a high diversity, irrespective of the benthic group or level of taxonomic analysis. A common decreasing bathymetric trend was detected for meiobenthic abundance, major taxa diversity and nematode genera richness, but no differences were found between the two habitats (basin vs slope). In contrast, microbial richness is significantly higher at the basin ecosystem and tends to increase with depth. Multivariate analyses (β- and δ-diversity and ordination analysis) complemented these results and underlined the high within-habitat variability of benthic communities. Meiofaunal communities in particular were found to change gradually and vary more towards the abyss. On the other hand, microbial communities were highly variable, even among samples of the same area, habitat and bathymetry. A significant proportion of the variation of benthic communities and their descriptors was explained by depth and proxies of food availability (sedimentary pigments and organic content), but the combination of predictor variables and the strength of the relationship varied depending on the data set used (based on type of habitat, benthic component, taxonomic level). This, along with the observed high within-habitat variability suggests that other factors, which tend to vary at local scale (hydrodynamics, substrate structure, geochemistry, food quality, etc.), may also relate to the observed benthic patterns. Overall, the results presented here suggest that differences in small-size benthos between the basin and slope habitats are neither strong nor consistent; it appears that within-habitat variability is high, differences among depth ranges are important and further investigation of possible environmental drivers of benthic patterns is needed.

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.

Effects of shelter and enrichment on the ecology and nutrient cycling of microbial communities of subtidal carbonate sediments.

PubMed

Forehead, Hugh I; Kendrick, Gary A; Thompson, Peter A

2012-04-01

The interactions between physical disturbances and biogeochemical cycling are fundamental to ecology. The benthic microbial community controls the major pathway of nutrient recycling in most shallow-water ecosystems. This community is strongly influenced by physical forcing and nutrient inputs. Our study tests the hypotheses that benthic microbial communities respond to shelter and enrichment with (1) increased biomass, (2) change in community composition and (3) increased uptake of inorganic nutrients from the water column. Replicate in situ plots were sheltered from physical disturbance and enriched with inorganic nutrients or left without additional nutrients. At t(0) and after 10 days, sediment-water fluxes of nutrients, O(2) and N(2) , were measured, the community was characterized with biomarkers. Autochthonous benthic microalgal (BMA) biomass increased 30% with shelter and a natural fivefold increase in nutrient concentration; biomass did not increase with greater enrichment. Diatoms remained the dominant taxon of BMA, suggesting that the sediments were not N or Si limited. Bacteria and other heterotrophic organisms increased with enrichment and shelter. Daily exchanges of inorganic nutrients between sediments and the water column did not change in response to shelter or nutrient enrichment. In these sediments, physical disturbance, perhaps in conjunction with nutrient enrichment, was the primary determinant of microbial biomass. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. 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.

2D-Visualization of metabolic activity with planar optical chemical sensors (optodes)

NASA Astrophysics Data System (ADS)

Meier, R. J.; Liebsch, G.

2015-12-01

Microbia plays an outstandingly important role in many hydrologic compartments, such as e.g. the benthic community in sediments, or biologically active microorganisms in the capillary fringe, in ground water, or soil. Oxygen, pH, and CO2 are key factors and indicators for microbial activity. They can be measured using optical chemical sensors. These sensors record changing fluorescence properties of specific indicator dyes. The signals can be measured in a non-contact mode, even through transparent walls, which is important for many lab-experiments. They can measure in closed (transparent) systems, without sampling or intruding into the sample. They do not consume the analytes while measuring, are fully reversible and able to measure in non-stirred solutions. These sensors can be applied as high precision fiberoptic sensors (for profiling), robust sensor spots, or as planar sensors for 2D visualization (imaging). Imaging enables to detect thousands of measurement spots at the same time and generate 2D analyte maps over a region of interest. It allows for comparing different regions within one recorded image, visualizing spatial analyte gradients, or more important to identify hot spots of metabolic activity. We present ready-to-use portable imaging systems for the analytes oxygen, pH, and CO2. They consist of a detector unit, planar sensor foils and a software for easy data recording and evaluation. Sensors foils for various analytes and measurement ranges enable visualizing metabolic activity or analyte changes in the desired range. Dynamics of metabolic activity can be detected in one shot or over long time periods. We demonstrate the potential of this analytical technique by presenting experiments on benthic disturbance-recovery dynamics in sediments and microbial degradation of organic material in the capillary fringe. We think this technique is a new tool to further understand how microbial and geochemical processes are linked in (not solely) hydrologic systems.

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.

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

Black reefs: iron-induced phase shifts on coral reefs.

PubMed

Kelly, Linda Wegley; Barott, Katie L; Dinsdale, Elizabeth; Friedlander, Alan M; Nosrat, Bahador; Obura, David; Sala, Enric; Sandin, Stuart A; Smith, Jennifer E; Vermeij, Mark J A; Williams, Gareth J; Willner, Dana; Rohwer, Forest

2012-03-01

The Line Islands are calcium carbonate coral reef platforms located in iron-poor regions of the central Pacific. Natural terrestrial run-off of iron is non-existent and aerial deposition is extremely low. However, a number of ship groundings have occurred on these atolls. The reefs surrounding the shipwreck debris are characterized by high benthic cover of turf algae, macroalgae, cyanobacterial mats and corallimorphs, as well as particulate-laden, cloudy water. These sites also have very low coral and crustose coralline algal cover and are call black reefs because of the dark-colored benthic community and reduced clarity of the overlying water column. Here we use a combination of benthic surveys, chemistry, metagenomics and microcosms to investigate if and how shipwrecks initiate and maintain black reefs. Comparative surveys show that the live coral cover was reduced from 40 to 60% to <10% on black reefs on Millennium, Tabuaeran and Kingman. These three sites are relatively large (>0.75 km(2)). The phase shift occurs rapidly; the Kingman black reef formed within 3 years of the ship grounding. Iron concentrations in algae tissue from the Millennium black reef site were six times higher than in algae collected from reference sites. Metagenomic sequencing of the Millennium Atoll black reef-associated microbial community was enriched in iron-associated virulence genes and known pathogens. Microcosm experiments showed that corals were killed by black reef rubble through microbial activity. Together these results demonstrate that shipwrecks and their associated iron pose significant threats to coral reefs in iron-limited regions.

Impact of refined petroleum spills on water quality, macro-invertebrate and microbial communities of a tropical aquatic environment.

PubMed

Chukwu, L O; Nwachukwu, S C U

2005-07-01

Water quality characteristics, benthic macro-invertebrates and microbial communities of three first order streams in South West Nigeria were investigated to assess the effects of refined petroleum five months after spillage. All physical and chemical conditions except temperature and pH were significantly different (P<0.01) at the upstream control stations and impacted stations reflecting the perturbational stress. The benthic macro-invertebrate fauna were dominated by arthropods, but the faunal spectrum was dissimilar at all the stations studied. Sampling stations at the epicentre of the spill showed considerable reduction in faunal compositions and relative abundance. Generally, the microbial density and diversity were highest in both soil and water samples from impacted sites than in control sites. There was a significantly higher proportion (P < 0.05) of hydrocarbon utilizers in soil than in water samples in all stations except in samples from stations (P<0.05).

Biogeochemical malfunctioning in sediments beneath a deep-water fish farm.

PubMed

Valdemarsen, Thomas; Bannister, Raymond J; Hansen, Pia K; Holmer, Marianne; Ervik, Arne

2012-11-01

We investigated the environmental impact of a deep water fish farm (190 m). Despite deep water and low water currents, sediments underneath the farm were heavily enriched with organic matter, resulting in stimulated biogeochemical cycling. During the first 7 months of the production cycle benthic fluxes were stimulated >29 times for CO(2) and O(2) and >2000 times for NH(4)(+), when compared to the reference site. During the final 11 months, however, benthic fluxes decreased despite increasing sedimentation. Investigations of microbial mineralization revealed that the sediment metabolic capacity was exceeded, which resulted in inhibited microbial mineralization due to negative feed-backs from accumulation of various solutes in pore water. Conclusions are that (1) deep water sediments at 8 °C can metabolize fish farm waste corresponding to 407 and 29 mmol m(-2) d(-1) POC and TN, respectively, and (2) siting fish farms at deep water sites is not a universal solution for reducing benthic impacts. Copyright © 2012 Elsevier Ltd. All rights reserved.

Farming behaviour of reef fishes increases the prevalence of coral disease associated microbes and black band disease

PubMed Central

Casey, Jordan M.; Ainsworth, Tracy D.; Choat, J. Howard; Connolly, Sean R.

2014-01-01

Microbial community structure on coral reefs is strongly influenced by coral–algae interactions; however, the extent to which this influence is mediated by fishes is unknown. By excluding fleshy macroalgae, cultivating palatable filamentous algae and engaging in frequent aggression to protect resources, territorial damselfish (f. Pomacentridae), such as Stegastes, mediate macro-benthic dynamics on coral reefs and may significantly influence microbial communities. To elucidate how Stegastes apicalis and Stegastes nigricans may alter benthic microbial assemblages and coral health, we determined the benthic community composition (epilithic algal matrix and prokaryotes) and coral disease prevalence inside and outside of damselfish territories in the Great Barrier Reef, Australia. 16S rDNA sequencing revealed distinct bacterial communities associated with turf algae and a two to three times greater relative abundance of phylotypes with high sequence similarity to potential coral pathogens inside Stegastes's territories. These potentially pathogenic phylotypes (totalling 30.04% of the community) were found to have high sequence similarity to those amplified from black band disease (BBD) and disease affected corals worldwide. Disease surveys further revealed a significantly higher occurrence of BBD inside S. nigricans's territories. These findings demonstrate the first link between fish behaviour, reservoirs of potential coral disease pathogens and the prevalence of coral disease. PMID:24966320

Free-Living Nematodes in the Freshwater Food Web: A Review

PubMed Central

Majdi, Nabil; Traunspurger, Walter

2015-01-01

Free-living nematodes are well-recognized as an abundant and ubiquitous component of benthic communities in inland waters. Compelling evidence from soil and marine ecosystems has highlighted the importance of nematodes as trophic intermediaries between microbial production and higher trophic levels. However, the paucity of empirical evidence of their role in freshwater ecosystems has hampered their inclusion in our understanding of freshwater food web functioning. This literature survey provides an overview of research efforts in the field of freshwater nematode ecology and of the complex trophic interactions between free-living nematodes and microbes, other meiofauna, macro-invertebrates, and fishes. Based on an analysis of the relevant literature and an appreciation of the potential of emerging approaches for the evaluation of nematode trophic ecology, we point out research gaps and recommend relevant directions for further research. The latter include (i) interactions of nematodes with protozoans and fungi; (ii) nonconsumptive effects of nematodes on microbial activity and the effects of nematodes on associated key ecosystem processes (decomposition, primary production); and (iii) the feeding selectivity and intraspecific feeding variability of nematodes and their potential impacts on the structure of benthic communities. PMID:25861114

Demonstration of the SeptiStrand benthic microbial fuel cell powering a magnetometer for ship detection

NASA Astrophysics Data System (ADS)

Arias-Thode, Y. Meriah; Hsu, Lewis; Anderson, Greg; Babauta, Jerome; Fransham, Roy; Obraztsova, Anna; Tukeman, Gabriel; Chadwick, D. Bart

2017-07-01

The Navy has a need for monitoring conditions and gathering information in marine environments. Sensors can monitor and report environmental parameters and potential activities such as animal movements, ships, or personnel. However, there has to be a means to power these sensors. One promising enabling technology that has been shown to provide long-term power production in underwater environments is the benthic microbial fuel cells (BMFC). BMFCs are devices that generate energy by coupling bioanodes and biocathodes through an external energy harvester. Recent studies have demonstrated success for usage of BMFCs in powering small instruments and other devices on the seafloor over limited periods of time. In this effort, a seven-stranded BMFC linear array of 30 m was designed to power a seafloor magnetometer to detect passing ship movements through Pearl Harbor, Hawaii. The BMFC system was connected to a flyback energy harvesting circuit that charged the battery powering the magnetometer. The deployment was demonstrated the BMFC supplied power to the battery for approximately 38 days. This is the first large-scale demonstration system for usage of the SeptiStrand BMFC technology to power a relevant sensor.

Metal-Macrofauna Interactions Determine Microbial Community Structure and Function in Copper Contaminated Sediments

PubMed Central

Mayor, Daniel J.; Gray, Nia B.; Elver-Evans, Joanna; Midwood, Andrew J.; Thornton, Barry

2013-01-01

Copper is essential for healthy cellular functioning, but this heavy metal quickly becomes toxic when supply exceeds demand. Marine sediments receive widespread and increasing levels of copper contamination from antifouling paints owing to the 2008 global ban of organotin-based products. The toxicity of copper will increase in the coming years as seawater pH decreases and temperature increases. We used a factorial mesocosm experiment to investigate how increasing sediment copper concentrations and the presence of a cosmopolitan bioturbating amphipod, Corophium volutator, affected a range of ecosystem functions in a soft sediment microbial community. The effects of copper on benthic nutrient release, bacterial biomass, microbial community structure and the isotopic composition of individual microbial membrane [phospholipid] fatty acids (PLFAs) all differed in the presence of C. volutator. Our data consistently demonstrate that copper contamination of global waterways will have pervasive effects on the metabolic functioning of benthic communities that cannot be predicted from copper concentrations alone; impacts will depend upon the resident macrofauna and their capacity for bioturbation. This finding poses a major challenge for those attempting to manage the impacts of copper contamination on ecosystem services, e.g. carbon and nutrient cycling, across different habitats. Our work also highlights the paucity of information on the processes that result in isotopic fractionation in natural marine microbial communities. We conclude that the assimilative capacity of benthic microbes will become progressively impaired as copper concentrations increase. These effects will, to an extent, be mitigated by the presence of bioturbating animals and possibly other processes that increase the influx of oxygenated seawater into the sediments. Our findings support the move towards an ecosystem approach for environmental management. PMID:23741430

Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments.

PubMed

Mayor, Daniel J; Gray, Nia B; Elver-Evans, Joanna; Midwood, Andrew J; Thornton, Barry

2013-01-01

Copper is essential for healthy cellular functioning, but this heavy metal quickly becomes toxic when supply exceeds demand. Marine sediments receive widespread and increasing levels of copper contamination from antifouling paints owing to the 2008 global ban of organotin-based products. The toxicity of copper will increase in the coming years as seawater pH decreases and temperature increases. We used a factorial mesocosm experiment to investigate how increasing sediment copper concentrations and the presence of a cosmopolitan bioturbating amphipod, Corophium volutator, affected a range of ecosystem functions in a soft sediment microbial community. The effects of copper on benthic nutrient release, bacterial biomass, microbial community structure and the isotopic composition of individual microbial membrane [phospholipid] fatty acids (PLFAs) all differed in the presence of C. volutator. Our data consistently demonstrate that copper contamination of global waterways will have pervasive effects on the metabolic functioning of benthic communities that cannot be predicted from copper concentrations alone; impacts will depend upon the resident macrofauna and their capacity for bioturbation. This finding poses a major challenge for those attempting to manage the impacts of copper contamination on ecosystem services, e.g. carbon and nutrient cycling, across different habitats. Our work also highlights the paucity of information on the processes that result in isotopic fractionation in natural marine microbial communities. We conclude that the assimilative capacity of benthic microbes will become progressively impaired as copper concentrations increase. These effects will, to an extent, be mitigated by the presence of bioturbating animals and possibly other processes that increase the influx of oxygenated seawater into the sediments. Our findings support the move towards an ecosystem approach for environmental management.

Microbial to reef scale interactions between the reef-building coral Montastraea annularis and benthic algae.

PubMed

Barott, Katie L; Rodriguez-Mueller, Beltran; Youle, Merry; Marhaver, Kristen L; Vermeij, Mark J A; Smith, Jennifer E; Rohwer, Forest L

2012-04-22

Competition between reef-building corals and benthic algae is of key importance for reef dynamics. These interactions occur on many spatial scales, ranging from chemical to regional. Using microprobes, 16S rDNA pyrosequencing and underwater surveys, we examined the interactions between the reef-building coral Montastraea annularis and four types of benthic algae. The macroalgae Dictyota bartayresiana and Halimeda opuntia, as well as a mixed consortium of turf algae, caused hypoxia on the adjacent coral tissue. Turf algae were also associated with major shifts in the bacterial communities at the interaction zones, including more pathogens and virulence genes. In contrast to turf algae, interactions with crustose coralline algae (CCA) and M. annularis did not appear to be antagonistic at any scale. These zones were not hypoxic, the microbes were not pathogen-like and the abundance of coral-CCA interactions was positively correlated with per cent coral cover. We propose a model in which fleshy algae (i.e. some species of turf and fleshy macroalgae) alter benthic competition dynamics by stimulating bacterial respiration and promoting invasion of virulent bacteria on corals. This gives fleshy algae a competitive advantage over corals when human activities, such as overfishing and eutrophication, remove controls on algal abundance. Together, these results demonstrate the intricate connections and mechanisms that structure coral reefs.

Bacterial Liasons: Bacteria Associated With Marine Benthic Meiofauna in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Diaz, K. S.; Sevigny, J.; Leasi, F.; Thomas, W. K.

2017-12-01

All macroorganisms are colonized by and harbor microbial associates that form their microbiome. Some microbial associates establish predictable symbioses across a host species. Other microbial assemblages, such as the human gut microbiome, exhibit semi-predictable patterns dependent on various factors such as host habitat and diet. Host species typically share core microbiota that remain temporally and spatially stable, but turnover of accessory microbiota due to to environmental change often confers adaptive advantage to the host would not receive from its own genome or core microbiome. Benthic meiofauna, microscopic eukaryotes that live in marine sediments, harbor bacterial associates that may confer functional advantages in the face of environmental perturbation that allow the host to persist and adapt during an environmental disturbance such as an oil spill. However, benthic meiofauna and their microbiota represent relatively unknown components of marine environments. In 2010, the Deepwater Horizon oil spill poured over 0.5 million metric tons of crude oil into the Gulf of Mexico. Now, much of the oil has dispersed, but some still lingers in environments such as marine sediments. Benthic meiofauna remain affected by these lingering hydrocarbons. Their inability to simply leave their habitat makes them ideal sentinels of environmental change that can factor into understanding oil spill impacts and inform response and mitigation of similar future events. Binning bacterial sequences from host whole shotgun genomes allows for analysis of microbiome gene coding and functional potentials that may assist the host through environmental disturbances, such as genes involved in hydrocarbon degradation pathways. 16S rRNA gene surveys reveal of microbiome composition of diverse meiofaunal taxa collected throughout the Gulf of Mexico. This work will examine structure and distribution of benthic meiofauna microbiomes in the Gulf of Mexico. Thus far, 16S surveys display differences between host microbiome composition and environmental microbiota. Microbiomes cluster based on host taxonomy and sampling location around the gulf.

Nutrients and temperature additively increase stream microbial respiration

Treesearch

David W. P. Manning; Amy D. Rosemond; Vladislav Gulis; Jonathan P. Benstead; John S. Kominoski

2017-01-01

Rising temperatures and nutrient enrichment are co‐occurring global‐change drivers that stimulate microbial respiration of detrital carbon, but nutrient effects on the temperature dependence of respiration in aquatic ecosystems remain uncertain. We measured respiration rates associated with leaf litter, wood, and fine benthic organic matter (FBOM) across...

Benthic flux of dissolved organic matter from lake sediment at different redox conditions and the possible effects of biogeochemical processes.

PubMed

Yang, Liyang; Choi, Jung Hyun; Hur, Jin

2014-09-15

The benthic fluxes of dissolved organic carbon (DOC), chromophoric and fluorescent dissolved organic matter (CDOM and FDOM) were studied for the sediment from an artificial lake, based on laboratory benthic chamber experiments. Conservative estimates for the benthic flux of DOC were 71 ± 142 and 51 ± 101 mg m(-2) day(-1) at hypoxic and oxic conditions, respectively. Two humic-like (C1 and C2), one tryptophan-like (C3), and one microbial humic-like (C4) components were identified from the samples using fluorescence excitation emission matrices and parallel factor analysis (EEM-PARAFAC). During the incubation period, C3 was removed while C4 was accumulated in the overlying water with no significant difference in the trends between the redox conditions. The humification index (HIX) increased with time. The combined results for C3, C4 and HIX suggested that microbial transformation may be an important process affecting the flux behaviors of DOM. In contrast, the overall accumulations of CDOM, C1, and C2 in the overlying water occurred only for the hypoxic condition, which was possibly explained by their enhanced photo-degradation and sorption to redox-sensitive minerals under the oxic condition. Our study demonstrated significant benthic flux of DOM in lake sediment and also the possible involvement of biogeochemical transformation in the processes, providing insight into carbon cycling in inland waters. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

Biological Diversity Comprising Microbial Structures of Antarctic Ice Covered Lakes

NASA Astrophysics Data System (ADS)

Matys, E. D.

2015-12-01

Analysis of microbial membrane lipids is a rapid and non-selective method for evaluating the composition of microbial communities. To fully realise the diagnostic potential of these lipids, we must first understand their structural diversity, biological sources, physiological functions, and pathways of preservation. Particular environmental conditions likely prompt the production of different membrane lipid structures. Antarctica's McMurdo Dry Valleys host numerous ice-covered lakes with sharp chemical gradients that vary in illumination, geochemical structure, and benthic mat morphologies that are structured by nutrient availability and water chemistry. The lipid contents of these benthic mats have not received extensive study nor have the communities yet been thoroughly characterized. Accordingly, a combination of lipid biomarker and nucleic acid sequence data provides the means of assessing species diversity and environmental controls on the composition and diversity of membrane lipid assemblages. We investigated the richness and diversity of benthic microbial communities and accumulated organic matter in Lake Vanda of the McMurdo Dry Valleys. We have identified diverse glycolipids, aminolipids, and phospholipids in addition to many unknown compounds that may be specific to these particular environments. Light levels fluctuate seasonally, favoring low-light-tolerant cyanobacteria and specific lipid assemblages. Adaptations to nutrient limitations are reflected in contrasting intact polar lipid assemblages. For example, under P-limiting conditions, phospholipids are subsidiary to membrane-forming lipids that do not contain P (i.e. ornithine, betaine, and sulfolipids). The bacteriohopanepolyol (BHP) composition is dominated by bacteriohopanetetrol (BHT), a ubiquitous BHP, and 2-methylhopanoids. The relative abundance of 2-methylhopanoids is unprecedented and may reflect the unusual seasonal light regime of this polar environment. By establishing correlations between environmental conditions, microbial community composition and the lipid assemblages of microbial structures in ice-covered lakes of Antarctica's McMurdo Dry Valleys, our data provides important ecological and evolutionary insights into these unusual environments.

Black reefs: iron-induced phase shifts on coral reefs

PubMed Central

Kelly, Linda Wegley; Barott, Katie L; Dinsdale, Elizabeth; Friedlander, Alan M; Nosrat, Bahador; Obura, David; Sala, Enric; Sandin, Stuart A; Smith, Jennifer E; Vermeij, Mark J A; Williams, Gareth J; Willner, Dana; Rohwer, Forest

2012-01-01

The Line Islands are calcium carbonate coral reef platforms located in iron-poor regions of the central Pacific. Natural terrestrial run-off of iron is non-existent and aerial deposition is extremely low. However, a number of ship groundings have occurred on these atolls. The reefs surrounding the shipwreck debris are characterized by high benthic cover of turf algae, macroalgae, cyanobacterial mats and corallimorphs, as well as particulate-laden, cloudy water. These sites also have very low coral and crustose coralline algal cover and are call black reefs because of the dark-colored benthic community and reduced clarity of the overlying water column. Here we use a combination of benthic surveys, chemistry, metagenomics and microcosms to investigate if and how shipwrecks initiate and maintain black reefs. Comparative surveys show that the live coral cover was reduced from 40 to 60% to <10% on black reefs on Millennium, Tabuaeran and Kingman. These three sites are relatively large (>0.75 km2). The phase shift occurs rapidly; the Kingman black reef formed within 3 years of the ship grounding. Iron concentrations in algae tissue from the Millennium black reef site were six times higher than in algae collected from reference sites. Metagenomic sequencing of the Millennium Atoll black reef-associated microbial community was enriched in iron-associated virulence genes and known pathogens. Microcosm experiments showed that corals were killed by black reef rubble through microbial activity. Together these results demonstrate that shipwrecks and their associated iron pose significant threats to coral reefs in iron-limited regions. PMID:21881615

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

Carbon foam anode modified by urea and its higher electrochemical performance in marine benthic microbial fuel cell

NASA Astrophysics Data System (ADS)

Fu, Yubin; Lu, Zhikai; Zai, Xuerong; Wang, Jian

2015-08-01

Electrode materials have an important effect on the property of microbial fuel cell (MFC). Carbon foam is utilized as an anode and further modified by urea to improve its performance in marine benthic microbial fuel cell (BMFC) with higher voltage and output power. The electrochemical properties of plain carbon foam (PC) and urea-modified carbon foam (UC) are measured respectively. Results show that the UC obtains better wettability after its modification and higher anti-polarization ability than the PC. A novel phenomenon has been found that the electrical potential of the modified UC anode is nearly 100 mV lower than that of the PC, reaching -570 ±10 mV ( vs. SCE), and that it also has a much higher electron transfer kinetic activity, reaching 9399.4 mW m-2, which is 566.2-fold higher than that from plain graphite anode (PG). The fuel cell containing the UC anode has the maximum power density (256.0 mW m-2) among the three different BMFCs. Urea would enhance the bacteria biofilm formation with a more diverse microbial community and maintain more electrons, leading to a lower anodic redox potential and higher power output. The paper primarily analyzes why the electrical potential of the modified anode becomes much lower than that of others after urea modification. These results can be utilized to construct a novel BMFC with higher output power and to design the conditioner of voltage booster with a higher conversion ratio. Finally, the carbon foam with a bigger pore size would be a potential anodic material in conventional MFC.

Farming behaviour of reef fishes increases the prevalence of coral disease associated microbes and black band disease.

PubMed

Casey, Jordan M; Ainsworth, Tracy D; Choat, J Howard; Connolly, Sean R

2014-08-07

Microbial community structure on coral reefs is strongly influenced by coral-algae interactions; however, the extent to which this influence is mediated by fishes is unknown. By excluding fleshy macroalgae, cultivating palatable filamentous algae and engaging in frequent aggression to protect resources, territorial damselfish (f. Pomacentridae), such as Stegastes, mediate macro-benthic dynamics on coral reefs and may significantly influence microbial communities. To elucidate how Stegastes apicalis and Stegastes nigricans may alter benthic microbial assemblages and coral health, we determined the benthic community composition (epilithic algal matrix and prokaryotes) and coral disease prevalence inside and outside of damselfish territories in the Great Barrier Reef, Australia. 16S rDNA sequencing revealed distinct bacterial communities associated with turf algae and a two to three times greater relative abundance of phylotypes with high sequence similarity to potential coral pathogens inside Stegastes's territories. These potentially pathogenic phylotypes (totalling 30.04% of the community) were found to have high sequence similarity to those amplified from black band disease (BBD) and disease affected corals worldwide. Disease surveys further revealed a significantly higher occurrence of BBD inside S. nigricans's territories. These findings demonstrate the first link between fish behaviour, reservoirs of potential coral disease pathogens and the prevalence of coral disease. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Partitioning the contributions of mega-, macro- and meiofauna to benthic metabolism on the upper continental slope of New Zealand: Potential links with environmental factors and trawling intensity

NASA Astrophysics Data System (ADS)

Leduc, Daniel; Pilditch, Conrad A.; Nodder, Scott D.

2016-02-01

Understanding and predicting change in deep-sea benthic ecosystem function remains a major challenge. Here, we conducted analyses combining data on the abundance and biomass of benthic fauna and sediment community oxygen consumption (SCOC) on New Zealand's continental margin to estimate and compare the contributions of meio-, macro-, and megafauna to total benthic metabolism and identify potential links with environmental factors and trawling intensity. We focussed on two regions in close proximity-the high surface primary productivity Chatham Rise and low surface productivity Challenger Plateau. Mean megafauna biomass was twenty times greater on Chatham Rise than Challenger Plateau, likely reflecting differences in food supply between the two regions; this contrast in megafaunal biomass was mainly due to differences in mean body weight rather than abundance. Meio- and macrofauna made similar contributions to SCOC and together accounted for 12% of benthic metabolism on average. In contrast, the estimated contribution of megafauna never exceeded 1.5%. Significant positive correlations between faunal respiration and food availability indicate a link between food supply and benthic community function. Our analyses also show that fauna made a greater contribution to SCOC in conditions of high food availability, and that microorganisms (i.e., the proportion of SCOC not accounted for by the fauna) tended to be more dominant at sites with low food availability. These findings provide support for the concept that large organisms are more strongly affected by a reduction in food resources than small organisms, which in turn underlies one of the most widely described patterns in the deep-sea benthos, i.e., the reduction in organism body size with depth. Because metabolism in deep-sea sediments is typically dominated by microorganisms and small fauna, the absence of a relationship between bottom trawling intensity and the respiration of benthic fauna in the present study may be explained by benthic communities shifting towards smaller body size following physical disturbance. Future studies of deep-sea benthic ecosystem function will need to quantify the indirect influence of fauna on microbial metabolism through activities such as feeding and bioturbation in order to better understand the total contribution of benthic fauna to benthic processes.

Microbial to reef scale interactions between the reef-building coral Montastraea annularis and benthic algae

PubMed Central

Barott, Katie L.; Rodriguez-Mueller, Beltran; Youle, Merry; Marhaver, Kristen L.; Vermeij, Mark J. A.; Smith, Jennifer E.; Rohwer, Forest L.

2012-01-01

Competition between reef-building corals and benthic algae is of key importance for reef dynamics. These interactions occur on many spatial scales, ranging from chemical to regional. Using microprobes, 16S rDNA pyrosequencing and underwater surveys, we examined the interactions between the reef-building coral Montastraea annularis and four types of benthic algae. The macroalgae Dictyota bartayresiana and Halimeda opuntia, as well as a mixed consortium of turf algae, caused hypoxia on the adjacent coral tissue. Turf algae were also associated with major shifts in the bacterial communities at the interaction zones, including more pathogens and virulence genes. In contrast to turf algae, interactions with crustose coralline algae (CCA) and M. annularis did not appear to be antagonistic at any scale. These zones were not hypoxic, the microbes were not pathogen-like and the abundance of coral–CCA interactions was positively correlated with per cent coral cover. We propose a model in which fleshy algae (i.e. some species of turf and fleshy macroalgae) alter benthic competition dynamics by stimulating bacterial respiration and promoting invasion of virulent bacteria on corals. This gives fleshy algae a competitive advantage over corals when human activities, such as overfishing and eutrophication, remove controls on algal abundance. Together, these results demonstrate the intricate connections and mechanisms that structure coral reefs. PMID:22090385

Pilot-scale benthic microbial electrochemical system (BMES) for the bioremediation of polluted river sediment

NASA Astrophysics Data System (ADS)

Li, Henan; He, Weihua; Qu, Youpeng; Li, Chao; Tian, Yan; Feng, Yujie

2017-07-01

A benthic microbial electrochemical system (BMES) of 350 L is built for the bioremediation of river sediment (Ashi river, Harbin, China). Carbon mesh anode with honeycomb-structure supports and activated carbon cathodes are applied for the construction. Synthesis wastewater with glucose is added to simulate the natural condition of Ashi River as an intermittent pollutant-holding water body and accelerate the removal of accumulated bio-refractory organic contents in sediment, represented by the concentration changes of polycyclic aromatic hydrocarbons, as the co-metabolic substrate for bacteria. The effluent TOC in the water layer of BMES is stable at 40 ± 2 mg L-1 and further reduced to 19 ± 5 mg L-1 after the addition of synthesis wastewater, while the removal of polycyclic aromatic hydrocarbons(Benzo(b)fluoranthene, Benzo(k)fluoranthene and Benzo(a)pyrene) in sediment samples reaches 74%. A maximum power density of 63 ± 3 mW m-2 is achieved by BMES, which decrease to 42 ± 2 mW m-2 due to cathode degradation and further reduce to 30 ± 3 mW m-2 attributed to substrate limitation at the end of operation. Community analyses show the diversity of anode community is improved during operation and the abundance of Chloroflexi, Firmicutes and exoelectrogenic microbes like G. psychrophilus increase.

Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems

PubMed Central

Danovaro, Roberto; Molari, Massimiliano; Corinaldesi, Cinzia; Dell’Anno, Antonio

2016-01-01

Bacteria and archaea dominate the biomass of benthic deep-sea ecosystems at all latitudes, playing a crucial role in global biogeochemical cycles, but their macroscale patterns and macroecological drivers are still largely unknown. We show the results of the most extensive field study conducted so far to investigate patterns and drivers of the distribution and structure of benthic prokaryote assemblages from 228 samples collected at latitudes comprising 34°N to 79°N, and from ca. 400- to 5570-m depth. We provide evidence that, in deep-sea ecosystems, benthic bacterial and archaeal abundances significantly increase from middle to high latitudes, with patterns more pronounced for archaea, and particularly for Marine Group I Thaumarchaeota. Our results also reveal that different microbial components show varying sensitivities to changes in temperature conditions and food supply. We conclude that climate change will primarily affect deep-sea benthic archaea, with important consequences on global biogeochemical cycles, particularly at high latitudes. PMID:27386507

Methane fates in the benthos and water column at cold seep sites along the continental margin of Central and North America

NASA Astrophysics Data System (ADS)

Hansman, Roberta L.; Thurber, Andrew R.; Levin, Lisa A.; Aluwihare, Lihini I.

2017-02-01

The potential influence of methane seeps on carbon cycling is a key question for global assessments, but the study of carbon cycling in surface sediments and the water column of cold seep environments is complicated by the high temporal and spatial variability of fluid and gas fluxes at these sites. In this study we directly examined carbon sources supporting benthic and planktonic food webs at venting methane seeps using isotopic and molecular approaches that integrate this variability. At four seep environments located along North and Central America, microorganisms from two size fractions were collected over several days from 2800 to 9050 l of seawater to provide a time-integrated measure of key microbial groups and the carbon sources supporting the overall planktonic microbial community. In addition to water column measurements, the extent of seafloor methane release was estimated at two of the sites by examining the stable carbon isotopic signature (δ13C) of benthic metazoan infauna. This signature reveals carbon sources fueling the base of the food chain and thus provides a metric that represents a time-integrated view of the dominant microbial processes within the sediment. The stable carbon isotopic composition of microbial DNA (δ13C-DNA), which had values between -17.0 and -19.5‰, indicated that bulk planktonic microbial production was not ultimately linked to methane or other 13C-depleted seep-derived carbon sources. Instead these data support the importance of organic carbon derived from either photo- or chemoautotrophic CO2 fixation to the planktonic food web. Results of qPCR of microbial DNA sequences coding for a subunit of the particulate methane monooxygenase gene (pmoA) showed that only a small percentage of the planktonic microbial community were potential methane oxidizers possessing pmoA (<5% of 16S rRNA gene copies). There was an overall decrease of 13C-depleted carbon fueling the benthic metazoan community from 3 to 5 cm below the seafloor to the sediment surface, reflecting limited use of isotopically depleted carbon at the sediment surface. Rare methane emission as indicated by limited aerobic methane oxidation acts to corroborate our findings for the planktonic microbial community.

Microbial Ecology of Four Coral Atolls in the Northern Line Islands

PubMed Central

Smriga, Steven; Edwards, Robert A.; Angly, Florent; Wegley, Linda; Hatay, Mark; Hall, Dana; Brown, Elysa; Haynes, Matthew; Krause, Lutz; Sala, Enric; Sandin, Stuart A.; Thurber, Rebecca Vega; Willis, Bette L.; Azam, Farooq; Knowlton, Nancy; Rohwer, Forest

2008-01-01

Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated (∼5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems worldwide. PMID:18301735

Microbial ecology of four coral atolls in the Northern Line Islands.

PubMed

Dinsdale, Elizabeth A; Pantos, Olga; Smriga, Steven; Edwards, Robert A; Angly, Florent; Wegley, Linda; Hatay, Mark; Hall, Dana; Brown, Elysa; Haynes, Matthew; Krause, Lutz; Sala, Enric; Sandin, Stuart A; Thurber, Rebecca Vega; Willis, Bette L; Azam, Farooq; Knowlton, Nancy; Rohwer, Forest

2008-02-27

Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated ( approximately 5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems worldwide.

Modelling temporal and spatial dynamics of benthic fauna in North-West-European shelf seas

NASA Astrophysics Data System (ADS)

Lessin, Gennadi; Bruggeman, Jorn; Artioli, Yuri; Butenschön, Momme; Blackford, Jerry

2017-04-01

Benthic zones of shallow shelf seas receive high amounts of organic material. Physical processes such as resuspension, as well as complex transformations mediated by diverse faunal and microbial communities, define fate of this material, which can be returned to the water column, reworked within sediments or ultimately buried. In recent years, numerical models of various complexity and serving different goals have been developed and applied in order to better understand and predict dynamics of benthic processes. ERSEM includes explicit parameterisations of several groups of benthic biota, which makes it particularly applicable for studies of benthic biodiversity, biological interactions within sediments and benthic-pelagic coupling. To assess model skill in reproducing temporal (inter-annual and seasonal) dynamics of major benthic macrofaunal groups, 1D model simulation results were compared with data from the Western Channel Observatory (WCO) benthic survey. The benthic model was forced with organic matter deposition rates inferred from observed phytoplankton abundance and model parameters were subsequently recalibrated. Based on model results and WCO data comparison, deposit-feeders exert clear seasonal variability, while for suspension-feeders inter-annual variability is more pronounced. Spatial distribution of benthic fauna was investigated using results of a full-scale NEMO-ERSEM hindcast simulation of the North-West European Shelf Seas area, covering the period of 1981-2014. Results suggest close relationship between spatial distribution of biomass of benthic faunal functional groups in relation to bathymetry, hydrodynamic conditions and organic matter supply. Our work highlights that it is feasible to construct, implement and validate models that explicitly include functional groups of benthic macrofauna. Moreover, the modelling approach delivers detailed information on benthic biogeochemistry and food-web at spatial and temporal scales that are unavailable through other sources but highly relevant to marine management, planning and policy.

Archive of bacterial community in anhydrite crystals from a deep-sea basin provides evidence of past oil-spilling in a benthic environment in the Red Sea

NASA Astrophysics Data System (ADS)

Wang, Yong; Li, Tie Gang; Wang, Meng Ying; Lai, Qi Liang; Li, Jiang Tao; Gao, Zhao Ming; Shao, Zong Ze; Qian, Pei-Yuan

2016-11-01

In deep-sea sediment, the microbes present in anhydrite crystals are potential markers of the past environment. In the Atlantis II Deep, anhydrite veins were produced by mild mixture of calcium-rich hydrothermal solutions and sulfate in the bottom water, which had probably preserved microbial inhabitants in the past seafloor of the Red Sea. In this study, this hypothesis was tested by analyzing the metagenome of an anhydrite crystal sample from the Atlantis II Deep. The estimated age of the anhydrite layer was between 750 and 770 years, which might span the event of hydrothermal eruption into the benthic floor. The 16S/18S rRNA genes in the metagenome were assigned to bacteria, archaea, fungi and even invertebrate species. The dominant species in the crystals was an oil-degrading Alcanivorax borkumensis bacterium, which was not detected in the adjacent sediment layer. Fluorescence microscopy using 16S rRNA and marker gene probes revealed intact cells of the Alcanivorax bacterium in the crystals. A draft genome of A. borkumensis was binned from the metagenome. It contained all functional genes for alkane utilization and the reduction of nitrogen oxides. Moreover, the metagenomes of the anhydrites and control sediment contained aromatic degradation pathways, which were mostly derived from Ochrobactrum sp. Altogether, these results indicate an oxic, oil-spilling benthic environment in the Atlantis II basin of the Red Sea in approximately the 14th century. The original microbial inhabitants probably underwent a dramatic selection process via drastic environmental changes following the formation of an overlying anoxic brine pool in the basin due to hydrothermal activities.

Extensive metazoan reefs from the Ediacaran Nama Group, Namibia: the rise of benthic suspension feeding.

PubMed

Wood, R; Curtis, A

2015-03-01

We describe new, ecologically complex reef types from the Ediacaran Nama Group, Namibia, dated at ~548 million years ago (Ma), where the earliest known skeletal metazoans, Cloudina riemkeae and Namacalathus, formed extensive reefs up to 20 m in height and width. C. riemkeae formed densely aggregating assemblages associated with microbialite and thrombolite, each from 30 to 100 mm high, which successively colonised former generations to create stacked laminar or columnar reef frameworks. C. riemkeae individuals show budding, multiple, radiating attachment sites and cementation between individuals. Isolated Namacalathus either intergrew with C. riemkeae or formed dense, monospecific aggregations succeeding C. riemkeae frameworks, providing a potential example of environmentally mediated ecological succession. Cloudina and Namacalathus also grow cryptically, either as pendent aggregations from laminar crypt ceilings in microbial framework reefs or as clusters associated with thrombolite attached to neptunian dyke walls. These reefs are notable for their size, exceeding that of the succeeding Lower Cambrian archaeocyath-microbial communities. The repeated colonisation shown by C. riemkeae of former assemblages implies philopatric larval aggregation to colonise limited favourable substrates. As such, not only were skeletal metazoans more important contributors to reef building in the Ediacaran, but there were also more variable reef types with more complex ecologies, than previously thought. Such an abundance of inferred suspension feeders with biomineralised skeletons indicates the efficient exploitation of new resources, more active carbon removal with a strengthened energy flow between planktic and benthic realms, and the rise of biological control over benthic carbonate production. These mark the prelude to the Cambrian Explosion and the modernisation of the global carbon cycle. © 2014 John Wiley & Sons Ltd.

Bioturbation determines the response of benthic ammonia-oxidizing microorganisms to ocean acidification

PubMed Central

Laverock, B.; Kitidis, V.; Tait, K.; Gilbert, J. A.; Osborn, A. M.; Widdicombe, S.

2013-01-01

Ocean acidification (OA), caused by the dissolution of increasing concentrations of atmospheric carbon dioxide (CO2) in seawater, is projected to cause significant changes to marine ecology and biogeochemistry. Potential impacts on the microbially driven cycling of nitrogen are of particular concern. Specifically, under seawater pH levels approximating future OA scenarios, rates of ammonia oxidation (the rate-limiting first step of the nitrification pathway) have been shown to dramatically decrease in seawater, but not in underlying sediments. However, no prior study has considered the interactive effects of microbial ammonia oxidation and macrofaunal bioturbation activity, which can enhance nitrogen transformation rates. Using experimental mesocosms, we investigated the responses to OA of ammonia oxidizing microorganisms inhabiting surface sediments and sediments within burrow walls of the mud shrimp Upogebia deltaura. Seawater was acidified to one of four target pH values (pHT 7.90, 7.70, 7.35 and 6.80) in comparison with a control (pHT 8.10). At pHT 8.10, ammonia oxidation rates in burrow wall sediments were, on average, fivefold greater than in surface sediments. However, at all acidified pH values (pH ≤ 7.90), ammonia oxidation rates in burrow sediments were significantly inhibited (by 79–97%; p < 0.01), whereas rates in surface sediments were unaffected. Both bacterial and archaeal abundances increased significantly as pHT declined; by contrast, relative abundances of bacterial and archaeal ammonia oxidation (amoA) genes did not vary. This research suggests that OA could cause substantial reductions in total benthic ammonia oxidation rates in coastal bioturbated sediments, leading to corresponding changes in coupled nitrogen cycling between the benthic and pelagic realms. PMID:23980243

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.

A Pilot-scale Benthic Microbial Electrochemical System (BMES) for Enhanced Organic Removal in Sediment Restoration

NASA Astrophysics Data System (ADS)

Li, Henan; Tian, Yan; Qu, Youpeng; Qiu, Ye; Liu, Jia; Feng, Yujie

2017-01-01

A benthic microbial electrochemical systems (BMES) of 195 L (120 cm long, 25 cm wide and 65 cm height) was constructed for sediment organic removal. Sediment from a natural river (Ashi River) was used as test sediments in the present research. Three-dimensional anode (Tri-DSA) with honeycomb structure composed of carbon cloth and supporting skeleton was employed in this research for the first time. The results demonstrated that BMES performed good in organic-matter degradation and energy generation from sediment and could be considered for river sediments in situ restoration as novel method. Community analysis from the soil and anode using 16S rDNA gene sequencing showed that more electrogenic functional bacteria was accumulated in anode area when circuit connected than control system.

Environmental Genomic Analysis of Stratified Microbial Communities and Climate Active Gases in the Subarctic Pacific Oxygen Minimum Zone

NASA Astrophysics Data System (ADS)

Wright, J.; Hallam, S.; Merzouk, A.; Tortell, P.

2008-12-01

Oxygen minimum zones (OMZs) are areas of low dissolved oxygen concentrations that play a major role in biogeochemical cycling within the world's oceans. They are major sinks for nitrogen and sources for the greenhouse gases carbon dioxide and nitrous oxide. Therefore, microbial mediated biological activity associated with these systems directly impacts ocean productivity and global climate balance. There is increasing evidence that ocean warming trends will decrease dissolved oxygen concentrations within the coastal and interior regions of the subarctic Pacific, causing an expansion of the hypoxic boundary layer. This expansion will have a direct effect on coastal benthic ecosystems and the productivity of marine fisheries due to habitat loss and changes in nutrient cycling. In order to understand the potential implications of these transitions, we are performing environmental genomic analyses of indigenous microbial communities found in coastal and open ocean OMZs in the subarctic Pacific Ocean in relation to dissolved gas and nutrient concentrations. In addition to identifying and describing the key microbial players and biochemical pathways contributing to carbon, nitrogen and sulfur metabolism within the subarctic Pacific Ocean, this work provides a solid comparative genomic foundation for understanding the biogeochemical processes at work in marine OMZs around the globe.

Infection Paradox: High Abundance but Low Impact of Freshwater Benthic Viruses

PubMed Central

Filippini, Manuela; Buesing, Nanna; Bettarel, Yvan; Sime-Ngando, Télesphore; Gessner, Mark O.

2006-01-01

The discovery of an abundant and diverse virus community in oceans and lakes has profoundly reshaped ideas about global carbon and nutrient fluxes, food web dynamics, and maintenance of microbial biodiversity. These roles are exerted through massive viral impact on the population dynamics of heterotrophic bacterioplankton and primary producers. We took advantage of a shallow wetland system with contrasting microhabitats in close proximity to demonstrate that in marked contrast to pelagic systems, viral infection, determined directly by transmission electron microscopy, and consequently mortality of prokaryotes were surprisingly low in benthic habitats in all seasons. This was true even though free viruses were abundant throughout the year and bacterial infection and mortality rates were high in surrounding water. The habitats in which we found this pattern include sediment, decomposing plant litter, and biofilms on aquatic vegetation. Overall, we detected viruses in only 4 of a total of ∼15,000 bacterial cells inspected in these three habitats; for comparison, nearly 300 of ∼5,000 cells suspended in the water column were infected. The strikingly low incidence of impact of phages in the benthos may have important implications, since a major portion of microbial biodiversity and global carbon and nutrient turnover are associated with surfaces. Therefore, if failure to infect benthic bacteria is a widespread phenomenon, then the global role of viruses in controlling microbial diversity, food web dynamics, and biogeochemical cycles would be greatly diminished compared to predictions based on data from planktonic environments. PMID:16820485

Heterotrophic Protists in Hypersaline Microbial Mats and Deep Hypersaline Basin Water Columns

PubMed Central

Edgcomb, Virginia P.; Bernhard, Joan M.

2013-01-01

Although hypersaline environments pose challenges to life because of the low water content (water activity), many such habitats appear to support eukaryotic microbes. This contribution presents brief reviews of our current knowledge on eukaryotes of water-column haloclines and brines from Deep Hypersaline Anoxic Basins (DHABs) of the Eastern Mediterranean, as well as shallow-water hypersaline microbial mats in solar salterns of Guerrero Negro, Mexico and benthic microbialite communities from Hamelin Pool, Shark Bay, Western Australia. New data on eukaryotic diversity from Shark Bay microbialites indicates eukaryotes are more diverse than previously reported. Although this comparison shows that eukaryotic communities in hypersaline habitats with varying physicochemical characteristics are unique, several groups are commonly found, including diverse alveolates, strameonopiles, and fungi, as well as radiolaria. Many eukaryote sequences (SSU) in both regions also have no close homologues in public databases, suggesting that these environments host unique microbial eukaryote assemblages with the potential to enhance our understanding of the capacity of eukaryotes to adapt to hypersaline conditions. PMID:25369746

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.

Year-round N2O production by benthic NOx reduction in a monomictic south-alpine lake

NASA Astrophysics Data System (ADS)

Freymond, C. V.; Wenk, C. B.; Frame, C. H.; Lehmann, M. F.

2013-12-01

Nitrous oxide (N2O) is a potent greenhouse gas, generated through microbial nitrogen (N) turnover processes, such as nitrification, nitrifier denitrification, and denitrification. Previous studies quantifying natural sources have mainly focused on soils and the ocean, but the potential role of terrestrial water bodies in the global N2O budget has been widely neglected. Furthermore, the biogeochemical controls on the production rates and the microbial pathways that produce benthic N2O in lakes are essentially unknown. In this study, benthic N2O fluxes and the contributions of the microbial pathways that produce N2O were assessed using 15N label flow-through sediment incubations in the eutrophic, monomictic south basin of Lake Lugano in Switzerland. The sediments were a significant source of N2O throughout the year, with production rates ranging between 140 and 2605 nmol N2O h-1 m-2, and the highest observed rates coinciding with periods of water column stratification and stably anoxic conditions in the overlying bottom water. Nitrate (NO3-) reduction via denitrification was found to be the major N2O production pathway in the sediments under both oxygen-depleted and oxygen-replete conditions in the overlying water, while ammonium oxidation did not contribute significantly to the benthic N2O flux. A marked portion (up to 15%) of the total NO3- consumed by denitrification was reduced only to N2O, without complete denitrification to N2. These fluxes were highest when the bottom water had stabilized to a low-oxygen state, in contrast with the notion that stable anoxia is particularly conducive to complete denitrification without accumulation of N2O. This study provides evidence that lake sediments are a significant source of N2O to the overlying water and may produce large N2O fluxes to the atmosphere during seasonal mixing events.

Seasonal relationships between planktonic microorganisms and dissolved organic material in an alpine stream

USGS Publications Warehouse

McKnight, Diane M.; Smith, R.L.; Harnish, R.A.; Miller, C.L.; Bencala, K.E.

1993-01-01

The relationships between the abundance and activity of planktonic, heterotrophic microorganisms and the quantity and characteristics of dissolved organic carbon (DOC) in a Rocky Mountain stream were evaluated. Peak values of glucose uptake, 2.1 nmol L-1 hr-1, and glucose concentration, 333 nM, occurred during spring snowmelt when the water temperature was 4.0??C and the DOC concentration was greatest. The turnover time of the in situ glucose pool ranged seasonally from 40-1110 hours, with a mean of 272 hr. Seasonal uptake of3H-glucose, particulate ATP concentrations, and direct counts of microbial biomass were independent of temperature, but were positively correlated with DOC concentrations and negatively correlated with stream discharge. Heterotrophic activity in melted snow was generally low, but patchy. In the summer, planktonic heterotrophic activity and microbial biomass exhibited small-scale diel cycles which did not appear to be related to fluctuations in discharge or DOC, but could be related to the activity of benthic invertebrates. Leaf-packs placed under the snow progressively lost weight and leachable organic material during the winter, indicating that the annual litterfall in the watershed may be one source of the spring flush of DOC. These results indicate that the availability of labile DOC to the stream ecosystem is the primary control on seasonal variation in heterotrophic activity of planktonic microbial populations. ?? 1993 Kluwer Academic Publishers.

Influence of Sedimentary and Seagrass Microbial Communities on Shallow-Water Benthic Optical Properties

DTIC Science & Technology

2008-09-30

grass, Thalassia testudinum) and in Monterey Bay (eel grass, Zostera marina). Assess how the microbial community affects the flux of photons to and...optical properties and photosynthetic potential of the seagrasses Thalassia testudinum and Zostera marina”. The manuscript will be submitted to the...crystals in Thalassia from LSI. We have pursued this serendipitous discovery, and at the Estuarine Research Federation meeting this fall, we will

Stability characterization and modeling of robust distributed benthic microbial fuel cell (DBMFC) system.

PubMed

Karra, Udayarka; Huang, Guoxian; Umaz, Ridvan; Tenaglier, Christopher; Wang, Lei; Li, Baikun

2013-09-01

A novel and robust distributed benthic microbial fuel cell (DBMFC) was developed to address the energy supply issues for oceanographic sensor network applications, especially under scouring and bioturbation by aquatic life. Multi-anode/cathode configuration was employed in the DBMFC system for enhanced robustness and stability in the harsh ocean environment. The results showed that the DBMFC system achieved peak power and current densities of 190mW/m(2) and 125mA/m(2) respectively. Stability characterization tests indicated the DBMFC with multiple anodes achieved higher power generation over the systems with single anode. A computational model that integrated physical, electrochemical and biological factors of MFCs was developed to validate the overall performance of the DBMFC system. The model simulation well corresponded with the experimental results, and confirmed the hypothesis that using a multi anode/cathode MFC configuration results in reliable and robust power generation. Published by Elsevier Ltd.

Benthic biological and biogeochemical patterns and processes across an oxygen minimum zone (Pakistan margin, NE Arabian Sea)

NASA Astrophysics Data System (ADS)

Cowie, Gregory L.; Levin, Lisa A.

2009-03-01

Oxygen minimum zones (OMZs) impinging on continental margins present sharp gradients ideal for testing environmental factors thought to influence C cycling and other benthic processes, and for identifying the roles that biota play in these processes. Here we introduce the objectives and initial results of a multinational research program designed to address the influences of water depth, the OMZ (˜150-1300 m), and organic matter (OM) availability on benthic communities and processes across the Pakistan Margin of the Arabian Sea. Hydrologic, sediment, and faunal characterizations were combined with in-situ and shipboard experiments to quantify and compare biogeochemical processes and fluxes, OM burial efficiency, and the contributions of benthic communities, across the OMZ. In this introductory paper, we briefly review previous related work in the Arabian Sea, building the rationale for integrative biogeochemical and ecological process studies. This is followed by a summary of individual volume contributions and a brief synthesis of results. Five primary stations were studied, at 140, 300, 940, 1200 and 1850 m water depth, with sampling in March-May (intermonsoon) and August-October (late-to-postmonsoon) 2003. Taken together, the contributed papers demonstrate distinct cross-margin gradients, not only in oxygenation and sediment OM content, but in benthic community structure and function, including microbial processes, the extent of bioturbation, and faunal roles in C cycling. Hydrographic studies demonstrated changes in the intensity and extent of the OMZ during the SW monsoon, with a shoaling of the upper OMZ boundary that engulfed the previously oxygenated 140-m site. Oxygen profiling and microbial process rate determinations demonstrated dramatic differences in oxygen penetration and consumption across the margin, and in the relative importance of anaerobic processes, but surprisingly little seasonal change. A broad maximum in sediment OM content occurred on the upper slope, roughly coincident with the OMZ; but the otherwise poor correlation with bottom-water oxygen concentrations indicated that other factors are important in determining sediment OM distributions. Downcore profiles generally showed little clear evidence of in-situ OM alteration, and there was little sign of OM enrichment resulting from the southwest monsoon in sediments collected in the late-to-postmonsoon sampling. This is interpreted to be due to rapid cycling of labile OM. Organic geochemical studies confirmed that sediment OM is overwhelmingly of marine origin across the margin, but also that it is heavily altered, with only small changes in degradation state across the OMZ. More negative stable C isotopic compositions in surficial sediments at hypoxic sites within the OMZ core are attributed to a chemosynthetic bacterial imprint. Dramatic changes in benthic community structure occurred across the lower OMZ transition, apparently related to OM availability and quality as well as to DO concentrations. High-resolution sampling, biomarkers and isotope tracer studies revealed that oxygen availability appears to exert threshold-type controls on benthic community structure and early faunal C processing. Biomarker studies also provided evidence of faunal influence on sediment OM composition. Together, the results offer strong evidence that benthic fauna at sites across the margin play important roles in the early cycling of sediment OM through differential feeding and bioturbation activities.

Role of macrofauna on benthic oxygen consumption in sandy sediments of a high-energy tidal beach

NASA Astrophysics Data System (ADS)

Charbonnier, Céline; Lavesque, Nicolas; Anschutz, Pierre; Bachelet, Guy; Lecroart, Pascal

2016-06-01

Sandy beaches exposed to tide and waves are characterized by low abundance and diversity of benthic macrofauna, because of high-energy conditions. This is the reason why there are few studies on benthic communities living in such highly dynamic environments. It has been shown recently that tidal sandy beaches may act as biogeochemical reactors. Marine organic matter that is supplied in the sand during each flood tide is efficiently mineralized through aerobic respiration. In order to quantify the role of macrofauna in the whole beach benthic respiration, we studied the macrofauna and the pore water oxygen content of an exposed sandy beach (Truc Vert, SW of France) during four seasons in 2011. The results showed that macrofauna was characterised by a low number of species of specialized organisms such as the crustaceans Eurydice naylori and Gastrosaccus spp. and the polychaetes Ophelia bicornis and Scolelepis squamata. The distribution and abundance of macrofauna were clearly affected by exposure degree and emersion time. The combined monitoring of benthic macrofauna and pore waters chemistry allowed us to estimate (1) the macrofauna oxygen uptake, calculated with a standard allometric relationship using biomass data, and (2) the total benthic oxygen uptake, calculated from the oxygen deficit measured in pore waters. This revealed that benthic macrofauna respiration represented a variable but low (<10%) contribution to the total benthic oxygen consumption. This suggests that oxygen was mainly consumed by microbial respiration.

Ocean Microbial Fuel Cell: Power Source and Research Tool for Studying Marine Biogeochemistry

NASA Astrophysics Data System (ADS)

Reimers, C. E.; Girguis, P.; Westall, J. C.; Nielsen, M. E.

2007-05-01

Ocean microbial fuel cells (OMFCs) are devices capable of producing modest levels of electrical power. The cells are ultimately driven by the oxidation of marine organic matter at the anode and reduction of dissolved oxygen at the cathode, but microbial transformations and electrochemically active intermediates play important roles in the overall process of electricity generation. By separating the factors that affect the performance of OMFCs into components of an equivalent circuit and manipulating these factors in laboratory and field experiments, we are gaining new insight into how specific redox reactions, sources of organic matter, and mass transport at small and intermediate scales may enrich environments with certain groups of microorganisms that in turn regulate anaerobic organic matter degradation. This talk will illustrate these relationships with the results from at least four experiments in which either fresh plankton, or substrates within continental margin sediments, fuelled the OMFCs. In each example, reduced sulfur compounds were found to be major electron carriers to the fuel cell anode. These intermediates came from a variety of sources including sulfide generated from sulfate reduction in mixed solutions surrounding the electrode, sulfide generated distally but transported by pore-water diffusion and advection, iron monosulfides and pyrite present is a sediment matrix centimeters from the electrode, and sulfide or polysulfide produced within an electrode biofilm. To illustrate a practical application of an OMFC, we are currently constructing a benthic cell that will power a sonic receiver in a network of underwater sensors. The form of this OMFC resembles a benthic chamber with a footprint of one square meter. It should be capable of supplying electrical power and regulating its output for years to decades.

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

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.

Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway

PubMed Central

2018-01-01

ABSTRACT Growing demands for potable water have led to extensive reliance on waterways in tropical megacities. Attempts to manage these waterways in an environmentally sustainable way generally lack an understanding of microbial processes and how they are influenced by urban factors, such as land use and rain. Here, we describe the composition and functional potential of benthic microbial communities from an urban waterway network and analyze the effects of land use and rain perturbations on these communities. With a sequence depth of 3 billion reads from 48 samples, these metagenomes represent nearly full coverage of microbial communities. The predominant taxa in these waterways were Nitrospira and Coleofasciculus, indicating the presence of nitrogen and carbon fixation in this system. Gene functions from carbohydrate, protein, and nucleic acid metabolism suggest the presence of primary and secondary productivity in such nutrient-deficient systems. Comparison of microbial communities by land use type and rain showed that while there are significant differences in microbial communities in land use, differences due to rain perturbations were rain event specific. The more diverse microbial communities in the residential areas featured a higher abundance of reads assigned to genes related to community competition. However, the less diverse communities from industrial areas showed a higher abundance of reads assigned to specialized functions such as organic remediation. Finally, our study demonstrates that microbially diverse populations in well-managed waterways, where contaminant levels are within defined limits, are comparable to those in other relatively undisturbed freshwater systems. IMPORTANCE Unravelling the microbial metagenomes of urban waterway sediments suggest that well-managed urban waterways have the potential to support diverse sedimentary microbial communities, similar to those of undisturbed natural freshwaters. Despite the fact that these urban waterways are well managed, our study shows that environmental pressures from land use and rain perturbations play a role in shaping the structure and functions of microbial communities in these waterways. We propose that although pulsed disturbances, such as rain perturbations, influence microbial communities, press disturbances, including land usage history, have a long-term and stronger influence on microbial communities. Our study found that the functions of microbial communities were less affected by environmental factors than the structure of microbial communities was, indicating that core microbial functions largely remain conserved in challenging environments. PMID:29896568

Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway.

PubMed

Saxena, Gourvendu; Mitra, Suparna; Marzinelli, Ezequiel M; Xie, Chao; Wei, Toh Jun; Steinberg, Peter D; Williams, Rohan B H; Kjelleberg, Staffan; Lauro, Federico M; Swarup, Sanjay

2018-01-01

Growing demands for potable water have led to extensive reliance on waterways in tropical megacities. Attempts to manage these waterways in an environmentally sustainable way generally lack an understanding of microbial processes and how they are influenced by urban factors, such as land use and rain. Here, we describe the composition and functional potential of benthic microbial communities from an urban waterway network and analyze the effects of land use and rain perturbations on these communities. With a sequence depth of 3 billion reads from 48 samples, these metagenomes represent nearly full coverage of microbial communities. The predominant taxa in these waterways were Nitrospira and Coleofasciculus , indicating the presence of nitrogen and carbon fixation in this system. Gene functions from carbohydrate, protein, and nucleic acid metabolism suggest the presence of primary and secondary productivity in such nutrient-deficient systems. Comparison of microbial communities by land use type and rain showed that while there are significant differences in microbial communities in land use, differences due to rain perturbations were rain event specific. The more diverse microbial communities in the residential areas featured a higher abundance of reads assigned to genes related to community competition. However, the less diverse communities from industrial areas showed a higher abundance of reads assigned to specialized functions such as organic remediation. Finally, our study demonstrates that microbially diverse populations in well-managed waterways, where contaminant levels are within defined limits, are comparable to those in other relatively undisturbed freshwater systems. IMPORTANCE Unravelling the microbial metagenomes of urban waterway sediments suggest that well-managed urban waterways have the potential to support diverse sedimentary microbial communities, similar to those of undisturbed natural freshwaters. Despite the fact that these urban waterways are well managed, our study shows that environmental pressures from land use and rain perturbations play a role in shaping the structure and functions of microbial communities in these waterways. We propose that although pulsed disturbances, such as rain perturbations, influence microbial communities, press disturbances, including land usage history, have a long-term and stronger influence on microbial communities. Our study found that the functions of microbial communities were less affected by environmental factors than the structure of microbial communities was, indicating that core microbial functions largely remain conserved in challenging environments.

Response of estuarine biofilm microbial community development to changes in dissolved oxygen and nutrient concentrations.

PubMed

Nocker, Andreas; Lepo, Joe Eugene; Martin, Linda Lin; Snyder, Richard Allan

2007-10-01

The information content and responsiveness of microbial biofilm community structure, as an integrative indicator of water quality, was assessed against short-term changes in oxygen and nutrient loading in an open-water estuarine setting. Biofilms were grown for 7-day periods on artificial substrates in the Pensacola Bay estuary, Florida, in the vicinity of a wastewater treatment plant (WWTP) outfall and a nearby reference site. Substrates were deployed floating at the surface and near the benthos in 5.4 m of water. Three sampling events covered a 1-month period coincident with declining seasonal WWTP flow and increasing dissolved oxygen (DO) levels in the bottom waters. Biomass accumulation in benthic biofilms appeared to be controlled by oxygen rather than nutrients. The overriding effect of DO was also seen in DNA fingerprints of community structure by terminal restriction fragment length polymorphism (T-RFLP) of amplified 16S rRNA genes. Ribotype diversity in benthic biofilms at both sites dramatically increased during the transition from hypoxic to normoxic. Terminal restriction fragment length polymorphism patterns showed pronounced differences between benthic and surface biofilm communities from the same site in terms of signal type, strength, and diversity, but minor differences between sites. Sequencing of 16S rRNA gene clone libraries from benthic biofilms at the WWTP site suggested that low DO levels favored sulfate-reducing prokaryotes (SRP), which decreased with rising oxygen levels and increasing overall diversity. A 91-bp ribotype in the CfoI-restricted 16S rRNA gene T-RFLP profiles, indicative of SRP, tracked the decrease in relative SRP abundance over time.

Sediment Microbial Community Dynamics and Geochemistry During Oxic and Hypoxic Periods in the Gulf of Mexico

EPA Science Inventory

Seasonal hypoxia in the benthic waters of the Louisiana Coastal Shelf contributes to the Gulf of Mexico "dead zone" phenomena. Limited information is available on sedimentary biogeochemical interactions during periods of hypoxia.

Potential impact of global climate change on benthic deep-sea microbes.

PubMed

Danovaro, Roberto; Corinaldesi, Cinzia; Dell'Anno, Antonio; Rastelli, Eugenio

2017-12-15

Benthic deep-sea environments are the largest ecosystem on Earth, covering ∼65% of the Earth surface. Microbes inhabiting this huge biome at all water depths represent the most abundant biological components and a relevant portion of the biomass of the biosphere, and play a crucial role in global biogeochemical cycles. Increasing evidence suggests that global climate changes are affecting also deep-sea ecosystems, both directly (causing shifts in bottom-water temperature, oxygen concentration and pH) and indirectly (through changes in surface oceans' productivity and in the consequent export of organic matter to the seafloor). However, the responses of the benthic deep-sea biota to such shifts remain largely unknown. This applies particularly to deep-sea microbes, which include bacteria, archaea, microeukaryotes and their viruses. Understanding the potential impacts of global change on the benthic deep-sea microbial assemblages and the consequences on the functioning of the ocean interior is a priority to better forecast the potential consequences at global scale. Here we explore the potential changes in the benthic deep-sea microbiology expected in the coming decades using case studies on specific systems used as test models. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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 activities at the benthic boundary layer in the Aegean Sea

NASA Astrophysics Data System (ADS)

Bianchi, A.; Tholosan, O.; Garcin, J.; Polychronaki, T.; Tselepides, A.; Buscail, R.; Duineveld, G.

2003-05-01

During the Aegean Sea component of the EU MTP-MATER project, benthic samples were acquired along a depth gradient from two continental margins in the Aegean Sea. Sampling was undertaken during spring and summer 1997 and the microbial metabolic activities measured (Vmax for aminopeptidase activity, 14C-glutamate respiration and assimilation) displayed seasonal variability even in deep-sea conditions. The metabolic rates encountered in the North Aegean (average depth 566±234 m), were approximately five-fold higher than in the deeper (1336±140 m) Southern part of the Aegean. The aminopeptidase rates, however, were the exception with higher values recorded in the more oligotrophic sediments of the Southern stations (1383±152 vs. 766±297 nmol MCA cm-2 h-1). A discrepancy in bacterial metabolism also appeared in the near bottom waters. In the Southern stations, 80% of the glutamate uptake was used for energy yielding processes and only 20% devoted to biomass production, while in the North Aegean, most of the used glutamate was incorporated into bacterial cells. During the early burial stages, bacterial mineralization rates estimated from 14C-glutamate respiration decreased drastically compared to the rates of biopolymer hydrolysis estimated by aminopeptidase assays. Thus, at the 2-cm depth layer, these rates were only 32 and up to 77% of the corresponding average values, respectively, in the superficial layer. Such a discrepancy between the evolution of these two metabolic activities is possibly due to the rapid removal of readily utilizable monomers in the surface deposits. The correlation between bacterial respiration and total organic carbon, or total organic nitrogen, is higher in the surficial sediment (0-2 and 2-4 cm) than in the underlying layer. Conversely, it is only at 4-cm depth layer that the hydrolysis rates appear correlated with organic carbon and nitrogen concentrations. This pattern confirms the drastic degradation of organic matter during the early burial stages.

Effects of Triclosan on Marine Benthic and Epibenthic Organisms

EPA Science Inventory

Triclosan is an anti-microbial and anti-bacterial compound that has been widely used since the 1970s in consumer products, such as toothpaste, deodorant, and shampoo. Due to its widespread use, triclosan has been detected in various environmental media including wastewater sludg...

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.

Epiphytic cyanobacteria of the seagrass Cymodocea rotundata: diversity, diel nifH expression and nitrogenase activity.

PubMed

Hamisi, Mariam; Díez, Beatriz; Lyimo, Thomas; Ininbergs, Karolina; Bergman, Birgitta

2013-06-01

Seagrasses are photoautotrophic, ecologically important components of many globally widespread coastal ecosystems, in which combined nitrogen may limit their production. We examined the biodiversity and diazotrophic capacity of microbial epiphytes associated with the phyllosphere of the seagrass Cymodocea rotundata of the Western Indian Ocean. Light microscopy, 16S rRNA and nifH gene analysis revealed the dominance of cyanobacteria in the epiphytic microbial community. Most phylotypes were related to free-living uncultured benthic cyanobacteria, while some to cyanobacterial endosymbionts of marine diatoms. Novel and potentially diazotrophic species, some of known pantropical distribution, were also discovered. Significant diel nitrogenase activities (acetylene reduction assay) were recorded (up to 358 ± 232 nmol C2H4 g(-1) of seagrass FW h(-1)). The nifH gene expression patterns showed that heterocystous phylotypes may be the dominant diazotrophs during the day and non-heterocystous at night. These data show that C. rotundata is colonized by diverse diazotrophic cyanobacteria species and suggest that these may be beneficial partners of seagrasses in nitrogen-depleted waters. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Benthic methylmercury production in lacustrine ecosystems of Nahuel Huapi National Park, Patagonia, Argentina

USGS Publications Warehouse

Ribeiro, Guevara S.; Catan, S.P.; Marvin-DiPasquale, M.

2009-01-01

Seasonal trends of benthic methylmercury (methyl-Hg) production were examined in both littoral and open water sites of three lakes (Escondido, Moreno, and Morenito) in the North Andean Patagonia region of Argentina. Potentials of methyl-Hg production were measured by amending sediment samples with inorganic 197Hg(II), incubating for either 24 and 32 h at room temperature, and subsequently assaying the radiolabelled organomercury produced. Seasonal variations of benthic methyl-Hg production were studied but no significant correlation was observed. Lake littoral sites exhibited up to two fold higher methyl-Hg production potentials in most cases. Sediment from lakes Moreno and Morenito generally exhibited much lower (up to 10 fold) methyl-Hg production potentials than those from Lake Escondido, possibly due to differences in particulate and dissolved organic matter quantity and quality, which is higher in Lake Escondido and primarily allochthonous, whereas in lakes Moreno and Morenito is primarily autochthonous. This study represents the first to directly examine benthic microbial Hg(II)-methylation in aquatic ecosystems of Patagonia. ?? 2009 Elsevier Ltd. All rights reserved.

The natural diet of a hexactinellid sponge: Benthic pelagic coupling in a deep-sea microbial food web

NASA Astrophysics Data System (ADS)

Pile, Adele J.; Young, Craig M.

2006-07-01

Dense communities of shallow-water suspension feeders are known to sidestep the microbial loop by grazing on ultraplankton at its base. We quantified the diet, rates of water processing, and abundance of the deep-sea hexactinellid sponge Sericolophus hawaiicus, and found that, like their demosponge relatives in shallow water, hexactinellids are a significant sink for ultraplankton. S. hawaiicus forms a dense bed of sponges on the Big Island of Hawaii between 360 and 460 m depth, with a mean density of 4.7 sponges m -2. Grazing of S. hawaiicus on ultraplankton was quantified from in situ samples using flow cytometry, and was found to be unselective. Rates of water processing were determined with dye visualization and ranged from 1.62 to 3.57 cm s -1, resulting in a processing rate of 7.9±2.4 ml sponge -1 s -1. The large amount of water processed by these benthic suspension feeders results in the transfer of approximately 55 mg carbon and 7.3 mg N d -1 m -2 from the water column to the benthos. The magnitude of this flux places S. hawaiicus squarely within the functional group of organisms that link the pelagic microbial food web to the benthos.

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.

Rates of total oxygen uptake of sediments and benthic nutrient fluxes measured using an in situ autonomous benthic chamber in the sediment of the slope off the southwestern part of Ulleung Basin, East Sea

NASA Astrophysics Data System (ADS)

Lee, Jae Seong; An, Sung-Uk; Park, Young-Gyu; Kim, Eunsoo; Kim, Dongseon; Kwon, Jung No; Kang, Dong-Jin; Noh, Jae-Hoon

2015-09-01

We have developed a new autonomous benthic lander for deep-sea research, the Korea Institute of Ocean Science and Technology (KIOST) Belc II and Belp II. The benthic lander was successfully tested at 950 and 1450 m water depths on the slope off the southwestern part of the Ulleung Basin in the East Sea of Korea. The ex situ measurements of the total oxygen uptake (TOU) rates at all the stations exceeded the in situ measurement values, and may indicate artificial effects from onboard incubation. The TOU rates were estimated to be 5.80 mmol m-2 d-1 and 3.77 mmol m-2 d-1 at water depths of 950 m and 1450 m, respectively. The benthic nutrient fluxes were also higher at water depths of 950 m, which indicates a partitioning of organic degradation with water depth. In addition, the negative phosphate and nitrogen benthic flux ratios and the higher nitrate removal flux via the sediment-water interface at the slope imply that the nitrogen in the bottom water may be preferentially removed via microbial respiration processes in the sediments, and may be coupled with the low nitrogen-to-phosphate ratio found in the deep water. Although our measurements comprised just two experiments in the slope sediment, the robust in situ measurement of the benthic fluxes in the slope sediment is a forerunner for new research into the biogeochemical cycles across the shelf edge-slope-basin system in the East Sea.

Rates of total oxygen uptake of sediments and benthic nutrient fluxes measured by an in situ autonomous benthic chamber in the sediment of the slope off the southwestern part of Ulleung Basin, East Sea

NASA Astrophysics Data System (ADS)

Lee, J. S.; An, S. U.; Park, Y. G.; Kim, E.; Kim, D.; Kwon, J. N.; Kang, D. J.; Noh, J. H.

2016-02-01

We have developed a new autonomous benthic lander for deep-sea research, the Korea Institute of Ocean Science and Technology (KIOST) BelcII and BelpII. The benthic lander was successfully tested at 950 and 1450 m water depths on the slope off the southwestern part of the Ulleung Basin in the East Sea of Korea. The ex situ measurements of the total oxygen uptake (TOU) rates at all the stations exceeded the in situ measurement values, and may indicate artificial effects from onboard incubation. The TOU rates were estimated to be 5.80 mmol m-2 d-1 and 3.77 mmol m-2 d-1 at water depths of 950 m and 1450 m, respectively. The benthic nutrient fluxes were also higher at water depths of 950 m, which indicates a partitioning of organic degradation with water depth. In addition, the negative phosphate and nitrogen benthic flux ratios and the higher nitrate removal flux via the sediment-water interface at the slope imply that the nitrogen in the bottom water may be preferentially removed via microbial respiration processes in the sediments, and may be coupled with the low nitrogen-to-phosphate ratio found in the deep water. Although our measurements comprised just two experiments in the slope sediment, the robust in situ measurement of the benthic fluxes in the slope sediment is a forerunner for new research into the biogeochemical cycles across the shelf edge- slope-basin system in the East Sea.

Diatoms in sediments of perennially ice-covered Lake Hoare, and implications for interpreting lake history in the McMurdo Dry Valleys of Antarctica

USGS Publications Warehouse

Spaulding, S.A.; McKnight, Diane M.; Stoermer, E.F.; Doran, P.T.

1997-01-01

Diatom assemblages in surficial sediments, sediment cores, sediment traps, and inflowing streams of perennially ice-covered Lake Hore, South Victorialand, Antarctica were examined to determine the distribution of diatom taxa, and to ascertain if diatom species composition has changed over time. Lake Hoare is a closed-basin lake with an area of 1.8 km2, maximum depth of 34 m, and mean depth of 14 m, although lake level has been rising at a rate of 0.09 m yr-1 in recent decades. The lake has an unusual regime of sediment deposition: coarse grained sediments accumulate on the ice surface and are deposited episodically on the lake bottom. Benthic microbial mats are covered in situ by the coarse episodic deposits, and the new surfaces are recolonized. Ice cover prevents wind-induced mixing, creating the unique depositional environment in which sediment cores record the history of a particular site, rather than a lake=wide integration. Shallow-water (<1 m) diatom assemblages (Stauroneis anceps, Navicula molesta, Diadesmis contenta var. parallela, Navicula peraustralis) were distinct from mid-depth (4-16 m) assemblages (Diadesmis contenta, Luticola muticopsis fo. reducta, Stauroneis anceps, Diadesmis contenta var. parallela, Luticola murrayi) and deep-water (2-31 m) assemblages (Luticola murrayi, Luticola muticopsis fo. reducta, Navicula molesta. Analysis of a sediment core (30 cm long, from 11 m water depth) from Lake Hoare revealed two abrupt changes in diatom assemblages. The upper section of the sediment core contained the greatest biomass of benthic microbial mat, as well as the greatest total abundance and diversity of diatoms. Relative abundances of diatoms in this section are similar to the surficial samples from mid-depths. An intermediate zone contained less organic material and lower densities of diatoms. The bottom section of core contained the least amount of microbial mat and organic material, and the lowest density of diatoms. The dominant process influencing species composition and abundance of diatom assemblages in the benthic microbial mats is episodic deposition of coarse sediment from the ice surface.

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.

An ecological model of the Northern and Central Adriatic Sea: Analysis of ecosystem structure and fishing impacts

NASA Astrophysics Data System (ADS)

Coll, Marta; Santojanni, Alberto; Palomera, Isabel; Tudela, Sergi; Arneri, Enrico

2007-08-01

A trophic mass-balance model was developed to characterise the food web structure and functioning of the Northern and Central Adriatic Sea and to quantify the ecosystem impacts of fishing during the 1990s. Forty functional groups were described, including target and non-target fish and invertebrate groups, and three detritus groups (natural detritus, discards and by-catch of cetaceans and marine turtles). Results highlighted that there was an important coupling between pelagic-benthic production of plankton, benthic invertebrates and detritus. Organisms located at low and medium trophic levels, (i.e. benthic invertebrates, zooplankton and anchovy), as well as dolphins, were identified as keystone groups of the ecosystem. Jellyfish were an important element in terms of consumption and production of trophic flows within the ecosystem. The analysis of trophic flows of zooplankton and detritus groups indirectly underlined the importance of the microbial food web in the Adriatic Sea. Fishing activities inflicted notable impacts on the ecosystem during the 1990s, with a high gross efficiency of the fishery, a high consumption of fishable production, high exploitation rates for various target and non target species, a low trophic level of the catch and medium values of primary production required to sustain the fishery. Moreover, the analysis of Odum's ecological indicators highlighted that the ecosystem was in a low-medium developmental stage. Bottom trawling ( Strascico), mid-water trawling ( Volante) and beam trawling ( Rapido) fleets had the highest impacts on both target and non target ecological groups. On the contrary, purse seining ( Lampara) showed medium to low impacts on the ecosystem; cetaceans, marine turtles and sea birds were not significantly involved in competition with fishing activity.

Crustose coralline algae and associated microbial biofilms deter seaweed settlement on coral reefs

NASA Astrophysics Data System (ADS)

Gomez-Lemos, Luis A.; Diaz-Pulido, Guillermo

2017-06-01

Crustose coralline algae (CCA), a group of calcifying red algae found commonly in benthic marine ecosystems worldwide, perform essential ecological functions on coral reefs, including creating benthic substrate, stabilizing the reef structure and inducing coral settlement. An important feature of CCA is the ability to keep their surfaces free of epiphytic algae, thereby reducing algal overgrowth and allowing them access to light. However, the mechanisms by which CCA prevent settlement of opportunistic seaweeds (fleshy macroalgae) are not fully understood, nor is whether these mechanisms vary among CCA species. In our study based on the Great Barrier Reef, we demonstrate that three common CCA species ( Titanoderma pustulatum, Porolithon onkodes and Neogoniolithon sp.) have a remarkable ability to deter settlement of seaweed spores. We provide experimental evidence that the CCA use allelopathy and microbial inhibition against the settlement of spores of the brown seaweed Padina boergesenii. Methanol extracts of allelopathic compounds from T. pustulatum, Po. onkodes and Neogoniolithon sp. significantly reduced the settlement of Pa. boergesenii spores by 4.3 times, 3.0 and 3.8 times, respectively. Further, we found that microbial biofilms, while having a lower inhibitory effect than allelopathic compounds, also reduced seaweed settlement of Pa. boergesenii. Our study demonstrates that allelopathy and microbial inhibition, in addition to epithallial tissue sloughing, are mechanisms employed by CCA to prevent the settlement of epiphytic algae. Understanding the mechanisms by which CCA avoid seaweed overgrowth contributes to our understanding of the dynamics of seaweed proliferations on reefs and to the ecological knowledge of this important group of reef-building organisms.

Sinkhole-like structures as bioproductivity hotspots in the Abrolhos Bank

NASA Astrophysics Data System (ADS)

Cavalcanti, Giselle S.; Gregoracci, Gustavo B.; Longo, Leila de L.; Bastos, Alex C.; Ferreira, Camilo M.; Francini-Filho, Ronaldo B.; Paranhos, Rodolfo; Ghisolfi, Renato D.; Krüger, Ricardo; Güth, Arthur Z.; Sumida, Paulo Y. G.; Bruce, Thiago; Maia-Neto, Oswaldo; de O. Santos, Eidy; Iida, Tetsuya; Moura, Rodrigo L.; Amado-Filho, Gilberto M.; Thompson, Fabiano L.

2013-11-01

We performed a biological survey in the novel system of sinkhole-like structures ("buracas") of the Abrolhos Bank, Brazil. We found dissimilar benthic assemblages and higher nutrient concentration, microbial abundance (and activity) and fish abundance inside the buracas than in the surrounding rhodolith beds. Our results support the view that these cup-shaped structures trap and accumulate organic matter, functioning as productivity hotspots in the mid and outer shelf of the central portion of the Abrolhos Bank shelf, where they aggregate biomass of commercially important fishes. This distinctive system is being increasingly pressured by commercial fisheries and needs urgent management measures such as fishing effort control and representation in the network of Marine Protected Areas (MPAS).

Questioning the Origin of the Great Salt Lake "Microbialites"

NASA Astrophysics Data System (ADS)

Frantz, C.; Matyjasik, M.; Newell, D. L.; Vanden Berg, M. D.; Park, C.

2017-12-01

The Great Salt Lake (GSL) of Utah contains abundant carbonate mounds that have been described in the literature as "biostromes", "bioherms", "stromatolites", and "microbialites". The structures are commonly cited as being rare examples of modern lacustrine microbialites, which implies that they are actively-forming and biogenic. Indeed, at least in some regions of the lake, the mounds are covered in a mixed community of cyanobacteria, algae, insect larval casings, microbial heterotrophs, and other organisms that is thought to contribute significantly to benthic primary productivity in GSL. However, the presence of a modern surface microbial community does not implicate a biogenic or modern origin for the mounds. The few studies to date GSL microbialites indicate that they are ancient, with radiocarbon calendar ages in the late Pleistocene and Holocene ( 13 - 3 cal ka). However, could they still be actively growing, and are the surface microbial communities playing a role? Here, we present results of a suite geochemical measurements used to constrain parameters—including groundwater seepage—influencing carbonate saturation and precipitation in the vicinity of one currently-submerged "microbialite reef" on the northern shore of Antelope Island in the South Arm of GSL. Our data suggests that calcium-charged brackish groundwater input to the lake through a permeable substratum in this location results in locally supersaturated conditions for aragonite, which could lead to modern, abiogenic mineralization. In addition, a series of laboratory experiments suggest that the modern surface microbial communities that coat the mounds do not appreciably facilitate carbonate precipitation in simulated GSL conditions, although they may serve as a template for precipitation when local waters become supersaturated.

A microbial role in the construction of Mono Lake carbonate chimneys?

PubMed

Brasier, Alexander; Wacey, David; Rogerson, Mike; Guagliardo, Paul; Saunders, Martin; Kellner, Siri; Mercedes-Martin, Ramon; Prior, Tim; Taylor, Colin; Matthews, Anna; Reijmer, John

2018-06-09

Lacustrine carbonate chimneys are striking, metre-scale constructions. If these were bioinfluenced constructions, they could be priority targets in the search for early and extraterrestrial microbial life. However, there are questions over whether such chimneys are built on a geobiological framework or are solely abiotic geomorphological features produced by mixing of lake and spring waters. Here, we use correlative microscopy to show that microbes were living around Pleistocene Mono Lake carbonate chimneys during their growth. A plausible interpretation, in line with some recent works by others on other lacustrine carbonates, is that benthic cyanobacteria and their associated extracellular organic material (EOM) formed tubular biofilms around rising sublacustrine spring vent waters, binding calcium ions and trapping and binding detrital silicate sediment. Decay of these biofilms would locally have increased calcium and carbonate ion activity, inducing calcite precipitation on and around the biofilms. Early manganese carbonate mineralisation was directly associated with cell walls, potentially related to microbial activity though the precise mechanism remains to be elucidated. Much of the calcite crystal growth was likely abiotic, and no strong evidence for either authigenic silicate growth or a clay mineral precursor framework was observed. Nevertheless, it seems likely that the biofilms provided initial sites for calcite nucleation and encouraged the primary organised crystal growth. We suggest that the nano-, micro- and macroscale fabrics of these Pleistocene Mono Lake chimneys were affected by the presence of centimetre-thick tubular and vertically stacked calcifying microbial mats. Such carbonate chimneys represent a promising macroscale target in the exploration for ancient or extraterrestrial life. © 2018 John Wiley & Sons Ltd.

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

Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru

PubMed Central

Biddle, Jennifer F.; Lipp, Julius S.; Lever, Mark A.; Lloyd, Karen G.; Sørensen, Ketil B.; Anderson, Rika; Fredricks, Helen F.; Elvert, Marcus; Kelly, Timothy J.; Schrag, Daniel P.; Sogin, Mitchell L.; Brenchley, Jean E.; Teske, Andreas; House, Christopher H.; Hinrichs, Kai-Uwe

2006-01-01

Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane–carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100–2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea. PMID:16505362

A precision multi-sampler for deep-sea hydrothermal microbial mat studies

NASA Astrophysics Data System (ADS)

Breier, J. A.; Gomez-Ibanez, D.; Reddington, E.; Huber, J. A.; Emerson, D.

2012-12-01

A new tool was developed for deep-sea microbial mat studies by remotely operated vehicles and was successfully deployed during a cruise to the hydrothermal vent systems of the Mid-Cayman Rise. The Mat Sampler allows for discrete, controlled material collection from complex microbial structures, vertical-profiling within thick microbial mats and particulate and fluid sample collection from venting seafloor fluids. It has a reconfigurable and expandable sample capacity based on magazines of 6 syringes, filters, or water bottles. Multiple magazines can be used such that 12-36 samples can be collected routinely during a single dive; several times more if the dive is dedicated for this purpose. It is capable of hosting in situ physical, electrochemical, and optical sensors, including temperature and oxygen probes in order to guide sampling and to record critical environmental parameters at the time and point of sample collection. The precision sampling capability of this instrument will greatly enhance efforts to understand the structured, delicate, microbial mat communities that grow in diverse benthic habitats.

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.

Viral Impact on Prokaryotic and Microalgal Activities in the Microphytobenthic Biofilm of an Intertidal Mudflat (French Atlantic Coast)

PubMed Central

Montanié, Hélène; De Crignis, Margot G.; Lavaud, Johann

2015-01-01

This is the first report on viriobenthos activity within the microbial biofilm located at the top-surface of the intertidal mudflat during emersion in Marennes-Oléron Bay (France). By combining in situ and ex situ approaches, the viral production (VP) was linked to the dynamics of prokaryotes and microphytobenthos (MPB). VP averaged 2–4 × 108 viruses ml−1 h−1. VP correlated positively with the Virus to Prokaryote Ratio, and both were correlated negatively with the water content. The virus-induced mortality of prokaryotes was lower in winter than in summer (6.8 vs. 39.7% of the production) and the C-shunting may supply 2–12% of their Carbon Demand, respectively. VP accounted for 79% of loss in Prokaryotes but the response was delayed compared to the increase in VP suggesting a simultaneous release of viruses of MPB origin. This hypothesis is supported by capsid-sizing of virions by transmission electronic microscopy and bioassays. Harvesting and ex situ maintenance of top-surface sediments was carried out to monitor the dynamics of viruses, prokaryotes and MPB after inoculation with benthic or planktonic viruses. Benthic viruses modified the prokaryotic and MPB dynamics and decreased the photosynthesis efficiency in contrast to planktonic viruses that impacted MPB but not the prokaryotes. PMID:26617575

Extracellular enzyme activity and microbial diversity measured on seafloor exposed basalts from Loihi seamount indicate the importance of basalts to global biogeochemical cycling.

PubMed

Jacobson Meyers, Myrna E; Sylvan, Jason B; Edwards, Katrina J

2014-08-01

Seafloor basalts are widely distributed and host diverse prokaryotic communities, but no data exist concerning the metabolic rates of the resident microbial communities. We present here potential extracellular enzyme activities of leucine aminopeptidase (LAP) and alkaline phosphatase (AP) measured on basalt samples from different locations on Loihi Seamount, HI, coupled with analysis of prokaryotic biomass and pyrosequencing of the bacterial 16S rRNA gene. The community maximum potential enzyme activity (Vmax) of LAP ranged from 0.47 to 0.90 nmol (g rock)(-1) h(-1); the Vmax for AP was 28 to 60 nmol (g rock)(-1) h(-1). The Km of LAP ranged from 26 to 33 μM, while the Km for AP was 2 to 7 μM. Bacterial communities on Loihi basalts were comprised primarily of Alpha-, Delta-, andGammaproteobacteria, Bacteroidetes, and Planctomycetes. The putative ability to produce LAP is evenly distributed across the most commonly detected bacterial orders, but the ability to produce AP is likely dominated by bacteria in the orders Xanthomonadales, Flavobacteriales, and Planctomycetales. The enzyme activities on Loihi basalts were compared to those of other marine environments that have been studied and were found to be similar in magnitude to those from continental shelf sediments and orders of magnitude higher than any measured in the water column, demonstrating that the potential for exposed basalts to transform organic matter is substantial. We propose that microbial communities on basaltic rock play a significant, quantifiable role in benthic biogeochemical processes. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Modeling Biogeochemical Cycling of Heavy Metals in Lake Coeur d'Alene Sediments

NASA Astrophysics Data System (ADS)

Sengor, S. S.; Spycher, N.; Belding, E.; Curthoys, K.; Ginn, T. R.

2005-12-01

Mining of precious metals since the late 1800's have left Lake Coeur d'Alene (LCdA) sediments heavily enriched with toxic metals, including Cd, Cu, Pb, and Zn. Indigenous microbes however are capable of catalyzing reactions that detoxify the benthic and aqueous lake environments, and thus constitute an important driving component in the biogeochemical cycles of these metals. Here we report on the development of a quantitative model of transport, fate, exposure and effects of toxic compounds on benthic microbial communities at LCdA. First, chemical data from the LCdA area have been compiled from multiple sources to investigate trends in chemical occurrence, as well as to define model boundary conditions. The model is structured as 1-D diffusive reactive transport model to simulate spatial and temporal distribution of metals through the benthic sediments. Inorganic reaction processes included in the model are aqueous speciation, surface complexation, mineral precipitation/dissolution and abiotic redox reactions. Simulations with and without surface complexation are carried out to evaluate the effect of sorption and the conservative behaviour of metals within the benthic sediments under abiotic and purely diffusive transport. The 1-D inorganic diffusive transport model is then coupled to a biotic reaction network including consortium biodegradation kinetics with multiple electron acceptors, product toxicity, and energy partitioning. Multiyear simulations are performed, with water column chemistry established as a boundary condition from extant data, to explore the role of biogeochemical dynamics on benthic fluxes of metals in the long term.

Hawaii Energy and Environmental Technologies Initiative

DTIC Science & Technology

2005-06-01

include a hydrate synthesis system, benthic pressure chambers to simulate deep seafloor sediment, and specialized instrumentation for high pressure...the high probability that a sulfide/oxygen microbial fuel cell can generate electricity in deep ocean sediments, and that prolonged power generation may...hydrogen generation (using an electrolyser) and storage, and on-line high -resolution gas analysis. In addition to installation and commissioning of

Observations and Models of Heat and Salt Generation at a Deepwater Gulf of Mexico Vent

NASA Astrophysics Data System (ADS)

Sweetman, A. K.; Bøe, C.; Reigstad, L. J.; Durand, D.

2011-12-01

CO2 capture and storage (CCS) is, at present, one of the most promising measures for immediate regulation of CO2 emissions, while non-petroleum energy sources are being sought. Norway has taken a leading role in developing and implementing CCS, whilst international conventions, such as London and OSPAR, and regulations (EU directives) are defining the regulatory framework for CCS, in particular, for CO2 storage in geological structures including those under the seabed. To implement sub-seabed CCS on a global scale it is first necessary to understand how leakage from a CCS reservoir will impact marine ecosystems. To quantify how deep-sea benthic ecosystems respond to elevated levels of CO2, we conducted 4 in-situ benthic chamber lander deployments in a Norwegian fjord at 350m depth in September 2011. During each lander deployment, sediments in one benthic respirometry chamber were exposed to elevated levels of CO2 acidified seawater (up to 20,000 μatm), while those in a control chamber were exposed to seawater bubbled with air. Each experiment lasted approximately 40 hours. In the CO2 exposed chambers, benthic oxygen demand (respiration) increased and was negatively linearly correlated to pH. While bacterial and archael abundance showed no significant difference between the CO2 exposed chambers and the controls, bacterial and archael abundance was exponentially correlated to benthic oxygen demand, implying that microbial communities played a large role in forcing the strong correlation between respiration and pH. In terms of the effects of CO2 on sediment infauna, more macrofauna burrowed to deeper sediment depths in the CO2 exposed chambers relative to the control to potentially flee the low pH conditions in the experimental treatment. No large differences were seen in Pielou's evenness (J') (a measure of stress in diversity metrics) or the expected number of species between the control and experimental treatments, suggesting that no short-term (< 40 hrs) impacts on infaunal diversity are likely to be seen during a CO2 leakage event. Overall, the results collectively show that sedimentary ecosystems may respond very rapidly to CO2 exposure from a leakage event, and these responses may be manifested by higher respiration, but not necessarily by changes in sediment microbial abundance and faunal diversity. Results on faunal carbon uptakes rates between the 2 treatments will also be presented.

Modular spectral imaging system for discrimination of pigments in cells and microbial communities.

PubMed

Polerecky, Lubos; Bissett, Andrew; Al-Najjar, Mohammad; Faerber, Paul; Osmers, Harald; Suci, Peter A; Stoodley, Paul; de Beer, Dirk

2009-02-01

Here we describe a spectral imaging system for minimally invasive identification, localization, and relative quantification of pigments in cells and microbial communities. The modularity of the system allows pigment detection on spatial scales ranging from the single-cell level to regions whose areas are several tens of square centimeters. For pigment identification in vivo absorption and/or autofluorescence spectra are used as the analytical signals. Along with the hardware, which is easy to transport and simple to assemble and allows rapid measurement, we describe newly developed software that allows highly sensitive and pigment-specific analyses of the hyperspectral data. We also propose and describe a number of applications of the system for microbial ecology, including identification of pigments in living cells and high-spatial-resolution imaging of pigments and the associated phototrophic groups in complex microbial communities, such as photosynthetic endolithic biofilms, microbial mats, and intertidal sediments. This system provides new possibilities for studying the role of spatial organization of microorganisms in the ecological functioning of complex benthic microbial communities or for noninvasively monitoring changes in the spatial organization and/or composition of a microbial community in response to changing environmental factors.

Modular Spectral Imaging System for Discrimination of Pigments in Cells and Microbial Communities▿ †

PubMed Central

Polerecky, Lubos; Bissett, Andrew; Al-Najjar, Mohammad; Faerber, Paul; Osmers, Harald; Suci, Peter A.; Stoodley, Paul; de Beer, Dirk

2009-01-01

Here we describe a spectral imaging system for minimally invasive identification, localization, and relative quantification of pigments in cells and microbial communities. The modularity of the system allows pigment detection on spatial scales ranging from the single-cell level to regions whose areas are several tens of square centimeters. For pigment identification in vivo absorption and/or autofluorescence spectra are used as the analytical signals. Along with the hardware, which is easy to transport and simple to assemble and allows rapid measurement, we describe newly developed software that allows highly sensitive and pigment-specific analyses of the hyperspectral data. We also propose and describe a number of applications of the system for microbial ecology, including identification of pigments in living cells and high-spatial-resolution imaging of pigments and the associated phototrophic groups in complex microbial communities, such as photosynthetic endolithic biofilms, microbial mats, and intertidal sediments. This system provides new possibilities for studying the role of spatial organization of microorganisms in the ecological functioning of complex benthic microbial communities or for noninvasively monitoring changes in the spatial organization and/or composition of a microbial community in response to changing environmental factors. PMID:19074609

Direct and indirect influence of parental bedrock on streambed microbial community structure in forested streams.

PubMed

Mosher, Jennifer J; Findlay, Robert H

2011-11-01

A correlative study was performed to determine if variation in streambed microbial community structure in low-order forested streams can be directly or indirectly linked to the chemical nature of the parental bedrock of the environments through which the streams flow. Total microbial and photosynthetic biomass (phospholipid phosphate [PLP] and chlorophyll a), community structure (phospholipid fatty acid analysis), and physical and chemical parameters were measured in six streams, three located in sandstone and three in limestone regions of the Bankhead National Forest in northern Alabama. Although stream water flowing through the two different bedrock types differed significantly in chemical composition, there were no significant differences in total microbial and photosynthetic biomass in the sediments. In contrast, sedimentary microbial community structure differed between the bedrock types and was significantly correlated with stream water ion concentrations. A pattern of seasonal variation in microbial community structure was also observed. Further statistical analysis indicated dissolved organic matter (DOM) quality, which was previously shown to be influenced by geological variation, correlated with variation in bacterial community structure. These results indicate that the geology of underlying bedrock influences benthic microbial communities directly via changes in water chemistry and also indirectly via stream water DOM quality.

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.

Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms

PubMed Central

Wilhelm, Linda; Besemer, Katharina; Fragner, Lena; Peter, Hannes; Weckwerth, Wolfram; Battin, Tom J

2015-01-01

Resources structure ecological communities and potentially link biodiversity to energy flow. It is commonly believed that functional traits (generalists versus specialists) involved in the exploitation of resources depend on resource availability and environmental fluctuations. The longitudinal nature of stream ecosystems provides changing resources to stream biota with yet unknown effects on microbial functional traits and community structure. We investigated the impact of autochthonous (algal extract) and allochthonous (spruce extract) resources, as they change along alpine streams from above to below the treeline, on microbial diversity, community composition and functions of benthic biofilms. Combining bromodeoxyuridine labelling and 454 pyrosequencing, we showed that diversity was lower upstream than downstream of the treeline and that community composition changed along the altitudinal gradient. We also found that, especially for allochthonous resources, specialisation by biofilm bacteria increased along that same gradient. Our results suggest that in streams below the treeline biofilm diversity, specialisation and functioning are associated with increasing niche differentiation as potentially modulated by divers allochthonous and autochthonous constituents contributing to resources. These findings expand our current understanding on biofilm structure and function in alpine streams. PMID:25978543

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.

Ferrous iron- and ammonium-rich diffuse vents support habitat-specific communities in a shallow hydrothermal field off the Basiluzzo Islet (Aeolian Volcanic Archipelago).

PubMed

Bortoluzzi, G; Romeo, T; La Cono, V; La Spada, G; Smedile, F; Esposito, V; Sabatino, G; Di Bella, M; Canese, S; Scotti, G; Bo, M; Giuliano, L; Jones, D; Golyshin, P N; Yakimov, M M; Andaloro, F

2017-09-01

Ammonium- and Fe(II)-rich fluid flows, known from deep-sea hydrothermal systems, have been extensively studied in the last decades and are considered as sites with high microbial diversity and activity. Their shallow-submarine counterparts, despite their easier accessibility, have so far been under-investigated, and as a consequence, much less is known about microbial communities inhabiting these ecosystems. A field of shallow expulsion of hydrothermal fluids has been discovered at depths of 170-400 meters off the base of the Basiluzzo Islet (Aeolian Volcanic Archipelago, Southern Tyrrhenian Sea). This area consists predominantly of both actively diffusing and inactive 1-3 meters-high structures in the form of vertical pinnacles, steeples and mounds covered by a thick orange to brown crust deposits hosting rich benthic fauna. Integrated morphological, mineralogical, and geochemical analyses revealed that, above all, these crusts are formed by ferrihydrite-type Fe 3+ oxyhydroxides. Two cruises in 2013 allowed us to monitor and sampled this novel ecosystem, certainly interesting in terms of shallow-water iron-rich site. The main objective of this work was to characterize the composition of extant communities of iron microbial mats in relation to the environmental setting and the observed patterns of macrofaunal colonization. We demonstrated that iron-rich deposits contain complex and stratified microbial communities with a high proportion of prokaryotes akin to ammonium- and iron-oxidizing chemoautotrophs, belonging to Thaumarchaeota, Nitrospira, and Zetaproteobacteria. Colonizers of iron-rich mounds, while composed of the common macrobenthic grazers, predators, filter-feeders, and tube-dwellers with no representatives of vent endemic fauna, differed from the surrounding populations. Thus, it is very likely that reduced electron donors (Fe 2+ and NH 4 + ) are important energy sources in supporting primary production in microbial mats, which form a habitat-specific trophic base of the whole Basiluzzo hydrothermal ecosystem, including macrobenthic fauna. © 2017 John Wiley & Sons Ltd.

Hyporheic Microbial Biofilms as Indicators of Heavy and Rare Earth Metals in the Clark Fork Basin, Montana

NASA Astrophysics Data System (ADS)

Barnhart, E. P.; Hornberger, M.; Hwang, C.; Dror, I.; Bouskill, N.; Short, T.; Cain, D.; Fields, M. W.

2016-12-01

The ability to effectively monitor the impact of hard rock mining activities on rivers and streams is a growing concern given the large number of active and abandoned mines in the western United States. One such example, the Clark Fork Basin (CFB), western Montana, was extensively mined for copper in the early 20th century: it is now one of largest U.S. EPA superfund sites. Microbial biofilms are at the base of the lotic food chain and may provide a useful biomonitoring tool for the assessment of metal toxicity due to their environmental ubiquity, rapidity of response to environmental perturbation, and importance in determining metal mobility. Hyporheic microbial biofilms from the CFB were sampled in 2014, concurrent with the USGS National Research Programs (NRP) long-term site monitoring of metals in bed sediment and aquatic benthic insects. Integration of the DNA sequencing results from the hyporheic biofilms with the sediment and insect metal concentrations correlated several bacterial phyla with metal contamination. For example, the genus Lysobacter was strongly associated with copper (Cu) bioaccumulation in the aquatic insect Hydropsyche. These results support previous studies identifying Lysobacter as a bacterial genus that is resistant to Cu ions. Our analysis is the first to indicate that specific microorganisms can act as biomarkers of Cu contamination in rivers. Moreover, our work demonstrates that changes at the microbial community level in the hyporheic zone can be coupled to observed perturbations across higher trophic levels. In 2015, extensive remediation occurred at several of the sites sampled in 2014, providing an excellent opportunity to revisit the sites and examine the temporal variability of identified biomarkers and the short-term effectiveness of remediation. In addition, samples were analyzed for rare earth metals, of which little is known, and could provide additional insight into other metals that change the microbial community structure.

Nitrous oxide emissions and denitrification rates: A blueprint for smart management and remediation of agricultural landscapes.

NASA Astrophysics Data System (ADS)

Tomasek, A.; Hondzo, M.; Kozarek, J. L.

2015-12-01

Anthropogenic activities have greatly altered the global nitrogen cycle, especially in the agriculturally dominated Midwest, with severe consequences on human and aquatic health. Complete microbial denitrification can be viewed as a nitrogen sink, converting soluble nitrate into inert nitrogen gas. This research aims to quantify and correlate the driving parameters in microbial denitrification and explore the relationship to the abundance of denitrifying genes and the microbial communities at these sites. Denitrifying genes for each step in the denitrification process have been quantified. Data from a field site in Southern Minnesota has been collected throughout the season for two years enabling investigation into the temporal variability of denitrification. Data was collected at two cross-sections across the channel to determine the effect of bank location and moisture content on denitrification. Data were collected in an experimental basin in the summer of 2015 to determine the effect of flooding and benthic organic matter content and quality on microbial denitrification and nitrous oxide production. Four sediment types were investigated in three different flood regimes. After each raising or lowering of the water level, soil cores were taken to determine soil characteristics, the potential denitrification using the denitrification enzyme activity method, nitrous oxide production using a static core method, and the denitrifying gene abundance. Chambers were also deployed over each soil amendment in each flood regime to determine the nitrous oxide production over time. Results from these studies will convey a more complete explanation of denitrification and nitrous oxide production under varying environmental conditions. By determining the driving parameters for microbial denitrification, denitrification hot spots and hot moments can be created and enhanced. One potential consequence of increased denitrification is the possibility of incomplete denitrification resulting in the release of nitrous oxide, a greenhouse gas with 300 times the warming potential of carbon dioxide. The investigation of nitrous oxide emissions and correlation to denitrification rates will facilitate smart management and remediation efforts of agricultural landscapes.

Mn/Ca intra- and inter-test variability in the benthic foraminifer Ammonia tepida

NASA Astrophysics Data System (ADS)

Petersen, Jassin; Barras, Christine; Bézos, Antoine; La, Carole; de Nooijer, Lennart J.; Meysman, Filip J. R.; Mouret, Aurélia; Slomp, Caroline P.; Jorissen, Frans J.

2018-01-01

The adaptation of some benthic foraminiferal species to low-oxygen conditions provides the prospect of using the chemical composition of their tests as proxies for bottom water oxygenation. Manganese may be particularly suitable as such a geochemical proxy because this redox element is soluble in reduced form (Mn2+) and hence can be incorporated into benthic foraminiferal tests under low-oxygen conditions. Therefore, intra- and inter-test differences in foraminiferal Mn/Ca ratios may hold important information about short-term variability in pore water Mn2+ concentrations and sediment redox conditions. Here, we studied Mn/Ca intra- and inter-test variability in living individuals of the shallow infaunal foraminifer Ammonia tepida sampled in Lake Grevelingen (the Netherlands) in three different months of 2012. The deeper parts of this lake are characterized by seasonal hypoxia/anoxia with associated shifts in microbial activity and sediment geochemistry, leading to seasonal Mn2+ accumulation in the pore water. Earlier laboratory experiments with similar seawater Mn2+ concentrations as encountered in the pore waters of Lake Grevelingen suggest that intra-test variability due to ontogenetic trends (i.e. size-related effects) and/or other vital effects occurring during calcification in A. tepida (11-25 % relative SD, RSD) is responsible for part of the observed variability in Mn/Ca. Our present results show that the seasonally highly dynamic environmental conditions in the study area lead to a strongly increased Mn/Ca intra- and inter-test variability (average of 45 % RSD). Within single specimens, both increasing and decreasing trends in Mn/Ca ratios with size are observed. Our results suggest that the variability in successive single-chamber Mn/Ca ratios reflects the temporal variability in pore water Mn2+. Additionally, active or passive migration of the foraminifera in the surface sediment may explain part of the observed Mn/Ca variability.

Nutrients in estuaries--an overview and the potential impacts of climate change.

PubMed

Statham, Peter J

2012-09-15

The fate and cycling of macronutrients introduced into estuaries depend upon a range of interlinked processes. Hydrodynamics and morphology in combination with freshwater inflow control the freshwater flushing time, and the timescale for biogeochemical processes to operate that include microbial activity, particle-dissolved phase interactions, and benthic exchanges. In some systems atmospheric inputs and exchanges with coastal waters can also be important. Climate change will affect nutrient inputs and behaviour through modifications to temperature, wind patterns, the hydrological cycle, and sea level rise. Resulting impacts include: 1) inundation of freshwater systems 2) changes in stratification, flushing times and phytoplankton productivity 3) increased coastal storm activity 4) changes in species and ecosystem function. A combination of continuing high inputs of nutrients through human activity and climate change is anticipated to lead to enhanced eutrophication in the future. The most obvious impacts of increasing global temperature will be in sub-arctic systems where permafrost zones will be reduced in combination with enhanced inputs from glacial systems. Improved process understanding in several key areas including cycling of organic N and P, benthic exchanges, resuspension, impact of bio-irrigation, particle interactions, submarine groundwater discharges, and rates and magnitude of bacterially-driven recycling processes, is needed. Development of high frequency in situ nutrient analysis systems will provide data to improve predictive models that need to incorporate a wider variety of key factors, although the complexity of estuarine systems makes such modelling a challenge. However, overall a more holistic approach is needed to effectively understand, predict and manage the impact of macronutrients on estuaries. Copyright © 2011 Elsevier B.V. All rights reserved.

Contribution of sea ice microbial production to Antarctic benthic communities is driven by sea ice dynamics and composition of functional guilds.

PubMed

Wing, Stephen R; Leichter, James J; Wing, Lucy C; Stokes, Dale; Genovese, Sal J; McMullin, Rebecca M; Shatova, Olya A

2018-04-28

Organic matter produced by the sea ice microbial community (SIMCo) is an important link between sea ice dynamics and secondary production in near-shore food webs of Antarctica. Sea ice conditions in McMurdo Sound were quantified from time series of MODIS satellite images for Sept. 1 through Feb. 28 of 2007-2015. A predictable sea ice persistence gradient along the length of the Sound and evidence for a distinct change in sea ice dynamics in 2011 were observed. We used stable isotope analysis (δ 13 C and δ 15 N) of SIMCo, suspended particulate organic matter (SPOM) and shallow water (10-20 m) macroinvertebrates to reveal patterns in trophic structure of, and incorporation of organic matter from SIMCo into, benthic communities at eight sites distributed along the sea ice persistence gradient. Mass-balance analysis revealed distinct trophic architecture among communities and large fluxes of SIMCo into the near-shore food web, with the estimates ranging from 2 to 84% of organic matter derived from SIMCo for individual species. Analysis of patterns in density, and biomass of macroinvertebrate communities among sites allowed us to model net incorporation of organic matter from SIMCo, in terms of biomass per unit area (g/m 2 ), into benthic communities. Here, organic matter derived from SIMCo supported 39 to 71 per cent of total biomass. Furthermore, for six species, we observed declines in contribution of SIMCo between years with persistent sea ice (2008-2009) and years with extensive sea ice breakout (2012-2015). Our data demonstrate the vital role of SIMCo in ecosystem function in Antarctica and strong linkages between sea ice dynamics and near-shore secondary productivity. These results have important implications for our understanding of how benthic communities will respond to changes in sea ice dynamics associated with climate change and highlight the important role of shallow water macroinvertebrate communities as sentinels of change for the Antarctic marine ecosystem. © 2018 John Wiley & Sons Ltd.

Microbial mats in playa lakes and other saline habitats: Early Mars analog?

NASA Technical Reports Server (NTRS)

Bauld, John

1989-01-01

Microbial mats are cohesive benthic microbial communities which inhabit various Terra (Earth-based) environments including the marine littoral and both permanent and ephemeral (playa) saline lakes. Certain geomorphological features of Mars, such as the Margaritifer Sinus, were interpreted as ancient, dried playa lakes, presumably formed before or during the transition to the present Mars climate. Studies of modern Terran examples suggest that microbial mats on early Mars would have had the capacity to survive and propagate under environmental constraints that would have included irregularly fluctuating regimes of water activity and high ultraviolet flux. Assuming that such microbial communities did indeed inhabit early Mars, their detection during the Mars Rover Sample Return (MRSR) mission depends upon the presence of features diagnostic of the prior existence of these communities or their component microbes or, as an aid to choosing suitable landing, local exploration or sampling sites, geomorphological, sedimentological or chemical features characteristic of their playa lake habitats. Examination of modern Terran playas (e.g., the Lake Eyre basin) shows that these features span several orders of magnitude in size. While stromatolites are commonly centimeter-meter scale features, bioherms or fields of individuals may extend to larger scales. Preservation of organic matter (mats and microbes) would be favored in topographic lows such as channels or ponds of high salinity, particularly those receiving silica-rich groundwaters. These areas are likely to be located near former zones of groundwater emergence and/or where flood channels entered the paleo-playa. Fossil playa systems which may aid in assessing the applicability of this particular Mars analog include the Cambrian Observatory Hill Beds of the Officer Basin and the Eocene Wilkins Peak Member of the Green River Formation.

Carbon isotope discrepancy between precambrian stromatolites and their modern analogs: Inferences from hypersaline microbial mats of the sinai coast

NASA Astrophysics Data System (ADS)

Schidlowski, Manfred

1985-12-01

The isotopic composition of organic carbon from extant stromatolite-type microbial ecosystems is commonly slanted toward heavy δ13 C values as compared to respective compositions of average organic matter (including that from Precambrian stromatolites). This seems the more enigmatic as the bulk of primary producers from benthic microbial communities are known to fix carbon via the C3 pathway normally entailing the sizable fractionations of the RuBP carboxylase reaction. There is reason to believe that the small fractionations displayed by aquatic microorganisms result from the limitations of a diffusion-controlled assimilatory pathway in which the isotope effect of the enzymatic reaction is largely suppressed. Apart from the diffusion-control exercised by the aqueous environment, transport of CO2 to the photosynthetically active sites will be further impeded by the protective slime (polysaccharide) coatings commonly covering microbial mats in which gas diffusivities are extremely low. Ineffective discrimination against13C becomes, however, most pronounced in hypersaline environments where substantially reduced CO2 solubilities tend to push carbon into the role of a limiting nutrient (brine habitats constitute preferential sanctuaries of mat-forming microbenthos since the emergence of Metazoan grazers ˜ 0.7 Ga ago). As the same microbial communities had been free to colonize normal marine environments during the Precambrian, the CO2 concentration effect was irrelevant to the carbon-fixing pathway of these ancient forms. Therefore, it might not surprise that organic matter from Precambrian stromatolites displays the large fractionations commonly associated with C3 photosynthesis. Increased mixing ratios of CO2 in the Precambrian atmosphere may have additionally contributed to the elimination of the diffusion barrier in the carbon-fixing pathways of ancient mat-forming microbiota.

Collection, Culturing, and Genome Analyses of Tropical Marine Filamentous Benthic Cyanobacteria.

PubMed

Moss, Nathan A; Leao, Tiago; Glukhov, Evgenia; Gerwick, Lena; Gerwick, William H

2018-01-01

Decreasing sequencing costs has sparked widespread investigation of the use of microbial genomics to accelerate the discovery and development of natural products for therapeutic uses. Tropical marine filamentous cyanobacteria have historically produced many structurally novel natural products, and therefore present an excellent opportunity for the systematic discovery of new metabolites via the information derived from genomics and molecular genetics. Adequate knowledge transfer and institutional know-how are important to maintain the capability for studying filamentous cyanobacteria due to their unusual microbial morphology and characteristics. Here, we describe workflows, procedures, and commentary on sample collection, cultivation, genomic DNA generation, bioinformatics tools, and biosynthetic pathway analysis concerning filamentous cyanobacteria. © 2018 Elsevier Inc. All rights reserved.

Authigenic minerals related to carbon and sulfur biogeochemical cycling from deep-sea active methane seeps offshore South-West Africa

NASA Astrophysics Data System (ADS)

Pierre, C.; Blanc-Valleron, M.; Demange, J.; Boudouma, O.; Pape, T.; Himmler, T.; Fekete, N.; Spiess, V.

2011-12-01

The South-West African continental margin is well known for occurrences of active methane-rich fluid seeps that are associated with seafloor pockmarks in a broad range of water depths, from the shelf to the deep basins. High gas flares in the water column, luxurious oases of benthic fauna, gas hydrate accumulations and diagenetic carbonate crusts have been observed at these seeps. During the M76/3a expedition of R/V METEOR (summer 2008) gravity cores recovered abundant authigenic carbonate concretions from five pockmarks of the South-West African margin including previously studied sites (Hydrate Hole, Worm Hole, Regab Pockmark) and two sites (Deep Hole, Baboon Cluster) newly discovered during the cruise. Carbonate concretions were mostly associated to sediments settled by seep-associated benthic macrofauna and bearing shallow gas hydrates. We present new results of the comprehensive analysis of the mineralogy and isotope geochemistry of the diagenetic carbonates sampled in the five pockmarks. The mineralogy of authigenic carbonates is dominated by magnesian calcite and aragonite, associated occasionally with dolomite. The oxygen and carbon isotopic compositions of authigenic carbonates (+2.4 < δ18O % V-PDB < +6.2 ; -61.0 < δ13C % V-PDB < -40.1) indicate that microbial anaerobic oxidation of methane (AOM) was the main process controling carbonate precipitation within sub-seafloor sediments deposited from the glacial-time up to the present. The frequent occurrence of diagenetic gypsum crystals within the sediments demonstrates that bio-irrigation with oxygenated bottom water by the burrowing activity of benthic fauna caused the secondary oxidation of reduced sulfur (hydrogen sulfide and pyrite) that was produced by sulfate reducting bacteria as a by-product of AOM; during the sulfide oxidation process, the released acidity induced the partial dissolution of carbonates. Our results demonstrate also the strong link that existed between the carbon and sulfur cycles in cold seep systems where the anoxic-oxic boundary may move within the sediment due to variations in the strength of the methane flux.

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.

RELATIONSHIPS BETWEEN ENVIRONMENTAL VARIABLES AND BENTHIC DIATOM ASSEMBLAGES IN CALIFORNIA CENTRAL VALLEY STREAMS (USA)

EPA Science Inventory

Streams and rivers in the California Central Valley Ecoregion have been substantially modified by human activities. This study examines distributional patterns of benthic diatom assemblages in relation to environmental characteristics in streams and rivers of this region. Benthic...

Draft Genome Sequence of Cyanobacterium sp. Strain HL-69, Isolated from a Benthic Microbial Mat from a Magnesium Sulfate-Dominated Hypersaline Lake

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

Mobberley, J. M.; Romine, M. F.; Cole, J. K.

ABSTRACT The complete genome sequence ofCyanobacteriumsp. strain HL-69 consists of 3,155,247 bp and contains 2,897 predicted genes comprising a chromosome and two plasmids. The genome is consistent with a halophilic nondiazotrophic phototrophic lifestyle, and this organism is able to synthesize most B vitamins and produces several secondary metabolites.

Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data.

PubMed

Meirelles, Pedro M; Amado-Filho, Gilberto M; Pereira-Filho, Guilherme H; Pinheiro, Hudson T; de Moura, Rodrigo L; Joyeux, Jean-Christophe; Mazzei, Eric F; Bastos, Alex C; Edwards, Robert A; Dinsdale, Elizabeth; Paranhos, Rodolfo; Santos, Eidy O; Iida, Tetsuya; Gotoh, Kazuyoshi; Nakamura, Shota; Sawabe, Tomoo; Rezende, Carlos E; Gadelha, Luiz M R; Francini-Filho, Ronaldo B; Thompson, Cristiane; Thompson, Fabiano L

2015-01-01

Seamounts are considered important sources of biodiversity and minerals. However, their biodiversity and health status are not well understood; therefore, potential conservation problems are unknown. The mesophotic reefs of the Vitória-Trindade Seamount Chain (VTC) were investigated via benthic community and fish surveys, metagenomic and water chemistry analyses, and water microbial abundance estimations. The VTC is a mosaic of reef systems and includes fleshy algae dominated rhodolith beds, crustose coralline algae (CCA) reefs, and turf algae dominated rocky reefs of varying health levels. Macro-carnivores and larger fish presented higher biomass at the CCA reefs (4.4 kg per frame) than in the rhodolith beds and rocky reefs (0.0 to 0.1 kg per frame). A larger number of metagenomic sequences identified as primary producers (e.g., Chlorophyta and Streptophyta) were found at the CCA reefs. However, the rocky reefs contained more diseased corals (>90%) than the CCA reefs (~40%) and rhodolith beds (~10%). Metagenomic analyses indicated a heterotrophic and fast-growing microbiome in rocky reef corals that may possibly lead to unhealthy conditions possibly enhanced by environmental features (e.g. light stress and high loads of labile dissolved organic carbon). VTC mounts represent important hotspots of biodiversity that deserve further conservation actions.

Sulfur oxidation to sulfate coupled with electron transfer to electrodes by Desulfuromonas strain TZ1

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

Zhang, T; Bain, TS; Barlett, MA

2014-01-02

Microbial oxidation of elemental sulfur with an electrode serving as the electron acceptor is of interest because this may play an important role in the recovery of electrons from sulfidic wastes and for current production in marine benthic microbial fuel cells. Enrichments initiated with a marine sediment inoculum, with elemental sulfur as the electron donor and a positively poised (+300 mV versus Ag/AgCl) anode as the electron acceptor, yielded an anode biofilm with a diversity of micro-organisms, including Thiobacillus, Sulfurimonas, Pseudomonas, Clostridium and Desulfuromonas species. Further enrichment of the anode biofilm inoculum in medium with elemental sulfur as the electronmore » donor and Fe(III) oxide as the electron acceptor, followed by isolation in solidified sulfur/Fe(III) medium yielded a strain of Desulfuromonas, designated strain TZ1. Strain TZ1 effectively oxidized elemental sulfur to sulfate with an anode serving as the sole electron acceptor, at rates faster than Desulfobulbus propionicus, the only other organism in pure culture previously shown to oxidize S with current production. The abundance of Desulfuromonas species enriched on the anodes of marine benthic fuel cells has previously been interpreted as acetate oxidation driving current production, but the results presented here suggest that sulfur-driven current production is a likely alternative.« less

Food web flows through a sub-arctic deep-sea benthic community

NASA Astrophysics Data System (ADS)

Gontikaki, E.; van Oevelen, D.; Soetaert, K.; Witte, U.

2011-11-01

The benthic food web of the deep Faroe-Shetland Channel (FSC) was modelled by using the linear inverse modelling methodology. The reconstruction of carbon pathways by inverse analysis was based on benthic oxygen uptake rates, biomass data and transfer of labile carbon through the food web as revealed by a pulse-chase experiment. Carbon deposition was estimated at 2.2 mmol C m -2 d -1. Approximately 69% of the deposited carbon was respired by the benthic community with bacteria being responsible for 70% of the total respiration. The major fraction of the labile detritus flux was recycled within the microbial loop leaving merely 2% of the deposited labile phytodetritus available for metazoan consumption. Bacteria assimilated carbon at high efficiency (0.55) but only 24% of bacterial production was grazed by metazoans; the remaining returned to the dissolved organic matter pool due to viral lysis. Refractory detritus was the basal food resource for nematodes covering ∼99% of their carbon requirements. On the contrary, macrofauna seemed to obtain the major part of their metabolic needs from bacteria (49% of macrofaunal consumption). Labile detritus transfer was well-constrained, based on the data from the pulse-chase experiment, but appeared to be of limited importance to the diet of the examined benthic organisms (<1% and 5% of carbon requirements of nematodes and macrofauna respectively). Predation on nematodes was generally low with the exception of sub-surface deposit-feeding polychaetes that obtained 35% of their energy requirements from nematode ingestion. Carnivorous polychaetes also covered 35% of their carbon demand through predation although the preferred prey, in this case, was other macrofaunal animals rather than nematodes. Bacteria and detritus contributed 53% and 12% to the total carbon ingestion of carnivorous polychaetes suggesting a high degree of omnivory among higher consumers in the FSC benthic food web. Overall, this study provided a unique insight into the functioning of a deep-sea benthic community and demonstrated how conventional data can be exploited further when combined with state-of-the-art modelling approaches.

Bacterial Production and Enzymatic Activities in Deep-Sea Sediments of the Pacific Ocean: Biogeochemical Implications of Different Temperature Constraints

NASA Astrophysics Data System (ADS)

Danovaro, R.; Corinaldesi, C.; dell'Anno, A.

2002-12-01

The deep-sea bed, acting as the ultimate sink for organic material derived from the upper oceans primary production, is now assumed to play a key role in biogeochemical cycling of organic matter on global scale. Early diagenesis of organic matter in marine sediments is dependent upon biological processes (largely mediated by bacterial activity) and by molecular diffusion. Organic matter reaching the sea floor by sedimentation is subjected to complex biogeochemical transformations that make organic matter largely unsuitable for direct utilization by benthic heterotrophs. Extracellular enzymatic activities in the sediment is generally recognized as the key step in the degradation and utilization of organic polymers by bacteria and a key role in biopolymeric carbon mobilization is played by aminopeptidase, alkaline phosphatase and glucosidase activities. In the present study we investigated bacterial density, bacterial C production and exo-enzymatic activities (aminopeptidase, glucosidase and phosphatase activity) in deep-sea sediments of the Pacific Ocean in relation with the biochemical composition of sediment organic matter (proteins, carbohydrates and lipids), in order to gather information on organic matter cycling and diagenesis. Benthic viral abundance was also measured to investigate the potential role of viruses on microbial loop functioning. Sediment samples were collected at eight stations (depth ranging from 2070-3100 m) along two transects located at the opposite side (north and south) of ocean seismic ridge Juan Fernandez (along latitudes 33° 20' - 33° 40'), constituted by the submerged vulcanoes, which connects the Chilean coasts to Rapa Nui Island. Since the northern and southern sides of this ridge apparently displayed small but significant differences in deep-sea temperature (related to the general ocean circulation), this sampling strategy allowed also investigating the role of different temperature constraints on bacterial activity and biogeochemical processes and to define possible scenarios dealing with climate induced changes in deep-sea conditions.

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.

The interaction between the proliferating macroalga Asparagopsis taxiformis and the coral Astroides calycularis induces changes in microbiome and metabolomic fingerprints.

PubMed

Greff, Stéphane; Aires, Tânia; Serrão, Ester A; Engelen, Aschwin H; Thomas, Olivier P; Pérez, Thierry

2017-02-20

Mediterranean Sea ecosystems are considered as hotspots of biological introductions, exposed to possible negative effects of non-indigenous species. In such temperate marine ecosystems, macroalgae may be dominant, with a great percentage of their diversity represented by introduced species. Their interaction with temperate indigenous benthic organisms have been poorly investigated. To provide new insights, we performed an experimental study on the interaction between the introduced proliferative red alga Asparagopsis taxiformis and the indigenous Mediterranean coral Astroides calycularis. The biological response measurements included meta-barcoding of the associated microbial communities and metabolomic fingerprinting of both species. Significant changes were detected among both associated microbial communities, the interspecific differences decreasing with stronger host interaction. No short term effects of the macroalga on the coral health, neither on its polyp activity or its metabolism, were detected. In contrast, the contact interaction with the coral induced a change in the macroalgal metabolomic fingerprint with a significant increase of its bioactivity against the marine bacteria Aliivibrio fischeri. This induction was related to the expression of bioactive metabolites located on the macroalgal surface, a phenomenon which might represent an immediate defensive response of the macroalga or an allelopathic offense against coral.

The interaction between the proliferating macroalga Asparagopsis taxiformis and the coral Astroides calycularis induces changes in microbiome and metabolomic fingerprints

NASA Astrophysics Data System (ADS)

Greff, Stéphane; Aires, Tânia; Serrão, Ester A.; Engelen, Aschwin H.; Thomas, Olivier P.; Pérez, Thierry

2017-02-01

Mediterranean Sea ecosystems are considered as hotspots of biological introductions, exposed to possible negative effects of non-indigenous species. In such temperate marine ecosystems, macroalgae may be dominant, with a great percentage of their diversity represented by introduced species. Their interaction with temperate indigenous benthic organisms have been poorly investigated. To provide new insights, we performed an experimental study on the interaction between the introduced proliferative red alga Asparagopsis taxiformis and the indigenous Mediterranean coral Astroides calycularis. The biological response measurements included meta-barcoding of the associated microbial communities and metabolomic fingerprinting of both species. Significant changes were detected among both associated microbial communities, the interspecific differences decreasing with stronger host interaction. No short term effects of the macroalga on the coral health, neither on its polyp activity or its metabolism, were detected. In contrast, the contact interaction with the coral induced a change in the macroalgal metabolomic fingerprint with a significant increase of its bioactivity against the marine bacteria Aliivibrio fischeri. This induction was related to the expression of bioactive metabolites located on the macroalgal surface, a phenomenon which might represent an immediate defensive response of the macroalga or an allelopathic offense against coral.

Benthic Food Webs of the Chukchi and Beaufort Seas: Relative Importance of Ultimate Carbon Sources in a Changing Climate

NASA Astrophysics Data System (ADS)

Dunton, K. H.; Schonberg, S. V.; Mctigue, N.; Bucolo, P. A.; Connelly, T. L.; McClelland, J. W.

2014-12-01

Changes in sea-ice cover, coastal erosion, and freshwater run-off have the potential to greatly influence carbon assimilation pathways and affect trophic structure in benthic communities across the western Arctic. In the Chukchi Sea, variations in the duration and timing of ice cover affect the delivery of ice algae to a relatively shallow (40-50 m) shelf benthos. Although ice algae are known as an important spring carbon subsidy for marine benthic fauna, ice algal contributions may also help initiate productivity of an active microphytobenthos. Recent studies provide clear evidence that the microphytobenthos are photosynthetically active, and have sufficient light and nutrients for in situ growth. The assimilation of benthic diatoms from both sources may explain the 13C enrichment observed in benthic primary consumers throughout the northern Chukchi. On the eastern Beaufort Sea coast, shallow (2-4 m) estuarine lagoon systems receive massive subsidies of terrestrial carbon that is assimilated by a benthic fauna of significant importance to upper trophic level species, but again, distinct 13C enrichment in benthic primary consumers suggests the existence of an uncharacterized food source. Since ice algae are absent, we believe the 13C enrichment in benthic fauna is caused by the assimilation of benthic microalgae, as reflected in seasonally high benthic chlorophyll in spring under replete light and nutrient conditions. Our observations suggest that changes in ice cover, on both temporal and spatial scales, are likely to have significant effects on the magnitude and timing of organic matter delivery to both shelf and nearshore systems, and that locally produced organic matter may become an increasingly important carbon subsidy that affects trophic assimilation and secondary ecosystem productivity.

Controls on development and diversity of Early Archean stromatolites

PubMed Central

Allwood, Abigail C.; Grotzinger, John P.; Knoll, Andrew H.; Burch, Ian W.; Anderson, Mark S.; Coleman, Max L.; Kanik, Isik

2009-01-01

The ≈3,450-million-year-old Strelley Pool Formation in Western Australia contains a reef-like assembly of laminated sedimentary accretion structures (stromatolites) that have macroscale characteristics suggestive of biological influence. However, direct microscale evidence of biology—namely, organic microbial remains or biosedimentary fabrics—has to date eluded discovery in the extensively-recrystallized rocks. Recently-identified outcrops with relatively good textural preservation record microscale evidence of primary sedimentary processes, including some that indicate probable microbial mat formation. Furthermore, we find relict fabrics and organic layers that covary with stromatolite morphology, linking morphologic diversity to changes in sedimentation, seafloor mineral precipitation, and inferred microbial mat development. Thus, the most direct and compelling signatures of life in the Strelley Pool Formation are those observed at the microscopic scale. By examining spatiotemporal changes in microscale characteristics it is possible not only to recognize the presence of probable microbial mats during stromatolite development, but also to infer aspects of the biological inputs to stromatolite morphogenesis. The persistence of an inferred biological signal through changing environmental circumstances and stromatolite types indicates that benthic microbial populations adapted to shifting environmental conditions in early oceans. PMID:19515817

Taxonomic and Functional Metagenomic Signature of Turfs in the Abrolhos Reef System (Brazil)

PubMed Central

Walter, Juline M.; Tschoeke, Diogo A.; Meirelles, Pedro M.; de Oliveira, Louisi; Leomil, Luciana; Tenório, Márcio; Valle, Rogério; Salomon, Paulo S.; Thompson, Cristiane C.; Thompson, Fabiano L.

2016-01-01

Turfs are widespread assemblages (consisting of microbes and algae) that inhabit reef systems. They are the most abundant benthic component in the Abrolhos reef system (Brazil), representing greater than half the coverage of the entire benthic community. Their presence is associated with a reduction in three-dimensional coral reef complexity and decreases the habitats available for reef biodiversity. Despite their importance, the taxonomic and functional diversity of turfs remain unclear. We performed a metagenomics and pigments profile characterization of turfs from the Abrolhos reefs. Turf microbiome primarily encompassed Proteobacteria (mean 40.57% ± s.d. 10.36, N = 1.548,192), Cyanobacteria (mean 35.04% ± s.d. 15.5, N = 1.337,196), and Bacteroidetes (mean 11.12% ± s.d. 4.25, N = 424,185). Oxygenic and anoxygenic phototrophs, chemolithotrophs, and aerobic anoxygenic phototrophic (AANP) bacteria showed a conserved functional trait of the turf microbiomes. Genes associated with oxygenic photosynthesis, AANP, sulfur cycle (S oxidation, and DMSP consumption), and nitrogen metabolism (N2 fixation, ammonia assimilation, dissimilatory nitrate and nitrite ammonification) were found in the turf microbiomes. Principal component analyses of the most abundant taxa and functions showed that turf microbiomes differ from the other major Abrolhos benthic microbiomes (i.e., corals and rhodoliths) and seawater. Taken together, these features suggest that turfs have a homogeneous functional core across the Abrolhos Bank, which holds diverse microbial guilds when comparing with other benthic organisms. PMID:27548380

Effect of bottom water oxygenation on oxygen consumption and benthic biogeochemical processes at the Crimean Shelf (Black Sea)

NASA Astrophysics Data System (ADS)

Lichtschlag, A.; Janssen, F.; Wenzhöfer, F.; Holtappels, M.; Struck, U.; Jessen, G.; Boetius, A.

2012-04-01

Hypoxia occurs where oxygen concentrations fall below a physiological threshold of many animals, usually defined as <63 µmol L-1. Oxygen depletion can be caused by anthropogenic influences, such as global warming and eutrophication, but as well occurs naturally due to restricted water exchange in combination with high nutrient loads (e.g. upwelling). Bottom-water oxygen availability not only influences the composition of faunal communities, but is also one of the main factors controlling sediment-water exchange fluxes and organic carbon degradation in the sediment, usually shifting processes towards anaerobic mineralization pathways mediated by microorganisms. The Black Sea is one of the world's largest meromictic marine basins with an anoxic water column below 180m. The outer shelf edge, where anoxic waters meet the seafloor, is an ideal natural laboratory to study the response of benthic ecosystems to hypoxia, including benthic biogeochemical processes. During the MSM 15/1 expedition with the German research vessel MARIA S. MERIAN, the NW area of the Black Sea (Crimean Shelf) was studied. The study was set up to investigate the influence of bottom water oxygenation on, (1) the respective share of fauna-mediated oxygen uptake, microbial respiration, or re-oxidation of reduced compounds formed in the deeper sediments for the total oxygen flux and (2) on the efficiency of benthic biogeochemical cycles. During our study, oxygen consumption and pathways of organic carbon degradation were estimated from benthic chamber incubations, oxygen microprofiles measured in situ, and pore water and solid phase profiles measured on retrieved cores under oxic, hypoxic, and anoxic water column conditions. Benthic oxygen fluxes measured in Crimean Shelf sediments in this study were comparable to fluxes from previous in situ and laboratory measurements at similar oxygen concentrations (total fluxes -8 to -12 mmol m-2 d-1; diffusive fluxes: -2 to -5 mmol m-2 d-1) with oxygen penetrating less than 5 mm into the seafloor. In total oxygen uptake by the seafloor, the fraction of the diffusive flux, which comprises microbial consumption plus re-oxidation of reduced compounds, increased with declining oxygen concentrations. Measurements and modeling of penetration depths and fluxes of the electron acceptors nitrate, iron- and manganese oxides, sulfate suggest that as long as oxygen is available in the oxic and the hypoxic zones of the Crimean shelf, the largest fraction of oxygen is consumed directly during aerobic mineralization of organic matter and re-oxidation processes play only a minor role. Furthermore, the combination of rapid and strong fluctuation of bottom water oxygen concentration and low sedimentation rates appear to repress anaerobic organic matter degradation. This study was carried out within the framework of the EU-funded project HYPOX (www.hypox.net), which is set up to improve our understanding of hypoxia formation and to develop capacities and know-how for hypoxia monitoring.

Dissolved organic matter (DOM) in pore water of Arctic Ocean sediments: linking DOM molecular composition with microbial community structure

NASA Astrophysics Data System (ADS)

Rossel, P. E.; Bienhold, C.; Boetius, A.; Dittmar, T.

2016-02-01

Marine organic matter (OM) that sinks from surface waters to the seafloor is the energy and carbon source for benthic communities. These communities produce dissolved organic matter (DOM) in the process of remineralization, enriching the sediment porewater with fresh DOM compounds. In the Arctic Ocean, primary production is limited by nutrients and light and is thus strongly influenced by sea ice cover. Ice cover is expected to further decrease due to global warming, which may have important consequences for primary production and the quantity and quality of OM exported to the seafloor. This study focused on: 1) the molecular composition of the DOM in sediment pore waters of the deep Eurasian Arctic basins, 2) whether there is any relation between Arctic Ocean ice cover and DOM composition and 3) whether the DOM composition correlates with microbial community structure. Molecular data, obtained via 15 Tesla Fourier transform ion cyclotron resonance mass spectrometry, were statistically correlated with environmental parameters. The productive ice margin stations showed higher abundances of molecular formulae of peptides, unsaturated aliphatics and saturated fatty acids. This molecular trend is indicative of fresh OM and phytodetritus deposition, compared to the northernmost, ice-covered stations which had stronger aromatic signals. Benthic bacterial community structure, as assessed with the fingerprinting method ARISA, was significantly correlated with DOM molecular composition. Further analyses using Illumina next-generation sequencing will enable the taxonomic identification of specific bacterial groups and their interdependence with DOM compounds. This study contributes to the understanding of the coupling between Arctic Ocean productivity and its depositional regime, and provides first insights into potential links between microbial community structure and DOM molecular composition in Arctic sediments

Biological, habitat, and water quality conditions in the upper Merced River drainage, Yosemite National Park, California, 1993-1996

USGS Publications Warehouse

Brown, Larry R.; Short, Terry M.

1999-01-01

The general conclusion from these studies is that water quality in the upper Merced River was very good from 1993-1996, despite high levels of human activities in some areas. Fish communities did not appear to be a useful indicator of habitat and water quality because of low species richness and the apparent importance of physical barriers in determining species distributions. Measurements of fish densities and size-distributions might be useful, but would be logistically difficult. Benthic algae and benthic invertebrates do appear to be useful in monitoring environmental conditions. Benthic algae may be more sensitive than benthic invertebrates to small environmental differences within years. Benthic algae were also more responsive than benthic invertebrates to differences in discharge between years. Thus, benthic invertebrates may be more useful in comparing environmental conditions between years, independent of discharge conditions.

Benthic communities in the deep Mediterranean Sea: exploring microbial and meiofaunal patterns in slope and basin ecosystems

NASA Astrophysics Data System (ADS)

Sevastou, K.; Lampadariou, N.; Polymenakou, P. N.; Tselepides, A.

2012-12-01

The long held perception of the deep sea consisting of monotonous slopes and uniform oceanic basins has over the decades given way to the idea of a complex system with wide habitat heterogeneity. Under the prism of a highly diverse environment, a large dataset was used to describe and compare spatial patterns of the dominant small-size components of deep-sea benthos, metazoan meiofauna and bacteria, from Mediterranean basins and slopes. A grid of 73 stations sampled at five geographical areas along the central-eastern Mediterranean basin (central Mediterranean, northern Aegean Sea, Cretan Sea, Libyan Sea, eastern Levantine) spanning over 4 km in depth revealed a high diversity in terms of both metazoan meiofauna and microbial communities. The higher meiofaunal abundance and richness observed in the northern Aegean Sea highlights the effect of productivity on benthic patterns. Non parametric analyses detected no differences for meiobenthic standing stocks and major taxa diversity (α, β, γ and δ components) between the two habitats (basin vs. slope) for the whole investigated area and within each region, but revealed significant bathymetric trends: abundance and richness follow the well-known gradient of decreasing values with increasing depth, whereas differentiation diversity (β- and δ-diversity) increases with depth. In spite of a similar bathymetric trend observed for nematode genera richness, no clear pattern was detected with regard to habitat type; the observed number of nematode genera suggests higher diversity in slopes, whereas richness estimator Jack1 found no differences between habitats. On the other hand, δ-diversity was higher at the basin habitat, but no differences were found among depth ranges, though turnover values were high in all pairwise comparisons of the different depth categories. Results of multivariate analysis are in line with the above findings, indicating high within habitat variability of meiofaunal communities and a gradual change of meiofaunal structure towards the abyssal stations. In contrast to meiobenthic results, microbial richness is significantly higher at the basin ecosystem and tends to increase with depth, while community structure varies greatly among samples regardless of the type of habitat, depth or area. The results presented here suggest that differences in benthic parameters between the two habitats are neither strong nor consistent; it appears that within habitat variability is high and differences among depth ranges are more important.

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.

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.

Role of surface and subsurface processes in scaling N2O emissions along riverine networks

PubMed Central

Marzadri, Alessandra; Dee, Martha M.; Tonina, Daniele; Bellin, Alberto; Tank, Jennifer L.

2017-01-01

Riverine environments, such as streams and rivers, have been reported as sources of the potent greenhouse gas nitrous oxide (N2O) to the atmosphere mainly via microbially mediated denitrification. Our limited understanding of the relative roles of the near-surface streambed sediment (hyporheic zone), benthic, and water column zones in controlling N2O production precludes predictions of N2O emissions along riverine networks. Here, we analyze N2O emissions from streams and rivers worldwide of different sizes, morphology, land cover, biomes, and climatic conditions. We show that the primary source of N2O emissions varies with stream and river size and shifts from the hyporheic–benthic zone in headwater streams to the benthic–water column zone in rivers. This analysis reveals that N2O production is bounded between two N2O emission potentials: the upper N2O emission potential results from production within the benthic–hyporheic zone, and the lower N2O emission potential reflects the production within the benthic–water column zone. By understanding the scaling nature of N2O production along riverine networks, our framework facilitates predictions of riverine N2O emissions globally using widely accessible chemical and hydromorphological datasets and thus, quantifies the effect of human activity and natural processes on N2O production. PMID:28400514

Organic carbon mineralization in the Santa Catalina Basin: benthic boundary layer metabolism

NASA Astrophysics Data System (ADS)

Smith, K. L.; Carlucci, A. F.; Jahnke, R. A.; Craven, D. B.

1987-02-01

Organic carbon mineralization rates in the benthic boundary layer (BBL) of the Santa Catalina Basin (1300 m depth) were estimated to identify the primary sites and organisms involved in the turnover of carbon and to compare these rates with the supply of particulate organic matter entering the system from above. Concurrent in situ measurements of macrozooplankton, epibenthic megafauna, and sediment community oxygen consumption, and bacterioplankton and total microbial (microplankton) metabolism were made on 12 dives with DSRV Alvin in November 1984. Pore water and solid phase chemistries, and sediment microbial activity were measured on samples from box cores. Macrozooplankton oxygen consumption, integrated over the 100 m BBL, was 25.8 μmol O 2 m -2 d -1 (0.3 mg C m -2 d -1). Microplankton carbon mineralization rates were 13-29 mg C m -2 d -1 for the BBL with an assimilation efficiency of 80-90%. The estimated oxygen consumption of the dominant population of epibenthic megafauna, Ophiophthalmus normani, at observed densities was 237.8 μmol O 2 m -2 d -1 (2.4 mg C m -2 d -1). Sediment community oxygen consumption was 2776.8 μmol O 2 m -2 d -1 (28.6 mg C m -2 d -1) which is similar to the estimated microbial carbon mineralization estimate for the sediments of 32 mg C m -2 d -1 assuming a 90% assimilation efficiency. These rates were corroborated further by the observed total inorganic carbon pore water gradients from which a mineralization rate of 10-31 mg C m -2 d -1 was estimated. The combined carbon mineralization by the three consumer groups ranged from 25.7 to 63.7 mg C m -2 d -1. For comparison, the oxygen consumption in the BBL based on hydrographic data from the center and sills of the basin was 3.1-20.0 mg C m -2 d -1. Given the large uncertainties in all of the calculations, there was reasonable agreement between these diverse methods of estimating carbon mineralization. The concurrently measured flux of small particulate organic carbon into the BBL using sediment traps was 11.1 ± 2.4 mg C m -2 d -1, providing 17-43% of the estimated carbon mineralized by the three consumer groups.

Lipid Biomarkers for a Hypersaline Microbial Mat Community

NASA Technical Reports Server (NTRS)

Jahnke, Linda L.; Embaye, Tsege; Turk, Kendra A.

2003-01-01

The use of lipid biomarkers and their carbon isotopic compositions are valuable tools for establishing links to ancient microbial ecosystems. As witnessed by the stromatolite record, benthic microbial mats grew in shallow water lagoonal environments where microorganisms had virtually no competition apart from the harsh conditions of hypersalinity, desiccation and intense light. Today, the modern counterparts of these microbial ecosystems find appropriate niches in only a few places where extremes eliminate eukaryotic grazers. Answers to many outstanding questions about the evolution of microorganisms and their environments on early Earth are best answered through study of these extant analogs. Lipids associated with various groups of bacteria can be valuable biomarkers for identification of specific groups of microorganisms both in ancient organic-rich sedimentary rocks (geolipids) and contemporary microbial communities (membrane lipids). Use of compound specific isotope analysis adds additional refinement to the identification of biomarker source, so that it is possible to take advantage of the 3C-depletions associated with various functional groups of organisms (i.e. autotrophs, heterotrophs, methanotrophs, methanogens) responsible for the cycling of carbon within a microbial community. Our recent work has focused on a set of hypersaline evaporation ponds at Guerrero Negro, Baja California Sur, Mexico which support the abundant growth of Microcoleus-dominated microbial mats. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface.

The Identification of Cable Bacteria Attached to the Anode of a Benthic Microbial Fuel Cell: Evidence of Long Distance Extracellular Electron Transport to Electrodes

PubMed Central

Reimers, Clare E.; Li, Cheng; Graw, Michael F.; Schrader, Paul S.; Wolf, Michael

2017-01-01

Multicellular, filamentous, sulfur-oxidizing bacteria, known as cable bacteria, were discovered attached to fibers of a carbon brush electrode serving as an anode of a benthic microbial fuel cell (BMFC). The BMFC had been operated in a temperate estuarine environment for over a year before collecting anode samples for scanning electron microscopy and phylogenetic analyses. Individual filaments were attached by single terminus cells with networks of pilus-like nano-filaments radiating out from these cells, across the anode fiber surface, and between adjacent attachment locations. Current harvesting by the BMFC poised the anode at potentials of ~170–250 mV vs. SHE, and these surface potentials appear to have allowed the cable bacteria to use the anode as an electron acceptor in a completely anaerobic environment. A combination of catalyzed reporter deposition fluorescent in situ hybridization (CARD-FISH) and 16S rRNA gene sequence analysis confirmed the phylogeny of the cable bacteria and showed that filaments often occurred in bundles and in close association with members of the genera Desulfuromonas. However, the Desulfobulbaceae Operational Taxonomic Units (OTUs) from the 16S sequencing did not cluster closely with other putative cable bacteria sequences suggesting that the taxonomic delineation of cable bacteria is far from complete. PMID:29114243

Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data

PubMed Central

Meirelles, Pedro M.; Amado-Filho, Gilberto M.; Pereira-Filho, Guilherme H.; Pinheiro, Hudson T.; de Moura, Rodrigo L.; Joyeux, Jean-Christophe; Mazzei, Eric F.; Bastos, Alex C.; Edwards, Robert A.; Dinsdale, Elizabeth; Paranhos, Rodolfo; Santos, Eidy O.; Iida, Tetsuya; Gotoh, Kazuyoshi; Nakamura, Shota; Sawabe, Tomoo; Rezende, Carlos E.; Gadelha, Luiz M. R.; Francini-Filho, Ronaldo B.; Thompson, Cristiane; Thompson, Fabiano L.

2015-01-01

Seamounts are considered important sources of biodiversity and minerals. However, their biodiversity and health status are not well understood; therefore, potential conservation problems are unknown. The mesophotic reefs of the Vitória-Trindade Seamount Chain (VTC) were investigated via benthic community and fish surveys, metagenomic and water chemistry analyses, and water microbial abundance estimations. The VTC is a mosaic of reef systems and includes fleshy algae dominated rhodolith beds, crustose coralline algae (CCA) reefs, and turf algae dominated rocky reefs of varying health levels. Macro-carnivores and larger fish presented higher biomass at the CCA reefs (4.4 kg per frame) than in the rhodolith beds and rocky reefs (0.0 to 0.1 kg per frame). A larger number of metagenomic sequences identified as primary producers (e.g., Chlorophyta and Streptophyta) were found at the CCA reefs. However, the rocky reefs contained more diseased corals (>90%) than the CCA reefs (~40%) and rhodolith beds (~10%). Metagenomic analyses indicated a heterotrophic and fast-growing microbiome in rocky reef corals that may possibly lead to unhealthy conditions possibly enhanced by environmental features (e.g. light stress and high loads of labile dissolved organic carbon). VTC mounts represent important hotspots of biodiversity that deserve further conservation actions. PMID:26090804

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.

Patterns of benthic bacterial diversity in coastal areas contaminated by heavy metals, polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs)

PubMed Central

Quero, Grazia Marina; Cassin, Daniele; Botter, Margherita; Perini, Laura; Luna, Gian Marco

2015-01-01

Prokaryotes in coastal sediments are fundamental players in the ecosystem functioning and regulate processes relevant in the global biogeochemical cycles. Nevertheless, knowledge on benthic microbial diversity patterns across spatial scales, or as function to anthropogenic influence, is still limited. We investigated the microbial diversity in two of the most chemically polluted sites along the coast of Italy. One site is the Po River Prodelta (Northern Adriatic Sea), which receives contaminant discharge from one of the largest rivers in Europe. The other site, the Mar Piccolo of Taranto (Ionian Sea), is a chronically polluted area due to steel production plants, oil refineries, and intense maritime traffic. We collected sediments from 30 stations along gradients of contamination, and studied prokaryotic diversity using Illumina sequencing of amplicons of a 16S rDNA gene fragment. The main sediment variables and the concentration of eleven metals, polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) were measured. Chemical analyses confirmed the high contamination in both sites, with concentrations of PCBs particularly high and often exceeding the sediment guidelines. The analysis of more than 3 millions 16S rDNA sequences showed that richness decreased with higher contamination levels. Multivariate analyses showed that contaminants significantly shaped community composition. Assemblages differed significantly between the two sites, but showed wide within-site variations related with spatial gradients in the chemical contamination, and the presence of a core set of OTUs shared by the two geographically distant sites. A larger importance of PCB-degrading taxa was observed in the Mar Piccolo, suggesting their potential selection in this historically polluted site. Our results indicate that sediment contamination by multiple contaminants significantly alter benthic prokaryotic diversity in coastal areas, and suggests considering the potential contribution of the resident microbes to contaminant bioremediation actions. PMID:26528247

Effects of Lumbriculus variegatus (Annelida, Oligochaete) bioturbation on zinc sediment chemistry and toxicity to the epi-benthic invertebrate Chironomus tepperi (Diptera: Chironomidae).

PubMed

Colombo, Valentina; Pettigrove, Vincent J; Hoffmann, Ary A; Golding, Lisa A

2016-09-01

Classical laboratory-based single-species sediment bioassays do not account for modifications to toxicity from bioturbation by benthic organisms which may impact predictions of contaminated sediment risk to biota in the field. This study aims to determine the effects of bioturbation on the toxicity of zinc measured in a standard laboratory bioassay conducted with chironomid larvae (Chironomus tepperi). The epi-benthic chironomid larvae were exposed to two different levels of sediment contamination (1600 and 1980 mg/kg of dry weight zinc) in the presence or absence of annelid worms (Lumbriculus variegatus) which are known to be tolerant to metal and to have a large impact on sediment properties through bioturbation. Chironomids had 5-6x higher survival in the presence of L. variegatus which shows that bioturbation had a beneficial effect on the chironomid larvae. Chemical analyses showed that bioturbation induced a flux of zinc from the pore water into the water column, thereby reducing the bioavailability of zinc in pore water to the chironomid larvae. This also suggested that pore water was the major exposure path for the chironomids to metals in sediment. During the study, annelid worms (Oligochaetes) produced a thin layer of faecal pellets at the sediment surface, a process known to: (i) create additional adsorption sites for zinc, thus reducing its availability, (ii) increase the microbial abundance that in turn could represent an additional food source for opportunistic C. tepperi larvae, and (iii) modify the microbial community's structure and alter the biogeochemical processes it governs thus indirectly impact zinc toxicity. This study represents a contribution in recognising bioturbating organisms as "ecological engineers" as they directly and indirectly influence metal bioavailability and impact other sediment-inhabiting species. This is significant and should be considered in risk assessment of zinc levels (and other metals) in contaminated sediment when extrapolating from laboratory studies to the field. Copyright © 2016 Elsevier Ltd. All rights reserved.

Origin of Cretaceous phosphorites from the onshore of Tamil Nadu, India

NASA Astrophysics Data System (ADS)

Purnachandra Rao, V.; Kessarkar, Pratima M.; Nagendra, R.; Babu, E. V. S. S. K.

2007-12-01

Cretaceous phosphorites from the onshore of Tamil Nadu have been investigated for their origin and compared with those in the offshore. Cretaceous phosphorites occur as light brown to yellowish brown or white nodules in Karai Shale of the Uttatur Group in the onshore Cauvery basin. Nodules exhibit phosphatic nucleus encrusted by a chalky shell of carbonate. The nucleus of the nodules consists of light and dark coloured laminae, phosphate peloids/coated grains and detrital particles interspersed between the laminae. Scanning electron microscope (SEM) studies reveal trapping and binding activity of microbial filaments. A mat structure with linearly arranged microbial filaments and hollow, cell-based coccoid cyanobacterial mat are present. Nodules contain abundant carbonate fluorapatite, followed by minor calcite, quartz and feldspar. The P2O5 content of the phosphorites ranges from 18 to 26%. The CaO/P2O5, Sr and F contents are higher than that of pure carbonate fluorapatite. Concentrations of Si, Al, K, Fe, and Ti are low. We suggest that the nuclei of the nodules represent phosphate clasts related to phosphate stromatolites formed at intertidal conditions. At high energy levels the microbial mats were disintegrated into phosphate clasts, coated with carbonate and then reworked into Karai Shale. On the other hand, Quaternary phosphorites occur as irregular to rounded, grey coloured phosphate clasts at water depths between 180 and 320m on the continental shelf of Tamil Nadu. They exhibit grain-supported texture. Despite Quaternary in age, they also resemble phosphate stromatolites of intertidal origin and reworked as phosphate clasts onto the shelf margin depressions. Benthic microbial mats probably supplied high phosphorus to the sediments. Availability of excess phosphorus seems to be a pre-requisite for the formation of phosphate stromatolites.

Methane-Carbon Flow into the Benthic Food Web at Cold Seeps – A Case Study from the Costa Rica Subduction Zone

PubMed Central

Niemann, Helge; Linke, Peter; Knittel, Katrin; MacPherson, Enrique; Boetius, Antje; Brückmann, Warner; Larvik, Gaute; Wallmann, Klaus; Schacht, Ulrike; Omoregie, Enoma; Hilton, David; Brown, Kevin; Rehder, Gregor

2013-01-01

Cold seep ecosystems can support enormous biomasses of free-living and symbiotic chemoautotrophic organisms that get their energy from the oxidation of methane or sulfide. Most of this biomass derives from animals that are associated with bacterial symbionts, which are able to metabolize the chemical resources provided by the seeping fluids. Often these systems also harbor dense accumulations of non-symbiotic megafauna, which can be relevant in exporting chemosynthetically fixed carbon from seeps to the surrounding deep sea. Here we investigated the carbon sources of lithodid crabs (Paralomis sp.) feeding on thiotrophic bacterial mats at an active mud volcano at the Costa Rica subduction zone. To evaluate the dietary carbon source of the crabs, we compared the microbial community in stomach contents with surface sediments covered by microbial mats. The stomach content analyses revealed a dominance of epsilonproteobacterial 16S rRNA gene sequences related to the free-living and epibiotic sulfur oxidiser Sulfurovum sp. We also found Sulfurovum sp. as well as members of the genera Arcobacter and Sulfurimonas in mat-covered surface sediments where Epsilonproteobacteria were highly abundant constituting 10% of total cells. Furthermore, we detected substantial amounts of bacterial fatty acids such as i-C15∶0 and C17∶1ω6c with stable carbon isotope compositions as low as −53‰ in the stomach and muscle tissue. These results indicate that the white microbial mats at Mound 12 are comprised of Epsilonproteobacteria and that microbial mat-derived carbon provides an important contribution to the crab's nutrition. In addition, our lipid analyses also suggest that the crabs feed on other 13C-depleted organic matter sources, possibly symbiotic megafauna as well as on photosynthetic carbon sources such as sedimentary detritus. PMID:24116017

Methane-carbon flow into the benthic food web at cold seeps--a case study from the Costa Rica subduction zone.

PubMed

Niemann, Helge; Linke, Peter; Knittel, Katrin; MacPherson, Enrique; Boetius, Antje; Brückmann, Warner; Larvik, Gaute; Wallmann, Klaus; Schacht, Ulrike; Omoregie, Enoma; Hilton, David; Brown, Kevin; Rehder, Gregor

2013-01-01

Cold seep ecosystems can support enormous biomasses of free-living and symbiotic chemoautotrophic organisms that get their energy from the oxidation of methane or sulfide. Most of this biomass derives from animals that are associated with bacterial symbionts, which are able to metabolize the chemical resources provided by the seeping fluids. Often these systems also harbor dense accumulations of non-symbiotic megafauna, which can be relevant in exporting chemosynthetically fixed carbon from seeps to the surrounding deep sea. Here we investigated the carbon sources of lithodid crabs (Paralomis sp.) feeding on thiotrophic bacterial mats at an active mud volcano at the Costa Rica subduction zone. To evaluate the dietary carbon source of the crabs, we compared the microbial community in stomach contents with surface sediments covered by microbial mats. The stomach content analyses revealed a dominance of epsilonproteobacterial 16S rRNA gene sequences related to the free-living and epibiotic sulfur oxidiser Sulfurovum sp. We also found Sulfurovum sp. as well as members of the genera Arcobacter and Sulfurimonas in mat-covered surface sediments where Epsilonproteobacteria were highly abundant constituting 10% of total cells. Furthermore, we detected substantial amounts of bacterial fatty acids such as i-C15∶0 and C17∶1ω6c with stable carbon isotope compositions as low as -53‰ in the stomach and muscle tissue. These results indicate that the white microbial mats at Mound 12 are comprised of Epsilonproteobacteria and that microbial mat-derived carbon provides an important contribution to the crab's nutrition. In addition, our lipid analyses also suggest that the crabs feed on other (13)C-depleted organic matter sources, possibly symbiotic megafauna as well as on photosynthetic carbon sources such as sedimentary detritus.

Benthic food web structure in the Comau fjord, Chile (∼42°S): Preliminary assessment including a site with chemosynthetic activity

NASA Astrophysics Data System (ADS)

Zapata-Hernández, Germán; Sellanes, Javier; Mayr, Christoph; Muñoz, Práxedes

2014-12-01

Using C and N stable isotopes we analyzed different trophic aspects of the benthic fauna at two sites in the Comau fjord: one with presence of venting of chemically reducing fluids and extensive patches of bacterial mats (XH: X-Huinay), and one control site (PG: Punta Gruesa) with a typical fjord benthic habitat. Due to the widespread presence of such microbial patches in the fjord and their recognized trophic role in reducing environments, we hypothesize that these microbial communities could be contributing to the assimilated food of consumers and transferring carbon into high trophic levels in the food web. Food sources in the area included macroalgae with a wide range of δ13C values (-34.7 to -11.9‰), particulate organic matter (POM, δ13C = -20.1‰), terrestrial organic matter (TOM, δ13C = -32.3‰ to -27.9‰) and chemosynthetic filamentous bacteria (δ13C = ∼-33‰). At both sites, fauna depicted typical values indicating photosynthetic production as a main food source (>-20‰). However, at XH selected taxa reported lower δ13C values (e.g. -26.5‰ in Nacella deaurata), suggesting a partial use of chemosynthetic production. Furthermore, enhanced variability at this site in δ13C values of the polyplacophoran Chiton magnificus, the limpet Fissurella picta and the tanaid Zeuxoides sp. may also be responding to the use of a wider scope of primary food sources. Trophic position estimates suggest three trophic levels of consumers at both sites. However, low δ15N values in some grazer and suspension-feeder species suggest that these taxa could be using other sources still to be identified (e.g. bacterial films, microalgae and organic particles of small size-fractions). Furthermore, between-site comparisons of isotopic niche width measurements in some trophic guilds indicate that grazers from XH have more heterogenic trophic niches than at PG (measured as mean distance to centroid and standard deviation of nearest neighbor distance). This last could be ascribed to the utilization of a mixture of photosynthetic and chemosynthetic carbon sources. In addition, corrected standard ellipses area (SEAc) values in suspension-feeders and carnivores at both sites suggest a similar magnitude of exploitation of food sources. However, grazers from XH have a greater expansion of their isotopic niche (SEAc), probably explained by the presence of species with low δ13C and δ15N values, and directly associated to chemosynthetic carbon incorporation.

New multi-scale perspectives on the stromatolites of Shark Bay, Western Australia.

PubMed

Suosaari, E P; Reid, R P; Playford, P E; Foster, J S; Stolz, J F; Casaburi, G; Hagan, P D; Chirayath, V; Macintyre, I G; Planavsky, N J; Eberli, G P

2016-02-03

A recent field-intensive program in Shark Bay, Western Australia provides new multi-scale perspectives on the world's most extensive modern stromatolite system. Mapping revealed a unique geographic distribution of morphologically distinct stromatolite structures, many of them previously undocumented. These distinctive structures combined with characteristic shelf physiography define eight 'Stromatolite Provinces'. Morphological and molecular studies of microbial mat composition resulted in a revised growth model where coccoid cyanobacteria predominate in mat communities forming lithified discrete stromatolite buildups. This contradicts traditional views that stromatolites with the best lamination in Hamelin Pool are formed by filamentous cyanobacterial mats. Finally, analysis of internal fabrics of stromatolites revealed pervasive precipitation of microcrystalline carbonate (i.e. micrite) in microbial mats forming framework and cement that may be analogous to the micritic microstructures typical of Precambrian stromatolites. These discoveries represent fundamental advances in our knowledge of the Shark Bay microbial system, laying a foundation for detailed studies of stromatolite morphogenesis that will advance our understanding of benthic ecosystems on the early Earth.

Origin of marine planktonic cyanobacteria.

PubMed

Sánchez-Baracaldo, Patricia

2015-12-01

Marine planktonic cyanobacteria contributed to the widespread oxygenation of the oceans towards the end of the Pre-Cambrian and their evolutionary origin represents a key transition in the geochemical evolution of the Earth surface. Little is known, however, about the evolutionary events that led to the appearance of marine planktonic cyanobacteria. I present here phylogenomic (135 proteins and two ribosomal RNAs), Bayesian relaxed molecular clock (18 proteins, SSU and LSU) and Bayesian stochastic character mapping analyses from 131 cyanobacteria genomes with the aim to unravel key evolutionary steps involved in the origin of marine planktonic cyanobacteria. While filamentous cell types evolved early on at around 2,600-2,300 Mya and likely dominated microbial mats in benthic environments for most of the Proterozoic (2,500-542 Mya), marine planktonic cyanobacteria evolved towards the end of the Proterozoic and early Phanerozoic. Crown groups of modern terrestrial and/or benthic coastal cyanobacteria appeared during the late Paleoproterozoic to early Mesoproterozoic. Decrease in cell diameter and loss of filamentous forms contributed to the evolution of unicellular planktonic lineages during the middle of the Mesoproterozoic (1,600-1,000 Mya) in freshwater environments. This study shows that marine planktonic cyanobacteria evolved from benthic marine and some diverged from freshwater ancestors during the Neoproterozoic (1,000-542 Mya).

Origin of marine planktonic cyanobacteria

PubMed Central

Sánchez-Baracaldo, Patricia

2015-01-01

Marine planktonic cyanobacteria contributed to the widespread oxygenation of the oceans towards the end of the Pre-Cambrian and their evolutionary origin represents a key transition in the geochemical evolution of the Earth surface. Little is known, however, about the evolutionary events that led to the appearance of marine planktonic cyanobacteria. I present here phylogenomic (135 proteins and two ribosomal RNAs), Bayesian relaxed molecular clock (18 proteins, SSU and LSU) and Bayesian stochastic character mapping analyses from 131 cyanobacteria genomes with the aim to unravel key evolutionary steps involved in the origin of marine planktonic cyanobacteria. While filamentous cell types evolved early on at around 2,600–2,300 Mya and likely dominated microbial mats in benthic environments for most of the Proterozoic (2,500–542 Mya), marine planktonic cyanobacteria evolved towards the end of the Proterozoic and early Phanerozoic. Crown groups of modern terrestrial and/or benthic coastal cyanobacteria appeared during the late Paleoproterozoic to early Mesoproterozoic. Decrease in cell diameter and loss of filamentous forms contributed to the evolution of unicellular planktonic lineages during the middle of the Mesoproterozoic (1,600–1,000 Mya) in freshwater environments. This study shows that marine planktonic cyanobacteria evolved from benthic marine and some diverged from freshwater ancestors during the Neoproterozoic (1,000–542 Mya). PMID:26621203

Diverse microbially induced sedimentary structures from 1 Ga lakes of the Diabaig Formation, Torridon Group, northwest Scotland

NASA Astrophysics Data System (ADS)

Callow, Richard H. T.; Battison, Leila; Brasier, Martin D.

2011-08-01

The siliciclastic lacustrine rocks of the ~ 1000 Ma Diabaig Formation, northwest Scotland, contain a remarkable diversity of macroscopic structures on bedding planes that can be compared with various kinds of microbially induced sedimentary structures (MISS). Field sedimentological investigations, combined with laboratory analysis of bedding planes and petrographic study of thin sections have allowed us to characterise a range of depositional environments and document the spectrum of biological structures. MISS are reported from frequently subaerial environments, through commonly submerged facies, and down to permanently sub-wavebase settings. Palaeoenvironmental conditions (water depth, exposure, hydrodynamic energy) control the distribution of MISS within these facies. This demonstrates that mat-forming microbial communities were arguably well adapted to low light levels or periodic exposure. Some MISS from the Diabaig Formation are typical of Precambrian microbial mats, including reticulate fabrics and 'old elephant skin' textures. In addition to these, a number of new and unusual fabrics of putative microbial origin are described, including linear arrays of ridges and grooves (cf. 'Arumberia') and discoidal structures that are comparable with younger Ediacaran fossils such as Beltanelliformis. These observations indicate that benthic microbial ecosystems were thriving in freshwater lake systems ~ 1000 Ma, and indicate how microbially induced sedimentary structures may be applied as facies indicators for Proterozoic lacustrine environments. The discovery of structures closely resembling Ediacaran fossils (cf. Beltanelliformis) also serves to highlight the difficulty of interpreting simple discoidal bedding plane structures as metazoan fossils.

Biologically induced mineralization of dypingite by cyanobacteria from an alkaline wetland near Atlin, British Columbia, Canada

PubMed Central

Power, Ian M; Wilson, Siobhan A; Thom, James M; Dipple, Gregory M; Southam, Gordon

2007-01-01

Background This study provides experimental evidence for biologically induced precipitation of magnesium carbonates, specifically dypingite (Mg5(CO3)4(OH)2·5H2O), by cyanobacteria from an alkaline wetland near Atlin, British Columbia. This wetland is part of a larger hydromagnesite (Mg5(CO3)4(OH)2·4H2O) playa. Abiotic and biotic processes for magnesium carbonate precipitation in this environment are compared. Results Field observations show that evaporation of wetland water produces carbonate films of nesquehonite (MgCO3·3H2O) on the water surface and crusts on exposed surfaces. In contrast, benthic microbial mats possessing filamentous cyanobacteria (Lyngbya sp.) contain platy dypingite (Mg5(CO3)4(OH)2·5H2O) and aragonite. Bulk carbonates in the benthic mats (δ13C avg. = 6.7‰, δ18O avg. = 17.2‰) were isotopically distinguishable from abiotically formed nesquehonite (δ13C avg. = 9.3‰, δ18O avg. = 24.9‰). Field and laboratory experiments, which emulated natural conditions, were conducted to provide insight into the processes for magnesium carbonate precipitation in this environment. Field microcosm experiments included an abiotic control and two microbial systems, one containing ambient wetland water and one amended with nutrients to simulate eutrophic conditions. The abiotic control developed an extensive crust of nesquehonite on its bottom surface during which [Mg2+] decreased by 16.7% relative to the starting concentration. In the microbial systems, precipitation occurred within the mats and was not simply due to the capturing of mineral grains settling out of the water column. Magnesium concentrations decreased by 22.2% and 38.7% in the microbial systems, respectively. Laboratory experiments using natural waters from the Atlin site produced rosettes and flakey globular aggregates of dypingite precipitated in association with filamentous cyanobacteria dominated biofilms cultured from the site, whereas the abiotic control again precipitated nesquehonite. Conclusion Microbial mats in the Atlin wetland create ideal conditions for biologically induced precipitation of dypingite and have presumably played a significant role in the development of this natural Mg-carbonate playa. This biogeochemical process represents an important link between the biosphere and the inorganic carbon pool. PMID:18053262

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.

Characterizing Microbial Mat Morphology with Structure from Motion Techniques in Ice-Covered Lake Joyce, McMurdo Dry Valleys, Antarctica

NASA Astrophysics Data System (ADS)

Mackey, T. J.; Leidman, S. Z.; Allen, B.; Hawes, I.; Lawrence, J.; Jungblut, A. D.; Krusor, M.; Coleman, L.; Sumner, D. Y.

2015-12-01

Structure from Motion (SFM) techniques can provide quantitative morphological documentation of otherwise inaccessible benthic ecosystems such as microbial mats in Lake Joyce, a perennially ice-covered lake of the Antarctic McMurdo Dry Valleys (MDV). Microbial mats are a key ecosystem of MDV lakes, and diverse mat morphologies like pinnacles emerge from interactions among microbial behavior, mineralization, and environmental conditions. Environmental gradients can be isolated to test mat growth models, but assessment of mat morphology along these gradients is complicated by their inaccessibility: the Lake Joyce ice cover is 4-5 m thick, water depths containing diverse pinnacle morphologies are 9-14 m, and relevant mat features are cm-scale. In order to map mat pinnacle morphology in different sedimentary settings, we deployed drop cameras (SeaViewer and GoPro) through 29 GPS referenced drill holes clustered into six stations along a transect spanning 880 m. Once under the ice cover, a boom containing a second GoPro camera was unfurled and rotated to collect oblique images of the benthic mats within dm of the mat-water interface. This setup allowed imaging from all sides over a ~1.5 m diameter area of the lake bottom. Underwater lens parameters were determined for each camera in Agisoft Lens; images were reconstructed and oriented in space with the SFM software Agisoft Photoscan, using the drop camera axis of rotation as up. The reconstructions were compared to downward facing images to assess accuracy, and similar images of an object with known geometry provided a test for expected error in reconstructions. Downward facing images identify decreasing pinnacle abundance in higher sedimentation settings, and quantitative measurements of 3D reconstructions in KeckCAVES LidarViewer supplement these mat morphological facies with measurements of pinnacle height and orientation. Reconstructions also help isolate confounding variables for mat facies trends with measurements of lake bottom slope and underlying relief that could influence pinnacle growth. Comparison of 3D reconstructions to downward-facing drop camera images demonstrate that SFM is a powerful tool for documenting diverse mat morphologies across environmental gradients in ice-covered lakes.

Macrofaunal communities associated with chemosynthetic habitats from the U.S. Atlantic margin: A comparison among depth and habitat types

USGS Publications Warehouse

Bourque, Jill R.; Robertson, Craig M.; Brooke, Sandra; Demopoulos, Amanda W.J.

2016-01-01

Hydrocarbon seeps support distinct benthic communities capable of tolerating extreme environmental conditions and utilizing reduced chemical compounds for nutrition. In recent years, several locations of methane seepage have been mapped along the U.S. Atlantic continental slope. In 2012 and 2013, two newly discovered seeps were investigated in this region: a shallow site near Baltimore Canyon (BCS, 366–412 m) and a deep site near Norfolk Canyon (NCS, 1467–1602 m), with both sites containing extensive chemosynthetic mussel bed and microbial mat habitats. Sediment push cores, suction samples, and Ekman box cores were collected to quantify the abundance, diversity, and community structure of benthic macrofauna (>300 μm) in mussel beds, mats, and slope habitats at both sites. Community data from the deep site were also assessed in relation to the associated sediment environment (organic carbon and nitrogen, stable carbon and nitrogen isotopes, grain size, and depth). Infaunal assemblages and densities differed both between depths and among habitat types. Macrofaunal densities in microbial mats were four times greater than those present in mussel beds and slope sediments and were dominated by the annelid families Dorvilleidae, Capitellidae, and Tubificidae, while mussel habitats had higher proportions of crustaceans. Diversity was lower in BCS microbial mat habitats, but higher in mussel and slope sediments compared to NCS habitats. Multivariate statistical analysis revealed specific sediment properties as important for distinguishing the macrofaunal communities, including larger grain sizes present within NCS microbial mat habitats and depleted stable carbon isotopes (δ13C) in sediments present at mussel beds. These results suggest that habitat differences in the quality and source of organic matter are driving the observed patterns in the infaunal assemblages, including high β diversity and high variability in the macrofaunal community composition. This study is the first investigation of seep infauna along the U.S. Atlantic slope north of the Blake Ridge Diapir and provides a baseline for future regional comparisons to other seep habitats along the Atlantic margin.

Macrofaunal communities associated with chemosynthetic habitats from the U.S. Atlantic margin: A comparison among depth and habitat types

NASA Astrophysics Data System (ADS)

Bourque, Jill R.; Robertson, Craig M.; Brooke, Sandra; Demopoulos, Amanda W. J.

2017-03-01

Hydrocarbon seeps support distinct benthic communities capable of tolerating extreme environmental conditions and utilizing reduced chemical compounds for nutrition. In recent years, several locations of methane seepage have been mapped along the U.S. Atlantic continental slope. In 2012 and 2013, two newly discovered seeps were investigated in this region: a shallow site near Baltimore Canyon (BCS, 366-412 m) and a deep site near Norfolk Canyon (NCS, 1467-1602 m), with both sites containing extensive chemosynthetic mussel bed and microbial mat habitats. Sediment push cores, suction samples, and Ekman box cores were collected to quantify the abundance, diversity, and community structure of benthic macrofauna (>300 μm) in mussel beds, mats, and slope habitats at both sites. Community data from the deep site were also assessed in relation to the associated sediment environment (organic carbon and nitrogen, stable carbon and nitrogen isotopes, grain size, and depth). Infaunal assemblages and densities differed both between depths and among habitat types. Macrofaunal densities in microbial mats were four times greater than those present in mussel beds and slope sediments and were dominated by the annelid families Dorvilleidae, Capitellidae, and Tubificidae, while mussel habitats had higher proportions of crustaceans. Diversity was lower in BCS microbial mat habitats, but higher in mussel and slope sediments compared to NCS habitats. Multivariate statistical analysis revealed specific sediment properties as important for distinguishing the macrofaunal communities, including larger grain sizes present within NCS microbial mat habitats and depleted stable carbon isotopes (δ13C) in sediments present at mussel beds. These results suggest that habitat differences in the quality and source of organic matter are driving the observed patterns in the infaunal assemblages, including high β diversity and high variability in the macrofaunal community composition. This study is the first investigation of seep infauna along the U.S. Atlantic slope north of the Blake Ridge Diapir and provides a baseline for future regional comparisons to other seep habitats along the Atlantic margin.

Dinitrogen-fixing cyanobacteria in microbial mats of two shallow coral reef ecosystems.

PubMed

Charpy, Loic; Palinska, Katarzyna A; Casareto, Beatriz; Langlade, Marie José; Suzuki, Yoshimi; Abed, Raeid M M; Golubic, Stjepko

2010-01-01

Dinitrogen-fixing organisms in cyanobacterial mats were studied in two shallow coral reef ecosystems: La Reunion Island, southwestern Indian Ocean, Sesoko (Okinawa) Island, and northwestern Pacific Ocean. Rapidly expanding benthic miniblooms, frequently dominated by a single cyanobacterial taxon, were identified by microscopy and molecular tools. In addition, nitrogenase activity by these blooms was measured in situ. Dinitrogen fixation and its contribution to mat primary production were calculated using (15)N(2) and (13)C methods. Dinitrogen-fixing cyanobacteria from mats in La Reunion and Sesoko showed few differences in taxonomic composition. Anabaena sp. among heterocystous and Hydrocoleum majus and Symploca hydnoides among nonheterocystous cyanobacteria occurred in microbial mats of both sites. Oscillatoria bonnemaisonii and Leptolyngbya spp. occurred only in La Reunion, whereas Hydrocoleum coccineum dominated in Sesoko. Other mats dominated by Hydrocoleum lyngbyaceum, Phormidium laysanense, and Trichocoleus tenerrimus occurred at lower frequencies. The 24-h nitrogenase activity, as measured by acetylene reduction, varied between 11 and 324 nmoles C(2)H(2) reduced microg(-1) Chl a. The highest values were achieved by heterocystous Anabaena sp. performed mostly during the day. Highest values for nonheterocystous cyanobacteria were achieved by H. coccineum mostly during the night. Daily nitrogen fixation varied from nine (Leptolyngbya) to 238 nmoles N(2) microg(-1) Chl day(-1) (H. coccineum). Primary production rates ranged from 1,321 (S. hydnoides) to 9,933 nmoles C microg(-1) Chl day(-1) (H. coccineum). Dinitrogen fixation satisfied between 5% and 21% of the nitrogen required for primary production.

Early diagenesis in the sediments of the Congo deep-sea fan dominated by massive terrigenous deposits: Part II - Iron-sulfur coupling

NASA Astrophysics Data System (ADS)

Taillefert, Martial; Beckler, Jordon S.; Cathalot, Cécile; Michalopoulos, Panagiotis; Corvaisier, Rudolph; Kiriazis, Nicole; Caprais, Jean-Claude; Pastor, Lucie; Rabouille, Christophe

2017-08-01

Deep-sea fans are well known depot centers for organic carbon that should promote sulfate reduction. At the same time, the high rates of deposition of unconsolidated metal oxides from terrigenous origin may also promote metal-reducing microbial activity. To investigate the eventual coupling between the iron and sulfur cycles in these environments, shallow sediment cores (< 50 cm) across various channels and levees in the Congo River deep-sea fan ( 5000 m) were profiled using a combination of geochemical methods. Interestingly, metal reduction dominated suboxic carbon remineralization processes in most of these sediments, while dissolved sulfide was absent. In some 'hotspot' patches, however, sulfate reduction produced large sulfide concentrations which supported chemosynthetic-based benthic megafauna. These environments were characterized by sharp geochemical boundaries compared to the iron-rich background environment, suggesting that FeS precipitation efficiently titrated iron and sulfide from the pore waters. A companion study demonstrated that methanogenesis was active in the deep sediment layers of these patchy ecosystems, suggesting that sulfate reduction was promoted by alternative anaerobic processes. These highly reduced habitats could be fueled by discrete, excess inputs of highly labile natural organic matter from Congo River turbidites or by exhumation of buried sulfide during channel flank erosion and slumping. Sulfidic conditions may be maintained by the mineralization of decomposition products from local benthic macrofauna or bacterial symbionts or by the production of more crystalline Fe(III) oxide phases that are less thermodynamically favorable than sulfate reduction in these bioturbated sediments. Overall, the iron and sulfur biogeochemical cycling in this environment is unique and much more similar to a coastal ecosystem than a deep-sea environment.

Composition and extracellular enzymatic function of pelagic, particle-associated, and benthic bacterial communities in the central Arctic Ocean

NASA Astrophysics Data System (ADS)

Balmonte, J. P.; Teske, A.; Arnosti, C.

2016-02-01

The structure and function of Arctic bacterial communities have rarely been studied in concert, but are crucial to our understanding of biogeochemical cycles. As the Arctic transitions to become seasonally-ice free, a critical priority is to elucidate the present ecological role and environmental dependence of Arctic bacterial communities. We investigated the depth and regional variations in Central Arctic bacterial community composition (BCC) and extracellular enzymatic activities (EEA)—the initial step in organic matter breakdown—to explore links between community structure and function. Samples were collected across a gradient of sea-ice cover (open ocean, first year ice, multi-year ice) from 79°N to 88°N and from surface to bottom waters ( 3.5 to 4.5 km). Pelagic BCC most strongly varies with hydrography and with particle-association, which likely selects for a specialized community of heterotrophic opportunists; benthic BCC show little regional variation. In contrast, EEA reveal significant depth and regional differences in hydrolysis rates as well as in the spectrum of substrates hydrolyzed. Particle-associated EEA reveal an equal or greater range of enzymatic capabilities than in bulk-seawater measurements, supporting previous findings that particles are hotspots of microbial heterotrophic activity. These patterns suggest a complex relationship between BCC, EEA, and the environment: while water mass characteristics consistently differentiate bacterial communities, additional local factors shape their capabilities to hydrolyze organic matter. Multivariate analyses will be used to further explore the relationships between composition and function as well as their correlations with environmental data. Our findings provide a baseline for future comparisons and initial insight into the functionality and biogeography of Arctic bacterial communities.

Benthic microbial fuel cell as direct power source for an acoustic modem and seawater oxygen/temperature sensor system.

PubMed

Gong, Yanming; Radachowsky, Sage E; Wolf, Michael; Nielsen, Mark E; Girguis, Peter R; Reimers, Clare E

2011-06-01

Supported by the natural potential difference between anoxic sediment and oxic seawater, benthic microbial fuel cells (BMFCs) promise to be ideal power sources for certain low-power marine sensors and communication devices. In this study a chambered BMFC with a 0.25 m(2) footprint was used to power an acoustic modem interfaced with an oceanographic sensor that measures dissolved oxygen and temperature. The experiment was conducted in Yaquina Bay, Oregon over 50 days. Several improvements were made in the BMFC design and power management system based on lessons learned from earlier prototypes. The energy was harvested by a dynamic gain charge pump circuit that maintains a desired point on the BMFC's power curve and stores the energy in a 200 F supercapacitor. The system also used an ultralow power microcontroller and quartz clock to read the oxygen/temperature sensor hourly, store data with a time stamp, and perform daily polarizations. Data records were transmitted to the surface by the acoustic modem every 1-5 days after receiving an acoustic prompt from a surface hydrophone. After jump-starting energy production with supplemental macroalgae placed in the BMFC's anode chamber, the average power density of the BMFC adjusted to 44 mW/m(2) of seafloor area which is better than past demonstrations at this site. The highest power density was 158 mW/m(2), and the useful energy produced and stored was ≥ 1.7 times the energy required to operate the system.

Molar tooth carbonates and benthic methane fluxes in Proterozoic oceans.

PubMed

Shen, Bing; Dong, Lin; Xiao, Shuhai; Lang, Xianguo; Huang, Kangjun; Peng, Yongbo; Zhou, Chuanming; Ke, Shan; Liu, Pengju

2016-01-07

Molar tooth structures are ptygmatically folded and microspar-filled structures common in early- and mid-Proterozoic (∼2,500-750 million years ago, Ma) subtidal successions, but extremely rare in rocks <750 Ma. Here, on the basis of Mg and S isotopes, we show that molar tooth structures may have formed within sediments where microbial sulphate reduction and methanogenesis converged. The convergence was driven by the abundant production of methyl sulphides (dimethyl sulphide and methanethiol) in euxinic or H2S-rich seawaters that were widespread in Proterozoic continental margins. In this convergence zone, methyl sulphides served as a non-competitive substrate supporting methane generation and methanethiol inhibited anaerobic oxidation of methane, resulting in the buildup of CH4, formation of degassing cracks in sediments and an increase in the benthic methane flux from sediments. Precipitation of crack-filling microspar was driven by methanogenesis-related alkalinity accumulation. Deep ocean ventilation and oxygenation around 750 Ma brought molar tooth structures to an end.

Biogeochemistry and community ecology in a spring-fed urban river following a major earthquake.

PubMed

Wells, Naomi S; Clough, Tim J; Condron, Leo M; Baisden, W Troy; Harding, Jon S; Dong, Y; Lewis, G D; Lear, Gavin

2013-11-01

In February 2011 a MW 6.3 earthquake in Christchurch, New Zealand inundated urban waterways with sediment from liquefaction and triggered sewage spills. The impacts of, and recovery from, this natural disaster on the stream biogeochemistry and biology were assessed over six months along a longitudinal impact gradient in an urban river. The impact of liquefaction was masked by earthquake triggered sewage spills (~20,000 m(3) day(-1) entering the river for one month). Within 10 days of the earthquake dissolved oxygen in the lowest reaches was <1 mg l(-1), in-stream denitrification accelerated (attenuating 40-80% of sewage nitrogen), microbial biofilm communities changed, and several benthic invertebrate taxa disappeared. Following sewage system repairs, the river recovered in a reverse cascade, and within six months there were no differences in water chemistry, nutrient cycling, or benthic communities between severely and minimally impacted reaches. This study highlights the importance of assessing environmental impact following urban natural disasters. Copyright © 2013 Elsevier Ltd. All rights reserved.

Molar tooth carbonates and benthic methane fluxes in Proterozoic oceans

PubMed Central

Shen, Bing; Dong, Lin; Xiao, Shuhai; Lang, Xianguo; Huang, Kangjun; Peng, Yongbo; Zhou, Chuanming; Ke, Shan; Liu, Pengju

2016-01-01

Molar tooth structures are ptygmatically folded and microspar-filled structures common in early- and mid-Proterozoic (∼2,500–750 million years ago, Ma) subtidal successions, but extremely rare in rocks <750 Ma. Here, on the basis of Mg and S isotopes, we show that molar tooth structures may have formed within sediments where microbial sulphate reduction and methanogenesis converged. The convergence was driven by the abundant production of methyl sulphides (dimethyl sulphide and methanethiol) in euxinic or H2S-rich seawaters that were widespread in Proterozoic continental margins. In this convergence zone, methyl sulphides served as a non-competitive substrate supporting methane generation and methanethiol inhibited anaerobic oxidation of methane, resulting in the buildup of CH4, formation of degassing cracks in sediments and an increase in the benthic methane flux from sediments. Precipitation of crack-filling microspar was driven by methanogenesis-related alkalinity accumulation. Deep ocean ventilation and oxygenation around 750 Ma brought molar tooth structures to an end. PMID:26739600

Meet the Arctic Benthos. Arctic Ocean Exploration--Grades 7-8. Benthic Invertebrate Groups in the Deep Arctic Ocean.

ERIC Educational Resources Information Center

National Oceanic and Atmospheric Administration (DOC), Rockville, MD.

This activity introduces students to major groups of invertebrates that have been found in other polar ocean expeditions and acquaints them with the feeding habits of these animals as a basis for making inferences about benthic communities and their connection to other components of the Artic Ocean ecosystem. The activity provides learning…

Nitrogen fixation dynamics of two diazotrophic communities in Mono Lake, California

USGS Publications Warehouse

Oremland, R.S.

1990-01-01

Two types of diazotrophic microbial communities were found in the littoral zone of alkaline hypersaline Mono Lake, California. One consisted of anaerobic bacteria inhabiting the flocculent surface layers of sediments. Nitrogen fixation (acetylene reduction) by flocculent surface layers occurred under anaerobic conditions, was not stimulated by light or by additions of organic substrates, and was inhibited by O2, nitrate, and ammonia. The second community consisted of a ball-shaped association of a filamentous chlorophyte (Ctenocladus circinnatus) with diazotrophic, nonheterocystous cyanobacteria, as well as anaerobic bacteria (Ctenocladus balls). Nitrogen fixation by Ctenocladus balls was usually, but not always, stimulated by light. Rates of anaerobic dark fixation equaled those in the light under air. Fixation in the light was stimulated by 3-(3,4-dichlorophenyl)-1,1-dimethylurea and by propanil [N-(3,4-dichlorophenyl)propanamide]. 3-(3,4-Dichlorophenyl)-1,1-dimethyl urea-elicited nitrogenase activity was inhibited by ammonia (96%) and nitrate (65%). Fixation was greatest when Ctenocladus balls were incubated anaerobically in the light with sulfide. Dark anaerobic fixation was not stimulated by organic substrates in short-term (4-h) incubations, but was in long-term (67-h) ones. Areal estimates of benthic N2 fixation were measured seasonally, using chambers. Highest rates (~29.3 ??mol of C2H4 m-2 h-1) occurred under normal diel regimens of light and dark. These estimates indicate that benthic N2 fixation has the potential to be a significant nitrogen source in Mono Lake.

Effects of natural and human-induced hypoxia on coastal benthos

NASA Astrophysics Data System (ADS)

Levin, L. A.; Ekau, W.; Gooday, A. J.; Jorissen, F.; Middelburg, J. J.; Naqvi, W.; Neira, C.; Rabalais, N. N.; Zhang, J.

2009-04-01

Coastal hypoxia (<1.42 ml L-1; 62.5 μM; 2 mg L-1, approx. 30% oxygen saturation) occurs seasonally in many estuaries, fjords, and along open coasts subject to upwelling or excessive riverine nutrient input, and permanently in some isolated seas and marine basins. Underlying causes of hypoxia include enhanced nutrient input from natural causes (upwelling) or anthropogenic origin (eutrophication) and reduction of mixing by limited circulation or enhanced stratification; combined these lead to higher surface water production, microbial respiration and eventual oxygen depletion. Advective inputs of low-oxygen waters may initiate or expand hypoxic conditions. Responses of estuarine, enclosed sea, and open shelf benthos to hypoxia depend on the duration, predictability, and intensity of oxygen depletion and on whether H2S is formed. Under suboxic conditions, large mats of filamentous sulfide oxidizing bacteria cover the seabed and consume sulfide, thereby providing a detoxified microhabitat for eukaryotic benthic communities. Calcareous foraminiferans and nematodes are particularly tolerant of low oxygen concentrations and may attain high densities and dominance, often in association with microbial mats. When oxygen is sufficient to support metazoans, small, soft-bodied invertebrates (typically annelids), often with short generation times and elaborate branchial structures, predominate. Large taxa are more sensitive than small taxa to hypoxia. Crustaceans and echinoderms are typically more sensitive to hypoxia, with lower oxygen thresholds, than annelids, sipunculans, molluscs and cnidarians. Mobile fish and shellfish will migrate away from low-oxygen areas. Within a species, early life stages may be more subject to oxygen stress than older life stages. Hypoxia alters both the structure and function of benthic communities, but effects may differ with regional hypoxia history. Human-caused hypoxia is generally linked to eutrophication, and occurs adjacent to watersheds with large populations or agricultural activities. Many occurrences are seasonal, within estuaries, fjords or enclosed seas of the North Atlantic and the NW Pacific Oceans. Benthic faunal responses, elicited at oxygen levels below 2 ml L-1, typically involve avoidance or mortality of large species and elevated abundances of enrichment opportunists, sometimes prior to population crashes. Areas of low oxygen persist seasonally or continuously beneath upwelling regions, associated with the upper parts of oxygen minimum zones (SE Pacific, W Africa, N Indian Ocean). These have a distribution largely distinct from eutrophic areas and support a resident fauna that is adapted to survive and reproduce at oxygen concentrations <0.5 ml L-1. Under both natural and eutrophication-caused hypoxia there is loss of diversity, through attrition of intolerant species and elevated dominance, as well as reductions in body size. These shifts in species composition and diversity yield altered trophic structure, energy flow pathways, and corresponding ecosystem services such as production, organic matter cycling and organic C burial. Increasingly the influences of nature and humans interact to generate or exacerbate hypoxia. A warmer ocean is more stratified, holds less oxygen, and may experience greater advection of oxygen-poor source waters, making new regions subject to hypoxia. Future understanding of benthic responses to hypoxia must be established in the context of global climate change and other human influences such as overfishing, pollution, disease, habitat loss, and species invasions.

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.

Two distinct microbial communities revealed in the sponge Cinachyrella

PubMed Central

Cuvelier, Marie L.; Blake, Emily; Mulheron, Rebecca; McCarthy, Peter J.; Blackwelder, Patricia; Thurber, Rebecca L. Vega; Lopez, Jose V.

2014-01-01

Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes), which can constitute up to 50% of the sponge biomass. Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rRNA gene tag pyrosequencing. Cinachyrella specimens and seawater samples were collected from the same South Florida reef at two different times of year. In total, 639 OTUs (12 archaeal and 627 bacterial) belonging to 2 archaeal and 21 bacterial phyla were detected in the sponges. Based on their microbiomes, the six sponge samples formed two distinct groups, namely sponge group 1 (SG1) with lower diversity (Shannon-Weiner index: 3.73 ± 0.22) and SG2 with higher diversity (Shannon-Weiner index: 5.95 ± 0.25). Hosts' 28S rRNA gene sequences further confirmed that the sponge specimens were composed of two taxa closely related to Cinachyrella kuekenthalli. Both sponge groups were dominated by Proteobacteria, but Alphaproteobacteria were significantly more abundant in SG1. SG2 harbored many bacterial phyla (>1% of sequences) present in low abundance or below detection limits (<0.07%) in SG1 including: Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, PAUC34f, Poribacteria, and Verrucomicrobia. Furthermore, SG1 and SG2 only had 95 OTUs in common, representing 30.5 and 22.4% of SG1 and SG2's total OTUs, respectively. These results suggest that the sponge host may exert a pivotal influence on the nature and structure of the microbial community and may only be marginally affected by external environment parameters. PMID:25408689

A depocenter of organic matter at 7800 m depth in the SE Pacific Ocean

NASA Astrophysics Data System (ADS)

Danovaro, R.; Della Croce, N.; Dell'Anno, A.; Pusceddu, A.

2003-12-01

The Atacama trench, the deepest ecosystem of the southern Pacific Ocean (ca. 8000 m depth) was investigated during the Atacama Trench International Expedition. Sediments, collected at three bathyal stations (1040-1355 m depth) and at a hadal site (7800 m) were analyzed for organic matter quantity and biochemical composition (in terms of phytopigments, proteins, carbohydrates and lipids), bacterial abundance, biomass and carbon production and extracellular enzymatic activities. Functional chlorophyll- a (18.0±0.10 mg m -2), phytodetritus (322.2 mg m -2) and labile organic carbon (16.9±4.3 g C m -2) deposited on surface sediments at hadal depth (7800 m) reached concentrations similar to those encountered in highly productive shallow coastal areas. High values of bacterial C production and aminopeptidase activity were also measured (at in situ temperature and 1 atm). The chemical analyses of the Atacama hadal sediments indicate that this trench behaves as a deep oceanic trap for organic material. We hypothesize that, despite the extreme physical conditions, benthic microbial processes might be accelerated as a result of the organic enrichment.

History of benthic research in the English Channel: From general patterns of communities to habitat mosaic description

NASA Astrophysics Data System (ADS)

Dauvin, Jean-Claude

2015-06-01

Benthic studies in the English Channel (EC), a shallow megatidal and epicontinental sea, began in the 1960s and 1970s with the work of teams led by Norman Holme (UK) and Louis Cabioch (F). During this period, benthic sampling was mainly qualitative, i.e. using a device such as the 'Rallier du Baty' dredge in the case of the French team and a modified anchor dredge in the case of the British team. Studies were focused on acquiring knowledge of the main distributions of benthic communities and species. Surveys on the scale of the whole EC led to the recognition of general features and two main patterns were identified: 1) the role of hydrodynamics on the spatial distribution of sediment, benthic species and communities; 2) the presence of a west-east climatic gradient of faunal impoverishment. Benthic studies in the 1980s-1990s were focused on the beginning of the implementation of long-term survey at a limited number of sites to identify seasonal and multi-annual changes. In the first decade of the 2000s, the implementation of the European Water Framework Directive and the Marine Strategy Framework Directive to define the Ecological Quality Status of marine environments increased the need to acquire better information of the structure and functioning of benthic communities, since benthic species and habitats were recognised as good indicators of human pressure on marine ecosystems. Faced with the increase of human maritime activities, the appearance of invasive species and the need to preserve sensitive marine habitats, benthic studies have been focused on developing a 'toolkit' to help in the decision-making and planning for both sound governance and sustainable management of marine resources and human activities in the English Channel. Multidisciplinary approaches were used to differentiate habitats in a more precise detail. Both indirect (side-scan sonar, ROV) and direct (grab sampling with benthos identification and grain-size analyses) approaches were used and combined to allow the description of benthic habitats using numerous descriptors. These approaches were mainly applied on a local scale, leading to the identification of habitat mosaics mainly in coarse sands, gravels and pebbly areas which cover 80% of the EC seabed. They also allowed the enrichment of the EUNIS habitat classification for infralittoral and circalittoral zones taking into account the scale of observations of benthic habitats. Moreover, several recommendations for future benthic studies are proposed within a HABITAT approach.

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems

PubMed Central

Zinger, Lucie; Amaral-Zettler, Linda A.; Fuhrman, Jed A.; Horner-Devine, M. Claire; Huse, Susan M.; Welch, David B. Mark; Martiny, Jennifer B. H.; Sogin, Mitchell; Boetius, Antje; Ramette, Alban

2011-01-01

Background Marine microbial communities have been essential contributors to global biomass, nutrient cycling, and biodiversity since the early history of Earth, but so far their community distribution patterns remain unknown in most marine ecosystems. Methodology/Principal Findings The synthesis of 9.6 million bacterial V6-rRNA amplicons for 509 samples that span the global ocean's surface to the deep-sea floor shows that pelagic and benthic communities greatly differ, at all taxonomic levels, and share <10% bacterial types defined at 3% sequence similarity level. Surface and deep water, coastal and open ocean, and anoxic and oxic ecosystems host distinct communities that reflect productivity, land influences and other environmental constraints such as oxygen availability. The high variability of bacterial community composition specific to vent and coastal ecosystems reflects the heterogeneity and dynamic nature of these habitats. Both pelagic and benthic bacterial community distributions correlate with surface water productivity, reflecting the coupling between both realms by particle export. Also, differences in physical mixing may play a fundamental role in the distribution patterns of marine bacteria, as benthic communities showed a higher dissimilarity with increasing distance than pelagic communities. Conclusions/Significance This first synthesis of global bacterial distribution across different ecosystems of the World's oceans shows remarkable horizontal and vertical large-scale patterns in bacterial communities. This opens interesting perspectives for the definition of biogeographical biomes for bacteria of ocean waters and the seabed. PMID:21931760

Organic matter degradation drives benthic cyanobacterial mat abundance on Caribbean coral reefs.

PubMed

Brocke, Hannah J; Polerecky, Lubos; de Beer, Dirk; Weber, Miriam; Claudet, Joachim; Nugues, Maggy M

2015-01-01

Benthic cyanobacterial mats (BCMs) are impacting coral reefs worldwide. However, the factors and mechanisms driving their proliferation are unclear. We conducted a multi-year survey around the Caribbean island of Curaçao, which revealed highest BCM abundance on sheltered reefs close to urbanised areas. Reefs with high BCM abundance were also characterised by high benthic cover of macroalgae and low cover of corals. Nutrient concentrations in the water-column were consistently low, but markedly increased just above substrata (both sandy and hard) covered with BCMs. This was true for sites with both high and low BCM coverage, suggesting that BCM growth is stimulated by a localised, substrate-linked release of nutrients from the microbial degradation of organic matter. This hypothesis was supported by a higher organic content in sediments on reefs with high BCM coverage, and by an in situ experiment which showed that BCMs grew within days on sediments enriched with organic matter (Spirulina). We propose that nutrient runoff from urbanised areas stimulates phototrophic blooms and enhances organic matter concentrations on the reef. This organic matter is transported by currents and settles on the seabed at sites with low hydrodynamics. Subsequently, nutrients released from the organic matter degradation fuel the growth of BCMs. Improved management of nutrients generated on land should lower organic loading of sediments and other benthos (e.g. turf and macroalgae) to reduce BCM proliferation on coral reefs.

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.

Effect of recreational diving on Patagonian rocky reefs.

PubMed

Bravo, Gonzalo; Márquez, Federico; Marzinelli, Ezequiel M; Mendez, María M; Bigatti, Gregorio

2015-03-01

Tourism has grown considerably in the last decades, promoting activities such as recreational SCUBA diving that may affect marine benthic communities. In Puerto Madryn, Patagonia Argentina, sub-aquatic tourism areas (STA) receive about 7,000 divers per year. Diving is concentrated on a few small rocky reefs and 50% of the dives occur in summer. In this work, we evaluated the effect of recreational diving activities on benthic communities and determined whether diving causes a press (long-term) or a pulse (short-term) response. We quantified the percentage cover of benthic organisms and compared benthic assemblage structure and composition between two sites with contrasting usage by divers, 'highly disturbed' and 'moderately disturbed' sites, and two 'control' sites with similar physical characteristics but no diving activity, twice before and after the diving peak in summer. We found differences in benthic assemblage structure (identity and relative abundance of taxa) and composition (identity only) among diving sites and controls. These differences were consistent before and after the peak of diving in summer, suggesting that recreational diving may produce a press impact on overall benthic assemblage structure and composition in these STA. At the moderately disturbed site, however, covers of specific taxa, such as some key habitat-forming or highly abundant species, usually differed from those in controls only immediately after summer, after which they begun to resemble controls, suggesting a pulse impact. Thus, STA in Golfo Nuevo seem to respond differently to disturbances of diving depending on the usage of the sites. This information is necessary to develop sound management strategies in order to preserve local biodiversity. Copyright © 2014 Elsevier Ltd. All rights reserved.

Isotope and fatty acid trends along continental shelf depth gradients: Inshore versus offshore hydrological influences on benthic trophic functioning

NASA Astrophysics Data System (ADS)

Chouvelon, T.; Schaal, G.; Grall, J.; Pernet, F.; Perdriau, M.; A-Pernet, E. J.; Le Bris, H.

2015-11-01

Anthropogenic activities and land-based inputs into the sea may influence the trophic structure and functioning of coastal and continental shelf ecosystems, despite the numerous opportunities and services the latter offer to humans and wildlife. In addition, hydrological structures and physical dynamics potentially influence the sources of organic matter (e.g., terrestrial versus marine, or fresh material versus detrital material) entering marine food webs. Understanding the significance of the processes that influence marine food webs and ecosystems (e.g., terrestrial inputs, physical dynamics) is crucially important because trophic dynamics are a vital part of ecosystem integrity. This can be achieved by identifying organic matter sources that enter food webs along inshore-offshore transects. We hypothesised that regional hydrological structures over wide continental shelves directly control the benthic trophic functioning across the shelf. We investigated this issue along two transects in the northern ecosystem of the Bay of Biscay (north-eastern Atlantic). Carbon and nitrogen stable isotope analysis (SIA) and fatty acid analysis (FAA) were conducted on different complementary ecosystem compartments that include suspended particulate organic matter (POM), sedimentary organic matter (SOM), and benthic consumers such as bivalves, large crustaceans and demersal fish. Samples were collected from inshore shallow waters (at ∼1 m in depth) to more than 200 m in depth on the offshore shelf break. Results indicated strong discrepancies in stable isotope (SI) and fatty acid (FA) compositions in the sampled compartments between inshore and offshore areas, although nitrogen SI (δ15N) and FA trends were similar along both transects. Offshore the influence of a permanently stratified area (described previously as a ;cold pool;) was evident in both transects. The influence of this hydrological structure on benthic trophic functioning (i.e., on the food sources available for consumers) was especially apparent across the northern transect, due to unusual carbon isotope compositions (δ13C) in the compartments. At stations under the cold pool, SI and FA organism compositions indicated benthic trophic functioning based on a microbial food web, including a significant contribution of heterotrophic planktonic organisms and/or of SOM, notably in stations under the cold pool. On the contrary, inshore and shelf break areas were characterised by a microalgae-based food web (at least in part for the shelf break area, due to slope current and upwelling that can favour fresh primary production sinking on site). SIA and FAA were relevant and complementary tools, and consumers better medium- to long-term system integrators than POM samples, for depicting the trophic functioning and dynamics along inshore-offshore transects over continental shelves.

Benthic Foraminifera as bio-indicators of anthropogenic impacts in coastal environments: Acqua dei Corsari area case study (Palermo, Italy).

PubMed

Musco, Marianna; Cuttitta, Angela; Bicchi, Erica; Quinci, Enza Maria; Sprovieri, Mario; Tranchida, Giorgio; Giaramita, Luigi; Traina, Anna; Salvagio Manta, Daniela; Gherardi, Serena; Mercurio, Pietro; Siragusa, Angelo; Mazzola, Salvatore

2017-04-15

This study investigates living benthic foraminiferal assemblages as bio-indicators of anthropogenic activities in a coastal area within the Gulf of Palermo (Sicily, Italy), affected by industrial and urban activities, and evaluates the environmental quality through the calibration of a Tolerant Species index (%TS std ). Sediments from 6 stations were sampled along a bathymetric transect from the coast to offshore. Sediment grain size, TOC, major, minor and trace elements and polycyclic aromatic hydrocarbons (PAHs) were compared to benthic foraminiferal assemblages and species at each station. Diversity and density of benthic foraminiferal assemblages were not affected by the presence of pollutants, while tolerant species increased with organic (TOC and PAHs) or chemical (As and Pb) concentrations. Moreover, the calibration of the %TS std formula to >125μm foraminiferal assemblage, gives a detailed description of environmental quality along the transect, representing a good and sensitive tool to evaluate marine coastal environment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Growth, physiochemical and antioxidant responses of overwintering benthic cyanobacteria to hydrogen peroxide.

PubMed

Chen, Chao; Yang, Zhen; Kong, Fanxiang; Zhang, Min; Yu, Yang; Shi, Xiaoli

2016-12-01

The recruitment of overwintering benthic cyanobacteria from the sediment surface is important for the development of cyanobacterial blooms during warm spring seasons. Thus, controlling the growth of cyanobacteria at the benthic stage to inhibit their recruitment is vital to control or delay the formation of summer blooms. In this study, overwintering benthic cyanobacteria were exposed to ascending hydrogen peroxide (H 2 O 2 ) concentrations (0, 1, 5, and 20 mg/L) in a simulated overwintering environment. Photosynthetic pigments, physiochemical features, and antioxidant responses were evaluated to determine the inhibitory effects of H 2 O 2 on the growth of benthic cyanobacteria and to identify the potential mechanisms thereof. These H 2 O 2 -treated cyanobacteria were then collected through filtration and transferred to an optimum environment to evaluate their recovery capacity. The results showed that chlorophyll a and phycocyanin contents, photosynthetic yield, and esterase activity decreased significantly in H 2 O 2 treated groups compared to the control. The activities of superoxide dismutase (SOD) and catalase (CAT) in benthic cyanobacteria were inhibited after 72 h exposure to H 2 O 2 , while the malondialdehyde (MDA) contents were stimulated at the same time. These results indicate that H 2 O 2 can inhibit the growth of benthic cyanobacteria, and H 2 O 2 -induced oxidative damage might be one of the mechanisms involved. The recovery experiment showed that the impairment of benthic cyanobacteria was temporary at a low dose of 1 mg/L H 2 O 2 , but permanent damage was induced when H 2 O 2 concentrations were increased to 5 and 20 mg/L. Overall, our results highlight that H 2 O 2 is a potential cyanobacteria inhibitor and can be used to decreasing the biomass of overwintering cyanobacteria, and could further control the intensity of cyanobacteria during the growth seasons. Copyright © 2016. Published by Elsevier Ltd.

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.

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.

Impact of particulate sediment, bentonite and barite (oil-drilling waste) on net fluxes of oxygen and nitrogen in Arctic-boreal sponges.

PubMed

Fang, James K H; Rooks, Christine A; Krogness, Cathinka M; Kutti, Tina; Hoffmann, Friederike; Bannister, Raymond J

2018-07-01

To meet the increasing global energy demand, expanding exploration for oil and gas reserves as well as associated drilling activities are expected in the Arctic-boreal region where sponge aggregations contribute to up to 90% of benthic biomass. These deep-water sponges along with their microbial endobionts play key roles in the nitrogen cycling in Arctic-boreal ecosystems. This study aimed to investigate the effects of drilling discharges and associated sediment resuspension events on net fluxes of oxygen, ammonium, nitrate and nitrite in three common deep-water sponge species in the form of explants. Sponges were exposed to suspended bentonite and barite, the primary particulate compounds in drilling waste, as well as suspended natural sediment particles for a period of 33 days (on average 10 mg L -1 for 12 h day -1 ). The exposure period was followed by a pollution abatement period for a further 33 days. No sponge mortality was observed during the experiment. However, exposure to these particles, especially to barite, led to reduced oxygen consumption by up to 33% that was linearly correlated with reduced nitrite/nitrate release by the sponges. The changes in net fluxes were accompanied by decreased tissue oxygenation by up to 54% within the sponges. These findings reveal the effects of fine particles on sponge metabolic processes by reducing aerobic respiration and microbial nitrification, and possibly by favouring anaerobic processes such as microbial denitrification. Most of the sponge responses recovered to their control levels upon the pollution abatement period, but the effects caused by barite may not be reversible. Our findings provide the first insight into the ecological consequences of oil and gas drilling activities on sponge-mediated nitrogen cycling in the Arctic-boreal region. Copyright © 2017 Elsevier Ltd. All rights reserved.

The biogeodynamics of microbial landscapes

NASA Astrophysics Data System (ADS)

Battin, T. J.; Hödl, I.; Bertuzzo, E.; Mari, L.; Suweis, S. S.; Rinaldo, A.

2011-12-01

Spatial configuration is fundamental in defining the structural and functional properties of biological systems. Biofilms, surface-attached and matrix-enclosed microorganisms, are a striking example of spatial organisation. Coupled biotic and abiotic processes shape the spatial organisation across scales of the landscapes formed by these benthic biofilms in streams and rivers. Experimenting with such biofilms in streams, we found that, depending on the streambed topography and the related hydrodynamic microenvironment, biofilm landscapes form increasingly diverging spatial patterns as they grow. Strikingly, however, cluster size distributions tend to converge even in contrasting hydrodynamic microenvironments. To reproduce the observed cluster size distributions we used a continuous, size-structured population model. The model accounts for the formation, growth, erosion and merging of biofilm clusters. Our results suggest not only that hydrodynamic forcing induce the diverging patterning of the microbial landscape, but also that microorganisms have developed strategies to equally exploit spatial resources independently of the physical structure of the microenvironment where they live.

Mud, Macrofauna and Microbes: An ode to benthic organism-abiotic interactions at varying scales

EPA Science Inventory

Benthic environments are dynamic habitats, subject to variable sources and rates of sediment delivery, reworking from the abiotic and biotic processes, and complex biogeochemistry. These activities do not occur in a vacuum, and interact synergistically to influence food webs, bi...

Diazotrophy in the Deep: An analysis of the distribution, magnitude, geochemical controls, and biological mediators of deep-sea benthic nitrogen fixation

NASA Astrophysics Data System (ADS)

Dekas, Anne Elizabeth

Biological nitrogen fixation (the conversion of N2 to NH3) is a critical process in the oceans, counteracting the production of N2 gas by dissimilatory bacterial metabolisms and providing a source of bioavailable nitrogen to many nitrogen-limited ecosystems. One currently poorly studied and potentially underappreciated habitat for diazotrophic organisms is the sediments of the deep-sea. Although nitrogen fixation was once thought to be negligible in non-photosynthetically driven benthic ecosystems, the present study demonstrates the occurrence and expression of a diversity of nifH genes (those necessary for nitrogen fixation), as well as a widespread ability to fix nitrogen at high rates in these locations. The following research explores the distribution, magnitude, geochemical controls, and biological mediators of nitrogen fixation at several deep-sea sediment habitats, including active methane seeps (Mound 12, Costa Rica; Eel River Basin, CA, USA; Hydrate Ridge, OR, USA; and Monterey Canyon, CA, USA), whale-fall sites (Monterey Canyon, CA), and background deep-sea sediment (off-site Mound 12 Costa Rica, off-site Hydrate Ridge, OR, USA; and Monterey Canyon, CA, USA). The first of the five chapters describes the FISH-NanoSIMS method, which we optimized for the analysis of closely associated microbial symbionts in marine sediments. The second describes an investigation of methane seep sediment from the Eel River Basin, where we recovered nifH sequences from extracted DNA, and used FISH-NanoSIMS to identify methanotrophic archaea (ANME-2) as diazotrophs, when associated with functional sulfate-reducing bacterial symbionts. The third and fourth chapters focus on the distribution and diversity of active diazotrophs (respectively) in methane seep sediment from Mound 12, Costa Rica, using a combination of 15N-labeling experiments, FISH-NanoSIMS, and RNA and DNA analysis. The fifth chapter expands the scope of the investigation by targeting diverse samples from methane seep, whale-fall, and background sediment collected along the Eastern Pacific Margin, and comparing the rates of nitrogen fixation observed to geochemical measurements collected in parallel. Together, these analyses represent the most extensive investigation of deep-sea nitrogen fixation to date, and work towards understanding the contribution of benthic nitrogen fixation to global marine nitrogen cycling.

Mercury Cycling in Agricultural and Non-agricultural Wetlands of the Yolo Bypass Wildlife Area, California: Sediment Biogeochemistry

NASA Astrophysics Data System (ADS)

Marvin-Dipasquale, M. C.; Windham-Myers, L.; Alpers, C. N.; Agee, J. L.; Cox, M. H.; Kakouros, E.; Wren, S. L.

2007-12-01

The Yolo Bypass Wildlife Area (YBWA) is part of the larger Yolo Bypass floodwater protection zone associated with the Sacramento River and the Sacramento-San Joaquin Delta, California. Land use in the YBWA consists of white and wild rice fields, seasonally flooded fallow agricultural fields, and permanently and seasonally flooded non-agricultural wetlands used for resident and migratory waterfowl. A recent assessment of mercury (Hg) and methylmercury (MeHg) loads indicates that the Yolo Bypass is responsible for a high proportion of the aqueous MeHg entering the Delta, and that biota from the Yolo Bypass are considerably elevated in MeHg. The current study examines benthic MeHg production and biogeochemical controls on this process, as a function of YBWA land use, wetland management, and agricultural practices during the 2007 rice growing season (June to October). Preliminary results indicate that in the week following initial flooding of agricultural fields, prior to the establishment of rice plants, the microbial community in the 0-2 cm surface sediment zone exhibited very little potential Hg(II)-methylation activity compared to the permanent wetland habitat (as assessed via the 203Hg(II)- methylation assay). Approximately 1 month after flooding, rice plants were established and the activity of the resident Hg(II)-methylating microbial community had increased substantially in all agricultural fields, although the observed rates of MeHg production were still much lower than those observed in the permanent wetland setting. Ongoing field sampling includes analysis of reactive Hg(II) in sediments and of iron and sulfur redox species in sediments and pore waters.

Cretaceous tropical carbonate platform changes used as paleoclimatic and paleoceanic indicators: the three lower Cretaceous platform crises

NASA Astrophysics Data System (ADS)

Arnaud-Vanneau, A.; Vrielynck, B.

2009-04-01

Carbonate platform sediments are of biogenic origin. More commonly the bioclasts are fragments of shells and skeletons. The bioclastic composition of a limestone may reflect the nature of biota inhabiting the area and a carbonate platform can be estimated as a living factory, which reflects the prevailing ecological factors. The rate of carbonate production is highest in the tropics, in oligotrophic environments, and in the photic zone. The rate of carbonate production varies greatly with temperature and nutrient input. Three types of biotic carbonate platform can be distinguished. The highest carbonate production is linked to oligotrophic carbonate platform characterized by the presence of assemblages with hermatypic corals. This type of platform is developed in shallow marine environment, nutrient poor water and warm tropical sea. A less efficient production of carbonate platform is related to mesotrophic environments in cooler and/or deeper water and associated to nutrient flux with, sometime, detrital input. The biota includes red algae, solitary coral and branching ahermatypic corals, common bryozoans, crinoids and echinoids. The less productive carbonate platform is the eutrophic muddy platform where the mud is due to the intense bacterial activity, probably related to strong nutrient flux. All changes of type of carbonate platform can be related to climatic and oceanic changes. Three platform crises occurred during lower Cretaceous time. They are followed by important turnover of microfauna (large benthic foraminifers) and microflora (marine algae). They start with the demise of the previous oligotrophic platform, they continue with oceanic perturbations, expression of which was the widespread deposition of organic-rich sediments, well expressed during Late Aptian/Albian and Cenomanian Turonian boundary and the replacement of previous oligotrophic platforms by mesotrophic to eutrophic platforms. The first crisis occurred during Valanginian and Hauterivian time and is related to the opening of the North Atlantic and the neocimerian tectonic phase. It could be linked to cooling periods. Geographically, the warm oligotrophic tropical carbonate platforms of the northern Tethyan margin migrated towards the equator from more than 500kms. The Upper Valanginian-Hauterivian mesotrophic to eutrophic carbonate platforms are muddier and microbially dominated (algal mats, oolites). 60% of benthic foraminifers living in carbonate platform became extinct. The second crisis occurred during Late Aptian to Albian time. It is coeval to the increasing plate movement and the opening of the central Atlantic Ocean. It is linked to massive detrital input on both margins of the Tethys. Tropical carbonate platform are mostly mesotrophic to eutrophic with abundance of opportunistic species such as Orbitolina, which took advantage of abundance of clastic grains. 50% of benthic foraminifers living in carbonate platform became extinct. The last crisis coincides with the Cenomanian-Turonian boundary. This period corresponds to a rapid northward movement of Africa and Spain and the opening of the North-South Atlantic connection. At the boundary we note the disappearance of organisms such as large benthic foraminifers, corals and rudists, which had a symbiotic relationship with green algae. More than 90% of large benthic foraminifers living in carbonate platform became extinct, but this extinction is not available for small size benthic foraminifers, which had not symbiosis.

Growing Rocks: Implications of Lithification for Microbial Communities and Nutrient Cycling

NASA Astrophysics Data System (ADS)

Corman, J. R.; Poret-Peterson, A. T.; Elser, J. J.

2014-12-01

Lithifying microbial communities ("microbialites") have left their signature on Earth's rock record for over 3.4 billion years and are regarded as important players in paleo-biogeochemical cycles. In this project, we study extant microbialites to understand the interactions between lithification and resource availability. All microbes need nutrients and energy for growth; indeed, nutrients are often a factor limiting microbial growth. We hypothesize that calcium carbonate deposition can sequester bioavailable phosphorus (P) and expect the growth of microbialites to be P-limited. To test our hypothesis, we first compared nutrient limitation in lithifying and non-lithifying microbial communities in Río Mesquites, Cuatro Ciénegas. Then, we experimentally manipulated calcification rates in the Río Mesquites microbialites. Our results suggest that lithifying microbialites are indeed P-limited, while non-lithifying, benthic microbial communities tend towards co-limitation by nitrogen (N) and P. Indeed, in microbialites, photosynthesis and aerobic respiration responded positively to P additions (P<0.05). Organic carbon (OC) additions caused shifts in bacterial community composition based on analysis of 16S rRNA genes. Unexpectedly, calcification rates increased with OC additions (P<0.05), but not with P additions, suggesting that sulfate reduction may be an important pathway for calcification. Experimental reductions in calcification rates caused changes to microbial biomass OC and P concentrations (P<0.01 and P<0.001, respectively), although shifts depended on whether calcification was decreased abiotically or biotically. These results show that resource availability does influence microbialite formation and that lithification may promote phosphorus limitation; however, further investigation is required to understand the mechanism by which the later occurs.

Metabolic Activity and Functional Diversity Changes in Sediment Prokaryotic Communities Organically Enriched with Mussel Biodeposits

PubMed Central

Pollet, Thomas; Cloutier, Olivier; Nozais, Christian; McKindsey, Christopher W.; Archambault, Philippe

2015-01-01

This experimental microcosm study reports the influence of organic enrichments by mussel biodeposits on the metabolic activity and functional diversity of benthic prokaryotic communities. The different biodeposit enrichment regimes created, which mimicked the quantity of faeces and pseudo-faeces potentially deposited below mussel farms, show a clear stimulatory effect of this organic enrichment on prokaryotic metabolic activity. This effect was detected once a certain level of biodeposition was attained with a tipping point estimated between 3.25 and 10 g day-1 m-2. Prokaryotic communities recovered their initial metabolic activity by 11 days after the cessation of biodeposit additions. However, their functional diversity remained greater than prior to the disturbance suggesting that mussel biodeposit enrichment may disturb the functioning and perhaps the role of prokaryotic communities in benthic ecosystems. This manipulative approach provided new information on the influence of mussel biodeposition on benthic prokaryotic communities and dose-response relationships and may support the development of carrying capacity models for bivalve culture. PMID:25923715

Metabolic activity and functional diversity changes in sediment prokaryotic communities organically enriched with mussel biodeposits.

PubMed

Pollet, Thomas; Cloutier, Olivier; Nozais, Christian; McKindsey, Christopher W; Archambault, Philippe

2015-01-01

This experimental microcosm study reports the influence of organic enrichments by mussel biodeposits on the metabolic activity and functional diversity of benthic prokaryotic communities. The different biodeposit enrichment regimes created, which mimicked the quantity of faeces and pseudo-faeces potentially deposited below mussel farms, show a clear stimulatory effect of this organic enrichment on prokaryotic metabolic activity. This effect was detected once a certain level of biodeposition was attained with a tipping point estimated between 3.25 and 10 g day-1 m-2. Prokaryotic communities recovered their initial metabolic activity by 11 days after the cessation of biodeposit additions. However, their functional diversity remained greater than prior to the disturbance suggesting that mussel biodeposit enrichment may disturb the functioning and perhaps the role of prokaryotic communities in benthic ecosystems. This manipulative approach provided new information on the influence of mussel biodeposition on benthic prokaryotic communities and dose-response relationships and may support the development of carrying capacity models for bivalve culture.

Salinity Responses of Benthic Microbial Communities in a Solar Saltern (Eilat, Israel)

PubMed Central

Sørensen, Ketil Bernt; Canfield, Donald E.; Oren, Aharon

2004-01-01

The salinity responses of cyanobacteria, anoxygenic phototrophs, sulfate reducers, and methanogens from the laminated endoevaporitic community in the solar salterns of Eilat, Israel, were studied in situ with oxygen microelectrodes and in the laboratory in slurries. The optimum salinity for the sulfate reduction rate in sediment slurries was between 100 and 120‰, and sulfate reduction was strongly inhibited at an in situ salinity of 215‰. Nevertheless, sulfate reduction was an important respiratory process in the crust, and reoxidation of formed sulfide accounted for a major part of the oxygen budget. Methanogens were well adapted to the in situ salinity but contributed little to the anaerobic mineralization in the crust. In slurries with a salinity of 180‰ or less, methanogens were inhibited by increased activity of sulfate-reducing bacteria. Unicellular and filamentous cyanobacteria metabolized at near-optimum rates at the in situ salinity, whereas the optimum salinity for anoxygenic phototrophs was between 100 and 120‰. PMID:15006785

Alkaline Phosphatase Activity : an overlooked player on the phosphate behavior in macrotidal estuaries

NASA Astrophysics Data System (ADS)

Delmas, Daniel; Labry, Claire; Youenou, Agnes; Quere, Julien; Auguet, Jean Christophe; Montanie, Helene

2014-05-01

The non-conservative behavior of phosphate within the estuarine salinity gradient is essentially assigned to physico-chemical processes, such as desorption at low salinity and to benthic exchanges. Microbial phosphatase activity (APA), generally related to phosphate deficiency, is seldom studied in phosphate rich estuarine waters. In order to address the impact of microbial activity (bacterial abundance, production BSP, APA) on phosphate behavior, we studied these activities on a seasonal basis within the salinity gradient of two macrotidal estuaries presenting different levels of suspended solids. Whatever the season the Charente estuary is characterized by high levels of Suspended Particulate Matter (SPM > 1g.L-1), particularly in the Maximum Turbidity Zone (MTZ) located at the 5-10 psu. In this area characterized by high BSP and APA there is a significant increase of PO4 levels especially during summer. In the Aulne estuary the particle load is significantly lower (1/10) but high BSP and APA are equally recorded. In the highly turbid waters of the Charente estuary, active phytoplankton is virtually absent as pheopigments constitute up to 80% of the total pigments, particularly in the MTZ, therefore APA may essentially have a bacterial origin. In the Aulne estuary attached bacteria are dominant, both in numbers and production, and their distribution along the haline gradient perfectly follows those of APA and phosphate levels. These observations, associated with the very close relationships observed between APA, SPM and BSP, suggest that APA derive mainly from bacterial (attached) origin and operate at the expense of particulate phosphorus and hence contribute to PO4 regeneration, especially in spring and summer. Finally, as APA increased as PO4, whereas the reverse is observed in both fresh and marine waters, an original scheme for APA regulation, related to the large dominance of attached bacteria can be described for the estuarine waters.

Assessment of benthic flux of dissolved organic carbon in wetland and estuarine sediments using the eddy-correlation technique

NASA Astrophysics Data System (ADS)

Swett, M. P.; Amirbahman, A.; Boss, E.

2009-12-01

Wetland and estuarine sediments release significant amounts of dissolved organic carbon (DOC) due to high levels of microbial activity, particularly sulfate reduction. Changes in climate and hydrologic conditions have a potential to alter DOC release from these systems as well. This is a concern, as high levels of DOC can lead to mobilization of toxic metals and organics in natural waters. In addition, source waters high in DOC produce undesirable disinfection byproducts in water treatment. Various in situ methods, such as peepers and sediment core centrifugation, exist to quantify vertical benthic fluxes of DOC and other dissolved species from the sediment-water interface (SWI). These techniques, however, are intrusive and involve disturbance of the sediment environment. Eddy-correlation allows for real-time, non-intrusive, in situ flux measurement of important analytes, such as O2 and DOC. An Acoustic Doppler Velocimeter (ADV) is used to obtain three-dimensional fluid velocity measurements. The eddy-correlation technique employs the mathematical separation of fluid velocity into mean velocity and fluctuating velocity components, with the latter representing turbulent eddy velocity. DOC concentrations are measured using a colored dissolved organic matter (CDOM) fluorometer, and instantaneous vertical flux is determined from the correlated data. This study assesses DOC flux at three project sites: a beaver pond in the Lower Penobscot Watershed, Maine; a mudflat in Penobscot River, Maine; and a mudflat in Great Bay, New Hampshire. Eddy flux values are compared with results obtained using peepers and centrifugation, as well as vertical profiling.

Wastewater Treatment Effluent Reduces the Abundance and Diversity of Benthic Bacterial Communities in Urban and Suburban Rivers

PubMed Central

Drury, Bradley; Rosi-Marshall, Emma

2013-01-01

In highly urbanized areas, wastewater treatment plant (WWTP) effluent can represent a significant component of freshwater ecosystems. As it is impossible for the composition of WWTP effluent to match the composition of the receiving system, the potential exists for effluent to significantly impact the chemical and biological characteristics of the receiving ecosystem. We assessed the impacts of WWTP effluent on the size, activity, and composition of benthic microbial communities by comparing two distinct field sites in the Chicago metropolitan region: a highly urbanized river receiving effluent from a large WWTP and a suburban river receiving effluent from a much smaller WWTP. At sites upstream of effluent input, the urban and suburban rivers differed significantly in chemical characteristics and in the composition of their sediment bacterial communities. Although effluent resulted in significant increases in inorganic nutrients in both rivers, surprisingly, it also resulted in significant decreases in the population size and diversity of sediment bacterial communities. Tag pyrosequencing of bacterial 16S rRNA genes revealed significant effects of effluent on sediment bacterial community composition in both rivers, including decreases in abundances of Deltaproteobacteria, Desulfococcus, Dechloromonas, and Chloroflexi sequences and increases in abundances of Nitrospirae and Sphingobacteriales sequences. The overall effect of the WWTP inputs was that the two rivers, which were distinct in chemical and biological properties upstream of the WWTPs, were almost indistinguishable downstream. These results suggest that WWTP effluent has the potential to reduce the natural variability that exists among river ecosystems and indicate that WWTP effluent may contribute to biotic homogenization. PMID:23315724

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.

Leaf litter breakdown, microbial respiration and shredder production in metal-polluted streams

USGS Publications Warehouse

Carlisle, D.M.; Clements, W.H.

2005-01-01

1. If species disproportionately influence ecosystem functioning and also differ in their sensitivities to environmental conditions, the selective removal of species by anthropogenic stressors may lead to strong effects on ecosystem processes. We evaluated whether these circumstances held for several Colorado, U.S.A. streams stressed by Zn. 2. Benthic invertebrates and chemistry were sampled in five second-third order streams for 1 year. Study streams differed in dissolved metal concentrations, but were otherwise similar in chemical and physical characteristics. Secondary production of leaf-shredding insects was estimated using the increment summation and size-frequency methods. Leaf litter breakdown rates were estimated by retrieving litter-bags over a 171 day period. Microbial activity on leaf litter was measured in the laboratory using changes in oxygen concentration over a 48 h incubation period. 3. Dissolved Zn concentrations varied eightfold among two reference and three polluted streams. Total secondary production of shredders was negatively associated with metal contamination. Secondary production in reference streams was dominated by Taenionema pallidum. Results of previous studies and the current investigation demonstrate that this shredder is highly sensitive to metals in Colorado headwater streams. Leaf litter breakdown rates were similar between reference streams and declined significantly in the polluted streams. Microbial respiration at the most contaminated site was significantly lower than at reference sites. 4. Our results supported the hypothesis that some shredder species contribute disproportionately to leaf litter breakdown. Furthermore, the functionally dominant taxon was also the most sensitive to metal contamination. We conclude that leaf litter breakdown in our study streams lacked functional redundancy and was therefore highly sensitive to contaminant-induced alterations in community structure. We argue for the necessity of simultaneously measuring community structure and ecosystem function in anthropogenically stressed ecosystems.

Small benthic size classes along the N.W. European Continental Margin: spatial and temporal variability in activity and biomass

NASA Astrophysics Data System (ADS)

Pfannkuche, O.; Soltwedel, T.

1998-12-01

In the context of the European OMEX Programme this investigation focused on gradients in the biomass and activity of the small benthic size spectrum along a transect across the Goban Spur from the outer Celtic Sea into Porcupine Abyssal Plain. The effects of food pulses (seasonal, episodic) on this part of the benthic size spectrum were investigated. Sediments sampled during eight expeditions at different seasons covering a range from 200 m to 4800 m water depth were assayed with biochemical bulk measurements: determinations of chloroplastic pigment equivalents (CPE), the sum of chlorophyll a and its breakdown products, provide information concerning the input of phytodetrital matter to the seafloor; phospholipids were analyzed to estimate the total biomass of small benthic organisms (including bacteria, fungi, flagellata, protozoa and small metazoan meiofauna). A new term `small size class biomass' (SSCB) is introduced for the biomass of the smallest size classes of sediment-inhabiting organisms; the reduction of fluorescein-di-acetate (FDA) was determined to evaluate the potential activity of ester-cleaving bacterial exoenzymes in the sediment samples. At all stations benthic biomass was predominantly composed of the small size spectrum (90% on the shelf; 97-98% in the bathyal and abyssal parts of the transect). Small size class biomass (integrated over a 10 cm sediment column) ranged from 8 g C m -2 on the shelf to 2.1 g C m -2 on the adjacent Porcupine Abyssal Plain, exponentially decreasing with increasing water depth. However, a correlation between water depth and SSCB, macrofauna biomass as well as metazoan meiofauna biomass exhibited a significantly flatter slope for the small size classes in comparison to the larger organisms. CPE values indicated a pronounced seasonal cycle on the shelf and upper slope with twin peaks of phytodetrital deposition in mid spring and late summer. The deeper stations seem to receive a single annual flux maximum in late summer. SSCB and heterotrophic activity are significantly correlated to the amount of sediment-bound pigments. Seasonality in pigment concentrations is clearly followed by SSCB and activity. In contrast to macro- and megafauna which integrate over larger periods (months/years), the small benthic size classes, namely bacteria and foraminifera, proved to be the most reactive potential of the benthic communities to any perturbations on short time scales (days/weeks). The small size classes, therefore, occupy a key role in early diagenetic processes.

Inland diatoms from the McMurdo Dry Valleys and James Ross Island, Antarctica

USGS Publications Warehouse

Esposito, R.M.M.; Spaulding, S.A.; McKnight, Diane M.; Van De Vijver, B.; Kopalova, K.; Lubinski, D.; Hall, B.; Whittaker, T.

2008-01-01

Diatom taxa present in the inland streams and lakes of the McMurdo Dry Valleys and James Ross Island, Antarctica, are presented in this paper. A total of nine taxa are illustrated, with descriptions of four new species (Luticola austroatlantica sp. nov., Luticola dolia sp. nov., Luticola laeta sp. nov., Muelleria supra sp. nov.). In the perennially ice-covered lakes of the McMurdo Dry Valleys, diatoms are confined to benthic mats within the photic zone. In streams, diatoms are attached to benthic surfaces and within the microbial mat matrix. One species, L. austroatlantica, is found on James Ross Island, of the southern Atlantic archipelago, and the McMurdo Dry Valleys. The McMurdo Dry Valley populations are at the lower range of the size spectrum for the species. Streams flow for 6-10 weeks during the austral summer, when temperatures and solar radiation allow glacial ice to melt. The diatom flora of the region is characterized by species assemblages favored under harsh conditions, with naviculoid taxa as the dominant group and several major diatom groups conspicuously absent. ?? 2008 NRC.

Microbial methanogenesis in the sulfate-reducing zone of sediments in the Eckernförde Bay, SW Baltic Sea

NASA Astrophysics Data System (ADS)

Maltby, Johanna; Steinle, Lea; Löscher, Carolin R.; Bange, Hermann W.; Fischer, Martin A.; Schmidt, Mark; Treude, Tina

2018-01-01

Benthic microbial methanogenesis is a known source of methane in marine systems. In most sediments, the majority of methanogenesis is located below the sulfate-reducing zone, as sulfate reducers outcompete methanogens for the major substrates hydrogen and acetate. The coexistence of methanogenesis and sulfate reduction has been shown before and is possible through the usage of noncompetitive substrates by methanogens such as methanol or methylated amines. However, knowledge about the magnitude, seasonality, and environmental controls of this noncompetitive methane production is sparse. In the present study, the presence of methanogenesis within the sulfate reduction zone (SRZ methanogenesis) was investigated in sediments (0-30 cm below seafloor, cm b.s.f.) of the seasonally hypoxic Eckernförde Bay in the southwestern Baltic Sea. Water column parameters such as oxygen, temperature, and salinity together with porewater geochemistry and benthic methanogenesis rates were determined in the sampling area Boknis Eck quarterly from March 2013 to September 2014 to investigate the effect of seasonal environmental changes on the rate and distribution of SRZ methanogenesis, to estimate its potential contribution to benthic methane emissions, and to identify the potential methanogenic groups responsible for SRZ methanogenesis. The metabolic pathway of methanogenesis in the presence or absence of sulfate reducers, which after the addition of a noncompetitive substrate was studied in four experimental setups: (1) unaltered sediment batch incubations (net methanogenesis), (2) 14C-bicarbonate labeling experiments (hydrogenotrophic methanogenesis), (3) manipulated experiments with the addition of either molybdate (sulfate reducer inhibitor), 2-bromoethanesulfonate (methanogen inhibitor), or methanol (noncompetitive substrate, potential methanogenesis), and (4) the addition of 13C-labeled methanol (potential methylotrophic methanogenesis). After incubation with methanol, molecular analyses were conducted to identify key functional methanogenic groups during methylotrophic methanogenesis. To also compare the magnitudes of SRZ methanogenesis with methanogenesis below the sulfate reduction zone (> 30 cm b.s.f.), hydrogenotrophic methanogenesis was determined by 14C-bicarbonate radiotracer incubation in samples collected in September 2013.SRZ methanogenesis changed seasonally in the upper 30 cm b.s.f. with rates increasing from March (0.2 nmol cm-3 d-1) to November (1.3 nmol cm-3 d-1) 2013 and March (0.2 nmol cm-3 d-1) to September (0.4 nmol cm-3 d-1) 2014. Its magnitude and distribution appeared to be controlled by organic matter availability, C / N, temperature, and oxygen in the water column, revealing higher rates in the warm, stratified, hypoxic seasons (September-November) compared to the colder, oxygenated seasons (March-June) of each year. The majority of SRZ methanogenesis was likely driven by the usage of noncompetitive substrates (e.g., methanol and methylated compounds) to avoid competition with sulfate reducers, as was indicated by the 1000-3000-fold increase in potential methanogenesis activity observed after methanol addition. Accordingly, competitive hydrogenotrophic methanogenesis increased in the sediment only below the depth of sulfate penetration (> 30 cm b.s.f.). Members of the family Methanosarcinaceae, which are known for methylotrophic methanogenesis, were detected by PCR using Methanosarcinaceae-specific primers and are likely to be responsible for the observed SRZ methanogenesis.The present study indicates that SRZ methanogenesis is an important component of the benthic methane budget and carbon cycling in Eckernförde Bay. Although its contributions to methane emissions from the sediment into the water column are probably minor, SRZ methanogenesis could directly feed into methane oxidation above the sulfate-methane transition zone.

Macroalgae Decrease Growth and Alter Microbial Community Structure of the Reef-Building Coral, Porites astreoides

PubMed Central

Vega Thurber, Rebecca; Burkepile, Deron E.; Correa, Adrienne M. S.; Thurber, Andrew R.; Shantz, Andrew A.; Welsh, Rory; Pritchard, Catharine; Rosales, Stephanie

2012-01-01

With the continued and unprecedented decline of coral reefs worldwide, evaluating the factors that contribute to coral demise is of critical importance. As coral cover declines, macroalgae are becoming more common on tropical reefs. Interactions between these macroalgae and corals may alter the coral microbiome, which is thought to play an important role in colony health and survival. Together, such changes in benthic macroalgae and in the coral microbiome may result in a feedback mechanism that contributes to additional coral cover loss. To determine if macroalgae alter the coral microbiome, we conducted a field-based experiment in which the coral Porites astreoides was placed in competition with five species of macroalgae. Macroalgal contact increased variance in the coral-associated microbial community, and two algal species significantly altered microbial community composition. All macroalgae caused the disappearance of a γ-proteobacterium previously hypothesized to be an important mutualist of P. astreoides. Macroalgal contact also triggered: 1) increases or 2) decreases in microbial taxa already present in corals, 3) establishment of new taxa to the coral microbiome, and 4) vectoring and growth of microbial taxa from the macroalgae to the coral. Furthermore, macroalgal competition decreased coral growth rates by an average of 36.8%. Overall, this study found that competition between corals and certain species of macroalgae leads to an altered coral microbiome, providing a potential mechanism by which macroalgae-coral interactions reduce coral health and lead to coral loss on impacted reefs. PMID:22957055

Macroalgae decrease growth and alter microbial community structure of the reef-building coral, Porites astreoides.

PubMed

Vega Thurber, Rebecca; Burkepile, Deron E; Correa, Adrienne M S; Thurber, Andrew R; Shantz, Andrew A; Welsh, Rory; Pritchard, Catharine; Rosales, Stephanie

2012-01-01

With the continued and unprecedented decline of coral reefs worldwide, evaluating the factors that contribute to coral demise is of critical importance. As coral cover declines, macroalgae are becoming more common on tropical reefs. Interactions between these macroalgae and corals may alter the coral microbiome, which is thought to play an important role in colony health and survival. Together, such changes in benthic macroalgae and in the coral microbiome may result in a feedback mechanism that contributes to additional coral cover loss. To determine if macroalgae alter the coral microbiome, we conducted a field-based experiment in which the coral Porites astreoides was placed in competition with five species of macroalgae. Macroalgal contact increased variance in the coral-associated microbial community, and two algal species significantly altered microbial community composition. All macroalgae caused the disappearance of a γ-proteobacterium previously hypothesized to be an important mutualist of P. astreoides. Macroalgal contact also triggered: 1) increases or 2) decreases in microbial taxa already present in corals, 3) establishment of new taxa to the coral microbiome, and 4) vectoring and growth of microbial taxa from the macroalgae to the coral. Furthermore, macroalgal competition decreased coral growth rates by an average of 36.8%. Overall, this study found that competition between corals and certain species of macroalgae leads to an altered coral microbiome, providing a potential mechanism by which macroalgae-coral interactions reduce coral health and lead to coral loss on impacted reefs.

Benthic perspective on Earth's oldest evidence for oxygenic photosynthesis.

PubMed

Lalonde, Stefan V; Konhauser, Kurt O

2015-01-27

The Great Oxidation Event (GOE) is currently viewed as a protracted process during which atmospheric oxygen increased above ∼10(-5) times the present atmospheric level (PAL). This threshold represents an estimated upper limit for sulfur isotope mass-independent fractionation (S-MIF), an Archean signature of atmospheric anoxia that begins to disappear from the rock record at 2.45 Ga. However, an increasing number of papers have suggested that the timing for oxidative continental weathering, and by conventional thinking the onset of atmospheric oxygenation, was hundreds of million years earlier than previously thought despite the presence of S-MIF. We suggest that this apparent discrepancy can be resolved by the earliest oxidative-weathering reactions occurring in benthic and soil environments at profound redox disequilibrium with the atmosphere, such as biological soil crusts and freshwater microbial mats covering riverbed, lacustrine, and estuarine sediments. We calculate that oxygenic photosynthesis in these millimeter-thick ecosystems provides sufficient oxidizing equivalents to mobilize sulfate and redox-sensitive trace metals from land to the oceans while the atmosphere itself remained anoxic with its attendant S-MIF signature. As continental freeboard increased significantly between 3.0 and 2.5 Ga, the chemical and isotopic signatures of benthic oxidative weathering would have become more globally significant from a mass-balance perspective. These observations help reconcile evidence for pre-GOE oxidative weathering with the history of atmospheric chemistry, and support the plausible antiquity of a terrestrial biosphere populated by cyanobacteria well before the GOE.

Benthic perspective on Earth’s oldest evidence for oxygenic photosynthesis

PubMed Central

Konhauser, Kurt O.

2015-01-01

The Great Oxidation Event (GOE) is currently viewed as a protracted process during which atmospheric oxygen increased above ∼10−5 times the present atmospheric level (PAL). This threshold represents an estimated upper limit for sulfur isotope mass-independent fractionation (S-MIF), an Archean signature of atmospheric anoxia that begins to disappear from the rock record at 2.45 Ga. However, an increasing number of papers have suggested that the timing for oxidative continental weathering, and by conventional thinking the onset of atmospheric oxygenation, was hundreds of million years earlier than previously thought despite the presence of S-MIF. We suggest that this apparent discrepancy can be resolved by the earliest oxidative-weathering reactions occurring in benthic and soil environments at profound redox disequilibrium with the atmosphere, such as biological soil crusts and freshwater microbial mats covering riverbed, lacustrine, and estuarine sediments. We calculate that oxygenic photosynthesis in these millimeter-thick ecosystems provides sufficient oxidizing equivalents to mobilize sulfate and redox-sensitive trace metals from land to the oceans while the atmosphere itself remained anoxic with its attendant S-MIF signature. As continental freeboard increased significantly between 3.0 and 2.5 Ga, the chemical and isotopic signatures of benthic oxidative weathering would have become more globally significant from a mass-balance perspective. These observations help reconcile evidence for pre-GOE oxidative weathering with the history of atmospheric chemistry, and support the plausible antiquity of a terrestrial biosphere populated by cyanobacteria well before the GOE. PMID:25583484

AN INTERACTIVE DEMONSTRATION OF 3D COMPUTER-AIDED TOMOGRAPHY IMAGERY FOR INTERPRETING AND QUANTIFYING ANTHROPOGENIC IMPACTS TO MARINE BENTHIC COMMUNITIES

EPA Science Inventory

Two dimensional CT analysis has allowed the quantification of biologically derived structures (tubes and tunnels) within benthic sediments. The percent tube and tunnel area (PTTA) and the sediment bulk density (SXA) resulting from these activities have been shown be to highly cor...

On diel variability of marine sediment backscattering properties caused by microphytobenthos photosynthesis: Impact of environmental factors

NASA Astrophysics Data System (ADS)

Gorska, Natalia; Kowalska-Duda, Ewa; Pniewski, Filip; Latała, Adam

2018-06-01

The study has been motivated by the development of the hydroacoustic techniques for mapping and classifying the benthic habitats and for the research of the microbenthos photosynthesis in the semi-enclosed Baltic Sea, particularly sensitive to human activity. The investigation of the effect of the benthic microalgal photosynthesis on the echo signal from the Baltic sandy sediments is continuing. The study clarifies the impact of the abiotic and biotic factors on the diel variation of the backscattering caused by the benthic microalgal photosynthetic activity. Five multiday laboratory experiments, different in hydrophysical or biological conditions, were conducted. During each measurement series, the "day" (illumination) and "night" (darkness) conditions (L:D cycle) were simulated and the diel variations of the echo energy of the backscattered signal were analyzed. The hydroacoustic data were acquired along with measuring biological and biooptical parameters and oxygen concentration. The study demonstrated the impact of microphytobenthos photosynthesis on the backscattering properties of the marine sediment which is sensitive to the illumination level, benthic microalgal biomass and macrozoobenthos bioturbation.

Response of marine benthic fauna to thin-layer capping with activated carbon in a large-scale field experiment in the Grenland fjords, Norway.

PubMed

Samuelsson, Göran S; Raymond, Caroline; Agrenius, Stefan; Schaanning, Morten; Cornelissen, Gerard; Gunnarsson, Jonas S

2017-06-01

A field experiment with thin-layer capping was conducted in the Grenland fjords, Norway, for remediation in situ of mercury and dioxin-contaminated sediments. Experimental fields at 30 and 95 m depth were capped with (i) powdered activated carbon (AC) mixed with clay (AC+cla`y), (ii) clay, and (iii) crushed limestone. Ecological effects on the benthic community and species-feeding guilds were studied 1 and 14 months after capping, and a total of 158 species were included in the analyses. The results show that clay and limestone had only minor effects on the benthic community, while AC+clay caused severe perturbations. AC+clay reduced the abundance, biomass, and number of species by up to 90% at both 30 and 95 m depth, and few indications of recovery were found during the period of this investigation. The negative effects of AC+clay were observed on a wide range of species with different feeding strategies, although the suspension feeding brittle star Amphiura filiformis was particularly affected. Even though activated carbon is effective in reducing sediment-to-water fluxes of dioxins and other organic pollutants, this study shows that capping with powdered AC can lead to substantial disturbances to the benthic community.

High light intensity mediates a shift from allochthonous to autochthonous carbon use in phototrophic stream biofilms

NASA Astrophysics Data System (ADS)

Wagner, Karoline; Bengtsson, Mia M.; Findlay, Robert H.; Battin, Tom J.; Ulseth, Amber J.

2017-07-01

Changes in the riparian vegetation along stream channels, diurnal light availability, and longitudinal fluctuations in the local light regime in streams influence primary production and carbon (C) cycling in benthic stream biofilms. To investigate the influence of light availability on the uptake dynamics of autochthonous and allochthonous dissolved organic carbon (DOC) in benthic biofilms, we experimentally added 13C-labeled allochthonous DOC to biofilms grown under light intensities ranging from 5 to 152 μmol photons m-2 s-1. We calculated the net C flux, which showed that benthic biofilms released autochthonous DOC across the entire light gradient. Light availability and diurnal light patterns influenced C uptake by benthic biofilms. More allochthonous DOC was respired under low light availability and at night, whereas under high light availability and during the day mainly autochthonous C was respired by the benthic biofilm community. Furthermore, phenol oxidase activity (indicative of allochthonous DOC uptake) was more elevated under low light availability, whereas beta-glucosidase activity (indicative of autochthonous DOC use) increased with light intensity. Collectively, our results suggest that biofilms exposed to high light inputs preferentially used autochthonous DOC, whereas biofilms incubated at attenuated levels showed greater use of allochthonous DOC. This has implications for the spatial dynamics of DOC uptake in streams and speaks against the occurrence of priming effects in algal-dominated stream biofilms.

Benthic marine debris, with an emphasis on fishery-related items, surrounding Kodiak Island, Alaska, 1994-1996

USGS Publications Warehouse

Hess, N.A.; Ribic, C.A.; Vining, I.

1999-01-01

Composition and abundance of benthic marine debris were investigated during three bottom trawl surveys in inlet and offshore locations surrounding Kodiak Island, Alaska, 1994-1996. Debris items were primarily plastic and metal regardless of trawl location. Plastic bait jars, fishing line, and crab pots were the most common fishery-related debris items and were encountered in large amounts in inlets (20-25 items km-2), but were less abundant outside of inlets (4.5-11 items km-2). Overall density of debris was also significantly greater in inlets than outside of inlets. Plastic debris densities in inlets ranged 22-31.5 items km-2, 7.8-18.8 items km-2 outside of inlets. Trawls in inlets contained almost as much metal debris as plastic debris. Density of metal debris ranged from 21.2 to 23.7 items km-2 in inlets, a maximum of 2.7 items km-2 outside of inlets. Inlets around the town of Kodiak had the highest densities of fishery-related and total benthic debris. Differences in benthic debris density between inlets and outside of inlets and differences by area may be due to differences in fishing activity and water circulation patterns. At the current reduced levels of fishing activity, however, yearly monitoring of benthic debris appears unnecessary. Copyright (C) 1999.

Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt

PubMed Central

Jungbluth, Sean P; Bowers, Robert M; Lin, Huei-Ting; Cowen, James P; Rappé, Michael S

2016-01-01

Although little is known regarding microbial life within our planet's rock-hosted deep subseafloor biosphere, boreholes drilled through deep ocean sediment and into the underlying basaltic crust provide invaluable windows of access that have been used previously to document the presence of microorganisms within fluids percolating through the deep ocean crust. In this study, the analysis of 1.7 million small subunit ribosomal RNA genes amplified and sequenced from marine sediment, bottom seawater and basalt-hosted deep subseafloor fluids that span multiple years and locations on the Juan de Fuca Ridge flank was used to quantitatively delineate a subseafloor microbiome comprised of distinct bacteria and archaea. Hot, anoxic crustal fluids tapped by newly installed seafloor sampling observatories at boreholes U1362A and U1362B contained abundant bacterial lineages of phylogenetically unique Nitrospirae, Aminicenantes, Calescamantes and Chloroflexi. Although less abundant, the domain Archaea was dominated by unique, uncultivated lineages of marine benthic group E, the Terrestrial Hot Spring Crenarchaeotic Group, the Bathyarchaeota and relatives of cultivated, sulfate-reducing Archaeoglobi. Consistent with recent geochemical measurements and bioenergetic predictions, the potential importance of methane cycling and sulfate reduction were imprinted within the basalt-hosted deep subseafloor crustal fluid microbial community. This unique window of access to the deep ocean subsurface basement reveals a microbial landscape that exhibits previously undetected spatial heterogeneity. PMID:26872042

Responses of benthic bacteria to experimental drying in sediments from Mediterranean temporary rivers.

PubMed

Amalfitano, Stefano; Fazi, Stefano; Zoppini, Annamaria; Barra Caracciolo, Anna; Grenni, Paola; Puddu, Alberto

2008-02-01

In the semiarid Mediterranean regions, water scarcity represents a common physiological stress for microbial communities residing in river sediments. However, the effect of drying has not yet adequately been evaluated when analyzing riverine microbiological processes. The bacterial community structure (abundance, biomass, composition) and functioning (carbon production, live cell percentage) were assessed during experimental desiccation in microcosms with sediments from different Mediterranean temporary rivers (Tagliamento, Krathis, Mulargia, Pardiela). Our results showed that the overall responses to drying of the bacterial community were independent from sediment origin and strictly related to water content. During desiccation, a prompt decline (up to 100%) of the initial bacterial carbon production was followed by a slower decrease in abundance and biomass, with an overall reduction of 74% and 78%, respectively. By the end of the experiment, live cells were still abundant but depressed in their main metabolic functions, thus resulting in a drastic increase in the community turnover time. Only 14% of the initial live cell biomass was available in dry sediments to immediately start the reactivation of the aquatic microbial food web after the arrival of new water. Community composition analysis showed a relative increase in alpha- and beta-Proteobacteria, when passing from wet to dry conditions. Our results suggest that the occurrence of drought events could affect carbon cycling through the freshwater microbial compartment, by temporarily limiting microbial mineralization and altering bacterial community structure.

Ecohydrological Interfaces as Dynamic Hotspots of Biogeochemical Cycling

NASA Astrophysics Data System (ADS)

Krause, Stefan; Lewandowski, Joerg; Hannah, David; McDonald, Karlie; Folegot, Silvia; Baranov, Victor

2016-04-01

Ecohydrological interfaces, represent the boundaries between water-dependent ecosystems that can alter substantially the fluxes of energy and matter. There is still a critical gap of understanding the organisational principles of the drivers and controls of spatially and temporally variable ecohydrological interface functions. This knowledge gap limits our capacity to efficiently quantify, predict and manage the services provided by complex ecosystems. Many ecohydrological interfaces are characterized by step changes in microbial metabolic activity, steep redox gradients and often even thermodynamic phase shifts, for instance at the interfaces between atmosphere and water or soil matrix and macro-pores interfaces. This paper integrates investigations from point scale laboratory microcosm experiments with reach and subcatchment scale tracer experiments and numerical modeling studies to elaborate similarities in the drivers and controls that constitute the enhanced biogeochemical activity of different types of ecohydrologica interfaces across a range of spatial and temporal scales. We therefore combine smart metabolic activity tracers to quantify the impact of bioturbating benthic fauna onto ecosystem respiration and oxygen consumption and investigate at larger scale, how microbial metabolic activity and carbon turnover at the water-sediment interface are controlled by sediment physical and chemical properties as well as water temperatures. Numerical modeling confirmed that experimentally identified hotspots of streambed biogeochemical cycling were controlled by patterns of physical properties such as hydraulic conductivities or bioavailability of organic matter, impacting on residence time distributions and hence reaction times. In contrast to previous research, our investigations thus confirmed that small-scale variability of physical and chemical interface properties had a major impact on biogeochemical processing at the investigated ecohydrological interfaces. Our results furthermore indicate that to fully understand spatial patterns and temporal dynamics of ecohydrological interface functioning, including hotspots and hot moments, detailed knowledge of the impacts of biological behavior on the physic-chemical ecosystem conditions, and vice-versa, is required.

Ecohydrological Interfaces as Dynamic Hotspots of Biogeochemical Cycling

NASA Astrophysics Data System (ADS)

Krause, S.

2015-12-01

Ecohydrological interfaces, represent the boundaries between water-dependent ecosystems that can alter substantially the fluxes of energy and matter. There is still a critical gap of understanding the organisational principles of the drivers and controls of spatially and temporally variable ecohydrological interface functions. This knowledge gap limits our capacity to efficiently quantify, predict and manage the services provided by complex ecosystems. Many ecohydrological interfaces are characterized by step changes in microbial metabolic activity, steep redox gradients and often even thermodynamic phase shifts, for instance at the interfaces between atmosphere and water or soil matrix and macro-pores interfaces. This paper integrates investigations from point scale microcosm experiments with reach and subcatchment scale tracer experiments and numerical modeling studies to elaborate similarities in the drivers and controls that constitute the enhanced biogeochemical activity of different types of ecohydrologica interfaces across a range of spatial and temporal scales. We therefore combine smart metabolic activity tracers to quantify the impact of bioturbating benthic fauna onto ecosystem respiration and oxygen consumption and investigate at larger scale, how microbial metabolic activity and carbon turnover at the water-sediment interface are controlled by sediment physical and chemical properties as well as water temperatures. Numerical modeling confirmed that experimentally identified hotspots of streambed biogeochemical cycling were controlled by patterns of physical properties such as hydraulic conductivities or bioavailability of organic matter, impacting on residence time distributions and hence reaction times. In contrast to previous research, our investigations thus confirmed that small-scale variability of physical and chemical interface properties had a major impact on biogeochemical processing at the investigated ecohydrological interfaces. Our results furthermore indicate that to fully understand spatial patterns and temporal dynamics of ecohydrological interface functioning, including hotspots and hot moments, detailed knowledge of the impacts of biological behavior on the physic-chemical ecosystem conditions, and vice-versa, is required.

The isolation and characterization of actinobacteria from dominant benthic macroinvertebrates endemic to Lake Baikal.

PubMed

Axenov-Gribanov, Denis; Rebets, Yuriy; Tokovenko, Bogdan; Voytsekhovskaya, Irina; Timofeyev, Maxim; Luzhetskyy, Andriy

2016-03-01

The high demand for new antibacterials fosters the isolation of new biologically active compounds producing actinobacteria. Here, we report the isolation and initial characterization of cultured actinobacteria from dominant benthic organisms' communities of Lake Baikal. Twenty-five distinct strains were obtained from 5 species of Baikal endemic macroinvertebrates of amphipods, freshwater sponges, turbellaria worms, and insects (caddisfly larvae). The 16S ribosomal RNA (rRNA)-based phylogenic analysis of obtained strains showed their affiliation to Streptomyces, Nocardia, Pseudonocardia, Micromonospora, Aeromicrobium, and Agromyces genera, revealing the diversity of actinobacteria associated with the benthic organisms of Lake Baikal. The biological activity assays showed that 24 out of 25 strains are producing compounds active against at least one of the test cultures used, including Gram-negative bacteria and Candida albicans. Complete dereplication of secondary metabolite profiles of two isolated strains led to identification of only few known compounds, while the majority of detected metabolites are not listed in existing antibiotic databases.

Benthic metabolism over the emersion - immersion alternation in sands colonized by the invasive Manila clam Ruditapes philippinarum

NASA Astrophysics Data System (ADS)

Migné, Aline; Trigui, Rima Jihane; Davoult, Dominique; Desroy, Nicolas

2018-01-01

The effect of an invasive infaunal suspension-feeding bivalve, the Manila clam Ruditapes philippinarum, on benthic inorganic carbon and nutrient fluxes was examined through in situ incubations. Measurements were performed in spring and summer on a tidal sandflat of the Rance estuary (south part of the Western English Channel) colonized by the Manila clam after its deliberate introduction in the 1990's. Benthic inorganic carbon fluxes were measured using light and dark benthic chambers both at emersion and immersion. Benthic nutrient fluxes were measured using dark benthic chambers at immersion. Inorganic carbon (IC) and ammonium sediment release under darkness at immersion reached 5.60 mmol m-2 h-1 and 441 μmol m-2 h-1 respectively for a clam density of 291 ind m-2. The sediment IC-release under darkness was lower during emersion than during immersion, probably due to the reduced activity of infauna at low tide. Under ambient light, a sediment IC-uptake was systematically measured at emersion, indicating a net autotrophy under the condition of measurements (125 < surface PAR < 1670 μmol m-2 s-1), while either sediment IC-uptake or release was measured at immersion according to light variation (20 < underwater PAR < 990 μmol m-2 s-1). The highest gross community primary production, calculated from highest IC-fluxes at light (i.e. net community production) and highest IC-fluxes at dark (i.e. community respiration), was similar at emersion and immersion and reached 6.2 mmolC m-2 h-1. These results suggest that the metabolic activity of the invasive Manila clam Ruditapes philippinarum contributes to increase inorganic C and ammonium sediment release. These regenerated nutrients may support microphytobenthic production which appeared particularly high on this intertidal sand flat.

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.

Budget of coral-derived organic carbon in a fringing coral reef of the Gulf of Aqaba, Red Sea

NASA Astrophysics Data System (ADS)

Naumann, Malik S.; Richter, Claudio; Mott, Claudius; el-Zibdah, Mohammad; Manasrah, Riyad; Wild, Christian

2012-12-01

The continuous release of organic C-rich material by reef-building corals can contribute substantially to biogeochemical processes and concomitant rapid nutrient recycling in coral reef ecosystems. However, our current understanding of these processes is limited to platform reefs exhibiting a high degree of ecosystem closure compared to the globally most common fringing reef type. This study carried out in the northern Gulf of Aqaba (Red Sea) presents the first quantitative budget for coral-derived organic carbon (COC) in a fringing reef and highlights the importance of local hydrodynamics. Diel reef-wide COC release amounted to 1.1 ± 0.2 kmol total organic carbon (TOC) representing 1-3% of gross benthic primary production. Most COC (73%) was released as particulate organic C (POC), the bulk of which (34-63%) rapidly settled as mucus string aggregates accounting for approximately 28% of total POC sedimentation. Sedimentation of mucus strings, but also dilution of suspended and dissolved COC in reef waters retained 82% of diel COC release in the fringing reef, providing a potentially important organic source for a COC-based food web. Pelagic COC degradation represented 0.1-1.6% of pelagic microbial respiration recycling 32% of diel retained COC. Benthic COC degradation contributed substantially (29-47%) to reef-wide microbial respiration in reef sands, including 20-38% by mucus string POC, and consumed approximately 52% of all retained COC. These findings point out the importance of COC as a C carrier for different reef types. COC may further represent a source of organic carbon for faunal communities colonising reef framework cavities complementing the efficient retention and recycling of COC within fringing reef environments.

Plankton assembly in an ultra-oligotrophic Antarctic lake over the summer transition from the ice-cover to ice-free period: A size spectra approach

NASA Astrophysics Data System (ADS)

Rochera, Carlos; Quesada, Antonio; Toro, Manuel; Rico, Eugenio; Camacho, Antonio

2017-03-01

Lakes from the Antarctic maritime region experience climate change as a main stressor capable of modifying their plankton community structure and function, essentially because summer temperatures are commonly over the freezing point and the lake's ice cap thaws. This study was conducted in such seasonally ice-covered lake (Lake Limnopolar, Byers Peninsula, Livingston Is., Antarctica), which exhibits a microbial dominated pelagic food web. An important feature is also the occurrence of benthic mosses (Drepanocladus longifolius) covering the lake bottom. Plankton dynamics were investigated during the ice-thawing transition to the summer maximum. Both bacterioplankton and viral-like particles were higher near the lake's bottom, suggesting a benthic support. When the lake was under dim conditions because of the snow-and-ice cover, autotrophic picoplankters dominated at deep layers. The taxa-specific photopigments indicated dominance of picocyanobacteria among them when the light availability was lower. By contrast, larger and less edible phytoplankton dominated at the onset of the ice melting. The plankton size spectra were fitted to the continuous model of Pareto distribution. Spectra evolved similarly at two sampled depths, in surface and near the bottom, with slopes increasing until mid-January. However, slopes were less steep (i.e., size classes more uniformly distributed) at the bottom, thus denoting a more efficient utilization of resources. These findings suggest that microbial loop pathways in the lake are efficiently channelized during some periods to the metazoan production (mainly the copepod Boeckella poppei). Our results point to that trophic interactions may still occur in these lakes despite environmental harshness. This results of interest in a framework of increasing temperatures that may reduce the climatic restrictions and therefore stimulate biotic interactions.

Long-term impact of bottom trawling on pelagic-benthic coupling in the southern North Sea (German Bight)

NASA Astrophysics Data System (ADS)

Friedrich, Jana; van Beusekom, Justus E. E.; Neumann, Andreas; Naderipour, Celine; Janssen, Felix; Ahmerkamp, Soeren; Holtappels, Moritz; Schueckel, Ulrike

2016-04-01

The southern North Sea, and the German Bight, has been systematically bottom-trawled at least since the late 19th century (Christiansen, 2009; Reiss et al., 2009; Kröncke 2011; Emeis et al., 2015, Neumann et al., 2016). As a result, benthic habitats and benthic biogenic structures created by bivalves, polychaetes and hydroids where destroyed or reduced. The parallel removal of hard substrate (gravel and boulders) avoids the resettlement of hard-substrate depended species. For example, the Oyster ground, a huge oyster bank a hundred years ago (Olsen, 1883), turned into a muddy depression today. In addition, shallow depth of max 40 m, strong tidal currents and frequent storms result in a high-energy environment with low sedimentation rates and recurrent sediment resuspension. The decrease in benthic filtering capacity by disturbance in epifauna and bottom roughness (Callaway et al., 2007) apparently influence pelagic-benthic coupling of biogeochemical fluxes. Heip et al. (1995) indicate that benthic respiration at depths prevailing in the German Bight accounts for 10-40% of total respiration, whereas pelagic respiration accounts for 60-90%. Previous estimates are in the middle of this range (Heip et al., 1995). To test these hypotheses and to assess the partitioning of benthic and pelagic processes, and the factors influencing organic matter mineralization, we measured pelagic production and respiration based on Winkler titration, in-situ benthic fluxes using chamber landers, we did ex-situ incubations of intact sediment cores and analysed still images from a towed benthic video sled. In addition, O2 fluxes in permeable sediments were estimated by integrating the volumetric rate measurements of the upper sediment layer over in-situ microsensor-measured O2 penetration depth. Our current results show significant seasonality in benthic respiration, with highest rates in summer and lowest rates in winter. No significant differences in total benthic respiration rates were measured on sandy (permeable) and silty (diffusive) sediments, whereas significant differences of microbial O2 uptake were observed indeed between permeable and diffusive sediments. Nevertheless, when considering the multitude of different methods, we found that benthic respiration over the season seemed to be governed mainly by settling of fresh organic matter during calm periods and its rapid turnover in a region where strong tidal and wind-forced currents distribute suspended particles over large areas. Summer pelagic respiration rates were an order of magnitude higher then benthic rates, and account for 88-93% of total respiration, which represents 79-98% of pelagic primary production. Our measurements of benthic respiration account for 7-12% of the total in the German Bight, which is lower compared to earlier studies. Strong tidal and wind-forced currents along with the lack of complex three-dimensional biogenic structures seem to prevent settling of suspended matter and foster resuspension, thereby supporting pelagic turnover processes. Hence, we assume that benthic turnover might have been higher before systematic bottom trawling destroyed the bottom hydrobiological regime. Today, due to the strong current regime in the German Bight, the pelagic system appears to be a largely closed system of production and respiration, with comparably little for export to the benthic system due to absence of biogenic structures. References Callaway R, Engelhard GH, Dann J, Cotter J, Rumohr H (2007) One century of North Sea epibenthos and fishing: comparison between 1902-1912, 1982-1985 and 2000. Marine Ecology Progress Series 346, 27-43. Christiansen S (2009) Towards good environmental status - A network of marine protected areas for the North Sea. In: Lutter S (ed) WWF Germany, Fankfurt/Main Emeis K-C, van Beusekom J, Callies U, Ebinghaus R, Kannen A, Kraus G, Kröncke I, Lenhart H, Lorkowski I, Matthias V, Möllmann C, Pätsch J, Scharfe M, Thomas H, Weisse R, Zorita E (2015) The North Sea -A shelf sea in the Anthropocene. Journal of Marine Systems 141:18-33 Heip CHR, Goosen NK, Herman PMJ, Kromkamp J, Middelburg JJ, Soetaerd K (1995) Production and consumption of biological particles in temperate tidal estuaries. Oceanography and Marine Biology: an Annual Review 33:1-149 Kröncke I (2011) Changes in Dogger Bank macrofauna communities in the 20th century caused by fishing and climate. Estuarine, Coastal and Shelf Sciences 94 (3): 234-245. Neumann H, Diekmann R, Kröncke I (2016) The influence of habitat characteristics and fishing effort on functional composition of epifauna in the south-eastern North Sea. Estuarine, Coastal and Shelf Sciences 169: 182-194. Olsen OT (1883) The Piscatorial Atlas of the North Sea, English and St. George's Channels. Taylor and Francis, London Reiss H, Greenstreet S, Sieben K, Ehrich S, Piet G, Quirijns F, Robinson F, Wolff W, Kröncke I (2009) Effects of fishing disturbance on benthic communities and secondary production within an intensively fished area. Marine Ecology Progress Series 394:201-213

Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat.

PubMed

Babauta, Jerome T; Atci, Erhan; Ha, Phuc T; Lindemann, Stephen R; Ewing, Timothy; Call, Douglas R; Fredrickson, James K; Beyenal, Haluk

2014-01-01

Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode-associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1-V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community.

Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

PubMed Central

Babauta, Jerome T.; Atci, Erhan; Ha, Phuc T.; Lindemann, Stephen R.; Ewing, Timothy; Call, Douglas R.; Fredrickson, James K.; Beyenal, Haluk

2014-01-01

Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode-associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1–V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community. PMID:24478768

Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

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

Babauta, Jerome T.; Atci, Erhan; Ha, Phuc T.

2014-01-01

Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell wasmore » light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode- associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1-V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community.« less

Linking Archaeal Molecular Diversity and Lipid Biomarker Composition in a Hypersaline Microbial Mat Community

NASA Technical Reports Server (NTRS)

Jahnke, Linda; Orphan, Victoria; Turk, Kendra; Embaye, Tsegereda; Kubo, Mike; Summons, Roger

2005-01-01

Lipid biomarkers for discrete microbial groups are a valuable tool for establishing links to ancient microbial ecosystems. Lipid biomarkers can establish organism source and function in contemporary microbial ecosystems (membrane lipids) and by analogy, potential relevance to the fossilized carbon skeletons (geolipids) extracted from ancient sedimentary rock. The Mars Exploration Rovers have provided clear evidence for an early wet Mars and the presence of hypersaline evaporitic basins. Ongoing work on an early Earth analog, the hypersaline benthic mats in Guerrero Negro, Baja California Sur, may provide clues to what may have evolved and flourished on an early wet Mars, if only for a short period. Cyanobacterial mats are a pertinent early Earth analog for consideration of evolutionary and microbial processes within the aerobic photosynthetic and adjacent anoxic layers. Fluctuations in physio-chemical parameters associated with spatial and temporal scales are expressed through vast microbial metabolic diversity. Our recent work hopes to establish the dynamic of archaeal diversity, particularly as it relates to methane production in this high sulfate environment, through the use of lipid biomarker and phylogenetic analyses. Archaeal 16s rRNA and mcrA gene assemblages, demonstrated distinct spatial separation over the 130 mm core of at least three distinct genera within the order Methanosarcinales, as well as an abundance of uncultured members of the Thermoplasmales and Crenarchaeota. Ether-bound lipid analysis identified abundant 0-alkyl and 0-isopranyl chains throughout the core, and the presence of sn-2 hydroxyarchaeol, a biomarker for methylotrophic methanogens. A unique ether isoprenoid chain, a C30:1 , possibly related to the geolipid squalane, a paleobiomarker associated with hypersaline environments, was most abundant within the oxic-anoxic transition zone.

The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling

PubMed Central

Lindemann, Stephen R.; Moran, James J.; Stegen, James C.; Renslow, Ryan S.; Hutchison, Janine R.; Cole, Jessica K.; Dohnalkova, Alice C.; Tremblay, Julien; Singh, Kanwar; Malfatti, Stephanie A.; Chen, Feng; Tringe, Susannah G.; Beyenal, Haluk; Fredrickson, James K.

2013-01-01

Phototrophic microbial mats are compact ecosystems composed of highly interactive organisms in which energy and element cycling take place over millimeter-to-centimeter-scale distances. Although microbial mats are common in hypersaline environments, they have not been extensively characterized in systems dominated by divalent ions. Hot Lake is a meromictic, epsomitic lake that occupies a small, endorheic basin in north-central Washington. The lake harbors a benthic, phototrophic mat that assembles each spring, disassembles each fall, and is subject to greater than tenfold variation in salinity (primarily Mg2+ and SO2−4) and irradiation over the annual cycle. We examined spatiotemporal variation in the mat community at five time points throughout the annual cycle with respect to prevailing physicochemical parameters by amplicon sequencing of the V4 region of the 16S rRNA gene coupled to near-full-length 16S RNA clone sequences. The composition of these microbial communities was relatively stable over the seasonal cycle and included dominant populations of Cyanobacteria, primarily a group IV cyanobacterium (Leptolyngbya), and Alphaproteobacteria (specifically, members of Rhodobacteraceae and Geminicoccus). Members of Gammaproteobacteria (e.g., Thioalkalivibrio and Halochromatium) and Deltaproteobacteria (e.g., Desulfofustis) that are likely to be involved in sulfur cycling peaked in summer and declined significantly by mid-fall, mirroring larger trends in mat community richness and evenness. Phylogenetic turnover analysis of abundant phylotypes employing environmental metadata suggests that seasonal shifts in light variability exert a dominant influence on the composition of Hot Lake microbial mat communities. The seasonal development and organization of these structured microbial mats provide opportunities for analysis of the temporal and physical dynamics that feed back to community function. PMID:24312082

The Epsomitic Phototrophic Microbial Mat of Hot Lake, Washington. Community Structural Responses to Seasonal Cycling

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

Lindemann, Stephen R.; Moran, James J.; Stegen, James C.

2013-11-13

Phototrophic microbial mats are compact ecosystems composed of highly interactive organisms in which energy and element cycling take place over millimeter-to-centimeter-scale distances. Although microbial mats are common in hypersaline environments, they have not been extensively characterized in systems dominated by divalent ions. Hot Lake is a meromictic, epsomitic lake that occupies a small, endorheic basin in north-central Washington. The lake harbors a benthic, phototrophic mat that assembles each spring, disassembles each fall, and is subject to greater than tenfold variation in salinity (primarily Mg 2+ and SO 2 -4) and irradiation over the annual cycle. We examined spatiotemporal variation inmore » the mat community at five time points throughout the annual cycle with respect to prevailing physicochemical parameters by amplicon sequencing of the V4 region of the 16S rRNA gene coupled to near-full-length 16S RNA clone sequences. The composition of these microbial communities was relatively stable over the seasonal cycle and included dominant populations of Cyanobacteria, primarily a group IV cyanobacterium (Leptolyngbya), and Alphaproteobacteria (specifically, members of Rhodobacteraceae and Geminicoccus). Members of Gammaproteobacteria (e.g., Thioalkalivibrio and Halochromatium) and Deltaproteobacteria (e.g., Desulfofustis) that are likely to be involved in sulfur cycling peaked in summer and declined significantly by mid-fall, mirroring larger trends in mat community richness and evenness. Phylogenetic turnover analysis of abundant phylotypes employing environmental metadata suggests that seasonal shifts in light variability exert a dominant influence on the composition of Hot Lake microbial mat communities. The seasonal development and organization of these structured microbial mats provide opportunities for analysis of the temporal and physical dynamics that feed back to community function.« less

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

Geobiology: A Conceptual Framework for Understanding Earth's Surface

NASA Astrophysics Data System (ADS)

Sumner, D. Y.

2016-12-01

A topic of study becomes a new field when it provides a useful conceptual framework for understanding suites of important processes. Geobiology integrates microbial biology with Earth sciences in a way that allows us to ask - and answer - deeper questions about Earth and the life on it. Recent studies of the oxidation of Earth's surface exemplify the impact of Geobiology as a new field. For decades, scientists have understood that Earth's surface was oxidized by photosynthesis. Geochemical records indicate dramatic redox changes both globally, e.g. the loss of MIF sulfur signatures due to formation of an ozone layer, and locally, as preserved in sedimentary rocks. However, these records depend critically on the dynamics of both the global biosphere and local microbial ecology. For example, an increase in global redox due to photosynthetic iron oxidation has different biogeochemical implications than an increase from oxygenic photosynthesis; O2 reacts very differently with organic matter and minerals than iron oxyhydroxides do, influencing microbial ecology as well as potential geochemical signatures in sedimentary rocks. Thus, studies of modern microbial communities provide insights into the interactions among metabolisms and geochemical gradients that have shaped Earth's redox history. For example, the ability of cyanobacteria to create O2 oases in benthic mats and soils on land provides a new framework for evaluating redox-sensitive elemental fluxes to the ocean. Similarly, genomic studies of Cyanobacteria have revealed close relatives, Melainabacteria, that are mostly obligate anaerobes. The evolutionary relationships between these two groups, as preserved in their genomes, reflect important microbial processes that led to oxidation of Earth's surface. By combining insights from microbial biology and sedimentary geochemistry, geobiologists will develop significantly more accurate models of the interactions between life and Earth.

Methane gas seepage - Disregard of significant water column filter processes?

NASA Astrophysics Data System (ADS)

Schneider von Deimling, Jens; Schmale, Oliver

2016-04-01

Marine methane seepage represents a potential contributor for greenhouse gas in the atmosphere and is discussed as a driver for climate change. The ultimate question is how much methane is released from the seafloor on a global scale and what fraction may reach the atmosphere? Dissolved fluxes from methane seepage sites on the seabed were found to be very efficiently reduced by benthic microbial oxidation, whereas transport of free gas bubbles from the seabed is considered to bypass the effective benthic methane filter. Numerical models are available today to predict the fate of such methane gas bubble release to the water column in regard to gas exchange with the ambient water column, respective bubble lifetime and rise height. However, the fate of rising gas bubbles and dissolved methane in the water column is not only governed by dissolution, but is also affected by lateral oceanographic currents and vertical bubble-induced upwelling, microbial oxidation, and physico-chemical processes that remain poorly understood so far. According to this gap of knowledge we present data from two study sites - the anthropogenic North Sea 22/4b Blowout and the natural Coal Oil point seeps - to shed light into two new processes gathered with hydro-acoustic multibeam water column imaging and microbial investigations. The newly discovered processes are hereafter termed Spiral Vortex and Bubble Transport Mechanism. Spiral Vortex describes the evolution of a complex vortical fluid motion of a bubble plume in the wake of an intense gas release site (Blowout, North Sea). It appears very likely that it dramatically changes the dissolution kinetics of the seep gas bubbles. Bubble Transport Mechanism prescribes the transport of sediment-hosted bacteria into the water column via rising gas bubbles. Both processes act as filter mechanisms in regard to vertical transport of seep related methane, but have not been considered before. Spiral Vortex and Bubble Transport Mechanism represent the basis for a follow up research scheduled for August 2016 with the R/V POSEIDON with the aim to better constrain their mechanisms and to quantify their overall importance.

Linking metatranscriptomic to bioremediation processes of oil contaminated marine sediments

NASA Astrophysics Data System (ADS)

Cuny, P.; Atkinson, A.; Léa, S.; Guasco, S.; Jezequel, R.; Armougom, F.; Michotey, V.; Bonin, P.; Militon, C.

2016-02-01

Oil-derived hydrocarbons are one major source of pollution of marine ecosystems. In coastal marine areas they tend to accumulate in the sediment where they can impact the benthic communities. Oil hydrocarbons biodegradation by microorganisms is known to be one of the prevalent processes acting in the removal of these contaminants from sediments. The redox oscillation regimes generated by bioturbation, and the efficiency of metabolic coupling between functional groups associated to these specific redox regimes, are probably determinant factors controlling hydrocarbon biodegradation. Metatranscriptomic analysis appears like a promising approach to shed new light on the metabolic processes involved in the response of microbial communities to oil contamination in such oxic/anoxic oscillating environments. In the framework of the DECAPAGE project (ANR CESA-2011-006 01), funded by the French National Agency for Research, the metatranscriptomes (RNA-seq) of oil contaminated or not (Ural blend crude oil, 5 000 ppm) and bioturbated or not (addition of the common burrowing organism Hediste diversicolor, 1000 ind/m2) mudflat sediments, incubated in microcosms during 4 months at 19±1°C, were compared. The analysis of active microbial communities by SSU rRNA barcoding shows that the main observable changes are due to the presence of H. diversicolor. On the contrary, oil addition is the main factor explaining the observed changes in the genes expression patterns with 1949 genes specifically up or down-regulated (which is the case of only 245 genes when only H. diversicolor worms are added). In particular, the oil contamination leads to a marked overexpression (i) of benzyl- and alkylsuccinate synthase genes (ass and bss) that are involved in the anaerobic metabolism of aromatics (toluene) and alkanes, respectively and, (ii) of genes coding for nucleotide excision repair exonucleases indicating that DNA repair processes are also activated.

Inorganic mercury (Hg2+) accumulation in autotrophic and mixotrophic planktonic protists: Implications for Hg trophodynamics in ultraoligotrophic Andean Patagonian lakes.

PubMed

Soto Cárdenas, Carolina; Gerea, Marina; Queimaliños, Claudia; Ribeiro Guevara, Sergio; Diéguez, María C

2018-05-01

Microbial assemblages are typical of deep ultraoligotrophic Andean Patagonian lakes and comprise picoplankton and protists (phytoflagellates and mixotrophic ciliates), having a central role in the C cycle, primary production and in the incorporation of dissolved inorganic mercury (Hg 2+ ) into lake food webs. In this study we evaluated the mechanisms of Hg 2+ incorporation in hetero- and autotrophic bacteria, in the autotrophic dinoflagellate (Gymnodinium paradoxum) and in two mixotrophic ciliates (Stentor araucanus and Ophrydium naumanni) dominating the planktonic microbial assemblage. The radioisotope 197 Hg was used to trace the Hg 2+ incorporation in microbiota. Hg uptake was analyzed as a function of cell abundance (BCF: bioconcentration factor), cell surface (SCF: surface concentration factor) and cell volume (VCF: volume concentration factor). Overall, the results obtained showed that these organisms incorporate substantial amounts of dissolved Hg 2+ passively (adsorption) and actively (bacteria consumption or attachment), displaying different Hg internalization and therefore, varying potential for Hg transfer. Surface area and quality, and surface:volume ratio (S:V) control the passive uptake in all the organisms. Active incorporation depends on bacteria consumption in the mixotrophic ciliates, or on bacteria association to surface in the autotrophic dinoflagellate. Hg bioaccumulated by pelagic protists can be transferred to higher trophic levels through plankton and fish feeding, regenerated to the dissolved phase by excretion, and/or transferred to the sediments by particle sinking. In ultraoligotrophic Andean Patagonian lakes, picoplankton and planktonic protists are key components of lake food webs, linking the pelagic and benthic Hg pathways, and thereby playing a central role in Hg trophodynamics. Copyright © 2018 Elsevier Ltd. All rights reserved.

A multitrophic approach to monitoring the effects of metal mining in otherwise pristine and ecologically sensitive rivers in northern Canada.

PubMed

Spencer, Paula; Bowman, Michelle F; Dubé, Monique G

2008-07-01

It is not known if current chemical and biological monitoring methods are appropriate for assessing the impacts of growing industrial development on ecologically sensitive northern waters. We used a multitrophic level approach to evaluate current monitoring methods and to determine whether metal-mining activities had affected 2 otherwise pristine rivers that flow into the South Nahanni River, Northwest Territories, a World Heritage Site. We compared upstream reference conditions in the rivers to sites downstream and further downstream of mines. The endpoints we evaluated included concentrations of metals in river water, sediments, and liver and flesh of slimy sculpin (Cottus cognatus); benthic algal and macroinvertebrate abundance, richness, diversity, and community composition; and various slimy sculpin measures, our sentinel forage fish species. Elevated concentrations of copper and iron in liver tissue of sculpin from the Flat River were associated with high concentrations of mine-derived iron in river water and copper in sediments that were above national guidelines. In addition, sites downstream of the mine on the Flat River had increased algal abundances and altered benthic macroinvertebrate communities, whereas the sites downstream of the mine on Prairie Creek had increased benthic macroinvertebrate taxa richness and improved sculpin condition. Biological differences in both rivers were consistent with mild enrichment of the rivers downstream of current and historical mining activity. We recommend that monitoring in these northern rivers focus on indicators in epilithon and benthic macroinvertebrate communities due to their responsiveness and as alternatives to lethal fish sampling in habitats with low fish abundance. We also recommend monitoring of metal burdens in periphyton and benthic invertebrates for assessment of exposure to mine effluent and causal association. Although the effects of mining activities on riverine biota currently are limited, our results show that there is potential for effects to occur with proposed growth in mining activities.

Microbial colonization and degradation of polyethylene and biodegradable plastic bags in temperate fine-grained organic-rich marine sediments.

PubMed

Nauendorf, Alice; Krause, Stefan; Bigalke, Nikolaus K; Gorb, Elena V; Gorb, Stanislav N; Haeckel, Matthias; Wahl, Martin; Treude, Tina

2016-02-15

To date, the longevity of plastic litter at the sea floor is poorly constrained. The present study compares colonization and biodegradation of plastic bags by aerobic and anaerobic benthic microbes in temperate fine-grained organic-rich marine sediments. Samples of polyethylene and biodegradable plastic carrier bags were incubated in natural oxic and anoxic sediments from Eckernförde Bay (Western Baltic Sea) for 98 days. Analyses included (1) microbial colonization rates on the bags, (2) examination of the surface structure, wettability, and chemistry, and (3) mass loss of the samples during incubation. On average, biodegradable plastic bags were colonized five times higher by aerobic and eight times higher by anaerobic microbes than polyethylene bags. Both types of bags showed no sign of biodegradation during this study. Therefore, marine sediment in temperate coastal zones may represent a long-term sink for plastic litter and also supposedly compostable material. Copyright © 2016 Elsevier Ltd. All rights reserved.

Bacterial exopolymer utilization by a harpacticoid copepod: A methodology and results

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

Decho, A.W.; Moriarty, D.J.W.

1990-07-01

Exopolymer mucus secretions of bacteria and diatoms are potential foods for benthic animals. These secretions are coincidently ingested by animals during consumption of microbial cells and sediments. The utilization of microbial secretions was investigated with exopolymer derived from a marine bacterium (pseudomonas sp.) from seagrass beds and a harpacticoid copepod Laophonte sp. from the same habitat. A new technique was developed to examine ingestion, absorption, and absorption efficiencies of these bacterial secretions by consumers. Exopolymer mucus (from the bacterium in stationary phase) was labeled with {sup 14}C, collected, purified, and bound onto bacterium-sized beads. The exopolymer slime coating mimicked themore » coatings associated with many marine bacteria. Results from feeding experiments where the coated beads were mixed with sediment demonstrated that the mucus-exopolymer secretions of bacteria were ingested and utilized by Laophonte sp. Absorption efficiencies, determined directly, were > 80% in the presence of other food resources, indicating that exopolymer is potentially a highly labile C resource for this animal.« less

Unseen players shape benthic competition on coral reefs.

PubMed

Barott, Katie L; Rohwer, Forest L

2012-12-01

Recent work has shown that hydrophilic and hydrophobic organic matter (OM) from algae disrupts the function of the coral holobiont and promotes the invasion of opportunistic pathogens, leading to coral morbidity and mortality. Here we refer to these dynamics as the (3)DAM [dissolved organic matter (DOM), direct contact, disease, algae and microbes] model. There is considerable complexity in coral-algae interactions; turf algae and macroalgae promote heterotrophic microbial overgrowth of coral, macroalgae also directly harm the corals via hydrophobic OM, whereas crustose coralline algae generally encourage benign microbial communities. In addition, complex flow patterns transport OM and pathogens from algae to downstream corals, and direct algal contact enhances their delivery. These invisible players (microbes, viruses, and OM) are important drivers of coral reefs because they have non-linear responses to disturbances and are the first to change in response to perturbations, providing near real-time trajectories for a coral reef, a vital metric for conservation and restoration. Copyright © 2012 Elsevier Ltd. All rights reserved.

Benthic and Plankton Foraminifers in Hydrothermally Active Zones of the Mid-Atlantic Ridge (MAR)

NASA Astrophysics Data System (ADS)

Khusid, T. A.; Os'kina, N. S.; Lukashina, N. P.; Gablina, I. F.; Libina, N. V.; Matul, A. G.

2018-01-01

Comparison of benthic foraminiferal assemblages from the core obtained within the Peterburgskoe ore field (Mid-Atlantic Ridge) and from the core taken five kilometers away from the ore field revealed evident differences in their composition, in the appearance of their shells, and also in the benthic-plankton species ratio. It was noted that the foraminiferal assemblage from the ore-bearing sediments of the Petersburg field was characterized by a higher relative content of benthic species and a large number of chemically altered and broken shells. The first occurrence of the species Osangularia umbonifera, which is able to exist in lowoxygen and CaCO3-undersaturated bottom waters at the boundary of biogenic sediments surrounding the ore field and in the ore-bearing sediments, was established. In the core section sampled beyond the ore field, the composition of foraminiferal assemblages differs insignificantly from typical oceanic ones.

Benthic plastic debris in marine and fresh water environments.

PubMed

Corcoran, Patricia L

2015-08-01

This review provides a discussion of the published literature concerning benthic plastic debris in ocean, sea, lake, estuary and river bottoms throughout the world. Although numerous investigations of shoreline, surface and near-surface plastic debris provide important information on plastic types, distribution, accumulation, and degradation, studies of submerged plastic debris have been sporadic in the past and have become more prominent only recently. The distribution of benthic debris is controlled mainly by combinations of urban proximity and its association with fishing-related activities, geomorphology, hydrological conditions, and river input. High density plastics, biofouled products, polymers with mineral fillers or adsorbed minerals, and plastic-metal composites all have the potential to sink. Once deposited on the bottoms of water basins and channels, plastics are shielded from UV light, thus slowing the degradation process significantly. Investigations of the interactions between benthic plastic debris and bottom-dwelling organisms will help shed light on the potential dangers of submerged plastic litter.

Use of benthic invertebrate community structure and the sediment quality triad to evaluate metal-contaminated sediment in the upper Clark Fork River, Montana

USGS Publications Warehouse

Canfield, Timothy J.; Kemble, Nile E.; Brumbaugh, William G.; Dwyer, F. James; Ingersoll, Christopher G.; Fairchild, James F.

1994-01-01

The upper Clark Fork River, above Flathead River, is contaminated with large amounts of As, Cd, Cu, Pb, Mn, and Zn ores from past mining activities. The contaminated area extends from the Butte and Anaconda area to at least 230 km downstream to Milltown Reservoir. Both the upper Clark Fork River and Milltown Reservoir have been designated as U.S. Environmental Protection Agency Superfund sites because of metal-contaminated bottom sediments. We evaluated the impacts of past mining activities on the Clark Fork River ecosystem using benthic invertebrate community assessment, residue chemistry, and toxicity testing. Oligochaeta and Chironomidae generally accounted for over 90% of the benthic invertebrate community in the soft sediment depositional areas. Taxa of Oligochaeta and Chironomidae were predominantly pollution tolerant. Higher numbers of Chironomidae genera were present at stations with higher concentrations of metals in sediment identified as toxic by the amphipod Hyalella azteca in 28-d exposures. Frequency of mouthpart deformities in genera of Chironomidae was low and did not correspond to concentrations of metals in sediment. Total abundance of organisms/m2 did not correspond to concentrations of metals in the sediment samples. Chemical analyses, laboratory toxicity tests, and benthic community evaluations all provide evidence of metal-induced degradation to aquatic communities in both the reservoir and the river. Using a weight-of-evidence approach-the Sediment Quality Triad - provided good concurrence among measures of benthic community structure, sediment chemistry, and laboratory toxicity.

Ecological engineering to control bioclogging: an original field study coupling infiltration and biological measurements

NASA Astrophysics Data System (ADS)

Gette-bouvarot, Morgane; Mermillod-Blondin, Florian; Lassabatere, Laurent; Lemoine, Damien; Delolme, Cécile; Volatier, Laurence

2014-05-01

Infiltration systems are increasingly used in urban areas for several purposes such as flood prevention and groundwater recharge. However, their functioning is often impacted by clogging that leads to decreases in hydraulic and water treatment performances. These systems are commonly built with sand as infiltration medium, a media subject to rapid clogging by the combined and overlapping processes of pore occlusion by fine particles and biofilm development. In a previous study, we pointed out that the phototrophic component of biofilms developed at the surface layer of infiltration systems (algae, cyanobacteria) could reduce by up to 60-fold the saturated hydraulic conductivity. Consequently, it appears crucial to control biofilm growth to maintain porous infiltration media performances. The present study aimed to test the influence of biotic (addition of animals or macrophytes) and abiotic (light reduction) treatments on biofilm development and associated hydraulic properties in an infiltration device dedicated to aquifer recharge with river water in Lyon Area (France). Twenty-five benthic enclosures were used to test 5 "treatments" on non-manipulated surface layer under field conditions. Three biotic treatments consisted in the introduction of: (i) an invertebrate acting as algae grazer (Viviparus viviparus), (ii) an invertebrate that digs galleries in sediments (Tubifex tubifex), and (iii) a macrophyte that could inhibit benthic biofilm by allelopathic activity (Vallisneria spiralis L). The fourth treatment was designed to simulate shading. The last "treatment" was a control which monitored the evolution of the system during the experiment without manipulation (addition of macro-organisms or shading). Each treatment was replicated five times. The experiment was conducted for 6 weeks, and sampling of the surface layer (0-1 cm) was carried out in each enclosure at the beginning (t0) and the end (tf). We coupled biological characterizations (organic matter, algal biomass, bacterial abundances, microbial enzymatic activities, EPS composition, and photosynthetic efficiency) with in situ hydraulic conductivity measurements (falling head method, five measures per enclosure at t0 and tf). Our results showed that some treatments could regulate benthic biofilm growth and improve infiltration rate. For instance, V. viviparus treatment resulted in a decrease in chlorophyll-a, EPS sugar and protein contents and an associated increase of infiltration rate, while it decreased in the control treatment. These results are very promising for the future development of ecological engineering solutions to prevent biological clogging in systems dedicated to infiltration. To our knowledge, this study is the first to highlight such potential role of macro-organisms under field conditions.

Dynamics of submarine groundwater discharge and associated fluxes of dissolved nutrients, carbon, and trace gases to the coastal zone (Okatee River estuary, South Carolina)

USGS Publications Warehouse

Porubsky, W.P.; Weston, N.B.; Moore, W.S.; Ruppel, C.; Joye, S.B.

2014-01-01

Multiple techniques, including thermal infrared aerial remote sensing, geophysical and geological data, geochemical characterization and radium isotopes, were used to evaluate the role of groundwater as a source of dissolved nutrients, carbon, and trace gases to the Okatee River estuary, South Carolina. Thermal infrared aerial remote sensing surveys illustrated the presence of multiple submarine groundwater discharge sites in Okatee headwaters. Significant relationships were observed between groundwater geochemical constituents and 226Ra activity in groundwater with higher 226Ra activity correlated to higher concentrations of organics, dissolved inorganic carbon, nutrients, and trace gases to the Okatee system. A system-level radium mass balance confirmed a substantial submarine groundwater discharge contribution of these constituents to the Okatee River. Diffusive benthic flux measurements and potential denitrification rate assays tracked the fate of constituents in creek bank sediments. Diffusive benthic fluxes were substantially lower than calculated radium-based submarine groundwater discharge inputs, showing that advection of groundwater-derived nutrients dominated fluxes in the system. While a considerable potential for denitrification in tidal creek bank sediments was noted, in situ denitrification rates were nitrate-limited, making intertidal sediments an inefficient nitrogen sink in this system. Groundwater geochemical data indicated significant differences in groundwater chemical composition and radium activity ratios between the eastern and western sides of the river; these likely arose from the distinct hydrological regimes observed in each area. Groundwater from the western side of the Okatee headwaters was characterized by higher concentrations of dissolved organic and inorganic carbon, dissolved organic nitrogen, inorganic nutrients and reduced metabolites and trace gases, i.e. methane and nitrous oxide, than groundwater from the eastern side. Differences in microbial sulfate reduction, organic matter supply, and/or groundwater residence time likely contributed to this pattern. The contrasting features of the east and west sub-marsh zones highlight the need for multiple techniques for characterization of submarine groundwater discharge sources and the impact of biogeochemical processes on the delivery of nutrients and carbon to coastal areas via submarine groundwater discharge.

Sources and cycling of major ions and nutrients in Devils Lake, North Dakota

USGS Publications Warehouse

Lent, R.M.

1994-01-01

Devils Lake is a saline lake in a large, closed drainage basin in northeastern North Dakota. Previous studies determined that major-ion and nutrient concentrations in Devils Lake are strongly affected by microbially mediated sulfate reduction and dissolution of sulfate and carbonate minerals in the bottom sediments. These studies documented substantial spatial variability in the magnitude of calculated benthic fluxes coincident with the horizontal salinity gradient in Devils Lake. The purpose of the present study is to evaluate seasonal variability in benthic-flux rates, and to understand the effect of these fluxes on the major-ion and nutrient chemistries in Devils Lake between May and October 1991. During the study period, the water column was well mixed, and specific conductance, pH, and temperature did not vary with depth. Dissolved oxygen was enriched near the lake surface due to photosynthesis. Major-ion concentrations and nutrient concentrations did not vary with depth. Because the water-quality data were obtained during open-water periods, the vertical profiles reflect well-mixed conditions. However, the first and last profiles for the study period did document near-bottom maxima of major cations. Secchi-disk depth varied from 0.82 meter on May 7,1991, to 2.13 meters on June 5, 1991. The mean Secchi-disk depth during the study period was 1.24 meters. Seasonal variations in Secchi-disk depths were attributed to variations in primary productivity and phytoplankton communities. Nutrient cycles in Devils Lake were evaluated using gross primary productivity rate data, sediment trap data, and major-ion and nutrient benthic-flux rate data. Gross primary productivity rate was smallest in May (0.076 gram of carbon per square meter per day) and largest in September (1.8 grams of carbon per square meter per day). Average gross primary productivity for the study period was 0.87 gram of carbon per square meter per day. Average gross primary productivity is consistent with historic data from Devils Lake and with data from other eutrophic lakes.The average flux of organic carbon for the study period was 12 grams per square meter per day. The calculated carbon to nitrogen to phosphorus ratio (317:25:1) is similar to the Redfield ratio (106:16:1); therefore, most organic matter probably is derived from lacustrine phytoplankton.Calculated benthic-flux rates indicated that bottom sediments are important sources of majorions and nutrients to Devils Lake. Only one of the cores collected during this study indicated a net sulfate flux from the lake into the sediments. Seasonal variations in major-ion and nutrient benthic fluxes generally were small. However, there were important differences between the calculated benthic fluxes for this study and the calculated benthic fluxes for 1990. Calculated benthic fluxes of bicarbonate, ammonia, and phosphorus for this study were smaller than calculated benthic fluxes for 1990. The large differences between fluxes for 1990 and 1991 were attributed to calm, stratified water-column conditions in 1990 and well-mixed water-column conditions in 1991.The role of benthic fluxes in the chemical mass balances in Devils Lake was evaluated by calculating response times for major ions and nutrients in Devils Lake. The calculated response times for major ions in Devils Lake ranged from 6.7 years for bicarbonate to 34 years for sulfur (as 804). The response times for major ions are significantly shorter than previous estimates that did not include benthic fluxes. In addition, the relatively short response times for nitrogen (4.2 years) and phosphorus (0.95 year) indicate that nutrients are recycled rapidly between bottom sediments and the lake. During the study period, benthic fluxes were the dominant source of major ions and nutrients to Devils Lake and greatly reduced the response times of all major ions and nutrients for Devils Lake. As a result, bottom-sediment processes appear to buffer major-ion and nutrient concentrations in the lake. Any future attempt to evaluate water quality in Devils Lake should include the effects of bottom-sediment processes.

Chemical defense of early life stages of benthic marine invertebrates.

PubMed

Lindquist, Niels

2002-10-01

Accurate knowledge of factors affecting the survival of early life stages of marine invertebrates is critically important for understanding their population dynamics and the evolution of their diverse reproductive and life-history characteristics. Chemical defense is an important determinant of survival for adult stages of many sessile benthic invertebrates, yet relatively little consideration has been given to chemical defenses at the early life stages. This review examines the taxonomic breadth of early life-stage chemical defense in relation to various life-history and reproductive characteristics, as well as possible constraints on the expression of chemical defense at certain life stages. Data on the localization of defensive secondary metabolites in larvae and the fitness-related consequences of consuming even a small amount of toxic secondary metabolites underpin proposals regarding the potential for Müllerian and Batesian mimicry to occur among marine larvae. The involvement of microbial symbionts in the chemical defense of early life stages illustrates its complexity for some species. As our knowledge of chemical defenses in early life stages grows, we will be able to more rigorously examine connections among phylogeny, chemical defenses, and the evolution of reproductive and life-history characteristics among marine invertebrates.

Nitrogen Fixation in the Intertidal Sediments of the Yangtze Estuary: Occurrence and Environmental Implications

NASA Astrophysics Data System (ADS)

Hou, Lijun; Wang, Rong; Yin, Guoyu; Liu, Min; Zheng, Yanling

2018-03-01

Nitrogen fixation is a microbial-mediated process converting atmospheric dinitrogen gas to biologically available ammonia or other molecules, and it plays an important role in regulating nitrogen budgets in coastal marine ecosystems. In this study, nitrogen fixation in the intertidal sediments of the Yangtze Estuary was investigated using nitrogen isotope tracing technique. The abundance of nitrogen fixation functional gene (nifH) was also quantified. The measured rates of sediment nitrogen fixation ranged from 0.37 to 7.91 nmol N g-1 hr-1, while the abundance of nifH gene varied from 2.28 × 106 to 1.28 × 108 copies g-1 in the study area. The benthic nitrogen fixation was correlated closely to the abundance of nifH gene and was affected significantly by salinity, pH, and availability of sediment organic carbon and ammonium. It is estimated that sediment nitrogen fixation contributed approximately 9.3% of the total terrigenous inorganic nitrogen transported annually into the Yangtze estuarine and coastal environment. This result implies that the occurrence of benthic nitrogen fixation acts as an important internal source of reactive nitrogen and to some extent exacerbates nitrogen pollution in this aquatic ecosystem.

Benthic boundary layer processes in the Lower Florida Keys

USGS Publications Warehouse

Lavoie, D.L.; Richardson, M.D.; Holmes, C.

1997-01-01

This special issue of Geo-Marine Letters, "Benthic Boundary Layer Processes in the Lower Florida Keys," includes 12 papers that present preliminary results from the Key West Campaign. The Dry Tortugas and Marquesas Keys test sites were selected by a group of 115 scientists and technicians to study benthic boundary layer processes in a carbonate environment controlled by bioturbation and biogeochemical processes. Major activities included remote sediment classification; high-frequency acoustic scattering experiments; sediment sampling for radiological, geotechnical, biological, biogeochemical, physical, and geoacoustic studies; and hydrodynamic studies using an instrumented tetrapod. All these data are being used to improve our understanding of the effects of environmental processes on sediment structure and behavior.

Benthic algae compensate for phytoplankton losses in large aquatic ecosystems.

PubMed

Brothers, Soren; Vadeboncoeur, Yvonne; Sibley, Paul

2016-12-01

Anthropogenic activities can induce major trophic shifts in aquatic systems, yet we have an incomplete understanding of the implication of such shifts on ecosystem function and on primary production (PP) in particular. In recent decades, phytoplankton biomass and production in the Laurentian Great Lakes have declined in response to reduced nutrient concentrations and invasive mussels. However, the increases in water clarity associated with declines in phytoplankton may have positive effects on benthic PP at the ecosystem scale. Have these lakes experienced oligotrophication (a reduction of algal production), or simply a shift in autotrophic structure with no net decline in PP? Benthic contributions to ecosystem PP are rarely measured in large aquatic systems, but our calculations based on productivity rates from the Great Lakes indicate that a significant proportion (up to one half, in Lake Huron) of their whole-lake production may be benthic. The large declines (5-45%) in phytoplankton production in the Great Lakes from the 1970s to 2000s may be substantially compensated by benthic PP, which increased by up to 190%. Thus, the autotrophic productive capacity of large aquatic ecosystems may be relatively resilient to shifts in trophic status, due to a redirection of production to the near-shore benthic zone, and large lakes may exhibit shifts in autotrophic structure analogous to the regime shifts seen in shallow lakes. © 2016 John Wiley & Sons Ltd.

Microbial mat structures in the basal Ediacaran Doushantuo cap dolostone from the Yangtze Gorges area of South China and their environmental implications

NASA Astrophysics Data System (ADS)

Wang, Z.; Wang, J.; Xiao, S.; Hu, J.

2014-12-01

Environmental changes after the terminal Cryogenian snowball Earth event have been debated extensively in the literature. But there have been relatively few studies on the biotic response in the aftermath of this snowball Earth event. In fact, a variety of potential microbial facies are preserved in basal Ediacaran cap dolostones as peloids, clotted fabrics, and morphologically diverse microbialites (e. g., tube-like stromatolites and stratiform biolaminites). In South China, centimeter-sized domal and conical stromatolites consisting of wavy or wrinkled microbial mats occur at the top of the Doushantuo cap dolostone. Sedimentological investigation of these stromatolites on outcrop and in core samples from the Yangtze Gorges area suggests that they are likely biological in origin. These stromatolites are characterized by vertical accumulation of dark and light laminae. The dark laminae are sub-millimetric in thickness and are composed of probably biogenic kerogen as determined by Raman spectroscopy. The dark laminae is also rich in pyrite, likely derived from organic degradation by sulfate reduction bacteria. Microsparry calcite occur as cements between the dark laminae. Within the Doushantuo stromatolites, there are patches of randomly oriented calcite needles. The precipitation of these calcite needles may have also been facilitated by microbial processes such bacterial sulfate reduction. Our study shows that shallow marine environment became habitable soon after the snowball Earth glaciation ended and benthic microbes were among some of the first organisms to colonize these environments.

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate‐reducing benthic microbial populations

PubMed Central

Saad, Sainab; Bhatnagar, Srijak; Tegetmeyer, Halina E.; Geelhoed, Jeanine S.; Strous, Marc

2017-01-01

Summary For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate‐reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum, appeared to have coupled both acetate‐ and hydrogen oxidation to sulfate reduction. We describe a novel representative of the widespread uncultured candidate phylum Fermentibacteria (formerly candidate division Hyd24‐12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name ‘USabulitectum silens’ and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the function of fermentative, as well as sulfate‐reducing microbial communities and their adaptation to a dynamic environment. PMID:28836729

Hypoxia causes preservation of labile organic matter and changes seafloor microbial community composition (Black Sea).

PubMed

Jessen, Gerdhard L; Lichtschlag, Anna; Ramette, Alban; Pantoja, Silvio; Rossel, Pamela E; Schubert, Carsten J; Struck, Ulrich; Boetius, Antje

2017-02-01

Bottom-water oxygen supply is a key factor governing the biogeochemistry and community composition of marine sediments. Whether it also determines carbon burial rates remains controversial. We investigated the effect of varying oxygen concentrations (170 to 0 μM O 2 ) on microbial remineralization of organic matter in seafloor sediments and on community diversity of the northwestern Crimean shelf break. This study shows that 50% more organic matter is preserved in surface sediments exposed to hypoxia compared to oxic bottom waters. Hypoxic conditions inhibit bioturbation and decreased remineralization rates even within short periods of a few days. These conditions led to the accumulation of threefold more phytodetritus pigments within 40 years compared to the oxic zone. Bacterial community structure also differed between oxic, hypoxic, and anoxic zones. Functional groups relevant in the degradation of particulate organic matter, such as Flavobacteriia , Gammaproteobacteria , and Deltaproteobacteria , changed with decreasing oxygenation, and the microbial community of the hypoxic zone took longer to degrade similar amounts of deposited reactive matter. We conclude that hypoxic bottom-water conditions-even on short time scales-substantially increase the preservation potential of organic matter because of the negative effects on benthic fauna and particle mixing and by favoring anaerobic processes, including sulfurization of matter.

Hypoxia causes preservation of labile organic matter and changes seafloor microbial community composition (Black Sea)

PubMed Central

Jessen, Gerdhard L.; Lichtschlag, Anna; Ramette, Alban; Pantoja, Silvio; Rossel, Pamela E.; Schubert, Carsten J.; Struck, Ulrich; Boetius, Antje

2017-01-01

Bottom-water oxygen supply is a key factor governing the biogeochemistry and community composition of marine sediments. Whether it also determines carbon burial rates remains controversial. We investigated the effect of varying oxygen concentrations (170 to 0 μM O2) on microbial remineralization of organic matter in seafloor sediments and on community diversity of the northwestern Crimean shelf break. This study shows that 50% more organic matter is preserved in surface sediments exposed to hypoxia compared to oxic bottom waters. Hypoxic conditions inhibit bioturbation and decreased remineralization rates even within short periods of a few days. These conditions led to the accumulation of threefold more phytodetritus pigments within 40 years compared to the oxic zone. Bacterial community structure also differed between oxic, hypoxic, and anoxic zones. Functional groups relevant in the degradation of particulate organic matter, such as Flavobacteriia, Gammaproteobacteria, and Deltaproteobacteria, changed with decreasing oxygenation, and the microbial community of the hypoxic zone took longer to degrade similar amounts of deposited reactive matter. We conclude that hypoxic bottom-water conditions—even on short time scales—substantially increase the preservation potential of organic matter because of the negative effects on benthic fauna and particle mixing and by favoring anaerobic processes, including sulfurization of matter. PMID:28246637

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river

NASA Astrophysics Data System (ADS)

Atashgahi, Siavash; Aydin, Rozelin; Dimitrov, Mauricio R.; Sipkema, Detmer; Hamonts, Kelly; Lahti, Leo; Maphosa, Farai; Kruse, Thomas; Saccenti, Edoardo; Springael, Dirk; Dejonghe, Winnie; Smidt, Hauke

2015-11-01

The impact of the installation of a technologically advanced wastewater treatment plant (WWTP) on the benthic microbial community of a vinyl chloride (VC) impacted eutrophic river was examined two years before, and three and four years after installation of the WWTP. Reduced dissolved organic carbon and increased dissolved oxygen concentrations in surface water and reduced total organic carbon and total nitrogen content in the sediment were recorded in the post-WWTP samples. Pyrosequencing of bacterial 16S rRNA gene fragments in sediment cores showed reduced relative abundance of heterotrophs and fermenters such as Chloroflexi and Firmicutes in more oxic and nutrient poor post-WWTP sediments. Similarly, quantitative PCR analysis showed 1-3 orders of magnitude reduction in phylogenetic and functional genes of sulphate reducers, denitrifiers, ammonium oxidizers, methanogens and VC-respiring Dehalococcoides mccartyi. In contrast, members of Proteobacteria adapted to nutrient-poor conditions were enriched in post-WWTP samples. This transition in the trophic state of the hyporheic sediments reduced but did not abolish the VC respiration potential in the post-WWTP sediments as an important hyporheic sediment function. Our results highlight effective nutrient load reduction and parallel microbial ecological state restoration of a human-stressed urban river as a result of installation of a WWTP.

Carbon isotope variations in a solar pond microbial mat: Role of environmental gradients as steering variables

NASA Astrophysics Data System (ADS)

Schidlowski, Manfred; Gorzawski, Hendrik; Dor, Inka

1994-05-01

A biogeochemical traverse is presented for a juvenile benthic mat covering the depth profile of an artificially stratified and eutrophicated hypersaline heliothermal pond with known gradients of temperature, salinity, pH, and light transmission. It can be shown that visual mat development depends primarily on temperature and salinity as main environmental steering variables whose increase with depth goes along with the attenuation and final disappearance of a visible microbial film in the pond's hypolimnic compartment. Recorded biogeochemical parameters (C org content, cell numbers, chlorophyll-a content) evidently reflect, as either biomass- or productivity-related index functions, the visually perceptible growth gradient of the microbial ecosystem along the pond slope. The observed coincidence of maxima in these index functions with maxima in δ13Corg clearly identifies high rates of primary productivity as the agent ultimately responsible for the generation of isotopically heavy ( 13C-enriched) biomass in these and related environments. Extreme demands placed on the local feeder pool of dissolved inorganic carbon by high rates of primary productivity entertained by the mat-forming microbenthos obviously give rise to severe CO 2 limitation, enforcing the operation of a diffusion-(supply-)limited assimilatory pathway with an isotopically indiscriminate metabolization of the available CO 2 resources.

Benthic Carbon Mineralization in Hadal Trenches: Insights From In Situ Determination of Benthic Oxygen Consumption

NASA Astrophysics Data System (ADS)

Luo, Min; Glud, Ronnie N.; Pan, Binbin; Wenzhöfer, Frank; Xu, Yunping; Lin, Gang; Chen, Duofu

2018-03-01

Hadal trenches have been proposed as depocenters of organic material and hot spots for organic matter mineralization. In this study, we for the first time quantified the total benthic O2 uptake in hadal trenches using in situ chamber incubations. Three trenches in the tropical Pacific were targeted and exhibited relatively high diagenetic activity given the great water depths, that is, the Mariana Trench (2.0 × 102 μmol O2 m-2 d-1, 10,853 m), the Mussau Trench (2.7 ± 0.1 × 102 μmol O2 m-2 d-1, 7,011 m), and the New Britain Trench (6.0 ± 0.1 × 102 μmol O2 m-2 d-1, 8,225 m). Combined with the analyses of total organic carbon and δ13C of total organic carbon in the sediments and previously published in situ O2 microprofiles from hadal settings, we suggest that hadal benthic carbon mineralization partly is governed by the surface production and also is linked to the distance from land. Therefore, we highlight that terrestrial organic matter can be of importance in sustaining benthic communities in some hadal settings.

How marine debris ingestion differs among megafauna species in a tropical coastal area.

PubMed

Di Beneditto, Ana Paula Madeira; Awabdi, Danielle Rodrigues

2014-11-15

The marine debris ingested by megafauna species (Trichiurus lepturus, Chelonia mydas, Pontoporia blainvillei, and Sotalia guianensis) was recorded in a coastal area of southeastern Brazil (21-23°S). Marine debris was recorded in all species, mainly consisting of plastic material (flexible and hard plastics - clear, white, and colored- and nylon filaments). The 'pelagic predators' T. lepturus and S. guianesis showed the lowest percent frequencies of debris ingestion (0.7% and 1.3%, respectively), followed by the 'benthic predator' P. blainvillei (15.7%) and the 'benthic herbivorous C. mydas (59.2%). The debris found in C. mydas stomachs was opportunistically ingested during feeding activities on local macroalgal banks. In the study area, the benthic environment accumulates more anthropogenic debris than the pelagic environment, and benthic/demersal feeders are more susceptible to encounters and ingestion. The sub-lethal effects observed in C. mydas, such as intestinal obstruction due to hardened fecal material, should be considered a local conservation concern. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effects of mining-derived metals on riffle-dwelling benthic fishes in Southeast Missouri, USA

USGS Publications Warehouse

Allert, A.L.; Fairchild, J.F.; Schmitt, C.J.; Besser, J.M.; Brumbaugh, W.G.; Olson, S.J.

2009-01-01

We studied the ecological effects of mining-derived metals on riffle-dwelling benthic fishes at 16 sites in the Viburnum Trend lead-zinc mining district of southeast Missouri. Fish community attributes were compared to watershed features and to physical and chemical variables including metal concentrations in sediment pore water and fish. Ozark sculpin (Cottus hypselurus), rainbow darter (Etheostoma caeruleum), Ozark madtom (Noturus albater), and banded sculpin (Cottus carolinae) were the most abundant fishes collected. Species richness and density of riffle-dwelling benthic fishes were negatively correlated with metal concentrations in pore water and in fish. Sculpin densities were also negatively correlated with metal concentrations in pore water and in fish, but positively correlated with distance from mines and upstream watershed area. These findings indicate that metals associated with active lead-zinc mining adversely affect riffle-dwelling benthic fishes downstream of mining areas in the Viburnum Trend. Sculpins may be useful as a sentinel species for assessing mining-related impacts on fish communities.

Turnover of microbial lipids in the deep biosphere and growth of benthic archaeal populations

PubMed Central

Xie, Sitan; Lipp, Julius S.; Wegener, Gunter; Ferdelman, Timothy G.; Hinrichs, Kai-Uwe

2013-01-01

Deep subseafloor sediments host a microbial biosphere with unknown impact on global biogeochemical cycles. This study tests previous evidence based on microbial intact polar lipids (IPLs) as proxies of live biomass, suggesting that Archaea dominate the marine sedimentary biosphere. We devised a sensitive radiotracer assay to measure the decay rate of ([14C]glucosyl)-diphytanylglyceroldiether (GlcDGD) as an analog of archaeal IPLs in continental margin sediments. The degradation kinetics were incorporated in model simulations that constrained the fossil fraction of subseafloor IPLs and rates of archaeal turnover. Simulating the top 1 km in a generic continental margin sediment column, we estimated degradation rate constants of GlcDGD being one to two orders of magnitude lower than those of bacterial IPLs, with half-lives of GlcDGD increasing with depth to 310 ky. Given estimated microbial community turnover times of 1.6–73 ky in sediments deeper than 1 m, 50–96% of archaeal IPLs represent fossil signals. Consequently, previous lipid-based estimates of global subseafloor biomass probably are too high, and the widely observed dominance of archaeal IPLs does not rule out a deep biosphere dominated by Bacteria. Reverse modeling of existing concentration profiles suggest that archaeal IPL synthesis rates decline from around 1,000 pg⋅mL−1 sediment⋅y−1 at the surface to 0.2 pg⋅mL−1⋅y−1 at 1 km depth, equivalent to production of 7 × 105 to 140 archaeal cells⋅mL−1 sediment⋅y−1, respectively. These constraints on microbial growth are an important step toward understanding the relationship between the deep biosphere and the carbon cycle. PMID:23530229

Turnover of microbial lipids in the deep biosphere and growth of benthic archaeal populations.

PubMed

Xie, Sitan; Lipp, Julius S; Wegener, Gunter; Ferdelman, Timothy G; Hinrichs, Kai-Uwe

2013-04-09

Deep subseafloor sediments host a microbial biosphere with unknown impact on global biogeochemical cycles. This study tests previous evidence based on microbial intact polar lipids (IPLs) as proxies of live biomass, suggesting that Archaea dominate the marine sedimentary biosphere. We devised a sensitive radiotracer assay to measure the decay rate of ([(14)C]glucosyl)-diphytanylglyceroldiether (GlcDGD) as an analog of archaeal IPLs in continental margin sediments. The degradation kinetics were incorporated in model simulations that constrained the fossil fraction of subseafloor IPLs and rates of archaeal turnover. Simulating the top 1 km in a generic continental margin sediment column, we estimated degradation rate constants of GlcDGD being one to two orders of magnitude lower than those of bacterial IPLs, with half-lives of GlcDGD increasing with depth to 310 ky. Given estimated microbial community turnover times of 1.6-73 ky in sediments deeper than 1 m, 50-96% of archaeal IPLs represent fossil signals. Consequently, previous lipid-based estimates of global subseafloor biomass probably are too high, and the widely observed dominance of archaeal IPLs does not rule out a deep biosphere dominated by Bacteria. Reverse modeling of existing concentration profiles suggest that archaeal IPL synthesis rates decline from around 1,000 pg⋅mL(-1) sediment⋅y(-1) at the surface to 0.2 pg⋅mL(-1)⋅y(-1) at 1 km depth, equivalent to production of 7 × 10(5) to 140 archaeal cells⋅mL(-1) sediment⋅y(-1), respectively. These constraints on microbial growth are an important step toward understanding the relationship between the deep biosphere and the carbon cycle.

Substrate growth dynamics and biomineralization of an Ediacaran encrusting poriferan.

PubMed

Wood, Rachel; Penny, Amelia

2018-01-10

The ability to encrust in order to secure and maintain growth on a substrate is a key competitive innovation in benthic metazoans. Here we describe the substrate growth dynamics, mode of biomineralization and possible affinity of Namapoikia rietoogensis , a large (up to 1 m), robustly skeletal, and modular Ediacaran metazoan which encrusted the walls of synsedimentary fissures within microbial-metazoan reefs. Namapoikia formed laminar or domal morphologies with an internal structure of open tubules and transverse elements, and had a very plastic, non-deterministic growth form which could encrust both fully lithified surfaces as well as living microbial substrates, the latter via modified skeletal holdfasts. Namapoikia shows complex growth interactions and substrate competition with contemporary living microbialites and thrombolites, including the production of plate-like dissepiments in response to microbial overgrowth which served to elevate soft tissue above the microbial surface. Namapoikia could also recover from partial mortality due to microbial fouling. We infer initial skeletal growth to have propagated via the rapid formation of an organic scaffold via a basal pinacoderm prior to calcification. This is likely an ancient mode of biomineralization with similarities to the living calcified demosponge Vaceletia. Namapoikia also shows inferred skeletal growth banding which, combined with its large size, implies notable individual longevity. In sum, Namapoikia was a large, relatively long-lived Ediacaran clonal skeletal metazoan that propagated via an organic scaffold prior to calcification, enabling rapid, effective and dynamic substrate occupation and competition in cryptic reef settings. The open tubular internal structure, highly flexible, non-deterministic skeletal organization, and inferred style of biomineralization of Namapoikia places probable affinity within total-group poriferans. © 2018 The Author(s).

Benthic N2 fixation in coral reefs and the potential effects of human-induced environmental change

PubMed Central

Cardini, Ulisse; Bednarz, Vanessa N; Foster, Rachel A; Wild, Christian

2014-01-01

Tropical coral reefs are among the most productive and diverse ecosystems, despite being surrounded by ocean waters where nutrients are in short supply. Benthic dinitrogen (N2) fixation is a significant internal source of “new” nitrogen (N) in reef ecosystems, but related information appears to be sparse. Here, we review the current state (and gaps) of knowledge on N2 fixation associated with coral reef organisms and their ecosystems. By summarizing the existing literature, we show that benthic N2 fixation is an omnipresent process in tropical reef environments. Highest N2 fixation rates are detected in reef-associated cyanobacterial mats and sea grass meadows, clearly showing the significance of these functional groups, if present, to the input of new N in reef ecosystems. Nonetheless, key benthic organisms such as hard corals also importantly contribute to benthic N2 fixation in the reef. Given the usually high coral coverage of healthy reef systems, these results indicate that benthic symbiotic associations may be more important than previously thought. In fact, mutualisms between carbon (C) and N2 fixers have likely evolved that may enable reef communities to mitigate N limitation. We then explore the potential effects of the increasing human interferences on the process of benthic reef N2 fixation via changes in diazotrophic populations, enzymatic activities, or availability of benthic substrates favorable to these microorganisms. Current knowledge indicates positive effects of ocean acidification, warming, and deoxygenation and negative effects of increased ultraviolet radiation on the amount of N fixed in coral reefs. Eutrophication may either boost or suppress N2 fixation, depending on the nutrient becoming limiting. As N2 fixation appears to play a fundamental role in nutrient-limited reef ecosystems, these assumptions need to be expanded and confirmed by future research efforts addressing the knowledge gaps identified in this review. PMID:24967086

A new Arctic seepage site? Preliminary evidence from benthic community

NASA Astrophysics Data System (ADS)

Caridi, Francesca; Sabbatini, Anna; Morigi, Caterina; Giulia Lucchi, Renata

2017-04-01

The Kveithola Trough is an abrupt and narrow sedimentary system located in the NW Barents Sea. The hydrographic, bio-geochemical conditions and the possible existence of gas seepage activity of the area have been investigated during the Eurofleets 2- BURSTER cruise, conducted on board the German icebreaker RV Polarstern. The aim of our work is to characterize the benthic biota and more specifically the macrofaunal community structure coupled to the study of benthic foraminiferal meiofauna. Preliminary qualitative results revealed that in the inner Kveithola Trough, the macrofaunal community is composed by abundant black worm tubes (Chaetopteridae worms and Siboglinidae-like taxa) with presence of Thyasiridae bivalve species. The occurrence of these macrofaunal taxa is usually associated to oxygen-reduced environments, hydrothermal vents and cold seeps. The living benthic foraminiferal assemblage in the same stations is characterized by the presence of typically oxygen-depleted environmental taxa including the calcareous species Nonionellina labradorica and Globobulimina spp.. Conversely, in the outer Kveithola trough, both benthic macrofauna and foraminiferal meiofauna assemblages are characterized by less opportunistic taxa with a higher biodiversity suggesting very distinct oceanographic sea bottom conditions. The organic matter richness plays a large role in the Kveithola Trough environmental setting and may bring anoxic conditions that could affect the biota of the area. In fact, the benthic community structure of this area inhabits suboxic, anoxic and organic-enriched sediments and disturbed environments, forming assemblages with low diversity and high abundances of a few tolerant and/or specialized species. This preliminary finding could be consistent with other studies examining benthic community structure around Svalbard and in particular cold seep and vents habitats where faunal characteristics are patchy, suggesting small-scale heterogeneity in the environment surrounding cold seeps. For said reasons we envisage the presence of a new Arctic seepage site having a strong local impact on the benthic system.

Herbivorous snails can increase water clarity by stimulating growth of benthic algae.

PubMed

Zhang, Xiufeng; Taylor, William D; Rudstam, Lars G

2017-11-01

Eutrophication in shallow lakes is characterized by a switch from benthic to pelagic dominance of primary productivity that leads to turbid water, while benthification is characterized by a shift in primary production from the pelagic zone to the benthos associated with clear water. A 12-week mesocosm experiment tested the hypothesis that the herbivorous snail Bellamya aeruginosa stimulates the growth of pelagic algae through grazing on benthic algae and through accelerating nutrient release from sediment. A tube-microcosm experiment using 32 P-PO 4 as a tracer tested the effects of the snails on the release of sediment phosphorus (P). The mesocosm experiment recorded greater total nitrogen (TN) concentrations and a higher ratio of TN:TP in the overlying water, and a higher light intensity and biomass of benthic algae as measured by chlorophyll a (Chl a) in the snail treatment than in the control. Concentrations of total phosphorus (TP), total suspended solids (TSSs), and inorganic suspended solids (ISSs) in the overlying water were lower in the snail treatment than in the control, though no significant difference in Chl a of pelagic algae between the snail treatment and control was observed. In the microcosm experiment, 32 P activity in the overlying water was higher in the snail treatment than in the control, indicating that snails accelerated P release from the sediment. Our interpretation of these results is that snails enhanced growth of benthic algae and thereby improved water clarity despite grazing on the benthic algae and enhancing P release from the sediment. The rehabilitation of native snail populations may therefore enhance the recovery of eutrophic shallow lakes to a clear water state by stimulating growth of benthic algae.

Benthic foraminifera as indicators of pollution in high latitude marine environments

NASA Astrophysics Data System (ADS)

Dijkstra, N.; Junttila, J.; Husum, K.; Carroll, J.; Klitgaard-Kristensen, D.; Hald, M.

2012-04-01

An increasing number of studies demonstrate the potential of benthic foraminifera to characterize ecological status. However, the use of benthic foraminifera as bio-indicators has previously not been tested in high latitudes. This research contributes to the development of foraminifera as a bio-monitoring technique for the Arctic region, as industrial activities in this region will increase in the coming years. Surface sediments (0-1 cm) from sites close to gas fields in the SW Barents Sea were studied. In addition, to elucidate the range from less to very affected, surface sediments from the harbor of the town of Hammerfest (70° N) were studied. At least 300 living benthic foraminifera from the size fraction 100 µm-1 mm were counted and identified at species level. Pollution levels (heavy metals and persistent organic pollutants) and sediment properties (grainsize and TOC) were also analyzed. Pollution levels at the sea floor in the SW Barents Sea are of background to good level (level I-II) according to the definitions by the Water Framework Directorate (WFD). Benthic foraminiferal assemblages are influenced by natural environmental parameters such as water mass properties, water depth, nutrient availability, bottom current strength, and grain size. Surface sediments from the Hammerfest harbor are of moderate environmental status (WFD level II-III) based on heavy metal concentrations and of bad environmental status (WFD IV-V) based on persistent organic pollutant concentrations. Opportunistic benthic foraminifera are dominating the assemblages. The most polluted areas in the harbor are barren for foraminifera or have high amounts of deformed shells. In both environments the foraminiferal diversity of the samples, does not correspond to expected environmental status based on the pollution levels of the sediments. Environmental status classes, based on benthic foraminifera instead of macrofauna, would allow rapid analyses of the environmental impact of pollution.

Effect of settled diatom‐aggregates on benthic nitrogen cycling

PubMed Central

Thamdrup, Bo; Stief, Peter; Glud, Ronnie N.

2017-01-01

Abstract The marine sediment hosts a mosaic of microhabitats. Recently it has been demonstrated that the settlement of phycodetrital aggregates can induce local changes in the benthic O2 distribution due to confined enrichment of organic material and alteration of the diffusional transport. Here, we show how this microscale O2 shift substantially affects benthic nitrogen cycling. In sediment incubations, the settlement of diatom‐aggregates markedly enhanced benthic O2 and NO3− consumption and stimulated NO2− and NH4+ production. Oxygen microprofiles revealed the rapid development of anoxic niches within and underneath the aggregates. During 120 h following the settling of the aggregates, denitrification of NO3− from the overlying water increased from 13.5 μmol m−2 h−1 to 24.3 μmol m−2 h−1, as quantified by 15N enrichment experiment. Simultaneously, N2 production from coupled nitrification‐denitrification decreased from 33.4 μmol m−2 h−1 to 25.9 μmol m−2 h−1, probably due to temporary inhibition of the benthic nitrifying community. The two effects were of similar magnitude and left the total N2 production almost unaltered. At the aggregate surface, nitrification was, conversely, very efficient in oxidizing NH4+ liberated by mineralization of the aggregates. The produced NO3− was preferentially released into the overlying water and only a minor fraction contributed to denitrification activity. Overall, our data indicate that the abrupt change in O2 microdistribution caused by aggregates stimulates denitrification of NO3− from the overlying water, and loosens the coupling between benthic nitrification and denitrification both in time and space. The study contributes to expanding the conceptual and quantitative understanding of how nitrogen cycling is regulated in dynamic benthic environments. PMID:29456269

Distinct responses of bacterial communities to agricultural and urban impacts in temperate southern African estuaries

NASA Astrophysics Data System (ADS)

Matcher, G. F.; Froneman, P. W.; Meiklejohn, I.; Dorrington, R. A.

2018-01-01

Worldwide, estuaries are regarded as amongst the most ecologically threatened ecosystems and are increasingly being impacted by urban development, agricultural activities and reduced freshwater inflow. In this study, we examined the influence of different human activities on the diversity and structure of bacterial communities in the water column and sediment in three distinct, temperate permanently open estuarine systems within the same geographic region of southern Africa. The Kariega system is freshwater-deprived and is considered to be relatively pristine; the Kowie estuary is marine-dominated and impacted by urban development, while the Sundays system is fresh-water dominated and impacted by agricultural activity in its catchment. The bacterial communities in all three systems comprise predominantly heterotrophic species belonging to the Bacteroidetes and Proteobacteria phyla with little overlap between bacterioplankton and benthic bacterial communities at the species level. There was overlap between the operational taxonomic units (OTUs) of the Kowie and Kariega, both marine-influenced estuaries. However, lower species richness in the Kowie, likely reflects the impact of human settlements along the estuary. The dominant OTUs in the Sundays River system were distinct from those of the Kariega and Kowie estuaries with an overall decrease in species richness and evenness. This study provides an important snapshot into the microbial population structures of permanently open temperate estuarine systems and the influence of anthropogenic impacts on bacterial diversity and community structure.

Benthic nutrient fluxes in the Eastern Gotland Basin (Baltic Sea) with particular focus on microbial mat ecosystems

NASA Astrophysics Data System (ADS)

Noffke, A.; Sommer, S.; Dale, A. W.; Hall, P. O. J.; Pfannkuche, O.

2016-06-01

Benthic fluxes and water column distributions of dissolved inorganic nitrogen (DIN) and total dissolved phosphate (PO43 -) were measured in situ at 7 sites across a redox gradient from oxic to anoxic bottom waters in the Eastern Gotland Basin (Baltic Sea). The study area was divided into the oxic zone (60 to ca. 80 m water depth, O2 > 30 μM), the hypoxic transition zone (HTZ, ca. 80 to 120 m, O2 < 30 μM) and the deep anoxic and sulfidic basin (> ca. 120 m). Sediments in the HTZ were covered by mats of vacuolated sulfur bacteria. Ammonium (NH4+) fluxes in the deep basin and the HTZ were elevated at 0.6 mmol m- 2 d- 1 and 1 mmol m- 2 d- 1, respectively. Nitrate (NO3-) fluxes were directed into the sediment at all stations in the HTZ and were zero in the deep basin. PO43 - release was highest in the HTZ at 0.23 mmol m- 2 d- 1, with a further release of 0.2 mmol m- 2 d- 1 in the deep basin. Up-scaling the benthic fluxes to the Baltic Proper equals 109 kt yr- 1 of PO43 - and 266 kt yr- 1 of DIN. This is eight- and two-fold higher than the total external load of P (14 kt yr- 1) and DIN (140 kt yr- 1) in 2006 (HELCOM 2009b). The HTZ makes an important contribution to the internal nutrient loading in the Baltic Proper, releasing 70% of P (76 kt yr- 1) and 75% of DIN (200 kt yr- 1) despite covering only 51% of area.

Tracing carbon flow through coral reef food webs using a compound-specific stable isotope approach.

PubMed

McMahon, Kelton W; Thorrold, Simon R; Houghton, Leah A; Berumen, Michael L

2016-03-01

Coral reefs support spectacularly productive and diverse communities in tropical and sub-tropical waters throughout the world's oceans. Debate continues, however, on the degree to which reef biomass is supported by new water column production, benthic primary production, and recycled detrital carbon (C). We coupled compound-specific stable C isotope ratio (δ(13)C) analyses with Bayesian mixing models to quantify C flow from primary producers to coral reef fishes across multiple feeding guilds and trophic positions in the Red Sea. Analyses of reef fishes with putative diets composed primarily of zooplankton (Amblyglyphidodon indicus), benthic macroalgae (Stegastes nigricans), reef-associated detritus (Ctenochaetus striatus), and coral tissue (Chaetodon trifascialis) confirmed that δ(13)C values of essential amino acids from all baseline C sources were both isotopically diagnostic and accurately recorded in consumer tissues. While all four source end-members contributed to the production of coral reef fishes in our study, a single-source end-member often dominated dietary C assimilation of a given species, even for highly mobile, generalist top predators. Microbially reworked detritus was an important secondary C source for most species. Seascape configuration played an important role in structuring resource utilization patterns. For instance, Lutjanus ehrenbergii showed a significant shift from a benthic macroalgal food web on shelf reefs (71 ± 13 % of dietary C) to a phytoplankton-based food web (72 ± 11 %) on oceanic reefs. Our work provides insights into the roles that diverse C sources play in the structure and function of coral reef ecosystems and illustrates a powerful fingerprinting method to develop and test nutritional frameworks for understanding resource utilization.

Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan

PubMed Central

Yoshida, Mitsuhiro; Mochizuki, Tomohiro; Urayama, Syun-Ichi; Yoshida-Takashima, Yukari; Nishi, Shinro; Hirai, Miho; Nomaki, Hidetaka; Takaki, Yoshihiro; Nunoura, Takuro; Takai, Ken

2018-01-01

Previous studies on marine environmental virology have primarily focused on double-stranded DNA (dsDNA) viruses; however, it has recently been suggested that single-stranded DNA (ssDNA) viruses are more abundant in marine ecosystems. In this study, we performed a quantitative viral community DNA analysis to estimate the relative abundance and composition of both ssDNA and dsDNA viruses in offshore upper bathyal sediment from Tohoku, Japan (water depth = 500 m). The estimated dsDNA viral abundance ranged from 3 × 106 to 5 × 106 genome copies per cm3 sediment, showing values similar to the range of fluorescence-based direct virus counts. In contrast, the estimated ssDNA viral abundance ranged from 1 × 108 to 3 × 109 genome copies per cm3 sediment, thus providing an estimation that the ssDNA viral populations represent 96.3–99.8% of the benthic total DNA viral assemblages. In the ssDNA viral metagenome, most of the identified viral sequences were associated with ssDNA viral families such as Circoviridae and Microviridae. The principle components analysis of the ssDNA viral sequence components from the sedimentary ssDNA viral metagenomic libraries found that the different depth viral communities at the study site all exhibited similar profiles compared with deep-sea sediment ones at other reference sites. Our results suggested that deep-sea benthic ssDNA viruses have been significantly underestimated by conventional direct virus counts and that their contributions to deep-sea benthic microbial mortality and geochemical cycles should be further addressed by such a new quantitative approach. PMID:29467725

Energy transfer in the Congo deep-sea fan: From terrestrially-derived organic matter to chemosynthetic food webs

NASA Astrophysics Data System (ADS)

Pruski, A. M.; Decker, C.; Stetten, E.; Vétion, G.; Martinez, P.; Charlier, K.; Senyarich, C.; Olu, K.

2017-08-01

Large amounts of recent terrestrial organic matter (OM) from the African continent are delivered to the abyssal plain by turbidity currents and accumulate in the Congo deep-sea fan. In the recent lobe complex, large clusters of vesicomyid bivalves are found all along the active channel in areas of reduced sediment. These soft-sediment communities resemble those fuelled by chemoautotrophy in cold-seep settings. The aim of this study was to elucidate feeding strategies in these macrofaunal assemblages as part of a greater effort to understand the link between the inputs of terrestrially-derived OM and the chemosynthetic habitats. The biochemical composition of the sedimentary OM was first analysed in order to evaluate how nutritious the available particulate OM is for the benthic macrofauna. The terrestrial OM is already degraded when it reaches the final depositional area. However, high biopolymeric carbon contents (proteins, carbohydrates and lipids) are found in the channel of the recent lobe complex. In addition, about one to two thirds of the nitrogen can be assigned to peptide-like material. Even if this soil-derived OM is poorly digestible, turbiditic deposits contain such high amounts of organic carbon that there is enough biopolymeric carbon and proteacinous nitrogen to support dense benthic communities that contrast with the usual depauperate abyssal plains. Stable carbon and nitrogen isotopes and fatty acid biomarkers were then used to shed light on the feeding strategies allowing the energy transfer from the terrestrial OM brought by the turbidity currents to the abyssal food web. In the non-reduced sediment, surface detritivorous holothurians and suspension-feeding poriferans rely on detritic OM, thereby depending directly on the turbiditic deposits. The sulphur-oxidising symbiont bearing vesicomyids closely depend on the reprocessing of OM with methane and sulphide as final products. Their carbon and nitrogen isotopic signatures vary greatly among sites and could reflect the intensity of the anaerobic oxidation of methane (AOM) in the sediments. Within the vesicomyid habitats, the heterotrophic fauna exhibits a distinctively light carbon isotopic signature in comparison to the background sediments, clearly indicating the utilisation of chemosynthetically-derived OM. Fatty acid biomarkers further confirm that dorvilleid polychaetes consume aggregates that perform AOM. Terrestrial OM reprocessing by microbial consortium thus ensures its transfer to the benthic food web in the Congo deep-sea fan.

Polar marine biology science in Portugal and Spain: Recent advances and future perspectives

NASA Astrophysics Data System (ADS)

Xavier, José C.; Barbosa, Andrés; Agustí, Susana; Alonso-Sáez, Laura; Alvito, Pedro; Ameneiro, Julia; Ávila, Conxita; Baeta, Alexandra; Canário, João; Carmona, Raquel; Catry, Paulo; Ceia, Filipe; Clark, Melody S.; Cristobo, Francisco J.; Cruz, Bruno; Duarte, Carlos M.; Figuerola, Blanca; Gili, Josep-Maria; Gonçalves, Ana R.; Gordillo, Francisco J. L.; Granadeiro, José P.; Guerreiro, Miguel; Isla, Enrique; Jiménez, Carlos; López-González, Pablo J.; Lourenço, Sílvia; Marques, João C.; Moreira, Elena; Mota, Ana M.; Nogueira, Marta; Núñez-Pons, Laura; Orejas, Covadonga; Paiva, Vitor H.; Palanques, Albert; Pearson, Gareth A.; Pedrós-Alió, Carlos; Peña Cantero, Álvaro L.; Power, Deborah M.; Ramos, Jaime A.; Rossi, Sergi; Seco, José; Sañé, Elisabet; Serrão, Ester A.; Taboada, Sergi; Tavares, Sílvia; Teixidó, Núria; Vaqué, Dolors; Valente, Tiago; Vázquez, Elsa; Vieira, Rui P.; Viñegla, Benjamin

2013-10-01

Polar marine ecosystems have global ecological and economic importance because of their unique biodiversity and their major role in climate processes and commercial fisheries, among others. Portugal and Spain have been highly active in a wide range of disciplines in marine biology of the Antarctic and the Arctic. The main aim of this paper is to provide a synopsis of some of the results and initiatives undertaken by Portuguese and Spanish polar teams within the field of marine sciences, particularly on benthic and pelagic biodiversity (species diversity and abundance, including microbial, molecular, physiological and chemical mechanisms in polar organisms), conservation and ecology of top predators (particularly penguins, albatrosses and seals), and pollutants and evolution of marine organisms associated with major issues such as climate change, ocean acidification and UV radiation effects. Both countries have focused their polar research more in the Antarctic than in the Arctic. Portugal and Spain should encourage research groups to continue increasing their collaborations with other countries and develop multi-disciplinary research projects, as well as to maintain highly active memberships within major organizations, such as the Scientific Committee for Antarctic Research (SCAR), the International Arctic Science Council (IASC) and the Association of Polar Early Career Scientists (APECS), and in international research projects.

Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea.

PubMed

Lösekann, Tina; Knittel, Katrin; Nadalig, Thierry; Fuchs, Bernhard; Niemann, Helge; Boetius, Antje; Amann, Rudolf

2007-05-01

Submarine mud volcanoes are formed by expulsions of mud, fluids, and gases from deeply buried subsurface sources. They are highly reduced benthic habitats and often associated with intensive methane seepage. In this study, the microbial diversity and community structure in methane-rich sediments of the Haakon Mosby Mud Volcano (HMMV) were investigated by comparative sequence analysis of 16S rRNA genes and fluorescence in situ hybridization. In the active volcano center, which has a diameter of about 500 m, the main methane-consuming process was bacterial aerobic oxidation. In this zone, aerobic methanotrophs belonging to three bacterial clades closely affiliated with Methylobacter and Methylophaga species accounted for 56%+/-8% of total cells. In sediments below Beggiatoa mats encircling the center of the HMMV, methanotrophic archaea of the ANME-3 clade dominated the zone of anaerobic methane oxidation. ANME-3 archaea form cell aggregates mostly associated with sulfate-reducing bacteria of the Desulfobulbus (DBB) branch. These ANME-3/DBB aggregates were highly abundant and accounted for up to 94%+/-2% of total microbial biomass at 2 to 3 cm below the surface. ANME-3/DBB aggregates could be further enriched by flow cytometry to identify their phylogenetic relationships. At the outer rim of the mud volcano, the seafloor was colonized by tubeworms (Siboglinidae, formerly known as Pogonophora). Here, both aerobic and anaerobic methane oxidizers were found, however, in lower abundances. The level of microbial diversity at this site was higher than that at the central and Beggiatoa species-covered part of the HMMV. Analysis of methyl-coenzyme M-reductase alpha subunit (mcrA) genes showed a strong dominance of a novel lineage, mcrA group f, which could be assigned to ANME-3 archaea. Our results further support the hypothesis of Niemann et al. (54), that high methane availability and different fluid flow regimens at the HMMV provide distinct niches for aerobic and anaerobic methanotrophs.

Isotopic biosignatures in carbonate-rich, cyanobacteria-dominated microbial mats of the Cariboo Plateau, B.C.

PubMed

Brady, A L; Druschel, G; Leoni, L; Lim, D S S; Slater, G F

2013-09-01

Photosynthetic activity in carbonate-rich benthic microbial mats located in saline, alkaline lakes on the Cariboo Plateau, B.C. resulted in pCO2 below equilibrium and δ(13) CDIC values up to +6.0‰ above predicted carbon dioxide (CO2 ) equilibrium values, representing a biosignature of photosynthesis. Mat-associated δ(13) Ccarb values ranged from ~4 to 8‰ within any individual lake, with observations of both enrichments (up to 3.8‰) and depletions (up to 11.6‰) relative to the concurrent dissolved inorganic carbon (DIC). Seasonal and annual variations in δ(13) C values reflected the balance between photosynthetic (13) C-enrichment and heterotrophic inputs of (13) C-depleted DIC. Mat microelectrode profiles identified oxic zones where δ(13) Ccarb was within 0.2‰ of surface DIC overlying anoxic zones associated with sulphate reduction where δ(13) Ccarb was depleted by up to 5‰ relative to surface DIC reflecting inputs of (13) C-depleted DIC. δ(13) C values of sulphate reducing bacteria biomarker phospholipid fatty acids (PLFA) were depleted relative to the bulk organic matter by ~4‰, consistent with heterotrophic synthesis, while the majority of PLFA had larger offsets consistent with autotrophy. Mean δ(13) Corg values ranged from -18.7 ± 0.1 to -25.3 ± 1.0‰ with mean Δ(13) Cinorg-org values ranging from 21.1 to 24.2‰, consistent with non-CO2 -limited photosynthesis, suggesting that Precambrian δ(13) Corg values of ~-26‰ do not necessitate higher atmospheric CO2 concentrations. Rather, it is likely that the high DIC and carbonate content of these systems provide a non-limiting carbon source allowing for expression of large photosynthetic offsets, in contrast to the smaller offsets observed in saline, organic-rich and hot spring microbial mats. © 2013 John Wiley & Sons Ltd.

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.

Diversity and Abundance of Aerobic and Anaerobic Methane Oxidizers at the Haakon Mosby Mud Volcano, Barents Sea▿

PubMed Central

Lösekann, Tina; Knittel, Katrin; Nadalig, Thierry; Fuchs, Bernhard; Niemann, Helge; Boetius, Antje; Amann, Rudolf

2007-01-01

Submarine mud volcanoes are formed by expulsions of mud, fluids, and gases from deeply buried subsurface sources. They are highly reduced benthic habitats and often associated with intensive methane seepage. In this study, the microbial diversity and community structure in methane-rich sediments of the Haakon Mosby Mud Volcano (HMMV) were investigated by comparative sequence analysis of 16S rRNA genes and fluorescence in situ hybridization. In the active volcano center, which has a diameter of about 500 m, the main methane-consuming process was bacterial aerobic oxidation. In this zone, aerobic methanotrophs belonging to three bacterial clades closely affiliated with Methylobacter and Methylophaga species accounted for 56% ± 8% of total cells. In sediments below Beggiatoa mats encircling the center of the HMMV, methanotrophic archaea of the ANME-3 clade dominated the zone of anaerobic methane oxidation. ANME-3 archaea form cell aggregates mostly associated with sulfate-reducing bacteria of the Desulfobulbus (DBB) branch. These ANME-3/DBB aggregates were highly abundant and accounted for up to 94% ± 2% of total microbial biomass at 2 to 3 cm below the surface. ANME-3/DBB aggregates could be further enriched by flow cytometry to identify their phylogenetic relationships. At the outer rim of the mud volcano, the seafloor was colonized by tubeworms (Siboglinidae, formerly known as Pogonophora). Here, both aerobic and anaerobic methane oxidizers were found, however, in lower abundances. The level of microbial diversity at this site was higher than that at the central and Beggiatoa species-covered part of the HMMV. Analysis of methyl-coenzyme M-reductase alpha subunit (mcrA) genes showed a strong dominance of a novel lineage, mcrA group f, which could be assigned to ANME-3 archaea. Our results further support the hypothesis of Niemann et al. (54), that high methane availability and different fluid flow regimens at the HMMV provide distinct niches for aerobic and anaerobic methanotrophs. PMID:17369343

The structure of soft-bottom benthic communities in the vicinity of the Texas Flower Garden Banks, Gulf of Mexico

NASA Astrophysics Data System (ADS)

Yingst, Josephine Y.; Rhoads, Donald C.

1985-05-01

Biological and sedimentological samples were obtained in June 1980 from box cores taken in 100-200 m of water on sandy-mud sediments near the East and West Flower Garden Bank reefs, on the Texas-Louisiana Continental Shelf. The objective was to obtain baseline information about sedimentary parameters and organisms adjacent to the FGB environments in order to allow inferences to be made about potential effects of physical disturbance of the seafloor on the resident benthos. Most infaunal organisms are found in the upper 3-5 cm of the bottom. Permanent meiofauna dominate in both numbers and biomass. X-radiographs of sediment fabrics show all stations to be reworked by head-down deposit-feeders or errant bioturbators. Taxa responsible for this bioturbation were not quantitatively sampled. Macrofaunal densities range from 3000 to 25000 m -2 and total meiofauna from 221 to 892 × (10 cm) -2. Nematodes dominate followed in equal abundance by foraminiferans, polychaetes, and copepods. Seventy-five percent of the total sediment ATP in the top 3 cm is contributed by meiofauna. These benthic assemblages are hypothesized to represent a mixture of pioneering and high-order successional stages. Bacterial abundances are positively correlated with organic content and inversely correlated with macro- and meiofaunal densities. This inverse relationship may reflect consumer cropping intensities. Both microbial ATP and bacterial biomass are lower than reported for the Georgia Bight Shelf, Cape Blanc, West African Shelf, western coast of Norway, and Long Island Sound. Bacterial counts are lower than those recorded for the East China Sea and the Amazon River shelf. Moderate to low standing stocks of benthos, dominated by meiofaunal-sized taxa, further suggest that this area of the Gulf of Mexico is a relatively oligotrophic system for infaunal benthic consumers. Higher order successional stages are, in general, adversely affected to a greater extent than pioneering stages by physical disturbance. In the Texas-Louisiana shelf region, dilution of an already food limited system by inert barium sulphate would be expected to result in even lower standing stocks of benthic infaunal invertebrates.

Dinoflagellate cysts and benthic foraminifera in surface sediments from the Mar Piccolo in Taranto (Ionian Sea, Southern Italy)

NASA Astrophysics Data System (ADS)

Ferraro, L.; Rubino, F.; Frontalini, F.; Belmonte, M.; Di Leo, A.; Giandomenico, S.; Greco, M.; Lirer, F.; Spada, L.; Vallefuoco, M.

2012-12-01

Coastal areas have traditionally been places of human settlement, with the increasing development of cities, industries and other human-related activities possibly having an impact on the aquatic ecosystem. These impacts may take the form of pollution from industrial, domestic, agricultural or mining activities. For this reason, attention to marine environmental problems has recently increased and the search for new methodologies and techniques for the monitoring of coastal-marine areas become more and more active and accurate. In this context biological indicators result a useful tool to provide indication of environmental conditions including the presence or absence of contaminants; in fact biological monitoring is more directly related to the ecological health of an ecosystem than are chemical data. The increasing importance of bioindicators is also encouraged within the European Union's Water Framework Directive (WFD), which aims to achieve a good ecological status in all European water bodies (i.e., rivers, lakes and coastal waters). Among the wide range of bioindicators, 5 biological elements are listed within the WFD: phytoplankton, macroalgae, angiosperms, benthic invertebrates and fishes. Benthic invertebrates as foraminifera represent a group of protozoa widely distributed in all brackish and marine environments which are used in studies assessing the environmental quality of areas subject to intense human activity. Moreover in coastal marine environments benthic and pelagic domain present several relationships, one of these is represented by the life cycles of phytoplankton species, as Dinoflagellates, which include the production of benthic stages (cysts). These dormant stages, which accumulate in confined marine muddy areas, such as ports, lagoons or estuaries, can reach high densities, similar to the seed banks of terrestrial plants. The cysts have a high preservation potential and can rest in/on the sediments for decades. Due to this peculiar characteristic, cysts constitute a reservoir of potential biodiversity but can also be useful indicators of productivity, eutrophication and pollution in recent marine environments. In this way, the sampling sediments of a coastal marine area, allows to monitor the responses of both microplankton and microbenthos to possible disturbance events of the ecosystem. A preliminary study, preparatory to a more detailed sampling survey during winter 2013, was carried out in December 2011 in the Mar Piccolo of Taranto (Ionian Sea), on surface sediment samples which were analyzed to identify living benthic foraminiferal assemblages and dormant stages of plankton in order to establish the potentiality of these organisms as bio-indicators of environmental stress conditions.

Rhythmic behaviour of marine benthopelagic species and the synchronous dynamics of benthic communities

NASA Astrophysics Data System (ADS)

Aguzzi, Jacopo; Sbragaglia, Valerio; Tecchio, Samuele; Navarro, Joan; Company, Joan B.

2015-01-01

Light-intensity cycles drive the relentless motion of species in the oceans, and water column migrants may cyclically make contact with the seabed, hence influencing the temporal dynamism of benthic ecosystems. The influence of light on this process remains largely unknown to date. In this study, we focus on the occurrence of day-night changes in benthic communities on the western Mediterranean continental shelf (100 m depth) and slope (400 m depth) as a potential result of a behaviourally sustained benthopelagic coupling. We analysed fluctuations in species abundance based on trawling at hourly intervals over a 4-day period as a proxy of activity rhythms at the seabed. We also measured light in situ to assess how the depth-related decrease of its intensity influences species rhythms and the occurrence of the putative benthopelagic synchronisation. Temporal similarities in the catch patterns for different species were screened by dendrogram analysis. On the continental shelf, species performing diel migrations (i.e., over a 24 h period) that were either vertical (i.e., benthopelagic) or horizontal across depths (i.e., nektobenthic) clustered together separately from the more sedentary endobenthic and epibenthic species. At the same depth, waveform analysis showed a significant diurnal increase in the catch of water column species and benthic species at night. Such coupling was absent on the continental slope, where light intensity was several orders of magnitude lower than that on the shelf. Our data indicate that diel activity rhythms, which are well known for vertical pelagic migrators, are also evident in the benthos. We discuss the role of light as a major evolutionary driver shaping the composition and biodiversity of benthic communities via visual predation.

High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems

PubMed Central

Lejzerowicz, Franck; Esling, Philippe; Pillet, Loïc; Wilding, Thomas A.; Black, Kenneth D.; Pawlowski, Jan

2015-01-01

Environmental diversity surveys are crucial for the bioassessment of anthropogenic impacts on marine ecosystems. Traditional benthic monitoring relying on morphotaxonomic inventories of macrofaunal communities is expensive, time-consuming and expertise-demanding. High-throughput sequencing of environmental DNA barcodes (metabarcoding) offers an alternative to describe biological communities. However, whether the metabarcoding approach meets the quality standards of benthic monitoring remains to be tested. Here, we compared morphological and eDNA/RNA-based inventories of metazoans from samples collected at 10 stations around a fish farm in Scotland, including near-cage and distant zones. For each of 5 replicate samples per station, we sequenced the V4 region of the 18S rRNA gene using the Illumina technology. After filtering, we obtained 841,766 metazoan sequences clustered in 163 Operational Taxonomic Units (OTUs). We assigned the OTUs by combining local BLAST searches with phylogenetic analyses. We calculated two commonly used indices: the Infaunal Trophic Index and the AZTI Marine Biotic Index. We found that the molecular data faithfully reflect the morphology-based indices and provides an equivalent assessment of the impact associated with fish farms activities. We advocate that future benthic monitoring should integrate metabarcoding as a rapid and accurate tool for the evaluation of the quality of marine benthic ecosystems. PMID:26355099

Effects of reduced dissolved oxygen concentrations on physiology and fluorescence of hermatypic corals and benthic algae

PubMed Central

Smith, Jennifer E.; Thompson, Melissa

2014-01-01

While shifts from coral to seaweed dominance have become increasingly common on coral reefs and factors triggering these shifts successively identified, the primary mechanisms involved in coral-algae interactions remain unclear. Amongst various potential mechanisms, algal exudates can mediate increases in microbial activity, leading to localized hypoxic conditions which may cause coral mortality in the direct vicinity. Most of the processes likely causing such algal exudate induced coral mortality have been quantified (e.g., labile organic matter release, increased microbial metabolism, decreased dissolved oxygen availability), yet little is known about how reduced dissolved oxygen concentrations affect competitive dynamics between seaweeds and corals. The goals of this study were to investigate the effects of different levels of oxygen including hypoxic conditions on a common hermatypic coral Acropora yongei and the common green alga Bryopsis pennata. Specifically, we examined how photosynthetic oxygen production, dark and daylight adapted quantum yield, intensity and anatomical distribution of the coral innate fluorescence, and visual estimates of health varied with differing background oxygen conditions. Our results showed that the algae were significantly more tolerant to extremely low oxygen concentrations (2–4 mg L−1) than corals. Furthermore corals could tolerate reduced oxygen concentrations, but only until a given threshold determined by a combination of exposure time and concentration. Exceeding this threshold led to rapid loss of coral tissue and mortality. This study concludes that hypoxia may indeed play a significant role, or in some cases may even be the main cause, for coral tissue loss during coral-algae interaction processes. PMID:24482757

Effects of reduced dissolved oxygen concentrations on physiology and fluorescence of hermatypic corals and benthic algae.

PubMed

Haas, Andreas F; Smith, Jennifer E; Thompson, Melissa; Deheyn, Dimitri D

2014-01-01

While shifts from coral to seaweed dominance have become increasingly common on coral reefs and factors triggering these shifts successively identified, the primary mechanisms involved in coral-algae interactions remain unclear. Amongst various potential mechanisms, algal exudates can mediate increases in microbial activity, leading to localized hypoxic conditions which may cause coral mortality in the direct vicinity. Most of the processes likely causing such algal exudate induced coral mortality have been quantified (e.g., labile organic matter release, increased microbial metabolism, decreased dissolved oxygen availability), yet little is known about how reduced dissolved oxygen concentrations affect competitive dynamics between seaweeds and corals. The goals of this study were to investigate the effects of different levels of oxygen including hypoxic conditions on a common hermatypic coral Acropora yongei and the common green alga Bryopsis pennata. Specifically, we examined how photosynthetic oxygen production, dark and daylight adapted quantum yield, intensity and anatomical distribution of the coral innate fluorescence, and visual estimates of health varied with differing background oxygen conditions. Our results showed that the algae were significantly more tolerant to extremely low oxygen concentrations (2-4 mg L(-1)) than corals. Furthermore corals could tolerate reduced oxygen concentrations, but only until a given threshold determined by a combination of exposure time and concentration. Exceeding this threshold led to rapid loss of coral tissue and mortality. This study concludes that hypoxia may indeed play a significant role, or in some cases may even be the main cause, for coral tissue loss during coral-algae interaction processes.

Impact of Salinity Gradients on Ammonia Bioattenuation Processes in a Photosynthetic Wetland Biomat

NASA Astrophysics Data System (ADS)

Vega, M.; Jones, Z.; Sharp, J.

2017-12-01

Shallow, open water treatment wetlands may be able to offset challenges associated with the reclamation of impaired waters (e.g., membrane fouling, aeration costs, etc.) due to natural biogeochemical fluctuations produced by a benthic, photoactive biomat. This diatomaceous, redox-stratified biomat has demonstrated significant nitrate and trace organic removal from municipal wastewater streams and the microbial community has been thoroughly characterized. However, research is required to predict shifts in community structure and function in response to the excess salinity, ammonia, and metal gradients of impaired waters. Batch microcosm studies inoculating biomat from an active open water treatment wetland with incremental dilutions of hydraulic fracturing produced water were conducted in a light chamber with oscillating twelve-hour light and dark cycles to assess the effect of an impaired water matrix on biomat functionality. Diurnal photosynthetic signatures and ammonia removal kinetics were quantified in various experiments probing the effects of oscillating light conditions, biomat depth, water column isolation, nitrogen source, and salinity gradients in conjunction with phylogenetic profiles and morphological characterization. Diurnal pH and dissolved oxygen fluctuations were present at all produced water permutations, perhaps indicating stabilization of photosynthetic communities. Ammonia attenuation results suggest that the biomat is effective at removing ammonia, although first order rate constants decrease with increasing produced water abundance. Microbial community diversity appears to decrease with increasing salinity, and it is likely that these shifts correspond to variation in ecosystem function and thus treatment effectiveness. The application of shallow, open water treatment wetlands to remediate impaired waters has the potential to address societally relevant problems while discerning fundamental biogeochemical phenomena.

Microbial Lipid and C Isotopic Biosignatures of a Unique Community at Grand Prismatic Spring, Yellowstone National Park

NASA Technical Reports Server (NTRS)

Jahnke, Linda; Parenteau, Mary; Farmer, Jack

2012-01-01

The microbial communities found in modern hot springs are considered analogs to ones that may have existed in hydrothermal systems on the early Earth and possibly Mars. Our goal was to characterize the microbial biosignatures and to assess the preservation of organic matter in the silica-depositing Grand Prismatic Spring in Yellowstone National Park. This study combines 16S rRNA surveys, lipid biomarkers, and C isotopes to query, "Who's there and what are they doing?" On the edge of the approximately 90 m diameter blue vent pool (56.1 C, pH 8.5), a floating green streamer community grew over a benthic pink community. The membrane lipids in the green streamers and pink mat were composed of unusual ester-linked fatty acids, indicating the presence of novel bacterial groups. In particular, we discovered a series of 2-methyl and 2,X-dimethyl phospholipid fatty acids (C18-22). We are attempting to use the 16S rRNA surveys to link these compounds to source organisms. Wax esters, biomarkers for Chloroflexi, were present in both communities, but displayed different profiles. A higher proportion of branched wax esters were found in the green streamers, and were associated with a relatively high concentration of long-chain di- and trienes (C29-31). This suggests that Chloroflexus primarily grew in the green streamers, while a pink mat of Roseiflexus grew on the sinter substrate underneath. Cyanobacterial alkanes were found in the green streamers (n-C17, 7-, 6- and 5-monomethyl-C17, 7,11-dimethyl-C17, n-C19, n-C19:1). We also detected a series of monoalkylglycerylethers and geologically relevant hopanoids in both communities. Carbon isotope analyses indicated that Chloroflexus was growing photoheterotrophically using cyanobacterial photosynthate. Roseiflexus also traditionally grows photoheterotrophically, but the C isotopic signatures of the lipids in the pink mat were approximately 10 %0 lighter than the cyanobacterial and Chloroflexus lipids, indicating a potentially novel metabolic mechanism or prior secondary reworking of substrates before reaching Roseiflexus. This arrangement of Synechococcus-Chloroflexus green streamers floating over a benthic pink community of Roseiflexus is different from the classical laminated Synechococcus-Chloroflexi mats at Octopus Hot Spring.

Spatio-temporal variations in the composition of organic matter in surface sediments of a mangrove receiving shrimp farm effluents (New Caledonia).

PubMed

Aschenbroich, Adélaïde; Marchand, Cyril; Molnar, Nathalie; Deborde, Jonathan; Hubas, Cédric; Rybarczyk, Hervé; Meziane, Tarik

2015-04-15

In order to investigate spatio-temporal variations in the composition and origin of the benthic organic matter (OM) at the sediment surface in mangrove receiving shrimp farm effluents, fatty acid (FA) biomarkers, natural stable isotopes (δ(13)C and δ(15)N), C:N ratios and chlorophyll-a (chl-a) concentrations were determined during the active and the non-active period of the farm. Fatty acid compositions in surface sediments within the mangrove forest indicated that organic matter inputs varied along the year as a result of farm activity. Effluents were the source of fresh particulate organic matter for the mangrove, as evidenced by the unsaturated fatty acid (UFA) distribution. The anthropogenic MUFA 18:1ω9 was not only accumulated at the sediment surface in some parts of the mangrove, but was also exported to the seafront. Direct release of bacteria and enhanced in situ production of fungi, as revealed by specific FAs, stimulated mangrove litter decomposition under effluent runoff condition. Also, microalgae released from ponds contributed to maintain high benthic chl-a concentrations in mangrove sediments in winter and to a shift in microphytobenthic community assemblage. Primary production was high whether the farm released effluent or not which questioned the temporary effect of shrimp farm effluent on benthic microalgae dynamic. This study outlined that mangrove benthic organic matter was qualitatively and quantitatively affected by shrimp farm effluent release and that responses to environmental condition changes likely depended on mangrove stand characteristics. Copyright © 2015 Elsevier B.V. All rights reserved.

Bioturbation and dissolved organic matter enhance contaminant fluxes from sediment treated with powdered and granular activated carbon.

PubMed

Kupryianchyk, D; Noori, A; Rakowska, M I; Grotenhuis, J T C; Koelmans, A A

2013-05-21

Sediment amendment with activated carbon (AC) is a promising technique for in situ sediment remediation. To date it is not clear whether this technique sufficiently reduces sediment-to-water fluxes of sediment-bound hydrophobic organic chemicals (HOCs) in the presence of bioturbators. Here, we report polychlorobiphenyl (PCB) pore water concentrations, fluxes, mass transfer coefficients, and survival data of two benthic species, for four treatments: no AC addition (control), powdered AC addition, granular AC addition and addition and subsequent removal of GAC (sediment stripping). AC addition decreased mass fluxes but increased apparent mass transfer coefficients because of dissolved organic carbon (DOC) facilitated transport across the benthic boundary layer (BBL). In turn, DOC concentrations depended on bioturbator activity which was high for the PAC tolerant species Asellus aquaticus and low for AC sensitive species Lumbriculus variegatus. A dual BBL resistance model combining AC effects on gradients, DOC facilitated transport and biodiffusion was evaluated against the data and showed how the type of resistance differs with treatment and chemical hydrophobicity. Data and simulations illustrate the complex interplay between AC and contaminant toxicity to benthic organisms and how differences in species tolerance affect mass fluxes from sediment to the water column.

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

NASA Astrophysics Data System (ADS)

Jungbluth, Sean P.; Amend, Jan P.; Rappé, Michael S.

2017-03-01

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids.

PubMed

Jungbluth, Sean P; Amend, Jan P; Rappé, Michael S

2017-03-28

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.

Microbenthic distribution of Proterozoic tidal flats: environmental and taphonomic considerations

NASA Technical Reports Server (NTRS)

Kah, L. C.; Knoll, A. H.

1996-01-01

Silicified carbonates of the late Mesoproterozoic to early Neoproterozoic Society Cliffs Formation, Baffin Island, contain distinctive microfabrics and microbenthic assemblages whose paleo-environmental distribution within the formation parallels the distribution of these elements through Proterozoic time. In the Society Cliffs Formation, restricted carbonates--including microdigitate stromatolites, laminated tufa, and tufted microbial mats--consist predominantly of synsedimentary cements; these facies and the cyanobacterial fossils they contain are common in Paleoproterozoic successions but rare in Neoproterozoic and younger rocks. Less restricted tidal-flat facies in the formation are composed of laminated microbialites dominated by micritic carbonate lithified early, yet demonstrably after compaction; these strata contain cyanobacteria that are characteristic in Neoproterozoic rocks. Within the formation, the facies-dependent distribution of microbial populations reflects both the style and timing of carbonate deposition because of the strong substrate specificity of benthic cyanobacteria. A reasonable conclusion is that secular changes in microbenthic assemblages through Proterozoic time reflect a decrease in the overall representation of rapidly lithified carbonate substrates in younger peritidal environments, as well as concomitant changes in the taphonomic window of silicification through which early life is observed.

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

PubMed Central

Jungbluth, Sean P.; Amend, Jan P.; Rappé, Michael S.

2017-01-01

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation. PMID:28350381

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

Bernstein, Hans C.; Brislawn, Colin J.; Dana, Karl

Benthic microbial ecosystems are widespread yet knowledge gaps still remain on the relationships between the diversity of species across kingdoms and productivity. Here, we ask two fundamental questions: 1) How does species diversity relate to the rates of primary and heterotrophic productivity? 2) How do diel variations in light-energy inputs influence productivity and microbiome diversity? To answer these questions, microbial mats from a magnesium sulfate hypersaline Lake were used to establish microcosms. Both the number and relatedness between bacterial and eukaryotic taxa in the microbiome were assayed via amplicon based sequencing of 16S and 18S rRNA genes over two dielmore » cycles. These results correlated with biomass productivity obtained from substrate-specific 13C stable isotope incorporation that enabled comparisons between primary and heterotrophic productivity. Both bacterial and eukaryotic species richness and evenness were related only to the rates of 13C labeled glucose and acetate biomass incorporation. Interestingly, measures of these heterotrophic relationships changed from positive and negative correlations depending on carbon derived from glucose and acetate, respectively. Bacterial and eukaryotic diversity of this ecosystem is also controlled, in part, energy constraints imposed by changing irradiance over a diel cycle.« less

Benthic flux measurements of Hg species in a northern Adriatic lagoon environment (Marano and Grado Lagoon, Italy)

NASA Astrophysics Data System (ADS)

Emili, Andrea; Acquavita, Alessandro; Koron, Neža; Covelli, Stefano; Faganeli, Jadran; Horvat, Milena; Žižek, Suzana; Fajon, Vesna

2012-11-01

As part of the "MIRACLE" project, the biogeochemical cycling of mercury (Hg) at the sediment-water interface was studied in the field in the Marano and Grado Lagoon (Northern Adriatic Sea). Seasonal investigations were conducted at selected experimental sites, where Manila Clams (Tapes philippinarum) were previously seeded. Measurements were performed seasonally during three campaigns, using two benthic chambers, one transparent and one dark, to evaluate the effect of light on Hg cycling. Total dissolved Hg (THg), methylmercury (MeHg), and dissolved gaseous Hg (DGM) species were considered. Diurnal benthic fluxes were found to significantly exceed the diffusive fluxes at all stations. The assessment of the annual recycling of Hg species from sediments to the water column showed that up to 99% of MeHg is recycled annually to the water column, while Hg recycling ranges from 30 to 60%. MeHg poses the higher risk for potential bioaccumulation in clams, but it is partially mitigated by Hg reduction, which seems to be an important process leading to evasion losses of Hg from these environments. Estimated benthic fluxes suggest that Hg recycling at the sediment-water interface is more active in the Grado sector. Hence, based on the estimated release of MeHg from sediments, it is suggested that the western sector seems to be more suitable for clam farming and the extension of rearing activities.

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.

Impacts of exploratory drilling for oil and gas on the benthic environment of Georges Bank

USGS Publications Warehouse

Neff, J. M.; Bothner, Michael H.; Maciolek, N. J.; Grassle, J. F.

1989-01-01

Cluster analysis revealed a strong relationship between community structure and both sediment type and water depth. Little seasonal variation was detected, but some interannual differences were revealed by cluster analysis and correspondence analysis. The replicates from a station always resembled each other more than they resembled any replicates from other stations. In addition, the combined replicates from a station always clustered with samples from that station taken on other cruises. This excellent replication and uniformity of the benthic infaunal community at a station over time made it possible to detect very subtle changes in community parameters that might be related to discharges of drilling fluid and drill cuttings. Nevertheless, no changes were detected in benthic communities of Georges Bank that could be attributed to drilling activities.

Transfer of radiocaesium from contaminated bottom sediments to marine organisms through benthic food chains in post-Fukushima and post-Chernobyl periods

NASA Astrophysics Data System (ADS)

Bezhenar, Roman; Jung, Kyung Tae; Maderich, Vladimir; Willemsen, Stefan; de With, Govert; Qiao, Fangli

2016-05-01

After the earthquake and tsunami on 11 March 2011 damaged the Fukushima Dai-ichi Nuclear Power Plant (FDNPP), an accidental release of a large amount of radioactive isotopes into both the air and the ocean occurred. Measurements provided by the Japanese agencies over the past 5 years show that elevated concentrations of 137Cs still remain in sediments, benthic organisms, and demersal fishes in the coastal zone around the FDNPP. These observations indicate that there are 137Cs transfer pathways from bottom sediments to the marine organisms. To describe the transfer quantitatively, the dynamic food chain biological uptake model of radionuclides (BURN) has been extended to include benthic marine organisms. The extended model takes into account both pelagic and benthic marine organisms grouped into several classes based on their trophic level and type of species: phytoplankton, zooplankton, and fishes (two types: piscivorous and non-piscivorous) for the pelagic food chain; deposit-feeding invertebrates, demersal fishes fed by benthic invertebrates, and bottom omnivorous predators for the benthic food chain; crustaceans, mollusks, and coastal predators feeding on both pelagic and benthic organisms. Bottom invertebrates ingest organic parts of bottom sediments with adsorbed radionuclides which then migrate up through the food chain. All organisms take radionuclides directly from water as well as food. The model was implemented into the compartment model POSEIDON-R and applied to the north-western Pacific for the period of 1945-2010, and then for the period of 2011-2020 to assess the radiological consequences of 137Cs released due to the FDNPP accident. The model simulations for activity concentrations of 137Cs in both pelagic and benthic organisms in the coastal area around the FDNPP agree well with measurements for the period of 2011-2015. The decrease constant in the fitted exponential function of simulated concentration for the deposit-feeding invertebrates (0.45 yr-1) is close to the observed decrease constant in sediments (0.44 yr-1). These results strongly indicate that the gradual decrease of activity in demersal fish (decrease constant is 0.46 yr-1) is caused by the transfer of activity from organic matter deposited in bottom sediment through the deposit-feeding invertebrates. The estimated model transfer coefficient from bulk sediment to demersal fish in the model for 2012-2020 (0.13) is larger than that to the deposit-feeding invertebrates (0.07). In addition, the transfer of 137Cs through food webs for the period of 1945-2020 has been modelled for the Baltic Sea contaminated due to global fallout and from the Chernobyl accident. The model simulation results obtained with generic parameters are also in good agreement with available measurements in the Baltic Sea. Unlike the open coastal system where the FDNPP is located, the dynamics of radionuclide transfer in the Baltic Sea reach a quasi-steady state due to the slow rate in water mass exchange in this semi-enclosed basin. Obtained results indicate a substantial contribution of the benthic food chain in the long-term transfer of 137Cs from contaminated bottom sediments to marine organisms and the potential application of a generic model in different regions of the world's oceans.

Light availability impacts structure and function of phototrophic stream biofilms across domains and trophic levels.

PubMed

Bengtsson, Mia M; Wagner, Karoline; Schwab, Clarissa; Urich, Tim; Battin, Tom J

2018-04-21

Phototrophic biofilms are ubiquitous in freshwater and marine environments where they are critical for biogeochemical cycling, food webs and in industrial applications. In streams, phototrophic biofilms dominate benthic microbial life and harbor an immense prokaryotic and eukaryotic microbial biodiversity with biotic interactions across domains and trophic levels. Here, we examine how community structure and function of these biofilms respond to varying light availability, as the crucial energy source for phototrophic biofilms. Using metatranscriptomics, we found that under light limitation dominant phototrophs, including diatoms and cyanobacteria, displayed a remarkable plasticity in their photosynthetic machinery manifested as higher abundance of messenger RNAs (mRNAs) involved in photosynthesis and chloroplast ribosomal RNA. Under higher light availability, bacterial mRNAs involved in phosphorus metabolism, mainly from Betaproteobacteria and Cyanobacteria, increased, likely compensating for nutrient depletion in thick biofilms with high biomass. Consumers, including diverse ciliates, displayed community shifts indicating preferential grazing on algae instead of bacteria under higher light. For the first time, we show that the functional integrity of stream biofilms under variable light availability is maintained by structure-function adaptations on several trophic levels. Our findings shed new light on complex biofilms, or "microbial jungles", where in analogy to forests, diverse and multi-trophic level communities lend stability to ecosystem functioning. This multi-trophic level perspective, coupling metatranscriptomics to process measurements, could advance understanding of microbial-driven ecosystems beyond biofilms, including planktonic and soil environments. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

The roles of biological interactions and pollutant contamination in shaping microbial benthic community structure.

PubMed

Louati, Hela; Said, Olfa Ben; Soltani, Amel; Got, Patrice; Mahmoudi, Ezzeddine; Cravo-Laureau, Cristiana; Duran, Robert; Aissa, Patricia; Pringault, Olivier

2013-11-01

Biological interactions between metazoans and the microbial community play a major role in structuring food webs in aquatic sediments. Pollutants can also strongly affect the structure of meiofauna and microbial communities. This study aims investigating, in a non-contaminated sediment, the impact of meiofauna on bacteria facing contamination by a mixture of three PAHs (fluoranthene, phenanthrene and pyrene). Sediment microcosms were incubated in the presence or absence of meiofauna during 30 days. Bioremediation treatments, nutrient amendment and addition of a hydrocarbon-degrading bacterium, were also tested to enhance PAH biodegradation. Results clearly show the important role of meiofauna as structuring factor for bacterial communities with significant changes observed in the molecular fingerprints. However, these structural changes were not concomitant with changes in biomass or function. PAH contamination had a severe impact on total meiofaunal abundance with a strong decrease of nematodes and the complete disappearance of polychaetes and copepods. In contrast, correspondence analysis, based on T-RFLP fingerprints, showed that contamination by PAH resulted in small shifts in microbial composition, with or without meiofauna, suggesting a relative tolerance of bacteria to the PAH cocktail. The PAH bioremediation treatments were highly efficient with more than 95% biodegradation. No significant difference was observed in presence or absence of meiofauna. Nutrient addition strongly enhanced bacterial and meiofaunal abundances as compared to control and contaminated microcosms, as well as inducing important changes in the bacterial community structure. Nutrients thus were the main structural factor in shaping bacterial community composition, while the role of meiofauna was less evident.

Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill

PubMed Central

Rodriguez-R, Luis M; Overholt, Will A; Hagan, Christopher; Huettel, Markus; Kostka, Joel E; Konstantinidis, Konstantinos T

2015-01-01

Although petroleum hydrocarbons discharged from the Deepwater Horizon (DWH) blowout were shown to have a pronounced impact on indigenous microbial communities in the Gulf of Mexico, effects on nearshore or coastal ecosystems remain understudied. This study investigated the successional patterns of functional and taxonomic diversity for over 1 year after the DWH oil was deposited on Pensacola Beach sands (FL, USA), using metagenomic and 16S rRNA gene amplicon techniques. Gamma- and Alphaproteobacteria were enriched in oiled sediments, in corroboration of previous studies. In contrast to previous studies, we observed an increase in the functional diversity of the community in response to oil contamination and a functional transition from generalist populations within 4 months after oil came ashore to specialists a year later, when oil was undetectable. At the latter time point, a typical beach community had reestablished that showed little to no evidence of oil hydrocarbon degradation potential, was enriched in archaeal taxa known to be sensitive to xenobiotics, but differed significantly from the community before the oil spill. Further, a clear succession pattern was observed, where early responders to oil contamination, likely degrading aliphatic hydrocarbons, were replaced after 3 months by populations capable of aromatic hydrocarbon decomposition. Collectively, our results advance the understanding of how natural benthic microbial communities respond to crude oil perturbation, supporting the specialization-disturbance hypothesis; that is, the expectation that disturbance favors generalists, while providing (microbial) indicator species and genes for the chemical evolution of oil hydrocarbons during degradation and weathering. PMID:25689026

Community structure and distribution of benthic cyanobacteria in Antarctic lacustrine microbial mats.

PubMed

Pessi, Igor S; Lara, Yannick; Durieu, Benoit; Maalouf, Pedro de C; Verleyen, Elie; Wilmotte, Annick

2018-05-01

The terrestrial Antarctic Realm has recently been divided into 16 Antarctic Conservation Biogeographic Regions (ACBRs) based on environmental properties and the distribution of biota. Despite their prominent role in the primary production and nutrient cycling in Antarctic lakes, cyanobacteria were only poorly represented in the biological dataset used to delineate these ACBRs. Here, we provide a first high-throughput sequencing insight into the spatial distribution of benthic cyanobacterial communities in Antarctic lakes located in four distinct, geographically distant ACBRs and covering a range of limnological conditions. Cyanobacterial community structure differed between saline and freshwater lakes. No clear bioregionalization was observed, as clusters of community similarity encompassed lakes from distinct ACBRs. Most phylotypes (77.0%) were related to cyanobacterial lineages (defined at ≥99.0% 16S rRNA gene sequence similarity) restricted to the cold biosphere, including lineages potentially endemic to Antarctica (55.4%). The latter were generally rare and restricted to a small number of lakes, while more ubiquitous phylotypes were generally abundant and present in different ACBRs. These results point to a widespread distribution of some cosmopolitan cyanobacterial phylotypes across the different Antarctic ice-free regions, but also suggest the existence of dispersal barriers both within and between Antarctica and the other continents.

Trace element distributions in the water column near the Deepwater Horizon well blowout.

PubMed

Joung, DongJoo; Shiller, Alan M

2013-03-05

To understand the impact of the Deepwater Horizon well blowout on dissolved trace element concentrations, samples were collected from areas around the oil rig explosion site during four cruises in early and late May 2010, October 2010, and October 2011. In surface waters, Ba, Fe, Cu, Ni, Mn, and Co were relatively well correlated with salinity during all cruises, suggesting mixing with river water was the main influence on metal distributions in these waters. However, in deep oil/gas plumes (1000-1400 m depth), modestly elevated concentrations of Co and Ba were observed in late May, compared with postblowout conditions. Analysis of the oil itself along with leaching experiments confirm the oil as the source of the Co, whereas increased Ba was likely due to drilling mud used in the top kill attempt. Deep plume dissolved Mn largely reflected natural benthic input, though some samples showed slight elevation probably associated with the top kill. Dissolved Fe concentrations were low and also appeared largely topographically controlled and reflective of benthic input. Estimates suggest that microbial Fe demand may have affected the Fe distribution but probably not to the extent of Fe becoming a growth-limiting factor. Experiments showed that the dispersant can have some limited impact on dissolved-particulate metal partitioning.

Size Matters: The Contribution of Mega-Infauna to the Food ...

EPA Pesticide Factsheets

Large-bodied, invertebrates are common to infaunal communities of NE Pacific estuaries (e.g., bivalves, polychaetes, burrowing shrimps), but their contribution to the ecological structure, function and ecosystem services of most estuaries has been poorly characterized because they are difficult to sample and quantify. In a study of Yaquina estuary (Oregon) food webs, particular effort was made to quantify intertidal and subtidal mega-infauna using suction-excavated 40-cm diameter corers in addition to conventional sampling of macro-infauna. Additionally, the abundance and biomass of all floral and other faunal guilds (except microbial and mammalian guilds) were directly quantified or estimated from published studies, carbon and nitrogen stable isotopes were measured for abundant species, and inverse analysis was used to generate models of carbon flow within food webs of the lower and upper reaches of Yaquina estuary. Benthic invertebrates dominated the biomass and respiration among faunal guilds in both estuarine reaches, whereas biomass and respiration of birds and fish were two orders-of-magnitude smaller. Mega-infauna, particularly intertidal burrowing shrimps and bivalves, constituted most of the benthic invertebrate biomass, respiration and secondary production in both reaches, although only a small fraction of the total infaunal abundance. Mega-infauna were dominant consumers of phytoplankton, major contributors of carbon to sediment organic matter, a

Impact of nitrogen deposition on forest and lake food webs in nitrogen-limited environments.

PubMed

Meunier, Cédric L; Gundale, Michael J; Sánchez, Irene S; Liess, Antonia

2016-01-01

Increased reactive nitrogen (Nr ) deposition has raised the amount of N available to organisms and has greatly altered the transfer of energy through food webs, with major consequences for trophic dynamics. The aim of this review was to: (i) clarify the direct and indirect effects of Nr deposition on forest and lake food webs in N-limited biomes, (ii) compare and contrast how aquatic and terrestrial systems respond to increased Nr deposition, and (iii) identify how the nutrient pathways within and between ecosystems change in response to Nr deposition. We present that Nr deposition releases primary producers from N limitation in both forest and lake ecosystems and raises plants' N content which in turn benefits herbivores with high N requirements. Such trophic effects are coupled with a general decrease in biodiversity caused by different N-use efficiencies; slow-growing species with low rates of N turnover are replaced by fast-growing species with high rates of N turnover. In contrast, Nr deposition diminishes below-ground production in forests, due to a range of mechanisms that reduce microbial biomass, and decreases lake benthic productivity by switching herbivore growth from N to phosphorus (P) limitation, and by intensifying P limitation of benthic fish. The flow of nutrients between ecosystems is expected to change with increasing Nr deposition. Due to higher litter production and more intense precipitation, more terrestrial matter will enter lakes. This will benefit bacteria and will in turn boost the microbial food web. Additionally, Nr deposition promotes emergent insects, which subsidize the terrestrial food web as prey for insectivores or by dying and decomposing on land. So far, most studies have examined Nr -deposition effects on the food web base, whereas our review highlights that changes at the base of food webs substantially impact higher trophic levels and therefore food web structure and functioning. © 2015 John Wiley & Sons Ltd.

Benthic community structure on coral reefs exposed to intensive recreational snorkeling.

PubMed

Renfro, Bobbie; Chadwick, Nanette E

2017-01-01

Chronic anthropogenic disturbances on coral reefs in the form of overfishing and pollution can shift benthic community composition away from stony corals and toward macroalgae. The use of reefs for recreational snorkeling and diving potentially can lead to similar ecological impacts if not well-managed, but impacts of snorkeling on benthic organisms are not well understood. We quantified variation in benthic community structure along a gradient of snorkeling frequency in an intensively-visited portion of the Mesoamerican Barrier Reef. We determined rates of snorkeling in 6 water sections and rates of beach visitation in 4 adjacent land sections at Akumal Bay, Mexico. For each in-water section at 1-3 m depth, we also assessed the percent cover of benthic organisms including taxa of stony corals and macroalgae. Rates of recreational snorkeling varied from low in the southwestern to very high (>1000 snorkelers d-1) in the northeastern sections of the bay. Stony coral cover decreased and macroalgal cover increased significantly with levels of snorkeling, while trends varied among taxa for other organisms such as gorgonians, fire corals, and sea urchins. We conclude that benthic organisms appear to exhibit taxon-specific variation with levels of recreational snorkeling. To prevent further degradation, we recommend limitation of snorkeler visitation rates, coupled with visitor education and in-water guides to reduce reef-damaging behaviors by snorkelers in high-use areas. These types of management activities, integrated with reef monitoring and subsequent readjustment of management, have the potential to reverse the damage potentially inflicted on coral reefs by the expansion of reef-based recreational snorkeling.

Benthic community structure on coral reefs exposed to intensive recreational snorkeling

PubMed Central

Renfro, Bobbie

2017-01-01

Chronic anthropogenic disturbances on coral reefs in the form of overfishing and pollution can shift benthic community composition away from stony corals and toward macroalgae. The use of reefs for recreational snorkeling and diving potentially can lead to similar ecological impacts if not well-managed, but impacts of snorkeling on benthic organisms are not well understood. We quantified variation in benthic community structure along a gradient of snorkeling frequency in an intensively-visited portion of the Mesoamerican Barrier Reef. We determined rates of snorkeling in 6 water sections and rates of beach visitation in 4 adjacent land sections at Akumal Bay, Mexico. For each in-water section at 1–3 m depth, we also assessed the percent cover of benthic organisms including taxa of stony corals and macroalgae. Rates of recreational snorkeling varied from low in the southwestern to very high (>1000 snorkelers d-1) in the northeastern sections of the bay. Stony coral cover decreased and macroalgal cover increased significantly with levels of snorkeling, while trends varied among taxa for other organisms such as gorgonians, fire corals, and sea urchins. We conclude that benthic organisms appear to exhibit taxon-specific variation with levels of recreational snorkeling. To prevent further degradation, we recommend limitation of snorkeler visitation rates, coupled with visitor education and in-water guides to reduce reef-damaging behaviors by snorkelers in high-use areas. These types of management activities, integrated with reef monitoring and subsequent readjustment of management, have the potential to reverse the damage potentially inflicted on coral reefs by the expansion of reef-based recreational snorkeling. PMID:28873449

Phylogenetic Analysis of a Microbialite-Forming Microbial Mat from a Hypersaline Lake of the Kiritimati Atoll, Central Pacific

PubMed Central

Schneider, Dominik; Arp, Gernot; Reimer, Andreas; Reitner, Joachim; Daniel, Rolf

2013-01-01

On the Kiritimati atoll, several lakes exhibit microbial mat-formation under different hydrochemical conditions. Some of these lakes trigger microbialite formation such as Lake 21, which is an evaporitic, hypersaline lake (salinity of approximately 170‰). Lake 21 is completely covered with a thick multilayered microbial mat. This mat is associated with the formation of decimeter-thick highly porous microbialites, which are composed of aragonite and gypsum crystals. We assessed the bacterial and archaeal community composition and its alteration along the vertical stratification by large-scale analysis of 16S rRNA gene sequences of the nine different mat layers. The surface layers are dominated by aerobic, phototrophic, and halotolerant microbes. The bacterial community of these layers harbored Cyanobacteria (Halothece cluster), which were accompanied with known phototrophic members of the Bacteroidetes and Alphaproteobacteria. In deeper anaerobic layers more diverse communities than in the upper layers were present. The deeper layers were dominated by Spirochaetes, sulfate-reducing bacteria (Deltaproteobacteria), Chloroflexi (Anaerolineae and Caldilineae), purple non-sulfur bacteria (Alphaproteobacteria), purple sulfur bacteria (Chromatiales), anaerobic Bacteroidetes (Marinilabiacae), Nitrospirae (OPB95), Planctomycetes and several candidate divisions. The archaeal community, including numerous uncultured taxonomic lineages, generally changed from Euryarchaeota (mainly Halobacteria and Thermoplasmata) to uncultured members of the Thaumarchaeota (mainly Marine Benthic Group B) with increasing depth. PMID:23762495

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations.

PubMed

Saad, Sainab; Bhatnagar, Srijak; Tegetmeyer, Halina E; Geelhoed, Jeanine S; Strous, Marc; Ruff, S Emil

2017-12-01

For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate-reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum, appeared to have coupled both acetate- and hydrogen oxidation to sulfate reduction. We describe a novel representative of the widespread uncultured candidate phylum Fermentibacteria (formerly candidate division Hyd24-12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name ' U Sabulitectum silens' and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the function of fermentative, as well as sulfate-reducing microbial communities and their adaptation to a dynamic environment. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Global deglaciation and the re-appearance of microbial matground-dominated ecosystems in the late Paleozoic of Gondwana.

PubMed

Buatois, L A; Netto, R G; Gabriela Mángano, M; Carmona, N B

2013-07-01

The extensive matgrounds in Carboniferous-Permian open-marine deposits of western Argentina constitute an anachronistic facies, because with the onset of penetrative bioturbation during the early Paleozoic microbial mats essentially disappeared from these settings. Abundant microbially induced sedimentary structures in the Argentinean deposits are coincident with the disappearance of trace and body fossils in the succession and with a landward facies shift indicative of transgressive conditions. Deposits of the Late Carboniferous-Early Permian glacial event are well developed in adjacent basins in eastern Argentina, Brazil, South Africa and Antarctica, but do not occur in the western Andean basins of Argentina. However, the deglaciation phase is indirectly recorded in the studied region by a rapid rise in sea level referred to as the Stephanian-Asselian transgression. We suggest that an unusual release of meltwater during the final deglaciation episode of the Gondwana Ice Age may have dramatically freshened peri-Gondwanan seas, impacting negatively on coastal and shallow-marine benthic faunas. Suppression of bioturbation was therefore conducive to a brief re-appearance of matground-dominated ecosystems, reminiscent of those in the precambrian. Bioturbation is essential for ecosystem performance and plays a major role in ocean and sediment geochemistry. Accordingly, the decimation of the mixed layer during deglaciation in the Gondwana basins may have altered ecosystem functioning and geochemical cycling. © 2013 John Wiley & Sons Ltd.

Temporal and Spatial Patterns of Plankton and Microbial Dynamics in the Offshore Gulf of Mexico After the Deepwater Horizon Oil Spill

NASA Astrophysics Data System (ADS)

Sutor, M.; Longnecker, K.

2016-02-01

The oligotrophic regions of the world oceans represent large and important marine ecosystems. The vast majority of animals in these zones are plankton and marine microbes and they play a key role in the export of carbon and organic matter to seafloor benthic communities and higher trophic levels. There is little published data on the ecology of plankton and microbes in the offshore waters of the Northern Gulf of Mexico. In the wake of the Deepwater Horizon oil spill, which was a primarily oceanic event, it is clear that understanding the microbial and planktonic community and how it responded to this event is critical to interpret any observed changes at higher trophic levels (i.e. fish). We conducted three cruises in the spring of 2011, 2012, and 2013 and measured the primary production, respiration, bacterial production, and community composition of plankton and marine microbes. The data show that there are important differences in these parameters between the surface waters and the deep chlorophyll maximum and proximity to the spill site in 2011. Spatial patterns in relation to the spill site are not pronounced in 2012 and 2013. These data represent an important estimate of the microbial and planktonic community ecology of this region and demonstrate the important role the deep chlorophyll maximum plays in this system.

Nitrous Oxide Production and Fluxes from Coastal Sediments under Varying Environmental Conditions

NASA Astrophysics Data System (ADS)

Ziebis, W.; Wankel, S. D.; de Beer, D.; Dentinger, J.; Buchwald, C.; Charoenpong, C.

2014-12-01

Although coastal zones represent important contributors to the increasing levels of atmospheric nitrous oxide (N2O), it is still unclear which role benthic processes play and whether marine sediments represent sinks or sources for N2O, since interactions among closely associated microbial groups lead to a high degree of variability. In addition, coastal areas are extremely dynamic regions, often exposed to increased nutrient loading and conditions of depleted oxygen. We investigated benthic N2O fluxes and how environmental conditions affect N2O production in different sediments at 2 different geographical locations (German Wadden Sea, a California coastal lagoon). At each location, a total of 32 sediment cores were taken in areas that differed in sediment type, organic content and pore-water nutrient concentrations, as well as in bioturbation activity. Parallel cores were incubated under in-situ conditions, low oxygen and increased nitrate levels for 10 days. Zones of N2O production and consumption were identified in intact cores by N2O microprofiles at the beginning and end of the experiments. In a collaborative effort to determine the dominant sources of N2O, samples were taken throughout the course of the experiments for the determination of the isotopic composition of N2O (as well as nitrate, nitrite and ammonium). Our results indicate that both, nitrate addition and low oxygen conditions in the overlying water, caused an increase of subsurface N2O production in most sediments, with a high variability between different sediment types. N2O production in the sediments was accompanied by N2O consumption, reducing the fluxes to the water column. In general, organic rich sediments showed the strongest response to environmental changes with increased production and efflux of N2O into the overlying water. Bioturbation activity added to the complexity of N2O dynamics by an increase in nitrification-denitrification processes, as well as enhanced pore-water transport. The results will be used in a metabolic modeling approach that will allow numerical simulation and prediction of sedimentary N2O dynamics.

Microbial biogeography of San Francisco Bay sediments

NASA Astrophysics Data System (ADS)

Lee, J. A.; Francis, C. A.

2014-12-01

The largest estuary on the west coast of North America, San Francisco Bay is an ecosystem of enormous biodiversity, and also enormous human impact. The benthos has experienced dredging, occupation by invasive species, and over a century of sediment input as a result of hydraulic mining. Although the Bay's great cultural and ecological importance has inspired numerous surveys of the benthic macrofauna, to date there has been almost no investigation of the microbial communities on the Bay floor. An understanding of those microbial communities would contribute significantly to our understanding of both the biogeochemical processes (which are driven by the microbiota) and the physical processes (which contribute to microbial distributions) in the Bay. Here, we present the first broad survey of bacterial and archaeal taxa in the sediments of the San Francisco Bay. We conducted 16S rRNA community sequencing of bacteria and archaea in sediment samples taken bimonthly for one year, from five sites spanning the salinity gradient between Suisun and Central Bay, in order to capture the effect of both spatial and temporal environmental variation on microbial diversity. From the same samples we also conducted deep sequencing of a nitrogen-cycling functional gene, nirS, allowing an assessment of evolutionary diversity at a much finer taxonomic scale within an important and widespread functional group of bacteria. We paired these sequencing projects with extensive geochemical metadata as well as information about macrofaunal distribution. Our data reveal a diversity of distinct biogeographical patterns among different taxa: clades ubiquitous across sites; clades that respond to measurable environmental drivers; and clades that show geographical site-specificity. These community datasets allow us to test the hypothesis that salinity is a major driver of both overall microbial community structure and community structure of the denitrifying bacteria specifically; and to assess whether patterns of diversity observed at the broadest of taxonomic scales also apply to patterns observed within a single extremely diverse gene (nirS). In sum, this project provides a first look at the forces driving the migration and selection of microbial communities in San Francisco Bay.

Neogene paleoceanographic events recorded in an active-margin setting: Humboldt basin, California

USGS Publications Warehouse

McCrory, P.A.

1990-01-01

Recognition of North Pacific paleoceanographic events in the marginal Humboldt (Eel River) basin of northern California enables correlation of stratigraphic sections and development of a chronostratigraphy. Paleoclimatically related coiling shifts in Neogloboquadrina pachyderma (Ehrenberg) and benthic foraminiferal datums form the basis of the chronostratigraphy. Benthic foraminiferal datums are defined by the occurrence of selected benthic species and abundance maxima of benthic biofacies. The compiled chronostratigraphy is used to refine reconstructions of the depositional history of Humboldt basin. Paleoceanographic events, recognized by the distribution of benthic foraminiferal biofacies, are used to infer paleoceanographic history along the northeastern Pacific margin. The similarity in coiling curves of N. pachyderma from the marine sequence at DSDP Site 173 and the coastal Centerville Beach section of Humboldt basin and at other independently dated sites along the northeastern Pacific margin demonstrates that matching records of climatic oscillations is a reliable method of correlating marine sequences. Benthic fauna from the Centerville Beach section vary in phase with climatically related coiling shifts in N. pachyderma. In particular these data show an increase in displaced neritic fauna during inferred warm intervals and resurgence of deeper bathyal fauna during inferred cool events. Similar data are observed from the inland Eel River section, demonstrating that benthic foraminiferal trends recognized at Centerville Beach can be identified elsewhere in Humboldt basin. This in-phase benthic response to climatic fluctuations probably results from changes in vertical depth range of many benthic species in response to paleoclimatically related vertical changes in water-mass position. Depositional histories reconstructed for two key sites in southern Humboldt basin indicate low rates of sediment accumulation during early basin filling with hemipelagic sediments. Initiation of turbidite sedimentation in the early Pliocene resulted in a sharp increase in rate of sediment accumulation. This increase in rate of sediment accumulation is partially a response to tectonic uplift in the northern Coast Ranges and may be an effect of realignment of motion between the Pacific and North American plates at about this time. The inland site shoaled more rapidly during turbidite sedimentation as a result of a higher rate of sediment accumulation. The rate of sediment accumulation increased again at this site in the late Pliocene during deposition of shelf and nearshore facies. The Eel River region subsided concurrent with deposition of these shallow-water deposits. ?? 1990.

Application of an eddy correlation system for the estimation of oxygen benthic fluxes in coastal permeable sediments impacted by submarine groundwater discharge

NASA Astrophysics Data System (ADS)

Donis, D.; Janssen, F.; Böttcher, M.; McGinnis, D.; Holtappels, M.; Wenzhöfer, F.

2012-04-01

Measurements of solute exchange across the sediment-water interface are crucial for marine environment monitoring. This interface has fundamental filter functions for the mass exchange between the seafloor and the water column. Being a non-invasive technique, the eddy correlation method, is probably the most accurate measurement for benthic fluxes. It does not interfere with local hydrodynamics and integrates over large areas, showing considerable advantages compared to traditional methods, i.e., microprofiles and benthic chambers. One of the most important exchange processes across the sediment-water interface is flux of oxygen, which is a predominant control factor for the biogeochemical activity in the sediment, carbon processing and the composition of benthic communities. The eddy correlation method performs simultaneous recordings of vertical velocities and oxygen concentrations at a specific distance to the seafloor and is becoming a standard method for resolving dissolved oxygen fluxes in aquatic systems. However, data treatment and interpretation, especially in shallow environments, is still challenging. One major concern in eddy correlation studies of coastal environments is how to consider surface wave motions that can dominate the turbulence range and that may bias flux calculations. A critical part of the data treatment thus is the removal of wave biases from the vertical velocity component, by separating the wave frequency oscillations (due to a tilted or miss-aligned sensor) from those containing meaningful flux contributions. Here we present in situ benthic oxygen exchange rates as determined by an eddy correlation system (ECS) and simultaneously deployed stirred benthic chambers. The study was carried out in a coastal ecosystem of the southern Baltic Sea that was impacted by low salinity groundwater discharge (Hel peninsula, Poland). Oxygen fluxes determined with ECS compared well with results from benthic chambers. Flux data and seepage rates are discussed in the context of groundwater and their importance for benthic biogeochemical processes in shallow sandy sediments. This work was supported by 7th framework EU ITN-project SENSEnet and BONUS+ project AMBER.

A newly developed dispersal metric indicates the succession of benthic invertebrates in restored rivers.

PubMed

Li, Fengqing; Sundermann, Andrea; Stoll, Stefan; Haase, Peter

2016-11-01

Dispersal capacity plays a fundamental role in the riverine benthic invertebrate colonization of new habitats that emerges following flash floods or restoration. However, an appropriate measure of dispersal capacity for benthic invertebrates is still lacking. The dispersal of benthic invertebrates occurs mainly during the aquatic (larval) and aerial (adult) life stages, and the dispersal of each stage can be further subdivided into active and passive modes. Based on these four possible dispersal modes, we first developed a metric (which is very similar to the well-known and widely used saprobic index) to estimate the dispersal capacity for 802 benthic invertebrate taxa by incorporating a weight for each mode. Second, we tested this metric using benthic invertebrate community data from a) 23 large restored river sites with substantial improvements of river bottom habitats dating back 1 to 10years, b) 23 unrestored sites very close to the restored sites, and c) 298 adjacent surrounding sites (mean±standard deviation: 13.0±9.5 per site) within a distance of up to 5km for each restored site in the low mountain and lowland areas of Germany. We hypothesize that our metric will reflect the temporal succession process of benthic invertebrate communities colonizing the restored sites, whereas no temporal changes are expected in the unrestored and surrounding sites. By applying our metric to these three river treatment categories, we found that the average dispersal capacity of benthic invertebrate communities in the restored sites significantly decreased in the early years following restoration, whereas there were no changes in either the unrestored or the surrounding sites. After all taxa had been divided into quartiles representing weak to strong dispersers, this pattern became even more obvious; strong dispersers colonized the restored sites during the first year after restoration and then significantly decreased over time, whereas weak dispersers continued to increase. The successful application of our metric to river restoration might be promising in further applications of this metric, for example, in analyzing metacommunity structure or community's recovery from extreme events such as floods, droughts or catastrophic pollution episodes. Copyright © 2016 Elsevier B.V. All rights reserved.

[Monthly changes in the benthic macro-invertebrate community structure in the habitats of Phragmites australis marsh in the Dongtan wetland of the Yangtze River estuary, China].

PubMed

Zhang, Heng; Ye, Jin Yu; Liang, Xiao Li; Zhu, Xiao Jing; Jin, Shao Fei; Chen, Yuan Ge; Zhang, Jia Rui; Dai, Yang

2017-04-18

Based on the data of the benthic macro-invertebrates community in the Phragmites australis marsh in the Dongtan Wetland of the Yangtze River estuary collected from May 2015 to April 2016, we evaluated the monthly variations in the species composition, biodiversity and community structure of the benthic macro-invertebrates. The results showed that the average height and degree of coverage for P. australis increased monthly from March to August, and then deceased from September. The density and aboveground biomass (dry mass, g) of P. australis peaked in July. A total of twenty species (including 2 species only identified to genus level and 2 species identified to family level) were found in the survey periods, including 11 Gastropoda, 5 Malacostraca, 2 Insecta and 2 Polychaeta. Three snail species (Assiminea latericea, Assiminea violacea and Cerithideopsis largillierti) dominated the benthic communities in terms of numerical abundance. The number of epifauna species was the most (11 species), followed by 5 burrowing species and 4 infauna species. There were significant monthly variations in the density and biomass of the macro-invertebrates. The density and biomass of benthic community reached the maximum in August. The Margalef's species richness index (D) and Shannon index (H) showed significant differences monthly, but Pielou's index (J) except in November. Three macro-zoobenthic assemblages were identified with the 42% similarity level. The non-Metric Multidimensional scaling plot indicates that the benthic community in May, October and November was distinct compared to that in the other months. The present study suggested the density of the benthic macro-invertebrates community in the P. australis marshes was somewhat correlated with water temperature, underground biomass and salinity. But those correlation were not significant (P>0.05). Because of the continuous impact of anthropogenic activities, the biodiversity of the benthic macro-invertebrate community has been decreasing for several years. More attention should be paid to the habitat value of the P. australis marshes in the future.

Benthic oxygen consumption on continental shelves off eastern Canada

NASA Astrophysics Data System (ADS)

Grant, Jonathan; Emerson, Craig W.; Hargrave, Barry T.; Shortle, Jeannette L.

1991-08-01

The consumption of phytoplankton production by the benthos is an important component of organic carbon budgets for continental shelves. Sediment texture is a major factor regulating benthic processes because fine sediment areas are sites of enhanced deposition from the water column, resulting in increased organic content, bacterial biomass and community metabolism. Although continental shelves at mid- to high latitudes consist primarily of coarse relict sediments ( PIPER, Continental Shelf Research, 11, 1013-1035), shelf regions of boreal and subarctic eastern Canada contain large areas of silt and clay sediments ( FADER, Continental Shelf Research, 11, 1123-1153). We collated estimates of benthic oxygen consumption in coarse (<20% silt-clay, <0.5% organic matter) and fine sediments (20% silt-clay, 0.5% organic matter) for northwest Atlantic continental shelves including new data for Georges Bank, the Scotian Shelf, the Grand Banks of Newfoundland and Labrador Shelf. Estimates were applied to the areal distribution of sediment type on these shelves to obtain a general relationship between sediment texture and benthic carbon consumption. Mean benthic oxygen demand was 2.7 times greater in fine sediment than in coarse sediment, when normalized to mean annual temperature. In terms of carbon equivalents, shelf regions with minimal fine sediment (Georges Bank, the Grand Banks of Newfoundland-northeast Newfoundland) consumed only 5-8% of annual primary production. Benthos of the Gulf of Maine (100% fine sediment) and the Scotian Shelf (35% fine sediment) utilized 16-19% of primary production. Although 32% of the Labrador Shelf area contained fine sediments, benthic consumption of pelagic production (8%) was apparently limited by low mean annual temperature (2°C). These results indicate that incorporation of sediment-specific oxygen uptake into shelf carbon budgets may increase estimates of benthic consumption by 50%. Furthermore, respiration and production by large macrofauna allow an even greater proportion of primary production to enter benthic pathways. Fine sediment areas (shelf basins or "depocenters") are postulated to be sites of enhanced biological activity which must be considered in the modelling of shelf carbon budgets and the role of the benthos in demersal fisheries.

Impact of the Phaeocystis globosa spring bloom on the intertidal benthic compartment in the eastern English Channel: a synthesis.

PubMed

Spilmont, Nicolas; Denis, Lionel; Artigas, Luis Felipe; Caloin, Frédéric; Courcot, Lucie; Créach, Anne; Desroy, Nicolas; Gevaert, François; Hacquebart, Pascal; Hubas, Cédric; Janquin, Marie-Andrée; Lemoine, Yves; Luczak, Christophe; Migné, Aline; Rauch, Mathieu; Davoult, Dominique

2009-01-01

From 1999 to 2005, studies carried out in the frame of regional and national French programs aimed to determine whether the Phaeocystis globosa bloom affected the intertidal benthic communities of the French coast of the eastern English Channel in terms of composition and/or functioning. Study sites were chosen to cover most of the typical shore types encountered on this coast (a rocky shore, an exposed sandy beach and a small estuary). Both the presence of active Phaeocystis cells and their degradation product (foam) did have a significant impact on the studied shores. The primary production and growth rates of the kelp Saccharina latissima decreased during the bloom because of a shortage of light and nutrient for the macroalgae. On sandy sediments, the benthic metabolism (community respiration and community primary production), as well as the nitrification rate, were enhanced during foam deposits, in relation with the presence of bacteria and active pelagic cells within the decaying colonies. In estuarine sediments, the most impressive impact was the formation of a crust at the sediment surface due to drying foam. This led to anoxic conditions in the surface sediment and resulted in a high mortality among the benthic community. Some organisms also tended to migrate upward and were then directly accessible to the higher trophic level represented by birds. Phaeocystis then created a shortcut in the estuarine trophic network. Most of these modifications lasted shortly and all the systems considered came back to their regular properties and activities a few weeks after the end of the bloom, except for the most impacted estuarine area.

Modeling Benthic Sediment Processes to Predict Water ...

EPA Pesticide Factsheets

The benthic sediment acts as a huge reservoir of particulate and dissolved material (within interstitial water) which can contribute to loading of contaminants and nutrients to the water column. A benthic sediment model is presented in this report to predict spatial and temporal benthic fluxes of nutrients and chemicals in Narragansett Bay. A benthic sediment model is presented in this report to identify benthic flux into the water column in Narragansett Bay. Benthic flux is essential to properly model water quality and ecology in estuarine and coastal systems.

Understanding the effects of predictability, duration, and spatial pattern of drying on benthic invertebrate assemblages in two contrasting intermittent streams

PubMed Central

von Schiller, Daniel; Barberá, Gonzalo G.; Díaz, Angela M.; Arce, Maria Isabel; del Campo, Rubén; Tockner, Klement

2018-01-01

In the present study, we examined the effects of different drying conditions on the composition, structure and function of benthic invertebrate assemblages. We approached this objective by comparing invertebrate assemblages in perennial and intermittent sites along two intermittent Mediterranean streams with contrasting predictability, duration, and spatial patterns of drying: Fuirosos (high predictability, short duration, downstream drying pattern) and Rogativa (low predictability, long duration, patchy drying pattern). Specifically, we quantified the contribution of individual taxa to those differences, the degree of nestedness, and shifts in the composition, structure and function of benthic invertebrate assemblages along flow intermittence gradients. We observed greater effects of drying on the benthic invertebrate composition in Fuirosos than in Rogativa, resulting in a higher dissimilarity of assemblages between perennial and intermittent sites, as well as a lower degree of nestedness. Furthermore, a higher number of biotic metrics related to richness, abundance and biological traits were significantly different between perennial and intermittent sites in Fuirosos, despite a shorter dry period compared to Rogativa. At the same time, slightly different responses were detected during post-drying (autumn) than pre-drying (spring) conditions in this stream. In Rogativa, shifts in benthic invertebrate assemblages along increasing gradients of flow intermittence were found for three metrics (Ephemeroptera, Plecoptera and Trichoptera (EPT) and Odonata, Coleoptera and Heteroptera (OCH) abundances and aerial active dispersal. Furthermore, we demonstrated that combined gradients of dry period duration and distance to nearest perennial reach can generate complex, and different, responses of benthic invertebrate assemblages, depending on the flow intermittence metric. Our study advances the notion that special attention should be paid to the predictability, duration and spatial patterns of drying in intermittent streams in order to disentangle the effects of drying on benthic invertebrate assemblages, in particular in areas subject to high spatial heterogeneity and temporal variability in drying conditions. PMID:29590140

Macrobenthic patterns at the shallow marine waters in the caldera of the active volcano of Deception Island, Antarctica

NASA Astrophysics Data System (ADS)

Angulo-Preckler, Carlos; Figuerola, Blanca; Núñez-Pons, Laura; Moles, Juan; Martín-Martín, Rafael; Rull-Lluch, Jordi; Gómez-Garreta, Amelia; Avila, Conxita

2018-04-01

Deception Island is an active volcano located at the southern end of the South Shetland Archipelago, in the Antarctic Ocean. After the last eruption in 1970, benthic recolonization took place within the bay, with echinoderms being the dominant epifauna (e.g., the ophiuroid Ophionotus victoriae, the echinoid Sterechinus neumayeri and the sea star Odontaster validus), together with dense infaunal communities (mostly composed by oligochaetes, polychaetes, and bivalves). Here, we aim to describe the actual status of the marine benthic ecosystems inhabiting the shallow subtidal areas of this volcanic island. Benthic species were qualitatively scored as presence versus absence, considering the different sampling effort between localities done over the years. A total of 139 species of macroorganisms, belonging to 16 phyla were found, including fauna and flora, increasing the species richness values previously reported in all sites surveyed within the volcano caldera. Moreover, a dramatic increase in biodiversity was found towards the entrance of the bay. We suggest, however, that recolonization from external waters may not be the only reason for this pattern. In fact, sediment flux rates and substrate instability are common disturbances within the bay, probably being among the major factors determining benthic community assemblages. These processes probably favour deposit feeding communities at the innermost locations of the bay. This study provides a remarkably increased and updated species inventory from previous reports, altogether with a description of the main communities inhabiting the bay and the abiotic factors regulating this, mainly the bottom type.

Effects of natural and human-induced hypoxia on coastal benthos

NASA Astrophysics Data System (ADS)

Levin, L. A.; Ekau, W.; Gooday, A. J.; Jorissen, F.; Middelburg, J. J.; Naqvi, S. W. A.; Neira, C.; Rabalais, N. N.; Zhang, J.

2009-10-01

Coastal hypoxia (defined here as <1.42 ml L-1; 62.5 μM; 2 mg L-1, approx. 30% oxygen saturation) develops seasonally in many estuaries, fjords, and along open coasts as a result of natural upwelling or from anthropogenic eutrophication induced by riverine nutrient inputs. Permanent hypoxia occurs naturally in some isolated seas and marine basins as well as in open slope oxygen minimum zones. Responses of benthos to hypoxia depend on the duration, predictability, and intensity of oxygen depletion and on whether H2S is formed. Under suboxic conditions, large mats of filamentous sulfide oxidizing bacteria cover the seabed and consume sulfide. They are hypothesized to provide a detoxified microhabitat for eukaryotic benthic communities. Calcareous foraminiferans and nematodes are particularly tolerant of low oxygen concentrations and may attain high densities and dominance, often in association with microbial mats. When oxygen is sufficient to support metazoans, small, soft-bodied invertebrates (typically annelids), often with short generation times and elaborate branchial structures, predominate. Large taxa are more sensitive than small taxa to hypoxia. Crustaceans and echinoderms are typically more sensitive to hypoxia, with lower oxygen thresholds, than annelids, sipunculans, molluscs and cnidarians. Mobile fish and shellfish will migrate away from low-oxygen areas. Within a species, early life stages may be more subject to oxygen stress than older life stages. Hypoxia alters both the structure and function of benthic communities, but effects may differ with regional hypoxia history. Human-caused hypoxia is generally linked to eutrophication, and occurs adjacent to watersheds with large populations or agricultural activities. Many occurrences are seasonal, within estuaries, fjords or enclosed seas of the North Atlantic and the NW Pacific Oceans. Benthic faunal responses, elicited at oxygen levels below 2 ml L-1, typically involve avoidance or mortality of large species and elevated abundances of enrichment opportunists, sometimes prior to population crashes. Areas of low oxygen persist seasonally or continuously beneath upwelling regions, associated with the upper parts of oxygen minimum zones (SE Pacific, W Africa, N Indian Ocean). These have a distribution largely distinct from eutrophic areas and support a resident fauna that is adapted to survive and reproduce at oxygen concentrations <0.5 ml L-1. Under both natural and eutrophication-caused hypoxia there is loss of diversity, through attrition of intolerant species and elevated dominance, as well as reductions in body size. These shifts in species composition and diversity yield altered trophic structure, energy flow pathways, and corresponding ecosystem services such as production, organic matter cycling and organic C burial. Increasingly the influences of nature and humans interact to generate or exacerbate hypoxia. A warmer ocean is more stratified, holds less oxygen, and may experience greater advection of oxygen-poor source waters, making new regions subject to hypoxia. Future understanding of benthic responses to hypoxia must be established in the context of global climate change and other human influences such as overfishing, pollution, disease, habitat loss, and species invasions.

Morphological deformities of benthic foraminifera in response to nearshore pollution of the Red Sea, Egypt.

PubMed

El-Kahawy, R; El-Shafeiy, M; Helal, S A; Aboul-Ela, N; El-Wahab, M Abd

2018-04-28

The Red Sea encompasses a wide range of tropical marine habitats that are stressed due to anthropogenic activities. The main anthropogenic activities are hydrocarbon exploration and important trading harbors. This work aims to assess the influence of the Red Sea coastal heavy metal contamination on the marine meiofauna along three sites (Ras Gharib, Safaga, and Quseir). Eight heavy metal (Cu, Cd, Zn, Pb, Cr, Co, Ni, and Mn) contents are considered in four benthic foraminiferal species (Elphidium striatopunctatum, Amphistegina lobifera, Amphisorus hemprichii, and Ammonia beccarii). Quseir Harbor showed the highest level of pollution followed by Safaga and Ras Gharib sites. The analyzed benthic foraminiferal tests displayed noteworthy high concentrations of Cd, Zn, and Pb in Quseir Harbor which could be attributed to the anthropogenic activities in the nearshore areas. Some foraminiferal tests exhibited abnormalities in their apertures, coiling, and shape of chambers. A comparison between normal and deformed foraminiferal tests revealed that the deformed ones are highly contaminated with elevated heavy metal contents such as Fe, Mn, Ni, and Cd. Statistics in addition to geo-accumulation and pollution load indices reveal a whistling alarm for the Quseir harbor. The present data are necessary to improve conservation and management of the Red Sea ecosystem in the near future.

Evaluating host-associated sources of marine methane supersaturation

NASA Astrophysics Data System (ADS)

Blanton, J. M.; Pieper, L. M.; Allen, E. E.

2013-12-01

Methane can be found in surface ocean waters at levels from 5% to 75% greater than expected from exchange with the atmosphere. Because oceanic emissions account for up to 4% of the planet's annual methane inventory, understanding marine sources and sinks is relevant to global greenhouse gas budgets. These methane levels are presumed to result from the activity of microorganisms in the water column, yet this presents a paradox: how can biotic methanogensis, primarily understood as an anaerobic process, take place in oxic waters? One working theory is that methanogens find safe harbor in the gastrointestinal tracts of marine animals. We investigate the possibility that microbial communities within fish, and the fecal material they produce, contribute to in-situ methane production in the open ocean. Using genetic markers, we test the GI tracts of benthic and pelagic marine teleosts for the presence of methanogenic organisms and for components of the methanogenesis pathway. Our results indicate that methanogens may be present in fish, but in low numbers. This work sets the scene for measurement of methane production rates from these gut-associated communities in order to elucidate their contribution to oceanic methane supersaturation.

[Effects of different straw recycling and tillage methods on soil respiration and microbial activity].

PubMed

Li, Xiao-sha; Wu, Ning; Liu, Ling; Feng, Yu-peng; Xu, Xu; Han, Hui-fang; Ning, Tang-yuan; Li, Zeng-jia

2015-06-01

To explore the effects of different tillage methods and straw recycling on soil respiration and microbial activity in summer maize field during the winter wheat and summer maize double cropping system, substrate induced respiration method and CO2 release method were used to determine soil microbial biomass carbon, microbial activity, soil respiration, and microbial respiratory quotient. The experiment included 3 tillage methods during the winter wheat growing season, i.e., no-tillage, subsoiling and conventional tillage. Each tillage method was companied with 2 straw management patterns, i.e., straw recycling and no straw. The results indicated that the conservation tillage methods and straw recycling mainly affected 0-10 cm soil layer. Straw recycling could significantly improve the microbial biomass carbon and microbial activity, while decrease microbial respiratory quotient. Straw recycling could improve the soil respiration at both seedling stage and anthesis, however, it could reduce the soil respiration at filling stage, wax ripeness, and harvest stage. Under the same straw application, compared with conventional tillage, the soil respiration and microbial respiratory quotient in both subsoiling and no-tillage were reduced, while the microbial biomass carbon and microbial activity were increased. During the summer maize growing season, soil microbial biomass carbon and microbial activity were increased in straw returning with conservation tillage, while the respiratory quotient was reduced. In 0-10 cm soil layer, compared with conventional tillage, straw recycling with subsoiling and no-tillage significantly increased soil microbial biomass carbon by 95.8% and 74.3%, and increased soil microbial activity by 97.1% and 74.2%, respectively.

Benthic Primary Production Budget of a Caribbean Reef Lagoon (Puerto Morelos, Mexico)

PubMed Central

Naumann, Malik S.; Jantzen, Carin; Haas, Andreas F.; Iglesias-Prieto, Roberto; Wild, Christian

2013-01-01

High photosynthetic benthic primary production (P) represents a key ecosystem service provided by tropical coral reef systems. However, benthic P budgets of specific ecosystem compartments such as macrophyte-dominated reef lagoons are still scarce. To address this, we quantified individual and lagoon-wide net (Pn) and gross (Pg) primary production by all dominant functional groups of benthic primary producers in a typical macrophyte-dominated Caribbean reef lagoon near Puerto Morelos (Mexico) via measurement of O2 fluxes in incubation experiments. The photosynthetically active 3D lagoon surface area was quantified using conversion factors to allow extrapolation to lagoon-wide P budgets. Findings revealed that lagoon 2D benthic cover was primarily composed of sand-associated microphytobenthos (40%), seagrasses (29%) and macroalgae (27%), while seagrasses dominated the lagoon 3D surface area (84%). Individual Pg was highest for macroalgae and scleractinian corals (87 and 86 mmol O2 m−2 specimen area d−1, respectively), however seagrasses contributed highest (59%) to the lagoon-wide Pg. Macroalgae exhibited highest individual Pn rates, but seagrasses generated the largest fraction (51%) of lagoon-wide Pn. Individual R was highest for scleractinian corals and macroalgae, whereas seagrasses again provided the major lagoon-wide share (68%). These findings characterise the investigated lagoon as a net autotrophic coral reef ecosystem compartment revealing similar P compared to other macrophyte-dominated coastal environments such as seagrass meadows and macroalgae beds. Further, high lagoon-wide P (Pg: 488 and Pn: 181 mmol O2 m−2 lagoon area d−1) and overall Pg:R (1.6) indicate substantial benthic excess production within the Puerto Morelos reef lagoon and suggest the export of newly synthesised organic matter to surrounding ecosystems. PMID:24367570

Benthic response to the sedimentation of particulate organic matter at the BIOTRANS station, 47°N, 20°W

NASA Astrophysics Data System (ADS)

Pfannkuche, O.

The benthic response to the sedimentation of particulate organic matter (POM) was investigated during 1985-1990 at 47°N, 20°W (BIOTRANS station). The first noticeable annual sedimentation of phytodetritus, as indicated by chlorophyll a concentrations in the sediment, occurred as early as late April-early May. Maximum amounts were found in June-July. Two different sedimentation pulses to the sea bed are described that demonstrate interannual variation: the occurrence of salp faecal pellets early in the year 1988 and the massive fall out of a plankton bloom in summer 1986, which deposited approximately 15 mmol C m -2. The benthic reaction to POM pulses was quite diverse. The mega-, macro- and meiobenthos showed no change in biomass, whereas bacterial biomass doubled between March and July. This corresponds to a seasonal maximum of total adenylate biomass. The relative abundance of Foraminifera among the meiobenthos increased during the summer. Benthic activity (ATP, ratio ATP/ETSA), as well as in situ sediment community oxygen consumption rates (SCOC), showed distinct seasonal maxima in July-August of 0.75 mmol C m -2 day -1. Based on SCOC and the carbon demand for growth, a benthic carbon consumption of 0.94 mmol C m -2 day -1 was estimated. This represents about 1.1% of spring bloom primary production and 9.6% of the export flux beneath the 150 m layer, measured during the North Atlantic Bloom Experiment. Bacteria and protozoans colonizing the epibenthic phytodetrital layer were responsible for 60-80% of the seasonal increase in SCOC. The strong reaction of the smaller benthic size groups (bacteria, protozoans) to POM pulses stresses their particular importance for sediment-water interface flux rates.

Assessing environmental impact from gas and oil exploration in the SW Barents Sea using benthic foraminiferal assemblages

NASA Astrophysics Data System (ADS)

Dijkstra, N.; Junttila, J.; Husum, K.; Carroll, J.; Hald, M.

2012-04-01

During the last decades petroleum industry and shipping activities have increased in the SW Barents Sea. Oil exploration wells were drilled in the 1980s with production starting in 2007. These activities are projected to expand in the coming years. As part of the Northern Environmental Waste Management (EWMA) project, a competence cluster for petroleum industry related waste handling, we investigate the impacts of enhanced anthropogenic activities on benthic foraminiferal assemblages in the SW Barents Sea. Sediment cores (0-20 cm) from sites in proximity to two oil- and gas fields are under investigation. These sediment cores, dated with the 210Pb method, represent the last 90 to 150 years. Both dead and living benthic foraminifera (100 µm-1 mm) were counted to elucidate differences in foraminiferal assemblages between pre-impact and recent conditions. In addition, the heavy metal concentrations, persistent organic pollutant (POP) concentrations, grain size and total organic content (TOC) of the sediment cores have been analyzed. Pollution levels of the surface sediments (0-1 cm) are of background to good level (level I-II) according to the definitions of the Water Framework Directorate (WFD). Patterns in living benthic foraminiferal assemblages identified in the sea floor surface sediments, are the result of natural environmental changes such as depth, water mass and sediment composition. Further downcore (1-20 cm) pollution levels are in general of background environmental status (WFD level I). However, at some depth intervals, especially in sediment cores from the near proximity of the oil- and gas- fields, pollution levels are slightly enhanced (WFD level II). Further work will include statistical comparison of dead and living foraminiferal assemblages with sediment pollution levels, sediment properties, and oceanographic conditions. This research contributes to the development of foraminifera as a useful bio-monitoring technique for the Arctic region as industrial activities increase in the coming years.

Benthic Oxygen Uptake in the Arctic Ocean Margins - A Case Study at the Deep-Sea Observatory HAUSGARTEN (Fram Strait)

PubMed Central

Cathalot, Cecile; Rabouille, Christophe; Sauter, Eberhard; Schewe, Ingo; Soltwedel, Thomas

2015-01-01

The past decades have seen remarkable changes in the Arctic, a hotspot for climate change. Nevertheless, impacts of such changes on the biogeochemical cycles and Arctic marine ecosystems are still largely unknown. During cruises to the deep-sea observatory HAUSGARTEN in July 2007 and 2008, we investigated the biogeochemical recycling of organic matter in Arctic margin sediments by performing shipboard measurements of oxygen profiles, bacterial activities and biogenic sediment compounds (pigment, protein, organic carbon, and phospholipid contents). Additional in situ oxygen profiles were performed at two sites. This study aims at characterizing benthic mineralization activity along local bathymetric and latitudinal transects. The spatial coverage of this study is unique since it focuses on the transition from shelf to Deep Ocean, and from close to the ice edge to more open waters. Biogeochemical recycling across the continental margin showed a classical bathymetric pattern with overall low fluxes except for the deepest station located in the Molloy Hole (5500 m), a seafloor depression acting as an organic matter depot center. A gradient in benthic mineralization rates arises along the latitudinal transect with clearly higher values at the southern stations (average diffusive oxygen uptake of 0.49 ± 0.18 mmol O2 m-2 d-1) compared to the northern sites (0.22 ± 0.09 mmol O2 m-2 d-1). The benthic mineralization activity at the HAUSGARTEN observatory thus increases southward and appears to reflect the amount of organic matter reaching the seafloor rather than its lability. Although organic matter content and potential bacterial activity clearly follow this gradient, sediment pigments and phospholipids exhibit no increase with latitude whereas satellite images of surface ocean chlorophyll a indicate local seasonal patterns of primary production. Our results suggest that predicted increases in primary production in the Arctic Ocean could induce a larger export of more refractory organic matter due to the longer production season and the extension of the ice-free zone. PMID:26465885

Synthesis of benthic flux components in the Patos Lagoon coastal zone, Rio Grande do Sul, Brazil

NASA Astrophysics Data System (ADS)

King, J. N.

2012-12-01

The primary objective of this work is to synthesize components of benthic flux in the Patos Lagoon coastal zone, Rio Grande do Sul, Brazil. Specifically, the component of benthic discharge flux forced by the terrestrial hydraulic gradient is 0.8 m3 d-1; components of benthic discharge and recharge flux associated with the groundwater tidal prism are both 2.1 m3 d-1; components of benthic discharge and recharge flux forced by surface-gravity wave setup are both 6.3 m3 d-1; the component of benthic discharge flux that transports radium-228 is 350 m3 d-1; and components of benthic discharge and recharge flux forced by surface-gravity waves propagating over a porous medium are both 1400 m3 d-1. (All models are normalized per meter shoreline.) Benthic flux is a function of components forced by individual mechanisms and nonlinear interactions that exist between components. Constructive and destructive interference may enhance or diminish the contribution of benthic flux components. It may not be possible to model benthic flux by summing component magnitudes. Geochemical tracer techniques may not accurately model benthic discharge flux or submarine groundwater discharge (SGD). A conceptual model provides a framework on which to quantitatively characterize benthic discharge flux and SGD with a multifaceted approach.

Synthesis of benthic flux components in the Patos Lagooncoastal zone, Rio Grande do Sul, Brazil

USGS Publications Warehouse

King, Jeffrey N.

2012-01-01

The primary objective of this work is to synthesize components of benthic flux in the Patos Lagoon coastal zone, Rio Grande do Sul, Brazil. Specifically, the component of benthic discharge flux forced by the terrestrial hydraulic gradient is 0.8 m3 d-1; components of benthic discharge and recharge flux associated with the groundwater tidal prism are both 2.1 m3 d-1; components of benthic discharge and recharge flux forced by surface-gravity wave setup are both 6.3 m3 d-1; the component of benthic discharge flux that transports radium-228 is 350 m3 d-1; and components of benthic discharge and recharge flux forced by surface-gravity waves propagating over a porous medium are both 1400 m3 d-1. (All models are normalized per meter shoreline.) Benthic flux is a function of components forced by individual mechanisms and nonlinear interactions that exist between components. Constructive and destructive interference may enhance or diminish the contribution of benthic flux components. It may not be possible to model benthic flux by summing component magnitudes. Geochemical tracer techniques may not accurately model benthic discharge flux or submarine groundwater discharge (SGD). A conceptual model provides a framework on which to quantitatively characterize benthic discharge flux and SGD with a multifaceted approach.

Metals-contaminated benthic invertebrates in the Clark Fork River, Montana: Effects on age-0 brown trout and rainbow trout

USGS Publications Warehouse

Woodward, Daniel F.; Farag, Aïda M.; Bergman, Harold L.; Delonay, Aaron J.; Little, Edward E.; Smiths, Charlie E.; Barrows, Frederic T.

1995-01-01

Benthic organisms in the upper Clark Fork River have recently been implicated as a dietary source of metals that may be a chronic problem for young-of-the-year rainbow trout (Oncorhynchus mykiss). In this present study, early life stage brown trout (Salmo trutta) and rainbow trout were exposed for 88 d to simulated Clark Fork River water and a diet of benthic invertebrates collected from the river. These exposures resulted in reduced growth and elevated levels of metals in the whole body of both species. Concentrations of As, Cd, Cu, and Pb increased in whole brown trout; in rainbow trout, As and Cd increased in whole fish, and As also increased in liver. Brown trout on the metals-contaminated diets exhibited constipation, gut impaction, increased cell membrane damage (lipid peroxidation), decreased digestive enzyme production (zymogen), and a sloughing of intestinal mucosal epithelial cells. Rainbow trout fed the contaminated diets exhibited constipation and reduced feeding activity. We believe that the reduced standing crop of trout in the Clark Fork River results partly from chronic effects of metals contamination in benthic invertebrates that are important as food for young-of-the-year fish.

Microbial Extremophiles in Aspect of Limits of Life

NASA Technical Reports Server (NTRS)

Pikuta, Elena V.; Hoover, Richard B.; Tang, Jane

2007-01-01

During Earth's evolution accompanied by geophysical and climatic changes a number of ecosystems have been formed. These ecosystems differ by the broad variety of physicochemical and biological factors composing our environment. Traditionally, pH and salinity are considered as geochemical extremes, as opposed to the temperature, pressure and radiation that are referred to as physical extremes (Van den Burg, 2003). Life inhabits all possible places on Earth interacting with the environment and within itself (cross species relations). In nature it is very rare when an ecotope is inhabited by a single species. As a rule, most ecosystems contain the functionally related and evolutionarily adjusted communities (consortia and populations). In contrast to the multicellular structure of eukaryotes (tissues, organs, systems of organs, whole organism), the highest organized form of prokaryotic life in nature is the benthic colonization in biofilms and microbial mats. In these complex structures all microbial cells of different species are distributed in space and time according to their functions and to physicochemical gradients that allow more effective system support, self-protection, and energy distribution. In vitro, of course, the most primitive organized structure for bacterial and archaeal cultures is the colony, the size, shape, color, consistency, and other characteristics of which could carry varies specifics on species or subspecies levels. In table 1 all known types of microbial communities are shown (Pikuta et a]., 2005). In deep underground (lithospheric) and deep-sea ecosystems an additional factor - pressure, and irradiation - could also be included in the list of microbial communities. Currently the beststudied ecosystems are: human body (due to the medical importance), and fresh water and marine ecosystems (due to the reason of an environmental safety). For a long time, extremophiles were terra incognita, since the environments with aggressive parameters (compared to the human body temperature, pH, mineralization, and pressure) were considered a priori as a dead zone.

Significance of microcystin production by benthic communities in water treatment systems of arid zones.

PubMed

Hurtado, I; Aboal, M; Zafra, E; Campillo, D

2008-02-01

The study of the dynamics of phytobenthic and phytoplankton communities was undertaken, during a year, in the regulation reservoir associated with a water treatment plant (WTP), which provides the city of Murcia (Spain) with drinking water. Water samples were collected in different stages of the treatment. In the reservoir, the presence of dissolved and intracellular microcystins is constant, both in benthos and in plankton. The collected samples show a positive correlation between the dissolved microcystins and the benthic ones in the reservoir itself, as well as in an upstream reservoir (Ojós Reservoir). The treatment process (ozone+clarification+ozone+activated carbon) is very effective in the removal of toxins, and the drinking water produced is totally free of microcystins. The incorporation of the benthic communities in the routine check for the presence of microcystins is recommended, since it is not compulsory according to the current legislation.

[Characteristics of microbial community and operation efficiency in biofilter process for drinking water purification].

PubMed

Xiang, Hong; Lü, Xi-Wu; Yang, Fei; Yin, Li-Hong; Zhu, Guang-Can

2011-04-01

In order to explore characteristics of microbial community and operation efficiency in biofilter (biologically-enhanced active filter and biological activated carbon filter) process for drinking water purification, Biolog and polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) techniques were applied to analyze the metabolic function and structure of microbial community developing in biofilters. Water quality parameters, such as NH; -N, NO; -N, permanganate index, UV254 and BDOC etc, were determined in inflow and outflow of biofilters for investigation of operation efficiency of the biofilters. The results show that metabolic capacity of microbial community of the raw water is reduced after the biofilters, which reflect that metabolically active microbial communities in the raw water can be intercepted by biofilters. After 6 months operation of biofilters, the metabolic profiles of microbial communities are similar between two kinds of biologically-enhanced active filters, and utilization of carbon sources of microbial communities in the two filters are 73.4% and 75.5%, respectively. The metabolic profiles of microbial communities in two biological activated carbon filters showed significant difference. The carbon source utilization rate of microbial community in granule-activated carbon filter is 79.6%, which is obviously higher than 53.8% of the rate in the columnar activated carbon filter (p < 0.01). The analysis results of PCR-SSCP indicate that microbial communities in each biofilter are variety, but the structure of dominant microorganisms is similar among different biofilters. The results also show that the packing materials had little effect on the structure and metabolic function of microbial community in biologically-enhanced active filters, and the difference between two biofilters for the water purification efficiency was not significant (p > 0.05). However, in biological activated carbon filters, granule-activated carbon is conducive to microbial growth and reproduction, and the microbial communities in the biofilter present high metabolic activities, and the removal efficiency for NH4(+)-N, permanganate index and BDOC is better than the columnar activated carbon filter(p < 0.05). The results also suggest that operation efficiency of biofilter is related to the metabolic capacity of microbial community in biofilter.

Identifying active foraminifera in the Sea of Japan using metatranscriptomic approach

NASA Astrophysics Data System (ADS)

Lejzerowicz, Franck; Voltsky, Ivan; Pawlowski, Jan

2013-02-01

Metagenetics represents an efficient and rapid tool to describe environmental diversity patterns of microbial eukaryotes based on ribosomal DNA sequences. However, the results of metagenetic studies are often biased by the presence of extracellular DNA molecules that are persistent in the environment, especially in deep-sea sediment. As an alternative, short-lived RNA molecules constitute a good proxy for the detection of active species. Here, we used a metatranscriptomic approach based on RNA-derived (cDNA) sequences to study the diversity of the deep-sea benthic foraminifera and compared it to the metagenetic approach. We analyzed 257 ribosomal DNA and cDNA sequences obtained from seven sediments samples collected in the Sea of Japan at depths ranging from 486 to 3665 m. The DNA and RNA-based approaches gave a similar view of the taxonomic composition of foraminiferal assemblage, but differed in some important points. First, the cDNA dataset was dominated by sequences of rotaliids and robertiniids, suggesting that these calcareous species, some of which have been observed in Rose Bengal stained samples, are the most active component of foraminiferal community. Second, the richness of monothalamous (single-chambered) foraminifera was particularly high in DNA extracts from the deepest samples, confirming that this group of foraminifera is abundant but not necessarily very active in the deep-sea sediments. Finally, the high divergence of undetermined sequences in cDNA dataset indicate the limits of our database and lack of knowledge about some active but possibly rare species. Our study demonstrates the capability of the metatranscriptomic approach to detect active foraminiferal species and prompt its use in future high-throughput sequencing-based environmental surveys.

Benthic nutrient fluxes and sediment oxygen consumption in a full-scale facultative pond in Patagonia, Argentina.

PubMed

Faleschini, M; Esteves, J L

2013-01-01

The study of benthic metabolism is an interesting tool to understand the process that occurs in bottom water at wastewater stabilization ponds. Here, rates of benthic oxygen consumption and nutrient exchange across the water-sludge interface were measured in situ using a benthic chamber. The research was carried out during autumn, winter, and summer at a municipal facultative stabilization pond working in a temperate region (Puerto Madryn city, Argentina). Both a site near the raw wastewater inlet (Inlet station) and a site near the outlet (Outlet station) were sampled. Important seasonal and spatial patterns were identified as being related to benthic fluxes. Ammonium release ranged from undetectable (autumn/summer - Inlet station) to +30.7 kg-NH4(+) ha(-1) d(-1) (autumn - Outlet station), denitrification ranged from undetectable (winter - in both sites) to -4.0 kg-NO3(-) ha(-1) d(-1) (autumn - Outlet station), and oxygen consumption ranged from 0.07 kg-O2ha(-1) d(-1) (autumn/summer - Outlet station) to 0.84 kg-O2ha(-1) d(-1) (autumn - Inlet station). During the warmer months, the mineralization of organic matter from the bottom pond acts as a source of nutrients, which seem to support the important development of phytoplankton and nitrification activity recorded in the surface water. Bottom processes could be related to the advanced degree and efficiency of the treatment, the temperature, and probably the strong and frequent wind present in the region.

Primary and heterotrophic productivity relate to multikingdom diversity in a hypersaline mat

DOE PAGES

Bernstein, Hans C.; Brislawn, Colin J.; Dana, Karl; ...

2017-10-17

Benthic microbial ecosystems are widespread yet knowledge gaps still remain on the relationships between the diversity of species across kingdoms and productivity. Here, we ask two fundamental questions: (i) How does species diversity relate to the rates of primary and heterotrophic productivity? (ii) How do diel variations in light-energy inputs influence productivity and microbiome diversity? To answer these questions, microbial mats from a magnesium sulfate hypersaline lake were used to establish microcosms. Both the number and relatedness between bacterial and eukaryotic taxa in the microbiome were assayed via amplicon-based sequencing of 16S and 18S rRNA genes over two diel cycles.more » These results correlated with biomass productivity obtained from substrate-specific 13C stable isotope tracers that enabled comparisons between primary and heterotrophic productivity. Both bacterial and eukaryotic species richness and evenness were related only to the rates of 13C-labeled glucose and acetate biomass incorporation. Interestingly, measures of these heterotrophic relationships changed from positive and negative correlations depending on carbon derived from glucose or acetate, respectively. The bacterial and eukaryotic diversity of this ecosystem is also controlled, in part, from energy constraints imposed by changing irradiance over a diel cycle.« less

Primary and heterotrophic productivity relate to multikingdom diversity in a hypersaline mat

PubMed Central

Brislawn, Colin J.; Dana, Karl; Flores-Wentz, Tobias; Cory, Alexandra B.; Fansler, Sarah J.; Fredrickson, James K.; Moran, James J.

2017-01-01

Abstract Benthic microbial ecosystems are widespread yet knowledge gaps still remain on the relationships between the diversity of species across kingdoms and productivity. Here, we ask two fundamental questions: (i) How does species diversity relate to the rates of primary and heterotrophic productivity? (ii) How do diel variations in light-energy inputs influence productivity and microbiome diversity? To answer these questions, microbial mats from a magnesium sulfate hypersaline lake were used to establish microcosms. Both the number and relatedness between bacterial and eukaryotic taxa in the microbiome were assayed via amplicon-based sequencing of 16S and 18S rRNA genes over two diel cycles. These results correlated with biomass productivity obtained from substrate-specific 13C stable isotope tracers that enabled comparisons between primary and heterotrophic productivity. Both bacterial and eukaryotic species richness and evenness were related only to the rates of 13C-labeled glucose and acetate biomass incorporation. Interestingly, measures of these heterotrophic relationships changed from positive and negative correlations depending on carbon derived from glucose or acetate, respectively. The bacterial and eukaryotic diversity of this ecosystem is also controlled, in part, from energy constraints imposed by changing irradiance over a diel cycle. PMID:29045626

Primary and heterotrophic productivity relate to multikingdom diversity in a hypersaline mat

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

Bernstein, Hans C.; Brislawn, Colin J.; Dana, Karl

Benthic microbial ecosystems are widespread yet knowledge gaps still remain on the relationships between the diversity of species across kingdoms and productivity. Here, we ask two fundamental questions: (i) How does species diversity relate to the rates of primary and heterotrophic productivity? (ii) How do diel variations in light-energy inputs influence productivity and microbiome diversity? To answer these questions, microbial mats from a magnesium sulfate hypersaline lake were used to establish microcosms. Both the number and relatedness between bacterial and eukaryotic taxa in the microbiome were assayed via amplicon-based sequencing of 16S and 18S rRNA genes over two diel cycles.more » These results correlated with biomass productivity obtained from substrate-specific 13C stable isotope tracers that enabled comparisons between primary and heterotrophic productivity. Both bacterial and eukaryotic species richness and evenness were related only to the rates of 13C-labeled glucose and acetate biomass incorporation. Interestingly, measures of these heterotrophic relationships changed from positive and negative correlations depending on carbon derived from glucose or acetate, respectively. The bacterial and eukaryotic diversity of this ecosystem is also controlled, in part, from energy constraints imposed by changing irradiance over a diel cycle.« less

Energy sustainability of Microbial Fuel Cell (MFC): A case study

NASA Astrophysics Data System (ADS)

Tommasi, Tonia; Lombardelli, Giorgia

2017-07-01

Energy sustainability analysis and durability of Microbial Fuel Cells (MFCs) as energy source are necessary in order to move from the laboratory scale to full-scale application. This paper focus on these two aspects by considering the energy performances of an original experimental test with MFC conducted for six months under an external load of 1000 Ω. Energy sustainability is quantified using Energy Payback Time, the time necessary to produce the energy already spent to construct the MFC device. The results of experiment reveal that the energy sustainability of this specific MFC is never reached due to energy expenditure (i.e. for pumping) and to the low amount of energy produced. Hence, different MFC materials and architectures were analysed to find guidelines for future MFC development. Among these, only sedimentary fuel cells (Benthic MFCs) seem sustainable from an energetic point of view, with a minimum duration of 2.7 years. An energy balance approach highlights the importance of energy calculation. However, this is very often not taken into account in literature. This study outlines promising methodology for the design of an alternative layout of energy sustainable MFC and wastewater management systems.

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank

PubMed Central

Leite, Márcio F. A.; Pan, Yao; Bloem, Jaap; Berge, Hein ten; Kuramae, Eiko E.

2017-01-01

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake. PMID:28198425

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.

PubMed

Leite, Márcio F A; Pan, Yao; Bloem, Jaap; Berge, Hein Ten; Kuramae, Eiko E

2017-02-15

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.

Microorganism-regulated mechanisms of temperature effects on the performance of anaerobic digestion.

PubMed

Lin, Qiang; He, Guihua; Rui, Junpeng; Fang, Xiaoyu; Tao, Yong; Li, Jiabao; Li, Xiangzhen

2016-06-03

Temperature is an important factor determining the performance and stability of the anaerobic digestion process. However, the microorganism-regulated mechanisms of temperature effects on the performance of anaerobic digestion systems remain further elusive. To address this issue, we investigated the changes in composition, diversity and activities of microbial communities under temperature gradient from 25 to 55 °C using 16S rRNA gene amplicon sequencing approach based on genomic DNA (refer to as "16S rDNA") and total RNA (refer to as "16S rRNA"). Microbial community structure and activities changed dramatically along the temperature gradient, which corresponded to the variations in digestion performance (e.g., daily CH4 production, total biogas production and volatile fatty acids concentration). The ratios of 16S rRNA to 16S rDNA of microbial taxa, as an indicator of the potentially relative activities in situ, and whole activities of microbial community assessed by the similarity between microbial community based on 16S rDNA and rRNA, varied strongly along the temperature gradient, reflecting different metabolic activities. The daily CH4 production increased with temperature from 25 to 50 °C and declined at 55 °C. Among all the examined microbial properties, the whole activities of microbial community and alpha-diversity indices of both microbial communities and potentially relative activities showed highest correlations to the performance. The whole activities of microbial community and alpha-diversity indices of both microbial communities and potentially relative activities were sensitive indicators for the performance of anaerobic digestion systems under temperature gradient, while beta-diversity could predict functional differences. Microorganism-regulated mechanisms of temperature effects on anaerobic digestion performance were likely realized through increasing alpha-diversity of both microbial communities and potentially relative activities to supply more functional pathways and activities for metabolic network, and increasing the whole activities of microbial community, especially methanogenesis, to improve the strength and efficiency in anaerobic digestion process.

Assessing the Efficacy of the Aerobic Methanotrophic Biofilter in Methane Hydrate Environments

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

Valentine, David

2012-09-30

In October 2008 the University of California at Santa Barbara (UCSB) initiated investigations of water column methane oxidation in methane hydrate environments, through a project funded by the National Energy Technology Laboratory (NETL) entitled: assessing the efficacy of the aerobic methanotrophic biofilter in methane hydrate environments. This Final Report describes the scientific advances and discoveries made under this award as well as the importance of these discoveries in the broader context of the research area. Benthic microbial mats inhabit the sea floor in areas where reduced chemicals such as sulfide reach the more oxidizing water that overlies the sediment. Wemore » set out to investigate the role that methanotrophs play in such mats at locations where methane reaches the sea floor along with sulfide. Mats were sampled from several seep environments and multiple sets were grown in-situ at a hydrocarbon seep in the Santa Barbara Basin. Mats grown in-situ were returned to the laboratory and used to perform stable isotope probing experiments in which they were treated with 13C-enriched methane. The microbial community was analyzed, demonstrating that three or more microbial groups became enriched in methane?s carbon: methanotrophs that presumably utilize methane directly, methylotrophs that presumably consume methanol excreted by the methanotrophs, and sulfide oxidizers that presumably consume carbon dioxide released by the methanotrophs and methylotrophs. Methanotrophs reached high relative abundance in mats grown on methane, but other bacterial processes include sulfide oxidation appeared to dominate mats, indicating that methanotrophy is not a dominant process in sustaining these benthic mats, but rather a secondary function modulated by methane availability. Methane that escapes the sediment in the deep ocean typically dissolved into the overlying water where it is available to methanotrophic bacteria. We set out to better understand the efficacy of this process as a biofilter by studying the distribution of methane oxidation and disposition of methanotrophic populations in the Pacific Ocean. We investigated several environments including the basins offshore California, the continental margin off Central America, and the shallow waters around gas seeps. We succeeded in identifying the distributions of activity in these environments, identified potential physical and chemical controls on methanotrophic activity, we further revealed details about the methanotrophic communities active in these settings, and we developed new approaches to study methanotrophic communities. These findings should improve our capacity to predict the methanotrophic response in ocean waters, and further our ability to generate specific hypotheses as to the ecology and efficacy of pelagic methanotrophic communites. The discharge of methane and other hydrocarbons to Gulf of Mexico that followed the sinking of the Deepwater Horizon provided a unique opportunity to study the methanotorphic biofilter in the deep ocean environment. We set out to understand the consumption of methane and the bloom of methanotrophs resulting from this event, as a window into the regional scale release of gas hydrate under rapid warming scenarios. We found that other hydrocarbon gases, notably propane and ethane, were preferred for consumption over methane, but that methane consumption accelerated rapidly and drove the depletion of methane within a matter of months after initial release. These results revealed the identity of the responsible community, and point to the importance of the seed population in determining the rate at which a methanotrophic community is able to respond to an input of methane. Collectively, these results provide a significant advance in our understanding of the marine methanotrohic biofilter, and further provide direction and context for future investigations of this important phenomenon. This project has resulted in fourteen publications to date, with five more circulating in draft form, and several others planned.« less

Intertidal foraminifera and stable isotope geochemistry from world's largest mangrove, Sundarbans: Assessing a multiproxy approach for studying changes in sea-level

NASA Astrophysics Data System (ADS)

Sen, Areen; Bhadury, Punyasloke

2017-06-01

Recent changes in sea level have appeared as a major threat to the existence of coastal habitats like mangroves and to the biodiversity characterizing such habitats. In this study benthic foraminifer analysis along with carbon isotopes (δ13C‰) and ratio between organic Carbon and Nitrogen (C/N) were analyzed from five intertidal stations in Sundarbans, the world's largest mangrove ecosystem to test the efficiency of these signatures toward tracking relative rise in sea level. The stability of these signatures with respect to gap of twenty months across varying elevations of the targeted stations has been tested. Benthic foraminifer abundance ranged from 0 to 118 individuals per 10 g and the assemblage was found to be mostly dominated by agglutinated species. The δ13C‰ values (-26.6 to -23.8) reflected that the origin of carbon is majorly from vascular land plants in some inputs from estuarine phytoplankton that are known to characterize tidal water of Sundarbans. The values of C/N (0.48-1.43) represented a microbially degraded total organic carbon (TOC) pool and thus were not a suitable proxy. Out of three signatures, δ13C‰ showed a strong co-relation with elevation and thus could be used as a reliable proxy to track relative sea level rise in mangrove environments.

Ten Years of Observatory Science from Saanich Inlet on the VENUS Cabled Ocean Observatory

NASA Astrophysics Data System (ADS)

Dewey, R. K.; Tunnicliffe, V.; Macoun, P.; Round, A.

2016-02-01

The Saanich Inlet array of the VENUS cabled ocean observatory, maintained and operated by Ocean Networks Canada, was installed in February 2006, and in 2016 will have supported ten years of comprehensive interactive science. Representing the first in the present generation of cabled observing technologies, this coastal array has provided continuous high power and broadband communications to a variety of instrument platforms, hundreds of sensors, and enabled dozens of short, medium, and long-term studies. Saanich Inlet is a protected fjord with limited tidal action, resulting in an extremely productive environment, with strong seasonal chemical variations driven by episodic deep water renewal events and oxygen reduction processes. The breadth of the research has included microbial and benthic community dynamics, biogeochemical cycles, forensics, quantifying inter-annual variations, benthic-pelagic coupling, sensor testing, plankton dynamics, and bio-turbulence. Observatory measurements include core water properties (CTD & O2) and water-column echo-sounder records, as well as experiment-oriented deployments utilizing cameras, Gliders, Dopplers, hydrophones, and a variety of biogeochemical sensors. With a recently installed Buoy Profiler System for monitoring the entire water column, community plans continue with a dedicated Redox experiment through the 2016-17 seasons. Highlights from the dozens of research papers and theses will be presented to demonstrate the achievements enabled by a comprehensive coastal cabled observing system.

Effects of a chronic lower range of triclosan exposure to a stream mesocosm community

USGS Publications Warehouse

Nietch, C.T.; Quinlan, E.L.; Lazorchak, J.; Impellitteri, C.; Raikow, D.; Walters, David M.

2013-01-01

Triclosan (5-chloro-2-(2,4-dichlorophenoxy)phenol) is an antimicrobial found in consumer soaps and toothpaste. It is in treated wastewater effluents at low part per billion concentrations, representing a potentially chronic exposure condition for biota inhabiting receiving streams. A naturally colonized benthos was created using flow-through indoor mesocosms. Then the benthic communities were dosed to achieve different in-stream triclosan concentrations (Control, 0.1, 0.5, 1.0, 5.0, and 10 µg/L) for 56 days. Water quality parameters and endpoints from bacteria to macroinvertebrates plus interacting abiotic components were measured. Effects of triclosan on specific microbial endpoints were observed at all doses, including an effect on litter decomposition dynamics at doses 1.0 µg/L and higher. Resistance of periphytic bacteria to triclosan significantly increased in doses 0.5 µg/L and above. By the end of dosing, the antimicrobial appeared to stimulate the stream periphyton at the three lowest doses while the two highest doses exhibited decreased stocks of periphyton, including significantly lower bacteria cell densities, and cyanobacteria abundance compared to the control. Beside an effect on benthic ostracods, the changes that occurred in the periphyton did not translate to significant change in the colonizing nematodes, the macroinvertebrate community as a whole, or other measurements of stream function. The results shed light on the role a low, chronic exposure to triclosan may play in effluent dominated streams.

Methane-Oxidizing Bacteria Shunt Carbon to Microbial Mats at a Marine Hydrocarbon Seep

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

Paul, Blair G.; Ding, Haibing; Bagby, Sarah C.

The marine subsurface is a reservoir of the greenhouse gas methane. While microorganisms living in water column and seafloor ecosystems are known to be a major sink limiting net methane transport from the marine subsurface to the atmosphere, few studies have assessed the flow of methane-derived carbon through the benthic mat communities that line the seafloor on the continental shelf where methane is emitted. We analyzed the abundance and isotope composition of fatty acids in microbial mats grown in the shallow Coal Oil Point seep field off Santa Barbara, CA, USA, where seep gas is a mixture of methane andmore » CO 2. We further used stable isotope probing (SIP) to track methane incorporation into mat biomass. We found evidence that multiple allochthonous substrates supported the rich growth of these mats, with notable contributions from bacterial methanotrophs and sulfur-oxidizers as well as eukaryotic phototrophs. Fatty acids characteristic of methanotrophs were shown to be abundant and 13C-enriched in SIP samples, and DNA-SIP identified members of the methanotrophic family Methylococcaceae as major 13CH 4 consumers. Members of Sulfuricurvaceae, Sulfurospirillaceae, and Sulfurovumaceae are implicated in fixation of seep CO 2. The mats’ autotrophs support a diverse assemblage of co-occurring bacteria and protozoa, with Methylophaga as key consumers of methane-derived organic matter. This study identifies the taxa contributing to the flow of seep-derived carbon through microbial mat biomass, revealing the bacterial and eukaryotic diversity of these remarkable ecosystems.« less

Methane-Oxidizing Bacteria Shunt Carbon to Microbial Mats at a Marine Hydrocarbon Seep

DOE PAGES

Paul, Blair G.; Ding, Haibing; Bagby, Sarah C.; ...

2017-02-27

The marine subsurface is a reservoir of the greenhouse gas methane. While microorganisms living in water column and seafloor ecosystems are known to be a major sink limiting net methane transport from the marine subsurface to the atmosphere, few studies have assessed the flow of methane-derived carbon through the benthic mat communities that line the seafloor on the continental shelf where methane is emitted. We analyzed the abundance and isotope composition of fatty acids in microbial mats grown in the shallow Coal Oil Point seep field off Santa Barbara, CA, USA, where seep gas is a mixture of methane andmore » CO 2. We further used stable isotope probing (SIP) to track methane incorporation into mat biomass. We found evidence that multiple allochthonous substrates supported the rich growth of these mats, with notable contributions from bacterial methanotrophs and sulfur-oxidizers as well as eukaryotic phototrophs. Fatty acids characteristic of methanotrophs were shown to be abundant and 13C-enriched in SIP samples, and DNA-SIP identified members of the methanotrophic family Methylococcaceae as major 13CH 4 consumers. Members of Sulfuricurvaceae, Sulfurospirillaceae, and Sulfurovumaceae are implicated in fixation of seep CO 2. The mats’ autotrophs support a diverse assemblage of co-occurring bacteria and protozoa, with Methylophaga as key consumers of methane-derived organic matter. This study identifies the taxa contributing to the flow of seep-derived carbon through microbial mat biomass, revealing the bacterial and eukaryotic diversity of these remarkable ecosystems.« less

Methane-Oxidizing Bacteria Shunt Carbon to Microbial Mats at a Marine Hydrocarbon Seep

PubMed Central

Paul, Blair G.; Ding, Haibing; Bagby, Sarah C.; Kellermann, Matthias Y.; Redmond, Molly C.; Andersen, Gary L.; Valentine, David L.

2017-01-01

The marine subsurface is a reservoir of the greenhouse gas methane. While microorganisms living in water column and seafloor ecosystems are known to be a major sink limiting net methane transport from the marine subsurface to the atmosphere, few studies have assessed the flow of methane-derived carbon through the benthic mat communities that line the seafloor on the continental shelf where methane is emitted. We analyzed the abundance and isotope composition of fatty acids in microbial mats grown in the shallow Coal Oil Point seep field off Santa Barbara, CA, USA, where seep gas is a mixture of methane and CO2. We further used stable isotope probing (SIP) to track methane incorporation into mat biomass. We found evidence that multiple allochthonous substrates supported the rich growth of these mats, with notable contributions from bacterial methanotrophs and sulfur-oxidizers as well as eukaryotic phototrophs. Fatty acids characteristic of methanotrophs were shown to be abundant and 13C-enriched in SIP samples, and DNA-SIP identified members of the methanotrophic family Methylococcaceae as major 13CH4 consumers. Members of Sulfuricurvaceae, Sulfurospirillaceae, and Sulfurovumaceae are implicated in fixation of seep CO2. The mats’ autotrophs support a diverse assemblage of co-occurring bacteria and protozoa, with Methylophaga as key consumers of methane-derived organic matter. This study identifies the taxa contributing to the flow of seep-derived carbon through microbial mat biomass, revealing the bacterial and eukaryotic diversity of these remarkable ecosystems. PMID:28289403

A new 0.9 Ma oxygen isotope stratigraphy for a shallow-water sedimentary transect across three IODP 317 sites in the Canterbury Bight of southwest Pacific Ocean

NASA Astrophysics Data System (ADS)

Ding, Xuan; Wu, YingYing

2016-04-01

Sedimentary records in shallow-water environment provide unique opportunity to further our understanding on the regional relative sea level changes in relation to global climate change. Here we present a new 0.9 Ma oxygen isotope stratigraphy for a shallow-water sedimentary transect across three IODP 317 sites in the Canterbury Bight of southwest Pacific Ocean. The three sites are located on the eastern margin of the South Island of New Zealand, including a continental slope site, IODP317-U1352 and two continental shelf sites, IODP317-U1354 and IODP317-U1351. We first generated high resolution benthic foraminifers (Nonionella flemingi) δ18O records for the three sites and a planktonic (Globigerina bulloides) record for the U1352B. An initial chronological framework for the benthic δ18O record of the U1352B was constructed using 8 accelerator mass spectrometry (AMS) radiocarbon dates and 4 biostratigraphic events. Then a refined age model was established by correlating the U1352B benthic δ18O record with the EDC δD record on the AICC2012 time-scale, and the LR04 benthic δ18O stack. Although the U1354B and U1351B have lower sedimentation rates, their benthic δ18O records correlate well with that of U1352B. In order to ensure the accuracy of the chronostratigraphic framework established, we also analyzed the characteristics of sedimentary grain size and the planktonic and benthic δ18O values. In accord with the adjacent sites, the results show that the melt of Southern Alps glaciers due to the warming climate during MIS 11 and 5.5 led to the increased fresh water delivery, with massive terrigenous deposit; and the warm SST during the MIS7 is related with the STF migration, which led to strong current activity, with coarser grain size. Meanwhile, records of benthic δ18O, sedimentation rate and content of >63μm coarse fraction of site U1352 all indicate the MIS 20 was indeed a colder interval compared to subsequent glacial times.

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.

Recent benthic foraminifera and sedimentary facies distribution of the Abu Dhabi (United Arab Emirates) coastline

NASA Astrophysics Data System (ADS)

Fiorini, Flavia; Lokier, Stephen W.

2014-05-01

The distribution of benthic foraminifera and sedimentary facies from Recent coastline environments adjacent to the coastline of Abu Dhabi (UAE) was studied in detail with the aim to: 1) provide reliable analogs for understanding and interpreting the depositional environment of ancient shallow-marine sediments from the UAE; 2) assess any modifications in the distribution of benthic environments and sedimentary facies in an area affected by significant anthropogenic activities - particular construction and land reclamation. A total of 100 sea-floor sediment samples were collected in different shallow-marine sedimentary environments (nearshore shelf, beach-front, channels, ooid shoals, lagoon and mangals) close to the coastline of Abu Dhabi Island. Where possible, we revisited the sampling sites used in several studies conducted in the middle of last century (prior to any significant anthropogenic activities) to assess temporal changes in Recent benthic foraminifera and sedimentary facies distribution during the last 50 years. Five foraminiferal assemblages were recognized in the studied area. Species with a porcellaneous test mainly belonging to the genera Quinqueloculina, Triloculina, Spiroloculina, Sigmoilinita are common in all studied areas. Larger benthic foraminifera Peneroplis and Spirolina are particularly abundant in samples collected on seaweed. Hyaline foraminifera mostly belonging to the genera Elphidium, Ammonia, Bolivina and Rosalina are also common together with Miliolidae in the nearshore shelf and beach front. Agglutinated foraminifera (Clavulina, Textularia, Ammobaculites and Reophax) are present in low percentages. The species belonging to the genera Ammobaculites and Reophax are present only in the finest grain samples particularly in lagoons and mangal environments and have not been reported previously in the studied area. The majority of the ooid shoal sediments, the coarser sediments of the beach-front and samples collected in dredged channels do not contain living foraminifera and the dead assemblage is mostly composed of a few specimens of coarse-sized Miliolidae with fragmented or abraded tests, probably transported from nearby environments. While the shallow-water settings of the Abu Dhabi coastline continue to be areas of active carbonate sedimentation, there have been significant changes in facies distributions over the last 50 years. In particular: × The opportunistic genera Ammonia and Elphidium have become more abundant. Reophax and Ammobaculites are reported in the area for the first time. × With anthropogenic activities some environments, such as inner lagoons, are lost whilst other areas show resilience to anthropogenic activities with little change in sedimentary facies distribution and foraminiferal assemblage. × No living foraminifera are found in dredged channels. The detailed analysis of these changes in foraminifera distribution and sedimentary facies allows us to further our understanding of the effects of anthropogenic activities on shallow-marine environments. By so doing, we are better able to distinguish between those changes that result from anthropogenic activities and those that are a result of naturally-occurring environmental perturbations.

Methane seep events of the southern Joetsu Knoll since middle Pleistocene based on benthic foraminifera

NASA Astrophysics Data System (ADS)

Oi, T.; Akiba, F.; Matsumoto, R.; Kakuwa, Y.

2016-12-01

Gas hydrates were collected at several sites off Joetsu which presented anomalous seismic structures. "Gas chimneys", major host structures for shallow gas hydrates, were recognized ROV off Joetsu in eastern margin of the Japan Sea, as were a number of active methane seeps. The assemblage components and carbon isotope of benthic foraminifera, which are ubiquitous in global marine settings, can indicate methane seep environments (Akimoto et al., 1994; Bhaumik and Gupta, 2007). Preliminary work by Oi et al. (2015) documented the obvious occurrences of methane related foraminifera, Rutherfordoides sp., in three core sediments recovered from Umitaka Spur, west Oki Trough and north Mogami Trough in the eastern margin of the Japan Sea, and found them to comprise the early part of the MIS 2, calculated to 28-25ka. These records suggest that active methane seep events might occur at the same time during early MIS 2, but were confined within the last 100ka. In this study, we analyzed benthic foraminiferal fossils from drilling core J04RB (core length 122 m; one of the gas hydrate bearing sites at a southern part of the Joetsu Knoll) in order to document methane seep events during the last 500ka. Firstly, we estimated sedimentation ages from diatom biostratigraphy and identification of Aso-1 tephra. Based on diatom components, we recognized a boundary between NPD (Neogene North Pacific diatom Zonations) 12 and NPD11, estimated at 300 ka (MIS8/9; Yanagisawa and Akiba, 1998). The bottom age was estimated to almost 530-560 ka (around MIS14) especially from the alternation with warm and cold diatom zones (Akiba et al., 2014). Secondary, we could suppose the paleoenvironments from benthic foraminifera as below. 1. The rare benthic foraminifera during the cold stages (MIS8, MIS10, and MIS12) indicate anoxic bottom conditions characteristic of falling sea level, just as with MIS 2. 2. We recognized the continuous distributions of tiny methane related specimens of Rutherfordoides sp. during MIS10. In order to confirm new records of active methane seep events in the Joetsu Knoll, we need to measure isotope records of this species. This study was conducted under the commission from AIST as a part of the methane hydrate research project of METI (the Ministry of Economy, Trade and Industry, Japan).

Planetary stations and Abyssal Benthic Laboratories: An overview of parallel approaches for long-term investigation in extreme environments

NASA Technical Reports Server (NTRS)

Dipippo, S.; Prendin, W.; Gasparoni, F.

1994-01-01

In spite of the apparent great differences between deep ocean and space environment, significant similarities can be recognized when considering the possible solutions and technologies enabling the development of remote automatic stations supporting the execution of scientific activities. In this sense it is believed that mutual benefits shall be derived from the exchange of experiences and results between people and organizations involved in research and engineering activities for hostile environments, such as space, deep sea, and polar areas. A significant example of possible technology transfer and common systematic approach is given, which describes in some detail how the solutions and the enabling technologies identified for an Abyssal Benthic Laboratory can be applied for the case of a lunar or planetary station.

Effects of N and P enrichment on competition between phytoplankton and benthic algae in shallow lakes: a mesocosm study.

PubMed

Zhang, Xiufeng; Mei, Xueying; Gulati, Ramesh D; Liu, Zhengwen

2015-03-01

Competition for resources between coexisting phytoplankton and benthic algae, but with different habitats and roles in functioning of lake ecosystems, profoundly affects dynamics of shallow lakes in the process of eutrophication. An experiment was conducted to test the hypothesis that combined enrichment with nitrogen (N) and phosphorus (P) would be a greater benefit to phytoplankton than benthic algae. The growth of phytoplankton and benthic algae was measured as chlorophyll a (Chl a) in 12 shallow aquatic mesocosms supplemented with N, P, or both. We found that enrichment with N enhanced growth of benthic algae, but not phytoplankton. P enrichment had a negative effect on benthic algal growth, and no effect on the growth of phytoplankton. N+P enrichment had a negative effect on benthic algae, but enhanced the growth of phytoplankton, thus reducing the proportion of benthic algae contributing to the combined biomass of these two groups of primary producers. Thus, combined N+P enrichment is more favorable to phytoplankton in competition with benthic algae than enrichment with either N or P alone. Our study indicates that combined enrichment with N+P promotes the dominance of phytoplankton over benthic algae, with consequences for the trophic dynamics of shallow lake ecosystems.

Impact of prolonged storm activity on the Ecological Status of intertidal benthic habitats within oyster (Crassostrea gigas) trestle cultivation sites.

PubMed

O'Carroll, Jack P J; Quinn, Christina; Forde, James; Patterson, Adrian; O'Beirn, Francis X; Kennedy, Robert

2016-09-15

The Ecological Status (ES; sensu the Water Framework Directive) of intertidal benthic communities within six oyster trestle cultivation sites was found to be negatively impacted along the access routes to trestles in a 2013 study. All cultivation sites occur within Natura 2000 sites. The current study revisited four of the 2013 cultivation sites in February 2014 one month after the storm activity of winter 2013/14 to test if the compaction effect along access routes persisted after the storms. Three levels of the fixed factor treatment were sampled; immediately below the trestles, along the access route and 300m away from any anthropogenic activity. The compaction effect at the Access treatment persisted in spite of the major storm activity. The current study showed the IQI to be effective for assessing the impacts of aquaculture and highlights the IQI as a tool for monitoring Conservation Status of intertidal communities under the Habitats Directive. Copyright © 2016 Elsevier Ltd. All rights reserved.

Recovery of microbial community structure and functioning after wildfire in semi-arid environments: optimising methods for monitoring and assessment

NASA Astrophysics Data System (ADS)

Muñoz-Rojas, Miriam; Martini, Dylan; Erickson, Todd; Merritt, David; Dixon, Kingsley

2015-04-01

Introduction In semi-arid areas such as northern Western Australia, wildfires are a natural part of the environment and many ecosystems in these landscapes have evolved and developed a strong relationship with fire. Soil microbial communities play a crucial role in ecosystem processes by regulating the cycling of nutrients via decomposition, mineralization, and immobilization processes. Thus, the structure (e.g. soil microbial biomass) and functioning (e.g. soil microbial activity) of microbial communities, as well as their changes after ecosystem disturbance, can be useful indicators of soil quality and health recovery. In this research, we assess the impacts of fire on soil microbial communities and their recovery in a biodiverse semi-arid environment of Western Australia (Pilbara region). New methods for determining soil microbial respiration as an indicator of microbial activity and soil health are also tested. Methodology Soil samples were collected from 10 similar ecosystems in the Pilbara with analogous native vegetation, but differing levels of post-fire disturbance (i.e. 3 months, 1 year, 5, 7 and 14 years after wildfire). Soil microbial activity was measured with the Solvita test which determines soil microbial respiration rate based on the measurement of the CO2 burst of a dry soil after it is moistened. Soils were dried and re-wetted and a CO2 probe was inserted before incubation at constant conditions of 25°C during 24 h. Measurements were taken with a digital mini spectrometer. Microbial (bacteria and fungi) biomass and community composition were measured by phospholipid fatty acid analysis (PLFA). Results Immediately after the fire (i.e. 3 months), soil microbial activity and microbial biomass are similar to 14 years 'undisturbed' levels (53.18±3.68 ppm CO2-CO and 14.07±0.65 mg kg-1, respectively). However, after the first year post-fire, with larger plant productivity, microbial biomass and microbial activity increase rapidly, peaking after 5-7 years post fire (70.70±8.94 ppm CO2-CO and 21.67±2.62 mg kg-1, respectively). Microbial activity measured with the Solvita test was significantly correlated (R Pearson > 0.7; P < 0.001) with microbial parameters analysed with PLFA such as microbial biomass, bacteria biomass or mycorrhizhal fungi. This method has proven to be reliable, fast and easy to interpret for assessment of soil microbial activity in the recovery of soil quality during the recovery after fire. Keywords Pilbara region, biodiverse ecosystems, microbial biomass, microbial respiration, Solvita test, CO2 burst.

Indices, multispecies and synthesis descriptors in benthic assessments: Intertidal organic enrichment from oyster farming

NASA Astrophysics Data System (ADS)

Quintino, Victor; Azevedo, Ana; Magalhães, Luísa; Sampaio, Leandro; Freitas, Rosa; Rodrigues, Ana Maria; Elliott, Michael

2012-09-01

Intertidal off-bottom oyster culture is shown to cause organic enrichment of the shore and although there are two stressors of interest (the presence of a structure, the trestles, and also the sediment and organic waste from the oysters), these can be separated and their relative impacts determined using an appropriate nested experimental design and data treatments. Although no artificial food sources are involved, the oysters feeding activity and intensity of culture enhances biodeposition and significantly increases the sediment fines content and total organic matter. This in general impoverished the benthic community in culture areas rather than a species succession with the installation of opportunists or a resulting increase in the abundance and biomass of benthic species; the findings can be a direct consequence of the intertidal situation which is less-amenable recruitment of species more common to the subtidal environment. Thus the most appropriate biological descriptors to diagnose the effects associated with the organic enrichment were the multispecies abundance data as well as the primary biological variables species richness and abundance. The effects were however spatially and statistically significantly confined to the area located directly underneath the culture bags compared to the corridors located between the trestles, which do not show such enrichment effects. Synthesis biotic indices were much less effective to diagnose the benthic alterations associated with this organic enrichment. These results show that special attention must be paid when using indices in areas where the organic enrichment induces an impoverishment of the benthic community but not necessarily a species replacement with the installation of opportunists.

Strong linkage between active microbial communities and microbial carbon usage in a deglaciated terrain of the High Arctic

NASA Astrophysics Data System (ADS)

Kim, M.; Gyeong, H. R.; Lee, Y. K.

2017-12-01

Soil microorganisms play pivotal roles in ecosystem development and carbon cycling in newly exposed glacier forelands. However, little is known about carbon utilization pattern by metabolically active microbes over the course of ecosystem succession in these nutrient-poor environments. We investigated RNA-based microbial community dynamics and its relation to microbial carbon usage along the chronosequence of a High Arctic glacier foreland. Among microbial taxa surveyed (bacteria, archaea and fungi), bacteria are among the most metabolically active taxa with a dominance of Cyanobacteria and Actinobacteria. There was a strong association between microbial carbon usage and active Actinobacterial communities, suggesting that member of Actinobacteria are actively involved in organic carbon degradation in glacier forelands. Both bacterial community and microbial carbon usage are converged towards later stage of succession, indicating that the composition of soil organic carbon plays important roles in structuring bacterial decomposer communities during ecosystem development.

Distribution of benthic foraminifera along the Iranian Coast

NASA Astrophysics Data System (ADS)

Amao, Abduljamiu; Kaminski, Michael

2017-04-01

This study focuses on the distribution of benthic foraminifera along the Iranian coast of the Gulf from the northeast close to Shatt Al-Arab/Arvand Rud to the southeast near the Strait of Hormuz where it connects to the Indian Ocean. The Gulf is a naturally stressed environment due to extremes of salinity, temperatures and anthropogenic influences such as rapid urbanization projects, maritime transport, large numbers of desalination plants and oil platforms. These activities over time continue to compound the already stressed environment. Historical records on foraminiferal diversity and distribution in the Gulf commonly underestimate its benthic foraminiferal composition and diversity. Thirty-two samples collected from depths ranging between 20 to 45 m were analyzed for total foraminiferal assemblages. A total of 224 benthic foraminiferal species and subspecies belonging to 63 genera, 34 families, 22 superfamilies and 6 orders were recognized. The assemblages are dominated by hyaline taxa (45.3%) and porcelaneous foraminiferal (35.3%), while agglutinated foraminiferal groups are comprise a lower proportion (19.4%). The ten most abundant genera include Asterorotalia (13.3%), Quinqueloculina (12.4%), Bolivina (9.8%), Nonion (8.6%), Ammonia (5.5%), Textularia (5.4%), Elphidium (5.2%), Cibicides (3.9%), Challengerella (3.6%) and Hanzawaia (3.4%). The most common species are Nonion sp. 1 (5.45%), Asterorotalia dentata (5.03%), Quinqueloculina sp. 1 (4.8%), Nonion sp. 2 (4.5%), Rotalinoides cf. R. gaimardii (3.3%), Asterorotalia sp. 3 (3.2%), Quinqueloculina sp. 8 (3.1%), Bolivina cf. B. persiensis (3.0%), Bolivina cf. B. striatula (2.9%), and Ammonia sp. 1 (2.9%). We speculate that feeding strategy, e.g., herbivore (Nonion, Ammonia, Elphidium and Asterorotalia), the proportion of finer sediments (mud), availability of nutrients and presence of oxygen are factors controlling the diversity and distribution of benthic foraminifera in the Gulf. Due to the importance of this water body in a changing world climate, this study updates the knowledge on the type and distribution of benthic foraminiferal groups.

Large-scale assessment of benthic communities across multiple marine protected areas using an autonomous underwater vehicle.

PubMed

Ferrari, Renata; Marzinelli, Ezequiel M; Ayroza, Camila Rezende; Jordan, Alan; Figueira, Will F; Byrne, Maria; Malcolm, Hamish A; Williams, Stefan B; Steinberg, Peter D

2018-01-01

Marine protected areas (MPAs) are designed to reduce threats to biodiversity and ecosystem functioning from anthropogenic activities. Assessment of MPAs effectiveness requires synchronous sampling of protected and non-protected areas at multiple spatial and temporal scales. We used an autonomous underwater vehicle to map benthic communities in replicate 'no-take' and 'general-use' (fishing allowed) zones within three MPAs along 7o of latitude. We recorded 92 taxa and 38 morpho-groups across three large MPAs. We found that important habitat-forming biota (e.g. massive sponges) were more prevalent and abundant in no-take zones, while short ephemeral algae were more abundant in general-use zones, suggesting potential short-term effects of zoning (5-10 years). Yet, short-term effects of zoning were not detected at the community level (community structure or composition), while community structure varied significantly among MPAs. We conclude that by allowing rapid, simultaneous assessments at multiple spatial scales, autonomous underwater vehicles are useful to document changes in marine communities and identify adequate scales to manage them. This study advanced knowledge of marine benthic communities and their conservation in three ways. First, we quantified benthic biodiversity and abundance, generating the first baseline of these benthic communities against which the effectiveness of three large MPAs can be assessed. Second, we identified the taxonomic resolution necessary to assess both short and long-term effects of MPAs, concluding that coarse taxonomic resolution is sufficient given that analyses of community structure at different taxonomic levels were generally consistent. Yet, observed differences were taxa-specific and may have not been evident using our broader taxonomic classifications, a classification of mid to high taxonomic resolution may be necessary to determine zoning effects on key taxa. Third, we provide an example of statistical analyses and sampling design that once temporal sampling is incorporated will be useful to detect changes of marine benthic communities across multiple spatial and temporal scales.

Large-scale assessment of benthic communities across multiple marine protected areas using an autonomous underwater vehicle

PubMed Central

Ayroza, Camila Rezende; Jordan, Alan; Figueira, Will F.; Byrne, Maria; Malcolm, Hamish A.; Williams, Stefan B.; Steinberg, Peter D.

2018-01-01

Marine protected areas (MPAs) are designed to reduce threats to biodiversity and ecosystem functioning from anthropogenic activities. Assessment of MPAs effectiveness requires synchronous sampling of protected and non-protected areas at multiple spatial and temporal scales. We used an autonomous underwater vehicle to map benthic communities in replicate ‘no-take’ and ‘general-use’ (fishing allowed) zones within three MPAs along 7o of latitude. We recorded 92 taxa and 38 morpho-groups across three large MPAs. We found that important habitat-forming biota (e.g. massive sponges) were more prevalent and abundant in no-take zones, while short ephemeral algae were more abundant in general-use zones, suggesting potential short-term effects of zoning (5–10 years). Yet, short-term effects of zoning were not detected at the community level (community structure or composition), while community structure varied significantly among MPAs. We conclude that by allowing rapid, simultaneous assessments at multiple spatial scales, autonomous underwater vehicles are useful to document changes in marine communities and identify adequate scales to manage them. This study advanced knowledge of marine benthic communities and their conservation in three ways. First, we quantified benthic biodiversity and abundance, generating the first baseline of these benthic communities against which the effectiveness of three large MPAs can be assessed. Second, we identified the taxonomic resolution necessary to assess both short and long-term effects of MPAs, concluding that coarse taxonomic resolution is sufficient given that analyses of community structure at different taxonomic levels were generally consistent. Yet, observed differences were taxa-specific and may have not been evident using our broader taxonomic classifications, a classification of mid to high taxonomic resolution may be necessary to determine zoning effects on key taxa. Third, we provide an example of statistical analyses and sampling design that once temporal sampling is incorporated will be useful to detect changes of marine benthic communities across multiple spatial and temporal scales. PMID:29547656

Understanding the relationships among phytoplankton, benthic macroinvertebrates, and water quality variables in peri-urban river systems.

PubMed

Pinto, Uthpala; Maheshwari, Basant L; Morris, E Charles

2014-12-01

In this article, using the Hawkesbury-Nepean River as a case study, the spatial and temporal trends of water quality variables over three sampling surveys in a peri-urban situation are examined for their effect on benthic macroinvertebrate communities and phytoplankton communities and whether phytoplankton and benthic macroinvertebrate species can be used as indicators for river health assessment. For this, the authors monitored the spatial and temporal difference of 10 water quality parameters: temperature, turbidity, pH, dissolved oxygen, electrical conductivity, oxidation reduction potential, total nitrogen, total phosphorus, manganese, and suspended solids. The variability in water quality parameters clearly indicated a complex pattern, depending on the season (interaction p = 0.001), which highlighted how the river condition is stressed at multiple points as a result of anthropogenic effects. In particular, the downstream locations indicated an accumulation of nutrients, the presence of increased sediments, and phytoplankton related variables such as total counts, bio-volumes, chlorophyll-a, and total phosphorus. The patterns of phytoplankton communities varied in a complex way depending on the season (interaction p = 0.001). Abundances of phytoplankton were also found in low concentrations where the water column is not severely disturbed by flow and tide. However, when the water clarity drops resulting from tidal cycles, inflows from tributaries, and intense boating activities, the phytoplankton abundances also increased considerably. On the other hand, benthic macroinvertebrates compositions were significantly different between locations (p = 0.001) with increased abundances associated with upstream sites. Aphanocapsa holsatica and chironomid larvae appeared as the important indicators for upstream and downstream site differences in water quality. Water temperature influenced the phytoplankton community pattern (ρ(w) = 0.408), whereas pH influenced the benthic macroinvertebrate community pattern (ρ(w) = 0.437). The findings of this study provide valuable insights into the interactions of water quality parameters on biotic assemblages and to the extent that benthic macroinvertebrates and phytoplankton assemblages are suitable as indicators for monitoring and assessing peri-urban river health.

Diachronous benthic δ18O responses during late Pleistocene terminations

NASA Astrophysics Data System (ADS)

Lisiecki, Lorraine E.; Raymo, Maureen E.

2009-09-01

Benthic δ18O is often used as a stratigraphic tool to place marine records on a common age model and as a proxy for the timing of ice volume/sea level change. However, Skinner and Shackleton (2005) found that the timing of benthic δ18O change at the last termination differed by 3900 years between one Atlantic site and one Pacific site. These results suggest that benthic δ18O change may not always accurately record the timing of deglaciation. We compare benthic δ18O records from 20 Atlantic sites and 14 Pacific sites to evaluate systematic differences in the timing of terminations in benthic δ18O. Analysis of sedimentation rates derived from the alignment of benthic δ18O suggests a statistically significant Atlantic lead over Pacific benthic δ18O change during the last six terminations. We estimate an average Pacific benthic δ18O lag of 1600 years for Terminations 1-5, slightly larger than the delay expected from ocean mixing rates given that most glacial meltwater probably enters the North Atlantic. We additionally find evidence of ˜4000-year Pacific δ18O lags at approximately 128 ka and 330 ka, suggesting that stratigraphic correlation of δ18O has the potential to generate age model errors of several thousand years during terminations. A simple model demonstrates that these lags can be generated by diachronous temperature changes and do not require slower circulation rates. Most importantly, diachronous benthic δ18O responses must be taken into account when comparing Atlantic and Pacific benthic δ18O records or when using benthic δ18O records as a proxy for the timing of ice volume change.

Potential microbial contamination during sampling of permafrost soil assessed by tracers

NASA Astrophysics Data System (ADS)

Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

2017-02-01

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

Potential microbial contamination during sampling of permafrost soil assessed by tracers.

PubMed

Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S

2017-02-23

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

Potential microbial contamination during sampling of permafrost soil assessed by tracers

PubMed Central

Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

2017-01-01

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores. PMID:28230151

Benthic Macroinvertebrate Assemblages and Environmental Correlates in Springs of the Ridge and Valley Province

EPA Science Inventory

Springs are unique features in the landscape that provide important habitat for benthic invertebrates, yet there are few studies characterizing the distribution of benthic macro invertebrates in springs. Benthic macroinvertebrate and water quality data were collected at 35 spring...

Evaluation of anti-microbial activities of ZnO, citric acid and a mixture of both against Propionibacterium acnes.

PubMed

Bae, J Y; Park, S N

2016-12-01

In this study, anti-microbial activities of ZnO of three different particle sizes of citric acid (CA) and of mixtures of ZnO and CA were confirmed against Propionibacterium acnes. ZnO with the smallest particle size showed relatively high anti-microbial activity by disc diffusion assay and broth macrodilution assay. The mixtures of ZnO and CA also showed relatively high anti-microbial activity when the particle size of ZnO was the smallest. Furthermore, anti-microbial activities of ZnO, CA and the mixtures of ZnO and CA were compared through the checkerboard assay. The results indicated that a 1 : 1 ratio of ZnO and CA resulted in the highest anti-microbial activity. The substances were confirmed to have synergic anti-microbial effects. With the time-kill curve assay, the mixture of ZnO-containing CA reduced the surviving microbial content the most after 24 h. The results of our study suggest that ZnO may not only be an anti-microbial ingredient for the prevention of and treatment of acne. The results of our study suggest that ZnO may be an anti-microbial ingredient for the prevention of and treatment of acne when mixed with CA. © 2016 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

Stoichiometry constrains microbial response to root exudation - insights from a model and a field experiment in a temperate forest

NASA Astrophysics Data System (ADS)

Drake, J. E.; Darby, B. A.; Giasson, M.-A.; Kramer, M. A.; Phillips, R. P.; Finzi, A. C.

2012-06-01

Healthy plant roots release a wide range of chemicals into soils. This process, termed root exudation, is thought to increase the activity of microbes and the exo-enzymes they synthesize, leading to accelerated rates of carbon (C) mineralization and nutrient cycling in rhizosphere soils relative to bulk soils. The causal role of exudation, however, is difficult to isolate with in-situ observations, given the complex nature of the rhizosphere environment. We investigated the potential effects of root exudation on microbial and exo-enzyme activity using a theoretical model of decomposition and a field experiment, with a specific focus on the stoichiometric constraint of nitrogen (N) availability. The field experiment isolated the effect of exudation by pumping solutions of exudate mimics through microlysimeter "root simulators" into intact forest soils over two 50-day periods. Using a combined model-experiment approach, we tested two hypotheses: (1) exudation alone is sufficient to stimulate microbial and exo-enzyme activity in rhizosphere soils, and (2) microbial response to C-exudates (carbohydrates and organic acids) is constrained by N-limitation. Experimental delivery of exudate mimics containing C and N significantly increased microbial respiration, microbial biomass, and the activity of exo-enzymes that decompose labile components of soil organic matter (SOM, e.g., cellulose, amino sugars), while decreasing the activity of exo-enzymes that degrade recalcitrant SOM (e.g., polyphenols, lignin). However, delivery of C-only exudates had no effect on microbial biomass or overall exo-enzyme activity, and only increased microbial respiration. The theoretical decomposition model produced complementary results; the modeled microbial response to C-only exudates was constrained by limited N supply to support the synthesis of N-rich microbial biomass and exo-enzymes, while exuding C and N together elicited an increase in modeled microbial biomass, exo-enzyme activity, and decomposition. Thus, hypothesis (2) was supported, while hypothesis (1) was only supported when C and N compounds were exuded together. This study supports a cause-and-effect relationship between root exudation and enhanced microbial activity, and suggests that exudate stoichiometry is an important and underappreciated driver of microbial activity in rhizosphere soils.

Substrate and environmental controls on microbial assimilation of soil organic carbon: a framework for Earth System Models

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

Xu, Xiaofeng; Schimel, Joshua; Thornton, Peter E

2014-01-01

Microbial assimilation of soil organic carbon is one of the fundamental processes of global carbon cycling and it determines the magnitude of microbial biomass in soils. Mechanistic understanding of microbial assimilation of soil organic carbon and its controls is important for to improve Earth system models ability to simulate carbon-climate feedbacks. Although microbial assimilation of soil organic carbon is broadly considered to be an important parameter, it really comprises two separate physiological processes: one-time assimilation efficiency and time-dependent microbial maintenance energy. Representing of these two mechanisms is crucial to more accurately simulate carbon cycling in soils. In this study, amore » simple modeling framework was developed to evaluate the substrate and environmental controls on microbial assimilation of soil organic carbon using a new term: microbial annual active period (the length of microbes remaining active in one year). Substrate quality has a positive effect on microbial assimilation of soil organic carbon: higher substrate quality (lower C:N ratio) leads to higher ratio of microbial carbon to soil organic carbon and vice versa. Increases in microbial annual active period from zero stimulate microbial assimilation of soil organic carbon; however, when microbial annual active period is longer than an optimal threshold, increasing this period decreases microbial biomass. The simulated ratios of soil microbial biomass to soil organic carbon are reasonably consistent with a recently compiled global dataset at the biome-level. The modeling framework of microbial assimilation of soil organic carbon and its controls developed in this study offers an applicable ways to incorporate microbial contributions to the carbon cycling into Earth system models for simulating carbon-climate feedbacks and to explain global patterns of microbial biomass.« less

APPLICATION OF TWO INDICES OF BENTHIC COMMUNITY CONDITION IN CHESAPEAKE BAY

EPA Science Inventory

The Chesapeake Bay Benthic Index of Biotic Integrity (B-161) and the Environmental Monitoring and Assessment Program's Virginian Province Benthic Index (EMAP-VP BI) were applied to 294 sampling events in Chesapeake Bay and the results were compared. These benthic indices are inte...

How do microlocal environmental variations affect microbial activities of a Pinus halepensis litter in a Mediterranean coastal area?

PubMed

Qasemian, Leila; Guiral, Daniel; Farnet, Anne-Marie

2014-10-15

Mediterranean coastal ecosystems suffer many different types of natural and anthropogenic environmental pressure. Microbial communities, major conductors of organic matter decomposition are also subject to these environmental constraints. In this study, our aim was to understand how microbial activities vary at a small spatio-temporal scale in a Mediterranean coastal environment. Microbial activities were monitored in a Pinus halepensis litter collected from two areas, one close to (10 m) and one far from (300 m) the French Mediterranean coast. Litters were transferred from one area to the other using litterbags and studied via different microbial indicators after 2, 5 and 13 months. Microbial Basal Respiration, qCO₂, certain enzyme activities (laccase, cellulase, β-glucosidase and acid phosphatase) and functional diversity via Biolog microplates were assayed in litterbags left in the area of origin as well as in litterbags transferred from one area to the other. Results highlight that microbial activities differ significantly in this short spatial scale over time. The influence of microlocal conditions more intensified for litters situated close to the sea, especially during summer seems to have a stressful effect on microbial communities, leading to less efficient functional activities. However, microbial activities were more strongly influenced by temporal variations linked to seasonality than by location. Copyright © 2014 Elsevier B.V. All rights reserved.

Ecological periodic tables for benthic macrofaunal usage of estuarine habitats: Insights from a case study in Tillamook Bay, Oregon, USA

NASA Astrophysics Data System (ADS)

Ferraro, Steven P.; Cole, Faith A.

2012-05-01

This study validates the ecological relevance of estuarine habitat types to the benthic macrofaunal community and, together with previous similar studies, suggests they can serve as elements in ecological periodic tables of benthic macrofaunal usage in the bioregion. We compared benthic macrofaunal Bray-Curtis similarity and the means of eight benthic macrofaunal community measures across seven habitat types in Tillamook Bay, Oregon, USA: intertidal eelgrass (Zostera marina), dwarf eelgrass (Zostera japonica), oyster (Crassostrea gigas) ground culture, burrowing mud shrimp (Upogebia pugettensis), burrowing ghost shrimp (Neotrypaea californiensis), sand and subtidal. Benthic macrofaunal Bray-Curtis similarity differed among all the habitats except ghost shrimp and sand. The habitat rank order on mean benthic macrofaunal species richness, abundance and biomass was dwarf eelgrass ≈ oyster ≥ mud shrimp ≈ eelgrass > sand ≈ ghost shrimp ≈ subtidal. The benthic macrofaunal habitat usage pattern in Tillamook Bay was, with a few exceptions, similar to that in two other US Pacific Northwest estuaries. The exceptions indicate variants of eelgrass and ghost shrimp habitat that differ in benthic macrofaunal usage perhaps due to differences in the coarseness of the sand fraction of the sediments in which they live. The similarities indicate periodic benthic macrofaunal usage patterns across the other habitat types extend over a wider geographic scale and range of environmental conditions than previously known.

Human Stressors Are Driving Coastal Benthic Long-Lived Sessile Fan Mussel Pinna nobilis Population Structure More than Environmental Stressors.

PubMed

Deudero, Salud; Vázquez-Luis, Maite; Álvarez, Elvira

2015-01-01

Coastal degradation and habitat disruption are severely compromising sessile marine species. The fan shell Pinna nobilis is an endemic, vulnerable species and the largest bivalve in the Mediterranean basin. In spite of species legal protection, fan shell populations are declining. Models analyzed the contributions of environmental (mean depth, wave height, maximum wave height, period of waves with high energy and mean direction of wave source) versus human-derived stressors (anchoring, protection status, sewage effluents, fishing activity and diving) as explanatory variables depicting Pinna nobilis populations at a mesoscale level. Human stressors were explaining most of the variability in density spatial distribution of fan shell, significantly disturbing benthic communities. Habitat protection affected P. nobilis structure and physical aggression by anchoring reveals a high impact on densities. Environmental variables instead played a secondary role, indicating that global change processes are not so relevant in coastal benthic communities as human-derived impacts.

Effect of abalone farming on seawater movement and benthic foraminiferal assemblage of Zostera marina in the inner bay of Wando, South Korea.

PubMed

Lee, Yeon Gyu; Choi, Yang Ho; Jeong, Da Un; Lee, Jung Sick; Kim, Yong Wan; Park, Jung Jun; Choi, Jae Ung

2016-08-15

Tidal current survey as well as geochemical and benthic foraminiferal analyses of sediment cores were conducted in an abalone farm and a Zostera bed to understand the degree to which the abalone farm facilities installed along a channel in a shallow sea affect the benthic environment and ecology. In the abalone farm, Ammonia beccarii-Pseudoparrella naraensis-Elphidium somaense-Rosalina globularis-Trochammina hadai and P. naraensis-E. somaense-A. beccarii-T. hadai assemblages appeared owing to an increase in the total nitrogen content from the biodeposits. The Zostera bed consisted of A. beccarii-P. naraensis-Buccella frigida-T. hadai assemblage owing to the gradual expansion of a brackish shallow-water environment by the rapidly decreasing current speed, and it may have flourished. Moreover, the total sulfur, Zn, Cr, and Cu contents in the sediments decreased remarkably more than those of the pre-abalone farming did, caused by the vigorous activity of Zostera marina physiology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Long-term effects of nickel oxide nanoparticles on performance, microbial enzymatic activity, and microbial community of a sequencing batch reactor.

PubMed

Wang, Sen; Li, Zhiwei; Gao, Mengchun; She, Zonglian; Guo, Liang; Zheng, Dong; Zhao, Yangguo; Ma, Bingrui; Gao, Feng; Wang, Xuejiao

2017-02-01

The nitrogen and phosphorus removal, microbial enzymatic activity, and microbial community of a sequencing batch reactor (SBR) were evaluated under long-term exposure to nickel oxide nanoparticles (NiO NPs). High NiO NP concentration (over 5 mg L -1 ) affected the removal of chemical oxygen demand, nitrogen, and phosphorus. The presence of NiO NP inhibited the microbial enzymatic activities and reduced the nitrogen and phosphorus removal rates of activated sludge. The microbial enzymatic activities of the activated sludge showed a similar variation trend to the nitrogen and phosphorus removal rates with the increase in NiO NP concentration from 0 to 60 mg L -1 . The Ni content in the effluent and activated sludge showed an increasing trend with the increase in NiO NP concentration. Some NiO NPs were absorbed on the sludge surface or penetrate the cell membrane into the interior of microbial cells in the activated sludge. NiO NP facilitated the increase in reactive oxygen species by disturbing the balance between the oxidation and anti-oxidation processes, and the variation in lactate dehydrogenase demonstrated that NiO NP could destroy the cytomembrane and cause variations in the microbial morphology and physiological function. High-throughput sequencing demonstrated that the microbial community of SBR had some obvious changes at 0-60 mg L -1 NiO NPs at the phyla, class and genus levels. Copyright © 2016 Elsevier Ltd. All rights reserved.

Distribution, vertical position and ecological implications of shallow gas in Bahía Blanca estuary (Argentina)

NASA Astrophysics Data System (ADS)

Bravo, M. E.; Aliotta, S.; Fiori, S.; Ginsberg, S.

2018-03-01

There has been a growing interest in the study of shallow gas due its importance in relation to the marine environment, climate change and human activities. In Bahía Blanca estuary, Argentina, shallow gas has a wide distribution. Acoustic turbidity and blanking are the main seismic evidence for the presence of shallow gas in the estuary. The former prevails in the inner sector of the estuary where gas is either near or in contact with the seabed. Gas deposits are generally associated with paleochannels corresponding to the Holocene paleodeltaic environment. Distribution studies of shallow gas in this estuary are necessary because its presence implies not only a geological risk for harbor activities but also because it may have noxious effects on the marine ecosystem, mainly on benthic communities. The comparison of benthic communities at a gas site (GS) with those at a control site (CS) indicated that gas could generate impoverishment in terms of individuals' abundance (GS: N = 357; CS: N = 724). Also, diversity indices showed great differences in the community structure at each site. This indicates that methane gas may act as a natural disturbance agent in estuarine ecosystems. The presence of gas in seabed sediments must therefore be taken into account when distribution studies are conducted of estuarine benthic communities.

COMPARISON OF TWO INDICES OF BENTHIC COMMUNITY CONDITION IN CHESAPEAKE BAY

EPA Science Inventory

The Chesapeake Benthic Index of Biotic Integrity (B-IBI) and the EMAP-VP Benthic Index were applied to samples from 239 sites in Chesapeake Bay. The B-IBI weights several community measures equally and uses a simple scoring system while the EMAP-VP Benthic Index uses discriminant...

Using Regional Distribution of Estuarine and Coastal Benthic Invertebrates to Calibrate Benthic Indices of Ecological Condition

EPA Science Inventory

The biogeography of marine benthic macroinvertebrates of the U.S. Atlantic coast from Delaware Bay north to Passamaquoddy Bay, Maine, was studied to define physical-chemical factors affecting broad taxa distributions and provide information needed to calibrate benthic indices of ...

Effects of Soil Organic Matter Properties and Microbial Community Composition on Enzyme Activities in Cryoturbated Arctic Soils

PubMed Central

Schnecker, Jörg; Wild, Birgit; Hofhansl, Florian; Eloy Alves, Ricardo J.; Bárta, Jiří; Čapek, Petr; Fuchslueger, Lucia; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Hofer, Angelika; Kienzl, Sandra; Knoltsch, Anna; Lashchinskiy, Nikolay; Mikutta, Robert; Šantrůčková, Hana; Shibistova, Olga; Takriti, Mounir; Urich, Tim; Weltin, Georg; Richter, Andreas

2014-01-01

Enzyme-mediated decomposition of soil organic matter (SOM) is controlled, amongst other factors, by organic matter properties and by the microbial decomposer community present. Since microbial community composition and SOM properties are often interrelated and both change with soil depth, the drivers of enzymatic decomposition are hard to dissect. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this subduction to test if SOM properties shape microbial community composition, and to identify controls of both on enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acid analysis), was similar in cryoturbated material and in surrounding subsoil, although carbon and nitrogen contents were similar in cryoturbated material and topsoils. This suggests that the microbial community in cryoturbated material was not well adapted to SOM properties. We also measured three potential enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) and used structural equation models (SEMs) to identify direct and indirect drivers of the three enzyme activities. The models included microbial community composition, carbon and nitrogen contents, clay content, water content, and pH. Models for regular horizons, excluding cryoturbated material, showed that all enzyme activities were mainly controlled by carbon or nitrogen. Microbial community composition had no effect. In contrast, models for cryoturbated material showed that enzyme activities were also related to microbial community composition. The additional control of microbial community composition could have restrained enzyme activities and furthermore decomposition in general. The functional decoupling of SOM properties and microbial community composition might thus be one of the reasons for low decomposition rates and the persistence of 400 Gt carbon stored in cryoturbated material. PMID:24705618

A new seepage site south of Svalbard? Results from Eurofleets-2 BURSTER cruise

NASA Astrophysics Data System (ADS)

Giulia Lucchi, Renata; Morigi, Caterina; Sabbatini, Anna; Mazzini, Adriano; Krueger, Martin; de Vittor, Cinzia; Kovacevic, Vedrana; Deponte, Davide; Stefano, Graziani; Bensi, Manuel; Langone, Leonardo; Eurofleets2-Burster*, Scientific Party Of

2017-04-01

The oceanographic and environmental characteristics of the Kveithola Glacial Trough, located south of Svalbard, have been investigated during the Eurofleets2-BURSTER project onboard the German icebreaker Polarstern (expedition PS99-1a, June, 19-20, 2016). The inner part of the glacial trough contains a complex sediment drift that deposited under persistent bottom currents, active in the area after Last Glacial Maximum. Notwithstanding the highly dynamic environment depicted from the morphological and structural characteristics of the Kveithola sediment drift, previous studies indicated the presence of an apparently "stagnant" environment with black anoxic sediments and absence of bottom current related sediment features. We present the preliminary results from the new dataset that includes micropaleontological, geochemical and microbial analyses of multi-core sediments; morphological analyses of sea floor sediments with benthic camera (Ocean Floor Observatory System); acoustic analyses of the sub-bottom record, and oceanographic analyses of CTD-Rosette sampling, all together indicating the possible presence of a new seepage site in the Arctic area south of 75°N Latitude. *Bazzaro, M., Biebow, N., Carbonara, K., Caridi, F., Dominiczak, A., Gamboa Sojo, V.M., Laterza R., Le Gall, C., Musco, M.E., Povea, P., Relitti, F., Ruggiero, L., Rui, L., Sánchez Guillamón, O., Tagliaferro, M., Topchiy, M., Wiberg, D., Zoch, D.

Survival of marine heterotrophic flagellates isolated from the surface and the deep sea at high hydrostatic pressure: Literature review and own experiments

NASA Astrophysics Data System (ADS)

Živaljić, Suzana; Schoenle, Alexandra; Nitsche, Frank; Hohlfeld, Manon; Piechocki, Julia; Reif, Farina; Shumo, Marwa; Weiss, Alexandra; Werner, Jennifer; Witt, Madeleine; Voss, Janine; Arndt, Hartmut

2018-02-01

Although the abyssal seafloor represents the most common benthic environment on Earth, eukaryotic microbial life at abyssal depths is still an uncharted territory. This is in striking contrast to their potential importance regarding the material flux and bacteria consumption in the deep sea. Flagellate genotypes determined from sedimentary DNA deep-sea samples might originate from vital deep-sea populations or from cysts of organisms sedimented down from surface waters. The latter one may have never been active under deep-sea conditions. We wanted to analyze the principal ability of cultivable heterotrophic flagellates of different phylogenetic groups (choanoflagellates, ancyromonads, euglenids, kinetoplastids, bicosoecids, chrysomonads, and cercozoans) to survive exposure to high hydrostatic pressure (up to 670 bar). We summarized our own studies and the few available data from literature on pressure tolerances of flagellates isolated from different marine habitats. Our results demonstrated that many different flagellate species isolated from the surface waters and deep-sea sediments survived drastic changes in hydrostatic pressure. Barophilic behavior was also recorded for several species isolated from the deep sea indicating their possible genetic adaptation to high pressures. This is in accordance with records of heterotrophic flagellates present in environmental DNA surveys based on clone libraries established for deep-sea environments.

Microbial Activity and Silica Degradation in Rice Straw

NASA Astrophysics Data System (ADS)

Kim, Esther Jin-kyung

Abundantly available agricultural residues like rice straw have the potential to be feedstocks for bioethanol production. Developing optimized conditions for rice straw deconstruction is a key step toward utilizing the biomass to its full potential. One challenge associated with conversion of rice straw to bioenergy is its high silica content as high silica erodes machinery. Another obstacle is the availability of enzymes that hydrolyze polymers in rice straw under industrially relevant conditions. Microbial communities that colonize compost may be a source of enzymes for bioconversion of lignocellulose to products because composting systems operate under thermophilic and high solids conditions that have been shown to be commercially relevant. Compost microbial communities enriched on rice straw could provide insight into a more targeted source of enzymes for the breakdown of rice straw polysaccharides and silica. Because rice straw is low in nitrogen it is important to understand the impact of nitrogen concentrations on the production of enzyme activity by the microbial community. This study aims to address this issue by developing a method to measure microbial silica-degrading activity and measure the effect of nitrogen amendment to rice straw on microbial activity and extracted enzyme activity during a high-solids, thermophilic incubation. An assay was developed to measure silica-degrading enzyme or silicase activity. This process included identifying methods of enzyme extraction from rice straw, identifying a model substrate for the assay, and optimizing measurement techniques. Rice straw incubations were conducted with five different levels of nitrogen added to the biomass. Microbial activity was measured by respiration and enzyme activity. A microbial community analysis was performed to understand the shift in community structure with different treatments. With increased levels of nitrogen, respiration and cellulose and hemicellulose degrading activity increased. Silicase activity did not change across nitrogen treatments despite a shift in microbial community with varied nitrogen concentration. Samples treated with different nitrogen concentrations had similar levels of diversity, however the microbial community composition differed with added nitrogen. The results demonstrated that adding nitrogen to rice straw during thermophilic decomposition nurtured a more active microbial community and promoted enzyme secretion thus improving the ability to discover enzymes for rice straw deconstruction. These results can inform future experiments for cultivating a unique, thriving compost-derived microbial community that can successfully decompose rice straw. Understanding the silicase activity of microorganisms may alleviate the challenges associated with silica in various feedstocks.

Microbenthic community structure and trophic status of sediments in the Mar Piccolo of Taranto (Mediterranean, Ionian Sea).

PubMed

Rubino, F; Cibic, T; Belmonte, M; Rogelja, M

2016-07-01

This study aimed to assess the benthic ecosystem trophic status in a heavily polluted marine area and the response of the microbenthic community to multiple and diffuse anthropogenic impacts, integrating information coming from the active and resting (plankton's cysts) components of microbenthos. Two sampling campaigns were carried out in the period 2013-2014 and four sampling sites at different levels of industrial contamination were chosen within the first and second inlet of the Mar Piccolo of Taranto. The chemical contamination affected to a higher extent the active microbenthos than the resting one. In the central part of the first inlet, characterised by more marine features, thrives a very rich and biodiverse microbenthic community. In contrast, at the polluted site near the military navy arsenal, extremely low densities (9576 ± 1732 cells cm(-3)) were observed for active microbenthos, but not for the resting community. Here, the high level of contamination selected for tychopelagic diatom species, i.e., thriving just above the surface sediments, while the other life forms died or moved away. Following the adoption of a 10 μm mesh, for the first time, resting spores produced by small diatoms of the genus Chaetoceros were found. Our results further indicate that although the Mar Piccolo is very shallow, the benthic system is scarcely productive, likely as a consequence of the accumulated contaminants in the surface sediments that probably interfere with the proper functioning of the benthic ecosystem.

Capturing the genetic makeup of the active microbiome in situ.

PubMed

Singer, Esther; Wagner, Michael; Woyke, Tanja

2017-09-01

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.

Capturing the genetic makeup of the active microbiome in situ

PubMed Central

Singer, Esther; Wagner, Michael; Woyke, Tanja

2017-01-01

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions. PMID:28574490

[Effects of bio-crust on soil microbial biomass and enzyme activities in copper mine tailings].

PubMed

Chen, Zheng; Yang, Gui-de; Sun, Qing-ye

2009-09-01

Bio-crust is the initial stage of natural primary succession in copper mine tailings. With the Yangshanchong and Tongguanshan copper mine tailings in Tongling City of Anhui Province as test objects, this paper studied the soil microbial biomass C and N and the activities of dehydrogenase, catalase, alkaline phosphatase, and urease under different types of bio-crust. The bio-crusts improved the soil microbial biomass and enzyme activities in the upper layer of the tailings markedly. Algal crust had the best effect in improving soil microbial biomass C and N, followed by moss-algal crust, and moss crust. Soil microflora also varied with the type of bio-crust. No'significant difference was observed in the soil enzyme activities under the three types of bio-crust. Soil alkaline phosphatase activity was significantly positively correlated with soil microbial biomass and dehydrogenase and urease activities, but negatively correlated with soil pH. In addition, moss rhizoid could markedly enhance the soil microbial biomass and enzyme activities in moss crust rhizoid.

Effects of plastic film residues on occurrence of phthalates and microbial activity in soils.

PubMed

Wang, Jun; Lv, Shenghong; Zhang, Manyun; Chen, Gangcai; Zhu, Tongbin; Zhang, Shen; Teng, Ying; Christie, Peter; Luo, Yongming

2016-05-01

Plastic film mulching has played an important role in Chinese agriculture, especially in vegetable production, but large amounts of film residues can accumulate in the soil. The present study investigated the effects of plastic film residues on the occurrence of soil PAEs and microbial activities using a batch pot experiment. PAE concentrations increased with increasing plastic film residues but the soil microbial carbon and nitrogen, enzyme activities and microbial diversity decreased significantly. At the end of the experiment the PAE concentrations were 0-2.02 mg kg(-1) in the different treatments. Soil microbial C and N, enzyme activities, AWCD value, and Shannon-Weaver and Simpson indices declined by about 28.9-76.2%, 14.9-59.0%, 4.9-22.7%, 23.0-42.0% and 1.8-18.7%, respectively. Soil microbial activity was positively correlated with soil PAE concentration, and soil PAE concentrations were impacted by plastic color and residue volume. Correlations among, and molecular mechanisms of, plastic film residues, PAE occurrence and microbial activity require further study. Copyright © 2016 Elsevier Ltd. All rights reserved.

Benthic protists: the under-charted majority.

PubMed

Forster, Dominik; Dunthorn, Micah; Mahé, Fréderic; Dolan, John R; Audic, Stéphane; Bass, David; Bittner, Lucie; Boutte, Christophe; Christen, Richard; Claverie, Jean-Michel; Decelle, Johan; Edvardsen, Bente; Egge, Elianne; Eikrem, Wenche; Gobet, Angélique; Kooistra, Wiebe H C F; Logares, Ramiro; Massana, Ramon; Montresor, Marina; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C; Romac, Sarah; Shalchian-Tabrizi, Kamran; Simon, Nathalie; Richards, Thomas A; Santini, Sébastien; Sarno, Diana; Siano, Raffaele; Vaulot, Daniel; Wincker, Patrick; Zingone, Adriana; de Vargas, Colomban; Stoeck, Thorsten

2016-08-01

Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Interactive effects of wildfire and permafrost on microbial communities and soil processes in an Alaskan black spruce forest

USGS Publications Warehouse

Waldrop, M.P.; Harden, J.W.

2008-01-01

Boreal forests contain significant quantities of soil carbon that may be oxidized to CO2 given future increases in climate warming and wildfire behavior. At the ecosystem scale, decomposition and heterotrophic respiration are strongly controlled by temperature and moisture, but we questioned whether changes in microbial biomass, activity, or community structure induced by fire might also affect these processes. We particularly wanted to understand whether postfire reductions in microbial biomass could affect rates of decomposition. Additionally, we compared the short-term effects of wildfire to the long-term effects of climate warming and permafrost decline. We compared soil microbial communities between control and recently burned soils that were located in areas with and without permafrost near Delta Junction, AK. In addition to soil physical variables, we quantified changes in microbial biomass, fungal biomass, fungal community composition, and C cycling processes (phenol oxidase enzyme activity, lignin decomposition, and microbial respiration). Five years following fire, organic surface horizons had lower microbial biomass, fungal biomass, and dissolved organic carbon (DOC) concentrations compared with control soils. Reductions in soil fungi were associated with reductions in phenol oxidase activity and lignin decomposition. Effects of wildfire on microbial biomass and activity in the mineral soil were minor. Microbial community composition was affected by wildfire, but the effect was greater in nonpermafrost soils. Although the presence of permafrost increased soil moisture contents, effects on microbial biomass and activity were limited to mineral soils that showed lower fungal biomass but higher activity compared with soils without permafrost. Fungal abundance and moisture were strong predictors of phenol oxidase enzyme activity in soil. Phenol oxidase enzyme activity, in turn, was linearly related to both 13C lignin decomposition and microbial respiration in incubation studies. Taken together, these results indicate that reductions in fungal biomass in postfire soils and lower soil moisture in nonpermafrost soils reduced the potential of soil heterotrophs to decompose soil carbon. Although in the field increased rates of microbial respiration can be observed in postfire soils due to warmer soil conditions, reductions in fungal biomass and activity may limit rates of decomposition. ?? 2008 The Authors Journal compilation ?? 2008 Blackwell Publishing.

Virus-host interactions and their roles in coral reef health and disease.

PubMed

Thurber, Rebecca Vega; Payet, Jérôme P; Thurber, Andrew R; Correa, Adrienne M S

2017-04-01

Coral reefs occur in nutrient-poor shallow waters, constitute biodiversity and productivity hotspots, and are threatened by anthropogenic disturbance. This Review provides an introduction to coral reef virology and emphasizes the links between viruses, coral mortality and reef ecosystem decline. We describe the distinctive benthic-associated and water-column- associated viromes that are unique to coral reefs, which have received less attention than viruses in open-ocean systems. We hypothesize that viruses of bacteria and eukaryotes dynamically interact with their hosts in the water column and with scleractinian (stony) corals to influence microbial community dynamics, coral bleaching and disease, and reef biogeochemical cycling. Last, we outline how marine viruses are an integral part of the reef system and suggest that the influence of viruses on reef function is an essential component of these globally important environments.

Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes

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

Wong, Hon Lun; Visscher, Pieter T.; White, III, Richard Allen

Modern microbial mats provide remarkable insights into assembly, function and origin of complex microbial ecosystems. An excellent model of such systems is located in Shark Bay, Australia. Although bacteria have been extensively investigated in these communities, the role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of specific niches associated with this domain. In the present study, high throughput amplicon sequencing was undertaken in conjunction with key biogeochemical properties of two mat types (smooth and pustular). A total of 13,547,552 unfiltered sequences were obtained, and classified sequences weremore » affiliated to three archaeal and candidate phyla, Parvarchaeota, Euryarchaeota and Crenarchaeota. One way analysis of similarity tests (ANOSIM) indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1 %). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota, followed by Thermoplasmata, Class marine benthic group B and Halobacteria. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Conversely, pustular mats were enriched with Halobacteria and Parvarchaeota. The rates of oxygen production/consumption as well as sulphate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic part of mats and was up to seven-fold higher in smooth than in pustular mats. Metabolic cooperation in putative surface anoxic niches is proposed to be key in efficient cycling of key nutrients in these systems.« less

Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes

DOE PAGES

Wong, Hon Lun; Visscher, Pieter T.; White, III, Richard Allen; ...

2017-04-11

Modern microbial mats provide remarkable insights into assembly, function and origin of complex microbial ecosystems. An excellent model of such systems is located in Shark Bay, Australia. Although bacteria have been extensively investigated in these communities, the role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of specific niches associated with this domain. In the present study, high throughput amplicon sequencing was undertaken in conjunction with key biogeochemical properties of two mat types (smooth and pustular). A total of 13,547,552 unfiltered sequences were obtained, and classified sequences weremore » affiliated to three archaeal and candidate phyla, Parvarchaeota, Euryarchaeota and Crenarchaeota. One way analysis of similarity tests (ANOSIM) indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1 %). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota, followed by Thermoplasmata, Class marine benthic group B and Halobacteria. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Conversely, pustular mats were enriched with Halobacteria and Parvarchaeota. The rates of oxygen production/consumption as well as sulphate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic part of mats and was up to seven-fold higher in smooth than in pustular mats. Metabolic cooperation in putative surface anoxic niches is proposed to be key in efficient cycling of key nutrients in these systems.« less

Reticulamoeba Is a Long-Branched Granofilosean (Cercozoa) That Is Missing from Sequence Databases

PubMed Central

Bass, David; Yabuki, Akinori; Santini, Sébastien; Romac, Sarah; Berney, Cédric

2012-01-01

We sequenced the 18S ribosomal RNA gene of seven isolates of the enigmatic marine amoeboflagellate Reticulamoeba Grell, which resolved into four genetically distinct Reticulamoeba lineages, two of which correspond to R. gemmipara Grell and R. minor Grell, another with a relatively large cell body forming lacunae, and another that has similarities to both R. minor and R. gemmipara but with a greater propensity to form cell clusters. These lineages together form a long-branched clade that branches within the cercozoan class Granofilosea (phylum Cercozoa), showing phylogenetic affinities with the genus Mesofila. The basic morphology of Reticulamoeba is a roundish or ovoid cell with a more or less irregular outline. Long and branched reticulopodia radiate from the cell. The reticulopodia bear granules that are bidirectionally motile. There is also a biflagellate dispersal stage. Reticulamoeba is frequently observed in coastal marine environmental samples. PCR primers specific to the Reticulamoeba clade confirm that it is a frequent member of benthic marine microbial communities, and is also found in brackish water sediments and freshwater biofilm. However, so far it has not been found in large molecular datasets such as the nucleotide database in NCBI GenBank, metagenomic datasets in Camera, and the marine microbial eukaryote sampling and sequencing consortium BioMarKs, although closely related lineages can be found in some of these datasets using a highly targeted approach. Therefore, although such datasets are very powerful tools in microbial ecology, they may, for several methodological reasons, fail to detect ecologically and evolutionary key lineages. PMID:23226495

Plant community influence on soil microbial response after a wildfire in Sierra Nevada National Park (Spain).

PubMed

Bárcenas-Moreno, Gema; García-Orenes, Fuensanta; Mataix-Solera, Jorge; Mataix-Beneyto, Jorge

2016-12-15

Plant community influence on microbial response after fire has been studied in a Sierra Nevada National Park area affected by a wildfire in 2005. Two different plant communities adapted to different altitudes were selected to analyse possible differences on soil microbial recolonisation process after fire, in oak forest and high mountain shrub communities. Microbial abundance, activity and community composition were monitored to evaluate medium-term changes. Microbial abundance was studied by mean of microbial biomass carbon and plate count methods; microbial activity was analysed by microbial respiration and bacterial growth while microbial community composition was determined by analysing phospholipid fatty acid pattern. Under unburnt conditions oak forest showed higher nutrient content, pH and microbial abundance and activity values than the high mountain shrubs community. Different parameters studied showed different trends with time, highlighting important changes in microbial community composition in high mountain shrubs from first sampling to the second one. Post-fire recolonisation process was different depending on plant community studied. Highlighting fungal response and microbial activity were stimulated in burnt high mountain shrubs community whilst it was negatively affected in oak forest. Fire induced changes in oak forest were almost neutralized 20months after the fire, while high mountain shrubs community still showed fire-induced changes at the end of the study. Copyright © 2016 Elsevier B.V. All rights reserved.

Compound-Specific Amino Acid Isotopic Analysis of Benthic Food Webs in the Chukchi Sea

NASA Astrophysics Data System (ADS)

Zhang, M.; Cooper, L. W.; Biasatti, D. M.; Grebmeier, J. M.

2014-12-01

The Chukchi Sea is known for locally high standing stocks of benthic macrofauna and strong coupling between pelagic-benthic components of the ecosystem. However, benthic food structure is not fully understood, due to varied sources of particulate organic matter (POM) and the high diversity of benthic invertebrates. We provide the first demonstration of the application of compound-specific amino acid isotope analysis to study the dietary sources and trophic structure for this Arctic marginal sea. About 20 stations in Chukchi Sea were sampled during cruises in August of 2012 and 2013. At each station, phytoplankton, POM and benthic fauna were collected, processed and analyzed using GC-C-IRMS (gas chromatography-combustion-isotope ratio mass spectrometry). Among benthic fauna, dominant species included the following taxonomic groups: Ophiuroidea, Amphipoda, Polychaeta, Gastropoda, Bivalvia, and Cnidaria. The benthic fauna showed similar patterns of individual amino acid δ13C, with glycine the most enriched in 13C and leucine the most depleted in 13C. Specific amino acids including phenylalanine showed spatial variability in δ13C and δ15N values within the sampled area, indicating contributions of different dietary sources including phytoplankton, sea ice algae, benthic algae and terrestrial organic materials. δ15N values of individual amino acids such as the difference between glutamic acid and phenylalanine, i.e. Δ15Nglu-phe (δ15Nglu - δ15Nphe), were also used to identify trophic levels of benthic invertebrates relative to estimates available from bulk δ15N values. These data will ultimately be used to evaluate the spatial variability of organic carbon sources and trophic level interactions of dominant benthic species in the Chukchi Sea.

A decline in benthic foraminifera following the deepwater horizon event in the northeastern Gulf of Mexico.

PubMed

Schwing, Patrick T; Romero, Isabel C; Brooks, Gregg R; Hastings, David W; Larson, Rebekka A; Hollander, David J

2015-01-01

Sediment cores were collected from three sites (1000-1200 m water depth) in the northeastern Gulf of Mexico from December 2010 to June 2011 to assess changes in benthic foraminiferal density related to the Deepwater Horizon (DWH) event (April-July 2010, 1500 m water depth). Short-lived radioisotope geochronologies (²¹⁰Pb, ²³⁴Th), organic geochemical assessments, and redox metal concentrations were determined to relate changes in sediment accumulation rate, contamination, and redox conditions with benthic foraminiferal density. Cores collected in December 2010 indicated a decline in density (80-93%). This decline was characterized by a decrease in benthic foraminiferal density and benthic foraminiferal accumulation rate (BFAR) in the surface 10 mm relative to the down-core mean in all benthic foraminifera, including the dominant genera (Bulimina spp., Uvigerina spp., and Cibicidoides spp.). Cores collected in February 2011 documented a site-specific response. There was evidence of a recovery in the benthic foraminiferal density and BFAR at the site closest to the wellhead (45 NM, NE). However, the site farther afield (60 NM, NE) recorded a continued decline in benthic foraminiferal density and BFAR down to near-zero values. This decline in benthic foraminiferal density occurred simultaneously with abrupt increases in sedimentary accumulation rates, polycyclic aromatic hydrocarbon (PAH) concentrations, and changes in redox conditions. Persistent reducing conditions (as many as 10 months after the event) in the surface of these core records were a possible cause of the decline. Another possible cause was the increase (2-3 times background) in PAH's, which are known to cause benthic foraminifera mortality and inhibit reproduction. Records of benthic foraminiferal density coupled with short-lived radionuclide geochronology and organic geochemistry were effective in quantifying the benthic response and will continue to be a valuable tool in determining the long-term effects of the DWH event on a larger spatial scale.

A Decline in Benthic Foraminifera following the Deepwater Horizon Event in the Northeastern Gulf of Mexico

PubMed Central

Schwing, Patrick T.; Romero, Isabel C.; Brooks, Gregg R.; Hastings, David W.; Larson, Rebekka A.; Hollander, David J.

2015-01-01

Sediment cores were collected from three sites (1000–1200 m water depth) in the northeastern Gulf of Mexico from December 2010 to June 2011 to assess changes in benthic foraminiferal density related to the Deepwater Horizon (DWH) event (April-July 2010, 1500 m water depth). Short-lived radioisotope geochronologies (210Pb, 234Th), organic geochemical assessments, and redox metal concentrations were determined to relate changes in sediment accumulation rate, contamination, and redox conditions with benthic foraminiferal density. Cores collected in December 2010 indicated a decline in density (80–93%). This decline was characterized by a decrease in benthic foraminiferal density and benthic foraminiferal accumulation rate (BFAR) in the surface 10 mm relative to the down-core mean in all benthic foraminifera, including the dominant genera (Bulimina spp., Uvigerina spp., and Cibicidoides spp.). Cores collected in February 2011 documented a site-specific response. There was evidence of a recovery in the benthic foraminiferal density and BFAR at the site closest to the wellhead (45 NM, NE). However, the site farther afield (60 NM, NE) recorded a continued decline in benthic foraminiferal density and BFAR down to near-zero values. This decline in benthic foraminiferal density occurred simultaneously with abrupt increases in sedimentary accumulation rates, polycyclic aromatic hydrocarbon (PAH) concentrations, and changes in redox conditions. Persistent reducing conditions (as many as 10 months after the event) in the surface of these core records were a possible cause of the decline. Another possible cause was the increase (2–3 times background) in PAH’s, which are known to cause benthic foraminifera mortality and inhibit reproduction. Records of benthic foraminiferal density coupled with short-lived radionuclide geochronology and organic geochemistry were effective in quantifying the benthic response and will continue to be a valuable tool in determining the long-term effects of the DWH event on a larger spatial scale. PMID:25785988

Simulated leakage of high pCO2 water negatively impacts bivalve dominated infaunal communities from the Western Baltic Sea

NASA Astrophysics Data System (ADS)

Schade, Hanna; Mevenkamp, Lisa; Guilini, Katja; Meyer, Stefanie; Gorb, Stanislav N.; Abele, Doris; Vanreusel, Ann; Melzner, Frank

2016-08-01

Carbon capture and storage is promoted as a mitigation method counteracting the increase of atmospheric CO2 levels. However, at this stage, environmental consequences of potential CO2 leakage from sub-seabed storage sites are still largely unknown. In a 3-month-long mesocosm experiment, this study assessed the impact of elevated pCO2 levels (1,500 to 24,400 μatm) on Cerastoderma edule dominated benthic communities from the Baltic Sea. Mortality of C. edule was significantly increased in the highest treatment (24,400 μatm) and exceeded 50%. Furthermore, mortality of small size classes (0-1 cm) was significantly increased in treatment levels ≥6,600 μatm. First signs of external shell dissolution became visible at ≥1,500 μatm, holes were observed at >6,600 μatm. C. edule body condition decreased significantly at all treatment levels (1,500-24,400 μatm). Dominant meiofauna taxa remained unaffected in abundance. Densities of calcifying meiofauna taxa (i.e. Gastropoda and Ostracoda) decreased in high CO2 treatments (>6,600 μatm), while the non - calcifying Gastrotricha significantly increased in abundance at 24,400 μatm. In addition, microbial community composition was altered at the highest pCO2 level. We conclude that strong CO2 leakage can alter benthic infauna community composition at multiple trophic levels, likely due to high mortality of the dominant macrofauna species C. edule.

Simulated leakage of high pCO2 water negatively impacts bivalve dominated infaunal communities from the Western Baltic Sea.

PubMed

Schade, Hanna; Mevenkamp, Lisa; Guilini, Katja; Meyer, Stefanie; Gorb, Stanislav N; Abele, Doris; Vanreusel, Ann; Melzner, Frank

2016-08-19

Carbon capture and storage is promoted as a mitigation method counteracting the increase of atmospheric CO2 levels. However, at this stage, environmental consequences of potential CO2 leakage from sub-seabed storage sites are still largely unknown. In a 3-month-long mesocosm experiment, this study assessed the impact of elevated pCO2 levels (1,500 to 24,400 μatm) on Cerastoderma edule dominated benthic communities from the Baltic Sea. Mortality of C. edule was significantly increased in the highest treatment (24,400 μatm) and exceeded 50%. Furthermore, mortality of small size classes (0-1 cm) was significantly increased in treatment levels ≥6,600 μatm. First signs of external shell dissolution became visible at ≥1,500 μatm, holes were observed at >6,600 μatm. C. edule body condition decreased significantly at all treatment levels (1,500-24,400 μatm). Dominant meiofauna taxa remained unaffected in abundance. Densities of calcifying meiofauna taxa (i.e. Gastropoda and Ostracoda) decreased in high CO2 treatments (>6,600 μatm), while the non - calcifying Gastrotricha significantly increased in abundance at 24,400 μatm. In addition, microbial community composition was altered at the highest pCO2 level. We conclude that strong CO2 leakage can alter benthic infauna community composition at multiple trophic levels, likely due to high mortality of the dominant macrofauna species C. edule.

Unraveling the interactive effects of climate change and oil contamination on laboratory-simulated estuarine benthic communities.

PubMed

Coelho, Francisco J R C; Cleary, Daniel F R; Rocha, Rui J M; Calado, Ricardo; Castanheira, José M; Rocha, Sílvia M; Silva, Artur M S; Simões, Mário M Q; Oliveira, Vanessa; Lillebø, Ana I; Almeida, Adelaide; Cunha, Ângela; Lopes, Isabel; Ribeiro, Rui; Moreira-Santos, Matilde; Marques, Catarina R; Costa, Rodrigo; Pereira, Ruth; Gomes, Newton C M

2015-05-01

There is growing concern that modifications to the global environment such as ocean acidification and increased ultraviolet radiation may interact with anthropogenic pollutants to adversely affect the future marine environment. Despite this, little is known about the nature of the potential risks posed by such interactions. Here, we performed a multifactorial microcosm experiment to assess the impact of ocean acidification, ultraviolet B (UV-B) radiation and oil hydrocarbon contamination on sediment chemistry, the microbial community (composition and function) and biochemical marker response of selected indicator species. We found that increased ocean acidification and oil contamination in the absence of UV-B will significantly alter bacterial composition by, among other things, greatly reducing the relative abundance of Desulfobacterales, known to be important oil hydrocarbon degraders. Along with changes in bacterial composition, we identified concomitant shifts in the composition of oil hydrocarbons in the sediment and an increase in oxidative stress effects on our indicator species. Interestingly, our study identifies UV-B as a critical component in the interaction between these factors, as its presence alleviates harmful effects caused by the combination of reduced pH and oil pollution. The model system used here shows that the interactive effect of reduced pH and oil contamination can adversely affect the structure and functioning of sediment benthic communities, with the potential to exacerbate the toxicity of oil hydrocarbons in marine ecosystems. © 2014 John Wiley & Sons Ltd.

Clam dredging effects and subsequent recovery of benthic communities at different depth ranges.

PubMed

Constantino, R; Gaspar, M B; Tata-Regala, J; Carvalho, S; Cúrdia, J; Drago, T; Taborda, R; Monteiro, C C

2009-03-01

This study aimed to assess the potential effects of clam dredging and the subsequent recovery of the benthic environment. Two experimental areas located at 6 and 18m depth were established in order to analyse whether impacts and recovery of benthic environment are depth-related. Study areas were located within an area closed to dredging and two different plots were established at both depths. One of the plots was subjected to intense clam dredge-fishing, while the other was undisturbed and therefore used as control. Sampling followed a BACI design, with samples for macrobenthic, meiobenthic and sediment particle size analysis being taken by SCUBA divers from both areas before and after fishing stress. For both depths, impacts on the benthic environment were very low resulting in high recovery rates. Nevertheless, at shallower depths communities demonstrated a faster recovery. It was shown that depending on the faunal component used as a bioindicator, different results can be observed. Generally deposit-feeding organisms with scales or chitinous plates and vermiform shape (mainly crustaceans, polychaetes and ophiuroids), without external protection, were the most affected by dredging, while some polychaetes without external protection and with a carnivorous feeding mode seemed to be enhanced by fishing. The low level of perturbations induced by the dredging activities was comparable to the impact of surface waves on the bottom, as experiments were undertaken in wave-dominated environments. The coexistence of storm events during the study period proved to have similar or even more deleterious effects on the benthic environment. It appears that communities from hydrodynamic fishing grounds that are well adapted to natural physical stress are not highly affected by dredging.

Relationships between lines of evidence of pollution in estuarine areas: Linking contaminant levels with biomarker responses in mussels and with structure of macroinvertebrate benthic communities.

PubMed

De Los Ríos, A; Echavarri-Erasun, B; Lacorte, S; Sánchez-Ávila, J; De Jonge, M; Blust, R; Orbea, A; Juanes, J A; Cajaraville, M P

2016-10-01

Data obtained in a pollution survey performed in estuarine areas were integrated using multivariate statistics. The sites selected for the study were areas affected by treated and untreated urban discharges, harbours or industrial activities as well as reference sites. Mussels were transplanted to each site and after different times of exposure, samples of water, sediments and mussels were collected. Biomarkers were analysed on mussels after 3 and 21 days of transplant whereas concentrations of contaminants were measured in water, sediments and mussels after 21 days of transplant. The structure of macroinvertebrate benthic communities was studied in sediment samples. Studied variables were organised into 5 datasets, each one constituting a line of evidence (LOE): contaminants in water, contaminants in sediments, contaminants accumulated by transplanted mussels, biomarkers in transplanted mussels and changes in the structure of macroinvertebrate benthic communities of each sampling site. Principal Component Analysis (PCA) identified the variables of each LOE best explaining variability among sites. In order to know how LOEs relate to each other, Pearson's correlations were performed. Contaminants in sediments were not correlated with the rest of LOEs. Contaminants in water were significantly correlated with contaminants and biomarkers in mussels and with structure of macroinvertebrate benthic communities. Similarly, significant correlations were found between contaminants and biomarkers in mussels and between biomarkers in mussels and structure of macroinvertebrate benthic communities. In conclusion, biomarker responses give relevant information on pollution in estuarine areas and provide a link between chemical and ecological statuses of water bodies in the context of the Water Framework Directive. Copyright © 2016 Elsevier Ltd. All rights reserved.

The resistance of the active microbiome as a fundamental compartment of soil quality in the face of climate change

NASA Astrophysics Data System (ADS)

Bastida, Felipe; Andrés, Manuela; Torres, Irene; García, Carlos; Ruiz Navarro, Antonio; Moreno, Francisco R.; López Serrano, Francisco R.

2017-04-01

Arid and semiarid ecosystems will be severely affected by drought derived from climate change. Forest management can promote the adaptations of plant and microbial communities to drought. For instance, thinning reduces competition for resources through a decrease in tree density and the promotion of plant survival. The resistance of soil microbial communities must be strongly related to the soil quality. However, in order to evaluate these properties, the active (and not only the total) microbial community should be carefully assessed. Here, we studied the functional and phylogenetic responses of the microbial community to six years of drought induced by rainfall exclusion and how thinning shapes its resistance to drought, in a semiarid ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel strategies against drought. The diversity and the composition of the total and active soil microbial communities were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially-mediated ecosystem multifunctionality was studied by the evaluation of enzyme activities related to C, N, and P dynamics. The microbial biomass and ecosystem multifunctionality decreased in plots subjected to drought, but this decrease was greater in unthinned plots. The diversity of the total bacterial and fungal communities were resistant to drought but were shaped by seasonal dynamics. However, the active community was more sensitive to drought and related to multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of multifunctionality to drought by changes in the active microbiome. Protein-based phylogeny was a better predictor of the impacts of drought and the adaptations of microbial communities. We highlight that the resistance of the microbial community and the active microbial community are ecological concepts strongly related to the concept of soil quality in the face of climate change.

Effect of Malathion on the Microbial Ecology of Activated Sludge

DTIC Science & Technology

2015-03-26

EFFECT OF MALATHION ON THE MICROBIAL ECOLOGY OF ACTIVATED SLUDGE THESIS Seth K. Martin, Senior Master Sergeant, USAF AFIT-ENV-MS-15-M-095 DEPARTMENT...Government and is not subject to copyright protection in the United States. AFIT-ENV-MS-15-M-095 EFFECT OF MALATHION ON THE MICROBIAL ECOLOGY OF ACTIVATED...UNLIMITED. AFIT-ENV-MS-15-M-095 EFFECT OF MALATHION ON THE MICROBIAL ECOLOGY OF ACTIVATED SLUDGE THESIS Seth K. Martin, B.S. Senior Master Sergeant

A Comparison of Response Surface Methodology and a One-Factor-At-A-Time Approach as Calibration Techniques for the Bioplume-II Simulation Model of Contaminant Biodegradation

DTIC Science & Technology

1995-12-01

Technology, 26:1404-1410 (July 1992). 4. Atlas , Ronald M. and Richard Bartha . Microbial Ecology , Fundamentals and Applica- tions (3rd Edition). Redwood... microbial metabolic activity. Leahy and Colwell (35:307) note the impact of physical factors on microbial activity. They cite research by Atlas and... Bartha observing that low temperatures inhibit microbial activity and research by Bossert and Bartha observing that higher temperatures increase activity

Long-term recovery of a Mountain Stream from Clearcut Logging: The Effects of Forest Succession on Benthic Invertebrate Community Structure

Treesearch

Michael K. Stone; J. Bruce Wallace

1998-01-01

Summary1. Changes in benthic invertebrate community structure following 16 years of forest succession after logging were examined by estimating benthic invertebrate abundance, biomass and secondary production in streams draining a forested reference and a recovering clear-cut catchment. Benthic invertebrate abundance was three times higher,...

[Characteristics of soil microbes and enzyme activities in different degraded alpine meadows].

PubMed

Yin, Ya Li; Wang, Yu Qin; Bao, Gen Sheng; Wang, Hong Sheng; Li, Shi Xiong; Song, Mei Ling; Shao, Bao Lian; Wen, Yu Cun

2017-12-01

Soil microbial biomass C and N, microbial diversities and enzyme activity in 0-10 cm and 10-20 cm soil layers of different degraded grasslands (non-degradation, ND; light degradation, LD; moderate degradation, MD; sever degradation, SD; and black soil beach, ED) were measured by Biolog and other methods. The results showed that: 1) There were significant diffe-rences between 0-10 cm and 10-20 cm soil layers in soil microbial biomass, diversities and inver-tase activities in all grasslands. 2) The ratio of soil microbial biomass C to N decreased significantly with the grassland degradation. In the 0-10 cm soil layer, microbial biomass C and N in ND and LD were significantly higher than that in MD, SD and ED. Among the latter three kinds of grasslands, there was no difference for microbial biomass C, but microbial biomass N was lower in MD than in the other grasslands. The average color change rate (AWCD) and McIntosh Index (U) also decreased with grassland degradation, but only the reduction from ND to MD was significant. There were no differences among all grasslands for Shannon index (H) and Simpson Index (D). The urease activity was highest in MD and SD, and the activity of phosphatase and invertase was lowest in ED. In the 10-20 cm soil layer, microbial biomass C in ND and LD were significantly higher than that in the other grasslands. Microbial biomass N in LD and ED were significantly higher than that in the other grasslands. Carbon metabolism index in MD was significantly lower than that in LD and SD. AWCD and U index in ND and LD were significantly higher than that in ED. H index and D index showed no difference among different grasslands. The urease activity in ND and MD was significantly higher than that in the other grasslands. The phosphatase activity was highest in MD, and the invertase activity was lowest in MD. 3) The belowground biomass was significantly positively correlated with microbial biomass, carbon metabolic index and phosphatase activity, and the urease activity was negatively correlated with microbial biomass N, H index and D index.

CO2 leakage alters biogeochemical and ecological functions of submarine sands

PubMed Central

Molari, Massimiliano; Guilini, Katja; Lott, Christian; Weber, Miriam; de Beer, Dirk; Meyer, Stefanie; Ramette, Alban; Wegener, Gunter; Wenzhöfer, Frank; Martin, Daniel; Cibic, Tamara; De Vittor, Cinzia; Vanreusel, Ann; Boetius, Antje

2018-01-01

Subseabed CO2 storage is considered a future climate change mitigation technology. We investigated the ecological consequences of CO2 leakage for a marine benthic ecosystem. For the first time with a multidisciplinary integrated study, we tested hypotheses derived from a meta-analysis of previous experimental and in situ high-CO2 impact studies. For this, we compared ecological functions of naturally CO2-vented seafloor off the Mediterranean island Panarea (Tyrrhenian Sea, Italy) to those of nonvented sands, with a focus on biogeochemical processes and microbial and faunal community composition. High CO2 fluxes (up to 4 to 7 mol CO2 m−2 hour−1) dissolved all sedimentary carbonate, and comigration of silicate and iron led to local increases of microphytobenthos productivity (+450%) and standing stocks (+300%). Despite the higher food availability, faunal biomass (−80%) and trophic diversity were substantially lower compared to those at the reference site. Bacterial communities were also structurally and functionally affected, most notably in the composition of heterotrophs and microbial sulfate reduction rates (−90%). The observed ecological effects of CO2 leakage on submarine sands were reproduced with medium-term transplant experiments. This study assesses indicators of environmental impact by CO2 leakage and finds that community compositions and important ecological functions are permanently altered under high CO2. PMID:29441359

Search for Martian fossil communities: Science strategies, sediment sites, and sample handling

NASA Technical Reports Server (NTRS)

Desmarais, David J.

1988-01-01

The strategy for locating and sampling possible fossilized Martian organisms benefits from our experience with fossil microbial ecosystems on Earth. Evidence of early life is typically preserved as stromatolites in carbonates and cherts, and as microfossils in cherts, carbonates and shales. Stromatolites, which are laminated flat or domal structures built by microbial communities, are very likely the oldest and most widespread relics of early life. These communities flourished in supratidal to subtidal coastal benthic environments, wherever sunlight was available and where incoming sediments were insufficient to bury the communities before they became established. A logical site for such communities on Mars might be those areas in an ancient lake bed which were furthest from sediment input, but were still sufficiently shallow to have received sunlight. Therefore, although some sites within Valles Marineris might have contained ponded water, the possibly abundant sediment inputs might have overwhelmed stromatolite-like communities. Localized depressions which acted as catchment basins for ancient branched valley systems might be superior sites. Perhaps such depressions received drainage which, because of the relatively modest water discharges implied for these streams, was relatively low in transported sediment. Multiple streams converging on a single basin might have been able to maintain a shallow water environment for extended periods of time.

Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes

NASA Astrophysics Data System (ADS)

Robinson, Georgina; Caldwell, Gary S.; Wade, Matthew J.; Free, Andrew; Jones, Clifford L. W.; Stead, Selina M.

2016-12-01

Deposit-feeding invertebrates are proposed bioremediators in microbial-driven sediment-based aquaculture effluent treatment systems. We elucidate the role of the sediment reduction-oxidation (redox) regime in structuring benthic bacterial communities, having direct implications for bioremediation potential and deposit-feeder nutrition. The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated (oxic) and redox stratified (oxic-anoxic). Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments. At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems. This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated.

Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges.

PubMed

Karimi, Elham; Slaby, Beate M; Soares, André R; Blom, Jochen; Hentschel, Ute; Costa, Rodrigo

2018-06-01

Marine sponges are early-branched metazoans known to harbor dense and diverse microbial communities. Yet the role of the so far uncultivable alphaproteobacterial lineages that populate these sessile invertebrates remains unclear. We applied a sequence composition-dependent binning approach to assemble one Rhodospirillaceae genome from the Spongia officinalis microbial metagenome and contrast its functional features with those of closely related sponge-associated and free-living genomes. Both symbiotic and free-living Rhodospirillaceae shared a suite of common features, possessing versatile carbon, nitrogen, sulfur and phosphorus metabolisms. Symbiotic genomes could be distinguished from their free-living counterparts by the lack of chemotaxis and motility traits, enrichment of genes required for the uptake and utilization of organic sulfur compounds-particularly taurine-, higher diversity and abundance of ABC transporters, and a distinct repertoire of genes involved in natural product biosynthesis, plasmid stability, cell detoxification and oxidative stress remediation. These sessile symbionts may more effectively contribute to host fitness via nutrient exchange, and also host detoxification and chemical defense. Considering the worldwide occurrence and high diversity of sponge-associated Rhodospirillaceae verified here using a tailored in silico approach, we suggest that these organisms are not only relevant to holobiont homeostasis but also to nutrient cycling in benthic ecosystems.

Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes

PubMed Central

Robinson, Georgina; Caldwell, Gary S.; Wade, Matthew J.; Free, Andrew; Jones, Clifford L. W.; Stead, Selina M.

2016-01-01

Deposit-feeding invertebrates are proposed bioremediators in microbial-driven sediment-based aquaculture effluent treatment systems. We elucidate the role of the sediment reduction-oxidation (redox) regime in structuring benthic bacterial communities, having direct implications for bioremediation potential and deposit-feeder nutrition. The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated (oxic) and redox stratified (oxic-anoxic). Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments. At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems. This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated. PMID:27941918

Microbes a Tool for the Remediation of Organotin Pollution Determined by Static Headspace Gas Chromatography-Mass Spectrometry.

PubMed

Finnegan, Christopher; Ryan, David; Enright, Anne-Marie; Garcia-Cabellos, Guiomar

2018-03-10

Tributyltin (TBT) is one of the most toxic anthropogenic compounds introduced into the marine environment. Despite its global ban in 2008, TBT is still a problem of great concern due to its high affinity for particulate matter, providing a direct and potentially persistent route of entry into benthic sediments. Bioremediation strategies may constitute an alternative approach to conventional physicochemical methods, benefiting from the microorganism's potential to metabolize anthropogenic compounds. In this work, a simple, precise and accurate static headspace gas chromatography method was developed to investigate the ability of TBT degrading microbes in sedimentary microcosms over a period of 120 days. The proposed method was validated for linearity, repeatability, accuracy, specificity, limit of detection and limit of quantification. The method was subsequently successfully applied for the detection and quantification of TBT and degradation compounds in sediment samples on day 0, 30, 60, 90 and 120 of the experiment employing the principles of green chemistry. On day 120 the concentration of TBT remaining in the microcosms ranged between 91.91 ng/g wet wt for the least effective microbial inoculant to 52.73 ng/g wet wt for the most effective microbial inoculant from a starting concentration of 100 ng/g wet wt.

High-throughput amplicon sequencing and stream benthic bacteria: identifying the best taxonomic level for multiple-stressor research

PubMed Central

Salis, R. K.; Bruder, A.; Piggott, J. J.; Summerfield, T. C.; Matthaei, C. D.

2017-01-01

Disentangling the individual and interactive effects of multiple stressors on microbial communities is a key challenge to our understanding and management of ecosystems. Advances in molecular techniques allow studying microbial communities in situ and with high taxonomic resolution. However, the taxonomic level which provides the best trade-off between our ability to detect multiple-stressor effects versus the goal of studying entire communities remains unknown. We used outdoor mesocosms simulating small streams to investigate the effects of four agricultural stressors (nutrient enrichment, the nitrification inhibitor dicyandiamide (DCD), fine sediment and flow velocity reduction) on stream bacteria (phyla, orders, genera, and species represented by Operational Taxonomic Units with 97% sequence similarity). Community composition was assessed using amplicon sequencing (16S rRNA gene, V3-V4 region). DCD was the most pervasive stressor, affecting evenness and most abundant taxa, followed by sediment and flow velocity. Stressor pervasiveness was similar across taxonomic levels and lower levels did not perform better in detecting stressor effects. Community coverage decreased from 96% of all sequences for abundant phyla to 28% for species. Order-level responses were generally representative of responses of corresponding genera and species, suggesting that this level may represent the best compromise between stressor sensitivity and coverage of bacterial communities. PMID:28327636

CO2 leakage alters biogeochemical and ecological functions of submarine sands.

PubMed

Molari, Massimiliano; Guilini, Katja; Lott, Christian; Weber, Miriam; de Beer, Dirk; Meyer, Stefanie; Ramette, Alban; Wegener, Gunter; Wenzhöfer, Frank; Martin, Daniel; Cibic, Tamara; De Vittor, Cinzia; Vanreusel, Ann; Boetius, Antje

2018-02-01

Subseabed CO 2 storage is considered a future climate change mitigation technology. We investigated the ecological consequences of CO 2 leakage for a marine benthic ecosystem. For the first time with a multidisciplinary integrated study, we tested hypotheses derived from a meta-analysis of previous experimental and in situ high-CO 2 impact studies. For this, we compared ecological functions of naturally CO 2 -vented seafloor off the Mediterranean island Panarea (Tyrrhenian Sea, Italy) to those of nonvented sands, with a focus on biogeochemical processes and microbial and faunal community composition. High CO 2 fluxes (up to 4 to 7 mol CO 2 m -2 hour -1 ) dissolved all sedimentary carbonate, and comigration of silicate and iron led to local increases of microphytobenthos productivity (+450%) and standing stocks (+300%). Despite the higher food availability, faunal biomass (-80%) and trophic diversity were substantially lower compared to those at the reference site. Bacterial communities were also structurally and functionally affected, most notably in the composition of heterotrophs and microbial sulfate reduction rates (-90%). The observed ecological effects of CO 2 leakage on submarine sands were reproduced with medium-term transplant experiments. This study assesses indicators of environmental impact by CO 2 leakage and finds that community compositions and important ecological functions are permanently altered under high CO 2 .

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.

Indicators: Benthic Macroinvertebrates

EPA Pesticide Factsheets

Benthic (meaning “bottom-dwelling”) macroinvertebrates are small aquatic animals and the aquatic larval stages of insects. Benthic macroinvertebrates are commonly used as indicators of the biological condition of waterbodies.

Antifouling activity in some benthic Antarctic invertebrates by "in situ" experiments at Deception Island, Antarctica.

PubMed

Angulo-Preckler, Carlos; Cid, Cristina; Oliva, Francesc; Avila, Conxita

2015-04-01

Competition for space is a remarkable ecological force, comparable to predation, producing a strong selective pressure on benthic invertebrates. Some invertebrates, thus, possess antimicrobial compounds to reduce surface bacterial growth. Antimicrobial inhibition is the first step in avoiding being overgrown by other organisms, which may have a negative impact in feeding, respiration, reproduction … The in situ inhibition of bacterial biofilm was used here as an indicator of antifouling activity by testing hydrophilic extracts of twelve Antarctic invertebrates. Using two different approaches (genetics and confocal techniques) different levels of activity were found in the tested organisms. In fact, differences within body parts of the studied organisms were determined, in agreement with the Optimal Defense Theory. Eight out of 15 extracts tested had negative effects on fouling after 28 days submerged in Antarctic waters. Thus, although chemical defenses may be quite species-specific in their ecological roles, these results suggest that different chemical strategies exist to deal with space competition. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microbial biomass carbon and enzyme activities of urban soils in Beijing.

PubMed

Wang, Meie; Markert, Bernd; Shen, Wenming; Chen, Weiping; Peng, Chi; Ouyang, Zhiyun

2011-07-01

To promote rational and sustainable use of soil resources and to maintain the urban soil quality, it is essential to assess urban ecosystem health. In this study, the microbiological properties of urban soils in Beijing and their spatial distribution patterns across the city were evaluated based on measurements of microbial biomass carbon and urease and invertase activities of the soils for the purpose of assessing the urban ecosystem health of Beijing. Grid sampling design, normal Kriging technique, and the multiple comparisons among different land use types were used in soil sampling and data treatment. The inherent chemical characteristics of urban soils in Beijing, e.g., soil pH, electronic conductivity, heavy metal contents, total N, P and K contents, and soil organic matter contents were detected. The size and diversity of microbial community and the extent of microbial activity in Beijing urban soils were measured as the microbial biomass carbon content and the ratio of microbial biomass carbon content to total soil organic carbon. The microbial community health measured in terms of microbial biomass carbon, urease, and invertase activities varied with the organic substrate and nutrient contents of the soils and were not adversely affected by the presence of heavy metals at p < 0.01. It was shown that the older and the biologically more stable part of city exhibited higher microbial activity levels than the more recently developed part of the city and the road areas of heavy traffic. It was concluded that the land use patterns in Beijing urban soils influenced the nature and activities of the microbial communities.

Lipid Biomarkers for a Hypersaline Microbial Mat Community

NASA Technical Reports Server (NTRS)

Jahnke, Linda; Orphan, Victoria; Embaye, Tsegereda; Turk, Kendra; Kubo, Mike; Summons, Roger

2004-01-01

The use of lipid biomarkers and their carbon isotopic compositions are valuable tools for establishing links to ancient microbial ecosystems. Various lipids associated with specific microbial groups can serve as biomarkers for establishing organism source and function in contemporary microbial ecosystems (membrane lipids), and by analogy, potential relevance to ancient organic-rich sedimentary rocks (geolipids). As witnessed by the stromatolite record, benthic microbial mats grew in shallow water lagoonal environments. Our recent work has focused on lipid biomarker analysis of a potential analogue for such ancient mats growing in a set of hypersaline evaporation ponds at Guerrero Negro, Baja California Sur, Mexico. The aerobic, surface layer of this mat (0 to 1 mm) contained a variety of ester-bound fatty acids (FA) representing a diverse bacterial population including cyanobacteria, sulphate reducers (SRB) and heterotrophs. Biomarkers for microeukaryotes detected in this layer included sterols, C-20 polyunsaturated FA and a highly branched isoprenoid, diagnostic for diatoms. Cyanobacteria were also indicated by the presence of a diagnostic set of mid-chain methylalkanes. C-28, to C-34 wax esters (WXE) present in relatively small amounts in the upper 3 mm of the mat are considered biomarkers for green non-sulphur bacteria. Ether-bound isoprenoids were also identified although in considerably lower abundance than ester-bound FA (approx. 1:l0). These complex ether lipids included archatol, hydroxyarchaeol and a C-40 tetraether, all in small amounts. After ether cleavage with boron tribromide, the major recovered isoprenyl was a C-30:1. This C(sub 30;1) yelded squalane after hydrogenation, a known geobiomarker for hypersaline environments in ancient oils and sediments. In this mat, it represents the dominant Archaeal population. The carbon isotopic composition of biomarker lipids were generally depleted relative to the bulk organic material (delta C-13 TOC -10%). Most depleted were the cyanobacterial methylalkanes at -27% with FA such as the SRB biomarker, 10- methyl C-I6, somewhat heavier at -16%, and WXE at -17%. The C-30:1 isoprenyl was most enriched with delta C-13 in the -7 to -11% range, much too heavy to represent the methanogen population responsible for mat methane values measured at -60%.

Influence of an oyster reef on development of the microbial heterotrophic community of an estuarine biofilm.

PubMed

Nocker, Andreas; Lepo, Joe E; Snyder, Richard A

2004-11-01

We characterized microbial biofilm communities developed over two very closely located but distinct benthic habitats in the Pensacola Bay estuary using two complementary cultivation-independent molecular techniques. Biofilms were grown for 7 days on glass slides held in racks 10 to 15 cm over an oyster reef and an adjacent muddy sand bottom. Total biomass and optical densities of dried biofilms showed dramatic differences for oyster reef versus non-oyster reef biofilms. This study assessed whether the observed spatial variation was reflected in the heterotrophic prokaryotic species composition. Genomic biofilm DNA from both locations was isolated and served as a template to amplify 16S rRNA genes with universal eubacterial primers. Fluorescently labeled PCR products were analyzed by terminal restriction fragment length polymorphism, creating a genetic fingerprint of the composition of the microbial communities. Unlabeled PCR products were cloned in order to construct a clone library of 16S rRNA genes. Amplified ribosomal DNA restriction analysis was used to screen and define ribotypes. Partial sequences from unique ribotypes were compared with existing database entries to identify species and to construct phylogenetic trees representative of community structures. A pronounced difference in species richness and evenness was observed at the two sites. The biofilm community structure from the oyster reef setting had greater evenness and species richness than the one from the muddy sand bottom. The vast majority of the bacteria in the oyster reef biofilm were related to members of the gamma- and delta-subdivisions of Proteobacteria, the Cytophaga-Flavobacterium -Bacteroides cluster, and the phyla Planctomyces and Holophaga-Acidobacterium. The same groups were also present in the biofilm harvested at the muddy sand bottom, with the difference that nearly half of the community consisted of representatives of the Planctomyces phylum. Total species richness was estimated to be 417 for the oyster reef and 60 for the muddy sand bottom, with 10.5% of the total unique species identified being shared between habitats. The results suggest dramatic differences in habitat-specific microbial diversity that have implications for overall microbial diversity within estuaries.

Characterizing the role benthos plays in large coastal seas and estuaries: A modular approach

USGS Publications Warehouse

Tenore, K.R.; Zajac, R.N.; Terwin, J.; Andrade, F.; Blanton, J.; Boynton, W.; Carey, D.; Diaz, R.; Holland, Austin F.; Lopez-Jamar, E.; Montagna, P.; Nichols, F.; Rosenberg, R.; Queiroga, H.; Sprung, M.; Whitlatch, R.B.

2006-01-01

Ecologists studying coastal and estuarine benthic communities have long taken a macroecological view, by relating benthic community patterns to environmental factors across several spatial scales. Although many general ecological patterns have been established, often a significant amount of the spatial and temporal variation in soft-sediment communities within and among systems remains unexplained. Here we propose a framework that may aid in unraveling the complex influence of environmental factors associated with the different components of coastal systems (i.e. the terrestrial and benthic landscapes, and the hydrological seascape) on benthic communities, and use this information to assess the role played by benthos in coastal ecosystems. A primary component of the approach is the recognition of system modules (e.g. marshes, dendritic systems, tidal rivers, enclosed basins, open bays, lagoons). The modules may differentially interact with key forcing functions (e.g. temperature, salinity, currents) that influence system processes and in turn benthic responses and functions. Modules may also constrain benthic characteristics and related processes within certain ecological boundaries and help explain their overall spatio-temporal variation. We present an example of how benthic community characteristics are related to the modular structure of 14 coastal seas and estuaries, and show that benthic functional group composition is significantly related to the modular structure of these systems. We also propose a framework for exploring the role of benthic communities in coastal systems using this modular approach and offer predictions of how benthic communities may vary depending on the modular composition and characteristics of a coastal system. ?? 2006 Elsevier B.V. All rights reserved.

Influence of different forms of acidities on soil microbiological properties and enzyme activities at an acid mine drainage contaminated site.

PubMed

Sahoo, Prafulla Kumar; Bhattacharyya, Pradip; Tripathy, Subhasish; Equeenuddin, Sk Md; Panigrahi, M K

2010-07-15

Assessment of microbial parameters, viz. microbial biomass, fluorescence diacetate, microbial respiration, acid phosphatase, beta-glucosidase and urease with respect to acidity helps in evaluating the quality of soils. This study was conducted to investigate the effects of different forms of acidities on soil microbial parameters in an acid mine drainage contaminated site around coal deposits in Jainta Hills of India. Total potential and exchangeable acidity, extractable and exchangeable aluminium were significantly higher in contaminated soil compared to the baseline (p<0.01). Different forms of acidity were significantly and positively correlated with each other (p<0.05). Further, all microbial properties were positively and significantly correlated with organic carbon and clay (p<0.05). The ratios of microbial parameters with organic carbon were negatively correlated with different forms of acidity. Principal component analysis and cluster analyses showed that the microbial activities are not directly influenced by the total potential acidity and extractable aluminium. Though acid mine drainage affected soils had higher microbial biomass and activities due to higher organic matter content than those of the baseline soils, the ratios of microbial parameters/organic carbon indicated suppression of microbial growth and activities due to acidity stress. 2010 Elsevier B.V. All rights reserved.

Classification of threespine stickleback along the benthic-limnetic axis.

PubMed

Willacker, James J; von Hippel, Frank A; Wilton, Peter R; Walton, Kelly M

2010-11-01

Many species of fish display morphological divergence between individuals feeding on macroinvertebrates associated with littoral habitats (benthic morphotypes) and individuals feeding on zooplankton in the limnetic zone (limnetic morphotypes). Threespine stickleback (Gasterosteus aculeatus L.) have diverged along the benthic-limnetic axis into allopatric morphotypes in thousands of populations and into sympatric species pairs in several lakes. However, only a few well known populations have been studied because identifying additional populations as either benthic or limnetic requires detailed dietary or observational studies. Here we develop a Fisher's linear discriminant function based on the skull morphology of known benthic and limnetic stickleback populations from the Cook Inlet Basin of Alaska and test the feasibility of using this function to identify other morphologically divergent populations. Benthic and limnetic morphotypes were separable using this technique and of 45 populations classified, three were identified as morphologically extreme (two benthic and one limnetic), nine as moderately divergent (three benthic and six limnetic) and the remaining 33 populations as morphologically intermediate. Classification scores were found to correlate with eye size, the depth profile of lakes, and the presence of invasive northern pike (Esox lucius). This type of classification function provides a means of integrating the complex morphological differences between morphotypes into a single score that reflects the position of a population along the benthic-limnetic axis and can be used to relate that position to other aspects of stickleback biology.

Classification of threespine stickleback along the benthic-limnetic axis

PubMed Central

Willacker, James J.; von Hippel, Frank A.; Wilton, Peter R.; Walton, Kelly M.

2010-01-01

Many species of fish display morphological divergence between individuals feeding on macroinvertebrates associated with littoral habitats (benthic morphotypes) and individuals feeding on zooplankton in the limnetic zone (limnetic morphotypes). Threespine stickleback (Gasterosteus aculeatus L.) have diverged along the benthic-limnetic axis into allopatric morphotypes in thousands of populations and into sympatric species pairs in several lakes. However, only a few well known populations have been studied because identifying additional populations as either benthic or limnetic requires detailed dietary or observational studies. Here we develop a Fisher’s linear discriminant function based on the skull morphology of known benthic and limnetic stickleback populations from the Cook Inlet Basin of Alaska and test the feasibility of using this function to identify other morphologically divergent populations. Benthic and limnetic morphotypes were separable using this technique and of 45 populations classified, three were identified as morphologically extreme (two benthic and one limnetic), nine as moderately divergent (three benthic and six limnetic) and the remaining 33 populations as morphologically intermediate. Classification scores were found to correlate with eye size, the depth profile of lakes, and the presence of invasive northern pike (Esox lucius). This type of classification function provides a means of integrating the complex morphological differences between morphotypes into a single score that reflects the position of a population along the benthic-limnetic axis and can be used to relate that position to other aspects of stickleback biology. PMID:21221422

NO3 uptake in shallow, oligotrophic, mountain lakes: The influence of elevated NO3 concentrations

USGS Publications Warehouse

Nydick, K.R.; LaFrancois, B.M.; Baron, Jill S.

2004-01-01

Nutrient enrichment experiments were conducted in 1.2-m deep enclosures in 2 shallow, oligotrophic, mountain lakes. 15N-NO3 isotope tracer was used to compare the importance of phytoplankton and benthic compartments (epilithon, surface sediment [epipelon], and subsurface sediment) for NO3 uptake under high and low NO3 conditions. NO3 uptake approached saturation in the high-N lake, but not in the low-N lake. The capacity of phytoplankton and benthic compartments to take up NO3 differed among treatments and between lakes, and depended on water-column nutrient conditions and the history of NO3 availability. Phytoplankton productivity responded strongly to addition of limiting nutrients, and NO3 uptake was related to phytoplankton biomass and photosynthesis. However, more NO3 usually was taken up by benthic compartments (57–92% combined) than by phytoplankton, even though the response of benthic algal biomass to nutrient additions was less pronounced than that of phytoplankton and benthic NO3 uptake was unrelated to benthic algal biomass. In the low-N lake where NO3 uptake was unsaturated, C content or % was related to NO3 uptake in benthic substrates, suggesting that heterotrophic bacterial processes could be important in benthic NO3 uptake. These results suggest that phytoplankton are most sensitive to nutrient additions, but benthic processes are important for NO3 uptake in shallow, oligotrophic lakes.

Benthic macrofaunal structure and secondary production in tropical estuaries on the Eastern Marine Ecoregion of Brazil.

PubMed

Bissoli, Lorena B; Bernardino, Angelo F

2018-01-01

Tropical estuaries are highly productive and support diverse benthic assemblages within mangroves and tidal flats habitats. Determining differences and similarities of benthic assemblages within estuarine habitats and between regional ecosystems may provide scientific support for management of those ecosystems. Here we studied three tropical estuaries in the Eastern Marine Ecoregion of Brazil to assess the spatial variability of benthic assemblages from vegetated (mangroves) and unvegetated (tidal flats) habitats. A nested sampling design was used to determine spatial scales of variability in benthic macrofaunal density, biomass and secondary production. Habitat differences in benthic assemblage composition were evident, with mangrove forests being dominated by annelids (Oligochaeta and Capitellidae) whereas peracarid crustaceans were also abundant on tidal flats. Macrofaunal biomass, density and secondary production also differed between habitats and among estuaries. Those differences were related both to the composition of benthic assemblages and to random spatial variability, underscoring the importance of hierarchical sampling in estuarine ecological studies. Given variable levels of human impacts and predicted climate change effects on tropical estuarine assemblages in Eastern Brazil, our data support the use of benthic secondary production to address long-term changes and improved management of estuaries in Eastern Brazil.

Benthic macrofaunal structure and secondary production in tropical estuaries on the Eastern Marine Ecoregion of Brazil

PubMed Central

Bissoli, Lorena B.

2018-01-01

Tropical estuaries are highly productive and support diverse benthic assemblages within mangroves and tidal flats habitats. Determining differences and similarities of benthic assemblages within estuarine habitats and between regional ecosystems may provide scientific support for management of those ecosystems. Here we studied three tropical estuaries in the Eastern Marine Ecoregion of Brazil to assess the spatial variability of benthic assemblages from vegetated (mangroves) and unvegetated (tidal flats) habitats. A nested sampling design was used to determine spatial scales of variability in benthic macrofaunal density, biomass and secondary production. Habitat differences in benthic assemblage composition were evident, with mangrove forests being dominated by annelids (Oligochaeta and Capitellidae) whereas peracarid crustaceans were also abundant on tidal flats. Macrofaunal biomass, density and secondary production also differed between habitats and among estuaries. Those differences were related both to the composition of benthic assemblages and to random spatial variability, underscoring the importance of hierarchical sampling in estuarine ecological studies. Given variable levels of human impacts and predicted climate change effects on tropical estuarine assemblages in Eastern Brazil, our data support the use of benthic secondary production to address long-term changes and improved management of estuaries in Eastern Brazil. PMID:29507833

Effects of an oil spill on benthic community production and respiration on subtropical intertidal sandflats.

PubMed

Lee, Li-Hua; Lin, Hsing-Juh

2013-08-15

This study determined effects of an oil spill on subtropical benthic community production and respiration by monitoring CO2 fluxes in benthic chambers on intertidal sandflats during emersion before and after an accidental spill. The oil spill decreased sediment chlorophyll a concentrations, altered benthic macrofaunal community, and affected ecological functioning by suppressing or even stopping microalgal production, increasing bacterial respiration, and causing a shift from an autotrophic system to a heterotrophic system. Effects of the oil spill on the macrofauna were more severe than on benthic microalgae, and affected sedentary infauna more than motile epifauna. Despite the oil spill's impact on the benthic community and carbon metabolism, the affected area appeared to return to normal in about 23 days. Our results suggest that the prompt response of benthic metabolism to exposure to petroleum hydrocarbons can serve as a useful indicator of the impact of an oil spill. Copyright © 2013 Elsevier Ltd. All rights reserved.

Dissolved organic carbon concentration controls benthic primary production: results from in situ chambers in north-temperate lakes

USGS Publications Warehouse

Godwin, Sean C.; Jones, Stuart E.; Weidel, Brian C.; Solomon, Christopher T.

2014-01-01

We evaluated several potential drivers of primary production by benthic algae (periphyton) in north-temperate lakes. We used continuous dissolved oxygen measurements from in situ benthic chambers to quantify primary production by periphyton at multiple depths across 11 lakes encompassing a broad range of dissolved organic carbon (DOC) and total phosphorous (TP) concentrations. Light-use efficiency (primary production per unit incident light) was inversely related to average light availability (% of surface light) in 7 of the 11 study lakes, indicating that benthic algal assemblages exhibit photoadaptation, likely through physiological or compositional changes. DOC alone explained 86% of the variability in log-transformed whole-lake benthic production rates. TP was not an important driver of benthic production via its effects on nutrient and light availability. This result is contrary to studies in other systems, but may be common in relatively pristine north-temperate lakes. Our simple empirical model may allow for the prediction of whole-lake benthic primary production from easily obtained measurements of DOC concentration.

Functional response of an adapted subtidal macrobenthic community to an oil spill: macrobenthic structure and bioturbation activity over time throughout an 18-month field experiment.

PubMed

Gilbert, Franck; Stora, Georges; Cuny, Philippe

2015-10-01

An experimental oil spill was carried out in order to assess in situ responses of a macrobenthic community of shallow subtidal sediments historically exposed to petroleum contamination. Both structural and functional (bioturbation activity) parameters of the community, subjected or not to a pulse acute contamination (25,000 ppm), were studied for 18 months. No difference in the community structure was detected between contaminated and control sediments, from 6 to 18 months of experimentation. Vertical distributions of organisms, however, were affected by the presence of oil contamination leading to a deeper burial of some polychaete species. In the same time, changes in sediment-reworking activity and more especially a deeper particle burying in sediments subjected to acute oil contamination were shown. These results highlight the need to complete the analysis of community structure by assessing functional aspects, such as bioturbation activity, a process integrating various aspects of benthic behaviour (e.g. feeding, locomotion, burrow building) in order to estimate real (structural and functional) and long-term effects of oil contamination on benthic communities.

Limited recovery of soil microbial activity after transient exposure to gasoline vapors.

PubMed

Modrzyński, Jakub J; Christensen, Jan H; Mayer, Philipp; Brandt, Kristian K

2016-09-01

During gasoline spills complex mixtures of toxic volatile organic compounds (VOCs) are released to terrestrial environments. Gasoline VOCs exert baseline toxicity (narcosis) and may thus broadly affect soil biota. We assessed the functional resilience (i.e. resistance and recovery of microbial functions) in soil microbial communities transiently exposed to gasoline vapors by passive dosing via headspace for 40 days followed by a recovery phase of 84 days. Chemical exposure was characterized with GC-MS, whereas microbial activity was monitored as soil respiration (CO2 release) and soil bacterial growth ([(3)H]leucine incorporation). Microbial activity was strongly stimulated and inhibited at low and high exposure levels, respectively. Microbial growth efficiency decreased with increasing exposure, but rebounded during the recovery phase for low-dose treatments. Although benzene, toluene, ethylbenzene and xylene (BTEX) concentrations decreased by 83-97% during the recovery phase, microbial activity in high-dose treatments did not recover and numbers of viable bacteria were 3-4 orders of magnitude lower than in control soil. Re-inoculation with active soil microorganisms failed to restore microbial activity indicating residual soil toxicity, which could not be attributed to BTEX, but rather to mixture toxicity of more persistent gasoline constituents or degradation products. Our results indicate a limited potential for functional recovery of soil microbial communities after transient exposure to high, but environmentally relevant, levels of gasoline VOCs which therefore may compromise ecosystem services provided by microorganisms even after extensive soil VOC dissipation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Capturing the genetic makeup of the active microbiome in situ

DOE PAGES

Singer, Esther; Wagner, Michael; Woyke, Tanja

2017-06-02

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and thatmore » have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.« less

Capturing the genetic makeup of the active microbiome in situ

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

Singer, Esther; Wagner, Michael; Woyke, Tanja

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and thatmore » have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.« less

Intraspecific variation in an Ediacaran skeletal metazoan: Namacalathus from the Nama Group, Namibia.

PubMed

Penny, A M; Wood, R A; Zhuravlev, A Yu; Curtis, A; Bowyer, F; Tostevin, R

2017-01-01

Namacalathus hermanastes is one of the oldest known skeletal metazoans, found in carbonate settings of the terminal Ediacaran (~550-541 million years ago [Ma]). The palaeoecology of this widespread, goblet-shaped, benthic organism is poorly constrained yet critical for understanding the dynamics of the earliest metazoan communities. Analysis of in situ assemblages from the Nama Group, Namibia (~548-541 Ma), shows that Namacalathus exhibited size variation in response to differing water depths, hydrodynamic conditions and substrate types. In low-energy, inner ramp environments, Namacalathus attains the largest average sizes but grew in transient, loosely aggregating, monospecific aggregations attached to microbial mats. In high-energy mid-ramp reefs, Namacalathus spatially segregated into different palaeoecological habitats with distinct size distributions. In outer ramp environments, individuals were small and formed patchy, dense, monospecific aggregations attached to thin microbial mats. Asexual budding is common in all settings. We infer that variations in size distribution in Namacalathus reflect differences in habitat heterogeneity and stability, including the longevity of mechanically stable substrates and oxic conditions. In the Nama Group, long-lived skeletal metazoan communities developed within topographically heterogeneous mid-ramp reefs, which provided diverse mechanically stable microbial substrates in persistently oxic waters, while inner and outer ramp communities were often ephemeral, developing during fleeting episodes of either oxia and/or substrate stability. We conclude that Namacalathus, which forms a component of these communities in the Nama Group, was a generalist that adapted to various palaeoecological habitats within a heterogeneous ecosystem landscape where favourable conditions persisted, and was also able to opportunistically colonise transiently hospitable environments. These early skeletal metazoans colonised previously unoccupied substrates in thrombolitic reefs and other microbial carbonate settings, and while they experienced relatively low levels of interspecific competition, they were nonetheless adapted to the diverse environments and highly dynamic redox conditions present in the terminal Ediacaran. © 2016 John Wiley & Sons Ltd.

16SrDNA Pyrosequencing of the Mediterranean Gorgonian Paramuricea clavata Reveals a Link among Alterations in Bacterial Holobiont Members, Anthropogenic Influence and Disease Outbreaks

PubMed Central

Vezzulli, Luigi; Pezzati, Elisabetta; Huete-Stauffer, Carla; Pruzzo, Carla; Cerrano, Carlo

2013-01-01

Mass mortality events of benthic invertebrates in the Mediterranean Sea are becoming an increasing concern with catastrophic effects on the coastal marine environment. Sea surface temperature anomalies leading to physiological stress, starvation and microbial infections were identified as major factors triggering animal mortality. However the highest occurrence of mortality episodes in particular geographic areas and occasionally in low temperature deep environments suggest that other factors play a role as well. We conducted a comparative analysis of bacterial communities associated with the purple gorgonian Paramuricea clavata, one of the most affected species, collected at different geographic locations and depth, showing contrasting levels of anthropogenic disturbance and health status. Using massive parallel 16SrDNA gene pyrosequencing we showed that the bacterial community associated with healthy P. clavata in pristine locations was dominated by a single genus Endozoicomonas within the order Oceanospirillales which represented ∼90% of the overall bacterial community. P. clavata samples collected in human impacted areas and during disease events had higher bacterial diversity and abundance of disease-related bacteria, such as vibrios, than samples collected in pristine locations whilst showed a reduced dominance of Endozoicomonas spp. In contrast, bacterial symbionts exhibited remarkable stability in P. clavata collected both at euphotic and mesophotic depths in pristine locations suggesting that fluctuations in environmental parameters such as temperature have limited effect in structuring the bacterial holobiont. Interestingly the coral pathogen Vibrio coralliilyticus was not found on diseased corals collected during a deep mortality episode suggesting that neither temperature anomalies nor recognized microbial pathogens are solely sufficient to explain for the events. Overall our data suggest that anthropogenic influence may play a significant role in determining the coral health status by affecting the composition of the associated microbial community. Environmental stressful events and microbial infections may thus be superimposed to compromise immunity and trigger mortality outbreaks. PMID:23840768

Molecular evidence for a microbial role in ooid formation and preservation of molecular biosignatures in ancient oolite

NASA Astrophysics Data System (ADS)

Mariotti, G.; O'Reilly, S. S.; Winter, A.; Newman, S. A.; Pruss, S. B.; Bosak, T.; Klepac-Ceraj, V.; McDermott, F. P.; Summons, R. E.

2015-12-01

Ooids are concentrically laminated carbonate grains, occurring in a limited number of modern shallow marine and lacustrine settings. Oolitic sedimentary rocks (oolite) are common in the geological record, particularly in the Precambrian, and subsequent to some mass extinction events. Despite their significance, controversy remains about processes that form and shape ooids. Abiotic models typically favour carbonate precipitation in suspension in supersaturated, agitated water while biotic models emphasise microbial benthic contribution to ooid carbonate precipitation in relatively low turbulence waters. While various interpretations of ooids in the geological record have been made, the ongoing formation debate, together with post-depositional diagenesis, hinders our ability to interpret and utilize ooids to reconstruct Earth's past environments and biodiversity. Recently, Neoproterozoic oolitic carbonates have been shown to preserve C-isotopic records of environmental change and carbon cycle anomalies. This prompts the question whether molecular organic biosignatures can be found in well-preserved oolite. Here, lipid biomarker analysis and Illumina sequencing of modern ooids at Pigeon Cay, the Bahamas, revealed colonization of ooids by biofim-producing α-proteobacteria and diatoms, sulfate-reducing bacteria, anoxygenic phototrophs, as well as some cyanobacteria, in calm waters adjacent to the surf zone. These were comparable to communities associated with microbially-cemented grapestones. Relict lipids bound within ooid carbonate were also dominated by bacterial fatty acids, hydroxy acids and hopanoids. This indicates that a common, bacteria-dominated, microbial community is directly involved in carbonate precipitation of ooids and grapestones, likely by autotrophic metabolism and organomineralization of biofilms. Analysis of oolites as old as Jurassic in age revealed the preservation of hydrocarbons, as well as appreciable amounts of fatty acids, and emphasises the potential utility of oolites to preserve organic biosignatures. Further comparison of biomarkers from ooids from different environmental conditions and preservation state will provide insight into syngenetic molecular signals of environmental conditions and biological diversity in ancient oolite.

INDIVIDUAL TURBULENT CELL INTERACTION: BASIS FOR BOUNDARY LAYER ESTABLISHMENT

EPA Science Inventory

Boundary layers are important in determining the forces on objects in flowing fluids, mixing characteristics, and other phenomena. For example, benthic boundary layers are frequently active resuspension layers that determine bottom turbidity and transniissivity. Traditionally, bo...

75 FR 38831 - Repair Kalaupapa Dock Structure: Kalaupapa National Historical Park, Hawaii; Notice of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-06

..., including minor to moderate effects on water quality, benthic resources, coral and essential fish habitats... required for the park's recycling program and other operations and activities). Originally the NPS planned...

Trace fossils and substrates of the terminal Proterozoic–Cambrian transition: Implications for the record of early bilaterians and sediment mixing

PubMed Central

Droser, Mary L.; Jensen, Sören; Gehling, James G.

2002-01-01

The trace fossil record is important in determining the timing of the appearance of bilaterian animals. A conservative estimate puts this time at ≈555 million years ago. The preservational potential of traces made close to the sediment–water interface is crucial to detecting early benthic activity. Our studies on earliest Cambrian sediments suggest that shallow tiers were preserved to a greater extent than typical for most of the Phanerozoic, which can be attributed both directly and indirectly to the low levels of sediment mixing. The low levels of sediment mixing meant that thin event beds were preserved. The shallow depth of sediment mixing also meant that muddy sediments were firm close to the sediment–water interface, increasing the likelihood of recording shallow-tier trace fossils in muddy sediments. Overall, trace fossils can provide a sound record of the onset of bilaterian benthic activity. PMID:12271130

Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils

USGS Publications Warehouse

Waldrop, M.P.; Firestone, M.K.

2006-01-01

Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA) . Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling microbial community composition and function. ?? 2006 Springer Science+Business Media, Inc.

Anti-Bacterial and Anti-Fungal Activity of Xanthones Obtained via Semi-Synthetic Modification of α-Mangostin from Garcinia mangostana.

PubMed

Narasimhan, Srinivasan; Maheshwaran, Shanmugam; Abu-Yousef, Imad A; Majdalawieh, Amin F; Rethavathi, Janarthanam; Das, Prince Edwin; Poltronieri, Palmiro

2017-02-12

The microbial contamination in food packaging has been a major concern that has paved the way to search for novel, natural anti-microbial agents, such as modified α-mangostin. In the present study, twelve synthetic analogs were obtained through semi-synthetic modification of α-mangostin by Ritter reaction, reduction by palladium-carbon (Pd-C), alkylation, and acetylation. The evaluation of the anti-microbial potential of the synthetic analogs showed higher bactericidal activity than the parent molecule. The anti-microbial studies proved that I E showed high anti-bacterial activity whereas I I showed the highest anti-fungal activity. Due to their microbicidal potential, modified α-mangostin derivatives could be utilized as active anti-microbial agents in materials for the biomedical and food industry.

Effects of Benthic Barriers on Macroinvertebrate Communities

DTIC Science & Technology

1993-10-01

Aquatic Plant Control Research Program Effects of Benthic Barriers on Macroinvertebrate Communities by Barry S. Payne, Andrew C. Miller Environmental...Plant Control Technical Report A-93-5Resear h Program Oct ber 1993 Effects of Benthic Barriers on Macroinvertebrate Communities by Barry S. Payne...Effects of benthic barriers on macroinvertebrate communities / by Barry S. Payne, Andrew C. Miller, [and] Thomas Ussery ; prepared for U.S. Army Corps of

Hydrothermal vents and methane seeps: Rethinking the sphere of influence

USGS Publications Warehouse

Levin, Lisa A.; Baco, Amy; Bowden, David; Colaco, Ana; Cordes, Erik E.; Cunha, Marina; Demopoulos, Amanda W.J.; Gobin, Judith; Grupe, Ben; Le, Jennifer; Metaxas, Anna; Netburn, Amanda; Rouse, Greg; Thurber, Andrew; Tunnicliffe, Verena; Van Dover, Cindy L.; Vanreusel, Ann; Watling, Les

2016-01-01

Although initially viewed as oases within a barren deep ocean, hydrothermal vent and methane seep communities are now recognized to interact with surrounding ecosystems on the sea floor and in the water column, and to affect global geochemical cycles. The importance of understanding these interactions is growing as the potential rises for disturbance from oil and gas extraction, seabed mining and bottom trawling. Here we synthesize current knowledge of the nature, extent and time and space scales of vent and seep interactions with background systems. We document an expanded footprint beyond the site of local venting or seepage with respect to elemental cycling and energy flux, habitat use, trophic interactions, and connectivity. Heat and energy are released, global biogeochemical and elemental cycles are modified, and particulates are transported widely in plumes. Hard and biotic substrates produced at vents and seeps are used by “benthic background” fauna for attachment substrata, shelter, and access to food via grazing or through position in the current, while particulates and fluid fluxes modify planktonic microbial communities. Chemosynthetic production provides nutrition to a host of benthic and planktonic heterotrophic background species through multiple horizontal and vertical transfer pathways assisted by flow, gamete release, animal movements, and succession, but these pathways remain poorly known. Shared species, genera and families indicate that ecological and evolutionary connectivity exists among vents, seeps, organic falls and background communities in the deep sea; the genetic linkages with inactive vents and seeps and background assemblages however, are practically unstudied. The waning of venting or seepage activity generates major transitions in space and time that create links to surrounding ecosystems, often with identifiable ecotones or successional stages. The nature of all these interactions is dependent on water depth, as well as regional oceanography and biodiversity. Many ecosystem services are associated with the interactions and transitions between chemosynthetic and background ecosystems, for example carbon cycling and sequestration, fisheries production, and a host of non-market and cultural services. The quantification of the sphere of influence of vents and seeps could be beneficial to better management of deep-sea environments in the face of growing industrialization.

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

Historical assessments and comparisons of benthic communities and physical habitat in two agricultural streams in California's San Joaquin watershed.

PubMed

Hall, Lenwood W; Killen, William D

2006-01-01

This study was designed to assess trends in physical habitat and benthic communities (macroinvertebrates) annually in two agricultural streams (Del Puerto Creek and Salt Slough) in California's San Joaquin Valley from 2001 to 2005, determine the relationship between benthic communities and both water quality and physical habitat from both streams over the 5-year period, and compare benthic communities and physical habitat in both streams from 2001 to 2005. Physical habitat, measured with 10 metrics and a total score, was reported to be fairly stable over 5 years in Del Puerto Creek but somewhat variable in Salt Slough. Benthic communities, measured with 18 metrics, were reported to be marginally variable over time in Del Puerto Creek but fairly stable in Salt Slough. Rank correlation analysis for both water bodies combined showed that channel alteration, embeddedness, riparian buffer, and velocity/depth/diversity were the most important physical habitat metrics influencing the various benthic metrics. Correlations of water quality parameters and benthic community metrics for both water bodies combined showed that turbidity, dissolved oxygen, and conductivity were the most important water quality parameters influencing the different benthic metrics. A comparison of physical habitat metrics (including total score) for both water bodies over the 5-year period showed that habitat metrics were more positive in Del Puerto Creek when compared to Salt Slough. A comparison of benthic metrics in both water bodies showed that approximately one-third of the metrics were significantly different between the two water bodies. Generally, the more positive benthic metric scores were reported in Del Puerto Creek, which suggests that the communities in this creek are more robust than Salt Slough.

Effects of lead contamination on soil microbial activity and rice physiological indices in soil-Pb-rice (Oryza sativa L.) system.

PubMed

Zeng, Lu-Sheng; Liao, Min; Chen, Cheng-Li; Huang, Chang-Yong

2006-10-01

The effect of lead (Pb) treatment on the soil microbial activities (soil microbial biomass and soil basal respiration) and rice physiological indices were studied by greenhouse pot experiment. Pb was applied as lead acetate at six different levels in two different paddy soils, namely 0 (control), 100, 300, 500, 700, 900 mg kg-1 soil. The results showed that the application of Pb at lower level (<300 mg kg-1) as lead acetate resulted in a slight increase in soil microbial activities compared with the control, and had an inhibitory influence at high concentration (>500 mg Pb kg-1 soil), which might be the critical concentration of Pb causing a significant decline in the soil microbial activities. However, the degree of influence on soil microbial activities by Pb was related to the clay and organic matter contents of the soils. On the other hand, when the level of Pb treatments increased to 500 mg kg-1, there was ecological risk for both soil microbial activities and plants. The results also revealed that there was a consistent trend that the chlorophyll contents increased initially, and then decreased gradually with increase in Pb concentration. Pb was effective in inducing proline accumulation and its toxicity causes oxidative stress in rice plants. In a word, soil microbial activities and rice physiological indices, therefore, may be sensitive indicators reflecting environmental stress in soil-Pb-rice system.

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau.

PubMed

Chen, Yong-Liang; Deng, Ye; Ding, Jin-Zhi; Hu, Hang-Wei; Xu, Tian-Le; Li, Fei; Yang, Gui-Biao; Yang, Yuan-He

2017-12-01

Permafrost represents an important understudied genetic resource. Soil microorganisms play important roles in regulating biogeochemical cycles and maintaining ecosystem function. However, our knowledge of patterns and drivers of permafrost microbial communities is limited over broad geographic scales. Using high-throughput Illumina sequencing, this study compared soil bacterial, archaeal and fungal communities between the active and permafrost layers on the Tibetan Plateau. Our results indicated that microbial alpha diversity was significantly higher in the active layer than in the permafrost layer with the exception of fungal Shannon-Wiener index and Simpson's diversity index, and microbial community structures were significantly different between the two layers. Our results also revealed that environmental factors such as soil fertility (soil organic carbon, dissolved organic carbon and total nitrogen contents) were the primary drivers of the beta diversity of bacterial, archaeal and fungal communities in the active layer. In contrast, environmental variables such as the mean annual precipitation and total phosphorus played dominant roles in driving the microbial beta diversity in the permafrost layer. Spatial distance was important for predicting the bacterial and archaeal beta diversity in both the active and permafrost layers, but not for fungal communities. Collectively, these results demonstrated different driving factors of microbial beta diversity between the active layer and permafrost layer, implying that the drivers of the microbial beta diversity observed in the active layer cannot be used to predict the biogeographic patterns of the microbial beta diversity in the permafrost layer. © 2017 John Wiley & Sons Ltd.

Mineralogical impact on long-term patterns of soil nitrogen and phosphorus enzyme activities

NASA Astrophysics Data System (ADS)

Mikutta, Robert; Turner, Stephanie; Meyer-Stüve, Sandra; Guggenberger, Georg; Dohrmann, Reiner; Schippers, Axel

2014-05-01

Soil chronosequences provide a unique opportunity to study microbial activity over time in mineralogical diverse soils of different ages. The main objective of this study was to test the effect of mineralogical properties, nutrient and organic matter availability over whole soil pro-files on the abundance and activity of the microbial communities. We focused on microbio-logical processes involved in nitrogen and phosphorus cycling at the 120,000-year Franz Josef soil chronosequence. Microbial abundances (microbial biomass and total cell counts) and enzyme activities (protease, urease, aminopeptidase, and phosphatase) were determined and related to nutrient contents and mineralogical soil properties. Both, microbial abundances and enzyme activities decreased with soil depth at all sites. In the organic layers, microbial biomass and the activities of N-hydrolyzing enzymes showed their maximum at the intermediate-aged sites, corresponding to a high aboveground biomass. In contrast, the phosphatase activity increased with site age. The activities of N-hydrolyzing enzymes were positively correlated with total carbon and nitrogen contents, whereas the phosphatase activity was negatively correlated with the phosphorus content. In the mineral soil, the enzyme activities were generally low, thus reflecting the presence of strongly sorbing minerals. Sub-strate-normalized enzyme activities correlated negatively to clay content as well as poorly crystalline Al and Fe oxyhydroxides, supporting the view that the evolution of reactive sec-ondary mineral phases alters the activity of the microbial communities by constraining sub-strate availability. Our data suggest a strong mineralogical influence on nutrient cycling par-ticularly in subsoil environments.

Analytical characterization of selective benthic flux components in estuarine and coastal waters

USGS Publications Warehouse

King, Jeffrey N.

2011-01-01

Benthic flux is the rate of flow across the bed of a water body, per unit area of bed. It is forced by component mechanisms, which interact. For example, pressure gradients across the bed, forced by tide, surface gravity waves, density gradients, bed–current interaction, turbulence, and terrestrial hydraulic gradients, drive an advective benthic flux of water and constituents between estuarine and coastal waters, and surficial aquifers. Other mechanisms also force benthic flux, such as chemical gradients, bioturbation, and dispersion. A suite of component mechanisms force a total benthic flux at any given location, where each member of the suite contributes a component benthic flux. Currently, the types and characteristics of component interactions are not fully understood. For example, components may interact linearly or nonlinearly, and the interaction may be constructive or destructive. Benthic flux is a surface water–groundwater interaction process. Its discharge component to a marine water body is referred to, in some literature, as submarine groundwater discharge. Benthic flux is important in characterizing water and constituent budgets of estuarine and coastal systems. Analytical models to characterize selective benthic flux components are reviewed. Specifically, these mechanisms are for the component associated with the groundwater tidal prism, and forced by surface gravity wave setup, surface gravity waves on a plane bed, and the terrestrial hydraulic gradient. Analytical models are applied to the Indian River Lagoon, Florida; Great South Bay, New York; and the South Atlantic Bight in South Carolina and portions of North Carolina.

Benthic Algal Community Structures and Their Response to Geographic Distance and Environmental Variables in the Qinghai-Tibetan Lakes With Different Salinity

PubMed Central

Yang, Jian; Jiang, Hongchen; Liu, Wen; Wang, Beichen

2018-01-01

Uncovering the limiting factors for benthic algal distributions in lakes is of great importance to understanding of their role in global carbon cycling. However, limited is known about the benthic algal community distribution and how they are influenced by geographic distance and environmental variables in alpine lakes. Here, we investigated the benthic algal community compositions in the surface sediments of six lakes on the Qinghai-Tibetan Plateau (QTP), China (salinity ranging from 0.8 to 365.6 g/L; pairwise geographic distance among the studied lakes ranging 8–514 km) employing an integrated approach including Illumina-Miseq sequencing and environmental geochemistry. The results showed that the algal communities of the studied samples were mainly composed of orders of Bacillariales, Ceramiales, Naviculales, Oscillatoriales, Spirulinales, Synechococcales, and Vaucheriales. The benthic algal community compositions in these QTP lakes were significantly (p < 0.05) correlated with many environmental (e.g., dissolved inorganic and organic carbon, illumination intensity, total nitrogen and phosphorus, turbidity and water temperature) and spatial factors, and salinity did not show significant influence on the benthic algal community structures in the studied lakes. Furthermore, geographic distance showed strong, significant correlation (r = 0.578, p < 0.001) with the benthic algal community compositions among the studied lakes, suggesting that spatial factors may play important roles in influencing the benthic algal distribution. These results expand our current knowledge on the influencing factors for the distributions of benthic alga in alpine lakes. PMID:29636745

Oyster reef restoration in the Northern Gulf of Mexico: effect of artificial substrate and sge on nekton and benthic macroinvertebrate assemblage use

USGS Publications Warehouse

Brown, Laura A.; Furlong, Jessica N.; Brown, Kenneth M.; LaPeyre, Megan K.

2013-01-01

In the northern Gulf of Mexico (GOM), reefs built by eastern oysters, Crassostrea virginica, provide critical habitat within shallow estuaries, and recent efforts have focused on restoring reefs to benefit nekton and benthic macroinvertebrates. We compared nekton and benthic macroinvertebrate assemblages at historic, newly created (<5years) and old (>6years) shell and rock substrate reefs. Using crab traps, gill-nets, otter trawls, cast nets, and benthic macroinvertebrate collectors, 20 shallow reefs (<5m) in the northern GOM were sampled throughout the summer of 2011. We compared nekton and benthic assemblage abundance, diversity and composition across reef types. Except for benthic macroinvertebrate abundance, which was significantly higher on old rock reefs as compared to historic reefs, all reefs were similar to historic reefs, suggesting created reefs provide similar support of nekton and benthic assemblages as historic reefs. To determine refuge value of oyster structure for benthic macroinvertebrates compared to bare bottom, we tested preferences of juvenile crabs across depth and refuge complexity in the presence and absence of adult blue crabs (Callinectes sapidus). Juveniles were more likely to use deep water with predators present only when provided oyster structure. Provision of structural material to support and sustain development of benthic and mobile reef communities may be the most important factor in determining reef value to these assemblages, with biophysical characteristics related to reef location influencing assemblage patterns in areas with structure; if so, appropriately locating created reefs is critical.

Blob-level active-passive data fusion for Benthic classification

NASA Astrophysics Data System (ADS)

Park, Joong Yong; Kalluri, Hemanth; Mathur, Abhinav; Ramnath, Vinod; Kim, Minsu; Aitken, Jennifer; Tuell, Grady

2012-06-01

We extend the data fusion pixel level to the more semantically meaningful blob level, using the mean-shift algorithm to form labeled blobs having high similarity in the feature domain, and connectivity in the spatial domain. We have also developed Bhattacharyya Distance (BD) and rule-based classifiers, and have implemented these higher-level data fusion algorithms into the CZMIL Data Processing System. Applying these new algorithms to recent SHOALS and CASI data at Plymouth Harbor, Massachusetts, we achieved improved benthic classification accuracies over those produced with either single sensor, or pixel-level fusion strategies. These results appear to validate the hypothesis that classification accuracy may be generally improved by adopting higher spatial and semantic levels of fusion.

Plant-soil-microbe interactions regulating soil C storage

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bach, E.; Williams, R.

2016-12-01

Integration across disciplines is required to identify the emergent microbial scale properties that regulate the release or occlusion of plant inputs in soil organic matter. To investigate how micro-scale processes influence soil carbon cycling, we measured microbial community composition and activity within soil aggregates monthly over two growing seasons of a long-term bioenergy field experiment. Using a biologically sensitive sieving technique, soil aggregates were isolated and microbial community activity and composition were measured. This aggregate approach revealed biogeochemical processes regulating C cycling that are not detected using whole soil approaches. Soil aggregation influenced microbe-substrate interactions, where diversified perennial grassland systems supported greater aggregation and reduced severity of aggregate turnover compared to corn systems. Aggregate turnover and concurrent increases in activity resulted in greater microbial biomass and physical protection of soil organic matter in prairie systems, especially fertilized prairies. Fertilized prairie enhanced microbial biomass, enzyme activity, and soil aggregation despite greater root biomass in unfertilized prairie. Independent of ecosystem or sampling date, N-acetyl-glucosaminidase activity and Nitrospirae abundance was greatest in large macroaggregates (>2000 µm), which harbored the highest C:N; cellobiohydrolase activity and Acidobacteria abundance was greatest in microaggregates (<250 µm) which had the lowest C:N. Aggregate fractions differed in microbial community composition (bacteria, archaea, and fungi) and potential enzyme activity, independent of cropping system. Microaggregates harbored significantly greater microbial diversity and richness across all bioenergy cropping systems. Together these results suggest that by mediating access to substrates, soil structure (aggregates) can influence the microbial community composition and extracellular enzyme activity to regulate ecosystem scale decomposition of soil organic matter.

Surfing the Pacific Island chains: linking internal wave energetics to coral reef benthic community patterns.

NASA Astrophysics Data System (ADS)

Painter Jones, Matilda; Green, Mattias; Gove, Jamison; Williams, Gareth

2017-04-01

The ocean is saturated with internal waves at tidal frequency. The energy associated with conversion from barotropic to baroclinic can enhance mixing and upwelling at sites of generation and dissipation, which in turn can drive primary production. Hotspots of internal wave generation are located at sudden changes in topography with the Hawaiian archipelago identified as an area of intense internal wave activity. The role of internal waves as a driver of benthic reef community is unexplored and could be key to coral reefs survival in the unknown future. Using a Pacific wide map of internal wave flux and barotropic-to-baroclinic conversion at an unprecedented 1/30th degree resolution, energy budgets were developed for four islands to evaluate dissipation and generation of internal waves. Spatiotemporal variations in benthic community structure were plotted around each island and related to changes in internal wave energetics using a boosted regression tree. Contrasting spatial patterns and species assemblages were seen around islands with distinct internal wave regimes. The relative importance and influence of internal waves on coral reef ecosystems is evaluated.

Dietary bioavailability of Cu adsorbed to colloidal hydrous ferric oxide

USGS Publications Warehouse

Cain, Daniel J.; Croteau, Marie-Noële; Fuller, Christopher C.

2013-01-01

The dietary bioavailability of copper (Cu) adsorbed to synthetic colloidal hydrous ferric oxide (HFO) was evaluated from the assimilation of 65Cu by two benthic grazers, a gastropod and a larval mayfly. HFO was synthesized, labeled with 65Cu to achieve a Cu/Fe ratio comparable to that determined in naturally formed HFO, and then aged. The labeled colloids were mixed with a food source (the diatom Nitzschia palea) to yield dietary 65Cu concentrations ranging from 211 to 2204 nmol/g (dry weight). Animals were pulse fed the contaminated diet and assimilation of 65Cu from HFO was determined following 1–3 days of depuration. Mass transfer of 65Cu from HFO to the diatom was less than 1%, indicating that HFO was the source of 65Cu to the grazers. Estimates of assimilation efficiency indicated that the majority of Cu ingested as HFO was assimilated (values >70%), implying that colloidal HFO potentially represents a source of dietary Cu to benthic grazers, especially where there is active formation and infiltration of these particles into benthic substrates.

Benthic foraminiferal assemblage formation: Theory and observation for the European Arctic margin

NASA Astrophysics Data System (ADS)

Loubere, Paul; Rayray, Shan

2016-09-01

We use theory and observation to determine how benthic foraminiferal populations living in a range of sedimentary microenvironments are translated into fossil assemblages along the continental margin of the European Arctic. We examine downcore stained (cell tracker green and rose Bengal) and total species shell abundances through the sediment mixing (bioturbation) zone. This, in combination with porewater geochemical measurements, allows us to establish zones of production and destruction for species' shells, and deduce how the fossil record is being generated by the living community. For many taxa, shell production is high in the upper, oxic, sedimentary layer, but destruction in this zone is also high. Hence, contribution to the fossil record is biased to more infaunal populations and species. Taxa producing near, or below, the anoxic boundary of the sediments are particularly important to the developing fossil record of the fjord environment. We find that taxon relative and absolute abundances change continuously through the biologically active sediment profile. This has implications for reconstructing paleoenvironments using benthic foraminiferal assemblages, and potentially for the geochemistry of individual fossil taxa.

Benthic foraminiferal assemblage formation: Theory and observation for the European Arctic Margin

NASA Astrophysics Data System (ADS)

Loubere, Paul; Rayray, Shan

2016-07-01

We use theory and observation to determine how benthic foraminiferal populations living in a range of sedimentary microenvironments are translated into fossil assemblages along the continental margin of the European Arctic. We examine downcore stained (cell tracker green and rose Bengal) and total species shell abundances through the sediment mixing (bioturbation) zone. This, in combination with porewater geochemical measurements, allows us to establish zones of production and destruction for species' shells, and deduce how the fossil record is being generated by the living community. For many taxa, shell production is high in the upper, oxic, sedimentary layer, but destruction in this zone is also high. Hence, contribution to the fossil record is biased to more infaunal populations and species. Taxa producing near, or below, the anoxic boundary of the sediments are particularly important to the developing fossil record of the fjord environment. We find that taxon relative and absolute abundances change continuously through the biologically active sediment profile. This has implications for reconstructing paleoenvironments using benthic foraminiferal assemblages, and potentially for the geochemistry of individual fossil taxa.

Community shelter use in response to two benthic decapod predators in the Long Island Sound

PubMed Central

Reagan, Dugan; Crivello, Joseph F.

2016-01-01

To investigate community shelter effects of two invasive decapod species, Hemigrapsus sanguineus and Carcinus maenas, in the Long Island Sound (LIS), we deployed artificial shelters in the intertidal and immediate subtidal zones. These consisted of five groups during the summer: a control, a resident H. sanguineus male or female group, and a resident C. maenas male or female group. We quantified utilization of the shelters at 24 h by counting crabs and fish present. We found significant avoidance of H. sanguineus in the field by benthic hermit crabs (Pagurus spp.) and significant avoidance of C. maenas by the seaboard goby (Gobiosoma ginsburgi). The grubby (Myoxocephalus aenaeus) avoided neither treatment, probably since it tends to be a predator of invertebrates. H. sanguineus avoided C. maenas treatments, whereas C. maenas did not avoid any treatment. Seasonal deployments in the subtidal indicated cohabitation of a number of benthic species in the LIS, with peak shelter use corresponding with increased predation and likely reproductive activity in spring and summer for green crabs (C. maenas), hermit crabs (Pagurus spp.), seaboard gobies (G. ginsburgi), and grubbies (Myoxocephalus aenaeus). PMID:27547570

Community shelter use in response to two benthic decapod predators in the Long Island Sound.

PubMed

Hudson, David M; Reagan, Dugan; Crivello, Joseph F

2016-01-01

To investigate community shelter effects of two invasive decapod species, Hemigrapsus sanguineus and Carcinus maenas, in the Long Island Sound (LIS), we deployed artificial shelters in the intertidal and immediate subtidal zones. These consisted of five groups during the summer: a control, a resident H. sanguineus male or female group, and a resident C. maenas male or female group. We quantified utilization of the shelters at 24 h by counting crabs and fish present. We found significant avoidance of H. sanguineus in the field by benthic hermit crabs (Pagurus spp.) and significant avoidance of C. maenas by the seaboard goby (Gobiosoma ginsburgi). The grubby (Myoxocephalus aenaeus) avoided neither treatment, probably since it tends to be a predator of invertebrates. H. sanguineus avoided C. maenas treatments, whereas C. maenas did not avoid any treatment. Seasonal deployments in the subtidal indicated cohabitation of a number of benthic species in the LIS, with peak shelter use corresponding with increased predation and likely reproductive activity in spring and summer for green crabs (C. maenas), hermit crabs (Pagurus spp.), seaboard gobies (G. ginsburgi), and grubbies (Myoxocephalus aenaeus).

Effect of Soil Amendments on Microbial Resilience Capacity of Acid Soil Under Copper Stress.

PubMed

Mounissamy, Vassanda Coumar; Kundu, Samaresh; Selladurai, Rajendiran; Saha, Jayanta Kumar; Biswas, Ashish Kumar; Adhikari, Tapan; Patra, Ashok Kumar

2017-11-01

An incubation study was undertaken to study microbial resilience capacity of acid soil amended with farmyard manure (FYM), charcoal and lime under copper (Cu) perturbation. Copper stress significantly reduced enzymatic activities and microbial biomass carbon (MBC) in soil. Percent reduction in microbial activity of soil due to Cu stress was 74.7% in dehydrogenase activity, 59.9% in MBC, 48.2% in alkaline phosphatase activity and 15.1% in acid phosphatase activity. Soil treated with FYM + charcoal showed highest resistance index for enzymatic activities and MBC. Similarly, the highest resilience index for acid phosphatase activity was observed in soil amended with FYM (0.40), whereas FYM + charcoal-treated soil showed the highest resilience indices for alkaline, dehydrogenase activity and MBC: 0.50, 0.22 and 0.25, respectively. This investigation showed that FYM and charcoal application, either alone or in combination, proved to be better than lime with respect to microbial functional resistance and resilience of acid soil under Cu perturbation.

Photosynthesis as a Possible Source of Gas Bubbles in Shallow Sandy Coastal Sediments

DTIC Science & Technology

2012-09-30

clearly demonstrates that gas bubbles can be formed when photosynthesis by benthic microalgae causes pore water to become supersaturated with oxygen...We also collected sediment samples from the upper few mm of sand to identify the dominant taxa of benthic microalgae present. Although benthic...Jan Rines (Graduate School of Oceanography / University of Rhode Island = GSO/URI) to identify the benthic microalgae in the samples. Following the

Nutrient and suspended-sediment concentrations and loads and benthic-invertebrate data for tributaries to the St. Croix River, Wisconsin and Minnesota, 1997-99

USGS Publications Warehouse

Lenz, Bernard N.; Robertson, Dale M.; Fallon, James D.; Ferrin, Randy

2001-01-01

Benthic invertebrates were sampled and indices of water quality were calculated at 16 tributaries in fall 1999. Benthic invertebrate indices indicated excellent to good water quality at all tributaries except Valley Creek, Willow River, and Kettle River. No relations were found between benthic invertebrate indices and the calculated and estimated 1999 annual tributary loads and yields.

Quantifying microbial activity in deep subsurface sediments using a tritium based hydrognease enzyme assay

NASA Astrophysics Data System (ADS)

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

2012-12-01

Microbial life is widespread in Earth's subsurface and estimated to represent a significant fraction of Earth's total living biomass. However, very little is known about subsurface microbial activity and its fundamental role in biogeochemical cycles of carbon and other biologically important elements. Hydrogen is one of the most important elements in subsurface anaerobic microbial metabolism. Heterotrophic and chemoautotrophic microorganisms use hydrogen in their metabolic pathways. They either consume or produce protons for ATP synthesis. 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 CO2 or sulfate. H2ase enzyme targets a key metabolic compound in cellular metabolism therefore the assay can be used as a measure for total microbial activity without the need to identify any specific metabolic process. Using the highly sensitive tritium assay we measured H2ase enzyme activity in the organic-rich sediments of Lake Van, a saline, alkaline lake in eastern Turkey, in marine sediments of the Barents Sea and in deep subseafloor sediments from the Nankai Trough. H2ase activity could be quantified at all depths of all sites but the activity distribution varied widely with depth and between sites. At the Lake Van sites H2ase activity ranged from ca. 20 mmol H2 cm-3d-1 close to the sediment-water interface to 0.5 mmol H2 cm-3d-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-3d-1 down to a depth of 1.60 m. At all sites the sulfate reduction rate profile followed the upper part of the H2ase activity profile until sulfate reduction reached the minimum detection limit (ca. 10 pmol cm-3d-1). H2ase activity could still be quantified after the decline of sulfate reduction, indicating that other microbial processes are becoming quantitatively more important. Similarly, H2ase activity could be quantified at greater depths (ca. 400 mbsf) in Nankai Trough sediments. Nankai Trough is one of the world's most geologically active accretionary wedges, where the Philippine Plate is subducting under the southwest of Japan. Due to the transient faulting, huge amounts of energy are liberated that enhance chemical transformations of organic and inorganic matter. An increase in H2ase activity could be observed at greater depth, which suggests that microbial activity is stimulated by the fault activity. Current techniques for the quantification of microbial activity in deep sediments have already reached their physical and technical limits and-in many cases- are still not sensitive enough to quantify extremely low rates of microbial activity. Additional to the quantification of specific processes, estimates of total microbial activity will provide valuable information on energy flux and microbial metabolism in the subsurface biosphere and other low-energy environments as well as help identifying hotspots of microbial activity. The tritium H2ase assay has a potential to become a valuable tool to measure total subsurface microbial activity.

Temporal dynamics of the compositions and activities of soil microbial communities post-application of the insecticide chlorantraniliprole in paddy soils.

PubMed

Wu, Meng; Liu, Jia; Li, Weitao; Liu, Ming; Jiang, Chunyu; Li, Zhongpei

2017-10-01

Chlorantraniliprole (CAP) is a newly developed insecticide widely used in rice fields in China. There has been few studies evaluating the toxicological effects of CAP on soil-associated microbes. An 85-day microcosm experiment was performed to reveal the dissipation dynamics of CAP in three types of paddy soils in subtropical China. The effects of CAP on microbial activities (microbial biomass carbon-MBC, basal soil respiration-BSR, microbial metabolic quotient-qCO 2 , acid phosphatase and sucrose invertase activities) in the soils were periodically evaluated. Microbial phospholipid fatty acid (PLFA) analysis was used to evaluate the change of soil microbial community composition on day 14 and 50 of the experiment. CAP residues were extracted using the quick, easy, cheap, effective, rugged, and safe (QuChERS) method and quantification was measured by high performance liquid chromatography (HPLC). The half-lives (DT 50 ) of CAP were in the range of 41.0-53.0 days in the three soils. The results showed that CAP did not impart negative effects on MBC during the incubation. CAP inhibited BSR, qCO 2 , acid phosphatase and sucrose invertase activities in the first 14 days of incubation in all the soils. After day 14, the soil microbial parameters of CAP-treated soils became statistically at par with their controls. Principal component analysis (PCA) determining abundance of biomarker PLFAs indicated that the application of CAP significantly changed the compositions of microbial communities in all three paddy soils on day 14 but the compositions of soil microbial communities recovered by day 50. This study indicates that CAP does not ultimately impair microbial activities and microbial compositions of these three paddy soil types. Copyright © 2017 Elsevier Inc. All rights reserved.

Potential contribution of surface-dwelling Sargassum algae to deep-sea ecosystems in the southern North Atlantic

NASA Astrophysics Data System (ADS)

Baker, Philip; Minzlaff, Ulrike; Schoenle, Alexandra; Schwabe, Enrico; Hohlfeld, Manon; Jeuck, Alexandra; Brenke, Nils; Prausse, Dennis; Rothenbeck, Marcel; Brix, Saskia; Frutos, Inmaculada; Jörger, Katharina M.; Neusser, Timea P.; Koppelmann, Rolf; Devey, Colin; Brandt, Angelika; Arndt, Hartmut

2018-02-01

Deep-sea ecosystems, limited by their inability to use primary production as a source of carbon, rely on other sources to maintain life. Sedimentation of organic carbon into the deep sea has been previously studied, however, the high biomass of sedimented Sargassum algae discovered during the VEMA Transit expedition in 2014/2015 to the southern North Atlantic, and its potential as a regular carbon input, has been an underestimated phenomenon. To determine the potential for this carbon flux, a literature survey of previous studies that estimated the abundance of surface water Sargassum was conducted. We compared these estimates with quantitative analyses of sedimented Sargassum appearing on photos taken with an autonomous underwater vehicle (AUV) directly above the abyssal sediment during the expedition. Organismal communities associated to Sargassum fluitans from surface waters were investigated and Sargassum samples collected from surface waters and the deep sea were biochemically analyzed (fatty acids, stable isotopes, C:N ratios) to determine degradation potential and the trophic significance within deep-sea communities. The estimated Sargassum biomass (fresh weight) in the deep sea (0.07-3.75 g/m2) was several times higher than that estimated from surface waters in the North Atlantic (0.024-0.84 g/m2). Biochemical analysis showed degradation of Sargassum occurring during sedimentation or in the deep sea, however, fatty acid and stable isotope analysis did not indicate direct trophic interactions between the algae and benthic organisms. Thus, it is assumed that components of the deep-sea microbial food web form an important link between the macroalgae and larger benthic organisms. Evaluation of the epifauna showed a diverse nano- micro-, meio, and macrofauna on surface Sargassum and maybe transported across the Atlantic, but we had no evidence for a vertical exchange of fauna components. The large-scale sedimentation of Sargassum forms an important trophic link between surface and benthic production and has to be further considered in the future as a regular carbon input to the deep-sea floor in the North Atlantic.

Food-web traits of the North Aegean Sea ecosystem (Eastern Mediterranean) and comparison with other Mediterranean ecosystems

NASA Astrophysics Data System (ADS)

Tsagarakis, K.; Coll, M.; Giannoulaki, M.; Somarakis, S.; Papaconstantinou, C.; Machias, A.

2010-06-01

A mass-balance trophic model was built to describe the food-web traits of the North Aegean Sea (Strymonikos Gulf and Thracian Sea, Greece, Eastern Mediterranean) during the mid-2000s and to explore the impacts of fishing. This is the first food-web model representing the Aegean Sea, and results were presented and discussed in comparison to other previous ecosystems modelled from the western and the central areas of the basin (South Catalan and North-Central Adriatic Seas). Forty functional groups were defined, covering the entire trophic spectrum from lower to higher trophic levels. Emphasis was placed on commercial invertebrates and fish. The potential ecological role of the invasive ctenophore, Mnemiopsis leidyi, and several vulnerable groups (e.g., dolphins) was also explored. Results confirmed the spatial productivity patterns known for the Mediterranean Sea showing, for example, that the total biomass is highest in N.C. Adriatic and lowest in N. Aegean Sea. Accordingly, food-web flows and several ecosystem indicators like the mean transfer efficiency were influenced by these patterns. Nevertheless, all three systems shared some common features evidencing similarities of Mediterranean Sea ecosystems such as dominance of the pelagic fraction in terms of flows and strong benthic-pelagic coupling of zooplankton and benthic invertebrates through detritus. The importance of detritus highlighted the role of the microbial food-web, which was indirectly considered through detritus dynamics. Ciliates, mesozooplankton and several benthic invertebrate groups were shown as important elements of the ecosystem linking primary producers and detritus with higher trophic levels in the N. Aegean Sea. Adult anchovy was shown as the most important fish group in terms of production, consumption and overall effect on the rest of the ecological groups in the model, in line with results from the Western Mediterranean Sea. The five fishing fleets considered (both artisanal and industrial) had high impacts on vulnerable species and numerous targeted groups given the multispecies nature of the fisheries in the N. Aegean Sea. Several exploitation indices highlighted that the N. Aegean Sea ecosystem was highly exploited and unlikely to be sustainably fished, similarly to other Mediterranean marine ecosystems.

Effects of biochar amendments on soil microbial biomass and activity.

PubMed

Zhang, H; Voroney, R P; Price, G W

2014-11-01

Environmental benefits reported in the literature of using biochar as a soil amendment are generally increased microbial activity and reduced greenhouse gas (GHG) emissions. This study determined the effects of amendment with biomass feedstocks (spent coffee grounds, wood pellets, and horse bedding compost) and that of biochars (700°C) produced from these feedstocks on soil microbial biomass (C and N) and activity. Soils were amended with these substrates at 0.75% by weight and incubated for up to 175 d under laboratory conditions. Biochar residual effects on soil microbial activity were also studied by amending these soils with either ammonium nitrate (NHNO, 35 mg N kg) or with glucose (864 mg C kg) plus NHNO. Soil microbial biomass C and N, net N mineralization, and CO, NO, and CH emissions were measured. Amendment with biomass feedstocks significantly increased soil microbial biomass and activity, whereas amendment with the biochars had no significant effect. Also, biochar amendment had no significant effect on either net N mineralization or NO and CH emissions from soil. These results indicate that production of biochars at this high temperature eliminated potential substrates. Microbial biomass C in biochar-amended and unamended soils was not significantly different following additions of NHNO or glucose plus NHNO, suggesting that microbial access to otherwise labile C and N was not affected. This study shows that biochars produced at 700°C, regardless of feedstock source, do not enhance soil microbial biomass or activity. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

[Effects of altitudes on soil microbial biomass and enzyme activity in alpine-gorge regions.

PubMed

Cao, Rui; Wu, Fu Zhong; Yang, Wan Qin; Xu, Zhen Feng; Tani, Bo; Wang, Bin; Li, Jun; Chang, Chen Hui

2016-04-22

In order to understand the variations of soil microbial biomass and soil enzyme activities with the change of altitude, a field incubation was conducted in dry valley, ecotone between dry valley and mountain forest, subalpine coniferous forest, alpine forest and alpine meadow from 1563 m to 3994 m of altitude in the alpine-gorge region of western Sichuan. The microbial biomass carbon and nitrogen, and the activities of invertase, urease and acid phosphorus were measured in both soil organic layer and mineral soil layer. Both the soil microbial biomass and soil enzyme activities showed the similar tendency in soil organic layer. They increased from 2158 m to 3028 m, then decreased to the lowest value at 3593 m, and thereafter increased until 3994 m in the alpine-gorge region. In contrast, the soil microbial biomass and soil enzyme activities in mineral soil layer showed the trends as, the subalpine forest at 3028 m > alpine meadow at 3994 m > montane forest ecotone at 2158 m > alpine forest at 3593 m > dry valley at 1563 m. Regardless of altitudes, soil microbial biomass and soil enzyme activities were significantly higher in soil organic layer than in mineral soil layer. The soil microbial biomass was significantly positively correlated with the activities of the measured soil enzymes. Moreover, both the soil microbial biomass and soil enzyme activities were significantly positively correlated with soil water content, organic carbon, and total nitrogen. The activity of soil invertase was significantly positively correlated with soil phosphorus content, and the soil acid phosphatase was so with soil phosphorus content and soil temperature. In brief, changes in vegetation and other environmental factors resulting from altitude change might have strong effects on soil biochemical properties in the alpine-gorge region.

Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study.

PubMed

Smith, A Peyton; Marín-Spiotta, Erika; Balser, Teri

2015-09-01

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. Understanding how microbial communities respond to changes in vegetation is critical for improving predictions of how land-cover change affects belowground carbon storage and nutrient availability. We measured intra- and interannual variability in soil and forest litter microbial community composition and activity via phospholipid fatty acid analysis (PLFA) and extracellular enzyme activity across a well-replicated, long-term chronosequence of secondary forests growing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Microbial community PLFA structure differed between young secondary forests and older secondary and primary forests, following successional shifts in tree species composition. These successional patterns held across seasons, but the microbial groups driving these patterns differed over time. Microbial community composition from the forest litter differed greatly from those in the soil, but did not show the same successional trends. Extracellular enzyme activity did not differ with forest succession, but varied by season with greater rates of potential activity in the dry seasons. We found few robust significant relationships among microbial community parameters and soil pH, moisture, carbon, and nitrogen concentrations. Observed inter- and intrannual variability in microbial community structure and activity reveal the importance of a multiple, temporal sampling strategy when investigating microbial community dynamics with land-use change. Successional control over microbial composition with forest recovery suggests strong links between above and belowground communities. © 2015 John Wiley & Sons Ltd.

Effects of Jet Fuel Spills on the Microbial Community of Soil †

PubMed Central

Song, Hong-Gyu; Bartha, Richard

1990-01-01

Hydrocarbon residues, microbial numbers, and microbial activity were measured and correlated in loam soil contaminated by jet fuel spills resulting in 50 and 135 mg of hydrocarbon g of soil−1. Contaminated soil was incubated at 27°C either as well-aerated surface soil or as poorly aerated subsurface soil. In the former case, the effects of bioremediation treatment on residues, microbial numbers, and microbial activity were also assessed. Hydrocarbon residues were measured by quantitative gas chromatography. Enumerations included direct counts of metabolically active bacteria, measurement of mycelial length, plate counts of aerobic heterotrophs, and most probable numbers of hydrocarbon degraders. Activity was assessed by fluorescein diacetate (FDA) hydrolysis. Jet fuel disappeared much more rapidly from surface soil than it did from subsurface soil. In surface soil, microbial numbers and mycelial length were increased by 2 to 2.5 orders of magnitude as a result of jet fuel contamination alone and by 3 to 4 orders of magnitude as a result of the combination of jet fuel contamination and bioremediation. FDA hydrolysis was stimulated by jet fuel and bioremediation, but was inhibited by jet fuel alone. The latter was traced to an inhibition of the FDA assay by jet fuel biodegradation products. In subsurface soil, oxygen limitation strongly attenuated microbial responses to jet fuel. An increase in the most probable numbers of hydrocarbon degraders was accompanied by a decline in other aerobic heterotrophs, so that total plate counts changed little. The correlations between hydrocarbon residues, microbial numbers, and microbial activity help in elucidating microbial contributions to jet fuel elimination from soil. PMID:16348138

Contribution of benthic microalgae to the temporal variation in phytoplankton assemblages in a macrotidal system.

PubMed

Hernández Fariñas, Tania; Ribeiro, Lourenço; Soudant, Dominique; Belin, Catherine; Bacher, Cédric; Lampert, Luis; Barillé, Laurent

2017-10-01

Suspended marine benthic microalgae in the water column reflect the close relationship between the benthic and pelagic components of coastal ecosystems. In this study, a 12-year phytoplankton time-series was used to investigate the contribution of benthic microalgae to the pelagic system at a site along the French-Atlantic coast. Furthermore, all taxa identified were allocated into different growth forms in order to study their seasonal patterns. The highest contribution of benthic microalgae was observed during the winter period, reaching up to 60% of the carbon biomass in the water column. The haptobenthic growth form showed the highest contribution in terms of biomass, dominant in the fall-winter period when the turbidity and the river flow were high. The epipelic growth form did not follow any seasonal pattern. The epiphytic diatom Licmophora was most commonly found during summer. As benthic microalgae were found in the water column throughout the year, the temporal variation detected in the structure of pelagic assemblages in a macrotidal ecosystem was partly derived from the differentiated contribution of several benthic growth forms. © 2017 Phycological Society of America.

Environmental characteristics and benthic invertebrate assemblages in Colorado mountain lakes

USGS Publications Warehouse

LaFrancois, B.M.; Carlisle, D.M.; Nydick, K.R.; Johnson, B.M.; Baron, Jill S.

2003-01-01

Twenty-two high-elevation lakes (>3000 m) in Rocky Mountain National Park and Indian Peaks Wilderness Area, Colorado, were surveyed during summer 1998 to explore relationships among benthic invertebrates, water chemistry (particularly nitrate concentrations), and other environmental variables. Water samples were collected from the deepest portion of each lake and analyzed for ions and other water chemistry parameters. Benthic invertebrates were collected from the littoral zone using both a sweep net and Hess sampler. Physical and geographical measurements were derived from maps. Relationships among benthic invertebrate assemblages and environmental variables were examined using canonical correspondence analysis, and the importance of sampling methodology and taxonomie resolution on these relationships was evaluated. Choice of sampling methodology strongly influenced the outcome of statistical analyses, whereas taxonomie resolution did not. Presence/absence of benthic invertebrate taxa among the study lakes was best explained by elevation and presence of fish. Relative abundance and density of benthic invertebrate taxa were more strongly influenced by sampling date and water chemistry. Nitrate (NO₃⁻) concentration, potentially on the rise due to regional nitrogen deposition, was unrelated to benthic invertebrate distribution regardless of sampling method or taxonomie resolution.

Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities

PubMed Central

Li, Jun-Min; Jin, Ze-Xin; Hagedorn, Frank; Li, Mai-He

2014-01-01

Native parasitic plants may be used to infect and control invasive plants. We established microcosms with invasive Mikania micrantha and native Coix lacryma-jobi growing in mixture on native soils, with M. micrantha being infected by parasitic Cuscuta campestris at four intensity levels for seven weeks to estimate the top-down effects of plant parasitism on the biomass and functional diversity of soil microbial communities. Parasitism significantly decreased root biomass and altered soil microbial communities. Soil microbial biomass decreased, but soil respiration increased at the two higher infection levels, indicating a strong stimulation of soil microbial metabolic activity (+180%). Moreover, a Biolog assay showed that the infection resulted in a significant change in the functional diversity indices of soil microbial communities. Pearson correlation analysis indicated that microbial biomass declined significantly with decreasing root biomass, particularly of the invasive M. micrantha. Also, the functional diversity indices of soil microbial communities were positively correlated with soil microbial biomass. Therefore, the negative effects on the biomass, activity and functional diversity of soil microbial community by the seven week long plant parasitism was very likely caused by decreased root biomass and root exudation of the invasive M. micrantha. PMID:25367357

Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities

NASA Astrophysics Data System (ADS)

Li, Jun-Min; Jin, Ze-Xin; Hagedorn, Frank; Li, Mai-He

2014-11-01

Native parasitic plants may be used to infect and control invasive plants. We established microcosms with invasive Mikania micrantha and native Coix lacryma-jobi growing in mixture on native soils, with M. micrantha being infected by parasitic Cuscuta campestris at four intensity levels for seven weeks to estimate the top-down effects of plant parasitism on the biomass and functional diversity of soil microbial communities. Parasitism significantly decreased root biomass and altered soil microbial communities. Soil microbial biomass decreased, but soil respiration increased at the two higher infection levels, indicating a strong stimulation of soil microbial metabolic activity (+180%). Moreover, a Biolog assay showed that the infection resulted in a significant change in the functional diversity indices of soil microbial communities. Pearson correlation analysis indicated that microbial biomass declined significantly with decreasing root biomass, particularly of the invasive M. micrantha. Also, the functional diversity indices of soil microbial communities were positively correlated with soil microbial biomass. Therefore, the negative effects on the biomass, activity and functional diversity of soil microbial community by the seven week long plant parasitism was very likely caused by decreased root biomass and root exudation of the invasive M. micrantha.

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

Durability and regeneration of activated carbon air-cathodes in long-term operated microbial fuel cells

NASA Astrophysics Data System (ADS)

Zhang, Enren; Wang, Feng; Yu, Qingling; Scott, Keith; Wang, Xu; Diao, Guowang

2017-08-01

The performance of activated carbon catalyst in air-cathodes in microbial fuel cells was investigated over one year. A maximum power of 1722 mW m-2 was produced within the initial one-month microbial fuel cell operation. The air-cathodes produced a maximum power >1200 mW m-2 within six months, but gradually became a limiting factor for the power output in prolonged microbial fuel cell operation. The maximum power decreased by 55% when microbial fuel cells were operated over one year due to deterioration in activated carbon air-cathodes. While salt/biofilm removal from cathodes experiencing one-year operation increased a limiting performance enhancement in cathodes, a washing-drying-pressing procedure could restore the cathode performance to its original levels, although the performance restoration was temporary. Durable cathodes could be regenerated by re-pressing activated carbon catalyst, recovered from one year deteriorated air-cathodes, with new gas diffusion layer, resulting in ∼1800 mW m-2 of maximum power production. The present study indicated that activated carbon was an effective catalyst in microbial fuel cell cathodes, and could be recovered for reuse in long-term operated microbial fuel cells by simple methods.

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.

Microbially assisted recording of the Earth's magnetic field in sediment.

PubMed

Zhao, Xiangyu; Egli, Ramon; Gilder, Stuart A; Müller, Sebastian

2016-02-11

Sediments continuously record variations of the Earth's magnetic field and thus provide an important archive for studying the geodynamo. The recording process occurs as magnetic grains partially align with the geomagnetic field during and after sediment deposition, generating a depositional remanent magnetization (DRM) or post-DRM (PDRM). (P)DRM acquisition mechanisms have been investigated for over 50 years, yet many aspects remain unclear. A key issue concerns the controversial role of bioturbation, that is, the mechanical disturbance of sediment by benthic organisms, during PDRM acquisition. A recent theory on bioturbation-driven PDRM appears to solve many inconsistencies between laboratory experiments and palaeomagnetic records, yet it lacks experimental proof. Here we fill this gap by documenting the important role of bioturbation-induced rotational diffusion for (P)DRM acquisition, including the control exerted on the recorded inclination and intensity, as determined by the equilibrium between aligning and perturbing torques acting on magnetic particles.

Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia

NASA Astrophysics Data System (ADS)

Dekas, Anne E.; Poretsky, Rachel S.; Orphan, Victoria J.

2009-10-01

Nitrogen-fixing (diazotrophic) microorganisms regulate productivity in diverse ecosystems; however, the identities of diazotrophs are unknown in many oceanic environments. Using single-cell-resolution nanometer secondary ion mass spectrometry images of 15N incorporation, we showed that deep-sea anaerobic methane-oxidizing archaea fix N2, as well as structurally similar CN-, and share the products with sulfate-reducing bacterial symbionts. These archaeal/bacterial consortia are already recognized as the major sink of methane in benthic ecosystems, and we now identify them as a source of bioavailable nitrogen as well. The archaea maintain their methane oxidation rates while fixing N2 but reduce their growth, probably in compensation for the energetic burden of diazotrophy. This finding extends the demonstrated lower limits of respiratory energy capable of fueling N2 fixation and reveals a link between the global carbon, nitrogen, and sulfur cycles.

Variation in benthic metabolism and nitrogen cycling across clam aquaculture sites.

PubMed

Murphy, Anna E; Nizzoli, Daniele; Bartoli, Marco; Smyth, Ashley R; Castaldelli, Giuseppe; Anderson, Iris C

2018-02-01

As bivalve aquaculture expands globally, an understanding of how it alters nitrogen is important to minimize impacts. This study investigated nitrogen cycling associated with clam aquaculture in the Sacca di Goro, Italy (Ruditapes philipinarum) and the Eastern Shore, USA (Mercenaria mercenaria). Ammonium and dissolved oxygen fluxes were positively correlated with clam biomass; R. philippinarum consumed ~6 times more oxygen and excreted ~5 times more NH 4 + than M. mercenaria. There was no direct effect of clams on denitrification or dissimilatory nitrate reduction to ammonium (DNRA); rather, nitrate availability controlled the competition between these microbial pathways. Highest denitrification rates were measured at sites where both water column nitrate and nitrification were elevated due to high densities of a burrowing amphipod (Corophium sp.). DNRA exceeded denitrification where water column nitrate was low and nitrification was suppressed in highly reduced sediment, potentially due to low hydrologic flow and high clam densities. Copyright © 2017 Elsevier Ltd. All rights reserved.

Report on the Biological Monitoring Program at Paducah Gaseous Diffusion Plant, January--December 1995

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

Kszos, L.A.

1996-04-01

The BMP for PGDP consists of three major tasks: (1) effluent and ambient toxicity monitoring, (2) bioaccumulation studies, and (3) ecological surveys of stream communities (benthic macroinvertebrates, fish). This report focuses on ESD activities occurring from Jan. 1995 to Dec. 1995, although activities conducted outside this period are included as appropriate.

Organic farming enhances soil microbial abundance and activity—A meta-analysis and meta-regression

PubMed Central

Symnaczik, Sarah; Mäder, Paul; De Deyn, Gerlinde; Gattinger, Andreas

2017-01-01

Population growth and climate change challenge our food and farming systems and provide arguments for an increased intensification of agriculture. A promising option is eco-functional intensification through organic farming, an approach based on using and enhancing internal natural resources and processes to secure and improve agricultural productivity, while minimizing negative environmental impacts. In this concept an active soil microbiota plays an important role for various soil based ecosystem services such as nutrient cycling, erosion control and pest and disease regulation. Several studies have reported a positive effect of organic farming on soil health and quality including microbial community traits. However, so far no systematic quantification of whether organic farming systems comprise larger and more active soil microbial communities compared to conventional farming systems was performed on a global scale. Therefore, we conducted a meta-analysis on current literature to quantify possible differences in key indicators for soil microbial abundance and activity in organic and conventional cropping systems. All together we integrated data from 56 mainly peer-reviewed papers into our analysis, including 149 pairwise comparisons originating from different climatic zones and experimental duration ranging from 3 to more than 100 years. Overall, we found that organic systems had 32% to 84% greater microbial biomass carbon, microbial biomass nitrogen, total phospholipid fatty-acids, and dehydrogenase, urease and protease activities than conventional systems. Exclusively the metabolic quotient as an indicator for stresses on microbial communities remained unaffected by the farming systems. Categorical subgroup analysis revealed that crop rotation, the inclusion of legumes in the crop rotation and organic inputs are important farming practices affecting soil microbial community size and activity. Furthermore, we show that differences in microbial size and activity between organic and conventional farming systems vary as a function of land use (arable, orchards, and grassland), plant life cycle (annual and perennial) and climatic zone. In summary, this study shows that overall organic farming enhances total microbial abundance and activity in agricultural soils on a global scale. PMID:28700609