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Liu X, Pan B, Liu X, Han X, Zhu P, Li G, Li D. Trophic level plays an enhanced role in shaping microbiota structure and assembly in lakes with decreased salinity on the Qinghai-Tibet and Inner Mongolia Plateaus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171316. [PMID: 38423321 DOI: 10.1016/j.scitotenv.2024.171316] [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: 11/15/2023] [Revised: 02/25/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
Plateau lakes characterized by salinization and eutrophication are essential aquatic ecosystems. A myriad of microorganisms serve as crucial biological resources in plateau lakes and drive the elemental cycles of these ecosystems. Currently, there is a paucity of knowledge regarding the impacts of salinization and eutrophication dynamics on the microbiota in plateau lakes. Here, high-throughput sequencing of the 16S ribosomal RNA genes (V4 region) was used to characterize microbial community structure and assembly in plateau lakes with different salinities and trophic levels. Water samples were collected at 191 sites across 24 lakes on the Qinghai-Tibet and Inner Mongolia Plateaus in northern China. The results showed that high salinity considerably reduced microbial alpha-diversity and niche breadth while increasing within-group similarity among various lake types. High salinity additionally decreased the complexity of microbial networks and enhanced network robustness. The assembly of microbial communities was primarily governed by deterministic processes in high-salinity and eutrophic low-salinity lakes. At decreased salinity, trophic level played a leading role in shaping microbial community structure, and the ecological processes shifted from deterministic processes driven by high salinity to eutrophication-driven deterministic processes. The biomarkers also varied from taxa adapted to high-salinity environments (e.g., Nanoarchaeaeota, Rhodothermia) to those suited for living in freshwater and low-salinity habitats (e.g., Alphaproteobacteria, Actinobacteria). In the case of eutrophication, Actinobacteria, Chloroflexi, and Cyanobacteria became the dominant taxa. Our findings indicate that decreased salinity enables trophic level to play an enhanced role in shaping microbial community structure and assembly in plateau lakes. This study enriches our knowledge about the ecological impacts of salinization and eutrophication in plateau lakes.
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Affiliation(s)
- Xing Liu
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
| | - Baozhu Pan
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China.
| | - Xinyuan Liu
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
| | - Xu Han
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
| | - Penghui Zhu
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
| | - Gang Li
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
| | - Dianbao Li
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi Province, China
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2
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Bendia AG, Moreira JCF, Ferreira JCN, Romano RG, Ferreira IGC, Franco DC, Evangelista H, Montone RC, Pellizari VH. Insights into Antarctic microbiomes: diversity patterns for terrestrial and marine habitats. AN ACAD BRAS CIENC 2023; 95:e20211442. [PMID: 37820122 DOI: 10.1590/0001-3765202320211442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 08/27/2022] [Indexed: 10/13/2023] Open
Abstract
Microorganisms in Antarctica are recognized for having crucial roles in ecosystems functioning and biogeochemical cycles. To explore the diversity and composition of microbial communities through different terrestrial and marine Antarctic habitats, we analyze 16S rRNA sequence datasets from fumarole and marine sediments, soil, snow and seawater environments. We obtained measures of alpha- and beta-diversities, as well as we have identified the core microbiome and the indicator microbial taxa of a particular habitat. Our results showed a unique microbial community structure according to each habitat, including specific taxa composing each microbiome. Marine sediments harbored the highest microbial diversity among the analyzed habitats. In the fumarole sediments, the core microbiome was composed mainly of thermophiles and hyperthermophilic Archaea, while in the majority of soil samples Archaea was absent. In the seawater samples, the core microbiome was mainly composed by cultured and uncultured orders usually identified on Antarctic pelagic ecosystems. Snow samples exhibited common taxa previously described for habitats of the Antarctic Peninsula, which suggests long-distance dispersal processes occurring from the Peninsula to the Continent. This study contributes as a baseline for further efforts on evaluating the microbial responses to environmental conditions and future changes.
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Affiliation(s)
- Amanda G Bendia
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Julio Cezar F Moreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Juliana C N Ferreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Renato G Romano
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Ivan G C Ferreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Diego C Franco
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Heitor Evangelista
- Universidade do Estado do Rio de Janeiro (UERJ), Instituto de Biologia Roberto Alcantara Gomes, Maracanã, 20550-013 Rio de Janeiro, RJ, Brazil
| | - Rosalinda C Montone
- Universidade de São Paulo (USP), Departamento de Oceanografia Física, Química e Geológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Vivian Helena Pellizari
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
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3
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Jameson BD, Murdock SA, Ji Q, Stevens CJ, Grundle DS, Kim Juniper S. Network analysis of 16S rRNA sequences suggests microbial keystone taxa contribute to marine N 2O cycling. Commun Biol 2023; 6:212. [PMID: 36823449 PMCID: PMC9950131 DOI: 10.1038/s42003-023-04597-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
The mechanisms by which large-scale microbial community function emerges from complex ecological interactions between individual taxa and functional groups remain obscure. We leveraged network analyses of 16S rRNA amplicon sequences obtained over a seven-month timeseries in seasonally anoxic Saanich Inlet (Vancouver Island, Canada) to investigate relationships between microbial community structure and water column N2O cycling. Taxa separately broadly into three discrete subnetworks with contrasting environmental distributions. Oxycline subnetworks were structured around keystone aerobic heterotrophs that correlated with nitrification rates and N2O supersaturations, linking N2O production and accumulation to taxa involved in organic matter remineralization. Keystone taxa implicated in anaerobic carbon, nitrogen, and sulfur cycling in anoxic environments clustered together in a low-oxygen subnetwork that correlated positively with nitrification N2O yields and N2O production from denitrification. Close coupling between N2O producers and consumers in the anoxic basin is indicated by strong correlations between the low-oxygen subnetwork, PICRUSt2-predicted nitrous oxide reductase (nosZ) gene abundances, and N2O undersaturation. This study implicates keystone taxa affiliated with common ODZ groups as a potential control on water column N2O cycling and provides a theoretical basis for further investigations into marine microbial interaction networks.
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Affiliation(s)
- Brett D Jameson
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada.
| | - Sheryl A Murdock
- Department of Biology, University of Victoria, P.O. Box 1700 CSC, Victoria, BC, V8W 2Y2, Canada
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
| | - Qixing Ji
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
- Thrust of Earth, Ocean & Atmospheric Sciences, Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou, Guangdong, 511400, China
| | - Catherine J Stevens
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada
| | - Damian S Grundle
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
- School of Ocean Futures & School of Earth & Space Exploration, Arizona State University, Tempe, AZ, 85287-7904, USA
| | - S Kim Juniper
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada
- Department of Biology, University of Victoria, P.O. Box 1700 CSC, Victoria, BC, V8W 2Y2, Canada
- Ocean Networks Canada, 2474 Arbutus Road, Victoria, BC, V8N 1V8, Canada
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4
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Debroas D, Hochart C, Galand PE. Seasonal microbial dynamics in the ocean inferred from assembled and unassembled data: a view on the unknown biosphere. ISME COMMUNICATIONS 2022; 2:87. [PMID: 37938749 PMCID: PMC9723795 DOI: 10.1038/s43705-022-00167-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 11/09/2023]
Abstract
In environmental metagenomic experiments, a very high proportion of the microbial sequencing data (> 70%) remains largely unexploited because rare and closely related genomes are missed in short-read assemblies. The identity and the potential metabolisms of a large fraction of natural microbial communities thus remain inaccessible to researchers. The purpose of this study was to explore the genomic content of unassembled metagenomic data and test their level of novelty. We used data from a three-year microbial metagenomic time series of the NW Mediterranean Sea, and conducted reference-free and database-guided analysis. The results revealed a significant genomic difference between the assembled and unassembled reads. The unassembled reads had a lower mean identity against public databases, and fewer metabolic pathways could be reconstructed. In addition, the unassembled fraction presented a clear temporal pattern, unlike the assembled ones, and a specific community composition that was similar to the rare communities defined by metabarcoding using the 16S rRNA gene. The rare gene pool was characterised by keystone bacterial taxa, and the presence of viruses, suggesting that viral lysis could maintain some taxa in a state of rarity. Our study demonstrates that unassembled metagenomic data can provide important information on the structure and functioning of microbial communities.
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Affiliation(s)
- Didier Debroas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, 63000, Clermont-Ferrand, France.
| | - Corentin Hochart
- Sorbonne Universités, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Pierre E Galand
- Sorbonne Universités, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
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5
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Vaksmaa A, Egger M, Lüke C, Martins PD, Rosselli R, Asbun AA, Niemann H. Microbial communities on plastic particles in surface waters differ from subsurface waters of the North Pacific Subtropical Gyre. MARINE POLLUTION BULLETIN 2022; 182:113949. [PMID: 35932724 DOI: 10.1016/j.marpolbul.2022.113949] [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: 06/21/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The long-term fate of plastics in the ocean and their interactions with marine microorganisms remain poorly understood. In particular, the role of sinking plastic particles as a transport vector for surface microbes towards the deep sea has not been investigated. Here, we present the first data on the composition of microbial communities on floating and suspended plastic particles recovered from the surface to the bathypelagic water column (0-2000 m water depth) of the North Pacific Subtropical Gyre. Microbial community composition of suspended plastic particles differed from that of plastic particles afloat at the sea surface. However, in both compartments, a diversity of hydrocarbon-degrading bacteria was identified. These findings indicate that microbial community members initially present on floating plastics are quickly replaced by microorganisms acquired from deeper water layers, thus suggesting a limited efficiency of sinking plastic particles to vertically transport microorganisms in the North Pacific Subtropical Gyre.
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Affiliation(s)
- Annika Vaksmaa
- Department of Marine Microbiology & Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, the Netherlands.
| | - Matthias Egger
- The Ocean Cleanup, Rotterdam, the Netherlands; Egger Research and Consulting, St. Gallen, Switzerland
| | - Claudia Lüke
- Radboud University, Department of Microbiology, Nijmegen, the Netherlands
| | | | - Riccardo Rosselli
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Spain; LABAQUA S.A.U, C/Dracma 16-18, Pol. Ind. Las Atalayas, 03114 Alicante, Spain
| | - Alejandro Abdala Asbun
- Department of Marine Microbiology & Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, the Netherlands
| | - Helge Niemann
- Department of Marine Microbiology & Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, the Netherlands; Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, the Netherlands
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6
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Milke F, Sanchez-Garcia S, Dlugosch L, McNichol J, Fuhrman J, Simon M, Wagner-Döbler I. Composition and Biogeography of Planktonic Pro- and Eukaryotic Communities in the Atlantic Ocean: Primer Choice Matters. Front Microbiol 2022; 13:895875. [PMID: 35836413 PMCID: PMC9273945 DOI: 10.3389/fmicb.2022.895875] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/18/2022] [Indexed: 01/02/2023] Open
Abstract
Basin-scale biogeographic observations of marine pelagic pro- and eukaryotic communities are necessary to understand forces driving community composition and for providing a baseline to monitor global change. Deep sequencing of rRNA genes provides community composition at high resolution; yet, it is unclear how the choice of primers affects biogeographic patterns. Here, we re-amplified 16S rRNA genes from DNA sampled during R/V Polarstern Cruise ANT28-5 over a latitudinal transect across the Atlantic Ocean from 52°S to 47°N using universal V4-V5 primers and compared the results with those obtained previously with V5-V6 bacteria-specific primers. For validation of our results, we inferred community composition based on 16S rRNA genes of metagenomes from the same stations and single amplified genomes (SAGs) from the Global Ocean Reference Genome (GORG) database. We found that the universal V4-V5 primers retrieved SAR11 clades with similar relative proportions as those found in the GORG database while the V5-V6 primers recovered strongly diverging clade abundances. We confirmed an inverse bell-shaped distance-decay relationship and a latitudinal diversity gradient that did not decline linearly with absolute latitude in the Atlantic Ocean. Patterns were modified by sampling depth, sequencing depth, choice of primers, and abundance filtering. Especially richness patterns were not robust to methodological change. This study offers a detailed picture of the Atlantic Ocean microbiome using a universal set of PCR primers that allow for the conjunction of biogeographical patterns among organisms from different domains of life.
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Affiliation(s)
- Felix Milke
- Institute for Chmistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Selene Sanchez-Garcia
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Leon Dlugosch
- Institute for Chmistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jesse McNichol
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jed Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Meinhard Simon
- Institute for Chmistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Irene Wagner-Döbler
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
- *Correspondence: Irene Wagner-Döbler,
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7
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Medina-Chávez NO, Travisano M. Archaeal Communities: The Microbial Phylogenomic Frontier. Front Genet 2022; 12:693193. [PMID: 35154237 PMCID: PMC8826477 DOI: 10.3389/fgene.2021.693193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
Archaea are a unique system for investigating the diversity of life. There are the most diverse group of organisms with the longest evolutionary history of life on Earth. Phylogenomic investigations reveal the complex evolutionary history of Archaea, overturning longstanding views of the history of life. They exist in the harshest environments and benign conditions, providing a system to investigate the basis for living in extreme environments. They are frequently members of microbial communities, albeit generally rare. Archaea were central in the evolution of Eukaryotes and can be used as a proxy for studying life on other planets. Future advances will depend not only upon phylogenomic studies but also on a better understanding of isolation and cultivation techniques.
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Affiliation(s)
- Nahui Olin Medina-Chávez
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States.,BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Michael Travisano
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States.,BioTechnology Institute, University of Minnesota, St. Paul, MN, United States.,Minnesota Center for the Philosophy of Science, University of Minnesota, Minneapolis, MN, United States
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8
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Fernandes L, Jesus H, Almeida P, Sandrini J, Bianchini A, Santos H. The influence of the Doce River mouth on the microbiome of nearby coastal areas three years after the Fundão Dam failure, Brazil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:151777. [PMID: 34808168 DOI: 10.1016/j.scitotenv.2021.151777] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 10/14/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
The failure of the Fundão Dam, considered the world's largest mining disaster, released more than 55 million m3 of ore tailings into the environment. The sediment plume formed by water and tailings spread along approximately 663 km of water bodies of the Doce River basin. It reached the Atlantic Ocean sixteen days after the dam failure. However, the effects of the dam failure in the marine coastal areas years after the disaster are still unknown. This study aims to evaluate water and sediment microbial communities of nearby coastal areas three years after the Fundão Dam failure, using 16S rRNA gene amplicon sequencing. A total of 441 samples from 25 locations were collected during two different seasons (dry and rainy). The results showed that the Doce River mouth seems to divide the microbial communities from the southern and northern stations into two groups. The plume of sediments from the Doce River seems to be impacting the marine microbiome even at the furthest sampling stations. Bacterial (Anaerolineaceae, Thermodesulfovibrionia and Rhodopirellula) and Archaeal (Bathyarchaeia and Woesearchaeia) taxa, found in high abundance in the sediment of the Doce River mouth, have been previously described in high abundance in heavy metal contaminated sediments, including the Doce River itself and in mine tailing sediments. Cyanobium, found in great abundance in the water samples from the Doce River mouth, was also reported as the most abundant in the water of the Doce River after the Fundão Dam failure. Overall, the farther from the Doce River mouth the sample was, the lower the relative abundances of these taxa were. These results provide strong evidence that the sediment plume released by the Fundão Dam failure is probably impacting the marine microbiome of nearby coastal areas, even three years after the dam failure.
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Affiliation(s)
- Luanny Fernandes
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ 24210-201, Brazil
| | - Hugo Jesus
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ 24210-201, Brazil
| | - Pedro Almeida
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ 24210-201, Brazil
| | - Juliana Sandrini
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Av. Itália, s/n, Carreiros, Rio Grande, RS 96203-900, Brazil
| | - Adalto Bianchini
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Av. Itália, s/n, Carreiros, Rio Grande, RS 96203-900, Brazil; Coral Vivo Institute, Rio de Janeiro, Brazil
| | - Henrique Santos
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ 24210-201, Brazil; Coral Vivo Institute, Rio de Janeiro, Brazil.
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9
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Abstract
Intestinal microbiota, dominated by bacteria, plays an important role in the occurrence and the development of alcohol-associated liver disease (ALD), which is one of the most common liver diseases around the world. With sufficient studies focusing on the gut bacterial community, chronic alcohol consumption is now known as a key factor that alters the composition of gut bacterial community, increases intestinal permeability, causes intestinal dysfunction, induces bacterial translocation, and exacerbates the process of ALD via gut-liver axis. However, gut non-bacterial communities including fungi, viruses, and archaea, which may also participate in the disease, has received little attention relative to the gut bacterial community. This paper will systematically collect the latest literatures reporting non-bacterial communities in mammalian health and disease, and review their mechanisms in promoting the development of ALD including CLEC7A pathway, Candidalysin (a peptide toxin secreted by Candida albicans), metabolites, and other chemical substances secreted or regulated by gut commensal mycobiome, virome, and archaeome, hoping to bring novel insights on our current knowledge of ALD.
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Affiliation(s)
- Wenkang Gao
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yixin Zhu
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Jin Ye
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huikuan Chu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,CONTACT Huikuan Chu Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
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10
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Blais MA, Matveev A, Lovejoy C, Vincent WF. Size-Fractionated Microbiome Structure in Subarctic Rivers and a Coastal Plume Across DOC and Salinity Gradients. Front Microbiol 2022; 12:760282. [PMID: 35046910 PMCID: PMC8762315 DOI: 10.3389/fmicb.2021.760282] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022] Open
Abstract
Little is known about the microbial diversity of rivers that flow across the changing subarctic landscape. Using amplicon sequencing (rRNA and rRNA genes) combined with HPLC pigment analysis and physicochemical measurements, we investigated the diversity of two size fractions of planktonic Bacteria, Archaea and microbial eukaryotes along environmental gradients in the Great Whale River (GWR), Canada. This large subarctic river drains an extensive watershed that includes areas of thawing permafrost, and discharges into southeastern Hudson Bay as an extensive plume that gradually mixes with the coastal marine waters. The microbial communities differed by size-fraction (separated with a 3-μm filter), and clustered into three distinct environmental groups: (1) the GWR sites throughout a 150-km sampling transect; (2) the GWR plume in Hudson Bay; and (3) small rivers that flow through degraded permafrost landscapes. There was a downstream increase in taxonomic richness along the GWR, suggesting that sub-catchment inputs influence microbial community structure in the absence of sharp environmental gradients. Microbial community structure shifted across the salinity gradient within the plume, with changes in taxonomic composition and diversity. Rivers flowing through degraded permafrost had distinct physicochemical and microbiome characteristics, with allochthonous dissolved organic carbon explaining part of the variation in community structure. Finally, our analyses of the core microbiome indicated that while a substantial part of all communities consisted of generalists, most taxa had a more limited environmental range and may therefore be sensitive to ongoing change.
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Affiliation(s)
- Marie-Amélie Blais
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
| | - Alex Matveev
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
| | - Connie Lovejoy
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Québec-Océan, Université Laval, Quebec City, QC, Canada
| | - Warwick F Vincent
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
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11
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Patin NV, Dietrich ZA, Stancil A, Quinan M, Beckler JS, Hall ER, Culter J, Smith CG, Taillefert M, Stewart FJ. Gulf of Mexico blue hole harbors high levels of novel microbial lineages. THE ISME JOURNAL 2021; 15:2206-2232. [PMID: 33612832 PMCID: PMC8319197 DOI: 10.1038/s41396-021-00917-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Exploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole's rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40-75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80-110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.
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Affiliation(s)
- N V Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA.
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA.
- Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA.
| | | | - A Stancil
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - M Quinan
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - J S Beckler
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - E R Hall
- Mote Marine Laboratory, Sarasota, FL, USA
| | - J Culter
- Mote Marine Laboratory, Sarasota, FL, USA
| | - C G Smith
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL, USA
| | - M Taillefert
- School of Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - F J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, USA
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12
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Pereira O, Hochart C, Boeuf D, Auguet JC, Debroas D, Galand PE. Seasonality of archaeal proteorhodopsin and associated Marine Group IIb ecotypes (Ca. Poseidoniales) in the North Western Mediterranean Sea. THE ISME JOURNAL 2021; 15:1302-1316. [PMID: 33288859 PMCID: PMC8115670 DOI: 10.1038/s41396-020-00851-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/09/2020] [Accepted: 11/18/2020] [Indexed: 01/04/2023]
Abstract
The Archaea Marine Group II (MGII) is widespread in the world's ocean where it plays an important role in the carbon cycle. Despite recent discoveries on the group's metabolisms, the ecology of this newly proposed order (Candidatus Poseidoniales) remains poorly understood. Here we used a combination of time-series metagenome-assembled genomes (MAGs) and high-frequency 16S rRNA data from the NW Mediterranean Sea to test if the taxonomic diversity within the MGIIb family (Candidatus Thalassarchaeaceae) reflects the presence of different ecotypes. The MAGs' seasonality revealed a MGIIb family composed of different subclades that have distinct lifestyles and physiologies. The vitamin metabolisms were notably different between ecotypes with, in some, a possible link to sunlight's energy. Diverse archaeal proteorhodopsin variants, with unusual signature in key amino acid residues, had distinct seasonal patterns corresponding to changing day length. In addition, we show that in summer, archaea, as opposed to bacteria, disappeared completely from surface waters. Our results shed light on the diversity and the distribution of the euryarchaeotal proteorhodopsin, and highlight that MGIIb is a diverse ecological group. The work shows that time-series based studies of the taxonomy, seasonality, and metabolisms of marine prokaryotes is critical to uncover their diverse role in the ocean.
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Affiliation(s)
- Olivier Pereira
- Sorbonne Universités, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls sur Mer, France
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Corentin Hochart
- Sorbonne Universités, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls sur Mer, France
| | - Dominique Boeuf
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States, Honolulu, HI, 96822, USA
| | - Jean Christophe Auguet
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France, Montpellier, France
| | - Didier Debroas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, 63000, Clermont-Ferrand, France
| | - Pierre E Galand
- Sorbonne Universités, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls sur Mer, France.
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13
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Biogeochemical Responses and Seasonal Dynamics of the Benthic Boundary Layer Microbial Communities during the El Niño 2015 in an Eastern Boundary Upwelling System. WATER 2021. [DOI: 10.3390/w13020180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Eastern South Pacific coastal zone is characterized by seasonal and interannual variability, driven by upwelling and El Niño Southern Oscillation (ENSO), respectively. These oceanographical conditions influence microbial communities and their contribution to nutrient and greenhouse gases recycling, especially in bottom waters due to oxygenation. This article addresses the seasonal hydrographic and biogeochemical conditions in the water and sediments during El Niño 2015. Bottom water active microbial communities, including nitrifiers, were studied using amplicon sequencing of 16S rRNA (cDNA) and RT-qPCR, respectively. The results of the hydrographic analysis showed changes in the water column associated with the predominance of sub-Antarctic Waters characterized by warmed and low nutrients in the surface and more oxygenated conditions at the bottom in comparison with El Niño 2014. The organic matter quantity and quality decreased during fall and winter. The bottom water active microbial assemblages were dominated by archaea (Ca. Poseidoniales) and putative ammonia oxidizing archaea. Active bacteria affiliated to SAR11, Marinimicrobia and Nitrospina, and oxygen deficient realms (Desulfobacterales, SUP05 clade and anammox) suffered variations, possibly associated with oxygen and redox conditions in the benthic boundary layer. Nitrifying functional groups contributed significantly more during late fall and winter which was consistent with higher bottom water oxygenation. Relationships between apparent oxygen utilization nitrate and nitrous oxide in the water support the contribution of nitrification to this greenhouse gas distribution in the water. In general, our study suggests that seasonal oceanographic variability during an El Niño year influences the microbial community and thus remineralization potential, which supports the need to carry out longer time series to identify the relevance of seasonality under ENSO in Eastern Boundary Upwelling Systems (EBUS) areas.
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14
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DeLong EF. Exploring Marine Planktonic Archaea: Then and Now. Front Microbiol 2021; 11:616086. [PMID: 33519774 PMCID: PMC7838436 DOI: 10.3389/fmicb.2020.616086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/18/2020] [Indexed: 12/24/2022] Open
Abstract
In 1977, Woese and Fox leveraged molecular phylogenetic analyses of ribosomal RNAs and identified a new microbial domain of life on Earth, the Archaebacteria (now known as Archaea). At the time of their discovery, only one archaebacterial group, the strictly anaerobic methanogens, was known. But soon, other phenotypically unrelated microbial isolates were shown to belong to the Archaea, many originating from extreme habitats, including extreme halophiles, extreme thermophiles, and thermoacidophiles. Since most Archaea seemed to inhabit extreme or strictly anoxic habitats, it came as a surprise in 1992 when two new lineages of archaea were reported to be abundant in oxygen rich, temperate marine coastal waters and the deep ocean. Since that time, studies of marine planktonic archaea have revealed many more surprises, including their unexpected ubiquity, unusual symbiotic associations, unpredicted physiologies and biogeochemistry, and global abundance. In this Perspective, early work conducted on marine planktonic Archaea by my lab group and others is discussed in terms of the relevant historical context, some of the original research motivations, and surprises and discoveries encountered along the way.
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Affiliation(s)
- Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawai'i at Mănoa, Honolulu, HI, United States
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15
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Quéméneur M, Bel Hassen M, Armougom F, Khammeri Y, Lajnef R, Bellaaj-Zouari A. Prokaryotic Diversity and Distribution Along Physical and Nutrient Gradients in the Tunisian Coastal Waters (South Mediterranean Sea). Front Microbiol 2020; 11:593540. [PMID: 33335519 PMCID: PMC7735998 DOI: 10.3389/fmicb.2020.593540] [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: 08/10/2020] [Accepted: 10/26/2020] [Indexed: 01/18/2023] Open
Abstract
Prokaryotes play an important role in biogeochemical cycling in marine ecosystems, but little is known about their diversity and composition, and how they may contribute to the ecological functioning of coastal areas in the South Mediterranean Sea. This study investigated bacterial and archaeal community diversity in seawater samples along the Tunisian coast subject to important physicochemical disturbances. The 16S amplicon sequencing survey revealed higher prokaryotic diversity in the northern Tunisian bays than in southeastern waters (Gulf of Gabès). The major taxonomic groups identified in all samples were Alphaproteobacteria (40.9%), Gammaproteobacteria (18.7%), Marine Group II Euryarchaeota (11.3%), and Cyanobacteria (10.9%). Among them, the relative abundance of Alteromonadales, Prochlorococcus, and some clades of Pelagibacterales (SAR11) significantly differed between the northern and the southern bays, whereas no difference was observed across coastal waters in the archaeal Candidatus Poseidoniales (MGII), Synechococcus, and Pelagibacteraceae (SAR11 clade Ia), for which no relationship was observed with the environmental variables. Both Pseudoalteromonas and Alteromonas levels increased with the increasing salinity, density and nutrients (NH4 + and/or PO4 3-) gradients detected toward the southern waters, while the SAR11 clades Ib and IV and Prochlorococcus, decreased in the shallow, salty and nutrient-rich coastal waters of the Gulf of Gabès. Rhodobacteraceae was positively correlated with Synechococcus and chlorophyll levels, suggesting a relationship with phytoplankton biomass. The present study provides the first insights into planktonic prokaryotic community composition in the South Mediterranean Sea through the analysis of Tunisian seawaters, which may support further investigations on the role of bacterioplankton in the biogeochemistry of these ecosystems.
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Affiliation(s)
- Marianne Quéméneur
- Aix-Marseille Univ, University of Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| | - Malika Bel Hassen
- Institut National des Sciences et Technologies de la Mer, Salammbô, Tunis, Tunisia
| | - Fabrice Armougom
- Aix-Marseille Univ, University of Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| | - Yosra Khammeri
- Institut National des Sciences et Technologies de la Mer, Salammbô, Tunis, Tunisia
| | - Rim Lajnef
- Institut National des Sciences et Technologies de la Mer, Salammbô, Tunis, Tunisia
| | - Amel Bellaaj-Zouari
- Institut National des Sciences et Technologies de la Mer, Salammbô, Tunis, Tunisia
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16
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Clifford EL, De Corte D, Amano C, Paliaga P, Ivančić I, Ortiz V, Najdek M, Herndl GJ, Sintes E. Mesozooplankton taurine production and prokaryotic uptake in the northern Adriatic Sea. LIMNOLOGY AND OCEANOGRAPHY 2020; 65:2730-2747. [PMID: 33664530 PMCID: PMC7891661 DOI: 10.1002/lno.11544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/30/2020] [Accepted: 05/29/2020] [Indexed: 05/28/2023]
Abstract
Dissolved free taurine, an important osmolyte in phytoplankton and metazoans, has been shown to be a significant carbon and energy source for prokaryotes in the North Atlantic throughout the water column. However, the extent of the coupling between taurine production and consumption over a seasonal cycle has not been examined yet. We determined taurine production by abundant crustacean zooplankton and its role as a carbon and energy source for several prokaryotic taxa in the northern Adriatic Sea over a seasonal cycle. Taurine concentrations were generally in the low nanomolar range, reaching a maximum of 22 nmol L-1 in fall during a Pseudonitzschia bloom and coinciding with the highest zooplankton taurine release rates. Taurine accounted for up to 5% of the carbon, 11% of the nitrogen, and up to 71% of the sulfur requirements of heterotrophic prokaryotes. Members of the Roseobacter clade, Alteromonas, Thaumarchaeota, and Euryarchaeota exhibited higher cell-specific taurine assimilation rates than SAR11 cells. However, cell-specific taurine and leucine assimilation were highly variable in all taxa, suggesting species and/or ecotype specific utilization patterns of taurine and dissolved free amino acids. Copepods were able to cover the bulk taurine requirements of the prokaryotic communities in fall and winter and partly in the spring-summer period. Overall, our study emphasizes the significance of taurine as a carbon and energy source for the prokaryotic community in the northern Adriatic Sea and the importance of crustacean zooplankton as a significant source of taurine and other organic compounds for the heterotrophic prokaryotic community.
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Affiliation(s)
| | - Daniele De Corte
- Research and Development Center for Marine BiosciencesJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan
| | - Chie Amano
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
| | - Paolo Paliaga
- Department of Natural and Health SciencesJuraj Dobrila University of PulaPulaCroatia
| | - Ingrid Ivančić
- Center for Marine ResearchRuđer Bošković InstituteRovinjCroatia
| | - Victor Ortiz
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
| | - Mirjana Najdek
- Center for Marine ResearchRuđer Bošković InstituteRovinjCroatia
| | - Gerhard J. Herndl
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and BiogeochemistryUtrecht UniversityDen BurgThe Netherlands
| | - Eva Sintes
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
- Instituto Español de Oceanografía (IEO)Centro Oceanográfico de BalearesPalma de MallorcaSpain
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17
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Abstract
Host-associated microbial communities have an important role in shaping the health and fitness of plants and animals. Most studies have focused on the bacterial, fungal or viral communities, but often the archaeal component has been neglected. The archaeal community, the so-called archaeome, is now increasingly recognized as an important component of host-associated microbiomes. It is composed of various lineages, including mainly Methanobacteriales and Methanomassiliicoccales (Euryarchaeota), as well as representatives of the Thaumarchaeota. Host-archaeome interactions have mostly been delineated from methanogenic archaea in the gastrointestinal tract, where they contribute to substantial methane production and are potentially also involved in disease-relevant processes. In this Review, we discuss the diversity and potential roles of the archaea associated with protists, plants and animals. We also present the current understanding of the archaeome in humans, the specific adaptations involved in interaction with the resident microbial community as well as with the host, and the roles of the archaeome in both health and disease.
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18
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Dai J, Ye Q, Wu Y, Zhang M, Zhang J. Simulation of Enhanced Growth of Marine Group II Euryarchaeota From the Deep Chlorophyll Maximum of the Western Pacific Ocean: Implication for Upwelling Impact on Microbial Functions in the Photic Zone. Front Microbiol 2020; 11:571199. [PMID: 33013804 PMCID: PMC7516215 DOI: 10.3389/fmicb.2020.571199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/13/2020] [Indexed: 11/13/2022] Open
Abstract
Mesoscale eddies can have a strong impact on regional biogeochemistry and primary productivity. To investigate the effect of the upwelling of seawater by western Pacific eddies on the composition of the active planktonic marine archaeal community composition of the deep chlorophyll maximum (DCM) layer, mesoscale cold-core eddies were simulated in situ by mixing western Pacific DCM layer water with mesopelagic layer (400 m) water. Illumina sequencing of the 16S rRNA gene and 16S rRNA transcripts indicated that the specific heterotrophic Marine Group IIb (MGIIb) taxonomic group of the DCM layer was rapidly stimulated after receiving fresh substrate from 400 m water, which was dominated by uncultured autotrophic Marine Group I (MGI) archaea. Furthermore, niche differentiation of autotrophic ammonia-oxidizing archaea (MGI) was demonstrated by deep sequencing of 16S rRNA, amoA, and accA genes, respectively. Similar distribution patterns of active Marine Group III (MGIII) were observed in the DCM layer with or without vertical mixing, indicating that they are inclined to utilize the substrates already present in the DCM layer. These findings underscore the importance of mesoscale cyclonic eddies in stimulating microbial processes involved in the regional carbon cycle.
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Affiliation(s)
- Jinlong Dai
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Qi Ye
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Ying Wu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Miao Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Jing Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
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19
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Pereira O, Hochart C, Auguet JC, Debroas D, Galand PE. Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean. Microbiologyopen 2019; 8:e00852. [PMID: 31264806 PMCID: PMC6741140 DOI: 10.1002/mbo3.852] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 01/22/2023] Open
Abstract
Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re‐analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co‐occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more specifically of MGII subgroups, and reveal their association to a number of gene‐coding sequences. In particular, we show that MGII proteorhodopsins were detected in both the surface and the deep chlorophyll maximum layer and that different clusters of these light harvesting proteins were present. Our approach helped describing the set of genes found together with specific MGII subgroups. We could thus define genomic environments that could theoretically describe ecologically meaningful units and the ecological niche that they occupy.
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Affiliation(s)
- Olivier Pereira
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Corentin Hochart
- Laboratoire Microorganismes: Génome et Environnement, UMR 6023, CNRS - Université Blaise Pascal, Aubière, France
| | - Jean Christophe Auguet
- Marine Biodiversity, Exploitation and Conservation (MARBEC), Université de Montpellier, CNRS, IFREMER, Montpellier, France
| | - Didier Debroas
- Laboratoire Microorganismes: Génome et Environnement, UMR 6023, CNRS - Université Blaise Pascal, Aubière, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
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