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Bydalek F, Webster G, Barden R, Weightman AJ, Kasprzyk-Hordern B, Wenk J. Microbial community and antimicrobial resistance niche differentiation in a multistage, surface flow constructed wetland. WATER RESEARCH 2024; 254:121408. [PMID: 38442607 DOI: 10.1016/j.watres.2024.121408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 03/07/2024]
Abstract
Free-living (FL) and particulate-associated (PA) communities are distinct bacterioplankton lifestyles with different mobility and dissemination routes. Understanding spatio-temporal dynamics of PA and FL fractions will allow improvement to wastewater treatment processes including pathogen and AMR bacteria removal. In this study, PA, FL and sediment community composition and antimicrobial resistance gene (ARG; tetW, ermB, sul1, intI1) dynamics were investigated in a full-scale municipal wastewater free-water surface polishing constructed wetland. Taxonomic composition of PA and FL microbial communities shifted towards less diverse communities (Shannon, Chao1) at the CW effluent but retained a distinct fraction-specific composition. Wastewater treatment plant derived PA communities introduced the bulk of AMR load (70 %) into the CW. However, the FL fraction was responsible for exporting over 60 % of the effluent AMR load given its high mobility and the effective immobilization (1-3 log removal) of PA communities. Strong correlations (r2>0.8, p < 0.05) were observed between the FL fraction, tetW and emrB dynamics, and amplicon sequence variants (ASVs) of potentially pathogenic taxa, including Bacteroides, Enterobacteriaceae, Aeromonadaceae, and Lachnospiraceae. This study reveals niche differentiation of microbial communities and associated AMR in CWs and shows that free-living bacteria are a primary escape route of pathogenic and ARG load from CWs under low-flow hydraulic conditions.
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Affiliation(s)
- Franciszek Bydalek
- Department of Chemical Engineering, University of Bath, Claverton Down, Bath BA2 7AY, UK; Water Innovation and Research Centre (WIRC), University of Bath, Bath BA2 7AY, UK; GW4 NERC CDT in Freshwater Biosciences and Sustainability, Cardiff University, Cardiff CF10 3AX, UK; Organisms and Environment Division, School of Biosciences, Microbiomes, Microbes and Informatics Group, Cardiff University, Cardiff CF10 3AX, UK
| | - Gordon Webster
- Organisms and Environment Division, School of Biosciences, Microbiomes, Microbes and Informatics Group, Cardiff University, Cardiff CF10 3AX, UK
| | | | - Andrew J Weightman
- Organisms and Environment Division, School of Biosciences, Microbiomes, Microbes and Informatics Group, Cardiff University, Cardiff CF10 3AX, UK
| | - Barbara Kasprzyk-Hordern
- Water Innovation and Research Centre (WIRC), University of Bath, Bath BA2 7AY, UK; Department of Chemistry, University of Bath, Bath BA2 7AY, UK
| | - Jannis Wenk
- Department of Chemical Engineering, University of Bath, Claverton Down, Bath BA2 7AY, UK; Water Innovation and Research Centre (WIRC), University of Bath, Bath BA2 7AY, UK.
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2
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Siebers R, Schultz D, Farza MS, Brauer A, Zühlke D, Mücke PA, Wang F, Bernhardt J, Teeling H, Becher D, Riedel K, Kirstein IV, Wiltshire KH, Hoff KJ, Schweder T, Urich T, Bengtsson MM. Marine particle microbiomes during a spring diatom bloom contain active sulfate-reducing bacteria. FEMS Microbiol Ecol 2024; 100:fiae037. [PMID: 38490736 PMCID: PMC11008741 DOI: 10.1093/femsec/fiae037] [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: 09/26/2023] [Revised: 02/08/2024] [Accepted: 03/14/2024] [Indexed: 03/17/2024] Open
Abstract
Phytoplankton blooms fuel marine food webs with labile dissolved carbon and also lead to the formation of particulate organic matter composed of living and dead algal cells. These particles contribute to carbon sequestration and are sites of intense algal-bacterial interactions, providing diverse niches for microbes to thrive. We analyzed 16S and 18S ribosomal RNA gene amplicon sequences obtained from 51 time points and metaproteomes from 3 time points during a spring phytoplankton bloom in a shallow location (6-10 m depth) in the North Sea. Particulate fractions larger than 10 µm diameter were collected at near daily intervals between early March and late May in 2018. Network analysis identified two major modules representing bacteria co-occurring with diatoms and with dinoflagellates, respectively. The diatom network module included known sulfate-reducing Desulfobacterota as well as potentially sulfur-oxidizing Ectothiorhodospiraceae. Metaproteome analyses confirmed presence of key enzymes involved in dissimilatory sulfate reduction, a process known to occur in sinking particles at greater depths and in sediments. Our results indicate the presence of sufficiently anoxic niches in the particle fraction of an active phytoplankton bloom to sustain sulfate reduction, and an important role of benthic-pelagic coupling for microbiomes in shallow environments. Our findings may have implications for the understanding of algal-bacterial interactions and carbon export during blooms in shallow-water coastal areas.
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Affiliation(s)
- Robin Siebers
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Doreen Schultz
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Mohamed S Farza
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Anne Brauer
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Pierre A Mücke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Fengqing Wang
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Inga V Kirstein
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, 27498 Helgoland, Germany
| | - Karen H Wiltshire
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, 27498 Helgoland, Germany
| | - Katharina J Hoff
- Institute of Mathematics and Computer Science, University of Greifswald, 17489 Greifswald, Germany
| | - Thomas Schweder
- Institute of Marine Biotechnology, 17489 Greifswald, Germany
- Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Mia M Bengtsson
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, 17489 Greifswald, Germany
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, 27498 Helgoland, Germany
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3
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Kalenborn S, Zühlke D, Riedel K, Amann RI, Harder J. Proteomic insight into arabinogalactan utilization by particle-associated Maribacter sp. MAR_2009_72. FEMS Microbiol Ecol 2024; 100:fiae045. [PMID: 38569650 PMCID: PMC11036162 DOI: 10.1093/femsec/fiae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/13/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024] Open
Abstract
Arabinose and galactose are major, rapidly metabolized components of marine particulate and dissolved organic matter. In this study, we observed for the first time large microbiomes for the degradation of arabinogalactan and report a detailed investigation of arabinogalactan utilization by the flavobacterium Maribacter sp. MAR_2009_72. Cellular extracts hydrolysed arabinogalactan in vitro. Comparative proteomic analyses of cells grown on arabinogalactan, arabinose, galactose, and glucose revealed the expression of specific proteins in the presence of arabinogalactan, mainly glycoside hydrolases (GH). Extracellular glycan hydrolysis involved five alpha-l-arabinofuranosidases affiliating with glycoside hydrolase families 43 and 51, four unsaturated rhamnogalacturonylhydrolases (GH105) and a protein with a glycoside hydrolase family-like domain. We detected expression of three induced TonB-dependent SusC/D transporter systems, one SusC, and nine glycoside hydrolases with a predicted periplasmatic location. These are affiliated with the families GH3, GH10, GH29, GH31, GH67, GH78, and GH115. The genes are located outside of and within canonical polysaccharide utilization loci classified as specific for arabinogalactan, for galactose-containing glycans, and for arabinose-containing glycans. The breadth of enzymatic functions expressed in Maribacter sp. MAR_2009_72 as response to arabinogalactan from the terrestrial plant larch suggests that Flavobacteriia are main catalysts of the rapid turnover of arabinogalactans in the marine environment.
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Affiliation(s)
- Saskia Kalenborn
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Daniela Zühlke
- Department for Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, D-17489 Greifswald, Germany
| | - Katharina Riedel
- Department for Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, D-17489 Greifswald, Germany
| | - Rudolf I Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
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4
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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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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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Sidhu C, Kirstein IV, Meunier CL, Rick J, Fofonova V, Wiltshire KH, Steinke N, Vidal-Melgosa S, Hehemann JH, Huettel B, Schweder T, Fuchs BM, Amann RI, Teeling H. Dissolved storage glycans shaped the community composition of abundant bacterioplankton clades during a North Sea spring phytoplankton bloom. MICROBIOME 2023; 11:77. [PMID: 37069671 PMCID: PMC10108472 DOI: 10.1186/s40168-023-01517-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/15/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Blooms of marine microalgae play a pivotal role in global carbon cycling. Such blooms entail successive blooms of specialized clades of planktonic bacteria that collectively remineralize gigatons of algal biomass on a global scale. This biomass is largely composed of distinct polysaccharides, and the microbial decomposition of these polysaccharides is therefore a process of prime importance. RESULTS In 2020, we sampled a complete biphasic spring bloom in the German Bight over a 90-day period. Bacterioplankton metagenomes from 30 time points allowed reconstruction of 251 metagenome-assembled genomes (MAGs). Corresponding metatranscriptomes highlighted 50 particularly active MAGs of the most abundant clades, including many polysaccharide degraders. Saccharide measurements together with bacterial polysaccharide utilization loci (PUL) expression data identified β-glucans (diatom laminarin) and α-glucans as the most prominent and actively metabolized dissolved polysaccharide substrates. Both substrates were consumed throughout the bloom, with α-glucan PUL expression peaking at the beginning of the second bloom phase shortly after a peak in flagellate and the nadir in bacterial total cell counts. CONCLUSIONS We show that the amounts and composition of dissolved polysaccharides, in particular abundant storage polysaccharides, have a pronounced influence on the composition of abundant bacterioplankton members during phytoplankton blooms, some of which compete for similar polysaccharide niches. We hypothesize that besides the release of algal glycans, also recycling of bacterial glycans as a result of increased bacterial cell mortality can have a significant influence on bacterioplankton composition during phytoplankton blooms. Video Abstract.
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Affiliation(s)
- Chandni Sidhu
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Inga V. Kirstein
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, P.O. Box 180, 27483 Helgoland, Germany
| | - Cédric L. Meunier
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, P.O. Box 180, 27483 Helgoland, Germany
| | - Johannes Rick
- Alfred Wegener Institute for Polar and Marine Research, Hafenstraße 43, 25992 List/Sylt, Germany
| | - Vera Fofonova
- Alfred Wegener Institute for Polar and Marine Research, Klußmannstraße 3, 27570 Bremerhaven, Germany
| | - Karen H. Wiltshire
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, P.O. Box 180, 27483 Helgoland, Germany
| | - Nicola Steinke
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Leobener Straße 8, 28359 Bremen, Germany
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Leobener Straße 8, 28359 Bremen, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Leobener Straße 8, 28359 Bremen, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Carl Von Linné-Weg 10, 50829 Cologne, 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
| | - Rudolf I. Amann
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
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7
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Heins A, Harder J. Particle-associated bacteria in seawater dominate the colony-forming microbiome on ZoBell marine agar. FEMS Microbiol Ecol 2022; 99:6895545. [PMID: 36513318 PMCID: PMC9798892 DOI: 10.1093/femsec/fiac151] [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: 07/27/2022] [Revised: 11/03/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Planktonic particle-associated bacteria comprise particle-attached and motile free-living cells. These groups were obtained by settlement in Imhoff cones. Dilution plating on marine agar 2216 (ZoBell marine agar) and microscopic counts indicated a cultivability of 0.7% (0.4%-1.2%) of bacteria in coastal seawater collected at Helgoland Roads, North Sea. Particle-associated bacteria presented a minority population in seawater, but had a larger cultivability of 25% (0.9%-100%) for populations collected by settlement of particles and 5.7% (0.9%-24%) for populations collected by filtration. Partial 16S rRNA gene sequences indicated that 84% of the cultured taxa were either enriched in particle-associated microbiomes or only found in these microbiomes, including Sulfitobacter and other Rhodobacteraceae, Pseudoalteromonas, Psychromonas, Arcobacter and many Flavobacteriaceae. Illumina-based 16S rRNA V3V4 amplicon sequences of plate communities revealed that nearly all operational taxonomic units had a cultivated and described strain in close phylogenetic proximity. This suggested that decades of strain isolation from seawater on ZoBell marine agar had achieved a very good coverage of cultivable genera abundant in nature. The majority belonged to particle-associated bacteria, complementing observations that abundant free-living seawater bacteria often require cultivation conditions closer to their natural habitat like liquid cultivation in oligotrophic medium.
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Affiliation(s)
- Anneke Heins
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr.1, D-28359 Bremen, Germany
| | - Jens Harder
- Corresponding author: Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr.1, D-28359 Bremen, Germany. E-mail:
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8
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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: 11] [Impact Index Per Article: 5.5] [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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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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