Differences in microbial community composition between injection and production water samples of water flooding petroleum reservoirs

Although mosquito microbiota are known to influence reproduction, nutrition, disease transmission, and pesticide resistance, the relationship between host-associated microbial community composition and geographical location is poorly understood. To begin addressing this knowledge gap, we characterized microbiota associated with adult females of Culex nigripalpus mosquito vectors of Saint Louis Encephalitis and West Nile viruses sampled from three locations in Florida (Vero Beach, Palmetto Inland, and Palmetto Coast). High-throughput sequencing of PCR-amplified 16S rRNA genes demonstrated significant differences among microbial communities of mosquitoes sampled from the three locations. Mosquitoes from Vero Beach (east coast Florida) were dominated by uncultivated Asaia sp. (Alphaproteobacteria), whereas microbiota associated with mosquitoes collected from two mosquito populations at Palmetto (west coast Florida) sites were dominated by uncultured Spironema culicis (Spirochaetes), Salinisphaera hydrothermalis (Gammaproteobacteria), Spiroplasma (Mollicutes), uncultured Enterobacteriaceae, Candidatus Megaira (Alphaproteobacteria; Rickettsiae), and Zymobacter (Gammaproteobacteria). The variation in taxonomic profiles of Cx. nigripalpus gut microbial communities, especially with respect to dominating taxa, is a potentially critical factor in understanding disease transmission and mosquito susceptibility to insecticides among different mosquito populations.

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Environmental conditions and diffusion-limited microbial transfer drive specific microbial communities detected at different sections in oil-production reservoir with water-flooding

10.1101/2020.12.07.415646 ◽

2020 ◽

Author(s):

Peike Gao ◽

Huimei Tian ◽

Guoqiang Li ◽

Feng Zhao ◽

Wenjie Xia ◽

...

Keyword(s):

Microbial Communities ◽

Water Injection ◽

Oil Production ◽

Environmental Variation ◽

Water Flooding ◽

Petroleum Reservoir ◽

Diffusion Limited ◽

Production Wells ◽

And Diffusion ◽

Production Facilities

ABSTRACTThis study investigated the distribution of microbial communities in the oilfield production facilities of a water-flooding petroleum reservoir and the roles of environmental variation, microorganisms in injected water, and diffusion-limited microbial transfer in structuring the microbial communities. Similar bacterial communities were observed in surface water-injection facilities dominated by aerobic or facultative anaerobic Betaproteobacteria, Alphaproteobacteria, and Flavobacteria. Distinct bacterial communities were observed in downhole of the water-injection wells dominated by Clostridia, Deltaproteobacteria, Anaerolineae, and Synergistia, and in the oil-production wells dominated by Gammaproteobacteria, Betaproteobacteria, and Epsilonproteobacteria. Methanosaeta, Methanobacterium, and Methanolinea were dominant archaeal taxa in the water-injection facilities, while the oil-production wells were predominated by Methanosaeta, Methanomethylovorans, and Methanocalculus. Energy, nucleotide, translation, and glycan biosynthesis metabolisms were more active in the downhole of the water-injection wells, while bacterial chemotaxis, biofilm formation, two-component system, and xenobiotic biodegradation was associated with the oil-production wells. The number of shared OTUs and its positive correlation with formation permeability revealed differential diffusion-limited microbial transfer in oil-production facilities. The overall results indicate that environmental variation and microorganisms in injected water are the determinants that structure microbial communities in water-injection facilities, and the determinants in oil-bearing strata are environmental variation and diffusion-limited microbial transfer.IMPORTANCEWater-flooding continually inoculates petroleum reservoirs with exogenous microorganisms, nutrients, and oxygen. However, how this process influences the subsurface microbial community of the whole production process remains unclear. In this study, we investigated the spatial distribution of microbial communities in the oilfield production facilities of a water-flooding petroleum reservoir, and comprehensively illustrate the roles of environmental variation, microorganisms in injected water, and diffusion-limited microbial transfer in structuring the microbial communities. The results advance fundamental understanding on petroleum reservoir ecosystems that subjected to anthropogenic perturbations during oil production processes.

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Microbiome succession during ammonification in eelgrass bed sediments

10.7287/peerj.preprints.2956 ◽

2017 ◽

Author(s):

Cassandra L Ettinger ◽

Susan L Williams ◽

Jessica M Abbott ◽

John J Stachowicz ◽

Jonathan A Eisen

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Sulfur Metabolism ◽

Microbial Community Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Ecosystem Functions ◽

Sediment Samples ◽

Functional Studies ◽

Elemental Cycling

Background. Eelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, or diagenesis, from plots at a field site in Bodega Bay, CA. Methods. Sediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples (n= 4 per plot) under a N2 atmosphere, incubated them at in situ temperatures (15 oC) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at 7, 13 and 19 days to characterize the relative abundances of microbial taxa and how they changed throughout early diagenesis. Results. Within-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in sulfur reducers (Desulfobacterales) and corresponding increases in sulfide oxidizers (Alteromonadales and Thiotrichales). None of these changes in composition or richness were associated with ammonification rates. Discussion. Overall, our results showed that the microbiome of sediment from different plots followed similar successional patterns, which we surmise to be due to changes related to sulfur metabolism. These large changes likely overwhelmed any potential changes in sediment microbiome related to ammonification rate. We found no relationship between eelgrass presence or genetic composition and the microbiome. This was likely due to our sampling of bulk sediments to measure ammonification rates rather than sampling microbes in sediment directly in contact with the plants and suggests that eelgrass influence on the sediment microbiome may be limited in spatial extent. More in-depth functional studies associated with eelgrass microbiome will be required in order to fully understand the implications of these microbial communities in broader host-plant and ecosystem functions (e.g. elemental cycling and eelgrass-microbe interactions).

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The shift of microbial population composition accompanying the injected water flowing in the water-flooding petroleum reservoirs

Biogeosciences Discussions ◽

10.5194/bgd-11-16773-2014 ◽

2014 ◽

Vol 11 (12) ◽

pp. 16773-16797 ◽

Cited By ~ 2

Author(s):

P. K. Gao ◽

G. Q. Li ◽

H. M. Tian ◽

Y. S. Wang ◽

H. W. Sun ◽

...

Keyword(s):

Dissolved Oxygen ◽

Produced Water ◽

Water Flooding ◽

Microbial Populations ◽

Petroleum Reservoir ◽

Injection Wells ◽

Production Wells ◽

Sieve Effect ◽

Pass Through ◽

A Minor

Abstract. In water-flooding petroleum reservoir, microbial populations in injected water are expected to migrate into oil-bearing strata and reach production wells. To demonstrate this, we firstly investigated microbial compositions in a homogeneous sandstone reservoir. The results indicated that the injected water harbored more microbial cells than produced water, and the shared populations and their abundance accounted for a minor fraction in injected water, while dominated in produced water, suggesting that most populations in injected water did hardly reach production wells in this reservoir. We further investigated microbial communities in water samples collected from wellhead and downhole of injection wells and production wells in a heterogeneous conglomerate reservoir. The results indicated that, except for the community reconstruction mainly resulted from dissolved oxygen, most populations were simultaneously detected in the wellhead and downhole of injection wells and production wells, suggesting that most microbial populations in injected water reached the production wells. This study suggest that microbial populations in injected water can pass through reservoir strata and reach production wells, but the reservoir heterogeneity, interwell spacing, sieve effect of strata and dissolved oxygen exert significant influence on microbial migration and distribution in reservoirs.

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A conceptual framework modeling of functional microbial communities in wastewater treatment electro-bioreactors

Water Science & Technology ◽

10.2166/wst.2020.553 ◽

2020 ◽

Vol 82 (12) ◽

pp. 3047-3061

Author(s):

Nancy A. ElNaker ◽

Abdelsattar M. Sallam ◽

El-Sayed M. El-Sayed ◽

H. El Ghandoor ◽

M. S. Talaat ◽

...

Keyword(s):

Wastewater Treatment ◽

Conceptual Framework ◽

Microbial Communities ◽

Conceptual Model ◽

High Throughput Sequencing ◽

Microbial Community Composition ◽

Operating Conditions ◽

Rrna Gene ◽

Sequencing Data ◽

Operational Parameters

Abstract Understanding the microbial ecology of a system allows linking members of the community and their metabolic functions to the performance of the wastewater bioreactor. This study provided a comprehensive conceptual framework for microbial communities in wastewater treatment electro-bioreactors (EBRs). The model was based on data acquired from monitoring the effect of altering different bioreactor operational parameters, such as current density and hydraulic retention time, on the microbial communities of an EBR and its nutrient removal efficiency. The model was also based on the 16S rRNA gene high-throughput sequencing data analysis and bioreactor efficiency data. The collective data clearly demonstrated that applying various electric currents affected the microbial community composition and stability and the reactor efficiency in terms of chemical oxygen demand, N and P removals. Moreover, a schematic that recommends operating conditions that are tailored to the type of wastewater that needs to be treated based on the functional microbial communities enriched at specific operating conditions was suggested. In this study, a conceptual model as a simplified representation of the behavior of microbial communities in EBRs was developed. The proposed conceptual model can be used to predict how biological treatment of wastewater in EBRs can be improved by varying several operating conditions.

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Reference-free comparison of microbial communities via de Bruijn graphs

10.1101/055020 ◽

2016 ◽

Cited By ~ 2

Author(s):

Serghei Mangul ◽

David Koslicki

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Microbial Community Composition ◽

De Bruijn Graph ◽

Data Sets ◽

Sequencing Data ◽

De Bruijn Graphs ◽

De Bruijn ◽

The Individual ◽

And Control

ABSTRACTMicrobial communities inhabiting the human body exhibit significant variability across different individuals and tissues, and are suggested to play an important role in health and disease. High-throughput sequencing offers unprecedented possibilities to profile microbial community composition, but limitations of existing taxonomic classification methods (including incompleteness of existing microbial reference databases) limits the ability to accurately compare microbial communities across different samples. In this paper, we present a method able to overcome these limitations by circumventing the classification step and directly using the sequencing data to compare microbial communities. The proposed method provides a powerful reference-free way to assess differences in microbial abundances across samples. This method, called EMDeBruijn, condenses the sequencing data into a de Bruijn graph. The Earth Mover's Distance (EMD) is then used to measure similarities and differences of the microbial communities associated with the individual graphs. We apply this method to RNA-Seq data sets from a coronary artery calcification (CAC) study and shown that EMDeBruijn is able to differentiate between case and control CAC samples while utilizing all the candidate microbial reads. We compare these results to current reference-based methods, which are shown to have a limited capacity to discriminate between case and control samples. We conclude that this reference-free approach is a viable choice in comparative metatranscriptomic studies.

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Mercury methylating microbial communities of boreal forest soils

10.1101/299248 ◽

2018 ◽

Cited By ~ 1

Author(s):

Jingying Xu ◽

Moritz Buck ◽

Karin Eklöf ◽

Omneya Osman ◽

Jeffra K. Schaefer ◽

...

Keyword(s):

Boreal Forest ◽

Microbial Communities ◽

Forest Soils ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Current Knowledge ◽

Microbial Populations ◽

Fundamental Understanding ◽

Relevant Role ◽

Shed Light

AbstractThe formation of the potent neurotoxic methylmercury (MeHg) is a microbially mediated process that has raised much concern because MeHg poses threats to wildlife and human health. Since boreal forest soils can be a source of MeHg in aquatic networks, it is crucial to understand the biogeochemical processes involved in the formation of this pollutant. High-throughput sequencing of 16S rRNA and the mercury methyltransferase,hgcA, combined with geochemical characterisation of soils, were used to determine the microbial populations contributing to MeHg formation in forest soils across Sweden. ThehgcAsequences obtained were distributed among diverse clades, includingProteobacteria, Firmicutes, andMethanomicrobia,withDeltaproteobacteria, particularlyGeobacteraceae, dominating the libraries across all soils examined. Our results also suggest that MeHg formation is linked to the composition of also non-mercury methylating bacterial communities, likely providing growth substrate (e.g. acetate) for thehgcA-carrying microorganisms responsible for the actual methylation process. While previous research focused on mercury methylating microbial communities of wetlands, this study provides some first insights into the diversity of mercury methylating microorganisms in boreal forest soils.ImportanceDespite a global state of awareness that mercury, and methylmercury in particular, is a neurotoxin that millions of people continue to be exposed to, there are sizable gaps in our fundamental understanding of the processes and organisms involved in methylmercury formation. In the present study we shed light on the diversity of the microorganisms responsible for methylmercury formation in boreal forest soils. All the microorganisms identified have a relevant role on the processing of organic matter in soils. Moreover, our results show that the formation of methylation formation is not only linked to mercury methylating microorganisms but also to the presence of non-mercury methylating bacterial communities that contribute to methylmercury formation by the appropriate substrate to the microorganisms responsible for the actual methylation process. This study improves current knowledge on the diversity of organisms involved in methylmercury formation in soils.

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Microbiome succession during ammonification in eelgrass bed sediments

10.7287/peerj.preprints.2956v1 ◽

2017 ◽

Author(s):

Cassandra L Ettinger ◽

Susan L Williams ◽

Jessica M Abbott ◽

John J Stachowicz ◽

Jonathan A Eisen

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Sulfur Metabolism ◽

Microbial Community Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Ecosystem Functions ◽

Sediment Samples ◽

Functional Studies ◽

Elemental Cycling

Background. Eelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, or diagenesis, from plots at a field site in Bodega Bay, CA. Methods. Sediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples (n= 4 per plot) under a N2 atmosphere, incubated them at in situ temperatures (15 oC) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at 7, 13 and 19 days to characterize the relative abundances of microbial taxa and how they changed throughout early diagenesis. Results. Within-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in sulfur reducers (Desulfobacterales) and corresponding increases in sulfide oxidizers (Alteromonadales and Thiotrichales). None of these changes in composition or richness were associated with ammonification rates. Discussion. Overall, our results showed that the microbiome of sediment from different plots followed similar successional patterns, which we surmise to be due to changes related to sulfur metabolism. These large changes likely overwhelmed any potential changes in sediment microbiome related to ammonification rate. We found no relationship between eelgrass presence or genetic composition and the microbiome. This was likely due to our sampling of bulk sediments to measure ammonification rates rather than sampling microbes in sediment directly in contact with the plants and suggests that eelgrass influence on the sediment microbiome may be limited in spatial extent. More in-depth functional studies associated with eelgrass microbiome will be required in order to fully understand the implications of these microbial communities in broader host-plant and ecosystem functions (e.g. elemental cycling and eelgrass-microbe interactions).

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Microbiome succession during ammonification in eelgrass bed sediments

PeerJ ◽

10.7717/peerj.3674 ◽

2017 ◽

Vol 5 ◽

pp. e3674 ◽

Cited By ~ 8

Author(s):

Cassandra L. Ettinger ◽

Susan L. Williams ◽

Jessica M. Abbott ◽

John J. Stachowicz ◽

Jonathan A. Eisen

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Sulfur Metabolism ◽

Microbial Community Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Ecosystem Functions ◽

Sediment Samples ◽

Functional Studies ◽

Elemental Cycling

BackgroundEelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, also known as diagenesis, from plots at a field site in Bodega Bay, CA.MethodsSediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples (n = 4 per plot) under a N2atmosphere, incubated them atin situtemperatures (15 °C) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at seven, 13 and 19 days to characterize changes in the relative abundances of microbial taxa throughout ammonification.ResultsWithin-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in predicted sulfur reducers (Desulfobacterales) and corresponding increases in predicted sulfide oxidizers (Thiotrichales). None of these changes in composition or richness were associated with variation in ammonification rates.DiscussionOur results showed that the microbiome of sediment from different plots followed similar successional patterns, which we infer to be due to changes related to sulfur metabolism. These large changes likely overwhelmed any potential changes in sediment microbiome related to ammonification rate. We found no relationship between eelgrass presence or genetic composition and the microbiome. This was likely due to our sampling of bulk sediments to measure ammonification rates rather than sampling microbes in sediment directly in contact with the plants and suggests that eelgrass influence on the sediment microbiome may be limited in spatial extent. More in-depth functional studies associated with eelgrass microbiome will be required in order to fully understand the implications of these microbial communities in broader host-plant and ecosystem functions (e.g., elemental cycling and eelgrass-microbe interactions).

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Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽

10.3390/fuels2020014 ◽

2021 ◽

Vol 2 (2) ◽

pp. 241-252

Author(s):

Dyah Asri Handayani Taroepratjeka ◽

Tsuyoshi Imai ◽

Prapaipid Chairattanamanokorn ◽

Alissara Reungsang

Keyword(s):

Microbial Communities ◽

High Throughput ◽

High Throughput Sequencing ◽

High Salinity ◽

Amplicon Sequencing ◽

Spatial Proximity ◽

Lignocellulosic Waste ◽

Evaporation Pond ◽

Operational Taxonomic Units ◽

Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

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