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Wang S, Tian R, Bi Y, Meng F, Zhang R, Wang C, Wang D, Liu L, Zhang B. A review of distribution and functions of extracellular DNA in the environment and wastewater treatment systems. CHEMOSPHERE 2024; 359:142264. [PMID: 38714248 DOI: 10.1016/j.chemosphere.2024.142264] [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: 02/18/2024] [Revised: 04/23/2024] [Accepted: 05/04/2024] [Indexed: 05/09/2024]
Abstract
Extracellular DNA refers to DNA fragments existing outside the cell, originating from various cell release mechanisms, including active secretion, cell lysis, and phage-mediated processes. Extracellular DNA serves as a vital environmental biomarker, playing crucial ecological and environmental roles in water bodies. This review is summarized the mechanisms of extracellular DNA release, including pathways involving cell lysis, extracellular vesicles, and type IV secretion systems. Then, the extraction and detection methods of extracellular DNA from water, soil, and biofilm are described and analyzed. Finally, we emphasize the role of extracellular DNA in microbial community systems, including its significant contributions to biofilm formation, biodiversity through horizontal gene transfer, and electron transfer processes. This review offers a comprehensive insight into the sources, distribution, functions, and impacts of extracellular DNA within aquatic environments, aiming to foster further exploration and understanding of extracellular DNA dynamics in aquatic environments as well as other environments.
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Affiliation(s)
- Shaopo Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Ruimin Tian
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Yanmeng Bi
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Fansheng Meng
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Rui Zhang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Chenchen Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Dong Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Lingjie Liu
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China.
| | - Bo Zhang
- Tianjin Eco-City Water Investment and Construction Co. Ltd, Hexu Road 276, Tianjin, 300467, China
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Sharma DK, Rajpurohit YS. Multitasking functions of bacterial extracellular DNA in biofilms. J Bacteriol 2024; 206:e0000624. [PMID: 38445859 PMCID: PMC11025335 DOI: 10.1128/jb.00006-24] [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] [Indexed: 03/07/2024] Open
Abstract
Bacterial biofilms are intricate ecosystems of microbial communities that adhere to various surfaces and are enveloped by an extracellular matrix composed of polymeric substances. Within the context of bacterial biofilms, extracellular DNA (eDNA) originates from cell lysis or is actively secreted, where it exerts a significant influence on the formation, stability, and resistance of biofilms to environmental stressors. The exploration of eDNA within bacterial biofilms holds paramount importance in research, with far-reaching implications for both human health and the environment. An enhanced understanding of the functions of eDNA in biofilm formation and antibiotic resistance could inspire the development of strategies to combat biofilm-related infections and improve the management of antibiotic resistance. This comprehensive review encapsulates the latest discoveries concerning eDNA, encompassing its origins, functions within bacterial biofilms, and significance in bacterial pathogenesis.
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Affiliation(s)
- Dhirendra Kumar Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Schools of Life Sciences, Homi Bhabha National Institute (DAE—Deemed University), Mumbai, India
| | - Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Schools of Life Sciences, Homi Bhabha National Institute (DAE—Deemed University), Mumbai, India
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Liu X, Song Y, Ni T, Yang Y, Ma B, Huang T, Chen S, Zhang H. Ecological evolution of algae in connected reservoirs under the influence of water transfer: Algal density, community structure, and assembly processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170086. [PMID: 38232825 DOI: 10.1016/j.scitotenv.2024.170086] [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: 08/19/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/19/2024]
Abstract
Reservoir connectivity provides a solution for regional water shortages. Understanding the water quality of reservoirs and the response of algal communities to water transfer could provide the basis for a long-term evolutionary model of reservoirs. In this study, a water-algal community model was established to study the effects of water transfer on water quality and algal communities in reservoirs. The results showed that water transfer significantly decreased total nitrogen and nitrate concentrations. However, the water transfer resulted in an increase in the CODMn concentration and conductivity in the receiving reservoir. Additionally, the algal density and chlorophyll-a (chl-a) concentration showed an increase with water transfer. Bacillariophyta, Cyanophyta, and Chlorophyta were the dominant algal phyllum in all three reservoirs. Water transfer induced the evolution of the algal community by driving changes in the chemical parameters of the receiving reservoir and led to more complex relationships within the algal community. The effects of stochastic processes on algal communities were also enhanced in the receiving reservoirs. These results provide specific information for water quality safety management and eutrophication prevention in connected reservoirs.
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Affiliation(s)
- Xiang Liu
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China
| | - Yutong Song
- School of Future Technology, Xi'an University of Architecture and Technology, Xi'an, China
| | - Tongchao Ni
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China
| | - Yansong Yang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China
| | - Ben Ma
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China
| | - Tinglin Huang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China
| | - Shengnan Chen
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China.
| | - Haihan Zhang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, China.
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Mejia MP, Rojas CA, Curd E, Renshaw MA, Edalati K, Shih B, Vincent N, Lin M, Nguyen PH, Wayne R, Jessup K, Parker SS. Soil Microbial Community Composition and Tolerance to Contaminants in an Urban Brownfield Site. MICROBIAL ECOLOGY 2023; 85:998-1012. [PMID: 35802172 PMCID: PMC10156844 DOI: 10.1007/s00248-022-02061-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/21/2022] [Indexed: 05/04/2023]
Abstract
Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microbiome composition and diversity at brownfields. This study focuses on an urban brownfield-a former rail yard in Los Angeles that is contaminated with heavy metals, volatile organic compounds, and petroleum-derived pollutants. We anticipate that heavy metals and organic pollutants will shape soil microbiome diversity and that several candidate fungi and bacteria will be tolerant to the contaminants. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA, and the fungal internal transcribed spacer (FITS)) in 55 soil samples collected at five depths to (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples included heavy metals, petroleum hydrocarbons, polycyclic aromatic hydrocarbons, and volatile organic compounds. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness and fungal richness were positively correlated with lead and cobalt levels, respectively. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and represent taxa of interest for future bioremediation research. Based on our results, we recommend incorporating DNA-based multi-marker microbial community profiling at multiple sites and depths in brownfield site assessment standard methods and restoration.
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Affiliation(s)
- Maura Palacios Mejia
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Connie A Rojas
- Ecology, Evolution, and Behavior Program, Michigan State University, Lansing, MI, USA
| | - Emily Curd
- Natural Science, Landmark College, Putney, VT, USA
| | - Mark A Renshaw
- Cherokee Federal, USGS Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - Kiumars Edalati
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Beverly Shih
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nitin Vincent
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Meixi Lin
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peggy H Nguyen
- Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
| | - Robert Wayne
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
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Al-Wahaibi ASM, Upstill-Goddard RC, Burgess JG. Isolation and Staining Reveal the Presence of Extracellular DNA in Marine Gel Particles. Gels 2023; 9:gels9030251. [PMID: 36975700 PMCID: PMC10048003 DOI: 10.3390/gels9030251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Marine gel particles (MGP) are amorphous hydrogel exudates from bacteria and microalgae that are ubiquitous in the oceans, but their biochemical composition and function are poorly understood. While dynamic ecological interactions between marine microorganisms and MGPs may result in the secretion and mixing of bacterial extracellular polymeric substances (EPS) such as nucleic acids, compositional studies currently are limited to the identification of acidic polysaccharides and proteins in transparent exopolymer particles (TEP) and Coomassie stainable particles (CSP). Previous studies targeted MGPs isolated by filtration. We developed a new way of isolating MGPs from seawater in liquid suspension and applied it to identify extracellular DNA (eDNA) in North Sea surface seawater. Seawater was filtered onto polycarbonate (PC) filters with gentle vacuum filtration, and then the filtered particles were gently resuspended in a smaller volume of sterile seawater. The resulting MGPs ranged in size from 0.4 to 100 µm in diameter. eDNA was detected by fluorescent microscopy using YOYO-1 (for eDNA), with Nile red (targeting cell membranes) as a counterstain. TOTO-3 was also used to stain eDNA, with ConA to localise glycoproteins and SYTO-9 for the live/dead staining of cells. Confocal laser scanning microscopy (CLSM) revealed the presence of proteins and polysaccharides. We found eDNA to be universally associated with MGPs. To further elucidate the role of eDNA, we established a model experimental MGP system using bacterial EPS from Pseudoalteromonas atlantica that also contained eDNA. Our results clearly demonstrate the occurrence of eDNA in MGPs, and should aid furthering our understanding of the micro-scale dynamics and fate of MGPs that underly the large-scale processes of carbon cycling and sedimentation in the ocean.
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Affiliation(s)
- Aisha S M Al-Wahaibi
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Muscat 123, Oman
| | - Robert C Upstill-Goddard
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - J Grant Burgess
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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Neethu CS, Saravanakumar C, Purvaja R, Robin RS, Ramesh R. Arsenic resistance and horizontal gene transfer are associated with carbon and nitrogen enrichment in bacteria. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 311:119937. [PMID: 35977641 DOI: 10.1016/j.envpol.2022.119937] [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: 04/01/2022] [Revised: 07/14/2022] [Accepted: 08/07/2022] [Indexed: 06/15/2023]
Abstract
Coastal waters are confluences receiving large amounts of point and non-point sources of pollution. An attempt was made to explore microbial community interactions in response to carbon, nitrogen and metal pollution. Additionally, experiments were designed to analyze the influence of these factors on horizontal gene transfer (HGT). Shift in bacterial diversity dynamics by arsenic stress and nutrient addition in coastal waters was explored by metagenomics of microcosm setups. Phylogenetic analysis revealed equal distribution of Gammaproteobacteria (29%) and Betaproteobacteria (28%) in control microcosm. This proportional diversity from control switched to unique distribution of Gammaproteobacteria (44.5%)> Flavobacteria (17.7%)> Bacteriodia (11.92%)> Betaproteobacteria (11.52%) in microcosm supplemented with carbon, nitrogen and metal (C + N + M). Among metal-stressed systems, alpha diversity analysis indicated highest diversity of genera in C + N + M followed by N + M > C+M> metal alone. Arsenic and ampicillin sensitive E. coli XL1 blue and environmental strains (Vibrio tubiashii W85 and E. coli W101) were tested for efficiency of uptake of plasmid (P) pUCminusMCS (arsBRampR) under varying stress conditions. Transformation experiments revealed that combined effect of carbon, nitrogen and metal on horizontal gene transfer (HGT) was significantly higher (p < 0.01) than individual factors. The effect of carbon on HGT was proved to be superior to nitrogen under metal stressed conditions. Presence of arsenic in experimental setups (P + M, P + N + M and P + C + M) enhanced the HGT compared to non-metal counterparts supplemented with carbon or nitrogen. Arsenic resistant bacterial isolates (n = 200) were tested for the ability to utilize various carbon and nitrogen substrates and distinct positive correlation (p < 0.001) was found between arsenic resistance and utilization of urea and nitrate. However, evident positive correlation was not found between carbon sources and arsenic resistance. Our findings suggest that carbon and nitrogen pollution in aquatic habitats under arsenic stress determine the microbial community dynamics and critically influence uptake of genetic material from the surrounding environment.
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Affiliation(s)
- C S Neethu
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai 600025, India
| | - C Saravanakumar
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai 600025, India
| | - R Purvaja
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai 600025, India
| | - R S Robin
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai 600025, India
| | - R Ramesh
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai 600025, India.
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Owen C, Wright-Foulkes D, Alvarez P, Delgado H, Durance EC, Wells GF, Poretsky R, Shrestha A. Reduction and discharge of SARS-CoV-2 RNA in Chicago-area water reclamation plants. FEMS MICROBES 2022; 3:xtac015. [PMID: 37332512 PMCID: PMC10117756 DOI: 10.1093/femsmc/xtac015] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/14/2022] [Accepted: 05/05/2022] [Indexed: 08/24/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA is commonly excreted in the feces and urine of infected individuals and is, therefore, detected in wastewaters where infection is present in the surrounding population. Water reclamation plants (WRPs) that treat these wastewaters commonly discharge treated effluents into the surrounding environment, yet little is known about the removal or persistence of SARS-CoV-2 RNA through wastewater treatment systems and potential for eventual release into the environment. We collected 361 24-hour composite influent and effluent samples from seven WRPs in the Greater Chicago Area in Illinois. Samples were collected over a period of 21 weeks for three large WRPs (with design max flows of 1.89-2.32 billion gallons per day and serving a combined population of 4.62 million people) and 11 weeks for four smaller WRPs (with design max flows of 96.3-186 million gallons per day and serving a combined population of >0.5 million people). A total of two of the larger WRPs implemented seasonal disinfection (using UV light or chlorination/dechlorination) for 8 weeks of this sampling period. SARS-CoV-2 RNA was quantified in the influent and effluent samples by reverse-transcription quantitative PCR (RT-qPCR) of the N1 and N2 targets of the nucleocapsid (N) gene. Although SARS-CoV-2 RNA was regularly detected in influent and effluent from all WRPs, viral RNA concentrations in the effluent samples were considerably lower, with mean effluent: influent gene copy concentration ratios ranging from 1:160 to 1:2.95 between WRPs. Samples collected while disinfection was active vs. inactive did not show any significant difference in the portion of RNA persisting through the treatment process (P > .05).
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Affiliation(s)
- Christopher Owen
- Department of Biological Sciences, University of Illinois Chicago, Chicago, IL 60607, United States
| | - Dorothy Wright-Foulkes
- Division of Environmental and Occupational Health Sciences, School of Public Health, University of Illinois Chicago, Chicago, IL 60610, United States
| | - Prisila Alvarez
- Department of Biological Sciences, University of Illinois Chicago, Chicago, IL 60607, United States
| | - Haidy Delgado
- Department of Biological Sciences, University of Illinois Chicago, Chicago, IL 60607, United States
| | - Eva C Durance
- Department of Biological Sciences, University of Illinois Chicago, Chicago, IL 60607, United States
| | - George F Wells
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL 60208, United States
| | - Rachel Poretsky
- Department of Biological Sciences, University of Illinois Chicago, Chicago, IL 60607, United States
| | - Abhilasha Shrestha
- Division of Environmental and Occupational Health Sciences, School of Public Health, University of Illinois Chicago, Chicago, IL 60610, United States
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Yakimov MM, Merkel AY, Gaisin VA, Pilhofer M, Messina E, Hallsworth JE, Klyukina AA, Tikhonova EN, Gorlenko VM. Cultivation of a vampire: 'Candidatus Absconditicoccus praedator'. Environ Microbiol 2021; 24:30-49. [PMID: 34750952 DOI: 10.1111/1462-2920.15823] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 12/12/2022]
Abstract
Halorhodospira halophila, one of the most-xerophilic halophiles, inhabits biophysically stressful and energetically expensive, salt-saturated alkaline brines. Here, we report an additional stress factor that is biotic: a diminutive Candidate-Phyla-Radiation bacterium, that we named 'Ca. Absconditicoccus praedator' M39-6, which predates H. halophila M39-5, an obligately photosynthetic, anaerobic purple-sulfur bacterium. We cultivated this association (isolated from the hypersaline alkaline Lake Hotontyn Nur, Mongolia) and characterized their biology. 'Ca. Absconditicoccus praedator' is the first stably cultivated species from the candidate class-level lineage Gracilibacteria (order-level lineage Absconditabacterales). Its closed-and-curated genome lacks genes for the glycolytic, pentose phosphate- and Entner-Doudoroff pathways which would generate energy/reducing equivalents and produce central carbon currencies. Therefore, 'Ca. Absconditicoccus praedator' is dependent on host-derived building blocks for nucleic acid-, protein-, and peptidoglycan synthesis. It shares traits with (the uncultured) 'Ca. Vampirococcus lugosii', which is also of the Gracilibacteria lineage. These are obligate parasitic lifestyle, feeding on photosynthetic anoxygenic Gammaproteobacteria, and absorption of host cytoplasm. Commonalities in their genomic composition and structure suggest that the entire Absconditabacterales lineage consists of predatory species which act to cull the populations of their respective host bacteria. Cultivation of vampire : host associations can shed light on unresolved aspects of their metabolism and ecosystem dynamics at life-limiting extremes.
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Affiliation(s)
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Vasil A Gaisin
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Enzo Messina
- Institute for Marine Biological Resources and Biotechnology, IRBIM-CNR, Messina, Italy
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Alexandra A Klyukina
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina N Tikhonova
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir M Gorlenko
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Prokaryotic Communities in the Thalassohaline Tuz Lake, Deep Zone, and Kayacik, Kaldirim and Yavsan Salterns (Turkey) Assessed by 16S rRNA Amplicon Sequencing. Microorganisms 2021; 9:microorganisms9071525. [PMID: 34361960 PMCID: PMC8304926 DOI: 10.3390/microorganisms9071525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 01/31/2023] Open
Abstract
Prokaryotic communities and physico-chemical characteristics of 30 brine samples from the thalassohaline Tuz Lake (Salt Lake), Deep Zone, Kayacik, Kaldirim, and Yavsan salterns (Turkey) were analyzed using 16S rRNA amplicon sequencing and standard methods, respectively. Archaea (98.41% of reads) was found to dominate in these habitats in contrast to the domain Bacteria (1.38% of reads). Representatives of the phylum Euryarchaeota were detected as the most predominant, while 59.48% and 1.32% of reads, respectively, were assigned to 18 archaeal genera, 19 bacterial genera, 10 archaeal genera, and one bacterial genus that were determined to be present, with more than 1% sequences in the samples. They were the archaeal genera Haloquadratum, Haloarcula, Halorhabdus, Natronomonas, Halosimplex, Halomicrobium, Halorubrum, Halonotius, Halolamina, Halobacterium, and Salinibacter within the domain Bacteria. The genera Haloquadratum and Halorhabdus were found in all sampling sites. While Haloquadratum, Haloarcula, and Halorhabdus were the most abundant genera, two uncultured Tuz Lake Halobacteria (TLHs) 1 and 2 were detected in high abundance, and an additional uncultured haloarchaeal TLH-3 was found as a minor abundant uncultured taxon. Their future isolation in pure culture would permit us to expand our knowledge on hypersaline thalassohaline habitats, as well as their ecological role and biomedical and biotechnological potential applications.
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Estrela S, Sánchez Á, Rebolleda-Gómez M. Multi-Replicated Enrichment Communities as a Model System in Microbial Ecology. Front Microbiol 2021; 12:657467. [PMID: 33897672 PMCID: PMC8062719 DOI: 10.3389/fmicb.2021.657467] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022] Open
Abstract
Recent advances in robotics and affordable genomic sequencing technologies have made it possible to establish and quantitatively track the assembly of enrichment communities in high-throughput. By conducting community assembly experiments in up to thousands of synthetic habitats, where the extrinsic sources of variation among replicates can be controlled, we can now study the reproducibility and predictability of microbial community assembly at different levels of organization, and its relationship with nutrient composition and other ecological drivers. Through a dialog with mathematical models, high-throughput enrichment communities are bringing us closer to the goal of developing a quantitative predictive theory of microbial community assembly. In this short review, we present an overview of recent research on this growing field, highlighting the connection between theory and experiments and suggesting directions for future work.
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Affiliation(s)
- Sylvie Estrela
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Álvaro Sánchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
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