Science Notes.

ERIC Educational Resources Information Center

School Science Review, 1985

1985-01-01

Presents biology, chemistry, physics, and health activities, experiments, demonstrations, and computer programs. Includes mechanism of stomatal opening, using aquatic plants to help demonstrate chemical buffering, microbial activity/contamination in milk samples, computer computation of fitness scores, reservoir project, complexes of transition…

Effect of pesticides on microbial communities in container aquatic habitats

USDA-ARS?s Scientific Manuscript database

Mosquitoes develop in a variety of aquatic habitats and feed on microbial communities associated with decaying organic matter. These aquatic habitats are often embedded within and around agricultural lands and are frequently exposed to agricultural chemicals. We used a microcosm approach to examine ...

Drastic changes in aquatic bacterial populations from the Cuatro Cienegas Basin (Mexico) in response to long-term environmental stress.

PubMed

Pajares, Silvia; Eguiarte, Luis E; Bonilla-Rosso, German; Souza, Valeria

2013-12-01

Understanding the changes of aquatic microbial community composition in response to changes in temperature and ultraviolet irradiation is relevant for predicting biogeochemical modifications in the functioning of natural microbial communities under global climate change scenarios. Herein we investigate shifts in the bacterioplankton composition in response to long-term changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with composite aquatic microbial communities from natural pools within the Cuatro Cienegas Basin (Mexican Chihuahuan desert) and were subject to different temperatures and UV conditions. 16S rRNA gene clone libraries were obtained from water samples at the mid-point (4 months) and the end of the experiment (8 months). An increase in bacterial diversity over time was found in the treatment of constant temperature and UV protection, which suggests that stable environments promote the establishment of complex and diverse bacterial community. Drastic changes in the phylogenetic bacterioplankton composition and structure were observed in response to fluctuating temperature and increasing UV radiation and temperature. Fluctuating temperature induced the largest decrease of bacterial richness during the experiment, indicating that frequent temperature changes drive the reduction in abundance of several species, most notably autotrophs. The long-term impact of these environmental stresses reduced diversity and selected for generalist aquatic bacterial populations, such as Porphyrobacter. These changes at the community level occur at an ecological time scale, suggesting that under global warming scenarios cascade effects on the food web are possible if the microbial diversity is modified.

Multipurpose floating platform for hyperspectral imaging, sampling and sensing of surface water sources used in irrigation and recreation

USDA-ARS?s Scientific Manuscript database

The objective of this work was to design, construct, and test the self-propelled aquatic platform for imaging, multi-tier water sampling, water quality sensing, and depth profiling to document microbial content and environmental covariates in the interior of irrigation ponds and reservoirs. The plat...

MICROBIAL INDICATORS OF AQUATIC ECOSYSTEM CHANGE: CURRENT APPLICATIONS TO EUTROPHICATION STUDIES. (R828677C001)

EPA Science Inventory

Human encroachment on aquatic ecosystems is increasing at an unprecedented rate. The impacts of human pollution and habitat alteration are most evident and of greatest concern at the microbial level, where a bulk of production and nutrient cycling takes place. Aquatic ecosyste...

The feasibility of automated online flow cytometry for in-situ monitoring of microbial dynamics in aquatic ecosystems

PubMed Central

Besmer, Michael D.; Weissbrodt, David G.; Kratochvil, Bradley E.; Sigrist, Jürg A.; Weyland, Mathias S.; Hammes, Frederik

2014-01-01

Fluorescent staining coupled with flow cytometry (FCM) is often used for the monitoring, quantification and characterization of bacteria in engineered and environmental aquatic ecosystems including seawater, freshwater, drinking water, wastewater, and industrial bioreactors. However, infrequent grab sampling hampers accurate characterization and subsequent understanding of microbial dynamics in all of these ecosystems. A logic technological progression is high throughput and full automation of the sampling, staining, measurement, and data analysis steps. Here we assess the feasibility and applicability of automated FCM by means of actual data sets produced with prototype instrumentation. As proof-of-concept we demonstrate examples of microbial dynamics in (i) flowing tap water from a municipal drinking water supply network and (ii) river water from a small creek subject to two rainfall events. In both cases, automated measurements were done at 15-min intervals during 12–14 consecutive days, yielding more than 1000 individual data points for each ecosystem. The extensive data sets derived from the automated measurements allowed for the establishment of baseline data for each ecosystem, as well as for the recognition of daily variations and specific events that would most likely be missed (or miss-characterized) by infrequent sampling. In addition, the online FCM data from the river water was combined and correlated with online measurements of abiotic parameters, showing considerable potential for a better understanding of cause-and-effect relationships in aquatic ecosystems. Although several challenges remain, the successful operation of an automated online FCM system and the basic interpretation of the resulting data sets represent a breakthrough toward the eventual establishment of fully automated online microbiological monitoring technologies. PMID:24917858

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).

Organo-mineral complexation alters carbon and nitrogen cycling in stream microbial assemblages

NASA Astrophysics Data System (ADS)

Hunter, William Ross; Wanek, Wolfgang; Prommer, Judith; Mooshammer, Maria; Battin, Tom

2014-05-01

Inland waters are of global biogeochemical importance receiving carbon inputs of ~ 4.8 Pg C y-1. Of this 12 % is buried, 18 % transported to the oceans, and 70 % supports aquatic secondary production. However, the mechanisms that determine the fate of organic matter (OM) in these systems are poorly defined. One important aspect is the formation of organo-mineral complexes in aquatic systems and their potential as a route for OM transport and burial vs. microbial utilization as organic carbon (C) and nitrogen (N) sources. Organo-mineral particles form by sorption of dissolved OM to freshly eroded mineral surfaces and may contribute to ecosystem-scale particulate OM fluxes. We tested the availability of mineral-sorbed OM as a C & N source for streamwater microbial assemblages and streambed biofilms. Organo-mineral particles were constructed in vitro by sorption of 13C:15N-labelled amino acids to hydrated kaolin particles, and microbial degradation of these particles compared with equivalent doses of 13C:15N-labelled free amino acids. Experiments were conducted in 120 ml mesocosms over 7 days using biofilms and streamwater sampled from the Oberer Seebach stream (Austria), tracing assimilation and mineralization of 13C and 15N labels from mineral-sorbed and dissolved amino acids. Here we present data on the effects of organo-mineral sorption upon amino acid mineralization and its C:N stoichiometry. Organo-mineral sorption had a significant effect upon microbial activity, restricting C and N mineralization by both the biofilm and streamwater treatments. Distinct differences in community response were observed, with both dissolved and mineral-stabilized amino acids playing an enhanced role in the metabolism of the streamwater microbial community. Mineral-sorption of amino acids differentially affected C & N mineralization and reduced the C:N ratio of the dissolved amino acid pool. The present study demonstrates that organo-mineral complexes restrict microbial degradation of OM and may, consequently, alter the carbon and nitrogen cycling dynamics within aquatic ecosystems.

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

PubMed

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

2018-04-01

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

Microbial Community Analysis in the Roots of Aquatic Plants and Isolation of Novel Microbes Including an Organism of the Candidate Phylum OP10

PubMed Central

Tanaka, Yasuhiro; Tamaki, Hideyuki; Matsuzawa, Hiroaki; Nigaya, Masahiro; Mori, Kazuhiro; Kamagata, Yoichi

2012-01-01

A number of molecular ecological studies have revealed complex and unique microbial communities in various terrestrial plant roots; however, little is known about the microbial communities of aquatic plant roots in spite of their potential use for water quality improvement in aquatic environments (e.g. floating treatment wetland system). Here, we report the microbial communities inhabiting the roots of emerged plants, reed (Phragmites australis) and Japanese loosestrife (Lythrum anceps), collected from a floating treatment wetland in a pond by both culture-independent and culture-dependent approaches. Culture-independent analysis based on 16S rRNA gene sequences revealed that the microbial compositions between the two aquatic plant roots were clearly different (e.g. the predominant microbe was Betaproteobacteria for reed and Alphaproteobacteria for Japanese loosestrife). In comparisons of microbial communities between the plant roots and pond water taken from near the plants, the microbial diversity in the plant roots (e.g. 4.40–4.26 Shannon-Weiner index) were higher than that of pond water (e.g. 3.15 Shannon-Weiner index). Furthermore, the plant roots harbored 2.5–3.5 times more phylogenetically novel clone phylotypes than pond water. The culture-dependent approach also revealed differences in the microbial composition and diversity among the two plant roots and pond water. More importantly, compared to pond water, we succeeded in isolating approximately two times more novel isolate phylotypes, including a bacterium of candidate phylum OP10 (recently named Armatimonadetes) from the plant roots. These findings suggest that aquatic plants roots are significant sources for a variety of novel organisms. PMID:22791047

Minimizing microbial contamination of sperm samples

USGS Publications Warehouse

Jenkins, Jill A.; Tiersch, Terrence R.; Green, Christopher C.

2011-01-01

Taken from the Methods section: With the collection and translocation of gametes from aquatic species, a potential hazard exists for microbial transfer. Contamination of semen can occur during collection, processing, storage, and transport. Some preventative measures are described below for limiting the spread and amplification of microorganisms such as bacteria, viruses, fungi, mycoplasmas, and parasites. Generally, sanitation during collection is essential. Materials and equipment used to freeze semen should be sterile. Following good practice guidelines for handling and processing samples collected for freezing is especially important for non-domestic animals where disease-free status cannot be guaranteed and unsophisticated technology is used (Russell et al. 1977).

Connecting Water Quality With Air Quality Through Microbial Aerosols

NASA Astrophysics Data System (ADS)

Dueker, M. Elias

Aerosol production from surface waters results in the transfer of aquatic materials (including nutrients and bacteria) to air. These materials can then be transported by onshore winds to land, representing a biogeochemical connection between aquatic and terrestrial systems not normally considered. In urban waterfront environments, this transfer could result in emissions of pathogenic bacteria from contaminated waters. Despite the potential importance of this link, sources, near-shore deposition, identity and viability of microbial aerosols are largely uncharacterized. This dissertation focuses on the environmental and biological mechanisms that define this water-air connection, as a means to build our understanding of the biogeochemical, biogeographical, and public health implications of the transfer of surface water materials to the near-shore environment in both urban and non-urban environments. The effects of tidal height, wind speed and fog on coastal aerosols and microbial content were first quantified on a non-urban coast of Maine, USA. Culture-based, culture-independent, and molecular methods were used to simultaneously sample microbial aerosols while monitoring meteorological parameters. Aerosols at this site displayed clear marine influence and high concentrations of ecologically-relevant nutrients. Coarse aerosol concentrations significantly increased with tidal height, onshore wind speed, and fog presence. Tidal height and fog presence did not significantly influence total microbial aerosol concentrations, but did have a significant effect on culturable microbial aerosol fallout. Molecular analyses of the microbes settling out of near-shore aerosols provided further evidence of local ocean to terrestrial transport of microbes. Aerosol and surface ocean bacterial communities shared species and in general were dominated by organisms previously sampled in marine environments. Fog presence strengthened the microbial connection between water and land through air by increasing microbial aerosol settling rates and enhancing viability of aerosolized marine microbes. Using methods developed for the non-urban site, the role of local environment and winds in mediating water-air connections was further investigated in the urban environment. The local environment, including water surfaces, was an important source of microbial aerosols at urban sites. Large portions of the urban waterfront microbial aerosol communities were aquatic and, at a highly polluted Superfund waterfront, were closely related to bacteria previously described in environments contaminated with hydrocarbons, heavy metals, sewage and other industrial waste. Culturable urban aerosols and surface waters contained bacterial genera known to include human pathogens and asthma agents. High onshore winds strengthened this water-air connection by playing both a transport and production role. The microbial connection between water and air quality outlined by this dissertation highlights the need for information on the mechanisms that deliver surface water materials to terrestrial systems on a much larger scale. Moving from point measurements to landscape-level analyses will allow for the quantitative assessment of implications for this microbial water-air-land transfer in both urban and non-urban arenas.

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.

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

PubMed

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

2015-06-15

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

Non-target effects on aquatic decomposer organisms of imidacloprid as a systemic insecticide to control emerald ash borer in riparian trees.

PubMed

Kreutzweiser, David; Good, Kevin; Chartrand, Derek; Scarr, Taylor; Thompson, Dean

2007-11-01

Imidacloprid is effective against emerald ash borer when applied as a systemic insecticide. Following stem or soil injections to trees in riparian areas, imidacloprid residues could be indirectly introduced to aquatic systems via leaf fall or leaching. Either route of exposure may affect non-target, aquatic decomposer organisms. Leaves from ash trees treated with imidacloprid at two field rates and an intentionally-high concentration were added to aquatic microcosms. Leaves from trees treated at the two field rates contained imidacloprid concentrations of 0.8-1.3 ppm, and did not significantly affect leaf-shredding insect survival, microbial respiration or microbial decomposition rates. Insect feeding rates were significantly inhibited at foliar concentrations of 1.3 ppm but not at 0.8 ppm. Leaves from intentionally high-dose trees contained concentrations of about 80 ppm, and resulted in 89-91% mortality of leaf-shredding insects, but no adverse effects on microbial respiration and decomposition rates. Imidacloprid applied directly to aquatic microcosms to simulate leaching from soils was at least 10 times more toxic to aquatic insects than the foliar concentrations, with high mortality at 0.13 ppm and significant feeding inhibition at 0.012 ppm.

The development and implementation of a method using blue mussels (Mytilus spp.) as biosentinels of Cryptosporidium spp. and Toxoplasma gondii contamination in marine aquatic environments

EPA Science Inventory

It is estimated that protozoan parasites still account for greater than one third of waterborne disease outbreaks reported. Methods used to monitor microbial contamination typically involve collecting discrete samples at specific time-points and analyzing for a single contaminan...

FlowCam: Quantification and Classification of Phytoplankton by Imaging Flow Cytometry.

PubMed

Poulton, Nicole J

2016-01-01

The ability to enumerate, classify, and determine biomass of phytoplankton from environmental samples is essential for determining ecosystem function and their role in the aquatic community and microbial food web. Traditional micro-phytoplankton quantification methods using microscopic techniques require preservation and are slow, tedious and very laborious. The availability of more automated imaging microscopy platforms has revolutionized the way particles and cells are detected within their natural environment. The ability to examine cells unaltered and without preservation is key to providing more accurate cell concentration estimates and overall phytoplankton biomass. The FlowCam(®) is an imaging cytometry tool that was originally developed for use in aquatic sciences and provides a more rapid and unbiased method for enumerating and classifying phytoplankton within diverse aquatic environments.

N-15 NMR spectra of naturally abundant nitrogen in soil and aquatic natural organic matter samples of the International Humic Substances Society

USGS Publications Warehouse

Thorn, K.A.; Cox, L.G.

2009-01-01

The naturally abundant nitrogen in soil and aquatic NOM samples from the International Humic Substances Society has been characterized by solid state CP/MAS 15N NMR. Soil samples include humic and fulvic acids from the Elliot soil, Minnesota Waskish peat and Florida Pahokee peat, as well as the Summit Hill soil humic acid and the Leonardite humic acid. Aquatic samples include Suwannee River humic, fulvic and reverse osmosis isolates, Nordic humic and fulvic acids and Pony Lake fulvic acid. Additionally, Nordic and Suwannee River XAD-4 acids and Suwannee River hydrophobic neutral fractions were analyzed. Similar to literature reports, amide/aminoquinone nitrogens comprised the major peaks in the solid state spectra of the soil humic and fulvic acids, along with heterocyclic and amino sugar/terminal amino acid nitrogens. Spectra of aquatic samples, including the XAD-4 acids, contain resolved heterocyclic nitrogen peaks in addition to the amide nitrogens. The spectrum of the nitrogen enriched, microbially derived Pony Lake, Antarctica fulvic acid, appeared to contain resonances in the region of pyrazine, imine and/or pyridine nitrogens, which have not been observed previously in soil or aquatic humic substances by 15N NMR. Liquid state 15N NMR experiments were also recorded on the Elliot soil humic acid and Pony Lake fulvic acid, both to examine the feasibility of the techniques, and to determine whether improvements in resolution over the solid state could be realized. For both samples, polarization transfer (DEPT) and indirect detection (1H-15N gHSQC) spectra revealed greater resolution among nitrogens directly bonded to protons. The amide/aminoquinone nitrogens could also be observed by direct detection experiments.

N-15 NMR spectra of naturally abundant nitrogen in soil and aquatic natural organic matter samples of the International Humic Substances Society

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

Thorn, Kevin A.; Cox, Larry G.

2009-02-28

The naturally abundant nitrogen in soil and aquatic NOM samples from the International Humic Substances Society has been characterized by solid state CP/MAS ¹⁵N NMR. Soil samples include humic and fulvic acids from the Elliot soil, Minnesota Waskish peat and Florida Pahokee peat, as well as the Summit Hill soil humic acid and the Leonardite humic acid. Aquatic samples include Suwannee River humic, fulvic and reverse osmosis isolates, Nordic humic and fulvic acids and Pony Lake fulvic acid. Additionally, Nordic and Suwannee River XAD-4 acids and Suwannee River hydrophobic neutral fractions were analyzed. Similar to literature reports, amide/aminoquinone nitrogens comprisedmore » the major peaks in the solid state spectra of the soil humic and fulvic acids, along with heterocyclic and amino sugar/terminal amino acid nitrogens. Spectra of aquatic samples, including the XAD-4 acids, contain resolved heterocyclic nitrogen peaks in addition to the amide nitrogens. The spectrum of the nitrogen enriched, microbially derived Pony Lake, Antarctica fulvic acid, appeared to contain resonances in the region of pyrazine, imine and/or pyridine nitrogens, which have not been observed previously in soil or aquatic humic substances by ¹⁵N NMR. Liquid state ¹⁵N NMR experiments were also recorded on the Elliot soil humic acid and Pony Lake fulvic acid, both to examine the feasibility of the techniques, and to determine whether improvements in resolution over the solid state could be realized. For both samples, polarization transfer (DEPT) and indirect detection (¹H–¹⁵N gHSQC) spectra revealed greater resolution among nitrogens directly bonded to protons. The amide/aminoquinone nitrogens could also be observed by direct detection experiments.« less

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem.

PubMed

Northrop, Amanda C; Brooks, Rachel; Ellison, Aaron M; Gotelli, Nicholas J; Ballif, Bryan A

2017-10-01

Aquatic ecosystem enrichment can lead to distinct and irreversible changes to undesirable states. Understanding changes in active microbial community function and composition following organic-matter loading in enriched ecosystems can help identify biomarkers of such state changes. In a field experiment, we enriched replicate aquatic ecosystems in the pitchers of the northern pitcher plant, Sarracenia purpurea . Shotgun metaproteomics using a custom metagenomic database identified proteins, molecular pathways, and contributing microbial taxa that differentiated control ecosystems from those that were enriched. The number of microbial taxa contributing to protein expression was comparable between treatments; however, taxonomic evenness was higher in controls. Functionally active bacterial composition differed significantly among treatments and was more divergent in control pitchers than enriched pitchers. Aerobic and facultative anaerobic bacteria contributed most to identified proteins in control and enriched ecosystems, respectively. The molecular pathways and contributing taxa in enriched pitcher ecosystems were similar to those found in larger enriched aquatic ecosystems and are consistent with microbial processes occurring at the base of detrital food webs. Detectable differences between protein profiles of enriched and control ecosystems suggest that a time series of environmental proteomics data may identify protein biomarkers of impending state changes to enriched states.

EFFECT OF DIFFERENT REGIONS OF AMPLIFIED 16S RDNA ON A PERFORMANCE OF A MULTIPLEXED, BEAD-BASED METHOD FOR ANALYSIS OF DNA SEQUENCES IN ENVIRONMENTAL SAMPLES.

EPA Science Inventory

Using a bead-based method for multiplexed analysis of community DNA, the dynamics of aquatic microbial communities can be assessed. Capture probes, specific for a genus or species of bacteria, are attached to the surface of uniquely labeled, microscopic polystyrene beads. Primers...

Biogeochemical cycling at the aquatic-terrestrial interface is linked to parafluvial hyporheic zone inundation history

NASA Astrophysics Data System (ADS)

Goldman, Amy E.; Graham, Emily B.; Crump, Alex R.; Kennedy, David W.; Romero, Elvira B.; Anderson, Carolyn G.; Dana, Karl L.; Resch, Charles T.; Fredrickson, Jim K.; Stegen, James C.

2017-09-01

The parafluvial hyporheic zone combines the heightened biogeochemical and microbial interactions indicative of a hyporheic region with direct atmospheric/terrestrial inputs and the effects of wet-dry cycles. Therefore, understanding biogeochemical cycling and microbial interactions in this ecotone is fundamental to understanding biogeochemical cycling at the aquatic-terrestrial interface and to creating robust hydrobiogeochemical models of dynamic river corridors. We aimed to (i) characterize biogeochemical and microbial differences in the parafluvial hyporheic zone across a small spatial domain (6 lateral meters) that spans a breadth of inundation histories and (ii) examine how parafluvial hyporheic sediments respond to laboratory-simulated re-inundation. Surface sediment was collected at four elevations along transects perpendicular to flow of the Columbia River, eastern WA, USA. The sediments were inundated by the river 0, 13, 127, and 398 days prior to sampling. Spatial variation in environmental variables (organic matter, moisture, nitrate, glucose, % C, % N) and microbial communities (16S and internal transcribed spacer (ITS) rRNA gene sequencing, qPCR) were driven by differences in inundation history. Microbial respiration did not differ significantly across inundation histories prior to forced inundation in laboratory incubations. Forced inundation suppressed microbial respiration across all histories, but the degree of suppression was dramatically different between the sediments saturated and unsaturated at the time of sample collection, indicating a binary threshold response to re-inundation. We present a conceptual model in which irregular hydrologic fluctuations facilitate microbial communities adapted to local conditions and a relatively high flux of CO2. Upon rewetting, microbial communities are initially suppressed metabolically, which results in lower CO2 flux rates primarily due to suppression of fungal respiration. Following prolonged inundation, the microbial community adapts to saturation by shifting composition, and the CO2 flux rebounds to prior levels due to the subsequent change in respiration. Our results indicate that the time between inundation events can push the system into alternate states: we suggest (i) that, above some threshold of inundation interval, re-inundation suppresses respiration to a consistent, low rate and (ii) that, below some inundation interval, re-inundation has a minor effect on respiration. Extending reactive transport models to capture processes that govern such dynamics will provide more robust predictions of river corridor biogeochemical function under altered surface water flow regimes in both managed and natural watersheds.

Microplastic-associated bacterial assemblages in the intertidal zone of the Yangtze Estuary.

PubMed

Jiang, Peilin; Zhao, Shiye; Zhu, Lixin; Li, Daoji

2018-05-15

Plastic trash is common in oceans. Terrestrial and marine ecosystem interactions occur in the intertidal zone where accumulation of plastic frequently occurs. However, knowledge of the plastic-associated microbial community (the plastisphere) in the intertidal zone is scanty. We used high-throughput sequencing to profile the bacterial communities attached to microplastic samples from intertidal locations around the Yangtze estuary in China. The structure and composition of plastisphere communities varied significantly among the locations. We found the taxonomic composition on microplastic samples was related to their sedimentary and aquatic origins. Correlation network analysis was used to identify keystone bacterial genera (e.g. Rhodobacterales, Sphingomonadales and Rhizobiales), which represented important microbial associations within the plastisphere community. Other species (i.e. potential pathogens) were considered as hitchhikers in the plastic attached microbial communities. Metabolic pathway analysis suggested adaptations of these bacterial assemblages to the plastic surface-colonization lifestyle. These adaptations included reduced "cell motility" and greater "xenobiotics biodegradation and metabolism." The findings illustrate the diverse microbial assemblages that occur on microplastic and increase our understanding of plastisphere ecology. Copyright © 2017 Elsevier B.V. All rights reserved.

Phytotechnological purification of water and bio energy utilization of plant biomass

NASA Astrophysics Data System (ADS)

Stom, D. I.; Gruznych, O. V.; Zhdanova, G. O.; Timofeeva, S. S.; Kashevsky, A. V.; Saksonov, M. N.; Balayan, A. E.

2017-01-01

The aim of the study was to explore the possibility of using the phytomass of aquatic plants as the substrate in the microbial fuel cells and selection of microorganisms suitable for the generation of electricity on this substrate. The conversion of chemical energy of phytomass of aquatic plants to the electrical energy was carried out in a microbial fuel cells by biochemical transformation. As biological agents in the generation of electricity in the microbial fuel cells was used commercial microbial drugs “Doctor Robic 109K” and “Vostok-EM-1”. The results of evaluation of the characteristics of electrogenic (amperage, voltage) and the dynamics of the growth of microorganisms in the microbial fuel cells presents in the experimental part. As a source of electrogenic microorganisms is possible to use drugs “Dr. Robic 109K” and “Vostok-EM-1” was established. The possibility of utilization of excess phytomass of aquatic plants, formed during the implementation of phytotechnological purification of water, in microbial fuel cells, was demonstrated. The principal possibility of creating hybrid phytotechnology (plant-microbe cells), allowing to obtain electricity as a product, which can be used to ensure the operation of the pump equipment and the creation of a full cycle of resource-saving technologies for water treatment, was reviewed.

Identifying the core seed bank of a complex boreal bacterial metacommunity.

PubMed

Ruiz-González, Clara; Niño-García, Juan Pablo; Kembel, Steven W; Del Giorgio, Paul A

2017-09-01

Seed banks are believed to contribute to compositional changes within and across microbial assemblages, but the application of this concept to natural communities remains challenging. Here we describe the core seed bank of a bacterial metacommunity from a boreal watershed, using the spatial distribution of bacterial operational taxonomic units (OTUs) across 223 heterogeneous terrestrial, aquatic and phyllosphere bacterial assemblages. Taxa were considered potential seeds if they transitioned from rare to abundant somewhere within the metacommunity and if they were ubiquitous and able to persist under unfavorable conditions, the latter assessed by checking their presence in three deeply sequenced samples (one soil, one river and one lake, 2.2-3 million reads per sample). We show that only a small fraction (13%) of all detected OTUs constitute a metacommunity seed bank that is shared between all terrestrial and aquatic communities, but not by phyllosphere assemblages, which seem to recruit from a different taxa pool. Our results suggest directional recruitment driven by the flow of water in the landscape, since most aquatic sequences were associated to OTUs found in a single deeply-sequenced soil sample, but only 45% of terrestrial sequences belonged to OTUs found in the two deeply-sequenced aquatic communities. Finally, we hypothesize that extreme rarity, and its interplay with water residence time and growth rates, may further constrain the size of the potential seed bank.

A simple pore water hydrogen diffusion syringe sampler

USGS Publications Warehouse

Vroblesky, D.A.; Chapelle, F.H.; Bradley, P.M.

2007-01-01

Molecular hydrogen (H2) is an important intermediate product and electron donor in microbial metabolism. Concentrations of dissolved H 2 are often diagnostic of the predominant terminal electron-accepting processes in ground water systems or aquatic sediments. H2 concentrations are routinely measured in ground water monitoring wells but are rarely measured in saturated aquatic sediments due to a lack of simple and practical sampling methods. This report describes the design and development (including laboratory and field testing) of a simple, syringe-based H 2 sampler in (1) saturated, riparian sediments, (2) surface water bed sediments, and (3) packed intervals of a fractured bedrock borehole that are inaccessible by standard pumped methods. ?? 2007 National Ground Water Association.

Investigating microbial transformations of soil organic matter: synthesizing knowledge from disparate fields to guide new experimentation

NASA Astrophysics Data System (ADS)

Billings, S. A.; Tiemann, L. K.; Ballantyne, F., IV; Lehmeier, C. A.; Min, K.

2015-04-01

Discerning why some soil organic matter (SOM) leaves soil profiles relatively quickly while other compounds, especially at depth, can be retained for decades to millennia is challenging for a multitude of reasons. Simultaneous with soil-specific advances, multiple other disciplines have enhanced their knowledge bases in ways potentially useful for future investigations of SOM decay. In this article, we highlight observations highly relevant for those investigating SOM decay and retention but often emanating from disparate fields and residing in literature seldom cited in SOM research. We focus on recent work in two key areas. First, we turn to experimental approaches using natural and artificial aquatic environments to investigate patterns of microbially mediated OM transformations as environmental conditions change, and highlight how aquatic microbial responses to environmental change can reveal processes likely important to OM decay and retention in soils. Second, we emphasize the importance of establishing intrinsic patterns of decay kinetics for purified substrates commonly found in soils to develop baseline rates. These decay kinetics - which represent the upper limit of the reaction rates - can then be compared to substrate decay kinetics observed in natural samples, which integrate intrinsic decay reaction rates and edaphic factors essential to the site under study but absent in purified systems. That comparison permits the site-specific factors to be parsed from the fundamental decay kinetics, an important advance in our understanding of SOM decay (and thus persistence) in natural systems. We then suggest ways in which empirical observations from aquatic systems and purified substrate-enzyme reaction kinetics can be used to advance recent theoretical efforts in SOM-focused research. Finally, we suggest how the observations in aquatic and purified substrate-enzyme systems could be used to help unravel the puzzles presented by oft-observed patterns of SOM characteristics with depth, as one example of the many perplexing SOM-related problems.

40 CFR 158.2174 - Experimental use permit microbial pesticides nontarget organisms and environmental fate data...

Code of Federal Regulations, 2011 CFR

2011-07-01

... describe how to use this table to determine the terrestrial and aquatic nontarget organisms data... this section. (b) Use patterns. Aquatic uses include: food and feed, nonfood uses (e.g., outdoor... Organisms and Environmental Fate Data Requirements Guideline Number Data Requirement Use Patterns Aquatic...

Aquatic bacterial assemblage structure in Pozas Azules, Cuatro Cienegas Basin, Mexico: Deterministic vs. stochastic processes.

PubMed

Espinosa-Asuar, Laura; Escalante, Ana Elena; Gasca-Pineda, Jaime; Blaz, Jazmín; Peña, Lorena; Eguiarte, Luis E; Souza, Valeria

2015-06-01

The aim of this study was to determine the contributions of stochastic vs. deterministic processes in the distribution of microbial diversity in four ponds (Pozas Azules) within a temporally stable aquatic system in the Cuatro Cienegas Basin, State of Coahuila, Mexico. A sampling strategy for sites that were geographically delimited and had low environmental variation was applied to avoid obscuring distance effects. Aquatic bacterial diversity was characterized following a culture-independent approach (16S sequencing of clone libraries). The results showed a correlation between bacterial beta diversity (1-Sorensen) and geographic distance (distance decay of similarity), which indicated the influence of stochastic processes related to dispersion in the assembly of the ponds' bacterial communities. Our findings are the first to show the influence of dispersal limitation in the prokaryotic diversity distribution of Cuatro Cienegas Basin. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Microbial plant litter decomposition in aquatic and terrestrial boreal systems along a natural fertility gradient

NASA Astrophysics Data System (ADS)

Soares, A. Margarida P. M.; Kritzberg, Emma S.; Rousk, Johannes

2017-04-01

Plant litter decomposition is a global ecosystem process, with a crucial role in carbon and nutrient cycling. The majority of litter processing occurs in terrestrial systems, but an important fraction also takes place in inland waters. Among environmental factors, pH impacts the litter decomposition through its selective influence on microbial decomposers. Fungal communities are less affected by pH than bacteria, possibly owing to a wider pH tolerance by this group. On the other hand, bacterial pH optima are constrained to a narrower range of pH values. The microbial decomposition of litter is universally nutrient limited; but few comparisons exist between terrestrial and aquatic systems. We investigated the microbial colonisation and decomposition of plant litter along a fertility gradient, which varied in both pH and N availability in both soil and adjacent water. To do this we installed litterbags with birch (Betula pendula) in streams and corresponding soils in adjacent riparian areas in a boreal system, in Krycklan, Sweden. During the four months covering the ice-free growth season we monitored the successional dynamics of fungal (acetate incorporation into ergosterol) and bacterial growth (thymidine incorporation), microbial respiration in leaf litter, and quantitative and qualitative changes in litter over time. We observed that bacterial growth rates were initially higher in litter decomposing in streams than those in soils, but differences between terrestrial and aquatic bacterial production converged towards the end of the experiment. In litter bags installed in soils, bacterial growth was lower at sites with more acidic pH and lower N availability, while aquatic bacteria were relatively unaffected by the fertility level. Fungal growth rates were two-fold higher for litter decomposing in streams than in soils. In aquatic systems, fungal growth was initially lower in low fertility sites, but differences gradually disappeared over the time course. Fungal growth rates measured on litter-bags in soils were relatively stable over time, with unclear links to fertility. Microbial respiration rates were highest in litterbags buried in soils, and only initially negatively affected by pH. There was a large decrease in litter mass loss initially in aquatic systems. Subsequently the rates of loss stabilized to similar values to those in terrestrial systems, to finally be exceeded by the rates of loss in terrestrial systems. In conclusion, initial decomposition of litter appeared to be N-limited in aquatic systems, which was associated with a fungal dominance. In contrast, litter decomposition in terrestrial systems appeared to be lower in acidic sites, which coincided with lower growth rates of bacteria. Litter degradation was initially faster in aquatic systems, but overall mass-loss over the full time course was higher in terrestrial systems.

Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI

PubMed Central

Hengy, Miranda H.; Horton, Dean J.; Uzarski, Donald G.

2017-01-01

Lakes are dynamic and complex ecosystems that can be influenced by physical, chemical, and biological processes. Additionally, individual lakes are often chemically and physically distinct, even within the same geographic region. Here we show that differences in physicochemical conditions among freshwater lakes located on (and around) the same island, as well as within the water column of each lake, are significantly related to aquatic microbial community diversity. Water samples were collected over time from the surface and bottom-water within four freshwater lakes located around Beaver Island, MI within the Laurentian Great Lakes region. Three of the sampled lakes experienced seasonal lake mixing events, impacting either O2, pH, temperature, or a combination of the three. Microbial community alpha and beta diversity were assessed and individual microbial taxa were identified via high-throughput sequencing of the 16S rRNA gene. Results demonstrated that physical and chemical variability (temperature, dissolved oxygen, and pH) were significantly related to divergence in the beta diversity of surface and bottom-water microbial communities. Despite its correlation to microbial community structure in unconstrained analyses, constrained analyses demonstrated that dissolved organic carbon (DOC) concentration was not strongly related to microbial community structure among or within lakes. Additionally, several taxa were correlated (either positively or negatively) to environmental variables, which could be related to aerobic and anaerobic metabolisms. This study highlights the measurable relationships between environmental conditions and microbial communities within freshwater temperate lakes around the same island. PMID:29062609

Marcellus and mercury: Assessing potential impacts of unconventional natural gas extraction on aquatic ecosystems in northwestern Pennsylvania.

PubMed

Grant, Christopher J; Weimer, Alexander B; Marks, Nicole K; Perow, Elliott S; Oster, Jacob M; Brubaker, Kristen M; Trexler, Ryan V; Solomon, Caroline M; Lamendella, Regina

2015-01-01

Mercury (Hg) is a persistent element in the environment that has the ability to bioaccumulate and biomagnify up the food chain with potentially harmful effects on ecosystems and human health. Twenty-four streams remotely located in forested watersheds in northwestern PA containing naturally reproducing Salvelinus fontinalis (brook trout), were targeted to gain a better understanding of how Marcellus shale natural gas exploration may be impacting water quality, aquatic biodiversity, and Hg bioaccumulation in aquatic ecosystems. During the summer of 2012, stream water, stream bed sediments, aquatic mosses, macroinvertebrates, crayfish, brook trout, and microbial samples were collected. All streams either had experienced hydraulic fracturing (fracked, n = 14) or not yet experienced hydraulic fracturing (non-fracked, n = 10) within their watersheds at the time of sampling. Analysis of watershed characteristics (GIS) for fracked vs non-fracked sites showed no significant differences (P > 0.05), justifying comparisons between groups. Results showed significantly higher dissolved total mercury (FTHg) in stream water (P = 0.007), lower pH (P = 0.033), and higher dissolved organic matter (P = 0.001) at fracked sites. Total mercury (THg) concentrations in crayfish (P = 0.01), macroinvertebrates (P = 0.089), and predatory macroinvertebrates (P = 0.039) were observed to be higher for fracked sites. A number of positive correlations between amount of well pads within a watershed and THg in crayfish (r = 0.76, P < 0.001), THg in predatory macroinvertebrates (r = 0.71, P < 0.001), and THg in brook trout (r = 0.52, P < 0.01) were observed. Stream-water microbial communities within the Deltaproteobacteria also shared a positive correlation with FTHg and to the number of well pads, while stream pH (r = -0.71, P < 0.001), fish biodiversity (r = -0.60, P = 0.02), and macroinvertebrate taxa richness (r = -0.60, P = 0.01) were negatively correlated with the number of well pads within a watershed. Further investigation is needed to better elucidate relationships and pathways of observed differences in stream water chemistry, biodiversity, and Hg bioaccumulation, however, initial findings suggest Marcellus shale natural gas exploration is having an effect on aquatic ecosystems.

MICROBIAL ENZYME ACTIVITY FOR CHARACTERIZING NUTRIENT LOADING TO GREAT LAKES COASTAL WETLANDS

EPA Science Inventory

Energy and material flows in aquatic ecosystems are mediated by microbial carbon and nutrient cycling. Extracellular enzymes produced by the microbial community aid in the degradation of organic matter and the resultant acquisition of limiting nutrients. Organic carbon sequestrat...

Microbial ecology of the salmon necrobiome: evidence salmon carrion decomposition influences aquatic and terrestrial insect microbiomes.

PubMed

Pechal, Jennifer L; Benbow, M Eric

2016-05-01

Carrion decomposition is driven by complex relationships that affect necrobiome community (i.e. all organisms and their genes associated with a dead animal) interactions, such as insect species arrival time to carrion and microbial succession. Little is understood about how microbial communities interact with invertebrates at the aquatic-terrestrial habitat interface. The first objective of the study was to characterize internal microbial communities using high-throughput sequencing of 16S rRNA gene amplicons for aquatic insects (three mayfly species) in streams with salmon carcasses compared with those in streams without salmon carcasses. The second objective was to assess the epinecrotic microbial communities of decomposing salmon carcasses (Oncorhynchus keta) compared with those of terrestrial necrophagous insects (Calliphora terraenovae larvae and adults) associated with the carcasses. There was a significant difference in the internal microbiomes of mayflies collected in salmon carcass-bearing streams and in non-carcass streams, while the developmental stage of blow flies was the governing factor in structuring necrophagous insect internal microbiota. Furthermore, the necrophagous internal microbiome was influenced by the resource on which the larvae developed, and changes in the adult microbiome varied temporally. Overall, these carrion subsidy-driven networks respond to resource pulses with bottom-up effects on consumer microbial structure, as revealed by shifting communities over space and time. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Microplastic-associated Bacterial Assemblages in the Intertidal Zone

NASA Astrophysics Data System (ADS)

Jiang, P.; Zhao, S.; Zhu, L.; Li, D.

2017-12-01

Plastic debris is posing a planetary-scale threat. As a zone where terrestrial and marine ecosystems interactions occur, the accumulation of plastic marine debris (PMD) in intertidal environments has been well documented. But the information of plastic-associated microbial community (the "Plastisphere") in the intertidal zone is scanty. Utilizing the high-throughput sequencing, we profiled the bacterial communities attached to microplastic samples from the intertidal locations around Yangtze estuary. The structure and composition of Plastisphere communities in current study varied significantly with geographical stations. The taxonomic composition on microplastic samples implied their sedimental and aquatic origins. Some members of hydrocarbon degrading microorganisms and potential pathogens were detected on microplastic. Overall, our findings fuel the evidence for the occurrence of diverse microbial assemblages on PMD and improving our understanding of Plastisphere ecology, which could support the management action and policy change related to PMD.

Fate of organo-mineral particles in streams: Microbial degradation by streamwater & biofilm assemblages

NASA Astrophysics Data System (ADS)

Hunter, W. R.; Raich, M.; Wanek, W.; Battin, T. J.

2013-12-01

Inland waters are of global biogeochemical importance. They receive carbon inputs of ~ 4.8 Pg C/ y of which, 12 % is buried, 18 % transported to the oceans, and 70 % supports aquatic secondary production. However, the mechanisms that determine the fate of organic matter (OM) in these systems are poorly defined. One aspect of this is the formation of organo-mineral complexes in aquatic systems and their potential as a route for OM transport and burial vs. their use as carbon (C) and nitrogen (N) sources within aquatic systems. Organo-mineral particles form by sorption of dissolved OM to freshly eroded mineral surfaces and may contribute to ecosystem-scale particulate OM fluxes. We experimentally tested the availability of mineral-sorbed OM as a C & N source for streamwater microbial assemblages and streambed biofilms. Organo-mineral particles were constructed in vitro by sorption of 13C:15N-labelled amino acids to hydrated kaolin particles, and microbial degradation of these particles compared with equivalent doses of 13C:15N-labelled free amino acids. Experiments were conducted in 120 ml mesocosms over 7 days using biofilms and water sampled from the Oberer Seebach stream (Austria). Each incubation experienced a 16:8 light:dark regime, with metabolism monitored via changes in oxygen concentrations between photoperiods. The relative fate of the organo-mineral particles was quantified by tracing the mineralization of the 13C and 15N labels and their incorporation into microbial biomass. Here we present the initial results of 13C-label mineralization, incorporation and retention within dissolved organic carbon pool. The results indicate that 514 (× 219) μmol/ mmol of the 13:15N labeled free amino acids were mineralized over the 7-day incubations. By contrast, 186 (× 97) μmol/ mmol of the mineral-sorbed amino acids were mineralized over a similar period. Thus, organo-mineral complexation reduced amino acid mineralization by ~ 60 %, with no differences observed between the streamwater and biofilm assemblages. Throughout the incubations, biofilms were observed to leach dissolved organic carbon (DOC). However, within the streamwater assemblage the presence of both organo-mineral particles and kaolin particles was associated with significant DOC removal (-1.7 % and -7.5 % respectively). Consequently, the study demonstrates that mineral and organo-mineral particles can limit the availability of DOC in aquatic systems, providing nucleation sites for flocculation and fresh mineral surfaces, which facilitate OM-sorption. The formation of these organo-mineral particles subsequently restricts microbial OM degradation, potentially altering the transport and facilitating the burial of OM within streams.

Characterizing Microbial Community and Geochemical Dynamics at Hydrothermal Vents Using Osmotically Driven Continuous Fluid Samplers

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

Robidart, Julie C.; Callister, Stephen J.; Song, Peng F.

2013-05-07

Microbes play a key role in mediating all aquatic biogeochemical cycles, and ongoing efforts are aimed at better understanding the relationships between microbial phylogenetic and physiological diversity, and habitat physical and chemical characteristics. Establishing such relationships is facilitated by sampling and studying microbiology and geochemistry at the appropriate spatial and temporal scales, to access information on the past and current environmental state that contributes to observed microbial abundances and activities. A modest number of sampling systems exist to date, few of which can be used in remote, harsh environments such as hydrothermal vents, where the ephemeral nature of venting underscoresmore » the necessity for higher resolution sampling. We have developed a robust, continuous fluid sampling system for co-registered microbial and biogeochemical analyses. The osmosis-powered bio-osmosampling system (BOSS) use no electricity, collects fluids with daily resolution or better, can be deployed in harsh, inaccessible environments and can sample fluids continuously for up to five years. Here we present a series of tests to examine DNA, RNA and protein stability over time, as well as material compatability, via lab experiments. We also conducted two field deployments at deep-sea hydrothermal vents to assess changes in microbial diversity and protein expression as a function of the physico-chemical environment. Our data reveal significant changes in microbial community composition co-occurring with relatively modest changes in the geochemistry. These data additionally provide new insights into the distribution of an enigmatic sulfur oxidizing symbiont in its free-living state. Data from the second deployment reveal differences in the representation of peptides over time, underscoring the utility of the BOSS in meta-proteomic studies. In concert, these data demonstrate the efficacy of this approach, and illustrate the value of using this method to study microbial and geochemical phenomena.« less

Recent Advances in Microbial Single Cell Genomics Technology and Applications

NASA Astrophysics Data System (ADS)

Stepanauskas, R.

2016-02-01

Single cell genomics is increasingly utilized as a powerful tool to decipher the metabolic potential, evolutionary histories and in situ interactions of environmental microorganisms. This transformative technology recovers extensive information from cultivation-unbiased samples of individual, unicellular organisms. Thus, it does not require data binning into arbitrary phylogenetic or functional groups and therefore is highly compatible with agent-based modeling approaches. I will present several technological advances in this field, which significantly improve genomic data recovery from individual cells and provide direct linkages between cell's genomic and phenotypic properties. I will also demonstrate how these new technical capabilities help understanding the metabolic potential and viral infections of the "microbial dark matter" inhabiting aquatic and subsurface environments.

MICROBIAL TRANSFORMATION OF SELECTED ORGANIC CHEMICALS IN NATURAL AQUATIC SYSTEMS

EPA Science Inventory

A method for describing the microbial degradation of xenobiotics through the use of a second-order reaction equation was tested in several water bodies in the United States and Russia. he experiment was aimed at studying the microbial transformation of a herbicide widely used in ...

Virioplankton: Viruses in Aquatic Ecosystems†

PubMed Central

Wommack, K. Eric; Colwell, Rita R.

2000-01-01

The discovery that viruses may be the most abundant organisms in natural waters, surpassing the number of bacteria by an order of magnitude, has inspired a resurgence of interest in viruses in the aquatic environment. Surprisingly little was known of the interaction of viruses and their hosts in nature. In the decade since the reports of extraordinarily large virus populations were published, enumeration of viruses in aquatic environments has demonstrated that the virioplankton are dynamic components of the plankton, changing dramatically in number with geographical location and season. The evidence to date suggests that virioplankton communities are composed principally of bacteriophages and, to a lesser extent, eukaryotic algal viruses. The influence of viral infection and lysis on bacterial and phytoplankton host communities was measurable after new methods were developed and prior knowledge of bacteriophage biology was incorporated into concepts of parasite and host community interactions. The new methods have yielded data showing that viral infection can have a significant impact on bacteria and unicellular algae populations and supporting the hypothesis that viruses play a significant role in microbial food webs. Besides predation limiting bacteria and phytoplankton populations, the specific nature of virus-host interaction raises the intriguing possibility that viral infection influences the structure and diversity of aquatic microbial communities. Novel applications of molecular genetic techniques have provided good evidence that viral infection can significantly influence the composition and diversity of aquatic microbial communities. PMID:10704475

Balancing macronutrient stoichiometry to alleviate eutrophication.

PubMed

Stutter, M I; Graeber, D; Evans, C D; Wade, A J; Withers, P J A

2018-09-01

Reactive nitrogen (N) and phosphorus (P) inputs to surface waters modify aquatic environments, affect public health and recreation. Source controls dominate eutrophication management, whilst biological regulation of nutrients is largely neglected, although aquatic microbial organisms have huge potential to process nutrients. The stoichiometric ratio of organic carbon (OC) to N to P atoms should modulate heterotrophic pathways of aquatic nutrient processing, as high OC availability favours aquatic microbial processing. Heterotrophic microbial processing removes N by denitrification and captures N and P as organically-complexed, less eutrophying forms. With a global data synthesis, we show that the atomic ratios of bioavailable dissolved OC to either N or P in rivers with urban and agricultural land use are often distant from a "microbial optimum". This OC-deficiency relative to high availabilities of N and P likely overwhelms within-river heterotrophic processing. We propose that the capability of streams and rivers to retain N and P may be improved by active stoichiometric rebalancing. Although autotrophic OC production contributes to heterotrophic rates substantial control on nutrient processing from allochthonous OC is documented for N and an emerging field for P. Hence, rebalancing should be done by reconnecting appropriate OC sources such as wetlands and riparian forests that have become disconnected from rivers concurrent with agriculture and urbanisation. However, key knowledge gaps require research prior to the safe implementation of this approach in management: (i) to evaluate system responses to catchment inputs of dissolved OC forms and amounts relative to internal production of autotrophic dissolved OC and aquatic and terrestrial particulate OC and (ii) evaluate risk factors in anoxia-mediated P desorption with elevated OC scenarios. Still, we find stoichiometric rebalancing through reconnecting landscape beneficial OC sources has considerable potential for river management to alleviate eutrophication, improve water quality and aquatic ecosystem health, if augmenting nutrient source control. Copyright © 2018 Elsevier B.V. All rights reserved.

PHYLOGENETIC AND FUNCTIONAL DIVERSITY OF SEAGULL AND CANADIAN GEESE FECAL MICROBIAL COMMUNITIES

EPA Science Inventory

In spite of increasing public health concerns on the risks associated with swimming in waters contaminated with waterfowl feces, there is little information on the gut microbial communities of aquatic birds. To address the molecular microbial diversity of waterfowl, 16S rDNA and ...

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams

PubMed Central

Ren, Ze; Wang, Fang; Qu, Xiaodong; Elser, James J.; Liu, Yang; Chu, Limin

2017-01-01

Understanding microbial communities in terms of taxon and function is essential to decipher the biogeochemical cycling in aquatic ecosystems. Lakes and their input streams are highly linked. However, the differences between microbial assemblages in streams and lakes are still unclear. In this study, we conducted an intensive field sampling of microbial communities from lake water and stream biofilms in the Qinghai Lake watershed, the largest lake in China. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and predicted functional profiles using PICRUSt to determine the taxonomic and functional differences between microbial communities in stream biofilms and lake water. The results showed that stream biofilms and lake water harbored distinct microbial communities. The microbial communities were different taxonomically and functionally between stream and lake. Moreover, streams biofilms had a microbial network with higher connectivity and modularity than lake water. Functional beta diversity was strongly correlated with taxonomic beta diversity in both the stream and lake microbial communities. Lake microbial assemblages displayed greater predicted metabolic potentials of many metabolism pathways while the microbial assemblages in stream biofilms were more abundant in xenobiotic biodegradation and metabolism and lipid metabolism. Furthermore, lake microbial assemblages had stronger predicted metabolic potentials in amino acid metabolism, carbon fixation, and photosynthesis while stream microbial assemblages were higher in carbohydrate metabolism, oxidative phosphorylation, and nitrogen metabolism. This study adds to our knowledge of stream-lake linkages from the functional and taxonomic composition of microbial assemblages. PMID:29213266

Multispecies Biofilms Transform Selenium Oxyanions into Elemental Selenium Particles: Studies Using Combined Synchrotron X-ray Fluorescence Imaging and Scanning Transmission X-ray Microscopy.

PubMed

Yang, Soo In; George, Graham N; Lawrence, John R; Kaminskyj, Susan G W; Dynes, James J; Lai, Barry; Pickering, Ingrid J

2016-10-04

Selenium (Se) is an element of growing environmental concern, because low aqueous concentrations can lead to biomagnification through the aquatic food web. Biofilms, naturally occurring microbial consortia, play numerous important roles in the environment, especially in biogeochemical cycling of toxic elements in aquatic systems. The complexity of naturally forming multispecies biofilms presents challenges for characterization because conventional microscopic techniques require chemical and physical modifications of the sample. Here, multispecies biofilms biotransforming selenium oxyanions were characterized using X-ray fluorescence imaging (XFI) and scanning transmission X-ray microscopy (STXM). These complementary synchrotron techniques required minimal sample preparation and were applied correlatively to the same biofilm areas. Sub-micrometer XFI showed distributions of Se and endogenous metals, while Se K-edge X-ray absorption spectroscopy indicated the presence of elemental Se (Se 0 ). Nanoscale carbon K-edge STXM revealed the distributions of microbial cells, extracellular polymeric substances (EPS), and lipids using the protein, saccharide, and lipid signatures, respectively, together with highly localized Se 0 using the Se L III edge. Transmission electron microscopy showed the electron-dense particle diameter to be 50-700 nm, suggesting Se 0 nanoparticles. The intimate association of Se 0 particles with protein and polysaccharide biofilm components has implications for the bioavailability of selenium in the environment.

Multispecies Biofilms Transform Selenium Oxyanions into Elemental Selenium Particles: Studies Using Combined Synchrotron X-ray Fluorescence Imaging and Scanning Transmission X-ray Microscopy

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

Yang, Soo In; George, Graham N.; Lawrence, John R.

2016-10-04

Selenium (Se) is an element of growing environmental concern, because low aqueous concentrations can lead to biomagnification through the aquatic food web. Biofilms, naturally occurring microbial consortia, play numerous important roles in the environment, especially in biogeochemical cycling of toxic elements in aquatic systems. The complexity of naturally forming multispecies biofilms presents challenges for characterization because conventional microscopic techniques require chemical and physical modifications of the sample. Here, multispecies biofilms biotransforming selenium oxyanions were characterized using X-ray fluorescence imaging (XFI) and scanning transmission X-ray microscopy (STXM). These complementary synchrotron techniques required minimal sample preparation and were applied correlatively to themore » same biofilm areas. Sub-micrometer XFI showed distributions of Se and endogenous metals, while Se K-edge X-ray absorption spectroscopy indicated the presence of elemental Se (Se0). Nanoscale carbon K-edge STXM revealed the distributions of microbial cells, extracellular polymeric substances (EPS), and lipids using the protein, saccharide, and lipid signatures, respectively, together with highly localized Se0 using the Se LIII edge. Transmission electron microscopy showed the electron-dense particle diameter to be 50–700 nm, suggesting Se0 nanoparticles. The intimate association of Se0 particles with protein and polysaccharide biofilm components has implications for the bioavailability of selenium in the environment.« less

Microbial mediated retention/transformation of organic and inorganic materials in freshwater and marine ecosystems

EPA Science Inventory

Aquatic ecosystems are globally connected by hydrological and biogeochemical cycles. Microorganisms inhabiting aquatic ecosystems form the basis of food webs, mediate essential element cycles, decompose natural organic matter, transform inorganic nutrients and metals, and degrad...

A network-based approach to disturbance transmission through microbial interactions

PubMed Central

Hunt, Dana E.; Ward, Christopher S.

2015-01-01

Microbes numerically dominate aquatic ecosystems and play key roles in the biogeochemistry and the health of these environments. Due to their short generations times and high diversity, microbial communities are among the first responders to environmental changes, including natural and anthropogenic disturbances such as storms, pollutant releases, and upwelling. These disturbances affect members of the microbial communities both directly and indirectly through interactions with impacted community members. Thus, interactions can influence disturbance propagation through the microbial community by either expanding the range of organisms affected or buffering the influence of disturbance. For example, interactions may expand the number of disturbance-affected taxa by favoring a competitor or buffer the impacts of disturbance when a potentially disturbance-responsive clade’s growth is limited by an essential microbial partner. Here, we discuss the potential to use inferred ecological association networks to examine how disturbances propagate through microbial communities focusing on a case study of a coastal community’s response to a storm. This approach will offer greater insight into how disturbances can produce community-wide impacts on aquatic environments following transient changes in environmental parameters. PMID:26579091

Microbial reduction of uranium

USGS Publications Warehouse

Lovley, D.R.; Phillips, E.J.P.; Gorby, Y.A.; Landa, E.R.

1991-01-01

REDUCTION of the soluble, oxidized form of uranium, U(VI), to insoluble U(IV) is an important mechanism for the immobilization of uranium in aquatic sediments and for the formation of some uranium ores1-10. U(VI) reduction has generally been regarded as an abiological reaction in which sulphide, molecular hydrogen or organic compounds function as the reductant1,2,5,11. Microbial involvement in U(VI) reduction has been considered to be limited to indirect effects, such as microbial metabolism providing the reduced compounds for abiological U(VI) reduction and microbial cell walls providing a surface to stimulate abiological U(VI) reduction1,12,13. We report here, however, that dissimilatory Fe(III)-reducing microorganisms can obtain energy for growth by electron transport to U(VI). This novel form of microbial metabolism can be much faster than commonly cited abiological mechanisms for U(VI) reduction. Not only do these findings expand the known potential terminal electron acceptors for microbial energy transduction, they offer a likely explanation for the deposition of uranium in aquatic sediments and aquifers, and suggest a method for biological remediation of environments contaminated with uranium.

Assessment of the disinfection capacity and eco-toxicological impact of atmospheric cold plasma for treatment of food industry effluents.

PubMed

Patange, Apurva; Boehm, Daniela; Giltrap, Michelle; Lu, Peng; Cullen, P J; Bourke, Paula

2018-08-01

Generation of wastewater is one of the main environmental sustainability issues across food sector industries. The constituents of food process effluents are often complex and require high energy and processing for regulatory compliance. Wastewater streams are the subject of microbiological and chemical criteria, and can have a significant eco-toxicological impact on the aquatic life. Thus, innovative treatment approaches are required to mitigate environmental impact in an energy efficient manner. Here, dielectric barrier discharge atmospheric cold plasma (ACP) was evaluated for control of key microbial indicators encountered in food industry effluent. This study also investigated the eco-toxicological impact of cold plasma treatment of the effluents using a range of aquatic bioassays. Continuous ACP treatment was applied to synthetic dairy and meat effluents. Microbial inactivation showed treatment time dependence with significant reduction in microbial populations within 120 s, and to undetectable levels after 300 s. Post treatment retention time emerged as critical control parameter which promoted ACP bacterial inactivation efficiency. Moreover, ACP treatment for 20 min achieved significant reduction (≥2 Log 10 ) in Bacillus megaterium endospores in wastewater effluent. Acute aquatic toxicity was assessed using two fish cell lines (PLHC-1 and RTG-2) and a crustacean model (Daphnia magna). Untreated effluents were toxic to the aquatic models, however, plasma treatment limited the toxic effects. Differing sensitivities were observed to ACP treated effluents across the different test bio-assays in the following order: PLHC-1 > RTG-2 ≥ D. magna; with greater sensitivity retained to plasma treated meat effluent than dairy effluent. The toxic effects were dependent on concentration and treatment time of the ACP treated effluent; with 30% cytotoxicity in D. magna and fish cells observed after 24 h of exposure to ACP treated effluent for concentrations up to 5%. The findings suggest the need to employ wider variety of aquatic organisms for better understanding and complete toxicity evaluation of long-term effects. The study demonstrates the potential to tailor ACP system parameters to control pertinent microbial targets (mono/poly-microbial, vegetative or spore form) found in complex and nutritious wastewater effluents whilst maintaining a safe eco-toxicity profile for aquatic species. Copyright © 2018 Elsevier B.V. All rights reserved.

Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in Northwestern Pennsylvania

PubMed Central

Trexler, Ryan; Solomon, Caroline; Brislawn, Colin J.; Wright, Justin R.; Rosenberger, Abigail; McClure, Erin E.; Grube, Alyssa M.; Peterson, Mark P.; Keddache, Mehdi; Mason, Olivia U.; Hazen, Terry C.; Grant, Christopher J.; Lamendella, Regina

2014-01-01

Hydraulic fracturing and horizontal drilling have increased dramatically in Pennsylvania Marcellus shale formations, however the potential for major environmental impacts are still incompletely understood. High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial community structure of water, sediment, bryophyte, and biofilm samples from 26 headwater stream sites in northwestern Pennsylvania with different histories of fracking activity within Marcellus shale formations. Further, we describe the relationship between microbial community structure and environmental parameters measured. Approximately 3.2 million 16S rRNA gene sequences were retrieved from a total of 58 samples. Microbial community analyses showed significant reductions in species richness as well as evenness in sites with Marcellus shale activity. Beta diversity analyses revealed distinct microbial community structure between sites with and without Marcellus shale activity. For example, operational taxonomic units (OTUs) within the Acetobacteracea, Methylocystaceae, Acidobacteriaceae, and Phenylobacterium were greater than three log-fold more abundant in MSA+ sites as compared to MSA− sites. Further, several of these OTUs were strongly negatively correlated with pH and positively correlated with the number of wellpads in a watershed. It should be noted that many of the OTUs enriched in MSA+ sites are putative acidophilic and/or methanotrophic populations. This study revealed apparent shifts in the autochthonous microbial communities and highlighted potential members that could be responding to changing stream conditions as a result of nascent industrial activity in these aquatic ecosystems. PMID:25408683

Development of static system procedures to study aquatic biofilms and their responses to disinfection and invading species

NASA Technical Reports Server (NTRS)

Smithers, G. A.

1992-01-01

The microbial ecology facility in the Analytical and Physical Chemistry Branch at Marshall Space Flight Center is tasked with anticipation of potential microbial problems (and opportunities to exploit microorganisms) which may occur in partially closed systems such as space station/vehicles habitats and in water reclamation systems therein, with particular emphasis on the degradation of materials. Within this context, procedures for microbial biofilm research are being developed. Reported here is the development of static system procedures to study aquatic biofilms and their responses to disinfection and invading species. Preliminary investigations have been completed. As procedures are refined, it will be possible to focus more closely on the elucidation of biofilm phenomena.

Investigating microbial transformations of soil organic matter: synthesizing knowledge from disparate fields to guide new experimentation

NASA Astrophysics Data System (ADS)

Billings, S. A.; Tiemann, L. K.; Ballantyne, F., IV; Lehmeier, C.; Min, K.

2014-12-01

Investigators of soil organic matter (SOM) transformations struggle with a deceptively simple-sounding question: "Why does some SOM leave the soil profile relatively quickly, while other compounds, especially those at depth, appear to be retained on timescales ranging from the decadal to the millennial?" This question is important on both practical and academic levels, but addressing it is challenging for a multitude of reasons. Simultaneous with soil-specific advances, multiple other disciplines have enhanced their knowledge bases in ways potentially useful for future investigations of SOM decay. In this article, we highlight observations highly relevant for those investigating SOM decay and retention but often emanating from disparate fields and residing in literature seldom cited in SOM research. We focus on recent work in two key areas. First, we turn to experimental approaches using natural and artificial aquatic environments to investigate patterns of microbially-mediated OM transformations as environmental conditions change, and highlight how aquatic microbial responses to environmental change can reveal processes likely important to OM decay and retention in soils. Second, we emphasize the importance of establishing intrinsic patterns of decay kinetics for purified substrates commonly found in soils to develop baseline rates. These decay kinetics - which represent the upper limit of the reaction rates - can then be compared to substrate decay kinetics observed in natural samples, which integrate intrinsic decay reaction rates and edaphic factors essential to the site under study but absent in purified systems. That comparison permits the site-specific factors to be parsed from the fundamental decay kinetics, an important advance in our understanding of SOM decay (and thus persistence) in natural systems. We then suggest ways in which empirical observations from aquatic systems and purified enzyme-substrate reaction kinetics can be used to advance recent theoretical efforts in SOM-focused research. Finally, we suggest how the observations in aquatic and purified enzyme-substrate systems could be used to help unravel the puzzles presented by oft-observed patterns of SOM characteristics with depth, as one example of the many perplexing SOM-related problems.

Local environmental pollution strongly influences culturable bacterial aerosols at an urban aquatic superfund site.

PubMed

Dueker, M Elias; O'Mullan, Gregory D; Juhl, Andrew R; Weathers, Kathleen C; Uriarte, Maria

2012-10-16

In polluted environments, when microbial aerosols originate locally, species composition of the aerosols should reflect the polluted source. To test the connection between local environmental pollution and microbial aerosols near an urban waterfront, we characterized bacterial aerosols at Newtown Creek (NTC), a public waterway and Superfund site in a densely populated area of New York, NY, USA. Culturable bacterial aerosol fallout rate and surface water bacterial concentrations were at least an order of magnitude greater at NTC than at a neighboring, less polluted waterfront and a nonurban coastal site in Maine. The NTC culturable bacterial aerosol community was significantly different in taxonomic structure from previous urban and coastal aerosol studies, particularly in relative abundances of Actinobacteria and Proteobacteria. Twenty-four percent of the operational taxonomic units in the NTC overall (air + water) bacterial isolate library were most similar to bacterial 16S rRNA gene sequences previously described in terrestrial or aquatic environments contaminated with sewage, hydrocarbons, heavy metals, and other industrial waste. This study is the first to examine the community composition and local deposition of bacterial aerosols from an aquatic Superfund site. The findings have important implications for the use of aeration remediation in polluted aquatic environments and suggest a novel pathway of microbial exposure in densely populated urban communities containing contaminated soil and water.

Water Quality Criteria for Human Health and Aquatic Life

EPA Science Inventory

Collaborative effort with the Office of Water to provide science in support of the development and implementation of new or revised ambient water quality criteria for microbial and chemical contaminants for human health and aquatic life. The research also addresses implementation...

ANALYSIS OF AQUATIC MICROBIAL COMMUNITIES IMPACTED BY LARGE POULTRY FORMS

EPA Science Inventory

Microbial communities often respond more rapidly and extensively to environmental change than communities of higher organisms. Thus, characterizing shifts in the structure of native bacterial communities as a response to changes in nutrients, antimicrobials, and invading pathogen...

False positives in Biolog EcoPlates™ and MT2 MicroPlates™ caused by calcium.

PubMed

Pierce, Melissa L; Ward, J Evan; Dobbs, Fred C

2014-02-01

Biolog MicroPlates(TM) (e.g. EcoPlate(TM), MT2 MicroPlate(TM), GN MicroPlate(TM)) are useful tools for characterizing microbial communities, providing community-level physiological profiles to terrestrial and aquatic ecologists. The more recently designed Biolog EcoPlates have been used frequently in aquatic ecology with success. This study, however, reveals one major problem when using EcoPlates to evaluate samples within an estuarine or seawater matrix. At concentrations greater than 100 parts per million, the cation calcium begins to interfere with the microplate chemistry, causing false positive readings. Experiments, in which multiple treatments of natural and artificial seawater were tested, as well as calcium-addition experiments, demonstrate that calcium inhibits complete dissolution of the minimal growth medium in wells. Future studies involving Biolog EcoPlates and MicroPlates should take this effect into account, and the dilution of samples is strongly recommended to diminish the "calcium effect." Copyright © 2013 Elsevier B.V. All rights reserved.

Automated sample area definition for high-throughput microscopy.

PubMed

Zeder, M; Ellrott, A; Amann, R

2011-04-01

High-throughput screening platforms based on epifluorescence microscopy are powerful tools in a variety of scientific fields. Although some applications are based on imaging geometrically defined samples such as microtiter plates, multiwell slides, or spotted gene arrays, others need to cope with inhomogeneously located samples on glass slides. The analysis of microbial communities in aquatic systems by sample filtration on membrane filters followed by multiple fluorescent staining, or the investigation of tissue sections are examples. Therefore, we developed a strategy for flexible and fast definition of sample locations by the acquisition of whole slide overview images and automated sample recognition by image analysis. Our approach was tested on different microscopes and the computer programs are freely available (http://www.technobiology.ch). Copyright © 2011 International Society for Advancement of Cytometry.

Microbial community analysis and biodeterioration of waterlogged archaeological wood from the Nanhai No. 1 shipwreck during storage.

PubMed

Liu, Zijun; Fu, Tongtong; Hu, Cuiting; Shen, Dawa; Macchioni, Nicola; Sozzi, Lorena; Chen, Yue; Liu, Jie; Tian, Xingling; Ge, Qinya; Feng, Zhengteng; Liu, Huiru; Zhang, Zhiguo; Pan, Jiao

2018-05-08

Wooden shipwrecks are a significant part of the underwater cultural heritage. In 2007, the Nanhai No. 1 shipwreck was salvaged from the seabed and moved into the Marine Silk Road Museum, where it is still stored in a water tank. We analysed the microbial communities colonizing the hull surface of the Nanhai No. 1 shipwreck during storage. Six samples exposed to air were collected from different spots of the ship that exhibited obvious microbial plaques. High-throughput sequencing revealed the bacterial community includes both aquatic and terrestrial species, while in the fungal community, Fusarium was the most abundant genus across all samples and accounted for 84.91% to 98.40% of the total community composition. Two Fusarium species were isolated from the samples and were identified as F. solani and F. oxysporum. Both of the isolates were able to degrade cellulose, but only F. solani had the ability to degrade lignin. Antimicrobial efficacy in inhibiting the growth of Fusarium was assessed with five kinds of biocides, and isothiazolinones exhibited specific inhibition of Fusarium growth. These results provide critical background information to protect and reduce the biodegradation and destruction of this important historical shipwreck, and inform efforts to protect other similar artifacts.

Environmental safety to decomposer invertebrates of azadirachtin (neem) as a systemic insecticide in trees to control emerald ash borer.

PubMed

Kreutzweiser, David; Thompson, Dean; Grimalt, Susana; Chartrand, Derek; Good, Kevin; Scarr, Taylor

2011-09-01

The non-target effects of an azadirachtin-based systemic insecticide used for control of wood-boring insect pests in trees were assessed on litter-dwelling earthworms, leaf-shredding aquatic insects, and microbial communities in terrestrial and aquatic microcosms. The insecticide was injected into the trunks of ash trees at a rate of 0.2 gazadirachtin cm(-1) tree diameter in early summer. At the time of senescence, foliar concentrations in most (65%) leaves where at or below detection (<0.01 mg kg(-1) total azadirachtin) and the average concentration among leaves overall at senescence was 0.19 mg kg(-1). Leaves from the azadirachtin-treated trees at senescence were added to microcosms and responses by test organisms were compared to those in microcosms containing leaves from non-treated ash trees (controls). No significant reductions were detected among earthworm survival, leaf consumption rates, growth rates, or cocoon production, aquatic insect survival and leaf consumption rates, and among terrestrial and aquatic microbial decomposition of leaf material in comparison to controls. In a further set of microcosm tests containing leaves from intentional high-dose trees, the only significant, adverse effect detected was a reduction in microbial decomposition of leaf material, and only at the highest test concentration (∼6 mg kg(-1)). Results indicated no significant adverse effects on litter-dwelling earthworms or leaf-shredding aquatic insects at concentrations up to at least 30 × the expected field concentrations at operational rates, and at 6 × expected field concentrations for adverse effects on microbial decomposition. We conclude that when azadirachtin is used as a systemic insecticide in trees for control of insect pests such as the invasive wood-boring beetle, emerald ash borer, resultant foliar concentrations in senescent leaf material are likely to pose little risk of harm to decomposer invertebrates. Crown Copyright © 2011. Published by Elsevier Inc. All rights reserved.

Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups

PubMed Central

Le, Huong T.; Ho, Cuong T.; Trinh, Quan H.; Trinh, Duc A.; Luu, Minh T. N.; Tran, Hai S.; Orange, Didier; Janeau, Jean L.; Merroune, Asmaa; Rochelle-Newall, Emma; Pommier, Thomas

2016-01-01

Organic fertilizer application is often touted as an economical and effective method to increase soil fertility. However, this amendment may increase dissolved organic carbon (DOC) runoff into downstream aquatic ecosystems and may consequently alter aquatic microbial community. We focused on understanding the effects of DOC runoff from soils amended with compost, vermicompost, or biochar on the aquatic microbial community of a tropical reservoir. Runoff collected from a series of rainfall simulations on soils amended with different organic fertilizers was incubated for 16 days in a series of 200 L mesocosms filled with water from a downstream reservoir. We applied 454 high throughput pyrosequencing for bacterial 16S rRNA genes to analyze microbial communities. After 16 days of incubation, the richness and evenness of the microbial communities present decreased in the mesocosms amended with any organic fertilizers, except for the evenness in the mesocosms amended with compost runoff. In contrast, they increased in the reservoir water control and soil-only amended mesocosms. Community structure was mainly affected by pH and DOC concentration. Compared to the autochthonous organic carbon produced during primary production, the addition of allochthonous DOC from these organic amendments seemed to exert a stronger effect on the communities over the period of incubation. While the Proteobacteria and Actinobacteria classes were positively associated with higher DOC concentration, the number of sequences representing key bacterial groups differed between mesocosms particularly between the biochar runoff addition and the compost or vermi-compost runoff additions. The genera of Propionibacterium spp. and Methylobacterium spp. were highly abundant in the compost runoff additions suggesting that they may represent sentinel species of complex organic carbon inputs. Overall, this work further underlines the importance of studying the off-site impacts of organic fertilizers as their impact on downstream aquatic systems is not negligible. PMID:27379034

Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups.

PubMed

Le, Huong T; Ho, Cuong T; Trinh, Quan H; Trinh, Duc A; Luu, Minh T N; Tran, Hai S; Orange, Didier; Janeau, Jean L; Merroune, Asmaa; Rochelle-Newall, Emma; Pommier, Thomas

2016-01-01

Organic fertilizer application is often touted as an economical and effective method to increase soil fertility. However, this amendment may increase dissolved organic carbon (DOC) runoff into downstream aquatic ecosystems and may consequently alter aquatic microbial community. We focused on understanding the effects of DOC runoff from soils amended with compost, vermicompost, or biochar on the aquatic microbial community of a tropical reservoir. Runoff collected from a series of rainfall simulations on soils amended with different organic fertilizers was incubated for 16 days in a series of 200 L mesocosms filled with water from a downstream reservoir. We applied 454 high throughput pyrosequencing for bacterial 16S rRNA genes to analyze microbial communities. After 16 days of incubation, the richness and evenness of the microbial communities present decreased in the mesocosms amended with any organic fertilizers, except for the evenness in the mesocosms amended with compost runoff. In contrast, they increased in the reservoir water control and soil-only amended mesocosms. Community structure was mainly affected by pH and DOC concentration. Compared to the autochthonous organic carbon produced during primary production, the addition of allochthonous DOC from these organic amendments seemed to exert a stronger effect on the communities over the period of incubation. While the Proteobacteria and Actinobacteria classes were positively associated with higher DOC concentration, the number of sequences representing key bacterial groups differed between mesocosms particularly between the biochar runoff addition and the compost or vermi-compost runoff additions. The genera of Propionibacterium spp. and Methylobacterium spp. were highly abundant in the compost runoff additions suggesting that they may represent sentinel species of complex organic carbon inputs. Overall, this work further underlines the importance of studying the off-site impacts of organic fertilizers as their impact on downstream aquatic systems is not negligible.

Phylogenetic Structure and Metabolic Properties of Microbial Communities in Arsenic-Rich Waters of Geothermal Origin

PubMed Central

Crognale, Simona; Zecchin, Sarah; Amalfitano, Stefano; Fazi, Stefano; Casentini, Barbara; Corsini, Anna; Cavalca, Lucia; Rossetti, Simona

2017-01-01

Arsenic (As) is a toxic element released in aquatic environments by geogenic processes or anthropic activities. To counteract its toxicity, several microorganisms have developed mechanisms to tolerate and utilize it for respiratory metabolism. However, still little is known about identity and physiological properties of microorganisms exposed to natural high levels of As and the role they play in As transformation and mobilization processes. This work aims to explore the phylogenetic composition and functional properties of aquatic microbial communities in As-rich freshwater environments of geothermal origin and to elucidate the key microbial functional groups that directly or indirectly may influence As-transformations across a natural range of geogenic arsenic contamination. Distinct bacterial communities in terms of composition and metabolisms were found. Members of Proteobacteria, affiliated to Alpha- and Betaproteobacteria were mainly retrieved in groundwaters and surface waters, whereas Gammaproteobacteria were the main component in thermal waters. Most of the OTUs from thermal waters were only distantly related to 16S rRNA gene sequences of known taxa, indicating the occurrence of bacterial biodiversity so far unexplored. Nitrate and sulfate reduction and heterotrophic As(III)-oxidization were found as main metabolic traits of the microbial cultivable fraction in such environments. No growth of autotrophic As(III)-oxidizers, autotrophic and heterotrophic As(V)-reducers, Fe-reducers and oxidizers, Mn-reducers and sulfide oxidizers was observed. The ars genes, involved in As(V) detoxifying reduction, were found in all samples whereas aioA [As(III) oxidase] and arrA genes [As(V) respiratory reductase] were not found. Overall, we found that As detoxification processes prevailed over As metabolic processes, concomitantly with the intriguing occurrence of novel thermophiles able to tolerate high levels of As. PMID:29312179

Phylogenetic Structure and Metabolic Properties of Microbial Communities in Arsenic-Rich Waters of Geothermal Origin.

PubMed

Crognale, Simona; Zecchin, Sarah; Amalfitano, Stefano; Fazi, Stefano; Casentini, Barbara; Corsini, Anna; Cavalca, Lucia; Rossetti, Simona

2017-01-01

Arsenic (As) is a toxic element released in aquatic environments by geogenic processes or anthropic activities. To counteract its toxicity, several microorganisms have developed mechanisms to tolerate and utilize it for respiratory metabolism. However, still little is known about identity and physiological properties of microorganisms exposed to natural high levels of As and the role they play in As transformation and mobilization processes. This work aims to explore the phylogenetic composition and functional properties of aquatic microbial communities in As-rich freshwater environments of geothermal origin and to elucidate the key microbial functional groups that directly or indirectly may influence As-transformations across a natural range of geogenic arsenic contamination. Distinct bacterial communities in terms of composition and metabolisms were found. Members of Proteobacteria , affiliated to Alpha - and Betaproteobacteria were mainly retrieved in groundwaters and surface waters, whereas Gammaproteobacteria were the main component in thermal waters. Most of the OTUs from thermal waters were only distantly related to 16S rRNA gene sequences of known taxa, indicating the occurrence of bacterial biodiversity so far unexplored. Nitrate and sulfate reduction and heterotrophic As(III)-oxidization were found as main metabolic traits of the microbial cultivable fraction in such environments. No growth of autotrophic As(III)-oxidizers, autotrophic and heterotrophic As(V)-reducers, Fe-reducers and oxidizers, Mn-reducers and sulfide oxidizers was observed. The ars genes, involved in As(V) detoxifying reduction, were found in all samples whereas aioA [As(III) oxidase] and arrA genes [As(V) respiratory reductase] were not found. Overall, we found that As detoxification processes prevailed over As metabolic processes, concomitantly with the intriguing occurrence of novel thermophiles able to tolerate high levels of As.

An Eco-Safety Assessment of Glyoxal-Containing Cellulose Ether on Freeze-Dried Microbial Strain, Cyanobacteria, Daphnia, and Zebrafish

PubMed Central

Park, Chang-Beom; Song, Min Ju; Choi, Nak Woon; Kim, Sunghoon; Jeon, Hyun Pyo; Kim, Sanghun; Kim, Youngjun

2017-01-01

The objective of this study was to investigate the aquatic-toxic effects of glyoxal-containing cellulose ether with four different glyoxal concentrations (0%, 1.4%, 2.3%, and 6.3%) in response to global chemical regulations, e.g., European Union Classification, Labeling and Packaging (EU CLP). Toxicity tests of glyoxal-containing cellulose ether on 11 different microbial strains, Microcystis aeruginosa, Daphnia magna, and zebrafish embryos were designed as an initial stage of toxicity screening and performed in accordance with standardized toxicity test guidelines. Glyoxal-containing cellulose ether showed no significant toxic effects in the toxicity tests of the 11 freeze-dried microbial strains, Daphnia magna, and zebrafish embryos. Alternatively, 6.3% glyoxal-containing cellulose ether led to a more than 60% reduction in Microcystis aeruginosa growth after 7 days of exposure. Approximately 10% of the developmental abnormalities (e.g., bent spine) in zebrafish embryos were also observed in the group exposed to 6.3% glyoxal-containing cellulose ether after 6 days of exposure. These results show that 6.3% less glyoxal-containing cellulose ether has no acute toxic effects on aquatic organisms. However, 6.3% less glyoxal-containing cellulose ether may affect the health of aquatic organisms with long-term exposure. In order to better evaluate the eco-safety of cellulosic products containing glyoxal, further studies regarding the toxic effects of glyoxal-containing cellulose ether with long-term exposure are required. The results from this study allow us to evaluate the aquatic-toxic effects of glyoxal-containing cellulosic products, under EU chemical regulations, on the health of aquatic organisms. PMID:28335565

STABILITY AND CHANGE IN ESTUARINE BIOFILM BACTERIAL COMMUNITY DIVERSITY

EPA Science Inventory

Biofilms develop on all surfaces in aquatic environments and are defined as matrix-enclosed microbial populations adherent to each other and/or surfaces (1, 31). A substantial part of the microbial activity in nature is associated with surfaces (12). Surface association (biofou...

Factors Influencing the Diversity of Iron Uptake Systems in Aquatic Microorganisms

PubMed Central

Desai, Dhwani K.; Desai, Falguni D.; LaRoche, Julie

2012-01-01

Iron (Fe) is an essential micronutrient for many processes in all living cells. Dissolved Fe (dFe) concentrations in the ocean are of the order of a few nM, and Fe is often a factor limiting primary production. Bioavailability of Fe in aquatic environments is believed to be primarily controlled through chelation by Fe-binding ligands. Marine microbes have evolved different mechanisms to cope with the scarcity of bioavailable dFe. Gradients in dFe concentrations and diversity of the Fe-ligand pool from coastal to open ocean waters have presumably imposed selection pressures that should be reflected in the genomes of microbial communities inhabiting the pelagic realm. We applied a hidden Markov model (HMM)-based search for proteins related to cellular iron metabolism, and in particular those involved in Fe uptake mechanisms in 164 microbial genomes belonging to diverse taxa and occupying different aquatic niches. A multivariate statistical approach demonstrated that in phototrophic organisms, there is a clear influence of the ecological niche on the diversity of Fe uptake systems. Extending the analyses to the metagenome database from the Global Ocean Sampling expedition, we demonstrated that the Fe uptake and homeostasis mechanisms differed significantly across marine niches defined by temperatures and dFe concentrations, and that this difference was linked to the distribution of microbial taxa in these niches. Using the dN/dS ratios (which signify the rate of non-synonymous mutations) of the nucleotide sequences, we identified that genes encoding for TonB, Ferritin, Ferric reductase, IdiA, ZupT, and Fe2+ transport proteins FeoA and FeoB were evolving at a faster rate (positive selection pressure) while genes encoding ferrisiderophore, heme and Vitamin B12 uptake systems, siderophore biosynthesis, and IsiA and IsiB were under purifying selection pressure (evolving slowly). PMID:23087680

Biogeography of bacteriophages at four hydrothermal vent sites in the Antarctic based on g23 sequence diversity.

PubMed

Millard, Andrew D; Pearce, David; Zwirglmaier, Katrin

2016-04-01

In this study, which was carried out within the ChEsSO consortium project (Chemosynthetically driven ecosystems south of the Polar Front), we sampled two hydrothermal vent sites on the East Scotia Ridge, Scotia Sea, one in the Kemp Caldera, South Sandwich Arc and one in the Bransfield Strait, north-west of the Antarctic Peninsula, which exhibit strong differences in their chemical characteristics. We compared a subset of their bacteriophage population by Sanger- and 454-sequencing of g23, which codes for the major capsid protein of T4likeviruses. We found that the sites differ vastly in their bacteriophage diversity, which reflects the differences in the chemical conditions and therefore putatively the differences in microbial hosts living at these sites. Comparing phage diversity in the vent samples to other aquatic samples, the vent samples formed a distinct separate cluster, which also included the non-vent control samples that were taken several hundred meters above the vent chimneys. This indicates that the influence of the vents on the microbial population and therefore also the bacteriophage population extends much further than anticipated. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Atmospheric Sampling of Microorganisms with UAS

NASA Astrophysics Data System (ADS)

Schmale, D. G., III

2017-12-01

Many microorganisms relevant to crops, domestic animals, and humans are transported over long distances through the atmosphere. Some of these atmospheric microbes catalyze the freezing of water at higher temperatures and facilitate the onset of precipitation. A few have crossed continents. New technologies are needed to study the movement of microorganisms in the atmosphere. We have used unmanned aircraft systems (UAS) to study the transport of microorganisms tens to hundreds of meters above the ground. These UAS are equipped with unique devices for collecting microbes in the atmosphere during flight. Autonomous systems enable teams of UAS to perform complex atmospheric sampling tasks, and coordinate flight missions with one another. Data collected with UAS can be used to validate and improve disease forecasting models along highways in the sky, connecting transport scales across farms, states, and continents. Though terrestrial environments are often considered a major contributor to atmospheric microbial aerosols, little is known about aquatic sources of microbial aerosols. Droplets containing microorganisms can aerosolize from the water surface, liberating them into the atmosphere. We are using teams of unmanned surface vehicles (USVs) and UAS to study the aerosolization of microbes from aquatic environments. Controlled flume studies using highspeed video have allowed us to observe unique aerosolization phenomena that can launch microbes out of the water and into the air. Unmanned systems may be used to excite the next generation of biologists and engineers, and raise important ethical considerations about the future of human-robot interactions.

Protist-Bacteria Associations: Gammaproteobacteria and Alphaproteobacteria Are Prevalent as Digestion-Resistant Bacteria in Ciliated Protozoa

PubMed Central

Gong, Jun; Qing, Yao; Zou, Songbao; Fu, Rao; Su, Lei; Zhang, Xiaoli; Zhang, Qianqian

2016-01-01

Protistan bacterivory, a microbial process involving ingestion and digestion, is ecologically important in the microbial loop in aquatic and terrestrial ecosystems. While bacterial resistance to protistan ingestion has been relatively well understood, little is known about protistan digestion in which some ingested bacteria could not be digested in cells of major protistan grazers in the natural environment. Here we report the phylogenetic identities of digestion-resistant bacteria (DRB) that could survive starvation and form relatively stable associations with 11 marine and one freshwater ciliate species. Using clone library and sequencing of 16S rRNA genes, we found that the protistan predators could host a high diversity of DRB, most of which represented novel bacterial taxa that have not been cultivated. The localization inside host cells, quantity, and viability of these bacteria were checked using fluorescence in situ hybridization. The DRB were affiliated with Actinobacteria, Bacteroidetes, Firmicutes, Parcubacteria (OD1), Planctomycetes, and Proteobacteria, with Gammaproteobacteria and Alphaproteobacteria being the most frequently occurring classes. The dominance of Gamma- and Alphaproteobacteria corresponds well to a previous study of Global Ocean Sampling metagenomic data showing the widespread types of bacterial type VI and IV secretion systems (T6SS and T4SS) in these two taxa, suggesting a putatively significant role of secretion systems in promoting marine protist-bacteria associations. In the DRB assemblages, opportunistic bacteria such as Alteromonadaceae, Pseudoalteromonadaceae, and Vibrionaceae often presented with high proportions, indicating these bacteria could evade protistan grazing thus persist and accumulate in the community, which, however, contrasts with their well-known rarity in nature. This begs the question whether viral lysis is significant in killing these indigestible bacteria in microbial communities. Taken together, our study on the identity of DRB sheds new light on microbial interactions and generates further hypotheses including the potential importance of bacterial protein secretion systems in structuring bacterial community composition and functioning of “microbial black box” in aquatic environments. PMID:27148188

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

PubMed Central

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

2012-01-01

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

Experimental observations on the decay of environmental DNA from bighead and silver carps

USGS Publications Warehouse

Lance, Richard F.; Klymus, Katy E.; Richter, Cathy; Guan, Xin; Farrington, Heather L.; Carr, Matthew R.; Thompson, Nathan; Chapman, Duane C.; Baerwaldt, Kelly L.

2017-01-01

Interest in the field of environmental DNA (eDNA) is growing rapidly and eDNA surveys are becoming an important consideration for aquatic resource managers dealing with invasive species. However, in order for eDNA monitoring to mature as a research and management tool, there are several critical knowledge gaps that must be filled. One such gap is the fate of eDNA materials in the aquatic environment. Understanding the environmental factors that influence the decay of eDNA and how these factors impact detection probabilities over time and space could have significant implications for eDNA survey design and data interpretation. Here we experimentally explore decay of eDNA associated with bighead carp (Hypophthalmichthys nobilis) biological waste collected from an aquaculture filtration system and with sperm collected from captive silver carp (H. molitrix), and how decay may be influenced by differing levels of water turbulence, temperature, microbial load, and pH. We found that the decay patterns of eDNA associated with both H. nobilis biological waste and H. molitrix milt significantly fit monophasic exponential decay curves. Secondly, we observed that the highest temperature we tested resulted in a decay half-life as much as 5.5× more rapid than the lowest temperature we tested. When we suppressed microbial loads in eDNA samples, we observed that overall losses of eDNA were reduced by about 2.5×. When we amended eDNA samples with pond water the half-life of eDNA was reduced by about 2.25×, despite relatively little apparent increase in the overall microbial load. This pattern indicated that species constituency of the microbial community, in addition to microbial load, might play a critical role in eDNA degradation. A shift in pH from 6.5 to 8.0 in the samples resulted in a 1.6× reduction in eDNA halflife. Water turbulence in our study had no apparent effect on eDNA decay. When we combined different temperature, pH, and microbial load treatments to create a rapid decay condition and a slow decay condition, and tracked eDNA decay over 91 days, we observed a 5.0× greater loss of eDNA by Day 5 under rapid decay conditions than under slow decay conditions. At the end of the trials, the differences in eDNA loss between the rapid decay and baseline and slow decay conditions were 0.1× and 3.3×, respectively. Our results strongly demonstrate the potential for environmental factors to influence eDNA fate and, thus, the interpretation of eDNA survey results.

CHROMOPHORIC DISSOLVED ORGANIC MATTER (CDOM) DERIVED FROM DECOMPOSITION OF VARIOUS VASCULAR PLANT AND ALGAL SOURCES

EPA Science Inventory

Chromophoric dissolved organic (CDOM) in aquatic environments is derived from the microbial decomposition of terrestrial and microbial organic matter. Here we present results of studies of the spectral properties and photoreactivity of the CDOM derived from several organic matter...

Denitrification alternates between a source and sink of nitrous oxide in the hypolimnion of a thermally stratified reservoir

EPA Science Inventory

Nitrogen loading from developed watersheds to aquatic ecosystems can stimulate microbial denitrification, a process which reduces nitrate (NO3-) to dinitrogen (N2) or nitrous oxide (N2O), the latter a potent greenhouse gas. While aquatic ecosystems are a globally significant sou...

Seasonal and spatial patterns in coupled nitrification-denitrification rates in a large Great Lakes coastal system: The St. Louis River Estuary

EPA Science Inventory

Anthropogenic inputs of excess nitrogen (N) to aquatic systems are detrimental, but aquatic plants and sediments have the potential to mitigate N-loading. Sediment processes are driven by microbially mediated N-cycling. Coastal embayments purportedly play a significant role in N-...

Consumer-mediated nutrient recycling is influenced by interactions between nutrient enrichment and the anti-microbial agent triclosan

USDA-ARS?s Scientific Manuscript database

Triclosan (5-chloro-2-(2, 4-dichlorophenoxy)phenol) is a widely used antimicrobial agent in personal care products whose fate and transport in aquatic ecosystems is a growing environmental concern. Evidence for chronic ecological effects of triclosan in aquatic organisms is increasing. At larger sca...

Spatio-seasonal variability in dissolved organic matter optical properties and its bioavailability in a subalpine lake

NASA Astrophysics Data System (ADS)

Stadler, Masumi; Ejarque, Elisabet; Kainz, Martin J.

2017-04-01

Allochthonous and autochothonous dissolved organic matter (DOM) in lakes mainly originate from terrestrial and aquatic primary production, respectively. Due to their differing biochemical composition the degradability of DOM by microorganisms is expected to vary. The carbon use efficiency of bacteria and DOM biodegradability determine whether the consumed DOM is incorporated into microbial biomass or respired to CO2 and ultimately emitted into the atmosphere. Thus, understanding the interaction of biodegradable DOM and its consumers is crucial to increase our knowledge on the role of lakes in the global carbon cycling. However, interactions of specific aquatic DOM signatures and the microbial population still remain widely debated. The aim of this study was to explore how DOM biodegradability changes along a stream-lake continuum at different seasons of the year. We monitored DOM quantity and its optical properties, inorganic nutrients, CO2 and bacterial growth over 20 days in dark bioassays with water from the inflow, outflow and at three layers of an oligotrophic subalpine lake. Preliminary results reveal highest microbial abundance in the metalimnion in winter and summer (0.7 106 and 2.5 106 cells mL-1, respectively) and the inflow in spring and autumn (1 106 and 1.4 106 cells mL-1, respectively) after 20 days. Surprisingly, with the exception of winter samples final inflow bacterial abundance results high, despite its lowest initial natural cell concentration, providing evidence for effective utilisation of terrestrial DOM, even with its high humic signature as indicated by the humification index (HIX). Nonetheless, after a microbial biomass peak with the inflow yielding mostly highest after three days, at the final experimental stage microbial biomass does only marginally differ between all sites with the exception of autumn samples where outflow and metalimnion turn out most productive. Even though the DOM of all lake sites and the lake outflow were characterised by lower molecular weight (indicated by the slope ratio (SR)) and a higher autochthonous signature (BIX) in all seasons, rapid growth of inflow bacteria highlight the potential of terrestrially-derived DOM to support bacterial growth, and challenge previous ideas that autchthonously-produced DOM would be more labile than DOM of terrestrial origin.

Fire Effects on Soil and Dissolved Organic Matter in a Southern Appalachian Hardwood Forest: Movement of Fire-Altered Organic Matter Across the Terrestrial-Aquatic Interface Following the Great Smoky Mountains National Park Fire of 2016

NASA Astrophysics Data System (ADS)

Matosziuk, L.; Gallo, A.; Hatten, J. A.; Heckman, K. A.; Nave, L. E.; Sanclements, M.; Strahm, B. D.; Weiglein, T.

2017-12-01

Wildfire can dramatically affect the quantity and quality of soil organic matter (SOM), producing thermally altered organic material such as pyrogenic carbon (PyC) and polyaromatic hydrocarbons (PAHs). The movement of this thermally altered material through terrestrial and aquatic ecosystems can differ from that of unburned SOM, with far-reaching consequences for soil carbon cycling and water quality. Unfortunately, due to the rapid ecological changes following fire and the lack of robust pre-fire controls, the cycling of fire-altered carbon is still poorly understood. In December 2016, the Chimney Tops 2 fire in Great Smoky Mountains National Park burned over co-located terrestrial and aquatic NEON sites. We have leveraged the wealth of pre-fire data at these sites (chemical, physical, and microbial characterization of soils, continuous measurements of both soil and stream samples, and five soil cores up to 110 cm in depth) to conduct a thorough study of the movement of fire-altered organic matter through terrestrial and aquatic ecosystems. Stream samples have been collected weekly beginning 5 weeks post-fire. Grab samples of soil were taken at discrete time points in the first two months after the fire. Eight weeks post-fire, a second set of cores was taken and resin lysimeters installed at three different depths. A third set of cores and grab samples will be taken 8-12 months after the fire. In addition to routine soil characterization techniques, solid samples from cores and grab samples at all time points will be analyzed for PyC and PAHs. To determine the effect of fire on dissolved organic matter (DOM), hot water extracts of these soil samples, as well as the stream samples and lysimeter samples, will also be analyzed for PyC and PAHs. Selected samples will be analyzed by 1D- and 2D-NMR to further characterize the chemical composition of DOM. This extensive investigation of the quantity and quality of fire-altered organic material at discrete time points will provide insight into the production and cycling of thermally-altered SOM and DOM. We hypothesize that PyC will be an important source of SOM to surface mineral soil horizons, and that the quantity of DOM will increase after fire, providing a rapid pulse of C to deep soils and aquatic systems.

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community.

PubMed

Gómez-Consarnau, Laura; Sachdeva, Rohan; Gifford, Scott M; Cutter, Lynda S; Fuhrman, Jed A; Sañudo-Wilhelmy, Sergio A; Moran, Mary Ann

2018-04-16

Aquatic environments contain large communities of microorganisms whose synergistic interactions mediate the cycling of major and trace nutrients, including vitamins. B-vitamins are essential coenzymes that many organisms cannot synthesize. Thus, their exchange among de novo synthesizers and auxotrophs is expected to play an important role in the microbial consortia and explain some of the temporal and spatial changes observed in diversity. In this study, we analyzed metatranscriptomes of a natural marine microbial community, diel sampled quarterly over one year to try to identify the potential major B-vitamin synthesizers and consumers. Transcriptomic data showed that the best-represented taxa dominated the expression of synthesis genes for some B-vitamins but lacked transcripts for others. For instance, Rhodobacterales dominated the expression of vitamin-B 12 synthesis, but not of vitamin-B 7 , whose synthesis transcripts were mainly represented by Flavobacteria. In contrast, bacterial groups that constituted less than 4% of the community (e.g., Verrucomicrobia) accounted for most of the vitamin-B 1 synthesis transcripts. Furthermore, ambient vitamin-B 1 concentrations were higher in samples collected during the day, and were positively correlated with chlorophyll-a concentrations. Our analysis supports the hypothesis that the mosaic of metabolic interdependencies through B-vitamin synthesis and exchange are key processes that contribute to shaping microbial communities in nature. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

PHOTOREACTIVITY OF CHROMOPHORIC DISSOLVED ORGANIC MATTER (CDOM) DERIVED FROM DECOMPOSITION OF VARIOUS VASCULAR PLANT AND ALGAL SOURCES

EPA Science Inventory

Chromophoric dissolved organic matter (CDOM) in aquatic environments is derived from the microbial decomposition of terrestrial and microbial organic matter. Here we present results of studies of the spectral properties and photoreactivity of the CDOM derived from several organi...

Response of Aquatic Bacterial Communities to Hydraulic Fracturing in Northwestern Pennsylvania: A Five-Year Study.

PubMed

Ulrich, Nikea; Kirchner, Veronica; Drucker, Rebecca; Wright, Justin R; McLimans, Christopher J; Hazen, Terry C; Campa, Maria F; Grant, Christopher J; Lamendella, Regina

2018-04-09

Horizontal drilling and hydraulic fracturing extraction procedures have become increasingly present in Pennsylvania where the Marcellus Shale play is largely located. The potential for long-term environmental impacts to nearby headwater stream ecosystems and aquatic bacterial assemblages is still incompletely understood. Here, we perform high-throughput sequencing of the 16 S rRNA gene to characterize the bacterial community structure of water, sediment, and other environmental samples (n = 189) from 31 headwater stream sites exhibiting different histories of fracking activity in northwestern Pennsylvania over five years (2012-2016). Stream pH was identified as a main driver of bacterial changes within the streams and fracking activity acted as an environmental selector for certain members at lower taxonomic levels within stream sediment. Methanotrophic and methanogenic bacteria (i.e. Methylocystaceae, Beijerinckiaceae, and Methanobacterium) were significantly enriched in sites exhibiting Marcellus shale activity (MSA+) compared to MSA- streams. This study highlighted potential sentinel taxa associated with nascent Marcellus shale activity and some of these taxa remained as stable biomarkers across this five-year study. Identifying the presence and functionality of specific microbial consortia within fracking-impacted streams will provide a clearer understanding of the natural microbial community's response to fracking and inform in situ remediation strategies.

Is litter decomposition 'primed' by primary producer-release of labile carbon in terrestrial and aquatic experimental systems?

NASA Astrophysics Data System (ADS)

Soares, A. Margarida P. M.; Kritzberg, Emma S.; Rousk, Johannes

2015-04-01

It is possible that recalcitrant organic matter (ROM) can be 'activated' by inputs of labile organic matter (LOM) through the priming effect (PE). Investigating the PE is of major importance to fully understand the microbial use of ROM and its role on carbon (C) and nutrient cycling in both aquatic and terrestrial ecosystems. In aquatic ecosystems it is thought that the PE is triggered by periphytic algae release of LOM. Analogously, in terrestrial systems it is hypothesized that the LOM released in plant rhizospheres, or from the green crusts on the surface of agricultural soils, stimulate the activity and growth of ROM decomposers. Most previous studies on PE have utilised pulse additions of single substrates at high concentrations. However, to achieve an assessment of the true importance of the PE, it is important to simulate a realistic delivery of LOM. We investigated, in a series of 2-week laboratory experiments, how primary producer (PP)-release of LOM influence litter degradation in terrestrial and aquatic experimental systems. We used soil (terrestrial) and pond water (aquatic) microbial communities to which litter was added under light and dark conditions. In addition, glucose was added at PP delivery rates in dark treatments to test if the putative PE in light systems could be reproduced. We observed an initial peak of bacterial growth rate followed by an overall decrease over time with no treatment differences. In light treatments, periphytic algae growth and increased fungal production was stimulated when bacterial growth declined. In contrast, both fungal growth and algal production were negligible in dark treatments. This reveals a direct positive influence of photosynthesis on fungal growth. To investigate if PP LOM supplements, and the associated fungal growth, translate into a modulated litter decomposition, we are using stable isotopes to track the use of litter and algal-derived carbon by determining the δ13C in produced CO2. Fungi and bacteria are the fundamental microbial decomposers and thus the main agents involved in respiration, ROM mobilisation and carbon cycling. By describing if and how litter decomposition is primed by primary producer-release of labile carbon we gain a better understanding of how microbial communities degrade OM in terrestrial and aquatic systems.

On the use of high-throughput sequencing for the study of cyanobacterial diversity in Antarctic aquatic mats.

PubMed

Pessi, Igor Stelmach; Maalouf, Pedro De Carvalho; Laughinghouse, Haywood Dail; Baurain, Denis; Wilmotte, Annick

2016-06-01

The study of Antarctic cyanobacterial diversity has been mostly limited to morphological identification and traditional molecular techniques. High-throughput sequencing (HTS) allows a much better understanding of microbial distribution in the environment, but its application is hampered by several methodological and analytical challenges. In this work, we explored the use of HTS as a tool for the study of cyanobacterial diversity in Antarctic aquatic mats. Our results highlight the importance of using artificial communities to validate the parameters of the bioinformatics procedure used to analyze natural communities, since pipeline-dependent biases had a strong effect on the observed community structures. Analysis of microbial mats from five Antarctic lakes and an aquatic biofilm from the Sub-Antarctic showed that HTS is a valuable tool for the assessment of cyanobacterial diversity. The majority of the operational taxonomic units retrieved were related to filamentous taxa such as Leptolyngbya and Phormidium, which are common genera in Antarctic lacustrine microbial mats. However, other phylotypes related to different taxa such as Geitlerinema, Pseudanabaena, Synechococcus, Chamaesiphon, Calothrix, and Coleodesmium were also found. Results revealed a much higher diversity than what had been reported using traditional methods and also highlighted remarkable differences between the cyanobacterial communities of the studied lakes. The aquatic biofilm from the Sub-Antarctic had a distinct cyanobacterial community from the Antarctic lakes, which in turn displayed a salinity-dependent community structure at the phylotype level. © 2016 Phycological Society of America.

Microbial Activity in Aquatic Environments Measured by Dimethyl Sulfoxide Reduction and Intercomparison with Commonly Used Methods

PubMed Central

Griebler, Christian; Slezak, Doris

2001-01-01

A new method to determine microbial (bacterial and fungal) activity in various freshwater habitats is described. Based on microbial reduction of dimethyl sulfoxide (DMSO) to dimethyl sulfide (DMS), our DMSO reduction method allows measurement of the respiratory activity in interstitial water, as well as in the water column. DMSO is added to water samples at a concentration (0.75% [vol/vol] or 106 mM) high enough to compete with other naturally occurring electron acceptors, as determined with oxygen and nitrate, without stimulating or inhibiting microbial activity. Addition of NaN3, KCN, and formaldehyde, as well as autoclaving, inhibited the production of DMS, which proves that the reduction of DMSO is a biotic process. DMSO reduction is readily detectable via the formation of DMS even at low microbial activities. All water samples showed significant DMSO reduction over several hours. Microbially reduced DMSO is recovered in the form of DMS from water samples by a purge and trap system and is quantified by gas chromatography and detection with a flame photometric detector. The DMSO reduction method was compared with other methods commonly used for assessment of microbial activity. DMSO reduction activity correlated well with bacterial production in predator-free batch cultures. Cell-production-specific DMSO reduction rates did not differ significantly in batch cultures with different nutrient regimes but were different in different growth phases. Overall, a cell-production-specific DMSO reduction rate of 1.26 × 10−17 ± 0.12 × 10−17 mol of DMS per produced cell (mean ± standard error; R2 = 0.78) was calculated. We suggest that the relationship of DMSO reduction rates to thymidine and leucine incorporation is linear (the R2 values ranged from 0.783 to 0.944), whereas there is an exponential relationship between DMSO reduction rates and glucose uptake, as well as incorporation (the R2 values ranged from 0.821 to 0.931). Based on our results, we conclude that the DMSO reduction method is a nonradioactive alternative to other methods commonly used to assess microbial activity. PMID:11133433

Microbial activity in aquatic environments measured by dimethyl sulfoxide reduction and intercomparison with commonly used methods.

PubMed

Griebler, C; Slezak, D

2001-01-01

A new method to determine microbial (bacterial and fungal) activity in various freshwater habitats is described. Based on microbial reduction of dimethyl sulfoxide (DMSO) to dimethyl sulfide (DMS), our DMSO reduction method allows measurement of the respiratory activity in interstitial water, as well as in the water column. DMSO is added to water samples at a concentration (0.75% [vol/vol] or 106 mM) high enough to compete with other naturally occurring electron acceptors, as determined with oxygen and nitrate, without stimulating or inhibiting microbial activity. Addition of NaN(3), KCN, and formaldehyde, as well as autoclaving, inhibited the production of DMS, which proves that the reduction of DMSO is a biotic process. DMSO reduction is readily detectable via the formation of DMS even at low microbial activities. All water samples showed significant DMSO reduction over several hours. Microbially reduced DMSO is recovered in the form of DMS from water samples by a purge and trap system and is quantified by gas chromatography and detection with a flame photometric detector. The DMSO reduction method was compared with other methods commonly used for assessment of microbial activity. DMSO reduction activity correlated well with bacterial production in predator-free batch cultures. Cell-production-specific DMSO reduction rates did not differ significantly in batch cultures with different nutrient regimes but were different in different growth phases. Overall, a cell-production-specific DMSO reduction rate of 1.26 x 10(-17) +/- 0. 12 x 10(-17) mol of DMS per produced cell (mean +/- standard error; R(2) = 0.78) was calculated. We suggest that the relationship of DMSO reduction rates to thymidine and leucine incorporation is linear (the R(2) values ranged from 0.783 to 0.944), whereas there is an exponential relationship between DMSO reduction rates and glucose uptake, as well as incorporation (the R(2) values ranged from 0.821 to 0.931). Based on our results, we conclude that the DMSO reduction method is a nonradioactive alternative to other methods commonly used to assess microbial activity.

Selective preservation and origin of petroleum-forming aquatic kerogen

USGS Publications Warehouse

Hatcher, P.G.; Spiker, E. C.; Szeverenyi, N.M.; Maciel, G.E.

1983-01-01

Studies of a marine algal sapropel from Mangrove Lake, Bermuda, by 13C NMR and stable carbon isotopic methods show that precursors of aquatic kerogen (insoluble, macromolecular, paraffinic humic substances) are primary components of algae and possibly associated bacteria and that these substances survive microbial decomposition and are selectively preserved during early diagenesis. ?? 1983 Nature Publishing Group.

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

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

Parfrey, Laura Wegener; Walters, William A.; Lauber, Christian L.

2014-06-19

Eukaryotic microbes (protists) residing in the vertebrate gut influence host health and disease, but their diversity and distribution in healthy hosts is poorly understood. Protists found in the gut are typically considered parasites, but many are commensal and some are beneficial. Further, the hygiene hypothesis predicts that association with our co-evolved microbial symbionts may be important to overall health. It is therefore imperative that we understand the normal diversity of our eukaryotic gut microbiota to test for such effects and avoid eliminating commensal organisms. We assembled a dataset of healthy individuals from two populations, one with traditional, agrarian lifestyles andmore » a second with modern, westernized lifestyles, and characterized the human eukaryotic microbiota via high-throughput sequencing. To place the human gut microbiota within a broader context our dataset also includes gut samples from diverse mammals and samples from other aquatic and terrestrial environments. We curated the SILVA ribosomal database to reflect current knowledge of eukaryotic taxonomy and employ it as a phylogenetic framework to compare eukaryotic diversity across environment. We show that adults from the non-western population harbor a diverse community of protists, and diversity in the human gut is comparable to that in other mammals. However, the eukaryotic microbiota of the western population appears depauperate. The distribution of symbionts found in mammals reflects both host phylogeny and diet. Eukaryotic microbiota in the gut are less diverse and more patchily distributed than bacteria. More broadly, we show that eukaryotic communities in the gut are less diverse than in aquatic and terrestrial habitats, and few taxa are shared across habitat types, and diversity patterns of eukaryotes are correlated with those observed for bacteria. These results outline the distribution and diversity of microbial eukaryotic communities in the mammalian gut and across environments.« less

Dinitrogen fixation associated with shoots of aquatic carnivorous plants: is it ecologically important?

PubMed Central

Sirová, Dagmara; Šantrůček, Jiří; Adamec, Lubomír; Bárta, Jiří; Borovec, Jakub; Pech, Jiří; Owens, Sarah M.; Šantrůčková, Hana; Schäufele, Rudi; Štorchová, Helena; Vrba, Jaroslav

2014-01-01

Background and Aims Rootless carnivorous plants of the genus Utricularia are important components of many standing waters worldwide, as well as suitable model organisms for studying plant–microbe interactions. In this study, an investigation was made of the importance of microbial dinitrogen (N2) fixation in the N acquisition of four aquatic Utricularia species and another aquatic carnivorous plant, Aldrovanda vesiculosa. Methods 16S rRNA amplicon sequencing was used to assess the presence of micro-organisms with known ability to fix N2. Next-generation sequencing provided information on the expression of N2 fixation-associated genes. N2 fixation rates were measured following 15N2-labelling and were used to calculate the plant assimilation rate of microbially fixed N2. Key Results Utricularia traps were confirmed as primary sites of N2 fixation, with up to 16 % of the plant-associated microbial community consisting of bacteria capable of fixing N2. Of these, rhizobia were the most abundant group. Nitrogen fixation rates increased with increasing shoot age, but never exceeded 1·3 μmol N g–1 d. mass d–1. Plant assimilation rates of fixed N2 were detectable and significant, but this fraction formed less than 1 % of daily plant N gain. Although trap fluid provides conditions favourable for microbial N2 fixation, levels of nif gene transcription comprised <0·01 % of the total prokaryotic transcripts. Conclusions It is hypothesized that the reason for limited N2 fixation in aquatic Utricularia, despite the large potential capacity, is the high concentration of NH4-N (2·0–4·3 mg L–1) in the trap fluid. Resulting from fast turnover of organic detritus, it probably inhibits N2 fixation in most of the microorganisms present. Nitrogen fixation is not expected to contribute significantly to N nutrition of aquatic carnivorous plants under their typical growth conditions; however, on an annual basis the plant–microbe system can supply nitrogen in the order of hundreds of mg m–2 into the nutrient-limited littoral zone, where it may thus represent an important N source. PMID:24817095

The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes.

PubMed

Angly, Florent E; Willner, Dana; Prieto-Davó, Alejandra; Edwards, Robert A; Schmieder, Robert; Vega-Thurber, Rebecca; Antonopoulos, Dionysios A; Barott, Katie; Cottrell, Matthew T; Desnues, Christelle; Dinsdale, Elizabeth A; Furlan, Mike; Haynes, Matthew; Henn, Matthew R; Hu, Yongfei; Kirchman, David L; McDole, Tracey; McPherson, John D; Meyer, Folker; Miller, R Michael; Mundt, Egbert; Naviaux, Robert K; Rodriguez-Mueller, Beltran; Stevens, Rick; Wegley, Linda; Zhang, Lixin; Zhu, Baoli; Rohwer, Forest

2009-12-01

Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths. Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta-analysis of microbial and viral average genome lengths in over 150 metagenomes from four biomes to determine whether genome lengths vary consistently between and within biomes, and between microbial and viral communities from the same environment. Significant differences between biomes and within aquatic sub-biomes (oceans, hypersaline systems, freshwater, and microbialites) suggested that average genome length is a fundamental property of environments driven by factors at the sub-biome level. The behavior of paired viral and microbial metagenomes from the same environment indicated that microbial and viral average genome sizes are independent of each other, but indicative of community responses to stressors and environmental conditions.

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland: Bacterial, fungal, and plant communities

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

McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biologicalmore » soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.« less

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland: Bacterial, fungal, and plant communities

DOE PAGES

McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.; ...

2017-03-13

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biologicalmore » soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.« less

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

PubMed

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

2013-08-01

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

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland

USGS Publications Warehouse

McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.; Gallegos-Graves, La Verne; Kuske, Cheryl R.; Reed, Sasha C.

2017-01-01

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biological soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.

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...

Metagenome Sequencing of a Coastal Marine Microbial Community from Monterey Bay, California

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

Mueller, Ryan S.; Bryson, Sam; Kieft, Brandon

Heterotrophic microbes are critical components of aquatic food webs. Linkages between populations and the substrates they utilize are not well defined. Here we present the metagenome of microbial communities from the coastal Pacific Ocean exposed to various nutrient additions in order to better understand substrate utilization and partitioning in this environment.

40 CFR 158.2174 - Experimental use permit microbial pesticides nontarget organisms and environmental fate data...

Code of Federal Regulations, 2010 CFR

2010-07-01

... Freshwater invertebrate toxicity/pathogenicity NR R R R NR NR NR NR TGAI 1, 2, 3 885.4300 Nontarget... exposure. Freshwater invertebrates are preferred for invertebrate testing. 3. Required when there will be significant exposure to aquatic organisms (fish and invertebrates). 4. Required if the microbial pesticide is...

Metagenome Sequencing of a Coastal Marine Microbial Community from Monterey Bay, California

DOE PAGES

Mueller, Ryan S.; Bryson, Sam; Kieft, Brandon; ...

2015-04-30

Heterotrophic microbes are critical components of aquatic food webs. Linkages between populations and the substrates they utilize are not well defined. Here we present the metagenome of microbial communities from the coastal Pacific Ocean exposed to various nutrient additions in order to better understand substrate utilization and partitioning in this environment.

Optimization of 15 parameters influencing the long-term survival of bacteria in aquatic systems

NASA Technical Reports Server (NTRS)

Obenhuber, D. C.

1993-01-01

NASA is presently engaged in the design and development of a water reclamation system for the future space station. A major concern in processing water is the control of microbial contamination. As a means of developing an optimal microbial control strategy, studies were undertaken to determine the type and amount of contamination which could be expected in these systems under a variety of changing environmental conditions. A laboratory-based Taguchi optimization experiment was conducted to determine the ideal settings for 15 parameters which influence the survival of six bacterial species in aquatic systems. The experiment demonstrated that the bacterial survival period could be decreased significantly by optimizing environmental conditions.

A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater.

PubMed

Flaviani, Flavia; Schroeder, Declan C; Balestreri, Cecilia; Schroeder, Joanna L; Moore, Karen; Paszkiewicz, Konrad; Pfaff, Maya C; Rybicki, Edward P

2017-03-17

The aquatic microbiome is composed of a multi-phylotype community of microbes, ranging from the numerically dominant viruses to the phylogenetically diverse unicellular phytoplankton. They influence key biogeochemical processes and form the base of marine food webs, becoming food for secondary consumers. Due to recent advances in next-generation sequencing, this previously overlooked component of our hydrosphere is starting to reveal its true diversity and biological complexity. We report here that 250 mL of seawater is sufficient to provide a comprehensive description of the microbial diversity in an oceanic environment. We found that there was a dominance of the order Caudovirales (59%), with the family Myoviridae being the most prevalent. The families Phycodnaviridae and Mimiviridae made up the remainder of pelagic double-stranded DNA (dsDNA) virome. Consistent with this analysis, the Cyanobacteria dominate (52%) the prokaryotic diversity. While the dinoflagellates and their endosymbionts, the superphylum Alveolata dominates (92%) the microbial eukaryotic diversity. A total of 834 prokaryotic, 346 eukaryotic and 254 unique virus phylotypes were recorded in this relatively small sample of water. We also provide evidence, through a metagenomic-barcoding comparative analysis, that viruses are the likely source of microbial environmental DNA (meDNA). This study opens the door to a more integrated approach to oceanographic sampling and data analysis.

Internal nitrogen removal from sediments by the hybrid system of microbial fuel cells and submerged aquatic plants

PubMed Central

Xu, Peng; Xiao, En-Rong; Xu, Dan; Zhou, Yin; He, Feng; Liu, Bi-Yun; Zeng, Lei; Wu, Zhen-Bin

2017-01-01

Sediment internal nitrogen release is a significant pollution source in the overlying water of aquatic ecosystems. This study aims to remove internal nitrogen in sediment-water microcosms by coupling sediment microbial fuel cells (SMFCs) with submerged aquatic plants. Twelve tanks including four treatments in triplicates were designed: open-circuit (SMFC-o), closed-circuit (SMFC-c), aquatic plants with open-circuit (P-SMFC-o) and aquatic plants with closed-circuit (P-SMFC-c). The changes in the bio-electrochemical characteristics of the nitrogen levels in overlying water, pore water, sediments, and aquatic plants were documented to explain the migration and transformation pathways of internal nitrogen. The results showed that both electrogenesis and aquatic plants could facilitate the mineralization of organic nitrogen in sediments. In SMFC, electrogenesis promoted the release of ammonium from the pore water, followed by the accumulation of ammonium and nitrate in the overlying water. The increased redox potential of sediments due to electrogenesis also contributed to higher levels of nitrate in overlying water when nitrification in pore water was facilitated and denitrification at the sediment-water interface was inhibited. When the aquatic plants were introduced into the closed-circuit SMFC, the internal ammonium assimilation by aquatic plants was advanced by electrogenesis; nitrification in pore water and denitrification in sediments were also promoted. These processes might result in the maximum decrease of internal nitrogen with low nitrogen levels in the overlying water despite the lower power production. The P-SMFC-c reduced 8.1%, 16.2%, 24.7%, and 25.3% of internal total nitrogen compared to SMFC-o on the 55th, 82th, 136th, and 190th days, respectively. The smaller number of Nitrospira and the larger number of Bacillus and Pseudomonas on the anodes via high throughput sequencing may account for strong mineralization and denitrification in the sediments under closed-circuit. The coupled P-SMFC system has shown good potential for the efficient removal of internal nitrogen. PMID:28241072

Internal nitrogen removal from sediments by the hybrid system of microbial fuel cells and submerged aquatic plants.

PubMed

Xu, Peng; Xiao, En-Rong; Xu, Dan; Zhou, Yin; He, Feng; Liu, Bi-Yun; Zeng, Lei; Wu, Zhen-Bin

2017-01-01

Sediment internal nitrogen release is a significant pollution source in the overlying water of aquatic ecosystems. This study aims to remove internal nitrogen in sediment-water microcosms by coupling sediment microbial fuel cells (SMFCs) with submerged aquatic plants. Twelve tanks including four treatments in triplicates were designed: open-circuit (SMFC-o), closed-circuit (SMFC-c), aquatic plants with open-circuit (P-SMFC-o) and aquatic plants with closed-circuit (P-SMFC-c). The changes in the bio-electrochemical characteristics of the nitrogen levels in overlying water, pore water, sediments, and aquatic plants were documented to explain the migration and transformation pathways of internal nitrogen. The results showed that both electrogenesis and aquatic plants could facilitate the mineralization of organic nitrogen in sediments. In SMFC, electrogenesis promoted the release of ammonium from the pore water, followed by the accumulation of ammonium and nitrate in the overlying water. The increased redox potential of sediments due to electrogenesis also contributed to higher levels of nitrate in overlying water when nitrification in pore water was facilitated and denitrification at the sediment-water interface was inhibited. When the aquatic plants were introduced into the closed-circuit SMFC, the internal ammonium assimilation by aquatic plants was advanced by electrogenesis; nitrification in pore water and denitrification in sediments were also promoted. These processes might result in the maximum decrease of internal nitrogen with low nitrogen levels in the overlying water despite the lower power production. The P-SMFC-c reduced 8.1%, 16.2%, 24.7%, and 25.3% of internal total nitrogen compared to SMFC-o on the 55th, 82th, 136th, and 190th days, respectively. The smaller number of Nitrospira and the larger number of Bacillus and Pseudomonas on the anodes via high throughput sequencing may account for strong mineralization and denitrification in the sediments under closed-circuit. The coupled P-SMFC system has shown good potential for the efficient removal of internal nitrogen.

Soil Biogeochemical and Microbial Feedbacks along a Snowmelt-Dominated Hillslope-to-Floodplain Transect in Colorado.

NASA Astrophysics Data System (ADS)

Sorensen, P.; Beller, H. R.; Bill, M.; Bouskill, N.; Brodie, E.; Chakraborty, R.; Conrad, M. E.; Karaoz, U.; Polussa, A.; Steltzer, H.; Wang, S.; Williams, K. H.; Wilmer, C.; Wu, Y.

2017-12-01

Nitrogen export from mountainous watersheds is a product of multiple interactions among hydrological processes and soil-microbial-plant feedbacks along the continuum from terrestrial to aquatic environments. In snow-dominated systems, like the East River Watershed (CO), seasonal processes such as snowmelt exert significant influence on the annual hydrologic cycle and may also link spatially distinct catchment subsystems, such as hillslope and adjoining riparian floodplains. Further, snowmelt is occurring earlier each year and this is predicted to result in a temporal asynchrony between historically coupled microbial nutrient release and plant nutrient demand in spring, with the potential to increase N export from the East River Watershed. Here we summarize biogeochemical data collected along a hillslope-to-riparian floodplain transect at the East River site. Starting in Fall 2016, we sampled soils at 3 depths and measured dissolved pools of soil nutrients (e.g., NH4+, NO3-, DOC, P), microbial biomass CN, and microbial community composition over a seasonal time course, through periods of snow accumulation, snowmelt, and plant senescence. Soil moisture content in the top 5 cm of floodplain soils was nearly 4X greater across sampling dates, coinciding with 2X greater microbial biomass C, larger extractable pools of NH4+, and smaller pools of NO3- in floodplain vs. hillslope soils. These results suggest that microbially mediated redox processes played an important role in N cycling along the transect. Hillslope vs. floodplain location also appeared to be a key factor that differentiated soil microbial communities (e.g., a more important factor than seasonality or soil depth or type). Snow accumulation and snowmelt exerted substantial influence on soil biogeochemistry. For example, microbial biomass accumulation increased about 2X beneath the winter snowpack. Snowmelt resulted in a precipitous crash in the microbial population, with 2.5X reductions in floodplain and 2X reductions in hillslope soils. Immediately following snowmelt, NO3- concentrations in soil porewater and soil extracts increased dramatically. Overall, these results suggest that N export is strongly influenced by distinct soil biogeochemical and microbiological patterns along hillslope-to-floodplain transects at East River.

Effects of acute gamma-irradiation on the aquatic microbial microcosm in comparison with chemicals.

PubMed

Fuma, Shoichi; Ishii, Nobuyoshi; Takeda, Hiroshi; Miyamoto, Kiriko; Yanagisawa, Kei; Doi, Kazutaka; Kawaguchi, Isao; Tanaka, Nobuyuki; Inamori, Yuhei; Polikarpov, Gennady G

2009-12-01

Effects of acute gamma-irradiation were investigated in the aquatic microcosm consisting of green algae (Chlorella sp. and Scenedesmus sp.) and a blue-green alga (Tolypothrix sp.) as producers; an oligochaete (Aeolosoma hemprichi), rotifers (Lecane sp. and Philodina sp.) and a ciliate protozoan (Cyclidium glaucoma) as consumers; and more than four species of bacteria as decomposers. At 100 Gy, populations were not affected in any taxa. At 500-5000 Gy, one or three taxa died out and populations of two or three taxa decreased over time, while that of Tolypothrix sp. increased. This Tolypothrix sp. increase was likely an indirect effect due to interspecies interactions. The principal response curve analysis revealed that the main trend of the effects was a dose-dependent population decrease. For a better understanding of radiation risks in aquatic microbial communities, effect doses of gamma-rays compared with copper, herbicides and detergents were evaluated using the radiochemoecological conceptual model and the effect index for microcosm.

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

PubMed

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

2016-11-01

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

Heterogeneity in leaf litter decomposition in a temporary Mediterranean stream during flow fragmentation.

PubMed

Abril, Meritxell; Muñoz, Isabel; Menéndez, Margarita

2016-05-15

In temporary Mediterranean streams, flow fragmentation during summer droughts originates an ephemeral mosaic of terrestrial and aquatic habitat types. The heterogeneity of habitat types implies a particular ecosystem functioning in temporary streams that is still poorly understood. We assessed the initial phases of leaf litter decomposition in selected habitat types: running waters, isolated pools and moist and dry streambed sediments. We used coarse-mesh litter bags containing Populus nigra leaves to examine decomposition rates, microbial biomass, macroinvertebrate abundance and dissolved organic carbon (DOC) release rates in each habitat type over an 11-day period in late summer. We detected faster decomposition rates in aquatic (running waters and isolated pools) than in terrestrial habitats (moist and dry streambed sediments). Under aquatic conditions, decomposition was characterized by intense leaching and early microbial colonization, which swiftly started to decompose litter. Microbial colonization in isolated pools was primarily dominated by bacteria, whereas in running waters fungal biomass predominated. Under terrestrial conditions, leaves were most often affected by abiotic processes that resulted in small mass losses. We found a substantial decrease in DOC release rates in both aquatic habitats within the first days of the study, whereas DOC release rates remained relatively stable in the moist and dry sediments. This suggests that leaves play different roles as a DOC source during and after flow fragmentation. Overall, our results revealed that leaf decomposition is heterogeneous during flow fragmentation, which has implications related to DOC utilization that should be considered in future regional carbon budgets. Copyright © 2016 Elsevier B.V. All rights reserved.

Functional effects of the bacterial insecticide Bacillus thuringiensis var. kurstaki on aquatic microbial communities.

PubMed

Kreutzweiser, D P; Gringorten, J L; Thomas, D R; Butcher, J T

1996-04-01

Epilithic microbial communities were colonized on leaf disks and exposed to commercial preparations of Bacillus thuringiensis var. kurstaki (Btk) in aquatic microcosms. Responses in terms of microbial respiration, bacterial cell density, protozoan density, and microbial decomposition activity were measured. Test concentrations for treatments with Dipel 64AF and Dipel 8AF in microcosms were the expected environmental concentration (EEC) of 20 IU/ml, 100x the EEC, and 1000x the EEC. Bacterial cell density in the biofilm of leaf disks was significantly increased at concentrations as low as the EEC. There were no concomitant alterations in protozoan density. Microbial respiration was significantly increased, and decomposition activity was significantly decreased, but only at the artificially high concentration of 1000x the EEC. This effect was attributed to the spore-crystal component rather than formulation ingredients. Microbial decomposition of leaf material was also determined in outdoor stream channels treated at concentrations ranging from the EEC to 100x the EEC. Although there tended to be reduced decomposition activity in treated channels, there were no significant differences in mass loss of leaf material between treated and control channels. Various regression, classification, and ordination procedures were applied to the experimental data, and none indicated significant treatment effects. These results from laboratory and controlled field experiments indicate that contamination of watercourses with Btk is unlikely to result in significant adverse effects on microbial community function in terms of detrital decomposition.

Mass dependent stable isotope fractionation of mercury during mer mediated microbial degradation of monomethylmercury

NASA Astrophysics Data System (ADS)

Kritee, K.; Barkay, Tamar; Blum, Joel D.

2009-03-01

Controlling bioaccumulation of toxic monomethylmercury (MMHg) in aquatic food chains requires differentiation between biotic and abiotic pathways that lead to its production and degradation. Recent mercury (Hg) stable isotope measurements of natural samples suggest that Hg isotope ratios can be a powerful proxy for tracing dominant Hg transforming pathways in aquatic ecosystems. Specifically, it has been shown that photo-degradation of MMHg causes both mass dependent (MDF) and mass independent fractionation (MIF) of Hg isotopes. Because the extent of MDF and MIF observed in natural samples (e.g., fish, soil and sediments) can potentially be used to determine the relative importance of pathways leading to MMHg accumulation, it is important to determine the potential role of microbial pathways in contributing to the fractionation, especially MIF, observed in these samples. This study reports the extent of fractionation of Hg stable isotopes during degradation of MMHg to volatile elemental Hg and methane via the microbial Hg resistance ( mer) pathway in Escherichia coli carrying a mercury resistance ( mer) genetic system on a multi-copy plasmid. During experimental microbial degradation of MMHg, MMHg remaining in reactors became progressively heavier (increasing δ202Hg) with time and underwent mass dependent Rayleigh fractionation with a fractionation factor α202/198 = 1.0004 ± 0.0002 (2SD). However, MIF was not observed in any of the microbial MMHg degradation experiments indicating that the isotopic signature left by mer mediated MMHg degradation is significantly different from fractionation observed during DOC mediated photo-degradation of MMHg. Additionally, a clear suppression of Hg isotope fractionation, both during reduction of Hg(II) and degradation of MMHg, was observed when the cell densities increased, possibly due to a reduction in substrate bioavailability. We propose a multi-step framework for understanding the extent of fractionation seen in our MMHg degradation experiments and, based on estimates of the rates of the various steps involved in this mer mediated pathway, suggest which steps in the process could contribute towards the observed extent of fractionation. This framework suggests that at lower cell densities catalysis by MerB was the rate limiting step while at higher cell densities transport into the cell, which does not cause fractionation, became the rate limiting step. In addition to presenting evidence for absence of MIF during mer mediated Hg transformations, based on the nature of Hg compounds and microbe-Hg interactions, we suggest that the nuclear spin dependent MIF (i.e., the magnetic isotope effect) is also unlikely to occur during other non mer mediated 'dark' microbial Hg transformations (e.g., formation of MMHg and oxidative degradation of MMHg). Because of the important implications of the absence of MIF during biological processes on Hg isotope systematics, we discuss theoretical considerations and experimental strategies that could be used to confirm this suggestion.

Microbial competition between Bacillus subtilis and Staphylococcus aureus monitored by imaging mass spectrometry

PubMed Central

Gonzalez, David J.; Haste, Nina M.; Hollands, Andrew; Fleming, Tinya C.; Hamby, Matthew; Pogliano, Kit; Nizet, Victor

2011-01-01

Microbial competition exists in the general environment, such as soil or aquatic habitats, upon or within unicellular or multicellular eukaryotic life forms. The molecular actions that govern microbial competition, leading to niche establishment and microbial monopolization, remain undetermined. The emerging technology of imaging mass spectrometry (IMS) enabled the observation that there is directionality in the metabolic output of the organism Bacillus subtilis when co-cultured with Staphylococcus aureus. The directionally released antibiotic alters S. aureus virulence factor production and colonization. Therefore, IMS provides insight into the largely hidden nature of competitive microbial encounters and niche establishment, and provides a paradigm for future antibiotic discovery. PMID:21719540

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.

Cross-system nutrient transport: effects of locally-derived aeolian dust on oligotrophic lakes in West Greenland

NASA Astrophysics Data System (ADS)

Bullard, J. E.; Anderson, N. J.; McGowan, S.; Prater, C.; Watts, M.; Whitford, E.

2017-12-01

Terrestrially-derived nutrients can strongly affect production in aquatic environments. However, while some research has focused on nutrient delivery via hydrological inputs, the effects of atmospheric dry deposition are comparatively understudied. This paper examines the influence of aeolian-derived elements on water chemistry and microbial nutrient-limitation in oligotrophic lakes in West Greenland. Estimates of seasonal dust deposition and elemental leaching rates are combined with lake nutrient concentration measurements to establish the role of glacio-fluvial dust deposition in shaping nutrient stoichiometry of downwind lakes. The bioavailability of dust-associated elements is also explored using enzyme assays designed to indicate nutrient-limitation in microbial communities sampled across a dust deposition gradient. Together, these analyses demonstrate the importance of atmospheric dust inputs on hydrologically-isolated lakes found in arid high-latitude environments and demonstrate the need to better understand the role of aeolian deposition in cross-system nutrient transport.

Microbial Succession and Nitrogen Cycling in Cultured Biofilms as Affected by the Inorganic Nitrogen Availability.

PubMed

Li, Shuangshuang; Peng, Chengrong; Wang, Chun; Zheng, Jiaoli; Hu, Yao; Li, Dunhai

2017-01-01

Biofilms play important roles in nutrients and energy cycling in aquatic ecosystems. We hypothesized that as eutrophication could change phytoplankton community and decrease phytoplankton diversity, ambient inorganic nitrogen level will affect the microbial community and diversity of biofilms and the roles of biofilms in nutrient cycling. Biofilms were cultured using a flow incubator either with replete inorganic nitrogen (N-rep) or without exogenous inorganic nitrogen supply (N-def). The results showed that the biomass and nitrogen and phosphorous accumulation of biofilms were limited by N deficiency; however, as expected, the N-def biofilms had significantly higher microbial diversity than that of N-rep biofilms. The microbial community of biofilms shifted in composition and abundance in response to ambient inorganic nitrogen level. For example, as compared between the N-def and the N-rep biofilms, the former consisted of more diazotrophs, while the latter consisted of more denitrifying bacteria. As a result of the shift of the functional microbial community, the N concentration of N-rep medium kept decreasing, while that of N-def medium showed an increasing trend in the late stage. This indicates that biofilms can serve as the source or the sink of nitrogen in aquatic ecosystems, and it depends on the inorganic nitrogen availability.

Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar

PubMed Central

Bletz, Molly C.; Archer, Holly; Harris, Reid N.; McKenzie, Valerie J.; Rabemananjara, Falitiana C. E.; Rakotoarison, Andolalao; Vences, Miguel

2017-01-01

Host-associated microbiotas of vertebrates are diverse and complex communities that contribute to host health. In particular, for amphibians, cutaneous microbial communities likely play a significant role in pathogen defense; however, our ecological understanding of these communities is still in its infancy. Here, we take advantage of the fully endemic and locally species-rich amphibian fauna of Madagascar to investigate the factors structuring amphibian skin microbiota on a large scale. Using amplicon-based sequencing, we evaluate how multiple host species traits and site factors affect host bacterial diversity and community structure. Madagascar is home to over 400 native frog species, all of which are endemic to the island; more than 100 different species are known to occur in sympatry within multiple rainforest sites. We intensively sampled frog skin bacterial communities, from over 800 amphibians from 89 species across 30 sites in Madagascar during three field visits, and found that skin bacterial communities differed strongly from those of the surrounding environment. Richness of bacterial operational taxonomic units (OTUs) and phylogenetic diversity differed among host ecomorphs, with arboreal frogs exhibiting lower richness and diversity than terrestrial and aquatic frogs. Host ecomorphology was the strongest factor influencing microbial community structure, with host phylogeny and site parameters (latitude and elevation) explaining less but significant portions of the observed variation. Correlation analysis and topological congruency analyses revealed little to no phylosymbiosis for amphibian skin microbiota. Despite the observed geographic variation and low phylosymbiosis, we found particular OTUs that were differentially abundant between particular ecomorphs. For example, the genus Pigmentiphaga (Alcaligenaceae) was significantly enriched on arboreal frogs, Methylotenera (Methylophilaceae) was enriched on aquatic frogs, and Agrobacterium (Rhizobiaceae) was enriched on terrestrial frogs. The presence of shared bacterial OTUs across geographic regions for selected host genera suggests the presence of core microbial communities which in Madagascar, might be driven more strongly by a species’ preference for specific microhabitats than by the physical, physiological or biochemical properties of their skin. These results corroborate that both host and environmental factors are driving community assembly of amphibian cutaneous microbial communities, and provide an improved foundation for elucidating their role in disease resistance. PMID:28861051

Bacterial Community in Water and Air of Two Sub-Alpine Lakes in Taiwan.

PubMed

Tandon, Kshitij; Yang, Shan-Hua; Wan, Min-Tao; Yang, Chia-Chin; Baatar, Bayanmunkh; Chiu, Chih-Yu; Tsai, Jeng-Wei; Liu, Wen-Cheng; Tang, Sen-Lin

2018-04-21

Very few studies have attempted to profile the microbial communities in the air above freshwater bodies, such as lakes, even though freshwater sources are an important part of aquatic ecosystems and airborne bacteria are the most dispersible microorganisms on earth. In the present study, we investigated microbial communities in the waters of two high mountain sub-alpine montane lakes-located 21 km apart and with disparate trophic characteristics-and the air above them. Although bacteria in the lakes had locational differences, their community compositions remained constant over time. However, airborne bacterial communities were diverse and displayed spatial and temporal variance. Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria were dominant in both lakes, with different relative abundances between lakes, and Parcubacteria (OD1) was dominant in air samples for all sampling times, except two. We also identified certain shared taxa between lake water and the air above it. The results obtained on these communities in the present study provide putative candidates to study how airborne communities shape lake water bacterial compositions and vice versa.

Aquatic Plant Control Research Program: The Rhizosphere Microbiology of Rooted Aquatic Plants.

DTIC Science & Technology

1988-04-01

acids. Acetic acid postulated as agent Thalassia Nitrogen fixation in Capone 1983 testudinwn rhizosphere and phyllosphere 13. Fungi living in the...microbial population associated with the rhizome detritus. 26. Durako and Moffler (1987) examined responses of Thalassia testudinum to nitrogen enrichment...economy of seagrasses for communities of Thalassia testudinium and Zostera maina. He concluded that nitrogen fixation is probably more important for

Biofilm comprising phototrophic, diazotrophic, and hydrocarbon-utilizing bacteria: a promising consortium in the bioremediation of aquatic hydrocarbon pollutants.

PubMed

Al-Bader, Dhia; Kansour, Mayada K; Rayan, Rehab; Radwan, Samir S

2013-05-01

Biofilms harboring simultaneously anoxygenic and oxygenic phototrophic bacteria, diazotrophic bacteria, and hydrocarbon-utilizing bacteria were established on glass slides suspended in pristine and oily seawater. Via denaturing gradient gel electrophoresis analysis on PCR-amplified rRNA gene sequence fragments from the extracted DNA from biofilms, followed by band amplification, biofilm composition was determined. The biofilms contained anoxygenic phototrophs belonging to alphaproteobacteria; pico- and filamentous cyanobacteria (oxygenic phototrophs); two species of the diazotroph Azospirillum; and two hydrocarbon-utilizing gammaproteobacterial genera, Cycloclasticus and Oleibacter. The coexistence of all these microbial taxa with different physiologies in the biofilm makes the whole community nutritionally self-sufficient and adequately aerated, a condition quite suitable for the microbial biodegradation of aquatic pollutant hydrocarbons.

Emerging contaminants--pesticides, PPCPs, microbial degradation products and natural substances as inhibitors of multixenobiotic defense in aquatic organisms.

PubMed

Smital, Tvrtko; Luckenbach, Till; Sauerborn, Roberta; Hamdoun, Amro M; Vega, Rebecca L; Epel, David

2004-08-18

The environmental presence of chemosensitizers or inhibitors of the multixenobiotic resistance (MXR) defense system in aquatic organisms could cause increase in intracellular accumulation and toxic effects of other xenobiotics normally effluxed by MXR transport proteins (P-glycoprotein (P-gps), MRPs). MXR inhibition with concomitant detrimental effects has been shown in several studies with aquatic organisms exposed to both model MXR inhibitors and environmental pollutants. The presence of MXR inhibitors has been demonstrated in environmental samples from polluted locations at concentrations that could abolish P-gp transport activity. However, it is not clear whether the inhibition observed after exposure to environmental samples is a result of saturation of MXR transport proteins by numerous substrates present in polluted waters or results from the presence of powerful MXR inhibitors. And are potent environmental MXR inhibitors natural or man-made chemicals? As a consequence of these uncertainties, no official action has been taken to monitor and control the release and presence of MXR inhibitors into aquatic environments. In this paper we present our new results addressing these critical questions. Ecotoxicological significance of MXR inhibition was supported in in vivo studies that demonstrated an increase in the production of mutagenic metabolites by mussels and an increase in the number of sea urchin embryos with apoptotic cells after exposure to model MXR inhibitors. We also demonstrated that MXR inhibitors are present among both conventional and emerging man-made pollutants: some pesticides and synthetic musk fragrances show extremely high MXR inhibitory potential at environmentally relevant concentrations. In addition, we emphasized the biological transformation of crude oil hydrocarbons into MXR inhibitors by oil-degrading bacteria, and the risk potentially caused by powerful natural MXR inhibitors produced by invasive species.

Sustainable microbial water quality monitoring programme design using phage-lysis and multivariate techniques.

PubMed

Nnane, Daniel Ekane

2011-11-15

Contamination of surface waters is a pervasive threat to human health, hence, the need to better understand the sources and spatio-temporal variations of contaminants within river catchments. River catchment managers are required to sustainably monitor and manage the quality of surface waters. Catchment managers therefore need cost-effective low-cost long-term sustainable water quality monitoring and management designs to proactively protect public health and aquatic ecosystems. Multivariate and phage-lysis techniques were used to investigate spatio-temporal variations of water quality, main polluting chemophysical and microbial parameters, faecal micro-organisms sources, and to establish 'sentry' sampling sites in the Ouse River catchment, southeast England, UK. 350 river water samples were analysed for fourteen chemophysical and microbial water quality parameters in conjunction with the novel human-specific phages of Bacteroides GB-124 (Bacteroides GB-124). Annual, autumn, spring, summer, and winter principal components (PCs) explained approximately 54%, 75%, 62%, 48%, and 60%, respectively, of the total variance present in the datasets. Significant loadings of Escherichia coli, intestinal enterococci, turbidity, and human-specific Bacteroides GB-124 were observed in all datasets. Cluster analysis successfully grouped sampling sites into five clusters. Importantly, multivariate and phage-lysis techniques were useful in determining the sources and spatial extent of water contamination in the catchment. Though human faecal contamination was significant during dry periods, the main source of contamination was non-human. Bacteroides GB-124 could potentially be used for catchment routine microbial water quality monitoring. For a cost-effective low-cost long-term sustainable water quality monitoring design, E. coli or intestinal enterococci, turbidity, and Bacteroides GB-124 should be monitored all-year round in this river catchment. Copyright © 2011 Elsevier B.V. All rights reserved.

In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity

PubMed Central

Steinert, Georg; Taylor, Michael W.; Deines, Peter; Simister, Rachel L.; de Voogd, Nicole J.; Hoggard, Michael

2016-01-01

Sponges (phylum Porifera) are important members of almost all aquatic ecosystems, and are renowned for hosting often dense and diverse microbial communities. While the specificity of the sponge microbiota seems to be closely related to host phylogeny, the environmental factors that could shape differences within local sponge-specific communities remain less understood. On tropical coral reefs, sponge habitats can span from shallow areas to deeper, mesophotic sites. These habitats differ in terms of environmental factors such as light, temperature, and food availability, as well as anthropogenic impact. In order to study the host specificity and potential influence of varying habitats on the sponge microbiota within a local area, four tropical reef sponges, Rhabdastrella globostellata, Callyspongia sp., Rhaphoxya sp., and Acanthella cavernosa, were collected from exposed shallow reef slopes and a deep reef drop-off. Based on 16S rRNA gene pyrosequencing profiles, beta diversity analyses revealed that each sponge species possessed a specific microbiota that was significantly different to those of the other species and exhibited attributes that are characteristic of high- and/or low-microbial-abundance sponges. These findings emphasize the influence of host identity on the associated microbiota. Dominant sponge- and seawater-associated bacterial phyla were Chloroflexi, Cyanobacteria, and Proteobacteria. Comparison of individual sponge taxa and seawater samples between shallow and deep reef sites revealed no significant variation in alpha diversity estimates, while differences in microbial beta diversity (variation in community composition) were significant for Callyspongia sp. sponges and seawater samples. Overall, the sponge-associated microbiota is significantly shaped by host identity across all samples, while the effect of habitat differentiation seems to be less predominant in tropical reef sponges. PMID:27114882

Enzymatic versus nonenzymatic mechanisms for Fe(III) reduction in aquatic sediments

USGS Publications Warehouse

Lovley, D.R.; Phillips, E.J.P.; Lonergan, D.J.

1991-01-01

The potential for nonenzymatic reduction of Fe(III) either by organic compounds or by the development of a low redox potential during microbial metabolism was compared with direct, enzymatic Fe(III) reduction by Fe(III)-reducing microorganisms. At circumneutral pH, very few organic compounds nonenzymatically reduced Fe(III). In contrast, in the presence of the appropriate Fe(IH)-reducing microorganisms, most of the organic compounds examined could be completely oxidized to carbon dioxide with the reduction of Fe(III). Even for those organic compounds that could nonenzymatically reduce Fe(III), microbial Fe(III) reduction was much more extensive. The development of a low redox potential during microbial fermentation did not result in nonenzymatic Fe(III) reduction. Model organic compounds were readily oxidized in Fe(III)-reducing aquifer sediments, but not in sterilized sediments. These results suggest that microorganisms enzymatically catalyze most of the Fe(III) reduction in the Fe(III) reduction zone of aquatic sediments and aquifers.

Capabilities of Seven Species of Aquatic Macrophytes for Phytoremediation of Pentachlorophenol Contaminated Sediment

NASA Astrophysics Data System (ADS)

Zhao, Liangyuan; Guo, Weijie; Li, Qingyun; Li, Huan; Zhao, Weihua; Cao, Xiaohuan

2017-01-01

Sediments are regarded as the ultimate sink of pentachlorophenol(PCP) in aquatic environment, and capabilities of seven species of aquatic macrophytes for remediating PCP contaminated sediment were investigated. Seven species of aquatic macrophytes could significantly accelerate the degradation of PCP in sediments. Among all, canna indica L., Acorus calamus L. and Iris tectorum Maxim. can be used as efficient alternative plants for remediation of PCP contaminated sediment, which attained 98%, 92% and 88% of PCP removal in sediments, respectively. PCP was detected only in root tissues and the uptake was closely related to the root lipid contents of seven plants. The presence of seven aquatic macrophytes significantly increased microbial populations and the activities of dehydrogenase compared with control sediments, indicating that rhizosphere microorganism played important role in the remediation process. In conclusion, seven species of aquatic macrophytes may act as promising tools for the PCP phytoremediation in aquatic environment, especially Canna indica L., Acorus calamus L. and Iris tectorum Maxim.

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba

PubMed Central

Valdespino-Castillo, Patricia M.; Hu, Ping; Merino-Ibarra, Martín; López-Gómez, Luz M.; Cerqueda-García, Daniel; González-De Zayas, Roberto; Pi-Puig, Teresa; Lestayo, Julio A.; Holman, Hoi-Ying; Falcón, Luisa I.

2018-01-01

Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (Corg), nitrogen and Corg:Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations. PMID:29666607

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba.

PubMed

Valdespino-Castillo, Patricia M; Hu, Ping; Merino-Ibarra, Martín; López-Gómez, Luz M; Cerqueda-García, Daniel; González-De Zayas, Roberto; Pi-Puig, Teresa; Lestayo, Julio A; Holman, Hoi-Ying; Falcón, Luisa I

2018-01-01

Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (C org ), nitrogen and C org :Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations.

Development of a highly sensitive lateral immunochromatographic assay for rapid detection of Vibrio parahaemolyticus.

PubMed

Liu, Xinfeng; Guan, Yuyao; Cheng, Shiliang; Huang, Yidan; Yan, Qin; Zhang, Jun; Huang, Guanjun; Zheng, Jian; Liu, Tianqiang

2016-12-01

Vibrio parahaemolyticus is widely present in brackish water all over the world, causing infections in certain aquatic animals. It is also a foodborne pathogen that causes diarrhea in humans. The aim of this study is to develop an immunochromatographic lateral flow assay (LFA) for rapid detection of V. parahaemolyticus in both aquatic products and human feces of diarrheal patients. Two monoclonal antibody (MAb) pairs, GA1a-IC9 and IC9-KB4c, were developed and proven to be highly specific and sensitive to V. parahaemolyticus. Based on the two MAb pairs, two types of LFA strips were prepared. Their testing limits for V. parahaemolyticus culture were both 1.2×10 3 CFU/ml. The diagnostic sensitivities and specificities were both 100% for the 32 tested microbial species, including 6 Vibrio species. Subsequently, the LFA strips were used to test Whiteleg shrimps and human feces. The type II strip showed a higher diagnostic sensitivity. Its sensitivity and specificity for hepatopancreas and fecal samples from 13 Whiteleg shrimps and fecal samples from 146 human diarrheal patients were all 100%. In conclusion, our homemade type II LFA is a very promising testing device for rapid and convenient detection of V. parahaemolyticus infection not only in aquatic animals, but also in human diarrheal patients. This sensitive immunochromtographic LFA allows rapid detection of V. parahaemolyticus without requirement of culture enrichment. Copyright © 2016. Published by Elsevier B.V.

Implementation of artificial neural networks (ANNs) to analysis of inter-taxa communities of benthic microorganisms and macroinvertebrates in a polluted stream.

PubMed

Kim, Byunghyuk; Lee, Se-Eun; Song, Mi-Young; Choi, Jung-Hye; Ahn, Soon-Mo; Lee, Kun-Seop; Cho, Eungchun; Chon, Tae-Soo; Koh, Sung-Cheol

2008-02-01

This study was performed to gain an understanding of the structural and functional relationships between inter-taxa communities (macroinvertebrates as consumers, and microbes as decomposers or preys for the invertebrates) in a polluted stream using artificial neural networks techniques. Sediment samples, carrying microorganisms (eubacteria) and macroinvertebrates, were seasonally collected from similar habitats in streams with different levels of pollution. Microbial community taxa and densities were determined using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rDNA sequence analysis techniques. The identity and density of macroinvertebrates were concurrently determined. In general, differences were observed on grouping by self-organizing map (SOM) in polluted, clean and recovering sites based on the microbial densities, while the community patterns were partly dependent on the sampling period. A Spearman rank order correlation analysis revealed correlations of several eubacterial species with those of macroinvertebrates: a negative correlation was observed between Acidovorax sp. (from polluted sites) and Gammaridae (mostly from the clean site), while Herbaspirillum sp. and Janthinobacterium sp. appeared to have positive correlations with some macroinvertebrate species. The population dynamics of the tolerant texa, Tubificidae and Chironomidae, appeared to be related with changes in the densities of Acidovorax sp. This study revealed community relationships between macroinvertebrates and microorganisms, reflecting the connectivity between the two communities via the food chain. A further physio-ecological and symbiological study on the invertebrate-microorganism relationships will be required to understand the degradation and utilization of detritus in aquatic ecosystems as well as to elucidate the roles of the inter-taxa in the recovery of polluted aquatic environments.

Atrazine removal from aqueous solutions using submerged biological aerated filter.

PubMed

Baghapour, Mohammad Ali; Nasseri, Simin; Derakhshan, Zahra

2013-06-12

Atrazine is widely used in the agriculture as an herbicide. Due to its high mobility, Atrazine leaks into the groundwaters, surface waters, and drinking water wells. Many physical and chemical methods have been suggested for removing Atrazine from aquatic environments. However, these methods are very costly, have many performance problems, produce a lot of toxic intermediates which are very harmful and dangerous, and cannot completely mineralize Atrazine. In this study, biodegradation of Atrazine by microbial consortium was evaluated in the aquatic environment. In order to assess the Atrazine removal from the aquatic environment, submerged biological aerated filter (SBAF) was fed with synthetic wastewater based on sucrose and Atrazine at different hydraulic retention times (HRTs). The maximum efficiencies for Atrazine and Soluble Chemical Oxygen Demand (SCOD) removal were 97.9% and 98.9%, respectively. The study findings showed that Stover-Kincannon model had very good fitness (R2 > 99%) in loading Atrazine in the biofilter and by increasing the initial concentration of Atrazine, the removal efficiency increased. Aerobic mixed biofilm culture was observed to be suitable for the treatment of Atrazine from aquatic environment. There was no significant inhibition effect on mixed aerobic microbial consortia. Atrazine degradation depended on the strength of wastewater and the amount of Atrazine in the influent.

Atrazine removal from aqueous solutions using submerged biological aerated filter

PubMed Central

2013-01-01

Atrazine is widely used in the agriculture as an herbicide. Due to its high mobility, Atrazine leaks into the groundwaters, surface waters, and drinking water wells. Many physical and chemical methods have been suggested for removing Atrazine from aquatic environments. However, these methods are very costly, have many performance problems, produce a lot of toxic intermediates which are very harmful and dangerous, and cannot completely mineralize Atrazine. In this study, biodegradation of Atrazine by microbial consortium was evaluated in the aquatic environment. In order to assess the Atrazine removal from the aquatic environment, submerged biological aerated filter (SBAF) was fed with synthetic wastewater based on sucrose and Atrazine at different hydraulic retention times (HRTs). The maximum efficiencies for Atrazine and Soluble Chemical Oxygen Demand (SCOD) removal were 97.9% and 98.9%, respectively. The study findings showed that Stover-Kincannon model had very good fitness (R2 > 99%) in loading Atrazine in the biofilter and by increasing the initial concentration of Atrazine, the removal efficiency increased. Aerobic mixed biofilm culture was observed to be suitable for the treatment of Atrazine from aquatic environment. There was no significant inhibition effect on mixed aerobic microbial consortia. Atrazine degradation depended on the strength of wastewater and the amount of Atrazine in the influent. PMID:24499572

The Dinner Menu: Spatial Distribution of Organic Carbon Composition Across the San Francisco Bay-Delta

NASA Astrophysics Data System (ADS)

Harfmann, J.; Hernes, P.; Bergamaschi, B. A.

2016-12-01

The San Francisco Bay-Delta is a dynamic tidal system with multiple sources of carbon, both autochthonous (e.g. phytoplankton, submersed or floating aquatic vegetation, or non-phytoplankton microalgae) and allochthonous (e.g. riverine detritus, agricultural drainage, and urban runoff). Spatial variability in organic carbon (OC) sources translates into varying degrees of food quantity and quality for the aquatic food web, and yet surprisingly little is known about the implications of carbon source variability on the health of zooplankton populations, which form the base of the lower food chain. Particulate organic carbon (POC) is a critical component of zooplankton diet, and with the assistance of the microbial loop, dissolved organic carbon (DOC) may supplement their food. As part of a larger study linking OC sources with zooplankton growth, we collected water samples along a transect from San Pablo Bay to the Sacramento-San Joaquin Delta. Samples were analyzed for bulk POC and DOC, lignin, chlorophyll a, δ13C, and δ15N. Feeding experiments with the calanoid copepod Eurytemora affinis will be conducted in order to assess the relative bioavailability of collected OC across the transect.

Bacterioplankton assemblages in coastal ponds reflect the influence of hydrology and geomorphological setting.

PubMed

Huggett, Megan J; Kavazos, Christopher R J; Bernasconi, Rachele; Czarnik, Robert; Horwitz, Pierre

2017-06-01

The factors that shape microbial community assembly in aquatic ecosystems have been widely studied; yet it is still unclear how distinct communities within a connected landscape influence one another. Coastal lakes are recipients of, and thus are connected to, both marine and terrestrial environments. Thus, they may host microbial assemblages that reflect the relative degree of influence by, and connectivity to, either system. In order to address this idea, we interrogated microbial community diversity at 49 sites in seven ponds in two seasons in the Lake MacLeod basin, a system fed by seawater flowing inland through underground karst. Environmental and spatial variation within ponds explain <9% of the community structure, while identity of the pond that samples were taken from explains 50% of community variation. That is, ponds each host distinct assemblages despite similarities in size, environment and position in the landscape, indicating a dominant role for local species sorting. The ponds contain a substantial amount of previously unknown microbial taxa, reflecting the unusual nature of this inland system. Rare marine taxa, possibly dispersed from seawater assemblages via the underground karst connection, are abundant within the inland system, suggesting an important role for regional dispersal within the metacommunities. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Virophage control of antarctic algal host–virus dynamics

PubMed Central

Yau, Sheree; Lauro, Federico M.; DeMaere, Matthew Z.; Brown, Mark V.; Thomas, Torsten; Raftery, Mark J.; Andrews-Pfannkoch, Cynthia; Lewis, Matthew; Hoffman, Jeffrey M.; Gibson, John A.; Cavicchioli, Ricardo

2011-01-01

Viruses are abundant ubiquitous members of microbial communities and in the marine environment affect population structure and nutrient cycling by infecting and lysing primary producers. Antarctic lakes are microbially dominated ecosystems supporting truncated food webs in which viruses exert a major influence on the microbial loop. Here we report the discovery of a virophage (relative of the recently described Sputnik virophage) that preys on phycodnaviruses that infect prasinophytes (phototrophic algae). By performing metaproteogenomic analysis on samples from Organic Lake, a hypersaline meromictic lake in Antarctica, complete virophage and near-complete phycodnavirus genomes were obtained. By introducing the virophage as an additional predator of a predator–prey dynamic model we determined that the virophage stimulates secondary production through the microbial loop by reducing overall mortality of the host and increasing the frequency of blooms during polar summer light periods. Virophages remained abundant in the lake 2 y later and were represented by populations with a high level of major capsid protein sequence variation (25–100% identity). Virophage signatures were also found in neighboring Ace Lake (in abundance) and in two tropical lakes (hypersaline and fresh), an estuary, and an ocean upwelling site. These findings indicate that virophages regulate host–virus interactions, influence overall carbon flux in Organic Lake, and play previously unrecognized roles in diverse aquatic ecosystems. PMID:21444812

Virophage control of antarctic algal host-virus dynamics.

PubMed

Yau, Sheree; Lauro, Federico M; DeMaere, Matthew Z; Brown, Mark V; Thomas, Torsten; Raftery, Mark J; Andrews-Pfannkoch, Cynthia; Lewis, Matthew; Hoffman, Jeffrey M; Gibson, John A; Cavicchioli, Ricardo

2011-04-12

Viruses are abundant ubiquitous members of microbial communities and in the marine environment affect population structure and nutrient cycling by infecting and lysing primary producers. Antarctic lakes are microbially dominated ecosystems supporting truncated food webs in which viruses exert a major influence on the microbial loop. Here we report the discovery of a virophage (relative of the recently described Sputnik virophage) that preys on phycodnaviruses that infect prasinophytes (phototrophic algae). By performing metaproteogenomic analysis on samples from Organic Lake, a hypersaline meromictic lake in Antarctica, complete virophage and near-complete phycodnavirus genomes were obtained. By introducing the virophage as an additional predator of a predator-prey dynamic model we determined that the virophage stimulates secondary production through the microbial loop by reducing overall mortality of the host and increasing the frequency of blooms during polar summer light periods. Virophages remained abundant in the lake 2 y later and were represented by populations with a high level of major capsid protein sequence variation (25-100% identity). Virophage signatures were also found in neighboring Ace Lake (in abundance) and in two tropical lakes (hypersaline and fresh), an estuary, and an ocean upwelling site. These findings indicate that virophages regulate host-virus interactions, influence overall carbon flux in Organic Lake, and play previously unrecognized roles in diverse aquatic ecosystems.

Plant-microbe interaction in aquatic system and their role in the management of water quality: a review

NASA Astrophysics Data System (ADS)

Srivastava, Jatin K.; Chandra, Harish; Kalra, Swinder J. S.; Mishra, Pratibha; Khan, Hena; Yadav, Poonam

2017-06-01

Microbial assemblage as biofilm around the aquatic plant forms a firm association that largely depends upon the mutual supplies of nutrients, e.g., microbes interact with plants in an aquatic system most likely for organic carbon and oxygen, whereas plants receive defensive immunity and mineral exchange. Apart from the mutual benefits, plant-microbe interactions also influence the water quality especially at rhizosphere providing inherent ability to the aquatic system for the mitigation of pollution from the water column. The review presents and in-depth information along with certain research advancements made in the field of ecological and bio/chemical aspects of plant-microbe interactions and the underlying potential to improve water quality.

Microbial impact of Canada geese (Branta canadensis) and whistling swans (Cygnus columbianus columbianus) on aquatic ecosystems.

PubMed Central

Hussong, D; Damaré, J M; Limpert, R J; Sladen, W J; Weiner, R M; Colwell, R R

1979-01-01

Quantitative and qualitative analyses of the intestinal bacterial flora of Canada geese and whistling swans were carried out with the finding that wild birds harbor significantly more fecal coliforms than fecal streptococci. The reverse was typical of captive and fasting birds. Neither Salmonella spp. nor Shigella spp. were isolated from 44 migratory waterfowl that were wintering in the Chesapeake Bay region. Enteropathogenic Escherichia coli were detected in seven birds. Geese eliminated 10(7) and swans 10(9) fecal coliforms per day. Results of in situ studies showed that large flocks of waterfowl can cause elevated fecal coliform densities in the water column. From the data obtained in this study, it is possible to predict the microbial impact of migratory waterfowl upon aquatic roosting sites. PMID:104659

Impacts of fire on nitrogen cycling in aquatic and terrestrial ecosystems in the Yukon-Kuskokwim River Delta, AK

NASA Astrophysics Data System (ADS)

Schade, J. D.; Jardine, L. E.; Bristol, E. M.; Navarro-Perez, E.; Melton, S.; Jimmie, J. A.; Natali, S.; Mann, P. J.; Holmes, R. M.

2016-12-01

Global climate change is having a disproportionate impact on northern high latitudes, including rapid increases in temperature, changes in precipitation, and increasing fire frequency and severity. Wildfires have been shown to strongly influence ecosystem processes through acceleration of permafrost thaw and increased nitrogen (N) availability, the effects of which may increase gaseous loss of carbon (C) to the atmosphere, increase primary production by alleviating N limitation, or both. The extent of these fire impacts has not been well-documented in the Arctic, particularly in areas of discontinuous permafrost. In 2015, the Yukon-Kuskokwim River Delta (YK Delta) in southwestern Alaska experienced the largest fire season in recorded history, providing an opportunity to study wildfire impacts on an area particularly vulnerable to permafrost thaw. Our objectives were to study the impacts of these fires on nitrogen availability in a range of land cover classes, including peat plateaus, channel fens, and aquatic ecosystems distributed across the landscapes. We sampled soils from several vegetation patches on burned and unburned peat plateaus, and soil and surface waters from fens, small ponds, and streams downslope of these sites. All water samples were filtered through GFF filters in the field. Soils were transported frozen to the Woods Hole Research Center and extracted in KCl. All water samples and extracts were analyzed for NH4 and NO3 concentrations. We found substantially higher concentrations of extractable NH4 in burned soils, but very little extractable NO3 in either burned or unburned soils. Water samples also showed higher NH4 in aquatic ecosystems in burned watersheds, but, in contrast to soils, showed relatively high NO3 concentrations, particularly in waters from lower landscape positions. Overall, aquatic ecosystems exhibited higher NO3: NH4 ratios than soil extractions, and increasing NO3: NH4 downslope. These results suggest significant export of nitrogen after fire and the potential for nitrification as N is transported across the landscape. These changes in N cycling are likely to have substantial consequences for the recovery of plant communities post-fire and for microbial processes and greenhouse gas fluxes, including N2O, from burned watersheds.

Impacts of fire on nitrogen cycling in aquatic and terrestrial ecosystems in the Yukon-Kuskokwim River Delta, AK

NASA Astrophysics Data System (ADS)

Schade, J. D.; Jardine, L. E.; Bristol, E. M.; Navarro-Perez, E.; Melton, S.; Jimmie, J. A.; Natali, S.; Mann, P. J.; Holmes, R. M.

2017-12-01

Global climate change is having a disproportionate impact on northern high latitudes, including rapid increases in temperature, changes in precipitation, and increasing fire frequency and severity. Wildfires have been shown to strongly influence ecosystem processes through acceleration of permafrost thaw and increased nitrogen (N) availability, the effects of which may increase gaseous loss of carbon (C) to the atmosphere, increase primary production by alleviating N limitation, or both. The extent of these fire impacts has not been well-documented in the Arctic, particularly in areas of discontinuous permafrost. In 2015, the Yukon-Kuskokwim River Delta (YK Delta) in southwestern Alaska experienced the largest fire season in recorded history, providing an opportunity to study wildfire impacts on an area particularly vulnerable to permafrost thaw. Our objectives were to study the impacts of these fires on nitrogen availability in a range of land cover classes, including peat plateaus, channel fens, and aquatic ecosystems distributed across the landscapes. We sampled soils from several vegetation patches on burned and unburned peat plateaus, and soil and surface waters from fens, small ponds, and streams downslope of these sites. All water samples were filtered through GFF filters in the field. Soils were transported frozen to the Woods Hole Research Center and extracted in KCl. All water samples and extracts were analyzed for NH4 and NO3 concentrations. We found substantially higher concentrations of extractable NH4 in burned soils, but very little extractable NO3 in either burned or unburned soils. Water samples also showed higher NH4 in aquatic ecosystems in burned watersheds, but, in contrast to soils, showed relatively high NO3 concentrations, particularly in waters from lower landscape positions. Overall, aquatic ecosystems exhibited higher NO3: NH4 ratios than soil extractions, and increasing NO3: NH4 downslope. These results suggest significant export of nitrogen after fire and the potential for nitrification as N is transported across the landscape. These changes in N cycling are likely to have substantial consequences for the recovery of plant communities post-fire and for microbial processes and greenhouse gas fluxes, including N2O, from burned watersheds.

The role of biofilms as environmental reservoirs of antibiotic resistance

PubMed Central

Balcázar, José L.; Subirats, Jéssica; Borrego, Carles M.

2015-01-01

Antibiotic resistance has become a significant and growing threat to public and environmental health. To face this problem both at local and global scales, a better understanding of the sources and mechanisms that contribute to the emergence and spread of antibiotic resistance is required. Recent studies demonstrate that aquatic ecosystems are reservoirs of resistant bacteria and antibiotic resistance genes as well as potential conduits for their transmission to human pathogens. Despite the wealth of information about antibiotic pollution and its effect on the aquatic microbial resistome, the contribution of environmental biofilms to the acquisition and spread of antibiotic resistance has not been fully explored in aquatic systems. Biofilms are structured multicellular communities embedded in a self-produced extracellular matrix that acts as a barrier to antibiotic diffusion. High population densities and proximity of cells in biofilms also increases the chances for genetic exchange among bacterial species converting biofilms in hot spots of antibiotic resistance. This review focuses on the potential effect of antibiotic pollution on biofilm microbial communities, with special emphasis on ecological and evolutionary processes underlying acquired resistance to these compounds. PMID:26583011

Self-organization of dissolved organic matter to micelle-like microparticles in river water.

PubMed

Kerner, Martin; Hohenberg, Heinz; Ertl, Siegmund; Reckermann, Marcus; Spitzy, Alejandro

2003-03-13

In aquatic systems, the concept of the 'microbial loop' is invoked to describe the conversion of dissolved organic matter to particulate organic matter by bacteria. This process mediates the transfer of energy and matter from dissolved organic matter to higher trophic levels, and therefore controls (together with primary production) the productivity of aquatic systems. Here we report experiments on laboratory incubations of sterile filtered river water in which we find that up to 25% of the dissolved organic carbon (DOC) aggregates abiotically to particles of diameter 0.4-0.8 micrometres, at rates similar to bacterial growth. Diffusion drives aggregation of low- to high-molecular-mass DOC and further to larger micelle-like microparticles. The chemical composition of these microparticles suggests their potential use as food by planktonic bacterivores. This pathway is apparent from differences in the stable carbon isotope compositions of picoplankton and the microparticles. A large fraction of dissolved organic matter might therefore be channelled through microparticles directly to higher trophic levels--bypassing the microbial loop--suggesting that current concepts of carbon conversion in aquatic systems require revision.

The role of biofilms as environmental reservoirs of antibiotic resistance.

PubMed

Balcázar, José L; Subirats, Jéssica; Borrego, Carles M

2015-01-01

Antibiotic resistance has become a significant and growing threat to public and environmental health. To face this problem both at local and global scales, a better understanding of the sources and mechanisms that contribute to the emergence and spread of antibiotic resistance is required. Recent studies demonstrate that aquatic ecosystems are reservoirs of resistant bacteria and antibiotic resistance genes as well as potential conduits for their transmission to human pathogens. Despite the wealth of information about antibiotic pollution and its effect on the aquatic microbial resistome, the contribution of environmental biofilms to the acquisition and spread of antibiotic resistance has not been fully explored in aquatic systems. Biofilms are structured multicellular communities embedded in a self-produced extracellular matrix that acts as a barrier to antibiotic diffusion. High population densities and proximity of cells in biofilms also increases the chances for genetic exchange among bacterial species converting biofilms in hot spots of antibiotic resistance. This review focuses on the potential effect of antibiotic pollution on biofilm microbial communities, with special emphasis on ecological and evolutionary processes underlying acquired resistance to these compounds.

Linkages among geophysical facies, microbial composition, biogeochemical rates, and seasonal hydrology in the hyporheic zone

NASA Astrophysics Data System (ADS)

Stegen, J.

2016-12-01

The hyporheic zone is a critical ecosystem transition that links terrestrial, aquatic, and subsurface domains. To understand connections among physical, microbial, and biogeochemical components of the hyporheic zone, we obtained freeze cores along the Columbia River in the Hanford 300 Area and performed geologic, molecular, and microbial assays. Mud and sand content were found to be the primary drivers of microbial community attributes (in particular, of nitrite and carbon oxidizers). Microbial community analysis revealed an abundance of nitrifying Archaea (Thaumarchaea) and an absence of nitrifiying Bacteria. Network analysis revealed significant negative correlations between sand content and some statistical modules of microbial taxa, perhaps indicating the importance of pore water residence time on community composition. A similar set of microbial modules was positively correlated with total organic carbon. One such module that also positively correlated with aerobic metabolic rates was dominated by Thaumarchaea and Nitrospira, suggesting that ammonia oxidation was the dominant aerobic process. We also examined temporal changes in hyporheic microbial structure and activity through repeated sampling of attached and pore water microbes across a spatial gradient. We found that microbial communities remained distinct in river, hyporheic, and inland zones across seasonal variation in hydrologic mixing conditions. One reason was temperature-driven increases in microbial species richness in the hyporheic zone. We show that the relative importance of ecological selection and dispersal varied across environments and across geographic zones. Our results also indicated that while selection imposed short-term constraints on microbial community structure, hyporheic sediment communities did not respond to short-term hydrologic variation. Importantly, we demonstrated that the influence of selective pressures varied with phylogenetic affiliation, which may have been responsible for seasonal increases in Thaumarchaea and aerobic activity. Our results elucidate spatiotemporal shifts in composition and activity of hyporheic microbes across sedimentary and seasonal gradients in pore water environments that correlate with the contribution of Thaumarchaea to aerobic processes.

Comparison of tire and road wear particle concentrations in sediment for watersheds in France, Japan, and the United States by quantitative pyrolysis GC/MS analysis.

PubMed

Unice, Ken M; Kreider, Marisa L; Panko, Julie M

2013-08-06

Impacts of surface runoff to aquatic species are an ongoing area of concern. Tire and road wear particles (TRWP) are a constituent of runoff, and determining accurate TRWP concentrations in sediment is necessary in order to evaluate the likelihood that these particles present a risk to the aquatic environment. TRWP consist of approximately equal mass fractions of tire tread rubber and road surface mineral encrustations. Sampling was completed in the Seine (France), Chesapeake (U.S.), and Yodo-Lake Biwa (Japan) watersheds to quantify TRWP in the surficial sediment of watersheds characterized by a wide diversity of population densities and land uses. By using a novel quantitative pyrolysis-GC/MS analysis for rubber polymer, we detected TRWP in 97% of the 149 sediment samples collected. The mean concentrations of TRWP were 4500 (n = 49; range = 62-11 600), 910 (n = 50; range = 50-4400) and 770 (n = 50; range = 26-4600) μg/g d.w. for the characterized portions of the Seine, Chesapeake and Yodo-Lake Biwa watersheds, respectively. A subset of samples from the watersheds (n = 45) was pooled to evaluate TRWP metals, grain size and organic carbon correlations by principal components analysis (PCA), which indicated that four components explain 90% of the variance. The PCA components appeared to correspond to (1) metal alloys possibly from brake wear (primarily Cu, Pb, Zn), (2) crustal minerals (primarily Al, V, Fe), (3) metals mediated by microbial immobilization (primarily Co, Mn, Fe with TOC), and (4) TRWP and other particulate deposition (primarily TRWP with grain size and TOC). This study should provide useful information for assessing potential aquatic effects related to tire service life.

Degradation of Jet and Missile Fuels by Aquatic Microbial Communities.

DTIC Science & Technology

1987-07-01

and JP-9 resisted bio ’.,-Ork’-,"k when incubated with water/sediment suspensions collected from aquatic habitats. RJ - rCoIP9 were not toxic to the...polynuclear aromatic materials. These results support our observations (Reference 2) of rapid bio - degradation of many aromatic hydrocarbons but...minimal disturbance, and the residual oil content ot the sediment was deternined. In their case, very little bio - degradation of the oil occurreo

Standard filtration practices may significantly distort planktonic microbial diversity estimates.

PubMed

Padilla, Cory C; Ganesh, Sangita; Gantt, Shelby; Huhman, Alex; Parris, Darren J; Sarode, Neha; Stewart, Frank J

2015-01-01

Fractionation of biomass by filtration is a standard method for sampling planktonic microbes. It is unclear how the taxonomic composition of filtered biomass changes depending on sample volume. Using seawater from a marine oxygen minimum zone, we quantified the 16S rRNA gene composition of biomass on a prefilter (1.6 μm pore-size) and a downstream 0.2 μm filter over sample volumes from 0.05 to 5 L. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences matching Vibrionales decreased from ~40 to 60% of prefilter datasets at low volumes (0.05-0.5 L) to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Groups often associated with marine particles, including members of the Deltaproteobacteria, Planctomycetes, and Bacteroidetes, were among those showing the greatest increase with volume (4 to 27-fold). Taxon richness (97% similarity clusters) also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise concerns for studies using filter fractionation for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.

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

PubMed

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

2016-08-01

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

A microbial ecosystem beneath the West Antarctic ice sheet.

PubMed

Christner, Brent C; Priscu, John C; Achberger, Amanda M; Barbante, Carlo; Carter, Sasha P; Christianson, Knut; Michaud, Alexander B; Mikucki, Jill A; Mitchell, Andrew C; Skidmore, Mark L; Vick-Majors, Trista J

2014-08-21

Liquid water has been known to occur beneath the Antarctic ice sheet for more than 40 years, but only recently have these subglacial aqueous environments been recognized as microbial ecosystems that may influence biogeochemical transformations on a global scale. Here we present the first geomicrobiological description of water and surficial sediments obtained from direct sampling of a subglacial Antarctic lake. Subglacial Lake Whillans (SLW) lies beneath approximately 800 m of ice on the lower portion of the Whillans Ice Stream (WIS) in West Antarctica and is part of an extensive and evolving subglacial drainage network. The water column of SLW contained metabolically active microorganisms and was derived primarily from glacial ice melt with solute sources from lithogenic weathering and a minor seawater component. Heterotrophic and autotrophic production data together with small subunit ribosomal RNA gene sequencing and biogeochemical data indicate that SLW is a chemosynthetically driven ecosystem inhabited by a diverse assemblage of bacteria and archaea. Our results confirm that aquatic environments beneath the Antarctic ice sheet support viable microbial ecosystems, corroborating previous reports suggesting that they contain globally relevant pools of carbon and microbes that can mobilize elements from the lithosphere and influence Southern Ocean geochemical and biological systems.

Impacts of beach wrack removal via grooming on surf zone water quality.

PubMed

Russell, Todd L; Sassoubre, Lauren M; Zhou, Christina; French-Owen, Darien; Hassaballah, Abdulrahman; Boehm, Alexandria B

2014-02-18

Fecal indicator bacteria (FIB) are used to assess the microbial water quality of recreational waters. Increasingly, nonfecal sources of FIB have been implicated as causes of poor microbial water quality in the coastal environment. These sources are challenging to quantify and difficult to remediate. The present study investigates one nonfecal FIB source, beach wrack (decaying aquatic plants), and its impacts on water quality along the Central California coast. The prevalence of FIB on wrack was studied using a multibeach survey, collecting wrack throughout Central California. The impacts of beach grooming, to remove wrack, were investigated at Cowell Beach in Santa Cruz, California using a long-term survey (two summers, one with and one without grooming) and a 48 h survey during the first ever intensive grooming event. FIB were prevalent on wrack but highly variable spatially and temporally along the nine beaches sampled in Central California. Beach grooming was generally associated with either no change or a slight increase in coastal FIB concentrations and increases in surf zone turbidity and silicate, phosphate, and dissolved inorganic nitrogen concentrations. The findings suggest that beach grooming for wrack removal is not justified as a microbial pollution remediation strategy.

Differences in planktonic microbial communities associated with three types of macrophyte stands in a shallow lake.

PubMed

Mentes, Anikó; Szabó, Attila; Somogyi, Boglárka; Vajna, Balázs; Tugyi, Nóra; Csitári, Bianka; Vörös, Lajos; Felföldi, Tamás

2018-02-01

Little is known about how various substances from living and decomposing aquatic macrophytes affect the horizontal patterns of planktonic bacterial communities. Study sites were located within Lake Kolon, which is a freshwater marsh and can be characterised by open-water sites and small ponds with different macrovegetation (Phragmites australis, Nymphea alba and Utricularia vulgaris). Our aim was to reveal the impact of these macrophytes on the composition of the planktonic microbial communities using comparative analysis of environmental parameters, microscopy and pyrosequencing data. Bacterial 16S rRNA gene sequences were dominated by members of phyla Proteobacteria (36%-72%), Bacteroidetes (12%-33%) and Actinobacteria (5%-26%), but in the anoxic sample the ratio of Chlorobi (54%) was also remarkable. In the phytoplankton community, Cryptomonas sp., Dinobryon divergens, Euglena acus and chrysoflagellates had the highest proportion. Despite the similarities in most of the measured environmental parameters, the inner ponds had different bacterial and algal communities, suggesting that the presence and quality of macrophytes directly and indirectly controlled the composition of microbial plankton. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Combination of Competitive Quantitative PCR and Constant-Denaturant Capillary Electrophoresis for High-Resolution Detection and Enumeration of Microbial Cells

PubMed Central

Lim, Eelin L.; Tomita, Aoy V.; Thilly, William G.; Polz, Martin F.

2001-01-01

A novel quantitative PCR (QPCR) approach, which combines competitive PCR with constant-denaturant capillary electrophoresis (CDCE), was adapted for enumerating microbial cells in environmental samples using the marine nanoflagellate Cafeteria roenbergensis as a model organism. Competitive PCR has been used successfully for quantification of DNA in environmental samples. However, this technique is labor intensive, and its accuracy is dependent on an internal competitor, which must possess the same amplification efficiency as the target yet can be easily discriminated from the target DNA. The use of CDCE circumvented these problems, as its high resolution permitted the use of an internal competitor which differed from the target DNA fragment by a single base and thus ensured that both sequences could be amplified with equal efficiency. The sensitivity of CDCE also enabled specific and precise detection of sequences over a broad range of concentrations. The combined competitive QPCR and CDCE approach accurately enumerated C. roenbergensis cells in eutrophic, coastal seawater at abundances ranging from approximately 10 to 104 cells ml−1. The QPCR cell estimates were confirmed by fluorescent in situ hybridization counts, but estimates of samples with <50 cells ml−1 by QPCR were less variable. This novel approach extends the usefulness of competitive QPCR by demonstrating its ability to reliably enumerate microorganisms at a range of environmentally relevant cell concentrations in complex aquatic samples. PMID:11525983

Metaproteomics of aquatic microbial communities in a deep and stratified estuary.

PubMed

Colatriano, David; Ramachandran, Arthi; Yergeau, Etienne; Maranger, Roxane; Gélinas, Yves; Walsh, David A

2015-10-01

Here we harnessed the power of metaproteomics to assess the metabolic diversity and function of stratified aquatic microbial communities in the deep and expansive Lower St. Lawrence Estuary, located in eastern Canada. Vertical profiling of the microbial communities through the stratified water column revealed differences in metabolic lifestyles and in carbon and nitrogen processing pathways. In productive surface waters, we identified heterotrophic populations involved in the processing of high and low molecular weight organic matter from both terrestrial (e.g. cellulose and xylose) and marine (e.g. organic compatible osmolytes) sources. In the less productive deep waters, chemosynthetic production coupled to nitrification by MG-I Thaumarchaeota and Nitrospina appeared to be a dominant metabolic strategy. Similar to other studies of the coastal ocean, we identified methanol oxidation proteins originating from the common OM43 marine clade. However, we also identified a novel lineage of methanol-oxidizers specifically in the particle-rich bottom (i.e. nepheloid) layer. Membrane transport proteins assigned to the uncultivated MG-II Euryarchaeota were also specifically detected in the nepheloid layer. In total, these results revealed strong vertical structure of microbial taxa and metabolic activities, as well as the presence of specific "nepheloid" taxa that may contribute significantly to coastal ocean nutrient cycling. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optimization of microbial detoxification for an aquatic mercury-contaminated environment.

PubMed

Figueiredo, Neusa L; Canário, João; Serralheiro, Maria Luísa; Carvalho, Cristina

2017-01-01

Mercury (Hg) reduction performed by microorganisms is well recognized as a biological means for remediation of contaminated environment. Recently, studies demonstrated that Hg-resistant microorganisms of Tagus Estuary are involved in metal reduction processes. In the present study, aerobic microbial community isolated from a highly Hg-contaminated area of Tagus Estuary was used to determine the optimization of the reduction process in conditions such as the contaminated ecosystem. Factorial design methodology was employed to examine the influence of glucose, sulfate, iron, and chloride on Hg reduction. In the presence of several concentrations of these elements, microbial community reduced Hg in a range of 37-61% of the initial 0.1 mg/ml Hg 2+ levels. The response prediction through central composite design showed that the increase of sulfate concentration led to an optimal response in Hg reduction by microbial community, while the rise in chloride levels markedly decreased metal reduction. Iron may exert antagonistic effects depending upon the media composition. These results are useful in understanding the persistence of Hg contamination in Tagus Estuary after inactivation of critical industrial units, as well as data might also be beneficial for development of new bioremediation strategies either in Tagus Estuary and/or in other Hg-contaminated aquatic environments.

Biofilms as a sink for antibiotic resistance genes (ARGs) in the Yangtze Estuary

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

Guo, Xing-pan; Yang, Yi; Lu, Da-pei

Biofilms are ubiquitous throughout aquatic environments and they are thought to promote the acquisition and dissemination of antibiotic resistant genes (ARGs). This study focused on the occurrence and distribution of five types of ARG in naturally-occurring biofilms, in comparison to associated sediment and water samples, from the Yangtze Estuary, which borders the meta-city of Shanghai, China. The detection frequency and abundances of most ARGs showed the following order: biofilm > sediment > water, which can be attributed to a high level of antibiotics and metals that can accelerate the generation and propagation of ARGs in biofilms. Most of ARG abundancesmore » were contributed by extracellular DNA (eDNA) in biofilm and sediment samples. ARGs (sul1, sul2, tetAandtetW) in eDNA were significantly correlated with TOC in both biofilm and sediment samples. Furthermore, both intracellular DNA-associated ARGs per gram of microbial biomass carbon (MBC) and eDNA-associated ARGs per gram of non-MBC and were higher in biofilms than sediments, and the partitioning coefficients of ARGs in eDNA between biofilm and water were higher than those between sediment and water. Our results provide new insight for evaluating the occurrence and abundance of ARGs in aquatic environments, confirming that biofilms are a significant sink for ARGs in the estuarine environment.« less

Insights into microbial communities involved in mercury methylation in the San Francisco Bay estuary

NASA Astrophysics Data System (ADS)

Machak, C.; Francis, C. A.

2013-12-01

San Francisco Bay (SFB) estuary is the largest estuary on the western coast of the United States, draining a watershed covering more than one third of the state of California. Mercury (Hg) contamination in SFB, as a result of gold and mercury mining in the Coast Range and Sierra Nevada region, has been observed for at least 150 years. Additional sources of Hg contamination to SFB come from active oil refineries, manufacturing, and wastewater treatment plants in the area. Concentrations of methylmercury in the sediment at the time of sample collection for the present study ranged from 0.011-3.88 μg/kg (dry weight). At some sites, the concentration exceeds wetland toxicity limits, posing a threat to the health of the ecosystem and potentially endangering humans that use the estuary for food and recreation. This study attempts to understand the factors that control the transformation of Hg to methylmercury by microorganisms in aquatic sediments, where the majority of Hg methylation is known to occur. Under anoxic conditions, some sulfate- and iron-reducing bacteria have the capacity to transform Hg into methylmercury. To better understand the microbial communities involved in Hg methylation, an extensive library of 16S rRNA sequences was generated (via Illumina sequencing) from sediment samples at 20 sites throughout the SFB estuary. In addition to genomic data, we have access to a massive database of geochemical measurements made by the SFB Regional Monitoring Program at the sampling locations. These measurements show that our sediment samples have varying methylmercury concentrations and span gradients in porewater sulfate and Fe(III), which are the two known alternative electron acceptors for mercury-methylating anaerobic bacteria. The sampling sites also span gradients in other geochemical factors known to influence microbial community composition (and potentially Hg mercury methylation), such as available organic carbon, pH, and salinity. We will present the results of our analysis of the effect of various physical and geochemical parameters on the microbial community composition and abundance of known Hg methylators throughout SFB sediments.

Study to determine the aquatic biological effects on the Solid Rocket Booster (SRB). [technique for monitoring marine microbial fouling

NASA Technical Reports Server (NTRS)

Colwell, R. R.; Zachary, A.

1979-01-01

The surface of the reusable solid rocket boosters (SRB), which are jettisoned from the Shuttle Orbiter to parachute in the sea, are studied for colonization by marine life. Techniques for monitoring the marine microbial fouling of SRB materials are presented. An assessment of the nature and degree of the biofouling expected on the SRB materials in the recovery zone is reported. A determination of the degree and the effects of seasonal variation occurring on microbial fouling in the retrieval zone waters is made. The susceptibility of the SRB parachute recovery system to microbial fouling and biodeterioration is investigated. The development of scanning electron microscopy and epifluorescence microscopic observation techniques for rapid assessment of microbial fouling is discussed.

Visualizing Microbial Biogeochemistry: NanoSIMS and Stable Isotope Probing (Invited)

NASA Astrophysics Data System (ADS)

Pett-Ridge, J.; Weber, P. K.

2009-12-01

Linking phylogenetic information to function in microbial communities is a key challenge for microbial ecology. Isotope-labeling experiments provide a useful means to investigate the ecophysiology of microbial populations and cells in the environment and allow measurement of nutrient transfers between cell types, symbionts and consortia. The combination of Nano-Secondary Ion Mass Spectrometry (NanoSIMS) analysis, in situ labeling and high resolution microscopy allows isotopic analysis to be linked to phylogeny and morphology and holds great promise for fine-scale studies of microbial systems. In NanoSIMS analysis, samples are sputtered with an energetic primary beam (Cs+, O-) liberating secondary ions that are separated by the mass spectrometer and detected in a suite of electron multipliers. Five isotopic species may be analyzed concurrently with spatial resolution as fine as 50nm. A high sensitivity isotope ratio ‘map’ can then be generated for the analyzed area. NanoSIMS images of 13C, 15N and Mo (a nitrogenase co-factor) localization in diazotrophic cyanobacteria show how cells differentially allocate resources within filaments and allow calculation of nutrient uptake rates on a cell by cell basis. Images of AM fungal hyphae-root and cyanobacteria-rhizobia associations indicate the mobilization and sharing (stealing?) of newly fixed C and N. In a related technique, “El-FISH”, stable isotope labeled biomass is probed with oligonucleotide-elemental labels and then imaged by NanoSIMS. In microbial consortia and cyanobacterial mats, this technique helps link microbial structure and function simultaneously even in systems with unknown and uncultivated microbes. Finally, the combination of re-engineered universal 16S oligonucleotide microarrays with NanoSIMS analyses may allow microbial identity to be linked to functional roles in complex systems such as mats and cellulose degrading hindgut communities. These newly developed methods provide correlated oligonucleotide, functional enzyme and metabolic image data and should help unravel the metabolic processes of complex microbial communities in soils, biofilms and aquatic systems.

Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA)

PubMed Central

Morrison, Jessica M.; Baker, Kristina D.; Zamor, Richard M.; Nikolai, Steve; Elshahed, Mostafa S.

2017-01-01

Many freshwater lakes undergo seasonal stratification, where the formation of phototrophic blooms in the epilimnion and subsequent sedimentation induces hypoxia/anoxia in the thermocline and hypolimnion. This autochthonously produced biomass represents a major seasonal organic input that impacts the entire ecosystem. While the limnological aspects of this process are fairly well documented, relatively little is known regarding the microbial community response to such events, especially in the deeper anoxic layers of the water column. Here, we conducted a spatiotemporal survey of the particle-associated and free-living microbial communities in a warm monomictic freshwater reservoir (Grand Lake O’ the Cherokees) in northeastern Oklahoma, USA. Pre-stratification samples (March) harbored a homogeneous community throughout the oxygenated water column dominated by typical oligotrophic aquatic lineages (acl clade within Actinobacteria, and Flavobacterium within the Bacteroidetes). The onset of phototrophic blooming in June induced the progression of this baseline community into two distinct trajectories. Within the oxic epilimnion, samples were characterized by the propagation of phototrophic (Prochlorococcus), and heterotrophic (Planctomycetes, Verrucomicrobia, and Beta-Proteobacteria) lineages. Within the oxygen-deficient thermocline and hypolimnion, the sedimentation of surface biomass induced the development of a highly diverse community, with the enrichment of Chloroflexi, “Latescibacteria”, Armatimonadetes, and Delta-Proteobacteria in the particle-associated fraction, and Gemmatimonadetes and “Omnitrophica” in the free-living fraction. Our work documents the development of multiple spatially and temporally distinct niches during lake stratification, and supports the enrichment of multiple yet-uncultured and poorly characterized lineages in the lake’s deeper oxygen-deficient layers, an ecologically relevant microbial niche that is often overlooked in lakes diversity surveys. PMID:28493994

Contrasting effects of photochemical and microbial degradation on Cu(II) binding with fluorescent DOM from different origins.

PubMed

Xu, Huacheng; Guan, Dong-Xing; Zou, Li; Lin, Hui; Guo, Laodong

2018-08-01

Effects of photochemical and microbial degradation on variations in composition and molecular-size of dissolved organic matter (DOM) from different sources (algal and soil) and the subsequent influence on Cu(II) binding were investigated using UV-Vis, fluorescence excitation-emission matrices coupled with parallel factor analysis, flow field-flow fractionation (FlFFF), and metal titration. The degradation processes resulted in an initial rapid decline in the bulk dissolved organic carbon and chromophoric and fluorescent DOM components, followed by a small or little decrease. Specifically, photochemical reaction decreased the aromaticity, humification and apparent molecular weights of all DOM samples, whereas a reverse trend was observed during microbial degradation. The FlFFF fractograms revealed that coagulation of both protein- and humic-like DOM induced an increase in molecular weights for algal-DOM, while the molecular weight enhancement for allochthonous soil samples was mainly attributed to the self-assembly of humic-like components. The Cu(II) binding capacity of algal-derived humic-like and fulvic-like DOM consistently increased during photo- and bio-degradation, while the soil-derived DOM exhibited a slight decline in Cu(II) binding capacity during photo-degradation but a substantial increase during microbial degradation, indicating source- and degradation-dependent metal binding heterogeneities. Pearson correlation analysis demonstrated that the Cu(II) binding potential was mostly related with aromaticity and molecular size for allochthonous soil-derived DOM, but was regulated by both DOM properties and specific degradation processes for autochthonous algal-derived DOM. This study highlighted the coupling role of inherent DOM properties and external environmental processes in regulating metal binding, and provided new insights into metal-DOM interactions and the behavior and fate of DOM-bound metals in aquatic environments. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effects of COREXIT (registered trademark) EC9500A on Bacteria from a Beach Oiled by the Deepwater Horizon Spill

DTIC Science & Technology

2011-01-01

AQUATIC MICROBIAL ECOLOGY Aquat Microb Ecol Vol. 63: 101–109, 2011 doi: 10.3354/ame01482 Published online March 31 INTRODUCTION The mobile offshore...toxicity tests confirm that COREXIT® EC9500A does not pose a significant threat to invertebrate and adult fish pop- ulations, there is limited information on...Deepwater Horizon incident. Although toxicity tests confirm that COREXIT? EC9500A does not pose a significant threat to invertebrate and adult fish

Metagenomic insights into the effect of oxytetracycline on microbial structures, functions and functional genes in sediment denitrification.

PubMed

Zou, Yong; Lin, Manxia; Xiong, Wenguang; Wang, Mei; Zhang, Jiaxuan; Wang, Mianzhi; Sun, Yongxue

2018-06-02

Denitrification is an indispensable pathway of nitrogen removal in aquatic ecosystems, and plays an important role in decreasing eutrophication induced by excessive reactive nitrogen pollution. Aquatic environments also suffer from antibiotic pollution due to runoff from farms and sewage systems. The aim of this study was to investigate the effect of oxytetracycline stress on denitrifying functional genes, the microbial community and metabolic pathways in sediments using high-throughput sequencing and metagenomic analysis. The oxytetracycline was observed to significantly inhibit the abundance of nirK and nosZ genes (P < 0.001). KEGG pathway annotation indicated that oxytetracycline treatment decreased the abundance of nitrate reductase, nitrite reductase and N 2 O reductase. Functional annotations revealed that oxytetracycline exposure decreased the abundance of the protein metabolism subsystem in the bacterial community. Metagenomic sequencing demonstrated that the abundance of Proteobacteria and Firmicutes increased with oxytetracycline exposure while the Actinobacteria decreased. In sediments, Pseudomonas and Bradyrhizobium were major contributors to denitrification and oxytetracycline exposure resulted in a decreased abundance of Bradyrhizobium. These results indicated that oxytetracycline residues influences the denitrifier community and may heighten occurrence of reactive nitrogen in aquatic ecosystems. Copyright © 2018. Published by Elsevier Inc.

Wastewater Treatment: The Natural Way

NASA Technical Reports Server (NTRS)

1988-01-01

Wolverton Environmental Services, Inc. is widely acclaimed for innovative work in natural water purification which involves use of aquatic plants to remove pollutants from wastewater at a relatively low-cost. Haughton, Louisiana, visited Wolverton's artificial marsh test site and decided to use this method of wastewater treatment. They built an 11 acre sewage lagoon with a 70 by 900 foot artificial marsh called a vascular aquatic plant microbial filter cell. In the cell, microorganisms and rooted aquatic plants combine to absorb and digest wastewater pollutants, thereby converting sewage to relatively clean water. Raw waste water, after a period in the sewage lagoon, flows over a rock bed populated by microbes that digest nutrients and minerals from the sewage thus partially cleaning it. Additional treatment is provided by the aquatic plants growing in the rock bed, which absorb more of the pollutants and help deodorize the sewage.

Aquatic degradation of Cry1Ab protein and decomposition dynamics of transgenic corn leaves under controlled conditions.

PubMed

Böttger, Rita; Schaller, Jörg; Lintow, Sven; Gert Dudel, E

2015-03-01

The increasing cultivation of genetically modified corn plants (Zea mays) during the last decades is suggested as a potential risk to the environment. One of these genetically modified variety expressed the insecticidal Cry1Ab protein originating from Bacillus thuringiensis (Bt), resulting in resistance against Ostrinia nubilalis, the European corn borer. Transgenic litter material is extensively studied regarding the decomposition in soils. However, only a few field studies analyzed the fate of the Cry1Ab protein and the impact of green and senescent leaf litter from corn on the decomposition rate and related ecosystem functions in aquatic environments. Consequently, a microbial litter decomposition experiment was conducted under controlled semi-natural conditions in batch culture using two maize varieties: one variety with Cry1Ab and another one with the appertaining Iso-line as control treatment. The results showed no significant differences between the treatment with Cry1Ab and the Iso-line regarding loss of total mass in dry weight of 43% for Iso-line and 45% for Bt-corn litter, lignin content increased to 137.5% (Iso-line) and 115.7% (Bt-corn), and phenol loss decreased by 53.6% (Iso-line), 62.2% (Bt-corn) during three weeks of the experiment. At the end of the experiment Cry1Ab protein was still detected with 6% of the initial concentration. A slightly but significant lower cellulose content was found for the Cry1Ab treatment compared to the Iso-line litter at the end of the experiment. The significant higher total protein (25%) and nitrogen (25%) content in Bt corn, most likely due to the additionally expression of the transgenic protein, may increase the microbial cellulose degradation and decrease microbial lignin degradation. In conclusion a relevant year by year input of protein and therefore nitrogen rich Bt corn litter into aquatic environments may affect the balanced nutrient turnover in aquatic ecosystems. Copyright © 2014 Elsevier Inc. All rights reserved.

CHITIN TRANSFORMATION AND PESTICIDE INTERACTIONS IN A SIMULATED AQUATIC MICROENVIRONMENTAL SYSTEM

EPA Science Inventory

Interactions between the structural animo-polysaccharide, chitin, and the organophosphate pesticide, azinphosmethyl (Guthion), have been studied in a controlled continuous flow-through microcosm. Pesticide-induced microbial population changes and increases in substrate utilizatio...

Effects of Organic Amendments on Microbiota Associated with the Culex nigripalpus Mosquito Vector of the Saint Louis Encephalitis and West Nile Viruses.

PubMed

Duguma, Dagne; Hall, Michael W; Smartt, Chelsea T; Neufeld, Josh D

2017-01-01

Pollution from nutrients in aquatic habitats has been linked to increases in disease vectors, including mosquitoes and other pestiferous insects. One possibility is that changes in mosquito microbiomes are impacted by nutrient enrichments and that these changes affect various traits, including larval development, susceptibility to larval control agents, and susceptibility of the adult mosquitoes to pathogens. We tested this hypothesis using field mesocosms supplemented with low- and high-organic-nutrient regimens and then sampled microbial communities associated with the naturally colonizing Culex nigripalpus mosquito vector. By high-throughput sequencing of 16S rRNA gene sequences, we found no significant differences in overall microbial communities associated with sampled mosquitoes, despite detecting discernible differences in environmental variables, including pH, dissolved oxygen, and nutrient amendments. Nevertheless, indicator species analysis revealed that members of the Clostridiales were significantly associated with mosquitoes that originated from high-nutrient enrichments. In contrast, members of the Burkholderiales were associated with mosquitoes from the low-nutrient enrichment. High bacterial variability associated with the life stages of the C. nigripalpus was largely unaffected by levels of nutrient enrichments that impacted larval microbial resources, including bacteria, ciliates, and flagellates in the larval environments. IMPORTANCE Mosquito microbiota provide important physiological and ecological attributes to mosquitoes, including an impact on their susceptibility to pathogens, fitness, and sensitivity to mosquito control agents. Culex nigripalpus mosquito populations transmit various pathogens, including the Saint Louis and West Nile viruses, and proliferate in nutrient-rich environments, such as in wastewater treatment wetlands. Our study examined whether increases in nutrients within larval mosquito developmental habitats impact microbial communities associated with C. nigripalpus mosquitoes. We characterized the effects of organic enrichments on microbiomes associated with C. nigripalpus mosquitoes and identified potential bacterial microbiota that will be further investigated for whether they alter mosquito life history traits and for their potential role in the development of microbial-based control strategies.

Organochlorine compounds in Lake Superior: Chiral polychlorinated biphenyls and biotransformation in the aquatic food web

USGS Publications Warehouse

Wong, Charles S.; Mabury, Scott A.; Whittle, D. Michael; Backus, Sean M.; Teixeira, Camilla; DeVault, David S.; Bronte, Charles R.; Muir, Derek C.G.

2004-01-01

The enantiomeric composition of seven chiral PCB congeners was measured in the Lake Superior aquatic food web sampled in 1998, to determine the extent of enantioselective biotransformation in aquatic biota. All chiral PCB congeners studied (CBs 91, 95, 136, 149, 174, 176, and 183) biomagnified in the Lake Superior aquatic food web, based on biomagnification and food web magnification factors greater than unity. PCB atropisomers were racemic in phytoplankton and zooplankton, suggesting no biotransformation potential toward PCBs for these low trophic level organisms. However, Diporeia and mysids had significantly nonracemic residues for most chiral congeners studied. This observation suggests that these macrozooplankton can stereoselectively metabolize chiral congeners. Alternatively, macrozooplankton obtained nonracemic residues from feeding on organic-rich suspended particles and sediments, which would imply that stereoselective microbial PCB biotransformation may be occurring in Lake Superior sediments at PCB concentrations far lower than that previously associated with such activity. Widely nonracemic PCB residues in forage fish (lake herring, rainbow smelt, and slimy sculpin) and lake trout suggest a combination of both in vivo biotransformation and uptake of nonracemic residues from prey for these species. Minimum biotransformation rates, calculated from enantiomer mass balances between predators and prey, suggest metabolic half-lives on the order of 8 yr for CB 136 in lake trout and 2.6 yr for CB 95 in sculpins. This result suggests that significant biotransformation may occur for metaboliz able PCB congeners over the lifespan of these biota. This study highlights the potential of chiral analysis to study biotransformation processes in food webs.

Reconnaissance samplings and characterization of aquatic humic substances at the Yuma Desalting Test Facility, Arizona

USGS Publications Warehouse

Malcolm, R.L.; Wershaw, R. L.; Thurman, E.M.; Aiken, G.R.; Pinckney, D.J.; Kaakinen, J.

1981-01-01

Smectite clay minerals were found to be the principal compound on the surface of the cellulose-acetate, reverse-osmosis membranes at the Yuma Desalting Test Facility. These clay minerals were not present in the pumped ground water, but were blown into the conveyance canal from adjacent soils. Humic substances from the water and suspended sediments were associated with the clay films on the membrane, but no definitive results concerning their role in fouling were achieved. Microbial fouling is believed to be only a minor aspect of membrane fouling. Chemical and physical changes in humic substances were extensively studied at four points in the water-treatment process. Humic substances accounted for the largest component (over 25 percent) of organic constituents. Humic substances in the canal source water were similar to other aquatic humic substances present in natural waters. During the treatment process, these substances are brominated and decolorized. The effect of these halogenated humic substances on membrane fouling is unclear, but their presence in the reverse-osmosis product water and reverse-osmosis reject brine, along with volatile trihalomethanes, has led to environmental concerns. (USGS)

First report of predation of Giardia sp. cysts by ciliated protozoa and confirmation of predation of Cryptosporidium spp. oocysts by ciliate species.

PubMed

Siqueira-Castro, Isabel Cristina Vidal; Greinert-Goulart, Juliane Araújo; Bonatti, Tais Rondello; Yamashiro, Sandra; Franco, Regina Maura Bueno

2016-06-01

Ciliated protozoa are important components of the microbial food web in various habitats, especially aquatic environments. These organisms are useful bioindicators for both environmental quality assessment and the wastewater purification process. The pathogenic parasitic protozoan species Giardia and Cryptosporidium represent a significant concern for human health, being responsible for numerous disease outbreaks worldwide. The predation of cysts and oocysts in 15 ciliate species from water and sewage samples collected in Campinas, São Paulo, Brazil were verified under laboratory conditions. The ciliated protozoan species were selected based on their mode of nutrition, and only bacterivorous and suspension-feeders were considered for the experiments. The species Blepharisma sinuosum, Euplotes aediculatus, Sterkiella cavicola, Oxytricha granulifera, Vorticella infusionum, Spirostomum minus, and Stentor coeruleus ingested cysts and oocysts, the resistance forms of Giardia spp. and Cryptosporidium spp., respectively. This is the first time that the ingestion of Giardia cysts by ciliated protozoa has been reported. These findings may contribute to a better understanding of the biological removal of these pathogens from aquatic environments.

Microbial fuel cells for biosensor applications.

PubMed

Yang, Huijia; Zhou, Minghua; Liu, Mengmeng; Yang, Weilu; Gu, Tingyue

2015-12-01

Microbial fuel cells (MFCs) face major hurdles for real-world applications as power generators with the exception of powering small sensor devices. Despite tremendous improvements made in the last two decades, MFCs are still too expensive to build and operate and their power output is still too small. In view of this, in recently years, intensive researches have been carried out to expand the applications into other areas such as acid and alkali production, bioremediation of aquatic sediments, desalination and biosensors. Unlike power applications, MFC sensors have the immediate prospect to be practical. This review covers the latest developments in various proposed biosensor applications using MFCs including monitoring microbial activity, testing biochemical oxygen demand, detection of toxicants and detection of microbial biofilms that cause biocorrosion.

A Synthesis of the Effects of Pesticides on Microbial Persistence in Aquatic Ecosystems

PubMed Central

Staley, Zachery R.; Harwood, Valerie J.; Rohr, Jason R.

2016-01-01

Pesticides are a pervasive presence in aquatic ecosystems throughout the world. While pesticides are intended to control fungi, insects, and other pests, their mechanisms of action are often not specific enough to prevent unintended effects, such as on non-target microbial populations. Microorganisms, including algae and cyanobacteria, protozoa, aquatic fungi, and bacteria, form the basis of many food webs and are responsible for crucial aspects of biogeochemical cycling; therefore, the potential for pesticides to alter microbial community structures must be understood to preserve ecosystem services. This review examines studies that focused on direct population-level effects and indirect community-level effects of pesticides on microorganisms. Generally, insecticides, herbicides, and fungicides were found to have adverse direct effects on algal and fungal species. Insecticides and fungicides also had deleterious direct effects in the majority of studies examining protozoa species, although herbicides were found to have inconsistent direct effects on protozoans. Our synthesis revealed mixed or no direct effects on bacterial species among all pesticide categories, with results highly dependent on the target species, chemical, and concentration used in the study. Examination of community-level, indirect effects revealed that all pesticide categories had a tendency to reduce higher trophic levels, thereby diminishing top-down pressures and favoring lower trophic levels. Often, indirect effects exerted greater influence than direct effects. However, few studies have been conducted to specifically address community-level effects of pesticides on microorganisms and further research is necessary to better understand and predict the net effects of pesticides on ecosystem health. PMID:26565685

Impacts of Glutaraldehyde on Microbial Community Structure and Degradation Potential in Streams Impacted by Hydraulic Fracturing.

PubMed

Campa, Maria Fernanda; Techtmann, Stephen M; Gibson, Caleb M; Zhu, Xiaojuan; Patterson, Megan; Garcia de Matos Amaral, Amanda; Ulrich, Nikea; Campagna, Shawn R; Grant, Christopher J; Lamendella, Regina; Hazen, Terry C

2018-05-15

The environmental impacts of hydraulic fracturing, particularly those of surface spills in aquatic ecosystems, are not fully understood. The goals of this study were to (1) understand the effect of previous exposure to hydraulic fracturing fluids on aquatic microbial community structure and (2) examine the impacts exposure has on biodegradation potential of the biocide glutaraldehyde. Microcosms were constructed from hydraulic fracturing-impacted and nonhydraulic fracturing-impacted streamwater within the Marcellus shale region in Pennsylvania. Microcosms were amended with glutaraldehyde and incubated aerobically for 56 days. Microbial community adaptation to glutaraldehyde was monitored using 16S rRNA gene amplicon sequencing and quantification by qPCR. Abiotic and biotic glutaraldehyde degradation was measured using ultra-performance liquid chromatography--high resolution mass spectrometry and total organic carbon. It was found that nonhydraulic fracturing-impacted microcosms biodegraded glutaraldehyde faster than the hydraulic fracturing-impacted microcosms, showing a decrease in degradation potential after exposure to hydraulic fracturing activity. Hydraulic fracturing-impacted microcosms showed higher richness after glutaraldehyde exposure compared to unimpacted streams, indicating an increased tolerance to glutaraldehyde in hydraulic fracturing impacted streams. Beta diversity and differential abundance analysis of sequence count data showed different bacterial enrichment for hydraulic fracturing-impacted and nonhydraulic fracturing-impacted microcosms after glutaraldehyde addition. These findings demonstrated a lasting effect on microbial community structure and glutaraldehyde degradation potential in streams impacted by hydraulic fracturing operations.

Microbial source tracking as a tool for TMDL development, Little Blue River in Independence, Missouri

USGS Publications Warehouse

Christensen, Eric D.; Bushon, Rebecca N.; Brady, Amie M.G.

2013-01-01

The Little Blue River in Jackson County, Missouri has been listed by the Missouri Department of Natural Resources as impaired by bacteria for the protection of aquatic life and contact recreation from urban point and nonpoint sources. The Clean Water Act requires that a total maximum daily load (TMDL) for Escherichia coli (E. coli) be developed. Over a 5-year period, 108 base-flow, 87 stormflow, 48 fecal source, and 12 sewage influent samples were collected and analyzed for E. coli and Bacteroides general and host-associated microbial source tracking (MST) genetic markers. Less than half of the main-stem base-flow samples exceeded the E. coli state standard, whereas, all of the stormflow samples exceeded the standard during the recreation season (April through October). Both E. coli and MST markers were detected more frequently and at higher concentrations in stormflow samples. Only 14 percent of samples with E. coli detections greater than the Missouri state standard of 206 colonies per 100 milliliters had the human-associated Bacteroides marker as the only identified marker; therefore, Little Blue River TMDL development may require a broader scope beyond the municipal separate storm sewer system if bacteria sources are to be identified and addressed. Fecal samples showed a greater specificity with the human-associated marker than the dog- or ruminant-associated Bacteroides markers; however, false positives were at least one order of magnitude lower than true positives. MST data may be a useful tool for identifying probable sources of contamination and directing TMDL strategies.

A comprehensive insight into functional profiles of free-living microbial community responses to a toxic Akashiwo sanguinea bloom

NASA Astrophysics Data System (ADS)

Yang, Caiyun; Li, Yi; Zhou, Yanyan; Lei, Xueqian; Zheng, Wei; Tian, Yun; van Nostrand, Joy D.; He, Zhili; Wu, Liyou; Zhou, Jizhong; Zheng, Tianling

2016-10-01

Phytoplankton blooms are a worldwide problem and can greatly affect ecological processes in aquatic systems, but its impacts on the functional potential of microbial communities are limited. In this study, a high-throughput microarray-based technology (GeoChip) was used to profile the functional potential of free-living microbes from the Xiamen Sea Area in response to a 2011 Akashiwo sanguinea bloom. The bloom altered the overall community functional structure. Genes that were significantly (p < 0.05) increased during the bloom included carbon degradation genes and genes involved in nitrogen (N) and/or phosphorus (P) limitation stress. Such significantly changed genes were well explained by chosen environmental factors (COD, nitrite-N, nitrate-N, dissolved inorganic phosphorus, chlorophyll-a and algal density). Overall results suggested that this bloom might enhance the microbial converting of nitrate to N2 and ammonia nitrogen, decrease P removal from seawater, activate the glyoxylate cycle, and reduce infection activity of bacteriophage. This study presents new information on the relationship of algae to other microbes in aquatic systems, and provides new insights into our understanding of ecological impacts of phytoplankton blooms.

Microbial degradation of hydrocarbons in the environment.

PubMed Central

Leahy, J G; Colwell, R R

1990-01-01

The ecology of hydrocarbon degradation by microbial populations in the natural environment is reviewed, emphasizing the physical, chemical, and biological factors that contribute to the biodegradation of petroleum and individual hydrocarbons. Rates of biodegradation depend greatly on the composition, state, and concentration of the oil or hydrocarbons, with dispersion and emulsification enhancing rates in aquatic systems and absorption by soil particulates being the key feature of terrestrial ecosystems. Temperature and oxygen and nutrient concentrations are important variables in both types of environments. Salinity and pressure may also affect biodegradation rates in some aquatic environments, and moisture and pH may limit biodegradation in soils. Hydrocarbons are degraded primarily by bacteria and fungi. Adaptation by prior exposure of microbial communities to hydrocarbons increases hydrocarbon degradation rates. Adaptation is brought about by selective enrichment of hydrocarbon-utilizing microorganisms and amplification of the pool of hydrocarbon-catabolizing genes. The latter phenomenon can now be monitored through the use of DNA probes. Increases in plasmid frequency may also be associated with genetic adaptation. Seeding to accelerate rates of biodegradation has been shown to be effective in some cases, particularly when used under controlled conditions, such as in fermentors or chemostats. PMID:2215423

Aquatic urban ecology at the scale of a capital: community structure and interactions in street gutters.

PubMed

Hervé, Vincent; Leroy, Boris; Da Silva Pires, Albert; Lopez, Pascal Jean

2018-01-01

In most cities, streets are designed for collecting and transporting dirt, litter, debris, storm water and other wastes as a municipal sanitation system. Microbial mats can develop on street surfaces and form microbial communities that have never been described. Here, we performed the first molecular inventory of the street gutter-associated eukaryotes across the entire French capital of Paris and the non-potable waters sources. We found that the 5782 OTUs (operational taxonomic units) present in the street gutters which are dominated by diatoms (photoautotrophs), fungi (heterotrophs), Alveolata and Rhizaria, includes parasites, consumers of phototrophs and epibionts that may regulate the dynamics of gutter mat microbial communities. Network analyses demonstrated that street microbiome present many species restricted to gutters, and an overlapping composition between the water sources used for street cleaning (for example, intra-urban aquatic networks and the associated rivers) and the gutters. We propose that street gutters, which can cover a significant surface area of cities worldwide, potentially have important ecological roles in the remediation of pollutants or downstream wastewater treatments, might also be a niche for growth and dissemination of putative parasite and pathogens.

Aquatic urban ecology at the scale of a capital: community structure and interactions in street gutters

PubMed Central

Hervé, Vincent; Leroy, Boris; Da Silva Pires, Albert; Lopez, Pascal Jean

2018-01-01

In most cities, streets are designed for collecting and transporting dirt, litter, debris, storm water and other wastes as a municipal sanitation system. Microbial mats can develop on street surfaces and form microbial communities that have never been described. Here, we performed the first molecular inventory of the street gutter-associated eukaryotes across the entire French capital of Paris and the non-potable waters sources. We found that the 5782 OTUs (operational taxonomic units) present in the street gutters which are dominated by diatoms (photoautotrophs), fungi (heterotrophs), Alveolata and Rhizaria, includes parasites, consumers of phototrophs and epibionts that may regulate the dynamics of gutter mat microbial communities. Network analyses demonstrated that street microbiome present many species restricted to gutters, and an overlapping composition between the water sources used for street cleaning (for example, intra-urban aquatic networks and the associated rivers) and the gutters. We propose that street gutters, which can cover a significant surface area of cities worldwide, potentially have important ecological roles in the remediation of pollutants or downstream wastewater treatments, might also be a niche for growth and dissemination of putative parasite and pathogens. PMID:29027996

Understanding Aquatic Rhizosphere Processes Through Metabolomics and Metagenomics Approach

NASA Astrophysics Data System (ADS)

Lee, Yong Jian; Mynampati, Kalyan; Drautz, Daniela; Arumugam, Krithika; Williams, Rohan; Schuster, Stephan; Kjelleberg, Staffan; Swarup, Sanjay

2013-04-01

The aquatic rhizosphere is a region around the roots of aquatic plants. Many studies focusing on terrestrial rhizosphere have led to a good understanding of the interactions between the roots, its exudates and its associated rhizobacteria. The rhizosphere of free-floating roots, however, is a different habitat that poses several additional challenges, including rapid diffusion rates of signals and nutrient molecules, which are further influenced by the hydrodynamic forces. These can lead to rapid diffusion and complicates the studying of diffusible factors from both plant and/or rhizobacterial origins. These plant systems are being increasingly used for self purification of water bodies to provide sustainable solution. A better understanding of these processes will help in improving their performance for ecological engineering of freshwater systems. The same principles can also be used to improve the yield of hydroponic cultures. Novel toolsets and approaches are needed to investigate the processes occurring in the aquatic rhizosphere. We are interested in understanding the interaction between root exudates and the complex microbial communities that are associated with the roots, using a systems biology approach involving metabolomics and metagenomics. With this aim, we have developed a RhizoFlowCell (RFC) system that provides a controlled study of aquatic plants, observed the root biofilms, collect root exudates and subject the rhizosphere system to changes in various chemical or physical perturbations. As proof of concept, we have used RFC to test the response of root exudation patterns of Pandanus amaryllifolius after exposure to the pollutant naphthalene. Complexity of root exudates in the aquatic rhizosphere was captured using this device and analysed using LC-qTOF-MS. The highly complex metabolomic profile allowed us to study the dynamics of the response of roots to varying levels of naphthalene. The metabolic profile changed within 5mins after spiking with 20mg/L of naphthalene and reached a new steady state within 72 hours. An active microbial biofilm was formed during this process, which was imaged by light microscopy and confocal laser scanning microscopy and showed active changes in the biofilm. We have begun to unravel the complexity of rhizobacterial communities associated with aquatic plants. Using fluorescence in-situ hybridization (FISH) and Illumina Miseq Next Generation Sequencing of metagenomic DNA, we investigated the root-associated microbial community of P. amaryllifolius grown in two different water sources. The community structure of rhizobacteria from plants grown in freshwater lake or rainwater stored in tanks are highly similar. The top three phyla in both setups belonged to Proteobacteria, Bacteriocedes and Actinobacteria, as validated by FISH analyses. This suggests that the rhizosphere have an innate ability to attract and recruit rhizobacterial communities, possibly through the metabolic compounds secreted through root exudation. The selection pressure through plant host is higher compared to environmental pressures that are different between the two water sources. In comparison with the terrestrial rhizosphere, the aquatic rhizosphere microbiome seems more specialised and has a high influence by the host. We are using these findings to further understand the role of microbes in the performance of freshwater aquatic plants.

Effects of algal-derived carbon on sediment methane ...

EPA Pesticide Factsheets

Nutrient loading is known to have adverse consequences for aquatic ecosystems, particularly in the form of algal blooms that may result. These blooms pose problems for humans and wildlife, including harmful toxin release, aquatic hypoxia and increased costs for water treatment. Another potential disservice resulting from algal blooms is the enhanced production of methane (CH4), a potent greenhouse gas, in aquatic sediments. Laboratory experiments have shown that algal biomass additions to sediment cores increase rates of CH4 production, but it is unclear whether or not this effect occurs at the ecosystem scale. The goal of this research was to explore the link between algal-derived carbon and methane production in the sediment of a eutrophic reservoir located in southwest Ohio, using a sampling design that capitalized on spatial and temporal gradients in autochthonous carbon input to sediments. Specifically, we aimed to determine if the within-reservoir gradient of sediment algal-derived organic matter and sediment CH4 production rates correlate. This was done by retrieving sediment cores from 15 sites within the reservoir along a known gradient of methane emission rates, at two separate time points in 2016: late spring before the sediments had received large amounts of algal input and mid-summer after algal blooms had been prevalent in the reservoir. Potential CH4 production rates, sediment organic matter source, and microbial community composition were charac

From solid to liquid: Assessing the release of carbon from soil into solution in response to forest management

NASA Astrophysics Data System (ADS)

James, J. N.; Gross, C. D.; Butman, D. E.; Harrison, R. B.

2016-12-01

Dissolved organic matter (DOM) is a crucial conduit for internal cycling of carbon within soils as well as for the transfer of organic matter out of soil and into aquatic systems. Little is known about how the quantity, quality, lability and chemical characteristics of DOM changes in response to human management of forest soils. To examine the processes that release soil organic matter (SOM) into solution, we gathered samples from adjacent native and industrially managed Eucalyptus grandis plantation forests across Sao Paulo State, Brazil and from adjacent old-growth and Douglas-fir (Pseudotsuga menzisii) plantation forests in the coastal Pacific Northwest. Samples from each soil horizon were taken from soil profiles excavated to at least 1.5 m at each site. Water extractable organic matter (WEOM) was extracted twice from each sample using 0.5 M K2SO4 and Milli-Q water to quantify both dissolved and exchange phase organic matter. These extracts were measured for total organic carbon (TOC), 13C and 14C, and chemical characteristics were assessed by fluorescence spectroscopy (EEMs and SUVA254). At the same time, solid phase characteristics of the soil samples were quantified, including bulk density, pH, total carbon and nitrogen, microbial biomass, and 13C and 14C. Characterization of bulk SOM was undertaken by Fourier Transform Infrared Spectroscopy (FTIR) by subtracting mineral matrix spectra of each sample from the bulk spectra. Organic matter lability was assessed by incubations using difference in TOC for WEOM extracts and repeated measurement of CO2 efflux for bulk SOM. All together, these analyses permit a unique snapshot of the natural separation of organic matter from solid into liquid phase through the entire soil profile. Initial results reveal that small but measureable quantities of WEOM may be released from deep B and C horizons in soil, and that this material is labile to microbial decomposition. By identifying differences in SOM and DOM cycling due to forest management, this study aims to connect human management of terrestrial forest ecosystems to the transport of organic matter from surface and subsurface horizons to freshwater ecosystems, where it forms a major component of aquatic food webs.

The Arsenite Oxidation Potential of Native Microbial Communities from Arsenic-Rich Freshwaters.

PubMed

Fazi, Stefano; Crognale, Simona; Casentini, Barbara; Amalfitano, Stefano; Lotti, Francesca; Rossetti, Simona

2016-07-01

Microorganisms play an important role in speciation and mobility of arsenic in the environment, by mediating redox transformations of both inorganic and organic species. Since arsenite [As(III)] is more toxic than arsenate [As(V)] to the biota, the microbial driven processes of As(V) reduction and As(III) oxidation may play a prominent role in mediating the environmental impact of arsenic contamination. However, little is known about the ecology and dynamics of As(III)-oxidizing populations within native microbial communities exposed to natural high levels of As. In this study, two techniques for single cell quantification (i.e., flow cytometry, CARD-FISH) were used to analyze the structure of aquatic microbial communities across a gradient of arsenic (As) contamination in different freshwater environments (i.e., groundwaters, surface and thermal waters). Moreover, we followed the structural evolution of these communities and their capacity to oxidize arsenite, when experimentally exposed to high As(III) concentrations in experimental microcosms. Betaproteobacteria and Deltaproteobacteria were the main groups retrieved in groundwaters and surface waters, while Beta and Gammaproteobacteria dominated the bacteria community in thermal waters. At the end of microcosm incubations, the communities were able to oxidize up to 95 % of arsenite, with an increase of Alphaproteobacteria in most of the experimental conditions. Finally, heterotrophic As(III)-oxidizing strains (one Alphaproteobacteria and two Gammaproteobacteria) were isolated from As rich waters. Our findings underlined that native microbial communities from different arsenic-contaminated freshwaters can efficiently perform arsenite oxidation, thus contributing to reduce the overall As toxicity to the aquatic biota.

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

Graham, Emily B.; Tfaily, Malak M.; Crump, Alex R.

In light of increasing terrestrial carbon (C) transport across aquatic boundaries, the mechanisms governing organic carbon (OC) oxidation along terrestrial-aquatic interfaces are crucial to future climate predictions. Here, we investigate biochemistry, metabolic pathways, and thermodynamics corresponding to OC oxidation in the Columbia River corridor. We leverage natural vegetative differences to encompass variation in terrestrial C inputs. Our results suggest that decreases in terrestrial C deposition associated with diminished riparian vegetation induce oxidation of physically-bound (i.e., mineral and microbial) OC at terrestrial-aquatic interfaces. We also find that contrasting metabolic pathways oxidize OC in the presence and absence of vegetation and—in directmore » conflict with the concept of ‘priming’—that inputs of water-soluble and thermodynamically-favorable terrestrial OC protects bound-OC from oxidation. Based on our results, we propose a mechanistic conceptualization of OC oxidation along terrestrial-aquatic interfaces that can be used to model heterogeneous patterns of OC loss under changing land cover distributions.« less

Effects of 17β-estradiol on typical greenhouse gas emissions in aquatic anaerobic ecosystem.

PubMed

Ruan, Aidong; Liu, Chenxiao; Zhao, Ying; Zong, Fengjiao; Jiang, Shaopeng; Yu, Zhongbo

2015-01-01

Anaerobic microecosystems designed with different concentrations of 17β-estradiol (17β-E2) (0.0-10,000.0 ng/L) were simulated in this study. The influence of different concentrations of 17β-E2 on the emissions of typical greenhouse gases (CH4 and CO2) in simulated anaerobic microecosystems is analyzed to primarily explore the relationship between 17β-E2 and such emissions in aquatic anaerobic ecosystems. The results showed that 17β-E2 could promote or significantly stimulate aquatic anaerobic micro-organisms' production of CH4. The degree and the promotion time of CH4 production were both enhanced with the increase of 17β-E2 concentration. Furthermore, under higher concentration of 17β-E2 (≥500.0 ng/L), the increasing tendency of aquatic anaerobic microbial populations' activity and the function of methanogenic activity under corresponding experimental conditions had a synchronous relationship.

Are algae relevant to the detritus-based food web in tank-bromeliads?

PubMed

Brouard, Olivier; Le Jeune, Anne-Hélène; Leroy, Céline; Cereghino, Régis; Roux, Olivier; Pelozuelo, Laurent; Dejean, Alain; Corbara, Bruno; Carrias, Jean-François

2011-01-01

We assessed the occurrence of algae in five species of tank-bromeliads found in contrasting environmental sites in a Neotropical, primary rainforest around the Nouragues Research Station, French Guiana. The distributions of both algal abundance and biomass were examined based on physical parameters, the morphological characteristics of bromeliad species and with regard to the structure of other aquatic microbial communities held in the tanks. Algae were retrieved in all of the bromeliad species with mean densities ranging from ∼10(2) to 10(4) cells/mL. Their biomass was positively correlated to light exposure and bacterial biomass. Algae represented a tiny component of the detrital food web in shaded bromeliads but accounted for up to 30 percent of the living microbial carbon in the tanks of Catopsis berteroniana, located in a highly exposed area. Thus, while nutrient supplies are believed to originate from wind-borne particles and trapped insects (i.e., allochtonous organic matter), our results indicate that primary producers (i.e., autochtonous organic matter) are present in this insectivorous bromeliad. Using a 24-h incubation of size-fractionated and manipulated samples from this plant, we evaluated the impact of mosquito foraging on algae, other microorganisms and rotifers. The prey assemblages were greatly altered by the predation of mosquito larvae. Grazing losses indicated that the dominant algal taxon, Bumilleriopsis sp., like protozoa and rotifers, is a significant part of the diet of mosquito larvae. We conclude that algae are a relevant functional community of the aquatic food web in C. berteroniana and might form the basis of a complementary non-detrital food web.

Are Algae Relevant to the Detritus-Based Food Web in Tank-Bromeliads?

PubMed Central

Brouard, Olivier; Le Jeune, Anne-Hélène; Leroy, Céline; Cereghino, Régis; Roux, Olivier; Pelozuelo, Laurent; Dejean, Alain; Corbara, Bruno; Carrias, Jean-François

2011-01-01

We assessed the occurrence of algae in five species of tank-bromeliads found in contrasting environmental sites in a Neotropical, primary rainforest around the Nouragues Research Station, French Guiana. The distributions of both algal abundance and biomass were examined based on physical parameters, the morphological characteristics of bromeliad species and with regard to the structure of other aquatic microbial communities held in the tanks. Algae were retrieved in all of the bromeliad species with mean densities ranging from ∼102 to 104 cells/mL. Their biomass was positively correlated to light exposure and bacterial biomass. Algae represented a tiny component of the detrital food web in shaded bromeliads but accounted for up to 30 percent of the living microbial carbon in the tanks of Catopsis berteroniana, located in a highly exposed area. Thus, while nutrient supplies are believed to originate from wind-borne particles and trapped insects (i.e., allochtonous organic matter), our results indicate that primary producers (i.e., autochtonous organic matter) are present in this insectivorous bromeliad. Using a 24-h incubation of size-fractionated and manipulated samples from this plant, we evaluated the impact of mosquito foraging on algae, other microorganisms and rotifers. The prey assemblages were greatly altered by the predation of mosquito larvae. Grazing losses indicated that the dominant algal taxon, Bumilleriopsis sp., like protozoa and rotifers, is a significant part of the diet of mosquito larvae. We conclude that algae are a relevant functional community of the aquatic food web in C. berteroniana and might form the basis of a complementary non-detrital food web. PMID:21625603

Metagenomic investigation of the microbial diversity in a chrysotile asbestos mine pit pond, Lowell, Vermont, USA.

PubMed

Driscoll, Heather E; Vincent, James J; English, Erika L; Dolci, Elizabeth D

2016-12-01

Here we report on a metagenomics investigation of the microbial diversity in a serpentine-hosted aquatic habitat created by chrysotile asbestos mining activity at the Vermont Asbestos Group (VAG) Mine in northern Vermont, USA. The now-abandoned VAG Mine on Belvidere Mountain in the towns of Eden and Lowell includes three open-pit quarries, a flooded pit, mill buildings, roads, and > 26 million metric tons of eroding mine waste that contribute alkaline mine drainage to the surrounding watershed. Metagenomes and water chemistry originated from aquatic samples taken at three depths (0.5 m, 3.5 m, and 25 m) along the water column at three distinct, offshore sites within the mine's flooded pit (near 44°46'00.7673″, - 72°31'36.2699″; UTM NAD 83 Zone 18 T 0695720 E, 4960030 N). Whole metagenome shotgun Illumina paired-end sequences were quality trimmed and analyzed based on a translated nucleotide search of NCBI-NR protein database and lowest common ancestor taxonomic assignments. Our results show strata within the pit pond water column can be distinguished by taxonomic composition and distribution, pH, temperature, conductivity, light intensity, and concentrations of dissolved oxygen. At the phylum level, metagenomes from 0.5 m and 3.5 m contained a similar distribution of taxa and were dominated by Actinobacteria (46% and 53% of reads, respectively), Proteobacteria (45% and 38%, respectively), and Bacteroidetes (7% in both). The metagenomes from 25 m showed a greater diversity of phyla and a different distribution of reads than the two upper strata: Proteobacteria (60%), Actinobacteria (18%), Planctomycetes, (10%), Bacteroidetes (5%) and Cyanobacteria (2.5%), Armatimonadetes (< 1%), Verrucomicrobia (< 1%), Firmicutes (< 1%), and Nitrospirae (< 1%). Raw metagenome sequence data from each sample reside in NCBI's Short Read Archive (SRA ID: SRP056095) and are accessible through NCBI BioProject PRJNA277916.

Do Long-Term Changes in Organic Matter Inputs to Forest Soils Affect Dissolved Organic Matter Chemistry and Export?

NASA Astrophysics Data System (ADS)

Lajtha, K.; Strid, A.; Lee, B. S.

2014-12-01

Dissolved organic matter (DOM) production and transport play an important role in regulating organic matter (OM) distribution through a soil profile and ultimately, OM stabilization or export to aquatic systems. The contributions of varying OM inputs to the quality and amount of DOM as it passes through a soil profile remain relatively unknown. The Detrital Input and Removal Treatment (DIRT) site at the H. J. Andrews Experimental Forest in Oregon has undergone 17 years of litter, wood and root input manipulations and allows us to guage shifts in DOM chemistry induced by long-term changes to aboveground and belowground OM additions and exclusions. Using fluorescence and UV spectroscopy to characterize fluorescent properties, extent of decomposition, and sources of DOM in streams and soil solutions collected with lysimeters and soil extractions, we have assessed the importance of fresh OM inputs to DOM chemistry. Soil extracts from DIRT plots had a higher fluorescence index (FI) than lysimeter solutions or stream water. A high FI in surface water is generally interpreted as indicative of a high proportion of microbially-derived DOM. However, we suspect that the high FI in soil extracts is due to a higher proportion of non-aromatic DOM from fresh soil that microorganisms consume in transit through the soil profile to lysimeters or to streams. High redox index (RI) values were observed in lysimeters from the April 2014 sampling compared with the November 2013 sampling. These RI values show evidence of more reducing conditions at the end of the rainy season in the spring compared to the onset of the rainy season in the fall. Lysimeter water collected in No Input, No Litter, and No Root treatments contained high proportions of protein, suggesting the absence of carbon inputs changes activities of the microbial community. Observed variations reflect the viability of using fluorescent properties to explore the terrestrial-aquatic interface.

In situ grazing experiments apply new technology to gain insights into deep-sea microbial food webs

NASA Astrophysics Data System (ADS)

Pachiadaki, Maria G.; Taylor, Craig; Oikonomou, Andreas; Yakimov, Michail M.; Stoeck, Thorsten; Edgcomb, Virginia

2016-07-01

Predation by grazing protists in aquatic habitats can influence prokaryotic community structure and provides a source of new, labile organic matter. Due to methodological difficulties associated with studies of deep-sea (below photic zone) microbiota, trophic interactions between eukaryotes and prokaryotes in mesopelagic and bathypelagic realms are largely obscured. Further complicating matters, examinations of trophic interactions using water samples that have been exposed to upwards of hundreds of atmospheres of pressure change prior to initiating experiments can potentially introduce significant artifacts. Here we present results of the first study of protistan grazing in water layers ranging from the euphotic zone to the bathypelagic, utilizing the Microbial Sampler-Submersible Incubation Device (MS-SID) that makes possible in situ studies of microbial activities. Protistan grazing in the mesopelagic and bathypelagic realm of the East Mediterranean Sea was quantified using fluorescently labeled prokaryotes (FLP) prepared from the naturally-occurring prokaryotic assemblages. These studies reveal daily prokaryotic removal due to grazing ranging from 31.3±5.9% at 40 m depth to 0.5±0.3% at 950 m. At 3540 m depth, where a chemocline habitat exists with abundant and active prokaryotes above Urania basin, the daily consumption of prokaryotes by protists was 19.9±6.6% of the in situ abundance.

Suitability of a Saccharomyces cerevisiae-based assay to assess the toxicity of pyrimethanil sprayed soils via surface runoff: comparison with standard aquatic and soil toxicity assays.

PubMed

Gil, Fátima N; Moreira-Santos, Matilde; Chelinho, Sónia; Pereira, Carla; Feliciano, Joana R; Leitão, Jorge H; Sousa, José P; Ribeiro, Rui; Viegas, Cristina A

2015-02-01

The present study is aimed at evaluating whether a gene expression assay with the microbial eukaryotic model Saccharomyces cerevisiae could be used as a suitable warning tool for the rapid preliminary screening of potential toxic effects on organisms due to scenarios of soil and water contamination with pyrimethanil. The assay consisted of measuring changes in the expression of the selected pyrimethanil-responsive genes ARG3 and ARG5,6 in a standardized yeast population. Evaluation was held by assessing the toxicity of surface runoff, a major route of pesticide exposure in aquatic systems due to non-point-source pollution, which was simulated with a pyrimethanil formulation at a semifield scale mimicking worst-case scenarios of soil contamination (e.g. accident or improper disposal). Yeast cells 2-h exposure to the runoff samples led to a significant 2-fold increase in the expression of both indicator genes. These results were compared with those from assays with organisms relevant for the aquatic and soil compartments, namely the nematode Caenorhabditis elegans (reproduction), the freshwater cladoceran Daphnia magna (survival and reproduction), the benthic midge Chironomus riparius (growth), and the soil invertebrates Folsomia candida and Enchytraeus crypticus (survival and reproduction). Under the experimental conditions used to simulate accidental discharges into soil, runoff waters were highly toxic to the standard test organisms, except for C. elegans. Overall, results point out the usefulness of the yeast assay to provide a rapid preview of the toxicity level in preliminary screenings of environmental samples in situations of inadvertent high pesticide contamination. Advantages and limitations of this novel method are discussed. Copyright © 2014 Elsevier B.V. All rights reserved.

The Influence of Land-Use Change on Soil and Dissolved Organic Matter Age, Lability, and Chemical Characteristics in Brazilian Oxisols

NASA Astrophysics Data System (ADS)

James, J. N.; Harrison, R. B.; Gross, C. D.; Dwivedi, P.; Myers, T.; Butman, D. E.

2017-12-01

Recent advances in freshwater research indicate that the age of carbon exported from major rivers globally increases with greater human disturbance in the watershed. This implies that human land-use can release old, previously mineral-associated C into solution with subsequent export to groundwater and ultimately freshwater systems where terrestrial organic matter is either mineralized to CO2, stored in aquatic sediments, or exported to the ocean. It is important to understand the mechanisms that cause the release of mineral-bound soil organic matter (SOM) into solution in response to human disturbance and land-use change. To better characterize the response of the total soil organic matter (SOM) pool to disturbance, this study examines the interactions between dissolved and bulk soil pools in response to conversion of Brazilian Cerrado (savannah forest) to Eucalyptus plantations. Water-extractable organic matter (WEOM) was obtained from soil samples down to 150 cm at 4 sites in Sao Paulo State, Brazil. These WEOM samples were characterized using fluorescence and NMR spectroscopy, incubated to assess biolability, and carbon-dated. Simultaneously, bulk mineral soil samples were analyzed for microbial biomass, carbon content and age, and characterized using Fourier Transform Infrared Spectroscopy. FTIR spectra of SOM were obtained by washing subsamples with sodium hypochlorite and subtracting the subsequent mineral matrix spectra from bulk soil spectra. Preliminary results show that microbial biomass decreases much more quickly with depth than WEOM, suggesting that C released into solution from deeper horizons may be less likely to be intercepted, and thus preferentially leached to groundwater. Native Cerrado forests had substantially more roots compared to Eucalyptus, and also released substantially larger quantities of WEOM from their O horizons. Furthermore, the age of WEOM released under Eucalyptus forest was more similar in age to bulk SOM, while Cerrado forest WEOM was substantially younger than the bulk SOM. Processes operating at the interface between solid and liquid, terrestrial and aquatic are a key unknown in the global carbon cycle. This research permits a unique snapshot into the relationship between DOM and SOM and the response of these pools to forest conversion and management in Brazil.

Metagenomics Reveals the Impact of Wastewater Treatment Plants on the Dispersal of Microorganisms and Genes in Aquatic Sediments.

PubMed

Chu, Binh T T; Petrovich, Morgan L; Chaudhary, Adit; Wright, Dorothy; Murphy, Brian; Wells, George; Poretsky, Rachel

2018-03-01

Wastewater treatment plants (WWTPs) release treated effluent containing mobile genetic elements (MGEs), antibiotic resistance genes (ARGs), and microorganisms into the environment, yet little is known about their influence on nearby microbial communities and the retention of these factors in receiving water bodies. Our research aimed to characterize the genes and organisms from two different WWTPs that discharge into Lake Michigan, as well as from surrounding lake sediments to determine the dispersal and fate of these factors with respect to distance from the effluent outfall. Shotgun metagenomics coupled to distance-decay analyses showed a higher abundance of genes identical to those in WWTP effluent genes in sediments closer to outfall sites than in sediments farther away, indicating their possible WWTP origin. We also found genes attributed to organisms, such as those belonging to Helicobacteraceae , Legionellaceae , Moraxellaceae , and Neisseriaceae , in effluent from both WWTPs and decreasing in abundance in lake sediments with increased distance from WWTPs. Moreover, our results showed that the WWTPs likely influence the ARG composition in lake sediments close to the effluent discharge. Many of these ARGs were located on MGEs in both the effluent and sediment samples, indicating a relatively broad propensity for horizontal gene transfer (HGT). Our approach allowed us to specifically link genes to organisms and their genetic context, providing insight into WWTP impacts on natural microbial communities. Overall, our results suggest a substantial influence of wastewater effluent on gene content and microbial community structure in the sediments of receiving water bodies. IMPORTANCE Wastewater treatment plants (WWTPs) release their effluent into aquatic environments. Although treated, effluent retains many genes and microorganisms that have the potential to influence the receiving water in ways that are poorly understood. Here, we tracked the genetic footprint, including genes specific to antibiotic resistance and mobile genetic elements and their associated organisms, from WWTPs to lake sediments. Our work is novel in that we used metagenomic data sets to comprehensively evaluate total gene content and the genetic and taxonomic context of specific genes in environmental samples putatively impacted by WWTP inputs. Based on two different WWTPs with different treatment processes, our findings point to an influence of WWTPs on the presence, abundance, and composition of these factors in the environment. Copyright © 2018 Chu et al.

Metagenomics Reveals the Impact of Wastewater Treatment Plants on the Dispersal of Microorganisms and Genes in Aquatic Sediments

PubMed Central

Chu, Binh T. T.; Petrovich, Morgan L.; Chaudhary, Adit; Wright, Dorothy; Murphy, Brian; Wells, George

2017-01-01

ABSTRACT Wastewater treatment plants (WWTPs) release treated effluent containing mobile genetic elements (MGEs), antibiotic resistance genes (ARGs), and microorganisms into the environment, yet little is known about their influence on nearby microbial communities and the retention of these factors in receiving water bodies. Our research aimed to characterize the genes and organisms from two different WWTPs that discharge into Lake Michigan, as well as from surrounding lake sediments to determine the dispersal and fate of these factors with respect to distance from the effluent outfall. Shotgun metagenomics coupled to distance-decay analyses showed a higher abundance of genes identical to those in WWTP effluent genes in sediments closer to outfall sites than in sediments farther away, indicating their possible WWTP origin. We also found genes attributed to organisms, such as those belonging to Helicobacteraceae, Legionellaceae, Moraxellaceae, and Neisseriaceae, in effluent from both WWTPs and decreasing in abundance in lake sediments with increased distance from WWTPs. Moreover, our results showed that the WWTPs likely influence the ARG composition in lake sediments close to the effluent discharge. Many of these ARGs were located on MGEs in both the effluent and sediment samples, indicating a relatively broad propensity for horizontal gene transfer (HGT). Our approach allowed us to specifically link genes to organisms and their genetic context, providing insight into WWTP impacts on natural microbial communities. Overall, our results suggest a substantial influence of wastewater effluent on gene content and microbial community structure in the sediments of receiving water bodies. IMPORTANCE Wastewater treatment plants (WWTPs) release their effluent into aquatic environments. Although treated, effluent retains many genes and microorganisms that have the potential to influence the receiving water in ways that are poorly understood. Here, we tracked the genetic footprint, including genes specific to antibiotic resistance and mobile genetic elements and their associated organisms, from WWTPs to lake sediments. Our work is novel in that we used metagenomic data sets to comprehensively evaluate total gene content and the genetic and taxonomic context of specific genes in environmental samples putatively impacted by WWTP inputs. Based on two different WWTPs with different treatment processes, our findings point to an influence of WWTPs on the presence, abundance, and composition of these factors in the environment. PMID:29269503

Ecotoxic heavy metals transformation by bacteria and fungi in aquatic ecosystem.

PubMed

Chaturvedi, Amiy Dutt; Pal, Dharm; Penta, Santhosh; Kumar, Awanish

2015-10-01

Water is the most important and vital molecule of our planet and covers 75% of earth surface. But it is getting polluted due to high industrial growth. The heavy metals produced by industrial activities are recurrently added to it and considered as dangerous pollutants. Increasing concentration of toxic heavy metals (Pb(2+), Cd(2+), Hg(2+), Ni(2+)) in water is a severe threat for human. Heavy metal contaminated water is highly carcinogenic and poisonous at even relatively low concentrations. When they discharged in water bodies, they dissolve in the water and are distributed in the food chain. Bacteria and fungi are efficient microbes that frequently transform heavy metals and remove toxicity. The application of bacteria and fungi may offer cost benefit in water treatment plants for heavy metal transformation and directly related to public health and environmental safety issues. The heavy metals transformation rate in water is also dependent on the enzymatic capability of microorganisms. By transforming toxic heavy metals microbes sustain aquatic and terrestrial life. Therefore the application of microbiological biomass for heavy metal transformation and removal from aquatic ecosystem is highly significant and striking. This paper reviews the microbial transformation of heavy metal, microbe metal interaction and different approaches for microbial heavy metal remediation from water bodies.

WATER QUALITY MONITORING FOR PUBLIC HEALTH AND ENVIRONMENTAL PROTECTION

EPA Science Inventory

The applicability of using microbial population measures as indicators of aquatic condition has a rich history based primarily to study factors that affect the sanitary and ecological condition of fresh water streams. These studies are generally conducted by collecting water site...

Effects of triclosan on bacterial community composition and Vibrio populations in natural seawater microcosms

EPA Science Inventory

Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for select...

Development of Rapid Canine Fecal Source Identification PCR-based Assays

EPA Science Inventory

The extent to which dogs contribute to aquatic fecal contamination is unknown despite the potential for zoonotic transfer of harmful human pathogens. We used Genome Fragment Enrichment (GFE) to identify novel non-ribosomal microbial genetic markers potentially useful for detectin...

Ecological Forecasting: Microbial Contamination and Atmospheric Loadings of Nutrients to Land and Water

EPA Science Inventory

The development of ecological forecasts, namely, methodologies to predict the chemical, biological, and physical changes in terrestrial and aquatic ecosystems is desirable so that effective strategies for reducing the adverse impacts of human activities and extreme natural events...

Coastal Bacterioplankton Community Dynamics in Response to a Natural Disturbance

PubMed Central

Rappé, Michael S.

2013-01-01

In order to characterize how disturbances to microbial communities are propagated over temporal and spatial scales in aquatic environments, the dynamics of bacterial assemblages throughout a subtropical coastal embayment were investigated via SSU rRNA gene analyses over an 8-month period, which encompassed a large storm event. During non-perturbed conditions, sampling sites clustered into three groups based on their microbial community composition: an offshore oceanic group, a freshwater group, and a distinct and persistent coastal group. Significant differences in measured environmental parameters or in the bacterial community due to the storm event were found only within the coastal cluster of sampling sites, and only at 5 of 12 locations; three of these sites showed a significant response in both environmental and bacterial community characteristics. These responses were most pronounced at sites close to the shoreline. During the storm event, otherwise common bacterioplankton community members such as marine Synechococcus sp. and members of the SAR11 clade of Alphaproteobacteria decreased in relative abundance in the affected coastal zone, whereas several lineages of Gammaproteobacteria, Betaproteobacteria, and members of the Roseobacter clade of Alphaproteobacteria increased. The complex spatial patterns in both environmental conditions and microbial community structure related to freshwater runoff and wind convection during the perturbation event leads us to conclude that spatial heterogeneity was an important factor influencing both the dynamics and the resistance of the bacterioplankton communities to disturbances throughout this complex subtropical coastal system. This heterogeneity may play a role in facilitating a rapid rebound of regions harboring distinctly coastal bacterioplankton communities to their pre-disturbed taxonomic composition. PMID:23409156

Trace-Element Concentrations in Tissues of Aquatic Organisms from Rivers and Streams of the United States, 1992-1999

USGS Publications Warehouse

DeWeese, Lawrence R.; Stephens, Verlin C.; Short, Terry M.; Dubrovsky, Neil M.

2007-01-01

The U.S. Geological Survey National Water-Quality Assessment Program collected tissue samples from a variety of aquatic organisms during 1992-1999 within 47 study units across the United States. These tissue samples were collected to determine the occurrence and distribution of 20 major and minor trace elements in aquatic organisms. This report presents the tissue trace-element concentration data, sample summaries, and concentration statistics for 1,457 tissue samples representing 76 species or groups of fish, aquatic invertebrates, and plants were collected at 824 sampling sites.

Microbial Influences on Trace Metal Cycling in a Meromictic Lake, Fayetteville Green Lake, NY

NASA Astrophysics Data System (ADS)

Zerkle, A. L.; House, C.; Kump, L.

2002-12-01

Microorganisms can exist in aquatic environments at very high cell densities of up to 1011 cells/L, and can accumulate significant quantities of trace metals. Bacteria actively take up bioactive trace metals, including Fe, Zn, Mn, Co, Ni, Cu, and Mo, which function as catalytic centers in metalloproteins and metal-activated enzymes involved in virtually all cellular functions. In addition, bacteria may catalyze the release of trace metals from inorganic substrates by processes such as the reduction of iron and manganese oxides, suggesting that trace metal distributions within a natural environment dominated by microbial processes may be controlled primarily by microbial ecology. Fayetteville Green Lake (FGL), NY, is a permanently stratified meromictic lake that has a well-oxygenated surface water mass (mixolimnion) overlying a relatively stagnant, anoxic deep water mass (monimolimnion). A chemocline separates the water masses at around 20m depth, where oxygen concentrations decrease and sulfate and methane concentrations increase. In addition, previous studies have indicated that trace metals such as V, Cr, Co, Mn, and Fe reach elevated concentrations at the chemocline. Using fluorescent in situ hybridization (FISH) of FGL samples from depths of up to 40m with bacterial and archaeal probes, we have shown that fluctuating redox conditions within the FGL water column correlate with significant variations in the composition and distribution of microbial populations with depth. The mixolimnion is dominated by Eubacteria, with increasing concentrations of Archaea in the lower anoxic zone. Increases in microbial cell densities coincide with increases in trace metals at the chemocline, suggesting microbial activity may be responsible for trace metal release at this boundary. 16S rRNA PCR cloning techniques are currently being used to identify dominant microbial populations at various levels within the FGL water column. Future studies will focus on the potential for these dominant microorganisms to influence trace metal cycling and bioavailability in the FGL water column.

Metagenomic insights into particles and their associated microbiota in a coastal margin ecosystem

PubMed Central

Simon, Holly M.; Smith, Maria W.; Herfort, Lydie

2014-01-01

Our previously published research was one of the pioneering studies on the use of metagenomics to directly compare taxonomic and metabolic properties of aquatic microorganisms from different filter size-fractions. We compared size-fractionated water samples representing free-living and particle-attached communities from four diverse habitats in the Columbia River coastal margin, analyzing 12 metagenomes consisting of >5 million sequence reads (>1.6 Gbp). With predicted peptide and rRNA data we evaluated eukaryotic, bacterial and archaeal populations across size fractions and related their properties to attached and free-living lifestyles, and their potential roles in carbon and nutrient cycling. In this focused review, we expand our discussion on the use of high-throughput sequence data to relate microbial community structure and function to the origin, fate and transport of particulate organic matter (POM) in coastal margins. We additionally discuss the potential impact of the priming effect on organic matter cycling at the land-ocean interface, and build a case for the importance, in particle-rich estuaries and coastal margin waters, of microbial activities in low-oxygen microzones within particle interiors. PMID:25250019

Biostimulation of metal-resistant microbial consortium to remove zinc from contaminated environments.

PubMed

Mejias Carpio, Isis E; Franco, Diego Castillo; Zanoli Sato, Maria Inês; Sakata, Solange; Pellizari, Vivian H; Seckler Ferreira Filho, Sidney; Frigi Rodrigues, Debora

2016-04-15

Understanding the diversity and metal removal ability of microorganisms associated to contaminated aquatic environments is essential to develop metal remediation technologies in engineered environments. This study investigates through 16S rRNA deep sequencing the composition of a biostimulated microbial consortium obtained from the polluted Tietê River in São Paulo, Brazil. The bacterial diversity of the biostimulated consortium obtained from the contaminated water and sediment was compared to the original sample. The results of the comparative sequencing analyses showed that the biostimulated consortium and the natural environment had γ-Proteobacteria, Firmicutes, and uncultured bacteria as the major classes of microorganisms. The consortium optimum zinc removal capacity, evaluated in batch experiments, was achieved at pH=5 with equilibrium contact time of 120min, and a higher Zn-biomass affinity (KF=1.81) than most pure cultures previously investigated. Analysis of the functional groups found in the consortium demonstrated that amine, carboxyl, hydroxyl, and phosphate groups present in the consortium cells were responsible for zinc uptake. Copyright © 2016 Elsevier B.V. All rights reserved.

Cytometric methods for measuring bacteria in water: advantages, pitfalls and applications.

PubMed

Hammes, Frederik; Egli, Thomas

2010-06-01

Rapid detection of microbial cells is a challenge in microbiology, particularly when complex indigenous communities or subpopulations varying in viability, activity and physiological state are investigated. Flow cytometry (FCM) has developed during the last 30 years into a multidisciplinary technique for analysing bacteria. When used correctly, FCM can provide a broad range of information at the single-cell level, including (but not limited to) total counts, size measurements, nucleic acid content, cell viability and activity, and detection of specific bacterial groups or species. The main advantage of FCM is that it is fast and easy to perform. It is a robust technique, which is adaptable to different types of samples and methods, and has much potential for automation. Hence, numerous FCM applications have emerged in industrial biotechnology, food and pharmaceutical quality control, routine monitoring of drinking water and wastewater systems, and microbial ecological research in soils and natural aquatic habitats. This review focuses on the information that can be gained from the analysis of bacteria in water, highlighting some of the main advantages, pitfalls and applications.

Microbiological characterization of aquatic microbiomes targeting taxonomical marker genes and antibiotic resistance genes of opportunistic bacteria.

PubMed

Alexander, Johannes; Bollmann, Anna; Seitz, Wolfram; Schwartz, Thomas

2015-04-15

The dissemination of medically relevant antibiotic resistance genes (ARGs) (blaVIM-1, vanA, ampC, ermB, and mecA) and opportunistic bacteria (Enterococcus faecium/faecalis, Pseudomonas aeruginosa, Enterobacteriaceae, Staphylococcus aureus, and CNS) was determined in different anthropogenically influenced aquatic habitats in a selected region of Germany. Over a period of two years, four differently sized wastewater treatment plants (WWTPs) with and without clinical influence, three surface waters, four rain overflow basins, and three groundwater sites were analyzed by quantitative Polymerase Chain Reaction (qPCR). Results were calculated in cell equivalents per 100 ng of total DNA extracted from water samples and per 100 mL sample volume, which seems to underestimate the abundance of antibiotic resistance and opportunistic bacteria. High abundances of opportunistic bacteria and ARG were quantified in clinical wastewaters and influents of the adjacent WWTP. The removal capacities of WWTP were up to 99% for some, but not all investigated bacteria. The abundances of most ARG targets were found to be increased in the bacterial population after conventional wastewater treatment. As a consequence, downstream surface water and also some groundwater compartments displayed high abundances of all four ARGs. It became obvious that the dynamics of the ARG differed from the fate of the opportunistic bacteria. This underlines the necessity of an advanced microbial characterization of anthropogenically influenced environments. Copyright © 2015 Elsevier B.V. All rights reserved.

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer

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

Pan, Donald; Nolan, Jason; Williams, Kenneth H.

Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Coloradomore » River near Rifle, CO. Virus abundance ranged from 8.0 × 10 4 to 1.0 × 10 6 mL -1 and exceeded cell abundance in all samples (cell abundance ranged from 5.8 × 10 4 to 6.1 × 10 5 mL -1). The virus to microbial cell ratio ranged from 1.1 to 8.1 and averaged 3.0 ± 1.6 with virus abundance most strongly correlated to cell abundance (Spearman's ρ = 0.73, p < 0.001). Both viruses and cells were positively correlated to dissolved organic carbon (DOC) with cells having a slightly stronger correlation (Spearman's ρ = 0.46, p < 0.05 and ρ = 0.54, p < 0.05; respectively). Groundwater uranium was also strongly correlated with DOC and virus and cell abundance (Spearman's ρ = 0.62, p < 0.05; ρ = 0.46, p < 0.05; and ρ = 0.50, p < 0.05; respectively). Together the data indicate that microbial cell and virus abundance are correlated to the geochemical conditions in the aquifer. As such local geochemical conditions likely control microbial host cell abundance which in turn controls viral abundance. Given the potential impacts of viral-mediated cell lysis such as liberation of labile organic matter from lysed cells and changes in microbial community structure, viral interactions with the microbiota should be considered in an effort to understand subsurface biogeochemical cycling and contaminant mobility.« less

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer

DOE PAGES

Pan, Donald; Nolan, Jason; Williams, Kenneth H.; ...

2017-07-11

Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Coloradomore » River near Rifle, CO. Virus abundance ranged from 8.0 × 10 4 to 1.0 × 10 6 mL -1 and exceeded cell abundance in all samples (cell abundance ranged from 5.8 × 10 4 to 6.1 × 10 5 mL -1). The virus to microbial cell ratio ranged from 1.1 to 8.1 and averaged 3.0 ± 1.6 with virus abundance most strongly correlated to cell abundance (Spearman's ρ = 0.73, p < 0.001). Both viruses and cells were positively correlated to dissolved organic carbon (DOC) with cells having a slightly stronger correlation (Spearman's ρ = 0.46, p < 0.05 and ρ = 0.54, p < 0.05; respectively). Groundwater uranium was also strongly correlated with DOC and virus and cell abundance (Spearman's ρ = 0.62, p < 0.05; ρ = 0.46, p < 0.05; and ρ = 0.50, p < 0.05; respectively). Together the data indicate that microbial cell and virus abundance are correlated to the geochemical conditions in the aquifer. As such local geochemical conditions likely control microbial host cell abundance which in turn controls viral abundance. Given the potential impacts of viral-mediated cell lysis such as liberation of labile organic matter from lysed cells and changes in microbial community structure, viral interactions with the microbiota should be considered in an effort to understand subsurface biogeochemical cycling and contaminant mobility.« less

Sediment nitrification and denitrification rates in a Lake Superior estuary

EPA Science Inventory

Microbially-mediated nitrogen (N) cycling in aquatic sediments has been recognized as an ecosystem service due to mitigation of N-transport to receiving waters. In 2011 and 2012, we compared nitrification (NIT), unamended (DeNIT) and amended (DEA) denitrification rates among spat...

Nonstationary time series analysis of surface water microbial pathogen population dynamics using cointegration methods

EPA Science Inventory

Background/Question/Methods Bacterial pathogens in surface water present disease risks to aquatic communities and for human recreational activities. Sources of these pathogens include runoff from urban, suburban, and agricultural point and non-point sources, but hazardous micr...

Ecological theory as a foundation to control pathogenic invasion in aquaculture

PubMed Central

De Schryver, Peter; Vadstein, Olav

2014-01-01

Detrimental host–pathogen interactions are a normal phenomenon in aquaculture animal production, and have been counteracted by prophylactic use of antibiotics. Especially, the youngest life stages of cultivated aquatic animals are susceptible to pathogen invasion, resulting in disease and mortality. To establish a more sustainable aquatic food production, there is a need for new microbial management strategies that focus on ‘join them' and not the traditional ‘beat them' approaches. We argue that ecological theory could serve as a foundation for developing sustainable microbial management methods that prevent pathogenic disease in larviculture. Management of the water microbiota in aquaculture systems according to ecological selection principles has been shown to decrease opportunistic pathogen pressure and to result in an improved performance of the cultured animals. We hypothesize that manipulation of the biodiversity of the gut microbiota can increase the host's resistance against pathogenic invasion and infection. However, substantial barriers need to be overcome before active management of the intestinal microbiota can effectively be applied in larviculture. PMID:24892581

Ciliates in chalk-stream habitats congregate in biodiversity hot spots.

PubMed

Bradley, Mark W; Esteban, Genoveva F; Finlay, Bland J

2010-09-01

Free-living ciliates are a diverse group of microbial eukaryotes that inhabit aquatic environments. They have a vital role within the 'microbial loop', being consumers of microscopic prey such as bacteria, micro-algae, and flagellates, and representing a link between the microscopic and macroscopic components of aquatic food webs. This investigation describes the ciliate communities of four habitats located in the catchment of the River Frome, the major chalk-stream in southern Britain. The ciliate communities were characterised in terms of community assemblage, species abundance and size classes. The ciliate communities investigated proved to be highly diverse, yielding a total of 114 active species. An additional 15 'cryptic' ciliate species were also uncovered. Heterogeneity in the ciliate communities was evident at multiple spatial scales, revealing hot spots of species richness, both within and between habitats. The ciliate communities of habitats with flowing water were composed of smaller ciliates compared to the still-water habitats examined. Copyright 2010 Elsevier Masson SAS. All rights reserved.

Grazers structure the bacterial and algal diversity of aquatic metacommunities.

PubMed

Birtel, Julia; Matthews, Blake

2016-12-01

Consumers can have strong effects on the biotic and abiotic dynamics of spatially-structured ecosystems. In metacommunities, dispersing consumers can alter local assembly dynamics either directly through trophic interactions or indirectly by modifying local environmental conditions. In aquatic systems, very little is known about how key grazers, such as Daphnia, structure the microbial diversity of metacommunities and influence bacterial-mediated ecosystem functions. In an outdoor mesocosm experiment with replicate metacommunities (two 300 L mesocosms), we tested how the presence and absence of Daphnia and the initial density of the microbial community (manipulated via dilution) influenced the diversity and community structure of algae and bacteria, and several ecosystem properties (e.g., pH, dissolved substances) and functions (e.g., enzyme activity, respiration). We found that Daphnia strongly affected the local and regional diversity of both phytoplankton and bacteria, the taxonomic composition of bacterial communities, the biomass of algae, and ecosystem metabolism (i.e., respiration). Diluting the microbial inoculum (0.2-5 μm size fraction) to the metacommunities increased local phytoplankton diversity, decreased bacteria beta-diversity, and changed the relative abundance of bacterial classes. Changes in the rank abundance of different bacterial groups exhibited phylogenetic signal, implying that closely related bacteria species might share similar responses to the presence of Daphnia. © 2016 by the Ecological Society of America.

Soil Metabolome and Metabolic Fate: Microbial Insights into Freshwater Tidal Wetland Redox Biogeochemistry

NASA Astrophysics Data System (ADS)

Roy Chowdhury, T.; Bramer, L.; Hoyt, D. W.; Kim, Y. M.; Metz, T. O.; McCue, L. A.; Jansson, J.; Bailey, V. L.

2017-12-01

Earth System Models predict climate extremes that will impact regional and global hydrology. Aquatic-terrestrial transition zones like wetlands will experience the immediate consequence of climate change as shifts in the magnitude and dynamics of hydrologic flow. Such fluctuating hydrology can alter the structure and function of the soil microbial populations that in turn will alter the nature and rate of biogeochemical transformations and significantly impact the carbon balance of the ecosystem. We tested the impacts of shifting hydrology on the soil microbiome and the role of antecedent moisture condition on redox active microbial processes in soils sampled from a tidal freshwater wetland system in the lower Columbia River, WA, USA. Our objectives were to characterize changes in the soil microbial community composition in response to soil moisture legacy effects, and to elucidate relationships between community response, geochemical signatures and metabolite profiles in this soil. The 16S rRNA gene sequencing showed significant decreases in bacterial abundance capable of anaerobic metabolism in response to drying, but quickly recovered to the antecedent moisture condition, as observed by redox processes. Metabolomics and biogeochemical process rates generated evidence for moisture-driven redox conditions as principal controls on the community and metabolic function. Fluctuating redox conditions altered terminal electron acceptor and donor availability and recovery strengths of these pools in soil such that a disproportionate release of carbon dioxide stemmed from alternative anaerobic degradation processes like sulfate and iron reduction in compared to methanogenesis. Our results show that anoxic conditions impact microbial communities in both permanently and temporarily saturated conditions and that rapid change in hydrology can increase substrate availability for both aerobic and anaerobic decomposition processes, including methanogenesis.

Changes in River Organic Matter Through Time.

NASA Astrophysics Data System (ADS)

Hudson, N.; Baker, A.; Ward, D.

2006-12-01

Samples of river water from central England were collected during the summer base-flow period. They were analysed for BOD and filtered at 1.2μm and 0.1μm increments to obtain i) the colloidal and dissolved, and ii) dissolved filter sterilized fractions. Each filtered fraction was plated up for microbiological cell counts and the agar plates and water samples were stored under a range of environmental conditions (4° C dark, 11° C light/ dark, 11° C dark, and 20° C dark) for 26 days. Absorbance, fluorescence, pH, conductivity and total organic carbon (TOC) were measured and colony forming units (CFU) counted on days 1, 2, 3, 4, 5, 12, 19 and 26. The fluorescence intensity was recorded for 5 commonly studied regions: protein like fluorescence, indicative of microbial activity, represented by the fluorescent amino acids tyrosine and tryptophan (which has two clear fluorescence regions) and humic and fulvic acids derived from the break down of terrestrial and aquatic plant material. Humic and fulvic-like fluorescence increased in all samples under all storage conditions suggesting that peaks A and C probably include a microbial element, either a product of the living community or as dead cell material in all fraction sizes including <0.1μm. Tryptophan and tyrosine-like fluorescence intensities demonstrated less clear trends which may be reflective of the intrinsic variation in natural samples. Tryptophan-like fluorescence generally decreased or showed minimal change, except in samples exposed to light in which an increase was observed in line with algal growth. A decrease in intensity may relate to the use of the tryptophan-like material as a microbial substrate. The increase in tryptophan-like fluorescence intensity suggests that this fluorescent material is being produced, either by algae, or bacterial activity associated with algal growth. It may also occur as a result of changing water chemistry causing a change in molecular conformation, and resulting fluorescence, as an increase in pH was also observed in these samples. This work illustrates the dynamic character of river organic matter within a timescale and under conditions that are representative of the natural system.

MICROBIAL ACTIVITIES FOR THE REMEDIATION OF MERCURY CONTAMINATION

EPA Science Inventory

Methylmercury (MeHg) accumulation by aquatic biota could be reduced by stimulating bacterial degradation of MeHg and the reduction of Hg(II) to volatile Hg to zero power. Reduction of Hg(II) affects MeHg production by substrate limitation. The potential of bacterial reduction of ...

Association between fertilizer-mediated changes in microbial communities and Aedes albopictus growth and survival

USDA-ARS?s Scientific Manuscript database

Contamination of aquatic habitats with anthropogenic nutrients has been associated with an increase in mosquito larval populations but the underlying mechanisms remain poorly understood. We examined the individual and combined effects of two synthetic fertilizers (ammonium sulfate and potassium chlo...

Dredging effects on selected nutrient concentrations and ecoenzymatic activity in two drainage ditch sediments in the lower Mississippi River Valley

USDA-ARS?s Scientific Manuscript database

Agricultural drainage ditches are conduits between production acreage and receiving aquatic systems. Often overlooked for their mitigation capabilities, agricultural drainage ditches provide an important role for nutrient transformation via microbial metabolism. Variations in ecoenzyme activities ...

Influence of land use and land cover on the spatial variability of dissolved organic matter in multiple aquatic environments.

PubMed

Singh, Shatrughan; Dash, Padmanava; Silwal, Saurav; Feng, Gary; Adeli, Ardeshir; Moorhead, Robert J

2017-06-01

Water quality of lakes, estuaries, and coastal areas serves as an indicator of the overall health of aquatic ecosystems as well as the health of the terrestrial ecosystem that drains to the water body. Land use and land cover plays not only a significant role in controlling the quantity of the exported dissolved organic matter (DOM) but also influences the quality of DOM via various biogeochemical and biodegradation processes. We examined the characteristics and spatial distribution of DOM in five major lakes, in an estuary, and in the coastal waters of the Mississippi, USA, and investigated the influence of the land use and land cover of their watersheds on the DOM composition. We employed absorption and fluorescence spectroscopy including excitation-emission matrix (EEM) combined with parallel factor (PARAFAC) analysis modeling techniques to determine optical properties of DOM and its characteristics in this study. We developed a site-specific PARAFAC model to evaluate DOM characteristics resulting in five diverse DOM compositions that included two terrestrial humic-like (C1 and C3), two microbial humic-like (C2 and C5), and one protein-like (C4) DOM. Our results showed elevated fluorescence levels of microbial humic-like or protein-like DOM in the lakes and coastal waters, while the estuarine waters showed relatively high fluorescence levels of terrestrial humic-like DOM. The results also showed that percent forest and wetland coverage explained 68 and 82% variability, respectively, in terrestrial humic-like DOM exports, while 87% variability in microbially derived humiclike DOM was explained by percent agricultural lands. Strong correlations between microbial humic-like DOM and fluorescence-derived DOM indices such as biological index (BIX) and fluorescence index (FI) indicated autochthonous characteristics in the lakes, while the estuary showed largely allochthonous DOM of terrestrial origin. We also observed higher concentrations of total dissolved phosphorous (TDP) and ammonium nitrogen (NH 4 -N) in coastal waters potentially due to photodegradation of refractory DOM derived from the sediment-bound organic matter in the coastal wetlands. This study highlights the relationships between the DOM compositions in the water and the land use and land cover in the watershed. The spatial variability of DOM in three different types of aquatic environments enhances the understanding of the role of land use and land cover in carbon cycling through export of organic matter to the aquatic ecosystems..

Byers Peninsula: A reference site for coastal, terrestrial and limnetic ecosystem studies in maritime Antarctica

NASA Astrophysics Data System (ADS)

Quesada, A.; Camacho, A.; Rochera, C.; Velázquez, D.

2009-11-01

This article describes the development of an international and multidisciplinary project funded by the Spanish Polar Programme on Byers Peninsula (Livingston Island, South Shetlands). The project adopted Byers Peninsula as an international reference site for coastal and terrestrial (including inland waters) research within the framework of the International Polar Year initiative. Over 30 scientists from 12 countries and 26 institutions participated in the field work, and many others participated in the processing of the samples. The main themes investigated were: Holocene changes in climate, using both lacustrine sediment cores and palaeo-nests of penguins; limnology of the lakes, ponds, rivers and wetlands; microbiology of microbial mats, ecology of microbial food webs and viral effects on aquatic ecosystems; ornithology, with investigations on a Gentoo penguin rookery ( Pygoscelis papua) as well as the flying ornithofauna; biocomplexity and life cycles of species from different taxonomic groups; analysis of a complete watershed unit from a landscape perspective; and human impacts, specifically the effect of trampling on soil characteristics and biota. Byers Peninsula offers many features as an international reference site given it is one of the largest ice-free areas in the Antarctic Peninsula region, it has a variety of different landscape units, and it hosts diverse aquatic ecosystems. Moreover, the Byers Peninsula is a hotspot for Antarctic biodiversity, and because of its high level of environmental protection, it has been very little affected by human activities. Finally, the proximity to the Spanish polar installations on Livingston Island and the experience derived from previous expeditions to the site make it logistically feasible as a site for ongoing monitoring and research.

The evil within? Systemic fungicide application in trees enhances litter quality for an aquatic decomposer-detritivore system.

PubMed

Newton, Kymberly; Zubrod, Jochen P; Englert, Dominic; Lüderwald, Simon; Schell, Theresa; Baudy, Patrick; Konschak, Marco; Feckler, Alexander; Schulz, Ralf; Bundschuh, Mirco

2018-06-05

Waterborne exposure towards fungicides is known to trigger negative effects in aquatic leaf-associated microbial decomposers and leaf-shredding macroinvertebrates. We expected similar effects when these organisms use leaf material from terrestrial plants that were treated with systemic fungicides as a food source since the fungicides may remain within the leaves when entering aquatic systems. To test this hypothesis, we treated black alder (Alnus glutinosa) trees with a tap water control or a systemic fungicide mixture (azoxystrobin, cyprodinil, quinoxyfen, and tebuconazole) at two worst-case application rates. Leaves of these trees were used in an experiment targeting alterations in two functions provided by leaf-associated microorganisms, namely the decomposition and conditioning of leaf material. The latter was addressed via the food-choice response of the amphipod shredder Gammarus fossarum. During a second experiment, the potential impact of long-term consumption of leaves from trees treated with systemic fungicides on G. fossarum was assessed. Systemic fungicide treatment altered the resource quality of the leaf material resulting in trends of increased fungal spore production and an altered community composition of leaf-associated fungi. These changes in turn caused a significant preference of Gammarus for microbially conditioned leaves that had received the highest fungicide treatment over control leaves. This higher food quality ultimately resulted in a higher gammarid growth (up to 300% increase) during the long-term feeding assay. Although the underlying mechanisms still need to be addressed, the present study demonstrates a positive indirect response in aquatic organisms due to systemic pesticide application in a terrestrial system. As the effects from the introduction of plant material treated with systemic fungicides strongly differ from those mediated via other pathways (e.g., waterborne exposure), our study provides a novel perspective of fungicide-triggered effects in aquatic detritus-based food webs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Monitoring microbiological changes in drinking water systems using a fast and reproducible flow cytometric method.

PubMed

Prest, E I; Hammes, F; Kötzsch, S; van Loosdrecht, M C M; Vrouwenvelder, J S

2013-12-01

Flow cytometry (FCM) is a rapid, cultivation-independent tool to assess and evaluate bacteriological quality and biological stability of water. Here we demonstrate that a stringent, reproducible staining protocol combined with fixed FCM operational and gating settings is essential for reliable quantification of bacteria and detection of changes in aquatic bacterial communities. Triplicate measurements of diverse water samples with this protocol typically showed relative standard deviation values and 95% confidence interval values below 2.5% on all the main FCM parameters. We propose a straightforward and instrument-independent method for the characterization of water samples based on the combination of bacterial cell concentration and fluorescence distribution. Analysis of the fluorescence distribution (or so-called fluorescence fingerprint) was accomplished firstly through a direct comparison of the raw FCM data and subsequently simplified by quantifying the percentage of large and brightly fluorescent high nucleic acid (HNA) content bacteria in each sample. Our approach enables fast differentiation of dissimilar bacterial communities (less than 15 min from sampling to final result), and allows accurate detection of even small changes in aquatic environments (detection above 3% change). Demonstrative studies on (a) indigenous bacterial growth in water, (b) contamination of drinking water with wastewater, (c) household drinking water stagnation and (d) mixing of two drinking water types, univocally showed that this FCM approach enables detection and quantification of relevant bacterial water quality changes with high sensitivity. This approach has the potential to be used as a new tool for application in the drinking water field, e.g. for rapid screening of the microbial water quality and stability during water treatment and distribution in networks and premise plumbing. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

PubMed

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

2015-12-15

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

Comparative analysis of the intestinal bacterial communities in different species of carp by pyrosequencing.

PubMed

Li, Tongtong; Long, Meng; Gatesoupe, François-Joël; Zhang, Qianqian; Li, Aihua; Gong, Xiaoning

2015-01-01

Gut microbiota is increasingly regarded as an integral component of the host, due to important roles in the modulation of the immune system, the proliferation of the intestinal epithelium and the regulation of the dietary energy intake. Understanding the factors that influence the composition of these microbial communities is essential to health management, and the application to aquatic animals still requires basic investigation. In this study, we compared the bacterial communities harboured in the intestines and in the rearing water of grass carp (Ctenopharyngodon idellus), crucian carp (Carassius cuvieri), and bighead carp (Hypophthalmichthys nobilis), by using 454-pyrosequencing with barcoded primers targeting the V4 to V5 regions of the bacterial 16S rRNA gene. The specimens of the three species were cohabiting in the same pond. Between 6,218 and 10,220 effective sequences were read from each sample, resulting in a total of 110,398 sequences for 13 samples from gut microbiota and pond water. In general, the microbial communities of the three carps were dominated by Fusobacteria, Firmicutes, Proteobacteria and Bacteroidetes, but the abundance of each phylum was significantly different between species. At the genus level, the overwhelming group was Cetobacterium (97.29 ± 0.46 %) in crucian carp, while its abundance averaged c. 40 and 60 % of the sequences read in the other two species. There was higher microbial diversity in the gut of filter-feeding bighead carp than the gut of the two other species, with grazing feeding habits. The composition of intestine microbiota of grass carp and crucian carp shared higher similarity when compared with bighead carp. The principal coordinates analysis (PCoA) with the weighted UniFrac distance and the heatmap analysis suggested that gut microbiota was not a simple reflection of the microbial community in the local habitat but resulted from species-specific selective pressures, possibly dependent on behavioural, immune and metabolic characteristics.

Bacteria and fluorescent organic matter: processing and production.

NASA Astrophysics Data System (ADS)

Fox, B. G.; Thorn, R. M. S.; Reynolds, D. M.

2017-12-01

There is a need for a greater understanding of the importance of aquatic organic matter (OM) within global biogeochemical cycling. This need has prompted characterisation of OM using fluorescence spectroscopy. The origin, transformation and fate of fluorescent organic matter (FOM) is not fully understood within freshwater systems. This work demonstrates the importance of microbial processing in the creation and transformation of FOM, highlighting the dynamics of microbial-FOM interactions, using a model system. The FOM signature of different bacterial species common to surface freshwaters were analysed using a non-fluorescent media; Escherichia coli, Bacillus subtilis and Pseudomonas aeruginosa. By undertaking bacterial growth curves, alongside fluorescence spectroscopy, we have been able to determine FOM development in relation to population growth. Within this, we have identified that FOM peaks are associated with different species and driven by bacterial processes, such as cell multiplication or as metabolic by-products. The intracellular and extracellular fluorescence signature of each species has also been analysed to better understand how the microbial community structure may impact the FOM signal in aquatic systems. For example, Peak T develops within the growth curves of all the cultured species and has been identified as both intracellular and extracellular FOM. Whilst Peak T has been termed `microbially-derived' previously, other fluorescence peaks associated with terrestrial high molecular weight compounds, e.g. Peak C, have also been shown to be produced by bacteria throughout growth stages. Additionally, the notion that cell lysis is responsible for the presence of larger FOM compounds was also explored. Our work highlights the capacity of bacteria to not only utilise and process OM but to actively be a source of both labile and recalcitrant OM in situ. The bacteria fluorescence signatures seen are complex with comparable fluorescence peaks to those seen in real-world freshwaters. Interestingly, this includes a range of FOM currently considered high molecular weight compounds attributed to terrestrial origin. The role of bacterial processing in aquatic systems may prove to have a wider impact on DOM transformation along the hydrological continuum and global biogeochemical cycling.

Modelling sediment-microbial dynamics in the South Nation River, Ontario, Canada: Towards the prediction of aquatic and human health risk.

PubMed

Droppo, I G; Krishnappan, B G; Liss, S N; Marvin, C; Biberhofer, J

2011-06-01

Runoff from agricultural watersheds can carry a number of agricultural pollutants and pathogens; often associated with the sediment fraction. Deposition of this sediment can impact water quality and the ecology of the river, and the re-suspension of such sediment can become sources of contamination for reaches downstream. In this paper a modelling framework to predict sediment and associated microbial erosion, transport and deposition is proposed for the South Nation River, Ontario, Canada. The modelling framework is based on empirical relationships (deposition and re-suspension fluxes), derived from laboratory experiments in a rotating circular flume using sediment collected from the river bed. The bed shear stress governing the deposition and re-suspension processes in the stream was predicted using a one dimensional mobile boundary flow model called MOBED. Counts of live bacteria associated with the suspended and bed sediments were used in conjunction with measured suspended sediment concentration at an upstream section to allow for the estimation of sediment associated microbial erosion, transport and deposition within the modelled river reach. Results suggest that the South Nation River is dominated by deposition periods with erosion only occurring at flows above approximately 250 m(3) s(-1) (above this threshold, all sediment (suspended and eroded) with associated bacteria are transported through the modelled reach). As microbes are often associated with sediments, and can survive for extended periods of time, the river bed is shown to be a possible source of pathogenic organisms for erosion and transport downstream during large storm events. It is clear that, shear levels, bacteria concentrations and suspended sediment are interrelated requiring that these parameters be studied together in order to understand aquatic microbial dynamics. It is important that any management strategies and operational assessments for the protection of human and aquatic health incorporate the sediment compartments (suspended and bed sediment) and the energy dynamics within the system in order to better predict the concentration of indicator organism. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

IMPORTANCE OF THE DYNAMICS OF BACTERIOPHAGE-HOST INTERACTIONS TO BACTERIAL ABUNDANCE AND GENETIC DIVERSITY IN AQUATIC ENVIRONMENTS (RESEARCH BRIEF)

EPA Science Inventory

Using Pseudomonas aeruginosa and its bacteriophages as a model system, we have clearly demonstrated a significant potential for viral-mediated gene transfer (transduction) of both plasmid and chromosomal DNA in freshwater microbial populations. These investigations have predicted...

Phylogenetic Diversity and Molecular Detection of Bacteria in Gull Feces

EPA Science Inventory

In spite of increasing public health concerns about the potential risks associated with swimming in waters contaminated with waterfowl feces, little is known about the composition of the gut microbial community of aquatic birds. To address this, a gull 16S rDNA fecal clone librar...

EFFECTS OF LARGE-SCALE POULTRY FARMS ON AQUATIC MICROBIAL COMMUNITIES: A MOLECULAR INVESTIGATION.

EPA Science Inventory

The effects of large-scale poultry production operations on water quality and human health are largely unknown. Poultry litter is frequently applied as fertilizer to agricultural lands adjacent to large poultry farms. Run-off from the land introduces a variety of stressors into t...

ROAD SALT APPLICATION CREATES A UNIQUE CHLORIDE BIOCHEMISTRY IN AN URBAN STREAM OF THE CHESAPEAKE BAY WATERSHED

EPA Science Inventory

Recent evidence from the mid-Atlantic suggests that freshwater supplies are threatened by chronic chloride inputs from road salts applied to improve highway safety. Elevated chloride levels also may limit the ability of aquatic systems to microbially process nitrate nitrogen, a ...

ASSESSING ANTIBACTERIAL RESISTANCE DEVELOPMENT AND MICROBIAL COMMUNITY EFFECTS IN AQUATIC SYSTEMS EXPOSED TO ENROFLOXACIN USING DGGE. (R829008)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

The treatment of hospital wastewater: an appraisal.

PubMed

Pauwels, B; Verstraete, W

2006-12-01

Hospitals discharge considerable amounts of chemicals and microbial agents in their wastewaters. Problem chemicals present in hospital wastewater belong to different groups, such as antibiotics, X-ray contrast agents, disinfectants and pharmaceuticals. Many of these chemical compounds resist normal wastewater treatment. They end up in surface waters where they can influence the aquatic ecosystem and interfere with the food chain. Humans are particularly exposed by the drinking water, produced from surface water. Microbial agents of special concern are multiresistant microbial strains. The latter are suspected to contribute to the spread of antibiotic resistance. In this paper, we will discuss the different approaches towards hospital wastewater treatment. The principle of uncoupling hospitals from public sewers warrants indepth evaluation by technologists and ecotoxicologists as well as public health specialists.

Microbial methane production in oxygenated water column of an oligotrophic lake

PubMed Central

Grossart, Hans-Peter; Frindte, Katharina; Dziallas, Claudia; Eckert, Werner; Tang, Kam W.

2011-01-01

The prevailing paradigm in aquatic science is that microbial methanogenesis happens primarily in anoxic environments. Here, we used multiple complementary approaches to show that microbial methane production could and did occur in the well-oxygenated water column of an oligotrophic lake (Lake Stechlin, Germany). Oversaturation of methane was repeatedly recorded in the well-oxygenated upper 10 m of the water column, and the methane maxima coincided with oxygen oversaturation at 6 m. Laboratory incubations of unamended epilimnetic lake water and inoculations of photoautotrophs with a lake-enrichment culture both led to methane production even in the presence of oxygen, and the production was not affected by the addition of inorganic phosphate or methylated compounds. Methane production was also detected by in-lake incubations of lake water, and the highest production rate was 1.8–2.4 nM⋅h−1 at 6 m, which could explain 33–44% of the observed ambient methane accumulation in the same month. Temporal and spatial uncoupling between methanogenesis and methanotrophy was supported by field and laboratory measurements, which also helped explain the oversaturation of methane in the upper water column. Potentially methanogenic Archaea were detected in situ in the oxygenated, methane-rich epilimnion, and their attachment to photoautotrophs might allow for anaerobic growth and direct transfer of substrates for methane production. Specific PCR on mRNA of the methyl coenzyme M reductase A gene revealed active methanogenesis. Microbial methane production in oxygenated water represents a hitherto overlooked source of methane and can be important for carbon cycling in the aquatic environments and water to air methane flux. PMID:22089233

Ecology, Microbial

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

Konopka, Allan

2009-05-15

Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, theymore » interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.« less

Synthesis and anti-microbial potencies of 1-(2-hydroxyethyl)-3-alkylimidazolium chloride ionic liquids: microbial viabilities at different ionic liquids concentrations.

PubMed

Hossain, M Ismail; El-Harbawi, Mohanad; Alitheen, Noorjahan Banu Mohamed; Noaman, Yousr Abdulhadi; Lévêque, Jean-Marc; Yin, Chun-Yang

2013-01-01

Three 1-(2-hydroxyethyl)-3-alkylimidazolium chloride room temperature ionic liquids (ILs) [2OHimC(n)][Cl]; (n=0, 1, 4) have been synthesized from the appropriate imidazole precursors and characterized by IR and NMR spectroscopies and elemental analysis. Their anti-microbial activities were investigated using the well-diffusion method. The viabilities of Escherichia coli, Aeromonas hydrophila, Listeria monocytogenes and Salmonella enterica as a function of IL concentrations were studied. The minimal inhibitory concentrations (MICs) and EC₅₀ values for the present ILs were within the concentration range from 60 to 125 mM and 23 to 73 mM. The anti-microbial potencies of the present ILs were compared to a standard antibiotic, gentamicin. The finding affords additional perspective on the level of ILs toxicity to aquatic lifeforms and yet, this characteristic can be readily harnessed to detect microbial growth and activity. Copyright © 2012 Elsevier Inc. All rights reserved.

Composition of dissolved organic matter (DOM) from periodically submerged soils in the Three Gorges Reservoir areas as determined by elemental and optical analysis, infrared spectroscopy, pyrolysis-GC-MS and thermally assisted hydrolysis and methylation.

PubMed

Jiang, Tao; Kaal, Joeri; Liang, Jian; Zhang, Yaoling; Wei, Shiqiang; Wang, Dingyong; Green, Nelson W

2017-12-15

Soil-derived dissolved organic matter (DOM) has a major influence in biogeochemical processes related to contaminant dynamics and greenhouse gas emissions, due to its reactivity and its bridging role between the soil and aquatic systems. Within the Three Gorges Reservoir (TGR, China) area, an extensive water-fluctuation zone periodically submerges the surrounding soils. Here we report a characterization study of soil-derived DOM across the TGR areas, using elemental and optical analysis, infrared spectroscopy (FTIR), pyrolysis-GC-MS (Py-GC-MS) and thermally assisted hydrolysis and methylation (THM-GC-MS). The results showed that the soil DOM from the TGR area is a mixture of "allochthonous" (i.e., plant-derived/terrigenous) and "autochthonous" (i.e., microbial) origins. The terrigenous DOM is composed primarily of phenolic and aliphatic structures from lignin and aliphatic biopolymers (i.e. cutin, suberin), respectively. Multivariate statistics differentiated between two fractions of the microbial DOM, i.e. chitin-derived, perhaps from fungi and arthropods in soil, and protein-derived, partially sourced from algal or aquatic organisms. Molecular proxies of source and degradation state were in good agreement with optical parameters such as SUVA 254 , the fluorescence index (FI) and the humification index (HIX). The combined use of elemental analysis, fluorescence spectroscopy, and Py-GC-MS provides rigorous and detailed DOM characterization, whereas THM-GC-MS is useful for more precise but qualitative identification of the different phenolic (cinnamyl, p-hydroxyphenyl, guaiacyl, syringyl and tannin-derived) and aliphatic materials. With the multi-methodological approach used in this study, FTIR was the least informative, in part, because of the interference of inorganic matter in the soil DOM samples. The soil DOM from the TGR's water fluctuation zone exhibited considerable compositional diversity, mainly related to the balance between DOM source (microbial- or plant-derived), local vegetation and anthropogenic activities (e.g., agriculture). Finally, the relationship between DOM composition and its potential reactivity with substances of environmental concerns in the TGR area are also discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Compositional Characteristics of Dissolved Organic Matter released from the sediment of Han river in Korea.

NASA Astrophysics Data System (ADS)

Oh, H.; Choi, J. H.

2017-12-01

The dissolved organic matter (DOM) has variable characteristics depending on the sources. The DOM of a river is affected by rain water, windborne material, surface and groundwater flow, and sediments. In particular, sediments are sources and sinks of nutrients and pollutants in aquatic ecosystems by supplying large amounts of organic matter. The DOM which absorbs ultraviolet and visible light is called colored dissolved organic matter (CDOM). CDOM is responsible for the optical properties of natural waters in several biogeochemical and photochemical processes and absorbs UV-A (315-400 nm) and UV-B (280-315), which are harmful to aquatic ecosystems (Helms et al., 2008). In this study, we investigated the quantity and quality of DOM and CDOM released from the sediments of Han river which was impacted by anthropogenic activities and hydrologic alternation of 4 Major River Restoration Project. The target area of this study is Gangchenbo (GC), Yeojubo (YJ), and Ipobo(IP) of the Han River, Korea. Sediments and water samples were taken on July and August of 2016 and were incubated at 20° up to 7 days. Absorbance was measured with UV-visible spectrophotometer (Libra S32 PC, Biochrom). Fluorescence intensity determined with Fluorescence EEMs (F-7000, Hitachi). Absorbance and fluorescence intensity were used to calculate Specific Ultraviolet Absorbance (SUVA254), Humification index (HIX), Biological index (BIX), Spectral slope (SR) and component analysis. The DOC concentration increased after 3 days of incubation. According to the SUVA254 analysis, the microbial activity is highest in the initial overlying water of IP. HIX have range of 1.35-4.08, and decrease poly aromatic structures of organic matter during incubation. From the results of the BIX, autochthonous organic matter was released from the sediments. In all sites, Humic-like DOM, Microbial humic-like DOM and Protein-like DOM increased significantly between Day 0 and 3(except Humic-like, Microbial humic-like DOM in IP). Spectral slope ratio of all sites increased according to incubation, which means that the amount of CDOM increased from the sediment to overlying water.

Sorting Out the Ocean Crust Deep Biosphere with Single Cell Omics Approaches

NASA Astrophysics Data System (ADS)

Orcutt, B.; D'Angelo, T.; Goordial, J.; Jones, R. M.; Carr, S. A.

2017-12-01

Although oceanic crust comprises a large habitat for subsurface life, the structure, function, and dynamics of microbial communities living on rocks in the subsurface are poorly understood. Single cell level approaches can overcome limitations of low biomass in subsurface systems. Coupled with incubation experiments with amino acid orthologs, single cell level sorting can reveal high resolution information about identity, functional potential, and growth. Leveraging collaboration with the Single Cell Genomics Center and the Facility for Aquatic Cytometry at Bigelow Laboratory, we present recent results from single cell level sorting and -omics sequencing from several crustal environments, including the Atlantis Massif and the Juan de Fuca Ridge flank. We will also highlight new experiments conducted with samples recovered from the flank of the Mid-Atlantic Ridge.

Catabolism of Tritiated Thymidine by Aquatic Microbial Communities and Incorporation of Tritium into RNA and Protein †

PubMed Central

Brittain, Andrew M.; Karl, David M.

1990-01-01

The incorporation of tritiated thymidine by five microbial ecosystems and the distribution of tritium into DNA, RNA, and protein were determined. All microbial assemblages tested exhibited significant labeling of RNA and protein (i.e., nonspecific labeling), as determined by differential acid-base hydrolysis. Nonspecific labeling was greatest in sediment samples, for which ≥95% of the tritium was recovered with the RNA and protein fractions. The percentage of tritium recovered in the DNA fraction ranged from 15 to 38% of the total labeled macromolecules recovered. Nonspecific labeling was independent of both incubation time and thymidine concentration over very wide ranges. Four different RNA hydrolysis reagents (KOH, NaOH, piperidine, and enzymes) solubilized tritium from cold trichloroacetic acid precipitates. High-pressure liquid chromatography separation of piperidine hydrolysates followed by measurement of isolated monophosphates confirmed the labeling of RNA and indicated that tritium was recovered primarily in CMP and AMP residues. We also evaluated the specificity of [2-3H]adenine incorporation into adenylate residues in both RNA and DNA in parallel with the [3H]thymidine experiments and compared the degree of nonspecific labeling by [3H]adenine with that derived from [3H]thymidine. Rapid catabolism of tritiated thymidine was evaluated by determining the disappearance of tritiated thymidine from the incubation medium and the appearance of degradation products by high-pressure liquid chromatography separation of the cell-free medium. Degradation product formation, including that of both volatile and nonvolatile compounds, was much greater than the rate of incorporation of tritium into stable macromolecules. The standard degradation pathway for thymidine coupled with utilization of Krebs cycle intermediates for the biosynthesis of amino acids, purines, and pyrimidines readily accounts for the observed nonspecific labeling in environmental samples. PMID:16348180

Biodegradation of pesticides using fungi species found in the aquatic environment.

PubMed

Oliveira, B R; Penetra, A; Cardoso, V V; Benoliel, M J; Barreto Crespo, M T; Samson, R A; Pereira, V J

2015-08-01

Relatively limited attention has been given to the presence of fungi in the aquatic environment compared to their occurrence in other matrices. Taking advantage and recognizing the biodegradable capabilities of fungi is important, since these organisms may produce many potent enzymes capable of degrading toxic pollutants. Therefore, the aim of this study was to evaluate the potential ability of some species of filamentous fungi that occur in the aquatic environment to degrade pesticides in untreated surface water. Several laboratory-scale experiments were performed using the natural microbial population present in the aquatic environment as well as spiked fungi isolates that were found to occur in different water matrices, to test the ability of fungi to degrade several pesticides of current concern (atrazine, diuron, isoproturon and chlorfenvinphos). The results obtained in this study showed that, when spiked in sterile natural water, fungi were able to degrade chlorfenvinphos to levels below detection and unable to degrade atrazine, diuron and isoproturon. Penicillium citrinum, Aspergillus fumigatus, Aspergillus terreus and Trichoderma harzianum were found to be able to resist and degrade chlorfenvinphos. These fungi are therefore expected to play an important role in the degradation of this and other pollutants present in the aquatic environment.

Are leaves that fall from imidacloprid-treated maple trees to control Asian longhorned beetles toxic to non-target decomposer organisms?

PubMed

Kreutzweiser, David P; Good, Kevin P; Chartrand, Derek T; Scarr, Taylor A; Thompson, Dean G

2008-01-01

The systemic insecticide imidacloprid may be applied to deciduous trees for control of the Asian longhorned beetle, an invasive wood-boring insect. Senescent leaves falling from systemically treated trees contain imidacloprid concentrations that could pose a risk to natural decomposer organisms. We examined the effects of foliar imidacloprid concentrations on decomposer organisms by adding leaves from imidacloprid-treated sugar maple trees to aquatic and terrestrial microcosms under controlled laboratory conditions. Imidacloprid in maple leaves at realistic field concentrations (3-11 mg kg(-1)) did not affect survival of aquatic leaf-shredding insects or litter-dwelling earthworms. However, adverse sublethal effects at these concentrations were detected. Feeding rates by aquatic insects and earthworms were reduced, leaf decomposition (mass loss) was decreased, measurable weight losses occurred among earthworms, and aquatic and terrestrial microbial decomposition activity was significantly inhibited. Results of this study suggest that sugar maple trees systemically treated with imidacloprid to control Asian longhorned beetles may yield senescent leaves with residue levels sufficient to reduce natural decomposition processes in aquatic and terrestrial environments through adverse effects on non-target decomposer organisms.

Effects of Fungicides on Aquatic Fungi and Bacteria

NASA Astrophysics Data System (ADS)

Conners, D. E.; Rosemond, A. D.; Black, M. C.

2005-05-01

Aquatic microorganisms play an important role in conditioning leaf litter that enters streams and serves as an important base of production for consumers. Contamination of streams by fungicides may adversely affect microorganisms and alter leaf litter processing rates. Unfortunately, microorganisms are rarely used in acute toxicity tests for fungicide evaluation and registration. We adapted the resazurin reduction assay, which is used in medical microbiology, to assess the acute toxicity of four fungicides (azoxystrobin, trifloxystrobin, kresoxim-methyl and chlorothalonil) to aquatic fungi (Articulospora tetracladia) and bacteria (Cytophaga spp.), and investigated the ability of the toxicants to inhibit leaf breakdown in microcosms. Fungi were more sensitive to fungicides than many standard test organisms (cladocerans, green algae, trout), while bacteria were often the least sensitive. All of the fungicides except kresoxim-methyl, when added to microcosms at concentrations that inhibited the fungi by 90 percent in acute tests, reduced leaf breakdown rates by an average of 14.7 percent. Thus, aquatic fungi and their associated functions in streams may be relatively sensitive to fungicides applied terrestrially that enter streams through non-point sources. These data highlight the importance of including aquatic fungi in safety assessments of pesticides for protection of microbial function.

Estimating Aquatic Insect Populations. Introduction to Sampling.

ERIC Educational Resources Information Center

Chihuahuan Desert Research Inst., Alpine, TX.

This booklet introduces high school and junior high school students to the major groups of aquatic insects and to population sampling techniques. Chapter 1 consists of a short field guide which can be used to identify five separate orders of aquatic insects: odonata (dragonflies and damselflies); ephemeroptera (mayflies); diptera (true flies);…

Changes in organic - C, N, P and K and enzyme activities in vermicompost of biodegradable organic wastes under liming and microbial inoculants.

PubMed

Pramanik, P; Ghosh, G K; Ghosal, P K; Banik, P

2007-09-01

The aim of this work was to study the effect of different organic wastes, viz. cow dung, grass, aquatic weeds and municipal solid waste with lime and microbial inoculants on chemical and biochemical properties of vermicompost. Cow dung was the best substrate for vermicomposting. Application of lime (5 g/kg) and inoculation of microorganisms increased the nutrient content in vermicompost and also phosphatases and urease activities. Bacillus polymyxa, the free-living N-fixer, increased N-content of vermicompost significantly (p < or = 0.01) as compared to other inoculants.

Incorporation of hydrophobized mineral particles in activated sludge flocs: a way to assess ballasting efficiency.

PubMed

Defontaine, G; Thormann, J; Lartiges, B S; El Samrani, A G; Barrs, O

2005-01-01

The role of mineral surface hydrophobicity in attachment to activated sludge flocs was investigated. Fluorite and quartz particles of similar granulometry were hydrophobized by adsorbing sodium oleate and dodecylamine chloride, respectively. Mineral hydrophobicity was assessed by flotation expriments. The attachment of particles to microbial flocs was determined by optical microscopy. The results indicate that hydrophobized particles are always better incorporated within activated sludge flocs than non-coated particles. A comparison with Aquatal particles used as sludge ballast reveals that hydrophobized minerals are associated with microbial flocs to the same extent.

40 CFR 158.2150 - Microbial pesticides nontarget organisms and environmental fate data requirements table.

Code of Federal Regulations, 2014 CFR

2014-07-01

... product. Notes that apply to an individual test including specific conditions, qualifications, or exceptions to the designated test are listed in paragraph (e) of this section. (b) Use patterns. Aquatic uses... ingredient; All=All of the above. Specific conditions, qualifications, or exceptions to the designated test...

ENVIRONMENTAL BIODEGRADABILITY OF [14C] SINGLE-WALLED CARBON NANOTUBESBY TRAMETES VERSICOLOR AND NATURAL MICROBIAL CULTURES FOUND IN NEWBEDFORD HARBOR SEDIMENT AND AERATED WASTEWATER TREATMENT PLANT SLUDGE

EPA Science Inventory

Little is known about environmental biodegradability or biotransformations of single-walled carbon nanotubes (SWNT). Because of their strong association with aquatic organic matter, detailed knowledge of the ultimate fate and persistence of SWNT requires investigation of possible...

Ecological effects of nitrogen deposition in the western United States

Treesearch

Mark E. Fenn; Jill S. Baron; Edith B. Allen; Heather M. Rueth; Koren R. Nydick; Linda Geiser; William D. Bowman; James O. Sickman; Thomas Meixner; Dale W. Johnson; Peter Neitlich

2003-01-01

In the western United States vast acreages of land are exposed to low levels of atmospheric nitrogen (N) deposition, with interspersed hotspots of elevated N deposition downwind of large, expanding metropolitan centers or large agricultural operations. Biological response studies in western North America demonstrate that some aquatic and terrestrial plant and microbial...

Goethite promoted biodegradation of 2,4-dinitrophenol under nitrate reduction condition.

PubMed

Tang, Ting; Yue, Zhengbo; Wang, Jin; Chen, Tianhu; Qing, Chengsong

2018-02-05

Iron oxide may interact with other pollutants in the aquatic environments and further influence their toxicity, transport and fate. The current study was conducted to investigate the biodegradation of 2,4-dinitrophenol (2,4-DNP) in the presence of iron oxide of goethite under anoxic condition using nitrate as the electron acceptor. Experiment results showed that the degradation rate of 2,4-DNP was improved by goethite. High performance liquid chromatography-mass spectra analysis results showed that goethite promoted degradation and transformation of 2,4-diaminophenol and 2-amino-4-nitrophenol (2-nitro-4-aminophenol). Microbial community analysis results showed that the abundance of Actinobacteria, which have the potential ability to degrade PAHs, was increased when goethite was available. This might partially explain the higher degradation of 2,4-DNP. Furthermore, another bacterium of Desulfotomaculum reducens which could reduce soluble Fe(III) and nitrate was also increased. Results further confirmed that nanomaterials in the aquatic environment will influence the microbial community and further change the transformation process of toxic pollutants. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of the bacterial communities associated with different drinking water treatment processes.

PubMed

Zeng, Dan-Ning; Fan, Zhen-Yu; Chi, Liang; Wang, Xia; Qu, Wei-Dong; Quan, Zhe-Xue

2013-09-01

A drinking water plant was surveyed to determine the bacterial composition of different drinking water treatment processes (DWTP). Water samples were collected from different processing steps in the plant (i.e., coagulation, sedimentation, sand filtration, and chloramine disinfection) and from distantly piped water. The samples were pyrosequensed using sample-specific oligonucleotide barcodes. The taxonomic composition of the microbial communities of different DWTP and piped water was dominated by the phylum Proteobacteria. Additionally, a large proportion of the sequences were assigned to the phyla Actinobacteria and Bacteroidetes. The piped water exhibited increasing taxonomic diversity, including human pathogens such as the Mycobacterium, which revealed a threat to the safety of drinking water. Surprisingly, we also found that a sister group of SAR11 (LD12) persisted throughout the DWTP, which was always detected in freshwater aquatic systems. Moreover, Polynucleobacter, Rhodoferax, and a group of Actinobacteria, hgcI clade, were relatively consistent throughout the processes. It is concluded that smaller-size microorganisms tended to survive against the present treatment procedure. More improvement should be made to ensure the long-distance transmission drinking water.

Risk screening of pharmaceutical compounds in Romanian aquatic environment.

PubMed

Gheorghe, Stefania; Petre, Jana; Lucaciu, Irina; Stoica, Catalina; Nita-Lazar, Mihai

2016-06-01

The aquatic environment is under increased pressure by pharmaceutically active compounds (PhACs) due to anthropogenic activities. In spite of being found at very low concentrations (ng/L to μg/L) in the environment, PhACs represent a real danger to aquatic ecosystems due to their bioaccumulation and long-term effects. In this study, the presence in the aquatic environment of six non-steroidal anti-inflammatory drugs (ibuprofen, diclofenac, acetaminophen, naproxen, indomethacin, and ketoprofen), caffeine, and carbamazepine were monitored. Moreover, their aquatic risk and ecotoxicity by three biological models were evaluated. The monitoring studies performed in Romania showed that all studied PhACs were naturally present at concentrations >0.01 μg/L, pointing out the necessity to perform further toxicity tests for environmental risk assessment. The toxicity studies were carried out on aquatic organisms or bacteria and they indicated, for most of the tested PhACs, an insignificant or low toxicity effects: lethal concentrations (LC50) on fish Cyprinus carpio ranged from 42.60 mg/L to more than 100 mg/L; effective concentrations (EC50) on planktonic crustacean Daphnia magna ranged from 11.02 mg/L to more than 100 mg/L; inhibitory concentrations (IC50)/microbial toxic concentrations (MTC) on Vibrio fischeri and other bacterial strains ranged from 7.02 mg/L to more than 100 mg/L. The PhAC aquatic risk was assessed by using the ratio between measured environmental concentration (MEC) and predicted no effect concentration (PNEC) calculated for each type of organism. The average of quotient risks (RQs) revealed that the presence of these compounds in Romania's aquatic environment induced a lower or moderate aquatic risk.

Spatial distribution of enzyme driven reactions at micro-scales

NASA Astrophysics Data System (ADS)

Kandeler, Ellen; Boeddinghaus, Runa; Nassal, Dinah; Preusser, Sebastian; Marhan, Sven; Poll, Christian

2017-04-01

Studies of microbial biogeography can often provide key insights into the physiologies, environmental tolerances, and ecological strategies of soil microorganisms that dominate in natural environments. In comparison with aquatic systems, soils are particularly heterogeneous. Soil heterogeneity results from the interaction of a hierarchical series of interrelated variables that fluctuate at many different spatial and temporal scales. Whereas spatial dependence of chemical and physical soil properties is well known at scales ranging from decimetres to several hundred metres, the spatial structure of soil enzymes is less clear. Previous work has primarily focused on spatial heterogeneity at a single analytical scale using the distribution of individual cells, specific types of organisms or collective parameters such as bacterial abundance or total microbial biomass. There are fewer studies that have considered variations in community function and soil enzyme activities. This presentation will give an overview about recent studies focusing on spatial pattern of different soil enzymes in the terrestrial environment. Whereas zymography allows the visualization of enzyme pattern in the close vicinity of roots, micro-sampling strategies followed by MUF analyses clarify micro-scale pattern of enzymes associated to specific microhabitats (micro-aggregates, organo-mineral complexes, subsoil compartments).

Aerobic biodegradation potential of endocrine disrupting chemicals in surface-water sediment at Rocky Mountains National Park, USA

USGS Publications Warehouse

Bradley, Paul M.; Battaglin, William A.; Iwanowicz, Luke R.; Clark, Jimmy M.; Journey, Celeste A.

2016-01-01

Endocrine disrupting chemicals (EDC) in surface water and bed sediment threaten the structure and function of aquatic ecosystems. In natural, remote, and protected surface-water environments where contaminant releases are sporadic, contaminant biodegradation is a fundamental driver of exposure concentration, timing, duration, and, thus, EDC ecological risk. Anthropogenic contaminants, including known and suspected EDC, were detected in surface water and sediment collected from 2 streams and 2 lakes in Rocky Mountains National Park (ROMO). The potential for aerobic EDC biodegradation was assessed in collected sediments using 6 14C-radiolabeled model compounds. Aerobic microbial mineralization of natural (estrone and 17β-estradiol) and synthetic (17α-ethinylestradiol) estrogen was significant at all sites. ROMO bed sediment microbial communities also effectively degraded the xenoestrogens, bisphenol-A and 4-nonylphenol. The same sediment samples exhibited little potential for aerobic biodegradation of triclocarban, however, illustrating the need to assess a wider range of contaminant compounds. The current results support recent concerns over the widespread environmental occurrence of carbanalide antibacterials, like triclocarban and triclosan, and suggest that backcountry use of products containing these compounds should be discouraged.

Concentrations of biogenic amines in fish, squid and octopus and their changes during storage.

PubMed

Hu, Yue; Huang, Zhiyong; Li, Jian; Yang, Hong

2012-12-15

The concentrations of seven biogenic amines (BA) were simultaneously determined in 74 samples of fish, squid and octopus, by the method of HPLC coupled with pre-column derivatisation. The relationship between the formation of BA in aquatic products and the growth of microbial flora during storage was also investigated. Results showed that putrescine, cadaverine, histamine and tyramine were the dominant BA in the studied samples, but the concentrations of histamine and tyramine were mostly less than 50 and 100 mgkg(-1), respectively. Freezing can effectively prevent the formation of BA, but the levels of putrescine, cadaverine, histamine and tyramine significantly increased (p<0.05) during storage at 4 and 25°C. The growth of mesophilic or psychrophilic bacteria in blue scad and octopus strongly and positively correlated with the formation of amines (such as putrescine, cadaverine, histamine and tyramine) during storage, except for histamine in octopus. Copyright © 2012 Elsevier Ltd. All rights reserved.

Total Mercury, Methylmercury, Methylmercury Production Potential, and Ancillary Streambed-Sediment and Pore-Water Data for Selected Streams in Oregon, Wisconsin, and Florida, 2003-04

USGS Publications Warehouse

Marvin-DiPasquale, Mark C.; Lutz, Michelle A.; Krabbenhoft, David P.; Aiken, George R.; Orem, William H.; Hall, Britt D.; DeWild, John F.; Brigham, Mark E.

2008-01-01

Mercury contamination of aquatic ecosystems is an issue of national concern, affecting both wildlife and human health. Detailed information on mercury cycling and food-web bioaccumulation in stream settings and the factors that control these processes is currently limited. In response, the U.S. Geological Survey (USGS) National Water-Quality Assessment Program (NAWQA) conducted detailed studies from 2002 to 2006 on various media to enhance process-level understanding of mercury contamination, biogeochemical cycling, and trophic transfer. Eight streams were sampled for this study: two streams in Oregon, and three streams each in Wisconsin and Florida. Streambed-sediment and pore-water samples were collected between February 2003 and September 2004. This report summarizes the suite of geochemical and microbial constituents measured, the analytical methods used, and provides the raw data in electronic form for both bed-sediment and pore-water media associated with this study.

Microbial degradation of microcystin in Florida’s freshwaters

PubMed Central

Ramani, A.; Rein, K.; Shetty, K. G.

2012-01-01

Presence of microcystin (MC), a predominant freshwater algal toxin and a suspected liver carcinogen, in Florida’s freshwaters poses serious health threat to humans and aquatic species. Being recalcitrant to conventional physical and chemical water treatment methods, biological methods of MC removal is widely researched. Water samples collected from five sites of Lake Okeechobee (LO) frequently exposed to toxic Microcystis blooms were used as inoculum for enrichment with microcystin LR (MC-LR) supplied as sole C and N source. After 20 days incubation, MC levels were analyzed using high performance liquid chromatography (HPLC). A bacterial consortium consisting of two isolates DC7 and DC8 from the Indian Prairie Canal sample showed over 74% toxin degradation at the end of day 20. Optimal temperature requirement for biodegradation was identified and phosphorus levels did not affect the MC biodegradation. Based on 16S rRNA sequence similarity the isolate DC8 was found to have a match with Microbacterium sp. and the DC7 isolate with Rhizobium gallicum (AY972457). PMID:21611743

Patterns in DOC Concentration and Composition in Tundra Watersheds in the Kolyma River Basin

NASA Astrophysics Data System (ADS)

Behnke, M. I.; Schade, J. D.; Fiske, G. J.; Whittinghill, K. A.; Zimov, N.

2014-12-01

Much of the world's soil carbon is frozen in permafrost in the Arctic. As the climate warms and permafrost thaws, this carbon will again be actively cycled. Whether it is exported to the ocean or released as greenhouse gases to the atmosphere depends on the form of carbon compounds and conditions encountered during transport, and will determine the strength of permafrost thaw as a feedback on climate change. To better understand the fate of this carbon, we determined how and where in the landscape dissolved organic carbon (DOC) breaks down as water transports it from tundra to ocean. We compared DOC concentration and composition along flowpaths within watersheds and at the mouths of watersheds differing in drainage area. We incubated filtered water samples in light and dark, including filter-sterilized samples, to assess the interactions between light and microbial processing as mechanisms of DOC loss. Composition was assessed using optical measurements associated with the structure of organic compounds. DOC concentration declined along flowpaths within watersheds, with most loss occurring in aquatic environments high in the landscape. We also found a negative correlation between watershed size and DOC concentration. These results suggest that much of the processing of organic carbon occurs in small streams. In addition, the relationship with drainage area suggests that residence time in streams has a large impact on transformation of terrestrial carbon during transport. We found no substantial differences in optical characteristics of DOC, indicating that breakdown processes were not selective, and that light caused much of the breakdown. This conclusion is supported by the incubation experiment, which showed greater breakdown by light, and evidence that light stimulated higher rates of microbial processing. These results highlight the importance of inland aquatic ecosystems as processors of organic matter, and suggest that organic carbon from permafrost thaw is likely to be processed high in the landscape rather than transported to the ocean. Furthermore, the importance of light-induced breakdown as a mechanism for carbon loss suggests that the timing of DOC transport relative to seasonal changes in light intensity may influence the impact of permafrost thaw on climate change.

A simple technique for trapping Siren lacertina, Amphiuma means, and other aquatic vertebrates

USGS Publications Warehouse

Johnson, S.A.; Barichivich, W.J.

2004-01-01

We describe a commercially-available funnel trap for sampling aquatic vertebrates. The traps can be used in heavily vegetated wetlands and can be set in water up to 60 cm deep without concern for drowning the animals. They were especially useful for capturing the aquatic salamanders Siren lacertina and Amphiuma means, which have been difficult to capture with traditional sampling methods. They also were effective for sampling small fishes, particularly centrarchids, and larval anurans. In total, 14 species of amphibians, nine species of aquatic reptiles, and at least 32 fish species were captured. The trap we describe differs significantly from traditional funnel traps (e.g., minnow traps) and holds great promise for studies of small, aquatic vertebrates, in particular Siren and Amphiuma species.

Carbon Inputs From Riparian Vegetation Limit Oxidation of Physically Bound Organic Carbon Via Biochemical and Thermodynamic Processes: OC Oxidation Processes Across Vegetation

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

Graham, Emily B.; Tfaily, Malak M.; Crump, Alex R.

In light of increasing terrestrial carbon (C) transport across aquatic boundaries, the mechanisms governing organic carbon (OC) oxidation along terrestrial-aquatic interfaces are crucial to future climate predictions. Here, we investigate biochemistry, metabolic pathways, and thermodynamics corresponding to OC oxidation in the Columbia River corridor. We leverage natural vegetative differences to encompass variation in terrestrial C inputs. Our results suggest that decreases in terrestrial C deposition associated with diminished riparian vegetation induce oxidation of physically-bound (i.e., mineral and microbial) OC at terrestrial-aquatic interfaces. We also find that contrasting metabolic pathways oxidize OC in the presence and absence of vegetation and—in directmore » conflict with the concept of ‘priming’—that inputs of water-soluble and thermodynamically-favorable terrestrial OC protects bound-OC from oxidation. Based on our results, we propose a mechanistic conceptualization of OC oxidation along terrestrial-aquatic interfaces that can be used to model heterogeneous patterns of OC loss under changing land cover distributions.« less

Biodegradability and ecotoxicitiy of tramadol, ranitidine, and their photoderivatives in the aquatic environment.

PubMed

Bergheim, Marlies; Gieré, Reto; Kümmerer, Klaus

2012-01-01

This study was designed to assess the fate and the overall potential impacts of the widely prescribed drugs ranitidine and tramadol after their introduction into the aquatic environment. The probability to detect these two drugs in the aquatic environment was studied by analyzing their abiotic and biotic degradation properties. For this purpose, samples were irradiated with different light sources, and three widely used biodegradability tests from the OECD series, the closed bottle test (OECD 301 D), the manometric respirometry test (OECD 301 F) and the Zahn-Wellens test (OECD 302 B), were conducted. The ecotoxicity of the photolytically formed transformation products was assessed by performing the bacterial growth inhibition test (EN ISO 10712). Furthermore, quantitative structure-activity relationship analysis and a risk analysis based on the calculation of the predicted environmental concentrations have also been conducted to assess the environmental risk potential of the transformation products. The possible formation of stable products by microbial or photolytical transformation has been investigated with DOC and LC-MS analytics. In the present study, neither ranitidine, nor tramadol, nor their photoderivatives were found to be readily or inherently biodegradable according to test guidelines. The photolytic transformation was faster under a UV lamp compared to the reaction under an Xe lamp with a spectrum that mimics sunlight. No chronic toxicity against bacteria was found for ranitidine or its photolytic decomposition products, but a low toxicity was detected for the resulting mixture of the photolytic transformation products of tramadol. The study demonstrates that transformation products may have a higher environmental risk potential than the respective parent compounds.

Short-term degradation of terrestrial DOM in the coastal ocean: Implications for nutrient subsidies and marine microbial community structure

NASA Astrophysics Data System (ADS)

Oliver, A. A.; Tank, S. E.; Kellogg, C.

2015-12-01

The export of riverine dissolved organic matter (DOM) to the coastal ocean provides an important link between terrestrial and aquatic ecosystems. The coastal temperate rainforests of British Columbia contain extensive freshwater networks that export significant amounts of water and DOM to the ocean, representing significant cross-system hydrologic and biogeochemical linkages. To better understand the importance of these linkages and implications for ecosystem structure and function, we used an experimental approach to investigate the role of microbial and photodegradation transformations of DOM exported from small coastal catchments to the marine environment. At two time periods (August 2014, March 2015), stream water from the outlets of two coastal watersheds was filtered (<0.2 μm), and treated with microbial inoculums from across a salinity gradient (i.e., freshwater, estuarine, and marine). Treatments were incubated in the ocean under light and dark conditions for 8 days. At 0, 3 and 8 days, samples were analyzed for DOC, TDN, DIN, and DON. Changes in DOM composition were determined with optical characterization techniques such as absorbance (SUVA, S, Sr) and fluorescence (EEM). Microbial community response was measured using cell counts and DNA/RNA amplicon sequencing to determine changes in bacterial abundance and community composition. General patterns indicated that microbial communities from the high salinity treatment (i.e. most marine) were the most effective at utilizing freshwater DOM, especially under light conditions. In some treatments, DOM appeared as a potential source of inorganic nitrogen with corresponding shifts in microbial community composition. Incubations using inoculum from low and mid salinity levels demonstrated smaller changes, indicating that DOM exported from these streams may not be extensively utilized until exposed to higher salinity environments further from stream outlets. These results suggest a role for terrestrial sourced-DOM as a subsidy for microbial communities within the near shore marine environment, and emphasize that changes in DOM exports due to land development or climate change may have implications for coastal food web processes and biogeochemical cycling.

Comparative Metagenomics of Toxic Freshwater Cyanobacteria Bloom Communities on Two Continents

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

Steffen, Morgan M; Li, Zhou; Effler, Chad

2012-01-01

Toxic cyanobacterial blooms have persisted in freshwater systems around the world for centuries and appear to be globally increasing in frequency and severity. Toxins produced by bloom-associated cyanobacteria can have drastic impacts on the ecosystem and surrounding communities, and bloom biomass can disrupt aquatic food webs and act as a driver for hypoxia. Little is currently known regarding the genomic content of the Microcystis strains that form blooms or the companion heterotrophic community associated with bloom events. To address these issues, we examined the bloomassociated microbial communities in single samples from Lake Erie (North America), Lake Tai (Taihu, China), andmore » Grand Lakes St. Marys (OH, USA) using comparative metagenomics. Together the Cyanobacteria and Proteobacteria comprised .90% of each bloom bacterial community sample, although the dominant phylum varied between systems. Relative to the existing Microcystis aeruginosa NIES 843 genome, sequences from Lake Erie and Taihu revealed a number of metagenomic islands that were absent in the environmental samples. Moreover, despite variation in the phylogenetic assignments of bloomassociated organisms, the functional potential of bloom members remained relatively constant between systems. This pattern was particularly noticeable in the genomic contribution of nitrogen assimilation genes. In Taihu, the genetic elements associated with the assimilation and metabolism of nitrogen were predominantly associated with Proteobacteria, while these functions in the North American lakes were primarily contributed to by the Cyanobacteria. Our observations build on an emerging body of metagenomic surveys describing the functional potential of microbial communities as more highly conserved than that of their phylogenetic makeup within natural systems.« less

Physicochemical Characteristics of Larval Habitat Waters of Mosquitoes (Diptera: Culicidae) in Qom Province, Central Iran

PubMed Central

Abai, Mohammad Reza; Saghafipour, Abedin; Ladonni, Hossein; Jesri, Nahid; Omidi, Saeed; Azari-Hamidian, Shahyad

2016-01-01

Background: Mosquitoes lay eggs in a wide range of habitats with different physicochemical parameters. Ecological data, including physicochemical factors of oviposition sites, play an important role in integrated vector management. Those data help the managers to make the best decision in controlling the aquatic stages of vectors especially using source reduction. Methods: To study some physicochemical characteristics of larval habitat waters, an investigation was carried out in Qom Province, central Iran, during spring and summer 2008 and 2009. Water samples were collected during larval collection from ten localities. The chemical parameters of water samples were analyzed based on mg/l using standard methods. Water temperature (°C), turbidity (NTU), total dissolved solids (ppm), electrical conductivity (μS/cm), and acidity (pH) were measured using digital testers. Thermotolerant coliforms of water samples were analyzed based on MPN/100ml. Data were assessed by Kruskal-Wallis test and Spearman Correlation analysis. Results: In total, 371 mosquito larvae were collected including 14 species representing four genera. Some physicochemical parameters of water in Emamzadeh Esmail, Qomrood, Qom City, and Rahjerd showed significant differences among localities (P< 0.05). The physicochemical and microbial parameters did not show any significant differences among different species (P> 0.05). There was no significant correlation between the abundance of larvae and the different physicochemical and microbial parameters (P> 0.05). Conclusion: The means of EC, TDS, and phosphate of localities and species were remarkably higher than those of the previous studies. Other parameters seem to be in the range of other investigations. PMID:27047973

Physicochemical Characteristics of Larval Habitat Waters of Mosquitoes (Diptera: Culicidae) in Qom Province, Central Iran.

PubMed

Abai, Mohammad Reza; Saghafipour, Abedin; Ladonni, Hossein; Jesri, Nahid; Omidi, Saeed; Azari-Hamidian, Shahyad

2016-03-01

Mosquitoes lay eggs in a wide range of habitats with different physicochemical parameters. Ecological data, including physicochemical factors of oviposition sites, play an important role in integrated vector management. Those data help the managers to make the best decision in controlling the aquatic stages of vectors especially using source reduction. To study some physicochemical characteristics of larval habitat waters, an investigation was carried out in Qom Province, central Iran, during spring and summer 2008 and 2009. Water samples were collected during larval collection from ten localities. The chemical parameters of water samples were analyzed based on mg/l using standard methods. Water temperature (°C), turbidity (NTU), total dissolved solids (ppm), electrical conductivity (μS/cm), and acidity (pH) were measured using digital testers. Thermotolerant coliforms of water samples were analyzed based on MPN/100ml. Data were assessed by Kruskal-Wallis test and Spearman Correlation analysis. In total, 371 mosquito larvae were collected including 14 species representing four genera. Some physicochemical parameters of water in Emamzadeh Esmail, Qomrood, Qom City, and Rahjerd showed significant differences among localities (P< 0.05). The physicochemical and microbial parameters did not show any significant differences among different species (P> 0.05). There was no significant correlation between the abundance of larvae and the different physicochemical and microbial parameters (P> 0.05). The means of EC, TDS, and phosphate of localities and species were remarkably higher than those of the previous studies. Other parameters seem to be in the range of other investigations.

Effects of chronic γ-irradiation on the aquatic microbial microcosm: equi-dosimetric comparison with effects of heavy metals.

PubMed

Fuma, Shoichi; Kawaguchi, Isao; Kubota, Yoshihisa; Yoshida, Satoshi; Kawabata, Zen'ichiro; Polikarpov, Gennady G

2012-02-01

Effects of chronic γ-irradiation were investigated in the aquatic microcosm consisting of flagellate algae Euglena gracilis as producers, ciliate protozoa Tetrahymena thermophila as consumers and bacteria Escherichia coli as decomposers. At 1.1 Gy day(-1), no effects were observed. At 5.1 Gy day(-1), cell densities of E. coli showed a tendency to be lower than those of controls. At 9.7 and 24.7 Gy day(-1), population decrease was observed in E. coli. E. gracilis and T. thermophila died out after temporal population decrease and subsequent population increase in T. thermophila. It is likely that this temporal population increase was an indirect effect due to interspecies interactions. Effect dose rates of γ-rays were compared with effect concentrations of some metals using the radiochemoecological conceptual model and the effect index for microcosm. Comparison of these community-level effects data with environmental exposure data suggests that ionising radiation, gadolinium and dysprosium have low risks to affect aquatic microbial communities while manganese, nickel and copper have considerable risks. Effects of chronic irradiation were smaller than those of acute irradiation, and an acute to chronic ratio was calculated to be 28 by dividing an acute dose by chronic daily dose rate at which the effect index was 10%. This ratio would be useful for community-level extrapolation from acute to chronic radiation effects. Copyright © 2011 Elsevier Ltd. All rights reserved.

Metagenomic Frameworks for Monitoring Antibiotic Resistance in Aquatic Environments

PubMed Central

Port, Jesse A.; Cullen, Alison C.; Wallace, James C.; Smith, Marissa N.

2013-01-01

Background: High-throughput genomic technologies offer new approaches for environmental health monitoring, including metagenomic surveillance of antibiotic resistance determinants (ARDs). Although natural environments serve as reservoirs for antibiotic resistance genes that can be transferred to pathogenic and human commensal bacteria, monitoring of these determinants has been infrequent and incomplete. Furthermore, surveillance efforts have not been integrated into public health decision making. Objectives: We used a metagenomic epidemiology–based approach to develop an ARD index that quantifies antibiotic resistance potential, and we analyzed this index for common modal patterns across environmental samples. We also explored how metagenomic data such as this index could be conceptually framed within an early risk management context. Methods: We analyzed 25 published data sets from shotgun pyrosequencing projects. The samples consisted of microbial community DNA collected from marine and freshwater environments across a gradient of human impact. We used principal component analysis to identify index patterns across samples. Results: We observed significant differences in the overall index and index subcategory levels when comparing ecosystems more proximal versus distal to human impact. The selection of different sequence similarity thresholds strongly influenced the index measurements. Unique index subcategory modes distinguished the different metagenomes. Conclusions: Broad-scale screening of ARD potential using this index revealed utility for framing environmental health monitoring and surveillance. This approach holds promise as a screening tool for establishing baseline ARD levels that can be used to inform and prioritize decision making regarding management of ARD sources and human exposure routes. Citation: Port JA, Cullen AC, Wallace JC, Smith MN, Faustman EM. 2014. Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments. Environ Health Perspect 122:222–228; http://dx.doi.org/10.1289/ehp.1307009 PMID:24334622

Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments.

PubMed

Port, Jesse A; Cullen, Alison C; Wallace, James C; Smith, Marissa N; Faustman, Elaine M

2014-03-01

High-throughput genomic technologies offer new approaches for environmental health monitoring, including metagenomic surveillance of antibiotic resistance determinants (ARDs). Although natural environments serve as reservoirs for antibiotic resistance genes that can be transferred to pathogenic and human commensal bacteria, monitoring of these determinants has been infrequent and incomplete. Furthermore, surveillance efforts have not been integrated into public health decision making. We used a metagenomic epidemiology-based approach to develop an ARD index that quantifies antibiotic resistance potential, and we analyzed this index for common modal patterns across environmental samples. We also explored how metagenomic data such as this index could be conceptually framed within an early risk management context. We analyzed 25 published data sets from shotgun pyrosequencing projects. The samples consisted of microbial community DNA collected from marine and freshwater environments across a gradient of human impact. We used principal component analysis to identify index patterns across samples. We observed significant differences in the overall index and index subcategory levels when comparing ecosystems more proximal versus distal to human impact. The selection of different sequence similarity thresholds strongly influenced the index measurements. Unique index subcategory modes distinguished the different metagenomes. Broad-scale screening of ARD potential using this index revealed utility for framing environmental health monitoring and surveillance. This approach holds promise as a screening tool for establishing baseline ARD levels that can be used to inform and prioritize decision making regarding management of ARD sources and human exposure routes. Port JA, Cullen AC, Wallace JC, Smith MN, Faustman EM. 2014. Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments. Environ Health Perspect 122:222–228; http://dx.doi.org/10.1289/ehp.1307009

Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans.

PubMed

Shen, Tong; Xu, Shixia; Wang, Xiaohong; Yu, Wenhua; Zhou, Kaiya; Yang, Guang

2012-03-24

Cetaceans (whales, dolphins and porpoises) are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs), which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (ω) values along most (30 out of 33) examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS), and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo) and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans) habitat, and the other to the rapid diversification and radiation of oceanic dolphins. This is the first study thus far to characterize the TLR gene in cetaceans. Our data present evidences that cetacean TLR4 has undergone adaptive evolution against the background of purifying selection in response to the secondary aquatic adaptation and rapid diversification in the sea. It is suggested that microbial pathogens in different environments are important factors that promote adaptive changes at cetacean TLR4 and new functions of some amino acid sites specialized for recognizing pathogens in dramatically contrasted environments to enhance the fitness for the adaptation and survival of cetaceans.

Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans

PubMed Central

2012-01-01

Background Cetaceans (whales, dolphins and porpoises) are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs), which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. Results We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (ω) values along most (30 out of 33) examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS), and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo) and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans) habitat, and the other to the rapid diversification and radiation of oceanic dolphins. Conclusions This is the first study thus far to characterize the TLR gene in cetaceans. Our data present evidences that cetacean TLR4 has undergone adaptive evolution against the background of purifying selection in response to the secondary aquatic adaptation and rapid diversification in the sea. It is suggested that microbial pathogens in different environments are important factors that promote adaptive changes at cetacean TLR4 and new functions of some amino acid sites specialized for recognizing pathogens in dramatically contrasted environments to enhance the fitness for the adaptation and survival of cetaceans. PMID:22443485

Surface-water-quality assessment of the Yakima River basin in Washington: major-and minor-element data for sediment, water, and aquatic biota, 1987-91

USGS Publications Warehouse

Fuhrer, Gregory J.; Fluter, Shelley L.; McKenzie, Stuart W.; Rinella, Joseph F.; Crawford, J. Kent; Cain, Daniel J.; Hornberger, Michelle I.; Bridges, Jennifer L.; Skach, Kenneth A.

1994-01-01

Streambed-sediment samples were collected once from 27 sites in the basin during 1987-91. Suspended-sediment and filtered-water samples were collected monthly and during hydrologic events (including snowmelt and winter rainstorms) at seven sites, and filtered-water samples were collected at least once at an additional 37 sites during synoptic samplings. Unfiltered-water samples were collected at seven sites on a quarterly basis during 1987 only. Samples of aquatic plants were collected once in 1989, and aquatic insects, fish, and clams were collected from 34 sites three times during 1989-90.

Metagenomic profiling for assessing microbial diversity and microbial adaptation to degradation of hydrocarbons in two South African petroleum-contaminated water aquifers.

PubMed

Kachienga, Leonard; Jitendra, Keshri; Momba, Maggy

2018-05-15

Biodegradation of hydrocarbons by indigenous populations of microorganisms found in petroleum-contaminated water sources represents one of the primary mechanisms by which petroleum and other hydrocarbon pollutants are eliminated from the aquatic environment. The identification of these microorganisms, which have capabilities to convert the majority of toxic hydrocarbons into compounds that are less harmful for end-users, is therefore crucial for bioremediation purposes. The aim of this study was to profile the microbial diversity of two South African petroleum-contaminated water aquifer sites and to determine the microbial adaptation to hydrocarbon degradation using a metagenomics approach. The sequenced samples revealed that protozoa (62.04%) were found to be the most dominant group, followed by fungi (24.49%), unknown (12.87%), and finally other sequences such as Animalia and plantae which were <(0.10%) domains in the first oil-polluted aquifer site. In the second site, protozoa (61.90%), unknown (16.51%), fungi (11.41%) in that order. According to the classification at the genus level, the dominant group was Naegleria (15.21%), followed by Vorticella (6.67%) as the only ciliated protozoan genus, other species such as Arabidopsis (2.97%), Asarum (1.84%) Populus (1.04%) were significantly low and drastically lower in the first site. Regarding the second site, the dominant group was Naegleria (18.29%) followed by Colpoda (9.86%) with the remainder of the genera representing <2%. Overall results demonstrated the ability of various groups of microorganisms to adapt and survive in petroleum oil-polluted water sites regardless of their respective distributions and this can be explored further for their role in bioremediation and environmental management.

Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes

USGS Publications Warehouse

Chun, Chan Lan; Peller, Julie R.; Shively, Dawn; Byappanahalli, Muruleedhara N.; Whitman, Richard L.; Staley, Christopher; Zhang, Qian; Ishii, Satoshi; Sadowsky, Michael J.

2017-01-01

Cladophora mats that accumulate and decompose along shorelines of the Great Lakes create potential threats to the health of humans and wildlife. The decaying algae create a low oxygen and redox potential environment favoring growth and persistence of anaerobic microbial populations, including Clostridium botulinum, the causal agent of botulism in humans, birds, and other wildlife. In addition to the diverse population of microbes, a dynamic chemical environment is generated, which involves production of numerous organic and inorganic substances, many of which are believed to be toxic to the sand and aquatic biotic communities. In this study, we used 16S-rDNA-based-amplicon sequencing and microfluidic-based quantitative PCR approaches to characterize the bacterial community structure and the abundances of human pathogens associated with Cladophora at different stages (up to 90 days) of algal decay in laboratory microcosms. Oxygen levels were largely depleted after a few hours of incubation. As Cladophora decayed, the algal microbial biodiversity decreased within 24 h, and the mat transitioned from an aerobic to anaerobic environment. There were increasing abundances of enteric and pathogenic bacteria during decomposition of Cladophora, including Acinetobacter, Enterobacter, Kluyvera, Cedecea, and others. In contrast, there were no or very few sequences (< 0.07%) assigned to such groups in fresh Cladophora samples. Principal coordinate analysis indicated that the bacterial community structure was dynamic and changed significantly with decay time. Knowledge of microbial communities and chemical composition of decaying algal mats is critical to our further understanding of the role that Cladophora plays in a beach ecosystem's structure and function, including the algal role in trophic interactions. Based on these findings, public and environmental health concerns should be considered when decaying Cladophora mats accumulate Great Lakes shorelines.

Urban microbial ecology of a freshwater estuary of Lake Michigan.

PubMed

Fisher, Jenny C; Newton, Ryan J; Dila, Deborah K; McLellan, Sandra L

Freshwater estuaries throughout the Great Lakes region receive stormwater runoff and riverine inputs from heavily urbanized population centers. While human and animal feces contained in this runoff are often the focus of source tracking investigations, non-fecal bacterial loads from soil, aerosols, urban infrastructure, and other sources are also transported to estuaries and lakes. We quantified and characterized this non-fecal urban microbial component using bacterial 16S rRNA gene sequences from sewage, stormwater, rivers, harbor/estuary, and the lake surrounding Milwaukee, WI, USA. Bacterial communities from each of these environments had a distinctive composition, but some community members were shared among environments. We used a statistical biomarker discovery tool to identify the components of the microbial community that were most strongly associated with stormwater and sewage to describe an "urban microbial signature," and measured the presence and relative abundance of these organisms in the rivers, estuary, and lake. This urban signature increased in magnitude in the estuary and harbor with increasing rainfall levels, and was more apparent in lake samples with closest proximity to the Milwaukee estuary. The dominant bacterial taxa in the urban signature were Acinetobacter, Aeromonas , and Pseudomonas , which are organisms associated with pipe infrastructure and soil and not typically found in pelagic freshwater environments. These taxa were highly abundant in stormwater and sewage, but sewage also contained a high abundance of Arcobacter and Trichococcus that appeared in lower abundance in stormwater outfalls and in trace amounts in aquatic environments. Urban signature organisms comprised 1.7% of estuary and harbor communities under baseflow conditions, 3.5% after rain, and >10% after a combined sewer overflow. With predicted increases in urbanization across the Great Lakes, further alteration of freshwater communities is likely to occur with potential long term impacts on the function of estuarine and nearshore ecosystems.

Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes.

PubMed

Chun, Chan Lan; Peller, Julie R; Shively, Dawn; Byappanahalli, Muruleedhara N; Whitman, Richard L; Staley, Christopher; Zhang, Qian; Ishii, Satoshi; Sadowsky, Michael J

2017-01-01

Cladophora mats that accumulate and decompose along shorelines of the Great Lakes create potential threats to the health of humans and wildlife. The decaying algae create a low oxygen and redox potential environment favoring growth and persistence of anaerobic microbial populations, including Clostridium botulinum, the causal agent of botulism in humans, birds, and other wildlife. In addition to the diverse population of microbes, a dynamic chemical environment is generated, which involves production of numerous organic and inorganic substances, many of which are believed to be toxic to the sand and aquatic biotic communities. In this study, we used 16S-rDNA-based-amplicon sequencing and microfluidic-based quantitative PCR approaches to characterize the bacterial community structure and the abundances of human pathogens associated with Cladophora at different stages (up to 90days) of algal decay in laboratory microcosms. Oxygen levels were largely depleted after a few hours of incubation. As Cladophora decayed, the algal microbial biodiversity decreased within 24h, and the mat transitioned from an aerobic to anaerobic environment. There were increasing abundances of enteric and pathogenic bacteria during decomposition of Cladophora, including Acinetobacter, Enterobacter, Kluyvera, Cedecea, and others. In contrast, there were no or very few sequences (<0.07%) assigned to such groups in fresh Cladophora samples. Principal coordinate analysis indicated that the bacterial community structure was dynamic and changed significantly with decay time. Knowledge of microbial communities and chemical composition of decaying algal mats is critical to our further understanding of the role that Cladophora plays in a beach ecosystem's structure and function, including the algal role in trophic interactions. Based on these findings, public and environmental health concerns should be considered when decaying Cladophora mats accumulate Great Lakes shorelines. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbial communities mediating algal detritus turnover under anaerobic conditions

PubMed Central

Morrison, Jessica M.; Murphy, Chelsea L.; Baker, Kristina; Zamor, Richard M.; Nikolai, Steve J.; Wilder, Shawn; Elshahed, Mostafa S.

2017-01-01

Background Algae encompass a wide array of photosynthetic organisms that are ubiquitously distributed in aquatic and terrestrial habitats. Algal species often bloom in aquatic ecosystems, providing a significant autochthonous carbon input to the deeper anoxic layers in stratified water bodies. In addition, various algal species have been touted as promising candidates for anaerobic biogas production from biomass. Surprisingly, in spite of its ecological and economic relevance, the microbial community involved in algal detritus turnover under anaerobic conditions remains largely unexplored. Results Here, we characterized the microbial communities mediating the degradation of Chlorella vulgaris (Chlorophyta), Chara sp. strain IWP1 (Charophyceae), and kelp Ascophyllum nodosum (phylum Phaeophyceae), using sediments from an anaerobic spring (Zodlteone spring, OK; ZDT), sludge from a secondary digester in a local wastewater treatment plant (Stillwater, OK; WWT), and deeper anoxic layers from a seasonally stratified lake (Grand Lake O’ the Cherokees, OK; GL) as inoculum sources. Within all enrichments, the majority of algal biomass was metabolized within 13–16 weeks, and the process was accompanied by an increase in cell numbers and a decrease in community diversity. Community surveys based on the V4 region of the 16S rRNA gene identified different lineages belonging to the phyla Bacteroidetes, Proteobacteria (alpha, delta, gamma, and epsilon classes), Spirochaetes, and Firmicutes that were selectively abundant under various substrate and inoculum conditions. Within all kelp enrichments, the microbial communities structures at the conclusion of the experiment were highly similar regardless of the enrichment source, and were dominated by the genus Clostridium, or family Veillonellaceae within the Firmicutes. In all other enrichments the final microbial community was dependent on the inoculum source, rather than the type of algae utilized as substrate. Lineages enriched included the uncultured groups VadinBC27 and WCHB1-69 within the Bacteroidetes, genus Spirochaeta and the uncultured group SHA-4 within Spirochaetes, Ruminococcaceae, Lachnospiraceae, Yongiibacter, Geosporobacter, and Acidaminobacter within the Firmicutes, and genera Kluyvera, Pantoea, Edwardsiella and Aeromonas, and Buttiauxella within the Gamma-Proteobaceteria order Enterobacteriales. Conclusions Our results represent the first systematic survey of microbial communities mediating turnover of algal biomass under anaerobic conditions, and highlights the diversity of lineages putatively involved in the degradation process. PMID:28097050

Ecology of coliphages in southern California coastal waters.

PubMed

Reyes, V C; Jiang, S C

2010-08-01

This study aims to investigate the ecology of coliphages, an important microbial pollution indicator. Specifically, our experiments address (i) the ability of environmental Escherichia coli (E. coli) to serve as hosts for coliphage replication, and (ii) the temporal and spatial distribution of coliphages in coastal waters. Water samples from three locations in California's Newport Bay watershed were tested for the presence of coliphages every 2 weeks for an entire year. A total of nine E. coli strains isolated from various sources served as hosts for coliphage detection. Coliphage occurrence was significantly different between freshwater, estuarine and coastal locations and correlated with water temperature, salinity and rainfall in the watershed. The coliphages isolated on the environmental hosts had a broad host-range relative to the coliphages isolated on an E. coli strain from sewage and a US EPA recommended strain for coliphage detection. Coliphage occurrence was related to the temperature, rainfall and salinity within the bay. The adaptation to a broad host-range may enable the proliferation of coliphages in the aquatic environment. Understanding the seasonal variation of phages is useful for establishing a background level of coliphage presence in coastal waters. The broad host-range of coliphages isolated on the environmental E. coli host calls for investigation of coliphage replication in the aquatic environment.

Low-to-moderate nitrogen and phosphorus concentrations accelerate microbially driven litter breakdown rates

Treesearch

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

2015-01-01

Particulate organic matter (POM) processing is an important driver of aquatic ecosystem productivity that is sensitive to nutrient enrichment and drives ecosystem carbon (C) loss. Although studies of single concentrations of nitrogen (N) or phosphorus (P) have shown effects at relatively low concentrations, responses of litter breakdown rates along gradients of low-to-...

The seen and unseen world of the fallen tree.

Treesearch

Chris Maser; James M. Trappe

1984-01-01

Large, fallen trees in various stages of decay contribute much-needed diversity to terrestrial and aquatic habitats in western forests. When most biological activity in soil is limited by low moisture availability in summer, the fallen tree-soil interface offers a relatively cool, moist habitat for animals and a substrate for microbial and root activity. Intensified...

40 CFR 158.2150 - Microbial pesticides nontarget organisms and environmental fate data requirements table.

Code of Federal Regulations, 2013 CFR

2013-07-01

.../pathogenicity study is the upland game. There is also the option to test the passerine if there is a concern... product. Notes that apply to an individual test including specific conditions, qualifications, or exceptions to the designated test are listed in paragraph (e) of this section. (b) Use patterns. Aquatic uses...

40 CFR 158.2150 - Microbial pesticides nontarget organisms and environmental fate data requirements table.

Code of Federal Regulations, 2012 CFR

2012-07-01

.../pathogenicity study is the upland game. There is also the option to test the passerine if there is a concern... product. Notes that apply to an individual test including specific conditions, qualifications, or exceptions to the designated test are listed in paragraph (e) of this section. (b) Use patterns. Aquatic uses...

40 CFR 158.2150 - Microbial pesticides nontarget organisms and environmental fate data requirements table.

Code of Federal Regulations, 2011 CFR

2011-07-01

.../pathogenicity study is the upland game. There is also the option to test the passerine if there is a concern... product. Notes that apply to an individual test including specific conditions, qualifications, or exceptions to the designated test are listed in paragraph (e) of this section. (b) Use patterns. Aquatic uses...

40 CFR 158.2150 - Microbial pesticides nontarget organisms and environmental fate data requirements table.

Code of Federal Regulations, 2010 CFR

2010-07-01

.../pathogenicity study is the upland game. There is also the option to test the passerine if there is a concern... product. Notes that apply to an individual test including specific conditions, qualifications, or exceptions to the designated test are listed in paragraph (e) of this section. (b) Use patterns. Aquatic uses...

Microbial Contamination Detection in Water Resources: Interest of Current Optical Methods, Trends and Needs in the Context of Climate Change

PubMed Central

Jung, Aude-Valérie; Le Cann, Pierre; Roig, Benoit; Thomas, Olivier; Baurès, Estelle; Thomas, Marie-Florence

2014-01-01

Microbial pollution in aquatic environments is one of the crucial issues with regard to the sanitary state of water bodies used for drinking water supply, recreational activities and harvesting seafood due to a potential contamination by pathogenic bacteria, protozoa or viruses. To address this risk, microbial contamination monitoring is usually assessed by turbidity measurements performed at drinking water plants. Some recent studies have shown significant correlations of microbial contamination with the risk of endemic gastroenteresis. However the relevance of turbidimetry may be limited since the presence of colloids in water creates interferences with the nephelometric response. Thus there is a need for a more relevant, simple and fast indicator for microbial contamination detection in water, especially in the perspective of climate change with the increase of heavy rainfall events. This review focuses on the one hand on sources, fate and behavior of microorganisms in water and factors influencing pathogens’ presence, transportation and mobilization, and on the second hand, on the existing optical methods used for monitoring microbiological risks. Finally, this paper proposes new ways of research. PMID:24747537

Hadal biosphere: insight into the microbial ecosystem in the deepest ocean on Earth.

PubMed

Nunoura, Takuro; Takaki, Yoshihiro; Hirai, Miho; Shimamura, Shigeru; Makabe, Akiko; Koide, Osamu; Kikuchi, Tohru; Miyazaki, Junichi; Koba, Keisuke; Yoshida, Naohiro; Sunamura, Michinari; Takai, Ken

2015-03-17

Hadal oceans at water depths below 6,000 m are the least-explored aquatic biosphere. The Challenger Deep, located in the western equatorial Pacific, with a water depth of ∼11 km, is the deepest ocean on Earth. Microbial communities associated with waters from the sea surface to the trench bottom (0∼10,257 m) in the Challenger Deep were analyzed, and unprecedented trench microbial communities were identified in the hadal waters (6,000∼10,257 m) that were distinct from the abyssal microbial communities. The potentially chemolithotrophic populations were less abundant in the hadal water than those in the upper abyssal waters. The emerging members of chemolithotrophic nitrifiers in the hadal water that likely adapt to the higher flux of electron donors were also different from those in the abyssal waters that adapt to the lower flux of electron donors. Species-level niche separation in most of the dominant taxa was also found between the hadal and abyssal microbial communities. Considering the geomorphology and the isolated hydrotopographical nature of the Mariana Trench, we hypothesized that the distinct hadal microbial ecosystem was driven by the endogenous recycling of organic matter in the hadal waters associated with the trench geomorphology.

Measuring and modeling C flux rates through the central metabolic pathways in microbial communities using position-specific 13C-labeled tracers

NASA Astrophysics Data System (ADS)

Dijkstra, P.; van Groenigen, K.; Hagerty, S.; Salpas, E.; Fairbanks, D. E.; Hungate, B. A.; KOCH, G. W.; Schwartz, E.

2012-12-01

The production of energy and metabolic precursors occurs in well-known processes such as glycolysis and Krebs cycle. We use position-specific 13C-labeled metabolic tracers, combined with models of microbial metabolic organization, to analyze the response of microbial community energy production, biosynthesis, and C use efficiency (CUE) in soils, decomposing litter, and aquatic communities. The method consists of adding position-specific 13C -labeled metabolic tracers to parallel soil incubations, in this case 1-13C and 2,3-13C pyruvate and 1-13C and U-13C glucose. The measurement of CO2 released from the labeled tracers is used to calculate the C flux rates through the various metabolic pathways. A simplified metabolic model consisting of 23 reactions is solved using results of the metabolic tracer experiments and assumptions of microbial precursor demand. This new method enables direct estimation of fundamental aspects of microbial energy production, CUE, and soil organic matter formation in relatively undisturbed microbial communities. We will present results showing the range of metabolic patterns observed in these communities and discuss results from testing metabolic models.

Eco-Friendly Extraction of Biopolymer Chitin and Carotenoids from Shrimp Waste

NASA Astrophysics Data System (ADS)

Prameela, K.; Venkatesh, K.; Divya vani, K.; Sudesh Kumar, E.; Mohan, CH Murali

2017-08-01

Astaxanthin a nutraceutical and chitin a natural biopolymer present in shrimp waste. In current chemical extraction methods HCl and NaOH are used for extraction and these chemicals are introduced into aquatic ecosystems are spoiling aquatic flora and fauna, pollute the environment and destroy astaxanthin. Lactobacillus species were isolated from gut of Solenocera melantho and characterized phenotypically and genotypically. Initial screening experiments have shown to be an effective and identified as Lactobacillus plantaram based on morphological, biochemical characteristics and molecular analysis. Efficiency of fermentation has shown with good yield of astaxanthin and recovery of chitin. Hence this alternative microbial process is having advantage than existing hazardous, non-economical chemical process.

Potential of Phragmites australis for the removal of veterinary pharmaceuticals from aquatic media.

PubMed

Carvalho, Pedro N; Basto, M Clara P; Almeida, C Marisa R

2012-07-01

The potential of Phragmites australis was evaluated for the removal of three veterinary drugs, enrofloxacin (ENR), ceftiofur (CEF) and tetracycline (TET), from aquatic mediums. Results showed that the plant promoted the removal of 94% and 75% of ENR and TET, respectively, from wastewater. Microbial abundance estimation revealed that microorganisms were not a major participant. Occurrence of drugs adsorption to plant roots was observed in small extension. Therefore, main mechanisms occurring were drug removal by plant uptake and/or degradation. Present results demonstrated the potential of P. australis-planted beds to be used for removal of pharmaceuticals from livestock and slaughterhouse industries wastewater. Copyright © 2012 Elsevier Ltd. All rights reserved.

Effects of a ciliate protozoa predator on microbial communities in pitcher plant (Sarracenia purpurea) leaves.

PubMed

Paisie, Taylor K; Miller, Thomas E; Mason, Olivia U

2014-01-01

The aquatic communities found within the water filled leaves of the pitcher plant, Sarracenia purpurea, have a simple trophic structure providing an ideal system to study microscale interactions between protozoan predators and their bacterial prey. In this study, replicate communities were maintained with and without the presence of the bactivorous protozoan, Colpoda steinii, to determine the effects of grazing on microbial communities. Changes in microbial (Archaea and Bacteria) community structure were assessed using iTag sequencing of 16S rRNA genes. The microbial communities were similar with and without the protozoan predator, with>1000 species. Of these species, Archaea were negligible, with Bacteria comprising 99.99% of the microbial community. The Proteobacteria and Bacteroidetes were the most dominant phyla. The addition of a protozoan predator did not have a significant effect on microbial evenness nor richness. However, the presence of the protozoan did cause a significant shift in the relative abundances of a number of bacterial species. This suggested that bactivorous protozoan may target specific bacterial species and/or that certain bacterial species have innate mechanisms by which they evade predators. These findings help to elucidate the effect that trophic structure perturbations have on predator prey interactions in microbial systems.

Effects of a Ciliate Protozoa Predator on Microbial Communities in Pitcher Plant (Sarracenia purpurea) Leaves

PubMed Central

Paisie, Taylor K.; Miller, Thomas E.; Mason, Olivia U.

2014-01-01

The aquatic communities found within the water filled leaves of the pitcher plant, Sarracenia purpurea, have a simple trophic structure providing an ideal system to study microscale interactions between protozoan predators and their bacterial prey. In this study, replicate communities were maintained with and without the presence of the bactivorous protozoan, Colpoda steinii, to determine the effects of grazing on microbial communities. Changes in microbial (Archaea and Bacteria) community structure were assessed using iTag sequencing of 16S rRNA genes. The microbial communities were similar with and without the protozoan predator, with>1000 species. Of these species, Archaea were negligible, with Bacteria comprising 99.99% of the microbial community. The Proteobacteria and Bacteroidetes were the most dominant phyla. The addition of a protozoan predator did not have a significant effect on microbial evenness nor richness. However, the presence of the protozoan did cause a significant shift in the relative abundances of a number of bacterial species. This suggested that bactivorous protozoan may target specific bacterial species and/or that certain bacterial species have innate mechanisms by which they evade predators. These findings help to elucidate the effect that trophic structure perturbations have on predator prey interactions in microbial systems. PMID:25423622

Microbial community diversity, structure and assembly across oxygen gradients in meromictic marine lakes, Palau.

PubMed

Meyerhof, Matthew S; Wilson, Jesse M; Dawson, Michael N; Michael Beman, J

2016-12-01

Microbial communities consume oxygen, alter biogeochemistry and compress habitat in aquatic ecosystems, yet our understanding of these microbial-biogeochemical-ecological interactions is limited by a lack of systematic analyses of low-oxygen ecosystems. Marine lakes provide an ideal comparative system, as they range from well-mixed holomictic lakes to stratified, anoxic, meromictic lakes that vary in their vertical extent of anoxia. We examined microbial communities inhabiting six marine lakes and one ocean site using pyrosequencing of 16S rRNA genes. Microbial richness and evenness was typically highest in the anoxic monimolimnion of meromictic lakes, with common marine bacteria present in mixolimnion communities replaced by anoxygenic phototrophs, sulfate-reducing bacteria and SAR406 in the monimolimnion. These sharp changes in community structure were linked to environmental gradients (constrained variation in redundancy analysis = 68%-76%) - particularly oxygen and pH. However, in those lakes with the steepest oxygen gradients, salinity and dissolved nutrients were important secondary constraining variables, indicating that subtle but substantive differences in microbial communities occur within similar low-oxygen habitats. Deterministic processes were a dominant influence on whole community assembly (all nearest taxon index values >4), demonstrating that the strong environmental gradients present in meromictic marine lakes drive microbial community assembly. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Humus-reducing microorganisms and their valuable contribution in environmental processes.

PubMed

Martinez, Claudia M; Alvarez, Luis H; Celis, Lourdes B; Cervantes, Francisco J

2013-12-01

Humus constitutes a very abundant class of organic compounds that are chemically heterogeneous and widely distributed in terrestrial and aquatic environments. Evidence accumulated during the last decades indicating that humic substances play relevant roles on the transport, fate, and redox conversion of organic and inorganic compounds both in chemically and microbially driven reactions. The present review underlines the contribution of humus-reducing microorganisms in relevant environmental processes such as biodegradation of recalcitrant pollutants and mitigation of greenhouse gases emission in anoxic ecosystems, redox conversion of industrial contaminants in anaerobic wastewater treatment systems, and on the microbial production of nanocatalysts and alternative energy sources.

Bacteriophage in polar inland waters

USGS Publications Warehouse

Säwström, Christin; Lisle, John; Anesio, A.M.; Priscu, John C.; Laybourn-Parry, J.

2008-01-01

Bacteriophages are found wherever microbial life is present and play a significant role in aquatic ecosystems. They mediate microbial abundance, production, respiration, diversity, genetic transfer, nutrient cycling and particle size distribution. Most studies of bacteriophage ecology have been undertaken at temperate latitudes. Data on bacteriophages in polar inland waters are scant but the indications are that they play an active and dynamic role in these microbially dominated polar ecosystems. This review summarises what is presently known about polar inland bacteriophages, ranging from subglacial Antarctic lakes to glacial ecosystems in the Arctic. The review examines interactions between bacteriophages and their hosts and the abiotic and biotic variables that influence these interactions in polar inland waters. In addition, we consider the proportion of the bacteria in Arctic and Antarctic lake and glacial waters that are lysogenic and visibly infected with viruses. We assess the relevance of bacteriophages in the microbial loop in the extreme environments of Antarctic and Arctic inland waters with an emphasis on carbon cycling.

In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system

PubMed Central

Lee, On On; Wang, Yong; Tian, Renmao; Zhang, Weipeng; Shek, Chun Shum; Bougouffa, Salim; Al-Suwailem, Abdulaziz; Batang, Zenon B.; Xu, Wei; Wang, Guang Chao; Zhang, Xixiang; Lafi, Feras F.; Bajic, Vladmir B.; Qian, Pei-Yuan

2014-01-01

Using microscopic and molecular techniques combined with computational analysis, this study examined the structure and composition of microbial communities in biofilms that formed on different artificial substrates in a brine pool and on a seep vent of a cold seep in the Red Sea to test our hypothesis that initiation of the biofilm formation and spreading mode of microbial structures differs between the cold seep and the other aquatic environments. Biofilms on different substrates at two deployment sites differed morphologically, with the vent biofilms having higher microbial abundance and better structural features than the pool biofilms. Microbes in the pool biofilms were more taxonomically diverse and mainly composed of various sulfate-reducing bacteria whereas the vent biofilms were exclusively dominated by sulfur-oxidizing Thiomicrospira. These results suggest that the redox environments at the deployment sites might have exerted a strong selection on microbes in the biofilms at two sites whereas the types of substrates had limited effects on the biofilm development. PMID:24399144

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

Konopka, Allan

Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, theymore » interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.« less

Oxytetracycline removal from water by novel microbial embedding gel beads

NASA Astrophysics Data System (ADS)

Wu, Nan; Pan, Peng; Zeng, Ming; Wang, Wei; Xu, Chenshan; Zhang, Zongpeng; Liu, Xinyuan; Wang, Yichao

2018-01-01

As a common antibiotic in aquatic environment, excessive oxytetracycline (OTC) is urgent to be removed due to its great biological toxicity. Compared with the traditional activated sludge, microbial embedding can enhance the treating efficiency. In this study, novel microbial embedding gel beads were produced with the additional agent of cyclodextrin (CD). Results show that CD could increase the mass transfer of OTC into gel beads, possibly because of its strong affinity for organic matters. In terms of OTC biodegradation, gel beads with CD were comparable to gel beads without CD, while the former’s sucrose removal efficiency was higher than the latter. The biodegradation of OTC only occurred in the presence of sucrose. The respiration test also confirmed these findings. Overall, the produced novel gel beads modified with CD could improve the removal performance of OTC.

Could Methane Oxidation in Lakes Be Enhanced by Eutrophication?

NASA Astrophysics Data System (ADS)

Van Grinsven, S.; Villanueva, L.; Harrison, J.; S Sinninghe Damsté, J.

2017-12-01

Climate change and eutrophication both affect aquatic ecosystems. Eutrophication is caused by high nutrient inputs, leading to algal blooms, oxygen depletion and disturbances of the natural balances in aquatic systems. Methane, a potent greenhouse gas produced biologically by anaerobic degradation of organic matter, is often released from the sediments of lakes and marine systems to overlying water and the atmosphere. Methane oxidation, a microbial methane consumption process, can limit methane emission from lakes and reservoirs by 50-80%. Here, we studied methane oxidation in a seasonally stratified reservoir: Lacamas Lake in Washington, USA. We found this lake has a large summer storage capacity of methane in its deep water layer, with a very active microbial community capable of oxidizing exceptionally high amounts of methane. The natural presence of terminal electron acceptors is, however, too low to support these high potential rates. Addition of eutrophication-related nutrients such as nitrate and sulfate increased the methane removal rates by 4 to 7-fold. The microbial community was studied using 16S rRNA gene amplicon sequencing and preliminary results indicate the presence of a relatively unknown facultative anaerobic methane oxidizer of the genus Methylomonas, capable of using nitrate as an electron donor. Experiments in which anoxic and oxic conditions were rapidly interchanged showed this facultative anaerobic methane oxidizer has an impressive flexibility towards large, rapid changes in environmental conditions and this feature might be key to the unexpectedly high methane removal rates in eutrophied and anoxic watersheds.

The in situ bacterial production of fluorescent organic matter; an investigation at a species level.

PubMed

Fox, B G; Thorn, R M S; Anesio, A M; Reynolds, D M

2017-11-15

Aquatic dissolved organic matter (DOM) plays an essential role in biogeochemical cycling and transport of organic matter throughout the hydrological continuum. To characterise microbially-derived organic matter (OM) from common environmental microorganisms (Escherichia coli, Bacillus subtilis and Pseudomonas aeruginosa), excitation-emission matrix (EEM) fluorescence spectroscopy was employed. This work shows that bacterial organisms can produce fluorescent organic matter (FOM) in situ and, furthermore, that the production of FOM differs at a bacterial species level. This production can be attributed to structural biological compounds, specific functional proteins (e.g. pyoverdine production by P. aeruginosa), and/or metabolic by-products. Bacterial growth curve data demonstrates that the production of FOM is fundamentally related to microbial metabolism. For example, the majority of Peak T fluorescence (> 75%) is shown to be intracellular in origin, as a result of the building of proteins for growth and metabolism. This underpins the use of Peak T as a measure of microbial activity, as opposed to bacterial enumeration as has been previously suggested. This study shows that different bacterial species produce a range of FOM that has historically been attributed to high molecular weight allochthonous material or the degradation of terrestrial FOM. We provide definitive evidence that, in fact, it can be produced by microbes within a model system (autochthonous), providing new insights into the possible origin of allochthonous and autochthonous organic material present in aquatic systems. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

The maturing of microbial ecology.

PubMed

Schmidt, Thomas M

2006-09-01

A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe's Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe's contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology.

Aquatic toxicity testing for aquatic life impact assessments and recent scientific advancements

EPA Science Inventory

The focus of this presentation is to provide an overview of the use of aquatic toxicity testing for assessing possible impacts to aquatic life and how new scientific approaches are being researched. Toxicity testing of both ambient and effluent monitoring samples will be discusse...

Short- and medium-chain chlorinated paraffins in aquatic foods from 18 Chinese provinces: Occurrence, spatial distributions, and risk assessment.

PubMed

Wang, Runhua; Gao, Lirong; Zheng, Minghui; Tian, Yiling; Li, Jingguang; Zhang, Lei; Wu, Yongning; Huang, Huiting; Qiao, Lin; Liu, Wenbin; Su, Guijin; Liu, Guorui; Liu, Ying

2018-02-15

Short-chain chlorinated paraffins (SCCPs) are classed as persistent organic pollutants and were included in the Stockholm Convention in May 2017. Large amounts of chlorinated paraffins (CPs) are produced in China than in any other countries. CPs can be released into the environment while being produced and used, and can bioaccumulate in aquatic biota and be ingested by humans. Dietary intake is the main route through which humans are exposed to CPs. It has previously been found that persistent organic pollutant concentrations are usually higher in aquatic foods than in other foods. The risk of human exposure to SCCPs in aquatic foods should therefore be of concerns. However, SCCP concentrations in aquatic foods have not been systematically studied. A total of 1620 aquatic food samples were collected, and 18 pooled samples were analyzed by two-dimensional gas chromatography coupled with electron-capture negative-ionization time-of-flight mass spectrometry. The mean SCCP and MCCP concentrations were 1472 and 80.5ng/gwet weight, respectively. The dominant SCCP and MCCP congener groups were C 10 Cl 6-7 and C 14 Cl 7-8 , respectively. The concentrations were much higher than those have been found in aquatic foods in other countries. The CP concentrations in the samples consumed by local people from eastern and southern China were higher than the concentrations in samples from central and western China. Risk assessment results indicated that SCCPs and MCCPs in aquatic foods do not pose significant risks to residents of China. Copyright © 2017 Elsevier B.V. All rights reserved.

Determination of selected cardiovascular active compounds in environmental aquatic samples--Methods and results, a review of global publications from the last 10 years.

PubMed

Stankiewicz, Albert; Giebułtowicz, Joanna; Stankiewicz, Urszula; Wroczyński, Piotr; Nałęcz-Jawecki, Grzegorz

2015-11-01

In recent years cardiovascular diseases were the second most common cause of death worldwide. Therefore, the consumption of cardiovascular drugs is high, which might result in an increase of them in the environment. The major source of aquatic environmental contamination is still effluents of wastewater treatment plants (WWTPs). Unfortunately removal of cardiovascular active compounds and/or their metabolites in WWTP is still unsatisfactory. Among microbial and abiotic degradation of these compounds during wastewater processes, photolysis and photodegradation of cardiovascular drugs also play an important role. New formed compounds may be more toxic or retain the properties of parent compounds. Thus the main goal of this paper was to provide a detailed and comprehensive review of used analytical methods, coupled to liquid chromatography-tandem mass spectrometry, to determine the presence of cardiovascular compounds in surface waters as well as WTTPs effluents and influents. Exhaustive preparation for mass spectrometry detection and quantitation including samples pre-treatment, and the common problem of the matrix effect are thoroughly explored in this paper. Additionally, the article provides some hints in respect of recently noted problematic issue related to the availability of specific standards for the analysis of drug's metabolites. Furthermore, information concerning the metabolism of cardiovascular active compounds including differences in metabolism within enantiomers is described. This article also touches on the problems associated with environmental risk assessment due to the presence of cardiovasculars in the environment. The paper also tries to explain differences in concentrations among cardiovascular compounds between countries worldwide. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effects of agricultural practices on organic matter degradation in ditches

NASA Astrophysics Data System (ADS)

Hunting, Ellard R.; Vonk, J. Arie; Musters, C. J. M.; Kraak, Michiel H. S.; Vijver, Martina G.

2016-02-01

Agricultural practices can result in differences in organic matter (OM) and agricultural chemical inputs in adjacent ditches, but its indirect effects on OM composition and its inherent consequences for ecosystem functioning remain uncertain. This study determined the effect of agricultural practices (dairy farm grasslands and hyacinth bulb fields) on OM degradation by microorganisms and invertebrates with a consumption and food preference experiment in the field and in the laboratory using natural OM collected from the field. Freshly cut grass and hyacinths were also offered to control for OM composition and large- and small mesh-sizes were used to distinguish microbial decomposition and invertebrate consumption. Results show that OM decomposition by microorganisms and consumption by invertebrates was similar throughout the study area, but that OM collected from ditches adjacent grasslands and freshly cut grass and hyacinths were preferred over OM collected from ditches adjacent to a hyacinth bulb field. In the case of OM collected from ditches adjacent hyacinth bulb fields, both microbial decomposition and invertebrate consumption were strongly retarded, likely resulting from sorption and accumulation of pesticides. This outcome illustrates that differences in agricultural practices can, in addition to direct detrimental effects on aquatic organisms, indirectly alter the functioning of adjacent aquatic ecosystems.

Photos of Sampling for the National Aquatic Resource Surveys

EPA Pesticide Factsheets

The National Aquatic Resource Surveys study all types of waters: rivers and streams, lakes and reservoirs, Great Lakes, coastal waters and wetlands. These photos were taken during in-the-field sampling for recent reports.

Selection and screening of microbial consortia for efficient and ecofriendly degradation of plastic garbage collected from urban and rural areas of Bangalore, India.

PubMed

Skariyachan, Sinosh; Megha, M; Kini, Meghna Niranjan; Mukund, Kamath Manali; Rizvi, Alya; Vasist, Kiran

2015-01-01

Industrialization and urbanization have led to massive accumulation of plastic garbage all over India. The persistence of plastic in soil and aquatic environment has become ecological threat to the metropolitan city such as Bangalore, India. Present study investigates an ecofriendly, efficient and cost-effective approach for plastic waste management by the screening of novel microbial consortia which are capable of degrading plastic polymers. Plastic-contaminated soil and water samples were collected from six hot spots of urban and rural areas of Bangalore. The plastic-degrading bacteria were enriched, and degradation ability was determined by zone of clearance method. The percentage of polymer degradation was initially monitored by weight loss method, and the main isolates were characterized by standard microbiology protocols. These isolates were used to form microbial consortia, and the degradation efficiency of the consortia was compared with individual isolate and known strains obtained from the Microbial Type Culture Collection (MTCC) and Gene Bank, India. One of the main enzymes responsible for polymer degradation was identified, and the biodegradation mechanism was hypothesized by bioinformatics studies. From this study, it is evident that the bacteria utilized the plastic polymer as a sole source of carbon and showed 20-50% weight reduction over a period of 120 days. The two main bacteria responsible for the degradation were microbiologically characterized to be Pseudomonas spp. These bacteria could grow optimally at 37 °C in pH 9.0 and showed 35-40% of plastic weight reduction over 120 days. These isolates were showed better degradation ability than known strains from MTCC. The current study further revealed that the microbial consortia formulated by combining Psuedomonas spp. showed 40 plastic weight reduction over a period of 90 days. Further, extracellular lipase, one of the main enzymes responsible for polymer degradation, was identified. The computational docking studies suggested that polyethylene glycol and polystyrene present in the plastics might have good interaction towards the microbial lipase with stable binding and interacting forces which probably could be one of the reasons for the degradative mechanisms.

The Interplay Between Predation, Competition, and Nutrient Levels Influences the Survival of Escherichia coli in Aquatic Environments.

PubMed

Wanjugi, P; Fox, G A; Harwood, V J

2016-10-01

Nutrient levels, competition from autochthonous microorganisms, and protozoan predation may all influence survival of fecal microorganisms as they transition from the gastrointestinal tract to aquatic habitats. Although Escherichia coli is an important indicator of waterborne pathogens, the effects of environmental stressors on its survival in aquatic environments remain poorly understood. We manipulated organic nutrient, predation, and competition levels in outdoor microcosms containing natural river water, sediments, and microbial populations to determine their relative contribution to E. coli survival. The activities of predator (protozoa) and competitor (indigenous bacteria) populations were inhibited by adding cycloheximide or kanamycin. We developed a statistical model of E. coli density over time that fits with the data under all experimental conditions. Predation and competition had significant negative effects on E. coli survival, while higher nutrient levels increased survival. Among the main effects, predation accounted for the greatest variation (40 %) compared with nutrients (25 %) or competition (15 %). The highest nutrient level mitigated the effect of predation on E. coli survival. Thus, elevated organic nutrients may disproportionately enhance the survival of E. coli, and potentially that of other enteric bacteria, in aquatic habitats.

Antagonistic Microbial Interactions: Contributions and Potential Applications for Controlling Pathogens in the Aquatic Systems

PubMed Central

Feichtmayer, Judith; Deng, Li; Griebler, Christian

2017-01-01

Despite the active and intense treatment of wastewater, pathogenic microorganisms and viruses are frequently introduced into the aquatic environment. For most human pathogens, however, this is a rather hostile place, where starvation, continuous inactivation, and decay generally occur, rather than successful reproduction. Nevertheless, a great diversity of the pathogenic microorganisms can be detected, in particular, in the surface waters receiving wastewater. Pathogen survival depends majorly on abiotic factors such as irradiation, changes in water ionic strength, temperature, and redox state. In addition, inactivation is enhanced by the biotic interactions in the environment. Although knowledge of the antagonistic biotic interactions has been available since a long time, certain underlying processes and mechanisms still remain unclear. Others are well-appreciated and increasingly are applied to the present research. Our review compiles and discusses the presently known biotic interactions between autochthonous microbes and pathogens introduced into the aquatic environment, including protozoan grazing, virus-induced bacterial cell lysis, antimicrobial substances, and predatory bacteria. An overview is provided on the present knowledge, as well as on the obvious research gaps. Individual processes that appear promising for future applications in the aquatic environment are presented and discussed. PMID:29184541

Investigations of Sample Stability in Water Chemistry Samples: Implications for the National Aquatic Resource Surveys

EPA Science Inventory

Water samples collected for the EPA's National Aquatic Resource Surveys (NARS) typically arrive at an analytical laboratory 2 or 3 days after collection (longer if collected from a remote location), at which point they are stabilized (filtration and/or acid preservation) until an...

Map of National Aquatic Resource Surveys Sampling Locations

EPA Pesticide Factsheets

This map displays all of the lakes, rivers and streams, wetlands, and coastal waters sampled by the National Aquatic Resource Surveys, a collaborative EPA program that assesses the condition of the nation's waters using statistical designs.

Hydrological, water-quality, and ecological data for streams in Independence, Missouri, June 2005 through September 2013

USGS Publications Warehouse

Niesen, Shelley L.; Christensen, Eric D.

2015-01-01

Water-quality, hydrological, and ecological data collected from June 2005 through September 2013 from the Little Blue River and smaller streams within the City of Independence, Missouri, are presented in this report. These data were collected as a part of an ongoing cooperative study between the U.S. Geological Survey and the City of Independence Water Pollution Control Department to characterize the water quality and ecological condition of Independence streams. The quantities, sources of selected constituents, and processes affecting water quality and aquatic life were evaluated to determine the resulting ecological condition of streams within Independence. Data collected for this study fulfill the municipal separate sewer system permit requirements for the City of Independence and can be used to provide a baseline with which city managers can determine the effectiveness of current (2014) and future best management practices within Independence. Continuous streamflow and water-quality data, collected during base flow and stormflow, included physical and chemical properties, inorganic constituents, common organic micro-constituents, pesticides in streambed sediment and surface water, fecal indicator bacteria and microbial source tracking data, and suspended sediment. Dissolved oxygen, pH, specific conductance, water temperature, and turbidity data were measured continuously at seven sites within Independence. Base-flow and stormflow samples were collected at eight gaged and two ungaged sites. Fecal sources samples were collected for reference for microbial source tracking, and sewage influent samples were collected as additional source samples. Dry-weather screening was done on 11 basins within Independence to identify potential contaminant sources to the streams. Benthic macroinvertebrate community surveys and habitat assessments were done on 10 stream sites and 2 comparison sites outside the city. Sampling and laboratory procedures and quality-assurance and quality-control methods used in data collection for this study are described in this report.

Stream microbial diversity in response to environmental changes: review and synthesis of existing research

PubMed Central

Zeglin, Lydia H.

2015-01-01

The importance of microbial activity to ecosystem function in aquatic ecosystems is well established, but microbial diversity has been less frequently addressed. This review and synthesis of 100s of published studies on stream microbial diversity shows that factors known to drive ecosystem processes, such as nutrient availability, hydrology, metal contamination, contrasting land-use and temperature, also cause heterogeneity in bacterial diversity. Temporal heterogeneity in stream bacterial diversity was frequently observed, reflecting the dynamic nature of both stream ecosystems and microbial community composition. However, within-stream spatial differences in stream bacterial diversity were more commonly observed, driven specifically by different organic matter (OM) compartments. Bacterial phyla showed similar patterns in relative abundance with regard to compartment type across different streams. For example, surface water contained the highest relative abundance of Actinobacteria, while epilithon contained the highest relative abundance of Cyanobacteria and Bacteroidetes. This suggests that contrasting physical and/or nutritional habitats characterized by different stream OM compartment types may select for certain bacterial lineages. When comparing the prevalence of physicochemical effects on stream bacterial diversity, effects of changing metal concentrations were most, while effects of differences in nutrient concentrations were least frequently observed. This may indicate that although changing nutrient concentrations do tend to affect microbial diversity, other environmental factors are more likely to alter stream microbial diversity and function. The common observation of connections between ecosystem process drivers and microbial diversity suggests that microbial taxonomic turnover could mediate ecosystem-scale responses to changing environmental conditions, including both microbial habitat distribution and physicochemical factors. PMID:26042102

Bacterial community structure and dissolved organic matter in repeatedly flooded subsurface karst water pools.

PubMed

Shabarova, Tanja; Villiger, Jörg; Morenkov, Oleg; Niggemann, Jutta; Dittmar, Thorsten; Pernthaler, Jakob

2014-07-01

Bacterial diversity, community assembly, and the composition of the dissolved organic matter (DOM) were studied in three temporary subsurface karst pools with different flooding regimes. We tested the hypothesis that microorganisms introduced to the pools during floods faced environmental filtering toward a 'typical' karst water community, and we investigated whether DOM composition was related to floodings and the residence time of water in stagnant pools. As predicted, longer water residence consistently led to a decline of bacterial diversity. The microbial assemblages in the influx water harbored more 'exotic' lineages with large distances to known genotypes, yet these initial communities already appeared to be shaped by selective processes. β-Proteobacterial operational taxonomic units (OTUs) closely related to microbes from subsurface or surface aquatic environments were mainly responsible for the clustering of samples according to water residence time in the pools. By contrast, several Cytophagaceae and Flavobacteriaceae OTUs were related to different floodings, which were also the main determinants of DOM composition. A subset of compounds distinguishable by molecular mass and O/C content were characteristic for individual floods. Moreover, there was a transformation of DOM in stagnant pools toward smaller and more aromatic compounds, potentially also reflecting microbial utilization. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps.

PubMed

Yamazaki, Yohei; Meirelles, Pedro Milet; Mino, Sayaka; Suda, Wataru; Oshima, Kenshiro; Hattori, Masahira; Thompson, Fabiano L; Sakai, Yuichi; Sawabe, Toko; Sawabe, Tomoo

2016-02-24

Gut microbiome shapes various aspects of a host's physiology, but these functions in aquatic animal hosts have yet to be fully investigated. The sea cucumber Apostichopus japonicus Selenka is one such example. The large growth gap in their body size has delayed the development of intensive aquaculture, nevertheless the species is in urgent need of conservation. To understand possible contributions of the gut microbiome to its host's growth, individual fecal microbiome comparisons were performed. High-throughput 16S rRNA sequencing revealed significantly different microbiota in larger and smaller individuals; Rhodobacterales in particular was the most significantly abundant bacterial group in the larger specimens. Further shotgun metagenome of representative samples revealed a significant abundance of microbiome retaining polyhydroxybutyrate (PHB) metabolism genes in the largest individual. The PHB metabolism reads were potentially derived from Rhodobacterales. These results imply a possible link between microbial PHB producers and potential growth promotion in Deuterostomia marine invertebrates.

Systematic approaches to comprehensive analyses of natural organic matter

USGS Publications Warehouse

Leenheer, Jerry A.

2009-01-01

The more that is learned of the chemistry of aquatic natural organic matter (NOM) the greater is the scientific appreciation of the vast complexity of this subject. This complexity is due not only to a multiplicity of precursor molecules in any environment but to their associations with each other and with other components of local environments such as clays, mineral acids and dissolved metals. In addition, this complex system is subject to constant change owing to environmental variables and microbial action. Thus, there is a good argument that no two NOM samples are exactly the same even from the same source at nearly the same time. When ubiquity of occurrence, reaction with water treatment chemicals, and subsequent human exposure are added to the list of NOM issues, one can understand the appeal that this subject holds for a wide variety of environmental scientists.

Constraining Biomarkers of Dissolved Organic Matter Sourcing Using Microbial Incubations of Vascular Plant Leachates of the California landscape

NASA Astrophysics Data System (ADS)

Harfmann, J.; Hernes, P.; Chuang, C. Y.; Kaiser, K.; Spencer, R. G.; Guillemette, F.

2017-12-01

Source origin of dissolved organic matter (DOM) is crucial in determining reactivity, driving chemical and biological processing of carbon. DOM source biomarkers such as lignin (a vascular plant marker) and D-amino acids (bacterial markers) are well-established tools in tracing DOM origin and fate. The development of high-resolution mass spectrometry and optical studies has expanded our toolkit; yet despite these advances, our understanding of DOM sources and fate remains largely qualitative. Quantitative data on DOM pools and fluxes become increasingly necessary as we refine our comprehension of its composition. In this study, we aim to calibrate and quantify DOM source endmembers by performing microbial incubations of multiple vascular plant leachates, where total DOM is constrained by initial vascular plant input and microbial production. Derived endmembers may be applied to endmember mixing models to quantify DOM source contributions in aquatic systems.

Sampling and Analysis Plan for Supplemental Environmental Project: Aquatic Life Surveys

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

Berryhill, Jesse Tobias; Gaukler, Shannon Marie

As part of a settlement agreement for nuclear waste incidents in 2014, several supplemental environment projects (SEPs) were initiated at Los Alamos National Laboratory (LANL or the Laboratory) between the U.S. Department of Energy and the state of New Mexico. One SEP from this agreement consists of performing aquatic life surveys and will be used to assess the applicability of using generic ambient water-quality criteria (AWQC) for aquatic life. AWQC are generic criteria developed by the U.S. Environmental Protection Agency (EPA) to cover a broad range of aquatic species and are not unique to a specific region or state. AWQCmore » are established by a composition of toxicity data, called species sensitivity distributions (SSDs), and are determined by LC50 (lethal concentration of 50% of the organisms studied) acute toxicity experiments for chemicals of interest. It is of interest to determine whether aquatic species inhabiting waters on the Pajarito Plateau are adequately protected using the current generic AWQC. The focus of this study will determine which aquatic species are present in ephemeral, intermittent, and perennial waters within LANL boundaries and from reference waters adjacent to LANL. If the species identified from these waters do not generally represent species used in the SSDs, then SSDs may need to be modified and AWQC may need to be updated. This sampling and analysis plan details the sampling methodology, surveillance locations, temporal scheduling, and analytical approaches that will be used to complete aquatic life surveys. A significant portion of this sampling and analysis plan was formalized by referring to Appendix E: SEP Aquatic Life Surveys DQO (Data Quality Objectives).« less

Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth

PubMed Central

Nunoura, Takuro; Takaki, Yoshihiro; Hirai, Miho; Shimamura, Shigeru; Makabe, Akiko; Koide, Osamu; Kikuchi, Tohru; Miyazaki, Junichi; Koba, Keisuke; Yoshida, Naohiro; Sunamura, Michinari; Takai, Ken

2015-01-01

Hadal oceans at water depths below 6,000 m are the least-explored aquatic biosphere. The Challenger Deep, located in the western equatorial Pacific, with a water depth of ∼11 km, is the deepest ocean on Earth. Microbial communities associated with waters from the sea surface to the trench bottom (0 ∼10,257 m) in the Challenger Deep were analyzed, and unprecedented trench microbial communities were identified in the hadal waters (6,000 ∼10,257 m) that were distinct from the abyssal microbial communities. The potentially chemolithotrophic populations were less abundant in the hadal water than those in the upper abyssal waters. The emerging members of chemolithotrophic nitrifiers in the hadal water that likely adapt to the higher flux of electron donors were also different from those in the abyssal waters that adapt to the lower flux of electron donors. Species-level niche separation in most of the dominant taxa was also found between the hadal and abyssal microbial communities. Considering the geomorphology and the isolated hydrotopographical nature of the Mariana Trench, we hypothesized that the distinct hadal microbial ecosystem was driven by the endogenous recycling of organic matter in the hadal waters associated with the trench geomorphology. PMID:25713387

Sedimentary organic biomarkers suggest detrimental effects of PAHs on estuarine microbial biomass during the 20th century in San Francisco Bay, CA, USA

USGS Publications Warehouse

Nilsen, Elena B.; Rosenbauer, Robert J.; Fuller, Christopher C.; Jaffe, Bruce E.

2014-01-01

Hydrocarbon contaminants are ubiquitous in urban aquatic ecosystems, and the ability of some microbial strains to degrade certain polycyclic aromatic hydrocarbons (PAHs) is well established. However, detrimental effects of petroleum hydrocarbon contamination on nondegrader microbial populations and photosynthetic organisms have not often been considered. In the current study, fatty acid methyl ester (FAME) biomarkers in the sediment record were used to assess historical impacts of petroleum contamination on microbial and/or algal biomass in South San Francisco Bay, CA, USA. Profiles of saturated, branched, and monounsaturated fatty acids had similar concentrations and patterns downcore. Total PAHs in a sediment core were on average greater than 20× higher above ∼200 cm than below, which corresponds roughly to the year 1900. Isomer ratios were consistent with a predominant petroleum combustion source for PAHs. Several individual PAHs exceeded sediment quality screening values. Negative correlations between petroleum contaminants and microbial and algal biomarkers – along with high trans/cis ratios of unsaturated FA, and principle component analysis of the PAH and fatty acid records – suggest a negative impacts of petroleum contamination, appearing early in the 20th century, on microbial and/or algal ecology at the site.

What Are Probability Surveys used by the National Aquatic Resource Surveys?

EPA Pesticide Factsheets

The National Aquatic Resource Surveys (NARS) use probability-survey designs to assess the condition of the nation’s waters. In probability surveys (also known as sample-surveys or statistical surveys), sampling sites are selected randomly.

Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances.

PubMed

Xu, Jianping

2006-06-01

Microbial ecology examines the diversity and activity of micro-organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific sections, the applications of the genomics in microbial ecological research are highlighted. The first describes the widespread application of multilocus sequence typing and representational difference analysis in studying genetic variation within microbial species. Such investigations have identified that migration, horizontal gene transfer and recombination are common in natural microbial populations and that microbial strains can be highly variable in genome size and gene content. The second section highlights and summarizes the use of four specific genomics methods (phylogenetic analysis of ribosomal RNA, DNA-DNA re-association kinetics, metagenomics, and micro-arrays) in analysing the diversity and potential activity of microbial populations and communities from a variety of terrestrial and aquatic environments. Such analyses have identified many unexpected phylogenetic lineages in viruses, bacteria, archaea, and microbial eukaryotes. Functional analyses of environmental DNA also revealed highly prevalent, but previously unknown, metabolic processes in natural microbial communities. In the third section, the ecological implications of sequenced microbial genomes are briefly discussed. Comparative analyses of prokaryotic genomic sequences suggest the importance of ecology in determining microbial genome size and gene content. The significant variability in genome size and gene content among strains and species of prokaryotes indicate the highly fluid nature of prokaryotic genomes, a result consistent with those from multilocus sequence typing and representational difference analyses. The integration of various levels of ecological analyses coupled to the application and further development of high throughput technologies are accelerating the pace of discovery in microbial ecology.

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

Britton, L.J.; Greeson, P.E.

1989-01-01

The series of chapters on techniques describes methods used by the U.S. Geological Survey for planning and conducting water-resources investigations. The material is arranged under major subject headings called books and is further subdivided into sections and chapters. Book 5 is on laboratory analysis. Section A is on water. The unit of publication, the chapter, is limited to a narrow field of subject matter. "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" is the fourth chapter to be published under Section A of Book 5. The chapter number includes the letter of the section.This chapter was prepared by several aquatic biologists and microbiologists of the U.S. Geological Survey to provide accurate and precise methods for the collection and analysis of aquatic biological and microbiological samples.Use of brand, firm, and trade names in this chapter is for identification purposes only and does not constitute endorsement by the U.S. Geological Survey.This chapter supersedes "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" edited by P.E. Greeson, T.A. Ehlke, G.A. Irwin, B.W. Lium, and K.V. Slack (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4, 1977) and also supersedes "A Supplement to-Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" by P.E. Greeson (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4), Open-File Report 79-1279, 1979.

Evaluation of seven aquatic sampling methods for amphibians and other aquatic fauna

USGS Publications Warehouse

Gunzburger, M.S.

2007-01-01

To design effective and efficient research and monitoring programs researchers must have a thorough understanding of the capabilities and limitations of their sampling methods. Few direct comparative studies exist for aquatic sampling methods for amphibians. The objective of this study was to simultaneously employ seven aquatic sampling methods in 10 wetlands to compare amphibian species richness and number of individuals detected with each method. Four sampling methods allowed counts of individuals (metal dipnet, D-frame dipnet, box trap, crayfish trap), whereas the other three methods allowed detection of species (visual encounter, aural, and froglogger). Amphibian species richness was greatest with froglogger, box trap, and aural samples. For anuran species, the sampling methods by which each life stage was detected was related to relative length of larval and breeding periods and tadpole size. Detection probability of amphibians varied across sampling methods. Box trap sampling resulted in the most precise amphibian count, but the precision of all four count-based methods was low (coefficient of variation > 145 for all methods). The efficacy of the four count sampling methods at sampling fish and aquatic invertebrates was also analyzed because these predatory taxa are known to be important predictors of amphibian habitat distribution. Species richness and counts were similar for fish with the four methods, whereas invertebrate species richness and counts were greatest in box traps. An effective wetland amphibian monitoring program in the southeastern United States should include multiple sampling methods to obtain the most accurate assessment of species community composition at each site. The combined use of frogloggers, crayfish traps, and dipnets may be the most efficient and effective amphibian monitoring protocol. ?? 2007 Brill Academic Publishers.

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

Effects of selenium supplementation in cattle on aquatic ecosystems in northern California

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

Norman, B.; Nader, G.; Oliver, M.

1992-09-15

The potential impact on aquatic ecosystems of supplementing the diets of beef cattle with selenium (Se) was studied on 4 northern California ranches. All study sites included an area of concentrated use by cattle that had diets supplemented with Se. In each case, a stream flowed through the site and provided a control sampling area upstream and a treated sampling area downstream. Specimens of water, sediment, algae, aquatic plants, aquatic invertebrates, and fish were analyzed fluorometrically for total Se content. Significant differences in Se concentration were not found between specimens from upstream control areas and those from downstream areas subjectedmore » to use by Se-treated cattle. Evidence was not found that Se supplementation in cattle at maximal permitted concentrations caused Se accumulation in associated aquatic ecosystems.« less

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

PubMed Central

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

2015-01-01

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

Assessment of sources of human pathogens and fecal contamination in a Florida freshwater lake.

PubMed

Staley, Christopher; Reckhow, Kenneth H; Lukasik, Jerzy; Harwood, Valerie J

2012-11-01

We investigated the potential for a variety of environmental reservoirs to harbor or contribute fecal indicator bacteria (FIB), DNA markers of human fecal contamination, and human pathogens to a freshwater lake. We hypothesized that submerged aquatic vegetation (SAV), sediments, and stormwater act as reservoirs and/or provide inputs of FIB and human pathogens to this inland water. Analysis included microbial source tracking (MST) markers of sewage contamination (Enterococcus faecium esp gene, human-associated Bacteroides HF183, and human polyomaviruses), pathogens (Salmonella, Cryptosporidium, Giardia, and enteric viruses), and FIB (fecal coliforms, Escherichia coli, and enterococci). Bayesian analysis was used to assess relationships among microbial and physicochemical variables. FIB in the water were correlated with concentrations in SAV and sediment. Furthermore, the correlation of antecedent rainfall and major rain events with FIB concentrations and detection of human markers and pathogens points toward multiple reservoirs for microbial contaminants in this system. Although pathogens and human-source markers were detected in 55% and 21% of samples, respectively, markers rarely coincided with pathogen detection. Bayesian analysis revealed that low concentrations (<45 CFU × 100 ml(-1)) of fecal coliforms were associated with 93% probability that pathogens would not be detected; furthermore the Bayes net model showed associations between elevated temperature and rainfall with fecal coliform and enterococci concentrations, but not E. coli. These data indicate that many under-studied matrices (e.g. SAV, sediment, stormwater) are important reservoirs for FIB and potentially human pathogens and demonstrate the usefulness of Bayes net analysis for water quality assessment. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

PubMed

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

2015-01-01

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

Microbial community and treatment ability investigation in AOAO process for the optoelectronic wastewater treatment using PCR-DGGE biotechnology.

PubMed

Chen, Hsi-Jien; Lin, Yi-Zi; Fanjiang, Jen-Mao; Fan, Chihhao

2013-04-01

This study aimed to explore the microbial community variation and treatment ability of a full-scale anoxic-aerobic-anoxic-aerobic (AOAO) process used for optoelectronic wastewater treatment. The sludge samples in the biological treatment units were collected and subsequently subjected to polymerase chain reaction (PCR) amplification and denaturing gradient gel electrophoresis identification and the wastewater components such as BOD5 and NH3-N were evaluated during the processes. The group specific primers selected were targeting at the kingdom Bacteria, the Acidobacterium, the α-proteobacteria, the β-proteobacteria ammonia oxidizers, Actinobacteria and methyllotrophs, and the 16S rDNA clone libraries were established. Ten different clones were obtained using the Bacteria primers and eight different clones were obtained using the β-proteobacteria ammonia oxidizer primers. Over 95 % of BOD5 and 90 % of NH3-N were removed from the system. The microbial community analysis showed that the Janthinobacterium sp. An8 and Nitrosospira sp. were the dominant species throughout the AOAO process. Across the whole clone library, six clones showed closely related to Janthinobacterium sp. and these species seemed to be the dominant species with more than 50 % occupancy of the total population. Nitrosospira sp. was the predominant species within the β-proteobacteria and occupied more than 30 % of the total population in the system. These two strains were the novel species specific to the AOAO process for optoelectronic treatment, and they were found strongly related to the system capability of removing aquatic contaminants by inspecting the wastewater concentration variation across the system.

Mechanisms of nitrogen retention in forest ecosystems - A field experiment

NASA Technical Reports Server (NTRS)

Vitousek, P. M.; Matson, P. A.

1984-01-01

Intensive forest management led to elevated losses of nitrogen from a recently harvested loblolly pine plantation in North Carolina. Measurements of nitrogen-15 retention in the field demonstrated that microbial uptake of nitrogen during the decomposition of residual organic material was the most important process retaining nitrogen. Management practices that remove this material cause increased losses of nitrogen to aquatic ecosystems and the atmosphere.

Humic acids as electron acceptors for anaerobic microbial oxidation of vinyl chloride and dichloroethene

USGS Publications Warehouse

Bradley, P.M.; Chapelle, F.H.; Lovley, D.R.

1998-01-01

Anaerobic oxidation of [1,2-14C]vinyl chloride and [1,2- 14C]dichloroethene to 14CO2 under humic acid-reducing conditions was demonstrated. The results indicate that waterborne contaminants can be oxidized by using humic acid compounds as electron acceptors and suggest that natural aquatic systems have a much larger capacity for contaminant oxidation than previously thought.

Annual Report to Congress, Fiscal Year 1997. A Report by The Council of the Strategic Environmental Research and Development Program

DTIC Science & Technology

1998-03-01

Discovery of Novel Enzymatic Reactions and Determination of Biodegradation Mechanisms and Pathways. b. Phytoremediation of Explosives Contaminated...Groundwater using Wetlands and Aquatic Plants. c. Phytoremediation of Munitions Contaminated Soils. d. Enhanced TNT Biodegradation Through Genetic Manipulation...Microbial Communities Active in the Enhanced Aerobic Treatment of Chlorinated Ethenes. c. Phytoremediation of Shallow Chlorinated Solvent Plumes

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.

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

PubMed

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

2009-01-01

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

The responses of microbial temperature relationships to seasonal change and winter warming in a temperate grassland.

PubMed

Birgander, Johanna; Olsson, Pål Axel; Rousk, Johannes

2018-01-18

Microorganisms dominate the decomposition of organic matter and their activities are strongly influenced by temperature. As the carbon (C) flux from soil to the atmosphere due to microbial activity is substantial, understanding temperature relationships of microbial processes is critical. It has been shown that microbial temperature relationships in soil correlate with the climate, and microorganisms in field experiments become more warm-tolerant in response to chronic warming. It is also known that microbial temperature relationships reflect the seasons in aquatic ecosystems, but to date this has not been investigated in soil. Although climate change predictions suggest that temperatures will be mostly affected during winter in temperate ecosystems, no assessments exist of the responses of microbial temperature relationships to winter warming. We investigated the responses of the temperature relationships of bacterial growth, fungal growth, and respiration in a temperate grassland to seasonal change, and to 2 years' winter warming. The warming treatments increased winter soil temperatures by 5-6°C, corresponding to 3°C warming of the mean annual temperature. Microbial temperature relationships and temperature sensitivities (Q 10 ) could be accurately established, but did not respond to winter warming or to seasonal temperature change, despite significant shifts in the microbial community structure. The lack of response to winter warming that we demonstrate, and the strong response to chronic warming treatments previously shown, together suggest that it is the peak annual soil temperature that influences the microbial temperature relationships, and that temperatures during colder seasons will have little impact. Thus, mean annual temperatures are poor predictors for microbial temperature relationships. Instead, the intensity of summer heat-spells in temperate systems is likely to shape the microbial temperature relationships that govern the soil-atmosphere C exchange. © 2018 John Wiley & Sons Ltd.

Aquatic invertebrate sampling at selected outfalls in Operable Unit 1082; Technical areas 9, 11, 16 and 22

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

Cross, S.

The Ecological Studies Team (EST) of ESH-20 at Los Alamos National Laboratory conducted preliminary aquatic sampling at outfalls within Operable Unit 1082 and nearby natural waterways. Eleven outfalls were sampled a total of eighteen times. Three natural waterways (upper Pajarito Canyon, Starmer`s Gulch, and Bulldog Spring) in the vicinity were sampled a total of six times. At most sites, EST recorded hydrological condition, physico-chemical parameters, wildlife uses, and vegetation. At each outfall with water and each natural waterway, EST collected an aquatic invertebrate sample which was analyzed by taxa composition, Wilhm`s biodiversity index, the community tolerance quotient (CTQ), and density.more » The physico-chemical parameters at most outfalls and natural waterways fell within the normal range of natural waters in the area. However, the outfalls are characterized by low biodiversity and severely stressed communities composed of a restricted number of taxa. The habitat at the other outfalls could probably support well-developed aquatic communities if sufficient water was available. At present, the hydrology at these outfalls is too slight and/or sporadic to support such a community in the foreseeable future. In contrast to the outfalls, the natural waterways of the area had greater densities of aquatic invertebrates, higher biodiversities, and lower CTQs.« less

Microbial Food-Web Drivers in Tropical Reservoirs.

PubMed

Domingues, Carolina Davila; da Silva, Lucia Helena Sampaio; Rangel, Luciana Machado; de Magalhães, Leonardo; de Melo Rocha, Adriana; Lobão, Lúcia Meirelles; Paiva, Rafael; Roland, Fábio; Sarmento, Hugo

2017-04-01

Element cycling in aquatic systems is driven chiefly by planktonic processes, and the structure of the planktonic food web determines the efficiency of carbon transfer through trophic levels. However, few studies have comprehensively evaluated all planktonic food-web components in tropical regions. The aim of this study was to unravel the top-down controls (metazooplankton community structure), bottom-up controls (resource availability), and hydrologic (water residence time) and physical (temperature) variables that affect different components of the microbial food web (MFW) carbon stock in tropical reservoirs, through structural equation models (SEM). We conducted a field study in four deep Brazilian reservoirs (Balbina, Tucuruí, Três Marias, and Funil) with different trophic states (oligo-, meso-, and eutrophic). We found evidence of a high contribution of the MFW (up to 50% of total planktonic carbon), especially in the less-eutrophic reservoirs (Balbina and Tucuruí). Bottom-up and top-down effects assessed through SEM indicated negative interactions between soluble reactive phosphorus and phototrophic picoplankton (PPP), dissolved inorganic nitrogen, and heterotrophic nanoflagellates (HNF). Copepods positively affected ciliates, and cladocerans positively affected heterotrophic bacteria (HB) and PPP. Higher copepod/cladoceran ratios and an indirect positive effect of copepods on HB might strengthen HB-HNF coupling. We also found low values for the degree of uncoupling (D) and a low HNF/HB ratio compared with literature data (mostly from temperate regions). This study demonstrates the importance of evaluating the whole size spectrum (including microbial compartments) of the different planktonic compartments, in order to capture the complex carbon dynamics of tropical aquatic ecosystems.

Freshwater processing of terrestrial dissolved organic matter: What governs lability?

NASA Astrophysics Data System (ADS)

D'Andrilli, J.; Smith, H. J.; Junker, J. R.; Scholl, E. A.; Foreman, C. M.

2016-12-01

Aquatic and terrestrial ecosystems are linked through the transfer of energy and materials. Allochthonous organic matter (OM) is central to freshwater ecosystem function, influencing local food webs, trophic state, and nutrient availability. In order to understand the nature and fate of OM from inland headwaters to the open ocean, it is imperative to understand the links between OM lability and ecosystem function. Thus, biological, chemical, and physical factors need to be evaluated together to inform our understanding of environmental lability. We performed a laboratory processing experiment on naturally occurring OM leachates from riparian leaves, grasses, and pine needles. Measures of water chemistry, OM optical and molecular characterization, bacterial abundances, microbial assemblage composition, respiration, and C:N:P were integrated to discern the nature and fate of labile and recalcitrant OM in a freshwater stream. Peak processing of all OM sources in the stream water occurred after two days, with spikes in bacterial cell abundances, respiration rates, microbial assemblage shifts, and maximum C utilization. Respiration rates and microbial assemblages were dependent on the degree of lability of the OM molecular composition. Within the first few days, no differences in respiration rates were observed between leachate sources, however, beyond day five, the rates diverged with C processing efficiency correlated with OM lability. Originally comprised of amino acid-like, labile fluorescent species, the inoculated stream water OM became more recalcitrant after 16 days, indicating humification processing over time. Our study highlights the importance of interdisciplinary approaches for understanding the processing and fate of OM in aquatic ecosystems.

Aerobic Toluene Degraders in the Rhizosphere of a Constructed Wetland Model Show Diurnal Polyhydroxyalkanoate Metabolism.

PubMed

Lünsmann, Vanessa; Kappelmeyer, Uwe; Taubert, Anja; Nijenhuis, Ivonne; von Bergen, Martin; Heipieper, Hermann J; Müller, Jochen A; Jehmlich, Nico

2016-07-15

Constructed wetlands (CWs) are successfully applied for the treatment of waters contaminated with aromatic compounds. In these systems, plants provide oxygen and root exudates to the rhizosphere and thereby stimulate microbial degradation processes. Root exudation of oxygen and organic compounds depends on photosynthetic activity and thus may show day-night fluctuations. While diurnal changes in CW effluent composition have been observed, information on respective fluctuations of bacterial activity are scarce. We investigated microbial processes in a CW model system treating toluene-contaminated water which showed diurnal oscillations of oxygen concentrations using metaproteomics. Quantitative real-time PCR was applied to assess diurnal expression patterns of genes involved in aerobic and anaerobic toluene degradation. We observed stable aerobic toluene turnover by Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis was upregulated in these bacteria during the day, suggesting that they additionally feed on organic root exudates while reutilizing the stored carbon compounds during the night via the glyoxylate cycle. Although mRNA copies encoding the anaerobic enzyme benzylsuccinate synthase (bssA) were relatively abundant and increased slightly at night, the corresponding protein could not be detected in the CW model system. Our study provides insights into diurnal patterns of microbial processes occurring in the rhizosphere of an aquatic ecosystem. Constructed wetlands are a well-established and cost-efficient option for the bioremediation of contaminated waters. While it is commonly accepted knowledge that the function of CWs is determined by the interplay of plants and microorganisms, the detailed molecular processes are considered a black box. Here, we used a well-characterized CW model system treating toluene-contaminated water to investigate the microbial processes influenced by diurnal plant root exudation. Our results indicated stable aerobic toluene degradation by members of the Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis in these bacteria was higher during the day, suggesting that they additionally fed on organic root exudates and reutilized the stored carbon compounds during the night. Our study illuminates microbial processes occurring in the rhizosphere of an aquatic ecosystem. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Aerobic Toluene Degraders in the Rhizosphere of a Constructed Wetland Model Show Diurnal Polyhydroxyalkanoate Metabolism

PubMed Central

Lünsmann, Vanessa; Kappelmeyer, Uwe; Taubert, Anja; Nijenhuis, Ivonne; von Bergen, Martin; Müller, Jochen A.; Jehmlich, Nico

2016-01-01

ABSTRACT Constructed wetlands (CWs) are successfully applied for the treatment of waters contaminated with aromatic compounds. In these systems, plants provide oxygen and root exudates to the rhizosphere and thereby stimulate microbial degradation processes. Root exudation of oxygen and organic compounds depends on photosynthetic activity and thus may show day-night fluctuations. While diurnal changes in CW effluent composition have been observed, information on respective fluctuations of bacterial activity are scarce. We investigated microbial processes in a CW model system treating toluene-contaminated water which showed diurnal oscillations of oxygen concentrations using metaproteomics. Quantitative real-time PCR was applied to assess diurnal expression patterns of genes involved in aerobic and anaerobic toluene degradation. We observed stable aerobic toluene turnover by Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis was upregulated in these bacteria during the day, suggesting that they additionally feed on organic root exudates while reutilizing the stored carbon compounds during the night via the glyoxylate cycle. Although mRNA copies encoding the anaerobic enzyme benzylsuccinate synthase (bssA) were relatively abundant and increased slightly at night, the corresponding protein could not be detected in the CW model system. Our study provides insights into diurnal patterns of microbial processes occurring in the rhizosphere of an aquatic ecosystem. IMPORTANCE Constructed wetlands are a well-established and cost-efficient option for the bioremediation of contaminated waters. While it is commonly accepted knowledge that the function of CWs is determined by the interplay of plants and microorganisms, the detailed molecular processes are considered a black box. Here, we used a well-characterized CW model system treating toluene-contaminated water to investigate the microbial processes influenced by diurnal plant root exudation. Our results indicated stable aerobic toluene degradation by members of the Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis in these bacteria was higher during the day, suggesting that they additionally fed on organic root exudates and reutilized the stored carbon compounds during the night. Our study illuminates microbial processes occurring in the rhizosphere of an aquatic ecosystem. PMID:27129963

Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA.

PubMed

Miya, Masaki; Minamoto, Toshifumi; Yamanaka, Hiroki; Oka, Shin-Ichiro; Sato, Keiichi; Yamamoto, Satoshi; Sado, Tetsuya; Doi, Hideyuki

2016-11-25

Recent studies demonstrated the use of environmental DNA (eDNA) from fishes to be appropriate as a non-invasive monitoring tool. Most of these studies employed disk fiber filters to collect eDNA from water samples, although a number of microbial studies in aquatic environments have employed filter cartridges, because the cartridge has the advantage of accommodating large water volumes and of overall ease of use. Here we provide a protocol for filtration of water samples using the filter cartridge and extraction of eDNA from the filter without having to cut open the housing. The main portions of this protocol consists of 1) filtration of water samples (water volumes ≤4 L or >4 L); (2) extraction of DNA on the filter using a roller shaker placed in a preheated incubator; and (3) purification of DNA using a commercial kit. With the use of this and previously-used protocols, we perform metabarcoding analysis of eDNA taken from a huge aquarium tank (7,500 m 3 ) with known species composition, and show the number of detected species per library from the two protocols as the representative results. This protocol has been developed for metabarcoding eDNA from fishes, but is also applicable to eDNA from other organisms.

Distribution of greenhouse gases in hyper-arid and arid areas of northern Chile and the contribution of the high altitude wetland microbiome (Salar de Huasco, Chile).

PubMed

Molina, Verónica; Eissler, Yoanna; Cornejo, Marcela; Galand, Pierre E; Dorador, Cristina; Hengst, Martha; Fernandez, Camila; Francois, Jean Pierre

2018-04-06

Northern Chile harbors different bioclimatic zones including hyper-arid and arid ecosystems and hotspots of microbial life, such as high altitude wetlands, which may contribute differentially to greenhouse gases (GHG) such as carbon dioxide (CO 2 ), methane (CH 4 ) and nitrous oxide (N 2 O). In this study, we explored ground level GHG distribution and the potential role of a wetland situated at 3800 m.a.s.l, and characterized by high solar radiation < 1600 W m -2 , extreme temperature ranges (-12 to 24 °C) and wind stress (< 17 m s -1 ). The water source of the wetland is mainly groundwater springs, which generates streams and ponds surrounded by peatlands. These sites support a rich microbial aquatic life including diverse bacteria and archaea communities, which transiently form more complex structures, such as microbial mats. In this study, GHG were measured in the water and above ground level air at the wetland site and along an elevation gradient in different bioclimatic areas from arid to hyper-arid zones. The microbiome from the water and sediments was described by high-throughput sequencing 16S rRNA and rDNA genes. The results indicate that GHG at ground level were variable along the elevation gradient potentially associated with different bioclimatic zones, reaching high values at the high Andean steppe and variable but lower values in the Atacama Desert and at the wetland. The water areas of the wetland presented high concentrations of CH 4 and CO 2 , particularly at the spring areas and in air bubbles below microbial mats. The microbial community was rich (> 40 phyla), including archaea and bacteria potentially active in the different matrices studied (water, sediments and mats). Functional microbial groups associated with GHG recycling were detected at low frequency, i.e., < 2.5% of total sequences. Our results indicate that hyper-arid and arid areas of northern Chile are sites of GHG exchange associated with various bioclimatic zones and particularly in aquatic areas of the wetland where this ecosystem could represent a net sink of N 2 O and a source for CH 4 and CO 2 .

When is the best time to sample aquatic macroinvertebrates in ponds for biodiversity assessment?

PubMed

Hill, M J; Sayer, C D; Wood, P J

2016-03-01

Ponds are sites of high biodiversity and conservation value, yet there is little or no statutory monitoring of them across most of Europe. There are clear and standardised protocols for sampling aquatic macroinvertebrate communities in ponds, but the most suitable time(s) to undertake the survey(s) remains poorly specified. This paper examined the aquatic macroinvertebrate communities from 95 ponds within different land use types over three seasons (spring, summer and autumn) to determine the most appropriate time to undertake sampling to characterise biodiversity. The combined samples from all three seasons provided the most comprehensive record of the aquatic macroinvertebrate taxa recorded within ponds (alpha and gamma diversity). Samples collected during the autumn survey yielded significantly greater macroinvertebrate richness (76% of the total diversity) than either spring or summer surveys. Macroinvertebrate diversity was greatest during autumn in meadow and agricultural ponds, but taxon richness among forest and urban ponds did not differ significantly temporally. The autumn survey provided the highest measures of richness for Coleoptera, Hemiptera and Odonata. However, richness of the aquatic insect order Trichoptera was highest in spring and lowest in autumn. The results illustrate that multiple surveys, covering more than one season, provide the most comprehensive representation of macroinvertebrate biodiversity. When sampling can only be undertaken on one occasion, the most appropriate time to undertake surveys to characterise the macroinvertebrate community biodiversity is during autumn, although this may need to be modified if other floral and faunal groups need to be incorporated into the sampling programme.

From solid to liquid: assessing the release of organic matter into soil solution in response to land-use conversion in Brazilian Oxisols

NASA Astrophysics Data System (ADS)

James, Jason; Gross, Cole; Dwivedi, Pranjal; Bernardi, Rodolpho; Guerrini, Irae; Harrison, Rob; Butman, David

2017-04-01

Recent advances in freshwater research indicate that roughly double the quantity of carbon is exported from soils to streams and rivers than was previously estimated, and that the age of carbon exported from major rivers globally increases with greater human disturbance in the watershed. This implies that human land-use can release old, previously mineral-associated C into solution with subsequent export to groundwater and ultimately freshwater systems where terrestrial organic matter is either mineralized to CO2, stored in aquatic sediments, or exported to the ocean. Consequently, it is important to understand the mechanisms that cause the release of SOM that is mineral-bound into solution in response to human disturbance and land-use change. Research methods have been established to examine both the fast turnover, dissolved pool of soil organic matter (SOM), as well as the slow turnover, mineral-associated pool. However, to better characterize the response of the total SOM pool to disturbance, it is necessary to understand the interactions between these functional pools by examining them both simultaneously. This study seeks to examine the interaction between dissolved organic matter (DOM) and bulk SOM throughout the soil profile in response to conversion of Brazilian Cerrado (savannah forest) to Eucalyptus plantation forest on the same soil type. The water-extractable organic matter was obtained from soil samples down to 150 cm, characterized using fluorescence and NMR spectroscopy, and carbon-dated. Simultaneously, bulk mineral soil samples were analyzed for microbial biomass, carbon content and age, and characterized using Fourier Transform Infrared Spectroscopy. SOM spectra were obtained by washing subsamples with sodium hypochlorite and subtracting the subsequent mineral matrix spectra from bulk soil spectra. Preliminary results show that microbial biomass decreases much more quickly with depth than DOM, suggesting that C released into solution from deeper horizons may be less likely to be intercepted, and thus preferentially leached to groundwater. Native Cerrado forests had substantially more roots compared to Eucalyptus, and also released substantially larger quantities of DOM from their O horizons. Processes operating at the interface between solid and liquid, terrestrial and aquatic are a key unknown in the global carbon cycle. This research permits a unique snapshot into the relationship between DOM and SOM and the response of these pools to land-use change in Brazil.

Microfungal oasis in an oligotrophic desert: diversity patterns and community structure in three freshwater systems of Cuatro Ciénegas, Mexico

PubMed Central

Gasca-Pineda, Jaime; Rosique-Gil, Edmundo; Eguiarte, Luis E.; Espinosa-Asuar, Laura

2016-01-01

The Cuatro Ciénegas Basin (CCB) comprises several oligotrophic aquatic ecosystems limited by phosphorus. These aquatic systems are dominated by a high prokaryotic diversity, shaped by the stress of low nutrient supplies and interspecific competition. Although fungi constitute a diverse and important component of microbial diversity, the microfungal diversity in the CCB remains to be unveiled. With the aim to explore microfungal diversity and ecological patterns in this area, we present the first investigation analyzing cultivable taxa from sediment and water, as well as lignocellulolytic taxa obtained from incubated submerged plant debris, and wood panels in three contrasting freshwater systems in the CCB: Churince, Becerra and Pozas Rojas. We chose a culture-based approach to analyze sediment and water samples in order to obtain fungal cultures, providing opportunities for a posteriori studies, and the possibility of ex situ preservation of the diversity. We evaluated sequence data from the nuclear ribosomal internal transcribed spacer including the 5.8 rDNA region for 126 isolates, revealing 37 OTUs. These OTUs were phylogenetically affiliated to several genera in the fungal phyla: Zygomycota, Basidiomycota, and Ascomycota. We recorded two OTUs with saline affinity, agreeing with previous findings on the prokaryotic communities with ancestral marine resemblances. All the studied systems showed moderate diversity levels, however discrepancies among the diversity indexes were observed, due to the occurrence of abundant taxa in the samples. Our results indicated that lignocellulolytic microfungal communities are dominated by transient fungal taxa, as resident species were not recorded perhaps as a result of the long-term strong competition with the highly adapted prokaryotic community. Moreover, the obtained microfungal taxa occurred mostly on the resident plant debris, rather than submerged wood panels, perhaps as a result of the high adaptation to specific environmental conditions. In conclusion, the CCB possess a moderate taxonomical diversity compared to other arid environments, probably as a result of high selective pressures. Nonetheless, due to high spatial and temporal heterogeneity, the functional fungal diversity was considerable as predicted by the intermediate disturbance hypothesis. Decisively, the assessment of microfungal diversity freshwater systems is relevant, since this ecological group of microorganisms represents an important indicator of trophic complexity and biotic interactions among microbial communities, having important implications for understanding eukaryotic survival at the oligotrophic limit for life. PMID:27280070

Microbial Pre-exposure and Vectorial Competence of Anopheles Mosquitoes

PubMed Central

Dieme, Constentin; Rotureau, Brice; Mitri, Christian

2017-01-01

Anopheles female mosquitoes can transmit Plasmodium, the malaria parasite. During their aquatic life, wild Anopheles mosquito larvae are exposed to a huge diversity of microbes present in their breeding sites. Later, adult females often take successive blood meals that might also carry different micro-organisms, including parasites, bacteria, and viruses. Therefore, prior to Plasmodium ingestion, the mosquito biology could be modulated at different life stages by a suite of microbes present in larval breeding sites, as well as in the adult environment. In this article, we highlight several naturally relevant scenarios of Anopheles microbial pre-exposure that we assume might impact mosquito vectorial competence for the malaria parasite: (i) larval microbial exposures; (ii) protist co-infections; (iii) virus co-infections; and (iv) pathogenic bacteria co-infections. In addition, significant behavioral changes in African Anopheles vectors have been associated with increasing insecticide resistance. We discuss how these ethological modifications may also increase the repertoire of microbes to which mosquitoes could be exposed, and that might also influence their vectorial competence. Studying Plasmodium–Anopheles interactions in natural microbial environments would efficiently contribute to refining the transmission risks. PMID:29376030

Characterization of Microbial Communities Associated With Deep-Sea Hydrothermal Vent Animals of the East Pacific Rise and the Galápagos Rift

NASA Astrophysics Data System (ADS)

Ward, N.; Page, S.; Heidelberg, J.; Eisen, J. A.; Fraser, C. M.

2002-12-01

The composition of microbial communities associated with deep-sea hydrothermal vent animals is of interest because of the key role of bacterial symbionts in driving the chemosynthetic food chain of the vent system, and also because bacterial biofilms attached to animal exterior surfaces may play a part in settlement of larval forms. Sequence analysis of 16S ribosomal RNA (rRNA) genes from such communities provides a snapshot of community structure, as this gene is present in all Bacteria and Archaea, and a useful phylogenetic marker for both cultivated microbial species, and uncultivated species such as many of those found in the deep-sea environment. Specimens of giant tube worms (Riftia pachyptila), mussels (Bathymodiolus thermophilus), and clams (Calyptogena magnifica) were collected during the 2002 R/V Atlantis research cruises to the East Pacific Rise (9N) and Galápagos Rift. Microbial biofilms attached to the exterior surfaces of individual animals were sampled, as were tissues known to harbor chemosynthetic bacterial endosymbionts. Genomic DNA was extracted from the samples using a commercially available kit, and 16S rRNA genes amplified from the mixed bacterial communities using the polymerase chain reaction (PCR) and oligonucleotide primers targeting conserved terminal regions of the 16S rRNA gene. The PCR products obtained were cloned into a plasmid vector and the recombinant plasmids transformed into cells of Escherichia coli. Individual cloned 16S rRNA genes were sequenced at the 5' end of the gene (the most phylogenetically informative region in most taxa) and the sequence data compared to publicly available gene sequence databases, to allow a preliminary assignment of clones to taxonomic groups within the Bacteria and Archaea, and to determine the overall composition and phylogenetic diversity of the animal-associated microbial communities. Analysis of Riftia pachyptila exterior biofilm samples revealed the presence of members of the delta and epsilon proteobacteria, low GC Gram positive bacteria (firmicutes), spirochetes, CFB (Cytophaga-Flavobacterium-Bacteroides) group, green nonsulfur bacteria, acidobacteria, verrucomicrobia, and planctomycetes. The presence of the latter three taxonomic groups is of special interest, as they represent phylogenetically distinct groups within the Bacteria for which specific ecological functions have not yet been identified, but which have been found to be widely distributed and often numerically significant in diverse terrestrial and aquatic habitats. Although further sequencing is required to demonstrate the presence of a Riftia-associated microbial population distinct from that of the surrounding seawater, results available from three Riftia individuals from the East Pacific Rise suggest this to be the case. Analysis of microbial communities associated with the gill tissue of the mussel Bathymodiolus thermophilus shows a population dominated by gamma-Proteobacterial chemoautotrophic symbionts, although lower frequency novel phylotypes have been detected. Representatives of specific taxonomic groups have been selected for sequencing of the complete 16S rRNA gene, and the sequences used to reconstruct phylogenetic trees to more accurately determine the evolutionary relationships between the novel sequences, and available sequences for both cultured and non-cultured bacteria.

Ultrastructural and Single-Cell-Level Characterization Reveals Metabolic Versatility in a Microbial Eukaryote Community from an Ice-Covered Antarctic Lake

PubMed Central

Li, Wei; Podar, Mircea

2016-01-01

ABSTRACT The McMurdo Dry Valleys (MCM) of southern Victoria Land, Antarctica, harbor numerous ice-covered bodies of water that provide year-round liquid water oases for isolated food webs dominated by the microbial loop. Single-cell microbial eukaryotes (protists) occupy major trophic positions within this truncated food web, ranging from primary producers (e.g., chlorophytes, haptophytes, and cryptophytes) to tertiary predators (e.g., ciliates, dinoflagellates, and choanoflagellates). To advance the understanding of MCM protist ecology and the roles of MCM protists in nutrient and energy cycling, we investigated potential metabolic strategies and microbial interactions of key MCM protists isolated from a well-described lake (Lake Bonney). Fluorescence-activated cell sorting (FACS) of enrichment cultures, combined with single amplified genome/amplicon sequencing and fluorescence microscopy, revealed that MCM protists possess diverse potential metabolic capabilities and interactions. Two metabolically distinct bacterial clades (Flavobacteria and Methylobacteriaceae) were independently associated with two key MCM lake microalgae (Isochrysis and Chlamydomonas, respectively). We also report on the discovery of two heterotrophic nanoflagellates belonging to the Stramenopila supergroup, one of which lives as a parasite of Chlamydomonas, a dominate primary producer in the shallow, nutrient-poor layers of the lake. IMPORTANCE Single-cell eukaryotes called protists play critical roles in the cycling of organic matter in aquatic environments. In the ice-covered lakes of Antarctica, protists play key roles in the aquatic food web, providing the majority of organic carbon to the rest of the food web (photosynthetic protists) and acting as the major consumers at the top of the food web (predatory protists). In this study, we utilized a combination of techniques (microscopy, cell sorting, and genomic analysis) to describe the trophic abilities of Antarctic lake protists and their potential interactions with other microbes. Our work reveals that Antarctic lake protists rely on metabolic versatility for their energy and nutrient requirements in this unique and isolated environment. PMID:27084010

Ultrastructural and Single-Cell-Level Characterization Reveals Metabolic Versatility in a Microbial Eukaryote Community from an Ice-Covered Antarctic Lake.

PubMed

Li, Wei; Podar, Mircea; Morgan-Kiss, Rachael M

2016-06-15

The McMurdo Dry Valleys (MCM) of southern Victoria Land, Antarctica, harbor numerous ice-covered bodies of water that provide year-round liquid water oases for isolated food webs dominated by the microbial loop. Single-cell microbial eukaryotes (protists) occupy major trophic positions within this truncated food web, ranging from primary producers (e.g., chlorophytes, haptophytes, and cryptophytes) to tertiary predators (e.g., ciliates, dinoflagellates, and choanoflagellates). To advance the understanding of MCM protist ecology and the roles of MCM protists in nutrient and energy cycling, we investigated potential metabolic strategies and microbial interactions of key MCM protists isolated from a well-described lake (Lake Bonney). Fluorescence-activated cell sorting (FACS) of enrichment cultures, combined with single amplified genome/amplicon sequencing and fluorescence microscopy, revealed that MCM protists possess diverse potential metabolic capabilities and interactions. Two metabolically distinct bacterial clades (Flavobacteria and Methylobacteriaceae) were independently associated with two key MCM lake microalgae (Isochrysis and Chlamydomonas, respectively). We also report on the discovery of two heterotrophic nanoflagellates belonging to the Stramenopila supergroup, one of which lives as a parasite of Chlamydomonas, a dominate primary producer in the shallow, nutrient-poor layers of the lake. Single-cell eukaryotes called protists play critical roles in the cycling of organic matter in aquatic environments. In the ice-covered lakes of Antarctica, protists play key roles in the aquatic food web, providing the majority of organic carbon to the rest of the food web (photosynthetic protists) and acting as the major consumers at the top of the food web (predatory protists). In this study, we utilized a combination of techniques (microscopy, cell sorting, and genomic analysis) to describe the trophic abilities of Antarctic lake protists and their potential interactions with other microbes. Our work reveals that Antarctic lake protists rely on metabolic versatility for their energy and nutrient requirements in this unique and isolated environment. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Ultrastructural and Single-Cell-Level Characterization Reveals Metabolic Versatility in a Microbial Eukaryote Community from an Ice-Covered Antarctic Lake

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

Li, Wei; Podar, Mircea; Morgan-Kiss, Rachael M.

The McMurdo Dry Valleys (MCM) of southern Victoria Land, Antarctica, harbor numerous ice-covered bodies of water that provide year-round liquid water oases for isolated food webs dominated by the microbial loop. Single-cell microbial eukaryotes (protists) occupy major trophic positions within this truncated food web, ranging from primary producers (e.g., chlorophytes, haptophytes, and cryptophytes) to tertiary predators (e.g., ciliates, dinoflagellates, and choanoflagellates). To advance the understanding of MCM protist ecology and the roles of MCM protists in nutrient and energy cycling, we investigated potential metabolic strategies and microbial interactions of key MCM protists isolated from a well-described lake (Lake Bonney). Fluorescence-activatedmore » cell sorting (FACS) of enrichment cultures, combined with single amplified genome/amplicon sequencing and fluorescence microscopy, revealed that MCM protists possess diverse potential metabolic capabilities and interactions. Two metabolically distinct bacterial clades (FlavobacteriaandMethylobacteriaceae) were independently associated with two key MCM lake microalgae (IsochrysisandChlamydomonas, respectively). We also report on the discovery of two heterotrophic nanoflagellates belonging to the Stramenopila supergroup, one of which lives as a parasite ofChlamydomonas, a dominate primary producer in the shallow, nutrient-poor layers of the lake. Single-cell eukaryotes called protists play critical roles in the cycling of organic matter in aquatic environments. In the ice-covered lakes of Antarctica, protists play key roles in the aquatic food web, providing the majority of organic carbon to the rest of the food web (photosynthetic protists) and acting as the major consumers at the top of the food web (predatory protists). In this study, we utilized a combination of techniques (microscopy, cell sorting, and genomic analysis) to describe the trophic abilities of Antarctic lake protists and their potential interactions with other microbes. Ultimately, our work reveals that Antarctic lake protists rely on metabolic versatility for their energy and nutrient requirements in this unique and isolated environment.« less

Ultrastructural and Single-Cell-Level Characterization Reveals Metabolic Versatility in a Microbial Eukaryote Community from an Ice-Covered Antarctic Lake

DOE PAGES

Li, Wei; Podar, Mircea; Morgan-Kiss, Rachael M.

2016-04-15

The McMurdo Dry Valleys (MCM) of southern Victoria Land, Antarctica, harbor numerous ice-covered bodies of water that provide year-round liquid water oases for isolated food webs dominated by the microbial loop. Single-cell microbial eukaryotes (protists) occupy major trophic positions within this truncated food web, ranging from primary producers (e.g., chlorophytes, haptophytes, and cryptophytes) to tertiary predators (e.g., ciliates, dinoflagellates, and choanoflagellates). To advance the understanding of MCM protist ecology and the roles of MCM protists in nutrient and energy cycling, we investigated potential metabolic strategies and microbial interactions of key MCM protists isolated from a well-described lake (Lake Bonney). Fluorescence-activatedmore » cell sorting (FACS) of enrichment cultures, combined with single amplified genome/amplicon sequencing and fluorescence microscopy, revealed that MCM protists possess diverse potential metabolic capabilities and interactions. Two metabolically distinct bacterial clades (FlavobacteriaandMethylobacteriaceae) were independently associated with two key MCM lake microalgae (IsochrysisandChlamydomonas, respectively). We also report on the discovery of two heterotrophic nanoflagellates belonging to the Stramenopila supergroup, one of which lives as a parasite ofChlamydomonas, a dominate primary producer in the shallow, nutrient-poor layers of the lake. Single-cell eukaryotes called protists play critical roles in the cycling of organic matter in aquatic environments. In the ice-covered lakes of Antarctica, protists play key roles in the aquatic food web, providing the majority of organic carbon to the rest of the food web (photosynthetic protists) and acting as the major consumers at the top of the food web (predatory protists). In this study, we utilized a combination of techniques (microscopy, cell sorting, and genomic analysis) to describe the trophic abilities of Antarctic lake protists and their potential interactions with other microbes. Ultimately, our work reveals that Antarctic lake protists rely on metabolic versatility for their energy and nutrient requirements in this unique and isolated environment.« less

Measurement of undisturbed di-nitrogen emissions from aquatic ecosystems

NASA Astrophysics Data System (ADS)

Qin, Shuping, Clough, Timothy, Lou, Jiafa; Hu, Chunsheng; Oenema, Oene; Wrage-Mönnig, Nicole; Zhang, Yuming

2016-04-01

Increased production of reactive nitrogen (Nr) from atmospheric di-nitrogen (N2) during the last century has greatly contributed to increased food production1-4. However, enriching the biosphere with Nr through N fertilizer production, combustion, and biological N2 fixation has also caused a series of negative effects on global ecosystems 5,6, especially aquatic ecosystems7. The main pathway converting Nr back into the atmospheric N2 pool is the last step of the denitrification process, i.e., the reduction of nitrous oxide (N2O) into N2 by micro-organisms7,8. Despite several attempts9,10, there is not yet an accurate, fast and direct method for measuring undisturbed N2 fluxes from denitrification in aquatic sediments at the field scale11-14. Such a method is essential to study the feedback of aquatic ecosystems to Nr inputs1,2,7. Here we show that the measurement of both N2O emission and its isotope signature can be used to infer the undisturbed N2 fluxes from aquatic ecosystems. The microbial reduction of N2O increases the natural abundance of 15N-N2O relative to 14N-N2O (δ15N-N2O). We observed linear relationships between δ15N-N2O and the logarithmic transformed N2O/(N2+N2O) emission ratios. Through independent measurements, we verified that the undisturbed N2 flux from aquatic ecosystems can be inferred from measurements of N2O emissions and the δ15N-N2O signature. Our method allows the determination of field-scale N2 fluxes from undisturbed aquatic ecosystems, and thereby allows model predictions of denitrification rates to be tested. The undisturbed N2 fluxes observed are almost one order of magnitude higher than those estimated by the traditional method, where perturbation of the system occurs, indicating that the ability of aquatic ecosystems to remove Nr may have been severely underestimated.

Determination of the Biologically Relevant Sampling Depth for Terrestrial and Aquatic Ecological Risk Assessments (Final Report)

EPA Science Inventory

The Ecological Risk Assessment Support Center (ERASC) announced the release of the final report, Determination of the Biologically Relevant Sampling Depth for Terrestrial and Aquatic Ecological Risk Assessments. This technical paper provides defensible approximations fo...

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

2015-04-01

Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, D.; Tecon, R.; Ebrahimi, A.; Kleyer, H.; Ilie, O.; Wang, G.

2014-12-01

Microbial life in soil occurs within fragmented aquatic habitats in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world.

Occurrence of antimicrobial agents, drug-resistant bacteria, and genes in the sewage-impacted Vistula River (Poland).

PubMed

Giebułtowicz, Joanna; Tyski, Stefan; Wolinowska, Renata; Grzybowska, Wanda; Zaręba, Tomasz; Drobniewska, Agata; Wroczyński, Piotr; Nałęcz-Jawecki, Grzegorz

2018-02-01

Antimicrobial agents (antimicrobials) are a group of therapeutic and hygienic agents that either kill microorganisms or inhibit their growth. Their occurrence in surface water may reveal harmful effects on aquatic biota and challenge microbial populations. Recently, there is a growing concern over the contamination of surface water with both antimicrobial agents and multidrug-resistant bacteria. The aim of the study was the determination of the presence of selected antimicrobials at specific locations of the Vistula River (Poland), as well as in tap water samples originating from the Warsaw region. Analysis was performed using the liquid chromatography-electrospray ionization-tandem mass spectrometry method. In addition, the occurrence of drug-resistant bacteria and resistance genes was determined using standard procedures. This 2-year study is the first investigation of the simultaneous presence of antimicrobial agents, drug-resistant bacteria, and genes in Polish surface water. In Poland, relatively high concentrations of macrolides are observed in both surface and tap water. Simultaneous to the high macrolide levels in the environment, the presence of the erm B gene, coding the resistance to macrolides, lincosamides, and streptogramin, was detected in almost all sampling sites. Another ubiquitous gene was int1, an element of the 5'-conserved segment of class 1 integrons that encode site-specific integrase. Also, resistant isolates of Enterococcus faecium and Enterococcus faecalis and Gram-negative bacteria were recovered. Multidrug-resistant bacteria isolates of Gram-negative and Enterococcus were also detected. The results show that wastewater treatment plants (WWTP) are the main source of most antimicrobials, resistant bacteria, and genes in the aquatic environment, probably due to partial purification during wastewater treatment processes.

Aquatic Plant/microbial Filters for Treating Septic Tank Effluent

NASA Technical Reports Server (NTRS)

Wolverton, B. C.

1988-01-01

The use of natural biological processes for treating many types of wastewater have been developed by NASA at the John C. Stennis Space Center, NSTL, Mississippi, during the past 15 years. The simplest form of this technology involves the use of aquatic plant/marsh filters for treatment of septic tank effluent. Septic tank effluent from single home units can be treated to advanced secondary levels and beyond by using a 37.2 sq m (400 sq ft) surface area washed gravel filter. This filter is generally 0.3 m (1 ft) deep with a surface cover of approximately 0.15 m (6 in.) of gravel. The plants in this filter are usually aesthetic or ornamental such as calla lily (Zantedeschia aethiopica), canna lily (Canna flaccida), elephant ear (Colocasia esculenta), and water iris (Iris pseudacorus).

Micro-zooplankton grazing as a means of fecal bacteria removal in stormwater BMPs.

PubMed

Burtchett, Jade M; Mallin, Michael A; Cahoon, Lawrence B

2017-06-01

A priority for environmental managers is control of stormwater runoff pollution, especially fecal microbial pollution. This research was designed to determine if fecal bacterial grazing by micro-zooplankton is a significant control on fecal bacteria in aquatic best management practices (BMPs); if grazing differs between a wet detention pond and a constructed wetland; and if environmental factors enhance grazing. Both 3-day grazing tests and 24-h dilution assays were used to determine grazing differences between the two types of BMP. Micro-zooplankton grazing was a stronger bacteria removal mechanism in stormwater wetlands rich in aquatic vegetation compared to a standard wet detention pond, although grazing was important in detention ponds as well. Our experiments indicated that the majority of grazers that fed on fecal bacteria were <20 μm in size. Grazing rates were positively correlated with fecal coliform abundance and increased water temperatures. Enumeration of grazers demonstrated that protozoans were significantly more abundant among wetland vegetation than in open water, and open wetland waters contained more flagellates and dinoflagellates than open wet detention pond waters. Grazing on fecal bacteria in BMPs is enhanced by aquatic vegetation, and grazing in aquatic BMPs in warmer climates should be greater than in cooler climates.

Metal(loid) accumulation in aquatic plants of a mining area: Potential for water quality biomonitoring and biogeochemical prospecting.

PubMed

Favas, Paulo J C; Pratas, João; Rodrigues, Nelson; D'Souza, Rohan; Varun, Mayank; Paul, Manoj S

2018-03-01

Aquatic bryophytes can accumulate extremely high levels of chemical elements because of their unique morphology and physiology which is markedly different from vascular plants. Four aquatic mosses-Fontinalis squamosa, Brachythecium rivulare, Platyhypnidium riparioides, Thamnobryum alopecurum-and a freshwater red alga Lemanea fluviatilis along with water samples from the streams of Góis mine region in Central Portugal were analyzed for 46 elements. Despite being below detection levels in the water samples, the elements Zr, V, Cr, Mo, Ru, Os, Rh, Ir, Pt, Ag, Ge and Bi were obtained in the plant samples. The moss T. alopecurum had the highest mean concentrations of 19 elements followed by B. rivulare (15 elements). Maximum accumulation of Rb, Ta and Au, however, was seen in the alga L. fluviatilis. Bioconcentration factors > 10 6 were obtained for a few metals. The investigation confirms that aquatic bryophytes can be suitable for water quality biomonitoring and biogeochemical prospecting in fresh water bodies owing to their high accumulative capacity of multi-elements from their aquatic ambient. Copyright © 2017 Elsevier Ltd. All rights reserved.

Environmental microbiology as a mosaic of explored ecosystems and issues.

PubMed

Faure, Denis; Bonin, Patricia; Duran, Robert

2015-09-01

Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium's efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.

Environmental bacteriophages: viruses of microbes in aquatic ecosystems

PubMed Central

Sime-Ngando, Télesphore

2014-01-01

Since the discovery 2–3 decades ago that viruses of microbes are abundant in marine ecosystems, viral ecology has grown increasingly to reach the status of a full scientific discipline in environmental sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms, (http://www.isvm.org/) was recently launched. Increasing studies in viral ecology are sources of novel knowledge related to the biodiversity of living things, the functioning of ecosystems, and the evolution of the cellular world. This is because viruses are perhaps the most diverse, abundant, and ubiquitous biological entities in the biosphere, although local environmental conditions enrich for certain viral types through selective pressure. They exhibit various lifestyles that intimately depend on the deep-cellular mechanisms, and are ultimately replicated by members of all three domains of cellular life (Bacteria, Eukarya, Archaea), as well as by giant viruses of some eukaryotic cells. This establishes viral parasites as microbial killers but also as cell partners or metabolic manipulators in microbial ecology. The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e., phages) in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology. PMID:25104950

Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance.

PubMed

Shade, Ashley; Read, Jordan S; Welkie, David G; Kratz, Timothy K; Wu, Chin H; McMahon, Katherine D

2011-10-01

For lake microbes, water column mixing acts as a disturbance because it homogenizes thermal and chemical gradients known to define the distributions of microbial taxa. Our first objective was to isolate hypothesized drivers of lake bacterial response to water column mixing. To accomplish this, we designed an enclosure experiment with three treatments to independently test key biogeochemical changes induced by mixing: oxygen addition to the hypolimnion, nutrient addition to the epilimnion, and full water column mixing. We used molecular fingerprinting to observe bacterial community dynamics in the treatment and control enclosures, and in ambient lake water. We found that oxygen and nutrient amendments simulated the physical-chemical water column environment following mixing and resulted in similar bacterial communities to the mixing treatment, affirming that these were important drivers of community change. These results demonstrate that specific environmental changes can replicate broad disturbance effects on microbial communities. Our second objective was to characterize bacterial community stability by quantifying community resistance, recovery and resilience to an episodic disturbance. The communities in the nutrient and oxygen amendments changed quickly (had low resistance), but generally matched the control composition by the 10th day after treatment, exhibiting resilience. These results imply that aquatic bacterial assemblages are generally stable in the face of disturbance. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Biodegradability and aquatic toxicity of quaternary ammonium-based gemini surfactants: Effect of the spacer on their ecological properties.

PubMed

Garcia, M Teresa; Kaczerewska, Olga; Ribosa, Isabel; Brycki, Bogumił; Materna, Paulina; Drgas, Małgorzata

2016-07-01

Aerobic biodegradability and aquatic toxicity of five types of quaternary ammonium-based gemini surfactants have been examined. The effect of the spacer structure and the head group polarity on the ecological properties of a series of dimeric dodecyl ammonium surfactants has been investigated. Standard tests for ready biodegradability assessment (OECD 310) were conducted for C12 alkyl chain gemini surfactants containing oxygen, nitrogen or a benzene ring in the spacer linkage and/or a hydroxyethyl group attached to the nitrogen atom of the head groups. According to the results obtained, the gemini surfactants examined cannot be considered as readily biodegradable compounds. The negligible biotransformation of the gemini surfactants under the standard biodegradation test conditions was found to be due to their toxic effects on the microbial population responsible for aerobic biodegradation. Aquatic toxicity of gemini surfactants was evaluated against Daphnia magna. The acute toxicity values to Daphnia magna, IC50 at 48 h exposure, ranged from 0.6 to 1 mg/L. On the basis of these values, the gemini surfactants tested should be classified as toxic or very toxic to the aquatic environment. However, the dimeric quaternary ammonium-based surfactants examined result to be less toxic than their corresponding monomeric analogs. Nevertheless the aquatic toxicity of these gemini surfactants can be reduced by increasing the molecule hydrophilicity by adding a heteroatom to the spacer or a hydroxyethyl group to the polar head groups. Copyright © 2016 Elsevier Ltd. All rights reserved.

Improving Aquatic Warbler Population Assessments by Accounting for Imperfect Detection

PubMed Central

Oppel, Steffen; Marczakiewicz, Piotr; Lachmann, Lars; Grzywaczewski, Grzegorz

2014-01-01

Monitoring programs designed to assess changes in population size over time need to account for imperfect detection and provide estimates of precision around annual abundance estimates. Especially for species dependent on conservation management, robust monitoring is essential to evaluate the effectiveness of management. Many bird species of temperate grasslands depend on specific conservation management to maintain suitable breeding habitat. One such species is the Aquatic Warbler (Acrocephalus paludicola), which breeds in open fen mires in Central Europe. Aquatic Warbler populations have so far been assessed using a complete survey that aims to enumerate all singing males over a large area. Because this approach provides no estimate of precision and does not account for observation error, detecting moderate population changes is challenging. From 2011 to 2013 we trialled a new line transect sampling monitoring design in the Biebrza valley, Poland, to estimate abundance of singing male Aquatic Warblers. We surveyed Aquatic Warblers repeatedly along 50 randomly placed 1-km transects, and used binomial mixture models to estimate abundances per transect. The repeated line transect sampling required 150 observer days, and thus less effort than the traditional ‘full count’ approach (175 observer days). Aquatic Warbler abundance was highest at intermediate water levels, and detection probability varied between years and was influenced by vegetation height. A power analysis indicated that our line transect sampling design had a power of 68% to detect a 20% population change over 10 years, whereas raw count data had a 9% power to detect the same trend. Thus, by accounting for imperfect detection we increased the power to detect population changes. We recommend to adopt the repeated line transect sampling approach for monitoring Aquatic Warblers in Poland and in other important breeding areas to monitor changes in population size and the effects of habitat management. PMID:24713994

The C.E.B.A.S.-Minimodule: Behaviour of an Artificial Aquatic Ecological System During Spaceflight

NASA Astrophysics Data System (ADS)

Bluem, V.; Andriske, M.; Paris, F.; Voeste, D.

The C.E.B.A.S.-Minimodule, a closed aquatic ecosystem integrated into a middeck locker and consisting of a Zoological (animal tanks), a Botanical (plant bioreactor), a Microbial (bacteria filter) and an Electronic Component (data acquisition/control system) was flown on the STS-89 spaceshuttle mission in January 1998 for 9 days. Preflight the plant bioreactor was loaded with 53 g of Ceratophyllum demersum (coontail) and the animal tanks with 4 adult pregnant females of the fish, Xiphophorus helleri (sword-tails), 200 juveniles of the same species less than 1 week of age, 38 large and 30 juvenile Biomphalaria glabrata water snails. The filter compartment was filled with 200 g of lava grain inoculated with laboratory strains of ammonia-oxidizing bacteria. A ground reference was undertaken with the same biological setup with a delay of 4 d. After an adaptation period of 5 d the system was closed and integrated into the spaceshuttle one day before launch. Video recordings of the animals were automatically taken for 10 minutes in 2-hour periods; the tapes were changed daily by the astronauts. The chemical and physical data for the aquatic system were within the expected range and were closely comparable in comparison to the ground reference. After 9 d under space conditions, the plant biomass increased to 117 g. The plants were all found in very good condition. All 4 adult female fish were retrieved in a good physiological condition. The juvenile fishes had a survival rate of about 33 %. Almost 97 % of the snails had survived and produced more than 250 neonates and 40 spawning packs. All samples were distributed according to a defined schedule and satisfied all scientific needs of the involved 12 principal investigators. This was the first successful spaceflight of an artificial aquatic ecosystem containing vertebrates, invertebrates, higher plants and microorganisms self-sustained by its inhabitants only. C.E.B.A.S. in a modified form and biological setup is a promising candidate for the early space station utilization as a first midterm experiment

Groundwater geochemistry and microbial community structure in the aquifer transition from volcanic to alluvial areas.

PubMed

Amalfitano, S; Del Bon, A; Zoppini, A; Ghergo, S; Fazi, S; Parrone, D; Casella, P; Stano, F; Preziosi, E

2014-11-15

Groundwaters may act as sinks or sources of organic and inorganic solutes, depending on the relative magnitude of biochemical mobilizing processes and groundwater-surface water exchanges. The objective of this study was to link the lithological and hydrogeological gradients to the aquatic microbial community structure in the transition from aquifer recharge (volcanic formations) to discharge areas (alluvial deposits). A field-scale analysis was performed along a water table aquifer in which volcanic products decreased in thickness and areal extension, while alluvial deposits became increasingly important. We measured the main groundwater physical parameters and the concentrations of major and trace elements. In addition, the microbial community structure was assessed by estimating the occurrence of total coliforms and Escherichia coli, the prokaryotic abundance, the cytometric and phylogenetic community composition. The overall biogeochemical asset differed along the aquifer flow path. The concentration of total and live prokaryotic cells significantly increased in alluvial waters, together with the percentages of Beta- and Delta-Proteobacteria. The microbial propagation over a theoretical groundwater travel time allowed for the identification of microbial groups shifting significantly in the transition between the two different hydrogeochemical facies. The microbial community structure was intimately associated with geochemical changes, thus it should be further considered in view of a better understanding of groundwater ecology and sustainable management strategies. Copyright © 2014 Elsevier Ltd. All rights reserved.

Urban microbial ecology of a freshwater estuary of Lake Michigan

PubMed Central

Fisher, Jenny C.; Newton, Ryan J.; Dila, Deborah K.

2015-01-01

Freshwater estuaries throughout the Great Lakes region receive stormwater runoff and riverine inputs from heavily urbanized population centers. While human and animal feces contained in this runoff are often the focus of source tracking investigations, non-fecal bacterial loads from soil, aerosols, urban infrastructure, and other sources are also transported to estuaries and lakes. We quantified and characterized this non-fecal urban microbial component using bacterial 16S rRNA gene sequences from sewage, stormwater, rivers, harbor/estuary, and the lake surrounding Milwaukee, WI, USA. Bacterial communities from each of these environments had a distinctive composition, but some community members were shared among environments. We used a statistical biomarker discovery tool to identify the components of the microbial community that were most strongly associated with stormwater and sewage to describe an “urban microbial signature,” and measured the presence and relative abundance of these organisms in the rivers, estuary, and lake. This urban signature increased in magnitude in the estuary and harbor with increasing rainfall levels, and was more apparent in lake samples with closest proximity to the Milwaukee estuary. The dominant bacterial taxa in the urban signature were Acinetobacter, Aeromonas, and Pseudomonas, which are organisms associated with pipe infrastructure and soil and not typically found in pelagic freshwater environments. These taxa were highly abundant in stormwater and sewage, but sewage also contained a high abundance of Arcobacter and Trichococcus that appeared in lower abundance in stormwater outfalls and in trace amounts in aquatic environments. Urban signature organisms comprised 1.7% of estuary and harbor communities under baseflow conditions, 3.5% after rain, and >10% after a combined sewer overflow. With predicted increases in urbanization across the Great Lakes, further alteration of freshwater communities is likely to occur with potential long term impacts on the function of estuarine and nearshore ecosystems. PMID:26866046

RELATIONSIPS BETWEEN AQUATIC INVERTEBRATE ASSEMBLAGES AND REACH AND LANDSCAPE ATTRIBUTES ON WADEABLE, WILLAMETTE VALLEY STREAMS IN AGRICULTURAL WATERSHEDS

EPA Science Inventory

In summer 1997, we sampled reaches in 24 wadeable, Willamette Valley ecoregion streams draining agriculturally-infiuenced watersheds. Within these reaches, physical habitat, water chemistry, aquatic invertebrate and fish data and samples were collected. Low-level air photos were ...

ENVIRONMENTAL EFFECTS OF WESTERN COAL COMBUSTION. PART II. THE AQUATIC MACROINVERTEBRATES OF ROSEBUD CREEK, MONTANA

EPA Science Inventory

The aquatic macroinvertebrates of Rosebud Creek, Montana, were sampled between February 1976 and March 1977 to provide data on their abundance, distribution, and diversity. The sampling program was initiated during the first year of operation of the coal-fired power plants locate...

Hydrodynamics of microbial filter feeding

PubMed Central

Asadzadeh, Seyed Saeed; Dölger, Julia; Walther, Jens H.; Andersen, Anders

2017-01-01

Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate amounts of water. Also, the trade-off in the filter spacing remains unexplored, despite its simple formulation: A filter too coarse will allow suitably sized prey to pass unintercepted, whereas a filter too fine will cause strong flow resistance. We quantify the feeding flow of the filter-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), something notoriously difficult to visualize but sporadically observed in the related choanocytes (sponges). A CFD model with a flagellar vane correctly predicts the filtration rate of D. grandis, and using a simple model we can account for the filtration rates of other microbial filter feeders. We finally predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling. PMID:28808016

Hydrodynamics of microbial filter feeding.

PubMed

Nielsen, Lasse Tor; Asadzadeh, Seyed Saeed; Dölger, Julia; Walther, Jens H; Kiørboe, Thomas; Andersen, Anders

2017-08-29

Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate amounts of water. Also, the trade-off in the filter spacing remains unexplored, despite its simple formulation: A filter too coarse will allow suitably sized prey to pass unintercepted, whereas a filter too fine will cause strong flow resistance. We quantify the feeding flow of the filter-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), something notoriously difficult to visualize but sporadically observed in the related choanocytes (sponges). A CFD model with a flagellar vane correctly predicts the filtration rate of D. grandis , and using a simple model we can account for the filtration rates of other microbial filter feeders. We finally predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling.

Predator identity more than predator richness structures aquatic microbial assemblages in Sarracenia purpurea leaves.

PubMed

Canter, Erin J; Cuellar-Gempeler, Catalina; Pastore, Abigail I; Miller, Thomas E; Mason, Olivia U

2018-03-01

The importance of predators in influencing community structure is a well-studied area of ecology. However, few studies test ecological hypotheses of predation in multi-predator microbial communities. The phytotelmic community found within the water-filled leaves of the pitcher plant, Sarracenia purpurea, exhibits a simple trophic structure that includes multiple protozoan predators and microbial prey. Using this system, we sought to determine whether different predators target distinct microorganisms, how interactions among protozoans affect resource (microorganism) use, and how predator diversity affects prey community diversity. In particular, we endeavored to determine if protozoa followed known ecological patterns such as keystone predation or generalist predation. For these experiments, replicate inquiline microbial communities were maintained for seven days with five protozoan species. Microbial community structure was determined by 16S rRNA gene amplicon sequencing (iTag) and analysis. Compared to the control (no protozoa), two ciliates followed patterns of keystone predation by increasing microbial evenness. In pairwise competition treatments with a generalist flagellate, prey communities resembled the microbial communities of the respective keystone predator in monoculture. The relative abundance of the most common bacterial Operational Taxonomic Unit (OTU) in our system decreased compared to the control in the presence of these ciliates. This OTU was 98% similar to a known chitin degrader and nitrate reducer, important functions for the microbial community and the plant host. Collectively, the data demonstrated that predator identity had a greater effect on prey diversity and composition than overall predator diversity. © 2018 by the Ecological Society of America.

Does human activity impact the natural antibiotic resistance background? Abundance of antibiotic resistance genes in 21 Swiss lakes.

PubMed

Czekalski, Nadine; Sigdel, Radhika; Birtel, Julia; Matthews, Blake; Bürgmann, Helmut

2015-08-01

Antibiotic resistance genes (ARGs) are emerging environmental contaminants, known to be continuously discharged into the aquatic environment via human and animal waste. Freshwater aquatic environments represent potential reservoirs for ARG and potentially allow sewage-derived ARG to persist and spread in the environment. This may create increased opportunities for an eventual contact with, and gene transfer to, human and animal pathogens via the food chain or drinking water. However, assessment of this risk requires a better understanding of the level and variability of the natural resistance background and the extent of the human impact. We have analyzed water samples from 21 Swiss lakes, taken at sampling points that were not under the direct influence of local contamination sources and analyzed the relative abundance of ARG using quantitative real-time PCR. Copy numbers of genes mediating resistance to three different broad-spectrum antibiotic classes (sulfonamides: sul1, sul2, tetracyclines: tet(B), tet(M), tet(W) and fluoroquinolones: qnrA) were normalized to copy numbers of bacterial 16S rRNA genes. We used multiple linear regression to assess if ARG abundance is related to human activities in the catchment, microbial community composition and the eutrophication status of the lakes. Sul genes were detected in all sampled lakes, whereas only four lakes contained quantifiable numbers of tet genes, and qnrA remained below detection in all lakes. Our data indicate higher abundance of sul1 in lakes with increasing number and capacity of wastewater treatment plants (WWTPs) in the catchment. sul2 abundance was rather related to long water residence times and eutrophication status. Our study demonstrates the potential of freshwater lakes to preserve antibiotic resistance genes, and provides a reference for ARG abundance from lake systems with low human impact as a baseline for assessing ARG contamination in lake water. Copyright © 2015 Elsevier Ltd. All rights reserved.

Sources and sinks of methane beneath polar ice

NASA Astrophysics Data System (ADS)

Priscu, J. C.; Adams, H. E.; Hand, K. P.; Dore, J. E.; Matheus-Carnevali, P.; Michaud, A. B.; Murray, A. E.; Skidmore, M. L.; Vick-Majors, T.

2014-12-01

Several icy moons of the outer solar system carry subsurface oceans containing many times the volume of liquid water on Earth and may provide the greatest volume of habitable space in our solar system. Functional sub-ice polar ecosystems on Earth provide compelling models for the habitability of extraterrestrial sub-ice oceans. A key feature of sub-ice environments is that most of them receive little to no solar energy. Consequently, organisms inhabiting these environments must rely on chemical energy to assimilate either carbon dioxide or organic molecules to support their metabolism. Methane can be utilized by certain bacteria as both a carbon and energy source. Isotopic data show that methane in Earth's polar lakes is derived from both biogenic and thermogenic sources. Thermogenic sources of methane in the thermokarst lakes of the north slope of Alaska yield supersaturated water columns during winter ice cover that support active populations of methanotrophs during the polar night. Methane in the permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica varies widely in concentration and is produced either by contemporary methanogenesis or is a relic from subglacial flow. Rate measurements revealed that microbial methane oxidation occurs beneath the ice in both the arctic and Antarctic lakes. The first samples collected from an Antarctic subglacial environment beneath 800 m of ice (Subglacial Lake Whillans) revealed an active microbial ecosystem that has been isolated from the atmosphere for many thousands of years. The sediments of Lake Whillans contained high levels of methane with an isotopic signature that indicates it was produced via methanogenesis. The source of this methane appears to be from the decomposition of organic carbon deposited when this region of Antarctica was covered by the sea. Collectively, data from these sub-ice environments show that methane transformations play a key role in microbial community metabolism. The discovery of functional microbial ecosystems in Earth's sub-ice aquatic environments together with what we know about the geochemistry of extraterrestrial ice-covered water worlds provide a compelling case that sub-ice oceans, such as those on Europa and Enceladus, may support microbial life.

Microbe-surface interactions in biofouling and biocorrosion processes.

PubMed

Beech, Iwona B; Sunner, Jan A; Hiraoka, Kenzo

2005-09-01

The presence of microorganisms on material surfaces can have a profound effect on materials performance. Surface-associated microbial growth, i.e. a biofilm, is known to instigate biofouling. The presence of biofilms may promote interfacial physico-chemical reactions that are not favored under abiotic conditions. In the case of metallic materials, undesirable changes in material properties due to a biofilm (or a biofouling layer) are referred to as biocorrosion or microbially influenced corrosion (MIC). Biofouling and biocorrosion occur in aquatic and terrestrial habitats varying in nutrient content, temperature, pressure and pH. Interfacial chemistry in such systems reflects a wide variety of physiological activities carried out by diverse microbial populations thriving within biofilms. Biocorrosion can be viewed as a consequence of coupled biological and abiotic electron-transfer reactions, i.e. redox reactions of metals, enabled by microbial ecology. Microbially produced extracellular polymeric substances (EPS), which comprise different macromolecules, mediate initial cell adhesion to the material surface and constitute a biofilm matrix. Despite their unquestionable importance in biofilm development, the extent to which EPS contribute to biocorrosion is not well-understood. This review offers a current perspective on material/microbe interactions pertinent to biocorrosion and biofouling, with EPS as a focal point, while emphasizing the role atomic force spectroscopy and mass spectrometry techniques can play in elucidating such interactions.

Lysing bloom-causing alga Phaeocystis globosa with microbial algicide: An efficient process that decreases the toxicity of algal exudates

PubMed Central

Cai, Guanjing; Yang, Xujun; Lai, Qiliang; Yu, Xiaoqi; Zhang, Huajun; Li, Yi; Chen, Zhangran; Lei, Xueqian; Zheng, Wei; Xu, Hong; Zheng, Tianling

2016-01-01

Algicidal microbes could effectively remove the harmful algae from the waters. In this study, we were concerned with the ecological influence of an algicide extracted from Streptomyces alboflavus RPS, which could completely lyse the Phaeocystis globosa cells within two days. In microcosms, 4 μg/mL of the microbial algicide could efficiently remove P. globosa cells without suppressing other aquatic organisms. Bioluminescent assays confirmed that the toxicity of microbial algicide at this concentration was negligible. Interestingly, the toxicity of P. globosa exudates was also significantly reduced after being treated with the algicide. Further experiments revealed that the microbial algicide could instantly increase the permeability of the plasma membrane and disturb the photosynthetic system, followed by the deformation of organelles, vacuolization and increasing oxidative stress. The pre-incubation of N-acetyl cysteine (NAC) verified that the rapid damages to the plasma membrane and photosynthetic system caused the algal death in the early phase, and the increasing oxidative stress killed the rest. The late accumulation and possible release of CAT also explained the decreasing toxicity of the algal culture. These results indicated that this microbial algicide has great potential in controlling the growth of P. globosa on site. PMID:26847810

Microbial community structure across a wastewater-impacted riparian buffer zone in the southeastern coastal plain.

PubMed

Ducey, T F; Johnson, P R; Shriner, A D; Matheny, T A; Hunt, P G

2013-01-01

Riparian buffer zones are important for both natural and developed ecosystems throughout the world because of their ability to retain nutrients, prevent soil erosion, protect aquatic environments from excessive sedimentation, and filter pollutants. Despite their importance, the microbial community structures of riparian buffer zones remains poorly defined. Our objectives for this study were twofold: first, to characterize the microbial populations found in riparian buffer zone soils; and second, to determine if microbial community structure could be linked to denitrification enzyme activity (DEA). To achieve these objectives, we investigated the microbial populations of a riparian buffer zone located downslope of a pasture irrigated with swine lagoon effluent, utilizing DNA sequencing of the 16S rDNA, DEA, and quantitative PCR (qPCR) of the denitrification genes nirK, nirS, and nosZ. Clone libraries of the 16S rDNA gene were generated from each of twelve sites across the riparian buffer with a total of 986 partial sequences grouped into 654 operational taxonomic units (OTUs). The Proteobacteria were the dominant group (49.8% of all OTUs), with the Acidobacteria also well represented (19.57% of all OTUs). Analysis of qPCR results identified spatial relationships between soil series, site location, and gene abundance, which could be used to infer both incomplete and total DEA rates.

A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning

USGS Publications Warehouse

Wallenstein, Matthew D.; Hall, Edward K.

2012-01-01

As the earth system changes in response to human activities, a critical objective is to predict how biogeochemical process rates (e.g. nitrification, decomposition) and ecosystem function (e.g. net ecosystem productivity) will change under future conditions. A particular challenge is that the microbial communities that drive many of these processes are capable of adapting to environmental change in ways that alter ecosystem functioning. Despite evidence that microbes can adapt to temperature, precipitation regimes, and redox fluctuations, microbial communities are typically not optimally adapted to their local environment. For example, temperature optima for growth and enzyme activity are often greater than in situ temperatures in their environment. Here we discuss fundamental constraints on microbial adaptation and suggest specific environments where microbial adaptation to climate change (or lack thereof) is most likely to alter ecosystem functioning. Our framework is based on two principal assumptions. First, there are fundamental ecological trade-offs in microbial community traits that occur across environmental gradients (in time and space). These trade-offs result in shifting of microbial function (e.g. ability to take up resources at low temperature) in response to adaptation of another trait (e.g. limiting maintenance respiration at high temperature). Second, the mechanism and level of microbial community adaptation to changing environmental parameters is a function of the potential rate of change in community composition relative to the rate of environmental change. Together, this framework provides a basis for developing testable predictions about how the rate and degree of microbial adaptation to climate change will alter biogeochemical processes in aquatic and terrestrial ecosystems across the planet.

Terrestrially derived glomalin-related soil protein quality as a potential ecological indicator in a peri-urban watershed.

PubMed

Sui, Xueyan; Wu, Zhipeng; Lin, Chen; Zhou, Shenglu

2017-07-01

Glomalin, which sequesters substantial amounts of carbon, plays a critical role in sustaining terrestrial biome functions and contributes to the fate of many pollutants from terrestrial to aquatic ecosystems. Despite having focused on the amount of glomalin produced, very few attempts have been made to understand how landscapes and environmental conditions influence glomalin composition and characteristics. This study focused on glomalin-related soil protein (GRSP) exported as storm runoff including eroded sediment and water that was collected before flowing to surface waters in a peri-urban watershed. GRSP characteristics were assessed by Bradford protein analysis, fluorescence spectroscopy combined with parallel factor analysis (PARAFAC), and the determination of aromaticity based on the specific ultraviolet absorption value (280 nm) and molecular weight. General linear models (GLMs) was established by integrating microbial activity, land cover, water temperature, precipitation, and other solution chemical properties to explain the variations in GRSP characteristics. Results showed that a higher GRSP concentration in agricultural reference sites was produced in the form of specific materials with low molecular weight and aromaticity, as well as high percentage of C1 and C5 components which indicate microbial-processed sources, relative to urbanized and forested sites. Compared with forested land, urbanized land clearly produced runoff GRSP with low molecular weight and aromaticity, as well as more degradation of humic-like materials (C3 component). The highest GLM explaining 89% of the variables, including significant variables (p < 0.05) such as microbial activity, water temperature, and water conductivity, was observed for GRSP characteristics. Therefore, changes in eroded soil GRSP quality can serve as an indicator for improving watershed management and thus protecting aquatic ecosystems.

Extracellular enzyme kinetics scale with resource availability

USGS Publications Warehouse

Sinsabaugh, Robert L.; Belnap, Jayne; Findlay, Stuart G.; Follstad Shah, Jennifer J.; Hill, Brian H.; Kuehn, Kevin A.; Kuske, Cheryl; Litvak, Marcy E.; Martinez, Noelle G.; Moorhead, Daryl L.; Warnock, Daniel D.

2014-01-01

Microbial community metabolism relies on external digestion, mediated by extracellular enzymes that break down complex organic matter into molecules small enough for cells to assimilate. We analyzed the kinetics of 40 extracellular enzymes that mediate the degradation and assimilation of carbon, nitrogen and phosphorus by diverse aquatic and terrestrial microbial communities (1160 cases). Regression analyses were conducted by habitat (aquatic and terrestrial), enzyme class (hydrolases and oxidoreductases) and assay methodology (low affinity and high affinity substrates) to relate potential reaction rates to substrate availability. Across enzyme classes and habitats, the scaling relationships between apparent Vmax and apparent Km followed similar power laws with exponents of 0.44 to 0.67. These exponents, called elasticities, were not statistically distinct from a central value of 0.50, which occurs when the Km of an enzyme equals substrate concentration, a condition optimal for maintenance of steady state. We also conducted an ecosystem scale analysis of ten extracellular hydrolase activities in relation to soil and sediment organic carbon (2,000–5,000 cases/enzyme) that yielded elasticities near 1.0 (0.9 ± 0.2, n = 36). At the metabolomic scale, the elasticity of extracellular enzymatic reactions is the proportionality constant that connects the C:N:P stoichiometries of organic matter and ecoenzymatic activities. At the ecosystem scale, the elasticity of extracellular enzymatic reactions shows that organic matter ultimately limits effective enzyme binding sites. Our findings suggest that one mechanism by which microbial communities maintain homeostasis is regulating extracellular enzyme expression to optimize the short-term responsiveness of substrate acquisition. The analyses also show that, like elemental stoichiometry, the fundamental attributes of enzymatic reactions can be extrapolated from biochemical to community and ecosystem scales.

Legionella prevalence and risk of legionellosis in Japanese households.

PubMed

Kuroki, T; Watanabe, Y; Teranishi, H; Izumiyama, S; Amemura-Maekawa, J; Kura, F

2017-05-01

This study determined the occurrence of legionellae in private houses for which there were no available data on aquatic environments other than the water supply system. From June 2013 to November 2014, we collected 138 water and 90 swab samples from aquatic environments in 19 houses. Legionella DNA was detected via a loop-mediated isothermal amplification assay in 66 (47·8%) water and 17 (18·9%) swab samples. High Legionella DNA detection rates were observed in water samples from washing machines and aquariums. Legionella spp. was isolated from 9 (6·5%) water and 3 (3·3%) swab samples. Legionella pneumophila SG 1 was detected from the outlet water of a bathtub spout and a bath sponge. Use of amoebic co-culture effectively increased legionellae and Legionella DNA detection rates from all sample types. A logistic regression analysis revealed that the heterotrophic plate count was significantly related to Legionella contamination. Our findings indicate that there is a risk of legionellosis from exposure to Legionella spp. in a variety of aquatic environments in residential houses. Control measures for legionellae in houses should include frequent cleaning and disinfecting to reduce heterotrophic bacteria in water and, where possible, preventing aerosolization from aquatic environments.

Creating the spatial framework for National Aquatic Resource Surveys (NARS): Melding National Aquatic Data Sets with Survey Requirements

EPA Science Inventory

The U.S. EPA’s National Aquatic Resource Surveys (NARS) require a consistent spatial representation of the resource target populations being monitored (i.e., rivers and streams, lakes, coastal waters, and wetlands). A sample frame is the GIS representation of this target popula...

Exploring the Use of Participatory Information to Improve Monitoring, Mapping and Assessment of Aquatic Ecosystem Services at Landascape Scales

EPA Science Inventory

Traditionally, the EPA has monitored aquatic ecosystems using statistically rigorous sample designs and intensive field efforts which provide high quality datasets. But by their nature they leave many aquatic systems unsampled, follow a top down approach, have a long lag between ...

Investigating redox processes under diffusive and advective flow conditions using a coupled omics and synchrotron approach

NASA Astrophysics Data System (ADS)

Kemner, K. M.; Boyanov, M.; Flynn, T. M.; O'Loughlin, E. J.; Antonopoulos, D. A.; Kelly, S.; Skinner, K.; Mishra, B.; Brooks, S. C.; Watson, D. B.; Wu, W. M.

2015-12-01

FeIII- and SO42--reducing microorganisms and the mineral phases they produce have profound implications for many processes in aquatic and terrestrial systems. In addition, many of these microbially-catalysed geochemical transformations are highly dependent upon introduction of reactants via advective and diffusive hydrological transport. We have characterized microbial communities from a set of static microcosms to test the effect of ethanol diffusion and sulfate concentration on UVI-contaminated sediment. The spatial distribution, valence states, and speciation of both U and Fe were monitored in situ throughout the experiment by synchrotron x-ray absorption spectroscopy, in parallel with solution measurements of pH and the concentrations of sulfate, ethanol, and organic acids. After reaction initiation, a ~1-cm thick layer of sediment near the sediment-water (S-W) interface became visibly dark. Fe XANES spectra of the layer were consistent with the formation of FeS. Over the 4 year duration of the experiment, U LIII-edge XANES indicated reduction of U, first in the dark layer and then throughout the sediment. Next, the microcosms were disassembled and samples were taken from the overlying water and different sediment regions. We extracted DNA and characterized the microbial community by sequencing 16S rRNA gene amplicons with the Illumina MiSeq platform and found that the community evolved from its originally homogeneous composition, becoming significantly spatially heterogeneous. We have also developed an x-ray accessible column to probe elemental transformations as they occur along the flow path in a porous medium with the purpose of refining reactive transport models (RTMs) that describe coupled physical and biogeochemical processes in environmental systems. The elemental distribution dynamics and the RTMs of the redox driven processes within them will be presented.

Aquatic Plant Control Research Program: Host Specificity of Microbial Flora from Eurasian Watermilfoil

DTIC Science & Technology

1990-06-01

used. 22. When an endophytic fungal population was detected by the plating assay, FAA-preserved plants were examined for internal hyphae with a light...of the tightly attached populations for Colletotrichum and Acremonium, respec- tively. Hyphae of these two fungi growing on the plant surface were fre...revealed 13 intracellular hyphae within the epidermis. Acremonium did not survive this surface-sterilization regimen, and endophytic hyphae were not found

Aerobic biodegradation potential of endocrine-disrupting chemicals in surface-water sediment at Rocky Mountain National Park, USA.

PubMed

Bradley, Paul M; Battaglin, William A; Iwanowicz, Luke R; Clark, Jimmy M; Journey, Celeste A

2016-05-01

Endocrine-disrupting chemicals (EDCs) in surface water and bed sediment threaten the structure and function of aquatic ecosystems. In natural, remote, and protected surface-water environments where contaminant releases are sporadic, contaminant biodegradation is a fundamental driver of exposure concentration, timing, duration, and, thus, EDC ecological risk. Anthropogenic contaminants, including known and suspected EDCs, were detected in surface water and sediment collected from 2 streams and 2 lakes in Rocky Mountain National Park (Colorado, USA). The potential for aerobic EDC biodegradation was assessed in collected sediments using 6 (14) C-radiolabeled model compounds. Aerobic microbial mineralization of natural (estrone and 17β-estradiol) and synthetic (17α-ethinylestradiol) estrogen was significant at all sites. Bed sediment microbial communities in Rocky Mountain National Park also effectively degraded the xenoestrogens bisphenol-A and 4-nonylphenol. The same sediment samples exhibited little potential for aerobic biodegradation of triclocarban, however, illustrating the need to assess a wider range of contaminant compounds. The present study's results support recent concerns over the widespread environmental occurrence of carbanalide antibacterials, like triclocarban and triclosan, and suggest that backcountry use of products containing these compounds should be discouraged. Published 2015 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America.

Simultaneous Recovery of Extracellular and Intracellular DNA Suitable for Molecular Studies from Marine Sediments

PubMed Central

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

2005-01-01

The occurrence of high extracellular DNA concentrations in aquatic sediments (concentrations that are 3 to 4 orders of magnitude greater than those in the water column) might play an important role in biogeochemical cycling, as well as in horizontal gene transfer through natural transformation. Since isolation of extracellular DNA from sediments is a difficult and unsolved task, in this study we developed an efficient procedure to recover simultaneously DNA associated with microbial cells and extracellular DNA from the same sediment sample. This procedure is specifically suitable for studying extracellular DNA because it avoids any contamination with DNA released by cell lysis during handling and extraction. Applying this procedure to different sediment types, we obtained extracellular DNA concentrations that were about 10 to 70 times higher than the intracellular DNA concentrations. Using specific targeted prokaryotic primers, we obtained evidence that extracellular DNA recovered from different sediments did not contain amplifiable 16S rRNA genes. By contrast, using DNA extracted from microbial cells as the template, we always amplified 16S rRNA genes. Although 16S rRNA genes were not detected in extracellular DNA, analyses of the sizes of extracellular DNA indicated the presence of high-molecular-weight fragments that might have contained other gene sequences. This protocol allows investigation of extracellular DNA and its possible participation in natural transformation processes. PMID:15640168

Flow cytometric monitoring of bacterioplankton phenotypic diversity predicts high population-specific feeding rates by invasive dreissenid mussels.

PubMed

Props, Ruben; Schmidt, Marian L; Heyse, Jasmine; Vanderploeg, Henry A; Boon, Nico; Denef, Vincent J

2018-02-01

Species invasion is an important disturbance to ecosystems worldwide, yet knowledge about the impacts of invasive species on bacterial communities remains sparse. Using a novel approach, we simultaneously detected phenotypic and derived taxonomic change in a natural bacterioplankton community when subjected to feeding pressure by quagga mussels, a widespread aquatic invasive species. We detected a significant decrease in diversity within 1 h of feeding and a total diversity loss of 11.6 ± 4.1% after 3 h. This loss of microbial diversity was caused by the selective removal of high nucleic acid populations (29 ± 5% after 3 h). We were able to track the community diversity at high temporal resolution by calculating phenotypic diversity estimates from flow cytometry (FCM) data of minute amounts of sample. Through parallel FCM and 16S rRNA gene amplicon sequencing analysis of environments spanning a broad diversity range, we showed that the two approaches resulted in highly correlated diversity measures and captured the same seasonal and lake-specific patterns in community composition. Based on our results, we predict that selective feeding by invasive dreissenid mussels directly impacts the microbial component of the carbon cycle, as it may drive bacterioplankton communities toward less diverse and potentially less productive states. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

[Effect of sampling effort on taxa richness of aquatic macroinvertebrates and the BMWP/Atitlán index].

PubMed

Reyes-Morales, Fátima; Springer, Monika

2014-04-01

Aquatic macroinvertebrates are the group of organisms most commonly used to determine ecosystem health in water quality studies and freshwater biomonitoring. Nevertheless, the methods and collecting time of biomonitoring have not yet been sufficiently adapted and tested in tropical aquatic environments. Twelve rivers in the Lago de Atitlán watershed in Guatemala were assessed with different collecting times, during the dry season. The method involved the collection of organic and inorganic material including benthic organisms, from different microhabitats, for a pre-established time period (5, 10, 15 min) with a D-frame net. Samples were preserved with 95% ethanol in the field, and sorted in the laboratory. As expected, the analysis showed that the abundance and taxonomic richness was higher with increasing sampling effort. The water quality categories obtained from the newly proposed BMWP/Atitlán index varied among sampling times. However, the Kruskal-Wallis test showed no significant differences between the categories obtained with the index and the number of taxa collected at 10 and 15 min. Therefore, we recommend a reduction of sample time, but maintaining the tree subsamples in order to include most variety of microhabitats and assure a representative sample of the aquatic macroinvertebrates.

Effect of bait and gear type on channel catfish catch and turtle bycatch in a reservoir

USGS Publications Warehouse

Cartabiano, Evan C.; Stewart, David R.; Long, James M.

2014-01-01

Hoop nets have become the preferred gear choice to sample channel catfish Ictalurus punctatus but the degree of bycatch can be high, especially due to the incidental capture of aquatic turtles. While exclusion and escapement devices have been developed and evaluated, few have examined bait choice as a method to reduce turtle bycatch. The use of Zote™ soap has shown considerable promise to reduce bycatch of aquatic turtles when used with trotlines but its effectiveness in hoop nets has not been evaluated. We sought to determine the effectiveness of hoop nets baited with cheese bait or Zote™ soap and trotlines baited with shad or Zote™ soap as a way to sample channel catfish and prevent capture of aquatic turtles. We used a repeated-measures experimental design and treatment combinations were randomly assigned using a Latin-square arrangement. Eight sampling locations were systematically selected and then sampled with either hoop nets or trotlines using Zote™ soap (both gears), waste cheese (hoop nets), or cut shad (trotlines). Catch rates did not statistically differ among the gear–bait-type combinations. Size bias was evident with trotlines consistently capturing larger sized channel catfish compared to hoop nets. Results from a Monte Carlo bootstrapping procedure estimated the number of samples needed to reach predetermined levels of sampling precision to be lowest for trotlines baited with soap. Moreover, trotlines baited with soap caught no aquatic turtles, while hoop nets captured many turtles and had high mortality rates. We suggest that Zote™ soap used in combination with multiple hook sizes on trotlines may be a viable alternative to sample channel catfish and reduce bycatch of aquatic turtles.

Aquatic-macroinvertebrate communities of Prairie-Pothole wetlands and lakes under a changed climate

USGS Publications Warehouse

McLean, Kyle I.; Mushet, David M.; Renton, David A.; Stockwell, Craig A.

2016-01-01

Understanding how aquatic-macroinvertebrate communities respond to changes in climate is important for biodiversity conservation in the Prairie Pothole Region and other wetland-rich landscapes. We sampled macroinvertebrate communities of 162 wetlands and lakes previously sampled from 1966 to 1976, a much drier period compared to our 2012–2013 sampling timeframe. To identify possible influences of a changed climate and predation pressures on macroinvertebrates, we compared two predictors of aquatic-macroinvertebrate communities: ponded-water dissolved-ion concentration and vertebrate-predator presence/abundance. Further, we make inferences of how macroinvertebrate communities were structured during the drier period when the range of dissolved-ion concentrations was much greater and fish occurrence in aquatic habitats was rare. We found that aquatic-macroinvertebrate community structure was influenced by dissolved-ion concentrations through a complex combination of direct and indirect relationships. Ion concentrations also influenced predator occurrence and abundance, which indirectly affected macroinvertebrate communities. It is important to consider both abiotic and biotic gradients when predicting how invertebrate communities will respond to climate change. Generally, in the wetlands and lakes we studied, freshening of ponded water resulted in more homogenous communities than occurred during a much drier period when salinity range among sites was greater.

Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities

PubMed Central

Henderson, Gemma; Cox, Faith; Kittelmann, Sandra; Miri, Vahideh Heidarian; Zethof, Michael; Noel, Samantha J.; Waghorn, Garry C.; Janssen, Peter H.

2013-01-01

Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data from studies in which different sampling techniques, different rumen sample fractions or different DNA extraction methods were used should be avoided. PMID:24040342

Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities.

PubMed

Henderson, Gemma; Cox, Faith; Kittelmann, Sandra; Miri, Vahideh Heidarian; Zethof, Michael; Noel, Samantha J; Waghorn, Garry C; Janssen, Peter H

2013-01-01

Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data from studies in which different sampling techniques, different rumen sample fractions or different DNA extraction methods were used should be avoided.

GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU.

PubMed

Su, Xiaoquan; Wang, Xuetao; Jing, Gongchao; Ning, Kang

2014-04-01

The number of microbial community samples is increasing with exponential speed. Data-mining among microbial community samples could facilitate the discovery of valuable biological information that is still hidden in the massive data. However, current methods for the comparison among microbial communities are limited by their ability to process large amount of samples each with complex community structure. We have developed an optimized GPU-based software, GPU-Meta-Storms, to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples. Our results have shown that GPU-Meta-Storms would be able to compute the pair-wise similarity scores for 10 240 samples within 20 min, which gained a speed-up of >17 000 times compared with single-core CPU, and >2600 times compared with 16-core CPU. Therefore, the high-performance of GPU-Meta-Storms could facilitate in-depth data mining among massive microbial community samples, and make the real-time analysis and monitoring of temporal or conditional changes for microbial communities possible. GPU-Meta-Storms is implemented by CUDA (Compute Unified Device Architecture) and C++. Source code is available at http://www.computationalbioenergy.org/meta-storms.html.

Environmental Control on Microbial Turnover of Leaf Carbon in Streams – Ecological Function of Phototrophic-Heterotrophic Interactions

PubMed Central

Fabian, Jenny; Zlatanović, Sanja; Mutz, Michael; Grossart, Hans-Peter; van Geldern, Robert; Ulrich, Andreas; Gleixner, Gerd; Premke, Katrin

2018-01-01

In aquatic ecosystems, light availability can significantly influence microbial turnover of terrestrial organic matter through associated metabolic interactions between phototrophic and heterotrophic communities. However, particularly in streams, microbial functions vary significantly with the structure of the streambed, that is the distribution and spatial arrangement of sediment grains in the streambed. It is therefore essential to elucidate how environmental factors synergistically define the microbial turnover of terrestrial organic matter in order to better understand the ecological role of photo-heterotrophic interactions in stream ecosystem processes. In outdoor experimental streams, we examined how the structure of streambeds modifies the influence of light availability on microbial turnover of leaf carbon (C). Furthermore, we investigated whether the studied relationships of microbial leaf C turnover to environmental conditions are affected by flow intermittency commonly occurring in streams. We applied leaves enriched with a 13C-stable isotope tracer and combined quantitative and isotope analyses. We thereby elucidated whether treatment induced changes in C turnover were associated with altered use of leaf C within the microbial food web. Moreover, isotope analyses were combined with measurements of microbial community composition to determine whether changes in community function were associated with a change in community composition. In this study, we present evidence, that environmental factors interactively determine how phototrophs and heterotrophs contribute to leaf C turnover. Light availability promoted the utilization of leaf C within the microbial food web, which was likely associated with a promoted availability of highly bioavailable metabolites of phototrophic origin. However, our results additionally confirm that the structure of the streambed modifies light-related changes in microbial C turnover. From our observations, we conclude that the streambed structure influences the strength of photo-heterotrophic interactions by defining the spatial availability of algal metabolites in the streambed and the composition of microbial communities. Collectively, our multifactorial approach provides valuable insights into environmental controls on the functioning of stream ecosystems.

High taxonomic variability despite stable functional structure across microbial communities.

PubMed

Louca, Stilianos; Jacques, Saulo M S; Pires, Aliny P F; Leal, Juliana S; Srivastava, Diane S; Parfrey, Laura Wegener; Farjalla, Vinicius F; Doebeli, Michael

2016-12-05

Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate 'miniature' aquatic ecosystems contained within the foliage of wild bromeliads. We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups. We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable. Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift. Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.

Surface-water-quality assessment of the Yakima River basin in Washington; spatial and temporal distribution of trace elements in water, sediment, and aquatic biota, 1987-91; with a section on geology

USGS Publications Warehouse

Fuhrer, Gregory J.; Cain, Daniel J.; McKenzie, Stuart W.; Rinella, Joseph F.; Crawford, J. Kent; Skach, Kenneth A.; Hornberger, Michelle I.; Gannett, Marshall W.

1999-01-01

The report describes the distribution of trace elements in sediment, water, and aquatic biota in the Yakima River basin, Washington. Trace elements were determined from streambed sediment, suspended sediment, filtered and unfiltered water samples, aquatic insects, clams, fish livers, and fish fillets between 1987 and 1991. The distribution of trace elements in these media was related to local geology and anthropogenic sources. Additionally, annual and instantaneous loads were estimated for trace elements associated with suspended sediment and trace elements in filtered water samples. Trace elements also were screened against U.S. Environmental Protection Agency guidelines established for the protection of human health and aquatic life.

Aquatic fulvic acids in microbially based ecosystems: results from two desert lakes in Antarctica

USGS Publications Warehouse

McKnight, Diane M.; Aiken, G.R.; Smith, R.L.

1991-01-01

These lakes receive very limited input of organic material from the surrounding barren desert, but they sustain algal and bacterial populations under permanent ice cover. One lake has an extensive anoxic zone and high salinities; the other is oxic and has low salinities. Despite these differences, fulvic acids from both lakes had similar elemental compositions, carbon distributions, and amino acid contents, indicating that the chemistry of microbially derived fulvic acvids is not strongly influenced by chemical conditions in the water column. Compared to fulvic acids from other natural waters, these fulvic acids have low C:N atomic ratios (19-25) and low contents of aromatic carbons (5-7% of total carbon atoms); they are most similar to marine fulvic acids. -from Authors

Mixing alters the lytic activity of viruses in the dark ocean.

PubMed

Winter, Christian; Köstner, Nicole; Kruspe, Carl-Philip; Urban, Damaris; Muck, Simone; Reinthaler, Thomas; Herndl, Gerhard J

2018-03-01

In aquatic habitats, viral lysis of prokaryotic cells lowers the overall efficiency of the microbial loop, by which dissolved organic carbon is transfered to higher trophic levels. Mixing of water masses in the dark ocean occurs on a global scale and may have far reaching consequences for the different prokaryotic and virus communities found in these waters by altering the environmental conditions these communities experience. We hypothesize that mixing of deep ocean water masses enhances the lytic activity of viruses infecting prokaryotes. To address this hypothesis, major deep-sea water masses of the Atlantic Ocean such as North Atlantic Deep Water, Mediterranean Sea Overflow Water, Antarctic Intermediate Water, and Antarctic Bottom Water were sampled at five locations. Prokaryotic cells from these samples were collected by filtration and subsequently incubated in virus-reduced water from either the same (control) or a different water mass (transplantation treatment). Additionally, mixtures of prokaryotes obtained from two different water masses were incubated in a mixture of virus-reduced water from the same water masses (control) or in virus-reduced water from the source water masses separately (mixing treatments). Pronounced differences in productivity-related parameters (prokaryotic leucine incorporation, prokaryotic and viral abundance) between water masses caused strong changes in viral lysis of prokaryotes. Often, mixing of water masses increased viral lysis of prokaryotes, indicating that lysogenic viruses were induced into the lytic cycle. Mixing-induced changes in viral lysis had a strong effect on the community composition of prokaryotes and viruses. Our data show that mixing of deep-sea water masses alters levels of viral lysis of prokaryotes and in many cases weakens the efficiency of the microbial loop by enhancing the recycling of organic carbon in the deep ocean. © 2018 by the Ecological Society of America.

Ex situ study of Enterococcus faecalis survival in the recreational waters of the southern coast of the Caspian Sea.

PubMed

Irankhah, Sahar; Soudi, Mohammad Reza; Gharavi, Sara

2016-04-01

The US Environmental Protection Agency has suggested faecal enterococci as the primary bacterial indicators. Of more importance is their direct correlation with swimmer-associated gastroenteritis in recreation water quality monitoring. In contrast to other seawater bodies with 3.5% salinity, the recreational waters in the southern coast of the Caspian Sea possess its own salinity (about 1% w/v) and thus require further investigations to determine the capacity of Enterococcus faecalis as the sole primary microbial index in this unique aquatic environment. The survey of the presence and survival of E. faecalis as a microbial index in the recreational waters of the southern Caspian Sea was carried out using a microcosm as an experimental model. The concentration of E. faecalis cells in samples of seawater were estimated by a standard membrane filtration method using m-Enterococcus agar as the selective culture medium. As the current standard culture-based methods are not reliable enough for the detection of non-growing, damaged and under-tension bacteria, PCR was used to identify the possible VBNC form of the bacterium after disappearance of the culturable cells. A continuous decline in the number of culturable E. faecalis cells resulted in apparent elimination of the bacteria from seawater in a defined period. Detection of intact DNA was possible in the following 60 days. The salinity of about 1% and the self-purification properties of the Caspian Sea make the conditions feasible for the use of this microorganism as a measure of water quality throughout the region. The results confirmed the presence of damaged bacterial cells, namely VBNC forms, indicating the necessity of examining of the sea water samples by using molecular approaches or repair procedures.

Just Around the Riverbend: Seasonal hydrologic controls on dynamic hyporheic zone redox biogeochemistry

NASA Astrophysics Data System (ADS)

Saup, C. M.; Sawyer, A. H.; Williams, K. H.; Wilkins, M.

2017-12-01

Upland rivers host exceptionally strong linkages between the terrestrial and aquatic elemental cycles. The weathering of mineral phases, coupled with degradation of organic matter and anthropogenic influences can result in the export of carbon, metals, and nutrients in upland fluvial systems, often decreasing downstream water quality with negative impacts on both human usage and ecosystem functioning. Within these fluvial networks, zones of hyporheic mixing—regions within the riverbed where surface water and groundwater mix—are thought to represent hotspots of biogeochemical activity, thus exerting significant control over elemental cycling and solute export. To investigate how the deeper exchange of oxic river water into the riverbed during snowmelt-driven peak discharge affects microbial degradation (oxidation) of carbon pools, depth resolved pore water samples were recovered from multiple locations around a representative meander on the East River near Crested Butte, CO. At each location, a series of temperature and redox probes were installed in the riverbed to track the extent of hyporheic mixing and the impact of this process on riverbed biogeochemistry. We complemented this real-time data with discrete samples collected during peak flow, intermediate flow, and base flow at a 10 cm resolution over 70 cm vertical profiles for a suite of microbiological and geochemical analyses. Results revealed elevated pore fluid concentrations of dissolved metals and recalcitrant DOC species under reducing conditions induced by base flow, while regions that were more influenced by down-welling oxic surface water hosted distinct microbial communities and lower metal concentrations. Overall, our results indicate that mixing-driven vertical redox gradients exert a strong control on biogeochemical processing in riverbeds, with implications for downstream water quality and solute export from watersheds.

Wastewater and Saltwater: Studying the Biogeochemistry and Microbial Activity Associated with Wastewater Inputs to San Francisco Bay

NASA Astrophysics Data System (ADS)

Challenor, T.; Menendez, A. D.; Damashek, J.; Francis, C. A.; Casciotti, K. L.

2014-12-01

Nitrification is the process of converting ammonium (NH­­4+) into nitrate (NO3-), and is a crucial step in removing nitrogen (N) from aquatic ecosystems. This process is governed by ammonia-oxidizing bacteria (AOB) and archaea (AOA) that utilize the ammonia monooxygenase gene (amoA). Studying the rates of nitrification and the abundances of ammonia-oxidizing microorganisms in south San Francisco Bay's Artesian Slough, which receives treated effluent from the massive San Jose-Santa Clara Regional Wastewater Facility, are important for understanding the cycling of nutrients in this small but complex estuary. Wastewater inputs can have negative environmental impacts, such as the release of nitrous oxide, a byproduct of nitrification and a powerful greenhouse gas. Nutrient inputs can also increase productivity and sometimes lead to oxygen depletion. Assessing the relative abundance and diversity of AOA and AOB, along with measuring nitrification rates gives vital information about the biology and biogeochemistry of this important N-cycling process. To calculate nitrification rates, water samples were spiked with 15N-labeled ammonium and incubated in triplicate for 24 hours. Four time-points were extracted across the incubation and the "denitrifier" method was used to measure the isotopic ratio of nitrate in the samples over time. In order to determine relative ratios of AOB to AOA, DNA was extracted from water samples and used in clade-specific amoA PCR assays. Nitrification rates were detectable in all locations sampled and were higher than in other regions of the bay, as were concentrations of nitrate and ammonium. Rates were highest in the regions of Artesian Slough most directly affected by wastewater effluent. AOB vastly outnumbered AOA, which is consistent with other studies showing that AOB prefer high nutrient environments. AOB diversity includes clades of Nitrosospira and Nitrosomonas prevalent in estuarine settings. Many of the sequenced genes are related to estuarine sediment found at other sites in the San Francisco Bay as well as the Chesapeake Bay, China East Sea, and Pearl River Estuary. Our data provide evidence for the path that N takes once entering the estuary and also further characterize the behavior of nitrifying microorganisms in extremely high-nutrient aquatic environments.

Contrasting response to nutrient manipulation in Arctic mesocosms are reproduced by a minimum microbial food web model.

PubMed

Larsen, Aud; Egge, Jorun K; Nejstgaard, Jens C; Di Capua, Iole; Thyrhaug, Runar; Bratbak, Gunnar; Thingstad, T Frede

2015-03-01

A minimum mathematical model of the marine pelagic microbial food web has previously shown to be able to reproduce central aspects of observed system response to different bottom-up manipulations in a mesocosm experiment Microbial Ecosystem Dynamics (MEDEA) in Danish waters. In this study, we apply this model to two mesocosm experiments (Polar Aquatic Microbial Ecology (PAME)-I and PAME-II) conducted at the Arctic location Kongsfjorden, Svalbard. The different responses of the microbial community to similar nutrient manipulation in the three mesocosm experiments may be described as diatom-dominated (MEDEA), bacteria-dominated (PAME-I), and flagellated-dominated (PAME-II). When allowing ciliates to be able to feed on small diatoms, the model describing the diatom-dominated MEDEA experiment give a bacteria-dominated response as observed in PAME I in which the diatom community comprised almost exclusively small-sized cells. Introducing a high initial mesozooplankton stock as observed in PAME-II, the model gives a flagellate-dominated response in accordance with the observed response also of this experiment. The ability of the model originally developed for temperate waters to reproduce population dynamics in a 10°C colder Arctic fjord, does not support the existence of important shifts in population balances over this temperature range. Rather, it suggests a quite resilient microbial food web when adapted to in situ temperature. The sensitivity of the model response to its mesozooplankton component suggests, however, that the seasonal vertical migration of Arctic copepods may be a strong forcing factor on Arctic microbial food webs.

Contrasting response to nutrient manipulation in Arctic mesocosms are reproduced by a minimum microbial food web model

PubMed Central

Larsen, Aud; Egge, Jorun K; Nejstgaard, Jens C; Di Capua, Iole; Thyrhaug, Runar; Bratbak, Gunnar; Thingstad, T Frede

2015-01-01

A minimum mathematical model of the marine pelagic microbial food web has previously shown to be able to reproduce central aspects of observed system response to different bottom-up manipulations in a mesocosm experiment Microbial Ecosystem Dynamics (MEDEA) in Danish waters. In this study, we apply this model to two mesocosm experiments (Polar Aquatic Microbial Ecology (PAME)-I and PAME-II) conducted at the Arctic location Kongsfjorden, Svalbard. The different responses of the microbial community to similar nutrient manipulation in the three mesocosm experiments may be described as diatom-dominated (MEDEA), bacteria-dominated (PAME-I), and flagellated-dominated (PAME-II). When allowing ciliates to be able to feed on small diatoms, the model describing the diatom-dominated MEDEA experiment give a bacteria-dominated response as observed in PAME I in which the diatom community comprised almost exclusively small-sized cells. Introducing a high initial mesozooplankton stock as observed in PAME-II, the model gives a flagellate-dominated response in accordance with the observed response also of this experiment. The ability of the model originally developed for temperate waters to reproduce population dynamics in a 10°C colder Arctic fjord, does not support the existence of important shifts in population balances over this temperature range. Rather, it suggests a quite resilient microbial food web when adapted to in situ temperature. The sensitivity of the model response to its mesozooplankton component suggests, however, that the seasonal vertical migration of Arctic copepods may be a strong forcing factor on Arctic microbial food webs. PMID:26074626

Dissolved oxygen: Chapter 6

USGS Publications Warehouse

Senn, David; Downing-Kunz, Maureen; Novick, Emily

2016-01-01

Dissolved oxygen (DO) concentration serves as an important indicator of estuarine habitat condition, because all aquatic macro-organisms require some minimum DO level to survive and prosper. The instantaneous DO concentration, measured at a specific location in the water column, results from a balance between multiple processes that add or remove oxygen (Figure 6.1): primary production produces O2; aerobic respiration in the water column and sediments consumes O2; abiotic or microbially-mediated biogeochemical reactions utilize O2 as an oxidant (e.g., oxidation of ammonium, sulfide, and ferrous iron); O2 exchange occurs across the air:water interface in response to under- or oversaturated DO concentrations in the water column; and water currents and turbulent mixing transport DO into and out of zones in the water column. If the oxygen loss rate exceeds the oxygen production or input rate, DO concentration decreases. When DO losses exceed production or input over a prolonged enough period of time, hypoxia ((<2-3 mg/L) or anoxia can develop. Persistent hypoxia or anoxia causes stress or death in aquatic organism populations, or for organisms that can escape a hypoxic or anoxic area, the loss of habitat. In addition, sulfide, which is toxic to aquatic organisms and causes odor problems, escapes from sediments under low oxygen conditions. Low dissolved oxygen is a common aquatic ecosystem response to elevated organic

Global analysis of river systems: from Earth system controls to Anthropocene syndromes.

PubMed Central

Meybeck, Michel

2003-01-01

Continental aquatic systems from rivers to the coastal zone are considered within two perspectives: (i) as a major link between the atmosphere, pedosphere, biosphere and oceans within the Earth system with its Holocene dynamics, and (ii) as water and aquatic biota resources progressively used and transformed by humans. Human pressures have now reached a state where the continental aquatic systems can no longer be considered as being controlled by only Earth system processes, thus defining a new era, the Anthropocene. Riverine changes, now observed at the global scale, are described through a first set of syndromes (flood regulation, fragmentation, sediment imbalance, neo-arheism, salinization, chemical contamination, acidification, eutrophication and microbial contamination) with their related causes and symptoms. These syndromes have direct influences on water uses, either positive or negative. They also modify some Earth system key functions such as sediment, water, nutrient and carbon balances, greenhouse gas emissions and aquatic biodiversity. Evolution of river syndromes over the past 2000 years is complex: it depends upon the stages of regional human development and on natural conditions, as illustrated here for the chemical contamination syndrome. River damming, eutrophication and generalized decrease of river flow due to irrigation are some of the other global features of river changes. Future management of river systems should also consider these long-term impacts on the Earth system. PMID:14728790

Differential Regulation by Organic Compounds and Heavy Metals of Multiple Laccase Genes in the Aquatic Hyphomycete Clavariopsis aquatica

PubMed Central

Solé, Magali; Müller, Ines; Pecyna, Marek J.; Fetzer, Ingo; Harms, Hauke

2012-01-01

To advance the understanding of the molecular mechanisms controlling microbial activities involved in carbon cycling and mitigation of environmental pollution in freshwaters, the influence of heavy metals and natural as well as xenobiotic organic compounds on laccase gene expression was quantified using quantitative real-time PCR (qRT-PCR) in an exclusively aquatic fungus (the aquatic hyphomycete Clavariopsis aquatica) for the first time. Five putative laccase genes (lcc1 to lcc5) identified in C. aquatica were differentially expressed in response to the fungal growth stage and potential laccase inducers, with certain genes being upregulated by, e.g., the lignocellulose breakdown product vanillic acid, the endocrine disruptor technical nonylphenol, manganese, and zinc. lcc4 is inducible by vanillic acid and most likely encodes an extracellular laccase already excreted during the trophophase of the organism, suggesting a function during fungal substrate colonization. Surprisingly, unlike many laccases of terrestrial fungi, none of the C. aquatica laccase genes was found to be upregulated by copper. However, copper strongly increases extracellular laccase activity in C. aquatica, possibly due to stabilization of the copper-containing catalytic center of the enzyme. Copper was found to half-saturate laccase activity already at about 1.8 μM, in favor of a fungal adaptation to low copper concentrations of aquatic habitats. PMID:22544244

Viral impacts on microbial carbon cycling in thawing permafrost soils

NASA Astrophysics Data System (ADS)

Trubl, G. G.; Roux, S.; Bolduc, B.; Jang, H. B.; Emerson, J. B.; Solonenko, N.; Li, F.; Solden, L. M.; Vik, D. R.; Wrighton, K. C.; Saleska, S. R.; Sullivan, M. B.; Rich, V. I.

2017-12-01

Permafrost contains 30-50% of global soil carbon (C) and is rapidly thawing. While the fate of this C is unknown, it will be shaped in part by microbes and their associated viruses, which modulate host activities via mortality and metabolic control. To date, viral research in soils has been outpaced by that in aquatic environments, due to the technical challenges of accessing viruses as well as the dramatic physicochemical heterogeneity in soils. Here, we describe advances in soil viromics from our research on permafrost-associated soils, and their implications for associated terrestrial C cycling. First, we optimized viral resuspension-DNA extraction methods for a range of soil types. Second, we applied cutting-edge viral-specific informatics methods to recover viral populations, define their gene content, connect them to potential hosts, and analyze their relationships to environmental parameters. A total of 781 viral populations were recovered from size-fractionated virus samples of three soils along a permafrost thaw gradient. Ecological analyses revealed endemism as recovered viral populations were largely unique to each habitat and unlike those in aquatic communities. Genome- and network-based classification assigned these viruses into 226 viral clusters (VCs; genus-level taxonomy), 55% of which were novel. This increases the number of VCs by a third and triples the number of soil viral populations in the RefSeq database (currently contains 256 VCs and 316 soil viral populations). Genomic analyses revealed 85% of the genes were functionally unknown, though 5% of the annotatable genes contained C-related auxiliary metabolic genes (AMGs; e.g. glycoside hydrolases). Using sequence-based features and microbial population genomes, we were able to in silico predict hosts for 30% of the viral populations. The identified hosts spanned 3 phyla and 6 genera but suggested these viruses have species-specific host ranges as >80% of hosts for a given virus were in the same species. Several identified hosts (e.g. Acidobacterium) are dominant community members that play major roles in C cycling through organic matter degradation. Together these findings show that permafrost viruses play a major role in the fate of soil C through infection of key hosts and metabolic reprogramming using specific C cycling AMGs.

Towards a universal microbial inoculum for dissolved organic carbon degradation experiments

NASA Astrophysics Data System (ADS)

Pastor, Ada; Catalán, Núria; Gutiérrez, Carmen; Nagar, Nupur; Casas-Ruiz, Joan P.; Obrador, Biel; von Schiller, Daniel; Sabater, Sergi; Petrovic, Mira; Borrego, Carles M.; Marcé, Rafael

2017-04-01

Dissolved organic carbon (DOC) is the largest biologically available pool of organic carbon in aquatic ecosystems and its degradation along the land-to-ocean continuum has implications for carbon cycling from local to global scales. DOC biodegradability is usually assessed by incubating filtered water inoculated with native microbial assemblages in the laboratory. However, the use of a native inoculum from several freshwaters, without having a microbial-tailored design, hampers our ability to tease apart the relative contribution of the factors driving DOC degradation from the effects of local microbial communities. The use of a standard microbial inoculum would allow researchers to disentangle the drivers of DOC degradation from the metabolic capabilities of microbial communities operating in situ. With this purpose, we designed a bacterial inoculum to be used in experiments of DOC degradation in freshwater habitats. The inoculum is composed of six bacterial strains that easily grow under laboratory conditions, possess a versatile metabolism and are able to grow under both aerobic and anaerobic conditions. The mixed inoculum showed higher DOC degradation rates than those from their isolated bacterial components and the consumption of organic substrates was consistently replicated. Moreover, DOC degradation rates obtained using the designed inoculum were responsive across a wide range of natural water types differing in DOC concentration and composition. Overall, our results show the potential of the designed inoculum as a tool to discriminate between the effects of environmental drivers and intrinsic properties of DOC on degradation dynamics.

Exploration of Microbial Diversity and Community Structure of Lonar Lake: The Only Hypersaline Meteorite Crater Lake within Basalt Rock

PubMed Central

Paul, Dhiraj; Kumbhare, Shreyas V.; Mhatre, Snehit S.; Chowdhury, Somak P.; Shetty, Sudarshan A.; Marathe, Nachiket P.; Bhute, Shrikant; Shouche, Yogesh S.

2016-01-01

Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21–47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments. PMID:26834712

Influence of Salinity on Bacterioplankton Communities from the Brazilian Rain Forest to the Coastal Atlantic Ocean

PubMed Central

Silveira, Cynthia B.; Vieira, Ricardo P.; Cardoso, Alexander M.; Paranhos, Rodolfo; Albano, Rodolpho M.; Martins, Orlando B.

2011-01-01

Background Planktonic bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems, however, the taxa that make up these communities are poorly known. The aim of this study was to investigate bacterial communities in aquatic ecosystems at Ilha Grande, Rio de Janeiro, Brazil, a preserved insular environment of the Atlantic rain forest and how they correlate with a salinity gradient going from terrestrial aquatic habitats to the coastal Atlantic Ocean. Methodology/Principal Findings We analyzed chemical and microbiological parameters of water samples and constructed 16S rRNA gene libraries of free living bacteria obtained at three marine (two coastal and one offshore) and three freshwater (water spring, river, and mangrove) environments. A total of 836 sequences were analyzed by MOTHUR, yielding 269 freshwater and 219 marine operational taxonomic units (OTUs) grouped at 97% stringency. Richness and diversity indexes indicated that freshwater environments were the most diverse, especially the water spring. The main bacterial group in freshwater environments was Betaproteobacteria (43.5%), whereas Cyanobacteria (30.5%), Alphaproteobacteria (25.5%), and Gammaproteobacteria (26.3%) dominated the marine ones. Venn diagram showed no overlap between marine and freshwater OTUs at 97% stringency. LIBSHUFF statistics and PCA analysis revealed marked differences between the freshwater and marine libraries suggesting the importance of salinity as a driver of community composition in this habitat. The phylogenetic analysis of marine and freshwater libraries showed that the differences in community composition are consistent. Conclusions/Significance Our data supports the notion that a divergent evolutionary scenario is driving community composition in the studied habitats. This work also improves the comprehension of microbial community dynamics in tropical waters and how they are structured in relation to physicochemical parameters. Furthermore, this paper reveals for the first time the pristine bacterioplankton communities in a tropical island at the South Atlantic Ocean. PMID:21408023

Influence of salinity on bacterioplankton communities from the Brazilian rain forest to the coastal Atlantic Ocean.

PubMed

Silveira, Cynthia B; Vieira, Ricardo P; Cardoso, Alexander M; Paranhos, Rodolfo; Albano, Rodolpho M; Martins, Orlando B

2011-03-09

Planktonic bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems, however, the taxa that make up these communities are poorly known. The aim of this study was to investigate bacterial communities in aquatic ecosystems at Ilha Grande, Rio de Janeiro, Brazil, a preserved insular environment of the Atlantic rain forest and how they correlate with a salinity gradient going from terrestrial aquatic habitats to the coastal Atlantic Ocean. We analyzed chemical and microbiological parameters of water samples and constructed 16S rRNA gene libraries of free living bacteria obtained at three marine (two coastal and one offshore) and three freshwater (water spring, river, and mangrove) environments. A total of 836 sequences were analyzed by MOTHUR, yielding 269 freshwater and 219 marine operational taxonomic units (OTUs) grouped at 97% stringency. Richness and diversity indexes indicated that freshwater environments were the most diverse, especially the water spring. The main bacterial group in freshwater environments was Betaproteobacteria (43.5%), whereas Cyanobacteria (30.5%), Alphaproteobacteria (25.5%), and Gammaproteobacteria (26.3%) dominated the marine ones. Venn diagram showed no overlap between marine and freshwater OTUs at 97% stringency. LIBSHUFF statistics and PCA analysis revealed marked differences between the freshwater and marine libraries suggesting the importance of salinity as a driver of community composition in this habitat. The phylogenetic analysis of marine and freshwater libraries showed that the differences in community composition are consistent. Our data supports the notion that a divergent evolutionary scenario is driving community composition in the studied habitats. This work also improves the comprehension of microbial community dynamics in tropical waters and how they are structured in relation to physicochemical parameters. Furthermore, this paper reveals for the first time the pristine bacterioplankton communities in a tropical island at the South Atlantic Ocean.

Visible-light-enhanced Cr(VI) reduction at Pd-decorated silicon nanowire photocathode in photoelectrocatalytic microbial fuel cell.

PubMed

Han, He-Xing; Shi, Chen; Zhang, Nan; Yuan, Li; Sheng, Guo-Ping

2018-10-15

Hexavalent chromium (Cr(VI)) is a prominent toxic metal with significant adverse human health effects. Photocatalytic reduction of Cr(VI) to less-toxic trivalent chromium (Cr(III)) is a promising method for removing Cr(VI) from aquatic environments. However, this technique often suffers from electron-hole recombination of semiconductors and poor reduction efficiency. The photoelectrocatalytic microbial fuel cell (Photo-MFC), which can use wastewater and light to recover electricity, has recently been proven to improve the separation of photocarriers of semiconductors and enhance cathodic reduction of pollutants. Here, the reduction of Cr(VI) was investigated in a Photo-MFC with a Pd-decorated p-type silicon nanowire (Pd/SiNW) photocathode and a bioanode under visible light. The Cr(VI) reduction efficiency reached 98.7% in 8 h under visible light, which was much higher than that under dark condition (56.2%) and open-circuit condition (19.4%). The enhanced Cr(VI) removal was mainly attributed to the synergistic effect of Pd/SiNW photocathode and bioanode. Cr(VI) reduction in the Photo-MFC fitted well with pseudo-first-order kinetics. The kinetics constants and reduction efficiencies of Cr(VI) decreased with the increase of pH, initial Cr(VI) concentration and external resistance. This work provides a promising alternative to mitigate Cr(VI) pollution in aquatic environments. Copyright © 2018 Elsevier B.V. All rights reserved.

Defining Established and Emerging Microbial Risks in the Aquatic Environment: Current Knowledge, Implications, and Outlooks

PubMed Central

Rowan, Neil J.

2011-01-01

This timely review primarily addresses important but presently undefined microbial risks to public health and to the natural environment. It specifically focuses on current knowledge, future outlooks and offers some potential alleviation strategies that may reduce or eliminate the risk of problematic microbes in their viable but nonculturable (VBNC) state and Cryptosporidium oocysts in the aquatic environment. As emphasis is placed on water quality, particularly surrounding efficacy of decontamination at the wastewater treatment plant level, this review also touches upon other related emerging issues, namely, the fate and potential ecotoxicological impact of untreated antibiotics and other pharmaceutically active compounds in water. Deciphering best published data has elucidated gaps between science and policy that will help stakeholders work towards the European Union's Water Framework Directive (2000/60/EC), which provides an ambitious legislative framework for water quality improvements within its region and seeks to restore all water bodies to “good ecological status” by 2015. Future effective risk-based assessment and management, post definition of the plethora of dynamic inter-related factors governing the occurrence, persistence and/or control of these presently undefined hazards in water will also demand exploiting and harnessing tangential advances in allied disciplines such as mathematical and computer modeling that will permit efficient data generation and transparent reporting to be undertaken by well-balanced consortia of stakeholders. PMID:20976256

Effects of 2 fungicide formulations on microbial and macroinvertebrate leaf decomposition under laboratory conditions

USGS Publications Warehouse

Elskus, Adria; Smalling, Kelly L.; Hladik, Michelle; Kuivila, Kathryn

2016-01-01

Aquatic fungi contribute significantly to the decomposition of leaves in streams, a key ecosystem service. However, little is known about the effects of fungicides on aquatic fungi and macroinvertebrates involved with leaf decomposition. Red maple (Acer rubrum) leaves were conditioned in a stream to acquire microbes (bacteria and fungi), or leached in tap water (unconditioned) to simulate potential reduction of microbial biomass by fungicides. Conditioned leaves were exposed to fungicide formulations QUILT (azoxystrobin + propiconazole) or PRISTINE (boscalid + pyraclostrobin), in the presence and absence of the leaf shredder, Hyalella azteca (amphipods; 7-d old at start of exposures) for 14 d at 23 °C. QUILT formulation (~ 0.3 μg/L, 1.8 μg/L, 8 μg/L) tended to increase leaf decomposition by amphipods (not significant) without a concomitant increase in amphipod biomass, indicating potential increased consumption of leaves with reduced nutritional value. PRISTINE formulation (~ 33 μg/L) significantly reduced amphipod growth and biomass (p<0.05), effects similar to those observed with unconditioned controls. The significant suppressive effects of PRISTINE on amphipod growth, and the trend towards increased leaf decomposition with increasing QUILT concentration, indicate the potential for altered leaf decay in streams exposed to fungicides. Further work is needed to evaluate fungicide effects on leaf decomposition under conditions relevant to stream ecosystems, including temperature shifts and pulsed exposures to pesticide mixtures.

Occurrence of fungal metabolites--fumonisins at the ng/L level in aqueous environmental samples.

PubMed

Waśkiewicz, Agnieszka; Bocianowski, Jan; Perczak, Adam; Goliński, Piotr

2015-08-15

The B-series fumonisins (FBs) are some of the most prevalent mycotoxins produced as a secondary metabolite by Fusarium species growing on cereals. For decades they have been studied extensively in food and feed products, but there is no information about their occurrence in the aquatic environment or about how these mycotoxins are transported to the surface water and the groundwater. The aim of this study was to clarify the causes of fumonisin occurrence in aquatic ecosystems by examining the relation between mycotoxin contamination of crops and their levels in the aquatic environment. Water samples were collected from drainage ditches and wells or watercourses located in agricultural areas in the Wielkopolska region, Poland. Our research conducted on an annual basis showed the seasonal variability of fumonisin B1 concentration in the analyzed water samples, with the highest concentration in the post-harvest season (September to October) at 48.2 ng L(-1), and the lowest in winter and spring at 21.9 ng L(-1). Fumonisins B2 and B3 in water samples were not detected. Cereal samples were collected in the harvest season from each agricultural area close to tested water bodies. Mycotoxins were present in all cereal samples at concentrations from 43.3 to 1055.9 ng g(-1). Our results confirm that fumonisins are transported to aquatic systems by rainwater through soil. On the basis of available literature, this is the first report concerning the presence of fumonisin B1 in different aquatic environments. To date their ecotoxicological effects are largely unknown and require further investigation. Copyright © 2015 Elsevier B.V. All rights reserved.

Detection of viable Cronobacter spp. (Enterobacter sakazakii) by one-step RT-PCR in dry aquatic product.

PubMed

Ye, Yingwang; Wu, Qingping; Zhang, Jumei; Jiang, He; Hu, Wang

2012-11-01

Cronobacter are opportunistic food-borne pathogens associated with meningitis, sepsis, and necrotizing enterocolitis. Little attempt has focused on detection of viable cell of Cronobacter spp. in dry aquatic products, which were frequently used for raw materials of infant foods due to high nutrition. In this paper, one-step reverse transcription polymerase chain reaction (RT-PCR) was developed for detection of viable Cronobacter spp. in dry aquatic products. Specificity test indicated that clearly expected amplicon in size 469 bp was amplified from RNA of Cronobacter, but not from RNA of negative controls and DNA of Cronobacter strains. The sensitivity was 10(4) CFU/mL of Cronobacter strain in artificially fish meal samples and 10(1) CFU/mL of Cronobacter after 10-h enrichment. In a total of 81 dry aquatic products, 9.8%, 8.6%, and 9.8% of samples were found to be positive for Cronobacter by one-step RT-PCR, U.S. Food and Drug Administration method, and Druggan-Forsythe-Iversen medium, respectively. The results clearly indicated that one-step RT-PCR could avoid the interference of residual DNA of Cronobacter in food samples and be used to specifically detect viable Cronobacter spp. for large-scale monitoring of food samples. The use of rapid and specific detection of food borne pathogens in food samples was most of importance for control and precaution of food borne diseases. In this study, one-step RT-PCR was developed for detection of Cronobacter spp. in aquatic products. A comparison of different methods for detection of Cronobacter indicated that the newly developed method could be widely used to specifically detect Cronobacter spp. in food samples. © 2012 Institute of Food Technologists®

Manuals Used in the National Aquatic Resource Surveys

EPA Pesticide Factsheets

Various manuals are used to communicate the methods and guidelines for the National Aquatic Resource Surveys. The Field Operations Manual: outlines the field protocols that crews will utilize to sample sites.

A heteroskedastic error covariance matrix estimator using a first-order conditional autoregressive Markov simulation for deriving asympotical efficient estimates from ecological sampled Anopheles arabiensis aquatic habitat covariates

PubMed Central

Jacob, Benjamin G; Griffith, Daniel A; Muturi, Ephantus J; Caamano, Erick X; Githure, John I; Novak, Robert J

2009-01-01

Background Autoregressive regression coefficients for Anopheles arabiensis aquatic habitat models are usually assessed using global error techniques and are reported as error covariance matrices. A global statistic, however, will summarize error estimates from multiple habitat locations. This makes it difficult to identify where there are clusters of An. arabiensis aquatic habitats of acceptable prediction. It is therefore useful to conduct some form of spatial error analysis to detect clusters of An. arabiensis aquatic habitats based on uncertainty residuals from individual sampled habitats. In this research, a method of error estimation for spatial simulation models was demonstrated using autocorrelation indices and eigenfunction spatial filters to distinguish among the effects of parameter uncertainty on a stochastic simulation of ecological sampled Anopheles aquatic habitat covariates. A test for diagnostic checking error residuals in an An. arabiensis aquatic habitat model may enable intervention efforts targeting productive habitats clusters, based on larval/pupal productivity, by using the asymptotic distribution of parameter estimates from a residual autocovariance matrix. The models considered in this research extends a normal regression analysis previously considered in the literature. Methods Field and remote-sampled data were collected during July 2006 to December 2007 in Karima rice-village complex in Mwea, Kenya. SAS 9.1.4® was used to explore univariate statistics, correlations, distributions, and to generate global autocorrelation statistics from the ecological sampled datasets. A local autocorrelation index was also generated using spatial covariance parameters (i.e., Moran's Indices) in a SAS/GIS® database. The Moran's statistic was decomposed into orthogonal and uncorrelated synthetic map pattern components using a Poisson model with a gamma-distributed mean (i.e. negative binomial regression). The eigenfunction values from the spatial configuration matrices were then used to define expectations for prior distributions using a Markov chain Monte Carlo (MCMC) algorithm. A set of posterior means were defined in WinBUGS 1.4.3®. After the model had converged, samples from the conditional distributions were used to summarize the posterior distribution of the parameters. Thereafter, a spatial residual trend analyses was used to evaluate variance uncertainty propagation in the model using an autocovariance error matrix. Results By specifying coefficient estimates in a Bayesian framework, the covariate number of tillers was found to be a significant predictor, positively associated with An. arabiensis aquatic habitats. The spatial filter models accounted for approximately 19% redundant locational information in the ecological sampled An. arabiensis aquatic habitat data. In the residual error estimation model there was significant positive autocorrelation (i.e., clustering of habitats in geographic space) based on log-transformed larval/pupal data and the sampled covariate depth of habitat. Conclusion An autocorrelation error covariance matrix and a spatial filter analyses can prioritize mosquito control strategies by providing a computationally attractive and feasible description of variance uncertainty estimates for correctly identifying clusters of prolific An. arabiensis aquatic habitats based on larval/pupal productivity. PMID:19772590

A comparison of water solubility enhancements of organic solutes by aquatic humic materials and commercial humic acids

USGS Publications Warehouse

Chlou, C.T.; Kile, D.E.; Brinton, T.I.; Malcolm, R.L.; Leenheer, J.A.; MacCarthy, P.

1987-01-01

Water solubility enhancements of 1,1-bis(p-chloro-phenyl)-2,2,2-trichloroethane (p,p???-DDT), 2,4,5,2???,5???-pentachlorobiphenyl (2,4,5,2???,5???-PCB), and 2,4,4???-tri-chlorobiphenyl (2,4,4???-PCB) by dissolved organic matter have been studied with the following samples: (1) acidic water samples from the Suwannee River, Georgia, and the Sopchoppy River, Florida; (2) a humic extract of a nearly neutral pH water from the Calcasieu River, Louisiana; (3) commercial humic acids from the Aldrich Chemical Co. and Fluka-Tridom Chemical Corp. The calculated partition coefficients on a dissolved organic carbon basis (Kdoc) for organic solutes with water samples and aquatic humic extracts from this and earlier studies indicate that the enhancement effect varies with the molecular composition of the aquatic humic materials. The Kdoc values with water and aquatic humic samples are, however, far less than the observed Kdoc values obtained with the two commercial samples, by factors of about 4-20. In view of this finding, one should be cautious in interpreting the effects of the dissolved organic matter on solubility enhancement of organic solutes on the basis of the use of commercial humic acids.

Occurrence of antibiotics in water, sediments, aquatic plants, and animals from Baiyangdian Lake in North China.

PubMed

Li, Wenhui; Shi, Yali; Gao, Lihong; Liu, Jiemin; Cai, Yaqi

2012-11-01

This study investigated the presence and distribution of 22 antibiotics, including eight quinolones, nine sulfonamides and five macrolides, in the water, sediments, and biota samples from Baiyangdian Lake, China. A total of 132 samples were collected in 2008 and 2010, and laboratory analyses revealed that antibiotics were widely distributed in the lake. Sulfonamides were the dominant antibiotics in the water (0.86-1563 ng L(-1)), while quinolones were prominent in sediments (65.5-1166 μg kg(-1)) and aquatic plants (8.37-6532 μg kg(-1)). Quinolones (17.8-167 μg kg(-1)) and macrolides [from below detection limit (BDL) to 182 μg kg(-1)] were often found in aquatic animals and birds. Salvinia natans exhibited the highest bioaccumulation capability for quinolones among three species of aquatic plants. Geographical differences of antibiotic concentrations were greatly due to anthropogenic activities. Sewage discharged from Baoding City was likely the main source of antibiotics in the lake. Risk assessment of antibiotics on aquatic organisms suggested that algae and aquatic plants might be at risk in surface water, while animals were likely not at risk. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

PubMed

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

2015-01-01

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

Diversity and Abundance of Ammonia-Oxidizing Archaeal Nitrite Reductase (nirK) Genes in Estuarine Sediments of San Francisco Bay

NASA Astrophysics Data System (ADS)

Reji, L.; Lee, J. A.; Damashek, J.; Francis, C. A.

2013-12-01

Nitrification, the microbially-mediated aerobic oxidation of ammonia to nitrate via nitrite, is an integral component of the global biogeochemical nitrogen cycle. The first and rate-limiting step of nitrification, ammonia oxidation, is carried out by two distinct microbial groups: ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Molecular ecological studies targeting the amoA gene have revealed the abundance and ubiquity of AOA in terrestrial as well as aquatic environments. In addition to the ammonia oxidation machinery that includes the amoA gene, AOA also encode a gene for copper-containing nitrite reductase (nirK). The distribution patterns and functional role of nirK in AOA remain mostly unknown; proposed functions include the indirect involvement in ammonia oxidation through the production of nitric oxide during nitrite reduction, and (2) nitrite detoxification. In the present study, the diversity and abundance of archaeal nirK genes in estuarine sediments were investigated using quantitative polymerase chain reaction, cloning and sequencing approaches. In sediment samples collected from the San Francisco Bay estuary, two archaeal nirK variants (AnirKa and AnirKb) were amplified using specific primer sets. Overall, AnirKa was observed to be significantly more abundant than AnirKb in the sediment samples, with variation in relative abundance spanning two to three orders of magnitude between sampling sites. Phylogenetic analysis revealed a number of unique archaeal nirK sequence types, as well as many that clustered with sequences from previous estuarine studies and cultured AOA isolates, such as Nitrosopumilus maritimus. This study yielded new insights into the diversity and abundance of archaeal nirK genes in estuarine sediments, and highlights the importance of further investigating the physiological role of this gene in AOA, as well as its suitability as a marker gene for studying AOA in the environment.

Comparisons of discrete and integrative sampling accuracy in estimating pulsed aquatic exposures.

PubMed

Morrison, Shane A; Luttbeg, Barney; Belden, Jason B

2016-11-01

Most current-use pesticides have short half-lives in the water column and thus the most relevant exposure scenarios for many aquatic organisms are pulsed exposures. Quantifying exposure using discrete water samples may not be accurate as few studies are able to sample frequently enough to accurately determine time-weighted average (TWA) concentrations of short aquatic exposures. Integrative sampling methods that continuously sample freely dissolved contaminants over time intervals (such as integrative passive samplers) have been demonstrated to be a promising measurement technique. We conducted several modeling scenarios to test the assumption that integrative methods may require many less samples for accurate estimation of peak 96-h TWA concentrations. We compared the accuracies of discrete point samples and integrative samples while varying sampling frequencies and a range of contaminant water half-lives (t 50  = 0.5, 2, and 8 d). Differences the predictive accuracy of discrete point samples and integrative samples were greatest at low sampling frequencies. For example, when the half-life was 0.5 d, discrete point samples required 7 sampling events to ensure median values > 50% and no sampling events reporting highly inaccurate results (defined as < 10% of the true 96-h TWA). Across all water half-lives investigated, integrative sampling only required two samples to prevent highly inaccurate results and measurements resulting in median values > 50% of the true concentration. Regardless, the need for integrative sampling diminished as water half-life increased. For an 8-d water half-life, two discrete samples produced accurate estimates and median values greater than those obtained for two integrative samples. Overall, integrative methods are the more accurate method for monitoring contaminants with short water half-lives due to reduced frequency of extreme values, especially with uncertainties around the timing of pulsed events. However, the acceptability of discrete sampling methods for providing accurate concentration measurements increases with increasing aquatic half-lives. Copyright © 2016 Elsevier Ltd. All rights reserved.

Detection of the Amphibian Chytrid Fungus Batrachochytrium dendrobatidis in Museum Specimens of Andean Aquatic Birds: Implications for Pathogen Dispersal.

PubMed

Burrowes, Patricia A; De la Riva, Ignacio

2017-04-01

The occurrence of the pathogenic chytrid fungus Batrachochytrium dendrobatidis (Bd) in the feet of live waterfowl has been documented, but the potential role of birds as dispersers has not been studied. We report the presence of Bd in the feet of preserved aquatic birds in the Bolivian high Andes during the time of drastic amphibian declines in the country. We sampled 48 aquatic birds from the Bolivian Andes that were preserved in museum collections. Birds were sampled for the presence of Bd DNA by swabbing, taking small pieces of tissue from toe webbing, or both. We detected Bd by DNA using quantitative PCR in 42% of the birds sampled via toe tissue pieces. This method was significantly better than swabbing at detecting Bd from bird feet. We confirmed Bd presence by sequencing Bd -positive samples and found 91-98% homology with Bd sequences from GenBank. Our study confirms that aquatic birds can carry Bd and thus may serve as potential vectors of this pathogen across large distances and complex landscapes. In addition, we recommend using DNA from preserved birds as a novel source of data to test hypotheses on the spread of chytridiomycosis in amphibians.

Microbial community dynamics of an urban drinking water distribution system subjected to phases of chloramination and chlorination treatments.

PubMed

Hwang, Chiachi; Ling, Fangqiong; Andersen, Gary L; LeChevallier, Mark W; Liu, Wen-Tso

2012-11-01

Water utilities in parts of the U.S. control microbial regrowth in drinking water distribution systems (DWDS) by alternating postdisinfection methods between chlorination and chloramination. To examine how this strategy influences drinking water microbial communities, an urban DWDS (population ≅ 40,000) with groundwater as the source water was studied for approximately 2 years. Water samples were collected at five locations in the network at different seasons and analyzed for their chemical and physical characteristics and for their microbial community composition and structure by examining the 16S rRNA gene via terminal restriction fragment length polymorphism and DNA pyrosequencing technology. Nonmetric multidimension scaling and canonical correspondence analysis of microbial community profiles could explain >57% of the variation. Clustering of samples based on disinfection types (free chlorine versus combined chlorine) and sampling time was observed to correlate to the shifts in microbial communities. Sampling location and water age (<21.2 h) had no apparent effects on the microbial compositions of samples from most time points. Microbial community analysis revealed that among major core populations, Cyanobacteria, Methylobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae were more abundant in chlorinated water, and Methylophilaceae, Methylococcaceae, and Pseudomonadaceae were more abundant in chloraminated water. No correlation was observed with minor populations that were detected frequently (<0.1% of total pyrosequences), which were likely present in source water and survived through the treatment process. Transient microbial populations including Flavobacteriaceae and Clostridiaceae were also observed. Overall, reversible shifts in microbial communities were especially pronounced with chloramination, suggesting stronger selection of microbial populations from chloramines than chlorine.

Microbial Community Dynamics of an Urban Drinking Water Distribution System Subjected to Phases of Chloramination and Chlorination Treatments

PubMed Central

Hwang, Chiachi; Ling, Fangqiong; Andersen, Gary L.; LeChevallier, Mark W.

2012-01-01

Water utilities in parts of the U.S. control microbial regrowth in drinking water distribution systems (DWDS) by alternating postdisinfection methods between chlorination and chloramination. To examine how this strategy influences drinking water microbial communities, an urban DWDS (population ≅ 40,000) with groundwater as the source water was studied for approximately 2 years. Water samples were collected at five locations in the network at different seasons and analyzed for their chemical and physical characteristics and for their microbial community composition and structure by examining the 16S rRNA gene via terminal restriction fragment length polymorphism and DNA pyrosequencing technology. Nonmetric multidimension scaling and canonical correspondence analysis of microbial community profiles could explain >57% of the variation. Clustering of samples based on disinfection types (free chlorine versus combined chlorine) and sampling time was observed to correlate to the shifts in microbial communities. Sampling location and water age (<21.2 h) had no apparent effects on the microbial compositions of samples from most time points. Microbial community analysis revealed that among major core populations, Cyanobacteria, Methylobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae were more abundant in chlorinated water, and Methylophilaceae, Methylococcaceae, and Pseudomonadaceae were more abundant in chloraminated water. No correlation was observed with minor populations that were detected frequently (<0.1% of total pyrosequences), which were likely present in source water and survived through the treatment process. Transient microbial populations including Flavobacteriaceae and Clostridiaceae were also observed. Overall, reversible shifts in microbial communities were especially pronounced with chloramination, suggesting stronger selection of microbial populations from chloramines than chlorine. PMID:22941076

Presence and Persistence of Salmonella in Water: The Impact on Microbial Quality of Water and Food Safety.

PubMed

Liu, Huanli; Whitehouse, Chris A; Li, Baoguang

2018-01-01

Salmonella ranks high among the pathogens causing foodborne disease outbreaks. According to the Centers for Disease Control and Prevention, Salmonella contributed to about 53.4% of all foodborne disease outbreaks from 2006 to 2017, and approximately 32.7% of these foodborne Salmonella outbreaks were associated with consumption of produce. Trace-back investigations have suggested that irrigation water may be a source of Salmonella contamination of produce and a vehicle for transmission. Presence and persistence of Salmonella have been reported in surface waters such as rivers, lakes, and ponds, while ground water in general offers better microbial quality for irrigation. To date, culture methods are still the gold standard for detection, isolation and identification of Salmonella in foods and water. In addition to culture, other methods for the detection of Salmonella in water include most probable number, immunoassay, and PCR. The U.S. Food and Drug Administration (FDA) issued the Produce Safety Rule (PSR) in January 2013 based on the Food Safety Modernization Act (FSMA), which calls for more efforts toward enhancing and improving approaches for the prevention of foodborne outbreaks. In the PSR, agricultural water is defined as water used for in a way that is intended to, or likely to, contact covered produce, such as spray, wash, or irrigation. In summary, Salmonella is frequently present in surface water, an important source of water for irrigation. An increasing evidence indicates irrigation water as a source (or a vehicle) for transmission of Salmonella . This pathogen can survive in aquatic environments by a number of mechanisms, including entry into the viable but nonculturable (VBNC) state and/or residing within free-living protozoa. As such, assurance of microbial quality of irrigation water is critical to curtail the produce-related foodborne outbreaks and thus enhance the food safety. In this review, we will discuss the presence and persistence of Salmonella in water and the mechanisms Salmonella uses to persist in the aquatic environment, particularly irrigation water, to better understand the impact on the microbial quality of water and food safety due to the presence of Salmonella in the water environment.

Presence and Persistence of Salmonella in Water: The Impact on Microbial Quality of Water and Food Safety

PubMed Central

Liu, Huanli; Whitehouse, Chris A.; Li, Baoguang

2018-01-01

Salmonella ranks high among the pathogens causing foodborne disease outbreaks. According to the Centers for Disease Control and Prevention, Salmonella contributed to about 53.4% of all foodborne disease outbreaks from 2006 to 2017, and approximately 32.7% of these foodborne Salmonella outbreaks were associated with consumption of produce. Trace-back investigations have suggested that irrigation water may be a source of Salmonella contamination of produce and a vehicle for transmission. Presence and persistence of Salmonella have been reported in surface waters such as rivers, lakes, and ponds, while ground water in general offers better microbial quality for irrigation. To date, culture methods are still the gold standard for detection, isolation and identification of Salmonella in foods and water. In addition to culture, other methods for the detection of Salmonella in water include most probable number, immunoassay, and PCR. The U.S. Food and Drug Administration (FDA) issued the Produce Safety Rule (PSR) in January 2013 based on the Food Safety Modernization Act (FSMA), which calls for more efforts toward enhancing and improving approaches for the prevention of foodborne outbreaks. In the PSR, agricultural water is defined as water used for in a way that is intended to, or likely to, contact covered produce, such as spray, wash, or irrigation. In summary, Salmonella is frequently present in surface water, an important source of water for irrigation. An increasing evidence indicates irrigation water as a source (or a vehicle) for transmission of Salmonella. This pathogen can survive in aquatic environments by a number of mechanisms, including entry into the viable but nonculturable (VBNC) state and/or residing within free-living protozoa. As such, assurance of microbial quality of irrigation water is critical to curtail the produce-related foodborne outbreaks and thus enhance the food safety. In this review, we will discuss the presence and persistence of Salmonella in water and the mechanisms Salmonella uses to persist in the aquatic environment, particularly irrigation water, to better understand the impact on the microbial quality of water and food safety due to the presence of Salmonella in the water environment. PMID:29900166

The Effect of UV-B Radiation on Dissolved Organic Matter and Nitrogen Biogeochemistry in Aquatic Environments

NASA Astrophysics Data System (ADS)

Suddick, E. C.; Uher, G.; Woodward, M.; Upstill-Goddard, R. C.

2006-12-01

Peatlands are globally important reservoirs of carbon and represent important freshwater catchments in many regions. These waters generally contain high levels of dissolved organic matter (DOM), which contains a significant fraction of chromophoric, dissolved organic material (CDOM). CDOM is primarily responsible for light attenuation in these waters and affects a variety of biogeochemically relevant photo-processes including the formation of climatically active trace gases such as CO2, CO, COS and the release of essential plant micro-nutrients such as ammonium. Significant increases in DOM concentrations have been observed in various peatland waters over recent years, associated with increases in temperatures linked to global climate change. UV-B fluxes have also been projected to increase in the future as a consequence of stratospheric ozone depletion. Enhanced UV-B radiation can affect the balance between the biological processes that produce DOM and the chemical and microbial processes that degrade it. This infers that the rate of photochemical release of nutrients such as ammonium (photo-ammonification) is also likely to increase with increasing incident UV-B radiation. Samples of freshwater, riverine and marine, filtered (0.2 ìM) water were exposed to short-term natural and solar simulated irradiation which reduced their absorbance at 350 nm (a350) and total fluorescence intensity within the UV and visible regions and also produced changes in fluorescence excitation-emission matrix (EEM) measurements, such as the hypsochromic shift of peak A towards shorter wavelengths. Samples were taken from a variety of aqueous environments predominantly from Northern Scotland peatland freshwater catchments but also from the River Tyne, North East England and from the Iberian Coast, Atlantic Ocean, covering the a350 range 0.3 to 50 m-1. The photo-chemical release of ammonium from aquatic dissolved organic matter (DOM) was also concurrent with the photo-bleaching of DOM optical properties. Photochemical ammonium release was observed in all samples irradiated between four and ten hours, where either linear production or a three step production process was observed with release rates ranging from 0.001 to 3.57 ìM l-1 h-1. Preliminary data indicate that ammonium photo-production is independent of dissolved oxygen and we discuss implications of these findings with regard to the possible mechanism of ammonium photo-production. Photo-chemically induced nitrogen release indicates a new biologically labile source of nitrogen and can impact severely upon the biogeochemistry and nutrient limitation of aquatic environments.

Aquatic invertebrate ecology during a simulated botulism epizootic in a Sacramento Valley wetland

USGS Publications Warehouse

Hicks, Jane M.; Euliss, Ned H.; Harris, Stanley W.

1997-01-01

We investigated the effect of decomposing duck carcasses on aquatic invertebrate numbers, biomass, and taxonomic composition in a seasonally flooded, impounded wetland in the Sacramento Valley, California during August–November 1988 and 1989. Major invertebrate taxa were copepods (Cyclopoida, occurred in 8.3% of samples), water fleas (Daphnidae, 8.9%), water boatmen (Corisella, 10.4%), and midge larvae (Goeldichironomus, 9.3%;Chironomus, 11.5%;Tanypus, 17.2%). We found no treatment (carcass present or no carcass) by sampling day interaction for these taxa. We found a significant difference between sample plots with carcasses and those without carcasses only for Daphnidae counts andCorisella wet weights. We found significant differences among sampling days for these taxa that were probably statistical artifacts. We were unable to detect any effect of duck carcasses on aquatic invertebrate community structure and the potential availability of invertebrates as waterfowl food.

Specimen Sample Preservation for Cell and Tissue Cultures

NASA Technical Reports Server (NTRS)

Meeker, Gabrielle; Ronzana, Karolyn; Schibner, Karen; Evans, Robert

1996-01-01

The era of the International Space Station with its longer duration missions will pose unique challenges to microgravity life sciences research. The Space Station Biological Research Project (SSBRP) is responsible for addressing these challenges and defining the science requirements necessary to conduct life science research on-board the International Space Station. Space Station will support a wide range of cell and tissue culture experiments for durations of 1 to 30 days. Space Shuttle flights to bring experimental samples back to Earth for analyses will only occur every 90 days. Therefore, samples may have to be retained for periods up to 60 days. This presents a new challenge in fresh specimen sample storage for cell biology. Fresh specimen samples are defined as samples that are preserved by means other than fixation and cryopreservation. The challenge of long-term storage of fresh specimen samples includes the need to suspend or inhibit proliferation and metabolism pending return to Earth-based laboratories. With this challenge being unique to space research, there have not been any ground based studies performed to address this issue. It was decided hy SSBRP that experiment support studies to address the following issues were needed: Fixative Solution Management; Media Storage Conditions; Fresh Specimen Sample Storage of Mammalian Cell/Tissue Cultures; Fresh Specimen Sample Storage of Plant Cell/Tissue Cultures; Fresh Specimen Sample Storage of Aquatic Cell/Tissue Cultures; and Fresh Specimen Sample Storage of Microbial Cell/Tissue Cultures. The objective of these studies was to derive a set of conditions and recommendations that can be used in a long duration microgravity environment such as Space Station that will permit extended storage of cell and tissue culture specimens in a state consistent with zero or minimal growth, while at the same time maintaining their stability and viability.

Detection and identification of Malassezia species in domestic animals and aquatic birds by PCR-RFLP

PubMed Central

Zia, M.; Mirhendi, H.; Toghyani, M.

2015-01-01

The present study aimed at detection and species-level identification of the Malassezia yeasts in domestic animals and aquatic birds by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Samples were collected using tape strips and swabs from 471 animals including 97 horses, 102 cattle, 105 sheep, 20 camels, 60 dogs, 30 cats, 1 hamster, 1 squirrel, 50 aquatic birds and 5 turkeys. Tape-strip samples were examined by direct microscopy. All samples were inoculated on modified Leeming and Notman agar medium. DNA extracted from the yeast colonies was amplified by PCR using primers specific for 26S rDNA. RFLP of the PCR products was performed using Hin6I enzyme, and PCR and RFLP products were visualized by agarose gel electrophoresis. Malassezia yeasts were detected at the following frequencies: 15.46% in horses, 12.74% in cattle, 12.38% in sheep, 28.33% in dogs, 26.66% in cats and 26% in aquatic birds. Eighty colonies of 6 species were isolated: Malassezia globosa 41.25%, Malassezia furfur 22.5%, Malassezia restricta 15%, Malassezia sympodialis 15%, Malassezia pachydermatis 5% and Malassezia slooffiae 1.25%. Therefore different lipophilic Malassezia species are found in a wide diversity of animals and aquatic birds. PCR-RFLP is a suitable technique for identification of different Malassezia species. PMID:27175148

Qualitative perspectives on aquatic exercise initiation and satisfaction among persons with multiple sclerosis.

PubMed

Chard, Sarah

2017-06-01

To identify the individual and social experiences underlying the initiation and satisfaction with aquatic exercise among persons with MS. A convenience sample (n = 45) of persons aged ≥18 with MS who had engaged in water-based exercise within the previous six months completed a 60-90 min semi-structured telephone interview regarding their aquatic exercise experiences. An aquatic exercise history was not a prerequisite for the adoption of aquatic exercise. Rather, participants described aquatic exercise routines as stemming from recognition of a decline in physical function combined with encouragement and invitations to join aquatic programs. Despite regular visits, health care providers were not a common source of information regarding the feasibility of aquatic exercise. Participants' aquatic activities included MS-specific and generalized aquatics courses, with class satisfaction resting on the instructor, class "fit" and a feeling of acceptance. Communication regarding local aquatic opportunities is critical for ensuring aquatics engagement among persons with MS. Providers could play a stronger role in emphasizing the feasibility and benefits of aquatic programs. In addition, persons with MS should be encouraged to try local MS and more generalized aquatic programs in order to identify a program matching their social and physical goals. Implications for Rehabilitation Directed communication regarding aquatic opportunities is essential to prompting the initiation of aquatic exercise Both MS-specific and general aquatics classes can provide positive exercise experiences for persons with MS A history of regular exercise or aquatic experiences is not a prerequisite for the initiation of aquatic exercise among persons with MS Health care provider visits may represent missed opportunities for promoting aquatics; providers should consider the suitability of aquatics for all patients with MS, regardless of the patient's exercise history.

Malachite green and chloramphenicol in aquatic products from regions around Dongting Lake in Hunan, China.

PubMed

He, Jiang; Cui, Jingzhen

2016-01-01

Aquatic products are important sources of animal proteins in human diet, especially in developing countries. As such, the safety of aquatic products is of primary concern. In this study, a standard method is used to detect malachite green (MG) and chloramphenicol (CAP) and to analyse the contents of these banned chemicals in turtle, mandarin fish and grass carp sampled from the region surrounding Dongting Lake area in Hunan, China. Results showed that 10.6% of the samples were MG-positive, most of them turtles. CAP was found in 8.3% of the samples, mostly in mandarin fish. These data indicated that these banned substances are still used in the surveyed area. Hence, adequate strategies must be implemented by the local government to control these banned substances.

Comparison of Niskin vs. in situ approaches for analysis of gene expression in deep Mediterranean Sea water samples

NASA Astrophysics Data System (ADS)

Edgcomb, V. P.; Taylor, C.; Pachiadaki, M. G.; Honjo, S.; Engstrom, I.; Yakimov, M.

2016-07-01

Obtaining an accurate picture of microbial processes occurring in situ is essential for our understanding of marine biogeochemical cycles of global importance. Water samples are typically collected at depth and returned to the sea surface for processing and downstream experiments. Metatranscriptome analysis is one powerful approach for investigating metabolic activities of microorganisms in their habitat and which can be informative for determining responses of microbiota to disturbances such as the Deepwater Horizon oil spill. For studies of microbial processes occurring in the deep sea, however, sample handling, pressure, and other changes during sample recovery can subject microorganisms to physiological changes that alter the expression profile of labile messenger RNA. Here we report a comparison of gene expression profiles for whole microbial communities in a bathypelagic water column sample collected in the Eastern Mediterranean Sea using Niskin bottle sample collection and a new water column sampler for studies of marine microbial ecology, the Microbial Sampler - In Situ Incubation Device (MS-SID). For some taxa, gene expression profiles from samples collected and preserved in situ were significantly different from potentially more stressful Niskin sampling and preservation on deck. Some categories of transcribed genes also appear to be affected by sample handling more than others. This suggests that for future studies of marine microbial ecology, particularly targeting deep sea samples, an in situ sample collection and preservation approach should be considered.

Proteomics meets blue biotechnology: a wealth of novelties and opportunities.

PubMed

Hartmann, Erica M; Durighello, Emie; Pible, Olivier; Nogales, Balbina; Beltrametti, Fabrizio; Bosch, Rafael; Christie-Oleza, Joseph A; Armengaud, Jean

2014-10-01

Blue biotechnology, in which aquatic environments provide the inspiration for various products such as food additives, aquaculture, biosensors, green chemistry, bioenergy, and pharmaceuticals, holds enormous promise. Large-scale efforts to sequence aquatic genomes and metagenomes, as well as campaigns to isolate new organisms and culture-based screenings, are helping to push the boundaries of known organisms. Mass spectrometry-based proteomics can complement 16S gene sequencing in the effort to discover new organisms of potential relevance to blue biotechnology by facilitating the rapid screening of microbial isolates and by providing in depth profiles of the proteomes and metaproteomes of marine organisms, both model cultivable isolates and, more recently, exotic non-cultivable species and communities. Proteomics has already contributed to blue biotechnology by identifying aquatic proteins with potential applications to food fermentation, the textile industry, and biomedical drug development. In this review, we discuss historical developments in blue biotechnology, the current limitations to the known marine biosphere, and the ways in which mass spectrometry can expand that knowledge. We further speculate about directions that research in blue biotechnology will take given current and near-future technological advancements in mass spectrometry. Copyright © 2014 Elsevier B.V. All rights reserved.

Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

PubMed Central

Ulrich, Nikea; Rosenberger, Abigail; Brislawn, Colin; Wright, Justin; Kessler, Collin; Toole, David; Solomon, Caroline; Strutt, Steven; McClure, Erin

2016-01-01

ABSTRACT Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in which Betaproteobacteria and Gammaproteobacteria decreased in 16S rRNA gene relative abundance, while the relative abundance of members of the Firmicutes increased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains of Legionella, Campylobacter, Arcobacter, and Helicobacter, as well as bacteria of fecal origin (e.g., Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event. IMPORTANCE In order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial communities during and after Superstorm Sandy to provide fine time point resolution of dynamic changes in bacterial composition. This study adds to the current literature by revealing the variation in bacterial community structure during the course of a storm. This study employed high-throughput DNA sequencing, which generated a deep analysis of inter- and intracommunity responses during a significant storm event. This study has highlighted the utility of applying high-throughput sequencing for water quality monitoring purposes, as this approach enabled a more comprehensive investigation of the bacterial community structure. Altogether, these data suggest a drastic restructuring of the stream bacterial community during a storm event and highlight the potential of high-throughput sequencing approaches for assessing the microbiological quality of our environment. PMID:27060115

Streptomyces Bacteria as Potential Probiotics in Aquaculture

PubMed Central

Tan, Loh Teng-Hern; Chan, Kok-Gan; Lee, Learn-Han; Goh, Bey-Hing

2016-01-01

In response to the increased seafood demand from the ever-going human population, aquaculture has become the fastest growing animal food-producing sector. However, the indiscriminate use of antibiotics as a biological control agents for fish pathogens has led to the emergence of antibiotic resistance bacteria. Probiotics are defined as living microbial supplement that exert beneficial effects on hosts as well as improvement of environmental parameters. Probiotics have been proven to be effective in improving the growth, survival and health status of the aquatic livestock. This review aims to highlight the genus Streptomyces can be a good candidate for probiotics in aquaculture. Studies showed that the feed supplemented with Streptomyces could protect fish and shrimp from pathogens as well as increase the growth of the aquatic organisms. Furthermore, the limitations of Streptomyces as probiotics in aquaculture is also highlighted and solutions are discussed to these limitations. PMID:26903962

Biomarker Analysis of Samples Visually Identified as Microbial in the Eocene Green River Formation: An Analogue for Mars.

PubMed

Olcott Marshall, Alison; Cestari, Nicholas A

2015-09-01

One of the major exploration targets for current and future Mars missions are lithofacies suggestive of biotic activity. Although such lithofacies are not confirmation of biotic activity, they provide a way to identify samples for further analyses. To test the efficacy of this approach, we identified carbonate samples from the Eocene Green River Formation as "microbial" or "non-microbial" based on the macroscale morphology of their laminations. These samples were then crushed and analyzed by gas chromatography/mass spectroscopy (GC/MS) to determine their lipid biomarker composition. GC/MS analysis revealed that carbonates visually identified as "microbial" contained a higher concentration of more diverse biomarkers than those identified as "non-microbial," suggesting that this could be a viable detection strategy for selecting samples for further analysis or caching on Mars.

Microbiology and Crew Medical Events on the International Space Station

NASA Technical Reports Server (NTRS)

Oubre, Cherie M.; Charvat, Jacqueline M.; Kadwa, Biniafer; Taiym, Wafa; Ott, C. Mark; Pierson, Duane; Baalen, Mary Van

2014-01-01

The closed environment of the International Space Station (ISS) creates an ideal environment for microbial growth. Previous studies have identified the ubiquitous nature of microorganisms throughout the space station environment. To ensure safety of the crew, microbial monitoring of air and surface within ISS began in December 2000 and continues to be monitored on a quarterly basis. Water monitoring began in 2009 when the potable water dispenser was installed on ISS. However, it is unknown if high microbial counts are associated with inflight medical events. The microbial counts are determined for the air, surface, and water samples collected during flight operations and samples are returned to the Microbiology laboratory at the Johnson Space Center for identification. Instances of microbial counts above the established microbial limit requirements were noted and compared inflight medical events (any non-injury event such as illness, rashes, etc.) that were reported during the same calendar-quarter. Data were analyzed using repeated measures logistic regression for the forty-one US astronauts flew on ISS between 2000 and 2012. In that time frame, instances of microbial counts being above established limits were found for 10 times for air samples, 22 times for surface samples and twice for water. Seventy-eight inflight medical events were reported among the astronauts. A three times greater risk of a medical event was found when microbial samples were found to be high (OR = 3.01; p =.007). Engineering controls, crew training, and strict microbial limits have been established to mitigate the crew medical events and environmental risks. Due to the timing issues of sampling and the samples return to earth, identification of particular microorganisms causing a particular inflight medical event is difficult. Further analyses are underway.

Is there a risk associated with the insect repellent DEET (N,N-diethyl-m-toluamide) commonly found in aquatic environments?

USGS Publications Warehouse

Costanzo, S.D.; Watkinson, A.J.; Murby, E.J.; Kolpin, D.W.; Sandstrom, M.W.

2007-01-01

DEET (N,N-diethyl-m-toluamide) is the active ingredient of most commercial insect repellents. This compound has commonly been detected in aquatic water samples from around the world indicating that DEET is both mobile and persistent, despite earlier assumptions that DEET was unlikely to enter aquatic ecosystems. DEET's registration category does not require an ecological risk assessment, thus information on the ecological toxicity of DEET is sparse. This paper reviews the presence of DEET in aqueous samples from around the world (e.g. drinking water, streams, open seawater, groundwater and treated effluent) with reported DEET concentrations ranging from 40–3000 ng L− 1. In addition, new DEET data collected from 36 sites in coastal waterways from eastern Australia (detections ranging from 8 to 1500 ng L− 1) are examined. A summary of new and existing toxicity data are discussed with an emphasis on preparing a preliminary risk assessment for DEET in the aquatic environment. Collated information on DEET in the aquatic environment suggests risk to aquatic biota at observed environmental concentrations is minimal. However, the information available was not sufficient to conduct a full risk assessment due to data deficiencies in source characterisation, transport mechanisms, fate, and ecotoxicity studies. These risks warrant further investigation due to the high frequency that this organic contaminant is detected in aquatic environments around the world.

Biological Inventory Cape La Croix Creek Watershed, Cape Girardeau County, Missouri.

DTIC Science & Technology

1977-01-01

important stream flow characteristic of Cape La Croix Creek in this region is that it is a losing stream, or one which loses water to the groundwater system...flowing water habitat types (Capt. L7 Croix Creek and tributaries and Mississippi River) on the habitat map. Backwaters and oxbows are aquatic habitats...samples of 30 to 60 liters were collected at aquatic sampling stations 1 through 6 using a #25 plankton net. Sample volumes were dependent upon water

Microbial assessment of cabin air quality on commercial airliners

NASA Technical Reports Server (NTRS)

La Duc, Myron T.; Stuecker, Tara; Bearman, Gregory; Venkateswaran, Kasthuri

2005-01-01

The microbial burdens of 69 cabin air samples collected from commercial airliners were assessed via conventional culture-dependent, and molecular-based microbial enumeration assays. Cabin air samples from each of four separate flights aboard two different carriers were collected via air-impingement. Microbial enumeration techniques targeting DNA, ATP, and endotoxin were employed to estimate total microbial burden. The total viable microbial population ranged from 0 to 3.6 x10 4 cells per 100 liters of air, as assessed by the ATP-assay. When these same samples were plated on R2A minimal medium, anywhere from 2% to 80% of these viable populations were cultivable. Five of the 29 samples examined exhibited higher cultivable counts than ATP derived viable counts, perhaps a consequence of the dormant nature (and thus lower concentration of intracellular ATP) of cells inhabiting these air cabin samples. Ribosomal RNA gene sequence analysis showed these samples to consist of a moderately diverse group of bacteria, including human pathogens. Enumeration of ribosomal genes via quantitative-PCR indicated that population densities ranged from 5 x 10 1 ' to IO 7 cells per 100 liters of air. Each of the aforementioned strategies for assessing overall microbial burden has its strengths and weaknesses; this publication serves as a testament to the power of their use in concert.

Detection and identification of free-living amoeba from aquatic environment in Taiwan

NASA Astrophysics Data System (ADS)

Jiun Tzeng, Kai; Che Tung, Min; Hsu, Bing Mu; Tsai, Hsiu Feng; Huang, Po Hsiang; Hao Huang, Kuan; Kao, Po Min; Shen, Shu Min; Chen, Jung Sheng

2013-04-01

Free-living amoebae including Acanthamoeba, Naegleria, Balamuthia and Hartmannella are widely distributed in water, soil, and air. They can infect humans and can lead to serious illness even death. The aim of this study is to investigate the presence of free-living amoebae from aquatic environment in Taiwan, and to compare the differences between Acanthamoeba and Naegleria in different cultivation methods and conditions. In this study, we used molecular method with specific primers by Polymerase Chain Reaction (PCR) to amplify and to analyze the occurrence of free-living amoebae in aquatic environment. We collected 92 samples from environmental water in Taiwan. The results show that 33 water samples (35.9%) and 11 water samples (12.0%) were detected positive for Acanthamoeba and Naegleria, respectively. Furthermore, both Acanthamoeba and Naegleria can be cultured by PYG in 30° C, but not all free-living amoebae can be enriched and isolated by using storage-cultivation method. Due to the presence of Acanthamoeba and Naegleria in aquatic environment, the water quality monitoring should be more conscious. Keywords: free-living amoebae; Acanthamoeba; Naegleria; Balamuthia; Hartmannella; PCR

Rapid Development of Microbial Strains for Bioremediation of Military Soils and Dredged Materials Contaminated with Polycyclic Aromatic Hydrocarbons.

DTIC Science & Technology

1993-09-01

Ecology 20, 197-209. Bartha , R., and Atlas , R. M. (1977). ’"The microbiology of aquatic oil spills," Advances in Applied Microbiology 22, 225-226. Bellin, C...are reviewed by Atlas (1981); Jones (1977); Westlake, Jobson, and Cook (1978); Dibble and Bartha (1979): Fedorak and Westlake (1981); Aamand et al... Bartha and Atlas (1977), Atlas (1981), and the National Academy of Science (1984). According to this information, petroleum components, including the

A microbial survey of the International Space Station (ISS)

PubMed Central

Lang, Jenna M.; Coil, David A.; Neches, Russell Y.; Brown, Wendy E.; Cavalier, Darlene; Severance, Mark; Hampton-Marcell, Jarrad T.; Gilbert, Jack A.

2017-01-01

Background Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station (ISS). This ISS sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 surfaces sampled by swabs onboard the ISS. This sampling was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Learning more about the microbial inhabitants of the “buildings” in which we travel through space will take on increasing importance, as plans for human exploration continue, with the possibility of colonization of other planets and moons. Results Sterile swabs were used to sample 15 surfaces onboard the ISS. The sites sampled were designed to be analogous to samples collected for (1) the Wildlife of Our Homes project and (2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rDNA genes amplified from DNA extracted from each swab was used to produce a census of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both homes on Earth and data from the Human Microbiome Project. Conclusions While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the ISS was more similar to home surfaces than to the human microbiome samples. The ISS surfaces are species-rich with 1,036–4,294 operational taxonomic units (OTUs per sample). There was no discernible biogeography of microbes on the 15 ISS surfaces, although this may be a reflection of the small sample size we were able to obtain. PMID:29492330

A microbial survey of the International Space Station (ISS).

PubMed

Lang, Jenna M; Coil, David A; Neches, Russell Y; Brown, Wendy E; Cavalier, Darlene; Severance, Mark; Hampton-Marcell, Jarrad T; Gilbert, Jack A; Eisen, Jonathan A

2017-01-01

Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station (ISS). This ISS sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 surfaces sampled by swabs onboard the ISS. This sampling was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Learning more about the microbial inhabitants of the "buildings" in which we travel through space will take on increasing importance, as plans for human exploration continue, with the possibility of colonization of other planets and moons. Sterile swabs were used to sample 15 surfaces onboard the ISS. The sites sampled were designed to be analogous to samples collected for (1) the Wildlife of Our Homes project and (2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rDNA genes amplified from DNA extracted from each swab was used to produce a census of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both homes on Earth and data from the Human Microbiome Project. While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the ISS was more similar to home surfaces than to the human microbiome samples. The ISS surfaces are species-rich with 1,036-4,294 operational taxonomic units (OTUs per sample). There was no discernible biogeography of microbes on the 15 ISS surfaces, although this may be a reflection of the small sample size we were able to obtain.

Colloids as a sink for certain pharmaceuticals in the aquatic environment.

PubMed

Maskaoui, Khalid; Zhou, John L

2010-05-01

The occurrence and fate of pharmaceuticals in the aquatic environment is recognized as one of the emerging issues in environmental chemistry and as a matter of public concern. Existing data tend to focus on the concentrations of pharmaceuticals in the aqueous phase, with limited studies on their concentrations in particulate phase such as sediments. Furthermore, current water quality monitoring does not differentiate between soluble and colloidal phases in water samples, hindering our understanding of the bioavailability and bioaccumulation of pharmaceuticals in aquatic organisms. In this study, an investigation was conducted into the concentrations and phase association (soluble, colloidal, suspended particulate matter or SPM) of selected pharmaceuticals (propranolol, sulfamethoxazole, meberverine, thioridazine, carbamazepine, tamoxifen, indomethacine, diclofenac, and meclofenamic acid) in river water, effluents from sewage treatment works (STW), and groundwater in the UK. The occurrence and phase association of selected pharmaceuticals propranolol, sulfamethoxazole, meberverine, thioridazine, carbamazepine, tamoxifen, indomethacine, diclofenac, and meclofenamic acid in contrasting aquatic environments (river, sewage effluent, and groundwater) were studied. Colloids were isolated by cross-flow ultrafiltration (CFUF). Water samples were extracted by solid-phase extraction (SPE), while SPM was extracted by microwave. All sample extracts were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in the multiple reaction monitoring. Five compounds propranolol, sulfamethoxazole, carbamazepine, indomethacine, and diclofenac were detected in all samples, with carbamazepine showing the highest concentrations in all phases. The highest concentrations of these compounds were detected in STW effluents, confirming STW as a key source of these compounds in the aquatic environments. The calculation of partition coefficients of pharmaceuticals between SPM and filtrate (observed partition coefficients, Kobsp, Kobsoc), between SPM and soluble phase (intrinsic partition coefficients, Kintp, Kintoc), and between colloids and soluble phase (Kcoc) showed that intrinsic partition coefficients (Kintp, Kintoc) are between 25% and 96%, and between 18% and 82% higher than relevant observed partition coefficients values, and are much less variable. Secondly, Kcoc values are 3-4 orders of magnitude greater than Kintoc values, indicating that aquatic colloids are substantially more powerful sorbents for accumulating pharmaceuticals than sediments. Furthermore, mass balance calculations of pharmaceutical concentrations demonstrate that between 23% and 70% of propranolol, 17-62% of sulfamethoxazole, 7-58% of carbamazepine, 19-84% of indomethacine, and 9-74% of diclofenac are present in the colloidal phase. The results provide direct evidence that sorption to colloids provides an important sink for the pharmaceuticals in the aquatic environment. Such strong pharmaceutical/colloid interactions may provide a long-term storage of pharmaceuticals, hence, increasing their persistence while reducing their bioavailability in the environment. Pharmaceutical compounds have been detected not only in the aqueous phase but also in suspended particles; it is important, therefore, to have a holistic approach in future environmental fate investigation of pharmaceuticals. For example, more research is needed to assess the storage and long-term record of pharmaceutical residues in aquatic sediments by which benthic organisms will be most affected. Aquatic colloids have been shown to account for the accumulation of major fractions of total pharmaceutical concentrations in the aquatic environment, demonstrating unequivocally the importance of aquatic colloids as a sink for such residues in the aquatic systems. As aquatic colloids are abundant, ubiquitous, and highly powerful sorbents, they are expected to influence the bioavailability and bioaccumulation of such chemicals by aquatic organisms. It is therefore critical for colloids to be incorporated into water quality models for prediction and risk assessment purposes.

Optimization of whole-transcriptome amplification from low cell density deep-sea microbial samples for metatranscriptomic analysis.

PubMed

Wu, Jieying; Gao, Weimin; Zhang, Weiwen; Meldrum, Deirdre R

2011-01-01

Limitation in sample quality and quantity is one of the big obstacles for applying metatranscriptomic technologies to explore gene expression and functionality of microbial communities in natural environments. In this study, several amplification methods were evaluated for whole-transcriptome amplification of deep-sea microbial samples, which are of low cell density and high impurity. The best amplification method was identified and incorporated into a complete protocol to isolate and amplify deep-sea microbial samples. In the protocol, total RNA was first isolated by a modified method combining Trizol (Invitrogen, CA) and RNeasy (QIAGEN, CA) method, amplified with a WT-Ovation™ Pico RNA Amplification System (NuGEN, CA), and then converted to double-strand DNA from single-strand cDNA with a WT-Ovation™ Exon Module (NuGEN, CA). The products from the whole-transcriptome amplification of deep-sea microbial samples were assessed first through random clone library sequencing. The BLAST search results showed that marine-based sequences are dominant in the libraries, consistent with the ecological source of the samples. The products were then used for next-generation Roche GS FLX Titanium sequencing to obtain metatranscriptome data. Preliminary analysis of the metatranscriptomic data showed good sequencing quality. Although the protocol was designed and demonstrated to be effective for deep-sea microbial samples, it should be applicable to similar samples from other extreme environments in exploring community structure and functionality of microbial communities. Copyright © 2010 Elsevier B.V. All rights reserved.

Exploring ancient microbial community assemblages by creating complex lipid biomarker profiles for stromatolites and microbial mats in Hamelin Pool, Shark Bay, Australia

NASA Astrophysics Data System (ADS)

Myers, E.; Summons, R. E.; Schubotz, F.; Matys, E. D.

2015-12-01

Stromatolites that are biogenic in origin, a characteristic that can be determined by the coexistence of microbial mats (active microbial communities) and stromatolites (lithified structures) like in Hamelin Pool, comprise one of the best modern analogs to ancient microbial community assemblages. Comprehensive lipid biomarker profiles that include lipids of varying persistence in the rock record can help determine how previously living microbial communities are represented in lithified stromatolites. To create these profiles, the samples analyzed included non-lithified smooth, pustular, and colloform microbial mats, as well as smooth and colloform stromatolites. Select samples were separated into upper and lower layers of 5cm depth each. Intact polar lipids, glycerol dialkyl glycerol tetraethers, and bacteriohopanepolyols were analyzed via liquid chromatography-mass spectrometry (LC-MS) coupled to a Quadropole Time-of-Flight (QTOF) mass spectrometer; additionally, fatty acids from each sample were analyzed using gas chromatography-mass spectrometry (GC-MS) to prove consistent signatures with those determined by Allen et al. in 2010 for similar microbial mat samples. In accordance with those findings, 2-methylhopanoids were detected, as well as limited signals from higher (vascular) plants, the latter of which suggests terrestrial inputs, potentially from runoff. The rarely detected presence of 3-methylhopanoids appears in a significant portion of the samples, though further isolations of the molecule are needed to confirm. While all lipid profiles were relatively similar, certain differences in relative composition are likely attributable to morphological differences of the mats, some of which allow deeper oxygen and/or sunlight penetration, which influence the microbial community. However, overall similarities of transient and persistent lipids suggest that the microbial communities of both the non-lithified microbial mats and stromatolites are similar.

Monitoring and assessment of mercury pollution in the vicinity of a chloralkali plant. III. Concentration and genotoxicity of mercury in the industrial effluent and contaminated water of Rushikulya estuary, India.

PubMed

Panda, K K; Lenka, M; Panda, B B

1992-01-01

Aquatic mercury pollution of the Rushikulya estuary in the vicinity of the chloralkali plant at Ganjam, India was monitored over a period from October 1987 to May 1989. The concentrations of aquatic mercury in the water samples taken from the effluent channel and from different sites along the course of the estuary covering a distance of 2 km were periodically recorded and ranged from 0 to 0.5 mg/l. The bioconcentration and genotoxicity of aquatic mercury in the samples were assessed by the Allium micronucleus (MNC) assay. The frequency of cells with MNC was highly correlated not only with bioconcentrated mercury (root mercury) but also with the levels of aquatic mercury. The threshold assessment values such as effective concentration fifty (EC50) for root growth, lowest effective concentration tested (LECT), and highest ineffective concentration tested (HICT) for induction of MNC in Allium MNC assay for the present aquatic industrial mercury were determined to be 0.14, 0.06 and 0.02 mg/l, respectively.

Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks.

PubMed

Hale, Vanessa L; Tan, Chia L; Knight, Rob; Amato, Katherine R

2015-06-01

Studies of the gut microbiome have become increasingly common with recent technological advances. Gut microbes play an important role in human and animal health, and gut microbiome analysis holds great potential for evaluating health in wildlife, as microbiota can be assessed from non-invasively collected fecal samples. However, many common fecal preservation protocols (e.g. freezing at -80 °C) are not suitable for field conditions, or have not been tested for long-term (greater than 2 weeks) storage. In this study, we collected fresh fecal samples from captive spider monkeys (Ateles geoffroyi) at the Columbian Park Zoo (Lafayette, IN, USA). The samples were pooled, homogenized, and preserved for up to 8 weeks prior to DNA extraction and sequencing. Preservation methods included: freezing at -20 °C, freezing at -80 °C, immersion in 100% ethanol, application to FTA cards, and immersion in RNAlater. At 0 (fresh), 1, 2, 4, and 8 weeks from fecal collection, DNA was extracted and microbial DNA was amplified and sequenced. DNA concentration, purity, microbial diversity, and microbial composition were compared across all methods and time points. DNA concentration and purity did not correlate with microbial diversity or composition. Microbial composition of frozen and ethanol samples were most similar to fresh samples. FTA card and RNAlater-preserved samples had the least similar microbial composition and abundance compared to fresh samples. Microbial composition and diversity were relatively stable over time within each preservation method. Based on these results, if freezers are not available, we recommend preserving fecal samples in ethanol (for up to 8weeks) prior to microbial extraction and analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

Influences of Different Halophyte Vegetation on Soil Microbial Community at Temperate Salt Marsh.

PubMed

Chaudhary, Doongar R; Kim, Jinhyun; Kang, Hojeong

2018-04-01

Salt marshes are transitional zone between terrestrial and aquatic ecosystems, occupied mainly by halophytic vegetation which provides numerous ecological services to coastal ecosystem. Halophyte-associated microbial community plays an important role in the adaptation of plants to adverse condition and also affected habitat characteristics. To explore the relationship between halophytes and soil microbial community, we studied the soil enzyme activities, soil microbial community structure, and functional gene abundance in halophytes- (Carex scabrifolia, Phragmites australis, and Suaeda japonica) covered and un-vegetated (mud flat) soils at Suncheon Bay, South Korea. Higher concentrations of total, Gram-positive, Gram-negative, total bacterial, and actinomycetes PLFAs (phospholipid fatty acids) were observed in the soil underneath the halophytes compared with mud flat soil and were highest in Carex soil. Halophyte-covered soils had different microbial community composition due to higher abundance of Gram-negative bacteria than mud flat soil. Similar to PLFA concentrations, the increased activities of β-glucosidase, cellulase, phosphatase, and sulfatase enzymes were observed under halophyte soil compared to mud flat soil and Carex exhibited highest activities. The abundance of archaeal 16S rRNA, fungal ITS, and denitrifying genes (nirK, nirS, and nosZ) were not influenced by the halophytes. Abundance bacterial 16S rRNA and dissimilatory (bi)sulfite (dsrA) genes were highest in Carex-covered soil. The abundance of functional genes involved in methane cycle (mcrA and pmoA) was not affected by the halophytes. However, the ratios of mcrA/pmoA and mcrA/dsrA increased in halophyte-covered soils which indicate higher methanogenesis activities. The finding of the study also suggests that halophytes had increased the microbial and enzyme activities, and played a pivotal role in shaping microbial community structure.

Effects of temperature on decomposition of a potential nuisance species: the submerged aquatic macrophyte Egeria najas Planchon (Hydrocharitaceae).

PubMed

Carvalho, P; Thomaz, S M; Bini, L M

2005-02-01

Decomposition of aquatic plants is influenced by several biotic and abiotic factors. Among them, temperature plays an important role. Despite the increasing number of studies describing the effects of temperature on the decomposition of aquatic macrophytes, little attention has been given to the decay of submerged macrophytes. In this paper, we assessed the effect of temperature on weight loss and chemical composition of detritus of the submerged aquatic macrophyte Egeria najas Planchon (Hydrocharitaceae). Fresh plant material was maintained at 17 degrees C and 27 degrees C, in the dark, in incubation chambers. The overall decay process was best described by a linear model, with rates of 0.014 day(-1) (R2= 94%) and 0.045 day(-1) (R2= 96%) obtained at 17 degrees C and 27 degrees C, respectively. The analysis of covariance (ANCOVA) indicated a significant difference between the decomposition rates at the two temperatures. The rapid breakdown of E. najas detritus, indicated by the decay coefficient, may be explained by its low content of resistant compounds such as cellulose and lignin. The variables analyzed in this study (pH, electrical conductivity, dissolved oxygen in the water and organic matter, total nitrogen and total phosphorus concentration in detritus) showed accentuated responses at 27 degrees C. It is likely that the higher temperature increased microbial activity and, therefore, oxygen consumption in the water, consequently affecting the pH and the rate of ion and nutrient liberation into the aquatic ecosystem. Due to the rapid decomposition of E. najas at high temperatures, a small exportation is expected of this species from its stands to distant regions in tropical reservoirs, where it is considered a potential nuisance species.

Early Triassic wrinkle structures on land: stressed environments and oases for life

NASA Astrophysics Data System (ADS)

Chu, Daoliang; Tong, Jinnan; Song, Haijun; Benton, Michael J.; Bottjer, David J.; Song, Huyue; Tian, Li

2015-06-01

Wrinkle structures in rocks younger than the Permian-Triassic (P-Tr) extinction have been reported repeatedly in marine strata, but rarely mentioned in rocks recording land. Here, three newly studied terrestrial P-Tr boundary rock succession in North China have yielded diverse wrinkle structures. All of these wrinkles are preserved in barely bioturbated shore-shallow lacustrine siliciclastic deposits of the Liujiagou Formation. Conversely, both the lacustrine siliciclastic deposits of the underlying Sunjiagou Formation and the overlying Heshanggou Formation show rich bioturbation, but no wrinkle structures or other microbial-related structures. The occurrence of terrestrial wrinkle structures in the studied sections reflects abnormal hydrochemical and physical environments, presumably associated with the extinction of terrestrial organisms. Only very rare trace fossils occurred in the aftermath of the P-Tr extinction, but most of them were preserved together with the microbial mats. This suggests that microbial mats acted as potential oases for the surviving aquatic animals, as a source of food and oxygen. The new finds suggests that extreme environmental stresses were prevalent both in the sea and on land through most of the Early Triassic.

Oxidation of aromatic contaminants coupled to microbial iron reduction

USGS Publications Warehouse

Lovley, D.R.; Baedecker, M.J.; Lonergan, D.J.; Cozzarelli, I.M.; Phillips, E.J.P.; Siegel, D.I.

1989-01-01

THE contamination of sub-surface water supplies with aromatic compounds is a significant environmental concern1,2. As these contaminated sub-surface environments are generally anaerobic, the microbial oxidation of aromatic compounds coupled to nitrate reduction, sulphate reduction and methane production has been studied intensively1-7. In addition, geochemical evidence suggests that Fe(III) can be an important electron acceptor for the oxidation of aromatic compounds in anaerobic groundwater. Until now, only abiological mechanisms for the oxidation of aromatic compounds with Fe(III) have been reported8-12. Here we show that in aquatic sediments, microbial activity is necessary for the oxidation of model aromatic compounds coupled to Fe(III) reduction. Furthermore, a pure culture of the Fe(III)-reducing bacterium GS-15 can obtain energy for growth by oxidizing benzoate, toluene, phenol or p-cresol with Fe(III) as the sole electron acceptor. These results extend the known physiological capabilities of Fe(III)-reducing organisms and provide the first example of an organism of any type which can oxidize an aromatic hydrocarbon anaerobically. ?? 1989 Nature Publishing Group.

Optical properties of chromophoric dissolved organic matter (CDOM) in surface and pore waters adjacent to an oil well in a southern California salt marsh.

PubMed

Bowen, Jennifer C; Clark, Catherine D; Keller, Jason K; De Bruyn, Warren J

2017-01-15

Chromophoric dissolved organic matter (CDOM) optical properties were measured in surface and pore waters as a function of depth and distance from an oil well in a southern California salt marsh. Higher fluorescence and absorbances in pore vs. surface waters suggest soil pore water is a reservoir of CDOM in the marsh. Protein-like fluorophores in pore waters at distinct depths corresponded to variations in sulfate depletion and Fe(II) concentrations from anaerobic microbial activity. These variations were supported by fluorescence indexes and are consistent with differences in optical molecular weight and aromaticity indicators. Fluorescence indices were consistent with autochthonous material of aquatic origin in surface waters, with more terrestrial, humified allochthonous material in deeper pore waters. CDOM optical properties were consistent with significantly enhanced microbial activity in regions closest to the oil well, along with a three-dimensional excitation/emission matrix fluorescence spectrum peak attributable to oil, suggesting anaerobic microbial degradation of oil. Copyright © 2016 Elsevier Ltd. All rights reserved.

Best practices for germ-free derivation and gnotobiotic zebrafish husbandry

PubMed Central

Melancon, E.; De La Torre Canny, S. Gomez; Sichel, S.; Kelly, M.; Wiles, T.J.; Rawls, J.F.; Eisen, J.S.; Guillemin, K.

2017-01-01

All animals are ecosystems with resident microbial communities, referred to as microbiota, which play profound roles in host development, physiology, and evolution. Enabled by new DNA sequencing technologies, there is a burgeoning interest in animal–microbiota interactions, but dissecting the specific impacts of microbes on their hosts is experimentally challenging. Gnotobiology, the study of biological systems in which all members are known, enables precise experimental analysis of the necessity and sufficiency of microbes in animal biology by deriving animals germ-free (GF) and inoculating them with defined microbial lineages. Mammalian host models have long dominated gnotobiology, but we have recently adapted gnotobiotic approaches to the zebrafish (Danio rerio), an important aquatic model. Zebrafish offer several experimental attributes that enable rapid, large-scale gnotobiotic experimentation with high replication rates and exquisite optical resolution. Here we describe detailed protocols for three procedures that form the foundation of zebrafish gnotobiology: derivation of GF embryos, microbial association of GF animals, and long-term, GF husbandry. Our aim is to provide sufficient guidance in zebrafish gnotobiotic methodology to expand and enrich this exciting field of research. PMID:28129860

Rapid determination of soil quality and earthworm impacts on soil microbial communities using fluorescence-based respirometry

NASA Astrophysics Data System (ADS)

Prendergast-Miller, Miranda T.; Thurston, Josh; Taylor, Joe; Helgason, Thorunn; Ashauer, Roman; Hodson, Mark E.

2017-04-01

We applied a fluorescence-based respirometry method currently devised for aquatic ecotoxicology studies to rapidly measure soil microbial oxygen consumption as a function of soil quality. In this study, soil was collected from an arable wheat field and the field margin. These two soil habitats are known to differ in their soil quality due to differences in their use and management as well as plant, microbial and earthworm community. The earthworm Lumbricus terrestris was incubated in arable or margin soil for three weeks. After this initial phase, a transfer experiment was then conducted to test the hypothesis that earthworm 'migration' alters soil microbial community function and diversity. In this transfer experiment, earthworms incubated in margin soil were transferred to arable soil. The converse transfer (i.e. earthworms incubated in arable soil) was also conducted. Soils of each type with no earthworms were also incubated as controls. After a further four week incubation, the impact of earthworm migration on the soil microbial community was tested by measuring oxygen consumption. Replicated soil slurry subsamples were aliquoted into individual respirometer wells (600 μl volume) on a glass 24-well microplate (Loligo Systems, Denmark) fitted with non-invasive, reusable oxygen sensor spots. The sealed microplate was then attached to an oxygen fluorescence sensor (SDR SensorDish Reader, PreSens, Germany). Oxygen consumption was measured in real-time over a 2 hr period following standard operating procedures. Soil microbial activity was measured with and without an added carbon source (glucose or cellulose, 50 mg C L-1). Using this system, we were able to differentiate between soil type, earthworm treatment and C source. Earthworm-driven impacts on soil microbial oxygen consumption were also supported by changes in soil microbial community structure and diversity revealed using DNA-based sequencing techniques. This method provides a simple and rapid system for measuring soil quality and has the potential for use in a variety of scenarios investigating impacts on soil microbial function.

Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US

DOE PAGES

Kaleita, Amy L.; Schott, Linda R.; Hargreaves, Sarah K.; ...

2017-07-07

Soil microbial communities are structured by biogeochemical processes that occur at many different spatial scales, which makes soil sampling difficult. Because soil microbial communities are important in nutrient cycling and soil fertility, it is important to understand how microbial communities function within the heterogeneous soil landscape. In this study, a self-organizing map was used to determine whether landscape data can be used to characterize the distribution of microbial biomass and activity in order to provide an improved understanding of soil microbial community function. Points within a row crop field in south-central Iowa were clustered via a self-organizing map using sixmore » landscape properties into three separate landscape clusters. Twelve sampling locations per cluster were chosen for a total of 36 locations. After the soil samples were collected, the samples were then analysed for various metabolic indicators, such as nitrogen and carbon mineralization, extractable organic carbon, microbial biomass, etc. It was found that sampling locations located in the potholes and toe slope positions had significantly greater microbial biomass nitrogen and carbon, total carbon, total nitrogen and extractable organic carbon than the other two landscape position clusters, while locations located on the upslope did not differ significantly from the other landscape clusters. However, factors such as nitrate, ammonia, and nitrogen and carbon mineralization did not differ significantly across the landscape. Altogether, this research demonstrates the effectiveness of a terrain-based clustering method for guiding soil sampling of microbial communities.« less

Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US

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

Kaleita, Amy L.; Schott, Linda R.; Hargreaves, Sarah K.

Soil microbial communities are structured by biogeochemical processes that occur at many different spatial scales, which makes soil sampling difficult. Because soil microbial communities are important in nutrient cycling and soil fertility, it is important to understand how microbial communities function within the heterogeneous soil landscape. In this study, a self-organizing map was used to determine whether landscape data can be used to characterize the distribution of microbial biomass and activity in order to provide an improved understanding of soil microbial community function. Points within a row crop field in south-central Iowa were clustered via a self-organizing map using sixmore » landscape properties into three separate landscape clusters. Twelve sampling locations per cluster were chosen for a total of 36 locations. After the soil samples were collected, the samples were then analysed for various metabolic indicators, such as nitrogen and carbon mineralization, extractable organic carbon, microbial biomass, etc. It was found that sampling locations located in the potholes and toe slope positions had significantly greater microbial biomass nitrogen and carbon, total carbon, total nitrogen and extractable organic carbon than the other two landscape position clusters, while locations located on the upslope did not differ significantly from the other landscape clusters. However, factors such as nitrate, ammonia, and nitrogen and carbon mineralization did not differ significantly across the landscape. Altogether, this research demonstrates the effectiveness of a terrain-based clustering method for guiding soil sampling of microbial communities.« less

Assessing the Fauna of Aquatic Insects for Possible Use for Malaria Vector Control in Large River, Central Iran.

PubMed

Shayeghi, Mansoureh; Nejati, Jalil; Shirani-Bidabadi, Leila; Koosha, Mona; Badakhshan, Mehdi; Mohammadi Bavani, Mulood; Arzamani, Kourosh; Choubdar, Nayyereh; Bagheri, Fatemeh; Saghafipour, Abedin; Veysi, Arshad; Karimian, Fateh; Akhavan, Amir Ahamd; Vatandoost, Hassan

2015-01-01

Insects with over 30,000 aquatic species are known as very successful arthropods in freshwater habitats. Some of them are applied as biological indicators for water quality control, as well as the main food supply for fishes and amphibians. The faunistic studies are the basic step in entomological researches; the current study was carried out emphasizing on the fauna of aquatic insects in Karaj River, northern Iran. A field study was carried out in six various sampling site of Karaj River during spring 2013. The aquatic insects were collected using several methods such as D-frame nets, dipping and direct search on river floor stones. Specimens were collected and preserved in Ethanol and identified by standard identification keys. Totally, 211 samples were collected belonging to three orders; Plecoptera, Trichoptera and Ephemeroptera. Seven genuses (Perla, Isoperla, Hydropsyche, Cheumatopsyche, Baetis, Heptagenia and Maccafferium) from five families (Perlidae, Perlodidae, Hydropsychidae, Batidae, Heptagenidae) were identified. The most predominant order was Plecoptera followed by Trichoptera. Karaj River is a main and important river, which provides almost all of water of Karaj dam. So, identification of aquatic species which exist in this river is vital and further studies about systematic and ecological investigations should be performed. Also, monitoring of aquatic biota by trained health personnel can be a critical step to describe water quality in this river. Understanding the fauna of aquatic insects will provide a clue for possible biological control of medically important aquatic insects such as Anopheles as the malaria vectors.

Use of enzymatic tools for biomonitoring inorganic pollution in aquatic sediments: a case study (Bor, Serbia)

PubMed Central

2013-01-01

Background Sediment bacterial communities are key players in biogeochemical cycling of elements in the aquatic environment. Copper mining, smelting, and processing operations located in Bor area (Serbia) are major environmental hot spots in the lower Danube Basin and Western Balkans. In the present study, we evaluate the influence of trace element (TE) concentration in sediments and physico-chemical properties of water on sediment microbial communities in water streams adjacent to the Copper Smelter Complex Bor (RTB Bor, Serbia). The degree to which metabolic activities of bacterial biota inhabiting differently polluted sites is inhibited by inorganic pollution were compared using selected enzymatic bioindicators. Results Cu, Zn, Pb, and As concentrations systematically exceeded the target values for metal loadings in aquatic sediments. Water electrical conductivity (WEC) followed the same pattern of spatial variation, irrespective of season. Interestingly, the most intense enzymatic activity occurred at the reference site although this site showed the greatest TE levels in aquatic sediments. Catalase activity (CA), potential dehydrogenase activity (PDA), actual dehydrogenase activity (ADA), urease activity (UA), and phosphatase activity (PA) in aquatic sediments displayed heterogeneous patterns of spatio-temporal variation. Inorganic pollution greatly affected CA, ADA, and PDA, but much less so UA and PA. Canonical correlation analysis showed that pH and WEC were the strongest determinants of enzymatic activity in bacterial biota, with the latter variable being reversely correlated with the enzymatic indicator of sediment quality (EISQ). The median values of EISQ increased with distance from the major sources of pollution. In addition, it was found that sites with different degrees of inorganic pollution can be appropriately classified by applying cluster analysis to EISQ, TE levels in sediments, and physico-chemical properties of water. Conclusions Because EISQ can precisely identify changes in overall enzymatic activity of sediment bacterial communities, this enzymatic bioindicator has a great potential for biomonitoring the current status of inorganic pollution in aquatic ecosystems. PMID:23536970

Temporal dynamics of phosphorus during aquatic and terrestrial litter decomposition in an alpine forest.

PubMed

Peng, Yan; Yang, Wanqin; Yue, Kai; Tan, Bo; Huang, Chunping; Xu, Zhenfeng; Ni, Xiangyin; Zhang, Li; Wu, Fuzhong

2018-06-17

Plant litter decomposition in forested soil and watershed is an important source of phosphorus (P) for plants in forest ecosystems. Understanding P dynamics during litter decomposition in forested aquatic and terrestrial ecosystems will be of great importance for better understanding nutrient cycling across forest landscape. However, despite massive studies addressing litter decomposition have been carried out, generalizations across aquatic and terrestrial ecosystems regarding the temporal dynamics of P loss during litter decomposition remain elusive. We conducted a two-year field experiment using litterbag method in both aquatic (streams and riparian zones) and terrestrial (forest floors) ecosystems in an alpine forest on the eastern Tibetan Plateau. By using multigroup comparisons of structural equation modeling (SEM) method with different litter mass-loss intervals, we explicitly assessed the direct and indirect effects of several biotic and abiotic drivers on P loss across different decomposition stages. The results suggested that (1) P concentration in decomposing litter showed similar patterns of early increase and later decrease across different species and ecosystems types; (2) P loss shared a common hierarchy of drivers across different ecosystems types, with litter chemical dynamics mainly having direct effects but environment and initial litter quality having both direct and indirect effects; (3) when assessing at the temporal scale, the effects of initial litter quality appeared to increase in late decomposition stages, while litter chemical dynamics showed consistent significant effects almost in all decomposition stages across aquatic and terrestrial ecosystems; (4) microbial diversity showed significant effects on P loss, but its effects were lower compared with other drivers. Our results highlight the importance of including spatiotemporal variations and indicate the possibility of integrating aquatic and terrestrial decomposition into a common framework for future construction of models that account for the temporal dynamics of P in decomposing litter. Copyright © 2018 Elsevier B.V. All rights reserved.

Anaerobic degradation of benzene in diverse anoxic environments

USGS Publications Warehouse

Kazumi, J.; Caldwell, M.E.; Suflita, J.M.; Lovely, D.R.; Young, L.Y.

1997-01-01

Benzene has often been observed to be resistant to microbial degradation under anoxic conditions. A number of recent studies, however, have demonstrated that anaerobic benzene utilization can occur. This study extends the previous reports of anaerobic benzene degradation to sediments that varied with respect to contamination input, predominant redox condition, and salinity. In spite of differences in methodology, microbial degradation of benzene was noted in slurries constructed with sediments from various geographical locations and range from aquifer sands to fine-grained estuarine muds, under methanogenic, sulfate-reducing, and iron-reducing conditions. In aquifer sediments under methanogenic conditions, benzene loss was concomitant with methane production, and microbial utilization of [14C]benzene yielded 14CO2 and 14CH4. In slurries with estuarine and aquifer sediments under sulfate-reducing conditions, the loss of sulfate in amounts consistent with the stoichiometric degradation of benzene or the conversion of [14C]benzene to 14CO2 indicates that benzene was mineralized. Benzene loss also occurred in the presence of Fe(III) in sediments from freshwater environments. Microbial benzene utilization, however, was not observed under denitrifying conditions. These results indicate that the potential for the anaerobic degradation of benzene, which was once thought to be resistant to non-oxygenase attack, exists in a variety of aquatic sediments from widely distributed locations.

Thermal barriers constrain microbial elevational range size via climate variability.

PubMed

Wang, Jianjun; Soininen, Janne

2017-08-01

Range size is invariably limited and understanding range size variation is an important objective in ecology. However, microbial range size across geographical gradients remains understudied, especially on mountainsides. Here, the patterns of range size of stream microbes (i.e., bacteria and diatoms) and macroorganisms (i.e., macroinvertebrates) along elevational gradients in Asia and Europe were examined. In bacteria, elevational range size showed non-significant phylogenetic signals. In all taxa, there was a positive relationship between niche breadth and species elevational range size, driven by local environmental and climatic variables. No taxa followed the elevational Rapoport's rule. Climate variability explained the most variation in microbial mean elevational range size, whereas local environmental variables were more important for macroinvertebrates. Seasonal and annual climate variation showed negative effects, while daily climate variation had positive effects on community mean elevational range size for all taxa. The negative correlation between range size and species richness suggests that understanding the drivers of range is key for revealing the processes underlying diversity. The results advance the understanding of microbial species thermal barriers by revealing the importance of seasonal and diurnal climate variation, and highlight that aquatic and terrestrial biota may differ in their response to short- and long-term climate variability. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

The microbiome of glaciers and ice sheets.

PubMed

Anesio, Alexandre M; Lutz, Stefanie; Chrismas, Nathan A M; Benning, Liane G

2017-01-01

Glaciers and ice sheets, like other biomes, occupy a significant area of the planet and harbour biological communities with distinct interactions and feedbacks with their physical and chemical environment. In the case of the glacial biome, the biological processes are dominated almost exclusively by microbial communities. Habitats on glaciers and ice sheets with enough liquid water to sustain microbial activity include snow, surface ice, cryoconite holes, englacial systems and the interface between ice and overridden rock/soil. There is a remarkable similarity between the different specific glacial habitats across glaciers and ice sheets worldwide, particularly regarding their main primary producers and ecosystem engineers. At the surface, cyanobacteria dominate the carbon production in aquatic/sediment systems such as cryoconite holes, while eukaryotic Zygnematales and Chlamydomonadales dominate ice surfaces and snow dynamics, respectively. Microbially driven chemolithotrophic processes associated with sulphur and iron cycle and C transformations in subglacial ecosystems provide the basis for chemical transformations at the rock interface under the ice that underpin an important mechanism for the delivery of nutrients to downstream ecosystems. In this review, we focus on the main ecosystem engineers of glaciers and ice sheets and how they interact with their chemical and physical environment. We then discuss the implications of this microbial activity on the icy microbiome to the biogeochemistry of downstream ecosystems.

The effects of mixotrophy on the stability and dynamics of a simple planktonic food web

USGS Publications Warehouse

Jost, Christian; Lawrence, Cathryn A.; Campolongo, Francesca; Wouter, van de Bund; Hill, Sheryl; DeAngelis, Donald L.

2004-01-01

Recognition of the microbial loop as an important part of aquatic ecosystems disrupted the notion of simple linear food chains. However, current research suggests that even the microbial loop paradigm is a gross simplification of microbial interactions due to the presence of mixotrophs—organisms that both photosynthesize and graze. We present a simple food web model with four trophic species, three of them arranged in a food chain (nutrients–autotrophs–herbivores) and the fourth as a mixotroph with links to both the nutrients and the autotrophs. This model is used to study the general implications of inclusion of the mixotrophic link in microbial food webs and the specific predictions for a parameterization that describes open ocean mixed layer plankton dynamics. The analysis indicates that the system parameters reside in a region of the parameter space where the dynamics converge to a stable equilibrium rather than displaying periodic or chaotic solutions. However, convergence requires weeks to months, suggesting that the system would never reach equilibrium in the ocean due to alteration of the physical forcing regime. Most importantly, the mixotrophic grazing link seems to stabilize the system in this region of the parameter space, particularly when nutrient recycling feedback loops are included.

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.

Using solid 13C NMR coupled with solution 31P NMR spectroscopy to investigate molecular species and lability of organic carbon and phosphorus from aquatic plants in Tai Lake, China

USDA-ARS?s Scientific Manuscript database

Aquatic plants are involved in the storage and release capacity for organic matter and nutrients. In this study, solid 13C and solution 31P nuclear magnetic resonance (NMR) spectroscopy were used to characterize the biomass samples of six aquatic plants. Solid 13C NMR spectroscopy revealed the domin...

Characterization of the microbial community in a lotic environment to assess the effect of pollution on nitrifying and potentially pathogenic bacteria.

PubMed

Medeiros, J D; Araújo, L X; da Silva, V L; Diniz, C G; Cesar, D E; Del'Duca, A; Coelho, C M

2014-08-01

This study aimed to investigate microbes involved in the nitrogen cycle and potentially pathogenic bacteria from urban and rural sites of the São Pedro stream. Water samples were collected from two sites. A seasonal survey of bacterial abundance was conducted. The dissolved nutrient content was analysed. PCR and FISH analysis were performed to identify and quantify microbes involved in the nitrogen cycle and potentially pathogenic bacteria. The seasonal survey revealed that the bacterial abundance was similar along the year on the rural area but varied on the urban site. Higher concentration of dissolved nutrients in the urban area indicated a eutrophic system. Considering the nitrifying microbes, the genus Nitrobacter was found, especially in the urban area, and may act as the principal bacteria in converting nitrite into nitrate at this site. The molecular markers napA, amoA, and nfrA were more accumulated at the urban site, justifying the higher content of nutrients metabolised by these enzymes. Finally, high intensity of amplicons from Enterococcus, Streptococcus, Bacteroides/Prevotella/Porphyromonas, Salmonella, S. aureus, P. aeruginosa and the diarrheagenic lineages of E. coli were observed at the urban site. These results indicate a change in the structure of the microbial community imposed by anthrophic actions. The incidence of pathogenic bacteria in aquatic environments is of particular importance to public health, emphasising the need for sewage treatment to minimise the environmental impacts associated with urbanisation.

Photodegradation behaviour of estriol: An insight on natural aquatic organic matter influence.

PubMed

Oliveira, Cindy; Lima, Diana L D; Silva, Carla Patrícia; Otero, Marta; Esteves, Valdemar I

2016-09-01

Estriol (E3) is one of the steroidal estrogens ubiquitously found in the aquatic environment, photodegradation being an important pathway for the elimination of such endocrine disrupting compounds. However, it is important to understand how environmentally important components present in aquatic matrices, such as organic matter, may affect their photodegradation. The main objective of this work was to investigate the photodegradation of E3 in water, under simulated solar radiation, as well as the effect of humic substances (HS - humic acids (HA), fulvic acids (FA) and XAD-4 fraction) in E3 photodegradation. Moreover, the photodegradation behaviour of E3 when present in different environmental aquatic matrices (fresh, estuarine and waste water samples) was also assessed. Results showed a completely different E3 degradation rate depending on the aquatic matrix. In ultrapure water the half-life obtained was about 50 h, while in presence of HS it varied between 5 and 10 h. Then, half-life times between 1.6 and 9.5 h were determined in environmental samples, in which it was observed that the matrix composition contributed up to 97% for the overall E3 photodegradation. Therefore, E3 photodegradation in the considered aquatic matrices was mostly caused by photosensitizing reactions (indirect photodegradation). Copyright © 2016 Elsevier Ltd. All rights reserved.

Quantifying the contribution of single microbial cells to nitrogen assimilation in aquatic environments

NASA Astrophysics Data System (ADS)

Musat, N.; Kuypers, M. M. M.

2009-04-01

Nitrogen is a primary productivity-limiting nutrient in the ocean. The nitrogen limitation of productivity may be overcome by organisms capable of converting dissolved N2 into fixed nitrogen available to the ecosystem. In many oceanic regions, growth of phytoplankton is nitrogen limited because fixation of N2 cannot make up for the removal of fixed inorganic nitrogen (NH4+, NO2-, NO3-) by anaerobic microbial processes. The amount of available fixed nitrogen in the ocean can be changed by the biological processes of heterotrophic denitrification, anaerobic ammonium oxidation and nitrogen fixation. For a complete understanding of nitrogen cycling in the ocean a link between the microbial and biogeochemical processes at the single cell level and their role in global biogeochemical cycles is essential. Here we report a recently developed method, Halogen In Situ Hybridization-Secondary Ion Mass Spectroscopy (HISH-SIMS) and its potential application to study the nitrogen-cycle processes in the ocean. The method allows simultaneous phylogenetic identification and quantitation of metabolic activities of single microbial cells in the environment. It uses horseradish-peroxidase-labeled oligonucleotide probes and fluorine-containing tyramides for the identification of microorganisms in combination with stable-isotope-labeling experiments for analyzing the metabolic function of single microbial cells. HISH-SIMS was successfully used to study nitrogen assimilation and nitrogen fixation by anaerobic phototrophs in a meromictic alpine lake. The HISH-SIMS method enables studies of the ecophysiology of individual, phylogenetically identified microorganisms involved in the N-cycle and allows us to track the flow of nitrogen within microbial communities.

Rapid assay for microbially reducible ferric iron in aquatic sediments

USGS Publications Warehouse

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

1987-01-01

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

Processes of carbonate precipitation in modern microbial mats

NASA Astrophysics Data System (ADS)

Dupraz, Christophe; Reid, R. Pamela; Braissant, Olivier; Decho, Alan W.; Norman, R. Sean; Visscher, Pieter T.

2009-10-01

Microbial mats are ecosystems that arguably greatly affected the conditions of the biosphere on Earth through geological time. These laminated organosedimentary systems, which date back to > 3.4 Ga bp, are characterized by high metabolic rates, and coupled to this, rapid cycling of major elements on very small (mm-µm) scales. The activity of the mat communities has changed Earth's redox conditions (i.e. oxidation state) through oxygen and hydrogen production. Interpretation of fossil microbial mats and their potential role in alteration of the Earth's geochemical environment is challenging because these mats are generally not well preserved. Preservation of microbial mats in the fossil record can be enhanced through carbonate precipitation, resulting in the formation of lithified mats, or microbialites. Several types of microbially-mediated mineralization can be distinguished, including biologically-induced and biologically influenced mineralization. Biologically-induced mineralization results from the interaction between biological activity and the environment. Biologically-influenced mineralization is defined as passive mineralization of organic matter (biogenic or abiogenic in origin), whose properties influence crystal morphology and composition. We propose to use the term organomineralization sensu lato as an umbrella term encompassing biologically influenced and biologically induced mineralization. Key components of organomineralization sensu lato are the "alkalinity" engine (microbial metabolism and environmental conditions impacting the calcium carbonate saturation index) and an organic matrix comprised of extracellular polymeric substances (EPS), which may provide a template for carbonate nucleation. Here we review the specific role of microbes and the EPS matrix in various mineralization processes and discuss examples of modern aquatic (freshwater, marine and hypersaline) and terrestrial microbialites.

Fish biodiversity sampling in stream ecosystems: a process for evaluating the appropriate types and amount of gear

USGS Publications Warehouse

Smith, Joseph M.; Wells, Sarah P.; Mather, Martha E.; Muth, Robert M.

2014-01-01

When researchers and managers initiate sampling on a new stream or river system, they do not know how effective each gear type is and whether their sampling effort is adequate. Although the types and amount of gear may be different for other studies, systems, and research questions, the five-step process described here for making sampling decisions and evaluating sampling efficiency can be applied widely to any system to restore, manage, and conserve aquatic ecosystems. It is believed that incorporating this gear-evaluation process into a wide variety of studies and ecosystems will increase rigour within and across aquatic biodiversity studies.

Aquatic hazard and biodegradability of light and middle atmospheric distillate petroleum streams.

PubMed

Swigert, James P; Lee, Carol; Wong, Diana C L; Podhasky, Paula

2014-08-01

Light and middle atmospheric distillate petroleum substances are blended to produce fuels used in transportation and heating. These substances represent the majority by volume of crude oil refined products in the United States. The goal of this research was to develop biodegradability and aquatic toxicity data for four substances; heavy, straight-run naphtha (HSRN), hydro-desulfurized kerosene (HDK), hydro-cracked gas oil (HCGO), and catalytic-cracked gas oil (CCGO). Ready biodegradability tests demonstrated rapid and extensive microbial oxidation of these test substances, indicating a lack of persistence in the aquatic environment. Differences in biodegradation patterns reflected compositional differences in the constituent hydrocarbons. Results of aquatic toxicity tests on alga, cladocera, and fish demonstrated that toxicity was greatest for catalytic-cracked gas oil, which contained a high proportion of aromatic hydrocarbons. Aromatic hydrocarbons are more soluble, and hence more bioavailable, resulting in higher toxicity. When expressed on the basis of loading rates, acute toxicity values (LL/EL50) ranged between 0.3 and 5.5 mg L(-1) for all three species, while chronic no-observed-effect loading rates (NOELR) ranged between 0.05 and 0.64 mg L(-1). PETROTOX estimates for acute and chronic toxicity ranged from 0.18 to 2.3 mg L(-1) and 0.06 to 0.14 mg L(-1), respectively, which were generally more conservative than experimental data. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Integrated ecological risk assessment of pesticides in tropical ecosystems: a case study with carbofuran in Brazil.

PubMed

Chelinho, Sónia; Lopes, Isabel; Natal-da-Luz, Tiago; Domene, Xaxier; Nunes, Maria Edna Tenorio; Espíndola, Evaldo L G; Ribeiro, Rui; Sousa, Jose P

2012-02-01

The aim of the present study is to contribute an ecologically relevant assessment of the ecotoxicological effects of pesticide applications in agricultural areas in the tropics, using an integrated approach with information gathered from soil and aquatic compartments. Carbofuran, an insecticide/nematicide used widely on sugarcane crops, was selected as a model substance. To evaluate the toxic effects of pesticide spraying for soil biota, as well as the potential indirect effects on aquatic biota resulting from surface runoff and/or leaching, field and laboratory (using a cost-effective simulator of pesticide applications) trials were performed. Standard ecotoxicological tests were performed with soil (Eisenia andrei, Folsomia candida, and Enchytraeus crypticus) and aquatic (Ceriodaphnia silvestrii) organisms, using serial dilutions of soil, eluate, leachate, and runoff samples. Among soil organisms, sensitivity was found to be E. crypticus < E. andrei < F. candida. Among the aqueous extracts, mortality of C. silvestrii was extreme in runoff samples, whereas eluates were by far the least toxic samples. A generally higher toxicity was found in the bioassays performed with samples from the field trial, indicating the need for improvements in the laboratory simulator. However, the tool developed proved to be valuable in evaluating the toxic effects of pesticide spraying in soils and the potential risks for aquatic compartments. Copyright © 2011 SETAC.

Seasonal distribution and prevalence of diarrheagenic Escherichia coli in different aquatic environments in Taiwan.

PubMed

Huang, Wen-Chien; Hsu, Bing-Mu; Kao, Po-Min; Tao, Chi-Wei; Ho, Ying-Ning; Kuo, Chun-Wei; Huang, Yu-Li

2016-02-01

Diarrheagenic Escherichia coli (DEC) are the most common agents of diarrhea. Waterborne DEC could pose a potential health risk to human through agricultural, household, recreational, and industrial use. There are few published reports on the detection of DEC and its seasonal distribution in aquatic environments. The presence of DEC in different types of aquatic environments was investigated in this study. Water samples were collected from major rivers, water reservoirs, and recreational hot springs throughout Taiwan. Moreover, an intensive water sampling plan was carried out along Puzih River. The detection of DEC target genes was used to determine the presence of enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), and Shiga toxin-producing E. coli (STEC). Among the 383 water samples analyzed, DEC was found in 122 (31.8%) samples. The detection rate varied by genotype, raging from 3.6% for STEC to 17.2% for EPEC. The DEC detection rate was higher from river waters than reservoirs and hot springs. In addition, DEC was detected at a higher rate in spring and summer. The presence of EPEC was significantly associated with total coliform levels among hot spring samples. Moreover, the presence of ETEC in river water samples was associated with heterotrophic plate counts. Water with EPEC differed significantly in pH from Puzih River samples. These results suggest that seasonal characteristics may affect the presence of DEC in different aquatic environments, and water quality indicators may be indicative of the presence of DEC. Copyright © 2015 Elsevier Inc. All rights reserved.

Potential toxicity of pesticides measured in midwestern streams to aquatic organisms

USGS Publications Warehouse

Battaglin, W.; Fairchild, J.

2002-01-01

Society is becoming increasingly aware of the value of healthy aquatic ecosystems as well as the effects that man’s activities have on those ecosystems. In recent years, many urban and industrial sources of contamination have been reduced or eliminated. The agricultural community also has worked towards reducing off-site movement of agricultural chemicals, but their use in farming is still growing. A small fraction, estimated at <1 to 2% of the pesticides applied to crops are lost from fields and enter nearby streams during rainfall events. In many cases aquatic organisms are exposed to mixtures of chemicals, which may lead to greater non-target risk than that predicted based on traditional risk assessments for single chemicals. We evaluated the potential toxicity of environmental mixtures of 5 classes of pesticides using concentrations from water samples collected from ∼50 sites on midwestern streams during late spring or early summer runoff events in 1989 and 1998. Toxicity index values are calculated as the concentration of the compound in the sample divided by the EC50 or LC50 of an aquatic organism. These index values are summed within a pesticide class and for all classes to determine additive pesticide class and total pesticide toxicity indices. Toxicity index values greater than 1.0 indicate probable toxicity of a class of pesticides measured in a water sample to aquatic organisms. Results indicate that some samples had probable toxicity to duckweed and green algae, but few are suspected of having significant toxicity to bluegill sunfish or chorus frogs.

[Comparison between aquatic-biodanza and stretching for improving quality of life and pain in patients with fibromyalgia].

PubMed

López-Rodríguez, María del Mar; Castro-Sánchez, Adelaida María; Fernández-Martínez, Manuel; Matarán-Peñarrocha, Guillermo A; Rodríguez-Ferrer, María Encarnación

2012-11-01

To determine the level of improvement, as regards pain, impact on fibromyalgia and depression, achieved by patients with fibromyalgia by comparing aquatic biodanza and stretching exercises. Randomised controlled trial with two intervention groups. Five health centres (Almeria). A total of 82 fibromyalgia patients between 18 and 65 years old, diagnosed by American College of Rheumatology criteria, were included, with 12 patients declining to take part in the study. The 70 remaining patients were randomly assigned to two groups of 35 patients each: aquatic biodanza and stretching exercises. Those who did not attend in at least 14 sessions or changed their treatment during the studio were excluded. The final sample consisted of 19 patients in aquatic biodanza group and 20 in stretching group. The limitations of the study included, the open evaluation design and a sample size reduced by defaults. The outcome measures were sociodemographic data, quality of life (Fibromyalgia Impact Questionnaire), pain (McGill-Melzack questionnaire; and Visual Analogue Scale), pressure algometry (Wagner FPI10 algometer) and depression (Beck Inventory). These were carried out before and after a 12-week therapy. The mean age of the sample was 55.41 years. The mean period from diagnosis was 13.44 years. The sample consisted mainly of housewives. There were significant differences (P<.05) between groups, in pain (P<.01), fibromyalgia impact (P<.01), and depression (P<.04) after the treatment. The biodanza aquatic exercises improve pain and quality of life in fibromyalgia patients. Copyright © 2011 Elsevier España, S.L. All rights reserved.

Some New Windows into Terrestrial Deep Subsurface Microbial Ecosystems

NASA Astrophysics Data System (ADS)

Moser, D. P.

2011-12-01

Over the past several years, our group has surveyed the microbial ecology and biogeochemistry of a range of fracture rock subsurface ecosystems via deep mine boreholes in South Africa, the United States, and Canada; and boreholes from surface or deeply-sourced natural springs of the U.S. Great Basin. Collectively, these mostly unexplored habitats represent a wide range of geologic provinces, host rock types, aquatic chemistries, and the vast potential for biogeographic isolation. Thus, patterns of microbial diversity are of interest from the perspective of filling a fundamental knowledge gap; and while not necessarily expected, the detection of closely related microorganisms from geographically isolated settings would be noteworthy. Across these sample sets, microbial communities were invariably very low in biomass (e.g. 10e3 - 10e4 cells per mL) and dominated by deeply-branching bacterial lineages, particularly from the phyla Firmicutes and Nitrospira. In several cases, the Firmicutes have shown very close phylogenetic affiliations to lineages detected at divergent locations. For example, one abundant lineage from a new artesian well drilled into the Furnace Creek Fault of Death Valley, CA bears a very close phylogenetic relatedness to environmental DNA sequences (SSU rRNA gene) detected in one of the world's deepest mines (Tau Tona of South Africa) and what was North America's deepest gold mine (Homestake of South Dakota). Several radioactive wells from the Nevada National Security Site have produced rRNA gene sequences very close (e.g. greater than 99% identity) to that of Desulforudis audaxviator, a rarely detected microorganism thought to subsist as a single species ecosystem on the products of radiochemical reactions in deep crustal rocks from the South African Witwatersrand Basin. These sequences, along with more distantly related sequences from the marine subsurface (ridge flank basalt and mud volcanoes) and groundwater in Europe, hint at a role in certain hydrogen-rich subsurface settings for this group. Likewise, patterns of archaeal diversity across many of our Great Basin sites suggest shared deep lineages, particularly with the phylum, Thaumarchaeota. Here we will explore the possible significance of these patterns of diversity and discuss future research plans involving high throughput molecular techniques.

Seasonal variability in the persistence of dissolved environmental DNA (eDNA) in a marine system: The role of microbial nutrient limitation.

PubMed

Salter, Ian

2018-01-01

Environmental DNA (eDNA) can be defined as the DNA pool recovered from an environmental sample that includes both extracellular and intracellular DNA. There has been a significant increase in the number of recent studies that have demonstrated the possibility to detect macroorganisms using eDNA. Despite the enormous potential of eDNA to serve as a biomonitoring and conservation tool in aquatic systems, there remain some important limitations concerning its application. One significant factor is the variable persistence of eDNA over natural environmental gradients, which imposes a critical constraint on the temporal and spatial scales of species detection. In the present study, a radiotracer bioassay approach was used to quantify the kinetic parameters of dissolved eDNA (d-eDNA), a component of extracellular DNA, over an annual cycle in the coastal Northwest Mediterranean. Significant seasonal variability in the biological uptake and turnover of d-eDNA was observed, the latter ranging from several hours to over one month. Maximum uptake rates of d-eDNA occurred in summer during a period of intense phosphate limitation (turnover <5 hrs). Corresponding increases in bacterial production and uptake of adenosine triphosphate (ATP) demonstrated the microbial utilization of d-eDNA as an organic phosphorus substrate. Higher temperatures during summer may amplify this effect through a general enhancement of microbial metabolism. A partial least squares regression (PLSR) model was able to reproduce the seasonal cycle in d-eDNA persistence and explained 60% of the variance in the observations. Rapid phosphate turnover and low concentrations of bioavailable phosphate, both indicative of phosphate limitation, were the most important parameters in the model. Abiotic factors such as pH, salinity and oxygen exerted minimal influence. The present study demonstrates significant seasonal variability in the persistence of d-eDNA in a natural marine environment that can be linked to the metabolic response of microbial communities to nutrient limitation. Future studies should consider the effect of natural environmental gradients on the seasonal persistence of eDNA, which will be of particular relevance for time-series biomonitoring programs.

Seasonal variability in the persistence of dissolved environmental DNA (eDNA) in a marine system: The role of microbial nutrient limitation

PubMed Central

2018-01-01

Environmental DNA (eDNA) can be defined as the DNA pool recovered from an environmental sample that includes both extracellular and intracellular DNA. There has been a significant increase in the number of recent studies that have demonstrated the possibility to detect macroorganisms using eDNA. Despite the enormous potential of eDNA to serve as a biomonitoring and conservation tool in aquatic systems, there remain some important limitations concerning its application. One significant factor is the variable persistence of eDNA over natural environmental gradients, which imposes a critical constraint on the temporal and spatial scales of species detection. In the present study, a radiotracer bioassay approach was used to quantify the kinetic parameters of dissolved eDNA (d-eDNA), a component of extracellular DNA, over an annual cycle in the coastal Northwest Mediterranean. Significant seasonal variability in the biological uptake and turnover of d-eDNA was observed, the latter ranging from several hours to over one month. Maximum uptake rates of d-eDNA occurred in summer during a period of intense phosphate limitation (turnover <5 hrs). Corresponding increases in bacterial production and uptake of adenosine triphosphate (ATP) demonstrated the microbial utilization of d-eDNA as an organic phosphorus substrate. Higher temperatures during summer may amplify this effect through a general enhancement of microbial metabolism. A partial least squares regression (PLSR) model was able to reproduce the seasonal cycle in d-eDNA persistence and explained 60% of the variance in the observations. Rapid phosphate turnover and low concentrations of bioavailable phosphate, both indicative of phosphate limitation, were the most important parameters in the model. Abiotic factors such as pH, salinity and oxygen exerted minimal influence. The present study demonstrates significant seasonal variability in the persistence of d-eDNA in a natural marine environment that can be linked to the metabolic response of microbial communities to nutrient limitation. Future studies should consider the effect of natural environmental gradients on the seasonal persistence of eDNA, which will be of particular relevance for time-series biomonitoring programs. PMID:29474423

Survey of Legionella spp. in Mud Spring Recreation Area

NASA Astrophysics Data System (ADS)

Hsu, B.-M.; Ma, P.-H.; Su, I.-Z.; Chen, N.-S.

2009-04-01

Legionella genera are parasites of FLA, and intracellular bacterial replication within the FLA plays a major role in the transmission of disease. At least 13 FLA species—including Acanthamoeba spp., Naegleria spp., and Hartmannella spp.—support intracellular bacterial replication. In the study, Legionellae were detected with microbial culture or by direct DNA extraction and analysis from concentrated water samples or cultured free-living amoebae, combined with molecular methods that allow the taxonomic identification of these pathogens. The water samples were taken from a mud spring recreation area located in a mud-rock-formation area in southern Taiwan. Legionella were detected in 15 of the 34 samples (44.1%). Four of the 34 samples analyzed by Legionella culture were positive for Legionella, five of 34 were positive for Legionella when analyzed by direct DNA extraction and analysis, and 11 of 34 were positive for amoebae-resistant Legionella when analyzed by FLA culture. Ten samples were shown to be positive for Legionella by one analysis method and five samples were shown to be positive by two analysis methods. However, Legionella was detected in no sample by all three analysis methods. This suggests that the three analysis methods should be used together to detect Legionella in aquatic environments. In this study, L. pneumophila serotype 6 coexisted with A. polyphaga, and two uncultured Legionella spp. coexisted with either H. vermiformis or N. australiensis. Of the unnamed Legionella genotypes detected in six FLA culture samples, three were closely related to L. waltersii and the other three were closely related to L. pneumophila serotype 6. Legionella pneumophila serotype 6, L. drancourtii, and L. waltersii are noted endosymbionts of FLA and are categorized as pathogenic bacteria. This is significant for human health because these Legionella exist within FLA and thus come into contact with typically immunocompromised people.

Effect of gamma irradiation on the microbial load, nutrient composition and free radical scavenging activity of Nelumbo nucifera rhizome

NASA Astrophysics Data System (ADS)

Khattak, Khanzadi Fatima; Simpson, Thomas James; Ihasnullah

2009-03-01

The assurance of microbial quality is necessary to make plant materials suitable for human consumption and commercialization. The aim of the present study was to evaluate the possibility to apply the gamma radiation treatment on the rhizome samples of Nelumbo nucifera for microbial decontamination. The radiation processing was carried out at dose levels of 1, 2, 4 and 6 kGy. The irradiated and control samples were analyzed for microbial load, organoleptic acceptance, extraction yield, proximate composition, phenolic contents and DPPH scavenging activity. The results indicated that gamma radiation treatment significantly reduced microbial load and increased the storability of the irradiated samples. The treated samples were also acceptable sensorically. The extraction yield and phenolic contents increased with the increase of radiation dose. Gamma radiation also enhanced the DPPH scavenging activity.

Acoustically enriching, large-depth aquatic sampler.

PubMed

Jonsson, Jonas; Ogden, Sam; Johansson, Linda; Hjort, Klas; Thornell, Greger

2012-05-07

In marine biology, it is useful to collect water samples when exploring the distribution and diversity of microbial communities in underwater environments. In order to provide, e.g., a miniaturized submersible explorer with the capability of collecting microorganisms, a compact sample enrichment system has been developed. The sampler is 30 mm long, 15 mm wide, and just a few millimetres thick. Integrated in a multilayer steel, polyimide and glass construction is a microfluidic channel with piezoelectric transducers, where microorganism and particle samples are collected and enriched, using acoustic radiation forces for gentle and labelless trapping. High-pressure, latchable valves, using paraffin as the actuation material, at each end of the microfluidic channel keep the collected sample pristine. A funnel structure raised above the surface of the device directs water into the microfluidic channel as the vehicle propels itself or when there is a flow across its hull. The valves proved leak proof to a pressure of 2.1 MPa for 19 hours and momentary pressures of 12.5 MPa, corresponding to an ocean depth of more than 1200 metres. By reactivating the latching mechanism, small leakages through the valves could be remedied, which could thus increase the leak-less operational time. Fluorescent particles, 1.9 μm in diameter, were successfully trapped in the microfluidic channel at flow rates up to 15 μl min(-1), corresponding to an 18.5 cm s(-1) external flow rate of the sampler. In addition, liquid-suspended GFP-marked yeast cells were successfully trapped.

Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity

PubMed Central

Fujimoto, Masanori; Moyerbrailean, Gregory A.; Noman, Sifat; Gizicki, Jason P.; Ram, Michal L.; Green, Phyllis A.; Ram, Jeffrey L.

2014-01-01

The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies. PMID:25222021

Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.

PubMed

Fujimoto, Masanori; Moyerbrailean, Gregory A; Noman, Sifat; Gizicki, Jason P; Ram, Michal L; Green, Phyllis A; Ram, Jeffrey L

2014-01-01

The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies.