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Huang Z, Cai D, Sun Y. Towards more accurate microbial source tracking via non-negative matrix factorization (NMF). Bioinformatics 2024; 40:i68-i78. [PMID: 38940128 DOI: 10.1093/bioinformatics/btae227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION The microbiome of a sampled habitat often consists of microbial communities from various sources, including potential contaminants. Microbial source tracking (MST) can be used to discern the contribution of each source to the observed microbiome data, thus enabling the identification and tracking of microbial communities within a sample. Therefore, MST has various applications, from monitoring microbial contamination in clinical labs to tracing the source of pollution in environmental samples. Despite promising results in MST development, there is still room for improvement, particularly for applications where precise quantification of each source's contribution is critical. RESULTS In this study, we introduce a novel tool called SourceID-NMF towards more precise microbial source tracking. SourceID-NMF utilizes a non-negative matrix factorization (NMF) algorithm to trace the microbial sources contributing to a target sample. By leveraging the taxa abundance in both available sources and the target sample, SourceID-NMF estimates the proportion of available sources present in the target sample. To evaluate the performance of SourceID-NMF, we conducted a series of benchmarking experiments using simulated and real data. The simulated experiments mimic realistic yet challenging scenarios for identifying highly similar sources, irrelevant sources, unknown sources, low abundance sources, and noise sources. The results demonstrate the superior accuracy of SourceID-NMF over existing methods. Particularly, SourceID-NMF accurately estimated the proportion of irrelevant and unknown sources while other tools either over- or under-estimated them. In addition, the noise sources experiment also demonstrated the robustness of SourceID-NMF for MST. AVAILABILITY AND IMPLEMENTATION SourceID-NMF is available online at https://github.com/ZiyiHuang0708/SourceID-NMF.
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Affiliation(s)
- Ziyi Huang
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Dehan Cai
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
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Bergbusch NT, Wong AR, Russell JN, Swarbrick VJ, Freeman C, Bergsveinson J, Yost CK, Courtenay SC, Leavitt PR. Impact of wastewater treatment upgrade and nitrogen removal on bacterial communities and their interactions in eutrophic prairie streams. FEMS Microbiol Ecol 2023; 99:fiad142. [PMID: 37942568 PMCID: PMC10662661 DOI: 10.1093/femsec/fiad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/12/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023] Open
Abstract
Eutrophication can impact bacteria by altering fluxes and processing of nutrients and organic matter. However, relatively little is known of how bacterial communities, diversity, and interactions with phytoplankton might respond to nutrient management. We used 16S rRNA amplicon sequencing to compare bacterial assemblages in the water column upstream (control) and downstream (impact) of a wastewater treatment plant (WWTP) located on a eutrophic prairie stream. Sampling occurred before (2012) and after (2018) the 2016 biological nutrient removal (BNR) upgrade that removed >90% of nitrogen (N, mainly NH4+). Multivariate ordination suggested that effluent-impacted bacterial communities were associated mainly with elevated NH4+ concentrations before the upgrade, whereas those after BNR were characteristic of reference systems (low NO3-, diverse regulation). Genera such as Betaproteobacteria and Rhodocyclacea were abundant at impacted sites in 2012, whereas Flavobacterium and a potential pathogen (Legionella) were common at impacted sites in 2018. Nitrifier bacteria (Nitrospira and Nitrosomonas) were present but rare at all sites in 2012, but recorded only downstream of the WWTP in 2018. Generalized additive models showed that BNR reduced bacterial diversity, with ∼70% of the deviance in diversity explained by hydrology, pH, nutrients, and phytoplankton abundance. Overall, NH4+ removal reduced symptoms of cultural eutrophication in microbe assemblages.
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Affiliation(s)
- Nathanael T Bergbusch
- Limnology Laboratory, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Institute of Environmental Change and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Biology Department, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- School of Environment, Resources and Sustainability (SERS), University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Alicia R Wong
- School of Environment, Resources and Sustainability (SERS), University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Jennifer N Russell
- Biology Department, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Vanessa J Swarbrick
- Limnology Laboratory, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Office of the Chief Scientist, Government of Alberta, Edmonton T5J 5C6, Canada
| | - Claire Freeman
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Jordyn Bergsveinson
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Christopher K Yost
- Biology Department, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Simon C Courtenay
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Peter R Leavitt
- Limnology Laboratory, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Institute of Environmental Change and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Biology Department, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
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STENSL: Microbial Source Tracking with ENvironment SeLection. mSystems 2022; 7:e0099521. [PMID: 36047699 PMCID: PMC9599664 DOI: 10.1128/msystems.00995-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Microbial source tracking analysis has emerged as a widespread technique for characterizing the properties of complex microbial communities. However, this analysis is currently limited to source environments sampled in a specific study. In order to expand the scope beyond one single study and allow the exploration of source environments using large databases and repositories, such as the Earth Microbiome Project, a source selection procedure is required. Such a procedure will allow differentiating between contributing environments and nuisance ones when the number of potential sources considered is high. Here, we introduce STENSL (microbial Source Tracking with ENvironment SeLection), a machine learning method that extends common microbial source tracking analysis by performing an unsupervised source selection and enabling sparse identification of latent source environments. By incorporating sparsity into the estimation of potential source environments, STENSL improves the accuracy of true source contribution, while significantly reducing the noise introduced by noncontributing ones. We therefore anticipate that source selection will augment microbial source tracking analyses, enabling exploration of multiple source environments from publicly available repositories while maintaining high accuracy of the statistical inference. IMPORTANCE Microbial source tracking is a powerful tool to characterize the properties of complex microbial communities. However, this analysis is currently limited to source environments sampled in a specific study. In many applications there is a clear need to consider source selection over a large array of microbial environments, external to the study. To this end, we developed STENSL (microbial Source Tracking with ENvironment SeLection), an expectation-maximization algorithm with sparsity that enables the identification of contributing sources among a large set of potential microbial environments. With the unprecedented expansion of microbiome data repositories such as the Earth Microbiome Project, recording over 200,000 samples from more than 50 types of categorized environments, STENSL takes the first steps in performing automated source exploration and selection. STENSL is significantly more accurate in identifying the contributing sources as well as the unknown source, even when considering hundreds of potential source environments, settings in which state-of-the-art microbial source tracking methods add considerable error.
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Bärenstrauch M, Vanhove AS, Allégra S, Peuble S, Gallice F, Paran F, Lavastre V, Girardot F. Microbial diversity and geochemistry of groundwater impacted by steel slag leachates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:156987. [PMID: 35772557 DOI: 10.1016/j.scitotenv.2022.156987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
To understand long-term impacts of steel slag material on aquifer geochemistry and microbial communities, we conducted four sampling campaigns in the Gier alluvial groundwater (Loire, France). In its northern part, the aquifer flows under a 200,000 m3 steel slag exhibiting high levels of chromium and molybdenum. Geochemical analyses of the water table revealed the existence of water masses with different chemical signatures. They allowed us to identify an area particularly contaminated by leachates from the slag heap, whatever the sampling period. Water samples from this area were compared to non-contaminated samples, with geochemical characteristics similar to the river samples. To follow changes in microbial communities, the V3-V4 region of 16 s rRNA gene was sequenced. Overall, we observed lower diversity indices in contaminated areas, with higher relative abundances of Verrucomicrobiota and Myxococcota phyla, while several Proteobacteria orders exhibited lower relative abundances. In particular, one single genus among the Verrucomicrobiota, Candidatus Omnitrophus, represented up to 36 % of total taxon abundance in areas affected by steel slag leachates. A large proportion of taxa identified in groundwater were also detected in the upstream river, indicating strong river-groundwater interactions. Our findings pave the way for future research work on C. Omnitrophus remediation capacities.
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Affiliation(s)
- Margot Bärenstrauch
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France
| | - Audrey S Vanhove
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France
| | - Séverine Allégra
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France
| | - Steve Peuble
- Mines Saint-Étienne, Centre "Sciences des Processus Industriels et Naturels" (SPIN), Département "Procédés pour l'Environnement et les Géo-ressources" (PEG), UMR 5600 EVS, UMR 5307 LGF, F-42023 Saint-Etienne, France
| | - Frédéric Gallice
- Mines Saint-Étienne, Centre "Sciences des Processus Industriels et Naturels" (SPIN), Département "Procédés pour l'Environnement et les Géo-ressources" (PEG), UMR 5600 EVS, UMR 5307 LGF, F-42023 Saint-Etienne, France
| | - Frédéric Paran
- Mines Saint-Étienne, Centre "Sciences des Processus Industriels et Naturels" (SPIN), Département "Procédés pour l'Environnement et les Géo-ressources" (PEG), UMR 5600 EVS, UMR 5307 LGF, F-42023 Saint-Etienne, France
| | - Véronique Lavastre
- Université de Lyon, Université Jean Monnet Saint-Etienne, Laboratoire de Géologie de Lyon - Terre Planètes Environnement LGL-TPE, CNRS -UMR 5276, F-42023 Saint-Etienne, France
| | - Françoise Girardot
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France.
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Zhang Y, Huo Y, Zhang Z, Zhu S, Fan W, Wang X, Huo M. Deciphering the influence of multiple anthropogenic inputs on taxonomic and functional profiles of the microbial communities in Yitong River, Northeast China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:39973-39984. [PMID: 35112248 DOI: 10.1007/s11356-021-18386-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
We conducted the analysis of physicochemical parameters, 16S rRNA amplicon sequencing and real-time quantitative polymerase chain reaction to explore the impact of human inputs on the bacterioplankton communities within a tributary of the largest river flowing through a megacity in northeast China. Agriculture largely accounted for the alteration of diversity and functions of the microbial communities. Furthermore, nitrate and total phosphorus declined at the reservoir outlet. The WWTP effluent discharge caused a decrease of the relative abundance of Actinobacteria and Cyanobacteria, while the impact on the variation of alpha diversity of river microbial community was slight. Carbon fixation and nitrogen cycle varied with the change of land use type. The rare taxa contributed with a predominant role in the response to environmental variables and NH3-N as well as NO3--N were the main environmental factors that drove the shift in the bacterial community. The occurrence of the human-specific fecal indicator was mostly derived from agriculture, and its increase in relative abundance was observed in the WWTP effluent. Thus, our study provides guidance for ecological assessment and management of rivers by revealing the response pattern of river bacterioplankton to multiple types of anthropogenic stressors.
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Affiliation(s)
- Ying Zhang
- School of Environment, Northeast Normal University, Changchun, 130117, China
| | - Yang Huo
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China.
- School of Physics, Northeast Normal University, Changchun, 130024, China.
| | - Zhiruo Zhang
- Key Laboratory of Songliao Aquatic Environment, Ministry of Education, Jilin Jianzhu University, Changchun, 130118, China
| | - Suiyi Zhu
- School of Environment, Northeast Normal University, Changchun, 130117, China
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China
| | - Wei Fan
- School of Environment, Northeast Normal University, Changchun, 130117, China
| | - Xianze Wang
- School of Environment, Northeast Normal University, Changchun, 130117, China
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China
| | - Mingxin Huo
- School of Environment, Northeast Normal University, Changchun, 130117, China.
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China.
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Community-Based 16S rDNA Fingerprinting Analysis of Geographically Distinct Marine Sediments of Unexplored Coastal Regions of Palk Bay and Gulf of Mannar. Curr Microbiol 2022; 79:60. [PMID: 34982232 DOI: 10.1007/s00284-021-02692-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 10/01/2021] [Indexed: 11/03/2022]
Abstract
The present study aims to carefully delineate the bacterial community composition in marine sediments from different geographical coastal regions of Palk Bay and Gulf of Mannar that are known for human recreational activities. Bacterial richness in different marine sediments was assessed using 16S rRNA gene-based Denaturing Gradient Gel Electrophoresis (DGGE) which is a widely deployed fingerprinting technique. The DGGE profiles revealed that the bacterial community profiles of sediment from different coastal regions were complex and dynamic. The most dominant phylum present in the marine sediment samples were Proteobacteria followed by Cyanobacteria, Bacteriodetes, Firmicutes, Acidobacteria, and Actinobacteria. Cosmopolitan presence of Thioalkalivibrio sp. was observed in all the marine sediments. Sequencing of the abundant band reveals the presence of Vibrio spp. in all the marine sediments. Comparative illumina data analysis revealed the presence of 51 different Vibrio species in which Vibrio alginolyticus holds the highest abundance (67.2%) followed by V. harveyi (13.5%). This is the one of the very few reports that compared the complex microbial community composition of the marine sediments of different geographical regions of unexplored coastal region. Further in-depth analysis needs to be taken to understand the presence of complex microbial compositions and their functions through high-throughput whole metagenome sequencing and metaproteomic approaches.
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Zhou W, Dong J, Ding D, Long L, Suo A, Lin X, Yang Q, Lin L, Zhang Y, Ling J. Rhizosphere microbiome dynamics in tropical seagrass under short-term inorganic nitrogen fertilization. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:19021-19033. [PMID: 33394400 DOI: 10.1007/s11356-020-12048-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Rhizosphere microbes are crucial to seagrass meadows because they promote plant growth and heath. However, information concerning the response of rhizosphere microorganisms in seagrass sediment in the presence of different nitrogen sources is lacking. Here, by means of high-throughput sequencing, we investigated how addition of inorganic nitrogen affects the rhizosphere microbiome of the tropical seagrass Thalassia hemperichii. A seagrass culture system was set up to conduct a nitrogen addition (ammonium and nitrate) simulation experiment. We found that the relative abundance of Proteobacteria and Bacteroidetes was increased in inorganic nitrogen-enriched samples, whereas that of Acidobacteria decreased under ammonium enrichment, especially after 35 days. High levels of inorganic nitrogen addition caused a significant decrease in the relative abundance of Desulfobacteraceae, Sulfurovaceae, and Spirochaetes, which are primarily involved in sulfur cycling. Additionally, the abundance of microbes in the seagrass rhizosphere reached the highest after the ammonium-enrichment treatment. Among the analyzed seagrass photosynthetic characteristics, seagrass leaves presented the highest light utility in treatments receiving nitrate, followed by the control groups and ammonium-enrichment groups. Moreover, 16S rRNA gene-predicted functional analysis suggested that some functions related to metabolism of amino acids and signal transduction were enriched in samples receiving high ammonium, whereas nitrate addition enriched predicted functions related to diseases. These findings provide new insights into the response of microbial communities to different types of nitrogen additions in seagrass ecosystems.
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Affiliation(s)
- Weiguo Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, Guangdong Province, China
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, Guangdong Province, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China
| | - Dewen Ding
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, Guangdong Province, China
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, Guangdong Province, China
| | - Anning Suo
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, Guangdong Province, China
| | - Xiancheng Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, Guangdong Province, China
| | - Liyun Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yanying Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, Guangdong Province, China.
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Walker AM, Leigh MB, Mincks SL. Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope. Front Microbiol 2021; 12:581124. [PMID: 33584606 PMCID: PMC7876419 DOI: 10.3389/fmicb.2021.581124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/05/2021] [Indexed: 11/13/2022] Open
Abstract
The paradigm of tight pelagic-benthic coupling in the Arctic suggests that current and future fluctuations in sea ice, primary production, and riverine input resulting from global climate change will have major impacts on benthic ecosystems. To understand how these changes will affect benthic ecosystem function, we must characterize diversity, spatial distribution, and community composition for all faunal components. Bacteria and archaea link the biotic and abiotic realms, playing important roles in organic matter (OM) decomposition, biogeochemical cycling, and contaminant degradation, yet sediment microbial communities have rarely been examined in the North American Arctic. Shifts in microbial community structure and composition occur with shifts in OM inputs and contaminant exposure, with implications for shifts in ecological function. Furthermore, the characterization of benthic microbial communities provides a foundation from which to build focused experimental research. We assessed diversity and community structure of benthic prokaryotes in the upper 1 cm of sediments in the southern Beaufort Sea (United States and Canada), and investigated environmental correlates of prokaryotic community structure over a broad spatial scale (spanning 1,229 km) at depths ranging from 17 to 1,200 m. Based on hierarchical clustering, we identified four prokaryotic assemblages from the 85 samples analyzed. Two were largely delineated by the markedly different environmental conditions in shallow shelf vs. upper continental slope sediments. A third assemblage was mainly comprised of operational taxonomic units (OTUs) shared between the shallow shelf and upper slope assemblages. The fourth assemblage corresponded to sediments receiving heavier OM loading, likely resulting in a shallower anoxic layer. These sites may also harbor microbial mats and/or methane seeps. Substructure within these assemblages generally reflected turnover along a longitudinal gradient, which may be related to the quantity and composition of OM deposited to the seafloor; bathymetry and the Mackenzie River were the two major factors influencing prokaryote distribution on this scale. In a broader geographical context, differences in prokaryotic community structure between the Beaufort Sea and Norwegian Arctic suggest that benthic microbes may reflect regional differences in the hydrography, biogeochemistry, and bathymetry of Arctic shelf systems.
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Affiliation(s)
- Alexis M Walker
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Sarah L Mincks
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, United States
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Jurelevicius D, Cotta SR, Montezzi LF, Dias ACF, Mason OU, Picão RC, Jansson JK, Seldin L. Enrichment of potential pathogens in marine microbiomes with different degrees of anthropogenic activity. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115757. [PMID: 33168375 DOI: 10.1016/j.envpol.2020.115757] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
Anthropogenic activities in coastal marine ecosystems can lead to an increase in the abundance of potentially harmful microorganisms in the marine environment. To understand anthropogenic impacts on the marine microbiome, we first used publicly available microbial phylogenetic and functional data to establish a dataset of bacterial genera potentially related to pathogens that cause diseases (BGPRD) in marine organisms. Representatives of low-, medium- and highly impacted marine coastal environments were selected, and the abundance and composition of their microbial communities were determined by quantitative PCR and 16 S rRNA gene sequencing. In total, 72 BGPRD were cataloged, and 11, 36 and 37 BGPRD were found in low-, medium- and highly human-impacted ecosystems, respectively. The absolute abundance of BGPRD and the co-occurrence of antibiotic resistance genes (AGR) increased with the degree of anthropogenic perturbation in these ecosystems. Anthropogenically impacted coastal microbiomes were compositionally and functionally distinct from those of less impacted sites, presenting features that may contribute to adverse outcomes for marine macrobiota in the Anthropocene era.
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Affiliation(s)
- Diogo Jurelevicius
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Simone R Cotta
- ESALQ - Escola Superior de Agricultura Luiz de Queiroz, Piracicaba, SP, Brazil
| | - Lara F Montezzi
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Armando C F Dias
- ESALQ - Escola Superior de Agricultura Luiz de Queiroz, Piracicaba, SP, Brazil
| | - Olivia U Mason
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Renata C Picão
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Janet K Jansson
- Earth and Biological, Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Relationship between Rainfall, Fecal Pollution, Antimicrobial Resistance, and Microbial Diversity in an Urbanized Subtropical Bay. Appl Environ Microbiol 2020; 86:AEM.01229-20. [PMID: 32709726 PMCID: PMC7499047 DOI: 10.1128/aem.01229-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022] Open
Abstract
The presence of human enteric pathogens, stemming from fecal pollution, is a serious environmental and public health concern in recreational waters. Accurate assessments of fecal pollution are therefore needed to properly assess exposure risks and guide water quality policies and practices. In this study, the absence of a direct correlation between enterococci and source-specific human and animal markers disputes the utility of enterococci as an indicator of fecal pollution in urbanized subtropical bays. Moreover, the inverse correlation between enterococci and the human-specific marker HF183 indicates that recreational beach advisories, triggered by elevated enterococcus concentrations, are a misleading practice. This study clearly demonstrates that a multiparameter approach that includes the quantitation of host-specific markers, as well as analyses of microbial diversity, is a more effective means of assessing water quality in urbanized subtropical bays. Urbanized bays are vulnerable to fecal bacterial pollution, and the extent of this pollution, in marine recreational waters, is commonly assessed by quantifying enterococcus concentrations. Recent reports have questioned the utility of enterococci as an indicator of fecal bacterial pollution in subtropical bays impaired by non-point source pollution, and enterococcus data alone cannot identify fecal bacterial sources (i.e., hosts). The purpose of this study was to assess relationships between rainfall, fecal bacterial pollution, antimicrobial resistance, and microbial diversity in an urbanized subtropical bay. Thus, a comprehensive bacterial source tracking (BST) study was conducted using a combination of traditional and modern BST methods. Findings show that rainfall was directly correlated with elevated enterococcus concentrations, including the increased prevalence of Enterococcus faecium, although it was not correlated with an increase in the prevalence of antimicrobial-resistant strains. Rainfall was also correlated with decreased microbial diversity. In contrast, neither rainfall nor enterococcus concentrations were directly correlated with the concentrations of three omnipresent host-associated fecal markers (i.e., human, canine, and gull). Notably, the human fecal marker (HF183) was inversely correlated with enterococcus concentrations, signifying that traditional enterococcus data alone are not an accurate proxy for human fecal waste in urbanized subtropical bays. IMPORTANCE The presence of human enteric pathogens, stemming from fecal pollution, is a serious environmental and public health concern in recreational waters. Accurate assessments of fecal pollution are therefore needed to properly assess exposure risks and guide water quality policies and practices. In this study, the absence of a direct correlation between enterococci and source-specific human and animal markers disputes the utility of enterococci as an indicator of fecal pollution in urbanized subtropical bays. Moreover, the inverse correlation between enterococci and the human-specific marker HF183 indicates that recreational beach advisories, triggered by elevated enterococcus concentrations, are a misleading practice. This study clearly demonstrates that a multiparameter approach that includes the quantitation of host-specific markers, as well as analyses of microbial diversity, is a more effective means of assessing water quality in urbanized subtropical bays.
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11
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Noyer M, Reoyo-Prats B, Aubert D, Bernard M, Verneau O, Palacios C. Particle-attached riverine bacteriome shifts in a pollutant-resistant and pathogenic community during a Mediterranean extreme storm event. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 732:139047. [PMID: 32473395 DOI: 10.1016/j.scitotenv.2020.139047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/22/2020] [Accepted: 04/25/2020] [Indexed: 06/11/2023]
Abstract
Rivers are representative of the overall contamination found in their catchment area. Contaminant concentrations in watercourses depend on numerous factors including land use and rainfall events. Globally, in Mediterranean regions, rainstorms are at the origin of fluvial multipollution phenomena as a result of Combined Sewer Overflows (CSOs) and floods. Large loads of urban-associated microorganisms, including faecal bacteria, are released from CSOs which place public health - as well as ecosystems - at risk. The impacts of freshwater contamination on river ecosystems have not yet been adequately addressed, as is the case for the release of pollutant mixtures linked to extreme weather events. In this context, microbial communities provide critical ecosystem services as they are the only biological compartment capable of degrading or transforming pollutants. Through the use of 16S rRNA gene metabarcoding of environmental DNA at different seasons and during a flood event in a typical Mediterranean coastal river, we show that the impacts of multipollution phenomena on structural shifts in the particle-attached riverine bacteriome were greater than those of seasonality. Key players were identified via multivariate statistical modelling combined with network module eigengene analysis. These included species highly resistant to pollutants as well as pathogens. Their rapid response to contaminant mixtures makes them ideal candidates as potential early biosignatures of multipollution stress. Multiple resistance gene transfer is likely enhanced with drastic consequences for the environment and human-health, particularly in a scenario of intensification of extreme hydrological events.
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Affiliation(s)
- Mégane Noyer
- Univ. Perpignan Via Domitia, CEFREM, UMR5110, F-66860 Perpignan, France; CNRS, CEFREM, UMR5110, F-66860 Perpignan, France
| | - Brice Reoyo-Prats
- Univ. Perpignan Via Domitia, CEFREM, UMR5110, F-66860 Perpignan, France; CNRS, CEFREM, UMR5110, F-66860 Perpignan, France
| | - Dominique Aubert
- Univ. Perpignan Via Domitia, CEFREM, UMR5110, F-66860 Perpignan, France; CNRS, CEFREM, UMR5110, F-66860 Perpignan, France
| | - Maria Bernard
- Univ. Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France; INRAE, SIGENAE, 78350 Jouy-en-Josas, France
| | - Olivier Verneau
- Univ. Perpignan Via Domitia, CEFREM, UMR5110, F-66860 Perpignan, France; CNRS, CEFREM, UMR5110, F-66860 Perpignan, France; Unit. for Environmental Sciences and Management, North-West University, ZA-2520 Potchefstroom, South Africa
| | - Carmen Palacios
- Univ. Perpignan Via Domitia, CEFREM, UMR5110, F-66860 Perpignan, France; CNRS, CEFREM, UMR5110, F-66860 Perpignan, France.
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12
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Paulino GVB, Félix CR, Silvan CG, Andersen GL, Landell MF. Bacterial community and environmental factors associated to rivers runoff and their possible impacts on coral reef conservation. MARINE POLLUTION BULLETIN 2020; 156:111233. [PMID: 32510379 DOI: 10.1016/j.marpolbul.2020.111233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/27/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
Rivers potentially conduct important components as result of anthropogenic stressors for coral reefs. Molecular techniques are increasingly being used for monitoring biological and chemical monitoring of rivers and reefs. Here, we use PhyloChips™ to process surface water samples collected along two rivers and associated reefs in an environmental protection area in northeastern Brazil. Our results indicate that a significant part of Operational Taxonomic Units (OTUs) identified were able to survive the transition from freshwater to seawater, several of them belonging to genera implicated in human pathogenesis. The BBC:A ratio and functional prediction suggests that both study rivers are subject to fecal contamination and xenobiotics input and that the bacterial communities were more homogeneous in these environments. We suggest that protection actions adopted for reefs should be broadly extended to the surrounding environment, and that other bacterial group (besides cultivable coliforms) should be included in routine water quality monitoring.
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Affiliation(s)
| | - Ciro Ramon Félix
- Universidade Federal de Alagoas - UFAL, Campus A. C. Simões, Av. Lourival Melo Mota, s/n, CEP: 57072-900 Maceió, AL, Brazil
| | - Cinta Gomez Silvan
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Gary L Andersen
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Melissa Fontes Landell
- Universidade Federal de Alagoas - UFAL, Campus A. C. Simões, Av. Lourival Melo Mota, s/n, CEP: 57072-900 Maceió, AL, Brazil.
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13
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Zhang L, Fang W, Li X, Gao G, Jiang J. Linking bacterial community shifts with changes in the dissolved organic matter pool in a eutrophic lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 719:137387. [PMID: 32114229 DOI: 10.1016/j.scitotenv.2020.137387] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 06/10/2023]
Abstract
Aquatic bacterial communities play crucial roles in the circulation of nutrients in watershed ecosystems. However, the interaction between bacterial communities and chromophoric dissolved organic matter (CDOM) in freshwater ecosystems has not been studied in depth. In our study, we examined the constitution and interactions of CDOM with the bacterial community in Lake Chaohu and its inflow rivers under the influence of different exogenous pollutants. The results revealed that the bacterial community diversity in the inflow rivers was significantly lower than that in the lake sites. Clustering of different types of polluted inflow rivers integrated with the most abundant genera observed in specific areas indicated that environmentally guided species selection had a large impact on the composition of aquatic bacterial communities. Moreover, our study suggests that communities in lake environments may be more susceptible to interference through a variety of physiologies or via functional redundancy, allowing them to preserve their community structure. Through linear discriminant analysis effect size (Lefse) methods, we revealed that some taxa (from phylum to genus) were consistently enriched in the lake sites. Based on correlation network analysis results, the supersession niches of bacterial community members related to different CDOM in the biogeochemical process was determined. This study provides an ecological basis for the control of external pollution and the protection of the water environment in watershed ecosystems.
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Affiliation(s)
- Lei Zhang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Wangkai Fang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China
| | - Xingchen Li
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jiahu Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
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14
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Cheng WH, Lu HP, Chen CC, Jan S, Hsieh CH. Vertical Beta-Diversity of Bacterial Communities Depending on Water Stratification. Front Microbiol 2020; 11:449. [PMID: 32265880 PMCID: PMC7103642 DOI: 10.3389/fmicb.2020.00449] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/02/2020] [Indexed: 11/13/2022] Open
Abstract
Many studies indicate that variation of marine bacterial beta diversity in the horizontal dimension is mainly attributable to environmental and spatial effects. However, whether and how these two effects drive bacterial beta diversity in the vertical dimension remains unclear, especially when considering seasonal variation in the strength of water stratification. Here, we used 78 paired bacterioplankton community samples from surface and deep chlorophyll maximum (DCM) layers along a transect in the Kuroshio region east of Taiwan across multiple seasons. Variance partitioning was used to evaluate the mechanisms driving the vertical beta diversity between surface-DCM bacterioplankton communities during weak stratification periods (i.e., spring and fall) versus strong stratification periods (i.e., summer). During strong periods of stratification, vertical beta diversity was shaped by both environmental and spatial effects; notably, the strength of stratification played an important role in enhancing environmental dissimilarity and creating a barrier to dispersal. In contrast, during periods of weak stratification, environmental effects dominate, with a non-significant spatial effect due to mixing. Variation of vertical beta diversity for bacterioplankton communities in the Kuroshio region east of Taiwan was structured by different mechanisms across seasons, and was further dependent on stratification strength of the water column.
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Affiliation(s)
- Wan-Hsuan Cheng
- Taiwan International Graduate Program-Earth System Science Program, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program-Earth System Science Program, National Central University, Taoyuan, Taiwan
| | - Hsiao-Pei Lu
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.,Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chung-Chi Chen
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Sen Jan
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Chih-Hao Hsieh
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.,Institute of Ecology and Evolutionary Biology, Department of Life Science, National Taiwan University, Taipei, Taiwan.,Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.,National Center for Theoretical Sciences, Taipei, Taiwan
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15
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FEAST: fast expectation-maximization for microbial source tracking. Nat Methods 2019; 16:627-632. [DOI: 10.1038/s41592-019-0431-x] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 04/23/2019] [Indexed: 02/06/2023]
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16
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Zhu W, Liu Y, Wang S, Yu M, Qian W. Development of microbial community-based index of biotic integrity to evaluate the wetland ecosystem health in Suzhou, China. ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:377. [PMID: 31104161 DOI: 10.1007/s10661-019-7512-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
The development of microbial community-based biological indicators for assessing aquatic ecological status is urgently needed in heavily impaired regions, due to the local extinction of traditional indicator macro-organisms. The aim of this study was to develop and validate a microbial community-based index of biotic integrity (MC-IBI) to assess the health of wetlands in Suzhou, China. High-throughput sequencing was used to obtain information about microbial communities in wetlands and to investigate the health of the wetlands. When constructing the index, we selected what we considered were the most important environmental factors and biological parameters, and identified sensitive and tolerant species. We then used the index to evaluate the health of the inflows and outflows of 15 wetlands in Suzhou. The results showed that, of the 30 samples collected at the 10 impacted inflow sites, 2 were classified as "poor," 5 were "commonly," 18 were sub-healthy, and 5 were healthy; at the restored outflow sites, 24 were "healthy" and 6 were "sub-healthy." The health was worst at the inflows of wetlands that received agricultural effluent, followed by those that received industrial effluent, and was best at those that received urban effluent. The results from our study show that this newly developed MC-IBI gave reasonable evaluations of the health of wetland ecosystems. This application demonstrates that the evaluation system was feasible and we suggest that evaluations that further MC-IBI evaluation approaches should be developed further in the future.
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Affiliation(s)
- Wenting Zhu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Suzhou Polytechnic Institute of Agricultures, Suzhou, 215008, China
| | - Yingying Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Suzhou Polytechnic Institute of Agricultures, Suzhou, 215008, China
| | - Sitan Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Suzhou Polytechnic Institute of Agricultures, Suzhou, 215008, China
| | - Miao Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Suzhou Polytechnic Institute of Agricultures, Suzhou, 215008, China
| | - Wei Qian
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Suzhou University of Science and Technology, Suzhou, 215009, China.
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17
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Wang Y, Liu Y, Wang J, Luo T, Zhang R, Sun J, Zheng Q, Jiao N. Seasonal dynamics of bacterial communities in the surface seawater around subtropical Xiamen Island, China, as determined by 16S rRNA gene profiling. MARINE POLLUTION BULLETIN 2019; 142:135-144. [PMID: 31232286 DOI: 10.1016/j.marpolbul.2019.03.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 02/03/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
This study investigated the microbial structure in the surface seawater from five coastal sites around Xiamen Island, China, over four seasons to evaluate seasonal environmental fluctuations impact on them. This subtropical island is characterized by long, hot, humid summers, and short, mild, dry winters. All sites were dominated by Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes; microbial community composition was similar across four seasons. However, larger proportions of Gammaproteobacteria and Bacillus were observed during the summer than during any other season. The high ratio of Bacillus, Bacteroidetes, and Clostridia richness to Alphaproteobacteria richness in the summer, suggested that the sites we tested were heavily affected by waste water to other seasons. Correlation-based network analyses among the bacterial species and environmental variables indicated important connections between physiochemical variables and specific taxonomic groups. Collectively, our results suggested that seasonal shifts and wastewater pollution together shape the structures of the microbial communities around Xiamen Island.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Yanting Liu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Jianning Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Tingwei Luo
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Jia Sun
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China.
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China.
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18
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Yang N, Li Y, Zhang W, Wang L, Gao Y. Reduction of bacterial integrity associated with dam construction: A quantitative assessment using an index of biotic integrity improved by stability analysis. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 230:75-83. [PMID: 30273786 DOI: 10.1016/j.jenvman.2018.09.071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/14/2018] [Accepted: 09/22/2018] [Indexed: 06/08/2023]
Abstract
Rivers are extensively regulated by damming, yet the effects of such interruption on bacterial communities have not been assessed quantitatively. To fill this gap, we proposed a bacteria-based index of biotic integrity (Ba-IBI) by using bacterial community dataset collected from the Three Gorges Reservoir and its upper reaches. Stability analysis based on bacterial resistance (RS) and resilience (RL) to external disturbance was conducted to improve the performance of the index. Four core metrics, i.e. the ratio of Bacilli, Bacteroidetes and Clostridia to Alphaproteobacteria (BBC/A), Oxalobacteraceae, Methanotrophs and Thermophiles were selected after range, responsive and redundancy tests. The improved Ba-IBI, ranging from 1.04 to 4.10, was better at distinguishing sites with or without direct dam effects compared with the unimproved one. The index values maintained high in the riverine sites while reducing in the reservoir, demonstrating the negative influence of dam construction on bacterial integrity. Based on the assessment results, 23.1%, 46.2% and 30.8% sampling sites were large, moderately and little affected by damming, respectively. A Random Forest (RF) regression model was trained and tested, offering a valid prediction of the input Ba-IBI and environmental parameters. Sensitivity analysis revealed the significant contributions of flow velocity towards the predicting process performance, indicating the importance of hydrodynamic conditions on determining the spatial variability of bacterial communities. This study provides not only a first quantitative insight for assessing bacterial response to damming, but also a guideline for applying the improved index in the dam regulation and ecological protection.
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Affiliation(s)
- Nan Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Linqiong Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Yu Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
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19
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Dai T, Zhang Y, Ning D, Su Z, Tang Y, Huang B, Mu Q, Wen D. Dynamics of Sediment Microbial Functional Capacity and Community Interaction Networks in an Urbanized Coastal Estuary. Front Microbiol 2018; 9:2731. [PMID: 30487783 PMCID: PMC6246683 DOI: 10.3389/fmicb.2018.02731] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 10/25/2018] [Indexed: 11/23/2022] Open
Abstract
Coastal estuaries and bays are exposed to both natural and anthropogenic environmental changes, inflicting intensive stress on the microbial communities inhabiting these areas. However, it remains unclear how microbial community diversity and their eco-functions are affected by anthropogenic disturbances rather than natural environmental changes. Here, we explored sediment microbial functional genes dynamics and community interaction networks in Hangzhou Bay (HZB), one of the most severely polluted bays on China’s eastern coast. The results indicated key microbial functional gene categories, including N, P, S, and aromatic compound metabolism, and stress response, displayed significant spatial dynamics along environmental gradients. Sensitive feedbacks of key functional gene categories to N and P pollutants demonstrated potential impacts of human-induced seawater pollutants to microbial functional capacity. Seawater ammonia and dissolved inorganic nitrogen (DIN) was identified as primary drivers in selecting adaptive populations and varying community composition. Network analysis revealed distinct modules that were stimulated in inner or outer bay. Importantly, the network keystone species, which played a fundamental role in community interactions, were strongly affected by N-pollutants. Our results provide a systematic understanding of the microbial compositional and functional dynamics in an urbanized coastal estuary, and highlighted the impact of human activities on these communities.
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Affiliation(s)
- Tianjiao Dai
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Yan Zhang
- School of Environment and Civil Engineering, Jiangnan University, Wuxi, China
| | - Daliang Ning
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, OK, United States.,Consolidated Core Laboratory, University of Oklahoma, Norman, OK, United States.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Zhiguo Su
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Yushi Tang
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Bei Huang
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan, China
| | - Qinglin Mu
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
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20
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Jin D, Kong X, Cui B, Jin S, Xie Y, Wang X, Deng Y. Bacterial communities and potential waterborne pathogens within the typical urban surface waters. Sci Rep 2018; 8:13368. [PMID: 30190569 PMCID: PMC6127328 DOI: 10.1038/s41598-018-31706-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 05/10/2018] [Indexed: 12/11/2022] Open
Abstract
Waterborne pathogens have attracted a great deal of attention in the public health sector over the last several decades. However, little is known about the pathogenic microorganisms in urban water systems. In this study, the bacterial community structure of 16 typical surface waters in the city of Beijing were analyzed using Illumina MiSeq high-throughput sequencing based on 16S rRNA gene. The results showed that Bacteroidetes, Proteobacteria and Actinobacteria were the dominant groups in 16 surface water samples, and Betaproteobacteria, Alphaproteobacteria, Flavobacteriia, Sphingobacteriia and Actinobacteria were the most dominant classes. The dominant genus across all samples was Flavobacterium. In addition, fifteen genus level groups of potentialy pathogenic bacteria were detected within the 16 water samples, with Pseudomonas and Aeromonas the most frequently identified. Spearman correlation analysis demonstrated that richness estimators (OTUs and Chao1) were correlated with water temperature, nitrate and total nitrogen (p < 0.05), while ammonia-nitrogen and total nitrogen were significantly correlated with the percent of total potential pathogens (p ≤ 0.05). These results could provide insight into the ecological function and health risks of surface water bacterial communities during the process of urbanization.
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Affiliation(s)
- Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China. .,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiao Kong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bingjian Cui
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shulan Jin
- School of History Geography and Tourism, Shangrao Normal University, Shangrao, 334000, China
| | - Yunfeng Xie
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xingrun Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China. .,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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21
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Liu S, Jiang Z, Deng Y, Wu Y, Zhang J, Zhao C, Huang D, Huang X, Trevathan-Tackett SM. Effects of nutrient loading on sediment bacterial and pathogen communities within seagrass meadows. Microbiologyopen 2018. [PMID: 29521006 PMCID: PMC6182560 DOI: 10.1002/mbo3.600] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Eutrophication can play a significant role in seagrass decline and habitat loss. Microorganisms in seagrass sediments are essential to many important ecosystem processes, including nutrient cycling and seagrass ecosystem health. However, current knowledge of the bacterial communities, both beneficial and detrimental, within seagrass meadows in response to nutrient loading is limited. We studied the response of sediment bacterial and pathogen communities to nutrient enrichment on a tropical seagrass meadow in Xincun Bay, South China Sea. The bacterial taxonomic groups across all sites were dominated by the Gammaproteobacteria and Firmicutes. Sites nearest to the nutrient source and with the highest NH4+ and PO43− content had approximately double the relative abundance of putative denitrifiers Vibrionales, Alteromonadales, and Pseudomonadales. Additionally, the relative abundance of potential pathogen groups, especially Vibrio spp. and Pseudoalteromonas spp., was approximately 2‐fold greater at the sites with the highest nutrient loads compared to sites further from the source. These results suggest that proximity to sources of nutrient pollution increases the occurrence of potential bacterial pathogens that could affect fishes, invertebrates and humans. This study shows that nutrient enrichment does elicit shifts in bacterial community diversity and likely their function in local biogeochemical cycling and as a potential source of infectious diseases within seagrass meadows.
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Affiliation(s)
- Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China, Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China, Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yiqin Deng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China, Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China, Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Chunyu Zhao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China, Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Delian Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China, Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China, Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Stacey M Trevathan-Tackett
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Vic., Australia
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22
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Price JR, Ledford SH, Ryan MO, Toran L, Sales CM. Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in receiving streams. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 613-614:1104-1116. [PMID: 28954372 DOI: 10.1016/j.scitotenv.2017.09.162] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/30/2017] [Accepted: 09/16/2017] [Indexed: 05/20/2023]
Abstract
Through a combined approach using analytical chemistry, real-time quantitative polymerase chain reaction (qPCR), and targeted amplicon sequencing, we studied the impact of wastewater treatment plant effluent sources at six sites on two sampling dates on the chemical and microbial population regimes within the Wissahickon Creek, and its tributary, Sandy Run, in Montgomery County, Pennsylvania, USA. These water bodies contribute flow to the Schuylkill River, one of the major drinking water sources for Philadelphia, Pennsylvania. Effluent was observed to be a significant source of nutrients, human and non-specific fecal associated taxa. There was an observed increase in the alpha diversity at locations immediately below effluent outflows, which contributed many taxa involved in wastewater treatment processes and nutrient cycling to the stream's microbial community. Unexpectedly, modeling of microbial community shifts along the stream was not controlled by concentrations of measured nutrients. Furthermore, partial recovery, in the form of decreasing abundances of bacteria and nutrients associated with wastewater treatment plant processes, nutrient cycling bacteria, and taxa associated with fecal and sewage sources, was observed between effluent sources, which we hypothesize is controlled by distance from effluent source. Antecedent moisture conditions were observed to impact overall microbial community diversity, with higher diversity occurring after rainfall. Finally, the efficacy of using a subset of the microbial community including the orders of Bifidobacteriales, Bacteroidales, and Clostridiales to estimate the degree of influence due to sewage and fecal sources was explored and verified.
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Affiliation(s)
- Jacob R Price
- Civil, Architectural, and Environmental Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, United States
| | - Sarah H Ledford
- Earth and Environmental Science, Temple University, 1901 N. 13th St, Philadelphia, PA 19122, United States
| | - Michael O Ryan
- Civil, Architectural, and Environmental Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, United States
| | - Laura Toran
- Earth and Environmental Science, Temple University, 1901 N. 13th St, Philadelphia, PA 19122, United States
| | - Christopher M Sales
- Civil, Architectural, and Environmental Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, United States.
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23
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Lv B, Cui Y, Tian W, Feng D. Composition and influencing factors of bacterial communities in ballast tank sediments: Implications for ballast water and sediment management. MARINE ENVIRONMENTAL RESEARCH 2017; 132:14-22. [PMID: 29046225 DOI: 10.1016/j.marenvres.2017.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/08/2017] [Accepted: 10/08/2017] [Indexed: 06/07/2023]
Abstract
This study aims to reveal the composition and influencing factors of bacterial communities in ballast tank sediments. Nine samples were collected and their 16S rRNA gene sequences were analyzed by high-throughput sequencing. The analysis results showed the Shannon index in ballast tank sediments was in the range of 5.27-6.35, which was significantly higher than that in ballast water. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi and Proteobacteria were the dominant phyla and accounted for approximately 80% of all 16S rRNA gene sequences of the samples. Besides, the high contents of sulfate reducing bacteria (SRB) and sulfur oxidizing bacteria were detected in sediments, indicating that the corrosion of metal caused by SRB might occur in ballast tank. In addition, the trace of human fecal bacteria and candidate pathogens were also detected in ballast tank sediments, and these undesirable microbes reduced the effect of ballast water exchange. Furthermore, C and N had significant effects on the bacterial community composition in ballast tank sediments. In conclusion, our findings suggest that the proper management and disposal of the ballast tank sediments should be considered in order to reduce the negative impact and ecological risks related to ballast water and sediments.
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Affiliation(s)
- Baoyi Lv
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China.
| | - Yuxue Cui
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai 200241, China
| | - Wen Tian
- Jiangyin Entry-Exit Inspection and Quarantine Bureau, Jiangyin 214442, China
| | - Daolun Feng
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
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24
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Li J, Li Y, Qian B, Niu L, Zhang W, Cai W, Wu H, Wang P, Wang C. Development and validation of a bacteria-based index of biotic integrity for assessing the ecological status of urban rivers: A case study of Qinhuai River basin in Nanjing, China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 196:161-167. [PMID: 28284134 DOI: 10.1016/j.jenvman.2017.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/12/2017] [Accepted: 03/01/2017] [Indexed: 05/20/2023]
Abstract
With the increasing human disturbance to urban rivers, the extinction and biodiversity losses of some macroorganism species decreased the accuracy of bioassessment. In this study, a novel index of biotic integrity based on bacteria (Ba-IBI) was first developed for Qinhuai River in Nanjing city, China. Thirty-two biofilm samples were collected along the river bank and the bacterial communities were identified by high-throughput sequencing. By the range, responsive, and redundancy tests, four core metrics were selected from the dataset of 78 candidate metrics, including Pielou's evenness index, proportion of Paenibacillus, proportion of OTUs tolerant to organic pollution and proportion of Nitrosomonas. The results showed that the Ba-IBI was able to effectively discriminate different impaired site groups, and had a good correlation with the index of water quality (r = 0.79, p < 0.01) and the qualitative habitat evaluation index (r = 0.51, p < 0.01). Moreover, the Ba-IBI was negatively correlated with the number of population within a 1 km buffer (r = -0.71, p < 0.01). Application of the index showed that most of the sites were in the poor or bad class in the river. Our study revealed that the Ba-IBI is an effective and reliable approach for assessing the ecological status of Qinhuai River basin, which can complement the existing ecological assessment approaches for urban rivers. Meanwhile, repeted surveys and field validations are still needed to further improve the applicability of the index in future studies.
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Affiliation(s)
- Jie Li
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yi Li
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Bao Qian
- Hydrology Bureau of Changjiang Water Resources Commission, Wuhan, Hubei, 430010, PR China
| | - Lihua Niu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Wenlong Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Wei Cai
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Hainan Wu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Peifang Wang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Chao Wang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, PR China
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25
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Piceno YM, Pecora-Black G, Kramer S, Roy M, Reid FC, Dubinsky EA, Andersen GL. Bacterial community structure transformed after thermophilically composting human waste in Haiti. PLoS One 2017; 12:e0177626. [PMID: 28570610 PMCID: PMC5453478 DOI: 10.1371/journal.pone.0177626] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 05/01/2017] [Indexed: 11/19/2022] Open
Abstract
Recycling human waste for beneficial use has been practiced for millennia. Aerobic (thermophilic) composting of sewage sludge has been shown to reduce populations of opportunistically pathogenic bacteria and to inactivate both Ascaris eggs and culturable Escherichia coli in raw waste, but there is still a question about the fate of most fecal bacteria when raw material is composted directly. This study undertook a comprehensive microbial community analysis of composting material at various stages collected over 6 months at two composting facilities in Haiti. The fecal microbiota signal was monitored using a high-density DNA microarray (PhyloChip). Thermophilic composting altered the bacterial community structure of the starting material. Typical fecal bacteria classified in the following groups were present in at least half the starting material samples, yet were reduced below detection in finished compost: Prevotella and Erysipelotrichaceae (100% reduction of initial presence), Ruminococcaceae (98–99%), Lachnospiraceae (83–94%, primarily unclassified taxa remained), Escherichia and Shigella (100%). Opportunistic pathogens were reduced below the level of detection in the final product with the exception of Clostridium tetani, which could have survived in a spore state or been reintroduced late in the outdoor maturation process. Conversely, thermotolerant or thermophilic Actinomycetes and Firmicutes (e.g., Thermobifida, Bacillus, Geobacillus) typically found in compost increased substantially during the thermophilic stage. This community DNA-based assessment of the fate of human fecal microbiota during thermophilic composting will help optimize this process as a sanitation solution in areas where infrastructure and resources are limited.
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Affiliation(s)
- Yvette M. Piceno
- Ecology Department, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Gabrielle Pecora-Black
- Agricultural & Environmental Chemistry Graduate Group, University of California, Davis, CA, United States of America
| | - Sasha Kramer
- Sustainable Organic Integrated Livelihoods, Port-au-Prince, Haiti
| | - Monika Roy
- Sustainable Organic Integrated Livelihoods, Port-au-Prince, Haiti
| | - Francine C. Reid
- Ecology Department, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Eric A. Dubinsky
- Ecology Department, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Gary L. Andersen
- Ecology Department, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- * E-mail:
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26
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Suriya J, Chandra Shekar M, Nathani NM, Suganya T, Bharathiraja S, Krishnan M. Assessment of bacterial community composition in response to uranium levels in sediment samples of sacred Cauvery River. Appl Microbiol Biotechnol 2016; 101:831-841. [PMID: 27812801 DOI: 10.1007/s00253-016-7945-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 10/09/2016] [Accepted: 10/13/2016] [Indexed: 01/20/2023]
Abstract
Global industrialization is a major cause of effluent discharge from industries up to alarming concentrations. Especially, uranium concentrations in water bodies are of great concern, as its radioactivity significantly affects the persistent diversity of microbiota. Recently, continuous application of pesticides in the agricultural lands and accumulation of quartz that enter the Cauvery River has significantly increased the concentration of uranium (U) and other heavy metals. To perceive the impact of uranium on bacterial diversity in Cauvery River, sediment samples collected from polluted (UP) site with 32.4 Bq/K of U concentration and control (UNP) site were scrutinized for bacterial diversity through metagenomic analysis of the V3 region of 16S rDNA by Illumina sequencing. Taxonomic assignment revealed that the unpolluted sample was dominated by Bacteroidetes (27.7 %), and Firmicutes (25.9 %), while sediment sample from the highly polluted site revealed abundance of Proteobacteria (47.5 %) followed by Bacteroidetes (22.4 %) and Firmicutes (14.6 %). Among Proteobacteria, Gammaproteobacteria was the most prevalent group followed by alpha, delta, epsilon, and beta in the uranium-polluted sample. Rare and abundant species analysis revealed that species like Idiomarina loihiensis was abundant in the pollutant sample; however, it was rare (<0.1 %) in the sample from pristine environment. Similarly, the species distribution in both the samples varied, with the bacteria potentially active in redox activity and biosorption potential dominating in the polluted sample. Outcomes of the present study demonstrated the impact of uranium and metal accumulation on the bacterial communities and further confirmed the promising candidature of specific bacterial species as bioindicators of contamination.
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Affiliation(s)
- Jayaraman Suriya
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
| | - Mootapally Chandra Shekar
- CAS in Marine Biology, Annamalai University, Porto Novo, Tamil Nadu, 608502, India.,Department of Marine Science, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat, 364002, India
| | - Neelam Mustakali Nathani
- Department of Biosciences, Saurashtra University, Rajkot, Gujarat, 360005, India.,Department of Life Sciences, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat, 364002, India
| | - Thangaiyan Suganya
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
| | | | - Muthukalingan Krishnan
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
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27
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Uyaguari-Diaz MI, Chan M, Chaban BL, Croxen MA, Finke JF, Hill JE, Peabody MA, Van Rossum T, Suttle CA, Brinkman FSL, Isaac-Renton J, Prystajecky NA, Tang P. A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples. MICROBIOME 2016; 4:20. [PMID: 27391119 PMCID: PMC5011856 DOI: 10.1186/s40168-016-0166-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/04/2016] [Indexed: 05/16/2023]
Abstract
BACKGROUND Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic understanding of a microbiome, a strategy to characterize the viral, bacterial, and eukaryotic components is necessary. RESULTS We developed a method for metagenomic and amplicon-based analysis of freshwater samples involving the concentration and size-based separation of eukaryotic, bacterial, and viral fractions. Next-generation sequencing and culture-independent approaches were used to describe and quantify microbial communities in watersheds with different land use in British Columbia. Deep amplicon sequencing was used to investigate the distribution of certain viruses (g23 and RdRp), bacteria (16S rRNA and cpn60), and eukaryotes (18S rRNA and ITS). Metagenomic sequencing was used to further characterize the gene content of the bacterial and viral fractions at both taxonomic and functional levels. CONCLUSION This study provides a systematic approach to separate and characterize eukaryotic-, bacterial-, and viral-sized particles. Methodologies described in this research have been applied in temporal and spatial studies to study the impact of land use on watershed microbiomes in British Columbia.
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Affiliation(s)
- Miguel I. Uyaguari-Diaz
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Michael Chan
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
| | - Bonnie L. Chaban
- South Kensington Campus, Imperial College London, Sir Ernst Chain Building, London, SW7 2AZ UK
| | - Matthew A. Croxen
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
| | - Jan F. Finke
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4 Canada
| | - Michael A. Peabody
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Thea Van Rossum
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Curtis A. Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8 Canada
| | - Fiona S. L. Brinkman
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Judith Isaac-Renton
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Natalie A. Prystajecky
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
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28
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McLellan SL, Fisher JC, Newton RJ. The microbiome of urban waters. Int Microbiol 2015; 18:141-9. [PMID: 27036741 PMCID: PMC8793681 DOI: 10.2436/20.1501.01.244] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 09/10/2015] [Indexed: 11/15/2022]
Abstract
More than 50% of the world's population lives in urban centers. As collection basins for landscape activity, urban waters are an interface between human activity and the natural environment. The microbiome of urban waters could provide insight into the impacts of pollution, the presence of human health risks, or the potential for long-term consequences for these ecosystems and the people who depend upon them. An integral part of the urban water cycle is sewer infrastructure. Thousands of miles of pipes line cities as part of wastewater and stormwater systems. As stormwater and sewage are released into natural waterways, traces of human and animal microbiomes reflect the sources and magnitude of fecal pollution and indicate the presence of pollutants, such as nutrients, pathogens, and chemicals. Non-fecal organisms are also released as part of these systems. Runoff from impervious surfaces delivers microbes from soils, plants and the built environment to stormwater systems. Further, urban sewer infrastructure contains its own unique microbial community seemingly adapted to this relatively new artificial habitat. High microbial densities are conveyed via pipes to waterways, and these organisms can be found as an urban microbial signature imprinted on the natural community of rivers and urban coastal waters. The potential consequences of mass releases of non-indigenous microorganisms into natural waters include creation of reservoirs for emerging human pathogens, altered nutrient flows into aquatic food webs, and increased genetic exchange between two distinct gene pools. This review highlights the recent characterization of the microbiome of urban sewer and stormwater infrastructure and its connection to and potential impact upon freshwater systems.
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Affiliation(s)
- Sandra L. McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Jenny C. Fisher
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ryan J. Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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29
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Li X, Harwood VJ, Nayak B, Staley C, Sadowsky MJ, Weidhaas J. A novel microbial source tracking microarray for pathogen detection and fecal source identification in environmental systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:7319-7329. [PMID: 25970344 DOI: 10.1021/acs.est.5b00980] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pathogen detection and the identification of fecal contamination sources are challenging in environmental waters. Factors including pathogen diversity and ubiquity of fecal indicator bacteria hamper risk assessment and remediation of contamination sources. A custom microarray targeting pathogens (viruses, bacteria, protozoa), microbial source tracking (MST) markers, and antibiotic resistance genes was tested against DNA obtained from whole genome amplification (WGA) of RNA and DNA from sewage and animal (avian, cattle, poultry, and swine) feces. Perfect and mismatch probes established the specificity of the microarray in sewage, and fluorescence decrease of positive probes over a 1:10 dilution series demonstrated semiquantitative measurement. Pathogens, including norovirus, Campylobacter fetus, Helicobacter pylori, Salmonella enterica, and Giardia lamblia were detected in sewage, as well as MST markers and resistance genes to aminoglycosides, beta-lactams, and tetracycline. Sensitivity (percentage true positives) of MST results in sewage and animal waste samples (21-33%) was lower than specificity (83-90%, percentage of true negatives). Next generation DNA sequencing revealed two dominant bacterial families that were common to all sample types: Ruminococcaceae and Lachnospiraceae. Five dominant phyla and 15 dominant families comprised 97% and 74%, respectively, of sequences from all fecal sources. Phyla and families not represented on the microarray are possible candidates for inclusion in subsequent array designs.
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Affiliation(s)
- Xiang Li
- †Department of Civil and Environmental Engineering, West Virginia University, P.O. Box 6103, Morgantown, West Virginia 26506, United States
| | - Valerie J Harwood
- ‡Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, United States
| | - Bina Nayak
- ‡Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, United States
| | - Christopher Staley
- §BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Michael J Sadowsky
- ∥Department of Soil, Water, and Climate, BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Jennifer Weidhaas
- †Department of Civil and Environmental Engineering, West Virginia University, P.O. Box 6103, Morgantown, West Virginia 26506, United States
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30
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Barkovskii A, Babb C, Hurley D, Shin E. Origins and environmental mobility of antibiotic resistance genes, virulence factors and bacteria in a tidal creek's watershed. J Appl Microbiol 2015; 118:764-76. [DOI: 10.1111/jam.12735] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/03/2014] [Accepted: 12/19/2014] [Indexed: 11/30/2022]
Affiliation(s)
| | - C.M. Babb
- Georgia College & State University; Milledgeville GA USA
| | - D. Hurley
- Sapelo Island National Estuarine Research Reserve; Sapelo Island GA USA
| | - E. Shin
- Georgia College & State University; Milledgeville GA USA
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31
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Fisher JC, Newton RJ, Dila DK, McLellan SL. Urban microbial ecology of a freshwater estuary of Lake Michigan. ELEMENTA (WASHINGTON, D.C.) 2015; 3:000064. [PMID: 26866046 PMCID: PMC4746012 DOI: 10.12952/journal.elementa.000064] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Freshwater estuaries throughout the Great Lakes region receive stormwater runoff and riverine inputs from heavily urbanized population centers. While human and animal feces contained in this runoff are often the focus of source tracking investigations, non-fecal bacterial loads from soil, aerosols, urban infrastructure, and other sources are also transported to estuaries and lakes. We quantified and characterized this non-fecal urban microbial component using bacterial 16S rRNA gene sequences from sewage, stormwater, rivers, harbor/estuary, and the lake surrounding Milwaukee, WI, USA. Bacterial communities from each of these environments had a distinctive composition, but some community members were shared among environments. We used a statistical biomarker discovery tool to identify the components of the microbial community that were most strongly associated with stormwater and sewage to describe an "urban microbial signature," and measured the presence and relative abundance of these organisms in the rivers, estuary, and lake. This urban signature increased in magnitude in the estuary and harbor with increasing rainfall levels, and was more apparent in lake samples with closest proximity to the Milwaukee estuary. The dominant bacterial taxa in the urban signature were Acinetobacter, Aeromonas, and Pseudomonas, which are organisms associated with pipe infrastructure and soil and not typically found in pelagic freshwater environments. These taxa were highly abundant in stormwater and sewage, but sewage also contained a high abundance of Arcobacter and Trichococcus that appeared in lower abundance in stormwater outfalls and in trace amounts in aquatic environments. Urban signature organisms comprised 1.7% of estuary and harbor communities under baseflow conditions, 3.5% after rain, and >10% after a combined sewer overflow. With predicted increases in urbanization across the Great Lakes, further alteration of freshwater communities is likely to occur with potential long term impacts on the function of estuarine and nearshore ecosystems.
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Affiliation(s)
- Jenny C. Fisher
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States
| | - Ryan J. Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States
| | - Deborah K. Dila
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States
| | - Sandra L. McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States
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McLellan SL, Eren AM. Discovering new indicators of fecal pollution. Trends Microbiol 2014; 22:697-706. [PMID: 25199597 DOI: 10.1016/j.tim.2014.08.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/30/2014] [Accepted: 08/06/2014] [Indexed: 12/30/2022]
Abstract
Fecal pollution indicators are essential to identify and remediate contamination sources and protect public health. Historically, easily cultured facultative anaerobes such as fecal coliforms, Escherichia coli, or enterococci have been used but these indicators generally provide no information as to their source. More recently, molecular methods have targeted fecal anaerobes, which are much more abundant in humans and other mammals, and some strains appear to be associated with particular host sources. Next-generation sequencing and microbiome studies have created an unprecedented inventory of microbial communities associated with fecal sources, allowing reexamination of which taxonomic groups are best suited as informative indicators. The use of new computational methods, such as oligotyping coupled with well-established machine learning approaches, is providing new insights into patterns of host association. In this review we examine the basis for host-specificity and the rationale for using 16S rRNA gene targets for alternative indicators and highlight two taxonomic groups, Bacteroidales and Lachnospiraceae, which are rich in host-specific bacterial organisms. Finally, we discuss considerations for using alternative indicators for water quality assessments with a particular focus on detecting human sewage sources of contamination.
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Affiliation(s)
- Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
| | - A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
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Closek CJ, Sunagawa S, DeSalvo MK, Piceno YM, DeSantis TZ, Brodie EL, Weber MX, Voolstra CR, Andersen GL, Medina M. Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata. ISME JOURNAL 2014; 8:2411-22. [PMID: 24950107 DOI: 10.1038/ismej.2014.85] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 03/30/2014] [Accepted: 04/08/2014] [Indexed: 11/09/2022]
Abstract
Coral diseases impact reefs globally. Although we continue to describe diseases, little is known about the etiology or progression of even the most common cases. To examine a spectrum of coral health and determine factors of disease progression we examined Orbicella faveolata exhibiting signs of Yellow Band Disease (YBD), a widespread condition in the Caribbean. We used a novel combined approach to assess three members of the coral holobiont: the coral-host, associated Symbiodinium algae, and bacteria. We profiled three conditions: (1) healthy-appearing colonies (HH), (2) healthy-appearing tissue on diseased colonies (HD), and (3) diseased lesion (DD). Restriction fragment length polymorphism analysis revealed health state-specific diversity in Symbiodinium clade associations. 16S ribosomal RNA gene microarrays (PhyloChips) and O. faveolata complimentary DNA microarrays revealed the bacterial community structure and host transcriptional response, respectively. A distinct bacterial community structure marked each health state. Diseased samples were associated with two to three times more bacterial diversity. HD samples had the highest bacterial richness, which included components associated with HH and DD, as well as additional unique families. The host transcriptome under YBD revealed a reduced cellular expression of defense- and metabolism-related processes, while the neighboring HD condition exhibited an intermediate expression profile. Although HD tissue appeared visibly healthy, the microbial communities and gene expression profiles were distinct. HD should be regarded as an additional (intermediate) state of disease, which is important for understanding the progression of YBD.
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Affiliation(s)
- Collin J Closek
- 1] Department of Biology, The Pennsylvania State University, University Park, PA, USA [2] School of Natural Sciences, University of California, Merced, CA, USA
| | - Shinichi Sunagawa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Yvette M Piceno
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Eoin L Brodie
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michele X Weber
- 1] Department of Biology, The Pennsylvania State University, University Park, PA, USA [2] School of Natural Sciences, University of California, Merced, CA, USA
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Gary L Andersen
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mónica Medina
- 1] Department of Biology, The Pennsylvania State University, University Park, PA, USA [2] School of Natural Sciences, University of California, Merced, CA, USA
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Port JA, Cullen AC, Wallace JC, Smith MN, Faustman EM. Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments. ENVIRONMENTAL HEALTH PERSPECTIVES 2014; 122:222-228. [PMID: 24334622 PMCID: PMC3948035 DOI: 10.1289/ehp.1307009] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 12/10/2013] [Indexed: 05/29/2023]
Abstract
BACKGROUND High-throughput genomic technologies offer new approaches for environmental health monitoring, including metagenomic surveillance of antibiotic resistance determinants (ARDs). Although natural environments serve as reservoirs for antibiotic resistance genes that can be transferred to pathogenic and human commensal bacteria, monitoring of these determinants has been infrequent and incomplete. Furthermore, surveillance efforts have not been integrated into public health decision making. OBJECTIVES We used a metagenomic epidemiology-based approach to develop an ARD index that quantifies antibiotic resistance potential, and we analyzed this index for common modal patterns across environmental samples. We also explored how metagenomic data such as this index could be conceptually framed within an early risk management context. METHODS We analyzed 25 published data sets from shotgun pyrosequencing projects. The samples consisted of microbial community DNA collected from marine and freshwater environments across a gradient of human impact. We used principal component analysis to identify index patterns across samples. RESULTS We observed significant differences in the overall index and index subcategory levels when comparing ecosystems more proximal versus distal to human impact. The selection of different sequence similarity thresholds strongly influenced the index measurements. Unique index subcategory modes distinguished the different metagenomes. CONCLUSIONS Broad-scale screening of ARD potential using this index revealed utility for framing environmental health monitoring and surveillance. This approach holds promise as a screening tool for establishing baseline ARD levels that can be used to inform and prioritize decision making regarding management of ARD sources and human exposure routes. CITATION Port JA, Cullen AC, Wallace JC, Smith MN, Faustman EM. 2014. Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments. Environ Health Perspect 122:222–228; http://dx.doi.org/10.1289/ehp.1307009
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Affiliation(s)
- Jesse A Port
- Department of Environmental and Occupational Health Sciences, and
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Garrido L, Sánchez O, Ferrera I, Tomàs N, Mas J. Dynamics of microbial diversity profiles in waters of different qualities. Approximation to an ecological quality indicator. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 468-469:1154-1161. [PMID: 24121566 DOI: 10.1016/j.scitotenv.2013.08.065] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 08/20/2013] [Accepted: 08/22/2013] [Indexed: 06/02/2023]
Abstract
Over the past two decades, the amount of reclaimed water has increased throughout the world to face the current water shortage, and as a consequence there is an increasing interest to develop good indicators of water quality, beyond the traditional fecal indicators. In order to meet this need, in this work the microbial profiles of different wastewater treatment plant effluents, both secondary and tertiary, were studied and compared with water samples from an uncontaminated natural aquifer. Taking into account the most abundant phylogenetic groups found in these water samples, we calculated the Bacteroidetes, Gammaproteobacteria and Nitrospira/Betaproteobacteria (BGN:β) ratio and found significant differences between the mean ratios of the four water qualities. The secondary effluent ratios were never below 1.3 and the tertiary effluent and groundwater ratios were never over 0.85. Furthermore, calculation of this index with previous published data supports our results and indicates that the BGN:β ratio is a possible alternative indicator of water quality.
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Affiliation(s)
- L Garrido
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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Cao Y, Van De Werfhorst LC, Scott EA, Raith MR, Holden PA, Griffith JF. Bacteroidales terminal restriction fragment length polymorphism (TRFLP) for fecal source differentiation in comparison to and in combination with universal bacteria TRFLP. WATER RESEARCH 2013; 47:6944-6955. [PMID: 23880219 DOI: 10.1016/j.watres.2013.03.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 03/04/2013] [Accepted: 03/17/2013] [Indexed: 06/02/2023]
Abstract
Terminal restriction fragment length polymorphism (TRFLP) is an attractive community analysis method for microbial source tracking (MST) because it is accessible, relatively inexpensive, and can discern multiple fecal sources simultaneously. A new Bacteroidales TRFLP (Bac-TRFLP) method was developed and its source identification performance was evaluated by itself, in comparison to, and in combination with an existing universal bacterial TRFLP method in two laboratories. Sixty-four blind samples from 12 fecal sources (sewage, septage, human, dog, horse, cow, deer, pig, chicken, goose, pigeon, and gull) were used for evaluation. Bac- and Univ-TRFLP exhibited similarly high overall correct identification (>88% and >89%, respectively), excellent specificity regardless of fecal sources, variable sensitivity depending on the source, and stable performance across two laboratories. Compared to Univ-TRFLP, Bac-TRFLP had better sensitivity and specificity with horse, cow, and pig fecal sources but was not suited for certain avian sources such as goose, gull, and pigeon. Combining the general and more targeted TRFLP methods (Univ&Bac-TRFLP) achieved higher overall correct identification (>92%), higher sensitivity and specificity metrics, and higher reproducibility between laboratories. Our results suggest that the Bac-TRFLP and Univ&Bac-TRFLP methods are promising additions to the MST toolbox and warrant further evaluation and utilization in field MST applications.
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MESH Headings
- Animals
- Bacteroidetes/classification
- Bacteroidetes/genetics
- Bacteroidetes/isolation & purification
- Bacteroidetes/metabolism
- Birds/microbiology
- DNA, Bacterial/classification
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Environmental Monitoring/methods
- Feces/microbiology
- Humans
- Mammals/microbiology
- Polymerase Chain Reaction/methods
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 16S/classification
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Sensitivity and Specificity
- Wastewater/microbiology
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Affiliation(s)
- Yiping Cao
- Southern California Coastal Water Research Project Authority, Costa Mesa, CA 92626, USA
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Ultradeep 16S rRNA sequencing analysis of geographically similar but diverse unexplored marine samples reveal varied bacterial community composition. PLoS One 2013; 8:e76724. [PMID: 24167548 PMCID: PMC3805540 DOI: 10.1371/journal.pone.0076724] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 08/26/2013] [Indexed: 11/19/2022] Open
Abstract
Background Bacterial community composition in the marine environment differs from one geographical location to another. Reports that delineate the bacterial diversity of different marine samples from geographically similar location are limited. The present study aims to understand whether the bacterial community compositions from different marine samples harbour similar bacterial diversity since these are geographically related to each other. Methods and Principal Findings In the present study, 16S rRNA deep sequencing analysis targeting V3 region was performed using Illumina bar coded sequencing. A total of 22.44 million paired end reads were obtained from the metagenomic DNA of Marine sediment, Rhizosphere sediment, Seawater and the epibacterial DNA of Seaweed and Seagrass. Diversity index analysis revealed that Marine sediment has the highest bacterial diversity and the least bacterial diversity was observed in Rhizosphere sediment. Proteobacteria, Actinobacteria and Bacteroidetes were the dominant taxa present in all the marine samples. Nearly 62–71% of rare species were identified in all the samples and most of these rare species were unique to a particular sample. Further taxonomic assignment at the phylum and genus level revealed that the bacterial community compositions differ among the samples. Conclusion This is the first report that supports the fact that, bacterial community composition is specific for specific samples irrespective of its similar geographical location. Existence of specific bacterial community for each sample may drive overall difference in bacterial structural composition of each sample. Further studies like whole metagenomic sequencing will throw more insights to the key stone players and its interconnecting metabolic pathways. In addition, this is one of the very few reports that depicts the unexplored bacterial diversity of marine samples (Marine sediment, Rhizosphere sediment, Seawater) and the host associated marine samples (Seaweed and Seagrass) at higher depths from uncharacterised coastal region of Palk Bay, India using next generation sequencing technology.
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Newton RJ, Bootsma MJ, Morrison HG, Sogin ML, McLellan SL. A microbial signature approach to identify fecal pollution in the waters off an urbanized coast of Lake Michigan. MICROBIAL ECOLOGY 2013; 65:1011-23. [PMID: 23475306 PMCID: PMC4084971 DOI: 10.1007/s00248-013-0200-9] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 02/13/2013] [Indexed: 05/04/2023]
Abstract
Urban coasts receive watershed drainage from ecosystems that include highly developed lands with sewer and stormwater infrastructure. In these complex ecosystems, coastal waters are often contaminated with fecal pollution, where multiple delivery mechanisms that often contain multiple fecal sources make it difficult to mitigate the pollution. Here, we exploit bacterial community sequencing of the V6 and V6V4 hypervariable regions of the bacterial 16S rRNA gene to identify bacterial distributions that signal the presence of sewer, fecal, and human fecal pollution. The sequences classified to three sewer infrastructure-associated bacterial genera, Acinetobacter, Arcobacter, and Trichococcus, and five fecal-associated bacterial families, Bacteroidaceae, Porphyromonadaceae, Clostridiaceae, Lachnospiraceae, and Ruminococcaceae, served as signatures of sewer and fecal contamination, respectively. The human fecal signature was determined with the Bayesian source estimation program SourceTracker, which we applied to a set of 40 sewage influent samples collected in Milwaukee, WI, USA to identify operational taxonomic units (≥ 97 % identity) that were most likely of human fecal origin. During periods of dry weather, the magnitudes of all three signatures were relatively low in Milwaukee's urban rivers and harbor and nearly zero in Lake Michigan. However, the relative contribution of the sewer and fecal signature frequently increased to > 2 % of the measured surface water communities following sewer overflows. Also during combined sewer overflows, the ratio of the human fecal pollution signature to the fecal pollution signature in surface waters was generally close to that of sewage, but this ratio decreased dramatically during dry weather and rain events, suggesting that nonhuman fecal pollution was the dominant source during these weather-driven scenarios. The qPCR detection of two human fecal indicators, human Bacteroides and Lachno2, confirmed the urban fecal footprint in this ecosystem extends to at least 8 km offshore.
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Affiliation(s)
- Ryan J. Newton
- Great Lakes WATER Institute, School of Freshwater Sciences, University of Wisconsin—Milwaukee, 600 E. Greenfield Ave, Milwaukee, WI 53204, USA
| | - Melinda J. Bootsma
- Great Lakes WATER Institute, School of Freshwater Sciences, University of Wisconsin—Milwaukee, 600 E. Greenfield Ave, Milwaukee, WI 53204, USA
| | - Hilary G. Morrison
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Mitchell L. Sogin
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Sandra L. McLellan
- Great Lakes WATER Institute, School of Freshwater Sciences, University of Wisconsin—Milwaukee, 600 E. Greenfield Ave, Milwaukee, WI 53204, USA
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McLellan SL, Newton RJ, Vandewalle JL, Shanks OC, Huse SM, Eren AM, Sogin ML. Sewage reflects the distribution of human faecal Lachnospiraceae. Environ Microbiol 2013; 15:2213-27. [PMID: 23438335 DOI: 10.1111/1462-2920.12092] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/13/2013] [Accepted: 01/17/2013] [Indexed: 01/10/2023]
Abstract
Faecal pollution contains a rich and diverse community of bacteria derived from animals and humans, many of which might serve as alternatives to the traditional enterococci and Escherichia coli faecal indicators. We used massively parallel sequencing (MPS) of the 16S rRNA gene to characterize microbial communities from wastewater treatment plant (WWTP) influent sewage from 12 cities geographically distributed across the USA. We examined members of the Clostridiales, which included the families Clostridiaceae, Lachnospiraceae and Ruminococcaceae for their potential as sewage indicators. Lachnospiraceae was one of the most abundant groups of faecal bacteria in sewage, and several Lachnospiraceae high-abundance sewage pyrotags occurred in at least 46 of 48 human faecal samples. Clone libraries targeting Clostridium coccoides (C. coccoides) in sewage samples demonstrated that Lachnospiraceae-annotated V6 pyrotags encompassed the previously reported C. coccoides group. We used oligotyping to profile the genus Blautia within Lachnospiraceae and found oligotypes comprised of 24 entropy components that showed patterns of host specificity. These findings suggest that indicators based on Blautia might have the capacity to discriminate between different faecal pollution sources. Development of source-specific alternative indicators would enhance water quality assessments, which leads to improved ecosystem health and reduced human health risk due to waterborne disease.
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Affiliation(s)
- Sandra L McLellan
- Great Lakes Water Institute, School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E. Greenfield Ave, Milwaukee, WI 53204, USA.
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Botes M, de Kwaadsteniet M, Cloete TE. Application of quantitative PCR for the detection of microorganisms in water. Anal Bioanal Chem 2013; 405:91-108. [PMID: 23001336 PMCID: PMC7079929 DOI: 10.1007/s00216-012-6399-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/28/2012] [Accepted: 08/29/2012] [Indexed: 11/13/2022]
Abstract
The occurrence of microorganisms in water due to contamination is a health risk and control thereof is a necessity. Conventional detection methods may be misleading and do not provide rapid results allowing for immediate action. The quantitative polymerase chain reaction (qPCR) method has proven to be an effective tool to detect and quantify microorganisms in water within a few hours. Quantitative PCR assays have recently been developed for the detection of specific adeno- and polyomaviruses, bacteria and protozoa in different water sources. The technique is highly sensitive and able to detect low numbers of microorganisms. Quantitative PCR can be applied for microbial source tracking in water sources, to determine the efficiency of water and wastewater treatment plants and act as a tool for risk assessment. Different qPCR assays exist depending on whether an internal control is used or whether measurements are taken at the end of the PCR reaction (end-point qPCR) or in the exponential phase (real-time qPCR). Fluorescent probes are used in the PCR reaction to hybridise within the target sequence to generate a signal and, together with specialised systems, quantify the amount of PCR product. Quantitative reverse transcription polymerase chain reaction (q-RT-PCR) is a more sensitive technique that detects low copy number RNA and can be applied to detect, e.g. enteric viruses and viable microorganisms in water, and measure specific gene expression. There is, however, a need to standardise qPCR protocols if this technique is to be used as an analytical diagnostic tool for routine monitoring. This review focuses on the application of qPCR in the detection of microorganisms in water.
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Affiliation(s)
- Marelize Botes
- Department of Microbiology, University of Stellenbosch, Private Bag XI, Matieland 7602, Stellenbosch, Western Cape 7602, South Africa.
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Marine and Freshwater Fecal Indicators and Source Identification. Infect Dis (Lond) 2013. [DOI: 10.1007/978-1-4614-5719-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Salloto GRB, Cardoso AM, Coutinho FH, Pinto LH, Vieira RP, Chaia C, Lima JL, Albano RM, Martins OB, Clementino MM. Pollution impacts on bacterioplankton diversity in a tropical urban coastal lagoon system. PLoS One 2012; 7:e51175. [PMID: 23226484 PMCID: PMC3511411 DOI: 10.1371/journal.pone.0051175] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 10/30/2012] [Indexed: 01/29/2023] Open
Abstract
Despite a great number of published studies addressing estuarine, freshwater and marine bacterial diversity, few have examined urban coastal lagoons in tropical habitats. There is an increasing interest in monitoring opportunistic pathogens as well as indigenous microbial community members in these water bodies by current molecular and microbiological approaches. In this work, bacterial isolates were obtained through selective plate dilution methods to evaluate antibiotic resistances. In addition, 16S rRNA gene libraries were prepared from environmental waters and mixed cultures grown in BHI medium inoculated with Jacarepaguá lagoon waters. Denaturing gradient gel electrophoresis (DGGE) analyses showed distinct community profiles between environmental communities from each studied site and their cultured counterparts. A total of 497 bacterial sequences were analyzed by MOTHUR, yielding 245 operational taxonomic units (OTUs) grouped at 97% similarity. CCA diagrams showcased how several environmental variables affect the distribution of 18 bacterial orders throughout the three distinct habitats. UniFrac metrics and Venn diagrams revealed that bacterial communities retrieved through each experimental approach were significantly different and that only one OTU, closely related to Vibrio cholerae, was shared between them. Potentially pathogenic bacteria were isolated from most sampled environments, fifty percent of which showed antibiotic resistance.
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Affiliation(s)
- Gigliola R. B. Salloto
- Laboratório de Microrganismos de Referência, Instituto Nacional de Controle de Qualidade em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Alexander M. Cardoso
- Diretoria de Programa, Instituto Nacional de Metrologia, Qualidade e Tecnologia, Rio de Janeiro, Brazil
- * E-mail:
| | - Felipe H. Coutinho
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonardo H. Pinto
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ricardo P. Vieira
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Catia Chaia
- Laboratório de Microrganismos de Referência, Instituto Nacional de Controle de Qualidade em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Joyce L. Lima
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodolpho M. Albano
- Departamento de Bioquímica, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Orlando B. Martins
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maysa M. Clementino
- Laboratório de Microrganismos de Referência, Instituto Nacional de Controle de Qualidade em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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Port JA, Wallace JC, Griffith WC, Faustman EM. Metagenomic profiling of microbial composition and antibiotic resistance determinants in Puget Sound. PLoS One 2012; 7:e48000. [PMID: 23144718 PMCID: PMC3483302 DOI: 10.1371/journal.pone.0048000] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 09/25/2012] [Indexed: 11/26/2022] Open
Abstract
Human-health relevant impacts on marine ecosystems are increasing on both spatial and temporal scales. Traditional indicators for environmental health monitoring and microbial risk assessment have relied primarily on single species analyses and have provided only limited spatial and temporal information. More high-throughput, broad-scale approaches to evaluate these impacts are therefore needed to provide a platform for informing public health. This study uses shotgun metagenomics to survey the taxonomic composition and antibiotic resistance determinant content of surface water bacterial communities in the Puget Sound estuary. Metagenomic DNA was collected at six sites in Puget Sound in addition to one wastewater treatment plant (WWTP) that discharges into the Sound and pyrosequenced. A total of ∼550 Mbp (1.4 million reads) were obtained, 22 Mbp of which could be assembled into contigs. While the taxonomic and resistance determinant profiles across the open Sound samples were similar, unique signatures were identified when comparing these profiles across the open Sound, a nearshore marina and WWTP effluent. The open Sound was dominated by α-Proteobacteria (in particular Rhodobacterales sp.), γ-Proteobacteria and Bacteroidetes while the marina and effluent had increased abundances of Actinobacteria, β-Proteobacteria and Firmicutes. There was a significant increase in the antibiotic resistance gene signal from the open Sound to marina to WWTP effluent, suggestive of a potential link to human impacts. Mobile genetic elements associated with environmental and pathogenic bacteria were also differentially abundant across the samples. This study is the first comparative metagenomic survey of Puget Sound and provides baseline data for further assessments of community composition and antibiotic resistance determinants in the environment using next generation sequencing technologies. In addition, these genomic signals of potential human impact can be used to guide initial public health monitoring as well as more targeted and functionally-based investigations.
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Affiliation(s)
- Jesse A. Port
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States of America
- Institute for Risk Analysis and Risk Communication, School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - James C. Wallace
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States of America
- Institute for Risk Analysis and Risk Communication, School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - William C. Griffith
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States of America
- Institute for Risk Analysis and Risk Communication, School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Elaine M. Faustman
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States of America
- Institute for Risk Analysis and Risk Communication, School of Public Health, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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44
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Ishaq SL, Wright ADG. Insight into the bacterial gut microbiome of the North American moose (Alces alces). BMC Microbiol 2012; 12:212. [PMID: 22992344 PMCID: PMC3585231 DOI: 10.1186/1471-2180-12-212] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 09/17/2012] [Indexed: 02/07/2023] Open
Abstract
Background The work presented here provides the first intensive insight into the bacterial populations in the digestive tract of the North American moose (Alces alces). Eight free-range moose on natural pasture were sampled, producing eight rumen samples and six colon samples. Second generation (G2) PhyloChips were used to determine the presence of hundreds of operational taxonomic units (OTUs), representing multiple closely related species/strains (>97% identity), found in the rumen and colon of the moose. Results A total of 789 unique OTUs were used for analysis, which passed the fluorescence and the positive fraction thresholds. There were 73 OTUs, representing 21 bacterial families, which were found exclusively in the rumen samples: Lachnospiraceae, Prevotellaceae and several unclassified families, whereas there were 71 OTUs, representing 22 bacterial families, which were found exclusively in the colon samples: Clostridiaceae, Enterobacteriaceae and several unclassified families. Overall, there were 164 OTUs that were found in 100% of the samples. The Firmicutes were the most dominant bacteria phylum in both the rumen and the colon. Microarray data available at ArrayExpress, accession number E-MEXP-3721. Conclusions Using PhyloTrac and UniFrac computer software, samples clustered into two distinct groups: rumen and colon, confirming that the rumen and colon are distinct environments. There was an apparent correlation of age to cluster, which will be validated by a larger sample size in future studies, but there were no detectable trends based upon gender.
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Affiliation(s)
- Suzanne L Ishaq
- Department of Animal Science, College of Agriculture and Life Sciences, University of Vermont, 203 Terrill Building, 570 Main Street, Burlington, VT 05405, USA.
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Bacterial associates of two Caribbean coral species reveal species-specific distribution and geographic variability. Appl Environ Microbiol 2012; 78:6438-49. [PMID: 22773636 DOI: 10.1128/aem.01162-12] [Citation(s) in RCA: 177] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Scleractinian corals harbor microorganisms that form dynamic associations with the coral host and exhibit substantial genetic and ecological diversity. Microbial associates may provide defense against pathogens and serve as bioindicators of changing environmental conditions. Here we describe the bacterial assemblages associated with two of the most common and phylogenetically divergent reef-building corals in the Caribbean, Montastraea faveolata and Porites astreoides. Contrasting life history strategies and disease susceptibilities indicate potential differences in their microbiota and immune function that may in part drive changes in the composition of coral reef communities. The ribotype structure and diversity of coral-associated bacteria within the surface mucosal layer (SML) of healthy corals were assessed using denaturing gradient gel electrophoresis (DGGE) fingerprinting and 454 bar-coded pyrosequencing. Corals were sampled at disparate Caribbean locations representing various levels of anthropogenic impact. We demonstrate here that M. faveolata and P. astreoides harbor distinct, host-specific bacteria but that specificity varies by species and site. P. astreoides generally hosts a bacterial assemblage of low diversity that is largely dominated by one bacterial genus, Endozoicomonas, within the order Oceanospirillales. The bacterial assemblages associated with M. faveolata are significantly more diverse and exhibit higher specificity at the family level than P. astreoides assemblages. Both corals have more bacterial diversity and higher abundances of disease-related bacteria at sites closer to the mainland than at those furthest away. The most diverse bacterial taxa and highest relative abundance of disease-associated bacteria were seen for corals near St. Thomas, U.S. Virgin Islands (USVI) (2.5 km from shore), and the least diverse taxa and lowest relative abundance were seen for corals near our most pristine site in Belize (20 km from shore). We conclude that the two coral species studied harbor distinct bacterial assemblages within the SML, but the degree to which each species maintains specific microbial associations varies both within each site and across large spatial scales. The taxonomic scale (i.e., phylum versus genus) at which scientists examine coral-microbe associations, in addition to host-elicited factors and environmental fluctuations, must be considered carefully in future studies of the coral holobiont.
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Dubinsky EA, Esmaili L, Hulls JR, Cao Y, Griffith JF, Andersen GL. Application of phylogenetic microarray analysis to discriminate sources of fecal pollution. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:4340-4347. [PMID: 22360280 DOI: 10.1021/es2040366] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Conventional methods for fecal source tracking typically use single biomarkers to systematically identify or exclude sources. High-throughput DNA sequence analysis can potentially identify all sources of microbial contaminants in a single test by measuring the total diversity of fecal microbial communities. In this study, we used phylogenetic microarray analysis to determine the comprehensive suite of bacteria that define major sources of fecal contamination in coastal California. Fecal wastes were collected from 42 different populations of humans, birds, cows, horses, elk, and pinnipeds. We characterized bacterial community composition using a DNA microarray that probes for 16S rRNA genes of 59,316 different bacterial taxa. Cluster analysis revealed strong differences in community composition among fecal wastes from human, birds, pinnipeds, and grazers. Actinobacteria, Bacilli, and many Gammaproteobacteria taxa discriminated birds from mammalian sources. Diverse families within the Clostridia and Bacteroidetes taxa discriminated human wastes, grazers, and pinnipeds from each other. We found 1058 different bacterial taxa that were unique to either human, grazing mammal, or bird fecal wastes. These OTUs can serve as specific identifier taxa for these sources in environmental waters. Two field tests in marine waters demonstrate the capacity of phylogenetic microarray analysis to track multiple sources with one test.
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Affiliation(s)
- Eric A Dubinsky
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Berkeley, CA, USA
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Aw TG, Rose JB. Detection of pathogens in water: from phylochips to qPCR to pyrosequencing. Curr Opin Biotechnol 2011; 23:422-30. [PMID: 22153035 PMCID: PMC7126744 DOI: 10.1016/j.copbio.2011.11.016] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 10/30/2011] [Accepted: 11/11/2011] [Indexed: 12/24/2022]
Abstract
Waterborne pathogens pose a significant threat to human health and a proper assessment of microbial water quality is important for decision making regarding water infrastructure and treatment investments and eventually to provide early warning of disease, particularly given increasing global disasters associated with severe public health risks. Microbial water quality monitoring has undergone tremendous transition in recent years, with novel molecular tools beginning to offer rapid, high-throughput, sensitive and specific detection of a wide spectrum of microbial pathogens that challenge traditional culture-based techniques. High-density microarrays, quantitative real-time PCR (qPCR) and pyrosequencing which are considered to be breakthrough technologies borne out of the ‘molecular revolution’ are at present emerging rapidly as tools of pathogen detection and discovery. Future challenges lie in integrating these molecular tools with concentration techniques and bioinformatics platforms for unbiased guide of pathogen surveillance in water and developing standardized protocols.
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Affiliation(s)
- Tiong Gim Aw
- Department of Fisheries and Wildlife, 13 Natural Resources, Michigan State University, East Lansing, MI 48824, United States.
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Paliy O, Agans R. Application of phylogenetic microarrays to interrogation of human microbiota. FEMS Microbiol Ecol 2011; 79:2-11. [PMID: 22092522 DOI: 10.1111/j.1574-6941.2011.01222.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/09/2011] [Accepted: 09/28/2011] [Indexed: 12/22/2022] Open
Abstract
Human-associated microbiota is recognized to play vital roles in maintaining host health, and it is implicated in many disease states. While the initial surge in the profiling of these microbial communities was achieved with Sanger and next-generation sequencing, many oligonucleotide microarrays have also been developed recently for this purpose. Containing probes complementary to small ribosomal subunit RNA gene sequences of community members, such phylogenetic arrays provide direct quantitative comparisons of microbiota composition among samples and between sample groups. Some of the developed microarrays including PhyloChip, Microbiota Array, and HITChip can simultaneously measure the presence and abundance of hundreds and thousands of phylotypes in a single sample. This review describes the currently available phylogenetic microarrays that can be used to analyze human microbiota, delineates the approaches for the optimization of microarray use, and provides examples of recent findings based on microarray interrogation of human-associated microbial communities.
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Affiliation(s)
- Oleg Paliy
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH 45435, USA.
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Kellogg CA, Piceno YM, Tom LM, DeSantis TZ, Zawada DG, Andersen GL. PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology. J Microbiol Methods 2011; 88:103-9. [PMID: 22085912 DOI: 10.1016/j.mimet.2011.10.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 10/24/2011] [Accepted: 10/24/2011] [Indexed: 11/30/2022]
Abstract
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.
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Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS One 2011; 6:e24570. [PMID: 21931760 PMCID: PMC3169623 DOI: 10.1371/journal.pone.0024570] [Citation(s) in RCA: 340] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 08/12/2011] [Indexed: 11/19/2022] Open
Abstract
Background Marine microbial communities have been essential contributors to global biomass, nutrient cycling, and biodiversity since the early history of Earth, but so far their community distribution patterns remain unknown in most marine ecosystems. Methodology/Principal Findings The synthesis of 9.6 million bacterial V6-rRNA amplicons for 509 samples that span the global ocean's surface to the deep-sea floor shows that pelagic and benthic communities greatly differ, at all taxonomic levels, and share <10% bacterial types defined at 3% sequence similarity level. Surface and deep water, coastal and open ocean, and anoxic and oxic ecosystems host distinct communities that reflect productivity, land influences and other environmental constraints such as oxygen availability. The high variability of bacterial community composition specific to vent and coastal ecosystems reflects the heterogeneity and dynamic nature of these habitats. Both pelagic and benthic bacterial community distributions correlate with surface water productivity, reflecting the coupling between both realms by particle export. Also, differences in physical mixing may play a fundamental role in the distribution patterns of marine bacteria, as benthic communities showed a higher dissimilarity with increasing distance than pelagic communities. Conclusions/Significance This first synthesis of global bacterial distribution across different ecosystems of the World's oceans shows remarkable horizontal and vertical large-scale patterns in bacterial communities. This opens interesting perspectives for the definition of biogeographical biomes for bacteria of ocean waters and the seabed.
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