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Shih CY, Chen SY, Hsu CR, Chin CH, Chiu WC, Chang MH, Kang LK, Yang CH, Pai TW, Hu CH, Hsu PH, Tzou WS. Distinctive microbial community and genome structure in coastal seawater from a human-made port and nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean. PLoS One 2023; 18:e0284022. [PMID: 37294811 PMCID: PMC10256201 DOI: 10.1371/journal.pone.0284022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 03/21/2023] [Indexed: 06/11/2023] Open
Abstract
Pollution in human-made fishing ports caused by petroleum from boats, dead fish, toxic chemicals, and effluent poses a challenge to the organisms in seawater. To decipher the impact of pollution on the microbiome, we collected surface water from a fishing port and a nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean. By employing 16S rRNA gene amplicon sequencing and whole-genome shotgun sequencing, we discovered that Rhodobacteraceae, Vibrionaceae, and Oceanospirillaceae emerged as the dominant species in the fishing port, where we found many genes harboring the functions of antibiotic resistance (ansamycin, nitroimidazole, and aminocoumarin), metal tolerance (copper, chromium, iron and multimetal), virulence factors (chemotaxis, flagella, T3SS1), carbohydrate metabolism (biofilm formation and remodeling of bacterial cell walls), nitrogen metabolism (denitrification, N2 fixation, and ammonium assimilation), and ABC transporters (phosphate, lipopolysaccharide, and branched-chain amino acids). The dominant bacteria at the nearby offshore island (Alteromonadaceae, Cryomorphaceae, Flavobacteriaceae, Litoricolaceae, and Rhodobacteraceae) were partly similar to those in the South China Sea and the East China Sea. Furthermore, we inferred that the microbial community network of the cooccurrence of dominant bacteria on the offshore island was connected to dominant bacteria in the fishing port by mutual exclusion. By examining the assembled microbial genomes collected from the coastal seawater of the fishing port, we revealed four genomic islands containing large gene-containing sequences, including phage integrase, DNA invertase, restriction enzyme, DNA gyrase inhibitor, and antitoxin HigA-1. In this study, we provided clues for the possibility of genomic islands as the units of horizontal transfer and as the tools of microbes for facilitating adaptation in a human-made port environment.
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Affiliation(s)
- Chi-Yu Shih
- Bachelor Degree Program in Marine Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Taiwan Ocean Genome Center, National Taiwan Ocean University, Keelung, Taiwan
| | - Shiow-Yi Chen
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Chun-Ru Hsu
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Ching-Hsiang Chin
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Wei-Chih Chiu
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | | | - Lee-Kuo Kang
- Bachelor Degree Program in Marine Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Cing-Han Yang
- Department of Computer Science and Information Engineering, National Taipei University of Technology, Taipei, Taiwan
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Tun-Wen Pai
- Department of Computer Science and Information Engineering, National Taipei University of Technology, Taipei, Taiwan
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Chin-Hwa Hu
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Pang-Hung Hsu
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Wen-Shyong Tzou
- Taiwan Ocean Genome Center, National Taiwan Ocean University, Keelung, Taiwan
- Departent of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
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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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Oren A, Garrity GM. CANDIDATUS LIST No. 3. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 35100104 DOI: 10.1099/ijsem.0.005186] [Citation(s) in RCA: 251] [Impact Index Per Article: 125.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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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: 25] [Impact Index Per Article: 8.3] [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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Wolter LA, Mitulla M, Kalem J, Daniel R, Simon M, Wietz M. CAZymes in Maribacter dokdonensis 62-1 From the Patagonian Shelf: Genomics and Physiology Compared to Related Flavobacteria and a Co-occurring Alteromonas Strain. Front Microbiol 2021; 12:628055. [PMID: 33912144 PMCID: PMC8072126 DOI: 10.3389/fmicb.2021.628055] [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: 11/11/2020] [Accepted: 03/10/2021] [Indexed: 02/05/2023] Open
Abstract
Carbohydrate-active enzymes (CAZymes) are an important feature of bacteria in productive marine systems such as continental shelves, where phytoplankton and macroalgae produce diverse polysaccharides. We herein describe Maribacter dokdonensis 62–1, a novel strain of this flavobacterial species, isolated from alginate-supplemented seawater collected at the Patagonian continental shelf. M. dokdonensis 62–1 harbors a diverse array of CAZymes in multiple polysaccharide utilization loci (PUL). Two PUL encoding polysaccharide lyases from families 6, 7, 12, and 17 allow substantial growth with alginate as sole carbon source, with simultaneous utilization of mannuronate and guluronate as demonstrated by HPLC. Furthermore, strain 62-1 harbors a mixed-feature PUL encoding both ulvan- and fucoidan-targeting CAZymes. Core-genome phylogeny and pangenome analysis revealed variable occurrence of these PUL in related Maribacter and Zobellia strains, indicating specialization to certain “polysaccharide niches.” Furthermore, lineage- and strain-specific genomic signatures for exopolysaccharide synthesis possibly mediate distinct strategies for surface attachment and host interaction. The wide detection of CAZyme homologs in algae-derived metagenomes suggests global occurrence in algal holobionts, supported by sharing multiple adaptive features with the hydrolytic model flavobacterium Zobellia galactanivorans. Comparison with Alteromonas sp. 76-1 isolated from the same seawater sample revealed that these co-occurring strains target similar polysaccharides but with different genomic repertoires, coincident with differing growth behavior on alginate that might mediate ecological specialization. Altogether, our study contributes to the perception of Maribacter as versatile flavobacterial polysaccharide degrader, with implications for biogeochemical cycles, niche specialization and bacteria-algae interactions in the oceans.
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Affiliation(s)
- Laura A Wolter
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany.,JST ERATO Nomura Project, Faculty of Life and Environmental Sciences, Tsukuba, Japan
| | - Maximilian Mitulla
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Jovan Kalem
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany.,Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
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