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Giordano N, Gaudin M, Trottier C, Delage E, Nef C, Bowler C, Chaffron S. Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities. Nat Commun 2024; 15:2721. [PMID: 38548725 PMCID: PMC10978986 DOI: 10.1038/s41467-024-46374-w] [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: 06/30/2023] [Accepted: 02/26/2024] [Indexed: 04/01/2024] Open
Abstract
Marine microorganisms form complex communities of interacting organisms that influence central ecosystem functions in the ocean such as primary production and nutrient cycling. Identifying the mechanisms controlling their assembly and activities is a major challenge in microbial ecology. Here, we integrated Tara Oceans meta-omics data to predict genome-scale community interactions within prokaryotic assemblages in the euphotic ocean. A global genome-resolved co-activity network revealed a significant number of inter-lineage associations across diverse phylogenetic distances. Identified co-active communities include species displaying smaller genomes but encoding a higher potential for quorum sensing, biofilm formation, and secondary metabolism. Community metabolic modelling reveals a higher potential for interaction within co-active communities and points towards conserved metabolic cross-feedings, in particular of specific amino acids and group B vitamins. Our integrated ecological and metabolic modelling approach suggests that genome streamlining and metabolic auxotrophies may act as joint mechanisms shaping bacterioplankton community assembly in the global ocean surface.
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Affiliation(s)
- Nils Giordano
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Marinna Gaudin
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Camille Trottier
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Erwan Delage
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Charlotte Nef
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, F-75016, Paris, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, F-75016, Paris, 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.
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2
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Cooney C, Sommer B, Marzinelli EM, Figueira WF. The role of microbial biofilms in range shifts of marine habitat-forming organisms. Trends Microbiol 2024; 32:190-199. [PMID: 37633773 DOI: 10.1016/j.tim.2023.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/28/2023]
Abstract
Marine species, such as corals and kelp, are responding to climate change by altering their distributions. Microbial biofilms underpin key processes that affect the establishment, maintenance, and function of these dominant habitat-formers. Climate-mediated changes to microbial biofilms can therefore strongly influence species' range shifts. Here, we review emerging research on the interactions between benthic biofilms and habitat-formers and identify two key areas of interaction where climate change can impact this dynamic: (i) via direct effects on biofilm composition, and (ii) via impacts on the complex feedback loops which exist between the biofilm microbes and habitat-forming organisms. We propose that these key interactions will be fundamental in driving the speed and extent of tropicalisation of coastal ecosystems under climate change.
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Affiliation(s)
- Christopher Cooney
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Brigitte Sommer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Ezequiel M Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Will F Figueira
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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3
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Marcondes MA, Pessôa R, José da Silva Duarte A, Clissa PB, Sanabani SS. Temporal patterns of bacterial communities in the Billings Reservoir system. Sci Rep 2024; 14:2062. [PMID: 38267511 PMCID: PMC10808195 DOI: 10.1038/s41598-024-52432-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/18/2024] [Indexed: 01/26/2024] Open
Abstract
In this study, high-throughput sequencing of 16S rRNA amplicons and predictive PICRUSt functional profiles were used to perform a comprehensive analysis of the temporal bacterial distribution and metabolic functions of 19 bimonthly samples collected from July 2019 to January 2020 in the surface water of Billings Reservoir, São Paulo. The results revealed that most of the bacterial 16S rRNA gene sequences belonged to Cyanobacteria and Proteobacteria, which accounted for more than 58% of the total bacterial abundance. Species richness and evenness indices were highest in surface water from summer samples (January 2020), followed by winter (July 2019) and spring samples (September and November 2019). Results also showed that the highest concentrations of sulfate (SO4-2), phosphate (P), ammonia (NH3), and nitrate (NO3-) were detected in November 2019 and January 2020 compared with samples collected in July and September 2019 (P < 0.05). Principal component analysis suggests that physicochemical factors such as pH, DO, temperature, and NH3 are the most important environmental factors influencing spatial and temporal variations in the community structure of bacterioplankton. At the genus level, 18.3% and 9.9% of OTUs in the July and September 2019 samples, respectively, were assigned to Planktothrix, while 14.4% and 20% of OTUs in the November 2019 and January 2020 samples, respectively, were assigned to Microcystis. In addition, PICRUSt metabolic analysis revealed increasing enrichment of genes in surface water associated with multiple metabolic processes rather than a single regulatory mechanism. This is the first study to examine the temporal dynamics of bacterioplankton and its function in Billings Reservoir during the winter, spring, and summer seasons. The study provides comprehensive reference information on the effects of an artificial habitat on the bacterioplankton community that can be used to interpret the results of studies to evaluate and set appropriate treatment targets.
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Affiliation(s)
- Marta Angela Marcondes
- Post-Graduation Program in Translational Medicine, Department of Medicine, Federal University of São Paulo, São Paulo, 04021-001, Brazil
| | - Rodrigo Pessôa
- Post-Graduation Program in Translational Medicine, Department of Medicine, Federal University of São Paulo, São Paulo, 04021-001, Brazil
| | - Alberto José da Silva Duarte
- Laboratory of Dermatology and Immunodeficiency, Department of Dermatology LIM 56, Faculty of Medicine, University of São Paulo, São Paulo, 05403-000, Brazil
| | | | - Sabri Saeed Sanabani
- Laboratory of Medical Investigation 03 (LIM03), Clinics Hospital, Faculty of Medicine, University of São Paulo, São Paulo, 05403-000, Brazil.
- Laboratory of Dermatology and Immunodeficiency, LIM56/03, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Eneas de Carvalho Aguiar, 470 3º Andar, São Paulo, 05403 000, Brazil.
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4
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Barbour KM, Martiny JBH. Investigating eco-evolutionary processes of microbial community assembly in the wild using a model leaf litter system. THE ISME JOURNAL 2024; 18:wrae043. [PMID: 38506671 PMCID: PMC11008689 DOI: 10.1093/ismejo/wrae043] [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: 12/22/2023] [Revised: 02/13/2024] [Accepted: 03/19/2024] [Indexed: 03/21/2024]
Abstract
Microbial communities are not the easiest to manipulate experimentally in natural ecosystems. However, leaf litter-topmost layer of surface soil-is uniquely suitable to investigate the complexities of community assembly. Here, we reflect on over a decade of collaborative work to address this topic using leaf litter as a model system in Southern California ecosystems. By leveraging a number of methodological advantages of the system, we have worked to demonstrate how four processes-selection, dispersal, drift, and diversification-contribute to bacterial and fungal community assembly and ultimately impact community functioning. Although many dimensions remain to be investigated, our initial results demonstrate that both ecological and evolutionary processes occur simultaneously to influence microbial community assembly. We propose that the development of additional and experimentally tractable microbial systems will be enormously valuable to test the role of eco-evolutionary processes in natural settings and their implications in the face of rapid global change.
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Affiliation(s)
- Kristin M Barbour
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, United States
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, United States
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5
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Sun F, Wang Y, Wang Y, Sun C, Cheng H, Wu M. Insights into the spatial distributions of bacteria, archaea, ammonia-oxidizing bacteria and archaea communities in sediments of Daya Bay, northern South China Sea. MARINE POLLUTION BULLETIN 2024; 198:115850. [PMID: 38029671 DOI: 10.1016/j.marpolbul.2023.115850] [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: 06/29/2023] [Revised: 11/02/2023] [Accepted: 11/24/2023] [Indexed: 12/01/2023]
Abstract
Microbe plays an important role in the biogeochemical cycles of the coastal waters. However, comprehensive information about the microbe in the gulf waters is lacking. This study employed high-throughput sequencing and quantitative PCR (qPCR) to investigate the distribution patterns of bacterial, archaeal, ammonia-oxidizing bacterial (AOB), and archaeal (AOA) communities in Daya Bay. Community compositions and principal coordinates analysis (PCoA) exhibited significant spatial characteristics in the diversity and distributions of bacteria, archaea, AOB, and AOA. Notably, various microbial taxa (bacterial, archaeal, AOB, and AOA) exhibited significant differences in different regions, playing crucial roles in nitrogen, sulfur metabolism, and organic carbon mineralization. Canonical correlation analysis (CCA) or redundancy analysis (RDA) indicated that environmental parameters such as temperature, salinity, nitrate, total nitrogen, silicate, and phosphate strongly influenced the distributions of bacterial, archaeal, AOB, and AOA. This study deepens the understanding of the composition and ecological function of prokaryotes in the bay.
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Affiliation(s)
- Fulin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, China; Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, China
| | - Youshao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, China
| | - Yutu Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, China
| | - Cuici Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Meilin Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
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6
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Zhang Y, Liu J, Song D, Yao P, Zhu S, Zhou Y, Jin J, Zhang XH. Stochasticity-driven weekly fluctuations distinguished the temporal pattern of particle-associated microorganisms from its free-living counterparts in temperate coastal seawater. WATER RESEARCH 2024; 248:120849. [PMID: 37979570 DOI: 10.1016/j.watres.2023.120849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Microbial community dynamics directly determine their ecosystem functioning. Despite the well-known annual recurrence pattern, little is known how different lifestyles affect the temporal variation and how community assembly mechanisms change over different temporal scales. Here, through a high-resolution observation of size fractionated samples over 60 consecutive weeks, we investigate the distinction in weekly distribution pattern and assembly mechanism between free-living (FL) and particle-associated (PA) communities in highly dynamic coastal environments. A clear pattern of annual recurrence was observed, which was more pronounced in FL compared to PA, resulting in higher temporal specificity in the former samples. Both the two size fractions displayed significant temporal distance-decay patterns, yet the PA community showed a higher magnitude of community variation between adjacent weeks, likely caused by sudden, drastic and long-lived blooms of heterotrophic bacteria. Generally, determinism (environmental selection) had a greater effect on the community assembly than stochasticity (random birth, death, and dispersal events), with significant contributions from temperature and inorganic nutrients. However, a clear shift in the temporal assembly pattern was observed, transitioning from a prevalence of stochastic processes driving short-term (within a month) fluctuations to a dominance of deterministic processes over longer time intervals. Between adjacent weeks, stochasticity was more important in the community assembly of PA than FL. This study revealed that stochastic processes can lead to rapid, dramatic and irregular PA community fluctuations, indicating weak resistance and resilience to disturbances, which considering the role of PA microbes in carbon processing would significantly affect the coastal carbon cycle. Our results provided a new insight into the microbial community assembly mechanisms in the temporal dimension.
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Affiliation(s)
- Yulin Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jiwen Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Derui Song
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266237, China; Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Shaodong Zhu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yi Zhou
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jian Jin
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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7
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Ren K, Mo Y, Xiao P, Rønn R, Xu Z, Xue Y, Chen H, Rivera WL, Rensing C, Yang J. Microeukaryotic plankton evolutionary constraints in a subtropical river explained by environment and bacteria along differing taxonomic resolutions. ISME COMMUNICATIONS 2024; 4:ycae026. [PMID: 38559570 PMCID: PMC10980835 DOI: 10.1093/ismeco/ycae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024]
Abstract
Microeukaryotic plankton communities are keystone components for keeping aquatic primary productivity. Currently, variations in microeukaryotic plankton diversity have often been explained by local ecological factors but not by evolutionary constraints. We used amplicon sequencing of 100 water samples across five years to investigate the ecological preferences of the microeukaryotic plankton community in a subtropical riverine ecosystem. We found that microeukaryotic plankton diversity was less associated with bacterial abundance (16S rRNA gene copy number) than bacterial diversity. Further, environmental effects exhibited a larger influence on microeukaryotic plankton community composition than bacterial community composition, especially at fine taxonomic levels. The evolutionary constraints of microeukaryotic plankton community increased with decreasing taxonomic resolution (from 97% to 91% similarity levels), but not significant change from 85% to 70% similarity levels. However, compared with the bacterial community, the evolutionary constraints were shown to be more affected by environmental variables. This study illustrated possible controlling environmental and bacterial drivers of microeukaryotic diversity and community assembly in a subtropical river, thereby indirectly reflecting on the quality status of the water environment by providing new clues on the microeukaryotic community assembly.
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Affiliation(s)
- Kexin Ren
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yuanyuan Mo
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Peng Xiao
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- National and Local Joint Engineering Research Center for Ecological Treatment Technology of Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Regin Rønn
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Department of Biology, University of Copenhagen, Copenhagen DK2100, Denmark
| | - Zijie Xu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Xue
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Huihuang Chen
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Windell L Rivera
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Christopher Rensing
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Institute of Environmental Microbiology, College of Resources and the Environment, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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8
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Beauvais M, Schatt P, Montiel L, Logares R, Galand PE, Bouget FY. Functional redundancy of seasonal vitamin B 12 biosynthesis pathways in coastal marine microbial communities. Environ Microbiol 2023; 25:3753-3770. [PMID: 38031968 DOI: 10.1111/1462-2920.16545] [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: 07/14/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023]
Abstract
Vitamin B12 (cobalamin) is a major cofactor required by most marine microbes, but only produced by a few prokaryotes in the ocean, which is globally B12 -depleted. Despite the ecological importance of B12 , the seasonality of B12 metabolisms and the organisms involved in its synthesis in the ocean remain poorly known. Here we use metagenomics to assess the monthly dynamics of B12 -related pathways and the functional diversity of associated microbial communities in the coastal NW Mediterranean Sea over 7 years. We show that genes related to potential B12 metabolisms were characterized by an annual succession of different organisms carrying distinct production pathways. During the most productive winter months, archaea (Nitrosopumilus and Nitrosopelagicus) were the main contributors to B12 synthesis potential through the anaerobic pathway (cbi genes). In turn, Alphaproteobacteria (HIMB11, UBA8309, Puniceispirillum) contributed to B12 synthesis potential in spring and summer through the aerobic pathway (cob genes). Cyanobacteria could produce pseudo-cobalamin from spring to autumn. Finally, we show that during years with environmental perturbations, the organisms usually carrying B12 synthesis genes were replaced by others having the same gene, thus maintaining the potential for B12 production. Such ecological insurance could contribute to the long-term functional resilience of marine microbial communities exposed to contrasting inter-annual environmental conditions.
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Affiliation(s)
- Maxime Beauvais
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Philippe Schatt
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Lidia Montiel
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Écogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - François-Yves Bouget
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
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9
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Gazulla CR, Cabello AM, Sánchez P, Gasol JM, Sánchez O, Ferrera I. A Metagenomic and Amplicon Sequencing Combined Approach Reveals the Best Primers to Study Marine Aerobic Anoxygenic Phototrophs. MICROBIAL ECOLOGY 2023; 86:2161-2172. [PMID: 37148309 PMCID: PMC10497671 DOI: 10.1007/s00248-023-02220-y] [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: 01/12/2023] [Accepted: 04/07/2023] [Indexed: 05/08/2023]
Abstract
Studies based on protein-coding genes are essential to describe the diversity within bacterial functional groups. In the case of aerobic anoxygenic phototrophic (AAP) bacteria, the pufM gene has been established as the genetic marker for this particular functional group, although available primers are known to have amplification biases. We review here the existing primers for pufM gene amplification, design new ones, and evaluate their phylogenetic coverage. We then use samples from contrasting marine environments to evaluate their performance. By comparing the taxonomic composition of communities retrieved with metagenomics and with different amplicon approaches, we show that the commonly used PCR primers are biased towards the Gammaproteobacteria phylum and some Alphaproteobacteria clades. The metagenomic approach, as well as the use of other combinations of the existing and newly designed primers, show that these groups are in fact less abundant than previously observed, and that a great proportion of pufM sequences are affiliated to uncultured representatives, particularly in the open ocean. Altogether, the framework developed here becomes a better alternative for future studies based on the pufM gene and, additionally, serves as a reference for primer evaluation of other functional genes.
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Affiliation(s)
- Carlota R Gazulla
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalunya, Spain.
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain.
| | - Ana María Cabello
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, 29640, Fuengirola, Málaga, Spain
| | - Pablo Sánchez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Olga Sánchez
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalunya, Spain.
| | - Isabel Ferrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, 29640, Fuengirola, Málaga, Spain.
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10
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Jinbiao M, Yixiang D, Gaoying X, Deying Z, Zhen H, Tao Y. Long-term changes in major ion chemistry-similarities and differences between inflow rivers and the lake in Taihu watershed, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:100731-100742. [PMID: 37639101 DOI: 10.1007/s11356-023-29433-5] [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: 05/12/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023]
Abstract
The major ion chemistry in the Taihu watershed has dramatically changed due to human disturbances; however, little is known about the similarities and differences in the responses of the inflow rivers and Taihu lake to the disturbances. Using historical (1950s-1970s) and recent (2018-2021) water chemistry data of inflow rivers and the lake, as well as socioeconomic and land use data, we explored the drivers for the major ion chemistry change and different responses of the inflow rivers and the receiving lake. The results indicated that, compared with 1950s-1970s, all the major ions and TDS in rivers and Taihu lake significantly increased (by 91% for Mg2+ and by 395% for Cl- in rivers; by 68% for HCO3- and 134% for Na+ in the lake); however, their increases in major ion composition presented a clear difference, i.e., although current dominant cation remained Ca in inflow rivers, the second dominant cation has shifted from Mg2+ (1950s-1970s) to Na+ (2018-2021) for rivers, while for the lake, the second dominant cation has become frequently Na+ (2018-2021), followed by Ca2+, indicating a clear salinization tendency. Furthermore, the change of some indicative ratio indices of inflow rivers and the lake in the past decades presented an apparent difference, i.e., the river systems had a higher increase rate in Ca2+/Mg2+ and SO42-/Cl- than the lake, while the lake had a higher increase in (Ca2+ + Mg2+)/HCO3-, TH/TA, and Cl-/Na+ than the river systems. Analyses indicated that increased human disturbances were the major driver for the similar increase in the TDS and major ions for both river systems and the lake, while the different algal biomass in the rivers and lake, the land use change, and declined hydrological connectivity in this watershed played important roles in the different alterations of the water chemistry indices. Comparison of major ion correlation change between the running and stagnant waters indicated a clear "lacunification" trend of inflow rivers in terms of water chemistry characteristics in this dense river-network region. Our work revealed the cause and effect of the fundamental water chemistry change in a rapid development region and will provide scientific basis for the integrated management and recovery in the watershed.
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Affiliation(s)
- Ma Jinbiao
- College of Environment Science and Engineering, Yangzhou University, Yangzhou, 225217, China
| | - Deng Yixiang
- Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xu Gaoying
- College of Environment Science and Engineering, Yangzhou University, Yangzhou, 225217, China
| | - Zeng Deying
- College of Environment Science and Engineering, Yangzhou University, Yangzhou, 225217, China
| | - Huang Zhen
- College of Environment Science and Engineering, Yangzhou University, Yangzhou, 225217, China
| | - Yu Tao
- College of Environment Science and Engineering, Yangzhou University, Yangzhou, 225217, China.
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11
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Martiny JBH, Martiny AC, Brodie E, Chase AB, Rodríguez-Verdugo A, Treseder KK, Allison SD. Investigating the eco-evolutionary response of microbiomes to environmental change. Ecol Lett 2023; 26 Suppl 1:S81-S90. [PMID: 36965002 DOI: 10.1111/ele.14209] [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: 11/08/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/27/2023]
Abstract
Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free-living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome-functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.
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Affiliation(s)
- Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
- Department of Earth System Science, University of California, Irvine, California, USA
| | - Eoin Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Alexander B Chase
- Department of Earth Sciences, Southern Methodist University, Dallas, Texas, USA
| | | | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
- Department of Earth System Science, University of California, Irvine, California, USA
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12
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Ortmann AC, Cobanli SE, Wohlgeschaffen G, Poon HY, Ryther C, Greer CW, Wasserscheid J, Elias M, Robinson B, King TL. Factors that affect water column hydrocarbon concentrations have minor impacts on microbial responses following simulated diesel fuel spills. MARINE POLLUTION BULLETIN 2023; 194:115358. [PMID: 37567129 DOI: 10.1016/j.marpolbul.2023.115358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 07/24/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023]
Abstract
Effects of season and mixing on hydrocarbon concentrations and the microbial community response was explored in a series of mesocosm experiments simulating surface spills of diesel into coastal waters. Mixing of any amount contributed to hydrocarbons entering the water column, but diesel fuel composition had a significant effect on hydrocarbon concentrations. Higher initial concentrations of aromatic hydrocarbons resulted in higher water column concentrations, with minimal differences among seasons due to high variability. Regardless of the concentrations of hydrocarbons, prokaryotes increased and there were higher relative abundances of hydrocarbon affiliated bacteria with indications of biodegradation within 4 d of exposure. As concentrations decreased over time, the eukaryote community shifted from the initial community to one which appeared to be composed of organisms with some resilience to hydrocarbons. This series of experiments demonstrates the wide range of conditions under which natural attenuation of diesel fuel is an effective response.
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Affiliation(s)
- Alice C Ortmann
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada.
| | - Susan E Cobanli
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Gary Wohlgeschaffen
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Ho Yin Poon
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Camilla Ryther
- Dalhousie University, 6299 South Street, Halifax, NS B3H 4R2, Canada
| | - Charles W Greer
- National Research Council of Canada, Energy, Mining and Environment Research Centre, 6100 Royalmount Ave, Montreal, PQ H4P 2R2, Canada
| | - Jessica Wasserscheid
- National Research Council of Canada, Energy, Mining and Environment Research Centre, 6100 Royalmount Ave, Montreal, PQ H4P 2R2, Canada
| | - Miria Elias
- National Research Council of Canada, Energy, Mining and Environment Research Centre, 6100 Royalmount Ave, Montreal, PQ H4P 2R2, Canada
| | - Brian Robinson
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Thomas L King
- Centre for Offshore Oil, Gas and Energy Research, Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
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13
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Fletcher-Hoppe C, Yeh YC, Raut Y, Weissman JL, Fuhrman JA. Symbiotic UCYN-A strains co-occurred with El Niño, relaxed upwelling, and varied eukaryotes over 10 years off Southern California. ISME COMMUNICATIONS 2023; 3:63. [PMID: 37355737 PMCID: PMC10290647 DOI: 10.1038/s43705-023-00268-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/05/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
Biological nitrogen fixation, the conversion of N2 gas into a bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a focal point due to its streamlined metabolism, intimate partnership with a haptophyte host, and broad distribution. Here, we explore the environmental parameters that govern UCYN-A's presence at the San Pedro Ocean Time-series (SPOT), its host specificity, and statistically significant interactions with non-host eukaryotes from 2008-2018. 16S and 18S rRNA gene sequences were amplified by "universal primers" from monthly samples and resolved into Amplicon Sequence Variants, allowing us to observe multiple UCYN-A symbioses. UCYN-A1 relative abundances increased following the 2015-2016 El Niño event. This "open ocean ecotype" was present when coastal upwelling declined, and Ekman transport brought tropical waters into the region. Network analyses reveal all strains of UCYN-A co-occur with dinoflagellates including Lepidodinium, a potential predator, and parasitic Syndiniales. UCYN-A2 appeared to pair with multiple hosts and was not tightly coupled to its predominant host, while UCYN-A1 maintained a strong host-symbiont relationship. These biological relationships are particularly important to study in the context of climate change, which will alter UCYN-A distribution at regional and global scales.
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Affiliation(s)
- Colette Fletcher-Hoppe
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
| | - Yi-Chun Yeh
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
- Department of Global Ecology, Carnegie Institution for Science, Stanford University, Stanford, CA, USA
| | - Yubin Raut
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
| | - J L Weissman
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
- Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Jed A Fuhrman
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA.
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14
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Benincà E, Pinto S, Cazelles B, Fuentes S, Shetty S, Bogaards JA. Wavelet clustering analysis as a tool for characterizing community structure in the human microbiome. Sci Rep 2023; 13:8042. [PMID: 37198426 DOI: 10.1038/s41598-023-34713-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/05/2023] [Indexed: 05/19/2023] Open
Abstract
Human microbiome research is helped by the characterization of microbial networks, as these may reveal key microbes that can be targeted for beneficial health effects. Prevailing methods of microbial network characterization are based on measures of association, often applied to limited sampling points in time. Here, we demonstrate the potential of wavelet clustering, a technique that clusters time series based on similarities in their spectral characteristics. We illustrate this technique with synthetic time series and apply wavelet clustering to densely sampled human gut microbiome time series. We compare our results with hierarchical clustering based on temporal correlations in abundance, within and across individuals, and show that the cluster trees obtained by using either method are significantly different in terms of elements clustered together, branching structure and total branch length. By capitalizing on the dynamic nature of the human microbiome, wavelet clustering reveals community structures that remain obscured in correlation-based methods.
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Affiliation(s)
- Elisa Benincà
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
| | - Susanne Pinto
- Biomedical Data Sciences, Leiden UMC, Leiden, The Netherlands
| | - Bernard Cazelles
- CNRS UMR-8197, IBENS, Ecole Normale Supérieure, Paris, France
- Sorbonne Université, UMMISCO, Paris, France
| | - Susana Fuentes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Sudarshan Shetty
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Medical Microbiology and Infection Prevention, UMC Groningen, Groningen, The Netherlands
| | - Johannes A Bogaards
- Department of Epidemiology & Data Science, Amsterdam UMC location VUMC, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Amsterdam, The Netherlands
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15
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Subsurface Bacterioplankton Structure and Diversity in the Strongly-Stratified Water Columns within the Equatorial Eastern Indian Ocean. Microorganisms 2023; 11:microorganisms11030592. [PMID: 36985166 PMCID: PMC10058062 DOI: 10.3390/microorganisms11030592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
The consequences of climate change may directly or indirectly impact the marine biosphere. Although ocean stratification has been recognized as one of the crucial consequences of ocean warming, its impacts on several critical aspects of marine microbes remain largely unknown in the Indian Ocean. Here, we investigate the effects of water stratification, in both surface and subsurface layers, on hydrogeographic parameters and bacterioplankton diversity within the equatorial eastern Indian Ocean (EIO). Strong stratification in the upper 200 m of equatorial EIO was detected with evidential low primary productivity. The vertical bacterioplankton diversity of the whole water columns displayed noticeable variation, with lower diversity occurring in the surface layer than in the subsurface layers. Horizontal heterogeneity of bacterioplankton communities was also in the well-mixed layer among different stations. SAR11 and Prochlorococcus displayed uncharacteristic low abundance in the surface water. Some amplicon sequence variants (ASVs) were identified as potential biomarkers for their specific depths in strongly-stratified water columns. Thus, barriers resulting from stratification are proposed to function as an ‘ASV filter’ to regulate the vertical bacterioplankton community diversity along the water columns. Overall, our results suggest that the effects of stratification on the structure and diversity of bacterioplankton can extend up to the bathypelagic zone in the strongly-stratified waters of the equatorial EIO. This study provides the first insight into the effect of stratification on the subsurface microbial communities in the equatorial eastern Indian Ocean.
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16
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Lalzar M, Zvi-Kedem T, Kroin Y, Martinez S, Tchernov D, Meron D. Sediment Microbiota as a Proxy of Environmental Health: Discovering Inter- and Intrakingdom Dynamics along the Eastern Mediterranean Continental Shelf. Microbiol Spectr 2023; 11:e0224222. [PMID: 36645271 PMCID: PMC9927165 DOI: 10.1128/spectrum.02242-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Sedimentary marine habitats are the largest ecosystem on our planet in terms of area. Marine sediment microbiota govern most of the benthic biological processes and therefore are responsible for much of the global biogeochemical activity. Sediment microbiota respond, even rapidly, to natural change in environmental conditions as well as disturbances of anthropogenic sources. The latter greatly impact the continental shelf. Characterization and monitoring of the sediment microbiota may serve as an important tool for assessing environmental health and indicate changes in the marine ecosystem. This study examined the suitability of marine sediment microbiota as a bioindicator for environmental health in the eastern Mediterranean Sea. Integration of information from Bacteria, Archaea, and Eukaryota enabled robust assessment of environmental factors controlling sediment microbiota composition: seafloor-depth (here representing sediment grain size and total organic carbon), core depth, and season (11%, 4.2%, and 2.5% of the variance, respectively). Furthermore, inter- and intrakingdom cooccurrence patterns indicate that ecological filtration as well as stochastic processes may control sediment microbiota assembly. The results show that the sediment microbiota was robust over 3 years of sampling, in terms of both representation of region (outside the model sites) and robustness of microbial markers. Furthermore, anthropogenic disturbance was reflected by significant transformations in sediment microbiota. We therefore propose sediment microbiota analysis as a sensitive approach to detect disturbances, which is applicable for long-term monitoring of marine environmental health. IMPORTANCE Analysis of data, curated over 3 years of sediment sampling, improves our understanding of microbiota assembly in marine sediment. Furthermore, we demonstrate the importance of cross-kingdom integration of information in the study of microbial community ecology. Finally, the urgent need to propose an applicable approach for environmental health monitoring is addressed here by establishment of sediment microbiota as a robust and sensitive model.
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Affiliation(s)
- Maya Lalzar
- Bioinformatics Services Unit, University of Haifa, Haifa, Israel
| | - Tal Zvi-Kedem
- Morris Kahn Marine Research Station, Faculty of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Yael Kroin
- Morris Kahn Marine Research Station, Faculty of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Stephane Martinez
- Morris Kahn Marine Research Station, Faculty of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Dan Tchernov
- Morris Kahn Marine Research Station, Faculty of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Dalit Meron
- Morris Kahn Marine Research Station, Faculty of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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17
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Taniguchi A, Kuroyanagi Y, Aoki R, Eguchi M. Community Structure and Predicted Functions of Actively Growing Bacteria Responsive to Released Coral Mucus in Surrounding Seawater. Microbes Environ 2023; 38:ME23024. [PMID: 37704450 PMCID: PMC10522842 DOI: 10.1264/jsme2.me23024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/31/2023] [Indexed: 09/15/2023] Open
Abstract
A direct relationship exists between diverse corals and fish farming in Keten Bay, Amami-Oshima, Japan. The release of coral mucus has a significant impact on the microbial activity of surrounding seawater. To obtain a more detailed understanding of biogeochemical cycles in this environment, the effects of coral mucus on the community structure and function of bacteria in surrounding seawater need to be elucidated. We herein used a bromodeoxyuridine approach to investigate the structures and functions of bacterial communities growing close to mucus derived from two different Acropora corals, AC1 and AC2. The alpha diversities of actively growing bacteria (AGB) were lower in mucus-containing seawater than in control seawater and their community structures significantly differed, suggesting that the growth of specific bacteria was modulated by coral mucus. Rhodobacteraceae and Cryomorphaceae species were the most dominant AGB in response to the mucus of Acropora AC1 and AC2, respectively. In contrast, the growth of Actinomarinaceae, Alteromonadaceae, Flavobacteriaceae, and SAR86 clade bacteria was inhibited by coral mucus. The results of a Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) ana-lysis suggested that the predicted functions of AGB in mucus-containing seawater differed from those in seawater. These functions were related to the biosynthesis and degradation of the constituents of coral mucus, such as polysaccharides, sugar acids, and aromatic compounds. The present study demonstrated that complex bacterial community structures and functions may be shaped by coral mucus, suggesting that corals foster diverse bacterial communities that enhance the ecological resilience of this fish farming area.
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Affiliation(s)
- Akito Taniguchi
- Faculty of Agriculture, Kindai University, 3327-204 Naka-machi, Nara, Nara 631-8505, Japan
| | - Yuki Kuroyanagi
- Graduate School of Agriculture, Kindai University, 3327-204 Naka-machi, Nara, Nara 631-8505, Japan
| | - Ryuichiro Aoki
- Graduate School of Agriculture, Kindai University, 3327-204 Naka-machi, Nara, Nara 631-8505, Japan
| | - Mitsuru Eguchi
- Faculty of Agriculture, Kindai University, 3327-204 Naka-machi, Nara, Nara 631-8505, Japan
- Agricultural Technology and Innovation Research Institute, Kindai University, 3327-204 Naka-machi, Nara, Nara 631-8505, Japan
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18
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Effects of phytoplankton, viral communities, and warming on free-living and particle-associated marine prokaryotic community structure. Nat Commun 2022; 13:7905. [PMID: 36550140 PMCID: PMC9780322 DOI: 10.1038/s41467-022-35551-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Free-living and particle-associated marine prokaryotes have physiological, genomic, and phylogenetic differences, yet factors influencing their temporal dynamics remain poorly constrained. In this study, we quantify the entire microbial community composition monthly over several years, including viruses, prokaryotes, phytoplankton, and total protists, from the San-Pedro Ocean Time-series using ribosomal RNA sequencing and viral metagenomics. Canonical analyses show that in addition to physicochemical factors, the double-stranded DNA viral community is the strongest factor predicting free-living prokaryotes, explaining 28% of variability, whereas the phytoplankton (via chloroplast 16S rRNA) community is strongest with particle-associated prokaryotes, explaining 31% of variability. Unexpectedly, protist community explains little variability. Our findings suggest that biotic interactions are significant determinants of the temporal dynamics of prokaryotes, and the relative importance of specific interactions varies depending on lifestyles. Also, warming influenced the prokaryotic community, which largely remained oligotrophic summer-like throughout 2014-15, with cyanobacterial populations shifting from cold-water ecotypes to warm-water ecotypes.
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19
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Distributional Pattern of Bacteria, Protists, and Diatoms in Ocean according to Water Depth in the Northern South China Sea. Microbiol Spectr 2022; 10:e0275921. [PMID: 36222702 PMCID: PMC9769685 DOI: 10.1128/spectrum.02759-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Ocean microbiomes provide insightful details about the condition of water and the global impact of marine ecosystems. A fine-scale analysis of ocean microbes may shed light on the dynamics and function of the ocean microbiome community. In this study, we evaluated the changes in the community and function of marine bacteria, protists, and diatoms corresponding to different ocean depths using next-generation sequencing methods. We found that diatoms displayed a potential water-depth pattern in species richness (alpha diversity) and community composition (beta diversity). However, for bacteria and protists, there was no significant relationship between water depth and species richness. This may be related to the biological characteristics of diatoms. The photosynthesis of diatoms and their distribution may be associated with the fluctuating light regime in the underwater climate. Moreover, salinity displayed negative effects on the abundance of some diatom and bacterial groups, which indicates that salinity may be one of the factors restricting ocean microorganism diversity. In addition, compared to the global ocean microbiome composition, function, and antibiotic resistance genes, a water depth pattern due to the fine-scale region was not observed in this study. IMPORTANCE Fine-scale analysis of ocean microbes provides insights into the dynamics and functions of the ocean microbiome community. Here, using amplicon and metagenome sequencing methods, we found that diatoms in the northern South China Sea displayed a potential water-depth pattern in species richness and community composition, which may be related to their biological characteristics. The potential effects of the differences in geographic sites mainly occurred in the diatom and bacterial communities. Moreover, given the correlation between the environmental factors and relative abundance of antibiotic resistance genes (ARGs), the study of ocean ARG distribution patterns should integrate the potential effects of environmental factors.
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20
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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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21
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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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22
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Heterogeneous selection dominated the temporal variation of the planktonic prokaryotic community during different seasons in the coastal waters of Bohai Bay. Sci Rep 2022; 12:20475. [PMID: 36443487 PMCID: PMC9705714 DOI: 10.1038/s41598-022-24892-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
To explore temporal and spatial effects on the planktonic prokaryotic community composition (PCC) in the coastal region of the Bohai Sea, surface water samples were collected from 12 to 28 regularly distributed sites in Bohai Bay across 3 months from different seasons to characterize the PCC using high-throughput sequencing of the 16S rRNA V4 region. Prokaryotic α- and β-diversity showed significant temporal variation during the three sampling months. VPA analysis based on both weighted and unweighted UniFrac distances exhibited a shift of environmental and spatial effects on PCC variation with temporal variation. Quantification analysis of assembly processes on community turn over showed that "heterogeneous selection" dominated for PCC temporal variation, with basic abiotic parameters such as temperature, pH, ammonia nitrogen as the driving factors. Analysis of seasonal features showed that seasonal specific OTUs (ssOTUs) exhibited different seasonal attributions under the same phylum; meanwhile, the ssOTUs showed significant correlations with the driving environmental factors, which suggested that finer-level analysis was needed to more strictly reflect the temporal variation. Moreover, predicted nitrogen and sulfur metabolism were significantly shifted during the temporal variation. Our results clearly showed that seasonally varied environmental factors drive the "heterogeneous selection" process for PCC assembly in seawaters of Bohai Bay during different sampling seasons.
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23
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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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Succession of the intestinal bacterial community in Pacific bluefin tuna (Thunnus orientalis) larvae. PLoS One 2022; 17:e0275211. [PMID: 36201490 PMCID: PMC9536584 DOI: 10.1371/journal.pone.0275211] [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: 11/10/2021] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
We investigated the succession process of intestinal bacteria during seed production in full-cycle aquaculture of Pacific bluefin tuna (Thunnus orientalis). During the seed production, eggs, healthy fish, rearing water, and feeds from three experimental rounds in 2012 and 2013 were collected before transferring to offshore net cages and subjected to a fragment analysis of the bacterial community structure. We identified a clear succession of intestinal bacteria in bluefin tuna during seed production. While community structures of intestinal bacteria in the early stage of larvae were relatively similar to those of rearing water and feed, the bacterial community structures seen 17 days after hatching were different. Moreover, although intestinal bacteria in the late stage of larvae were less diverse than those in the early stage of larvae, the specific bacteria were predominant, suggesting that the developed intestinal environment of the host puts selection pressure on the bacteria in the late stage. The specific bacteria in the late stage of larvae, which likely composed 'core microbiota', were also found on the egg surface. The present study highlights that proper management of the seed production process, including the preparation of rearing water, feeds, and fish eggs, is important for the aquaculture of healthy fish.
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Anderson SR, Harvey EL. Estuarine microbial networks and relationships vary between environmentally distinct communities. PeerJ 2022; 10:e14005. [PMID: 36157057 PMCID: PMC9504456 DOI: 10.7717/peerj.14005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 08/14/2022] [Indexed: 01/19/2023] Open
Abstract
Microbial interactions have profound impacts on biodiversity, biogeochemistry, and ecosystem functioning, and yet, they remain poorly understood in the ocean and with respect to changing environmental conditions. We applied hierarchical clustering of an annual 16S and 18S amplicon dataset in the Skidaway River Estuary, which revealed two similar clusters for prokaryotes (Bacteria and Archaea) and protists: Cluster 1 (March-May and November-February) and Cluster 2 (June-October). We constructed co-occurrence networks from each cluster to explore how microbial networks and relationships vary between environmentally distinct periods in the estuary. Cluster 1 communities were exposed to significantly lower temperature, sunlight, NO3, and SiO4; only NH4 was higher at this time. Several network properties (e.g., edge number, degree, and centrality) were elevated for networks constructed with Cluster 1 vs. 2 samples. There was also evidence that microbial nodes in Cluster 1 were more connected (e.g., higher edge density and lower path length) compared to Cluster 2, though opposite trends were observed when networks considered Prokaryote-Protist edges only. The number of Prokaryote-Prokaryote and Prokaryote-Protist edges increased by >100% in the Cluster 1 network, mainly involving Flavobacteriales, Rhodobacterales, Peridiniales, and Cryptomonadales associated with each other and other microbial groups (e.g., SAR11, Bacillariophyta, and Strombidiida). Several Protist-Protist associations, including Bacillariophyta correlated with Syndiniales (Dino-Groups I and II) and an Unassigned Dinophyceae group, were more prevalent in Cluster 2. Based on the type and sign of associations that increased in Cluster 1, our findings indicate that mutualistic, competitive, or predatory relationships may have been more representative among microbes when conditions were less favorable in the estuary; however, such relationships require further exploration and validation in the field and lab. Coastal networks may also be driven by shifts in the abundance of certain taxonomic or functional groups. Sustained monitoring of microbial communities over environmental gradients, both spatial and temporal, is critical to predict microbial dynamics and biogeochemistry in future marine ecosystems.
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Affiliation(s)
- Sean R. Anderson
- Northern Gulf Institute, Mississippi State University, Mississippi State, MS, United States of America,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, United States of America
| | - Elizabeth L. Harvey
- Department of Biological Sciences, University of New Hampshire, Durham, NH, United States of America
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26
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Zufiaurre A, Felip M, Camarero L, Sala-Faig M, Juhanson J, Bonilla-Rosso G, Hallin S, Catalan J. Bacterioplankton seasonality in deep high-mountain lakes. Front Microbiol 2022; 13:935378. [PMID: 36187988 PMCID: PMC9519062 DOI: 10.3389/fmicb.2022.935378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/08/2022] [Indexed: 12/04/2022] Open
Abstract
Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. High-mountain lakes show snow-rich ice covers that determine contrasting conditions between ice-off and ice-on periods. We characterized the bacterioplankton seasonality in a deep high-mountain lake ice-covered for half a year. The lake shows a rich core bacterioplankton community consisting of three components: (i) an assemblage stable throughout the year, dominated by Actinobacteria, resistant to all environmental conditions; (ii) an ice-on-resilient assemblage dominating during the ice-covered period, which is more diverse than the other components and includes a high abundance of Verrucomicrobia; the deep hypolimnion constitutes a refuge for many of the typical under-ice taxa, many of which recover quickly during autumn mixing; and (iii) an ice-off-resilient assemblage, which members peak in summer in epilimnetic waters when the rest decline, characterized by a dominance of Flavobacterium, and Limnohabitans. The rich core community and low random elements compared to other relatively small cold lakes can be attributed to its simple hydrological network in a poorly-vegetated catchment, the long water-residence time (ca. 4 years), and the long ice-cover duration; features common to many headwater deep high-mountain lakes.
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Affiliation(s)
- Aitziber Zufiaurre
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- Área de Biodiversidad, Gestión ambiental de Navarra-Nafarroako Ingurumenkudeaketa (GAN-NIK), Pamplona-Iruñea, Navarra, Spain
| | - Marisol Felip
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Lluís Camarero
- Centre d’Estudis Avançats de Blanes (CEAB), CSIC, Blanes, Catalonia, Spain
| | - Marc Sala-Faig
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| | - Jaanis Juhanson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - German Bonilla-Rosso
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jordi Catalan
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- CSIC, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
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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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Li C, Liu J, Chen X, Ren H, Su B, Ma K, Tu Q. Determinism governs the succession of disturbed bacterioplankton communities in a coastal maricultural ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154457. [PMID: 35278542 DOI: 10.1016/j.scitotenv.2022.154457] [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: 10/19/2021] [Revised: 02/16/2022] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Bacterioplankton community is the major engine that drives the biogeochemical cycling of various nutrient and essential elements in the coastal ecosystem. Unraveling the mechanisms governing the succession of such complex bacterioplankton communities in dynamic environment is a challenging issue in environmental science. In this study, we investigated the diversity patterns and succession mechanisms of both free-living and particle-attached bacterioplankton communities that have been exposed to low oxygen and typhoon Lekima. The community evenness was the lowest in August when the temperature was high and dissolved oxygen was low. Similar patterns in community succession were observed for free-living and particle-attached bacterioplankton community after the passing through of typhoon Lekima. Both the free-living and particle-attached bacterioplankton communities in the surface and bottom water columns were strongly affected by geo-environmental factors, among which temperature was the common factor, suggesting that the metabolic theory of ecology also underlie the dynamic patterns of bacterioplankton communities. Although the surface and bottom bacterioplankton compositions were initially different taxonomically and shaped by different environmental conditions, they followed a similar succession pattern over the sampling months. Temperature, dissolved inorganic carbon and dissolved inorganic phosphorus were the major factors associated with the variations of surface bacterioplankton ASVs. Time-decay relationship, in which community similarity decreases with increasing time interval, was clearly observed. Such pattern shall be attributed to the combined effects of time and the changing environmental factors over the sampling months, rather than time alone. Integrating multiple lines of evidences, we demonstrated that determinism governed the succession of both free-living and particle-attached bacterioplankton communities in the coastal maricultural ecosystem, with higher stochastic ratio in habitable months (i.e. fall). This study is expected to provide valuable mechanistic insights into the succession of disturbed complex bacterioplankton communities.
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Affiliation(s)
- Chun Li
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, China; Joint Laboratory for Ocean Research and Education of Dalhousie University, Shandong University and Xiamen University, Qingdao 266237, China.
| | - Xiao Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, China
| | - Hongwei Ren
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Bei Su
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education of Dalhousie University, Shandong University and Xiamen University, Qingdao 266237, China
| | - Kai Ma
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Joint Laboratory for Ocean Research and Education of Dalhousie University, Shandong University and Xiamen University, Qingdao 266237, China.
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29
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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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30
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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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Haber M, Roth Rosenberg D, Lalzar M, Burgsdorf I, Saurav K, Lionheart R, Lehahn Y, Aharonovich D, Gómez-Consarnau L, Sher D, Krom MD, Steindler L. Spatiotemporal Variation of Microbial Communities in the Ultra-Oligotrophic Eastern Mediterranean Sea. Front Microbiol 2022; 13:867694. [PMID: 35464964 PMCID: PMC9022036 DOI: 10.3389/fmicb.2022.867694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Marine microbial communities vary seasonally and spatially, but these two factors are rarely addressed together. In this study, the temporal and spatial patterns of the bacterial and archaeal community were studied along a coast-to-offshore transect in the Eastern Mediterranean Sea (EMS) over six cruises, in three seasons of 2 consecutive years. Amplicon sequencing of 16S rRNA genes and transcripts was performed to determine presence and activity, respectively. The ultra-oligotrophic status of the Southeastern Mediterranean Sea was reflected in the microbial community composition dominated by oligotrophic bacterial groups such as SAR11, even at the most coastal station sampled, throughout the year. Seasons significantly affected the microbial communities, explaining more than half of the observed variability. However, the same few taxa dominated the community over the 2-year sampling period, varying only in their degree of dominance. While there was no overall effect of station location on the microbial community, the most coastal site (16 km offshore) differed significantly in community structure and activity from the three further offshore stations in early winter and summer. Our data on the microbial community compositions and their seasonality support previous notions that the EMS behaves like an oceanic gyre.
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Affiliation(s)
- Markus Haber
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.,Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, České Budějovice, Czechia
| | - Dalit Roth Rosenberg
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Maya Lalzar
- Bioinformatics Service Unit, University of Haifa, Haifa, Israel
| | - Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Kumar Saurav
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Regina Lionheart
- The Dr. Moses Strauss Department of Marine Geosciences, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Yoav Lehahn
- The Dr. Moses Strauss Department of Marine Geosciences, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Dikla Aharonovich
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Laura Gómez-Consarnau
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States.,Department of Biological Oceanography, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Mexico
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Michael D Krom
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.,Morris Kahn Marine Research Station, Environmental Geochemistry Lab., Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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32
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Gautam A, Lear G, Lewis GD. Time after time: Detecting annual patterns in stream bacterial biofilm communities. Environ Microbiol 2022; 24:2502-2515. [PMID: 35466520 PMCID: PMC9324112 DOI: 10.1111/1462-2920.16017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 04/03/2022] [Accepted: 04/13/2022] [Indexed: 11/26/2022]
Abstract
To quantify the major environmental drivers of stream bacterial population dynamics, we modelled temporal differences in stream bacterial communities to quantify community shifts, including those relating to cyclical seasonal variation and more sporadic bloom events. We applied Illumina MiSeq 16S rRNA bacterial gene sequencing of 892 stream biofilm samples, collected monthly for 36‐months from six streams. The streams were located a maximum of 118 km apart and drained three different catchment types (forest, urban and rural land uses). We identified repeatable seasonal patterns among bacterial taxa, allowing their separation into three ecological groupings, those following linear, bloom/trough and repeated, seasonal trends. Various physicochemical parameters (light, water and air temperature, pH, dissolved oxygen, nutrients) were linked to temporal community changes. Our models indicate that bloom events and seasonal episodes modify biofilm bacterial populations, suggesting that distinct microbial taxa thrive during these events including non‐cyanobacterial community members. These models could aid in determining how temporal environmental changes affect community assembly and guide the selection of appropriate statistical models to capture future community responses to environmental change.
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Affiliation(s)
- Anju Gautam
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Gavin Lear
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Gillian D Lewis
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
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33
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Yeh YC, Fuhrman JA. Contrasting diversity patterns of prokaryotes and protists over time and depth at the San-Pedro Ocean Time series. ISME COMMUNICATIONS 2022; 2:36. [PMID: 37938286 PMCID: PMC9723720 DOI: 10.1038/s43705-022-00121-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 06/18/2023]
Abstract
Community dynamics are central in microbial ecology, yet we lack studies comparing diversity patterns among marine protists and prokaryotes over depth and multiple years. Here, we characterized microbes at the San-Pedro Ocean Time series (2005-2018), using SSU rRNA gene sequencing from two size fractions (0.2-1 and 1-80 μm), with a universal primer set that amplifies from both prokaryotes and eukaryotes, allowing direct comparisons of diversity patterns in a single set of analyses. The 16S + 18S rRNA gene composition in the small size fraction was mostly prokaryotic (>92%) as expected, but the large size fraction unexpectedly contained 46-93% prokaryotic 16S rRNA genes. Prokaryotes and protists showed opposite vertical diversity patterns; prokaryotic diversity peaked at mid-depth, protistan diversity at the surface. Temporal beta-diversity patterns indicated prokaryote communities were much more stable than protists. Although the prokaryotic communities changed monthly, the average community stayed remarkably steady over 14 years, showing high resilience. Additionally, particle-associated prokaryotes were more diverse than smaller free-living ones, especially at deeper depths, contributed unexpectedly by abundant and diverse SAR11 clade II. Eukaryotic diversity was strongly correlated with the diversity of particle-associated prokaryotes but not free-living ones, reflecting that physical associations result in the strongest interactions, including symbioses, parasitism, and decomposer relationships.
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Affiliation(s)
- Yi-Chun Yeh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA.
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34
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Shu WS, Huang LN. Microbial diversity in extreme environments. Nat Rev Microbiol 2022; 20:219-235. [PMID: 34754082 DOI: 10.1038/s41579-021-00648-y] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
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Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
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35
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Kaiser T, Jahansouz C, Staley C. Network-based approaches for the investigation of microbial community structure and function using metagenomics-based data. Future Microbiol 2022; 17:621-631. [PMID: 35360922 DOI: 10.2217/fmb-2021-0219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Network-based approaches offer a powerful framework to evaluate microbial community organization and function as it relates to a variety of environmental processes. Emerging studies are exploring network theory as a method for data integration that is likely to be critical for the integration of 'omics' data using systems biology approaches. Intricacies of network theory and methodological and computational complexities in network construction, however, impede the use of these tools for translational science. We provide a perspective on the methods of network construction, interpretation and emerging uses for these techniques in understanding host-microbiota interactions.
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Affiliation(s)
- Thomas Kaiser
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA.,Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Cyrus Jahansouz
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Christopher Staley
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA.,Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
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36
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Liu S, Longnecker K, Kujawinski EB, Vergin K, Bolaños LM, Giovannoni SJ, Parsons R, Opalk K, Halewood E, Hansell DA, Johnson R, Curry R, Carlson CA. Linkages Among Dissolved Organic Matter Export, Dissolved Metabolites, and Associated Microbial Community Structure Response in the Northwestern Sargasso Sea on a Seasonal Scale. Front Microbiol 2022; 13:833252. [PMID: 35350629 PMCID: PMC8957919 DOI: 10.3389/fmicb.2022.833252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/31/2022] [Indexed: 01/04/2023] Open
Abstract
Deep convective mixing of dissolved and suspended organic matter from the surface to depth can represent an important export pathway of the biological carbon pump. The seasonally oligotrophic Sargasso Sea experiences annual winter convective mixing to as deep as 300 m, providing a unique model system to examine dissolved organic matter (DOM) export and its subsequent compositional transformation by microbial oxidation. We analyzed biogeochemical and microbial parameters collected from the northwestern Sargasso Sea, including bulk dissolved organic carbon (DOC), total dissolved amino acids (TDAA), dissolved metabolites, bacterial abundance and production, and bacterial community structure, to assess the fate and compositional transformation of DOM by microbes on a seasonal time-scale in 2016–2017. DOM dynamics at the Bermuda Atlantic Time-series Study site followed a general annual trend of DOC accumulation in the surface during stratified periods followed by downward flux during winter convective mixing. Changes in the amino acid concentrations and compositions provide useful indices of diagenetic alteration of DOM. TDAA concentrations and degradation indices increased in the mesopelagic zone during mixing, indicating the export of a relatively less diagenetically altered (i.e., more labile) DOM. During periods of deep mixing, a unique subset of dissolved metabolites, such as amino acids, vitamins, and benzoic acids, was produced or lost. DOM export and compositional change were accompanied by mesopelagic bacterial growth and response of specific bacterial lineages in the SAR11, SAR202, and SAR86 clades, Acidimicrobiales, and Flavobacteria, during and shortly following deep mixing. Complementary DOM biogeochemistry and microbial measurements revealed seasonal changes in DOM composition and diagenetic state, highlighting microbial alteration of the quantity and quality of DOM in the ocean.
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Affiliation(s)
- Shuting Liu
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Krista Longnecker
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Kevin Vergin
- Microbial DNA Analytics, Phoenix, OR, United States
| | - Luis M Bolaños
- School of Biosciences, University of Exeter, Exeter, United Kingdom.,Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Stephen J Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Rachel Parsons
- Bermuda Institute of Ocean Sciences, Saint George's, Bermuda
| | - Keri Opalk
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Elisa Halewood
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Dennis A Hansell
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Rod Johnson
- Bermuda Institute of Ocean Sciences, Saint George's, Bermuda
| | - Ruth Curry
- Bermuda Institute of Ocean Sciences, Saint George's, Bermuda
| | - Craig A Carlson
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
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37
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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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38
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Longobardi L, Dubroca L, Margiotta F, Sarno D, Zingone A. Photoperiod-driven rhythms reveal multi-decadal stability of phytoplankton communities in a highly fluctuating coastal environment. Sci Rep 2022; 12:3908. [PMID: 35273208 PMCID: PMC8913669 DOI: 10.1038/s41598-022-07009-6] [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: 10/19/2021] [Accepted: 02/09/2022] [Indexed: 11/09/2022] Open
Abstract
Phytoplankton play a pivotal role in global biogeochemical and trophic processes and provide essential ecosystem services. However, there is still no broad consensus on how and to what extent their community composition responds to environmental variability. Here, high-frequency oceanographic and biological data collected over more than 25 years in a coastal Mediterranean site are used to shed light on the temporal patterns of phytoplankton species and assemblages in their environmental context. Because of the proximity to the coast and due to large-scale variations, environmental conditions showed variability on the short and long-term scales. Nonetheless, an impressive regularity characterised the annual occurrence of phytoplankton species and their assemblages, which translated into their remarkable stability over decades. Photoperiod was the dominant factor related to community turnover and replacement, which points at a possible endogenous regulation of biological processes associated with species-specific phenological patterns, in analogy with terrestrial plants. These results highlight the considerable stability and resistance of phytoplankton communities in response to different environmental pressures, which contrast the view of these organisms as passively undergoing changes that occur at different temporal scales in their habitat, and show how, under certain conditions, biological processes may prevail over environmental forcing.
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Affiliation(s)
- Lorenzo Longobardi
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Laurent Dubroca
- Institut Français de Recherche Pour l'Exploitation de la Mer, IFREMER, Laboratoire Ressources Halieutiques de Port-en-Bessin, 14520, Port-en-Bessin-Huppain, France
| | - Francesca Margiotta
- Research Infrastructures for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Diana Sarno
- Research Infrastructures for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Adriana Zingone
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy. .,Research Infrastructures for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
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39
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Gleich SJ, Cram JA, Weissman JL, Caron DA. NetGAM: Using generalized additive models to improve the predictive power of ecological network analyses constructed using time-series data. ISME COMMUNICATIONS 2022; 2:23. [PMID: 37938660 PMCID: PMC9723797 DOI: 10.1038/s43705-022-00106-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/10/2022] [Accepted: 02/17/2022] [Indexed: 05/26/2023]
Abstract
Ecological network analyses are used to identify potential biotic interactions between microorganisms from species abundance data. These analyses are often carried out using time-series data; however, time-series networks have unique statistical challenges. Time-dependent species abundance data can lead to species co-occurrence patterns that are not a result of direct, biotic associations and may therefore result in inaccurate network predictions. Here, we describe a generalize additive model (GAM)-based data transformation that removes time-series signals from species abundance data prior to running network analyses. Validation of the transformation was carried out by generating mock, time-series datasets, with an underlying covariance structure, running network analyses on these datasets with and without our GAM transformation, and comparing the network outputs to the known covariance structure of the simulated data. The results revealed that seasonal abundance patterns substantially decreased the accuracy of the inferred networks. In addition, the GAM transformation increased the predictive power (F1 score) of inferred ecological networks on average and improved the ability of network inference methods to capture important features of network structure. This study underscores the importance of considering temporal features when carrying out network analyses and describes a simple, effective tool that can be used to improve results.
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Affiliation(s)
- Samantha J Gleich
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, AHF, Los Angeles, CA, 90089-0371, USA.
| | - Jacob A Cram
- Horn Point Laboratory, University of Maryland Center for Environmental Science, 2020 Horns Point Road, Cambridge, MD, 21613, USA
| | - J L Weissman
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, AHF, Los Angeles, CA, 90089-0371, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, AHF, Los Angeles, CA, 90089-0371, USA
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40
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Lian J, Steinert G, de Vree J, Meijer S, Heryanto C, Bosma R, Wijffels RH, Barbosa MJ, Smidt H, Sipkema D. Bacterial diversity in different outdoor pilot plant photobioreactor types during production of the microalga Nannochloropsis sp. CCAP211/78. Appl Microbiol Biotechnol 2022; 106:2235-2248. [PMID: 35166894 PMCID: PMC8930801 DOI: 10.1007/s00253-022-11815-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 12/22/2021] [Accepted: 01/29/2022] [Indexed: 11/25/2022]
Abstract
As large-scale outdoor production cannot be done in complete containment, cultures are (more) open for bacteria, which may affect the productivity and stability of the algae production process. We investigated the bacterial diversity in two indoor reactors and four pilot-scale outdoor reactors for the production of Nannochloropsis sp. CCAP211/78 spanning four months of operation from July to October. Illumina sequencing of 16S rRNA gene amplicons demonstrated that a wide variety of bacteria were present in all reactor types, with predominance of Bacteroidetes and Alphaproteobacteria. Bacterial communities were significantly different between all reactor types (except between the horizontal tubular reactor and the vertical tubular reactor) and also between runs in each reactor. Bacteria common to the majority of samples included one member of the Saprospiraceae family and one of the NS11-12_marine group (both Bacteroidetes). Hierarchical clustering analysis revealed two phases during the cultivation period separated by a major shift in bacterial community composition in the horizontal tubular reactor, the vertical tubular reactor and the raceway pond with a strong decrease of the Saprospiraceae and NS11-12_marine group that initially dominated the bacterial communities. Furthermore, we observed a less consistent pattern of bacterial taxa appearing in different reactors and runs, most of which belonging to the classes Deltaproteobacteria and Flavobacteriia. In addition, canonical correspondence analysis showed that the bacterial community composition was significantly correlated with the nitrate concentration. This study contributes to our understanding of bacterial diversity and composition in different types of outdoor reactors exposed to a range of dynamic biotic and abiotic factors. Key points • Reactor types had significantly different bacterial communities except HT and VT • The inoculum source and physiochemical factors together affect bacterial community • The bacterial family Saprospiraceae is positively correlated to microalgal growth.
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Affiliation(s)
- Jie Lian
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jeroen de Vree
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Sven Meijer
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Christa Heryanto
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Rouke Bosma
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - René H Wijffels
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, N8049, Bodø, Norway
| | - Maria J Barbosa
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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41
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Cordone A, D’Errico G, Magliulo M, Bolinesi F, Selci M, Basili M, de Marco R, Saggiomo M, Rivaro P, Giovannelli D, Mangoni O. Bacterioplankton Diversity and Distribution in Relation to Phytoplankton Community Structure in the Ross Sea Surface Waters. Front Microbiol 2022; 13:722900. [PMID: 35154048 PMCID: PMC8828583 DOI: 10.3389/fmicb.2022.722900] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/05/2022] [Indexed: 01/04/2023] Open
Abstract
Primary productivity in the Ross Sea region is characterized by intense phytoplankton blooms whose temporal and spatial distribution are driven by changes in environmental conditions as well as interactions with the bacterioplankton community. However, the number of studies reporting the simultaneous diversity of the phytoplankton and bacterioplankton in Antarctic waters are limited. Here, we report data on the bacterial diversity in relation to phytoplankton community structure in the surface waters of the Ross Sea during the Austral summer 2017. Our results show partially overlapping bacterioplankton communities between the stations located in the Terra Nova Bay (TNB) coastal waters and the Ross Sea Open Waters (RSOWs), with a dominance of members belonging to the bacterial phyla Bacteroidetes and Proteobacteria. In the TNB coastal area, microbial communities were characterized by a higher abundance of sequences related to heterotrophic bacterial genera such as Polaribacter spp., together with higher phytoplankton biomass and higher relative abundance of diatoms. On the contrary, the phytoplankton biomass in the RSOW were lower, with relatively higher contribution of haptophytes and a higher abundance of sequences related to oligotrophic and mixothrophic bacterial groups like the Oligotrophic Marine Gammaproteobacteria (OMG) group and SAR11. We show that the rate of diversity change between the two locations is influenced by both abiotic (salinity and the nitrogen to phosphorus ratio) and biotic (phytoplankton community structure) factors. Our data provide new insight into the coexistence of the bacterioplankton and phytoplankton in Antarctic waters, suggesting that specific rather than random interaction contribute to the organic matter cycling in the Southern Ocean.
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Affiliation(s)
- Angelina Cordone
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Giuseppe D’Errico
- Department of Life Sciences, DISVA, Polytechnic University of Marche, Ancona, Italy
| | - Maria Magliulo
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Francesco Bolinesi
- Department of Biology, University of Naples Federico II, Naples, Italy
- *Correspondence: Francesco Bolinesi,
| | - Matteo Selci
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Marco Basili
- National Research Council, Institute of Marine Biological Resources and Biotechnologies CNR-IRBIM, Ancona, Italy
| | - Rocco de Marco
- National Research Council, Institute of Marine Biological Resources and Biotechnologies CNR-IRBIM, Ancona, Italy
| | | | - Paola Rivaro
- Department of Chemistry and Industrial Chemistry, University of Genoa, Genoa, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples Federico II, Naples, Italy
- Department of Life Sciences, DISVA, Polytechnic University of Marche, Ancona, Italy
- National Research Council, Institute of Marine Biological Resources and Biotechnologies CNR-IRBIM, Ancona, Italy
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Donato Giovannelli,
| | - Olga Mangoni
- Department of Biology, University of Naples Federico II, Naples, Italy
- Consorzio Nazionale Interuniversitario delle Scienze del Mare (CoNISMa), Rome, Italy
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42
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Complex marine microbial communities partition metabolism of scarce resources over the diel cycle. Nat Ecol Evol 2022; 6:218-229. [DOI: 10.1038/s41559-021-01606-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/01/2021] [Indexed: 12/20/2022]
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43
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Wang H, Chen F, Zhang C, Wang M, Kan J. Estuarine gradients dictate spatiotemporal variations of microbiome networks in the Chesapeake Bay. ENVIRONMENTAL MICROBIOME 2021; 16:22. [PMID: 34838139 PMCID: PMC8627074 DOI: 10.1186/s40793-021-00392-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/10/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Annually reoccurring microbial populations with strong spatial and temporal variations have been identified in estuarine environments, especially in those with long residence time such as the Chesapeake Bay (CB). However, it is unclear how microbial taxa cooccurr and how the inter-taxa networks respond to the strong environmental gradients in the estuaries. RESULTS Here, we constructed co-occurrence networks on prokaryotic microbial communities in the CB, which included seasonal samples from seven spatial stations along the salinity gradients for three consecutive years. Our results showed that spatiotemporal variations of planktonic microbiomes promoted differentiations of the characteristics and stability of prokaryotic microbial networks in the CB estuary. Prokaryotic microbial networks exhibited a clear seasonal pattern where microbes were more closely connected during warm season compared to the associations during cold season. In addition, microbial networks were more stable in the lower Bay (ocean side) than those in the upper Bay (freshwater side). Multivariate regression tree (MRT) analysis and piecewise structural equation modeling (SEM) indicated that temperature, salinity and total suspended substances along with nutrient availability, particulate carbon and Chl a, affected the distribution and co-occurrence of microbial groups, such as Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia. Interestingly, compared to the abundant groups (such as SAR11, Saprospiraceae and Actinomarinaceae), the rare taxa including OM60 (NOR5) clade (Gammaproteobacteria), Micrococcales (Actinobacteria), and NS11-12 marine group (Bacteroidetes) contributed greatly to the stability of microbial co-occurrence in the Bay. Modularity and cluster structures of microbial networks varied spatiotemporally, which provided valuable insights into the 'small world' (a group of more interconnected species), network stability, and habitat partitioning/preferences. CONCLUSION Our results shed light on how estuarine gradients alter the spatiotemporal variations of prokaryotic microbial networks in the estuarine ecosystem, as well as their adaptability to environmental disturbances and co-occurrence network complexity and stability.
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Affiliation(s)
- Hualong Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, People's Republic of China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Min Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jinjun Kan
- Microbiology Division, Stroud Water Research Center, Avondale, PA, USA.
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, People's Republic of China.
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Sun FL, Wang YS, Wu ML, Sun CC, Jiang ZY, Cheng H, Fei J. Bacterial community variations in the South China Sea driven by different chemical conditions. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1808-1815. [PMID: 34269924 DOI: 10.1007/s10646-021-02455-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
In this study, Illumina MiSeq sequencing of the 16 S rRNA gene was used to describe the bacterial communities in the South China Sea (SCS) during the southwest monsoon period. We targeted different regions in the SCS and showed that bacterial community was driven by the effects of the river, upwelling, and mesoscale eddy through changing the environmental factors (salinity, temperature, and nutrients). Distinct bacterial communities were observed among different chemical conditions, especially between the estuary and the open sea. The abundance of Burkholderiales, Frankiales, Flavobacteriales, and Rhodobacterales dominated the estuary and its adjacent waters. Bacteria in cyclonic eddy were dominated by Methylophilales and Pseudomonadales, whereas Prochlorococcus, SAR11 clade, and Oceanospirillales had relatively high abundance in the anticyclonic eddy. Overall, the abundance of specific phylotypes significantly varied among samples with different chemical conditions. Chemical conditions probably act as a driver that shapes and controls the diversity of bacteria in the SCS. This study suggests that the interaction between microbial and environmental conditions needs to be further considered to fully understand the diversity and function of marine microbes.
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Affiliation(s)
- Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, 518121, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, 518121, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Mei-Lin Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, 518121, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Zhao-Yu Jiang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Jiao Fei
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
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45
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Traving SJ, Kellogg CTE, Ross T, McLaughlin R, Kieft B, Ho GY, Peña A, Krzywinski M, Robert M, Hallam SJ. Prokaryotic responses to a warm temperature anomaly in northeast subarctic Pacific waters. Commun Biol 2021; 4:1217. [PMID: 34686760 PMCID: PMC8536700 DOI: 10.1038/s42003-021-02731-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 09/23/2021] [Indexed: 11/23/2022] Open
Abstract
Recent studies on marine heat waves describe water temperature anomalies causing changes in food web structure, bloom dynamics, biodiversity loss, and increased plant and animal mortality. However, little information is available on how water temperature anomalies impact prokaryotes (bacteria and archaea) inhabiting ocean waters. This is a nontrivial omission given their integral roles in driving major biogeochemical fluxes that influence ocean productivity and the climate system. Here we present a time-resolved study on the impact of a large-scale warm water surface anomaly in the northeast subarctic Pacific Ocean, colloquially known as the Blob, on prokaryotic community compositions. Multivariate statistical analyses identified significant depth- and season-dependent trends that were accentuated during the Blob. Moreover, network and indicator analyses identified shifts in specific prokaryotic assemblages from typically particle-associated before the Blob to taxa considered free-living and chemoautotrophic during the Blob, with potential implications for primary production and organic carbon conversion and export.
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Affiliation(s)
- Sachia J Traving
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- HADAL and Nordcee, Department of Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | | | - Tetjana Ross
- Institute of Ocean Sciences, Fisheries and Ocean Canada, Sidney, BC, Canada
| | - Ryan McLaughlin
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Brandon Kieft
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Grace Y Ho
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Angelica Peña
- Institute of Ocean Sciences, Fisheries and Ocean Canada, Sidney, BC, Canada
| | - Martin Krzywinski
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Marie Robert
- Institute of Ocean Sciences, Fisheries and Ocean Canada, Sidney, BC, Canada
| | - Steven J Hallam
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Genome Science and Technology Program, University of British Columbia, 2329 West Mall, Vancouver, BC, V6T 1Z4, Canada.
- Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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Kobiyama A, Rashid J, Reza MS, Ikeda Y, Yamada Y, Kudo T, Mizusawa N, Yanagisawa S, Ikeda D, Sato S, Ogata T, Ikeo K, Kaga S, Watanabe S, Naiki K, Kaga Y, Segawa S, Tada Y, Musashi T, Mineta K, Gojobori T, Watabe S. Seasonal and annual changes in the microbial communities of Ofunato Bay, Japan, based on metagenomics. Sci Rep 2021; 11:17277. [PMID: 34446773 PMCID: PMC8390468 DOI: 10.1038/s41598-021-96641-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023] Open
Abstract
Five years of datasets from 2015 to 2019 of whole genome shotgun sequencing for cells trapped on 0.2-µm filters of seawater collected monthly from Ofunato Bay, an enclosed bay in Japan, were analysed, which included the 2015 data that we had reported previously. Nucleotide sequences were determined for extracted DNA from three locations for both the upper (1 m) and deeper (8 or 10 m) depths. The biotic communities analysed at the domain level comprised bacteria, eukaryotes, archaea and viruses. The relative abundance of bacteria was over 60% in most months for the five years. The relative abundance of the SAR86 cluster was highest in the bacterial group, followed by Candidatus Pelagibacter and Planktomarina. The relative abundance of Ca. Pelagibacter showed no relationship with environmental factors, and those of SAR86 and Planktomarina showed positive correlations with salinity and dissolved oxygen, respectively. The bacterial community diversity showed seasonal changes, with high diversity around September and low diversity around January for all five years. Nonmetric multidimensional scaling analysis also revealed that the bacterial communities in the bay were grouped in a season-dependent manner and linked with environmental variables such as seawater temperature, salinity and dissolved oxygen.
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Affiliation(s)
- Atsushi Kobiyama
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Jonaira Rashid
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
- Bangladesh Fisheries Research Institute, Freshwater Station, Mymensingh, 2201, Bangladesh
| | - Md Shaheed Reza
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
- Department of Fisheries Technology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Yuri Ikeda
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Yuichiro Yamada
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Toshiaki Kudo
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Nanami Mizusawa
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Saki Yanagisawa
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Daisuke Ikeda
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Shigeru Sato
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Takehiko Ogata
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Kazuho Ikeo
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
- National Institute of Genetics, Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Shinnosuke Kaga
- Iwate Fisheries Technology Center, Kamaishi, Iwate, 026-0001, Japan
| | - Shiho Watanabe
- Iwate Fisheries Technology Center, Kamaishi, Iwate, 026-0001, Japan
| | - Kimiaki Naiki
- Iwate Inland Fisheries Technology Center, Hachimantai, Iwate, 028-7302, Japan
| | - Yoshimasa Kaga
- Iwate Inland Fisheries Technology Center, Hachimantai, Iwate, 028-7302, Japan
| | - Satoshi Segawa
- Iwate Fisheries Technology Center, Kamaishi, Iwate, 026-0001, Japan
| | - Yumiko Tada
- Iwate Fisheries Technology Center, Kamaishi, Iwate, 026-0001, Japan
| | - Tatsuya Musashi
- Iwate Fisheries Technology Center, Kamaishi, Iwate, 026-0001, Japan
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
| | - Shugo Watabe
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan.
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Vignier J, Laroche O, Rolton A, Wadsworth P, Kumanan K, Trochel B, Pochon X, King N. Dietary Exposure of Pacific Oyster ( Crassostrea gigas) Larvae to Compromised Microalgae Results in Impaired Fitness and Microbiome Shift. Front Microbiol 2021; 12:706214. [PMID: 34504478 PMCID: PMC8421776 DOI: 10.3389/fmicb.2021.706214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/22/2021] [Indexed: 01/04/2023] Open
Abstract
The Pacific oyster Crassostrea gigas is the world's most cultivated oyster and seed supply is heavily reliant on hatchery production where recurring mass mortality events are a major constraint. Outbreaks of bacterial infection via microalgal feed are frequently implicated in these mortalities. This study assessed the effects of feeding compromised microalgae to developing oyster larvae. Intentionally 'stressed' (high pH) or non-stressed microalgae were fed to 11 day-old oyster larvae at two feeding rations for 96 h, followed by a recovery period. Biological endpoints of larval performance were measured following the 96 h exposure and subsequent recovery. Bacterial communities associated with the microalgae feed, rearing seawater, and the oyster larvae, were characterized and correlated with effects on oyster fitness parameters. Feeding stressed algae to oyster larvae for 96 h increased the occurrence of deformities (>70% vs. 20% in control), reduced feeding and swimming ability, and slowed development. Following the recovery period, fewer larvae reached pediveliger stage (2.7% vs. 36% in control) and became spat (1.5% vs. 6.6% in control). The quantity of stressed algae supplied to oyster larvae also influenced overall larval performance, with high feeding rations generally causing greater impairment than low rations. Bacterial profiling using 16S rRNA showed that most bacterial families characterized in larval tissue were also present in larval rearing seawater and in the microalgae feed (98%). The rearing seawater showed the highest bacterial richness compared to the larval and the microalgal compartments, regardless of feeding regime. In larval tissue, bacterial richness was highest in stressed and high-feed treatments, and negatively correlated with larval fitness parameters. These results suggest significant dysbiosis induced by compromised feed and/or increased feed ration. Several bacterial genera (e.g., Halomonas, Marinomonas) were strongly associated with impaired larval performance while the presence of genera in larvae including Vibrio was closely associated with overfeeding. Our research demonstrated that metabarcoding can be effectively used to identify microbiota features associated with larval fitness.
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Affiliation(s)
- Julien Vignier
- Aquaculture Group, Cawthron Institute, Nelson, New Zealand
| | - Olivier Laroche
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Anne Rolton
- Aquaculture Group, Cawthron Institute, Nelson, New Zealand
| | | | | | - Branwen Trochel
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, The University of Auckland, Warkworth, New Zealand
| | - Nick King
- Aquaculture Group, Cawthron Institute, Nelson, New Zealand
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48
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Zimmer-Faust AG, Steele JA, Xiong X, Staley C, Griffith M, Sadowsky MJ, Diaz M, Griffith JF. A Combined Digital PCR and Next Generation DNA-Sequencing Based Approach for Tracking Nearshore Pollutant Dynamics Along the Southwest United States/Mexico Border. Front Microbiol 2021; 12:674214. [PMID: 34421839 PMCID: PMC8377738 DOI: 10.3389/fmicb.2021.674214] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/25/2021] [Indexed: 12/27/2022] Open
Abstract
Ocean currents, multiple fecal bacteria input sources, and jurisdictional boundaries can complicate pollution source tracking and associated mitigation and management efforts within the nearshore coastal environment. In this study, multiple microbial source tracking tools were employed to characterize the impact and reach of an ocean wastewater treatment facility discharge in Mexico northward along the coast and across the Southwest United States- Mexico Border. Water samples were evaluated for fecal indicator bacteria (FIB), Enterococcus by culture-based methods, and human-associated genetic marker (HF183) and Enterococcus by droplet digital polymerase chain reaction (ddPCR). In addition, 16S rRNA gene sequence analysis was performed and the SourceTracker algorithm was used to characterize the bacterial community of the wastewater treatment plume and its contribution to beach waters. Sampling dates were chosen based on ocean conditions associated with northern currents. Evidence of a gradient in human fecal pollution that extended north from the wastewater discharge across the United States/Mexico border from the point source was observed using human-associated genetic markers and microbial community analysis. The spatial extent of fecal contamination observed was largely dependent on swell and ocean conditions. These findings demonstrate the utility of a combination of molecular tools for understanding and tracking specific pollutant sources in dynamic coastal water environments.
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Affiliation(s)
- Amity G Zimmer-Faust
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States
| | - Xianyi Xiong
- BioTechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Christopher Staley
- BioTechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Madison Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States
| | - Michael J Sadowsky
- Department of Soil, Water, and Climate, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Margarita Diaz
- Proyecto Fronterizo de Educación Ambiental, A.C., Tijuana, Mexico
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA, United States
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49
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Yan L, Hermans SM, Totsche KU, Lehmann R, Herrmann M, Küsel K. Groundwater bacterial communities evolve over time in response to recharge. WATER RESEARCH 2021; 201:117290. [PMID: 34130083 DOI: 10.1016/j.watres.2021.117290] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Time series analyses are a crucial tool for uncovering the patterns and processes shaping microbial communities and their functions, especially in aquatic ecosystems. Subsurface aquatic environments are perceived to be more stable than surface oceans and lakes, due to the lack of sunlight, the absence of photosysnthetically-driven primary production, low temperature variations, and oligotrophic conditions. However, periodic groundwater recharge should affect the structure and succession of groundwater microbiomes. To disentangle the long-term temporal changes in bacterial communities of shallow fractured bedrock groundwater, and identify the drivers of the observed patterns, we analysed bacterial 16S rRNA gene sequencing data for samples collected monthly from three groundwater wells over a six-year period (n = 230) along a hillslope recharge area. We showed that the bacterial communities in the groundwater of limestone-mudstone alternations were not stable over time and exhibited non-linear dissimilarity patterns which corresponded to periods of groundwater recharge. Further, we observed an increase in dissimilarity over time (generalized additive model P < 0.001) indicating that the successive recharge events result in communities that are increasingly more dissimilar to the initial reference time point. The sampling period was able to explain up to 29.5% of the variability in bacterial community composition and the impact of recharge events on the groundwater microbiome was linked to the strength of the recharge and local environmental selection. Many groundwater bacteria originated from the recharge-related sources (mean = 66.5%, SD = 15.1%) and specific bacterial taxa were identified as being either enriched or repressed during recharge events. Overall, similar to surface aquatic environments, the microbiomes in shallow fractured-rock groundwater vary through time, though we revealed groundwater recharges as unique driving factors for these patterns. The high temporal resolution employed here highlights the dynamics of bacterial communities in groundwater, which is an essential resource for the provision of clean drinking water; understanding the biological complexities of these systems is therefore crucial.
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Affiliation(s)
- Lijuan Yan
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany
| | - Syrie M Hermans
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany
| | - Kai Uwe Totsche
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Germany
| | - Robert Lehmann
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Germany
| | - Martina Herrmann
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany.
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50
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Sun C, Zhang B, Ning D, Zhang Y, Dai T, Wu L, Li T, Liu W, Zhou J, Wen X. Seasonal dynamics of the microbial community in two full-scale wastewater treatment plants: Diversity, composition, phylogenetic group based assembly and co-occurrence pattern. WATER RESEARCH 2021; 200:117295. [PMID: 34091223 DOI: 10.1016/j.watres.2021.117295] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
The optimal operation and functional stability of a wastewater treatment plant (WWTP) strongly depend on the properties of its microbial community. However, a knowledge gap remains regarding the seasonal dynamics of microbial community properties, especially phylogenetic group based assembly and co-occurrence patterns. Accordingly, in this study, influent and activated sludge (AS) samples were weekly collected from 2 full-scale WWTPs for one year (89 influent and 103 AS samples in total) and examined by high-throughput Illumina-MiSeq sequencing. The results suggested that the microbial community diversity and composition in the influent fluctuated substantially with season, while those in the AS had a relatively more stable pattern throughout the year. The phylogenetic group based assembly mechanisms of AS community were identified by using "Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP)". The results showed that drift accounted for the largest proportion (52.8%), while homogeneous selection (18.2%) was the most important deterministic process. Deterministic processes dominated in 47 microbial groups (bins), which were also found (~40%) in the AS core taxa dataset. Moreover, the results suggested that Nitrospira were more susceptible to stochastic processes in winter, which may provide a possible explanation for nitrification failure in winter. Network analysis results suggested that the network structure of the AS community could be more stable in summer and autumn. In addition, there were no identical keystone taxa found in different networks (constructed from different plants, sources, and seasons), which supported the context dependency theory. The results of this study deepened our understanding of the microbial ecology in AS systems and provided a foundation for further studies on the community regulation strategy of WWTPs.
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Affiliation(s)
- Chenxiang Sun
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China; Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA
| | - Bing Zhang
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Daliang Ning
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA
| | - Ya Zhang
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA
| | - Tianjiao Dai
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Linwei Wu
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA
| | - Tianle Li
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Wei Liu
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jizhong Zhou
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China; Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xianghua Wen
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China.
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