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Suffridge CP, Shannon KC, Matthews H, Johnson RC, Jeffres C, Mantua N, Ward AE, Holmes E, Kindopp J, Aidoo M, Colwell FS. Connecting thiamine availability to the microbial community composition in Chinook salmon spawning habitats of the Sacramento River basin. Appl Environ Microbiol 2024; 90:e0176023. [PMID: 38084986 PMCID: PMC10807462 DOI: 10.1128/aem.01760-23] [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: 10/05/2023] [Accepted: 10/27/2023] [Indexed: 01/25/2024] Open
Abstract
Thiamine deficiency complex (TDC) is a major emerging threat to global populations of culturally and economically important populations of salmonids. Salmonid eggs and embryos can assimilate exogenous thiamine, and evidence suggests that microbial communities in benthic environments can produce substantial amounts of thiamine. We therefore hypothesize that natural dissolved pools of thiamine exist in the surface water and hyporheic zones of riverine habitats where salmonids with TDC migrate, spawn, and begin their lives. To examine the relationship between dissolved thiamine-related compounds (dTRCs) and their microbial source, we determined the concentrations of these metabolites and the compositions of microbial communities in surface and hyporheic waters of the Sacramento River, California and its tributaries. Here we determine that all dTRCs are present in femto-picomolar concentrations in a range of critically important salmon spawning habitats. We observed that thiamine concentrations in the Sacramento River system are orders of magnitude lower than those of marine waters, indicating substantial differences in thiamine cycling between these two environments. Our data suggest that the hyporheic zone is likely the source of thiamine to the overlying surface water. Temporal variations in dTRC concentrations were observed where the highest concentrations existed when Chinook salmon were actively spawning. Significant correlations were seen between the richness of microbial taxa and dTRC concentrations, particularly in the hyporheic zone, which would influence the conditions where embryonic salmon incubate. Together, these results indicate a connection between microbial communities in freshwater habitats and the availability of thiamine to spawning TDC-impacted California Central Valley Chinook salmon.IMPORTANCEPacific salmon are keystone species with considerable economic importance and immeasurable cultural significance to Pacific Northwest indigenous peoples. Thiamine deficiency complex has recently been diagnosed as an emerging threat to the health and stability of multiple populations of salmonids ranging from California to Alaska. Microbial biosynthesis is the major source of thiamine in marine and aquatic environments. Despite this importance, the concentrations of thiamine and the identities of the microbial communities that cycle it are largely unknown. Here we investigate microbial communities and their relationship to thiamine in Chinook salmon spawning habitats in California's Sacramento River system to gain an understanding of how thiamine availability impacts salmonids suffering from thiamine deficiency complex.
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Affiliation(s)
| | - Kelly C. Shannon
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - H. Matthews
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - R. C. Johnson
- Fisheries Ecology Division, NOAA Fisheries, Southwest Fisheries Science Center, Santa Cruz, California, USA
- University of California, Center for Watershed Sciences, Davis, California, USA
| | - C. Jeffres
- University of California, Center for Watershed Sciences, Davis, California, USA
| | - N. Mantua
- Fisheries Ecology Division, NOAA Fisheries, Southwest Fisheries Science Center, Santa Cruz, California, USA
| | - A. E. Ward
- University of California, Center for Watershed Sciences, Davis, California, USA
| | - E. Holmes
- University of California, Center for Watershed Sciences, Davis, California, USA
- California Department of Water Resources, West Sacramento, California, USA
| | - J. Kindopp
- California Department of Water Resources, Division of Integrated Science and Engineering, Oroville, California, USA
| | - M. Aidoo
- Bronx Community College, Bronx, New York, USA
| | - F. S. Colwell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, USA
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2
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Pozzi ACM, Petit S, Marjolet L, Youenou B, Lagouy M, Namour P, Schmitt L, Navratil O, Breil P, Branger F, Cournoyer B. Ecological assessment of combined sewer overflow management practices through the analysis of benthic and hyporheic sediment bacterial assemblages from an intermittent stream. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167854. [PMID: 37848137 DOI: 10.1016/j.scitotenv.2023.167854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/19/2023]
Abstract
Combined sewer overflows (CSO) are used to avoid overloading unitary sewers and wastewater treatment plants. Following the European Council Directive on Urban Wastewater Treatment (UWT), CSO discharges are regulated using guidelines that aim to reduce their ecological impact on aquatic systems. A model CSO, which is part of a long-term experimental field observatory, was modified according to these guidelines and used to evaluate the benefits of compliance through analyses of the bacteriological and chemical states of the receiving intermittent stream. The benthic and hyporheic sediments of similar geomorphic units located upstream and downstream of a monitored CSO outlet were compared before and after changes in CSO regimes. Hydrological, pollutants (Metal Trace Elements, MTE; Polycyclic Aromatic Hydrocarbons, PAH; fecal indicator bacteria, FIB), and tpm-based DNA meta-barcoding datasets resolving the occurrences of >700 bacterial species of nearly 200 genera were studied. The frequency of overflow was confirmed to have significantly decreased following the application of the UWT guidelines. Overflows became almost limited to periods of heavy summer thunderstorm events. These changes were not associated with a significant decrease in most of the surveyed MTE, PAH, and FIB among stream sediments, except for chromium. Ecological benefits were highlighted by significant changes in tpm-based meta-barcoding community patterns between the UWT compliant sampling period and the previous one. Bacterial community change point analyses confirmed this segregation in the meta-barcoding dataset according to hydrological indices such as the number of CSO events and discharged volumes. A significant decline in CSO bacterial taxa in the benthic and hyporheic sediments was observed. Thirty-four CSO indicator species were identified, including Aeromonas caviae, Aeromonas media, and Pseudomonas oleovorans. These indicators, often documented as opportunistic pathogens (to humans, animals or plants) and/or pollutant degraders, were proposed as ecological sentinels for the assessment of CSO impacts.
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Affiliation(s)
- Adrien C M Pozzi
- Université Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Research Team "Bacterial Opportunistic Pathogens and Environment" (BPOE), 69280 Marcy L'Etoile, France.
| | - Stéphanie Petit
- Université Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Research Team "Bacterial Opportunistic Pathogens and Environment" (BPOE), 69280 Marcy L'Etoile, France
| | - Laurence Marjolet
- Université Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Research Team "Bacterial Opportunistic Pathogens and Environment" (BPOE), 69280 Marcy L'Etoile, France
| | - Benjamin Youenou
- Université Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Research Team "Bacterial Opportunistic Pathogens and Environment" (BPOE), 69280 Marcy L'Etoile, France
| | - Mickaël Lagouy
- UR RiverLy, INRAE Centre Lyon-Grenoble, Auvergne-Rhône-Alpes, 69625 Villeurbanne Cedex, France
| | - Philippe Namour
- UR RiverLy, INRAE Centre Lyon-Grenoble, Auvergne-Rhône-Alpes, 69625 Villeurbanne Cedex, France
| | - Laurent Schmitt
- Université de Strasbourg, UMR 7362 Unistra-CNRS-ENGEES, Faculté de Géographie et d'Aménagement, 67000 Strasbourg, France
| | - Oldrich Navratil
- UMR 5600 Environnement Ville Société, Université Lyon 2, CNRS, Lyon, France
| | - Pascal Breil
- UR RiverLy, INRAE Centre Lyon-Grenoble, Auvergne-Rhône-Alpes, 69625 Villeurbanne Cedex, France
| | - Flora Branger
- UR RiverLy, INRAE Centre Lyon-Grenoble, Auvergne-Rhône-Alpes, 69625 Villeurbanne Cedex, France
| | - Benoit Cournoyer
- Université Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Research Team "Bacterial Opportunistic Pathogens and Environment" (BPOE), 69280 Marcy L'Etoile, France.
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3
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Richards SC, King WL, Sutherland JL, Bell TH. Leveraging aquatic-terrestrial interfaces to capture putative habitat generalists. FEMS Microbiol Lett 2024; 371:fnae025. [PMID: 38553956 DOI: 10.1093/femsle/fnae025] [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: 08/20/2023] [Revised: 02/03/2024] [Accepted: 03/28/2024] [Indexed: 04/21/2024] Open
Abstract
Habitat type is a strong determinant of microbial composition. Habitat interfaces, such as the boundary between aquatic and terrestrial systems, present unique combinations of abiotic factors for microorganisms to contend with. Aside from the spillover of certain harmful microorganisms from agricultural soils into water (e.g. fecal coliform bacteria), we know little about the extent of soil-water habitat switching across microbial taxa. In this study, we developed a proof-of-concept system to facilitate the capture of putatively generalist microorganisms that can colonize and persist in both soil and river water. We aimed to examine the phylogenetic breadth of putative habitat switchers and how this varies across different source environments. Microbial composition was primarily driven by recipient environment type, with the strongest phylogenetic signal seen at the order level for river water colonizers. We also identified more microorganisms colonizing river water when soil was collected from a habitat interface (i.e. soil at the side of an intermittently flooded river, compared to soil collected further from water sources), suggesting that environmental interfaces could be important reservoirs of microbial habitat generalists. Continued development of experimental systems that actively capture microorganisms that thrive in divergent habitats could serve as a powerful tool for identifying and assessing the ecological distribution of microbial generalists.
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Affiliation(s)
- Sarah C Richards
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, United States
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, United States
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, United States
- International Agriculture and Development Graduate Program, The Pennsylvania State University, University Park, PA, 16802, United States
| | - William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, United States
- School of Biological Sciences, University of Southampton, SO17 1BJ, United Kingdom
| | - Jeremy L Sutherland
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, United States
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, United States
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, United States
- International Agriculture and Development Graduate Program, The Pennsylvania State University, University Park, PA, 16802, United States
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, Toronto, ON, M1C1A4, Canada
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4
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Koike K, Honda R, Aoki M, Yamamoto‐Ikemoto R, Syutsubo K, Matsuura N. A quantitative sequencing method using synthetic internal standards including functional and phylogenetic marker genes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:497-511. [PMID: 37465846 PMCID: PMC10667660 DOI: 10.1111/1758-2229.13189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/23/2023] [Indexed: 07/20/2023]
Abstract
The method of spiking synthetic internal standard genes (ISGs) to samples for amplicon sequencing, generating sequences and converting absolute gene numbers from read counts has been used only for phylogenetic markers and has not been applied to functional markers. In this study, we developed ISGs, including gene sequences of the 16S rRNA, pmoA, encoding a subunit of particulate methane monooxygenase and amoA, encoding a subunit of ammonia monooxygenase. We added ISGs to the samples, amplified the target genes and performed amplicon sequencing. For the mock community, the copy numbers converted from read counts using ISGs were equivalent to those obtained by the quantitative real-time polymerase chain reaction (4.0 × 104 versus 4.1 × 104 and 3.0 × 103 versus 4.0 × 103 copies μL-DNA-1 for 16S rRNA and pmoA genes, respectively), but we also identified underestimation, possibly due to primer coverage (7.8 × 102 versus 3.7 × 103 μL-DNA-1 for amoA gene). We then applied this method to environmental samples and analysed phylogeny, functional diversity and absolute quantities. One Methylocystis population was most abundant in the sludge samples [16S rRNA gene (3.8 × 109 copies g-1 ) and the pmoA gene (2.3 × 109 copies g-1 )] and were potentially interrelated. This study demonstrates that ISG spiking is useful for evaluating sequencing data processing and quantifying functional markers.
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Affiliation(s)
- Kazuyoshi Koike
- Graduate School of Natural Science and TechnologyKanazawa UniversityKanazawaJapan
| | - Ryo Honda
- Faculty of Geosciences and Civil EngineeringKanazawa UniversityKanazawaJapan
| | - Masataka Aoki
- Regional Environment Conservation DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
| | | | - Kazuaki Syutsubo
- Regional Environment Conservation DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
- Research Center for Water Environment Technology, School of Engineeringthe University of TokyoTokyoJapan
| | - Norihisa Matsuura
- Faculty of Geosciences and Civil EngineeringKanazawa UniversityKanazawaJapan
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5
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Liu B, Wang Y, Zhang H, Zhou Y, Zhang C, Yang N, Wang W. The Variations of Microbial Diversity and Community Structure Along Different Stream Orders in Wuyi Mountains. MICROBIAL ECOLOGY 2023; 86:2330-2343. [PMID: 37222804 DOI: 10.1007/s00248-023-02240-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 05/08/2023] [Indexed: 05/25/2023]
Abstract
The surface water is an important habitat for freshwater microorganisms, but there is a lack of understanding of the pattern of microbial diversity and structure in stream continuums of small subtropical forest watersheds. Therefore, this study aimed to understand the variations in microbial diversity and community structure along stream orders (1-5) in the small subtropical forest catchments of the Wuyi Mountains. Using GIS software, 20 streams were chosen and classified into 5 orders. Illumina sequencing was used to analyze the dynamics of microbial communities, along with stream orders and hydro-chemical properties of stream water were also determined. Our results indicated that the bacterial and fungal richness (ACE index) was higher in low-order (1 and 2 orders) streams than in high-order (3, 4, and 5 orders) streams, with the highest value in the order 2 streams (P < 0.05). The water temperature and dissolved oxygen were positively correlated with fungal richness (P < 0.05). The bacterial rare taxa had a significant correlation with the abundance taxa (P < 0.05). The relative abundances of Bacteroidetes, Actinobacteria, and Chytridiomycota microbial phyla were significantly different among different order streams (P < 0.05). Using the neutral community model, we found that the fungal community structure was significantly shaped by hydro-chemical properties, while the bacterial community structure was largely regulated by stochastic processes. Our findings suggest that variations in microbial community structure in subtropical headwaters are largely shaped by the water temperature and dissolved oxygen.
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Affiliation(s)
- Boran Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
- National Observation and Research Station of Fujian Wuyishan Forest Ecosystem, Wuyishan, 354300, Fujian, China
| | - Yuchao Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
- National Observation and Research Station of Fujian Wuyishan Forest Ecosystem, Wuyishan, 354300, Fujian, China
| | - Huiguang Zhang
- National Observation and Research Station of Fujian Wuyishan Forest Ecosystem, Wuyishan, 354300, Fujian, China
- Wuyishan National Park Research and Monitoring Center, Wuyishan, 354300, Fujian, China
| | - Yan Zhou
- National Observation and Research Station of Fujian Wuyishan Forest Ecosystem, Wuyishan, 354300, Fujian, China
- Wuyishan National Park Research and Monitoring Center, Wuyishan, 354300, Fujian, China
| | - Chenhui Zhang
- National Observation and Research Station of Fujian Wuyishan Forest Ecosystem, Wuyishan, 354300, Fujian, China
- Wuyishan National Park Research and Monitoring Center, Wuyishan, 354300, Fujian, China
| | - Nan Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
| | - Weifeng Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
- National Observation and Research Station of Fujian Wuyishan Forest Ecosystem, Wuyishan, 354300, Fujian, China.
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6
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Bier RL, Mosher JJ, Kaplan LA, Kan J. Spatial scale impacts microbial community composition and distribution within and across stream ecosystems in North and Central America. Environ Microbiol 2023; 25:1860-1874. [PMID: 37177981 DOI: 10.1111/1462-2920.16396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
A mechanistic understanding of factors that structure spatiotemporal community composition is a major challenge in microbial ecology. Our study of microbial communities in the headwaters of three freshwater stream networks showed significant community changes at the small spatial scale of benthic habitats when compared to changes at mid- and large-spatial scales associated with stream order and catchment. Catchment (which included temperate and tropical catchments) had the strongest influence on community composition followed by habitat type (epipsammon or epilithon) and stream orders. Alpha diversity of benthic microbiomes resulted from interactions between catchment, habitat, and canopy. Epilithon contained relatively more Cyanobacteria and algae while Acidobacteria and Actinobacteria proportions were higher in epipsammic habitats. Turnover from replacement created ~60%-95% of beta diversity differences among habitats, stream orders, and catchments. Turnover within a habitat type generally decreased downstream indicating longitudinal linkages in stream networks while between habitat turnover also shaped benthic microbial community assembly. Our study suggests that factors influencing microbial community composition shift in dominance across spatial scales, with habitat dominating locally and catchment dominating globally.
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Affiliation(s)
- Raven L Bier
- Stroud Water Research Center, Avondale, Pennsylvania, USA
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, USA
| | - Jennifer J Mosher
- Stroud Water Research Center, Avondale, Pennsylvania, USA
- Marshall University, Department of Biological Sciences, Huntington, West Virginia, USA
| | - Louis A Kaplan
- Stroud Water Research Center, Avondale, Pennsylvania, USA
| | - Jinjun Kan
- Stroud Water Research Center, Avondale, Pennsylvania, USA
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7
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Beaudry MS, Thomas JC, Baptista RP, Sullivan AH, Norfolk W, Devault A, Enk J, Kieran TJ, Rhodes OE, Perry-Dow KA, Rose LJ, Bayona-Vásquez NJ, Oladeinde A, Lipp EK, Sanchez S, Glenn TC. Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture. Environ Microbiol 2021; 23:7523-7537. [PMID: 34519156 DOI: 10.1111/1462-2920.15767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 11/30/2022]
Abstract
Finding, characterizing and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples. We demonstrate the continued utility of a set of 19 933 hybridization capture baits designed from the Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 and Pathogenicity Island Database (PAIDB)v2.0, targeting 3565 unique nucleotide sequences that confer resistance. We demonstrate the efficiency of our bait set on a custom-made resistance mock community and complex environmental samples to increase the proportion of on-target reads as much as >200-fold. However, keeping pace with newly discovered ARGs poses a challenge when studying AMR, because novel ARGs are continually being identified and would not be included in bait sets designed prior to discovery. We provide imperative information on how our bait set performs against CARDv3.3.1, as well as a generalizable approach for deciding when and how to update hybridization capture bait sets. This research encapsulates the full life cycle of baits for hybridization capture of the resistome from design and validation (both in silico and in vitro) to utilization and forecasting updates and retirement.
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Affiliation(s)
- Megan S Beaudry
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Jesse C Thomas
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, 29808, USA
| | - Rodrigo P Baptista
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.,Center for Tropical and Emerging Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Amanda H Sullivan
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - William Norfolk
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Alison Devault
- Daicel Arbor Biosciences, 5840 Interface Dr., Suite 101, Ann Arbor, MI, 48103, USA
| | - Jacob Enk
- Daicel Arbor Biosciences, 5840 Interface Dr., Suite 101, Ann Arbor, MI, 48103, USA
| | - Troy J Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Olin E Rhodes
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, 29808, USA.,Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
| | - K Allison Perry-Dow
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Laura J Rose
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Natalia J Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.,Division of Natural Science and Mathematics, Oxford College, Emory University, Oxford, GA, 30054, USA
| | - Adelumola Oladeinde
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA Agricultural Research Service, Athens, GA, 30605, USA
| | - Erin K Lipp
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Susan Sanchez
- Department of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
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8
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David GM, López-García P, Moreira D, Alric B, Deschamps P, Bertolino P, Restoux G, Rochelle-Newall E, Thébault E, Simon M, Jardillier L. Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns. Mol Ecol 2021; 30:2162-2177. [PMID: 33639035 DOI: 10.1111/mec.15864] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/27/2022]
Abstract
Despite small freshwater ecosystems being biodiversity reservoirs and contributing significantly to greenhouse fluxes, their microbial communities remain largely understudied. Yet, microorganisms intervene in biogeochemical cycling and impact water quality. Because of their small size, these ecosystems are in principle more sensitive to disturbances, seasonal variation and pluri-annual climate change. However, how microbial community composition varies over space and time, and whether archaeal, bacterial and microbial eukaryote communities behave similarly remain unanswered. Here, we aim to unravel the composition and intra/interannual temporal dynamic patterns for archaea, bacteria and microbial eukaryotes in a set of small freshwater ecosystems. We monitored archaeal and bacterial community composition during 24 consecutive months in four ponds and one brook from northwestern France by 16S rRNA gene amplicon sequencing (microbial eukaryotes were previously investigated for the same systems). Unexpectedly for oxic environments, bacterial Candidate Phyla Radiation (CPR) were highly diverse and locally abundant. Our results suggest that microbial community structure is mainly driven by environmental conditions acting over space (ecosystems) and time (seasons). A low proportion of operational taxonomic units (OTUs) (<1%) was shared by the five ecosystems despite their geographical proximity (2-9 km away), making microbial communities almost unique in each ecosystem and highlighting the strong selective influence of local environmental conditions. Marked and similar seasonality patterns were observed for archaea, bacteria and microbial eukaryotes in all ecosystems despite strong turnovers of rare OTUs. Over the 2-year survey, microbial community composition varied despite relatively stable environmental parameters. This suggests that biotic associations play an important role in interannual community assembly.
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Affiliation(s)
- Gwendoline M David
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | | | - David Moreira
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Benjamin Alric
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, Villeurbanne, France
| | - Philippe Deschamps
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Paola Bertolino
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Gwendal Restoux
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Emma Rochelle-Newall
- Sorbonne Université, UPEC, CNRS, IRD, INRAE, Institute d'Ecologie de des Sciences de l'Environnement de Paris, iEES-Paris, Paris, France
| | - Elisa Thébault
- Sorbonne Université, UPEC, CNRS, IRD, INRAE, Institute d'Ecologie de des Sciences de l'Environnement de Paris, iEES-Paris, Paris, France
| | - Marianne Simon
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Ludwig Jardillier
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
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9
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Chung T, Weller DL, Kovac J. The Composition of Microbial Communities in Six Streams, and Its Association With Environmental Conditions, and Foodborne Pathogen Isolation. Front Microbiol 2020; 11:1757. [PMID: 32849385 PMCID: PMC7403445 DOI: 10.3389/fmicb.2020.01757] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/06/2020] [Indexed: 12/16/2022] Open
Abstract
Surface water used for produce production is a potential source of pre-harvest contamination with foodborne pathogens. Decisions on how to mitigate food safety risks associated with pre-harvest water use currently rely on generic Escherichia coli-based water quality tests, although multiple studies have suggested that E. coli levels are not a suitable indicator of the food safety risks under all relevant environmental conditions. Hence, improved understanding of spatiotemporal variability in surface water microbiota composition is needed to facilitate identification of alternative or supplementary indicators that co-occur with pathogens. To this end, we aimed to characterize the composition of bacterial and fungal communities in the sediment and water fractions of 68 agricultural water samples collected from six New York streams. We investigated potential associations between the composition of microbial communities, environmental factors and Salmonella and/or Listeria monocytogenes isolation. We found significantly different composition of fungal and bacterial communities among sampled streams and among water fractions of collected samples. This indicates that geography and the amount of sediment in a collected water sample may affect its microbial composition, which was further supported by identified associations between the flow rate, turbidity, pH and conductivity, and microbial community composition. Lastly, we identified specific microbial families that were weakly associated with the presence of Salmonella or Listeria monocytogenes, however, further studies on samples from additional streams are needed to assess whether identified families may be used as indicators of pathogen presence.
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Affiliation(s)
- Taejung Chung
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
- Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Daniel L. Weller
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
- Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
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