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.

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

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.

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.

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.

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.

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.

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

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

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

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

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.

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.

It's all relative: ranking the diversity of aquatic bacterial communities.

PubMed

Shaw, Allison K; Halpern, Aaron L; Beeson, Karen; Tran, Bao; Venter, J Craig; Martiny, Jennifer B H

2008-09-01

The study of microbial diversity patterns is hampered by the enormous diversity of microbial communities and the lack of resources to sample them exhaustively. For many questions about richness and evenness, however, one only needs to know the relative order of diversity among samples rather than total diversity. We used 16S libraries from the Global Ocean Survey to investigate the ability of 10 diversity statistics (including rarefaction, non-parametric, parametric, curve extrapolation and diversity indices) to assess the relative diversity of six aquatic bacterial communities. Overall, we found that the statistics yielded remarkably similar rankings of the samples for a given sequence similarity cut-off. This correspondence, despite the different underlying assumptions of the statistics, suggests that diversity statistics are a useful tool for ranking samples of microbial diversity. In addition, sequence similarity cut-off influenced the diversity ranking of the samples, demonstrating that diversity statistics can also be used to detect differences in phylogenetic structure among microbial communities. Finally, a subsampling analysis suggests that further sequencing from these particular clone libraries would not have substantially changed the richness rankings of the samples.

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

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

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

Can the black box be cracked? The augmentation of microbial ecology by high-resolution, automated sensing technologies.

PubMed

Shade, Ashley; Carey, Cayelan C; Kara, Emily; Bertilsson, Stefan; McMahon, Katherine D; Smith, Matthew C

2009-08-01

Automated sensing technologies, 'ASTs,' are tools that can monitor environmental or microbial-related variables at increasingly high temporal resolution. Microbial ecologists are poised to use AST data to couple microbial structure, function and associated environmental observations on temporal scales pertinent to microbial processes. In the context of aquatic microbiology, we discuss three applications of ASTs: windows on the microbial world, adaptive sampling and adaptive management. We challenge microbial ecologists to push AST potential in helping to reveal relationships between microbial structure and function.

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...

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

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.

Microbial Condition of Water Samples from Foreign Fuel Storage Facilities

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

Berry, C.J.; Fliermans, C.B.; Santo Domingo, J.

1997-10-30

In order to assess the microbial condition of foreign nuclear fuel storage facilities, fourteen different water samples were received from facilities outside the United States that have sent spent nuclear fuel to SRS for wet storage. Each water sample was analyzed for microbial content and activity as determined by total bacteria, viable aerobic bacteria, viable anaerobic bacteria, viable sulfate- reducing bacteria, viable acid-producing bacteria and enzyme diversity. The results for each water sample were then compared to other foreign samples and to data from the receiving basin for off- site fuel (RBOF) at SRS.

Mesocosms of aquatic bacterial communities from the Cuatro Cienegas Basin (Mexico): a tool to test bacterial community response to environmental stress.

PubMed

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

2012-08-01

Microbial communities are responsible for important ecosystem processes, and their activities are regulated by environmental factors such as temperature and solar ultraviolet radiation. Here we investigate changes in aquatic microbial community structure, diversity, and evenness in response to changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with both microbial mat communities and plankton from natural pools within the Cuatro Cienegas Basin (Mexico). Clone libraries (16S rRNA) were obtained from water samples at the beginning and at the end of the experiment (40 days). Phylogenetic analysis indicated substantial changes in aquatic community composition and structure in response to temperature and UV radiation. Extreme treatments with elevation in temperature or UV radiation reduced diversity in relation to the Control treatments, causing a reduction in richness and increase in dominance, with a proliferation of a few resistant operational taxonomic units. Each phylum was affected differentially by the new conditions, which translates in a differential modification of ecosystem functioning. This suggests that the impact of environmental stress, at least at short term, will reshape the aquatic bacterial communities of this unique ecosystem. This work also demonstrates the possibility of designing manageable synthetic microbial community ecosystems where controlled environmental variables can be manipulated. Therefore, microbial model systems offer a complementary approach to field and laboratory studies of global research problems associated with the environment.

Microbial community composition and endolith colonization at an Arctic thermal spring are driven by calcite precipitation

USGS Publications Warehouse

Starke, Verena; Kirshtein, Julie; Fogel, Marilyn L.; Steele, Andrew

2013-01-01

Environmental conditions shape community composition. Arctic thermal springs provide an opportunity to study how environmental gradients can impose strong selective pressures on microbial communities and provide a continuum of niche opportunities. We use microscopic and molecular methods to conduct a survey of microbial community composition at Troll Springs on Svalbard, Norway, in the high Arctic. Microorganisms there exist under a wide range of environmental conditions: in warm water as periphyton, in moist granular materials, and in cold, dry rock as endoliths. Troll Springs has two distinct ecosystems, aquatic and terrestrial, together in close proximity, with different underlying environmental factors shaping each microbial community. Periphyton are entrapped during precipitation of calcium carbonate from the spring's waters, providing microbial populations that serve as precursors for the development of endolithic communities. This process differs from most endolith colonization, in which the rock predates the communities that colonize it. Community composition is modulated as environmental conditions change within the springs. At Troll, the aquatic environments show a small number of dominant operational taxonomic units (OTUs) that are specific to each sample. The terrestrial environments show a more even distribution of OTUs common to multiple samples.

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

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.

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

PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology

USGS Publications Warehouse

Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Zawada, David G.; Andersen, Gary L.

2012-01-01

Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease.

PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology.

PubMed

Kellogg, Christina A; Piceno, Yvette M; Tom, Lauren M; DeSantis, Todd Z; Zawada, David G; Andersen, Gary L

2012-01-01

Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease. Published by Elsevier B.V.

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

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.

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.

[Microbial air monitoring in operating theatre: active and passive samplings].

PubMed

Pasquarella, C; Masia, M D; Nnanga, Nga; Sansebastiano, G E; Savino, A; Signorelli, C; Veronesi, L

2004-01-01

Microbial air contamination was evaluated in 11 operating theatres using active and passive samplings. SAS (Surface Air System) air sampling was used to evaluate cfu/m3 and settle plates were used to measure the index of microbial air contamination (IMA). Samplings were performed at the same time on three different days, at three different times (before, during and after the surgical activity). Two points were monitored (patient area and perimeter of the operating theatre). Moreover, the cfu/m3 were evaluated at the air inlet of the conditioner system. 74.7% of samplings performed at the air inlet and 66.7% of the samplings performed at the patient area before the beginning of the surgical activity (at rest) exceeded the 35 cfu/m3 used as threshold value. 100% of IMA values exceeded the threshold value of 5. Using both active and passive sampling, the microbial contamination was shown to increase significantly during activity. The cfu values were higher at the patient area than at the perimeter of the operating theatre. Mean values of the cfu/m3 during activity at the patient area ranged from a minimum of 61+/-41 cfu/m3 to a maximum of 242+/-136 cfu/m3; IMA values ranged from a minimum of 19+/-10 to a maximum of 129+/-60. 15.2% of samplings performed at the patient area using SAS and 75.8% of samplings performed using settle plates exceeded the threshold values of 180 cfu/m3 and 25 respectively, with a significant difference of the percentages. The highest values were found in the operating theatre with inadequate structural and managerial conditions. These findings confirm that the microbiological quality of air may be considered a mirror of the hygienic conditions of the operating theatre. Settle plates proved to be more sensitive in detecting the increase of microbial air contamination related to conditions that could compromise the quality of the air in operating theatres.

Harmonisation of microbial sampling and testing methods for distillate fuels

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

Hill, G.C.; Hill, E.C.

1995-05-01

Increased incidence of microbial infection in distillate fuels has led to a demand for organisations such as the Institute of Petroleum to propose standards for microbiological quality, based on numbers of viable microbial colony forming units. Variations in quality requirements, and in the spoilage significance of contaminating microbes plus a tendency for temporal and spatial changes in the distribution of microbes, makes such standards difficult to implement. The problem is compounded by a diversity in the procedures employed for sampling and testing for microbial contamination and in the interpretation of the data obtained. The following paper reviews these problems andmore » describes the efforts of The Institute of Petroleum Microbiology Fuels Group to address these issues and in particular to bring about harmonisation of sampling and testing methods. The benefits and drawbacks of available test methods, both laboratory based and on-site, are discussed.« less

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

[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.

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

Elucidating Microbial Adaptation Dynamics via Autonomous Exposure and Sampling

NASA Technical Reports Server (NTRS)

Grace, Joseph M.; Verseux, Cyprien; Gentry, Diana; Moffet, Amy; Thayabaran, Ramanen; Wong, Nathan; Rothschild, Lynn

2013-01-01

The adaptation of micro-organisms to their environments is a complex process of interaction between the pressures of the environment and of competition. Reducing this multifactorial process to environmental exposure in the laboratory is a common tool for elucidating individual mechanisms of evolution, such as mutation rates. Although such studies inform fundamental questions about the way adaptation and even speciation occur, they are often limited by labor-intensive manual techniques. Current methods for controlled study of microbial adaptation limit the length of time, the depth of collected data, and the breadth of applied environmental conditions. Small idiosyncrasies in manual techniques can have large effects on outcomes; for example, there are significant variations in induced radiation resistances following similar repeated exposure protocols. We describe here a project under development to allow rapid cycling of multiple types of microbial environmental exposure. The system allows continuous autonomous monitoring and data collection of both single species and sampled communities, independently and concurrently providing multiple types of controlled environmental pressure (temperature, radiation, chemical presence or absence, and so on) to a microbial community in dynamic response to the ecosystem's current status. When combined with DNA sequencing and extraction, such a controlled environment can cast light on microbial functional development, population dynamics, inter- and intra-species competition, and microbe-environment interaction. The project's goal is to allow rapid, repeatable iteration of studies of both natural and artificial microbial adaptation. As an example, the same system can be used both to increase the pH of a wet soil aliquot over time while periodically sampling it for genetic activity analysis, or to repeatedly expose a culture of bacteria to the presence of a toxic metal, automatically adjusting the level of toxicity based on the

A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.

PubMed

Olesen, Scott W; Vora, Suhani; Techtmann, Stephen M; Fortney, Julian L; Bastidas-Oyanedel, Juan R; Rodríguez, Jorge; Hazen, Terry C; Alm, Eric J

2016-01-01

Many microbial ecology experiments use sequencing data to measure a community's response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method's validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of "bottle effects".

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.

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

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

Environmental DNA sampling protocol - filtering water to capture DNA from aquatic organisms

USGS Publications Warehouse

Laramie, Matthew B.; Pilliod, David S.; Goldberg, Caren S.; Strickler, Katherine M.

2015-09-29

Environmental DNA (eDNA) analysis is an effective method of determining the presence of aquatic organisms such as fish, amphibians, and other taxa. This publication is meant to guide researchers and managers in the collection, concentration, and preservation of eDNA samples from lentic and lotic systems. A sampling workflow diagram and three sampling protocols are included as well as a list of suggested supplies. Protocols include filter and pump assembly using: (1) a hand-driven vacuum pump, ideal for sample collection in remote sampling locations where no electricity is available and when equipment weight is a primary concern; (2) a peristaltic pump powered by a rechargeable battery-operated driver/drill, suitable for remote sampling locations when weight consideration is less of a concern; (3) a 120-volt alternating current (AC) powered peristaltic pump suitable for any location where 120-volt AC power is accessible, or for roadside sampling locations. Images and detailed descriptions are provided for each step in the sampling and preservation process.

A novel analysis method for paired-sample microbial ecology experiments

DOE PAGES

Olesen, Scott W.; Vora, Suhani; Techtmann, Stephen M.; ...

2016-05-06

Many microbial ecology experiments use sequencing data to measure a community s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samplesmore » and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Furthermore, our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of bottle effects .« less

A novel analysis method for paired-sample microbial ecology experiments

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

Olesen, Scott W.; Vora, Suhani; Techtmann, Stephen M.

Many microbial ecology experiments use sequencing data to measure a community s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samplesmore » and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Furthermore, our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of bottle effects .« less

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.

Investigations of the microbial transformation of cortisol to prednisolone in urine samples.

PubMed

Bredehöft, Michael; Baginski, Rainer; Parr, Maria-Kristina; Thevis, Mario; Schänzer, Wilhelm

2012-03-01

Doping control samples are normally collected under non-sterile conditions and sometimes, storage and transportation are influenced by parameters such as the temperature. Therefore, microbial contamination and subsequent alteration of a sample's composition are possible. Studies regarding sample collection in cattle breeding have already shown enzymatic transformation of endogenous testosterone to boldenone causing false-positive findings. The aim of the present study was to investigate whether positive doping cases with the synthetic corticosteroids prednisolone and prednisone may result from microbial transformation of the endogenous corticosteroids cortisol and cortisone, respectively. A method comprising parameters such as pH values and screening results for synthetic glucocorticosteroids as well as incubation experiments followed by liquid chromatographic and mass spectrometric analysis was employed to test for contaminating germs with Δ(1)-dehydrogenase activity. Over 700 urine samples comprising inpatient and doping control specimens were investigated. In none of them, 1,2-dehydrogenating activity was confirmed. These findings are in accordance with other studies. However, the problem of microbial alteration of doping control specimens with special respect to 1,2-dehydrogenation must not be underestimated. Article from a special issue on steroids and microorganisms. Copyright © 2010 Elsevier Ltd. All rights reserved.

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...

Microbial Habitability in Gale Crater: Sample Analysis at Mars (SAM) Instrument Detection of Microbial Essential Carbon and Nitrogen

NASA Technical Reports Server (NTRS)

Sutter, B.; Ming, D. W.; Eigenbrode, J. E.; Steele, A.; Stern, J. C.; Gonzalez, R. N.; McAdam, A. C.; Mahaffy, P. R.

2016-01-01

Chemical analyses of Mars soils and sediments from previous landed missions have demonstrated that Mars surface materials possessed major (e.g., P, K, Ca, Mg, S) and minor (e.g., Fe, Mn, Zn, Ni, Cl) elements essential to support microbial life. However, the detection of microbial essential organic-carbon (C) and nitrate have been more elusive until the Mars Science Laboratory (MSL) rover mission. Nitrate and organic-C in Gale Crater, Mars have been detected by the Sample Analysis at Mars (SAM) instrument onboard the MSL Curiosity rover. Eolian fines and drilled sedimentary rock samples were heated in the SAM oven from approximately 30 to 860 degrees Centigrade where evolved gases (e.g., nitrous oxide (NO) and CO2) were released and analyzed by SAM’s quadrupole mass spectrometer (MS). The temperatures of evolved NO was assigned to nitrate while evolved CO2 was assigned to organic-C and carbonate. The CO2 releases in several samples occurred below 450 degrees Centigrade suggesting organic-C dominated in those samples. As much as 7 micromoles NO3-N per gram and 200 micromoles CO2-C per gram have been detected in the Gale Crater materials. These N and C levels coupled with assumed microbial biomass (9 x 10 (sup -7) micrograms per cell) C (0.5 micrograms C per micrograms cell) and N (0.14 micrograms N per micrograms cell) requirements, suggests that less than 1 percent and less than 10 percent of Gale Crater C and N, respectively, would be required if available, to accommodate biomass requirements of 1 by 10 (sup 5) cells per gram sediment. While nitrogen is the limiting nutrient, the potential exists that sufficient N and organic-C were present to support limited heterotrophic microbial populations that may have existed on ancient Mars.

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 diversity within Juan de Fuca ridge basement fluids sampled from oceanic borehole observatories

NASA Astrophysics Data System (ADS)

Jungbluth, S.; Bowers, R.; Lin, H.; Hsieh, C.; Cowen, J. P.; Rappé, M.

2012-12-01

Three generations of sampling and instrumentation platforms known as Circulation Obviation Retrofit Kit (CORK) observatories affixed to Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP) boreholes are providing unrivaled access to fluids originating from 1.2-3.5 million-years (Myr) old basaltic crust of the eastern flank of the Juan de Fuca ridge. Borehole fluid samples obtained via a custom seafloor fluid pumping and sampling system coupled to CORK continuous fluid delivery lines are yielding critical insights into the biogeochemistry and nature of microbial life inhabiting the sediment-covered basement environment. Direct microscopic enumeration revealed microbial cell abundances that are 2-41% of overlying bottom seawater. Snapshots of basement fluid microbial diversity and community structure have been obtained through small subunit ribosomal RNA (SSU rRNA) gene cloning and sequencing from five boreholes that access a range of basement ages and temperatures at the sediment-basement interface. SSU rRNA gene clones were derived from four different CORK installations (1026B, 1301A, 1362A, and 1362B) accessing relatively warmer (65°C) and older (3.5 Myr) ridge flank, and one location (1025C) accessing relatively cooler (39°C) and younger (1.2 Myr) ridge flank, revealing that warmer basement fluids had higher microbial diversity. A sampling time-series collected from borehole 1301A has revealed a microbial community that is temporally variable, with the dominant lineages changing between years. Each of the five boreholes sampled contained a unique microbial assemblage, however, common members are found from both cultivated and uncultivated lineages within the archaeal and bacterial domains, including meso- and thermophilic microbial lineages involved with sulfur cycling (e.g Thiomicrospira, Sulfurimonas, Desulfocapsa, Desulfobulbus). In addition, borehole fluid environmental gene clones were also closely related to uncultivated lineages

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...

Molecular analysis of microbial diversity in corrosion samples from energy transmission towers.

PubMed

Oliveira, Valéria M; Lopes-Oliveira, Patrícia F; Passarini, Michel R Z; Menezes, Claudia B A; Oliveira, Walter R C; Rocha, Adriano J; Sette, Lara D

2011-04-01

Microbial diversity in corrosion samples from energy transmission towers was investigated using molecular methods. Ribosomal DNA fragments were used to assemble gene libraries. Sequence analysis indicated 10 bacterial genera within the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. In the two libraries generated from corroded screw-derived samples, the genus Acinetobacter was the most abundant. Acinetobacter and Clostridium spp. dominated, with similar percentages, in the libraries derived from corrosion scrapings. Fungal clones were affiliated with 14 genera belonging to the phyla Ascomycota and Basidiomycota; of these, Capnobotryella and Fellomyces were the most abundant fungi observed. Several of the microorganisms had not previously been associated with biofilms and corrosion, reinforcing the need to use molecular techniques to achieve a more comprehensive assessment of microbial diversity in environmental samples.

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 ...

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.

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

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

1988-01-01

Chapter A4, methods for collection and analyses of aquatic biological and microbiological samples, contains methods used by the U.S. Geological Survey to collect, preserve, and analyze waters to determine their biological and microbiological properties. Part 1 consists of detailed descriptions of more than 45 individual methods, including those for bacteria, phytoplankton, zooplankton, seston, periphyton, macrophytes, benthic invertebrates, fish and other vertebrates, cellular contents, productivity and bioassay. Each method is summarized, and the applications, interferences, apparatus, reagents, analyses, calculations, reporting of results, precisions, and references are given. Part 2 consists of a glossary. Part 3 is a list of taxonomic references. (USGS)

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.

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

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

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

Elucidating Microbial Adaptation Dynamics via Autonomous Exposure and Sampling

NASA Astrophysics Data System (ADS)

Grace, J. M.; Verseux, C.; Gentry, D.; Moffet, A.; Thayabaran, R.; Wong, N.; Rothschild, L.

2013-12-01

The adaptation of micro-organisms to their environments is a complex process of interaction between the pressures of the environment and of competition. Reducing this multifactorial process to environmental exposure in the laboratory is a common tool for elucidating individual mechanisms of evolution, such as mutation rates[Wielgoss et al., 2013]. Although such studies inform fundamental questions about the way adaptation and even speciation occur, they are often limited by labor-intensive manual techniques[Wassmann et al., 2010]. Current methods for controlled study of microbial adaptation limit the length of time, the depth of collected data, and the breadth of applied environmental conditions. Small idiosyncrasies in manual techniques can have large effects on outcomes; for example, there are significant variations in induced radiation resistances following similar repeated exposure protocols[Alcántara-Díaz et al., 2004; Goldman and Travisano, 2011]. We describe here a project under development to allow rapid cycling of multiple types of microbial environmental exposure. The system allows continuous autonomous monitoring and data collection of both single species and sampled communities, independently and concurrently providing multiple types of controlled environmental pressure (temperature, radiation, chemical presence or absence, and so on) to a microbial community in dynamic response to the ecosystem's current status. When combined with DNA sequencing and extraction, such a controlled environment can cast light on microbial functional development, population dynamics, inter- and intra-species competition, and microbe-environment interaction. The project's goal is to allow rapid, repeatable iteration of studies of both natural and artificial microbial adaptation. As an example, the same system can be used both to increase the pH of a wet soil aliquot over time while periodically sampling it for genetic activity analysis, or to repeatedly expose a culture of

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...

Relationships between processing delay and microbial load of broiler neck skin samples.

PubMed

Lucianez, A; Holmes, M A; Tucker, A W

2010-01-01

The measurable microbial load on poultry carcasses during processing is determined by a number of factors including farm or origin, processing hygiene, and external temperature. This study investigated associations between carcass microbial load and progressive delays to processing. A total of 30 carcasses were delayed immediately after defeathering and before evisceration in a commercial abattoir in groups of five, and were held at ambient temperature for 1, 2, 3, 4, 6, and 8 h. Delayed carcasses were reintroduced to the processing line, and quantitative assessment of total viable count, coliforms, Staphylococcus aureus, and Pseudomonas spp. was undertaken on neck skin flap samples collected after carcass chilling and then pooled for each group. Sampling was repeated on 5 separate days, and the data were combined. Significant increases in total viable count (P = 0.001) and coliforms (P = 0.004), but not for S. aureus or Pseudomonas loads, were observed across the 8-h period of delay. In line with previous studies, there was significant variation in microbiological data according to sampling day. In conclusion, there is a significant and measurable decline in microbiological status of uneviscerated but defeathered poultry carcasses after an 8-h delay, but the variability of sampling results, reflecting the wide range of factors that impact microbial load, means that it is not possible to determine maximum or minimum acceptable periods of processing delay based on this criterion alone.

A method for sampling microbial aerosols using high altitude balloons.

PubMed

Bryan, N C; Stewart, M; Granger, D; Guzik, T G; Christner, B C

2014-12-01

Owing to the challenges posed to microbial aerosol sampling at high altitudes, very little is known about the abundance, diversity, and extent of microbial taxa in the Earth-atmosphere system. To directly address this knowledge gap, we designed, constructed, and tested a system that passively samples aerosols during ascent through the atmosphere while tethered to a helium-filled latex sounding balloon. The sampling payload is ~ 2.7 kg and comprised of an electronics box and three sampling chambers (one serving as a procedural control). Each chamber is sealed with retractable doors that can be commanded to open and close at designated altitudes. The payload is deployed together with radio beacons that transmit GPS coordinates (latitude, longitude and altitude) in real time for tracking and recovery. A cut mechanism separates the payload string from the balloon at any desired altitude, returning all equipment safely to the ground on a parachute. When the chambers are opened, aerosol sampling is performed using the Rotorod® collection method (40 rods per chamber), with each rod passing through 0.035 m3 per km of altitude sampled. Based on quality control measurements, the collection of ~ 100 cells rod(-1) provided a 3-sigma confidence level of detection. The payload system described can be mated with any type of balloon platform and provides a tool for characterizing the vertical distribution of microorganisms in the troposphere and stratosphere. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

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

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...

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).

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.

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.

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.

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

NASA Astrophysics Data System (ADS)

Krueger, Martin; Straaten, Nontje; Mazzini, Adriano

2015-04-01

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

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

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

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

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 ...

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.

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.

Quantitative microbial faecal source tracking with sampling guided by hydrological catchment dynamics.

PubMed

Reischer, G H; Haider, J M; Sommer, R; Stadler, H; Keiblinger, K M; Hornek, R; Zerobin, W; Mach, R L; Farnleitner, A H

2008-10-01

The impairment of water quality by faecal pollution is a global public health concern. Microbial source tracking methods help to identify faecal sources but the few recent quantitative microbial source tracking applications disregarded catchment hydrology and pollution dynamics. This quantitative microbial source tracking study, conducted in a large karstic spring catchment potentially influenced by humans and ruminant animals, was based on a tiered sampling approach: a 31-month water quality monitoring (Monitoring) covering seasonal hydrological dynamics and an investigation of flood events (Events) as periods of the strongest pollution. The detection of a ruminant-specific and a human-specific faecal Bacteroidetes marker by quantitative real-time PCR was complemented by standard microbiological and on-line hydrological parameters. Both quantitative microbial source tracking markers were detected in spring water during Monitoring and Events, with preponderance of the ruminant-specific marker. Applying multiparametric analysis of all data allowed linking the ruminant-specific marker to general faecal pollution indicators, especially during Events. Up to 80% of the variation of faecal indicator levels during Events could be explained by ruminant-specific marker levels proving the dominance of ruminant faecal sources in the catchment. Furthermore, soil was ruled out as a source of quantitative microbial source tracking markers. This study demonstrates the applicability of quantitative microbial source tracking methods and highlights the prerequisite of considering hydrological catchment dynamics in source tracking study design.

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

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.

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.

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.

Microbial and chemical analysis of illicit drugs samples confiscated from different areas of PakistanMicrobial and chemical analysis of illicit drugs samples confiscated from different areas of Pakistan.

PubMed

Hussain, Shahzad; Khattak, Zainab; Mahmood, Sidra; Malik, Farnaz; Riaz, Humayun; Raza, Syed Atif; Khan, Samiullah

2016-09-01

The microbial and chemical analysis of illicit drug samples from different areas of Pakistan i.e. Quetta, Karachi, Lahore and Islamabad was conducted in a cross-sectional study at National Institute of Health, Islamabad. The drug samples were confiscated by Anti Narcotics Force (ANF), Pakistan. Microbial analysis was done by estimating bioburden which revealed the presence of gram negative and positive bacteria's, fungus, Streptococcus, Staphylococcus species. Trypton soya agar was used for total aerobic count, MacConkey agar for gram-negative bacteria, Sabouraud dextrose agar for fungus and Vogel-Johnson agar for Streptococcus and Staphylococcus species. Colour tests were applied to identify the drug samples. Qualitative and quantitative analysis of suspected samples of Heroin, morphine, cocaine and acetic anhydride was made by employing different chromatographic techniques i.e. Thin-layer chromatography (TLC) and High-performance liquid chromatography (HPLC). The samples were found to be adulterated with paracetamol, diazepam and Dextromethorphen. Acetic anhydride was adulterated with hydrochloric acid (HCl). There is lack of information providing structured advice on responses to the consequences of illicit drug adulteration. Robust and rehearsed interventions and communication strategies would provide a basis for response for a wide variety of organisations. Research into the usefulness of media warnings about adulteration of illicit drugs is required.

Fitting distributions to microbial contamination data collected with an unequal probability sampling design.

PubMed

Williams, M S; Ebel, E D; Cao, Y

2013-01-01

The fitting of statistical distributions to microbial sampling data is a common application in quantitative microbiology and risk assessment applications. An underlying assumption of most fitting techniques is that data are collected with simple random sampling, which is often times not the case. This study develops a weighted maximum likelihood estimation framework that is appropriate for microbiological samples that are collected with unequal probabilities of selection. A weighted maximum likelihood estimation framework is proposed for microbiological samples that are collected with unequal probabilities of selection. Two examples, based on the collection of food samples during processing, are provided to demonstrate the method and highlight the magnitude of biases in the maximum likelihood estimator when data are inappropriately treated as a simple random sample. Failure to properly weight samples to account for how data are collected can introduce substantial biases into inferences drawn from the data. The proposed methodology will reduce or eliminate an important source of bias in inferences drawn from the analysis of microbial data. This will also make comparisons between studies and the combination of results from different studies more reliable, which is important for risk assessment applications. © 2012 No claim to US Government works.

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

Community-Level Physiological Profiling of Microbial Communities in Constructed Wetlands: Effects of Sample Preparation.

PubMed

Button, Mark; Weber, Kela; Nivala, Jaime; Aubron, Thomas; Müller, Roland Arno

2016-03-01

Community-level physiological profiling (CLPP) using BIOLOG® EcoPlates™ has become a popular method for characterizing and comparing the functional diversity, functional potential, and metabolic activity of heterotrophic microbial communities. The method was originally developed for profiling soil communities; however, its usage has expanded into the fields of ecotoxicology, agronomy, and the monitoring and profiling of microbial communities in various wastewater treatment systems, including constructed wetlands for water pollution control. When performing CLPP on aqueous samples from constructed wetlands, a wide variety of sample characteristics can be encountered and challenges may arise due to excessive solids, color, or turbidity. The aim of this study was to investigate the impacts of different sample preparation methods on CLPP performed on a variety of aqueous samples covering a broad range of physical and chemical characteristics. The results show that using filter paper, centrifugation, or settling helped clarify samples for subsequent CLPP analysis, however did not do so as effectively as dilution for the darkest samples. Dilution was able to provide suitable clarity for the darkest samples; however, 100-fold dilution significantly affected the carbon source utilization patterns (CSUPs), particularly with samples that were already partially or fully clear. Ten-fold dilution also had some effect on the CSUPs of samples which were originally clear; however, the effect was minimal. Based on these findings, for this specific set of samples, a 10-fold dilution provided a good balance between ease of use, sufficient clarity (for dark samples), and limited effect on CSUPs. The process and findings outlined here can hopefully serve future studies looking to utilize CLPP for functional analysis of microbial communities and also assist in comparing data from studies where different sample preparation methods were utilized.

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.

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

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)

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

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 Indicator Profiling of Fresh Produce and Environmental Samples from Farms and Packing Facilities in Northern Mexico.

PubMed

Heredia, Norma; Caballero, Cindy; Cárdenas, Carmen; Molina, Karina; García, Rafael; Solís, Luisa; Burrowes, Vanessa; Bartz, Faith E; de Aceituno, Anna Fabiszewski; Jaykus, Lee-Ann; García, Santos; Leon, Juan

2016-07-01

To compare microbiological indicator and pathogen contamination among different types of fresh produce and environmental samples along the production chain, 636 samples of produce (rinsates from cantaloupe melons, jalapeño peppers, and tomatoes) and environmental samples (rinsates from hands of workers, soil, and water) were collected at four successive steps in the production process (from the field before harvest through the packing facility) on 11 farms in northern Mexico during 2011 and 2012. Samples were assayed for enteric pathogens (Escherichia coli O157:H7, other Shiga toxigenic E. coli, Salmonella, and Listeria monocytogenes) and microbial indicators (coliforms, other E. coli strains, and Enterococcus spp.). Salmonella was the only pathogen detected; it was found in one preharvest jalapeño sample (detection limits: 0.0033 CFU/ml in produce and hand samples, 0.0013 CFU/ml in water, and 0.04 CFU/g in soil). Microbial indicator profiles for produce, worker hands, and soil from jalapeño and tomato farms were similar, but cantaloupe farm samples had higher indicator levels (P < 0.05 for all comparisons) on fruit (6.5, 2.8, and 7.2 log CFU per fruit) and hands (6.6, 3.1, and 7.1 log CFU per hand) for coliforms, E. coli, and Enterococcus, respectively, and lower E. coli levels in soil (<1 CFU/g). In water from tomato farms, E. coli indicators were significantly more prevalent (70 to 89% of samples were positive; P = 0.01 to 0.02), and geometric mean levels were higher (0.3 to 0.6 log CFU/100 ml) than those in cantaloupe farm water (32 to 38% of samples were positive, geometric mean <1 CFU/100 ml). Microbial indicators were present during all production steps, but prevalence and levels were generally highest at the final on-farm production step (the packing facility) (P < 0.03 for significant comparisons). The finding that microbial contamination on produce farms is influenced by produce type and production step can inform the design of effective approaches to

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

Vibrational spectroscopy for imaging single microbial cells in complex biological samples

DOE PAGES

Harrison, Jesse P.; Berry, David

2017-04-13

Here, vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of themore » samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of singlecell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.« less

Vibrational spectroscopy for imaging single microbial cells in complex biological samples

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

Harrison, Jesse P.; Berry, David

Here, vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of themore » samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of singlecell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.« less

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.

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.

Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems.

PubMed

Imchen, Madangchanok; Kumavath, Ranjith; Barh, Debmalya; Azevedo, Vasco; Ghosh, Preetam; Viana, Marcus; Wattam, Alice R

2017-08-18

In this study, we categorize the microbial community in mangrove sediment samples from four different locations within a vast mangrove system in Kerala, India. We compared this data to other samples taken from the other known mangrove data, a tropical rainforest, and ocean sediment. An examination of the microbial communities from a large mangrove forest that stretches across southwestern India showed strong similarities across the higher taxonomic levels. When ocean sediment and a single isolate from a tropical rain forest were included in the analysis, a strong pattern emerged with Bacteria from the phylum Proteobacteria being the prominent taxon among the forest samples. The ocean samples were predominantly Archaea, with Euryarchaeota as the dominant phylum. Principal component and functional analyses grouped the samples isolated from forests, including those from disparate mangrove forests and the tropical rain forest, from the ocean. Our findings show similar patterns in samples were isolated from forests, and these were distinct from the ocean sediment isolates. The taxonomic structure was maintained to the level of class, and functional analysis of the genes present also displayed these similarities. Our report for the first time shows the richness of microbial diversity in the Kerala coast and its differences with tropical rain forest and ocean microbiome.

High-throughput automated microfluidic sample preparation for accurate microbial genomics

PubMed Central

Kim, Soohong; De Jonghe, Joachim; Kulesa, Anthony B.; Feldman, David; Vatanen, Tommi; Bhattacharyya, Roby P.; Berdy, Brittany; Gomez, James; Nolan, Jill; Epstein, Slava; Blainey, Paul C.

2017-01-01

Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (∼10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence ∼400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications. PMID:28128213

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

Estimating site occupancy rates for aquatic plants using spatial sub-sampling designs when detection probabilities are less than one

USGS Publications Warehouse

Nielson, Ryan M.; Gray, Brian R.; McDonald, Lyman L.; Heglund, Patricia J.

2011-01-01

Estimation of site occupancy rates when detection probabilities are <1 is well established in wildlife science. Data from multiple visits to a sample of sites are used to estimate detection probabilities and the proportion of sites occupied by focal species. In this article we describe how site occupancy methods can be applied to estimate occupancy rates of plants and other sessile organisms. We illustrate this approach and the pitfalls of ignoring incomplete detection using spatial data for 2 aquatic vascular plants collected under the Upper Mississippi River's Long Term Resource Monitoring Program (LTRMP). Site occupancy models considered include: a naïve model that ignores incomplete detection, a simple site occupancy model assuming a constant occupancy rate and a constant probability of detection across sites, several models that allow site occupancy rates and probabilities of detection to vary with habitat characteristics, and mixture models that allow for unexplained variation in detection probabilities. We used information theoretic methods to rank competing models and bootstrapping to evaluate the goodness-of-fit of the final models. Results of our analysis confirm that ignoring incomplete detection can result in biased estimates of occupancy rates. Estimates of site occupancy rates for 2 aquatic plant species were 19–36% higher compared to naive estimates that ignored probabilities of detection <1. Simulations indicate that final models have little bias when 50 or more sites are sampled, and little gains in precision could be expected for sample sizes >300. We recommend applying site occupancy methods for monitoring presence of aquatic species.

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.

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

Microbial environmental contamination in Italian dental clinics: A multicenter study yielding recommendations for standardized sampling methods and threshold values.

PubMed

Pasquarella, Cesira; Veronesi, Licia; Napoli, Christian; Castiglia, Paolo; Liguori, Giorgio; Rizzetto, Rolando; Torre, Ida; Righi, Elena; Farruggia, Patrizia; Tesauro, Marina; Torregrossa, Maria V; Montagna, Maria T; Colucci, Maria E; Gallè, Francesca; Masia, Maria D; Strohmenger, Laura; Bergomi, Margherita; Tinteri, Carola; Panico, Manuela; Pennino, Francesca; Cannova, Lucia; Tanzi, Marialuisa

2012-03-15

A microbiological environmental investigation was carried out in ten dental clinics in Italy. Microbial contamination of water, air and surfaces was assessed in each clinic during the five working days, for one week per month, for a three-month period. Water and surfaces were sampled before and after clinical activity; air was sampled before, after, and during clinical activity. A wide variation was found in microbial environmental contamination, both within the participating clinics and for the different sampling times. Before clinical activity, microbial water contamination in tap water reached 51,200cfu/mL (colony forming units per milliliter), and that in Dental Unit Water Systems (DUWSs) reached 872,000cfu/mL. After clinical activity, there was a significant decrease in the Total Viable Count (TVC) in tap water and in DUWSs. Pseudomonas aeruginosa was found in 2.38% (7/294) of tap water samples and in 20.06% (59/294) of DUWS samples; Legionella spp. was found in 29.96% (89/297) of tap water samples and 15.82% (47/297) of DUWS samples, with no significant difference between pre- and post-clinical activity. Microbial air contamination was highest during dental treatments, and decreased significantly at the end of the working activity (p<0.05). The microbial buildup on surfaces increased significantly during the working hours. This study provides data for the establishment of standardized sampling methods, and threshold values for contamination monitoring in dentistry. Some very critical situations have been observed which require urgent intervention. Furthermore, the study emphasizes the need for research aimed at defining effective managing strategies for dental clinics. Copyright © 2012 Elsevier B.V. All rights reserved.

Aquatic Acoustic Metrics Interface

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

2012-12-18

Fishes and marine mammals may suffer a range of potential effects from exposure to intense underwater sound generated by anthropogenic activities such as pile driving, shipping, sonars, and underwater blasting. Several underwater sound recording (USR) devices have been built to acquire samples of the underwater sound generated by anthropogenic activities. Software becomes indispensable for processing and analyzing the audio files recorded by these USRs. The new Aquatic Acoustic Metrics Interface Utility Software (AAMI) is specifically designed for analysis of underwater sound recordings to provide data in metrics that facilitate evaluation of the potential impacts of the sound on aquatic animals.more » In addition to the basic functions, such as loading and editing audio files recorded by USRs and batch processing of sound files, the software utilizes recording system calibration data to compute important parameters in physical units. The software also facilitates comparison of the noise sound sample metrics with biological measures such as audiograms of the sensitivity of aquatic animals to the sound, integrating various components into a single analytical frame.« less

Microbial Groundwater Sampling Protocol for Fecal-Rich Environments

PubMed Central

Harter, Thomas; Watanabe, Naoko; Li, Xunde; Atwill, Edward R; Samuels, William

2014-01-01

Inherently, confined animal farming operations (CAFOs) and other intense fecal-rich environments are potential sources of groundwater contamination by enteric pathogens. The ubiquity of microbial matter poses unique technical challenges in addition to economic constraints when sampling wells in such environments. In this paper, we evaluate a groundwater sampling protocol that relies on extended purging with a portable submersible stainless steel pump and Teflon® tubing as an alternative to equipment sterilization. The protocol allows for collecting a large number of samples quickly, relatively inexpensively, and under field conditions with limited access to capacity for sterilizing equipment. The protocol is tested on CAFO monitoring wells and considers three cross-contamination sources: equipment, wellbore, and ambient air. For the assessment, we use Enterococcus, a ubiquitous fecal indicator bacterium (FIB), in laboratory and field tests with spiked and blank samples, and in an extensive, multi-year field sampling campaign on 17 wells within 2 CAFOs. The assessment shows that extended purging can successfully control for equipment cross-contamination, but also controls for significant contamination of the well-head, within the well casing and within the immediate aquifer vicinity of the well-screen. Importantly, our tests further indicate that Enterococcus is frequently entrained in water samples when exposed to ambient air at a CAFO during sample collection. Wellbore and air contamination pose separate challenges in the design of groundwater monitoring strategies on CAFOs that are not addressed by equipment sterilization, but require adequate QA/QC procedures and can be addressed by the proposed sampling strategy. PMID:24903186

Microbial Air and Surface Monitoring Results from International Space Station Samples

NASA Technical Reports Server (NTRS)

Ott, C. Mark; Bruce, Rebekah J.; Castro, Victoria A.; Novikova, Natalia D.; Pierson, D. L.

2005-01-01

Over the course of long-duration spaceflight, spacecraft develop a microbial ecology that directly interacts with the crew of the vehicle. While most microorganisms are harmless or beneficial to the inhabitants of the vehicle, the presence of medically significant organisms appearing in this semi-closed environment could adversely affect crew health and performance. The risk of exposure of the crew to medically significant organisms during a mission is estimated using information gathered during nominal and contingency environmental monitoring. Analysis of the air and surface microbiota in the habitable compartments of the International Space Station (ISS) over the last four years indicate a high presence of Staphylococcus species reflecting the human inhabitants of the vehicle. Generally, air and surface microbial concentrations are below system design specifications, suggesting a lower risk of contact infection or biodegradation. An evaluation of sample frequency indicates a decrease in the identification of new species, suggesting a lower potential for unknown microorganisms to be identified. However, the opportunistic pathogen, Staphylococcus aureus, has been identified in 3 of the last 5 air samples and 5 of the last 9 surface samples. In addition, 47% of the coagulase negative Staphylococcus species that were isolated from the crew, ISS, and its hardware were found to be methicillin resistance. In combination, these observations suggest the potential of methicillin resistant infectious agents over time.

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

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

Rapid Microbial Sample Preparation from Blood Using a Novel Concentration Device

PubMed Central

Boardman, Anna K.; Campbell, Jennifer; Wirz, Holger; Sharon, Andre; Sauer-Budge, Alexis F.

2015-01-01

Appropriate care for bacteremic patients is dictated by the amount of time needed for an accurate diagnosis. However, the concentration of microbes in the blood is extremely low in these patients (1–100 CFU/mL), traditionally requiring growth (blood culture) or amplification (e.g., PCR) for detection. Current culture-based methods can take a minimum of two days, while faster methods like PCR require a sample free of inhibitors (i.e., blood components). Though commercial kits exist for the removal of blood from these samples, they typically capture only DNA, thereby necessitating the use of blood culture for antimicrobial testing. Here, we report a novel, scaled-up sample preparation protocol carried out in a new microbial concentration device. The process can efficiently lyse 10 mL of bacteremic blood while maintaining the microorganisms’ viability, giving a 30‑μL final output volume. A suite of six microorganisms (Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli, Haemophilus influenzae, Pseudomonas aeruginosa, and Candida albicans) at a range of clinically relevant concentrations was tested. All of the microorganisms had recoveries greater than 55% at the highest tested concentration of 100 CFU/mL, with three of them having over 70% recovery. At the lowest tested concentration of 3 CFU/mL, two microorganisms had recoveries of ca. 40–50% while the other four gave recoveries greater than 70%. Using a Taqman assay for methicillin-sensitive S. aureus (MSSA)to prove the feasibility of downstream analysis, we show that our microbial pellets are clean enough for PCR amplification. PCR testing of 56 spiked-positive and negative samples gave a specificity of 0.97 and a sensitivity of 0.96, showing that our sample preparation protocol holds great promise for the rapid diagnosis of bacteremia directly from a primary sample. PMID:25675242

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.

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

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.

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.

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...

Impact of temperature and time storage on the microbial detection of oral samples by Checkerboard DNA-DNA hybridization method.

PubMed

do Nascimento, Cássio; dos Santos, Janine Navarro; Pedrazzi, Vinícius; Pita, Murillo Sucena; Monesi, Nadia; Ribeiro, Ricardo Faria; de Albuquerque, Rubens Ferreira

2014-01-01

Molecular diagnosis methods have been largely used in epidemiological or clinical studies to detect and quantify microbial species that may colonize the oral cavity in healthy or disease. The preservation of genetic material from samples remains the major challenge to ensure the feasibility of these methodologies. Long-term storage may compromise the final result. The aim of this study was to evaluate the effect of temperature and time storage on the microbial detection of oral samples by Checkerboard DNA-DNA hybridization. Saliva and supragingival biofilm were taken from 10 healthy subjects, aliquoted (n=364) and processed according to proposed protocols: immediate processing and processed after 2 or 4 weeks, and 6 or 12 months of storage at 4°C, -20°C and -80°C. Either total or individual microbial counts were recorded in lower values for samples processed after 12 months of storage, irrespective of temperatures tested. Samples stored up to 6 months at cold temperatures showed similar counts to those immediately processed. The microbial incidence was also significantly reduced in samples stored during 12 months in all temperatures. Temperature and time of oral samples storage have relevant impact in the detection and quantification of bacterial and fungal species by Checkerboard DNA-DNA hybridization method. Samples should be processed immediately after collection or up to 6 months if conserved at cold temperatures to avoid false-negative results. Copyright © 2013 Elsevier Ltd. All rights reserved.

Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community.

PubMed

Tapio, Ilma; Shingfield, Kevin J; McKain, Nest; Bonin, Aurélie; Fischer, Daniel; Bayat, Ali R; Vilkki, Johanna; Taberlet, Pierre; Snelling, Timothy J; Wallace, R John

2016-01-01

Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial, fungal and archaeal communities were substantially different to ruminal digesta. Buccal and bolus samples gave much more similar profiles to ruminal digesta, although fewer archaea were detected in buccal and bolus samples. Bolus samples overall were most similar to ruminal samples. The differences between both buccal and bolus samples and ruminal digesta were consistent across all treatments. It can be concluded that either proxy sample type could be used as a predictor of the rumen microbial community, thereby enabling more convenient large-scale animal sampling for phenotyping and possible use in future animal breeding programs aimed at selecting cattle with a lower environmental footprint.

Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community

PubMed Central

Tapio, Ilma; Shingfield, Kevin J.; McKain, Nest; Bonin, Aurélie; Fischer, Daniel; Bayat, Ali R.; Vilkki, Johanna; Taberlet, Pierre; Snelling, Timothy J.; Wallace, R. John

2016-01-01

Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial, fungal and archaeal communities were substantially different to ruminal digesta. Buccal and bolus samples gave much more similar profiles to ruminal digesta, although fewer archaea were detected in buccal and bolus samples. Bolus samples overall were most similar to ruminal samples. The differences between both buccal and bolus samples and ruminal digesta were consistent across all treatments. It can be concluded that either proxy sample type could be used as a predictor of the rumen microbial community, thereby enabling more convenient large-scale animal sampling for phenotyping and possible use in future animal breeding programs aimed at selecting cattle with a lower environmental footprint. PMID:26986467

Efficiency of Different Sampling Tools for Aquatic Macroinvertebrate Collections in Malaysian Streams

PubMed Central

Ghani, Wan Mohd Hafezul Wan Abdul; Rawi, Che Salmah Md; Hamid, Suhaila Abd; Al-Shami, Salman Abdo

2016-01-01

This study analyses the sampling performance of three benthic sampling tools commonly used to collect freshwater macroinvertebrates. Efficiency of qualitative D-frame and square aquatic nets were compared to a quantitative Surber sampler in tropical Malaysian streams. The abundance and diversity of macroinvertebrates collected using each tool evaluated along with their relative variations (RVs). Each tool was used to sample macroinvertebrates from three streams draining different areas: a vegetable farm, a tea plantation and a forest reserve. High macroinvertebrate diversities were recorded using the square net and Surber sampler at the forested stream site; however, very low species abundance was recorded by the Surber sampler. Relatively large variations in the Surber sampler collections (RVs of 36% and 28%) were observed for the vegetable farm and tea plantation streams, respectively. Of the three sampling methods, the square net was the most efficient, collecting a greater diversity of macroinvertebrate taxa and a greater number of specimens (i.e., abundance) overall, particularly from the vegetable farm and the tea plantation streams (RV<25%). Fewer square net sample passes (<8 samples) were sufficient to perform a biological assessment of water quality, but each sample required a slightly longer processing time (±20 min) compared with those gathered via the other samplers. In conclusion, all three apparatuses were suitable for macroinvertebrate collection in Malaysian streams and gathered assemblages that resulted in the determination of similar biological water quality classes using the Family Biotic Index (FBI) and the Biological Monitoring Working Party (BMWP). However, despite a slightly longer processing time, the square net was more efficient (lowest RV) at collecting samples and more suitable for the collection of macroinvertebrates from deep, fast flowing, wadeable streams with coarse substrates. PMID:27019685

Impacts of Sampling and Handling Procedures on DNA- and RNA-based Microbial Characterization and Quantification of Groundwater and Saturated Soil

DTIC Science & Technology

2012-07-01

use of molecular biological techniques (MBTs) has allowed microbial ecologists and environmental engineers to determine microbial community...metabolic genes). The most common approaches used in bioremediation research are those based on the polymerase chain reaction (PCR) amplification of... bioremediation . Because of its sensitivity compared to direct hybridization/probing, PCR is increasingly used to analyze groundwater samples and soil samples

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

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

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.

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.

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.

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...

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

Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array.

PubMed

Devault, Alison M; McLoughlin, Kevin; Jaing, Crystal; Gardner, Shea; Porter, Teresita M; Enk, Jacob M; Thissen, James; Allen, Jonathan; Borucki, Monica; DeWitte, Sharon N; Dhody, Anna N; Poinar, Hendrik N

2014-03-06

Ancient human remains of paleopathological interest typically contain highly degraded DNA in which pathogenic taxa are often minority components, making sequence-based metagenomic characterization costly. Microarrays may hold a potential solution to these challenges, offering a rapid, affordable, and highly informative snapshot of microbial diversity in complex samples without the lengthy analysis and/or high cost associated with high-throughput sequencing. Their versatility is well established for modern clinical specimens, but they have yet to be applied to ancient remains. Here we report bacterial profiles of archaeological and historical human remains using the Lawrence Livermore Microbial Detection Array (LLMDA). The array successfully identified previously-verified bacterial human pathogens, including Vibrio cholerae (cholera) in a 19th century intestinal specimen and Yersinia pestis ("Black Death" plague) in a medieval tooth, which represented only minute fractions (0.03% and 0.08% alignable high-throughput shotgun sequencing reads) of their respective DNA content. This demonstrates that the LLMDA can identify primary and/or co-infecting bacterial pathogens in ancient samples, thereby serving as a rapid and inexpensive paleopathological screening tool to study health across both space and time.

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

Supercritical fluid extraction and ultra performance liquid chromatography of respiratory quinones for microbial community analysis in environmental and biological samples.

PubMed

Hanif, Muhammad; Atsuta, Yoichi; Fujie, Koichi; Daimon, Hiroyuki

2012-03-05

Microbial community structure plays a significant role in environmental assessment and animal health management. The development of a superior analytical strategy for the characterization of microbial community structure is an ongoing challenge. In this study, we developed an effective supercritical fluid extraction (SFE) and ultra performance liquid chromatography (UPLC) method for the analysis of bacterial respiratory quinones (RQ) in environmental and biological samples. RQ profile analysis is one of the most widely used culture-independent tools for characterizing microbial community structure. A UPLC equipped with a photo diode array (PDA) detector was successfully applied to the simultaneous determination of ubiquinones (UQ) and menaquinones (MK) without tedious pretreatment. Supercritical carbon dioxide (scCO(2)) extraction with the solid-phase cartridge trap proved to be a more effective and rapid method for extracting respiratory quinones, compared to a conventional organic solvent extraction method. This methodology leads to a successful analytical procedure that involves a significant reduction in the complexity and sample preparation time. Application of the optimized methodology to characterize microbial communities based on the RQ profile was demonstrated for a variety of environmental samples (activated sludge, digested sludge, and compost) and biological samples (swine and Japanese quail feces).

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

Potential microbial contamination during sampling of permafrost soil assessed by tracers

NASA Astrophysics Data System (ADS)

Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

2017-02-01

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

Potential microbial contamination during sampling of permafrost soil assessed by tracers.

PubMed

Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S

2017-02-23

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

Potential microbial contamination during sampling of permafrost soil assessed by tracers

PubMed Central

Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

2017-01-01

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores. PMID:28230151

Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples

PubMed Central

Beckers, Kalie F.; Childers, Gary W.

2017-01-01

Advances have been made to standardize 16S rRNA gene amplicon based studies for inter-study comparisons, yet there are many opportunities for systematic error that may render these comparisons improper and misleading. The fecal microbiome of horses has been examined previously, however, no universal horse fecal collection method and sample processing procedure has been established. This study was initialized in large part to ensure that samples collected by different individuals from different geographical areas (i.e., crowdsourced) were not contaminated due to less than optimal sampling or holding conditions. In this study, we examined the effect of sampling the surface of fecal pellets compared to homogenized fecal pellets, and also the effect of time of sampling after defecation on ‘bloom’ taxa (bloom taxa refers to microbial taxa that can grow rapidly in horse feces post-defecation) using v4 16S rRNA amplicon libraries. A total of 1,440,171 sequences were recovered from 65 horse fecal samples yielding a total of 3,422 OTUs at 97% similarity. Sampling from either surface or homogenized feces had no effect on diversity and little effect on microbial composition. Sampling at various time points (0, 2, 4, 6, 12 h) had a significant effect on both diversity and community composition of fecal samples. Alpha diversity (Shannon index) initially increased with time as regrowth taxa were detected in the amplicon libraries, but by 12 h the diversity sharply decreased as the community composition became dominated by a few bloom families, including Bacillaceae, Planococcaeae, and Enterococcaceae, and other families to a lesser extent. The results show that immediate sampling of horse feces must be done in order to ensure accurate representation of horse fecal samples. Also, several of the bloom taxa found in this study are known to occur in human and cattle feces post defecation. The dominance of these taxa in feces shortly after defecation suggests that the feces is an

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

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.

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

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 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

Gold-FISH: A correlative approach to microscopic imaging of single microbial cells in environmental samples

NASA Astrophysics Data System (ADS)

Schmidt, Hannes; Seki, David; Woebken, Dagmar; Eickhorst, Thilo

2017-04-01

Fluorescence in situ hybridization (FISH) is routinely used for the phylogenetic identification, detection, and quantification of single microbial cells environmental microbiology. Oligonucleotide probes that match the 16S rRNA sequence of target organisms are generally applied and the resulting signals are visualized via fluorescence microscopy. Consequently, the detection of the microbial cells of interest is limited by the resolution and the sensitivity of light microscopy where objects smaller than 0.2 µm can hardly be represented. Visualizing microbial cells at magnifications beyond light microscopy, however, can provide information on the composition and potential complexity of microbial habitats - the actual sites of nutrient cycling in soil and sediments. We present a recently developed technique that combines (1) the phylogenetic identification and detection of individual microorganisms by epifluorescence microscopy, with (2) the in situ localization of gold-labelled target cells on an ultrastructural level by SEM. Based on 16S rRNA targeted in situ hybridization combined with catalyzed reporter deposition, a streptavidin conjugate labeled with a fluorescent dye and nanogold particles is introduced into whole microbial cells. A two-step visualization process including an autometallographic enhancement of nanogold particles then allows for either fluorescence or electron microscopy, or a correlative application thereof. We will present applications of the Gold-FISH protocol to samples of marine sediments, agricultural soils, and plant roots. The detection and enumeration of bacterial cells in soil and sediment samples was comparable to CARD-FISH applications via fluorescence microscopy. Examples of microbe-surface interaction analysis will be presented on the basis of bacteria colonizing the rhizoplane of rice roots. In principle, Gold-FISH can be performed on any material to give a snapshot of microbe-surface interactions and provides a promising tool for

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.

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.

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.

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).

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.

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.

Effect of short-term room temperature storage on the microbial community in infant fecal samples.

PubMed

Guo, Yong; Li, Sheng-Hui; Kuang, Ya-Shu; He, Jian-Rong; Lu, Jin-Hua; Luo, Bei-Jun; Jiang, Feng-Ju; Liu, Yao-Zhong; Papasian, Christopher J; Xia, Hui-Min; Deng, Hong-Wen; Qiu, Xiu

2016-05-26

Sample storage conditions are important for unbiased analysis of microbial communities in metagenomic studies. Specifically, for infant gut microbiota studies, stool specimens are often exposed to room temperature (RT) conditions prior to analysis. This could lead to variations in structural and quantitative assessment of bacterial communities. To estimate such effects of RT storage, we collected feces from 29 healthy infants (0-3 months) and partitioned each sample into 5 portions to be stored for different lengths of time at RT before freezing at -80 °C. Alpha diversity did not differ between samples with storage time from 0 to 2 hours. The UniFrac distances and microbial composition analysis showed significant differences by testing among individuals, but not by testing between different time points at RT. Changes in the relative abundance of some specific (less common, minor) taxa were still found during storage at room temperature. Our results support previous studies in children and adults, and provided useful information for accurate characterization of infant gut microbiomes. In particular, our study furnished a solid foundation and justification for using fecal samples exposed to RT for less than 2 hours for comparative analyses between various medical conditions.

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.

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.

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.

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

Diversity of Microbial Carbohydrate-Active enZYmes (CAZYmes) Associated with Freshwater and Soil Samples from Caatinga Biome.

PubMed

Andrade, Ana Camila; Fróes, Adriana; Lopes, Fabyano Álvares Cardoso; Thompson, Fabiano L; Krüger, Ricardo Henrique; Dinsdale, Elizabeth; Bruce, Thiago

2017-07-01

Semi-arid and arid areas occupy about 33% of terrestrial ecosystems. However, little information is available about microbial diversity in the semi-arid Caatinga, which represents a unique biome that extends to about 11% of the Brazilian territory and is home to extraordinary diversity and high endemism level of species. In this study, we characterized the diversity of microbial genes associated with biomass conversion (carbohydrate-active enzymes, or so-called CAZYmes) in soil and freshwater of the Caatinga. Our results showed distinct CAZYme profiles in the soil and freshwater samples. Glycoside hydrolases and glycosyltransferases were the most abundant CAZYme families, with glycoside hydrolases more dominant in soil (∼44%) and glycosyltransferases more abundant in freshwater (∼50%). The abundances of individual glycoside hydrolase, glycosyltransferase, and carbohydrate-binding module subfamilies varied widely between soil and water samples. A predominance of glycoside hydrolases was observed in soil, and a higher contribution of enzymes involved in carbohydrate biosynthesis was observed in freshwater. The main taxa associated with the CAZYme sequences were Planctomycetia (relative abundance in soil, 29%) and Alphaproteobacteria (relative abundance in freshwater, 27%). Approximately 5-7% of CAZYme sequences showed low similarity with sequences deposited in non-redundant databases, suggesting putative homologues. Our findings represent a first attempt to describe specific microbial CAZYme profiles for environmental samples. Characterizing these enzyme groups associated with the conversion of carbohydrates in nature will improve our understanding of the significant roles of enzymes in the carbon cycle. We identified a CAZYme signature that can be used to discriminate between soil and freshwater samples, and this signature may be related to the microbial species adapted to the habitat. The data show the potential ecological roles of the CAZYme repertoire and

A strategy to sample nutrient dynamics across the terrestrial-aquatic interface at NEON sites

NASA Astrophysics Data System (ADS)

Hinckley, E. S.; Goodman, K. J.; Roehm, C. L.; Meier, C. L.; Luo, H.; Ayres, E.; Parnell, J.; Krause, K.; Fox, A. M.; SanClements, M.; Fitzgerald, M.; Barnett, D.; Loescher, H. W.; Schimel, D.

2012-12-01

The construction of the National Ecological Observatory Network (NEON) across the U.S. creates the opportunity for researchers to investigate biogeochemical transformations and transfers across ecosystems at local-to-continental scales. Here, we examine a subset of NEON sites where atmospheric, terrestrial, and aquatic observations will be collected for 30 years. These sites are located across a range of hydrological regimes, including flashy rain-driven, shallow sub-surface (perched, pipe-flow, etc), and deep groundwater, which likely affect the chemical forms and quantities of reactive elements that are retained and/or mobilized across landscapes. We present a novel spatial and temporal sampling design that enables researchers to evaluate long-term trends in carbon, nitrogen, and phosphorus biogeochemical cycles under these different hydrological regimes. This design focuses on inputs to the terrestrial system (atmospheric deposition, bulk precipitation), transfers (soil-water and groundwater sources/chemistry), and outputs (surface water, and evapotranspiration). We discuss both data that will be collected as part of the current NEON design, as well as how the research community can supplement the NEON design through collaborative efforts, such as providing additional datasets, including soil biogeochemical processes and trace gas emissions, and developing collaborative research networks. Current engagement with the research community working at the terrestrial-aquatic interface is critical to NEON's success as we begin construction, to ensure that high-quality, standardized and useful data are not only made available, but inspire further, cutting-edge research.

Microbial profiling of South African acid mine water samples using next generation sequencing platform.

PubMed

Kamika, I; Azizi, S; Tekere, M

2016-07-01

This study monitored changes in bacterial and fungal structure in a mine water in a monthly basis over 4 months. Over the 4-month study period, mine water samples contained more bacteria (91.06 %) compared to fungi (8.94 %). For bacteria, mine water samples were dominated by Proteobacteria (39.14 to 65.06 %) followed by Firmicutes (26.34 to 28.9 %) in summer, and Cyanobacteria (27.05 %) in winter. In the collected samples, 18 % of bacteria could not be assigned to a phylum and remained unclassified suggesting hitherto vast untapped microbial diversity especially during winter. The fungal domain was the sole eukaryotic microorganism found in the mine water samples with unclassified fungi (68.2 to 91 %) as the predominant group, followed by Basidiomycota (6.9 to 27.8 %). The time of collection, which was linked to the weather, had higher impact on bacterial community than fungal community. The bacterial operational taxonomic units (OTUs) ranged from 865 to 4052 over the 4-month sampling period, while fungal OTUs varied from 73 to 249. The diversity indices suggested that the bacterial community inhabiting the mine water samples were more diverse than the fungal community. The canonical correspondence analysis (CCA) results highlighted that the bacterial community variance had the strongest relationship with water temperature, conductivity, pH, and dissolved oxygen (DO) content, as compared to fungi and water characteristics, had the greatest contribution to both bacterial and fungal community variance. The results provided the relationships between microbial community and environmental variables in the studied mining sites.

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.

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

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.

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

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.

Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements

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

Qian, Chen; Hettich, Robert L.

The microbial composition and their activities in soil environments play a critical role in organic matter transformation and nutrient cycling, perhaps most specifically with respect to impact on plant growth but also more broadly to global impact on carbon and nitrogen-cycling. Liquid chromatography coupled to high performance mass spectrometry provides a powerful approach to characterize soil microbiomes; however, the limited microbial biomass and the presence of abundant interferences in soil samples present major challenges to soil proteome extraction and subsequent MS measurement. To address some of the major issues, we have designed and optimized an experimental method to enhance microbialmore » proteome extraction concomitant with minimizing the soil-borne humic substances co-extraction from soils. Among the range of interferences, humic substances are often the worst in terms of adversely impacting proteome extraction and mass spectrometry measurement. Our approach employs an in-situ detergent-based microbial lysis / TCA precipitation coupled with an additional acidification precipitation step at the peptide level which efficiently removes humic acids. By combing filtration and pH adjustment of the final peptide solution, the remaining humic acids can be differentially precipitated and removed with a membrane filter, thereby leaving much cleaner proteolytic peptide samples for MS measurement. As a result, this modified method is a reliable and straight-forward protein extraction method that efficiently removes soil-borne humic substances without inducing proteome sample loss or reducing or biasing protein identification in mass spectrometry.« less

Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements

DOE PAGES

Qian, Chen; Hettich, Robert L.

2017-05-24

The microbial composition and their activities in soil environments play a critical role in organic matter transformation and nutrient cycling, perhaps most specifically with respect to impact on plant growth but also more broadly to global impact on carbon and nitrogen-cycling. Liquid chromatography coupled to high performance mass spectrometry provides a powerful approach to characterize soil microbiomes; however, the limited microbial biomass and the presence of abundant interferences in soil samples present major challenges to soil proteome extraction and subsequent MS measurement. To address some of the major issues, we have designed and optimized an experimental method to enhance microbialmore » proteome extraction concomitant with minimizing the soil-borne humic substances co-extraction from soils. Among the range of interferences, humic substances are often the worst in terms of adversely impacting proteome extraction and mass spectrometry measurement. Our approach employs an in-situ detergent-based microbial lysis / TCA precipitation coupled with an additional acidification precipitation step at the peptide level which efficiently removes humic acids. By combing filtration and pH adjustment of the final peptide solution, the remaining humic acids can be differentially precipitated and removed with a membrane filter, thereby leaving much cleaner proteolytic peptide samples for MS measurement. As a result, this modified method is a reliable and straight-forward protein extraction method that efficiently removes soil-borne humic substances without inducing proteome sample loss or reducing or biasing protein identification in mass spectrometry.« less

Microplastic in Aquatic Ecosystems.

PubMed

Ivleva, Natalia P; Wiesheu, Alexandra C; Niessner, Reinhard

2017-02-06

The contamination of marine and freshwater ecosystems with plastic, and especially with microplastic (MP), is a global ecological problem of increasing scientific concern. This has stimulated a great deal of research on the occurrence of MP, interaction of MP with chemical pollutants, the uptake of MP by aquatic organisms, and the resulting (negative) impact of MP. Herein, we review the major issues of MP in aquatic environments, with the principal aims 1) to characterize the methods applied for MP analysis (including sampling, processing, identification and quantification), indicate the most reliable techniques, and discuss the required further improvements; 2) to estimate the abundance of MP in marine/freshwater ecosystems and clarify the problems that hamper the comparability of such results; and 3) to summarize the existing literature on the uptake of MP by living organisms. Finally, we identify knowledge gaps, suggest possible strategies to assess environmental risks arising from MP, and discuss prospects to minimize MP abundance in aquatic ecosystems. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microbial sequences retrieved from environmental samples from seasonal arctic snow and meltwater from Svalbard, Norway.

PubMed

Larose, Catherine; Berger, Sibel; Ferrari, Christophe; Navarro, Elisabeth; Dommergue, Aurélien; Schneider, Dominique; Vogel, Timothy M

2010-03-01

16S rRNA gene (rrs) clone libraries were constructed from two snow samples (May 11, 2007 and June 7, 2007) and two meltwater samples collected during the spring of 2007 in Svalbard, Norway (79 degrees N). The libraries covered 19 different microbial classes, including Betaproteobacteria (21.3%), Sphingobacteria (16.4%), Flavobacteria (9.0%), Acidobacteria (7.7%) and Alphaproteobacteria (6.5%). Significant differences were detected between the two sets of sample libraries. First, the meltwater libraries had the highest community richness (Chao1: 103.2 and 152.2) and Shannon biodiversity indices (between 3.38 and 3.59), when compared with the snow libraries (Chao1: 14.8 and 59.7; Shannon index: 1.93 and 3.01). Second, integral-LIBSHUFF analyses determined that the bacterial communities in the snow libraries were significantly different from those of the meltwater libraries. Despite these differences, our data also support the theory that a common core group of microbial populations exist within a variety of cryohabitats. Electronic supplementary material The online version of this article (doi:10.1007/s00792-009-0299-2) contains supplementary material, which is available to authorized users.

Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children.

PubMed

Pérez-Losada, Marcos; Crandall, Keith A; Freishtat, Robert J

2016-06-16

The nasopharynx is a reservoir for pathogens associated with respiratory illnesses, such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome during health and disease. Most studies so far have surveyed the nasopharynx as a whole; however, less is known about spatial variation (biogeography) in nasal microenvironments and how sampling techniques may capture that microbial diversity. We used targeted 16S rRNA MiSeq sequencing and two different sampling strategies [nasal washes (NW) and nasal brushes (NB)] to characterize the nasopharyngeal microbiota in 30 asthmatic children. Nasal brushing is more abrasive than nasal washing and targeted the inner portion of the inferior turbinate. This region is expected to be different from other nasal microenvironments. Nasal washing is not spatially specific. Our 30 × 2 nasal microbiomes generated 1,474,497 sequences, from which we identified an average of 157 and 186 OTUs per sample in the NW and NB groups, respectively. Microbiotas from NB showed significantly higher alpha-diversity than microbiotas from NW. Similarly, both nasal microbiotas were distinct from each other (PCoA) and significantly differed in their community composition and abundance in at least 9 genera (effective size ≥1 %). Nasopharyngeal microenvironments in asthmatic children contain microbiotas with different diversity and structure. Nasal washes and brushes capture that diversity differently. Future microbial studies of the nasopharynx need to be aware of potential spatial variation (biogeography).

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

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.

Microbial diversity in degraded and non-degraded petroleum samples and comparison across oil reservoirs at local and global scales.

PubMed

Sierra-Garcia, Isabel Natalia; Dellagnezze, Bruna M; Santos, Viviane P; Chaves B, Michel R; Capilla, Ramsés; Santos Neto, Eugenio V; Gray, Neil; Oliveira, Valeria M

2017-01-01

Microorganisms have shown their ability to colonize extreme environments including deep subsurface petroleum reservoirs. Physicochemical parameters may vary greatly among petroleum reservoirs worldwide and so do the microbial communities inhabiting these different environments. The present work aimed at the characterization of the microbiota in biodegraded and non-degraded petroleum samples from three Brazilian reservoirs and the comparison of microbial community diversity across oil reservoirs at local and global scales using 16S rRNA clone libraries. The analysis of 620 16S rRNA bacterial and archaeal sequences obtained from Brazilian oil samples revealed 42 bacterial OTUs and 21 archaeal OTUs. The bacterial community from the degraded oil was more diverse than the non-degraded samples. Non-degraded oil samples were overwhelmingly dominated by gammaproteobacterial sequences with a predominance of the genera Marinobacter and Marinobacterium. Comparisons of microbial diversity among oil reservoirs worldwide suggested an apparent correlation of prokaryotic communities with reservoir temperature and depth and no influence of geographic distance among reservoirs. The detailed analysis of the phylogenetic diversity across reservoirs allowed us to define a core microbiome encompassing three bacterial classes (Gammaproteobacteria, Clostridia, and Bacteroidia) and one archaeal class (Methanomicrobia) ubiquitous in petroleum reservoirs and presumably owning the abilities to sustain life in these environments.

Methane emissions to the atmosphere through aquatic plants

NASA Technical Reports Server (NTRS)

Sebacher, D. I.; Harriss, R. C.; Bartlett, K. B.

1985-01-01

The movement of methane (CH4) from anaerobic sediments through the leaves, stems, and flowers of aquatic plants and into the atmosphere was found to provide a significant pathway for the emission of CH4 from the aquatic substrates of flooded wetlands. Methane concentrations well above the surrounding ambient air levels were found in the mesophyll of 16 varies of aquatic plants and are attributed to transpiration, diffusion, and pressure-induced flow of gaseous CH4 from the roots when they are embedded in CH4-saturated anaerobic sediments. Methane emissions from the emergent parts of aquatic plants were measured using floating chamber techniques and by enclosing the plants in polyethylene bags of known volume. Concentration changes were monitored in the trapped air using syringes and gas chromatographic techniques. Vertical profiles of dissolved CH4 in sediment pore water surrounding the aquatic plants' rhizomes were obtained using an interstitial sampling technique. Methane emissions from the aquatic plants studied varied from 14.8 mg CH4/d to levels too low to be detectable. Rooted and unrooted freshwater aquatic plants were studied as well as saltwater and brackish water plants. Included in the experiment is detailed set of measurements on CH4 emissions from the common cattail (Typha latifolia). This paper illustrates that aquatic plants play an important gas exchange role in the C cycle between wetlands and the atmosphere.

Microbial diversity in firework chemical exposed soil and water samples collected in Virudhunagar district, Tamil Nadu, India.

PubMed

Dhasarathan, P; Theriappan, P; Ashokraja, C

2010-03-01

Microbial diversity of soil and water samples collected from pyrochemicals exposed areas of Virdhunagar district (Tamil Nadu, India) was studied. Soil and water samples from cultivable area, waste land and city area of the same region were also studied for a comparative acount. There is a remarkable reduction in total heterotrophic bacterial population (THB) in pyrochemicals exposed soil and water samples (42 × 10(4) CFU/g and 5.6 × 10(4) CFU/ml respectively), compared to the THB of cultivable area soil and water samples (98 × 10(7) CFU/g and 38.6 × 10(7) CFU/ml). The generic composition the THB of the pyrochemicals exposed samples too exhibited considerable change compared to other samples. Pseudomonas sp. was the predominant one (41.6%) followed by Achromobacter sp. (25%) in pyrochemical exposed soil and Pseudomonas sp. was the predominant one (25%) in pyrochemical exposed water samples followed by Bacillus sp. (25%) and Micrococcus sp. (16.6%). It was observed that Cornybacterium sp. and Micrococcus sp. were absent completely in pyrochemical exposed soil and Achromobacter sp. was missing in the pyrochemical exposed water samples, which were present in the other samples. The outcome of this study clearly demonstrates that pollutants such as chemicals used in pyrotechniques affect the microbial biodiversity and suitable measures have to be taken to control the pollution level and to save biodiversity.

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.

Can Particulate Air Sampling Predict Microbial Load in Operating Theatres for Arthroplasty?

PubMed Central

Cristina, Maria Luisa; Spagnolo, Anna Maria; Sartini, Marina; Panatto, Donatella; Gasparini, Roberto; Orlando, Paolo; Ottria, Gianluca; Perdelli, Fernanda

2012-01-01

Several studies have proposed that the microbiological quality of the air in operating theatres be indirectly evaluated by means of particle counting, a technique derived from industrial clean-room technology standards, using airborne particle concentration as an index of microbial contamination. However, the relationship between particle counting and microbiological sampling has rarely been evaluated and demonstrated in operating theatres. The aim of the present study was to determine whether particle counting could predict microbiological contamination of the air in an operating theatre during 95 surgical arthroplasty procedures. This investigation was carried out over a period of three months in 2010 in an orthopedic operating theatre devoted exclusively to prosthetic surgery. During each procedure, the bacterial contamination of the air was determined by means of active sampling; at the same time, airborne particulate contamination was assessed throughout the entire procedure. On considering the total number of surgical operations, the mean value of the total bacterial load in the center of the operating theatre proved to be 35 CFU/m3; the mean particle count was 4,194,569 no./m3 for particles of diameter ≥0.5 µm and 13,519 no./m3 for particles of diameter ≥5 µm. No significant differences emerged between the median values of the airborne microbial load recorded during the two types of procedure monitored. Particulates with a diameter of ≥0.5 µm were detected in statistically higher concentrations (p<0.001) during knee-replacement procedures. By contrast, particulates with a diameter of ≥5 µm displayed a statistically higher concentration during hip-replacement procedures (p<0.05). The results did not reveal any statistically significant correlation between microbial loads and particle counts for either of the particle diameters considered (≥0.5 µm and ≥5 µm). Consequently, microbiological monitoring remains the most suitable method of

Can particulate air sampling predict microbial load in operating theatres for arthroplasty?

PubMed

Cristina, Maria Luisa; Spagnolo, Anna Maria; Sartini, Marina; Panatto, Donatella; Gasparini, Roberto; Orlando, Paolo; Ottria, Gianluca; Perdelli, Fernanda

2012-01-01

Several studies have proposed that the microbiological quality of the air in operating theatres be indirectly evaluated by means of particle counting, a technique derived from industrial clean-room technology standards, using airborne particle concentration as an index of microbial contamination. However, the relationship between particle counting and microbiological sampling has rarely been evaluated and demonstrated in operating theatres. The aim of the present study was to determine whether particle counting could predict microbiological contamination of the air in an operating theatre during 95 surgical arthroplasty procedures. This investigation was carried out over a period of three months in 2010 in an orthopedic operating theatre devoted exclusively to prosthetic surgery. During each procedure, the bacterial contamination of the air was determined by means of active sampling; at the same time, airborne particulate contamination was assessed throughout the entire procedure. On considering the total number of surgical operations, the mean value of the total bacterial load in the center of the operating theatre proved to be 35 CFU/m(3); the mean particle count was 4,194,569 no./m(3) for particles of diameter ≥0.5 µm and 13,519 no./m(3) for particles of diameter ≥5 µm. No significant differences emerged between the median values of the airborne microbial load recorded during the two types of procedure monitored. Particulates with a diameter of ≥0.5 µm were detected in statistically higher concentrations (p<0.001) during knee-replacement procedures. By contrast, particulates with a diameter of ≥5 µm displayed a statistically higher concentration during hip-replacement procedures (p<0.05). The results did not reveal any statistically significant correlation between microbial loads and particle counts for either of the particle diameters considered (≥0.5 µm and ≥5 µm). Consequently, microbiological monitoring remains the most suitable method of

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.

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

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.

Identification of beta-lactam antibiotics in tissue samples containing unknown microbial inhibitors.

PubMed

Moats, W A; Romanowski, R D; Medina, M B

1998-01-01

Antibiotic residues in animal tissues can be detected by various screening tests based on microbial inhibition. In the 7-plate assay used by the U.S. Department of Agriculture's Food Safety and Inspection Service (FSIS), penicillinase is incorporated into all but one plate to distinguish beta-lactam antibiotics from other types. However, beta-lactams such as cloxacillin and the cephalosporins are resistant to degradation by penicillinase. They may not be identified as beta-lactams by this procedure, and thus, they may be identified as unidentified microbial inhibitors (UMIs). However, these penicillinase-resistant compounds can be degraded by other beta-lactamases. The present study describes an improved screening protocol to identify beta-lactam antibiotics classified as UMIs. A multiresidue liquid chromatographic procedure based on a method for determining beta-lactams in milk was also used to identify and quantitate residues. The 2 methods were tested with 24 tissue FSIS samples classified as containing UMIs. Of these, 3 contained penicillin G, including one at a violative level, and 5 contained a metabolite of ceftiofur. The others were negative for beta-lactam antibiotics.

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.

Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements.

PubMed

Qian, Chen; Hettich, Robert L

2017-07-07

The microbial composition and their activities in soil environments play a critical role in organic matter transformation and nutrient cycling. Liquid chromatography coupled to high-performance mass spectrometry provides a powerful approach to characterize soil microbiomes; however, the limited microbial biomass and the presence of abundant interferences in soil samples present major challenges to proteome extraction and subsequent MS measurement. To this end, we have designed an experimental method to improve microbial proteome measurement by removing the soil-borne humic substances coextraction from soils. Our approach employs an in situ detergent-based microbial lysis/TCA precipitation coupled to an additional cleanup step involving acidified precipitation and filtering at the peptide level to remove most of the humic acid interferences prior to proteolytic peptide measurement. The novelty of this approach is an integration to exploit two different characteristics of humic acids: (1) Humic acids are insoluble in acidic solution but should not be removed at the protein level, as undesirable protein removal may also occur. Rather it is better to leave the humics acids in the samples until the peptide level, at which point the significant differential solubility of humic acids versus peptides at low pH can be exploited very efficiently. (2) Most of the humic acids have larger molecule weights than the peptides. Therefore, filtering a pH 2 to 3 peptide solution with a 10 kDa filter will remove most of the humic acids. This method is easily interfaced with normal proteolytic processing approaches and provides a reliable and straightforward protein extraction method that efficiently removes soil-borne humic substances without inducing proteome sample loss or biasing protein identification in mass spectrometry. In general, this humic acid removal step is universal and can be adopted by any workflow to effectively remove humic acids to avoid them negatively competing

Expedition Six Flight Engineer Pettit uses a chemical/microbial analysis bag to collect water sample

NASA Image and Video Library

2002-12-18

ISS006-E-08628 (18 December 2002) --- Astronaut Donald R. Pettit, Expedition Six NASA ISS science officer, is pictured in the Zvezda Service Module on the International Space Station (ISS) during the scheduled Week 3 potable water sampling and on-orbit chemical/microbial analysis of the SM environment control and life support system.

Expedition Six Flight Engineer Pettit uses a chemical/microbial analysis bag to collect water sample

NASA Image and Video Library

2002-12-18

ISS006-E-08616 (18 December 2002) --- Astronaut Donald R. Pettit, Expedition Six NASA ISS science officer, is pictured in the Zvezda Service Module on the International Space Station (ISS) during the scheduled Week 3 potable water sampling and on-orbit chemical/microbial analysis of the SM environment control and life support system.

Sampling design for aquatic invasive species early detection in Great Lakes ports

EPA Science Inventory

From 2006-2012, we evaluated a pilot aquatic invasive species (AIS) early detection monitoring program in Lake Superior that was designed to detect newly introduced fishes. We established survey protocols for three major ports (Duluth-Superior, Sault Ste. Marie, Thunder Bay) and ...

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.

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.

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

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

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.

Occurrence and quantitative microbial risk assessment of Cryptosporidium and Giardia in soil and air samples.

PubMed

Balderrama-Carmona, Ana Paola; Gortáres-Moroyoqui, Pablo; Álvarez-Valencia, Luis Humberto; Castro-Espinoza, Luciano; Mondaca-Fernández, Iram; Balderas-Cortés, José de Jesús; Chaidez-Quiroz, Cristóbal; Meza-Montenegro, María Mercedes

2014-09-01

Cryptosporidium oocysts and Giardia cysts can be transmitted by the fecal-oral route and may cause gastrointestinal parasitic zoonoses. These zoonoses are common in rural zones due to the parasites being harbored in fecally contaminated soil. This study assessed the risk of illness (giardiasis and cryptosporidiosis) from inhaling and/or ingesting soil and/or airborne dust in Potam, Mexico. To assess the risk of infection, Quantitative Microbial Risk Assessment (QMRA) was employed, with the following steps: (1) hazard identification, (2) hazard exposure, (3) dose-response, and (4) risk characterization. Cryptosporidium oocysts and Giardia cysts were observed in 52% and 57%, respectively, of total soil samples (n=21), and in 60% and 80%, respectively, of air samples (n=12). The calculated annual risks were higher than 9.9 × 10(-1) for both parasites in both types of sample. Soil and air inhalation and/or ingestion are important vehicles for these parasites. To our knowledge, the results obtained in the present study represent the first QMRAs for cryptosporidiosis and giardiasis due to soil and air inhalation/ingestion in Mexico. In addition, this is the first evidence of the microbial air quality around these parasites in rural zones. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Submersed Aquatic Vegetation Modeling Output Online

USGS Publications Warehouse

Yin, Yao; Rogala, Jim; Sullivan, John; Rohweder, Jason J.

2005-01-01

Introduction The ability to predict the distribution of submersed aquatic vegetation in the Upper Mississippi River on the basis of physical or chemical variables is useful to resource managers. Wildlife managers have a keen interest in advanced estimates of food quantity such as American wildcelery (Vallisneria americana) population status to give out more informed advisories to hunters before the fall hunting season. Predictions for distribution of submerged aquatic vegetation beds can potentially increase hunter observance of voluntary avoidance zones where foraging birds are left alone to feed undisturbed. In years when submersed aquatic vegetation is predicted to be scarce in important wildlife habitats, managers can get the message out to hunters well before the hunting season (Jim Nissen, Upper Mississippi River National Wildlife and Fish Refuge, La Crosse District Manager, La Crosse, Wisconsin, personal communication). We developed a statistical model to predict the probability of occurrence of submersed aquatic vegetation in Pool 8 of the Upper Mississippi River on the basis of a few hydrological, physical, and geomorphic variables. Our model takes into consideration flow velocity, wind fetch, bathymetry, growing-season daily water level, and light extinction coefficient in the river (fig. 1) and calculates the probability of submersed aquatic vegetation existence in Pool 8 in individual 5- x 5-m grid cells. The model was calibrated using the data collected in 1998 (516 sites), 1999 (595 sites), and 2000 (649 sites) using a stratified random sampling protocol (Yin and others, 2000b). To validate the model, we chose the data from the Long Term Resource Monitoring Program (LTRMP) transect sampling in backwater areas (Rogers and Owens 1995; Yin and others, 2000a) and ran the model for each 5- x 5-m grid cell in every growing season from 1991 to 2001. We tallied all the cells and came up with an annual average percent frequency of submersed aquatic vegetation

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

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

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.

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.

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.

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.

Characterisation of intact proteins in aquatic samples from the Florida Everglades

NASA Astrophysics Data System (ADS)

Jones, V.; Ruddell, C. J.; Wainwright, G.; Rees, H. H.; Jaffe, R.; Penkman, K. E. H.; Collins, C. J.; Wolff, G. A.

2003-04-01

Dissolved organic nitrogen (DON) is the largest reservoir of reduced nitrogen in the oceans. Limited knowledge of the molecular composition of DON hinders our understanding of its cycling. The need to comprehend the DON cycle is nowadays more imperative than ever, as there is evidence that concentrations of nitrate are decreasing, while concentrations of DON are increasing in the surface ocean, as an indirect effect of global warming and hence stratification of the water column (Karl et al., 2001). Proteins typically account for 5-10% of DON. Recently, it has been suggested that certain, bacterially-derived, proteins found in the ocean are not as labile as was originally thought (e.g. Tanoue et al., 1995) and may therefore form a crucial part of the long term DON cycle. Here, we have applied gel electrophoresis in combination with mass spectrometry and amino acid enantiomer (D/L) analysis, to characterise proteins from aquatic samples and consider their origin. Samples were collected in the Florida Everglades at locations selected to represent an array of ecosystems, ranging from marsh water to marine coastal environments. Application of gel electrophoresis in combination with mass spectrometry revealed that each sample had a complex and characteristic protein distribution. Some proteins were common to more than one site. The bacterial protein of 48 kDa, previously reported as ubiquitous in the open ocean (e.g. Tanoue et al., 1995), was only present at one sampling location strongly affected by offshore currents. Amino acid enantiomer (D/L) analysis revealed that the bacterial input to amino acid nitrogen was an order of magnitude smaller than that reported for open ocean samples (McCarthy et al., 1998), although a trend towards higher bacterial input was observed from freshwater to marine sampling locations. We suggest that this is due to the presence of additional sources of protein to the DON pool, such as the higher plant vegetation, in freshwater and coastal

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

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

Rapid estimation of microbial populations in fish samples by using terminal restriction fragment length polymorphism analysis of 16S rDNA.

PubMed

Tanaka, Yuichiro; Takahashi, Hajime; Kitazawa, Nao; Kimura, Bon

2010-01-01

A rapid system using terminal restriction fragment length polymorphism (T-RFLP) analysis targeting 16S rDNA is described for microbial population analysis in edible fish samples. The defined terminal restriction fragment database was constructed by collecting 102 strains of bacteria representing 53 genera that are associated with fish. Digestion of these 102 strains with two restriction enzymes, HhaI and MspI, formed 54 pattern groups with discrimination to the genus level. This T-RFLP system produced results comparable to those from a culture-based method in six natural fish samples with a qualitative correspondence of 71.4 to 92.3%. Using the T-RFLP system allowed an estimation of the microbial population within 7 h. Rapid assay of the microbial population is advantageous for food manufacturers and testing laboratories; moreover, the strategy presented here allows adaptation to specific testing applications.

Does aquatic foraging impact head shape evolution in snakes?

PubMed

Segall, Marion; Cornette, Raphaël; Fabre, Anne-Claire; Godoy-Diana, Ramiro; Herrel, Anthony

2016-08-31

Evolutionary trajectories are often biased by developmental and historical factors. However, environmental factors can also impose constraints on the evolutionary trajectories of organisms leading to convergence of morphology in similar ecological contexts. The physical properties of water impose strong constraints on aquatic feeding animals by generating pressure waves that can alert prey and potentially push them away from the mouth. These hydrodynamic constraints have resulted in the independent evolution of suction feeding in most groups of secondarily aquatic tetrapods. Despite the fact that snakes cannot use suction, they have invaded the aquatic milieu many times independently. Here, we test whether the aquatic environment has constrained head shape evolution in snakes and whether shape converges on that predicted by biomechanical models. To do so, we used three-dimensional geometric morphometrics and comparative, phylogenetically informed analyses on a large sample of aquatic snake species. Our results show that aquatic snakes partially conform to our predictions and have a narrower anterior part of the head and dorsally positioned eyes and nostrils. This morphology is observed, irrespective of the phylogenetic relationships among species, suggesting that the aquatic environment does indeed drive the evolution of head shape in snakes, thus biasing the evolutionary trajectory of this group of animals. © 2016 The Author(s).

Does aquatic foraging impact head shape evolution in snakes?

PubMed Central

Cornette, Raphaël; Fabre, Anne-Claire; Godoy-Diana, Ramiro; Herrel, Anthony

2016-01-01

Evolutionary trajectories are often biased by developmental and historical factors. However, environmental factors can also impose constraints on the evolutionary trajectories of organisms leading to convergence of morphology in similar ecological contexts. The physical properties of water impose strong constraints on aquatic feeding animals by generating pressure waves that can alert prey and potentially push them away from the mouth. These hydrodynamic constraints have resulted in the independent evolution of suction feeding in most groups of secondarily aquatic tetrapods. Despite the fact that snakes cannot use suction, they have invaded the aquatic milieu many times independently. Here, we test whether the aquatic environment has constrained head shape evolution in snakes and whether shape converges on that predicted by biomechanical models. To do so, we used three-dimensional geometric morphometrics and comparative, phylogenetically informed analyses on a large sample of aquatic snake species. Our results show that aquatic snakes partially conform to our predictions and have a narrower anterior part of the head and dorsally positioned eyes and nostrils. This morphology is observed, irrespective of the phylogenetic relationships among species, suggesting that the aquatic environment does indeed drive the evolution of head shape in snakes, thus biasing the evolutionary trajectory of this group of animals. PMID:27581887

Avian Influenza Virus Surveillance in South-Central Spain Using Fecal Samples of Aquatic Birds Foraging at Landfills

PubMed Central

Bárbara, Andreia; Torrontegi, Olalla; Camacho, Maria-Cruz; Barral, Marta; Hernández, Jose-Manuel; Höfle, Ursula

2017-01-01

Aquatic wild birds have been intensively studied to better understand their role in avian influenza virus (AIV) maintenance and spread. To date, AIV surveillance has primarily focused on natural aquatic environments where different bird species aggregate and viral survival is enhanced. However, artificial habitats such as landfills are attracting substantial numbers of wild birds, AIV reservoir species included. The use of landfills as a predictable food source has significantly influenced population size, migratory traits, and feeding behavior of white storks (Ciconia ciconia) and black-headed gulls (Chroicocephalus ridibundus) among others. Considering the proximity of landfills to urban settlements and frequently poultry-farms, targeted monitoring of AIV in bird species that forage at landfills but are known to also frequent urban and agricultural habitats could be a useful means for monitoring of AIV, especially during periods of bird aggregation. During the wintering season 2014–2015, the prevalence of AIV in five avian species at two landfills in South-Central Spain was explored by rRT-PCR and species related temporal variation in AIV prevalence determined. We collected and tested 1,186 fresh fecal samples from white storks (N = 689), cattle egrets (Bubulcus ibis, N = 116) and mixed flocks of gulls (N = 381) as well as cloacal and oral swabs from five birds found dead. Seven samples contained AIV, five from gulls and one each from a stork and a cattle egret. Overall, AIV prevalence was 0.60%. No significant temporal variation was observed in AIV prevalence. Prevalence differed significantly among the sampled taxonomic groups, being highest in gulls (1.31%). H16N3 subtype was detected from a cattle egret and H11N9 subtype from a white stork, whereas gulls harbored both subtypes in addition to H11N3 subtype. H16 subtype detection in a cattle egret evidences its host range may not be restricted to gulls. Our results indicate that wild birds

I Environmental DNA sampling is more sensitive than a traditional survey technique for detecting an aquatic invader.

PubMed

Smart, Adam S; Tingley, Reid; Weeks, Andrew R; van Rooyen, Anthony R; McCarthy, Michael A

2015-10-01

Effective management of alien species requires detecting populations in the early stages of invasion. Environmental DNA (eDNA) sampling can detect aquatic species at relatively low densities, but few studies have directly compared detection probabilities of eDNA sampling with those of traditional sampling methods. We compare the ability of a traditional sampling technique (bottle trapping) and eDNA to detect a recently established invader, the smooth newt Lissotriton vulgaris vulgaris, at seven field sites in Melbourne, Australia. Over a four-month period, per-trap detection probabilities ranged from 0.01 to 0.26 among sites where L. v. vulgaris was detected, whereas per-sample eDNA estimates were much higher (0.29-1.0). Detection probabilities of both methods varied temporally (across days and months), but temporal variation appeared to be uncorrelated between methods. Only estimates of spatial variation were strongly correlated across the two sampling techniques. Environmental variables (water depth, rainfall, ambient temperature) were not clearly correlated with detection probabilities estimated via trapping, whereas eDNA detection probabilities were negatively correlated with water depth, possibly reflecting higher eDNA concentrations at lower water levels. Our findings demonstrate that eDNA sampling can be an order of magnitude more sensitive than traditional methods, and illustrate that traditional- and eDNA-based surveys can provide independent information on species distributions when occupancy surveys are conducted over short timescales.

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

Selective whole genome amplification for resequencing target microbial species from complex natural samples.

PubMed

Leichty, Aaron R; Brisson, Dustin

2014-10-01

Population genomic analyses have demonstrated power to address major questions in evolutionary and molecular microbiology. Collecting populations of genomes is hindered in many microbial species by the absence of a cost effective and practical method to collect ample quantities of sufficiently pure genomic DNA for next-generation sequencing. Here we present a simple method to amplify genomes of a target microbial species present in a complex, natural sample. The selective whole genome amplification (SWGA) technique amplifies target genomes using nucleotide sequence motifs that are common in the target microbe genome, but rare in the background genomes, to prime the highly processive phi29 polymerase. SWGA thus selectively amplifies the target genome from samples in which it originally represented a minor fraction of the total DNA. The post-SWGA samples are enriched in target genomic DNA, which are ideal for population resequencing. We demonstrate the efficacy of SWGA using both laboratory-prepared mixtures of cultured microbes as well as a natural host-microbe association. Targeted amplification of Borrelia burgdorferi mixed with Escherichia coli at genome ratios of 1:2000 resulted in >10(5)-fold amplification of the target genomes with <6.7-fold amplification of the background. SWGA-treated genomic extracts from Wolbachia pipientis-infected Drosophila melanogaster resulted in up to 70% of high-throughput resequencing reads mapping to the W. pipientis genome. By contrast, 2-9% of sequencing reads were derived from W. pipientis without prior amplification. The SWGA technique results in high sequencing coverage at a fraction of the sequencing effort, thus allowing population genomic studies at affordable costs. Copyright © 2014 by the Genetics Society of America.

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.

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

Sampling design for early detection of aquatic invasive species in Great Lakes ports

EPA Science Inventory

We evaluated a pilot adaptive monitoring program for aquatic invasive species (AIS) early detection in Lake Superior. The monitoring program is designed to detect newly-introduced fishes, and encompasses the lake’s three major ports (Duluth-Superior, Sault Ste. Marie, Thund...

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.

Application of the BMWP-Costa Rica biotic index in aquatic biomonitoring: sensitivity to collection method and sampling intensity.

PubMed

Gutiérrez-Fonseca, Pablo E; Lorion, Christopher M

2014-04-01

The use of aquatic macroinvertebrates as bio-indicators in water quality studies has increased considerably over the last decade in Costa Rica, and standard biomonitoring methods have now been formulated at the national level. Nevertheless, questions remain about the effectiveness of different methods of sampling freshwater benthic assemblages, and how sampling intensity may influence biomonitoring results. In this study, we compared the results of qualitative sampling using commonly applied methods with a more intensive quantitative approach at 12 sites in small, lowland streams on the southern Caribbean slope of Costa Rica. Qualitative samples were collected following the official protocol using a strainer during a set time period and macroinvertebrates were field-picked. Quantitative sampling involved collecting ten replicate Surber samples and picking out macroinvertebrates in the laboratory with a stereomicroscope. The strainer sampling method consistently yielded fewer individuals and families than quantitative samples. As a result, site scores calculated using the Biological Monitoring Working Party-Costa Rica (BMWP-CR) biotic index often differed greatly depending on the sampling method. Site water quality classifications using the BMWP-CR index differed between the two sampling methods for 11 of the 12 sites in 2005, and for 9 of the 12 sites in 2006. Sampling intensity clearly had a strong influence on BMWP-CR index scores, as well as perceived differences between reference and impacted sites. Achieving reliable and consistent biomonitoring results for lowland Costa Rican streams may demand intensive sampling and requires careful consideration of sampling methods.

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples.

PubMed

Yu, Feiqiao Brian; Blainey, Paul C; Schulz, Frederik; Woyke, Tanja; Horowitz, Mark A; Quake, Stephen R

2017-07-05

Metagenomics and single-cell genomics have enabled genome discovery from unknown branches of life. However, extracting novel genomes from complex mixtures of metagenomic data can still be challenging and represents an ill-posed problem which is generally approached with ad hoc methods. Here we present a microfluidic-based mini-metagenomic method which offers a statistically rigorous approach to extract novel microbial genomes while preserving single-cell resolution. We used this approach to analyze two hot spring samples from Yellowstone National Park and extracted 29 new genomes, including three deeply branching lineages. The single-cell resolution enabled accurate quantification of genome function and abundance, down to 1% in relative abundance. Our analyses of genome level SNP distributions also revealed low to moderate environmental selection. The scale, resolution, and statistical power of microfluidic-based mini-metagenomics make it a powerful tool to dissect the genomic structure of microbial communities while effectively preserving the fundamental unit of biology, the single cell.

INNOVATIVE TECHNOLOGY EVALUATION REPORT, SEDIMENT SAMPLING TECHNOLOGY, AQUATIC RESEARCH INSTRUMENTS, RUSSIAN PEAT BORER

EPA Science Inventory

The Russian Peat Borer designed and fabricated by Aquatic Research Instruments was demonstrated under the U.S. Environmental Protection Agency (EPA) Superfund Innovative Technology Evaluation Program in April and May 1999 at sites in EPA Regions 1 and 5, respectively. In additio...

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

Trends in monitoring pharmaceuticals and personal-care products in the aquatic environment by use of passive sampling devices

USGS Publications Warehouse

Mills, G.A.; Vrana, B.; Allan, I.; Alvarez, D.A.; Huckins, J.N.; Greenwood, R.

2007-01-01

The use of passive sampling in monitoring pharmaceuticals and personal-care products (PPCPs) in the aquatic environment is discussed. The utility of passive sampling methods for monitoring the fraction of heavy metals and the biologically available fraction of non-polar organic priority pollutants is recognized and these technologies are being used in surveys of water quality. These devices are used to measure the dissolved fraction and they can yield information that can be used in the development of risk assessments models. These devices can also be used to locate illegal dumping and to monitor specific sources of input of PPCPs into the environment, or to monitor the effectiveness of water treatment processes in the removal of these compounds from wastewater. These devices can provide representative information at low cost which necessitate a combination of laboratory calibration and field studies for emerging pollutants.

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

Diversity and Distribution of Aquatic Fungal Communities in the Ny-Ålesund Region, Svalbard (High Arctic): Aquatic Fungi in the Arctic.

PubMed

Zhang, Tao; Wang, Neng-Fei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2016-04-01

We assessed the diversity and distribution of fungi in 13 water samples collected from four aquatic environments (stream, pond, melting ice water, and estuary) in the Ny-Ålesund Region, Svalbard (High Arctic) using 454 pyrosequencing with fungi-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Aquatic fungal communities in this region showed high diversity, with a total of 43,061 reads belonging to 641 operational taxonomic units (OTUs) being found. Of these OTUs, 200 belonged to Ascomycota, 196 to Chytridiomycota, 120 to Basidiomycota, 13 to Glomeromycota, and 10 to early diverging fungal lineages (traditional Zygomycota), whereas 102 belonged to unknown fungi. The major orders were Helotiales, Eurotiales, and Pleosporales in Ascomycota; Chytridiales and Rhizophydiales in Chytridiomycota; and Leucosporidiales and Sporidiobolales in Basidiomycota. The common fungal genera Penicillium, Rhodotorula, Epicoccum, Glaciozyma, Holtermanniella, Betamyces, and Phoma were identified. Interestingly, the four aquatic environments in this region harbored different aquatic fungal communities. Salinity, conductivity, and temperature were important factors in determining the aquatic fungal diversity and community composition. The results suggest the presence of diverse fungal communities and a considerable number of potentially novel fungal species in Arctic aquatic environments, which can provide reliable data for studying the ecological and evolutionary responses of fungi to climate change in the Arctic ecosystem.

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

Microbial populations in contaminant plumes

USGS Publications Warehouse

Haack, S.K.; Bekins, B.A.

2000-01-01

Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation.

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

Microbial community structures differentiated in a single-chamber air-cathode microbial fuel cell fueled with rice straw hydrolysate.

PubMed

Wang, Zejie; Lee, Taekwon; Lim, Bongsu; Choi, Chansoo; Park, Joonhong

2014-01-17

The microbial fuel cell represents a novel technology to simultaneously generate electric power and treat wastewater. Both pure organic matter and real wastewater can be used as fuel to generate electric power and the substrate type can influence the microbial community structure. In the present study, rice straw, an important feedstock source in the world, was used as fuel after pretreatment with diluted acid method for a microbial fuel cell to obtain electric power. Moreover, the microbial community structures of anodic and cathodic biofilm and planktonic culturewere analyzed and compared to reveal the effect of niche on microbial community structure. The microbial fuel cell produced a maximum power density of 137.6 ± 15.5 mW/m2 at a COD concentration of 400 mg/L, which was further increased to 293.33 ± 7.89 mW/m2 through adjusting the electrolyte conductivity from 5.6 mS/cm to 17 mS/cm. Microbial community analysis showed reduction of the microbial diversities of the anodic biofilm and planktonic culture, whereas diversity of the cathodic biofilm was increased. Planktonic microbial communities were clustered closer to the anodic microbial communities compared to the cathodic biofilm. The differentiation in microbial community structure of the samples was caused by minor portion of the genus. The three samples shared the same predominant phylum of Proteobacteria. The abundance of exoelectrogenic genus was increased with Desulfobulbus as the shared most abundant genus; while the most abundant exoelectrogenic genus of Clostridium in the inoculum was reduced. Sulfate reducing bacteria accounted for large relative abundance in all the samples, whereas the relative abundance varied in different samples. The results demonstrated that rice straw hydrolysate can be used as fuel for microbial fuel cells; microbial community structure differentiated depending on niches after microbial fuel cell operation; exoelectrogens were enriched; sulfate from rice straw

Microbial community structures differentiated in a single-chamber air-cathode microbial fuel cell fueled with rice straw hydrolysate

PubMed Central

2014-01-01

Background The microbial fuel cell represents a novel technology to simultaneously generate electric power and treat wastewater. Both pure organic matter and real wastewater can be used as fuel to generate electric power and the substrate type can influence the microbial community structure. In the present study, rice straw, an important feedstock source in the world, was used as fuel after pretreatment with diluted acid method for a microbial fuel cell to obtain electric power. Moreover, the microbial community structures of anodic and cathodic biofilm and planktonic culturewere analyzed and compared to reveal the effect of niche on microbial community structure. Results The microbial fuel cell produced a maximum power density of 137.6 ± 15.5 mW/m2 at a COD concentration of 400 mg/L, which was further increased to 293.33 ± 7.89 mW/m2 through adjusting the electrolyte conductivity from 5.6 mS/cm to 17 mS/cm. Microbial community analysis showed reduction of the microbial diversities of the anodic biofilm and planktonic culture, whereas diversity of the cathodic biofilm was increased. Planktonic microbial communities were clustered closer to the anodic microbial communities compared to the cathodic biofilm. The differentiation in microbial community structure of the samples was caused by minor portion of the genus. The three samples shared the same predominant phylum of Proteobacteria. The abundance of exoelectrogenic genus was increased with Desulfobulbus as the shared most abundant genus; while the most abundant exoelectrogenic genus of Clostridium in the inoculum was reduced. Sulfate reducing bacteria accounted for large relative abundance in all the samples, whereas the relative abundance varied in different samples. Conclusion The results demonstrated that rice straw hydrolysate can be used as fuel for microbial fuel cells; microbial community structure differentiated depending on niches after microbial fuel cell operation; exoelectrogens were

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...

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

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

Air sampling methods to evaluate microbial contamination in operating theatres: results of a comparative study in an orthopaedics department.

PubMed

Napoli, C; Tafuri, S; Montenegro, L; Cassano, M; Notarnicola, A; Lattarulo, S; Montagna, M T; Moretti, B

2012-02-01

To evaluate the level of microbial contamination of air in operating theatres using active [i.e. surface air system (SAS)] and passive [i.e. index of microbial air contamination (IMA) and nitrocellulose membranes positioned near the wound] sampling systems. Sampling was performed between January 2010 and January 2011 in the operating theatre of the orthopaedics department in a university hospital in Southern Italy. During surgery, the mean bacterial loads recorded were 2232.9 colony-forming units (cfu)/m(2)/h with the IMA method, 123.2 cfu/m(3) with the SAS method and 2768.2 cfu/m(2)/h with the nitrocellulose membranes. Correlation was found between the results of the three methods. Staphylococcus aureus was detected in 12 of 60 operations (20%) with the membranes, five (8.3%) operations with the SAS method, and three operations (5%) with the IMA method. Use of nitrocellulose membranes placed near a wound is a valid method for measuring the microbial contamination of air. This method was more sensitive than the IMA method and was not subject to any calibration bias, unlike active air monitoring systems. Copyright © 2011 The Healthcare Infection Society. Published by Elsevier Ltd. 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

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.

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...

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

A Microbial Assessment Scheme to measure microbial performance of Food Safety Management Systems.

PubMed

Jacxsens, L; Kussaga, J; Luning, P A; Van der Spiegel, M; Devlieghere, F; Uyttendaele, M

2009-08-31

A Food Safety Management System (FSMS) implemented in a food processing industry is based on Good Hygienic Practices (GHP), Hazard Analysis Critical Control Point (HACCP) principles and should address both food safety control and assurance activities in order to guarantee food safety. One of the most emerging challenges is to assess the performance of a present FSMS. The objective of this work is to explain the development of a Microbial Assessment Scheme (MAS) as a tool for a systematic analysis of microbial counts in order to assess the current microbial performance of an implemented FSMS. It is assumed that low numbers of microorganisms and small variations in microbial counts indicate an effective FSMS. The MAS is a procedure that defines the identification of critical sampling locations, the selection of microbiological parameters, the assessment of sampling frequency, the selection of sampling method and method of analysis, and finally data processing and interpretation. Based on the MAS assessment, microbial safety level profiles can be derived, indicating which microorganisms and to what extent they contribute to food safety for a specific food processing company. The MAS concept is illustrated with a case study in the pork processing industry, where ready-to-eat meat products are produced (cured, cooked ham and cured, dried bacon).

Do diatoms run downhill? Using biodiversity of terrestrial and aquatic diatoms to identify hydrological connectivity between aquatic zones in Luxembourg

NASA Astrophysics Data System (ADS)

Pfister, L.; Wetzel, C. E.; Martinez-Carreras, N.; Frentress, J.; Ector, L.; Hoffmann, L.; McDonnell, J. J.

2011-12-01

Diatoms are siliceous unicellular algae, and range in size between a few and more than 500 micrometers. Diatoms are spread worldwide, live in many aquatic habitats, have many life forms and their short generation time make them respond rapidly to environmental changes. Their taxonomic diversity represents a valuable tool to assess water quality as each taxon has specific responses to environmental factors. Recently, diatoms have been used as tracers to detect the onset/cessation of surface runoff through binary classification of terrestrial and aquatic species in the Attert basin in Luxembourg. In order to continue the validation of these first results, we have collected samples during rain events at different seasons of the year using automatic stream water samplers, grab samples of diatoms from various terrestrial and subaerial substrates (bryophytes, litter and leaves), as well as from aquatic habitats (epilithon, epipelon and drift samples). This new type of information will be used to constrain assumptions of the conventional tracer-based hydrograph separation technique (i.e. using geochemistry and stable isotopes). The first results concerning the diatom flora, based on 39 samples, revealed 152 species belonging to 38 genera. The most species-rich genera were Pinnularia (15.8% - 24 taxa), Eunotia (13.2% - 20 taxa), Gomphonema (8.6% - 13 taxa), Navicula (7.2% - 11 taxa) and Stauroneis (5.3% - 8 taxa). The flora are mainly composed of oligotrophic and/or acidophilic taxa (32.0%), ubiquitous (14.0%) or poorly known ecologically species (43.0%). The most important taxa found in drift samples were Fragilariforma virescens, Fragilaria capucina sensu lato, Planothidium lanceolatum, Eunotia minor, Achnanthidium kranzii, Karayevia oblongella and Eunotia incisa. In the riparian zone (n = 10), 102 species were observed, with Eunotia exigua var. tenella, Eunotia botuliformis and Pinnularia perirrorata being among the most frequent. Epilithic samples from the main channel

Epigenetic Segregation of Microbial Genomes from Complex Samples Using Restriction Endonucleases HpaII and McrB.

PubMed

Liu, Guohong; Weston, Christopher Q; Pham, Long K; Waltz, Shannon; Barnes, Helen; King, Paula; Sphar, Dan; Yamamoto, Robert T; Forsyth, R Allyn

2016-01-01

We describe continuing work to develop restriction endonucleases as tools to enrich targeted genomes of interest from diverse populations. Two approaches were developed in parallel to segregate genomic DNA based on cytosine methylation. First, the methyl-sensitive endonuclease HpaII was used to bind non-CG methylated DNA. Second, a truncated fragment of McrB was used to bind CpG methylated DNA. Enrichment levels of microbial genomes can exceed 100-fold with HpaII allowing improved genomic detection and coverage of otherwise trace microbial genomes from sputum. Additionally, we observe interesting enrichment results that correlate with the methylation states not only of bacteria, but of fungi, viruses, a protist and plants. The methods presented here offer promise for testing biological samples for pathogens and global analysis of population methylomes.

Air sampling procedures to evaluate microbial contamination: a comparison between active and passive methods in operating theatres.

PubMed

Napoli, Christian; Marcotrigiano, Vincenzo; Montagna, Maria Teresa

2012-08-02

Since air can play a central role as a reservoir for microorganisms, in controlled environments such as operating theatres regular microbial monitoring is useful to measure air quality and identify critical situations. The aim of this study is to assess microbial contamination levels in operating theatres using both an active and a passive sampling method and then to assess if there is a correlation between the results of the two different sampling methods. The study was performed in 32 turbulent air flow operating theatres of a University Hospital in Southern Italy. Active sampling was carried out using the Surface Air System and passive sampling with settle plates, in accordance with ISO 14698. The Total Viable Count (TVC) was evaluated at rest (in the morning before the beginning of surgical activity) and in operational (during surgery). The mean TVC at rest was 12.4 CFU/m3 and 722.5 CFU/m2/h for active and passive samplings respectively. The mean in operational TVC was 93.8 CFU/m3 (SD = 52.69; range = 22-256) and 10496.5 CFU/m2/h (SD = 7460.5; range = 1415.5-25479.7) for active and passive samplings respectively. Statistical analysis confirmed that the two methods correlate in a comparable way with the quality of air. It is possible to conclude that both methods can be used for general monitoring of air contamination, such as routine surveillance programs. However, the choice must be made between one or the other to obtain specific information.

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.

AQUATIC ECOSYSTEMS,

EPA Science Inventory

Aquatic ecosystems are a vital part of the urban water cycle (and of urban areas more broadly), and, if healthy, provide a range of goods and services valued by humans (Meyer 1997). For example, aquatic ecosystems (e.g., rivers, lakes, wetlands) provide potable water, food resou...

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.

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

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

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples

PubMed Central

Yu, Feiqiao Brian; Blainey, Paul C; Schulz, Frederik; Woyke, Tanja; Horowitz, Mark A; Quake, Stephen R

2017-01-01

Metagenomics and single-cell genomics have enabled genome discovery from unknown branches of life. However, extracting novel genomes from complex mixtures of metagenomic data can still be challenging and represents an ill-posed problem which is generally approached with ad hoc methods. Here we present a microfluidic-based mini-metagenomic method which offers a statistically rigorous approach to extract novel microbial genomes while preserving single-cell resolution. We used this approach to analyze two hot spring samples from Yellowstone National Park and extracted 29 new genomes, including three deeply branching lineages. The single-cell resolution enabled accurate quantification of genome function and abundance, down to 1% in relative abundance. Our analyses of genome level SNP distributions also revealed low to moderate environmental selection. The scale, resolution, and statistical power of microfluidic-based mini-metagenomics make it a powerful tool to dissect the genomic structure of microbial communities while effectively preserving the fundamental unit of biology, the single cell. DOI: http://dx.doi.org/10.7554/eLife.26580.001 PMID:28678007

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.

Microbial stratification and microbially catalyzed processes along a hypersaline chemocline

NASA Astrophysics Data System (ADS)

Hyde, A.; Joye, S. B.; Teske, A.

2017-12-01

Orca Basin is the largest deep hypersaline anoxic basin in the world, covering over 400 km2. Located at the bottom of the Gulf of Mexico, this body of water reaches depths of 200 meters and is 8 times denser (and more saline) than the overlying seawater. The sharp pycnocline prevents any significant vertical mixing and serves as a particle trap for sinking organic matter. These rapid changes in salinity, oxygen, organic matter, and other geochemical parameters present unique conditions for the microbial communities present. We collected samples in 10m intervals throughout the chemocline. After filtering the water, we used high-throughput bacterial and archaeal 16S rRNA gene sequencing to characterize the changing microbial community along the Orca Basin chemocline. The results reveal a dominance of microbial taxa whose biogeochemical function is entirely unknown. We then used metagenomic sequencing and reconstructed genomes for select samples, revealing the potential dominant metabolic processes in the Orca Basin chemocline. Understanding how these unique geochemical conditions shape microbial communities and metabolic capabilities will have implications for the ocean's biogeochemical cycles and the consequences of expanding oxygen minimum zones.

Aquatic cycling-What do we know? A scoping review on head-out aquatic cycling.

PubMed

Rewald, Stefanie; Mesters, Ilse; Lenssen, Antoine F; Bansi, Jens; Lambeck, Johan; de Bie, Rob A; Waller, Benjamin

2017-01-01

Over the past few years, aquatic cycling has become a trending fitness activity. However, the literature has not been reviewed exhaustively. Therefore, using scoping review methodology, the aim of this review was to explore the current state of the literature concerning aquatic cycling. This study specifically focused on study designs, populations and outcomes. A comprehensive search of seven databases (PubMed, MEDLINE, Cinahl, Embase, PEDro,Web of Science, WorldCat) was conducted up to 30th September 2016. GoogleScholar, World Cat, ResearchGate, specific aquatic therapy websites and aquatic therapy journals were searched to identify additional literature. Full-text publications in English, German or Dutch were included. Studies were included when the intervention involved head-out cycling carried out in 10° to 35° Celsius water. Exclusion criteria were the use of wet suits or confounding interventions that would affect participants' homeostasis. 63 articles were included and the study parameters of these studies were summarized. Using three grouping themes, included studies were categorised as 1) single session tests comparing aquatic versus land cycling, or 2) aquatic cycling only sessions investigating different exercise conditions and 3) aquatic cycling intervention programmes. Although the experimental conditions differed noticeably across the studies, shared characteristics were identified. Cardiovascular parameters were investigated by many of the studies with the results suggesting that the cardiac demand of aquatic cycling seems similar to land-based cycling. Only six studies evaluated the effect of aquatic cycling interventions. Therefore, future research should investigate the effects of aquatic cycling interventions, preferably in individuals that are expected to gain health benefits from aquatic cycling. Moreover, this comprehensive outline of available literature could serve as a starting point for systematic reviews or clinical studies on the

Aquatic cycling—What do we know? A scoping review on head-out aquatic cycling

PubMed Central

Bansi, Jens; Lambeck, Johan; de Bie, Rob A.; Waller, Benjamin

2017-01-01

Over the past few years, aquatic cycling has become a trending fitness activity. However, the literature has not been reviewed exhaustively. Therefore, using scoping review methodology, the aim of this review was to explore the current state of the literature concerning aquatic cycling. This study specifically focused on study designs, populations and outcomes. A comprehensive search of seven databases (PubMed, MEDLINE, Cinahl, Embase, PEDro,Web of Science, WorldCat) was conducted up to 30th September 2016. GoogleScholar, World Cat, ResearchGate, specific aquatic therapy websites and aquatic therapy journals were searched to identify additional literature. Full-text publications in English, German or Dutch were included. Studies were included when the intervention involved head-out cycling carried out in 10° to 35° Celsius water. Exclusion criteria were the use of wet suits or confounding interventions that would affect participants’ homeostasis. 63 articles were included and the study parameters of these studies were summarized. Using three grouping themes, included studies were categorised as 1) single session tests comparing aquatic versus land cycling, or 2) aquatic cycling only sessions investigating different exercise conditions and 3) aquatic cycling intervention programmes. Although the experimental conditions differed noticeably across the studies, shared characteristics were identified. Cardiovascular parameters were investigated by many of the studies with the results suggesting that the cardiac demand of aquatic cycling seems similar to land-based cycling. Only six studies evaluated the effect of aquatic cycling interventions. Therefore, future research should investigate the effects of aquatic cycling interventions, preferably in individuals that are expected to gain health benefits from aquatic cycling. Moreover, this comprehensive outline of available literature could serve as a starting point for systematic reviews or clinical studies on the

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

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.

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.

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.

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.

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.

Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome

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

Miller, Ian J.; Weyna, Theodore R.; Fong, Stephen S.

Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain “universal” 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of “microbial darkmore » matter,” or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Lastly, our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.« less

Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome

DOE PAGES

Miller, Ian J.; Weyna, Theodore R.; Fong, Stephen S.; ...

2016-09-29

Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain “universal” 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of “microbial darkmore » matter,” or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Lastly, our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.« less

Aquatic Organic Matter Fluorescence - from phenomenon to application

NASA Astrophysics Data System (ADS)

Reynolds, Darren

2014-05-01

(bioluminescent reporter bacteria) for the discovery and characterization of bacteriophage and to assess their potential use as a bio-control/antimicrobial in the health and agri-food sectors. Presently, he is developing, in collaboration with industrial partners, in-situ fluorescence sensors to help further understand the role of dissolved organic matter in underpinning the microbial processes in aquatic systems through time, a project funded by the Natural Environment Research Council, UK.

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

Air sampling procedures to evaluate microbial contamination: a comparison between active and passive methods in operating theatres

PubMed Central

2012-01-01

Background Since air can play a central role as a reservoir for microorganisms, in controlled environments such as operating theatres regular microbial monitoring is useful to measure air quality and identify critical situations. The aim of this study is to assess microbial contamination levels in operating theatres using both an active and a passive sampling method and then to assess if there is a correlation between the results of the two different sampling methods. Methods The study was performed in 32 turbulent air flow operating theatres of a University Hospital in Southern Italy. Active sampling was carried out using the Surface Air System and passive sampling with settle plates, in accordance with ISO 14698. The Total Viable Count (TVC) was evaluated at rest (in the morning before the beginning of surgical activity) and in operational (during surgery). Results The mean TVC at rest was 12.4 CFU/m3 and 722.5 CFU/m2/h for active and passive samplings respectively. The mean in operational TVC was 93.8 CFU/m3 (SD = 52.69; range = 22-256) and 10496.5 CFU/m2/h (SD = 7460.5; range = 1415.5-25479.7) for active and passive samplings respectively. Statistical analysis confirmed that the two methods correlate in a comparable way with the quality of air. Conclusion It is possible to conclude that both methods can be used for general monitoring of air contamination, such as routine surveillance programs. However, the choice must be made between one or the other to obtain specific information. PMID:22853006

Aquatic Therapy for Children

ERIC Educational Resources Information Center

Kucher, Greta; Moore, Kelsey; Rodia, Rachel; Moser, Christy Szczech

2015-01-01

Aquatic therapy has long been highlighted in the literature as a potentially powerful therapeutic intervention. This review will highlight basic definitions of aquatic therapy, review salient research, and identify specific diagnoses that may benefit from aquatic therapy. Online resources, blogs, and books that occupational therapists may find…

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.

IV. Aquatics

Treesearch

Michael K. Young

2011-01-01

The problem of invasive aquatic species has long been recognized by scientists at the Rocky Mountain Research Station. Fausch and others (2006, 2009) recently overviewed this issue. A point that often distinguishes nonnative aquatic species from nonnatives in other environments is that the presence of some species is frequently prized by managers and the public. 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.

Organic Geochemistry and Sources of Natural Aquatic Foams

USGS Publications Warehouse

Mills, M.S.; Thurman, E.M.; Ertel, J.; Thorn, K.A.

1996-01-01

Aquatic foams and stream-water samples were collected from two pristine sites for humic substances isolation and characterization. Biomarker compounds identified in foam and stream humic substances included phospholipid fatty acids, steroids, and lignin. Results showed that foams had a 10 to 20 fold greater DOC concentration and were enriched in humic substances (90% by weight of DOC) that showed increased hydrophobicity, aliphatic character, and compositional complexity compared to host stream humic substances (55 to 81% by weight of DOC). Foam humic substances also were enriched in humic acid (36 to 83% by weight) compared to host stream humic substances (10 to 14% by weight). Biomarkers, which contributed less than 5% by weight to the DOC pool, indicated higher plants, bacteria, algae, fungi, and diatoms as DOC sources. It is proposed that aquatic foams may be important media for the concentration and transport of organic substances in the aquatic environment.

Human Streptococcus agalactiae strains in aquatic mammals and fish

PubMed Central

2013-01-01

Background In humans, Streptococcus agalactiae or group B streptococcus (GBS) is a frequent coloniser of the rectovaginal tract, a major cause of neonatal infectious disease and an emerging cause of disease in non-pregnant adults. In addition, Streptococcus agalactiae causes invasive disease in fish, compromising food security and posing a zoonotic hazard. We studied the molecular epidemiology of S. agalactiae in fish and other aquatic species to assess potential for pathogen transmission between aquatic species and humans. Methods Isolates from fish (n = 26), seals (n = 6), a dolphin and a frog were characterized by pulsed-field gel electrophoresis, multilocus sequence typing and standardized 3-set genotyping, i.e. molecular serotyping and profiling of surface protein genes and mobile genetic elements. Results Four subpopulations of S. agalactiae were identified among aquatic isolates. Sequence type (ST) 283 serotype III-4 and its novel single locus variant ST491 were detected in fish from Southeast Asia and shared a 3-set genotype identical to that of an emerging ST283 clone associated with invasive disease of adult humans in Asia. The human pathogenic strain ST7 serotype Ia was also detected in fish from Asia. ST23 serotype Ia, a subpopulation that is normally associated with human carriage, was found in all grey seals, suggesting that human effluent may contribute to microbial pollution of surface water and exposure of sea mammals to human pathogens. The final subpopulation consisted of non-haemolytic ST260 and ST261 serotype Ib isolates, which belong to a fish-associated clonal complex that has never been reported from humans. Conclusions The apparent association of the four subpopulations of S. agalactiae with specific groups of host species suggests that some strains of aquatic S. agalactiae may present a zoonotic or anthroponotic hazard. Furthermore, it provides a rational framework for exploration of pathogenesis and host-associated genome content of S

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

Regulation of Hydrolytic Enzyme Activity in Aquatic Microbial Communities Hosted by Carnivorous Pitcher Plants.

PubMed

Young, Erica B; Sielicki, Jessica; Grothjan, Jacob J

2018-04-20

Carnivorous pitcher plants Sarracenia purpurea host diverse eukaryotic and bacterial communities which aid in insect prey digestion, but little is known about the functional processes mediated by the microbial communities. This study aimed to connect pitcher community diversity with functional nutrient transformation processes, identifying bacterial taxa, and measuring regulation of hydrolytic enzyme activity in response to prey and alternative nutrient sources. Genetic analysis identified diverse bacterial taxa known to produce hydrolytic enzyme activities. Chitinase, protease, and phosphatase activities were measured using fluorometric assays. Enzyme activity in field pitchers was positively correlated with bacterial abundance, and activity was suppressed by antibiotics suggesting predominantly bacterial sources of chitinase and protease activity. Fungi, algae, and rotifers observed could also contribute enzyme activity, but fresh insect prey released minimal chitinase activity. Activity of chitinase and proteases was upregulated in response to insect additions, and phosphatase activity was suppressed by phosphate additions. Particulate organic P in prey was broken down, appearing as increasing dissolved organic and inorganic P pools within 14 days. Chitinase and protease were not significantly suppressed by availability of dissolved organic substrates, though organic C and N stimulated bacterial growth, resulting in elevated enzyme activity. This comprehensive field and experimental study show that pitcher plant microbial communities dynamically regulate hydrolytic enzyme activity, to digest prey nutrients to simpler forms, mediating biogeochemical nutrient transformations and release of nutrients for microbial and host plant uptake.

Nitrogen cycle in microbial mats: completely unknown?

NASA Astrophysics Data System (ADS)

Coban, O.; Bebout, B.

2015-12-01

Microbial mats are thought to have originated around 3.7 billion years ago, most likely in the areas around submarine hydrothermal vents, which supplied a source of energy in the form of reduced chemical species from the Earth's interior. Active hydrothermal vents are also believed to exist on Jupiter's moon Europa, Saturn's moon Enceladus, and on Mars, earlier in that planet's history. Microbial mats have been an important force in the maintenance of Earth's ecosystems and the first photosynthesis was also originated there. Microbial mats are believed to exhibit most, if not all, biogeochemical processes that exist in aquatic ecosystems, due to the presence of different physiological groups of microorganisms therein. While most microbially mediated biogeochemical transformations have been shown to occur within microbial mats, the nitrogen cycle in the microbial mats has received very little study in spite of the fact that nitrogen usually limits growth in marine environments. We will present the first results in the determination of a complete nitrogen budget for a photosynthetic microbial mat. Both in situ sources and sinks of nitrogen in photosynthetic microbial mats are being measured using stable isotope techniques. Our work has a particular focus on recently described, but poorly understood, processes, e.g., anammox and dissimilatory nitrate reduction, and an emphasis on understanding the role that nitrogen cycling may play in generating biogenic nitrogen isotopic signatures and biomarker molecules. Measurements of environmental controls on nitrogen cycling should offer insight into the nature of co-evolution of these microbial communities and their planets of origin. Identifying the spatial (microscale) as well as temporal (diel and seasonal) distribution of nitrogen transformations, e.g., rates of nitrification and denitrification, within mats, particularly with respect to the distribution of photosynthetically-produced oxygen, is anticipated. The results

HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes.

PubMed

Forster, Samuel C; Browne, Hilary P; Kumar, Nitin; Hunt, Martin; Denise, Hubert; Mitchell, Alex; Finn, Robert D; Lawley, Trevor D

2016-01-04

The Human Pan-Microbe Communities (HPMC) database (http://www.hpmcd.org/) provides a manually curated, searchable, metagenomic resource to facilitate investigation of human gastrointestinal microbiota. Over the past decade, the application of metagenome sequencing to elucidate the microbial composition and functional capacity present in the human microbiome has revolutionized many concepts in our basic biology. When sufficient high quality reference genomes are available, whole genome metagenomic sequencing can provide direct biological insights and high-resolution classification. The HPMC database provides species level, standardized phylogenetic classification of over 1800 human gastrointestinal metagenomic samples. This is achieved by combining a manually curated list of bacterial genomes from human faecal samples with over 21000 additional reference genomes representing bacteria, viruses, archaea and fungi with manually curated species classification and enhanced sample metadata annotation. A user-friendly, web-based interface provides the ability to search for (i) microbial groups associated with health or disease state, (ii) health or disease states and community structure associated with a microbial group, (iii) the enrichment of a microbial gene or sequence and (iv) enrichment of a functional annotation. The HPMC database enables detailed analysis of human microbial communities and supports research from basic microbiology and immunology to therapeutic development in human health and disease. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

Tropical Aquatic Archaea Show Environment-Specific Community Composition

PubMed Central

Silveira, Cynthia B.; Cardoso, Alexander M.; Coutinho, Felipe H.; Lima, Joyce L.; Pinto, Leonardo H.; Albano, Rodolpho M.; Clementino, Maysa M.; Martins, Orlando B.; Vieira, Ricardo P.

2013-01-01

The Archaea domain is ubiquitously distributed and extremely diverse, however, environmental factors that shape archaeal community structure are not well known. Aquatic environments, including the water column and sediments harbor many new uncultured archaeal species from which metabolic and ecological roles remain elusive. Some environments are especially neglected in terms of archaeal diversity, as is the case of pristine tropical areas. Here we investigate the archaeal composition in marine and freshwater systems from Ilha Grande, a South Atlantic tropical environment. All sampled habitats showed high archaeal diversity. No OTUs were shared between freshwater, marine and mangrove sediment samples, yet these environments are interconnected and geographically close, indicating environment-specific community structuring. Group II Euryarchaeota was the main clade in marine samples, while the new putative phylum Thaumarchaeota and LDS/RCV Euryarchaeota dominated freshwaters. Group III Euryarchaeota , a rare clade, was also retrieved in reasonable abundance in marine samples. The archaeal community from mangrove sediments was composed mainly by members of mesophilic Crenarchaeota and by a distinct clade forming a sister-group to Crenarchaeota and Thaumarchaeota. Our results show strong environment-specific community structuring in tropical aquatic Archaea, as previously seen for Bacteria. PMID:24086729

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.

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.

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

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

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.

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

EPA Region 7 Aquatic Focus Areas (ECO_RES.R7_AQUATIC_FOCUS_AREAS)

EPA Pesticide Factsheets

This shapefile consists of 347 individual Aquatic Ecological System (AES) polygons that are the Aquatic Conservation Focus Areas for EPA Region 7. The focus areas are those areas within each aquatic ecological system types that, if preserved, would maintain the biological and ecological diversity extant within that ecological system type. The layer consists of those polygons from the R7_AES.shp shapefile that had the highest ranks. The AES polygons in the Missouri portion of the file were appended and are those that contain the 158 aquatic conservation opportunity areas identified in Missouri as part of another project (Missouri Department of Conservation Aquatic Biodiversity Assessment 2005). Note that the identifiers in the Missouri portion of this file will not match the ID's in any Missouri specific files.

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

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.

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.

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 Load Monitor

NASA Technical Reports Server (NTRS)

Gibson, S. F.; Royer, E. R.

1979-01-01

The Microbial Load Monitor (MLM) is an automated and computerized system for detection and identification of microorganisms. Additionally, the system is designed to enumerate and provide antimicrobic susceptibility profiles for medically significant bacteria. The system is designed to accomplish these tasks in a time of 13 hours or less versus the traditional time of 24 hours for negatives and 72 hours or more for positives usually required for standard microbiological analysis. The MLM concept differs from other methods of microbial detection in that the system is designed to accept raw untreated clinical samples and to selectively identify each group or species that may be present in a polymicrobic sample.

Development and Antarctic Testing of a Maneuverable Probe for Clean In-Situ Analysis and Sampling of Subsurface Ice and Subglacial Aquatic Ecosystems

NASA Astrophysics Data System (ADS)

Francke, G.; Dachwald, B.; Kowalski, J.; Digel, I.; Tulaczyk, S. M.; Mikucki, J.; Feldmann, M.; Espe, C.; Schöngarth, S.; Hiecker, S.; Blandfort, D.; Schüller, K.; Plescher, E.

2016-12-01

There is significant interest in sampling subglacial environments for geochemical and microbiological studies, but those environments are difficult to access. Such environments exist not only on Earth but are also expected beneath the icy crusts of some outer solar system bodies, like the Jovian moon Europa and the Saturnian moon Enceladus. Existing ice drilling technologies make it cumbersome to maintain microbiologically clean access for sample acquisition and environmental stewardship of potentially fragile subglacial aquatic ecosystems. The "IceMole" is a maneuverable subsurface ice probe for clean in-situ analysis and sampling of glacial ice and subglacial materials. The design is based on combining melting and mechanical propulsion, using an ice screw at the tip of the melting head to maintain firm contact between the melting head and the ice. It can change melting direction by differential heating of the melting head and optional side wall heaters. The first two prototypes were successfully tested between 2010 and 2012 on glaciers in Switzerland and Iceland, where they demonstrated downward, horizontal and upward melting, as well as curve driving and dirt layer penetration. Hence, the IceMole allows maneuvers which may be necessary for obstacle avoidance or target selection. Maneuverability, however, necessitates a sophisticated on-board navigation system capable of autonomous operations. Therefore, between 2012 and 2014, a more advanced probe was developed as part of the "Enceladus Explorer" (EnEx) project. The EnEx-IceMole offers systems for relative positioning based on in-ice attitude determination, acoustic positioning, ultrasonic obstacle and target detection, which is all integrated through a high-level sensor fusion. In December 2014, it was used for clean access into a unique subglacial aquatic environment at Blood Falls, Antarctica, where a subglacial brine sample was successfully obtained after about 17 meters of oblique melting. Particular

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.

Microbial and Antibiotic Susceptibility Profile among Clinical Samples of Patients with Acute Leukemia.

PubMed

Abdollahi, Alireza; Hakimi, Faezeh; Doomanlou, Mahsa; Azadegan, Azadeh

2016-04-01

Preventing and starting early treatment of infections in patients whose immunity system is weak due to malignancies like leukemia can reduce mortality. This study aimed to determine microbial and antibiotic resistance patterns in clinical samples of patients with acute leukemia to start early treatment before the results of clinical tests are known. In this cross-sectional study, the clinical samples of all patients hospitalized with the diagnosis of acute leukemia were cultured and their antibiogram was evaluated. Then, the data were analyzed by SPSS 18 based on the objectives of the study. Of a total of 2,366 samples, 18.95% were reported to be positive blood samples, 22.96% were reported to be urine samples and 36% wound samples. E. coli was the most common bacteria isolated from the blood and urine cultures (34% in blood, 32% in urine culture) while Staphylococcus Aureus was the most common in the wound culture (35%). The highest level of sensitivity in the organisms with positive blood culture was to Ciprofloxacin, while in positive urine and wound culture was to Imipenem. The highest resistance in blood, urine and wound culture was to Cotrimoxazole. According to results obtained from this study, it is necessary to conduct appropriate studies on this issue in specific conditions in our country. The findings of this study can be used in clinics for more accurate diagnosis, more effective treatment before the results of clinical tests are known and also for prevention of infection in cancer patients.

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.

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

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

Modern Microbial Fossilization Processes as Signatures for Interpreting Ancient Terrestrial and Extraterrestrial Microbial Forms

NASA Technical Reports Server (NTRS)

Morris, Penny A.; Wentworth, Susan J.; Nelman, Mayra; Byrne, Monica; Longazo, Teresa; Galindo, Charles; McKay, David S.; Sams, Clarence

2003-01-01

Terrestrial biotas from microbially dominated hypersaline environments will help us understand microbial fossilization processes. Hypersaline tolerant biota from Storr's Lake, San Salvador Island (Bahamas), Mono Lake (California), and the Dead Sea (Israel) represent marine and nonmarine sites for comparative studies of potential analogs for interpreting some Mars meteorites and Mars sample return rocks [1,2,3,4,5,6]. The purpose of this study is to compare microbial fossilization processes, the dominant associated minerals, and potential diagenic implications.

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

Tool use by aquatic animals

PubMed Central

Mann, Janet; Patterson, Eric M.

2013-01-01

Tool-use research has focused primarily on land-based animals, with less consideration given to aquatic animals and the environmental challenges and conditions they face. Here, we review aquatic tool use and examine the contributing ecological, physiological, cognitive and social factors. Tool use among aquatic animals is rare but taxonomically diverse, occurring in fish, cephalopods, mammals, crabs, urchins and possibly gastropods. While additional research is required, the scarcity of tool use can likely be attributable to the characteristics of aquatic habitats, which are generally not conducive to tool use. Nonetheless, studying tool use by aquatic animals provides insights into the conditions that promote and inhibit tool-use behaviour across biomes. Like land-based tool users, aquatic animals tend to find tools on the substrate and use tools during foraging. However, unlike on land, tool users in water often use other animals (and their products) and water itself as a tool. Among sea otters and dolphins, the two aquatic tool users studied in greatest detail, some individuals specialize in tool use, which is vertically socially transmitted possibly because of their long dependency periods. In all, the contrasts between aquatic- and land-based tool users enlighten our understanding of the adaptive value of tool-use behaviour. PMID:24101631

Tool use by aquatic animals.

PubMed

Mann, Janet; Patterson, Eric M

2013-11-19

Tool-use research has focused primarily on land-based animals, with less consideration given to aquatic animals and the environmental challenges and conditions they face. Here, we review aquatic tool use and examine the contributing ecological, physiological, cognitive and social factors. Tool use among aquatic animals is rare but taxonomically diverse, occurring in fish, cephalopods, mammals, crabs, urchins and possibly gastropods. While additional research is required, the scarcity of tool use can likely be attributable to the characteristics of aquatic habitats, which are generally not conducive to tool use. Nonetheless, studying tool use by aquatic animals provides insights into the conditions that promote and inhibit tool-use behaviour across biomes. Like land-based tool users, aquatic animals tend to find tools on the substrate and use tools during foraging. However, unlike on land, tool users in water often use other animals (and their products) and water itself as a tool. Among sea otters and dolphins, the two aquatic tool users studied in greatest detail, some individuals specialize in tool use, which is vertically socially transmitted possibly because of their long dependency periods. In all, the contrasts between aquatic- and land-based tool users enlighten our understanding of the adaptive value of tool-use behaviour.

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.

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

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

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

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

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.

Bisphenol A in the aquatic environment and its endocrine-disruptive effects on aquatic organisms.

PubMed

Kang, Jeong-Hun; Asai, Daisuke; Aasi, Daisuke; Katayama, Yoshiki

2007-01-01

Bisphenol A [BPA; 2,2-bis(4-hydroxyphenyl)propane], which is mainly used in the production of epoxy resins and polycarbonate plastics, is a known endocrine disruptor and is acutely toxic to aquatic organisms. Due to intensified usage of these products, exposure of organisms to BPA via several routes, such as the environment and food, has increased. The aquatic environment is an important area for the study of BPA. This report reviews the literature concerning contamination routes and degradation of BPA in the aquatic environment and its endocrine-disruptive effects on aquatic organisms.

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

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

Methylmercury enters an aquatic food web through acidophilic microbial mats in Yellowstone National Park, Wyoming.

PubMed

Boyd, Eric S; King, Susan; Tomberlin, Jeffery K; Nordstrom, D Kirk; Krabbenhoft, David P; Barkay, Tamar; Geesey, Gill G

2009-04-01

Microbial mats are a visible and abundant life form inhabiting the extreme environments in Yellowstone National Park (YNP), WY, USA. Little is known of their role in food webs that exist in the Park's geothermal habitats. Eukaryotic green algae associated with a phototrophic green/purple Zygogonium microbial mat community that inhabits low-temperature regions of acidic (pH approximately 3.0) thermal springs were found to serve as a food source for stratiomyid (Diptera: Stratiomyidae) larvae. Mercury in spring source water was taken up and concentrated by the mat biomass. Monomethylmercury compounds (MeHg(+)), while undetectable or near the detection limit (0.025 ng l(-1)) in the source water of the springs, was present at concentrations of 4-7 ng g(-1) dry weight of mat biomass. Detection of MeHg(+) in tracheal tissue of larvae grazing the mat suggests that MeHg(+) enters this geothermal food web through the phototrophic microbial mat community. The concentration of MeHg(+) was two to five times higher in larval tissue than mat biomass indicating MeHg(+) biomagnification occurred between primary producer and primary consumer trophic levels. The Zygogonium mat community and stratiomyid larvae may also play a role in the transfer of MeHg(+) to species in the food web whose range extends beyond a particular geothermal feature of YNP.

Methods for Aquatic Resource Assessment

EPA Science Inventory

The Methods for Aquatic Resource Assessment (MARA) project consists of three main activities in support of assessing the conditions of the nation’s aquatic resources: 1) scientific support for EPA Office of Water’s national aquatic resource surveys; 2) spatial predications of riv...

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.

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.

Intra-storm variability in microbial partitioning and microbial loading rates.

PubMed

Krometis, Leigh-Anne H; Characklis, Gregory W; Simmons, Otto D; Dilts, Mackenzie J; Likirdopulos, Christina A; Sobsey, Mark D

2007-01-01

Association with particles in the water column can have a significant impact on microbial fate and transport. This study analyzed multiple stormwater samples taken throughout the duration of three separate storms (at two different sites) to evaluate the fraction of microbes partitioning to denser "settleable" particles and to examine how partitioning behavior varied over the course of a storm. Intra-storm sampling also allowed for estimates of microbial loading rates (both total and particle-associated) and cumulative storm-induced microbial load. Five different indicator organisms were examined, with the fraction of microbes associated with settleable particles assessed via a calibrated centrifugation method. Partitioning behavior varied across microorganism type, with an average of 40% of fecal coliforms, Escherichia coli, and enterococci associating with settleable particles, compared to approximately 65% of Clostridium perfringens spores and only 13% of total coliphage. Partitioning remained fairly constant for each type of organism throughout storm events. Nonetheless, higher concentrations of both settleable particles and microbes entering the water column soon after the onset of a storm led to higher loading rates of settleable microbes in the storm's earliest stages, a trend that could have important implications for the design of stormwater management structures (e.g., detention basins). Estimates of cumulative storm-induced microbial loading suggested that one day's worth of storm loading can be the equivalent of months, or even years, of dry-weather loading.

Sampled-time control of a microbial fuel cell stack

NASA Astrophysics Data System (ADS)

Boghani, Hitesh C.; Dinsdale, Richard M.; Guwy, Alan J.; Premier, Giuliano C.

2017-07-01

Research into microbial fuel cells (MFCs) has reached the point where cubic metre-scale systems and stacks are being built and tested. Apart from performance enhancement through catalysis, materials and design, an important research area for industrial applicability is stack control, which can enhance MFCs stack power output. An MFC stack is controlled using a sampled-time digital control strategy, which has the advantage of intermittent operation with consequent power saving, and when used in a hybrid series stack connectivity, can avoid voltage reversals. A MFC stack comprising four tubular MFCs was operated hydraulically in series. Each MFC was connected to an independent controller and the stack was connected electrically in series, creating a hybrid-series connectivity. The voltage of each MFC in the stack was controlled such that the overall series stack voltage generated was the algebraic sum (1.26 V) of the individual MFC voltages (0.32, 0.32, 0.32 and 0.3). The controllers were able to control the individual voltages to the point where 2.52 mA was drawn from the stack at a load of 499.9 Ω (delivering 3.18 mW). The controllers were able to reject the disturbances and perturbations caused by electrical loading, temperature and substrate concentration.

Metaproteomics to investigate the impact of sampling-site biogeochemistry on structure and functionality of leaf-litter degrading microbial communities

NASA Astrophysics Data System (ADS)

Schneider, Thomas; Keiblinger, Katharina; Gerrits, Bertran; Schmid, Emanuel; Eberl, Leo; Zechmeister-Boltenstern, Sophie; Riedel, Kathrin

2010-05-01

The composition of organic matter in natural ecosystems is strongly influenced by the microorganisms present. Conversely, bacteria and fungi are limited by the amount and type of organic matter available in a given environment, most of which is ultimately derived from plants. Changes in the stoichiometry and biochemical constituents of plant litter may therefore alter species composition and elicit changes in the activities of microbial communities and their component parts. The identification of the microbial proteins of a given habitat together with the analysis of their phylogenetic origin and their spatial and temporal distribution are expected to provide fundamentally new insights into the role of microbial diversity in biogeochemical processes. To relate structure and functionality of microbial communities involved in leaf-litter decomposition we determined biogeochemistry, community structure by phospholipid fatty acid (PLFA)-analyses, enzymatic activities, and analysed the protein complement of different litter types, which were collected in winter and spring at various Austrian sampling sites, in a semi-quantitative proteomics approach by one dimensional polyacrylamide gel electrophoresis (1-D-SDS-PAGE) combined with liquid chromatography/tandem mass-spectrometry (LC-MS/MS). Protein abundances were determined by counting the number of MS/MS spectra assigned to each protein. In samples with high manganese and phosphor content a significant increase of fungal proteins from February to May was observed, which was in good agreement with the PLFA-analyses showing similar trends towards an increase of the fungal community. In contrast, the PLFA analysis revealed no temporal changes in the community at Achenkirch and even a decrease in the fungal/bacterial ratio at Klausen-Leopoldsdorf, two sampling sites low in P and Mn; similar trends are reflected in our spectral counts. In conclusion, semi-quantitative proteome- and PLFA-analyses suggest that fungal and

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.

Non-microbial sources of microbial volatile organic compounds.

PubMed

Choi, Hyunok; Schmidbauer, Norbert; Bornehag, Carl-Gustaf

2016-07-01

The question regarding the true sources of the purported microbial volatile organic compounds (MVOCs) remains unanswered. To identify microbial, as well as non-microbial sources of 28 compounds, which are commonly accepted as microbial VOCs (i.e. primary outcome of interest is Σ 28 VOCs). In a cross-sectional investigation of 390 homes, six building inspectors assessed water/mold damage, took air and dust samples, and measured environmental conditions (i.e., absolute humidity (AH, g/m(3)), temperature (°C), ventilation rate (ACH)). The air sample was analyzed for volatile organic compounds (μg/m(3)) and; dust samples were analyzed for total viable fungal concentration (CFU/g) and six phthalates (mg/g dust). Four benchmark variables of the underlying sources were defined as highest quartile categories of: 1) the total concentration of 17 propylene glycol and propylene glycol ethers (Σ17 PGEs) in the air sample; 2) 2,2,4-trimethyl-1,3-pentanediol monoisobutyrate (TMPD-MIB) in the air sample; 3) semi-quantitative mold index; and 4) total fungal load (CFU/g). Within severely damp homes, co-occurrence of the highest quartile concentration of either Σ17 PGEs or TMPD-MIB were respectively associated with a significantly higher median concentration of Σ 28 VOCs (8.05 and 13.38μg/m(3), respectively) compared to the reference homes (4.30 and 4.86μg/m(3), respectively, both Ps ≤0.002). Furthermore, the homes within the highest quartile range for Σ fungal load as well as AH were associated with a significantly increased median Σ 28 VOCs compared to the reference group (8.74 vs. 4.32μg/m(3), P=0.001). Within the final model of multiple indoor sources on Σ 28 VOCs, one natural log-unit increase in summed concentration of Σ17 PGEs, plus TMPD-MIB (Σ 17 PGEs + TMPD-MIB) was associated with 1.8-times (95% CI, 1.3-2.5), greater likelihood of having a highest quartile of Σ 28 VOCs, after adjusting for absolute humidity, history of repainting at least one room

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

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

Science: Aquatic Toxicology Matures, Gains Importance.

ERIC Educational Resources Information Center

Dagani, Ron

1980-01-01

Reviews recent advances in aquatic toxicology, whose major goal is to protect diverse aquatic organisms and whole ecological communities from the dire effects of man-made chemicals. Current legislation is reviewed. Differences in mammalian and aquatic toxicology are listed, and examples of research in aquatic toxicology are discussed. (CS)

Flow management for hydropower extirpates aquatic insects, undermining river food webs

USGS Publications Warehouse

Kennedy, Theodore A.; Muehlbauer, Jeffrey D.; Yackulic, Charles B.; Lytle, D.A.; Miller, S.A.; Dibble, Kimberly L.; Kortenhoeven, Eric W.; Metcalfe, Anya; Baxter, Colden V.

2016-01-01

Dams impound the majority of rivers and provide important societal benefits, especially daily water releases that enable on-peak hydroelectricity generation. Such “hydropeaking” is common worldwide, but its downstream impacts remain unclear. We evaluated the response of aquatic insects, a cornerstone of river food webs, to hydropeaking using a life history–hydrodynamic model. Our model predicts that aquatic-insect abundance will depend on a basic life-history trait—adult egg-laying behavior—such that open-water layers will be unaffected by hydropeaking, whereas ecologically important and widespread river-edge layers, such as mayflies, will be extirpated. These predictions are supported by a more-than-2500-sample, citizen-science data set of aquatic insects from the Colorado River in the Grand Canyon and by a survey of insect diversity and hydropeaking intensity across dammed rivers of the Western United States. Our study reveals a hydropeaking-related life history bottleneck that precludes viable populations of many aquatic insects from inhabiting regulated rivers.

Microbial incorporation of nitrogen in stream detritus

Treesearch

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

2001-01-01

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

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

Aquatic Pest Control. Manual 99.

ERIC Educational Resources Information Center

Missouri Univ., Columbia. Agricultural Experiment Station.

This training manual provides information needed to meet the minimum EPA standards for certification as a commercial applicator of pesticides in the aquatic pest control category. The text discusses various water use situations; aquatic weed identification; herbicide use and effects; and aquatic insects and their control. (CS)

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.

Faunistic Study of the Aquatic Arthropods in a Tourism Area in Northern Iran.

PubMed

Shaeghi, Mansoureh; Dehghan, Hossein; Pakdad, Kamran; Nikpour, Fatemeh; Absavaran, Azad; Sofizadeh, Aioub; Akhavan, Amir Ahmad; Vatandoost, Hassan; Aghai-Afshar, Abbass

2017-06-01

Aquatic insects are very abundant and divers groups of insects that are associated with an aquatic or semiaquatic environment in one or more of their life stages. These insects have been, in some cases, well studied because they are vectors of several diseases. This is the first comprehensive faunistic study of aquatic insects from Babol County. The results may provide basic data for further taxonomic and ecological studies of aquatic insects as biological control agent or classification of water quality for the country. The specimens were collected using different methods including: D-frame net collector, standard mosquito dipper (350ml), Sweep-Netting and plastic pipette. Sampling carried out in different part of breading places in several times. During this study a total of 196 aquatic specimens were collected from different habitats and were morphologically identified including 18 families classified in 6 orders: Diptera, Trichoptera, Ephemeroptera, Plecoptera, Hemiptera and Odonata. Babol and Amol district in Mazandaran Province are located in humid climate regions with suitable ecological factors of humidity, moderate temperature and the variety of plant species. There are different species of aquatic insects in different habitats. The results will provide information for biodeveristy, species richness, their role for biological control as well as calcification of rivers based on abundance of aquatic insects. Therefore the understanding of ecological specifications of aquatic insects could provide a clue for further Arthropod-borne disease control. Additionally aquatic insect could be used for classification of water bodies.

Fate and bioaccumulation of isoproturon in outdoor aquatic microcosms.

PubMed

Merlin, Gerard; Vuillod, Maryline; Lissolo, Thierry; Clement, Bernard

2002-06-01

To gain information concerning the ecotoxicity of isoproturon (IPU) on aquatic ecosystems, six experimental ponds of 5 m3 each were studied. All the experiments were conducted during the summer over two years. Three different types of ecosystems were tested in 1994 and one type of ecosystem was selected and repeated in 1995 with three replicates. In each case, the initial concentration of IPU contamination was set at 10 microg/L. The IPU concentration was determined in the water column and in different species (mainly plants) of the microcosms. A first-order kinetic decrease in IPU concentration was observed in 1994, with half-life ranging from 15 to 35 d, depending on the microcosms. This relatively fast decrease was also confirmed in 1995, but it reached a constant value after two months. A high variability of the IPU concentration was observed in exposed plants, with bioconcentration factors ranging from 100 to 1,200 with large coefficients of variation. The observed plant bioconcentration factors are higher than those predicted by usual numerical models, probably due to the specific binding of IPU on one protein of the photosynthetic apparatus. Our data show that bioconcentration does not occur in mollusks but is important in photosynthetic organisms. Plant bioconcentration and microbial biodegradation are the main processes involved in the IPU decay in our outdoor aquatic microcosms.

Composition of microbial communities in aerosol, snow and ice samples from remote glaciated areas (Antarctica, Alps, Andes)

NASA Astrophysics Data System (ADS)

Elster, J.; Delmas, R. J.; Petit, J.-R.; Řeháková, K.

2007-06-01

Taxonomical and ecological analyses were performed on micro-autotrophs (cyanobacteria and algae together with remnants of diatom valves), micro-fungi (hyphae and spores), bacteria (rod, cocci and red clusters), yeast, and plant pollen extracted from various samples: Alps snow (Mt. Blank area), Andean snow (Illimani, Bolivia), Antarctic aerosol filters (Dumont d'Urville, Terre Adélie), and Antarctic inland ice (Terre Adélie). Three methods for ice and snow sample's pre-concentration were tested (filtration, centrifugation and lyophilisation). Afterwards, cultivation methods for terrestrial, freshwater and marine microorganisms (micro-autotrophs and micro-fungi) were used in combination with liquid and solid media. The main goal of the study was to find out if micro-autotrophs are commonly transported by air masses, and later stored in snow and icecaps around the world. The most striking result of this study was the absence of culturable micro-autotrophs in all studied samples. However, an unusual culturable pigmented prokaryote was found in both alpine snow and aerosol samples. Analyses of many samples and proper statistical analyses (PCA, RDA- Monte Carlo permutation tests) showed that studied treatments highly significantly differ in both microbial community and biotic remnants composition F=9.33, p=0.001. In addition, GLM showed that studied treatments highly significantly differ in numbers of categories of microorganisms and remnants of biological material F=11.45, p=0.00005. The Antarctic aerosol samples were characterised by having red clusters of bacteria, the unusual prokaryote and yeasts. The high mountain snow from the Alps and Andes contained much more culturable heterotrophs. The unusual prokaryote was very abundant, as were coccoid bacteria, red clusters of bacteria, as well as yeasts. The Antarctic ice samples were quite different. These samples had higher numbers of rod bacteria and fungal hyphae. The microbial communities and biological remnants of

Molybdenum limitation of microbial nitrogen assimilation in aquatic ecosystems and pure cultures.

PubMed

Glass, Jennifer B; Axler, Richard P; Chandra, Sudeep; Goldman, Charles R

2012-01-01

Molybdenum (Mo) is an essential micronutrient for biological assimilation of nitrogen gas and nitrate because it is present in the cofactors of nitrogenase and nitrate reductase enzymes. Although Mo is the most abundant transition metal in seawater (107 nM), it is present in low concentrations in most freshwaters, typically <20 nM. In 1960, it was discovered that primary productivity was limited by Mo scarcity (2-4 nM) in Castle Lake, a small, meso-oligotrophic lake in northern California. Follow up studies demonstrated that Mo also limited primary productivity in lakes in New Zealand, Alaska, and the Sierra Nevada. Research in the 1970s and 1980s showed that Mo limited primary productivity and nitrate uptake in Castle Lake only during periods of the growing season when nitrate concentrations were relatively high because ammonium assimilation does not require Mo. In the years since, research has shifted to investigate whether Mo limitation also occurs in marine and soil environments. Here we review studies of Mo limitation of nitrogen assimilation in natural microbial communities and pure cultures. We also summarize new data showing that the simultaneous addition of Mo and nitrate causes increased activity of proteins involved in nitrogen assimilation in the hypolimnion of Castle Lake when ammonium is scarce. Furthermore, we suggest that meter-scale Mo and oxygen depth profiles from Castle Lake are consistent with the hypothesis that nitrogen-fixing cyanobacteria in freshwater periphyton communities have higher Mo requirements than other microbial communities. Finally, we present topics for future research related to Mo bioavailability through time and with changing oxidation state.

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.

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

The role of groundwater transport in aquatic mercury cycling

USGS Publications Warehouse

Krabbenhoft, David P.; Babiarz, Christopher L.

1992-01-01

Mercury, which is transported globally by atmospheric pathways to remote aquatic environments, is a ubiquitous contaminant at very low (nanograms Hg per liter) aqueous concentrations. Until recently, however, analytical and sampling techniques were not available for freshwater systems to quantify the actual levels of mercury concentrations without introducing significant contamination artifacts. Four different sampling strategies were used to evaluate ground water flow as a mercury source and transport mechanism within aquatic systems. The sampling strategies employ ultraclean techniques to determine mercury concentrations in groundwater and pore water near Pallette Lake, Wisconsin. Ambient groundwater concentrations are about 2–4 ng Hg L−1, whereas pore waters near the sediment/water interface average about 12 ng Hg L−1, emphasizing the importance of biogeochemical processes near the interface. Overall, the groundwater system removes about twice as much mercury (1.5 g yr−1) as it contributes (0.7 g yr−1) to Pallette Lake. About three fourths of the groundwater mercury load is recycled, thought to be derived from the water column.

Methylmercury enters an aquatic food web through acidophilic microbial mats in Yellowstone National Park, Wyoming

USGS Publications Warehouse

Boyd, E.S.; King, S.; Tomberlin, J.K.; Nordstrom, D. Kirk; Krabbenhoft, D.P.; Barkay, T.; Geesey, G.G.

2009-01-01

Summary Microbial mats are a visible and abundant life form inhabiting the extreme environments in Yellowstone National Park (YNP), WY, USA. Little is known of their role in food webs that exist in the Park's geothermal habitats. Eukaryotic green algae associated with a phototrophic green/purple Zygogonium microbial mat community that inhabits low-temperature regions of acidic (pH ??? 3.0) thermal springs were found to serve as a food source for stratiomyid (Diptera: Stratiomyidae) larvae. Mercury in spring source water was taken up and concentrated by the mat biomass. Monomethylmercury compounds (MeHg +), while undetectable or near the detection limit (0.025 ng l -1) in the source water of the springs, was present at concentrations of 4-7 ng g-1 dry weight of mat biomass. Detection of MeHg + in tracheal tissue of larvae grazing the mat suggests that MeHg+ enters this geothermal food web through the phototrophic microbial mat community. The concentration of MeHg+ was two to five times higher in larval tissue than mat biomass indicating MeHg+ biomagnification occurred between primary producer and primary consumer trophic levels. The Zygogonium mat community and stratiomyid larvae may also play a role in the transfer of MeHg+ to species in the food web whose range extends beyond a particular geothermal feature of YNP. ?? 2008 The Authors. Journal compilation ?? 2008 Society for Applied Microbiology and Blackwell Publishing Ltd.

Aquatic concentrations of chemical analytes compared to ecotoxicity estimates

EPA Science Inventory

We describe screening level estimates of potential aquatic toxicity posed by 227 chemical analytes that were measured in 25 ambient water samples collected as part of a joint USGS/USEPA drinking water plant study. Measured concentrations were compared to biological effect concent...

Toxicity of ferric chloride sludge to aquatic organisms.

PubMed

Sotero-Santos, Rosana B; Rocha, Odete; Povinelli, Jurandyr

2007-06-01

Iron-rich sludge from a drinking water treatment plant (DWTP) was investigated regarding its toxicity to aquatic organisms and physical and chemical composition. In addition, the water quality of the receiving stream near the DWTP was evaluated. Experiments were carried out in August 1998, February 1999 and May 1999. Acute toxicity tests were carried out on a cladoceran (Daphnia similis), a midge (Chironomus xanthus) and a fish (Hyphessobrycon eques). Chronic tests were conducted only on D. similis. Acute sludge toxicity was not detected using any of the aquatic organisms, but chronic effects were observed upon the fecundity of D. similis. Although there were relatively few sample dates, the results suggested that the DWTP sludge had a negative effect on the receiving body as here was increased suspended matter, turbidity, conductivity, chemical oxygen demand (COD) and hardness in the water downstream of the DWTP effluent discharge. The ferric chloride sludge also exhibited high heavy metal concentrations revealing a further potential for pollution and harmful chronic effects on the aquatic biota when the sludge is disposed of without previous treatment.

Aquatic Plants and their Control.

ERIC Educational Resources Information Center

Michigan State Dept. of Natural Resources, Lansing.

Aquatic plants can be divided into two types: algae and macrophytes. The goal of aquatic plant management is to maintain a proper balance of plants within a lake and still retain the lake's recreational and economic importance. Aquatic plant management programs have two phases: long-term management (nutrient control), and short-term management…

Protozoa interaction with aquatic invertebrate: interest for watercourses biomonitoring.

PubMed

Palos Ladeiro, M; Bigot, A; Aubert, D; Hohweyer, J; Favennec, L; Villena, I; Geffard, A

2013-02-01

Toxoplasma gondii, Cryptosporidium parvum, and Giardia duodenalis are human waterborne protozoa. These worldwide parasites had been detected in various watercourses as recreational, surface, drinking, river, and seawater. As of today, water protozoa detection was based on large water filtration and on sample concentration. Another tool like aquatic invertebrate parasitism could be used for sanitary and environmental biomonitoring. In fact, organisms like filter feeders could already filtrate and concentrate protozoa directly in their tissues in proportion to ambient concentration. So molluscan shellfish can be used as a bioindicator of protozoa contamination level in a site since they were sedentary. Nevertheless, only a few researches had focused on nonspecific parasitism like protozoa infection on aquatic invertebrates. Objectives of this review are twofold: Firstly, an overview of protozoa in worldwide water was presented. Secondly, current knowledge of protozoa parasitism on aquatic invertebrates was detailed and the lack of data of their biological impact was pointed out.

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

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

Soil microbial structure and function post-volcanic eruption on Kasatochi Island and regional controls on microbial heterogeneity

NASA Astrophysics Data System (ADS)

Zeglin, L. H.; Rainey, F.; Wang, B.; Waythomas, C.; Talbot, S. L.

2013-12-01

Microorganisms are abundant and diverse in soil and their integrated activity drives nutrient cycling on the ecosystem scale. Organic matter (OM) inputs from plant production support microbial heterotrophic life, and soil geochemistry constrains microbial activity and diversity. As vegetation and soil develops over time, these factors change, modifying the controls on microbial heterogeneity. Following a volcanic eruption, ash deposition creates new surfaces where both organismal growth and weathering processes are effectively reset. The trajectory of microbial community development following this disturbance depends on both organic matter accumulation and geochemical constraints. Also, dispersal of microbial cells to the sterile ash surface may determine microbial community succession. The Aleutian Islands (Alaska, USA) are a dynamic volcanic region, with active and dormant volcanoes distributed across the volcanic arc. One of these volcanoes, Kasatochi, erupted violently in August 2008, burying a small lush island in pryoclastic flows and fine ash. Since, plants and birds are beginning to re-establish on developing surfaces, including legacy soils exposed by rapid erosion of pyroclastic deposits, suggesting that recovery of microbial life is also proceeding. However, soil microbial diversity and function has not been examined on Kasatochi Island or across the greater Aleutian region. The project goal is to address these questions: How is soil microbial community structure and function developing following the Kasatochi eruption? What is the relative importance of dispersal, soil OM and geochemistry to microbial community heterogeneity across the Aleutians? Surface mineral soil (20-cm depth) samples were collected from Kasatochi Island in summer 2013, five years after the 2008 eruption, and from eight additional Aleutian islands. On Kasatochi, pryoclastic deposits, exposed legacy soils supporting regrowth of remnant dune wild-rye (Leymus mollis) and mesic meadow

Real-time monitoring of subsurface microbial metabolism with graphite electrodes

DOE PAGES

Wardman, Colin; Nevin, Kelly P.; Lovley, Derek R.

2014-11-21

Monitoring in situ microbial activity in anoxic submerged soils and aquatic sediments can be labor intensive and technically difficult, especially in dynamic environments in which a record of changes in microbial activity over time is desired. Microbial fuel cell concepts have previously been adapted to detect changes in the availability of relatively high concentrations of organic compounds in waste water but, in most soils and sediments, rates of microbial activity are not linked to the concentrations of labile substrates, but rather to the turnover rates of the substrate pools with steady state concentrations in the nM-μ M range. In ordermore » to determine whether levels of current produced at a graphite anode would correspond to the rates of microbial metabolism in anoxic sediments, small graphite anodes were inserted in sediment cores and connected to graphite brush cathodes in the overlying water. Currents produced were compared with the rates of [2- 14C]-acetate metabolism. There was a direct correlation between current production and the rate that [2- 14C]-acetate was metabolized to 14CO 2 and 14CH 4 in sediments in which Fe(III) reduction, sulfate reduction, or methane production was the predominant terminal electron-accepting process. At comparable acetate turnover rates, currents were higher in the sediments in which sulfate-reduction or Fe(III) reduction predominated than in methanogenic sediments. This was attributed to reduced products (Fe(II), sulfide) produced at distance from the anode contributing to current production in addition to the current that was produced from microbial oxidation of organic substrates with electron transfer to the anode surface in all three sediment types. In conclusion, the results demonstrate that inexpensive graphite electrodes may provide a simple strategy for real-time monitoring of microbial activity in a diversity of anoxic soils and sediments.« less

Mercury bioaccumulation in bats reflects dietary connectivity to aquatic food webs.

PubMed

Becker, Daniel J; Chumchal, Matthew M; Broders, Hugh G; Korstian, Jennifer M; Clare, Elizabeth L; Rainwater, Thomas R; Platt, Steven G; Simmons, Nancy B; Fenton, M Brock

2018-02-01

Mercury (Hg) is a persistent and widespread heavy metal with neurotoxic effects in wildlife. While bioaccumulation of Hg has historically been studied in aquatic food webs, terrestrial consumers can become contaminated with Hg when they feed on aquatic organisms (e.g., emergent aquatic insects, fish, and amphibians). However, the extent to which dietary connectivity to aquatic ecosystems can explain patterns of Hg bioaccumulation in terrestrial consumers has not been well studied. Bats (Order: Chiroptera) can serve as a model system for illuminating the trophic transfer of Hg given their high dietary diversity and foraging links to both aquatic and terrestrial food webs. Here we quantitatively characterize the dietary correlates of long-term exposure to Hg across a diverse local assemblage of bats in Belize and more globally across bat species from around the world with a comparative analysis of hair samples. Our data demonstrate considerable interspecific variation in hair total Hg concentrations in bats that span three orders of magnitude across species, ranging from 0.04 mg/kg in frugivorous bats (Artibeus spp.) to 145.27 mg/kg in the piscivorous Noctilio leporinus. Hg concentrations showed strong phylogenetic signal and were best explained by dietary connectivity of bat species to aquatic food webs. Our results highlight that phylogeny can be predictive of Hg concentrations through similarity in diet and how interspecific variation in feeding strategies influences chronic exposure to Hg and enables movement of contaminants from aquatic to terrestrial ecosystems. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

The National Nonindigenous Aquatic Species Database

USGS Publications Warehouse

Neilson, Matthew E.; Fuller, Pamela L.

2012-01-01

The U.S. Geological Survey (USGS) Nonindigenous Aquatic Species (NAS) Program maintains a database that monitors, records, and analyzes sightings of nonindigenous aquatic plant and animal species throughout the United States. The program is based at the USGS Wetland and Aquatic Research Center in Gainesville, Florida.The initiative to maintain scientific information on nationwide occurrences of nonindigenous aquatic species began with the Aquatic Nuisance Species Task Force, created by Congress in 1990 to provide timely information to natural resource managers. Since then, the NAS database has been a clearinghouse of information for confirmed sightings of nonindigenous, also known as nonnative, aquatic species throughout the Nation. The database is used to produce email alerts, maps, summary graphs, publications, and other information products to support natural resource managers.

Contribution of microbial carbon to soil fractions: significance of diverse microbial group biochemistry

NASA Astrophysics Data System (ADS)

Throckmorton, H.; Bird, J. A.; Dane, L.; Firestone, M. K.; Horwath, W. R.

2011-12-01

The importance of diverse microbial groups to soil C maintenance is still a matter of debate. This study follows the turnover of 13C labeled nonliving residues from diverse microbial groups into soil physical fractions in situ in a temperate forest in California (CA) and a tropical forest in Puerto Rico (PR), during 5 sampling points per site- over a 3 and 2 year period, respectively. Microbial groups include fungi, actinomycetes, Gm(+) bacteria, and Gm(-) bacteria, isolated from CA and PR soils to obtain temperate and tropical isolates composited of 3-4 species per group. The selected density fractionation approach isolated: a "light fraction" (LF), non-mineral aggregate "occluded fraction" (OF), and a "mineral bound fraction" (MF). Pyrolysis gas chromatography mass spectrometry (Py-GC-MS) was employed to characterize microbial group isolates, whole soils, and fractions. Microbial isolates contained unique biochemical fingerprints: temperate and tropical fungi and tropical Gm(-) were characterized by a low abundance of phenol, benzene, and N-compounds compared with other microbial group isolates. Py-GC-MS revealed compositional differences among soil fractions at both sites, likely attributed to differences in the decomposition stage and C source material (ie. plant vs. microbial). For both sites, benzene and N-compounds were greatest in the MF; lignin and phenol compounds were greatest in the LF; and lipids were greatest in the OF. The trend for polysaccharides differed between sites, with the greatest concentration in the CA OF; and for PR with the lowest concentration in the OF, and similar concentrations in the LF and MF. SOM chemistry was most similar between sites in the LF, compared with the OF and MF, suggesting that differences in SOM chemistry between sites may be more attributed to differential decomposition processes than unique litter quality inputs. A substantial portion of microbial C moved from the LF into the OF, and the MF by the first sampling

Dining local: the microbial diet of a snail that grazes microbial communities is geographically structured.

PubMed

O'Rorke, Richard; Cobian, Gerald M; Holland, Brenden S; Price, Melissa R; Costello, Vincent; Amend, Anthony S

2015-05-01

Achatinella mustelina is a critically endangered tree snail that subsists entirely by grazing microbes from leaf surfaces of native trees. Little is known about the fundamental aspects of these microbe assemblages: not taxonomic composition, how this varies with host plant or location, nor whether snails selectively consume microbes. To address these questions, we collected 102 snail faecal samples as a proxy for diet, and 102 matched-leaf samples from four locations. We used Illumina amplicon sequencing to determine bacterial and fungal community composition. Microbial community structure was significantly distinct between snail faeces and leaf samples, but the same microbes occurred in both. We conclude that snails are not 'picky' eaters at the microbial level, but graze the surface of whatever plant they are on. In a second experiment, the gut was dissected from non-endangered native tree snails in the same family as Achatinella to confirm that faecal samples reflect gut contents. Over 60% of fungal reads were shared between faeces, gut and leaf samples. Overall, location, sample type (faeces or leaf) and host plant identity all significantly explained the community composition and variation among samples. Understanding the microbial ecology of microbes grazed by tree snails enables effective management when conservation requires captive breeding or field relocation. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

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.

Faunistic Study of the Aquatic Arthropods in a Tourism Area in Northern Iran

PubMed Central

Shaeghi, Mansoureh; Dehghan, Hossein; Pakdad, Kamran; Nikpour, Fatemeh; Absavaran, Azad; Sofizadeh, Aioub; Akhavan, Amir Ahmad; Vatandoost, Hassan; Aghai-Afshar, Abbass

2017-01-01

Background: Aquatic insects are very abundant and divers groups of insects that are associated with an aquatic or semiaquatic environment in one or more of their life stages. These insects have been, in some cases, well studied because they are vectors of several diseases. This is the first comprehensive faunistic study of aquatic insects from Babol County. The results may provide basic data for further taxonomic and ecological studies of aquatic insects as biological control agent or classification of water quality for the country. Methods: The specimens were collected using different methods including: D-frame net collector, standard mosquito dipper (350ml), Sweep-Netting and plastic pipette. Sampling carried out in different part of breading places in several times. Results: During this study a total of 196 aquatic specimens were collected from different habitats and were morphologically identified including 18 families classified in 6 orders: Diptera, Trichoptera, Ephemeroptera, Plecoptera, Hemiptera and Odonata. Babol and Amol district in Mazandaran Province are located in humid climate regions with suitable ecological factors of humidity, moderate temperature and the variety of plant species. There are different species of aquatic insects in different habitats. Conclusion: The results will provide information for biodeveristy, species richness, their role for biological control as well as calcification of rivers based on abundance of aquatic insects. Therefore the understanding of ecological specifications of aquatic insects could provide a clue for further Arthropod-borne disease control. Additionally aquatic insect could be used for classification of water bodies PMID:29062853

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.

Characterization of Serpentine Samples from the Coast Range Ophiolite Microbial Observatory with μ-FTIR and XRD. ­­

NASA Astrophysics Data System (ADS)

Sousa, A.; Cardace, D.

2017-12-01

Serpentinizing systems hold much promise as potentially habitable environments in diverse planetary settings. They involve abundant and simple ingredients (i.e., the mineral olivine, liquid water), support subsurface microbial communities on Earth (Crespo-Medina et al. 2014; Suzuki et al. 2014; Kelley et al. 2005) and are thought to occur elsewhere in our solar system such as Mars (Schulte et al. 2006; Ehlmann et al. 2010)and possibly ocean worlds (Waite et al. 2017; Vance 2009). Although geochemical and microbial data collection continues in serpentinizing systems, the identification and resolution of potential biosignatures in serpentinites are not yet clear. Specifically, the micro-scale mineralogical contexts in which cell fragments or biofilm residues may be formed and preserved is lacking. Here we report preliminary transmission and reflection mode μ-FTIR spectral maps and XRD diffractograms, obtained with instruments relevant to robotic exploration missions (Blake et al. 2012; Igisu et al. 2009; Leroi et al. 2009). Samples analyzed include ultramafic rock and constituent mineral standards (e.g., olivine) and rocks collected from near surface sites associated with the NASA Astrobiology Institute-funded initiative, the Coast Range Ophiolite Microbial Observatory (CROMO), in Lower Lake, CA (Cardace et al. 2013). These new results provide co-registered, complementary data on astrobiologically important rock and mineral phases related to serpentinization (Crespo-Medina et al. 2014; Twing et al. 2017). Future work will leverage this data set in microbial colonization experiments aimed at parsing background organic loads in serpentinites from surficial/fracture-localized modern biofilm signatures.

Inferring nutrient loading of estuarine systems by remote sensing of aquatic vegetation

NASA Technical Reports Server (NTRS)

Anderson, R. R.

1978-01-01

THe use of remote sensing to record algal and vascular aquatic plant growths in estuarine waters is discussed. A technique is proposed that uses a combination of data to hierarchically classify watersheds with regard to severity of potential pollution. Specific nonpoint sources of nutrients in tributaries of the watershed are identified with lower altitude photography of vegetation and selected ground sampling. It is concluded that excessive growths of some aquatic plants may be related to nutrient pollution.

Molybdenum limitation of microbial nitrogen assimilation in aquatic ecosystems and pure cultures

PubMed Central

Glass, Jennifer B.; Axler, Richard P.; Chandra, Sudeep; Goldman, Charles R.

2012-01-01

Molybdenum (Mo) is an essential micronutrient for biological assimilation of nitrogen gas and nitrate because it is present in the cofactors of nitrogenase and nitrate reductase enzymes. Although Mo is the most abundant transition metal in seawater (107 nM), it is present in low concentrations in most freshwaters, typically <20 nM. In 1960, it was discovered that primary productivity was limited by Mo scarcity (2–4 nM) in Castle Lake, a small, meso-oligotrophic lake in northern California. Follow up studies demonstrated that Mo also limited primary productivity in lakes in New Zealand, Alaska, and the Sierra Nevada. Research in the 1970s and 1980s showed that Mo limited primary productivity and nitrate uptake in Castle Lake only during periods of the growing season when nitrate concentrations were relatively high because ammonium assimilation does not require Mo. In the years since, research has shifted to investigate whether Mo limitation also occurs in marine and soil environments. Here we review studies of Mo limitation of nitrogen assimilation in natural microbial communities and pure cultures. We also summarize new data showing that the simultaneous addition of Mo and nitrate causes increased activity of proteins involved in nitrogen assimilation in the hypolimnion of Castle Lake when ammonium is scarce. Furthermore, we suggest that meter-scale Mo and oxygen depth profiles from Castle Lake are consistent with the hypothesis that nitrogen-fixing cyanobacteria in freshwater periphyton communities have higher Mo requirements than other microbial communities. Finally, we present topics for future research related to Mo bioavailability through time and with changing oxidation state. PMID:22993512

Aquatic Plant Control Research Program: Literature Review of Economic Valuation of Aquatic Plant Control

DTIC Science & Technology

1991-02-01

200 words) Aquatic plant control is necessary to maintain the flow of benefits for which water resources projects are constructed and operated (e.g...but little work has been performed by the Corps to evaluate the economic benefits resulting from aquatic plant control programs. This report reviewed...the applicability of the project evaluation guidance, Principles and Guidelines (P&G), for the eval- uation of aquatic plant control benefits . It was

Preliminary biological sampling of GT3 and BT1 cores and the microbial community dynamics of existing subsurface wells

NASA Astrophysics Data System (ADS)

Kraus, E. A.; Stamps, B. W.; Rempfert, K. R.; Ellison, E. T.; Nothaft, D. B.; Boyd, E. S.; Templeton, A. S.; Spear, J. R.

2017-12-01

Subsurface microbial life is poorly understood but potentially very important to the search for life on other planets as well as increasing our understanding of Earth's geobiological processes. Fluids and rocks of actively serpentinizing subsurface environments are a recent target of biological study due to their apparent ubiquity across the solar system. Areas of serpentinization can contain high concentrations of molecular hydrogen, H2, that can serve as the dominant fuel source for subsurface microbiota. Working with the Oman Drilling Project, DNA and RNA were extracted from fluids of seven alkaline wells and two rock cores from drill sites GT3 and BT1 within the Samail ophiolite. DNA and cDNA (produced via reverse transcription from the recovered RNA) were sequenced using universal primers to identify microbial life across all three domains. Alkaline subsurface fluids support a microbial community that changes with pH and host-rock type. In peridotite with pH values of >11, wells NSHQ 14 and WAB 71 have high relative abundances of Meiothermus, Methanobacterium, the family Nitrospiraceae, and multiple types of the class Dehalococcoidia. While also hosted in peridotite but at pH 8.5, wells WAB 104 and 105 have a distinct, more diverse microbial community. This increased variance in community make-up is seen in wells that sit near/at the contact of gabbro and peridotite formations as well. Core results indicate both sampled rock types host a very low biomass environment subject to multiple sources of contamination during the drilling process. Suggestions for contaminant reduction, such as having core handlers wear nitrile gloves and flame-sterilizing the outer surfaces of core rounds for biological sampling, would have minimal impact to overall ODP coreflow and maximize the ability to better understand in situ microbiota in this low-biomass serpentinizing subsurface environment. While DNA extraction was successful with gram amounts of crushed rock, much can be

Stoichiometry of microbial carbon use efficiency in soils

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

Sinsabaugh, Robert L.; Turner, Benjamin L.; Talbot, Jennifer M.

The carbon use efficiency (CUE) of microbial communities partitions the flow of C from primary producers to the atmosphere, decomposer food webs, and soil C stores. CUE, usually defined as the ratio of growth to assimilation, is a critical parameter in ecosystem models, but is seldom measured directly in soils because of the methodological difficulty of measuring in situ rates of microbial growth and respiration. Alternatively, CUE can be estimated indirectly from the elemental stoichiometry of organic matter and microbial biomass, and the ratios of C to nutrient-acquiring ecoenzymatic activities. In this paper, we used this approach to estimate andmore » compare microbial CUE in >2000 soils from a broad range of ecosystems. Mean CUE based on C:N stoichiometry was 0.269 ± 0.110 (mean ± SD). A parallel calculation based on C:P stoichiometry yielded a mean CUE estimate of 0.252 ± 0.125. The mean values and frequency distributions were similar to those from aquatic ecosystems, also calculated from stoichiometric models, and to those calculated from direct measurements of bacterial and fungal growth and respiration. CUE was directly related to microbial biomass C with a scaling exponent of 0.304 (95% CI 0.237–0.371) and inversely related to microbial biomass P with a scaling exponent of -0.234 (95% CI -0.289 to -0.179). Relative to CUE, biomass specific turnover time increased with a scaling exponent of 0.509 (95% CI 0.467–0.551). CUE increased weakly with mean annual temperature. CUE declined with increasing soil pH reaching a minimum at pH 7.0, then increased again as soil pH approached 9.0, a pattern consistent with pH trends in the ratio of fungal : bacteria abundance and growth. Structural equation models that related geographic variables to CUE component variables showed the strongest connections for paths linking latitude and pH to β-glucosidase activity and soil C:N:P ratios. Finally, the integration of stoichiometric and metabolic models provides a

Stoichiometry of microbial carbon use efficiency in soils

DOE PAGES

Sinsabaugh, Robert L.; Turner, Benjamin L.; Talbot, Jennifer M.; ...

2016-03-23

The carbon use efficiency (CUE) of microbial communities partitions the flow of C from primary producers to the atmosphere, decomposer food webs, and soil C stores. CUE, usually defined as the ratio of growth to assimilation, is a critical parameter in ecosystem models, but is seldom measured directly in soils because of the methodological difficulty of measuring in situ rates of microbial growth and respiration. Alternatively, CUE can be estimated indirectly from the elemental stoichiometry of organic matter and microbial biomass, and the ratios of C to nutrient-acquiring ecoenzymatic activities. In this paper, we used this approach to estimate andmore » compare microbial CUE in >2000 soils from a broad range of ecosystems. Mean CUE based on C:N stoichiometry was 0.269 ± 0.110 (mean ± SD). A parallel calculation based on C:P stoichiometry yielded a mean CUE estimate of 0.252 ± 0.125. The mean values and frequency distributions were similar to those from aquatic ecosystems, also calculated from stoichiometric models, and to those calculated from direct measurements of bacterial and fungal growth and respiration. CUE was directly related to microbial biomass C with a scaling exponent of 0.304 (95% CI 0.237–0.371) and inversely related to microbial biomass P with a scaling exponent of -0.234 (95% CI -0.289 to -0.179). Relative to CUE, biomass specific turnover time increased with a scaling exponent of 0.509 (95% CI 0.467–0.551). CUE increased weakly with mean annual temperature. CUE declined with increasing soil pH reaching a minimum at pH 7.0, then increased again as soil pH approached 9.0, a pattern consistent with pH trends in the ratio of fungal : bacteria abundance and growth. Structural equation models that related geographic variables to CUE component variables showed the strongest connections for paths linking latitude and pH to β-glucosidase activity and soil C:N:P ratios. Finally, the integration of stoichiometric and metabolic models provides a

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

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.

Temporal variation in airborne microbial populations and microbially-derived allergens in a tropical urban landscape

NASA Astrophysics Data System (ADS)

Woo, Anthony C.; Brar, Manreetpal S.; Chan, Yuki; Lau, Maggie C. Y.; Leung, Frederick C. C.; Scott, James A.; Vrijmoed, Lilian L. P.; Zawar-Reza, Peyman; Pointing, Stephen B.

2013-08-01

The microbial component of outdoor aerosols was assessed along a gradient of urban development from inner-city to rural in the seasonal-tropical metropolis of Hong Kong. Sampling over a continuous one-year period was conducted, with molecular analyses to characterize bacterial and eukaryal microbial populations, immuno-assays to detect microbially-derived allergens and extensive environmental and meteorological observations. The data revealed bio-aerosol populations were not significantly impacted by the level of urban development as measured by anthropogenic pollutants and human population levels, but instead exhibited a strong seasonal trend related to general climatic variables. We applied back-trajectory analysis to establish sources of air masses and this allowed further explanation of urban bio-aerosols largely in terms of summer-marine and winter-continental origins. We also evaluated bio-aerosols for the potential to detect human health threats. Many samples supported bacterial and fungal phylotypes indicative of known pathogenic taxa, together with common indicators of human presence. The occurrence of allergenic endotoxins and beta-glucans generally tracked trends in microbial populations, with levels known to induce symptoms detected during summer months when microbial loading was higher. This strengthens calls for bio-aerosols to be considered in future risk assessments and surveillance of air quality, along with existing chemical and particulate indices.

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.

The ocean sampling day consortium.

PubMed

Kopf, Anna; Bicak, Mesude; Kottmann, Renzo; Schnetzer, Julia; Kostadinov, Ivaylo; Lehmann, Katja; Fernandez-Guerra, Antonio; Jeanthon, Christian; Rahav, Eyal; Ullrich, Matthias; Wichels, Antje; Gerdts, Gunnar; Polymenakou, Paraskevi; Kotoulas, Giorgos; Siam, Rania; Abdallah, Rehab Z; Sonnenschein, Eva C; Cariou, Thierry; O'Gara, Fergal; Jackson, Stephen; Orlic, Sandi; Steinke, Michael; Busch, Julia; Duarte, Bernardo; Caçador, Isabel; Canning-Clode, João; Bobrova, Oleksandra; Marteinsson, Viggo; Reynisson, Eyjolfur; Loureiro, Clara Magalhães; Luna, Gian Marco; Quero, Grazia Marina; Löscher, Carolin R; Kremp, Anke; DeLorenzo, Marie E; Øvreås, Lise; Tolman, Jennifer; LaRoche, Julie; Penna, Antonella; Frischer, Marc; Davis, Timothy; Katherine, Barker; Meyer, Christopher P; Ramos, Sandra; Magalhães, Catarina; Jude-Lemeilleur, Florence; Aguirre-Macedo, Ma Leopoldina; Wang, Shiao; Poulton, Nicole; Jones, Scott; Collin, Rachel; Fuhrman, Jed A; Conan, Pascal; Alonso, Cecilia; Stambler, Noga; Goodwin, Kelly; Yakimov, Michael M; Baltar, Federico; Bodrossy, Levente; Van De Kamp, Jodie; Frampton, Dion Mf; Ostrowski, Martin; Van Ruth, Paul; Malthouse, Paul; Claus, Simon; Deneudt, Klaas; Mortelmans, Jonas; Pitois, Sophie; Wallom, David; Salter, Ian; Costa, Rodrigo; Schroeder, Declan C; Kandil, Mahrous M; Amaral, Valentina; Biancalana, Florencia; Santana, Rafael; Pedrotti, Maria Luiza; Yoshida, Takashi; Ogata, Hiroyuki; Ingleton, Tim; Munnik, Kate; Rodriguez-Ezpeleta, Naiara; Berteaux-Lecellier, Veronique; Wecker, Patricia; Cancio, Ibon; Vaulot, Daniel; Bienhold, Christina; Ghazal, Hassan; Chaouni, Bouchra; Essayeh, Soumya; Ettamimi, Sara; Zaid, El Houcine; Boukhatem, Noureddine; Bouali, Abderrahim; Chahboune, Rajaa; Barrijal, Said; Timinouni, Mohammed; El Otmani, Fatima; Bennani, Mohamed; Mea, Marianna; Todorova, Nadezhda; Karamfilov, Ventzislav; Ten Hoopen, Petra; Cochrane, Guy; L'Haridon, Stephane; Bizsel, Kemal Can; Vezzi, Alessandro; Lauro, Federico M; Martin, Patrick; Jensen, Rachelle M; Hinks, Jamie; Gebbels, Susan; Rosselli, Riccardo; De Pascale, Fabio; Schiavon, Riccardo; Dos Santos, Antonina; Villar, Emilie; Pesant, Stéphane; Cataletto, Bruno; Malfatti, Francesca; Edirisinghe, Ranjith; Silveira, Jorge A Herrera; Barbier, Michele; Turk, Valentina; Tinta, Tinkara; Fuller, Wayne J; Salihoglu, Ilkay; Serakinci, Nedime; Ergoren, Mahmut Cerkez; Bresnan, Eileen; Iriberri, Juan; Nyhus, Paul Anders Fronth; Bente, Edvardsen; Karlsen, Hans Erik; Golyshin, Peter N; Gasol, Josep M; Moncheva, Snejana; Dzhembekova, Nina; Johnson, Zackary; Sinigalliano, Christopher David; Gidley, Maribeth Louise; Zingone, Adriana; Danovaro, Roberto; Tsiamis, George; Clark, Melody S; Costa, Ana Cristina; El Bour, Monia; Martins, Ana M; Collins, R Eric; Ducluzeau, Anne-Lise; Martinez, Jonathan; Costello, Mark J; Amaral-Zettler, Linda A; Gilbert, Jack A; Davies, Neil; Field, Dawn; Glöckner, Frank Oliver

2015-01-01

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

Predicting Hydrologic Function With Aquatic Gene Fragments

NASA Astrophysics Data System (ADS)

Good, S. P.; URycki, D. R.; Crump, B. C.

2018-03-01

Recent advances in microbiology techniques, such as genetic sequencing, allow for rapid and cost-effective collection of large quantities of genetic information carried within water samples. Here we posit that the unique composition of aquatic DNA material within a water sample contains relevant information about hydrologic function at multiple temporal scales. In this study, machine learning was used to develop discharge prediction models trained on the relative abundance of bacterial taxa classified into operational taxonomic units (OTUs) based on 16S rRNA gene sequences from six large arctic rivers. We term this approach "genohydrology," and show that OTU relative abundances can be used to predict river discharge at monthly and longer timescales. Based on a single DNA sample from each river, the average Nash-Sutcliffe efficiency (NSE) for predicted mean monthly discharge values throughout the year was 0.84, while the NSE for predicted discharge values across different return intervals was 0.67. These are considerable improvements over predictions based only on the area-scaled mean specific discharge of five similar rivers, which had average NSE values of 0.64 and -0.32 for seasonal and recurrence interval discharge values, respectively. The genohydrology approach demonstrates that genetic diversity within the aquatic microbiome is a large and underutilized data resource with benefits for prediction of hydrologic function.

Microbial Communities in Pre-Columbian Coprolites

PubMed Central

Santiago-Rodriguez, Tasha M.; Narganes-Storde, Yvonne M.; Chanlatte, Luis; Crespo-Torres, Edwin; Toranzos, Gary A.; Jimenez-Flores, Rafael; Hamrick, Alice; Cano, Raul J.

2013-01-01

The study of coprolites from earlier cultures represents a great opportunity to study an “unaltered” composition of the intestinal microbiota. To test this, pre-Columbian coprolites from two cultures, the Huecoid and Saladoid, were evaluated for the presence of DNA, proteins and lipids by cytochemical staining, human and/or dog-specific Bacteroides spp. by PCR, as well as bacteria, fungi and archaea using Terminal Restriction Fragment analyses. DNA, proteins and lipids, and human-specific Bacteroides DNA were detected in all coprolites. Multidimensional scaling analyses resulted in spatial arrangements of microbial profiles by culture, further supported by cluster analysis and ANOSIM. Differences between the microbial communities were positively correlated with culture, and SIMPER analysis indicated 68.8% dissimilarity between the Huecoid and Saladoid. Proteobacteria, Bacteroidetes and methanogens were found in all coprolite samples. Propionebacteria, Shewanella and lactic acid bacteria dominated in the Huecoid samples, while Acidobacteria, and peptococci were dominant in Saladoid samples. Yeasts, including Candida albicans and Crypotococcus spp. were found in all samples. Basidiomycetes were the most notable fungi in Huecoid samples while Ascomycetes predominated in Saladoid samples, suggesting differences in dietary habits. Our study provides an approach for the study of the microbial communities of coprolite samples from various cultures. PMID:23755194

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

Aquatic Acoustic Metrics Interface Utility for Underwater Sound Monitoring and Analysis

PubMed Central

Ren, Huiying; Halvorsen, Michele B.; Deng, Zhiqun Daniel; Carlson, Thomas J.

2012-01-01

Fishes and marine mammals may suffer a range of potential effects from exposure to intense underwater sound generated by anthropogenic activities such as pile driving, shipping, sonars, and underwater blasting. Several underwater sound recording (USR) devices have been built to acquire samples of the underwater sound generated by anthropogenic activities. Software becomes indispensable for processing and analyzing the audio files recorded by these USRs. In this paper, we provide a detailed description of a new software package, the Aquatic Acoustic Metrics Interface (AAMI), specifically designed for analysis of underwater sound recordings to provide data in metrics that facilitate evaluation of the potential impacts of the sound on aquatic animals. In addition to the basic functions, such as loading and editing audio files recorded by USRs and batch processing of sound files, the software utilizes recording system calibration data to compute important parameters in physical units. The software also facilitates comparison of the noise sound sample metrics with biological measures such as audiograms of the sensitivity of aquatic animals to the sound, integrating various components into a single analytical frame. The features of the AAMI software are discussed, and several case studies are presented to illustrate its functionality. PMID:22969353

Microbial Inactivation for Safe and Rapid Diagnostics of Infectious Samples ▿ †

PubMed Central

Sagripanti, Jose-Luis; Hülseweh, Birgit; Grote, Gudrun; Voß, Luzie; Böhling, Katrin; Marschall, Hans-Jürgen

2011-01-01

The high risk associated with biological threat agents dictates that any suspicious sample be handled under strict surety and safety controls and processed under high-level containment in specialized laboratories. This study attempted to find a rapid, reliable, and simple method for the complete inactivation of a wide range of pathogens, including spores, vegetative bacteria, and viruses, while preserving microbial nucleic acid fragments suitable for PCRs and proteinaceous epitopes for detection by immunoassays. Formaldehyde, hydrogen peroxide, and guanidium thiocyanate did not completely inactivate high titers of bacterial spores or viruses after 30 min at 21°C. Glutaraldehyde and sodium hypochlorite showed high microbicidal activity but obliterated the PCR or enzyme-linked immunosorbent assay (ELISA) detection of bacterial spores or viruses. High-level inactivation (more than 6 log10) of bacterial spores (Bacillus atrophaeus), vegetative bacteria (Pseudomonas aeruginosa), an RNA virus (the alphavirus Pixuna virus), or a DNA virus (the orthopoxvirus vaccinia virus) was attained within 30 min at 21°C by treatment with either peracetic acid or cupric ascorbate with minimal hindrance of subsequent PCR tests and immunoassays. The data described here should provide the basis for quickly rendering field samples noninfectious for further analysis under lower-level containment and considerably lower cost. PMID:21856830

Methanogenic and Sulfate-Reducing Activities in a Hypersaline Microbial Mat and Associated Microbial Diversity.

PubMed

Cadena, Santiago; García-Maldonado, José Q; López-Lozano, Nguyen E; Cervantes, Francisco J

2018-05-01

Methanogenesis and sulfate reduction are important microbial processes in hypersaline environments. However, key aspects determining substrate competition between these microbial processes have not been well documented. We evaluated competitive and non-competitive substrates for stimulation of both processes through microcosm experiments of hypersaline microbial mat samples from Guerrero Negro, Baja California Sur, Mexico, and we assessed the effect of these substrates on the microbial community composition. Methylotrophic methanogenesis evidenced by sequences belonging to methanogens of the family Methanosarcinaceae was found as the dominant methanogenic pathway in the studied hypersaline microbial mat. Nevertheless, our results showed that incubations supplemented with acetate and lactate, performed in absence of sulfate, also produced methane after 40 days of incubation, apparently driven by hydrogenotrophic methanogens affiliated to the family Methanomicrobiaceae. Sulfate reduction was mainly stimulated by addition of acetate and lactate; however, after 40 days of incubation, an increase of the H 2 S concentrations in microcosms amended with trimethylamine and methanol was also observed, suggesting that these substrates are putatively used for sulfate reduction. Moreover, 16S rRNA gene sequencing analysis showed remarkable differences in the microbial community composition among experimental treatments. In the analyzed sample amended with acetate, sulfate-reducing bacteria (SRB) belonging to the family Desulfobacteraceae were dominant, while members of Desulfohalobiaceae, Desulfomicrobiaceae, and Desulfovibrionaceae were found in the incubation with lactate. Additionally, we detected an unexpected high abundance of unclassified Hydrogenedentes (near 25%) in almost all the experimental treatments. This study contributes to better understand methanogenic and sulfate-reducing activities, which play an important role in the functioning of hypersaline environments.

Microbial source tracking: a forensic technique for microbial source identification?

PubMed

Stapleton, Carl M; Wyer, Mark D; Kay, David; Crowther, John; McDonald, Adrian T; Walters, Martin; Gawler, Andrew; Hindle, Terry

2007-05-01

As the requirements of the Water Framework Directive (WFD) and the US Clean Water Act (USCWA) for the maintenance of microbiological water quality in 'protected areas' highlight, there is a growing recognition that integrated management of point and diffuse sources of microbial pollution is essential. New information on catchment microbial dynamics and, in particular, the sources of faecal indicator bacteria found in bathing and shellfish harvesting waters is a pre-requisite for the design of any 'programme of measures' at the drainage basin scale to secure and maintain compliance with existing and new health-based microbiological standards. This paper reports on a catchment-scale microbial source tracking (MST) study in the Leven Estuary drainage basin, northwest England, an area for which quantitative faecal indicator source apportionment empirical data and land use information were also collected. Since previous MST studies have been based on laboratory trials using 'manufactured' samples or analyses of spot environmental samples without the contextual microbial flux data (under high and low flow conditions) and source information, such background data are needed to evaluate the utility of MST in USCWA total maximum daily load (TMDL) assessments or WFD 'Programmes of Measures'. Thus, the operational utility of MST remains in some doubt. The results of this investigation, using genotyping of Bacteroidetes using polymerase chain reaction (PCR) and male-specific ribonucleic acid coliphage (F + RNA coliphage) using hybridisation, suggest some discrimination is possible between livestock- and human-derived faecal indicator concentrations but, in inter-grade areas, the degree to which the tracer picture reflected the land use pattern and probable faecal indicator loading were less distinct. Interestingly, the MST data was more reliable on high flow samples when much of the faecal indicator flux from catchment systems occurs. Whilst a useful supplementary tool, the MST

Efficacy of trap modifications for increasing capture rates of aquatic snakes in floating aquatic funnel traps

USGS Publications Warehouse

Halstead, Brian J.; Wylie, Glenn D.; Casazza, Michael L.

2013-01-01

Increasing detection and capture probabilities of rare or elusive herpetofauna of conservation concern is important to inform the scientific basis for their management and recovery. The Giant Gartersnake (Thamnophis gigas) is an example of a secretive, wary, and generally difficult-to-sample species about which little is known regarding its patterns of occurrence and demography. We therefore evaluated modifications to existing traps to increase the detection and capture probabilities of the Giant Gartersnake to improve the precision with which occurrence, abundance, survival, and other demographic parameters are estimated. We found that adding a one-way valve constructed of cable ties to the small funnel opening of traps and adding hardware cloth extensions to the wide end of funnels increased capture rates of the Giant Gartersnake by 5.55 times (95% credible interval = 2.45–10.51) relative to unmodified traps. The effectiveness of these modifications was insensitive to the aquatic habitat type in which they were deployed. The snout-vent length of the smallest and largest captured snakes did not vary among trap modifications. These trap modifications are expected to increase detection and capture probabilities of the Giant Gartersnake, and show promise for increasing the precision with which demographic parameters can be estimated for this species. We anticipate that the trap modifications found effective in this study will be applicable to a variety of aquatic and semi-aquatic reptiles and amphibians and improve conservation efforts for these species.

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.

Spatially resolved sampling reveals dynamic microbial communities in rising hydrothermal plumes across a back-arc basin.

PubMed

Sheik, Cody S; Anantharaman, Karthik; Breier, John A; Sylvan, Jason B; Edwards, Katrina J; Dick, Gregory J

2015-06-01

Within hydrothermal plumes, chemosynthetic processes and microbe-mineral interactions drive primary productivity in deep-ocean food webs and may influence transport of elements such as iron. However, the source of microorganisms in plumes and the factors governing how these communities assemble are poorly understood, in part due to lack of data from early stages of plume formation. In this study, we examined microbial community composition of rising hydrothermal plumes from five vent fields along the Eastern Lau Spreading Center. Seafloor and plume microbial communities were significantly dissimilar and shared few phylotypes. Plume communities were highly similar to each other with significant differences in community membership only between Kilo Moana and Mariner, two vents that are separated by extremes in depth, latitude and geochemistry. Systematic sampling of waters surrounding the vents revealed that species richness and phylogenetic diversity was typically highest near the vent orifice, implying mixing of microbial communities from the surrounding habitats. Above-plume background communities were primarily dominated by SAR11, SAR324 and MG-I Archaea, while SUP05, Sulfurovum, Sulfurimonas, SAR324 and Alteromonas were abundant in plume and near-bottom background communities. These results show that the ubiquitous water-column microorganisms populate plume communities, and that the composition of background seawater exerts primary influence on plume community composition, with secondary influence from geochemical and/or physical properties of vents. Many of these pervasive deep-ocean organisms are capable of lithotrophy, suggesting that they are poised to use inorganic electron donors encountered in hydrothermal plumes.

Spatially resolved sampling reveals dynamic microbial communities in rising hydrothermal plumes across a back-arc basin

PubMed Central

Sheik, Cody S; Anantharaman, Karthik; Breier, John A; Sylvan, Jason B; Edwards, Katrina J; Dick, Gregory J

2015-01-01

Within hydrothermal plumes, chemosynthetic processes and microbe–mineral interactions drive primary productivity in deep-ocean food webs and may influence transport of elements such as iron. However, the source of microorganisms in plumes and the factors governing how these communities assemble are poorly understood, in part due to lack of data from early stages of plume formation. In this study, we examined microbial community composition of rising hydrothermal plumes from five vent fields along the Eastern Lau Spreading Center. Seafloor and plume microbial communities were significantly dissimilar and shared few phylotypes. Plume communities were highly similar to each other with significant differences in community membership only between Kilo Moana and Mariner, two vents that are separated by extremes in depth, latitude and geochemistry. Systematic sampling of waters surrounding the vents revealed that species richness and phylogenetic diversity was typically highest near the vent orifice, implying mixing of microbial communities from the surrounding habitats. Above-plume background communities were primarily dominated by SAR11, SAR324 and MG-I Archaea, while SUP05, Sulfurovum, Sulfurimonas, SAR324 and Alteromonas were abundant in plume and near-bottom background communities. These results show that the ubiquitous water-column microorganisms populate plume communities, and that the composition of background seawater exerts primary influence on plume community composition, with secondary influence from geochemical and/or physical properties of vents. Many of these pervasive deep-ocean organisms are capable of lithotrophy, suggesting that they are poised to use inorganic electron donors encountered in hydrothermal plumes. PMID:25489728

COASTAL SUBMERGED VEGETATION: AQUATIC HABITAT RESEARCH

EPA Science Inventory

Aquatic vegetation is one of the most widespread and important types of aquatic habitat, in part because of the exceptional productivity of the plants. Aquatic vegetation also strongly influences local physical and chemical habitat conditions of significance to fish and shellfis...

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.

Aquatics for Disabled Persons.

ERIC Educational Resources Information Center

Priest, Louise

1983-01-01

Rising energy costs and staff reductions pose problems for those who direct aquatic programs for the disabled. At the same time, aquatics programs for the disabled are increasing in number, broadening in scope, and offering new opportunities for research and development of materials. (PP)

Cryobanking of aquatic species.

PubMed

Martínez-Páramo, Sonia; Horváth, Ákos; Labbé, Catherine; Zhang, Tiantian; Robles, Vanesa; Herráez, Paz; Suquet, Marc; Adams, Serean; Viveiros, Ana; Tiersch, Terrence R; Cabrita, Elsa

2017-04-01

This review is focused on the applications of genome cryobanking of aquatic species including freshwater and marine fish, as well as invertebrates. It also reviews the latest advances in cryobanking of model species, widely used by the scientific community worldwide, because of their applications in several fields. The state of the art of cryopreservation of different cellular types (sperm, oocytes, embryos, somatic cells and primordial germ cells or early spermatogonia) is discussed focusing on the advantages and disadvantages of each procedure according to different applications. A special review on the need of standardization of protocols has also been carried out. In summary, this comprehensive review provides information on the practical details of applications of genome cryobanking in a range of aquatic species worldwide, including the cryobanks established in Europe, USA, Brazil, Australia and New Zealand, the species and type of cells that constitute these banks and the utilization of the samples preserved. This review compiles the last advances on germplasm cryobanking of freshwater and marine fish species and invertebrates, with high value for commercial aquaculture or conservation. It is reviewed the most promising cryopreservation protocols for different cell types, embryos and larvae that could be applied in programs for genetic improvement, broodstock management or conservation of stocks to guarantee culture production.

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

Developing Water Sampling Standards

ERIC Educational Resources Information Center

Environmental Science and Technology, 1974

1974-01-01

Participants in the D-19 symposium on aquatic sampling and measurement for water pollution assessment were informed that determining the extent of waste water stream pollution is not a cut and dry procedure. Topics discussed include field sampling, representative sampling from storm sewers, suggested sampler features and application of improved…

Detection of ostreid herpesvirus 1 microvariant DNA in aquatic invertebrate species, sediment and other samples collected from the Georges River estuary, New South Wales, Australia.

PubMed

Evans, Olivia; Paul-Pont, Ika; Whittington, Richard J

2017-01-24

Ostreid herpesvirus 1 microvariants (OsHV-1) present a serious threat to the Australian Crassostrea gigas industry. Of great concern is the propensity for mortality due to the virus recurring each season in farmed oysters. However, the source of the virus in recurrent outbreaks remains unclear. Reference strain ostreid herpesvirus 1 (OsHV-1 ref) and other related variants have been detected in several aquatic invertebrate species other than C. gigas in Europe, Asia and the USA. The aim of this study was to confirm the presence or absence of OsHV-1 in a range of opportunistically sampled aquatic invertebrate species inhabiting specific locations within the Georges River estuary in New South Wales, Australia. OsHV-1 DNA was detected in samples of wild C. gigas, Saccostrea glomerata, Anadara trapezia, mussels (Mytilus spp., Trichomya hirsuta), whelks (Batillaria australis or Pyrazus ebeninus) and barnacles Balanus spp. collected from several sites between October 2012 and April 2013. Viral loads in non-ostreid species were consistently low, as was the prevalence of OsHV-1 DNA detection. Viral concentrations were highest in wild C. gigas and S. glomerata; the prevalence of detectable OsHV-1 DNA in these oysters reached approximately 68 and 43%, respectively, at least once during the study. These species may be important to the transmission and/or persistence of OsHV-1 in endemically infected Australian estuaries.

Aquatic insect community of lake, Phulbari anua in Cachar, Assam.

PubMed

Gupta, Susmita; Narzary, Rupali

2013-05-01

An investigation on the water quality and aquatic insect community of an oxbow lake (Phulbari anua) of south Assam, North-East India was carried out during February to April, 2010. Aquatic insect community of the oxbow lake was represented by 9 species belonging to 9 families and 4 orders during the study period. Order Ephemeroptera and Hemiptera were found to be dominant. Record of 5 species and 5 families from the order Hemiptera showed that this is the largest order in terms of aquatic insect diversity of the lake. Computation of dominance status of different species of aquatic insects of the lake based on Engelmann's Scale revealed that Anisops lundbladiana and Cloeon sp. were eudominant in the system. The Shannon- Weiner's Diversity Index (H') and Shannon evenness values (J') were found to range from 0.3-0.69 and 0.53 -0.97, respectively indicating perturbation of the system. Again in terms of physico-chemical properties of water the lake is in a satisfactory condition where all the parameters are well within the range of IS 10500. The DO values were found to range from 6.8 to 14.8 mgl(-1). Free CO2 fluctuated from 1 to 4.98 mgl(-1) and nitrate in water ranged from 0.4 to 2.1 mgl(-1). Margalef's water quality index values of most of the samplings also indicated clean water condition of the lake. Correlation coefficient analyses of the environmental variables, aquatic insect diversity and density of the lake revealed that aquatic insect diversity of the lake is mainly governed by dissolved oxygen, nitrate, and free carbon dioxide.

Developmental Aquatics: Assessment and Instructional Programming.

ERIC Educational Resources Information Center

Doremus, Wendy A.

1992-01-01

This article provides an assessment tool and guidelines for creating instructional programing in aquatic skills development for children with disabilities functioning below levels required for most adapted beginning aquatics programs. It covers individualized goals and objectives, adjustment to the water, and specific aquatic skills. (DB)

Modeling Aquatic Toxicity through Chromatographic Systems.

PubMed

Fernández-Pumarega, Alejandro; Amézqueta, Susana; Farré, Sandra; Muñoz-Pascual, Laura; Abraham, Michael H; Fuguet, Elisabet; Rosés, Martí

2017-08-01

Environmental risk assessment requires information about the toxicity of the growing number of chemical products coming from different origins that can contaminate water and become toxicants to aquatic species or other living beings via the trophic chain. Direct toxicity measurements using sensitive aquatic species can be carried out but they may become expensive and ethically questionable. Literature refers to the use of chromatographic measurements that correlate to the toxic effect of a compound over a specific aquatic species as an alternative to get toxicity information. In this work, we have studied the similarity in the response of the toxicity to different species and we have selected eight representative aquatic species (including tadpoles, fish, water fleas, protozoan, and bacteria) with known nonspecific toxicity to chemical substances. Next, we have selected four chromatographic systems offering good perspectives for surrogation of the eight selected aquatic systems, and thus prediction of toxicity from the chromatographic measurement. Then toxicity has been correlated to the chromatographic retention factor. Satisfactory correlation results have been obtained to emulate toxicity in five of the selected aquatic species through some of the chromatographic systems. Other aquatic species with similar characteristics to these five representative ones could also be emulated by using the same chromatographic systems. The final aim of this study is to model chemical products toxicity to aquatic species by means of chromatographic systems to reduce in vivo testing.

Aquatic insect assemblages associated with subalpine stream segment types in relict glaciated headwaters

USGS Publications Warehouse

Kubo, Joshua S.; Torgersen, Christian E.; Bolton, Susan M.; Weekes, Anne A.; Gara, Robert I.

2013-01-01

1. Aquatic habitats and biotic assemblages in subalpine headwaters are sensitive to climate and human impacts. Understanding biotic responses to such perturbations and the contribution of high-elevation headwaters to riverine biodiversity requires the assessment of assemblage composition among habitat types. We compared aquatic insect assemblages among headwater stream segment types in relict glaciated subalpine basins in Mt. Rainier National Park, Washington, USA. 2. Aquatic insects were collected during summer and autumn in three headwater basins. In each basin, three different stream segment types were sampled: colluvial groundwater sources, alluvial lake inlets, and cascade-bedrock lake outlets. Ward's hierarchical cluster analysis revealed high β diversity in aquatic insect assemblages, and non-metric multidimensional scaling indicated that spatial and temporal patterns in assemblage composition differed among headwater stream segment types. Aquatic insect assemblages showed more fidelity to stream segment types than to individual basins, and the principal environmental variables associated with assemblage structure were temperature and substrate. 3. Indicator species analyses identified specific aquatic insects associated with each stream segment type. Several rare and potentially endemic aquatic insect taxa were present, including the recently described species, Lednia borealis (Baumann and Kondratieff). 4. Our results indicate that aquatic insect assemblages in relict glaciated subalpine headwaters were strongly differentiated among stream segment types. These results illustrate the contribution of headwaters to riverine biodiversity and emphasise the importance of these habitats for monitoring biotic responses to climate change. Monitoring biotic assemblages in high-elevation headwaters is needed to prevent the potential loss of unique and sensitive biota.

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.

Development of a microbial population within a hot-drinks vending machine and the microbial load of vended hot chocolate drink.

PubMed

Hall, A; Short, K; Saltmarsh, M; Fielding, L; Peters, A

2007-09-01

In order to understand the development of the microbial population within a hot-drinks vending machine a new machine was placed in a staff area of a university campus vending only hot chocolate. The machine was cleaned weekly using a detergent based protocol. Samples from the mixing bowl, dispense area, and drink were taken over a 19-wk period and enumerated using plate count agar. Bacillus cereus was identified using biochemical methods. Vended drinks were sampled at 0, 3, 6, and 9 min after vending; the hot chocolate powder was also sampled. Over the 1st 8 wk, a significant increase in the microbial load of the machine components was observed. By the end of the study, levels within the vended drink had also increased significantly. Inactivation of the automatic flush over a subsequent 5-wk period led to a statistically but not operationally significant increase in the microbial load of the dispense area and vended drink. The simple weekly clean had a significant impact on the microbial load of the machine components and the vended drink. This study demonstrated that a weekly, detergent-based cleaning protocol was sufficient to maintain the microbial population of the mixing bowl and dispense point in a quasi-steady state below 3.5 log CFU/cm2 ensuring that the microbial load of the vended drinks was maintained below 3.4 log CFU/mL. The microbial load of the drinks showed no significant changes over 9 min after vending, suggesting only spores are present in the final product.

Successive DNA extractions improve characterization of soil microbial communities

PubMed Central

de Hollander, Mattias; Smidt, Hauke; van Veen, Johannes A.

2017-01-01

Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition. PMID:28168105

Deep and shallow water effects on developing preschoolers' aquatic skills.

PubMed

Costa, Aldo M; Marinho, Daniel A; Rocha, Helena; Silva, António J; Barbosa, Tiago M; Ferreira, Sandra S; Martins, Marta

2012-05-01

The aim of the study was to assess deep and shallow water teaching methods in swimming lessons for preschool children and identify variations in the basic aquatic skills acquired. The study sample included 32 swimming instructors (16 from deep water programs and 16 from shallow water programs) and 98 preschool children (50 from deep water swimming pool and 48 from shallow water swimming pool). The children were also studied regarding their previous experience in swimming (6, 12 and 18 months or practice). Chi-Square test and Fisher's exact test were used to compare the teaching methodology. A discriminant analysis was conducted with Λ wilk's method to predict under what conditions students are better or worse (aquatic competence). Results suggest that regardless of the non-significant variations found in teaching methods, the water depth can affect aquatic skill acquisition - shallow water lessons seem to impose greater water competence particularly after 6 months of practice. The discriminant function revealed a significant association between groups and all predictors for 6 months of swimming practice (p<0.001). Body position in gliding and leg displacements were the main predictors. For 12 and 18 months of practice, the discriminant function do not revealed any significant association between groups. As a conclusion, it seems that the teaching methodology of aquatic readiness based on deep and shallow water programs for preschoolers is not significantly different. However, shallow water lessons could be preferable for the development of basic aquatic skills.

Deep and Shallow Water Effects on Developing Preschoolers’ Aquatic Skills

PubMed Central

Costa, Aldo M.; Marinho, Daniel A.; Rocha, Helena; Silva, António J.; Barbosa, Tiago M.; Ferreira, Sandra S.; Martins, Marta

2012-01-01

The aim of the study was to assess deep and shallow water teaching methods in swimming lessons for preschool children and identify variations in the basic aquatic skills acquired. The study sample included 32 swimming instructors (16 from deep water programs and 16 from shallow water programs) and 98 preschool children (50 from deep water swimming pool and 48 from shallow water swimming pool). The children were also studied regarding their previous experience in swimming (6, 12 and 18 months or practice). Chi-Square test and Fisher’s exact test were used to compare the teaching methodology. A discriminant analysis was conducted with Λ wilk’s method to predict under what conditions students are better or worse (aquatic competence). Results suggest that regardless of the non-significant variations found in teaching methods, the water depth can affect aquatic skill acquisition - shallow water lessons seem to impose greater water competence particularly after 6 months of practice. The discriminant function revealed a significant association between groups and all predictors for 6 months of swimming practice (p<0.001). Body position in gliding and leg displacements were the main predictors. For 12 and 18 months of practice, the discriminant function do not revealed any significant association between groups. As a conclusion, it seems that the teaching methodology of aquatic readiness based on deep and shallow water programs for preschoolers is not significantly different. However, shallow water lessons could be preferable for the development of basic aquatic skills. PMID:23487406

Microbial micropatches within microbial hotspots

PubMed Central

Smith, Renee J.; Tobe, Shanan S.; Paterson, James S.; Seymour, Justin R.; Oliver, Rod L.; Mitchell, James G.

2018-01-01

The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have ‘hotspots’ of high abundance, and ‘coldspots’ of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur. PMID:29787564

Microbial micropatches within microbial hotspots.

PubMed

Dann, Lisa M; McKerral, Jody C; Smith, Renee J; Tobe, Shanan S; Paterson, James S; Seymour, Justin R; Oliver, Rod L; Mitchell, James G

2018-01-01

The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have 'hotspots' of high abundance, and 'coldspots' of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur.

The Effect of Aquatic Intervention on the Gross Motor Function and Aquatic Skills in Children with Cerebral Palsy

PubMed Central

Dimitrijević, Lidija; Aleksandrović, Marko; Madić, Dejan; Okičić, Tomislav; Radovanović, Dragan; Daly, Daniel

2012-01-01

The objective of this study was to investigate the effect of an aquatic intervention on the gross motor function and aquatic skills of children with cerebral palsy (CP). Twenty-nine children with CP, aged 5 to 14, were recruited. Fourteen children completed an aquatic intervention (EG), and 13 children served as controls (CG). Two participants dropped out due to events (illness) unrelated to the intervention. The aquatic intervention lasted 6 weeks (2 sessions per week at 55 minutes per session) with a follow-up period of 3 weeks. The outcome measures were the Gross Motor Function Measure (GMFM) for motor function and the Water Orientation Test Alyn 2 (WOTA 2) for aquatic skills assessment. A significant improvement was observed in the secondary assessment of GMFM and WOTA 2. In contrast to the aquatic skills improvement, the GMFM change was not maintained at follow-up. Our results indicate that children with CP can improve gross motor function on dry land and aquatic skills with a 6-week water intervention. The intervention period was too short for sustainable improvement in dry-land motor skills after intervention (follow-up), but time was sufficient to achieve sustainable improvements in aquatic skills. PMID:23487257

The effect of aquatic intervention on the gross motor function and aquatic skills in children with cerebral palsy.

PubMed

Dimitrijević, Lidija; Aleksandrović, Marko; Madić, Dejan; Okičić, Tomislav; Radovanović, Dragan; Daly, Daniel

2012-05-01

The objective of this study was to investigate the effect of an aquatic intervention on the gross motor function and aquatic skills of children with cerebral palsy (CP). Twenty-nine children with CP, aged 5 to 14, were recruited. Fourteen children completed an aquatic intervention (EG), and 13 children served as controls (CG). Two participants dropped out due to events (illness) unrelated to the intervention. The aquatic intervention lasted 6 weeks (2 sessions per week at 55 minutes per session) with a follow-up period of 3 weeks. The outcome measures were the Gross Motor Function Measure (GMFM) for motor function and the Water Orientation Test Alyn 2 (WOTA 2) for aquatic skills assessment. A significant improvement was observed in the secondary assessment of GMFM and WOTA 2. In contrast to the aquatic skills improvement, the GMFM change was not maintained at follow-up. Our results indicate that children with CP can improve gross motor function on dry land and aquatic skills with a 6-week water intervention. The intervention period was too short for sustainable improvement in dry-land motor skills after intervention (follow-up), but time was sufficient to achieve sustainable improvements in aquatic skills.

Investigating aquatic ecosystems of small lakes in Khorezm, Uzbekistan

USGS Publications Warehouse

Saito, L.; Scott, J.; Rosen, M.; Nishonov, Bakhriddin; Chandra, S.; Lamers, John P.A.; Fayzieva, Dilorom; Shanafield, M.

2009-01-01

The Khorezm province of Uzbekistan, located in the Aral Sea Basin, suffers from severe environmental and human health problems due to decades of unsustainable land and water management. Agriculture is the dominant land use in Khorezm, and agricultural runoff water has impacted many small lakes. In this water-scarce region, these lakes may provide a water source for irrigation or fish production. Samples have been collected from 13 of these lakes since 2006 to assess water quality, the aquatic food web, and possible limits to aquatic production. Lake salinity varied from 1 to >10 g/L both between and within lakes. Although hydrophobic contaminants concentrations were low (82-241 pg toxic equivalents/mL in June 2006, October 2006, and June 2007), aquatic species diversity and relative density were low in most lakes. Ongoing work is focused on 4 lakes with pelagic food webs to estimate fish production and assess anthropogenic impacts on the food web. Lake sediment cores are also being examined for organic contaminants, and hydrology is being assessed with stable isotopes. ?? 2009 ASCE.

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

Data Basin Aquatic Center: expanding access to aquatic conservation data, analysis tools, people and practical answers

NASA Astrophysics Data System (ADS)

Osborne-Gowey, J.; Strittholt, J.; Bergquist, J.; Ward, B. C.; Sheehan, T.; Comendant, T.; Bachelet, D. M.

2009-12-01

The world’s aquatic resources are experiencing anthropogenic pressures on an unprecedented scale and aquatic organisms are experiencing widespread population changes and ecosystem-scale habitat alterations. Climate change is likely to exacerbate these threats, in some cases reducing the range of native North American fishes by 20-100% (depending on the location of the population and the model assumptions). Scientists around the globe are generating large volumes of data that vary in quality, format, supporting documentation, and accessibility. Moreover, diverse models are being run at various temporal and spatial scales as scientists attempt to understand previous (and project future) human impacts to aquatic species and their habitats. Conservation scientists often struggle to synthesize this wealth of information for developing practical on-the-ground management strategies. As a result, the best available science is often not utilized in the decision-making and adaptive management processes. As aquatic conservation problems around the globe become more serious and the demand to solve them grows more urgent, scientists and land-use managers need a new way to bring strategic, science-based, and action-oriented approaches to aquatic conservation. The Conservation Biology Institute (CBI), with partners such as ESRI, is developing an Aquatic Center as part of a dynamic, web-based resource (Data Basin; http: databasin.org) that centralizes usable aquatic datasets and provides analytical tools to visualize, analyze, and communicate findings for practical applications. To illustrate its utility, we present example datasets of varying spatial scales and synthesize multiple studies to arrive at novel solutions to aquatic threats.

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.

Drivers of Non-Native Aquatic Species Invasions across the ...

EPA Pesticide Factsheets

Background/Question/Methods Mapping the geographic distribution of non-native aquatic species is a critically important precursor to understanding the anthropogenic and environmental factors that drive freshwater biological invasions. Such efforts are often limited to local scales and/or to a single taxa, missing the opportunity to observe and understand the drivers of macroscale invasion patterns at sub-continental or continental scales. Here we map the distribution of exotic freshwater species richness across the continental United States using publicly accessible species occurrence data (e.g GBIF) and investigate the role of human activity in driving macroscale patterns of aquatic invasion. Using a dasymetric model of human population density and a spatially explicit model of recreational freshwater fishing demand, we analyzed the effect of these metrics of human influence on non-native aquatic species richness at the watershed scale, while controlling for spatial and sampling bias. We also assessed the effects that a temporal mismatch between occurrence data (collected since 1815) and cross-sectional predictors (developed using 2010 data) may have on model fit. Results/Conclusions Our results indicated that non-native aquatic species richness exhibits a highly patchy distribution, with hotspots in the Northeast, Great Lakes, Florida, and human population centers on the Pacific coast. These richness patterns are correlated with population density, but are m

Trace fossils of microbial colonization on Mars: Criteria for search and for sample return

NASA Technical Reports Server (NTRS)

Friedmann, E. I.

1988-01-01

The recent discovery of microbial trace-fossil formation in the frigid Ross Desert of Antarctica suggests that early primitive life on Mars may have left behind similar signatures. These trace fossils are apparent as chemical or physical changes in rock (or sediment) structure (or chemistry) caused by the activity of organisms. Life on Mars, if it ever existed, almost certainly did not evolve above the level of microorganisms, and this should be considered in search for fossil life. For the reasons detailed here, microbial trace fossils seem to be a better and more realistic target for search than would be true microbial fossils (remnants of cellular structures).

Innovative biological approaches for monitoring and improving water quality

PubMed Central

Aracic, Sanja; Manna, Sam; Petrovski, Steve; Wiltshire, Jennifer L.; Mann, Gülay; Franks, Ashley E.

2015-01-01

Water quality is largely influenced by the abundance and diversity of indigenous microbes present within an aquatic environment. Physical, chemical and biological contaminants from anthropogenic activities can accumulate in aquatic systems causing detrimental ecological consequences. Approaches exploiting microbial processes are now being utilized for the detection, and removal or reduction of contaminants. Contaminants can be identified and quantified in situ using microbial whole-cell biosensors, negating the need for water samples to be tested off-site. Similarly, the innate biodegradative processes can be enhanced through manipulation of the composition and/or function of the indigenous microbial communities present within the contaminated environments. Biological contaminants, such as detrimental/pathogenic bacteria, can be specifically targeted and reduced in number using bacteriophages. This mini-review discusses the potential application of whole-cell microbial biosensors for the detection of contaminants, the exploitation of microbial biodegradative processes for environmental restoration and the manipulation of microbial communities using phages. PMID:26322034

Aquatic Activities for Youth.

ERIC Educational Resources Information Center

Greene, H. David; And Others

Designed to meet the diverse educational needs of youth groups, this aquatic program consists of eight individual lesson units, each devoted to one aspect of the aquatic world. Unit topics include: fish aquariums; raising earthworms; simulation of coastal planning; entomology and water; rope; calculating stream flow; saltwater aquariums; and fish…

Aquatic species and habitats

Treesearch

Danny C. Lee; James R. Sedell; Bruce E. Rieman; Russell F. Thurow; Jack E. Williams

1998-01-01

Continuing human activities threaten the highly prized aquatic resources of the interior Columbia basin. Precipitous declines in native species, particularly Pacific salmon, and a large influx of introduced species have radically altered the composition and distribution of native fishes. Fortunately, areas of relatively high aquatic integrity remain, much of it on...

Estimates of microbial quality and concentration of copper in distributed drinking water are highly dependent on sampling strategy.

PubMed

Lehtola, Markku J; Miettinen, Ilkka T; Hirvonen, Arja; Vartiainen, Terttu; Martikainen, Pertti J

2007-12-01

The numbers of bacteria generally increase in distributed water. Often household pipelines or water fittings (e.g., taps) represent the most critical location for microbial growth in water distribution systems. According to the European Union drinking water directive, there should not be abnormal changes in the colony counts in water. We used a pilot distribution system to study the effects of water stagnation on drinking water microbial quality, concentration of copper and formation of biofilms with two commonly used pipeline materials in households; copper and plastic (polyethylene). Water stagnation for more than 4h significantly increased both the copper concentration and the number of bacteria in water. Heterotrophic plate counts were six times higher in PE pipes and ten times higher in copper pipes after 16 h of stagnation than after only 40 min stagnation. The increase in the heterotrophic plate counts was linear with time in both copper and plastic pipelines. In the distribution system, bacteria originated mainly from biofilms, because in laboratory tests with water, there was only minor growth of bacteria after 16 h stagnation. Our study indicates that water stagnation in the distribution system clearly affects microbial numbers and the concentration of copper in water, and should be considered when planning the sampling strategy for drinking water quality control in distribution systems.

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.

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.

Guest editorial: Aquatic science in the Northwest

USGS Publications Warehouse

Sepulveda, Adam; Ray, Andrew M.

2017-01-01

In recent years, Northwest Science has seen a significant increase in the number of submissions representing aquatic science. Our region is punctuated by aquatic systems. The current issue in particular, presents a number of new aquatic science contributions. Accordingly, Northwest Science invited the authors of this guest editorial to address the question, why is aquatic science so important in the Northwest?

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 ...

Hydro-climatic Changes: Potential Non-linear Responses of Phosphorus Dynamic in Aquatic/Semi-aquatic Systems