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Van Le V, Kang M, Ko SR, Park CY, Lee JJ, Choi IC, Oh HM, Ahn CY. Response of particle-attached and free-living bacterial communities to Microcystis blooms. Appl Microbiol Biotechnol 2024; 108:42. [PMID: 38183480 DOI: 10.1007/s00253-023-12828-2] [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: 03/24/2023] [Revised: 07/29/2023] [Accepted: 11/13/2023] [Indexed: 01/08/2024]
Abstract
The massive proliferation of Microcystis threatens freshwater ecosystems and degrades water quality globally. Understanding the mechanisms that contribute to Microcystis growth is crucial for managing Microcystis blooms. The lifestyles of bacteria can be classified generally into two groups: particle-attached (PA; > 3 µm) and free-living (FL; 0.2-3.0 µm). However, little is known about the response of PA and FL bacteria to Microcystis blooms. Using 16S rRNA gene high-throughput sequencing, we investigated the stability, assembly process, and co-occurrence patterns of PA and FL bacterial communities during distinct bloom stages. PA bacteria were phylogenetically different from their FL counterparts. Microcystis blooms substantially influenced bacterial communities. The time decay relationship model revealed that Microcystis blooms might increase the stability of both PA and FL bacterial communities. A contrasting community assembly mechanism was observed between the PA and FL bacterial communities. Throughout Microcystis blooms, homogeneous selection was the major assembly process that impacted the PA bacterial community, whereas drift explained much of the turnover of the FL bacterial community. Both PA and FL bacterial communities could be separated into modules related to different phases of Microcystis blooms. Microcystis blooms altered the assembly process of PA and FL bacterial communities. PA bacterial community appeared to be more responsive to Microcystis blooms than FL bacteria. Decomposition of Microcystis blooms may enhance cooperation among bacteria. Our findings highlight the importance of studying bacterial lifestyles to understand their functions in regulating Microcystis blooms. KEY POINTS: • Microcystis blooms alter the assembly process of PA and FL bacterial communities • Microcystis blooms increase the stability of both PA and FL bacterial communities • PA bacteria seem to be more responsive to Microcystis blooms than FL bacteria.
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Affiliation(s)
- Ve Van Le
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Mingyeong Kang
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - So-Ra Ko
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
| | - Chan-Yeong Park
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Jay Jung Lee
- Geum River Environment Research Center, National Institute of Environmental Research, Chungbuk, 29027, Republic of Korea
| | - In-Chan Choi
- Geum River Environment Research Center, National Institute of Environmental Research, Chungbuk, 29027, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea.
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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Peng J, Wang D, He P, Wei P, Zhang L, Lan W, Li Y, Chen W, Zhao Z, Jiang L, Zhou L. Exploring the environmental influences and community assembly processes of bacterioplankton in a subtropical coastal system: Insights from the Beibu Gulf in China. ENVIRONMENTAL RESEARCH 2024; 259:119561. [PMID: 38972345 DOI: 10.1016/j.envres.2024.119561] [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: 03/08/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/09/2024]
Abstract
Due to rapid urbanization, the Beibu Gulf, a semi-closed gulf in the northwestern South China Sea, faces escalating ecological and environmental threats. Understanding the assembly mechanisms and driving factors of bacterioplankton in the Beibu Gulf is crucial for preserving its ecological functions and services. In the present study, we investigated the spatiotemporal dynamics of bacterioplankton communities and their assembly mechanisms in the Beibu Gulf based on the high-throughput sequencing of the bacterial 16 S rRNA gene. Results showed significantly higher bacterioplankton diversity during the wet season compared to the dry season. Additionally, distinct seasonal variations in bacterioplankton composition were observed, characterized by an increase in Cyanobacteria and Thermoplasmatota and a decrease in Proteobacteria and Bacteroidota during the wet season. Null model analysis revealed that stochastic processes governed bacterioplankton community assembly in the Beibu Gulf, with drift and homogenizing dispersal dominating during the dry and wet seasons, respectively. Enhanced deterministic assembly of bacterioplankton was also observed during the wet season. Redundancy and random forest model analyses identified the physical properties (e.g., temperature) and nutrient content (e.g., nitrate) of water as primary environmental drivers influencing bacterioplankton dynamics. Moreover, variation partitioning and distance-decay of similarity revealed that environmental filtering played a significant role in shaping bacterioplankton variations in this rapidly developed coastal ecosystem. These findings advance our understanding of bacterioplankton assembly in coastal ecosystems and establish a theoretical basis for effective ecological health management amidst ongoing global changes.
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Affiliation(s)
- Jinxia Peng
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 53002l, China
| | - Dapeng Wang
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 53002l, China
| | - Pingping He
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 53002l, China
| | - Pinyuan Wei
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 53002l, China
| | - Li Zhang
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 53002l, China
| | - Wenlu Lan
- Beibu Gulf Marine Ecological Environment Field Observation and Research Station of Guangxi, Marine Environmental Monitoring Centre of Guangxi, Beihai, 536000, China
| | - Yusen Li
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 53002l, China
| | - Wenjian Chen
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zelong Zhao
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Linyuan Jiang
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 53002l, China.
| | - Lei Zhou
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
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3
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Zhao S, Hu X, Li H, Zhang H, Lu J, Li Y, Chen Z, Bao M. Diversity and structure of pelagic microbial community in Kuroshio Extension. MARINE ENVIRONMENTAL RESEARCH 2024; 201:106697. [PMID: 39205358 DOI: 10.1016/j.marenvres.2024.106697] [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: 05/27/2024] [Revised: 07/27/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
Kuroshio Extension (KE) is the most active region of oceanic change in the North Pacific Ocean, which provides an essential place for the survival of marine microorganisms. However, Vertical changes in microbial communities in the Kuroshio Extension and the mechanisms by which environmental factors drive vertical changes in community structure remain unclear. In this work, microbial diversity, abundance, and community structure of 12 water layers (from surface to bottom) at five stations were uncovered by 16S rRNA gene high-throughput sequencing. Microbial diversity and richness decreased with increasing seawater depth. Microorganisms in the euphotic zone can be well separated from other zones based on NMDS analysis. Proteobacteria (65.20%), Bacteroidota (8.48%), Actinobacteriota (5.76%), and Crenarchaeota (4.49%) accounted for a relatively large proportion and their distribution is similar in four zones. Most of microorganisms were significantly (Spearman test, p < 0.05) correlated with salinity, density, pressure, and temperature. This work enhances our understanding of vertical microbial diversity and provides insights into the pelagic microbial community structure.
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Affiliation(s)
- Shanshan Zhao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province, 266100, China
| | - Xin Hu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province, 266100, China
| | - Haoshuai Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province, 266100, China
| | - Honghai Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province, 266100, China
| | - Jinren Lu
- College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province, 266100, China
| | - Yiming Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province, 266100, China
| | - Zhaohui Chen
- Frontier Science Center for Deep Ocean Multispheres and Earth System (FDOMES) and Physical Oceanography Laboratory, Ocean University of China, Qingdao, China; Laoshan Laboratory, Qingdao, China
| | - Mutai Bao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province, 266100, China.
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Madeira D, Madeira C, Calosi P, Vermandele F, Carrier-Belleau C, Barria-Araya A, Daigle R, Findlay HS, Poisot T. Multilayer biological networks to upscale marine research to global change-smart management and sustainable resource use. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173837. [PMID: 38866145 DOI: 10.1016/j.scitotenv.2024.173837] [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: 11/03/2023] [Revised: 05/30/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
Human activities are having a massive negative impact on biodiversity and ecological processes worldwide. The rate and magnitude of ecological transformations induced by climate change, habitat destruction, overexploitation and pollution are now so substantial that a sixth mass extinction event is currently underway. The biodiversity crisis of the Anthropocene urges scientists to put forward a transformative vision to promote the conservation of biodiversity, and thus indirectly the preservation of ecosystem functions. Here, we identify pressing issues in global change biology research and propose an integrative framework based on multilayer biological networks as a tool to support conservation actions and marine risk assessments in multi-stressor scenarios. Multilayer networks can integrate different levels of environmental and biotic complexity, enabling us to combine information on molecular, physiological and behaviour responses, species interactions and biotic communities. The ultimate aim of this framework is to link human-induced environmental changes to species physiology, fitness, biogeography and ecosystem impacts across vast seascapes and time frames, to help guide solutions to address biodiversity loss and ecological tipping points. Further, we also define our current ability to adopt a widespread use of multilayer networks within ecology, evolution and conservation by providing examples of case-studies. We also assess which approaches are ready to be transferred and which ones require further development before use. We conclude that multilayer biological networks will be crucial to inform (using reliable multi-levels integrative indicators) stakeholders and support their decision-making concerning the sustainable use of resources and marine conservation.
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Affiliation(s)
- Diana Madeira
- Laboratory for Innovation and Sustainability of Marine Biological Resources (ECOMARE), Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Aveiro, Portugal.
| | - Carolina Madeira
- Applied Molecular Biosciences Unit, Department of Life Sciences, School of Science and Technology, NOVA University of Lisbon, Caparica, Portugal; i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University of Lisbon, Caparica, Portugal
| | - Piero Calosi
- Laboratory of Marine Ecological and Evolutionary Physiology, Department of Biology, Chemistry and Geography, University of Quebec in Rimouski, 300 Allée des Ursulines, Rimouski, G5L 3A1, Québec, Canada
| | - Fanny Vermandele
- Laboratory of Marine Ecological and Evolutionary Physiology, Department of Biology, Chemistry and Geography, University of Quebec in Rimouski, 300 Allée des Ursulines, Rimouski, G5L 3A1, Québec, Canada
| | | | - Aura Barria-Araya
- Laboratory of Marine Ecological and Evolutionary Physiology, Department of Biology, Chemistry and Geography, University of Quebec in Rimouski, 300 Allée des Ursulines, Rimouski, G5L 3A1, Québec, Canada
| | - Remi Daigle
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, Nova Scotia, Canada; Marine Affairs Program, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Timothée Poisot
- Department of Biological Sciences, University of Montreal, Montreal, Canada
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Liu S, Chen Q, Hou C, Dong C, Qiu X, Tang K. Recovery of 1559 metagenome-assembled genomes from the East China Sea's low-oxygen region. Sci Data 2024; 11:994. [PMID: 39266528 PMCID: PMC11393323 DOI: 10.1038/s41597-024-03850-8] [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: 03/15/2024] [Accepted: 09/02/2024] [Indexed: 09/14/2024] Open
Abstract
The Changjiang Estuary and adjacent East China Sea are well-known hypoxic aquatic environments. Eutrophication-driven hypoxia frequently occurs in coastal areas, posing a major threat to the ecological environment, including altering community structure and metabolic processes of marine organisms, and enhancing diversion of energy shunt into microbial communities. However, the responses of microbial communities and their metabolic pathways to coastal hypoxia remain poorly understood. Here, we studied the microbial communities collected from spatiotemporal samplings using metagenomic sequencing in the Changjiang Estuary and adjacent East China Sea. This generated 1.31 Tbp of metagenomics data, distributed across 103 samples corresponding to 8 vertical profiles. We further reported 1,559 metagenome-assembled genomes (MAGs), of which 508 were high-quality MAGs (Completeness > 90% and Contamination < 10%). Phylogenomic analysis classified them into 181 archaeal and 1,378 bacterial MAGs. These results provided a valuable metagenomic dataset available for further investigation of the effects of hypoxia on marine microorganisms.
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Affiliation(s)
- Shujing Liu
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China
| | - Quanrui Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China
| | - Congcong Hou
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China
| | - Changjie Dong
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China
| | - Xuanyun Qiu
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China.
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West NJ, Landa M, Obernosterer I. Differential association of key bacterial groups with diatoms and Phaeocystis spp. during spring blooms in the Southern Ocean. Microbiologyopen 2024; 13:e1428. [PMID: 39119822 PMCID: PMC11310772 DOI: 10.1002/mbo3.1428] [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: 03/18/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024] Open
Abstract
Interactions between phytoplankton and heterotrophic bacteria significantly influence the cycling of organic carbon in the ocean, with many of these interactions occurring at the micrometer scale. We explored potential associations between specific phytoplankton and bacteria in two size fractions, 0.8-3 µm and larger than 3 µm, at three naturally iron-fertilized stations and one high nutrient low chlorophyll station in the Southern Ocean. The composition of phytoplankton and bacterial communities was determined by sequencing the rbcL gene and 16S rRNA gene from DNA and RNA extracts, which represent presence and potential activity, respectively. Diatoms, particularly Thalassiosira, contributed significantly to the DNA sequences in the larger size fractions, while haptophytes were dominant in the smaller size fraction. Correlation analysis between the most abundant phytoplankton and bacterial operational taxonomic units revealed strong correlations between Phaeocystis and picoeukaryotes with SAR11, SAR116, Magnetospira, and Planktomarina. In contrast, most Thalassiosira operational taxonomic units showed the highest correlations with Polaribacter, Sulfitobacteria, Erythrobacter, and Sphingobium, while Fragilariopsis, Haslea, and Thalassionema were correlated with OM60, Fluviicola, and Ulvibacter. Our in-situ observations suggest distinct associations between phytoplankton and bacterial taxa, which could play crucial roles in nutrient cycling in the Southern Ocean.
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Affiliation(s)
- Nyree J. West
- CNRS FR3724, Observatoire Océanologique de Banyuls (OOB)Sorbonne UniversitéBanyuls sur merFrance
| | - Marine Landa
- Laboratoire d'Océanographie Microbienne, LOMIC, CNRSSorbonne UniversitéBanyuls sur merFrance
| | - Ingrid Obernosterer
- Laboratoire d'Océanographie Microbienne, LOMIC, CNRSSorbonne UniversitéBanyuls sur merFrance
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Ferrera I, Auladell A, Balagué V, Reñé A, Garcés E, Massana R, Gasol JM. Seasonal and interannual variability of the free-living and particle-associated bacteria of a coastal microbiome. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13299. [PMID: 39081120 PMCID: PMC11289420 DOI: 10.1111/1758-2229.13299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 08/03/2024]
Abstract
Marine microbial communities differ genetically, metabolically, and ecologically according to their lifestyle, and they may respond differently to environmental changes. In this study, we investigated the seasonal dynamics of bacterial assemblies in the free-living (FL) and particle-associated (PA) fractions across a span of 6 years in the Blanes Bay Microbial Observatory in the Northwestern Mediterranean. Both lifestyles showed marked seasonality. The trends in alpha diversity were similar, with lower values in spring-summer than in autumn-winter. Samples from both fractions were grouped seasonally and the percentage of community variability explained by the measured environmental variables was comparable (32% in FL and 31% in PA). Canonical analyses showed that biotic interactions were determinants of bacterioplankton dynamics and that their relevance varies depending on lifestyles. Time-decay curves confirmed a high degree of predictability in both fractions. Yet, 'seasonal' Amplicon Sequence Variants (ASVs) (as defined by Lomb Scargle time series analysis) in the PA communities represented 46% of the total relative abundance while these accounted for 30% in the FL fraction. These results demonstrate that bacteria inhabiting both fractions exhibit marked seasonality, highlighting the importance of accounting for both lifestyles to fully comprehend the dynamics of marine prokaryotic communities.
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Affiliation(s)
- Isabel Ferrera
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC)BarcelonaCataloniaSpain
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía (IEO‐CSIC)MálagaSpain
| | - Adrià Auladell
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC)BarcelonaCataloniaSpain
- Present address:
Institut de Biologia Evolutiva (IBE‐UPF‐CSIC)BarcelonaCataloniaSpain
| | - Vanessa Balagué
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC)BarcelonaCataloniaSpain
| | - Albert Reñé
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC)BarcelonaCataloniaSpain
| | - Esther Garcés
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC)BarcelonaCataloniaSpain
| | - Ramon Massana
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC)BarcelonaCataloniaSpain
| | - Josep M. Gasol
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (ICM‐CSIC)BarcelonaCataloniaSpain
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Skouroliakou D, Breton E, Christaki U. Phaeocystis globosa and diatom blooms promote distinct bacterial communities and associations in a coastal ecosystem. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13313. [PMID: 38988030 PMCID: PMC11236930 DOI: 10.1111/1758-2229.13313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 06/26/2024] [Indexed: 07/12/2024]
Abstract
Phytoplankton and bacteria form the foundation of marine food webs. While most studies on phytoplankton bloom influence on bacteria dynamics focus on diatom-dominated blooms due to their global ecological significance, it is unclear if similar patterns extend to other species that compete with diatoms like Phaeocystis spp. This study aimed to contribute to the understanding of associations between phytoplankton and bacteria in a temperate ecosystem. For this, we studied the dynamics of phytoplankton and bacteria, combining 16S metabarcoding, microscopy, and flow cytometry over 4 years (282 samples). Phytoplankton and bacterial communities were studied throughout the year, particularly during contrasting phytoplankton blooms dominated by the Haptophyte Phaeocystis globosa or diatoms. We applied extended local similarity analysis (eLSA) to construct networks during blooming and non-blooming periods. Overall, the importance of seasonal and species-specific interactions between phytoplankton and bacteria is highlighted. In winter, mixed diatom communities were interconnected with bacteria, indicating a synergistic degradation of diverse phytoplankton-derived substrates. In spring, despite the intensity variations of P. globosa blooms, the composition of bacterial communities remained consistent over several years, suggesting establishing a stable-state environment for bacterial communities. Specific associations between monospecific diatom blooms and bacteria were evidenced in summer.
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Affiliation(s)
- Dimitra‐Ioli Skouroliakou
- UMR CNRS 8187 LOG, Université Littoral Côte d’Opale, Université de LilleWimereuxFrance
- Present address:
Laboratory of Protistology and Aquatic Ecology, Department of BiologyGhent UniversityGhentBelgium
| | - Elsa Breton
- UMR CNRS 8187 LOG, Université Littoral Côte d’Opale, Université de LilleWimereuxFrance
| | - Urania Christaki
- UMR CNRS 8187 LOG, Université Littoral Côte d’Opale, Université de LilleWimereuxFrance
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9
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Yang Y, Chen C, Yao K, Grossart HP. Seasonal dynamics of free-living (FL) and particle-attached (PA) bacterial communities in a plateau reservoir. Front Microbiol 2024; 15:1428701. [PMID: 39101032 PMCID: PMC11295932 DOI: 10.3389/fmicb.2024.1428701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 06/26/2024] [Indexed: 08/06/2024] Open
Abstract
In terms of lifestyle, bacterioplankton can be classified as free-living (FL) and particle-attached (PA) forms, and both play essential roles in biogeochemical cycling in aquatic ecosystems. Structure, distribution, and community assembly of FL and PA bacteria in plateau riverine waterbodies are largely unknown. Therefore, we explored the seasonal dynamics of FLand PA bacterial communities in the Wujiangdu reservoir, Yungui Plateau using 16S rRNA gene high-throughput sequencing. Results revealed there was a significant environmental heterogeneity in Wujiangdu reservoir seasonally. The dominant phylum was Actinomycetota for FL and Pseudomonadota for PA bacteria. Species richness and diversity was higher in autumn and winter compared to spring and summer. In general, PA diversity was greater than FL, but with some temporal variations. Species turnover was the major contributor to β-diversity of both FL and PA lifestyles, and significant differences were noticed between FL and PA bacterial community composition. Distinct co-occurrence network patterns implied that more connections exist between FL bacteria, while more complex PA networks were in parallel to their greater diversity and stronger interactions in biofilms on particles. Dispersal limitation was the major driving force for both FL and PA bacterial community assembly. Deterministic processes were of relatively low importance, with homogeneous selection for FL and heterogeneous selection for PA bacteria. Temperature was the most important environmental driver of seasonal bacterial dynamics, followed by nitrate for FL and Secchi depth for PA bacteria. This study allows for a better understanding of the temporal variability of different bacteria lifestyles in reservoirs in the vulnerable and rapidly changing plateau environment, facilitating further microbial research related to global warming and eutrophication.
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Affiliation(s)
- Yang Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Chen Chen
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Kai Yao
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Potsdam University, Potsdam, Germany
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Karlicki M, Bednarska A, Hałakuc P, Maciszewski K, Karnkowska A. Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning. FEMS Microbiol Ecol 2024; 100:fiae104. [PMID: 39039016 DOI: 10.1093/femsec/fiae104] [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: 03/04/2024] [Revised: 06/21/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024] Open
Abstract
Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and track spatio-temporal dynamics in both marine and freshwater environments. While marine ecosystems have been extensively studied, there is a notable research gap in understanding eukaryotic microbial communities in temperate lakes. Our study addresses this gap by investigating the free-living bacteria and small protist communities in Lake Roś (Poland), a dimictic temperate lake. Metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. Furthermore, machine learning and statistical methods identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the composition of analysed community are temperature, oxygen, and silicon concentration. Understanding these community structures and the underlying factors is important in the context of climate change potentially impacting mixing patterns and leading to prolonged stratification.
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Affiliation(s)
- Michał Karlicki
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Anna Bednarska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Department of Hydrobiology, Institute of Functional Biology and Ecology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Paweł Hałakuc
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Kacper Maciszewski
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
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11
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Sun F, Wang C, Xu Z, Song X, Cui H, Wang Z, Ouyang Z, Fu X. Temporal variations of bacterial and eukaryotic community in coastal waters-implications for aquaculture. Appl Microbiol Biotechnol 2024; 108:388. [PMID: 38900314 PMCID: PMC11189975 DOI: 10.1007/s00253-024-13176-5] [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: 06/27/2023] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 06/21/2024]
Abstract
Despite increased attention to the aquaculture environment, there is still a lack of understanding regarding the significance of water quality. To address this knowledge gap, this study utilized high-throughput sequencing of 16S rRNA and 18S rRNA to examine microbial communities (bacteria and eukaryotes) in coastal water over different months through long-term observations. The goal was to explore interaction patterns in the microbial community and identify potential pathogenic bacteria and red tide organisms. The results revealed significant differences in composition, diversity, and richness of bacterial and eukaryotic operational taxonomic units (OTUs) across various months. Principal coordinate analysis (PCoA) demonstrated distinct temporal variations in bacterial and eukaryotic communities, with significant differences (P = 0.001) among four groups: F (January-April), M (May), S (June-September), and T (October-December). Moreover, a strong association was observed between microbial communities and months, with most OTUs showing a distinct temporal preference. The Kruskal-Wallis test (P < 0.05) indicated significant differences in dominant bacterial and eukaryotic taxa among months, with each group exhibiting unique dominant taxa, including potential pathogenic bacteria and red tide organisms. These findings emphasize the importance of monitoring changes in potentially harmful microorganisms in aquaculture. Network analysis highlighted positive correlations between bacteria and eukaryotes, with bacteria playing a key role in network interactions. The key bacterial genera associated with other microorganisms varied significantly (P < 0.05) across different groups. In summary, this study deepens the understanding of aquaculture water quality and offers valuable insights for maintaining healthy aquaculture practices. KEY POINTS: • Bacterial and eukaryotic communities displayed distinct temporal variations. • Different months exhibited unique potential pathogenic bacteria and red tide organisms. • Bacteria are key taxonomic taxa involved in microbial network interactions.
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Affiliation(s)
- Fulin Sun
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, China
| | - Chunzhong Wang
- Putian Institute of Aquaculture Science of Fujian Province, Putian, China
| | - Zhantang Xu
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
| | - Xingyu Song
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Nansha Marine Ecological and Environmental Research Station, Chinese Academy of Sciences, Sansha, China
| | - Haiping Cui
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Nansha Marine Ecological and Environmental Research Station, Chinese Academy of Sciences, Sansha, China
| | - Zhen Wang
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Nansha Marine Ecological and Environmental Research Station, Chinese Academy of Sciences, Sansha, China
| | - Zhiyuan Ouyang
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Nansha Marine Ecological and Environmental Research Station, Chinese Academy of Sciences, Sansha, China
| | - Xiaoming Fu
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Nansha Marine Ecological and Environmental Research Station, Chinese Academy of Sciences, Sansha, China
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12
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Jing M, Yang W, Rao L, Chen J, Ding X, Zhou Y, Zhang Q, Lu K, Zhu J. Mechanisms of microbial coexistence in a patchy ecosystem: Differences in ecological niche overlap and species fitness between rhythmic and non-rhythmic species. WATER RESEARCH 2024; 256:121626. [PMID: 38642534 DOI: 10.1016/j.watres.2024.121626] [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: 11/24/2023] [Revised: 03/28/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
Resource patchiness caused by external events breaks the continuity and homogeneity of resource distribution in the original ecosystem. For local organisms, this leads to drastic changes in the availability of resources, breaks down the co-existence of species, and reshuffles the local ecosystem. West Lake is a freshwater lake with resource patchiness caused by multiple exogenous disturbances that has strong environmental heterogeneity that prevents clear observation of seasonal changes in the microbial communities. Despite this, the emergence of rhythmic species in response to irregular changes in the environment has been helpful for observing microbial communities dynamics in patchy ecosystems. We investigated the ecological mechanisms of seasonal changes in microbial communities in West Lake by screening rhythmic species based on the ecological niche and modern coexistence theories. The results showed that rhythmic species were the dominant factors in microbial community changes and the effects of most environmental factors on the microbial community were indirectly realised through the rhythmic species. Random forest analyses showed that seasonal changes in the microbial community were similarly predicted by the rhythmic species. In addition, we incorporated species interactions and community phylogenetic patterns into stepwise multiple regression analyses, the results of which indicate that ecological niches and species fitness may drive the coexistence of these subcommunities. Thus, this study extends our understanding of seasonal changes in microbial communities and provides new ways for observing seasonal changes in microbial communities, especially in ecosystems with resource patches. Our study also show that combining community phylogenies with co-occurrence networks based on ecological niches and modern coexistence theory can further help us understand the ecological mechanisms of interspecies coexistence.
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Affiliation(s)
- MingFei Jing
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Wen Yang
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Lihua Rao
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Jun Chen
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Xiuying Ding
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Yinying Zhou
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Quanxiang Zhang
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Kaihong Lu
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Jinyong Zhu
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China.
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13
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Puente‐Sánchez F, Macías‐Pérez LA, Campbell KL, Royo‐Llonch M, Balagué V, Sánchez P, Tamames J, Mundy CJ, Pedrós‐Alió C. Bacterioplankton taxa compete for iron along the early spring-summer transition in the Arctic Ocean. Ecol Evol 2024; 14:e11546. [PMID: 38895568 PMCID: PMC11183961 DOI: 10.1002/ece3.11546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 05/21/2024] [Accepted: 05/26/2024] [Indexed: 06/21/2024] Open
Abstract
Microbial assemblages under the sea ice of the Dease Strait, Canadian Arctic, were sequenced for metagenomes of a small size fraction (0.2-3 μm). The community from early March was typical for this season, with Alpha- and Gammaproteobacteria as the dominant taxa, followed by Thaumarchaeota and Bacteroidetes. Toward summer, Bacteroidetes, and particularly the genus Polaribacter, became increasingly dominant, followed by the Gammaproteobacteria. Analysis of genes responsible for microbial acquisition of iron showed an abundance of ABC transporters for divalent cations and ferrous iron. The most abundant transporters, however, were the outer membrane TonB-dependent transporters of iron-siderophore complexes. The abundance of iron acquisition genes suggested this element was essential for the microbial assemblage. Interestingly, Gammaproteobacteria were responsible for most of the siderophore synthesis genes. On the contrary, Bacteroidetes did not synthesize siderophores but accounted for most of the transporters, suggesting a role as cheaters in the competition for siderophores as public goods. This cheating ability of the Bacteroidetes may have contributed to their dominance in the summer.
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Affiliation(s)
- Fernando Puente‐Sánchez
- Department of Systems BiologyCentro Nacional de Biotecnología, CSICMadridSpain
- Microbial Ecology Division, Department of Aquatic Sciences and AssessmentSwedish University of Agricultural SciencesUppsalaSweden
- Present address:
Department of Aquatic Sciences and AssessmentSwedish University for Agricultural Sciences (SLU)UppsalaSweden
| | - Luis Alberto Macías‐Pérez
- Department of Systems BiologyCentro Nacional de Biotecnología, CSICMadridSpain
- Present address:
Department of Evolutionary and Integrative EcologyLeibniz Institute of Freshwater Ecology and Inland Fisheries (IGB)BerlinGermany
| | - Karley L. Campbell
- UiT The Arctic University of NorwayTromsøNorway
- Centre for Earth Observation Science, University of ManitobaWinnipegManitobaCanada
- Present address:
UiT The Arctic University of NorwayTromsøNorway
| | - Marta Royo‐Llonch
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar, CSICBarcelonaSpain
| | - Vanessa Balagué
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar, CSICBarcelonaSpain
| | - Pablo Sánchez
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar, CSICBarcelonaSpain
| | - Javier Tamames
- Department of Systems BiologyCentro Nacional de Biotecnología, CSICMadridSpain
| | | | - Carlos Pedrós‐Alió
- Department of Systems BiologyCentro Nacional de Biotecnología, CSICMadridSpain
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14
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Valencia‐Agami SS, Cerqueda‐García D, Gamboa‐Muñoz AM, Aguirre‐Macedo ML, García‐Maldonado JQ. Structure and composition of microbial communities in the water column from Southern Gulf of Mexico and detection of putative hydrocarbon-degrading microorganisms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13264. [PMID: 38692840 PMCID: PMC11062854 DOI: 10.1111/1758-2229.13264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/06/2024] [Indexed: 05/03/2024]
Abstract
This study assessed the bacterioplankton community and its relationship with environmental variables, including total petroleum hydrocarbon (TPH) concentration, in the Yucatan shelf area of the Southern Gulf of Mexico. Beta diversity analyses based on 16S rRNA sequences indicated variations in the bacterioplankton community structure among sampling sites. PERMANOVA indicated that these variations could be mainly related to changes in depth (5 to 180 m), dissolved oxygen concentration (2.06 to 5.93 mg L-1), and chlorophyll-a concentration (0.184 to 7.65 mg m3). Moreover, SIMPER and one-way ANOVA analyses showed that the shifts in the relative abundances of Synechococcus and Prochlorococcus were related to changes in microbial community composition and chlorophyll-a values. Despite the low TPH content measured in the studied sites (0.01 to 0.86 μL L-1), putative hydrocarbon-degrading bacteria such as Alteromonas, Acinetobacter, Balneola, Erythrobacter, Oleibacter, Roseibacillus, and the MWH-UniP1 aquatic group were detected. The relatively high copy number of the alkB gene detected in the water column by qPCR and the enrichment of hydrocarbon-degrading bacteria obtained during lab crude oil tests exhibited the potential of bacterioplankton communities from the Yucatan shelf to respond to potential hydrocarbon impacts in this important area of the Gulf Mexico.
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Affiliation(s)
- Sonia S. Valencia‐Agami
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de MéxicoMexico CityMexico
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Departamento de Recursos del MarMeridaYucatánMexico
| | - Daniel Cerqueda‐García
- Clúster Científico y Tecnológico BioMimic®, Red de Manejo Biorracional de Plagas y VectoresInstituto de Ecología, AC–INECOLXalapaVeracruzMexico
| | - Abril M. Gamboa‐Muñoz
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Departamento de Recursos del MarMeridaYucatánMexico
| | - M. Leopoldina Aguirre‐Macedo
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Departamento de Recursos del MarMeridaYucatánMexico
| | - José Q. García‐Maldonado
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Departamento de Recursos del MarMeridaYucatánMexico
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15
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Zhang W, Ye J, Liu X, Zhang Y, Zhang J, Shen L, Jin Y, Zhang J, Li H. Spatiotemporal dynamics of bacterioplankton communities in the estuaries of two differently contaminated coastal areas: Composition, driving factors and ecological process. MARINE POLLUTION BULLETIN 2024; 201:116263. [PMID: 38531208 DOI: 10.1016/j.marpolbul.2024.116263] [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: 12/06/2023] [Revised: 02/05/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024]
Abstract
Seasonal variations of environmental parameters usually lead to considerable changes in microbial communities. Nevertheless, the specific response patterns of these communities in coastal areas subjected to different levels of contamination remain unclear. Our results revealed notable fluctuations in the bacterioplankton community both seasonally and spatially, with seasonal variations being particularly significant. The diversity and composition of bacterioplankton communities in the estuaries varied significantly across seasons and between seas. Some bacterial phyla that were highly abundant in the dry season (e.g., Patescibacteria and Epsilonbacteraeota) were almost absent in the wet season. Furthermore, the network analysis revealed that the bacterioplankton networks were more complex during the wet season than in the dry season. In the wet season, the estuarine bacterioplankton network in the Yellow Sea region was more complex and stable, while the opposite was true in the dry season. According to the neutral community model, stochastic processes played a more significant role in the formation of bacterioplankton communities during the wet season than during the dry season. Estuarine bacterioplankton communities in the Yellow Sea region were more affected by stochastic processes compared to those in the Bohai Sea. In summary, in the estuaries of two differently contaminated coastal areas, the seasonal increase in nutrient levels enhanced the deterministic processes and network complexity of the bacterioplankton communities.
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Affiliation(s)
- Weiyue Zhang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Jinqing Ye
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China.
| | - Xiaohan Liu
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Yunlei Zhang
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Jinyong Zhang
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Lingyu Shen
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Yuan Jin
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Jianheng Zhang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian 116023, China.
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16
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Celussi M, Manna V, Banchi E, Fonti V, Bazzaro M, Flander-Putrle V, Klun K, Kralj M, Orel N, Tinta T. Annual recurrence of prokaryotic climax communities in shallow waters of the North Mediterranean. Environ Microbiol 2024; 26:e16595. [PMID: 38418391 DOI: 10.1111/1462-2920.16595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/02/2024] [Indexed: 03/01/2024]
Abstract
In temperate coastal environments, wide fluctuations of biotic and abiotic factors drive microbiome dynamics. To link recurrent ecological patterns with planktonic microbial communities, we analysed a monthly-sampled 3-year time series of 16S rRNA amplicon sequencing data, alongside environmental variables, collected at two stations in the northern Adriatic Sea. Time series multivariate analyses allowed us to identify three stable, mature communities (climaxes), whose recurrence was mainly driven by changes in photoperiod and temperature. Mixotrophs (e.g., Ca. Nitrosopumilus, SUP05 clade, and Marine Group II) thrived under oligotrophic, low-light conditions, whereas copiotrophs (e.g., NS4 and NS5 clades) bloomed at higher temperatures and substrate availability. The early spring climax was characterised by a more diverse set of amplicon sequence variants, including copiotrophs associated with phytoplankton-derived organic matter degradation, and photo-auto/heterotrophic organisms (e.g., Synechococcus sp., Roseobacter clade), whose rhythmicity was linked to photoperiod lengthening. Through the identification of recurrent climax assemblages, we begin to delineate a typology of ecosystem based on microbiome composition and functionality, allowing for the intercomparison of microbial assemblages among different biomes, a still underachieved goal in the omics era.
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Affiliation(s)
- Mauro Celussi
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Elisa Banchi
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Viviana Fonti
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
| | - Matteo Bazzaro
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
| | | | - Katja Klun
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Martina Kralj
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
| | - Neža Orel
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Tinkara Tinta
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
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17
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Genitsaris S, Stefanidou N, Hatzinikolaou D, Kourkoutmani P, Michaloudi E, Voutsa D, Gros M, García-Gómez E, Petrović M, Ntziachristos L, Moustaka-Gouni M. Marine Microbiota Responses to Shipping Scrubber Effluent Assessed at Community Structure and Function Endpoints. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024. [PMID: 38415986 DOI: 10.1002/etc.5834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/29/2024]
Abstract
The use of novel high-throughput sequencing (HTS) technologies to examine the responses of natural multidomain microbial communities to scrubber effluent discharges to the marine environment is still limited. Thus, we applied metabarcoding sequencing targeting the planktonic unicellular eukaryotic and prokaryotic fraction (phytoplankton, bacterioplankton, and protozooplankton) in mesocosm experiments with natural microbial communities from a polluted and an unpolluted site. Furthermore, metagenomic analysis revealed changes in the taxonomic and functional dominance of multidomain marine microbial communities after scrubber effluent additions. The results indicated a clear shift in the microbial communities after such additions, which favored bacterial taxa with known oil and polycyclic aromatic hydrocarbons (PAHs) biodegradation capacities. These bacteria exhibited high connectedness with planktonic unicellular eukaryotes employing variable trophic strategies, suggesting that environmentally relevant bacteria can influence eukaryotic community structure. Furthermore, Clusters of Orthologous Genes associated with pathways of PAHs and monocyclic hydrocarbon degradation increased in numbers at treatments with high scrubber effluent additions acutely. These genes are known to express enzymes acting at various substrates including PAHs. These indications, in combination with the abrupt decrease in the most abundant PAHs in the scrubber effluent below the limit of detection-much faster than their known half-lives-could point toward a bacterioplankton-initiated rapid ultimate biodegradation of the most abundant toxic contaminants of the scrubber effluent. The implementation of HTS could be a valuable tool to develop multilevel biodiversity indicators of the scrubber effluent impacts on the marine environment, which could lead to improved impact assessment. Environ Toxicol Chem 2024;00:1-18. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Savvas Genitsaris
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Section of Ecology and Taxonomy, School of Biology, National and Kapodistrian University of Athens, Zografou Campus, Athens, Greece
| | - Natassa Stefanidou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitris Hatzinikolaou
- Department of Botany, School of Biology, National and Kapodistrian University of Athens, Zografou Campus, Athens, Greece
| | - Polyxeni Kourkoutmani
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evangelia Michaloudi
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitra Voutsa
- Environmental Pollution Control Laboratory, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Meritxell Gros
- Catalan Institute for Water Research (ICRA), Girona, Spain
- University of Girona (UdG), Girona, Spain
| | - Elisa García-Gómez
- Catalan Institute for Water Research (ICRA), Girona, Spain
- University of Girona (UdG), Girona, Spain
| | - Mira Petrović
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Leonidas Ntziachristos
- Department of Mechanical Engineering, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Moustaka-Gouni
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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18
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Xu T, Novotny A, Zamora-Terol S, Hambäck PA, Winder M. Dynamics of Gut Bacteria Across Different Zooplankton Genera in the Baltic Sea. MICROBIAL ECOLOGY 2024; 87:48. [PMID: 38409540 PMCID: PMC10896951 DOI: 10.1007/s00248-024-02362-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/18/2024] [Indexed: 02/28/2024]
Abstract
In aquatic ecosystems, zooplankton-associated bacteria potentially have a great impact on the structure of ecosystems and trophic networks by providing various metabolic pathways and altering the ecological niche of host species. To understand the composition and drivers of zooplankton gut microbiota, we investigated the associated microbial communities of four zooplankton genera from different seasons in the Baltic Sea using the 16S rRNA gene. Among the 143 ASVs (amplified sequence variants) observed belonging to heterotrophic bacteria, 28 ASVs were shared across all zooplankton hosts over the season, and these shared core ASVs represented more than 25% and up to 60% of relative abundance in zooplankton hosts but were present at low relative abundance in the filtered water. Zooplankton host identity had stronger effects on bacterial composition than seasonal variation, with the composition of gut bacterial communities showing host-specific clustering patterns. Although bacterial compositions and dominating core bacteria were different between zooplankton hosts, higher gut bacteria diversity and more bacteria contributing to the temporal variation were found in Temora and Pseudocalanus, compared to Acartia and Synchaeta. Diet diatom and filamentous cyanobacteria negatively correlated with gut bacteria diversity, but the difference in diet composition did not explain the dissimilarity of gut bacteria composition, suggesting a general effect of diet on the inner conditions in the zooplankton gut. Synchaeta maintained high stability of gut bacterial communities with unexpectedly low bacteria-bacteria interactions as compared to the copepods, indicating host-specific regulation traits. Our results suggest that the patterns of gut bacteria dynamics are host-specific and the variability of gut bacteria is not only related to host taxonomy but also related to host behavior and life history traits.
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Affiliation(s)
- Tianshuo Xu
- Department of Ecology Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.
| | - Andreas Novotny
- Department of Ecology Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, Canada
| | - Sara Zamora-Terol
- Department of Ecology Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Institute of Marine Research, Bergen, Norway
| | - Peter A Hambäck
- Department of Ecology Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Monika Winder
- Department of Ecology Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.
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19
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Guo Z, Lu W, Minpeng S, Liyuan S, Zhenlin L, Wenjing C, Xiaoyong L, Bo Z, Jeong Ha K, Zhaoyang J. Seasonal dynamics response mechanism of benthic microbial community to artificial reef habitats. ENVIRONMENTAL RESEARCH 2024; 243:117867. [PMID: 38070848 DOI: 10.1016/j.envres.2023.117867] [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: 11/03/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 02/06/2024]
Abstract
Artificial reefs (ARs) have been globally deployed to enhance and restore coastal resource and ecosystems. Microorganisms play an essential role in marine ecosystems, while the knowledge regarding the impact of ARs on microecology is still limited, particularly data concerning the response of benthic microbial community to AR habitats. In this study, the seasonal dynamics of benthic microbial community in AR and adjacent non-artificial reef (NAR) areas surrounding Xiaoshi Island were investigated with high-throughput sequencing technology. The results revealed that the diversity and structure of microbial community between AR and NAR both displayed pronounced seasonal dynamics. There was a greater influence of season factors on microbial communities than that of habitat type. The microbial communities in AR and NAR habitats were characterized by a limited number of abundant taxa (ranging from 5 to 12 ASVs) with high relative abundance (8.35-25.53%) and numerous rare taxa (from 5994 to 12412 ASVs) with low relative abundance (11.91%-24.91%). Proteobacteria, Bacteroidota and Desulfobacterota were the common predominant phyla, with the relative abundances ranging from 50.94% to 76.76%. A total of 52 biomarkers were discovered, with 15, 4, 6, and 27 biomarkers identified in spring, summer, autumn and winter, respectively. Co-occurrence network analysis indicated that AR displayed a more complex interaction pattern and higher susceptibility to external disturbances. Furthermore, the neutral model and βNTI analyses revealed that the assembly of microbial communities in both AR and NAR is significantly influenced by stochastic processes. This study could provide valuable insights into the impact of ARs construction on the benthic ecosystems and would greatly facilitate the development and implementation of the future AR projects.
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Affiliation(s)
- Zhansheng Guo
- Marine College, Shandong University, Weihai, Shandong, 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, China
| | - Wang Lu
- Marine College, Shandong University, Weihai, Shandong, 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, China
| | - Song Minpeng
- Marine College, Shandong University, Weihai, Shandong, 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, China
| | - Sun Liyuan
- Shandong Fisheries Development and Resources Conservation Center, Yantai, 264003, China
| | - Liang Zhenlin
- Marine College, Shandong University, Weihai, Shandong, 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, China
| | - Chen Wenjing
- Marine College, Shandong University, Weihai, Shandong, 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, China
| | - Liu Xiaoyong
- Shandong Haizhibao Ocean Science and Technology Co., Ltd, Weihai, 264300, China
| | - Zhang Bo
- Shandong Haizhibao Ocean Science and Technology Co., Ltd, Weihai, 264300, China
| | - Kim Jeong Ha
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea.
| | - Jiang Zhaoyang
- Marine College, Shandong University, Weihai, Shandong, 264209, China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, China.
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20
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Lin L, Xiong J, Liu L, Wang F, Cao W, Xu W. Microbial interactions strengthen deterministic processes during community assembly in a subtropical estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167499. [PMID: 37778550 DOI: 10.1016/j.scitotenv.2023.167499] [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: 06/11/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Systematic studies on the assembly process and driving mechanisms of microbial communities in estuaries with diverse seasonal and spatial scales are still limited. In this study, high-throughput sequencing, and microbial network analysis were combined to decipher the impact of environmental changes and biological interactions on the maintenance of microbial diversity patterns in the Jiulong River Estuary (JRE). The results showed that overall, stochastic processes dominated the bacterioplankton community assembly in the estuary, accounting for 49.66-74.78 % of the total. Additionally, bacterioplankton community diversity varied significantly across seasons and subzones. Specifically, the concentration of soluble reactive phosphorus (SRP) in the estuary steadily reduced from winter to summer, and the corresponding bacterioplankton community interactions gradually shifted from the weakest interaction in winter to the strongest in summer. The deterministic processes contributed more than half (50.34 %) to microbial assembly in the summer, but only 25.22 % in winter. Deterministic processes prevailed in the seaward with low SRP concentrations and strong bacterioplankton community interactions, while stochastic processes contributed 70.14 % to the assembly of microbial communities riverward. Biotic and abiotic factors, such as nutrients and microbial interactions, jointly drove the seasonal and spatial patterns of bacterioplankton community assembly, but overall, nutrients played a dominant role. Nevertheless, the contributions of nutrients and microbial interactions were equivalent in spatial assembly processes, albeit nutrients were the primary seasonal driver of the bacterioplankton community assembly process. This study emphasizes the significance of microbial interactions in the bacterioplankton community assemblage. These findings provide new and comprehensive insights into the microbial communities' organization in estuaries.
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Affiliation(s)
- Ling Lin
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China
| | - Jiangzhiqian Xiong
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China
| | - Lihua Liu
- Fujian Xiamen Environmental Monitoring Central Station, Xing'lin South Road, Xiamen 361022, China
| | - Feifei Wang
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China
| | - Wenzhi Cao
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China.
| | - Wenfeng Xu
- Fujian Xiamen Environmental Monitoring Central Station, Xing'lin South Road, Xiamen 361022, China.
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21
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Brunet M, Le Duff N, Rigaut-Jalabert F, Romac S, Barbeyron T, Thomas F. Seasonal dynamics of a glycan-degrading flavobacterial genus in a tidally mixed coastal temperate habitat. Environ Microbiol 2023; 25:3192-3206. [PMID: 37722696 DOI: 10.1111/1462-2920.16505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/03/2023] [Indexed: 09/20/2023]
Abstract
Coastal marine habitats constitute hotspots of primary productivity. In temperate regions, this is due both to massive phytoplankton blooms and dense colonisation by macroalgae that mostly store carbon as glycans, contributing substantially to local and global carbon sequestration. Because they control carbon and energy fluxes, algae-degrading microorganisms are crucial for coastal ecosystem functions. Environmental surveys revealed consistent seasonal dynamics of alga-associated bacterial assemblages, yet resolving what factors regulate the in situ abundance, growth rate and ecological functions of individual taxa remains a challenge. Here, we specifically investigated the seasonal dynamics of abundance and activity for a well-known alga-degrading marine flavobacterial genus in a tidally mixed coastal habitat of the Western English Channel. We show that members of the genus Zobellia are a stable, low-abundance component of healthy macroalgal microbiota and can also colonise particles in the water column. This genus undergoes recurring seasonal variations with higher abundances in winter, significantly associated to biotic and abiotic variables. Zobellia can become a dominant part of bacterial communities on decaying macroalgae, showing a strong activity and high estimated in situ growth rates. These results provide insights into the seasonal dynamics and environmental constraints driving natural populations of alga-degrading bacteria that influence coastal carbon cycling.
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Affiliation(s)
- Maéva Brunet
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Nolwen Le Duff
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | | | - Sarah Romac
- Sorbonne Université, CNRS, Adaptation et Diversité en Milieu Marin (AD2M)-UMR7144, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Tristan Barbeyron
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - François Thomas
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
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22
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Wutkowska M, Vader A, Logares R, Pelletier E, Gabrielsen TM. Linking extreme seasonality and gene expression in Arctic marine protists. Sci Rep 2023; 13:14627. [PMID: 37669980 PMCID: PMC10480425 DOI: 10.1038/s41598-023-41204-3] [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: 02/27/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023] Open
Abstract
At high latitudes, strong seasonal differences in light availability affect marine organisms and regulate the timing of ecosystem processes. Marine protists are key players in Arctic aquatic ecosystems, yet little is known about their ecological roles over yearly cycles. This is especially true for the dark polar night period, which up until recently was assumed to be devoid of biological activity. A 12 million transcripts catalogue was built from 0.45 to 10 μm protist assemblages sampled over 13 months in a time series station in an Arctic fjord in Svalbard. Community gene expression was correlated with seasonality, with light as the main driving factor. Transcript diversity and evenness were higher during polar night compared to polar day. Light-dependent functions had higher relative expression during polar day, except phototransduction. 64% of the most expressed genes could not be functionally annotated, yet up to 78% were identified in Arctic samples from Tara Oceans, suggesting that Arctic marine assemblages are distinct from those from other oceans. Our study increases understanding of the links between extreme seasonality and biological processes in pico- and nanoplanktonic protists. Our results set the ground for future monitoring studies investigating the seasonal impact of climate change on the communities of microbial eukaryotes in the High Arctic.
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Affiliation(s)
- Magdalena Wutkowska
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway.
- Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway.
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia.
| | - Anna Vader
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Catalonia, Spain
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Tove M Gabrielsen
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway
- Department of Natural Sciences, University of Agder, Kristiansand, Norway
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23
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King NG, Wilmes SB, Browett SS, Healey A, McDevitt AD, McKeown NJ, Roche R, Skujina I, Smale DA, Thorpe JM, Malham S. Seasonal development of a tidal mixing front drives shifts in community structure and diversity of bacterioplankton. Mol Ecol 2023; 32:5201-5210. [PMID: 37555658 DOI: 10.1111/mec.17097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/10/2023]
Abstract
Bacterioplankton underpin biogeochemical cycles and an improved understanding of the patterns and drivers of variability in their distribution is needed to determine their wider functioning and importance. Sharp environmental gradients and dispersal barriers associated with ocean fronts are emerging as key determinants of bacterioplankton biodiversity patterns. We examined how the development of the Celtic Sea Front (CF), a tidal mixing front on the Northwest European Shelf affects bacterioplankton communities. We performed 16S-rRNA metabarcoding on 60 seawater samples collected from three depths (surface, 20 m and seafloor), across two research cruises (May and September 2018), encompassing the intra-annual range of the CF intensity. Communities above the thermocline of stratified frontal waters were clearly differentiated and less diverse than those below the thermocline and communities in the well-mixed waters of the Irish Sea. This effect was much more pronounced in September, when the CF was at its peak intensity. The stratified zone likely represents a stressful environment for bacterioplankton due to a combination of high temperatures and low nutrients, which fewer taxa can tolerate. Much of the observed variation was driven by Synechococcus spp. (cyanobacteria), which were more abundant within the stratified zone and are known to thrive in warm oligotrophic waters. Synechococcus spp. are key contributors to global primary productivity and carbon cycling and, as such, variability driven by the CF is likely to influence regional biogeochemical processes. However, further studies are required to explicitly link shifts in community structure to function and quantify their wider importance to pelagic ecosystems.
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Affiliation(s)
- Nathan G King
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, UK
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, UK
| | - Sophie-B Wilmes
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, UK
| | - Samuel S Browett
- Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, UK
- Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland
| | - Amy Healey
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
| | - Allan D McDevitt
- Department of Natural Resources and Environment, Atlantic Technological University, Galway, Ireland
| | - Niall J McKeown
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
| | - Ronan Roche
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, UK
| | - Ilze Skujina
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Dan A Smale
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, UK
| | - Jamie M Thorpe
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, UK
| | - Shelagh Malham
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, UK
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24
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Yang Q, Li D, Chen W, Zhu L, Zou X, Hu L, Yuan Y, He S, Shi F. Dynamics of Bacterioplankton Communities during Wet and Dry Seasons in the Danjiangkou Reservoir in Hubei, China. Life (Basel) 2023; 13:life13051206. [PMID: 37240851 DOI: 10.3390/life13051206] [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: 04/03/2023] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Water quality is directly linked to drinking water safety for millions of people receiving the water. The Danjiangkou Reservoir is the main water source for the Middle Route of the South-to-North Water Diversion Project (MR-SNWDP), located in the vicinity of Henan and Hubei provinces in China. Aquatic microorganisms are key indicators of biologically assessing and monitoring the water quality of the reservoir as they are sensitive to environmental and water quality changes. This study aimed to investigate the spatiotemporal variations in bacterioplankton communities during wet (April) and dry (October) seasons at eight monitoring points in Hanku reservoir and five monitoring points in Danku reservoir. Each time point had three replicates, labeled as wet season Hanku (WH), wet season Danku (WD), dry season Hanku (DH), and dry season Danku (DD) of Danjiangkou Reservoir in 2021. High-throughput sequencing (Illumina PE250) of the 16S rRNA gene was performed, and alpha (ACE and Shannon) and beta (PCoA and NDMS) diversity indices were analyzed. The results showed that the dry season (DH and DD) had more diverse bacterioplankton communities compared to the wet season (WH and WD). Proteobacteria, Actinobacteria, and Firmicutes were the most abundant phyla, and Acinetobacter, Exiguobacterium, and Planomicrobium were abundant in the wet season, while polynucleobacter was abundant in the dry season. The functional prediction of metabolic pathways revealed six major functions including carbohydrate metabolism, membrane transport, amino acid metabolism, signal transduction, and energy metabolism. Redundancy analysis showed that environmental parameters greatly affected bacterioplankton diversity during the dry season compared to the wet season. The findings suggest that seasonality has a significant impact on bacterioplankton communities, and the dry season has more diverse communities influenced by environmental parameters. Further, the relatively high abundance of certain bacteria such as Acinetobacter deteriorated the water quality during the wet season compared to the dry season. Our findings have significant implications for water resource management in China, and other countries facing similar challenges. However, further investigations are required to elucidate the role of environmental parameters in influencing bacterioplankton diversity in order to devise potential strategies for improving water quality management in the reservoir.
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Affiliation(s)
- Qing Yang
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Dewang Li
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Wei Chen
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Liming Zhu
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Xi Zou
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Lian Hu
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Yujie Yuan
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Shan He
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Fang Shi
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
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25
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Abreu CI, Dal Bello M, Bunse C, Pinhassi J, Gore J. Warmer temperatures favor slower-growing bacteria in natural marine communities. SCIENCE ADVANCES 2023; 9:eade8352. [PMID: 37163596 PMCID: PMC10171810 DOI: 10.1126/sciadv.ade8352] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Earth's life-sustaining oceans harbor diverse bacterial communities that display varying composition across time and space. While particular patterns of variation have been linked to a range of factors, unifying rules are lacking, preventing the prediction of future changes. Here, analyzing the distribution of fast- and slow-growing bacteria in ocean datasets spanning seasons, latitude, and depth, we show that higher seawater temperatures universally favor slower-growing taxa, in agreement with theoretical predictions of how temperature-dependent growth rates differentially modulate the impact of mortality on species abundances. Changes in bacterial community structure promoted by temperature are independent of variations in nutrients along spatial and temporal gradients. Our results help explain why slow growers dominate at the ocean surface, during summer, and near the tropics and provide a framework to understand how bacterial communities will change in a warmer world.
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Affiliation(s)
- Clare I Abreu
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Martina Dal Bello
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carina Bunse
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution of Microbial Model Systems, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
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26
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Ilicic D, Ionescu D, Woodhouse J, Grossart HP. Temperature-Related Short-Term Succession Events of Bacterial Phylotypes in Potter Cove, Antarctica. Genes (Basel) 2023; 14:genes14051051. [PMID: 37239412 DOI: 10.3390/genes14051051] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
In recent years, our understanding of the roles of bacterial communities in the Antarctic Ocean has substantially improved. It became evident that Antarctic marine bacteria are metabolically versatile, and even closely related strains may differ in their functionality and, therefore, affect the ecosystem differently. Nevertheless, most studies have been focused on entire bacterial communities, with little attention given to individual taxonomic groups. Antarctic waters are strongly influenced by climate change; thus, it is crucial to understand how changes in environmental conditions, such as changes in water temperature and salinity fluctuations, affect bacterial species in this important area. In this study, we show that an increase in water temperature of 1 °C was enough to alter bacterial communities on a short-term temporal scale. We further show the high intraspecific diversity of Antarctic bacteria and, subsequently, rapid intra-species succession events most likely driven by various temperature-adapted phylotypes. Our results reveal pronounced changes in microbial communities in the Antarctic Ocean driven by a single strong temperature anomaly. This suggests that long-term warming may have profound effects on bacterial community composition and presumably functionality in light of continuous and future climate change.
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Affiliation(s)
- Doris Ilicic
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 16775 Neuglobsow, Germany
| | - Danny Ionescu
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 16775 Neuglobsow, Germany
| | - Jason Woodhouse
- Institut für Zoologie, Universität Hamburg, 20146 Hamburg, Germany
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 16775 Neuglobsow, Germany
- Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
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27
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Deutschmann IM, Krabberød AK, Latorre F, Delage E, Marrasé C, Balagué V, Gasol JM, Massana R, Eveillard D, Chaffron S, Logares R. Disentangling temporal associations in marine microbial networks. MICROBIOME 2023; 11:83. [PMID: 37081491 PMCID: PMC10120119 DOI: 10.1186/s40168-023-01523-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 03/19/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Microbial interactions are fundamental for Earth's ecosystem functioning and biogeochemical cycling. Nevertheless, they are challenging to identify and remain barely known. Omics-based censuses are helpful in predicting microbial interactions through the statistical inference of single (static) association networks. Yet, microbial interactions are dynamic and we have limited knowledge of how they change over time. Here, we investigate the dynamics of microbial associations in a 10-year marine time series in the Mediterranean Sea using an approach inferring a time-resolved (temporal) network from a single static network. RESULTS A single static network including microbial eukaryotes and bacteria was built using metabarcoding data derived from 120 monthly samples. For the decade, we aimed to identify persistent, seasonal, and temporary microbial associations by determining a temporal network that captures the interactome of each individual sample. We found that the temporal network appears to follow an annual cycle, collapsing, and reassembling when transiting between colder and warmer waters. We observed higher association repeatability in colder than in warmer months. Only 16 associations could be validated using observations reported in literature, underlining our knowledge gap in marine microbial ecological interactions. CONCLUSIONS Our results indicate that marine microbial associations follow recurrent temporal dynamics in temperate zones, which need to be accounted for to better understand the functioning of the ocean microbiome. The constructed marine temporal network may serve as a resource for testing season-specific microbial interaction hypotheses. The applied approach can be transferred to microbiome studies in other ecosystems. Video Abstract.
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Affiliation(s)
- Ina Maria Deutschmann
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain.
| | - Anders K Krabberød
- Department of Biosciences/Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, p.b. 1066 Blindern, N-0316, Oslo, Norway
| | - Francisco Latorre
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Erwan Delage
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, F-75016, Paris, France
| | - Cèlia Marrasé
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Vanessa Balagué
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Josep M Gasol
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Ramon Massana
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Damien Eveillard
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, F-75016, Paris, France
| | - Samuel Chaffron
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, F-75016, Paris, France
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain.
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28
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Bech PK, Zhang SD, Henriksen NNSE, Bentzon-Tilia M, Strube ML, Gram L. The potential to produce tropodithietic acid by Phaeobacter inhibens affects the assembly of microbial biofilm communities in natural seawater. NPJ Biofilms Microbiomes 2023; 9:12. [PMID: 36959215 PMCID: PMC10036634 DOI: 10.1038/s41522-023-00379-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 03/10/2023] [Indexed: 03/25/2023] Open
Abstract
Microbial secondary metabolites play important roles in biotic interactions in microbial communities and yet, we do not understand how these compounds impact the assembly and development of microbial communities. To address the implications of microbial secondary metabolite production on biotic interactions in the assembly of natural seawater microbiomes, we constructed a model system where the assembly of a natural seawater biofilm community was influenced by the addition of the marine biofilm forming Phaeobacter inhibens that can produce the antibiotic secondary metabolite tropodithietic acid (TDA), or a mutant incapable of TDA production. Because of the broad antibiotic activity of TDA, we hypothesized that the potential of P. inhibens to produce TDA would strongly affect both biofilm and planktonic community assembly patterns. We show that 1.9 % of the microbial composition variance across both environments could be attributed to the presence of WT P. inhibens, and especially genera of the Bacteriodetes were increased by the presence of the TDA producer. Moreover, network analysis with inferred putative microbial interactions revealed that P. inhibens mainly displayed strong positive associations with genera of the Flavobacteriaceae and Alteromonadaceae, and that P. inhibens acts as a keystone OTU in the biofilm exclusively due to its potential to produce TDA. Our results demonstrate the potential impact of microbial secondary metabolites on microbial interactions and assembly dynamics of complex microbial communities.
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Affiliation(s)
| | - Sheng-Da Zhang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
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29
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Verma A, Amnebrink D, Pinhassi J, Wikner J. Prokaryotic maintenance respiration and growth efficiency field patterns reproduced by temperature and nutrient control at mesocosm scale. Environ Microbiol 2023; 25:721-737. [PMID: 36511634 DOI: 10.1111/1462-2920.16300] [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: 06/17/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
The distribution of prokaryotic metabolism between maintenance and growth activities has a profound impact on the transformation of carbon substrates to either biomass or CO2 . Knowledge of key factors influencing prokaryotic maintenance respiration is, however, highly limited. This mesocosm study validated the significance of prokaryotic maintenance respiration by mimicking temperature and nutrients within levels representative of winter and summer conditions. A global range of growth efficiencies (0.05-0.57) and specific growth rates (0.06-2.7 d-1 ) were obtained. The field pattern of cell-specific respiration versus specific growth rate and the global relationship between growth efficiency and growth rate were reproduced. Maintenance respiration accounted for 75% and 15% of prokaryotic respiration corresponding to winter and summer conditions, respectively. Temperature and nutrients showed independent positive effects for all prokaryotic variables except abundance and cell-specific respiration. All treatments resulted in different taxonomic diversity, with specific populations of amplicon sequence variants associated with either maintenance or growth conditions. These results validate a significant relationship between specific growth and respiration rate under productive conditions and show that elevated prokaryotic maintenance respiration can occur under cold and oligotrophic conditions. The experimental design provides a tool for further study of prokaryotic energy metabolism under realistic conditions at the mesocosm scale.
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Affiliation(s)
- Ashish Verma
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Hörnefors, Sweden
| | - Dennis Amnebrink
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Johan Wikner
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Hörnefors, Sweden
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30
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Marasco R, Fusi M, Coscolín C, Barozzi A, Almendral D, Bargiela R, Nutschel CGN, Pfleger C, Dittrich J, Gohlke H, Matesanz R, Sanchez-Carrillo S, Mapelli F, Chernikova TN, Golyshin PN, Ferrer M, Daffonchio D. Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes. Nat Commun 2023; 14:1045. [PMID: 36828822 PMCID: PMC9958047 DOI: 10.1038/s41467-023-36610-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 02/08/2023] [Indexed: 02/26/2023] Open
Abstract
Microbial communities respond to temperature with physiological adaptation and compositional turnover. Whether thermal selection of enzymes explains marine microbiome plasticity in response to temperature remains unresolved. By quantifying the thermal behaviour of seven functionally-independent enzyme classes (esterase, extradiol dioxygenase, phosphatase, beta-galactosidase, nuclease, transaminase, and aldo-keto reductase) in native proteomes of marine sediment microbiomes from the Irish Sea to the southern Red Sea, we record a significant effect of the mean annual temperature (MAT) on enzyme response in all cases. Activity and stability profiles of 228 esterases and 5 extradiol dioxygenases from sediment and seawater across 70 locations worldwide validate this thermal pattern. Modelling the esterase phase transition temperature as a measure of structural flexibility confirms the observed relationship with MAT. Furthermore, when considering temperature variability in sites with non-significantly different MATs, the broadest range of enzyme thermal behaviour and the highest growth plasticity of the enriched heterotrophic bacteria occur in samples with the widest annual thermal variability. These results indicate that temperature-driven enzyme selection shapes microbiome thermal plasticity and that thermal variability finely tunes such processes and should be considered alongside MAT in forecasting microbial community thermal response.
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Affiliation(s)
- Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Marco Fusi
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre for Conservation and Restoration Science, Edinburgh Napier University Sighthill Campus, Edinburgh, UK
| | | | - Alan Barozzi
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - David Almendral
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid, Spain
| | - Rafael Bargiela
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, UK
| | | | - Christopher Pfleger
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jonas Dittrich
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC) and Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ruth Matesanz
- Spectroscopy Laboratory, Centro de Investigaciones Biologicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Sergio Sanchez-Carrillo
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid, Spain
- Centro de Biologia Molecular Severo Ochoa (CBM), CSIC-UAM, Madrid, Spain
| | - Francesca Mapelli
- Department of Food Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Tatyana N Chernikova
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, UK
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, UK
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid, Spain.
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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31
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Tominaga K, Ogawa-Haruki N, Nishimura Y, Watai H, Yamamoto K, Ogata H, Yoshida T. Prevalence of Viral Frequency-Dependent Infection in Coastal Marine Prokaryotes Revealed Using Monthly Time Series Virome Analysis. mSystems 2023; 8:e0093122. [PMID: 36722950 PMCID: PMC9948707 DOI: 10.1128/msystems.00931-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/29/2022] [Indexed: 02/02/2023] Open
Abstract
Viruses infecting marine prokaryotes have a large impact on the diversity and dynamics of their hosts. Model systems suggest that viral infection is frequency dependent and constrained by the virus-host encounter rate. However, it is unclear whether frequency-dependent infection is pervasive among the abundant prokaryotic populations with different temporal dynamics. To address this question, we performed a comparison of prokaryotic and viral communities using 16S rRNA amplicon and virome sequencing based on samples collected monthly for 2 years at a Japanese coastal site, Osaka Bay. Concurrent seasonal shifts observed in prokaryotic and viral community dynamics indicated that the abundance of viruses correlated with that of their predicted host phyla (or classes). Cooccurrence network analysis between abundant prokaryotes and viruses revealed 6,423 cooccurring pairs, suggesting a tight coupling of host and viral abundances and their "one-to-many" correspondence. Although stable dominant species, such as SAR11, showed few cooccurring viruses, a fast succession of their viruses suggests that viruses infecting these populations changed continuously. Our results suggest that frequency-dependent viral infection prevails in coastal marine prokaryotes regardless of host taxa and temporal dynamics. IMPORTANCE There is little room for doubt that viral infection is prevalent among abundant marine prokaryotes regardless of their taxa or growth strategy. However, comprehensive evaluations of viral infections in natural prokaryotic communities are still technically difficult. In this study, we examined viral infection in abundant prokaryotes by monitoring the monthly dynamics of prokaryotic and viral communities at a eutrophic coastal site, Osaka Bay. We compared the community dynamics of viruses with those of their putative hosts based on genome-based in silico host prediction. We observed frequent cooccurrence among the predicted virus-host pairs, suggesting that viral infection is prevalent in abundant prokaryotes regardless of their taxa or temporal dynamics. This likely indicates that frequent lysis of the abundant prokaryotes via viral infection has a considerable contribution to the biogeochemical cycling and maintenance of prokaryotic community diversity.
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Affiliation(s)
- Kento Tominaga
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Yosuke Nishimura
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, Japan
| | - Hiroyasu Watai
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Keigo Yamamoto
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, Osaka, Japan
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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32
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Kodera SM, Sharma A, Martino C, Dsouza M, Grippo M, Lutz HL, Knight R, Gilbert JA, Negri C, Allard SM. Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades. ENVIRONMENTAL MICROBIOME 2023; 18:10. [PMID: 36805022 PMCID: PMC9938989 DOI: 10.1186/s40793-023-00470-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013-2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention. RESULTS Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality. CONCLUSIONS This study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.
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Affiliation(s)
- Sho M Kodera
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Anukriti Sharma
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | | | - Mark Grippo
- Environmental Science Division, Argonne National Laboratory, University of Chicago, Lemont, IL, USA
| | - Holly L Lutz
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jack A Gilbert
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Cristina Negri
- Environmental Science Division, Argonne National Laboratory, University of Chicago, Lemont, IL, USA.
| | - Sarah M Allard
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
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33
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Chen W, Sang S, Shao L, Li Y, Li T, Gan L, Liu L, Wang D, Zhou L. Biogeographic Patterns and Community Assembly Processes of Bacterioplankton and Potential Pathogens in Subtropical Estuaries in China. Microbiol Spectr 2023; 11:e0368322. [PMID: 36507672 PMCID: PMC9927264 DOI: 10.1128/spectrum.03683-22] [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: 09/20/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
Microbial communities in coastal waters are diverse and dynamic and play important roles in ecosystem functions and services. Despite the ecological impact of bacterioplankton or pathogens, little is known about whether bacterioplankton and pathogen communities exhibit similar patterns. Here, using 16S RNA gene amplicon sequencing, the geographic patterns and assembly processes of bacterioplankton and pathogen communities in 30 subtropical estuaries were studied. Results showed that the estuarine bacterioplankton communities mainly consisted of Proteobacteria (49.06%), Actinobacteria (17.62%), and Bacteroidetes (16.33%), among which 31 pathogen genera (186 amplicon sequence variants [ASVs]) were identified. Under the influence of salinity, bacterioplankton and pathogens showed similar biogeographic patterns. Redundancy and correlation analyses indicated that the bacterioplankton communities were strongly correlated with estuarine environmental factors, but potential pathogens were less influenced. Co-occurrence network analysis revealed a close relationship between bacterioplankton and potential pathogens, with two pathogens identified as connectors (i.e., ASV340 [Clostridium perfringens] and ASV1624 [Brevundimonas diminuta]), implying potential impacts of pathogens on structure, function, and stability of estuarine bacterioplankton communities. Null-model analysis revealed that deterministic processes (heterogeneous selection) dominated bacterioplankton community assembly, while stochastic processes (undominated effect) shaped the potential pathogen community. Our findings illustrate the biogeographic patterns and community assembly mechanisms of bacterioplankton and pathogens in estuaries, which should provide guidance and a reference for the control of potential pathogenic bacteria. IMPORTANCE Bacterioplankton play an important role in estuarine ecosystem functions and services; however, potentially pathogenic bacteria may exhibit infectivity and pose a serious threat to environmental and human health. In this study, geographic patterns and assembly processes of bacterioplankton communities in 30 subtropical estuaries were explored, and potential pathogenic bacteria in the estuaries were detected and profiled. Our results demonstrate here that bacterioplankton and pathogens show similar biogeographic patterns under the influence of salinity. Interestingly, heterogeneous selection dominated bacterioplankton assembly, while stochasticity dominated pathogen assembly. This study provides important information for future risk assessment of potential pathogenic bacteria as well as management in estuarine ecosystems.
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Affiliation(s)
- Wenjian Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Shilei Sang
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, MEE, Guangzhou, China
| | - Liyi Shao
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Yusen Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, China
| | - Tongzhou Li
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Lihong Gan
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Li Liu
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Dapeng Wang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, China
| | - Lei Zhou
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
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Yu Z, Peng X, Liu L, Yang JR, Zhai X, Xue Y, Mo Y, Yang J. Microbial one‑carbon and nitrogen metabolisms are beneficial to the reservoir recovery after cyanobacterial bloom. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159004. [PMID: 36155037 DOI: 10.1016/j.scitotenv.2022.159004] [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: 07/06/2022] [Revised: 09/03/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Cyanobacterial blooms have profound effects on the structure and function of plankton communities in inland waters, but few studies have focused on the effects of microbial-based processes in one‑carbon and nitrogen cycling on water quality improvement following the bloom. Here, we compared the structure and function of the bacterial community, focusing on microbial one‑carbon and nitrogen metabolisms during and after a cyanobacterial Microcystis bloom in a deep subtropical reservoir. Our data showed that microbial one‑carbon and nitrogen cycles were closely related to different periods of the bloom, and the changes of functional genes in microbial carbon and nitrogen cycling showed the same consistent trend as that of Methylomonas sp. With the receding of the bloom, the abundance of Methylomonas as well as the functional genes of microbial one‑carbon and nitrogen cycling reached the peak and then recovered. Our results indicate that microbial one‑carbon and nitrogen metabolisms were beneficial to the recovery of water quality from the cyanobacterial bloom. This study lays a foundation for a deep understanding of the cyanobacterial decomposition mediated by microbes in one‑carbon and nitrogen cycles in inland freshwaters.
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Affiliation(s)
- Zheng Yu
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, Hunan 410083, China; Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xuan Peng
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, Hunan 410083, China
| | - Lemian Liu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Jun R Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xingyu Zhai
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, Hunan 410083, China
| | - Yuanyuan Xue
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yuanyuan Mo
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Kopprio GA, Martínez A, Fricke A, Hupfer M, Lara RJ, Graeve M, Gärdes A. Towards the outwelling hypothesis in a Patagonian estuary: First support from lipid markers and bacterial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158670. [PMID: 36099952 DOI: 10.1016/j.scitotenv.2022.158670] [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: 06/24/2022] [Revised: 08/28/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Biogeochemical markers in combination with bacterial community composition were studied at two contrasting stations at the Río Negro (RN) estuary to assess the outwelling hypothesis in the Argentinian Patagonia. Inorganic nutrients and dissolved organic matter were exported clearly during the last hours of the ebb at the station Wetland. Moreover, a considerable outwelling of polyunsaturated fatty acids (PUFA), particulates and microalgae was inferred by this combined approach. The exported 22:6(n-3) and 20:5(n-3) contributed very likely to sustain higher trophic levels in the coasts of the Southwest Atlantic. The stable isotopes did not evidence clearly the outwelling; nevertheless, the combination of δ13C with fatty acid bacterial markers indicated organic matter degradation in the sediments. The dominance of Desulfobacterales and Desulfuromonadales suggested sulphate reduction in the sediments, a key mechanism for nutrient outwelling in salt marshes. Marivivens and other Rhodobacterales (Alphaproteobacteria) in the suspended particulate matter were clear indicators of the nutrient outwelling. The colonization of particles according to the island biogeography theory was a good hypothesis to explain the lower bacterial biodiversity at the wetland. The copiotrophic conditions of the RN estuary and particularly at the wetland were deduced also by the dynamic of some Actinobacteria, Bacteroidia and Gammaproteobacteria. This high-resolution snapshot combining isotopic, lipid and bacterial markers offers key pioneer insights into biogeochemical and ecological processes of the RN estuary.
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Affiliation(s)
- Germán A Kopprio
- Robert Koch Institute, Berlin, Germany; Leibniz Institute for Freshwater Ecology and Inland Fisheries, Berlin, Germany; Instituto Argentino de Oceanografía - Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca, Argentina.
| | - Ana Martínez
- Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Anna Fricke
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Michael Hupfer
- Leibniz Institute for Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Rubén J Lara
- Instituto Argentino de Oceanografía - Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca, Argentina
| | - Martin Graeve
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Astrid Gärdes
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany; University of Applied Sciences, Bremerhaven, Germany
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Pinhassi J, Farnelid H, García SM, Teira E, Galand PE, Obernosterer I, Quince C, Vila-Costa M, Gasol JM, Lundin D, Andersson AF, Labrenz M, Riemann L. Functional responses of key marine bacteria to environmental change – toward genetic counselling for coastal waters. Front Microbiol 2022; 13:869093. [DOI: 10.3389/fmicb.2022.869093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 11/11/2022] [Indexed: 12/04/2022] Open
Abstract
Coastal ecosystems deteriorate globally due to human-induced stress factors, like nutrient loading and pollution. Bacteria are critical to marine ecosystems, e.g., by regulating nutrient cycles, synthesizing vitamins, or degrading pollutants, thereby providing essential ecosystem services ultimately affecting economic activities. Yet, until now bacteria are overlooked both as mediators and indicators of ecosystem health, mainly due to methodological limitations in assessing bacterial ecosystem functions. However, these limitations are largely overcome by the advances in molecular biology and bioinformatics methods for characterizing the genetics that underlie functional traits of key bacterial populations – “key” in providing important ecosystem services, being abundant, or by possessing high metabolic rates. It is therefore timely to analyze and define the functional responses of bacteria to human-induced effects on coastal ecosystem health. We posit that categorizing the responses of key marine bacterial populations to changes in environmental conditions through modern microbial oceanography methods will allow establishing the nascent field of genetic counselling for our coastal waters. This requires systematic field studies of linkages between functional traits of key bacterial populations and their ecosystem functions in coastal seas, complemented with systematic experimental analyses of the responses to different stressors. Research and training in environmental management along with dissemination of results and dialogue with societal actors are equally important to ensure the role of bacteria is understood as fundamentally important for coastal ecosystems. Using the responses of microorganisms as a tool to develop genetic counselling for coastal ecosystems can ultimately allow for integrating bacteria as indicators of environmental change.
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37
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Garate L, Alonso‐Sáez L, Revilla M, Logares R, Lanzén A. Shared and contrasting associations in the dynamic nano- and picoplankton communities of two close but contrasting sites from the Bay of Biscay. Environ Microbiol 2022; 24:6052-6070. [PMID: 36054533 PMCID: PMC10087561 DOI: 10.1111/1462-2920.16153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/30/2022] [Indexed: 01/12/2023]
Abstract
Pico- and nanoplankton are key players in the marine ecosystems due to their implication in the biogeochemical cycles, nutrient recycling and the pelagic food webs. However, the specific dynamics and niches of most bacterial, archaeal and eukaryotic plankton remain unknown, as well as the interactions between them. Better characterization of these is critical for understanding and predicting ecosystem functioning under anthropogenic pressures. We used environmental DNA metabarcoding across a 6-year time series to explore the structure and seasonality of pico- and nanoplankton communities in two sites of the Bay of Biscay, one coastal and one offshore, and construct association networks to reveal potential keystone and connector taxa. Temporal trends in alpha diversity were similar between the two sites, and concurrent communities more similar than within the same site at different times. However, we found differences between the network topologies of the two sites, with both shared and site-specific keystones and connectors. For example, Micromonas, with lower abundance in the offshore site is a keystone here, indicating a stronger effect of associations such as resource competition. This study provides an example of how time series and association network analysis can reveal how similar communities may function differently despite being geographically close.
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Affiliation(s)
- Leire Garate
- AZTI, Marine ResearchBasque Research and Technology Alliance (BRTA)PasaiaSpain
| | - Laura Alonso‐Sáez
- AZTI, Marine ResearchBasque Research and Technology Alliance (BRTA)PasaiaSpain
| | - Marta Revilla
- AZTI, Marine ResearchBasque Research and Technology Alliance (BRTA)PasaiaSpain
| | - Ramiro Logares
- Institute of Marine Sciences (ICM)CSICBarcelonaCataloniaSpain
| | - Anders Lanzén
- AZTI, Marine ResearchBasque Research and Technology Alliance (BRTA)PasaiaSpain
- IKERBASQUEBasque Foundation for ScienceBilbaoBizkaiaSpain
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38
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Costas-Selas C, Martínez-García S, Logares R, Hernández-Ruiz M, Teira E. Role of Bacterial Community Composition as a Driver of the Small-Sized Phytoplankton Community Structure in a Productive Coastal System. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02125-2. [PMID: 36305941 DOI: 10.1007/s00248-022-02125-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
We present here the first detailed description of the seasonal patterns in bacterial community composition (BCC) in shelf waters off the Ría de Vigo (Spain), based on monthly samplings during 2 years. Moreover, we studied the relationship between bacterial and small-sized eukaryotic community composition to identify potential biotic interactions among components of these two communities. Bacterial operational taxonomic unit (OTU) richness and diversity systematically peaked in autumn-winter, likely related to low resource availability during this period. BCC showed seasonal and vertical patterns, with Rhodobacteraceae and Flavobacteriaceae families dominating in surface waters, and SAR11 clade dominating at the base of the photic zone (30 m depth). BCC variability was significantly explained by environmental variables (e.g., temperature of water, solar radiation, or dissolved organic matter). Interestingly, a strong and significant correlation was found between BCC and small-sized eukaryotic community composition (ECC), which suggests that biotic interactions may play a major role as structuring factors of the microbial plankton in this productive area. In addition, co-occurrence network analyses revealed strong and significant, mostly positive, associations between bacteria and small-sized phytoplankton. Positive associations likely result from mutualistic relationships (e.g., between Dinophyceae and Rhodobacteraceae), while some negative correlations suggest antagonistic interactions (e.g., between Pseudo-nitzchia sp. and SAR11). These results support the key role of biotic interactions as structuring factors of the small-sized eukaryotic community, mostly driven by positive associations between small-sized phytoplankton and bacteria.
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Affiliation(s)
- Cecilia Costas-Selas
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain.
| | - Sandra Martínez-García
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain
| | - Ramiro Logares
- Departament de Biologia Marina I Oceanografia, Institut de Ciéncies del Mar (ICM), CSIC, Catalonia, Barcelona, Spain
| | - Marta Hernández-Ruiz
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain
| | - Eva Teira
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain
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Shiah FK, Lai CC, Chen TY, Ko CY, Tai JH, Chang CW. Viral shunt in tropical oligotrophic ocean. SCIENCE ADVANCES 2022; 8:eabo2829. [PMID: 36223456 PMCID: PMC9555789 DOI: 10.1126/sciadv.abo2829] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Viruses cause massive bacterial mortality and thus modulate bacteria-governed carbon transfer and nutrient recycling at global scale. The viral shunt hypothesis states the crucial role of viral lysis in retaining microbial carbon into food web processes, while its applicability to nature has not been well identified for over two decades. Here, we conducted nine diel surveys in the tropical South China Sea and suggested that the time scale adopted in sampling and system trophic status determine the "visibility" of the viral shunt in the field. Specifically, viral abundance (VA), bacterial biomass (BB), and bacterial specific growth rate (SGR) varied synchronously and presented the significant VA-BB and VA-SGR linkages at an hourly scale, which reveals direct interactions between viruses and their hosts. The differential responses of the viral shunt to temperature, i.e., looser VA-SGR coupling in warm and tighter VA-SGR coupling in cold environments, imply an altered carbon cycling in tropical oceans under climatic warming.
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Affiliation(s)
- Fuh-Kwo Shiah
- Research Center for Environmental Changes, Academia Sinica, Taipei 11529, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Chao-Chen Lai
- Research Center for Environmental Changes, Academia Sinica, Taipei 11529, Taiwan
| | - Tzong-Yueh Chen
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Chia-Ying Ko
- Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan
- Institute of Ecology and Evolutionary Biology and Master’s Program in Biodiversity, National Taiwan University, Taipei 10617, Taiwan
| | - Jen-Hua Tai
- Research Center for Environmental Changes, Academia Sinica, Taipei 11529, Taiwan
| | - Chun-Wei Chang
- Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan
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Korlević M, Markovski M, Herndl GJ, Najdek M. Temporal variation in the prokaryotic community of a nearshore marine environment. Sci Rep 2022; 12:16859. [PMID: 36207405 PMCID: PMC9547059 DOI: 10.1038/s41598-022-20954-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Prokaryotic communities inhabiting surface waters of temperate areas exhibit patterns of seasonal succession. Generally, studies describing these temporal changes are not performed in the proximity to the coast. In the present study, temporal variation of these communities was determined in surface waters at two stations located in the close proximity to the eastern shore of the northern Adriatic Sea. Sequencing of the V4 region of the 16S rRNA gene identified the highest community richness in December with distinct shifts in community structure between periods from April to May, June to October, and November to March. Temperature was shown to be the main environmental force explaining community temporal variation. The NS5 marine group, uncultured Cryomorphaceae, SAR86 clade, and Synechococcus were present throughout the year. Members without know relatives within Rhodobacteraceae and the NS4 marine group were more pronounced in the period from April to May, the AEGEAN-169 marine group, SAR11 subclade III, and HIMB11 in the period from June to October, and SAR11 subclade Ia and Archaea in the period from November to March. Litoricola and OM60 (NOR5) clade were characteristic for both the community sampled from April to May and November to March. Taken together, prokaryotic communities inhabiting nearshore surface waters exhibit a general pattern in community structure similar to other surface associated assemblages of temperate areas. However, the identified specific community composition and temporal patterns differ from other coastal areas.
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Affiliation(s)
- Marino Korlević
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia.
| | - Marsej Markovski
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, The Netherlands
| | - Mirjana Najdek
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
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Scicchitano D, Lo Martire M, Palladino G, Nanetti E, Fabbrini M, Dell’Anno A, Rampelli S, Corinaldesi C, Candela M. Microbiome network in the pelagic and benthic offshore systems of the northern Adriatic Sea (Mediterranean Sea). Sci Rep 2022; 12:16670. [PMID: 36198901 PMCID: PMC9535000 DOI: 10.1038/s41598-022-21182-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/23/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractBecause of their recognized global importance, there is now the urgent need to map diversity and distribution patterns of marine microbial communities. Even if available studies provided some advances in the understanding the biogeographical patterns of marine microbiomes at the global scale, their degree of plasticity at the local scale it is still underexplored, and functional implications still need to be dissected. In this scenario here we provide a synoptical study on the microbiomes of the water column and surface sediments from 19 sites in a 130 km2 area located 13.5 km afar from the coast in the North-Western Adriatic Sea (Italy), providing the finest-scale mapping of marine microbiomes in the Mediterranean Sea. Pelagic and benthic microbiomes in the study area showed sector specific-patterns and distinct assemblage structures, corresponding to specific variations in the microbiome network structure. While maintaining a balanced structure in terms of potential ecosystem services (e.g., hydrocarbon degradation and nutrient cycling), sector-specific patterns of over-abundant modules—and taxa—were defined, with the South sector (the closest to the coast) characterized by microbial groups of terrestrial origins, both in the pelagic and the benthic realms. By the granular assessment of the marine microbiome changes at the local scale, we have been able to describe, to our knowledge at the first time, the integration of terrestrial microorganisms in the marine microbiome networks, as a possible natural process characterizing eutrophic coastal area. This raises the question about the biological threshold for terrestrial microorganisms to be admitted in the marine microbiome networks, without altering the ecological balance.
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Yuan Y, Luo B, Li Z, He Y, Xia L, Qin Y, Wang T, Ma K. Effects of green tide on microbial communities in waters of the Jiangsu coastal area, China. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2022; 94:e10797. [PMID: 36254385 PMCID: PMC9828100 DOI: 10.1002/wer.10797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 09/08/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Recently, green tide outbreaks have resulted in severe coastal ecology and economic effects in China. Jiangsu coastal areas are usually the site of early green tide outbreaks. To clarify the effects of green tide outbreaks in Jiangsu coastal areas, this study analyzed microbial communities during green tide-free and green tide outbreak periods (May and July, respectively) through 16S rDNA sequencing. Sequences were clustered into 4117 operational taxonomic units (OTUs), 1044 and 3834 of which were obtained from the May and July groups, respectively. Redundancy analysis indicated that green tide occurrence was closely associated with the temperature, pH, and concentrations of various nutrients. Diversity analysis revealed that the July group had a richer microbial community than the May group, in agreement with the results of propagule culture. Moreover, comparative analysis revealed that samples in the May and July groups clustered together. According to Megan analysis, the May group had much more Psychrobacter, Sulfitobacter, and Marinomonas than the July group, whereas the other genera were predominantly found in July, such as Ascidiacerhabitans, Synechococcus Hydrotalea, and Burkholderia-Paraburkholderia. These findings suggest that green tide outbreaks affect marine microbial communities, and detecting the changes in the identified genera during green tide outbreaks may contribute to green tide forecasting. PRACTITIONER POINTS: Jiangsu coastal areas are usually the site of early green tide outbreaks. Green tide occurrence was related to the concentrations of various nutrients. Microbial species and community structure significantly changed after green tide outbreak.
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Affiliation(s)
- Yiming Yuan
- Key Laboratory of Marine Ecological Monitoring and Restoration Technologies, MNREast China Sea Environmental Monitoring Center of State Oceanic AdministrationShanghaiChina
| | - Biyun Luo
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Collaborative Innovation for Aquatic Animal Genetics and BreedingShanghai Ocean UniversityShanghaiChina
| | - Zhien Li
- Key Laboratory of Marine Ecological Monitoring and Restoration Technologies, MNREast China Sea Environmental Monitoring Center of State Oceanic AdministrationShanghaiChina
| | - Yanlong He
- Key Laboratory of Marine Ecological Monitoring and Restoration Technologies, MNREast China Sea Environmental Monitoring Center of State Oceanic AdministrationShanghaiChina
| | - Lihua Xia
- Key Laboratory of Marine Ecological Monitoring and Restoration Technologies, MNREast China Sea Environmental Monitoring Center of State Oceanic AdministrationShanghaiChina
| | - Yutao Qin
- Key Laboratory of Marine Ecological Monitoring and Restoration Technologies, MNREast China Sea Environmental Monitoring Center of State Oceanic AdministrationShanghaiChina
| | - Teng Wang
- Key Laboratory of Marine Ecological Monitoring and Restoration Technologies, MNREast China Sea Environmental Monitoring Center of State Oceanic AdministrationShanghaiChina
| | - Keyi Ma
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Collaborative Innovation for Aquatic Animal Genetics and BreedingShanghai Ocean UniversityShanghaiChina
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Seasonal Succession and Temperature Response Pattern of a Microbial Community in the Yellow Sea Cold Water Mass. Appl Environ Microbiol 2022; 88:e0116922. [PMID: 36000863 PMCID: PMC9469719 DOI: 10.1128/aem.01169-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Explaining the temporal dynamics of marine microorganisms is critical for predicting their changing pattern under environmental disturbances. Although the effect of temperature on microbial seasonality has been widely studied, the phylogenetic structure of the temperature response pattern and the extent to which temperature shift leads to disruptive community changes are still unclear. Here, we explored the microbial seasonal dynamics in the Yellow Sea Cold Water Mass (YSCWM) that occurs in summer and disappears in winter and tested the temperature thresholds and phylogenetic coherence in response to temperature change. The existence of YSCWM generates strong temperature gradients in summer and confers little temperature change during seasonal transition, thus representing a unique intermediate state. The microbial community of YSCWM is more similar to that in the previous YSCWM in winter than that outside YSCWM. Temperature alone explains >50% of the community variation, suggesting that a temperature shift can induce a nearly seasonality-level community variance in summer. Persistence of most previous winter YSCWM inhabitants in YSCWM leads to conservation in predicted functional potentials and cooccurrence patterns, indicating a decisive role of temperature in maintaining functionality. Evaluation of the temperature threshold reveals that a small temperature change can lead to significant community turnover, with most taxa negatively responding to an elevation in temperature. The temperature response pattern is phylogenetically structured, and closely related taxa show an incohesive response. Our study provides novel insights into microbial seasonality and into how marine microorganisms respond to temperature fluctuations. IMPORTANCE Microbial seasonality is driven by a set of covarying factors including temperature. There is still a lack of understanding of the details of the phylogenetic structure and susceptibility of microbial communities in response to temperature variation. Through examination of the microbial community in a seasonally occurring summer cold water mass, which experiences little temperature change during seasonal transition, we show here that the cold water mass leads to nearly seasonality-level variations in community composition and predicted functional profile in summer. Moreover, massive community turnover occurs within a small temperature shift, with most taxa decreasing in abundance in response to increased temperature, and contrasting response patterns are observed between phylogenetically closely related taxa. These results suggest temperature as the fundamental factor over other covarying factors in structuring microbial seasonality, providing important insights into the variation mode of the microbial community under temperature disturbances.
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Mikhailov IS, Galachyants YP, Bukin YS, Petrova DP, Bashenkhaeva MV, Sakirko MV, Blinov VV, Titova LA, Zakharova YR, Likhoshway YV. Seasonal Succession and Coherence Among Bacteria and Microeukaryotes in Lake Baikal. MICROBIAL ECOLOGY 2022; 84:404-422. [PMID: 34510242 DOI: 10.1007/s00248-021-01860-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms exhibit seasonal succession governed by physicochemical factors and interspecies interactions, yet drivers of this process in different environments remain to be determined. We used high-throughput sequencing of 16S rRNA and 18S rRNA genes to study seasonal dynamics of bacterial and microeukaryotic communities at pelagic site of Lake Baikal from spring (under-ice, mixing) to autumn (direct stratification). The microbial community was subdivided into distinctive coherent clusters of operational taxonomic units (OTUs). Individual OTUs were consistently replaced during different seasonal events. The coherent clusters change their contribution to the microbial community depending on season. Changes of temperature, concentrations of silicon, and nitrates are the key factors affected the structure of microbial communities. Functional prediction revealed that some bacterial or eukaryotic taxa that switched with seasons had similar functional properties, which demonstrate their functional redundancy. We have also detected specific functional properties in different coherent clusters of bacteria or microeukaryotes, which can indicate their ability to adapt to seasonal changes of environment. Our results revealed a relationship between seasonal succession, coherency, and functional features of freshwater bacteria and microeukaryotes.
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Affiliation(s)
- Ivan S Mikhailov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia.
| | - Yuri P Galachyants
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yuri S Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Darya P Petrova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Maria V Bashenkhaeva
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Maria V Sakirko
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Vadim V Blinov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Lubov A Titova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yulia R Zakharova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yelena V Likhoshway
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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King NG, Smale DA, Thorpe JM, McKeown NJ, Andrews AJ, Browne R, Malham SK. Core Community Persistence Despite Dynamic Spatiotemporal Responses in the Associated Bacterial Communities of Farmed Pacific Oysters. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02083-9. [PMID: 35881247 DOI: 10.1007/s00248-022-02083-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
A breakdown in host-bacteria relationships has been associated with the progression of a number of marine diseases and subsequent mortality events. For the Pacific oyster, Crassostrea gigas, summer mortality syndrome (SMS) is one of the biggest constraints to the growth of the sector and is set to expand into temperate systems as ocean temperatures rise. Currently, a lack of understanding of natural spatiotemporal dynamics of the host-bacteria relationship limits our ability to develop microbially based monitoring approaches. Here, we characterised the associated bacterial community of C. gigas, at two Irish oyster farms, unaffected by SMS, over the course of a year. We found C. gigas harboured spatiotemporally variable bacterial communities that were distinct from bacterioplankton in surrounding seawater. Whilst the majority of bacteria-oyster associations were transient and highly variable, we observed clear patterns of stability in the form of a small core consisting of six persistent amplicon sequence variants (ASVs). This core made up a disproportionately large contribution to sample abundance (34 ± 0.14%), despite representing only 0.034% of species richness across the study, and has been associated with healthy oysters in other systems. Overall, our study demonstrates the consistent features of oyster bacterial communities across spatial and temporal scales and provides an ecologically meaningful baseline to track environmental change.
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Affiliation(s)
- Nathan G King
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, PL1 2PB, UK.
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, LL59 5AB, UK.
| | - Dan A Smale
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, PL1 2PB, UK
| | - Jamie M Thorpe
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, LL59 5AB, UK
| | - Niall J McKeown
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Adam J Andrews
- Bord Iascaigh Mhara, Dún Laoghaire, County Dublin, Ireland
| | - Ronan Browne
- Bord Iascaigh Mhara, Dún Laoghaire, County Dublin, Ireland
| | - Shelagh K Malham
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, LL59 5AB, UK
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Li Y, Khan FH, Wu J, Zhang Y, Jiang Y, Chen X, Yao Y, Pan Y, Han X. Drivers of Spatiotemporal Eukaryote Plankton Distribution in a Trans-Basin Water Transfer Canal in China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.899993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Planktonic eukaryotes are important components of aquatic ecosystems, and analyses of the whole eukaryotic planktonic community composition and function have far-reaching significance for water resource management. We aimed to understand the spatiotemporal variation and drivers of eukaryotic plankton distribution in the Middle Route Project of the South-to-North Water Diversion in Henan Province, China. Specifically, we examined planktonic assemblages and water quality at five stations along the canal and another one located before the dam in March, June, September, and December 2019. High-throughput sequencing revealed that the eukaryotic plankton community was primarily composed of 53 phyla, 200 genera, and 277 species, with Cryptophyta, Ciliophora, and norank_k_Cryptophyta being the dominant phyla. Redundancy analysis of the eukaryotic community and environmental factors showed that five vital factors affecting eukaryotic plankton distribution were oxidation-reduction potential, nitrate nitrogen, pH, total phosphorus, and water flow velocity. Furthermore, the geographical distribution of eukaryotic communities was consistent with the distance decay model. Importantly, environmental selection dominantly shaped the geographical distribution of the eukaryotic community. In summary, our study elucidates the ecological response of planktonic eukaryotes by identifying the diversity and ecological distribution of planktonic eukaryotes in trans-basin diversion channels.
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Zhang H, Yan Y, Lin T, Xie W, Hu J, Hou F, Han Q, Zhu X, Zhang D. Disentangling the Mechanisms Shaping the Prokaryotic Communities in a Eutrophic Bay. Microbiol Spectr 2022; 10:e0148122. [PMID: 35638815 PMCID: PMC9241920 DOI: 10.1128/spectrum.01481-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/08/2022] [Indexed: 11/24/2022] Open
Abstract
Eutrophication occurring in coastal bays is prominent in impacting local ecosystem structure and functioning. To understand how coastal bay ecosystem function responds to eutrophication, comprehending the ecological processes associated with microbial community assembly is critical. However, quantifying the contribution of ecological processes to the assembly of prokaryotic communities is still limited in eutrophic waters. Moreover, the influence of these ecological processes on microbial interactions is poorly understood. Here, we examined the assembly processes and co-occurrence patterns of prokaryotic communities in a eutrophic bay using 156 surface seawater samples collected over 12 months. The variation of prokaryotic community compositions (PCCs) could be mainly explained by environmental factors, of which temperature was the most important. Under high environmental heterogeneity conditions in low-temperature seasons, heterogeneous selection was the major assembly process, resulting in high β-diversity and more tightly connected co-occurrence networks. When environmental heterogeneity decreased in high-temperature seasons, drift took over, leading to decline in β-diversity and network associations. Microeukaryotes were found to be important biological factors affecting PCCs. Our results first disentangled the contribution of drift and microbial interactions to the large unexplained variation of prokaryotic communities in eutrophic waters. Furthermore, a new conceptual model linking microbial interactions to ecological processes was proposed under different environmental heterogeneity. Overall, our study sheds new light on the relationship between assembly processes and co-occurrence of prokaryotic communities in eutrophic waters. IMPORTANCE A growing number of studies have examined roles of microbial community assembly in modulating community composition. However, the relationships between community assembly and microbial interactions are not fully understood and rarely tested, especially in eutrophic waters. In this study, we built a conceptual model that links seasonal microbial interactions to ecological processes, which has not been reported before. The model showed that heterogeneous selection plays an important role in driving community assembly during low-temperature seasons, resulting in higher β-diversity and more tightly connected networks. In contrast, drift became a dominant force during high-temperature seasons, leading to declines in the β-diversity and network associations. This model could function as a new framework to predict how prokaryotic communities respond to intensified eutrophication induced by climate change in coastal environment.
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Affiliation(s)
- Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Yi Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Tenghui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Weijuan Xie
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Jian Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Fanrong Hou
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Qingxi Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Xiangyu Zhu
- Environmental Monitoring Center of Ningbo, Ningbo, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
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Caracciolo M, Rigaut-Jalabert F, Romac S, Mahé F, Forsans S, Gac JP, Arsenieff L, Manno M, Chaffron S, Cariou T, Hoebeke M, Bozec Y, Goberville E, Le Gall F, Guilloux L, Baudoux AC, de Vargas C, Not F, Thiébaut E, Henry N, Simon N. Seasonal dynamics of marine protist communities in tidally mixed coastal waters. Mol Ecol 2022; 31:3761-3783. [PMID: 35593305 PMCID: PMC9543310 DOI: 10.1111/mec.16539] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 12/29/2021] [Accepted: 04/19/2022] [Indexed: 12/01/2022]
Abstract
Major seasonal community reorganizations and associated biomass variations are landmarks of plankton ecology. However, the processes of plankton community turnover rates have not been fully elucidated so far. Here, we analyse patterns of planktonic protist community succession in temperate latitudes, based on quantitative taxonomic data from both microscopy counts (cells >10 μm) and ribosomal DNA metabarcoding (size fraction >3 μm, 18S rRNA gene) from plankton samples collected bimonthly over 8 years (2009–2016) at the SOMLIT‐Astan station (Roscoff, Western English Channel). Based on morphology, diatoms were clearly the dominating group all year round and over the study period. Metabarcoding uncovered a wider diversity spectrum and revealed the prevalence of Dinophyceae and diatoms but also of Cryptophyta, Chlorophyta, Cercozoa, Syndiniales and Ciliophora in terms of read counts and or richness. The use of morphological and molecular analyses in combination allowed improving the taxonomic resolution and to identify the sequence of the dominant species and OTUs (18S V4 rDNA‐derived taxa) that drive annual plankton successions. We detected that some of these dominant OTUs were benthic as a result of the intense tidal mixing typical of the French coasts in the English Channel. Our analysis of the temporal structure of community changes point to a strong seasonality and resilience. The temporal structure of environmental variables (especially Photosynthetic Active Radiation, temperature and macronutrients) and temporal structures generated by species life cycles and or species interactions, are key drivers of the observed cyclic annual plankton turnover.
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Affiliation(s)
| | | | | | | | | | | | - Laure Arsenieff
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | | | - Samuel Chaffron
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Laboratoire des Sciences du Numérique de Nantes (LS2N), CNRS, UMR6004, Université de Nantes, Ecole Centrale de Nantes, 44322, Nantes, France
| | - Thierry Cariou
- Institut de recherche pour le développement (IRD), Délégation Régionale Ouest, IMAGO, Plouzané, France
| | - Mark Hoebeke
- CNRS, Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff, 29680, Roscoff, France
| | | | - Eric Goberville
- Unité biologie des organismes et écosystèmes aquatiques (BOREA), Muséum National D'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS, IRD, CP53, 61 rue Buffon 75005, Paris, France
| | | | - Loïc Guilloux
- Sorbonne Université, Roscoff, France.,Mediterranean Institute of Oceanography (MIO), Campus de Luminy case 901, 163 Av. de Luminy, 13288 Marseille cedex 9, France
| | | | - Colomban de Vargas
- Sorbonne Université, Roscoff, France.,Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | | | - Eric Thiébaut
- Sorbonne Université, Roscoff, France.,Sorbonne Université, CNRS, OSU STAMAR, UMS2017, 4 Place Jussieu, 75252 Paris cedex 05, France
| | - Nicolas Henry
- Sorbonne Université, Roscoff, France.,Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,CNRS, Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff, 29680, Roscoff, France
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49
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Lu Y, Zhang Y, Wang J, Zhang M, Wu Y, Xiao X, Xu J. Dynamics in Bacterial Community Affected by Mesoscale Eddies in the Northern Slope of the South China Sea. MICROBIAL ECOLOGY 2022; 83:823-836. [PMID: 34272992 DOI: 10.1007/s00248-021-01816-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
Mesoscale eddies are common oceanographic processes that can enhance primary productivity by transporting nutrients to the euphotic zone. In the northern South China Sea (SCS), eddies were frequently found to promote the exchange between the nutrient-rich shelf water and the oligotrophic water at the slope area. However, the response of bacterial community to eddy perturbations remains unclear. In the present study, we examined the variation of bacterial community under the impact of eddies in early spring and summer. The results showed that both the summer cyclonic eddy and spring anticyclonic eddy enhanced the bacterial abundance in surface water. The bacterial community composition and their functional potentials of surface samples were also influenced by the summer cyclonic eddy, while no significant change was observed in the case of spring anticyclonic eddy. Salinity and nutrients, which varied between the inside and outside of the eddies, were the significant factors explaining the differentiation of the community composition and related functions. Taken together, the results of our present study reveal the effects of mesoscale eddies on the bacterial community and associated metagenomes, providing a better understanding of the dynamics of bacteria in the slope ecosystem of the SCS.
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Affiliation(s)
- Ye Lu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiahua Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Miao Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Ying Wu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, China.
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50
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Ansari MI, Calleja MLI, Silva L, Viegas M, Ngugi DK, Huete-Stauffer TM, Morán XAG. High-Frequency Variability of Bacterioplankton in Response to Environmental Drivers in Red Sea Coastal Waters. Front Microbiol 2022; 13:780530. [PMID: 35432231 PMCID: PMC9009512 DOI: 10.3389/fmicb.2022.780530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Autotrophic and heterotrophic bacterioplankton are essential to the biogeochemistry of tropical ecosystems. However, the processes that govern their dynamics are not well known. We provide here a high-frequency assessment of bacterial community dynamics and concurrent environmental factors in Red Sea coastal waters. Weekly sampling of surface samples during a full annual cycle at an enclosed station revealed high variability in ecological conditions, which reflected in changes of major bacterioplankton communities. Temperature varied between 23 and 34°C during the sampling period. Autotrophic (Synechococcus, 1.7–16.2 × 104 cells mL−1) and heterotrophic bacteria (1.6–4.3 × 105 cells mL−1) showed two maxima in abundance in spring and summer, while minima were found in winter and autumn. Heterotrophic cells with high nucleic acid content (HNA) peaked in July, but their contribution to the total cell counts (35–60%) did not show a clear seasonal pattern. Actively respiring cells (CTC+) contributed between 4 and 51% of the total number of heterotrophic bacteria, while live cells (with intact membrane) consistently accounted for over 90%. Sequenced 16S rRNA amplicons revealed a predominance of Proteobacteria in summer and autumn (>40%) and a smaller contribution in winter (21–24%), with members of the Alphaproteobacteria class dominating throughout the year. The contribution of the Flavobacteriaceae family was highest in winter (21%), while the Rhodobacteraceae contribution was lowest (6%). Temperature, chlorophyll-a, and dissolved organic carbon concentration were the environmental variables with the greatest effects on bacterial abundance and diversity patterns.
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Affiliation(s)
- Mohd Ikram Ansari
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Biosciences, Integral University, Lucknow, India
- *Correspondence: Mohd Ikram Ansari, ; Xosé Anxelu G. Morán,
| | - Maria LI. Calleja
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Climate Geochemistry, Max Planck Institute for Chemistry (MPIC), Mainz, Germany
| | - Luis Silva
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Miguel Viegas
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - David Kamanda Ngugi
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tamara Megan Huete-Stauffer
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xosé Anxelu G. Morán
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centro Oceanográfico de Gijón/Xixón (IEO, CSIC), Gijón/Xixón, Spain
- *Correspondence: Mohd Ikram Ansari, ; Xosé Anxelu G. Morán,
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