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Jing M, Yang W, Rao L, Chen J, Ding X, Zhou Y, Zhang Q, Lu K, Zhu J. Mechanisms of microbial coexistence in a patchy ecosystem: Differences in ecological niche overlap and species fitness between rhythmic and non-rhythmic species. WATER RESEARCH 2024; 256:121626. [PMID: 38642534 DOI: 10.1016/j.watres.2024.121626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/28/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
Resource patchiness caused by external events breaks the continuity and homogeneity of resource distribution in the original ecosystem. For local organisms, this leads to drastic changes in the availability of resources, breaks down the co-existence of species, and reshuffles the local ecosystem. West Lake is a freshwater lake with resource patchiness caused by multiple exogenous disturbances that has strong environmental heterogeneity that prevents clear observation of seasonal changes in the microbial communities. Despite this, the emergence of rhythmic species in response to irregular changes in the environment has been helpful for observing microbial communities dynamics in patchy ecosystems. We investigated the ecological mechanisms of seasonal changes in microbial communities in West Lake by screening rhythmic species based on the ecological niche and modern coexistence theories. The results showed that rhythmic species were the dominant factors in microbial community changes and the effects of most environmental factors on the microbial community were indirectly realised through the rhythmic species. Random forest analyses showed that seasonal changes in the microbial community were similarly predicted by the rhythmic species. In addition, we incorporated species interactions and community phylogenetic patterns into stepwise multiple regression analyses, the results of which indicate that ecological niches and species fitness may drive the coexistence of these subcommunities. Thus, this study extends our understanding of seasonal changes in microbial communities and provides new ways for observing seasonal changes in microbial communities, especially in ecosystems with resource patches. Our study also show that combining community phylogenies with co-occurrence networks based on ecological niches and modern coexistence theory can further help us understand the ecological mechanisms of interspecies coexistence.
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Affiliation(s)
- MingFei Jing
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Wen Yang
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Lihua Rao
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Jun Chen
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Xiuying Ding
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Yinying Zhou
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Quanxiang Zhang
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Kaihong Lu
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Jinyong Zhu
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China.
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Fournier C, Fiedler A, Weidele M, Kautz H, Schleheck D. Description of a 'plankton filtration bias' in sequencing-based bacterial community analysis and of an Arduino microcontroller-based flowmeter device that can help to resolve it. PLoS One 2024; 19:e0303937. [PMID: 38805423 PMCID: PMC11132488 DOI: 10.1371/journal.pone.0303937] [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: 07/18/2023] [Accepted: 05/03/2024] [Indexed: 05/30/2024] Open
Abstract
Diversity studies of aquatic picoplankton (bacterioplankton) communities using size-class filtration, DNA extraction, PCR and sequencing of phylogenetic markers, require a robust methodological pipeline, since biases have been demonstrated essentially at all levels, including DNA extraction, primer choice and PCR. Even different filtration volumes of the same plankton sample and, thus, different biomass loading of the filters, can distort the sequencing results. In this study, we designed an Arduino microcontroller-based flowmeter that records the decrease of initial (maximal) flowrate as proxy for increasing biomass loading and clogging of filters during plankton filtration. The device was tested using freshwater plankton of Lake Constance, and total DNA was extracted and an 16S rDNA amplicon was sequenced. We confirmed that different filtration volumes used for the same water sample affect the sequencing results. Differences were visible in alpha and beta diversities and across all taxonomic ranks. Taxa most affected were typical freshwater Actinobacteria and Bacteroidetes, increasing up to 38% and decreasing up to 29% in relative abundance, respectively. In another experiment, a lake water sample was filtered undiluted and three-fold diluted, and each filtration was stopped once the flowrate had reduced to 50% of initial flowrate, hence, at the same degree of filter clogging. The three-fold diluted sample required three-fold filtration volumes, while equivalent amounts of total DNA were extracted and differences across all taxonomic ranks were not statistically significant compared to the undiluted controls. In conclusion, this work confirms a volume/biomass-dependent bacterioplankton filtration bias for sequencing-based community analyses and provides an improved procedure for controlling biomass loading during filtrations and recovery of equivalent amounts of DNA from samples independent of the plankton density. The application of the device can also avoid the distorting of sequencing results as caused by the plankton filtration bias.
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Affiliation(s)
- Corentin Fournier
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Alexander Fiedler
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Maximilian Weidele
- Scientific Engineering and Manufacturing Services, University of Konstanz, Konstanz, Germany
| | - Harald Kautz
- Scientific Engineering and Manufacturing Services, University of Konstanz, Konstanz, Germany
| | - David Schleheck
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
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3
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Logares R. Decoding populations in the ocean microbiome. MICROBIOME 2024; 12:67. [PMID: 38561814 PMCID: PMC10983722 DOI: 10.1186/s40168-024-01778-0] [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: 09/27/2023] [Accepted: 02/12/2024] [Indexed: 04/04/2024]
Abstract
Understanding the characteristics and structure of populations is fundamental to comprehending ecosystem processes and evolutionary adaptations. While the study of animal and plant populations has spanned a few centuries, microbial populations have been under scientific scrutiny for a considerably shorter period. In the ocean, analyzing the genetic composition of microbial populations and their adaptations to multiple niches can yield important insights into ecosystem function and the microbiome's response to global change. However, microbial populations have remained elusive to the scientific community due to the challenges associated with isolating microorganisms in the laboratory. Today, advancements in large-scale metagenomics and metatranscriptomics facilitate the investigation of populations from many uncultured microbial species directly from their habitats. The knowledge acquired thus far reveals substantial genetic diversity among various microbial species, showcasing distinct patterns of population differentiation and adaptations, and highlighting the significant role of selection in structuring populations. In the coming years, population genomics is expected to significantly increase our understanding of the architecture and functioning of the ocean microbiome, providing insights into its vulnerability or resilience in the face of ongoing global change. Video Abstract.
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Affiliation(s)
- Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Catalonia, 08003, Spain.
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Wang T, Liu R, Huang G, Tian X, Zhang Y, He M, Wang C. Assembly dynamics of eukaryotic plankton and bacterioplankton in the Yangtze River estuary: A hybrid community perspective. MARINE ENVIRONMENTAL RESEARCH 2024; 196:106414. [PMID: 38394975 DOI: 10.1016/j.marenvres.2024.106414] [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: 10/30/2023] [Revised: 02/09/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024]
Abstract
Estuaries, acting as transitional habitats receiving species introductions from both freshwater and marine sources, undergo significant impacts from global climate changes. Planktonic microorganisms contribute significantly to estuarine biodiversity and ecological stability. These microorganisms primarily fall into three groups: eukaryotic plankton, particle-associated bacteria, and free-living bacteria. Understanding the structural characteristics and interactions within these subcommunities is crucial for comprehending estuarine dynamics. We collected samples from three distinct locations (< 0.1 PSU, 6.6 PSU, and 19 PSU) within the Yangtze River estuary. Samples underwent analysis for physicochemical indicators, while microbial communities were subjected to 16S/18S rRNA amplicon sequencing. Additionally, simulated mixing experiments were conducted using samples of varying salinities. Estuary samples, combined with simulated experiments, were employed to collectively examine the structural characteristics and assembly processes of estuarine microbes. Our research highlights the considerable impact of phylogenetic classification on prokaryotic behavior in these communities. We observed a transition in assembly processes from primarily stochastic for particle-associated bacteria to a predominant influence of homogeneous selection as salinity increased. Particle-associated bacterial communities exhibited a greater influence of stochastic processes compared to free-living bacteria, showcasing higher stability in diversity. The variations in composition and structure of estuarine microbial subcommunities were influenced by diverse environmental factors. Particle-associated bacteria displayed elevated network characterization values and established closer interactions with eukaryotic plankton. Structural equation modeling (SEM) analysis revealed that free-living bacteria displayed a heightened sensitivity to environmental factors and exerted a more significant influence on assembly processes and network characteristics. Simulated mixing in these environments resulted in the loss of species with similar microbial taxonomic relationships. The functioning of bacterioplankton is influenced by salinity and the processes governing their assembly, particularly in relation to different living states. These findings significantly contribute to our understanding of the intricate interplay between prokaryotic and eukaryotic plankton microorganisms in highly dynamic environments, laying a robust foundation for further exploration into the ecological mechanisms governing microbial dynamics in estuaries.
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Affiliation(s)
- Tong Wang
- Jiangsu Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruiqing Liu
- Jiangsu Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guolin Huang
- Jiangsu Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin Tian
- Jiangsu Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yaru Zhang
- Jiangsu Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Meilin He
- Jiangsu Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Changhai Wang
- Jiangsu Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China; Co-Innovation Center for Jiangsu Marine Bio-Industry Technology, Lianyungang, 222005, China
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Pan F, Yu X, Chen M, Liang Y. Vegetation recovery reshapes the composition and enhances the network connectivity of phoD-harboring microorganisms to promote P availability in a karst ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170561. [PMID: 38309358 DOI: 10.1016/j.scitotenv.2024.170561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/14/2024] [Accepted: 01/28/2024] [Indexed: 02/05/2024]
Abstract
Soil phoD-harboring microorganisms can facilitate phosphorus (P) transformation and increase the available P (AP) in P-limited soils; however, the mechanism by which these microorganisms enhance AP throughout the vegetation recovery process of karst ecosystems is poorly understood. Accordingly, this study investigates the effect of vegetation recovery on soil AP and the community composition and network connectivity of phoD-harboring microorganisms to elucidate the mechanism by which phoD-harboring microorganisms enhance soil AP in the four vegetation recovery stages (i.e., grassland, shrubland, shrub-arbor forest, and arbor forest) in a karst ecosystem. Results show that soil total P, AP, and microbial biomass P concentrations, as well as alkaline phosphatase activities, litter and soil nutrients, and plant diversity indices (Shannon-Wiener and Pielou) increase with advancing vegetation recovery. Moreover, the diversity indices (Shannon-Wiener and Simpson) and network complexity of the phoD-harboring microorganisms also increase with advancing vegetation recovery, leading to distinct communities among the four recovery stages. Rhizobiales, Pseudomonadales, and Burkholderiales comprise the dominant phoD-harboring microorganism orders. The relative abundances of Pseudomonadales and Burkholderiales increase with advancing vegetation recovery; Rhizobiales is the highest in shrubland and the lowest in grassland. The structural equation model results show that advanced vegetation recovery is associated with increased plant diversity, litter nutrients, and soil nutrients. The network connectivity is enhanced with advancing vegetation recovery accompanied by increasing soil phosphatase activity and P availability. These results suggest that regulating the phoD-harboring microorganism composition and network connectivity is essential to alleviate plant P limitation in karst ecosystems.
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Affiliation(s)
- Fujing Pan
- College of Environmental and Engineering, Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, Guilin University of Technology, Guilin 541004, China
| | - Xuan Yu
- College of Environmental and Engineering, Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, Guilin University of Technology, Guilin 541004, China
| | - Min Chen
- College of Environmental and Engineering, Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, Guilin University of Technology, Guilin 541004, China
| | - Yueming Liang
- Karst Dynamics Laboratory, Ministry of natural Resources & Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China.
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Shen S, Tominaga K, Tsuchiya K, Matsuda T, Yoshida T, Shimizu Y. Virus-prokaryote infection pairs associated with prokaryotic production in a freshwater lake. mSystems 2024; 9:e0090623. [PMID: 38193708 PMCID: PMC10878036 DOI: 10.1128/msystems.00906-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/06/2023] [Indexed: 01/10/2024] Open
Abstract
Viruses infect and kill prokaryotic populations in a density- or frequency-dependent manner and affect carbon cycling. However, the effects of the stratification transition, including the stratified and de-stratified periods, on the changes in prokaryotic and viral communities and their interactions remain unclear. We conducted a monthly survey of the surface and deep layers of a large and deep freshwater lake (Lake Biwa, Japan) for a year and analyzed the prokaryotic production and prokaryotic and viral community composition. Our analysis revealed that, in the surface layer, 19 prokaryotic species, accounting for approximately 40% of the total prokaryotic abundance, could potentially contribute to the majority of prokaryotic production, which is the highest during the summer and is suppressed by viruses. This suggests that a small fraction of prokaryotes and phages were the key infection pairs during the peak period of prokaryotic activity in the freshwater lake. We also found that approximately 50% of the dominant prokaryotic and viral species in the deep layer were present throughout the study period. This suggests that the "kill the winner" model could explain the viral impact on prokaryotes in the surface layer, but other dynamics may be at play in the deep layer. Furthermore, we found that annual vertical mixing could result in a similar rate of community change between the surface and deep layers. These findings may be valuable in understanding how communities and the interaction among them change when freshwater lake stratification is affected by global warming in the future.IMPORTANCEViral infection associated with prokaryotic production occurs in a density- or frequency-dependent manner and regulates the prokaryotic community. Stratification transition and annual vertical mixing in freshwater lakes are known to affect the prokaryotic community and the interaction between prokaryotes and viruses. By pairing measurements of virome analysis and prokaryotic production of a 1-year survey of the depths of surface and deep layers, we revealed (i) the prokaryotic infection pairs associated with prokaryotic production and (ii) the reset in prokaryotic and viral communities through annual vertical mixing in a freshwater lake. Our results provide a basis for future work into changes in stratification that may impact the biogeochemical cycling in freshwater lakes.
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Affiliation(s)
- Shang Shen
- Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, Japan
- Lake Biwa Branch Office, National Institute for Environmental Studies, Otsu, Shiga, Japan
- Department of Civil and Environmental Engineering, Ritsumeikan University, Kusatsu, Japan
| | - Kento Tominaga
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kenji Tsuchiya
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Tomonari Matsuda
- Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Yoshihisa Shimizu
- Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, Japan
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7
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Wang FQ, Bartosik D, Sidhu C, Siebers R, Lu DC, Trautwein-Schult A, Becher D, Huettel B, Rick J, Kirstein IV, Wiltshire KH, Schweder T, Fuchs BM, Bengtsson MM, Teeling H, Amann RI. Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides. MICROBIOME 2024; 12:32. [PMID: 38374154 PMCID: PMC10877868 DOI: 10.1186/s40168-024-01757-5] [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: 11/07/2023] [Accepted: 01/04/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND Marine microalgae (phytoplankton) mediate almost half of the worldwide photosynthetic carbon dioxide fixation and therefore play a pivotal role in global carbon cycling, most prominently during massive phytoplankton blooms. Phytoplankton biomass consists of considerable proportions of polysaccharides, substantial parts of which are rapidly remineralized by heterotrophic bacteria. We analyzed the diversity, activity, and functional potential of such polysaccharide-degrading bacteria in different size fractions during a diverse spring phytoplankton bloom at Helgoland Roads (southern North Sea) at high temporal resolution using microscopic, physicochemical, biodiversity, metagenome, and metaproteome analyses. RESULTS Prominent active 0.2-3 µm free-living clades comprised Aurantivirga, "Formosa", Cd. Prosiliicoccus, NS4, NS5, Amylibacter, Planktomarina, SAR11 Ia, SAR92, and SAR86, whereas BD1-7, Stappiaceae, Nitrincolaceae, Methylophagaceae, Sulfitobacter, NS9, Polaribacter, Lentimonas, CL500-3, Algibacter, and Glaciecola dominated 3-10 µm and > 10 µm particles. Particle-attached bacteria were more diverse and exhibited more dynamic adaptive shifts over time in terms of taxonomic composition and repertoires of encoded polysaccharide-targeting enzymes. In total, 305 species-level metagenome-assembled genomes were obtained, including 152 particle-attached bacteria, 100 of which were novel for the sampling site with 76 representing new species. Compared to free-living bacteria, they featured on average larger metagenome-assembled genomes with higher proportions of polysaccharide utilization loci. The latter were predicted to target a broader spectrum of polysaccharide substrates, ranging from readily soluble, simple structured storage polysaccharides (e.g., laminarin, α-glucans) to less soluble, complex structural, or secreted polysaccharides (e.g., xylans, cellulose, pectins). In particular, the potential to target poorly soluble or complex polysaccharides was more widespread among abundant and active particle-attached bacteria. CONCLUSIONS Particle-attached bacteria represented only 1% of all bloom-associated bacteria, yet our data suggest that many abundant active clades played a pivotal gatekeeping role in the solubilization and subsequent degradation of numerous important classes of algal glycans. The high diversity of polysaccharide niches among the most active particle-attached clades therefore is a determining factor for the proportion of algal polysaccharides that can be rapidly remineralized during generally short-lived phytoplankton bloom events. Video Abstract.
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Grants
- AM 73/9-3 Deutsche Forschungsgemeinschaft,Germany
- SCHW 595/10-3 Deutsche Forschungsgemeinschaft,Germany
- TE 813/2-3 Deutsche Forschungsgemeinschaft,Germany
- RI 969/9-2 Deutsche Forschungsgemeinschaft,Germany
- BE 3869/4-3 Deutsche Forschungsgemeinschaft,Germany
- SCHW 595/11-3 Deutsche Forschungsgemeinschaft,Germany
- FU 627/2-3 Deutsche Forschungsgemeinschaft,Germany
- RI 969/9-2 Deutsche Forschungsgemeinschaft,Germany
- TE 813/2-3 Deutsche Forschungsgemeinschaft,Germany
- AM 73/9-3 Deutsche Forschungsgemeinschaft,Germany
- AWI_BAH_o 1 Biological Station Helgoland, Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research
- AWI_BAH_o 1 Biological Station Helgoland, Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research
- Max Planck Institute for Marine Microbiology (2)
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Affiliation(s)
- Feng-Qing Wang
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Daniel Bartosik
- Institute of Pharmacy, University of Greifswald, Felix-Hausdorff-Straße 3, 17489, Greifswald, Germany
- Institute of Marine Biotechnology, Walther-Rathenau-Straße 49a, 17489, Greifswald, Germany
| | - Chandni Sidhu
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Robin Siebers
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - De-Chen Lu
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- Marine College, Shandong University, Weihai, 264209, China
| | - Anke Trautwein-Schult
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Carl von Linné-Weg 10, 50829, Cologne, Germany
| | - Johannes Rick
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, 27483, Germany
| | - Inga V Kirstein
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, 27483, Germany
| | - Karen H Wiltshire
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, 27483, Germany
| | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, Felix-Hausdorff-Straße 3, 17489, Greifswald, Germany
- Institute of Marine Biotechnology, Walther-Rathenau-Straße 49a, 17489, Greifswald, Germany
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Mia M Bengtsson
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany.
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
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Li H, Cai L, Wang L, Wang Y, Xu J, Zhang R. The structure and assembly mechanisms of T4-like cyanophages community in the South China Sea. Microbiol Spectr 2024; 12:e0200223. [PMID: 38193726 PMCID: PMC10846272 DOI: 10.1128/spectrum.02002-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024] Open
Abstract
Marine ecosystems contain an immense diversity of phages, many of which infect cyanobacteria (cyanophage) that are largely responsible for primary productivity. To characterize the genetic diversity and biogeographic distribution of the marine T4-like cyanophage community in the northern South China Sea, the T4-like cyanophage portal protein gene (g20) was amplified. Phylogenetic analysis revealed that marine T4-like cyanophages were highly diverse, with g20 operational taxonomic units being affiliated with five defined clades (Clusters I-V). Cluster II had a wide geographic distribution, Cluster IV was the most abundant in the open sea, and Cluster I was dominant in coastal shelf environments. Our results showed T4-like cyanophages (based on g20) community was generally shaped via heterogeneous selection. Highly variable environmental factors (such as salinity and temperature) can heterogeneously select different cyanophage communities. Nevertheless, the dominant drivers of the T4-like cyanophage community based on the g20 and g23 (T4-like phage major capsid protein gene) were different, probably due to different coverages by the primer sets. Furthermore, the community assembly processes of T4-like cyanophages were affected by host traits (abundance and distribution), viral traits (latent period, burst size, and host range), and environmental properties (temperature and salinity).IMPORTANCECyanophages are abundant and ubiquitous in the oceans, altering population structures and evolution of cyanobacteria, which account for a large portion of global carbon fixation, through host mortality, horizontal gene transfer, and the modulation of host metabolism. However, little is known about the biogeography and ecological drivers that shape the cyanophage community. Here, we use g20 and g23 genes to examine the biogeographic patterns and the assembly mechanisms of T4-like cyanophage community in the northern part of the South China Sea. The different coverages of primer sets might lead to the different dominant drivers of T4-like cyanophage community based on g20 and g23 genes. Our results showed that characteristics of viral traits (latent period, burst size, and host range) and host traits (abundance and distribution) were found to either limit or enhance the biogeographic distribution of T4-like cyanophages. Overall, both virus and host properties are critical to consider when determining rules of community assembly for viruses.
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Affiliation(s)
- Huifang Li
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Long Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Juntian Xu
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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9
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Tominaga K, Takebe H, Murakami C, Tsune A, Okamura T, Ikegami T, Onishi Y, Kamikawa R, Yoshida T. Population-level prokaryotic community structures associated with ferromanganese nodules in the Clarion-Clipperton Zone (Pacific Ocean) revealed by 16S rRNA gene amplicon sequencing. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13224. [PMID: 38146681 PMCID: PMC10866075 DOI: 10.1111/1758-2229.13224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 12/01/2023] [Indexed: 12/27/2023]
Abstract
Although deep-sea ferromanganese nodules are a potential resource for exploitation, their formation mechanisms remain unclear. Several nodule-associated prokaryotic species have been identified by amplicon sequencing of 16S rRNA genes and are assumed to contribute to nodule formation. However, the recent development of amplicon sequence variant (ASV)-level monitoring revealed that closely related prokaryotic populations within an operational taxonomic unit often exhibit distinct ecological properties. Thus, conventional species-level monitoring might have overlooked nodule-specific populations when distinct populations of the same species were present in surrounding environments. Herein, we examined the prokaryotic community diversity of nodules and surrounding environments at the Clarion-Clipperton Zone in Japanese licensed areas by 16S rRNA gene amplicon sequencing with ASV-level resolution for three cruises from 2017 to 2019. Prokaryotic community composition and diversity were distinct by habitat type: nodule, nodule-surface mud, sediment, bottom water and water column. Most ASVs (~80%) were habitat-specific. We identified 178 nodule-associated ASVs and 41 ASVs associated with nodule-surface mud via linear discriminant effect size analysis. Moreover, several ASVs, such as members of SAR324 and Woeseia, were highly specific to nodules. These nodule-specific ASVs are promising targets for future investigation of the nodule formation process.
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Affiliation(s)
- Kento Tominaga
- Graduate School of AgricultureKyoto UniversityKyotoJapan
| | - Hiroaki Takebe
- Graduate School of AgricultureKyoto UniversityKyotoJapan
| | | | - Akira Tsune
- Deep Ocean Resources Development Co., Ltd.TokyoJapan
| | | | | | | | - Ryoma Kamikawa
- Graduate School of AgricultureKyoto UniversityKyotoJapan
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10
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Guider JT, Yoshimura KM, Block KR, Biddle JF, Shah Walter SR. Archaeal blooms and busts in an estuarine time series. Environ Microbiol 2024; 26:e16584. [PMID: 38372423 DOI: 10.1111/1462-2920.16584] [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: 08/11/2023] [Accepted: 01/22/2024] [Indexed: 02/20/2024]
Abstract
Coastal bays, such as Delaware Bay, are highly productive, ecologically important transitions between rivers and the coastal ocean. They offer opportunities to investigate archaeal assemblages across seasons, with the exchange of water masses that occurs with tidal cycles, and in the context of variable organic matter quality. For a year-long estuarine, size-fractionated time series, we used amplicon sequencing, chemical measurements, and qPCR to follow archaeal groups through the seasons. We detected seasonally high abundances of Marine Group II archaea in summer months which correlate with indicators of phytoplankton production, although not phytoplankton biomass. Although previous studies have reported associations between Marine Group II archaea and particles, here they are almost entirely found in very small particles (0.22-0.7 μm), suggesting they are free-living cells. Populations of Nitrososphaeria did not vary with particle size or environmental conditions. Methanogens were significant fractions of archaeal sequences in large particles at low tide during winter months. Contrary to expectations, Nanoarchaeia were found predominantly in the free-living fraction despite the previous observation that they require an association with hosts. These results underscore the utility of time series studies in shallow, tidally mixed estuarine environments that capture variable conditions for understanding the ecology and biogeochemistry of planktic archaea.
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Affiliation(s)
- Justin T Guider
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
| | - Kristin M Yoshimura
- Department of Biology, James Madison University, Harrisonburg, Virginia, USA
| | - Kaleigh R Block
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
| | - Sunita R Shah Walter
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
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11
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Yu XA, McLean C, Hehemann JH, Angeles-Albores D, Wu F, Muszyński A, Corzett CH, Azadi P, Kujawinski EB, Alm EJ, Polz MF. Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics. THE ISME JOURNAL 2024; 18:wrad013. [PMID: 38365244 PMCID: PMC10811730 DOI: 10.1093/ismejo/wrad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 02/18/2024]
Abstract
Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.
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Affiliation(s)
- Xiaoqian Annie Yu
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Division of Microbial Ecology, Department of Microbiology and Ecosystems Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Craig McLean
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
- MIT/WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Jan-Hendrik Hehemann
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - David Angeles-Albores
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Fuqing Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Artur Muszyński
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Christopher H Corzett
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Eric J Alm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, United States
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Martin F Polz
- Division of Microbial Ecology, Department of Microbiology and Ecosystems Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
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12
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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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13
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Xue Y, Chen H, Xiao P, Jin L, Logares R, Yang J. Core taxa drive microeukaryotic community stability of a deep subtropical reservoir after complete mixing. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:769-782. [PMID: 37688478 PMCID: PMC10667671 DOI: 10.1111/1758-2229.13196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/17/2023] [Indexed: 09/11/2023]
Abstract
Microeukaryotes are key for predicting the change of ecosystem processes in the face of a disturbance. However, their vertical responses to multiple interconnected factors caused by water mixing remain unknown. Here, we conducted a 12-month high-frequency study to compare the impacts of mixing disturbances on microeukaryotic community structure and stability over different depths in a stratified reservoir. We demonstrate that core and satellite microeukaryotic compositions and interactions in surface waters were not resistant to water mixing, but significantly recovered. This was because the water temperature rebounded to the pre-mixing level. Core microeukaryotes maintained community stability in surface waters with high recovery capacity after water mixing. In contrast, the changes in water temperature, chlorophyll-a, and nutrients resulted in steep and prolonged variations in the bottom core and satellite microeukaryotic compositions and interactions. Under low environmental fluctuation, the recovery of microbial communities did not affect nutrient cycling in surface waters. Under high environmental fluctuation, core and satellite microeukaryotic compositions in bottom waters were significantly correlated with the multi-nutrient cycling index. Our findings shed light on different mechanisms of plankton community resilience in reservoir ecosystems to a major disturbance over depths, highlighting the role of bottom microeukaryotes in nutrient cycling.
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Affiliation(s)
- Yuanyuan Xue
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Huihuang Chen
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
| | - Peng Xiao
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Lei Jin
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
| | | | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
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14
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Câmara Dos Reis M, Romac S, Le Gall F, Marie D, Frada MJ, Koplovitz G, Cariou T, Henry N, de Vargas C, Jeanthon C. Exploring the phycosphere of Emiliania huxleyi: From bloom dynamics to microbiome assembly experiments. Mol Ecol 2023; 32:6507-6522. [PMID: 36541038 DOI: 10.1111/mec.16829] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 10/11/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Coccolithophores have global ecological and biogeochemical significance as the most important calcifying marine phytoplankton group. The structure and selection of prokaryotic communities associated with the most abundant coccolithophore and bloom-forming species, Emiliania huxleyi, are still poorly known. In this study, we assessed the diversity of bacterial communities associated with an E. huxleyi bloom in the Celtic Sea (Eastern North Atlantic), exposed axenic E. huxleyi cultures to prokaryotic communities derived from bloom and non-bloom conditions, and followed the dynamics of their microbiome composition over one year. Bloom-associated prokaryotic communities were dominated by SAR11, Marine group II Euryarchaeota and Rhodobacterales and contained substantial proportions of known indicators of phytoplankton bloom demises such as Flavobacteriaceae and Pseudoalteromonadaceae. The taxonomic richness of bacteria derived from natural communities associated with axenic E. huxleyi rapidly shifted and then stabilized over time. The succession of microorganisms recruited from the environment was consistently dependent on the composition of the initial bacterioplankton community. Phycosphere-associated communities derived from the E. huxleyi bloom were highly similar to one another, suggesting deterministic processes, whereas cultures from non-bloom conditions show an effect of stochasticity. Overall, this work sheds new light on the importance of the initial inoculum composition in microbiome recruitment and elucidates the temporal dynamics of its composition and long-term stability.
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Affiliation(s)
- Mariana Câmara Dos Reis
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Sarah Romac
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Florence Le Gall
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Dominique Marie
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Miguel J Frada
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
- Department of Ecology, Evolution and Behavior, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gil Koplovitz
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Thierry Cariou
- Sorbonne Université, Centre National de la Recherche Scientifique, FR2424, Station Biologique de Roscoff, Roscoff, France
| | - Nicolas Henry
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Christian Jeanthon
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
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15
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Kling JD, Lee MD, Walworth NG, Webb EA, Coelho JT, Wilburn P, Anderson SI, Zhou Q, Wang C, Phan MD, Fu F, Kremer CT, Litchman E, Rynearson TA, Hutchins DA. Dual thermal ecotypes coexist within a nearly genetically identical population of the unicellular marine cyanobacterium Synechococcus. Proc Natl Acad Sci U S A 2023; 120:e2315701120. [PMID: 37972069 PMCID: PMC10665897 DOI: 10.1073/pnas.2315701120] [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: 09/14/2023] [Accepted: 10/11/2023] [Indexed: 11/19/2023] Open
Abstract
The extent and ecological significance of intraspecific functional diversity within marine microbial populations is still poorly understood, and it remains unclear if such strain-level microdiversity will affect fitness and persistence in a rapidly changing ocean environment. In this study, we cultured 11 sympatric strains of the ubiquitous marine picocyanobacterium Synechococcus isolated from a Narragansett Bay (RI) phytoplankton community thermal selection experiment. Thermal performance curves revealed selection at cool and warm temperatures had subdivided the initial population into thermotypes with pronounced differences in maximum growth temperatures. Curiously, the genomes of all 11 isolates were almost identical (average nucleotide identities of >99.99%, with >99% of the genome aligning) and no differences in gene content or single nucleotide variants were associated with either cool or warm temperature phenotypes. Despite a very high level of genomic similarity, sequenced epigenomes for two strains showed differences in methylation on genes associated with photosynthesis. These corresponded to measured differences in photophysiology, suggesting a potential pathway for future mechanistic research into thermal microdiversity. Our study demonstrates that present-day marine microbial populations can harbor cryptic but environmentally relevant thermotypes which may increase their resilience to future rising temperatures.
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Affiliation(s)
- Joshua D. Kling
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Michael D. Lee
- ZOLL Medical Corporation, Chelmsford, MA01824
- Blue Marble Space Institute of Science, Seattle, WA98154
| | - Nathan G. Walworth
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Eric A. Webb
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Jordan T. Coelho
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Paul Wilburn
- ZOLL Medical Corporation, Chelmsford, MA01824
- Kellogg Biological Station, College of Natural Science, Michigan State University, Hickory Corners, MI49060
| | - Stephanie I. Anderson
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI02882
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Qianqian Zhou
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian361005, China
| | - Chunguang Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian361005, China
| | - Megan D. Phan
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Feixue Fu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
| | - Colin T. Kremer
- Kellogg Biological Station, College of Natural Science, Michigan State University, Hickory Corners, MI49060
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT06269
| | - Elena Litchman
- Kellogg Biological Station, College of Natural Science, Michigan State University, Hickory Corners, MI49060
- Department of Global Ecology, Carnegie Institution, Stanford University, Palo Alto, CA94305
| | - Tatiana A. Rynearson
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI02882
| | - David A. Hutchins
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90007
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16
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Zhang X, Cui L, Liu S, Li J, Wu Y, Ren Y, Huang X. Seasonal dynamics of bacterial community and co-occurrence with eukaryotic phytoplankton in the Pearl River Estuary. MARINE ENVIRONMENTAL RESEARCH 2023; 192:106193. [PMID: 37832281 DOI: 10.1016/j.marenvres.2023.106193] [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: 05/21/2023] [Revised: 08/23/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
In this study, we investigated the taxonomic composition of the bacteria and phytoplankton communities in the Pearl River Estuary (PRE) through Illumina sequencing of the V3-V4 region of the 16 S rRNA gene. Furthermore, their relationships as well as recorded environmental variables were explored by co-occurrence networks. Bacterial community composition was different in two size fractions, as well as along the salinity gradient across two seasons. Free-living (FL) communities were dominated by pico-sized Cyanobacteria (Synechococcus CC9902) while Exiguobacterium, Halomonas and Pseudomonas were predominantly associated with particle-associated (PA) lifestyle, and Cyanobium PCC-6307 exhibited seasonal shifts in lifestyles in different seasons. In wet season, bacterial community composition was characterized by abundance of Cyanobacteria, Actinobacteria, and Bacteroidetes, which were tightly linked with high riverine inflow. While in dry season, Proteobacteria increased in prevalence, especially for Psychrobacter, NOR5/OM60 clade and Pseudomonas, which were thrived in lower water temperature and higher salinity. Moreover, we discovered that differences between PA and FL composition were more significant in the wet season than in the dry season, which may be due to better nutritional conditions of particles (indicated by POC%) in the wet season and then attract more diverse PA populations. Based on the analysis of plastidial 16 S rRNA genes, abundant small-sized mixotrophic phytoplankton (Dinophyceae, Euglenida and Haptophyta) were identified in the PRE. The complexity of co-occurrence network increased from FL to PA fractions in both seasons, which suggested that suspended particles can provide ecological niches for particle-associated colonizers contributing to the maintenance of a more stable community structure. In addition, the majority of phytoplankton species exhibited positive co-occurrences with both other phytoplankton species and bacterial counterparts, indicating the mutual cooperation between phytoplankton assemblages and specific bacterial populations e likely benefited from phytoplankton-derived organic compounds. This study enhances our understanding of the seasonal and spatial dynamics of bacterial communities and their potential relationship with phytoplankton assembly in estuarine waters.
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Affiliation(s)
- Xia Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, 510301, China
| | - Lijun Cui
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, 510301, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, 510301, China
| | - Jinlong Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, 510301, China
| | - Yuzheng Ren
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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17
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Fu X, Fu Q, Zhu X, Yang X, Chen H, Li S. Microdiversity sustains the distribution of rhizosphere-associated bacterial species from the root surface to the bulk soil region in maize crop fields. FRONTIERS IN PLANT SCIENCE 2023; 14:1266218. [PMID: 37905168 PMCID: PMC10613529 DOI: 10.3389/fpls.2023.1266218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/22/2023] [Indexed: 11/02/2023]
Abstract
Over the years, the microbial community of maize (Zea mays) rhizosphere has been extensively studied; however, the role of microdiversity sustain rhizosphere-associated microbial species distribution from root surface to bulk soil in mature maize is still unclear. Although operational taxonomic units (OTUs) have been used to classify species, amplicon sequence variants (ASVs) have been shown to be effective in representing microdiversity within OTUs at a finer genetic scale. Therefore, the aim of this study was to examine the role of microdiversity in influencing the distribution of rhizosphere-associated microbial species across environmental gradients from root surface to bulk soil at the OTU and ASV levels. Here, the microbial community structures of bulk, loosely bound, and tightly bound soil samples from maize rhizosphere were examined at OTU and ASV levels. The results showed that OTU and ASV methods exhibited similar microbial community structures in rhizosphere. Additionally, different ecotypes with varying distributions and habitat preferences were observed within the same bacterial OTU at the ASV level, indicating a rich bacterial microdiversity. In contrast, the fungal community exhibited low microdiversity, with no significant relationship between fungal microdiversity and persistence and variability. Moreover, the ecotypes observed within the bacterial OTUs were found to be positively or negatively associated with environmental factors, such as soil organic carbon (SOC), NO3 --N, NH4 +-N contents, and pH. Overall, the results showed that the rich microdiversity could sustain the distribution of rhizosphere-associated bacterial species across environmental gradients from root surface to bulk soil. Further genetic analyses of rhizosphere-associated bacterial species could have considerable implications for potential mediation of microdiversity for sustainable crop production.
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Affiliation(s)
- Xianheng Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resource, Shaanxi, China
| | - Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Xiaozheng Zhu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resource, Shaanxi, China
| | - Xian Yang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Shiqing Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resource, Shaanxi, China
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18
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Robicheau BM, Tolman J, Desai D, LaRoche J. Microevolutionary patterns in ecotypes of the symbiotic cyanobacterium UCYN-A revealed from a Northwest Atlantic coastal time series. SCIENCE ADVANCES 2023; 9:eadh9768. [PMID: 37774025 PMCID: PMC10541017 DOI: 10.1126/sciadv.adh9768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/28/2023] [Indexed: 10/01/2023]
Abstract
UCYN-A is a globally important nitrogen-fixing symbiotic microbe often found in colder regions and coastal areas where nitrogen fixation has been overlooked. We present a 3-year coastal Northwest Atlantic time series of UCYN-A by integrating oceanographic data with weekly nifH and16S rRNA gene sequencing and quantitative PCR assays for UCYN-A ecotypes. High UCYN-A relative abundances dominated by A1 to A4 ecotypes reoccurred annually in the coastal Northwest Atlantic. Although UCYN-A was detected every summer/fall, the ability to observe separate ecotypes may be highly dependent on sampling time given intense interannual and weekly variability of ecotype-specific occurrences. Additionally, much of UCYN-A's rarer diversity was populated by short-lived neutral mutational variants, therefore providing insight into UCYN-A's microevolutionary patterns. For instance, rare ASVs exhibited community composition restructuring annually, while also sharing a common connection to a dominant ASV within each ecotype. Our study provides additional perspectives for interpreting UCYN-A intraspecific diversity and underscores the need for high-resolution datasets when deciphering spatiotemporal ecologies within UCYN-A.
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Affiliation(s)
- Brent M. Robicheau
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jennifer Tolman
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Dhwani Desai
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Integrated Microbiome Resource, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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19
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Li SH, Kang I, Cho JC. Metabolic Versatility of the Family Halieaceae Revealed by the Genomics of Novel Cultured Isolates. Microbiol Spectr 2023; 11:e0387922. [PMID: 36916946 PMCID: PMC10100682 DOI: 10.1128/spectrum.03879-22] [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: 09/22/2022] [Accepted: 02/16/2023] [Indexed: 03/16/2023] Open
Abstract
The family Halieaceae (OM60/NOR5 clade) is a gammaproteobacterial group abundant and cosmopolitan in coastal seawaters and plays an important role in response to phytoplankton blooms. However, the ecophysiology of this family remains understudied because of the vast gap between phylogenetic diversity and cultured representatives. Here, using six pure cultured strains isolated from coastal seawaters, we performed in-depth genomic analyses to provide an overview of the phylogeny and metabolic capabilities of this family. The combined analyses of 16S rRNA genes, genome sequences, and functional genes relevant to taxonomy demonstrated that each strain represents a novel species. Notably, two strains belonged to the hitherto-uncultured NOR5-4 and NOR5-12 subclades. Metabolic reconstructions revealed that the six strains likely have aerobic chemo- or photoheterotrophic lifestyles; five of them possess genes for proteorhodopsin or aerobic anoxygenic phototrophy. The presence of blue- or green-tuned proteorhodopsin in Halieaceae suggested their ability to adapt to light conditions varying with depth or coastal-to-open ocean transition. In addition to the genes of anaplerotic CO2 fixation, genes encoding a complete reductive glycine pathway for CO2 fixation were found in three strains. Putative polysaccharide utilization loci were detected in three strains, suggesting the association with phytoplankton blooms. Read mapping of various metagenomes and metatranscriptomes showed that the six strains are widely distributed and transcriptionally active in marine environments. Overall, the six strains genomically characterized in this study expand the phylogenetic and metabolic diversity of Halieaceae and likely serve as a culture resource for investigating the ecophysiological features of this environmentally relevant bacterial group. IMPORTANCE Although the family Halieaceae (OM60/NOR5 clade) is an abundant and cosmopolitan clade widely found in coastal seas and involved in interactions with phytoplankton, a limited number of cultured isolates are available. In this study, we isolated six pure cultured Halieaceae strains from coastal seawaters and performed a comparative physiological and genomic analysis to give insights into the phylogeny and metabolic potential of this family. The cultured strains exhibited diverse metabolic potential by harboring genes for anaplerotic CO2 fixation, proteorhodopsin, and aerobic anoxygenic phototrophy. Polysaccharide utilization loci detected in some of these strains also indicated an association with phytoplankton blooms. The cultivation of novel strains of Halieaceae and their genomic characteristics largely expanded the phylogenetic and metabolic diversity, which is important for future ecophysiological studies.
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Affiliation(s)
- Shan-Hui Li
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, Republic of Korea
| | - Ilnam Kang
- Center for Molecular and Cell Biology, Inha University, Incheon, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, Republic of Korea
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20
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Prevalence of Viral Frequency-Dependent Infection in Coastal Marine Prokaryotes Revealed Using Monthly Time Series Virome Analysis. mSystems 2023; 8:e0093122. [PMID: 36722950 PMCID: PMC9948707 DOI: 10.1128/msystems.00931-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Viruses infecting marine prokaryotes have a large impact on the diversity and dynamics of their hosts. Model systems suggest that viral infection is frequency dependent and constrained by the virus-host encounter rate. However, it is unclear whether frequency-dependent infection is pervasive among the abundant prokaryotic populations with different temporal dynamics. To address this question, we performed a comparison of prokaryotic and viral communities using 16S rRNA amplicon and virome sequencing based on samples collected monthly for 2 years at a Japanese coastal site, Osaka Bay. Concurrent seasonal shifts observed in prokaryotic and viral community dynamics indicated that the abundance of viruses correlated with that of their predicted host phyla (or classes). Cooccurrence network analysis between abundant prokaryotes and viruses revealed 6,423 cooccurring pairs, suggesting a tight coupling of host and viral abundances and their "one-to-many" correspondence. Although stable dominant species, such as SAR11, showed few cooccurring viruses, a fast succession of their viruses suggests that viruses infecting these populations changed continuously. Our results suggest that frequency-dependent viral infection prevails in coastal marine prokaryotes regardless of host taxa and temporal dynamics. IMPORTANCE There is little room for doubt that viral infection is prevalent among abundant marine prokaryotes regardless of their taxa or growth strategy. However, comprehensive evaluations of viral infections in natural prokaryotic communities are still technically difficult. In this study, we examined viral infection in abundant prokaryotes by monitoring the monthly dynamics of prokaryotic and viral communities at a eutrophic coastal site, Osaka Bay. We compared the community dynamics of viruses with those of their putative hosts based on genome-based in silico host prediction. We observed frequent cooccurrence among the predicted virus-host pairs, suggesting that viral infection is prevalent in abundant prokaryotes regardless of their taxa or temporal dynamics. This likely indicates that frequent lysis of the abundant prokaryotes via viral infection has a considerable contribution to the biogeochemical cycling and maintenance of prokaryotic community diversity.
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21
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Pushpakumara BLDU, Tandon K, Willis A, Verbruggen H. Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks. Sci Rep 2023; 13:2743. [PMID: 36797257 PMCID: PMC9935533 DOI: 10.1038/s41598-023-27816-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/09/2023] [Indexed: 02/18/2023] Open
Abstract
Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but the majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects to identify potential microalgal-bacterial associations in aquatic ecosystems. A high degree of clustering was observed in microalgal-bacterial modules, indicating densely connected neighbourhoods. Proteobacteria and Bacteroidetes predominantly co-occurred with microalgae and represented hubs of most modules. Our results also indicated that species-specificity may be a global characteristic of microalgal associated microbiomes. Several previously known associations were recovered from our network modules, validating that biologically meaningful results can be inferred using this approach. A range of previously unknown associations were recognised such as co-occurrences of Bacillariophyta with uncultured Planctomycetes OM190 and Deltaproteobacteria order NB1-j. Planctomycetes and Verrucomicrobia were identified as key associates of microalgae due to their frequent co-occurrences with several microalgal taxa. Despite no clear taxonomic pattern, bacterial associates appeared functionally similar across different environments. To summarise, we demonstrated the potential of 16S rRNA gene-based co-occurrence networks as a hypothesis-generating framework to guide more focused research on microalgal-bacterial associations.
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Affiliation(s)
| | - Kshitij Tandon
- School of Biosciences, University of Melbourne, Melbourne, VIC, Australia
| | - Anusuya Willis
- Australian National Algae Culture Collection, CSIRO, Hobart, TAS, 7000, Australia
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Melbourne, VIC, Australia.
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22
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Wu J, Zhu Z, Waniek JJ, Niu M, Wang Y, Zhang Z, Zhou M, Zhang R. The biogeography and co-occurrence network patterns of bacteria and microeukaryotes in the estuarine and coastal waters. MARINE ENVIRONMENTAL RESEARCH 2023; 184:105873. [PMID: 36628821 DOI: 10.1016/j.marenvres.2023.105873] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/02/2023] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
Community and diversity shifts of bacteria and microeukaryotes with strong environmental and spatial variations have been unveiled in the Pearl River Estuary (PRE) and northern coastal part of South China Sea (SCS). However, it is not clear what the determining factors shape the microbial community and how the biotic interactions respond to the estuarine and oceanic environment. Here, we established the multiple regression models (MRM) and co-occurrence networks on microbial communities in PRE and SCS habitats. The results showed that there were significant differences of the abiotic factors affecting the bacterial and microeukaryotic communities between PRE and SCS habitats. Salinity explained the largest variations to the microbial community dissimilarities in PRE. Whereas spatial and environmental factors determined the microbial community dissimilarities in SCS. Positive relations between parasitic lineages (e.g. Perkinsea and Cercozoa) and algal taxa (Dinophyceae, Cryptophyta, Chlorophyta and Ochrophyta) dominated in the PRE network. While parasites Syndiniales positively correlated with other Syndiniales and protists in SCS. Strong positive associations among autotrophic and heterotrophic groups were revealed in both niches. Therefore, the biotic interactions are also important and may be responsible for the unexplained variations of the abiotic factors from MRM models. Microbial network in the PRE estuarine water had weakened resistance to environmental disturbances, while the SCS network had greater capacity to maintain network stability. This study shed light on the different mechanisms of abiotic and biotic factors in shaping the compositions of bacteria and microeukaryotes between PRE and SCS niches, and highlights the weakening effect of environmental disturbances on the microbial network stability.
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Affiliation(s)
- Jinnan Wu
- School of Oceanography, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Zhu Zhu
- School of Oceanography, Shanghai Jiao Tong University, 200030, Shanghai, China.
| | - Joanna J Waniek
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, 18119, Rostock, Germany
| | - Mingyang Niu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Yuntao Wang
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, 310000, Hangzhou, Zhejiang, China
| | - Zhaoru Zhang
- School of Oceanography, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Meng Zhou
- School of Oceanography, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Ruifeng Zhang
- School of Oceanography, Shanghai Jiao Tong University, 200030, Shanghai, China.
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23
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Ji F, Sun Y, Yang Q. Early warning of red tides using bacterial and eukaryotic communities in nearshore waters. ENVIRONMENTAL RESEARCH 2023; 216:114711. [PMID: 36334824 DOI: 10.1016/j.envres.2022.114711] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/27/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Anthropogenic discharge activities have increased nutrient pollution in coastal areas, leading to algal blooms and microbial community changes. Particularly, microbial communities could easily be affected with variation in nutrient pollution, and thus offered a promising strategy to predict early red tides warning via microbial community-levels variation and their keystone taxa hysteretic responses to nutrient pollution. Herein high-throughput sequencing technology from 52 samples were used to explore the variation of microbial communities and find the significant tipping points with aggravating nutrient conditions in Xiaoping Island coastal area. Results indicated that bacterial and microeukaryote communities were generally spatial and seasonal heterogeneity and were influenced by the different nutrient conditions. Procrustes test results showed that the comprehensive index of organics polluting (OPI), total nitrogen (TN), inorganic nitrogen (DIN), and total phosphorus (TP) were significantly correlated with the composition of bacteria and microeukaryotes. A SEGMENTED analysis revealed that the threshold of TN, DIN, and NH4-N for bacterial community were 0.23 ± 0.091 mg/L, 0.21 ± 0.084 mg/L, 0.09 ± 0.057 mg/L, respectively. Tipping points for TN, DIN, and NH4-N agreed with the concentration during Ceratium tripos and Skeletonema costatum blooms. Co-occurrence network results found that Planktomarina, Acinetobacter, and Verrucomicrobiaceae were keystone and OPI-discriminatory taxa. The abundant changes of Planktomarina at station A1 were significantly correlated with the development of C. tripos blooms (r = 0.55, p < 0.05), and also significantly correlated with TN, DIN, and NO3-N (r≥|0.55|, p < 0.05). The abundant changes of Acinetobacter and Verrucomicrobiaceae at station C1 were significantly correlated with the development of C. tripos blooms (r ≥ 0.77, p < 0.05), and also significantly correlated with PO4-P (r ≥ 0.64, p < 0.05). The dynamic abundance of keystone taxa showed that the trend of rapid changes could be monitored 1.5 months before the occurrence of red tide. Therefore, this study provides an assessment method for early warning of red tide occurrence and factors that trigger red tide.
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Affiliation(s)
- Fengyun Ji
- Institute of Environmental Systems Biology, Environment Science and Engineering College, Dalian Maritime University, Dalian, Liaoning Province, 116026, China; Panjin Institute of Industrial Technology, Dalian University of Technology, Panjin 124221, Liaoning, China.
| | - Yeqing Sun
- Institute of Environmental Systems Biology, Environment Science and Engineering College, Dalian Maritime University, Dalian, Liaoning Province, 116026, China.
| | - Qing Yang
- Institute of Environmental Systems Biology, Environment Science and Engineering College, Dalian Maritime University, Dalian, Liaoning Province, 116026, China.
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24
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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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25
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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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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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27
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Duan L, Li JL, Yin LZ, Luo XQ, Ahmad M, Fang BZ, Li SH, Deng QQ, Wang P, Li WJ. Habitat-dependent prokaryotic microbial community, potential keystone species, and network complexity in a subtropical estuary. ENVIRONMENTAL RESEARCH 2022; 212:113376. [PMID: 35561827 DOI: 10.1016/j.envres.2022.113376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/09/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Microbes (e.g., bacteria and archaea) are indispensable components for the key biological processes of estuarine ecosystems and three main habitats (sediment, particle, and water) are harboring diverse estuarine microbes. However, we still know little about how the microbial community structures, potential keystone species, and network properties change among these three habitats in estuarine ecosystems. In this study, we collected size-fractioned water and sediment samples from the Pearl River Estuary to reveal their microbial diversity, community structures, network properties, and potential keystone taxa. We found that the sediment microbial community was remarkably more diverse than particle-attached (PA) and free-living (FL) communities, whereas its ecological network was less complex in terms of node distance and connectivity. TOC was determined as the main driver of sediment community, while the PA and FL communities were predominantly shaped by NO2-, non-ionic ammonia (NH) and pH. Among the bulk water, there were no significant differences between PA and FL communities in diversity, community structure, and network complexity. However, the PA community was more susceptible to metal elements, suggesting their higher level of involvement in physiological metabolism. Potential keystone taxa among community networks were taxonomically divergent in three habitats. Specifically, Synechococcales (Cyanobacteria) and Actinomarinales (Actinobacteria) exclusively served as the module-hubs in FL network, while members from phylum Proteobacteria and Bacteroidetes were the module-hubs and connectors in PA network. Potential keystone taxa in sediment network were more diverse and covered 9 phyla, including the only archaeal lineage Bathyarchaeia (Crenarchaeota). Overall, our study provided more detailed information about estuarine microbial communities in three habitats, especially the potential keystone species, which provided new perspectives on evaluating further effects of anthropogenic disturbances on estuarine microbes and facilitated the environment monitoring based on microbial community.
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Affiliation(s)
- Li Duan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ling-Zi Yin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiao-Qing Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Manzoor Ahmad
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Shan-Hui Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Qi-Qi Deng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Hubei Key Laboratory of Marine Geological Resources, China University of Geosciences, Wuhan 430074, China; School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.
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28
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Cao X, Zhao D, Li C, Röttjers L, Faust K, Zhang H. Regime transition Shapes the Composition, Assembly Processes, and Co-occurrence Pattern of Bacterioplankton Community in a Large Eutrophic Freshwater Lake. MICROBIAL ECOLOGY 2022; 84:336-350. [PMID: 34585289 DOI: 10.1007/s00248-021-01878-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
At certain nutrient concentrations, shallow freshwater lakes are generally characterized by two contrasting ecological regimes with disparate patterns of biodiversity and biogeochemical cycles: a macrophyte-dominated regime (MDR) and a phytoplankton-dominated regime (PDR). To reveal ecological mechanisms that affect bacterioplankton along the regime shift, Illumina MiSeq sequencing of the 16S rRNA gene combined with a novel network clustering tool (Manta) were used to identify patterns of bacterioplankton community composition across the regime shift in Taihu Lake, China. Marked divergence in the composition and ecological assembly processes of bacterioplankton community was observed under the regime shift. The alpha diversity of the bacterioplankton community consistently and continuously decreased with the regime shift from MDR to PDR, while the beta diversity presents differently. Moreover, as the regime shifted from MDR to PDR, the contribution of deterministic processes (such as environmental selection) to the assembly of bacterioplankton community initially decreased and then increased again as regime shift from MDR to PDR, most likely as a consequence of differences in nutrient concentration. The topological properties, including modularity, transitivity and network diameter, of the bacterioplankton co-occurrence networks changed along the regime shift, and the co-occurrences among species changed in structure and were significantly shaped by the environmental variables along the regime transition from MDR to PDR. The divergent environmental state of the regimes with diverse nutritional status may be the most important factor that contributes to the dissimilarity of bacterioplankton community composition along the regime shift.
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Affiliation(s)
- Xinyi Cao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.
| | - Chaoran Li
- Department of Civil, Environmental and Geomatic Engineering, University College London, London, UK
| | - Lisa Röttjers
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Karoline Faust
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Hongjie Zhang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
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Niche partitioning of the ubiquitous and ecologically relevant NS5 marine group. THE ISME JOURNAL 2022; 16:1570-1582. [PMID: 35169264 PMCID: PMC9122927 DOI: 10.1038/s41396-022-01209-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/24/2022] [Accepted: 02/02/2022] [Indexed: 11/08/2022]
Abstract
Niche concept is a core tenet of ecology that has recently been applied in marine microbial research to describe the partitioning of taxa based either on adaptations to specific conditions across environments or on adaptations to specialised substrates. In this study, we combine spatiotemporal dynamics and predicted substrate utilisation to describe species-level niche partitioning within the NS5 Marine Group. Despite NS5 representing one of the most abundant marine flavobacterial clades from across the world’s oceans, our knowledge on their phylogenetic diversity and ecological functions is limited. Using novel and database-derived 16S rRNA gene and ribosomal protein sequences, we delineate the NS5 into 35 distinct species-level clusters, contained within four novel candidate genera. One candidate species, “Arcticimaribacter forsetii AHE01FL”, includes a novel cultured isolate, for which we provide a complete genome sequence—the first of an NS5—along with morphological insights using transmission electron microscopy. Assessing species’ spatial distribution dynamics across the Tara Oceans dataset, we identify depth as a key influencing factor, with 32 species preferring surface waters, as well as distinct patterns in relation to temperature, oxygen and salinity. Each species harbours a unique substrate-degradation potential along with predicted substrates conserved at the genus-level, e.g. alginate in NS5_F. Successional dynamics were observed for three species in a time-series dataset, likely driven by specialised substrate adaptations. We propose that the ecological niche partitioning of NS5 species is mainly based on specific abiotic factors, which define the niche space, and substrate availability that drive the species-specific temporal dynamics.
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30
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Xie N, Wang Z, Hunt DE, Johnson ZI, He Y, Wang G. Niche Partitioning of Labyrinthulomycete Protists Across Sharp Coastal Gradients and Their Putative Relationships With Bacteria and Fungi. Front Microbiol 2022; 13:906864. [PMID: 35685928 PMCID: PMC9171235 DOI: 10.3389/fmicb.2022.906864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
While planktonic microbes play key roles in the coastal oceans, our understanding of heterotrophic microeukaryotes’ ecology, particularly their spatiotemporal patterns, drivers, and functions, remains incomplete. In this study, we focus on a ubiquitous marine fungus-like protistan group, the Labyrinthulomycetes, whose biomass can exceed that of bacterioplankton in coastal oceans but whose ecology is largely unknown. Using quantitative PCR and amplicon sequencing of their 18S rRNA genes, we examine their community variation in repeated five-station transects across the nearshore-to-offshore surface waters of North Carolina, United States. Their total 18S rRNA gene abundance and phylotype richness decrease significantly from the resource-rich nearshore to the oligotrophic offshore waters, but their Pielou’s community evenness appears to increase offshore. Similar to the bacteria and fungi, the Labyrinthulomycete communities are significantly structured by distance from shore, water temperature, and other environmental factors, suggesting potential niche partitioning. Nevertheless, only several Labyrinthulomycete phylotypes, which belong to aplanochytrids, thraustochytrids, or unclassified Labyrinthulomycetes, are prevalent and correlated with cohesive bacterial communities, while more phylotypes are patchy and often co-occur with fungi. Overall, these results complement previous time-series observations that resolve the Labyrinthulomycetes as persistent and short-blooming ecotypes with distinct seasonal preferences, further revealing their partitioning spatial patterns and multifaceted roles in coastal marine microbial food webs.
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Affiliation(s)
- Ningdong Xie
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Marine Laboratory, Duke University, Beaufort, NC, United States
| | - Zhao Wang
- Marine Laboratory, Duke University, Beaufort, NC, United States
| | - Dana E. Hunt
- Marine Laboratory, Duke University, Beaufort, NC, United States
- Biology Department, Duke University, Durham, NC, United States
| | - Zackary I. Johnson
- Marine Laboratory, Duke University, Beaufort, NC, United States
- Biology Department, Duke University, Durham, NC, United States
| | - Yaodong He
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Guangyi Wang
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- *Correspondence: Guangyi Wang,
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31
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Krabberød AK, Deutschmann IM, Bjorbækmo MFM, Balagué V, Giner CR, Ferrera I, Garcés E, Massana R, Gasol JM, Logares R. Long-term patterns of an interconnected core marine microbiota. ENVIRONMENTAL MICROBIOME 2022; 17:22. [PMID: 35526063 PMCID: PMC9080219 DOI: 10.1186/s40793-022-00417-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/20/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Ocean microbes constitute ~ 70% of the marine biomass, are responsible for ~ 50% of the Earth's primary production and are crucial for global biogeochemical cycles. Marine microbiotas include core taxa that are usually key for ecosystem function. Despite their importance, core marine microbes are relatively unknown, which reflects the lack of consensus on how to identify them. So far, most core microbiotas have been defined based on species occurrence and abundance. Yet, species interactions are also important to identify core microbes, as communities include interacting species. Here, we investigate interconnected bacteria and small protists of the core pelagic microbiota populating a long-term marine-coastal observatory in the Mediterranean Sea over a decade. RESULTS Core microbes were defined as those present in > 30% of the monthly samples over 10 years, with the strongest associations. The core microbiota included 259 Operational Taxonomic Units (OTUs) including 182 bacteria, 77 protists, and 1411 strong and mostly positive (~ 95%) associations. Core bacteria tended to be associated with other bacteria, while core protists tended to be associated with bacteria. The richness and abundance of core OTUs varied annually, decreasing in stratified warmers waters and increasing in colder mixed waters. Most core OTUs had a preference for one season, mostly winter, which featured subnetworks with the highest connectivity. Groups of highly associated taxa tended to include protists and bacteria with predominance in the same season, particularly winter. A group of 13 highly-connected hub-OTUs, with potentially important ecological roles dominated in winter and spring. Similarly, 18 connector OTUs with a low degree but high centrality were mostly associated with summer or autumn and may represent transitions between seasonal communities. CONCLUSIONS We found a relatively small and dynamic interconnected core microbiota in a model temperate marine-coastal site, with potential interactions being more deterministic in winter than in other seasons. These core microbes would be essential for the functioning of this ecosystem over the year. Other non-core taxa may also carry out important functions but would be redundant and non-essential. Our work contributes to the understanding of the dynamics and potential interactions of core microbes possibly sustaining ocean ecosystem function.
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Affiliation(s)
- Anders K Krabberød
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, 0316, Oslo, Norway.
| | - Ina M Deutschmann
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Marit F M Bjorbækmo
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, 0316, Oslo, Norway
| | - Vanessa Balagué
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Caterina R Giner
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Isabel Ferrera
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, 29640, Fuengirola, Málaga, Spain
| | - Esther Garcés
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Ramon Massana
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Josep M Gasol
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
- Centre for Marine Ecosystems Research, School of Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Ramiro Logares
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, 0316, Oslo, Norway.
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain.
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32
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Vanni C, Schechter MS, Acinas SG, Barberán A, Buttigieg PL, Casamayor EO, Delmont TO, Duarte CM, Eren AM, Finn RD, Kottmann R, Mitchell A, Sánchez P, Siren K, Steinegger M, Gloeckner FO, Fernàndez-Guerra A. Unifying the known and unknown microbial coding sequence space. eLife 2022; 11:67667. [PMID: 35356891 PMCID: PMC9132574 DOI: 10.7554/elife.67667] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/30/2022] [Indexed: 12/02/2022] Open
Abstract
Genes of unknown function are among the biggest challenges in molecular biology, especially in microbial systems, where 40–60% of the predicted genes are unknown. Despite previous attempts, systematic approaches to include the unknown fraction into analytical workflows are still lacking. Here, we present a conceptual framework, its translation into the computational workflow AGNOSTOS and a demonstration on how we can bridge the known-unknown gap in genomes and metagenomes. By analyzing 415,971,742 genes predicted from 1749 metagenomes and 28,941 bacterial and archaeal genomes, we quantify the extent of the unknown fraction, its diversity, and its relevance across multiple organisms and environments. The unknown sequence space is exceptionally diverse, phylogenetically more conserved than the known fraction and predominantly taxonomically restricted at the species level. From the 71 M genes identified to be of unknown function, we compiled a collection of 283,874 lineage-specific genes of unknown function for Cand. Patescibacteria (also known as Candidate Phyla Radiation, CPR), which provides a significant resource to expand our understanding of their unusual biology. Finally, by identifying a target gene of unknown function for antibiotic resistance, we demonstrate how we can enable the generation of hypotheses that can be used to augment experimental data. It is estimated that scientists do not know what half of microbial genes actually do. When these genes are discovered in microorganisms grown in the lab or found in environmental samples, it is not possible to identify what their roles are. Many of these genes are excluded from further analyses for these reasons, meaning that the study of microbial genes tends to be limited to genes that have already been described. These limitations hinder research into microbiology, because information from newly discovered genes cannot be integrated to better understand how these organisms work. Experiments to understand what role these genes have in the microorganisms are labor-intensive, so new analytical strategies are needed. To do this, Vanni et al. developed a new framework to categorize genes with unknown roles, and a computational workflow to integrate them into traditional analyses. When this approach was applied to over 400 million microbial genes (both with known and unknown roles), it showed that the share of genes with unknown functions is only about 30 per cent, smaller than previously thought. The analysis also showed that these genes are very diverse, revealing a huge space for future research and potential applications. Combining their approach with experimental data, Vanni et al. were able to identify a gene with a previously unknown purpose that could be involved in antibiotic resistance. This system could be useful for other scientists studying microorganisms to get a more complete view of microbial systems. In future, it may also be used to analyze the genetics of other organisms, such as plants and animals.
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Affiliation(s)
- Chiara Vanni
- Microbial Genomics and Bioinformatics Research G, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar-CMIMA (CSIC), Barcelona, Spain
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, United States
| | - Pier Luigi Buttigieg
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Bremerhaven, Germany
| | - Emilio O Casamayor
- Center for Advanced Studies of Blanes CEAB-CSIC, Spanish Council for Research, Blanes, Spain
| | - Tom O Delmont
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Paris, France
| | - Carlos M Duarte
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, United States
| | - Robert D Finn
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, United Kingdom
| | - Renzo Kottmann
- Microbial Genomics and Bioinformatics Research G, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Alex Mitchell
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, United Kingdom
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar-CMIMA (CSIC), Barcelona, Spain
| | - Kimmo Siren
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Frank Oliver Gloeckner
- MARUM, Helmholtz Center for Polar and Marine Research, University of Bremen, Bremen, Germany
| | - Antonio Fernàndez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
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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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Aguilar P, Vila I, Sommaruga R. Bacterioplankton Zonation Does Exist in High Elevation, Polymictic Lakes. Front Microbiol 2022; 13:764566. [PMID: 35250918 PMCID: PMC8891803 DOI: 10.3389/fmicb.2022.764566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/25/2022] [Indexed: 01/04/2023] Open
Abstract
The assessment of distribution patterns or zonation of planktonic microbes along the water column is a crucial step to interpret their function in the ecosystem. In lakes without seasonal thermal stratification or polymictic systems such as high elevation tropical lakes, planktonic bacterial taxa are probably homogeneously distributed in the water column in contrast to what is known for thermally stratified lakes. However, we know little about bacterial distribution patterns in polymictic lakes and their relation to environmental gradients other than temperature. Here we assessed the diversity, microdiversity, and bacterial community composition at different discrete depths in three high elevation lakes (4,400-4,550 m above sea level) from the Andean plateau to test whether bacterial zonation patterns exist along the water column. For this objective, we analyzed bulk DNA and the putatively active fraction (cDNA) of the 16S rRNA gene. Although a clear gradient of temperature and oxygen was not detected along the water column, a significant vertical spatial zonation of the bacterial communities was present in two out of the three lakes, with microdiversity contributing to such pattern. Our results provide a reference for understanding how changing environmental conditions could affect high elevation aquatic ecosystems, particularly when warming is amplified with elevation, accelerating changes in hydrological regimes and biodiversity. Finally, our results highlight the importance of incorporating the whole water column in ecological studies of aquatic ecosystems lacking temporal or permanent thermal stratification.
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Affiliation(s)
- Pablo Aguilar
- Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Núcleo Milenio INVASAL, Concepción, Chile
| | - Irma Vila
- Núcleo Milenio INVASAL, Concepción, Chile
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ruben Sommaruga
- Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
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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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36
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Auladell A, Barberán A, Logares R, Garcés E, Gasol JM, Ferrera I. Seasonal niche differentiation among closely related marine bacteria. THE ISME JOURNAL 2022; 16:178-189. [PMID: 34285363 PMCID: PMC8692485 DOI: 10.1038/s41396-021-01053-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023]
Abstract
Bacteria display dynamic abundance fluctuations over time in marine environments, where they play key biogeochemical roles. Here, we characterized the seasonal dynamics of marine bacteria in a coastal oligotrophic time series station, tested how similar the temporal niche of closely related taxa is, and what are the environmental parameters modulating their seasonal abundance patterns. We further explored how conserved the niche is at higher taxonomic levels. The community presented recurrent patterns of seasonality for 297 out of 6825 amplicon sequence variants (ASVs), which constituted almost half of the total relative abundance (47%). For certain genera, niche similarity decreased as nucleotide divergence in the 16S rRNA gene increased, a pattern compatible with the selection of similar taxa through environmental filtering. Additionally, we observed evidence of seasonal differentiation within various genera as seen by the distinct seasonal patterns of closely related taxa. At broader taxonomic levels, coherent seasonal trends did not exist at the class level, while the order and family ranks depended on the patterns that existed at the genus level. This study identifies the coexistence of closely related taxa for some bacterial groups and seasonal differentiation for others in a coastal marine environment subjected to a strong seasonality.
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Affiliation(s)
- Adrià Auladell
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain.
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA
| | - Ramiro Logares
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain.
- Center for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia.
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain.
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, Fuengirola, Málaga, Spain.
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37
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Prodinger F, Endo H, Takano Y, Li Y, Tominaga K, Isozaki T, Blanc-Mathieu R, Gotoh Y, Hayashi T, Taniguchi E, Nagasaki K, Yoshida T, Ogata H. Year-round dynamics of amplicon sequence variant communities differ among eukaryotes, Imitervirales, and prokaryotes in a coastal ecosystem. FEMS Microbiol Ecol 2021; 97:6486443. [PMID: 34962982 DOI: 10.1093/femsec/fiab167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 12/25/2021] [Indexed: 11/13/2022] Open
Abstract
Coastal microbial communities are affected by seasonal environmental change, biotic interactions, and fluctuating nutrient availability. We investigated the seasonal dynamics of communities of eukaryotes, a major group of double-stranded DNA viruses that infect eukaryotes (order Imitervirales; phylum Nucleocytoviricota), and prokaryotes in the Uranouchi Inlet, Kochi, Japan. We performed metabarcoding using ribosomal RNA genes and viral polB genes as markers in 43 seawater samples collected over 20 months. Eukaryotes, prokaryotes, and Imitervirales communities characterized by the compositions of amplicon sequence variants (ASVs) showed synchronic seasonal cycles. However, the community dynamics showed intriguing differences in several aspects, such as the recovery rate after a year. We also showed that the differences in community dynamics were at least partially explained by differences in recurrence/persistence levels of individual ASVs among eukaryotes, prokaryotes, and Imitervirales. Prokaryotic ASVs were the most persistent, followed by eukaryotic ASVs and Imitervirales ASVs, which were the least persistent. We argue that the differences in the specificity of interactions (virus-eukaryote vs. prokaryote-eukaryote) as well as the niche breadth of community members were at the origin of the distinct community dynamics among eukaryotes, their viruses, and prokaryotes.
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Affiliation(s)
- Florian Prodinger
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
| | - Hisashi Endo
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
| | - Yoshihito Takano
- Faculty of Science and Technology, Kochi University, Nankoku, Kochi, Japan
| | - Yanze Li
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
| | - Kento Tominaga
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Tatsuhiro Isozaki
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Romain Blanc-Mathieu
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan.,Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | | | - Keizo Nagasaki
- Faculty of Science and Technology, Kochi University, Nankoku, Kochi, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
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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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Alejandre-Colomo C, Francis B, Viver T, Harder J, Fuchs BM, Rossello-Mora R, Amann R. Cultivable Winogradskyella species are genomically distinct from the sympatric abundant candidate species. ISME COMMUNICATIONS 2021; 1:51. [PMID: 36747039 PMCID: PMC9723794 DOI: 10.1038/s43705-021-00052-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 02/08/2023]
Abstract
Winogradskyella is a genus within the phylum Bacteroidetes with a clear marine origin. Most members of this genus have been found associated with marine animals and algae, but also with inorganic surfaces such as sand. In this study, we analyzed genomes of eleven species recently isolated from surface seawater samples from the North Sea during a single spring algae bloom. Corresponding metagenomes yielded a single Candidatus species for this genus. All species in culture, with the exception of W. ursingii, affiliated with a Winogradskyella lineage characterized by large genomes (~4.3 ± 0.4 Mb), with high complexity in their carbohydrate and protein degradation genes. Specifically, the polysaccharide utilization loci (PULs) were diverse within each individual strain, indicating large substrate versatility. Although present in the North Sea, the abundances of these strains were at, or below, the detection limit of the metagenomes. In contrast, the single species, classified as Candidatus W. atlantica, to which all North Sea MAGs belonged, affiliated with a lineage in which the cultivated representatives showed small genomes of ~3.0-3.5 Mb, with the MAGs having ~2.3 Mb. In Ca. W. atlantica, genome streamlining has apparently resulted in the loss of biosynthesis pathways for several amino acids including arginine, methionine, leucine and valine, and the PUL loci were reduced to a single one for utilizing laminarin. This as-yet uncultivated species seems to capitalize on sporadically abundant substrates that are released by algae blooms, mainly laminarin. We also suggest that this streamlined genome might be responsible for the lack of growth on plates for this Candidatus species, in contrast to growth of the less abundant but coexisting members of the genus.
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Affiliation(s)
- Carlota Alejandre-Colomo
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marques 21, 07190, Esporles, Spain
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Ben Francis
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marques 21, 07190, Esporles, Spain
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Bernhard M Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marques 21, 07190, Esporles, Spain.
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany.
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Fodelianakis S, Washburne AD, Bourquin M, Pramateftaki P, Kohler TJ, Styllas M, Tolosano M, De Staercke V, Schön M, Busi SB, Brandani J, Wilmes P, Peter H, Battin TJ. Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome. ISME JOURNAL 2021; 16:666-675. [PMID: 34522009 PMCID: PMC8857233 DOI: 10.1038/s41396-021-01106-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/14/2021] [Accepted: 09/02/2021] [Indexed: 02/01/2023]
Abstract
Glacier-fed streams (GFSs) are extreme and rapidly vanishing ecosystems, and yet they harbor diverse microbial communities. Although our understanding of the GFS microbiome has recently increased, we do not know which microbial clades are ecologically successful in these ecosystems, nor do we understand potentially underlying mechanisms. Ecologically successful clades should be more prevalent across GFSs compared to other clades, which should be reflected as clade-wise distinctly low phylogenetic turnover. However, methods to assess such patterns are currently missing. Here we developed and applied a novel analytical framework, “phyloscore analysis”, to identify clades with lower spatial phylogenetic turnover than other clades in the sediment microbiome across twenty GFSs in New Zealand. These clades constituted up to 44% and 64% of community α-diversity and abundance, respectively. Furthermore, both their α-diversity and abundance increased as sediment chlorophyll a decreased, corroborating their ecological success in GFS habitats largely devoid of primary production. These clades also contained elevated levels of putative microdiversity than others, which could potentially explain their high prevalence in GFSs. This hitherto unknown microdiversity may be threatened as glaciers shrink, urging towards further genomic and functional exploration of the GFS microbiome.
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Affiliation(s)
- Stilianos Fodelianakis
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland.
| | | | - Massimo Bourquin
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Paraskevi Pramateftaki
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Tyler J Kohler
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Michail Styllas
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Matteo Tolosano
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Vincent De Staercke
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Martina Schön
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Susheel Bhanu Busi
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jade Brandani
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Paul Wilmes
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Hannes Peter
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Tom J Battin
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland.
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Tavares TCL, Bezerra WM, Normando LRO, Rosado AS, Melo VMM. Brazilian Semi-Arid Mangroves-Associated Microbiome as Pools of Richness and Complexity in a Changing World. Front Microbiol 2021; 12:715991. [PMID: 34512595 PMCID: PMC8427804 DOI: 10.3389/fmicb.2021.715991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/06/2021] [Indexed: 01/04/2023] Open
Abstract
Mangrove microbiomes play an essential role in the fate of mangroves in our changing planet, but the factors regulating the biogeographical distribution of mangrove microbial communities remain essentially vague. This paper contributes to our understanding of mangrove microbiomes distributed along three biogeographical provinces and ecoregions, covering the exuberant mangroves of Amazonia ecoregion (North Brazil Shelf) as well as mangroves located in the southern limit of distribution (Southeastern ecoregion, Warm Temperate Southwestern Atlantic) and mangroves localized on the drier semi-arid coast (Northeastern ecoregion, Tropical Southwestern Atlantic), two important ecotones where poleward and landward shifts, respectively, are expected to occur related to climate change. This study compared the microbiomes associated with the conspicuous red mangrove (Rhizophora mangle) root soils encompassing soil properties, latitudinal factors, and amplicon sequence variants of 105 samples. We demonstrated that, although the northern and southern sites are over 4,000 km apart, and despite R. mangle genetic divergences between north and south populations, their microbiomes resemble each other more than the northern and northeastern neighbors. In addition, the northeastern semi-arid microbiomes were more diverse and displayed a higher level of complexity than the northern and southern ones. This finding may reflect the endurance of the northeast microbial communities tailored to deal with the stressful conditions of semi-aridity and may play a role in the resistance and growing landward expansion observed in such mangroves. Minimum temperature, precipitation, organic carbon, and potential evapotranspiration were the main microbiota variation drivers and should be considered in mangrove conservation and recovery strategies in the Anthropocene. In the face of changes in climate, land cover, biodiversity, and chemical composition, the richness and complexity harbored by semi-arid mangrove microbiomes may hold the key to mangrove adaptability in our changing planet.
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Affiliation(s)
| | - Walderly Melgaço Bezerra
- Laboratory of Microbial Ecology and Biotechnology, Department of Biology, Federal University of Ceará (UFC), Fortaleza, Brazil
| | | | - Alexandre Soares Rosado
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Vânia Maria Maciel Melo
- Laboratory of Microbial Ecology and Biotechnology, Department of Biology, Federal University of Ceará (UFC), Fortaleza, Brazil
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Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms. ISME JOURNAL 2021; 16:630-641. [PMID: 34493810 PMCID: PMC8857213 DOI: 10.1038/s41396-021-01105-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/11/2022]
Abstract
Marine algae annually sequester petagrams of carbon dioxide into polysaccharides, which are a central metabolic fuel for marine carbon cycling. Diatom microalgae produce sulfated polysaccharides containing methyl pentoses that are challenging to degrade for bacteria compared to other monomers, implicating these sugars as a potential carbon sink. Free-living bacteria occurring in phytoplankton blooms that specialise on consuming microalgal sugars, containing fucose and rhamnose remain unknown. Here, genomic and proteomic data indicate that small, coccoid, free-living Verrucomicrobiota specialise in fucose and rhamnose consumption during spring algal blooms in the North Sea. Verrucomicrobiota cell abundance was coupled with the algae bloom onset and accounted for up to 8% of the bacterioplankton. Glycoside hydrolases, sulfatases, and bacterial microcompartments, critical proteins for the consumption of fucosylated and sulfated polysaccharides, were actively expressed during consecutive spring bloom events. These specialised pathways were assigned to novel and discrete candidate species of the Akkermansiaceae and Puniceicoccaceae families, which we here describe as Candidatus Mariakkermansia forsetii and Candidatus Fucivorax forsetii. Moreover, our results suggest specialised metabolic pathways could determine the fate of complex polysaccharides consumed during algae blooms. Thus the sequestration of phytoplankton organic matter via methyl pentose sugars likely depend on the activity of specialised Verrucomicrobiota populations.
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Isaac A, Francis B, Amann RI, Amin SA. Tight Adherence (Tad) Pilus Genes Indicate Putative Niche Differentiation in Phytoplankton Bloom Associated Rhodobacterales. Front Microbiol 2021; 12:718297. [PMID: 34447362 PMCID: PMC8383342 DOI: 10.3389/fmicb.2021.718297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/19/2021] [Indexed: 11/14/2022] Open
Abstract
The multiple interactions of phytoplankton and bacterioplankton are central for our understanding of aquatic environments. A prominent example of those is the consistent association of diatoms with Alphaproteobacteria of the order Rhodobacterales. These photoheterotrophic bacteria have traditionally been described as generalists that scavenge dissolved organic matter. Many observations suggest that members of this clade are specialized in colonizing the microenvironment of diatom cells, known as the phycosphere. However, the molecular mechanisms that differentiate Rhodobacterales generalists and phycosphere colonizers are poorly understood. We investigated Rhodobacterales in the North Sea during the 2010–2012 spring blooms using a time series of 38 deeply sequenced metagenomes and 10 metaproteomes collected throughout these events. Rhodobacterales metagenome assembled genomes (MAGs) were recurrently abundant. They exhibited the highest gene enrichment and protein expression of small-molecule transporters, such as monosaccharides, thiamine and polyamine transporters, and anaplerotic pathways, such as ethylmalonyl and propanoyl-CoA metabolic pathways, all suggestive of a generalist lifestyle. Metaproteomes indicated that the species represented by these MAGs were the dominant suppliers of vitamin B12 during the blooms, concomitant with a significant enrichment of genes related to vitamin B12 biosynthesis suggestive of association with diatom phycospheres. A closer examination of putative generalists and colonizers showed that putative generalists had persistently higher relative abundance throughout the blooms and thus produced more than 80% of Rhodobacterales transport proteins, suggesting rapid growth. In contrast, putative phycosphere colonizers exhibited large fluctuation in relative abundance across the different blooms and correlated strongly with particular diatom species that were dominant during the blooms each year. The defining feature of putative phycosphere colonizers is the presence of the tight adherence (tad) gene cluster, which is responsible for the assembly of adhesive pili that presumably enable attachment to diatom hosts. In addition, putative phycosphere colonizers possessed higher prevalence of secondary metabolite biosynthetic gene clusters, particularly homoserine lactones, which can regulate bacterial attachment through quorum sensing. Altogether, these findings suggest that while many members of Rhodobacterales are competitive during diatom blooms, only a subset form close associations with diatoms by colonizing their phycospheres.
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Affiliation(s)
- Ashley Isaac
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ben Francis
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Shady A Amin
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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Francis B, Urich T, Mikolasch A, Teeling H, Amann R. North Sea spring bloom-associated Gammaproteobacteria fill diverse heterotrophic niches. ENVIRONMENTAL MICROBIOME 2021; 16:15. [PMID: 34404489 PMCID: PMC8371827 DOI: 10.1186/s40793-021-00385-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND The planktonic bacterial community associated with spring phytoplankton blooms in the North Sea is responsible for a large amount of carbon turnover in an environment characterised by high primary productivity. Individual clades belonging to the Gammaproteobacteria have shown similar population dynamics to Bacteroidetes species, and are thus assumed to fill competing ecological niches. Previous studies have generated large numbers of metagenome assembled genomes and metaproteomes from these environments, which can be readily mined to identify populations performing potentially important ecosystem functions. In this study we attempt to catalogue these spring bloom-associated Gammaproteobacteria, which have thus far attracted less attention than sympatric Alphaproteobacteria and Bacteroidetes. METHODS We annotated 120 non-redundant species-representative gammaproteobacterial metagenome assembled genomes from spring bloom sampling campaigns covering the four years 2010-2012 and 2016 using a combination of Prokka and PfamScan, with further confirmation via BLAST against NCBI-NR. We also matched these gene annotations to 20 previously published metaproteomes covering those sampling periods plus the spring of 2009. RESULTS Metagenome assembled genomes with clear capacity for polysaccharide degradation via dedicated clusters of carbohydrate active enzymes were among the most abundant during blooms. Many genomes lacked gene clusters with clearly identifiable predicted polysaccharide substrates, although abundantly expressed loci for the uptake of large molecules were identified in metaproteomes. While the larger biopolymers, which are the most abundant sources of reduced carbon following algal blooms, are likely the main energy source, some gammaproteobacterial clades were clearly specialised for smaller organic compounds. Their substrates range from amino acids, monosaccharides, and DMSP, to the less expected, such as terpenoids, and aromatics and biphenyls, as well as many 'unknowns'. In particular we uncover a much greater breadth of apparent methylotrophic capability than heretofore identified, present in several order level clades without cultivated representatives. CONCLUSIONS Large numbers of metagenome assembled genomes are today publicly available, containing a wealth of readily accessible information. Here we identified a variety of predicted metabolisms of interest, which include diverse potential heterotrophic niches of spring bloom-associated Gammaproteobacteria. Features such as those identified here could well be fertile ground for future experimental studies.
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Affiliation(s)
- Ben Francis
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Tim Urich
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Annett Mikolasch
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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Heins A, Amann RI, Harder J. Cultivation of particle-associated heterotrophic bacteria during a spring phytoplankton bloom in the North Sea. Syst Appl Microbiol 2021; 44:126232. [PMID: 34399113 DOI: 10.1016/j.syapm.2021.126232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 07/05/2021] [Indexed: 11/29/2022]
Abstract
Seawater contains free-living and particle-attached bacteria. Only a small fraction is cultivable on plates. As free-living and particle-associated bacteria differ in their physiological traits, their cultivability on plates may coincide with particle association. Using filtration and Imhoff sedimentation cones, particles were collected during a spring phytoplankton bloom off Helgoland (North Sea) in order to obtain particle-associated bacteria as inocula. Direct dilution plating resulted in 526 strains from 3 µm filtration retentates and 597 strains from settled particles. Motile Gammaproteobacteria from the genera Pseudoalteromonas, Shewanella, Psychrobacter, Vibrio and Colwellia, as well as particle-attached Flavobacteriia affiliating with the genera Tenacibaculum and Gramella, were frequently isolated. As a result, a diverse collection comprised of 266 strains was deposited. Two strains were most likely to represent novel genera and 78 strains were probably novel species. Recently, a high-throughput cultivation study from the same site using seawater as an inoculum had retrieved 271 operational phylogenetic units (OPUs) that represented 88% of the 4136 characterized strains at the species level. A comparison of 16S rRNA gene sequences revealed that the collection obtained matched 104 of the 271 seawater OPUs at the species level and an additional 113 at the genus level. This large overlap indicated a significant contribution of particle-associated bacteria to the cultivable microbiome from seawater. The presence of 49 genera not identified in the larger seawater study suggested that sample fractionation was an efficient strategy to cultivate rare members of the planktonic microbiome. The diverse collection of heterotrophic bacteria retrieved in this study will be a rich source for future studies on the biology of particle-associated bacteria.
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Affiliation(s)
- Anneke Heins
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf I Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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Miksch S, Meiners M, Meyerdierks A, Probandt D, Wegener G, Titschack J, Jensen MA, Ellrott A, Amann R, Knittel K. Bacterial communities in temperate and polar coastal sands are seasonally stable. ISME COMMUNICATIONS 2021; 1:29. [PMID: 36739458 PMCID: PMC9723697 DOI: 10.1038/s43705-021-00028-w] [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: 05/11/2021] [Revised: 05/13/2021] [Accepted: 05/24/2021] [Indexed: 04/18/2023]
Abstract
Coastal sands are biocatalytic filters for dissolved and particulate organic matter of marine and terrestrial origin, thus, acting as centers of organic matter transformation. At high temporal resolution, we accessed the variability of benthic bacterial communities over two annual cycles at Helgoland (North Sea), and compared it with seasonality of communities in Isfjorden (Svalbard, 78°N) sediments, where primary production does not occur during winter. Benthic community structure remained stable in both, temperate and polar sediments on the level of cell counts and 16S rRNA-based taxonomy. Actinobacteriota of uncultured Actinomarinales and Microtrichales were a major group, with 8 ± 1% of total reads (Helgoland) and 31 ± 6% (Svalbard). Their high activity (frequency of dividing cells 28%) and in situ cell numbers of >10% of total microbes in Svalbard sediments, suggest Actinomarinales and Microtrichales as key heterotrophs for carbon mineralization. Even though Helgoland and Svalbard sampling sites showed no phytodetritus-driven changes of the benthic bacterial community structure, they harbored significantly different communities (p < 0.0001, r = 0.963). The temporal stability of benthic bacterial communities is in stark contrast to the dynamic succession typical of coastal waters, suggesting that pelagic and benthic bacterial communities respond to phytoplankton productivity very differently.
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Affiliation(s)
| | - Mirja Meiners
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - David Probandt
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Jürgen Titschack
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Senckenberg am Meer, Wilhelmshaven, Germany
| | - Maria A Jensen
- UNIS, The University Centre in Svalbard, Longyearbyen, Norway
| | - Andreas Ellrott
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katrin Knittel
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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47
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Artificial neural network analysis of microbial diversity in the central and southern Adriatic Sea. Sci Rep 2021; 11:11186. [PMID: 34045659 PMCID: PMC8159981 DOI: 10.1038/s41598-021-90863-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/17/2021] [Indexed: 11/29/2022] Open
Abstract
Bacteria are an active and diverse component of pelagic communities. The identification of main factors governing microbial diversity and spatial distribution requires advanced mathematical analyses. Here, the bacterial community composition was analysed, along with a depth profile, in the open Adriatic Sea using amplicon sequencing of bacterial 16S rRNA and the Neural gas algorithm. The performed analysis classified the sample into four best matching units representing heterogenic patterns of the bacterial community composition. The observed parameters were more differentiated by depth than by area, with temperature and identified salinity as important environmental variables. The highest diversity was observed at the deep chlorophyll maximum, while bacterial abundance and production peaked in the upper layers. The most of the identified genera belonged to Proteobacteria, with uncultured AEGEAN-169 and SAR116 lineages being dominant Alphaproteobacteria, and OM60 (NOR5) and SAR86 being dominant Gammaproteobacteria. Marine Synechococcus and Cyanobium-related species were predominant in the shallow layer, while Prochlorococcus MIT 9313 formed a higher portion below 50 m depth. Bacteroidota were represented mostly by uncultured lineages (NS4, NS5 and NS9 marine lineages). In contrast, Actinobacteriota were dominated by a candidatus genus Ca. Actinomarina. A large contribution of Nitrospinae was evident at the deepest investigated layer. Our results document that neural network analysis of environmental data may provide a novel insight into factors affecting picoplankton in the open sea environment.
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Thompson AW, Ward AC, Sweeney CP, Sutherland KR. Host-specific symbioses and the microbial prey of a pelagic tunicate (Pyrosoma atlanticum). ISME COMMUNICATIONS 2021; 1:11. [PMID: 36721065 PMCID: PMC9723572 DOI: 10.1038/s43705-021-00007-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/12/2021] [Accepted: 02/24/2021] [Indexed: 02/03/2023]
Abstract
Pyrosomes are widely distributed pelagic tunicates that have the potential to reshape marine food webs when they bloom. However, their grazing preferences and interactions with the background microbial community are poorly understood. This is the first study of the marine microorganisms associated with pyrosomes undertaken to improve the understanding of pyrosome biology, the impact of pyrosome blooms on marine microbial systems, and microbial symbioses with marine animals. The diversity, relative abundance, and taxonomy of pyrosome-associated microorganisms were compared to seawater during a Pyrosoma atlanticum bloom in the Northern California Current System using high-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry. We found that pyrosomes harbor a microbiome distinct from the surrounding seawater, which was dominated by a few novel taxa. In addition to the dominant taxa, numerous more rare pyrosome-specific microbial taxa were recovered. Multiple bioluminescent taxa were present in pyrosomes, which may be a source of the iconic pyrosome luminescence. We also discovered free-living marine microorganisms in association with pyrosomes, suggesting that pyrosome feeding impacts all microbial size classes but preferentially removes larger eukaryotic taxa. This study demonstrates that microbial symbionts and microbial prey are central to pyrosome biology. In addition to pyrosome impacts on higher trophic level marine food webs, the work suggests that pyrosomes also alter marine food webs at the microbial level through feeding and seeding of the marine microbial communities with their symbionts. Future efforts to predict pyrosome blooms, and account for their ecosystem impacts, should consider pyrosome interactions with marine microbial communities.
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Affiliation(s)
- Anne W Thompson
- Department of Biology, Portland State University, Portland, OR, USA.
| | - Anna C Ward
- Oregon Institute of Marine Biology, University of Oregon, Eugene, OR, USA
| | - Carey P Sweeney
- Department of Biology, Portland State University, Portland, OR, USA
| | - Kelly R Sutherland
- Oregon Institute of Marine Biology, University of Oregon, Eugene, OR, USA
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49
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Lambert S, Lozano JC, Bouget FY, Galand PE. Seasonal marine microorganisms change neighbours under contrasting environmental conditions. Environ Microbiol 2021; 23:2592-2604. [PMID: 33760330 DOI: 10.1111/1462-2920.15482] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/12/2020] [Accepted: 03/23/2021] [Indexed: 01/04/2023]
Abstract
Marine picoplankton contribute to global carbon sequestration and nutrient recycling. These processes are directly related to the composition of communities, which in turn depends on microbial interactions and environmental forcing. Under regular seasonal cycles, marine communities show strong predictable patterns of annual re-occurrences, but little is known about the effect of environmental perturbation on their organization. The aim of our study was to investigate the co-occurrence patterns of planktonic picoeukaryote, bacteria and archaea under contrasting environmental conditions. The study was designed to have high sampling frequency that could match both the biological rhythm of marine microbes and the short time scale of extreme weather events. Our results show that microbial networks changed from year to year depending on conditions. In addition, individual taxa became less interconnected and changed neighbours, which revealed an unfaithful relationship between marine microorganisms. This unexpected pattern suggests possible switches between organisms that have similar specific functions, or hints at the presence of organisms that share similar environmental niches without interacting. Despite the observed annual changes, the time series showed re-occurring communities that appear to recover from perturbations. Changing co-occurrence patterns between marine microorganisms may allow the long-term stability of ecosystems exposed to contrasting meteorological events.
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Affiliation(s)
- Stefan Lambert
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Jean-Claude Lozano
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), 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
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
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50
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Heins A, Reintjes G, Amann RI, Harder J. Particle Collection in Imhoff Sedimentation Cones Enriches Both Motile Chemotactic and Particle-Attached Bacteria. Front Microbiol 2021; 12:643730. [PMID: 33868201 PMCID: PMC8047139 DOI: 10.3389/fmicb.2021.643730] [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: 12/18/2020] [Accepted: 03/01/2021] [Indexed: 11/13/2022] Open
Abstract
Marine heterotrophic microorganisms remineralize about half of the annual primary production, with the microbiomes on and around algae and particles having a major contribution. These microbiomes specifically include free-living chemotactic and particle-attached bacteria, which are often difficult to analyze individually, as the standard method of size-selective filtration only gives access to particle-attached bacteria. In this study, we demonstrated that particle collection in Imhoff sedimentation cones enriches microbiomes that included free-living chemotactic bacteria and were distinct from particle microbiomes obtained by filtration or centrifugation. Coastal seawater was collected during North Sea phytoplankton spring blooms, and the microbiomes were investigated using 16S rRNA amplicon sequencing and fluorescence microscopy. Enrichment factors of individual operational taxonomic units (OTUs) were calculated for comparison of fractionated communities after separation with unfractionated seawater communities. Filtration resulted in a loss of cells and yielded particle fractions including bacterial aggregates, filaments, and large cells. Centrifugation had the lowest separation capacity. Particles with a sinking rate of >2.4 m day-1 were collected in sedimentation cones as a bottom fraction and enriched in free-living chemotactic bacteria, i.e., Sulfitobacter, Pseudoalteromonas, and Vibrio. Subfractions of these bottom fractions, obtained by centrifugation, showed enrichment of either free-living or particle-attached bacteria. We identified five distinct enrichment patterns across all separation techniques: mechano-sensitive and mechano-stable free-living bacteria and three groups of particle-attached bacteria. Simultaneous enrichment of particle-attached and chemotactic free-living bacteria in Imhoff sedimentation cones is a novel experimental access to these groups providing more insights into the diversity, structure, and function of particle-associated microbiomes, including members of the phycosphere.
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Affiliation(s)
- Anneke Heins
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Greta Reintjes
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Rudolf I Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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