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Balmonte JP, Giebel HA, Arnosti C, Simon M, Wietz M. Distinct bacterial succession and functional response to alginate in the South, Equatorial, and North Pacific Ocean. Environ Microbiol 2024; 26:e16594. [PMID: 38418376 DOI: 10.1111/1462-2920.16594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 01/26/2024] [Indexed: 03/01/2024]
Abstract
The availability of alginate, an abundant macroalgal polysaccharide, induces compositional and functional responses among marine microbes, but these dynamics have not been characterized across the Pacific Ocean. We investigated alginate-induced compositional and functional shifts (e.g., heterotrophic production, glucose turnover, hydrolytic enzyme activities) of microbial communities in the South Subtropical, Equatorial, and Polar Frontal North Pacific in mesocosms. We observed that shifts in response to alginate were site-specific. In the South Subtropical Pacific, prokaryotic cell counts, glucose turnover, and peptidase activities changed the most with alginate addition, along with the enrichment of the widest range of particle-associated taxa (161 amplicon sequence variants; ASVs) belonging to Alteromonadaceae, Rhodobacteraceae, Phormidiaceae, and Pseudoalteromonadaceae. Some of these taxa were detected at other sites but only enriched in the South Pacific. In the Equatorial Pacific, glucose turnover and heterotrophic prokaryotic production increased most rapidly; a single Alteromonas taxon dominated (60% of the community) but remained low (<2%) elsewhere. In the North Pacific, the particle-associated community response to alginate was gradual, with a more limited range of alginate-enriched taxa (82 ASVs). Thus, alginate-related ecological and biogeochemical shifts depend on a combination of factors that include the ability to utilize alginate, environmental conditions, and microbial interactions.
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Affiliation(s)
- John Paul Balmonte
- Department of Earth, Marine and Environmental Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Earth and Environmental Sciences, Lehigh University, Bethlehem, PA, USA
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Carol Arnosti
- Department of Earth, Marine and Environmental Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
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Wietz M, Engel A, Ramondenc S, Niwano M, von Appen WJ, Priest T, von Jackowski A, Metfies K, Bienhold C, Boetius A. The Arctic summer microbiome across Fram Strait: Depth, longitude, and substrate concentrations structure microbial diversity in the euphotic zone. Environ Microbiol 2024; 26:e16568. [PMID: 38268397 DOI: 10.1111/1462-2920.16568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024]
Abstract
The long-term dynamics of microbial communities across geographic, hydrographic, and biogeochemical gradients in the Arctic Ocean are largely unknown. To address this, we annually sampled polar, mixed, and Atlantic water masses of the Fram Strait (2015-2019; 5-100 m depth) to assess microbiome composition, substrate concentrations, and oceanographic parameters. Longitude and water depth were the major determinants (~30%) of microbial community variability. Bacterial alpha diversity was highest in lower-photic polar waters. Community composition shifted from west to east, with the prevalence of, for example, Dadabacteriales and Thiotrichales in Arctic- and Atlantic-influenced waters, respectively. Concentrations of dissolved organic carbon peaked in the western, compared to carbohydrates in the chlorophyll-maximum of eastern Fram Strait. Interannual differences due to the time of sampling, which varied between early (June 2016/2018) and late (September 2019) phytoplankton bloom stages, illustrated that phytoplankton composition and resulting availability of labile substrates influence bacterial dynamics. We identified 10 species clusters with stable environmental correlations, representing signature populations of distinct ecosystem states. In context with published metagenomic evidence, our microbial-biogeochemical inventory of a key Arctic region establishes a benchmark to assess ecosystem dynamics and the imprint of climate change.
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Affiliation(s)
- Matthias Wietz
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Anja Engel
- Biological Oceanography, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Simon Ramondenc
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Matomo Niwano
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Wilken-Jon von Appen
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Taylor Priest
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Anabel von Jackowski
- Biological Oceanography, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany
| | - Christina Bienhold
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antje Boetius
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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Oldenburg E, Popa O, Wietz M, von Appen WJ, Torres-Valdes S, Bienhold C, Ebenhöh O, Metfies K. Sea-ice melt determines seasonal phytoplankton dynamics and delimits the habitat of temperate Atlantic taxa as the Arctic Ocean atlantifies. ISME Commun 2024; 4:ycae027. [PMID: 38515865 PMCID: PMC10955684 DOI: 10.1093/ismeco/ycae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/23/2024]
Abstract
The Arctic Ocean is one of the regions where anthropogenic environmental change is progressing most rapidly and drastically. The impact of rising temperatures and decreasing sea ice on Arctic marine microbial communities is yet not well understood. Microbes form the basis of food webs in the Arctic Ocean, providing energy for larger organisms. Previous studies have shown that Atlantic taxa associated with low light are robust to more polar conditions. We compared to which extent sea ice melt influences light-associated phytoplankton dynamics and biodiversity over two years at two mooring locations in the Fram Strait. One mooring is deployed in pure Atlantic water, and the second in the intermittently ice-covered Marginal Ice Zone. Time-series analysis of amplicon sequence variants abundance over a 2-year period, allowed us to identify communities of co-occurring taxa that exhibit similar patterns throughout the annual cycle. We then examined how alterations in environmental conditions affect the prevalence of species. During high abundance periods of diatoms, polar phytoplankton populations dominated, while temperate taxa were weakly represented. Furthermore, we found that polar pelagic and ice-associated taxa, such as Fragilariopsis cylindrus and Melosira arctica, were more common in Atlantic conditions, while temperate taxa, such as Odontella aurita and Proboscia alata, were less abundant under polar conditions. This suggests that sea ice melt may act as a barrier to the northward expansion of temperate phytoplankton, preventing their dominance in regions still strongly influenced by polar conditions. Our findings highlight the complex interactions between sea ice melt, phytoplankton dynamics, and biodiversity in the Arctic.
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Affiliation(s)
- Ellen Oldenburg
- Institute of Quantitative and Theoretical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Ovidiu Popa
- Institute of Quantitative and Theoretical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Matthias Wietz
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1 D-28359 Bremen, Germany
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12 D-27570 Bremerhaven, Germany
| | - Wilken-Jon von Appen
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12 D-27570 Bremerhaven, Germany
| | - Sinhue Torres-Valdes
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12 D-27570 Bremerhaven, Germany
| | - Christina Bienhold
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1 D-28359 Bremen, Germany
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12 D-27570 Bremerhaven, Germany
| | - Oliver Ebenhöh
- Institute of Quantitative and Theoretical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12 D-27570 Bremerhaven, Germany
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Priest T, von Appen WJ, Oldenburg E, Popa O, Torres-Valdés S, Bienhold C, Metfies K, Boulton W, Mock T, Fuchs BM, Amann R, Boetius A, Wietz M. Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities. ISME J 2023; 17:1612-1625. [PMID: 37422598 PMCID: PMC10504371 DOI: 10.1038/s41396-023-01461-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 07/10/2023]
Abstract
The Arctic Ocean is experiencing unprecedented changes because of climate warming, necessitating detailed analyses on the ecology and dynamics of biological communities to understand current and future ecosystem shifts. Here, we generated a four-year, high-resolution amplicon dataset along with one annual cycle of PacBio HiFi read metagenomes from the East Greenland Current (EGC), and combined this with datasets spanning different spatiotemporal scales (Tara Arctic and MOSAiC) to assess the impact of Atlantic water influx and sea-ice cover on bacterial communities in the Arctic Ocean. Densely ice-covered polar waters harboured a temporally stable, resident microbiome. Atlantic water influx and reduced sea-ice cover resulted in the dominance of seasonally fluctuating populations, resembling a process of "replacement" through advection, mixing and environmental sorting. We identified bacterial signature populations of distinct environmental regimes, including polar night and high-ice cover, and assessed their ecological roles. Dynamics of signature populations were consistent across the wider Arctic; e.g. those associated with dense ice cover and winter in the EGC were abundant in the central Arctic Ocean in winter. Population- and community-level analyses revealed metabolic distinctions between bacteria affiliated with Arctic and Atlantic conditions; the former with increased potential to use bacterial- and terrestrial-derived substrates or inorganic compounds. Our evidence on bacterial dynamics over spatiotemporal scales provides novel insights into Arctic ecology and indicates a progressing Biological Atlantification of the warming Arctic Ocean, with consequences for food webs and biogeochemical cycles.
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Affiliation(s)
- Taylor Priest
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany.
| | - Wilken-Jon von Appen
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - Ellen Oldenburg
- Institute for Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Ovidiu Popa
- Institute for Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Sinhué Torres-Valdés
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - Christina Bienhold
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - William Boulton
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, 28359, Germany
| | - Matthias Wietz
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany.
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany.
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Rahlff J, Wietz M, Giebel HA, Bayfield O, Nilsson E, Bergström K, Kieft K, Anantharaman K, Ribas-Ribas M, Schweitzer HD, Wurl O, Hoetzinger M, Antson A, Holmfeldt K. Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick. ISME Commun 2023; 3:97. [PMID: 37723220 PMCID: PMC10507051 DOI: 10.1038/s43705-023-00307-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023]
Abstract
Visible surface films, termed slicks, can extensively cover freshwater and marine ecosystems, with coastal regions being particularly susceptible to their presence. The sea-surface microlayer (SML), the upper 1-mm at the air-water interface in slicks (herein slick SML) harbors a distinctive bacterial community, but generally little is known about SML viruses. Using flow cytometry, metagenomics, and cultivation, we characterized viruses and bacteria in a brackish slick SML in comparison to non-slick SML as well as seawater below slick and non-slick areas (subsurface water = SSW). Size-fractionated filtration of all samples distinguished viral attachment to hosts and particles. The slick SML contained higher abundances of virus-like particles, prokaryotic cells, and dissolved organic carbon compared to non-slick SML and SSW. The community of 428 viral operational taxonomic units (vOTUs), 426 predicted as lytic, distinctly differed across all size fractions in the slick SML compared to non-slick SML and SSW. Specific metabolic profiles of bacterial metagenome-assembled genomes and isolates in the slick SML included a prevalence of genes encoding motility and carbohydrate-active enzymes (CAZymes). Several vOTUs were enriched in slick SML, and many virus variants were associated with particles. Nine vOTUs were only found in slick SML, six of them being targeted by slick SML-specific clustered-regularly interspaced short palindromic repeats (CRISPR) spacers likely originating from Gammaproteobacteria. Moreover, isolation of three previously unknown lytic phages for Alishewanella sp. and Pseudoalteromonas tunicata, abundant and actively replicating slick SML bacteria, suggests that viral activity in slicks contributes to biogeochemical cycling in coastal ecosystems.
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Affiliation(s)
- Janina Rahlff
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.
| | - Matthias Wietz
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Center for Marine Sensors (ZfMarS), Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Wilhelmshaven, Germany
| | - Oliver Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Emelie Nilsson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Kristofer Bergström
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Kristopher Kieft
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Mariana Ribas-Ribas
- Center of Marine Sensors (ZfMarS), Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Wilhelmshaven, Germany
| | | | - Oliver Wurl
- Center of Marine Sensors (ZfMarS), Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Wilhelmshaven, Germany
| | - Matthias Hoetzinger
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Alfred Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Karin Holmfeldt
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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Fadeev E, Carpaneto Bastos C, Hennenfeind JH, Biller SJ, Sher D, Wietz M, Herndl GJ. Characterization of membrane vesicles in Alteromonas macleodii indicates potential roles in their copiotrophic lifestyle. Microlife 2022; 4:uqac025. [PMID: 37223730 PMCID: PMC10117737 DOI: 10.1093/femsml/uqac025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/05/2022] [Accepted: 12/16/2022] [Indexed: 05/25/2023]
Abstract
Bacterial membrane vesicles (MVs) are abundant in the oceans, but their potential functional roles remain unclear. In this study we characterized MV production and protein content of six strains of Alteromonas macleodii, a cosmopolitan marine bacterium. Alteromonas macleodii strains varied in their MV production rates, with some releasing up to 30 MVs per cell per generation. Microscopy imaging revealed heterogenous MV morphologies, including some MVs aggregated within larger membrane structures. Proteomic characterization revealed that A. macleodii MVs are rich in membrane proteins related to iron and phosphate uptake, as well as proteins with potential functions in biofilm formation. Furthermore, MVs harbored ectoenzymes, such as aminopeptidases and alkaline phosphatases, which comprised up to 20% of the total extracellular enzymatic activity. Our results suggest that A. macleodii MVs may support its growth through generation of extracellular 'hotspots' that facilitate access to essential substrates. This study provides an important basis to decipher the ecological relevance of MVs in heterotrophic marine bacteria.
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Affiliation(s)
- Eduard Fadeev
- Corresponding author: Bio-Oceanography and Marine Biology Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria. E-mail:
| | - Cécile Carpaneto Bastos
- Bio-Oceanography and Marine Biology Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Jennifer H Hennenfeind
- Bio-Oceanography and Marine Biology Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Steven J Biller
- Department of Biological Sciences, Wellesley College, Central Street 106, MA 02481, Wellesley, United States
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Aba Khoushy Ave. 199, 3498838 Haifa, Israel
| | - Matthias Wietz
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
| | - Gerhard J Herndl
- Bio-Oceanography and Marine Biology Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University,1790 AB Den Burg, The Netherlands
- Vienna Metabolomics & Proteomics Center, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
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Wietz M, López-Pérez M, Sher D, Biller SJ, Rodriguez-Valera F. Microbe Profile: Alteromonas macleodii - a widespread, fast-responding, 'interactive' marine bacterium. Microbiology (Reading) 2022; 168. [PMID: 36748580 DOI: 10.1099/mic.0.001236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Alteromonas macleodii is a marine heterotrophic bacterium with widespread distribution - from temperate to tropical oceans, and from surface to deep waters. Strains of A. macleodii exhibit considerable genomic and metabolic variability, and can grow rapidly on diverse organic compounds. A. macleodii is a model organism for the study of population genomics, physiological adaptations and microbial interactions, with individual genomes encoding diverse phenotypic traits influenced by recombination and horizontal gene transfer.
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Affiliation(s)
- Matthias Wietz
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Steven J Biller
- Department of Biological Sciences, Wellesley College, Wellesley, Massachusetts, USA
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Wietz M, Metfies K, Bienhold C, Wolf C, Janssen F, Salter I, Boetius A. Impact of preservation method and storage period on ribosomal metabarcoding of marine microbes: Implications for remote automated samplings. Front Microbiol 2022; 13:999925. [PMID: 36160263 PMCID: PMC9490091 DOI: 10.3389/fmicb.2022.999925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Automated sampling technologies can enhance the temporal and spatial resolution of marine microbial observations, particularly in remote and inaccessible areas. A critical aspect of automated microbiome sampling is the preservation of nucleic acids over long-term autosampler deployments. Understanding the impact of preservation method on microbial metabarcoding is essential for implementing genomic observatories into existing infrastructure, and for establishing best practices for the regional and global synthesis of data. The present study evaluates the effect of two preservatives commonly used in autosampler deployments (mercuric chloride and formalin) and two extraction kits (PowerWater and NucleoSpin) on amplicon sequencing of 16S and 18S rRNA gene over 50 weeks of sample storage. Our results suggest the combination of mercuric chloride preservation and PowerWater extraction as most adequate for 16S and 18S rRNA gene amplicon-sequencing from the same seawater sample. This approach provides consistent information on species richness, diversity and community composition in comparison to control samples (nonfixed, filtered and frozen) when stored up to 50 weeks at in situ temperature. Preservation affects the recovery of certain taxa, with specific OTUs becoming overrepresented (SAR11 and diatoms) or underrepresented (Colwellia and pico-eukaryotes) after preservation. In case eukaryotic sequence information is the sole target, formalin preservation and NucleoSpin extraction performed best. Our study contributes to the design of long-term autonomous microbial observations in remote ocean areas, allowing cross-comparison of microbiome dynamics across sampling devices (e.g., water and particle samplers) and marine realms.
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Affiliation(s)
- Matthias Wietz
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- *Correspondence: Matthias Wietz,
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany
| | - Christina Bienhold
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Christian Wolf
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Felix Janssen
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ian Salter
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Faroe Marine Research Institute, Torshavn, Faroe Islands
| | - Antje Boetius
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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9
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von Jackowski A, Becker KW, Wietz M, Bienhold C, Zäncker B, Nöthig EM, Engel A. Variations of microbial communities and substrate regimes in the eastern Fram Strait between summer and fall. Environ Microbiol 2022; 24:4124-4136. [PMID: 35590443 DOI: 10.1111/1462-2920.16036] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 04/22/2022] [Accepted: 05/03/2022] [Indexed: 11/26/2022]
Abstract
Seasonal variations in day length and temperature, in combination with dynamic factors such as advection from the North Atlantic, influence primary production and the microbial loop in the Fram Strait. Here, we investigated the seasonal variability of biopolymers, microbial abundance, and microbial composition within the upper 100 m during summer and fall. Flow cytometry revealed a shift in the autotrophic community from picoeukaryotes dominating in summer to a 34-fold increase of Synechococcus by fall. Furthermore, a significant decline in biopolymers concentrations covaried with increasing microbial diversity based on 16S rRNA gene sequencing along with a community shift towards fewer polymer-degrading genera in fall. The seasonal succession in the biopolymer pool and microbes indicates distinct metabolic regimes, with a higher relative abundance of polysaccharide-degrading genera in summer and a higher relative abundance of common taxa in fall. The parallel analysis of DOM and microbial diversity provides an important baseline for microbe-substrate relationships over the seasonal cycle in the Arctic Ocean. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Kevin W Becker
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Matthias Wietz
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Christina Bienhold
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Birthe Zäncker
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Eva-Maria Nöthig
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Anja Engel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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10
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Wietz M, Bienhold C, Metfies K, Torres-Valdés S, von Appen WJ, Salter I, Boetius A. The polar night shift: seasonal dynamics and drivers of Arctic Ocean microbiomes revealed by autonomous sampling. ISME Commun 2021; 1:76. [PMID: 37938651 PMCID: PMC9723606 DOI: 10.1038/s43705-021-00074-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/03/2021] [Accepted: 11/15/2021] [Indexed: 06/15/2023]
Abstract
The Arctic Ocean features extreme seasonal differences in daylight, temperature, ice cover, and mixed layer depth. However, the diversity and ecology of microbes across these contrasting environmental conditions remain enigmatic. Here, using autonomous samplers and sensors deployed at two mooring sites, we portray an annual cycle of microbial diversity, nutrient concentrations and physical oceanography in the major hydrographic regimes of the Fram Strait. The ice-free West Spitsbergen Current displayed a marked separation into a productive summer (dominated by diatoms and carbohydrate-degrading bacteria) and regenerative winter state (dominated by heterotrophic Syndiniales, radiolarians, chemoautotrophic bacteria, and archaea). The autumn post-bloom with maximal nutrient depletion featured Coscinodiscophyceae, Rhodobacteraceae (e.g. Amylibacter) and the SAR116 clade. Winter replenishment of nitrate, silicate and phosphate, linked to vertical mixing and a unique microbiome that included Magnetospiraceae and Dadabacteriales, fueled the following phytoplankton bloom. The spring-summer succession of Phaeocystis, Grammonema and Thalassiosira coincided with ephemeral peaks of Aurantivirga, Formosa, Polaribacter and NS lineages, indicating metabolic relationships. In the East Greenland Current, deeper sampling depth, ice cover and polar water masses concurred with weaker seasonality and a stronger heterotrophic signature. The ice-related winter microbiome comprised Bacillaria, Naviculales, Polarella, Chrysophyceae and Flavobacterium ASVs. Low ice cover and advection of Atlantic Water coincided with diminished abundances of chemoautotrophic bacteria while others such as Phaeocystis increased, suggesting that Atlantification alters microbiome structure and eventually the biological carbon pump. These insights promote the understanding of microbial seasonality and polar night ecology in the Arctic Ocean, a region severely affected by climate change.
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Affiliation(s)
- Matthias Wietz
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Christina Bienhold
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Sinhué Torres-Valdés
- Marine BioGeoScience, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Wilken-Jon von Appen
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Ian Salter
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Faroe Marine Research Institute, Tórshavn, Faroe Islands
| | - Antje Boetius
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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11
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Bunse C, Koch H, Breider S, Simon M, Wietz M. Sweet spheres: succession and CAZyme expression of marine bacterial communities colonizing a mix of alginate and pectin particles. Environ Microbiol 2021; 23:3130-3148. [PMID: 33876546 DOI: 10.1111/1462-2920.15536] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/06/2021] [Accepted: 04/15/2021] [Indexed: 12/24/2022]
Abstract
Polysaccharide particles are important substrates and microhabitats for marine bacteria. However, substrate-specific bacterial dynamics in mixtures of particle types with different polysaccharide composition, as likely occurring in natural habitats, are undescribed. Here, we studied the composition, functional diversity and gene expression of marine bacterial communities colonizing a mix of alginate and pectin particles. Amplicon, metagenome and metatranscriptome sequencing revealed that communities on alginate and pectin particles significantly differed from their free-living counterparts. Unexpectedly, microbial dynamics on alginate and pectin particles were similar, with predominance of amplicon sequence variants (ASVs) from Tenacibaculum, Colwellia, Psychrobium and Psychromonas. Corresponding metagenome-assembled genomes (MAGs) expressed diverse alginate lyases, several colocalized in polysaccharide utilization loci. Only a single, low-abundant MAG showed elevated transcript abundances of pectin-degrading enzymes. One specific Glaciecola ASV dominated the free-living fraction, possibly persisting on particle-derived oligomers through different glycoside hydrolases. Elevated ammonium uptake and metabolism signified nitrogen as an important factor for degrading carbon-rich particles, whereas elevated methylcitrate and glyoxylate cycles suggested nutrient limitation in surrounding waters. The bacterial preference for alginate, whereas pectin primarily served as colonization scaffold, illuminates substrate-driven dynamics within mixed polysaccharide pools. These insights expand our understanding of bacterial niche specialization and the biological carbon pump in macroalgae-rich habitats.
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Affiliation(s)
- Carina Bunse
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany.,Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Hanna Koch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.,Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Sven Breider
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany.,Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Wolter LA, Wietz M, Ziesche L, Breider S, Leinberger J, Poehlein A, Daniel R, Schulz S, Brinkhoff T. Pseudooceanicola algae sp. nov., isolated from the marine macroalga Fucus spiralis, shows genomic and physiological adaptations for an algae-associated lifestyle. Syst Appl Microbiol 2021; 44:126166. [PMID: 33310406 DOI: 10.1016/j.syapm.2020.126166] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/23/2022]
Abstract
The genus Pseudooceanicola from the alphaproteobacterial Roseobacter group currently includes ten validated species. We herein describe strain Lw-13eT, the first Pseudooceanicola species from marine macroalgae, isolated from the brown alga Fucus spiralis abundant at European and North American coasts. Physiological and pangenome analyses of Lw-13eT showed corresponding adaptive features. Adaptations to the tidal environment include a broad salinity tolerance, degradation of macroalgae-derived substrates (mannitol, mannose, proline), and resistance to several antibiotics and heavy metals. Notably, Lw-13eT can degrade oligomeric alginate via PL15 alginate lyase encoded in a polysaccharide utilization locus (PUL), rarely described for roseobacters to date. Plasmid localization of the PUL strengthens the importance of mobile genetic elements for evolutionary adaptations within the Roseobacter group. PL15 homologs were primarily detected in marine plant-associated metagenomes from coastal environments but not in the open ocean, corroborating its adaptive role in algae-rich habitats. Exceptional is the tolerance of Lw-13eT against the broad-spectrum antibiotic tropodithietic acid, produced by Phaeobacter spp. co-occurring in coastal habitats. Furthermore, Lw-13eT exhibits features resembling terrestrial plant-bacteria associations, i.e. biosynthesis of siderophores, terpenes and volatiles, which may contribute to mutual bacteria-algae interactions. Closest described relative of Lw-13eT is Pseudopuniceibacterium sediminis CY03T with 98.4% 16S rRNA gene sequence similarity. However, protein sequence-based core genome phylogeny and average nucleotide identity indicate affiliation of Lw-13eT with the genus Pseudooceanicola. Based on phylogenetic, physiological and (chemo)taxonomic distinctions, we propose strain Lw-13eT (=DSM 29013T=LMG 30557T) as a novel species with the name Pseudooceanicola algae.
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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.
| | - 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
| | - Lisa Ziesche
- Institute of Organic Chemistry, Technische Universität Braunschweig, Germany
| | - Sven Breider
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Janina Leinberger
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Anja Poehlein
- Institute of Microbiology and Genetics, Genomic and Applied Microbiology, and Göttingen Genomics Laboratory, Germany
| | - Rolf Daniel
- Institute of Microbiology and Genetics, Genomic and Applied Microbiology, and Göttingen Genomics Laboratory, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany.
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14
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Arnosti C, Wietz M, Brinkhoff T, Hehemann JH, Probandt D, Zeugner L, Amann R. The Biogeochemistry of Marine Polysaccharides: Sources, Inventories, and Bacterial Drivers of the Carbohydrate Cycle. Ann Rev Mar Sci 2021; 13:81-108. [PMID: 32726567 DOI: 10.1146/annurev-marine-032020-012810] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Polysaccharides are major components of macroalgal and phytoplankton biomass and constitute a large fraction of the organic matter produced and degraded in the ocean. Until recently, however, our knowledge of marine polysaccharides was limited due to their great structural complexity, the correspondingly complicated enzymatic machinery used by microbial communities to degrade them, and a lack of readily applied means to isolate andcharacterize polysaccharides in detail. Advances in carbohydrate chemistry, bioinformatics, molecular ecology, and microbiology have led to new insights into the structures of polysaccharides, the means by which they are degraded by bacteria, and the ecology of polysaccharide production and decomposition. Here, we survey current knowledge, discuss recent advances, and present a new conceptual model linking polysaccharide structural complexity and abundance to microbially driven mechanisms of polysaccharide processing. We conclude by highlighting specific future research foci that will shed light on this central but poorly characterized component of the marine carbon cycle.
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Affiliation(s)
- C Arnosti
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - M Wietz
- HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany, and Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - T Brinkhoff
- Institute for the Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - J-H Hehemann
- MARUM MPG Bridge Group Marine Glycobiology, Center for Marine Environmental Sciences (MARUM), University of Bremen, and Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - D Probandt
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - L Zeugner
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - R Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
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15
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Koch H, Germscheid N, Freese HM, Noriega-Ortega B, Lücking D, Berger M, Qiu G, Marzinelli EM, Campbell AH, Steinberg PD, Overmann J, Dittmar T, Simon M, Wietz M. Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii. Sci Rep 2020; 10:809. [PMID: 31964928 PMCID: PMC6972757 DOI: 10.1038/s41598-020-57526-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/23/2019] [Indexed: 01/28/2023] Open
Abstract
Ecological differentiation between strains of bacterial species is shaped by genomic and metabolic variability. However, connecting genotypes to ecological niches remains a major challenge. Here, we linked bacterial geno- and phenotypes by contextualizing pangenomic, exometabolomic and physiological evidence in twelve strains of the marine bacterium Alteromonas macleodii, illuminating adaptive strategies of carbon metabolism, microbial interactions, cellular communication and iron acquisition. In A. macleodii strain MIT1002, secretion of amino acids and the unique capacity for phenol degradation may promote associations with Prochlorococcus cyanobacteria. Strain 83-1 and three novel Pacific isolates, featuring clonal genomes despite originating from distant locations, have profound abilities for algal polysaccharide utilization but without detrimental implications for Ecklonia macroalgae. Degradation of toluene and xylene, mediated via a plasmid syntenic to terrestrial Pseudomonas, was unique to strain EZ55. Benzoate degradation by strain EC673 related to a chromosomal gene cluster shared with the plasmid of A. mediterranea EC615, underlining that mobile genetic elements drive adaptations. Furthermore, we revealed strain-specific production of siderophores and homoserine lactones, with implications for nutrient acquisition and cellular communication. Phenotypic variability corresponded to different competitiveness in co-culture and geographic distribution, indicating linkages between intraspecific diversity, microbial interactions and biogeography. The finding of "ecological microdiversity" helps understanding the widespread occurrence of A. macleodii and contributes to the interpretation of bacterial niche specialization, population ecology and biogeochemical roles.
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Affiliation(s)
- Hanna Koch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Nora Germscheid
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Heike M Freese
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Beatriz Noriega-Ortega
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Dominik Lücking
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Galaxy Qiu
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- Western Sydney University, Hawkesbury, Australia
| | - Ezequiel M Marzinelli
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Sydney Institute of Marine Science, Mosman, Australia
- University of Sydney, Camperdown, Australia
| | - Alexandra H Campbell
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- University of Sunshine Coast, Sunshine Coast, Australia
| | - Peter D Steinberg
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Sydney Institute of Marine Science, Mosman, Australia
| | - Jörg Overmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Braunschweig University of Technology, Braunschweig, Germany
| | - Thorsten Dittmar
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
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16
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Koch H, Freese HM, Hahnke RL, Simon M, Wietz M. Adaptations of Alteromonas sp. 76-1 to Polysaccharide Degradation: A CAZyme Plasmid for Ulvan Degradation and Two Alginolytic Systems. Front Microbiol 2019; 10:504. [PMID: 30936857 PMCID: PMC6431674 DOI: 10.3389/fmicb.2019.00504] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/27/2019] [Indexed: 11/16/2022] Open
Abstract
Studying the physiology and genomics of cultured hydrolytic bacteria is a valuable approach to decipher the biogeochemical cycling of marine polysaccharides, major nutrients derived from phytoplankton and macroalgae. We herein describe the profound potential of Alteromonas sp. 76-1, isolated from alginate-enriched seawater at the Patagonian continental shelf, to degrade the algal polysaccharides alginate and ulvan. Phylogenetic analyses indicated that strain 76-1 might represent a novel species, distinguished from its closest relative (Alteromonas naphthalenivorans) by adaptations to their contrasting habitats (productive open ocean vs. coastal sediments). Ecological distinction of 76-1 was particularly manifested in the abundance of carbohydrate-active enzymes (CAZymes), consistent with its isolation from alginate-enriched seawater and elevated abundance of a related OTU in the original microcosm. Strain 76-1 encodes multiple alginate lyases from families PL6, PL7, PL17, and PL18 largely contained in two polysaccharide utilization loci (PUL), which may facilitate the utilization of different alginate structures in nature. Notably, ulvan degradation relates to a 126 Kb plasmid dedicated to polysaccharide utilization, encoding several PL24 and PL25 ulvan lyases and monomer-processing genes. This extensive and versatile CAZyme repertoire allowed substantial growth on polysaccharides, showing comparable doubling times with alginate (2 h) and ulvan (3 h) in relation to glucose (3 h). The finding of homologous ulvanolytic systems in distantly related Alteromonas spp. suggests CAZyme plasmids as effective vehicles for PUL transfer that mediate niche gain. Overall, the demonstrated CAZyme repertoire substantiates the role of Alteromonas in marine polysaccharide degradation and how PUL exchange influences the ecophysiology of this ubiquitous marine taxon.
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Affiliation(s)
- Hanna Koch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Heike M. Freese
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Richard L. Hahnke
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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17
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Koch H, Dürwald A, Schweder T, Noriega-Ortega B, Vidal-Melgosa S, Hehemann JH, Dittmar T, Freese HM, Becher D, Simon M, Wietz M. Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides. ISME J 2019; 13:92-103. [PMID: 30116038 PMCID: PMC6298977 DOI: 10.1038/s41396-018-0252-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/10/2018] [Accepted: 07/19/2018] [Indexed: 11/08/2022]
Abstract
Algal polysaccharides are an important bacterial nutrient source and central component of marine food webs. However, cellular and ecological aspects concerning the bacterial degradation of polysaccharide mixtures, as presumably abundant in natural habitats, are poorly understood. Here, we contextualize marine polysaccharide mixtures and their bacterial utilization in several ways using the model bacterium Alteromonas macleodii 83-1, which can degrade multiple algal polysaccharides and contributes to polysaccharide degradation in the oceans. Transcriptomic, proteomic and exometabolomic profiling revealed cellular adaptations of A. macleodii 83-1 when degrading a mix of laminarin, alginate and pectin. Strain 83-1 exhibited substrate prioritization driven by catabolite repression, with initial laminarin utilization followed by simultaneous alginate/pectin utilization. This biphasic phenotype coincided with pronounced shifts in gene expression, protein abundance and metabolite secretion, mainly involving CAZymes/polysaccharide utilization loci but also other functional traits. Distinct temporal changes in exometabolome composition, including the alginate/pectin-specific secretion of pyrroloquinoline quinone, suggest that substrate-dependent adaptations influence chemical interactions within the community. The ecological relevance of cellular adaptations was underlined by molecular evidence that common marine macroalgae, in particular Saccharina and Fucus, release mixtures of alginate and pectin-like rhamnogalacturonan. Moreover, CAZyme microdiversity and the genomic predisposition towards polysaccharide mixtures among Alteromonas spp. suggest polysaccharide-related traits as an ecophysiological factor, potentially relating to distinct 'carbohydrate utilization types' with different ecological strategies. Considering the substantial primary productivity of algae on global scales, these insights contribute to the understanding of bacteria-algae interactions and the remineralization of chemically diverse polysaccharide pools, a key step in marine carbon cycling.
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Affiliation(s)
- Hanna Koch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Alexandra Dürwald
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Beatriz Noriega-Ortega
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
| | - Silvia Vidal-Melgosa
- MARUM-MPI Bridge Group for Marine Glycobiology, University of Bremen, Bremen, Germany
| | - Jan-Hendrik Hehemann
- MARUM-MPI Bridge Group for Marine Glycobiology, University of Bremen, Bremen, Germany
| | - Thorsten Dittmar
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
| | - Heike M Freese
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dörte Becher
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
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18
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Bakenhus I, Dlugosch L, Giebel HA, Beardsley C, Simon M, Wietz M. Distinct biogeographic patterns of bacterioplankton composition and single-cell activity between the subtropics and Antarctica. Environ Microbiol 2018; 20:3100-3108. [PMID: 30109757 DOI: 10.1111/1462-2920.14383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/26/2018] [Indexed: 11/26/2022]
Abstract
Bacterial biogeography and activity in the Southern Ocean are poorly understood to date. Here, we applied CARD-FISH to quantify bacterial community structure from the subtropics to Antarctica between 10°W and 10°E, covering four biogeographic provinces with distinct environmental properties. In addition, incorporation of radiolabeled glucose, amino acids and leucine via MAR-FISH served to quantify the contribution to substrate turnover by selected bacterial groups. SAR11, Bacteroidetes, Gammaproteobacteria and the Roseobacter group accounted for the majority of the bacterial community (52%-88% of DAPI-stained cells) but showed little distributional variation between provinces. In contrast, taxonomic subclades Polaribacter, NS5, NS2b (Bacteroidetes) as well as RCA (Roseobacter group) featured marked geographic variation, illustrated by NMDS and coefficients of variation. Roseobacter (specifically RCA) and Gammaproteobacteria constituted considerable fractions of cells incorporating glucose and amino acids respectively. Bacteroidetes had generally lower activities, but Polaribacter accounted for a major fraction of biomass production at one station near the Antarctic ice shelf. In conclusion, distributional patterns at finer taxonomic level and highest substrate turnover by less abundant taxa highlight the importance of taxonomic subclades in marine carbon fluxes, contributing to the understanding of functional bacterial biogeography in the Southern Ocean.
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Affiliation(s)
- Insa Bakenhus
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Christine Beardsley
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, 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
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Mitulla M, Dinasquet J, Guillemette R, Simon M, Azam F, Wietz M. Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain. Environ Microbiol 2016; 18:4369-4377. [PMID: 27059936 DOI: 10.1111/1462-2920.13314] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/23/2016] [Indexed: 11/29/2022]
Abstract
Alginate is a major cell wall polysaccharide from marine macroalgae and nutrient source for heterotrophic bacteria. Alginate can form gel particles in contact with divalent cations as found in seawater. Here, we tested the hypothesis that alginate gel particles serve as carbon source and microhabitat for marine bacteria by adding sterile alginate particles to microcosms with seawater from coastal California, a habitat rich in alginate-containing macroalgae. Alginate particles were rapidly colonized and degraded, with three- to eightfold higher bacterial abundances and production among alginate particle-associated (PA) bacteria. 16S rRNA gene amplicon sequencing showed that alginate PA bacteria were enriched in OTUs related to Cryomorphaceae, Saprospiraceae (Bacteroidetes) and Phaeobacter (Alphaproteobacteria) towards the end of the experiment. In microcosms amended with alginate particles and the proficient alginolytic bacterium Alteromonas macleodii strain 83-1, this strain dominated the community and outcompeted Cryomorphaceae, Saprospiraceae and Phaeobacter, and PA hydrolytic activities were over 50% higher. Thus, alginolytic activity by strain 83-1 did not benefit non-alginolytic strains by cross-feeding on alginate hydrolysis or other metabolic products. Considering the global distribution and extensive biomass of alginate-containing macroalgae, the observed bacterial dynamics associated with the utilization and remineralization of alginate microhabitats promote the understanding of carbon cycling in macroalgae-rich waters worldwide.
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Affiliation(s)
- Maximilian Mitulla
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany
| | - Julie Dinasquet
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA.,Laboratoire d'Oceanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls sur mer, Sorbonne Universités, UPMC, France
| | - Ryan Guillemette
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany
| | - Farooq Azam
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany
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Neumann AM, Balmonte JP, Berger M, Giebel HA, Arnosti C, Voget S, Simon M, Brinkhoff T, Wietz M. Different utilization of alginate and other algal polysaccharides by marine Alteromonas macleodii ecotypes. Environ Microbiol 2015; 17:3857-68. [PMID: 25847866 DOI: 10.1111/1462-2920.12862] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/29/2015] [Indexed: 10/23/2022]
Abstract
The marine bacterium Alteromonas macleodii is a copiotrophic r-strategist, but little is known about its potential to degrade polysaccharides. Here, we studied the degradation of alginate and other algal polysaccharides by A. macleodii strain 83-1 in comparison to other A. macleodii strains. Cell densities of strain 83-1 with alginate as sole carbon source were comparable to those with glucose, but the exponential phase was delayed. The genome of 83-1 was found to harbour an alginolytic system comprising five alginate lyases, whose expression was induced by alginate. The alginolytic system contains additional CAZymes, including two TonB-dependent receptors, and is part of a 24 kb genomic island unique to the A. macleodii 'surface clade' ecotype. In contrast, strains of the 'deep clade' ecotype contain only a single alginate lyase in a separate 7 kb island. This difference was reflected in an eightfold greater efficiency of surface clade strains to grow on alginate. Strain 83-1 furthermore hydrolysed laminarin, pullulan and xylan, and corresponding polysaccharide utilization loci were detected in the genome. Alteromonas macleodii alginate lyases were predominantly detected in Atlantic Ocean metagenomes. The demonstrated hydrolytic capacities are likely of ecological relevance and represent another level of adaptation among A. macleodii ecotypes.
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Affiliation(s)
- Anna M Neumann
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - John P Balmonte
- Department of Marine Sciences, University of North Carolina, 3117 Venable Hall, Chapel Hill, NC, USA
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina, 3117 Venable Hall, Chapel Hill, NC, USA
| | - Sonja Voget
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, 37077, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
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Wietz M, Wemheuer B, Simon H, Giebel HA, Seibt MA, Daniel R, Brinkhoff T, Simon M. Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans. Environ Microbiol 2015; 17:3822-31. [DOI: 10.1111/1462-2920.12842] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 03/04/2015] [Accepted: 03/04/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Institute of Microbiology and Genetics; University of Göttingen; Göttingen 37077 Germany
| | - Heike Simon
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
| | - Maren A. Seibt
- ICBM-MPI Bridging Group for Marine Geochemistry; Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Institute of Microbiology and Genetics; University of Göttingen; Göttingen 37077 Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
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Wietz M, Millán-Aguiñaga N, Jensen PR. CRISPR-Cas systems in the marine actinomycete Salinispora: linkages with phage defense, microdiversity and biogeography. BMC Genomics 2014; 15:936. [PMID: 25344663 PMCID: PMC4223832 DOI: 10.1186/1471-2164-15-936] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/29/2014] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Prokaryotic CRISPR-Cas systems confer resistance to viral infection and thus mediate bacteria-phage interactions. However, the distribution and functional diversity of CRISPRs among environmental bacteria remains largely unknown. Here, comparative genomics of 75 Salinispora strains provided insight into the diversity and distribution of CRISPR-Cas systems in a cosmopolitan marine actinomycete genus. RESULTS CRISPRs were found in all Salinispora strains, with the majority containing multiple loci and different Cas array subtypes. Of the six subtypes identified, three have not been previously described. A lower prophage frequency in S. arenicola was associated with a higher fraction of spacers matching Salinispora prophages compared to S. tropica, suggesting differing defensive capacities between Salinispora species. The occurrence of related prophages in strains from distant locations, as well as spacers matching those prophages inserted throughout spacer arrays, indicate recurring encounters with widely distributed phages over time. Linkages of CRISPR features with Salinispora microdiversity pointed to subclade-specific contacts with mobile genetic elements (MGEs). This included lineage-specific spacer deletions or insertions, which may reflect weak selective pressures to maintain immunity or distinct temporal interactions with MGEs, respectively. Biogeographic patterns in spacer and prophage distributions support the concept that Salinispora spp. encounter localized MGEs. Moreover, the presence of spacers matching housekeeping genes suggests that CRISPRs may have functions outside of viral defense. CONCLUSIONS This study provides a comprehensive examination of CRISPR-Cas systems in a broadly distributed group of environmental bacteria. The ubiquity and diversity of CRISPRs in Salinispora suggests that CRISPR-mediated interactions with MGEs represent a major force in the ecology and evolution of this cosmopolitan marine actinomycete genus.
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Affiliation(s)
- Matthias Wietz
- />Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037 USA
- />Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany
| | - Natalie Millán-Aguiñaga
- />Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037 USA
| | - Paul R Jensen
- />Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037 USA
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Wietz M, Duncan K, Patin NV, Jensen PR. Antagonistic interactions mediated by marine bacteria: the role of small molecules. J Chem Ecol 2013; 39:879-91. [PMID: 23852047 DOI: 10.1007/s10886-013-0316-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/17/2013] [Accepted: 06/25/2013] [Indexed: 12/21/2022]
Abstract
Marine bacteria are known to produce a wide variety of structurally diverse and biologically active secondary metabolites. Considerably less is known about the ecological functions of these compounds, in part due to methodological challenges associated with this field of research. Here, we review the antagonistic activities mediated by marine bacteria with a focus on activities linked to structurally defined secondary metabolites. Bacterial antagonism has been documented against other marine bacteria as well as eukaryotes, and includes antibiosis, the inhibition of quorum sensing, larval settlement deterrence, and defense against predation. These compounds likely play important ecological roles that ultimately affect ecosystem structure and function, however, much remains to be learned before these roles can be fully appreciated. Recent technological advances coupled with a better understanding of the diverse processes mediated by secondary metabolites provide new opportunities to expand our understanding of the chemical ecology of bacterial antagonism in the marine environment.
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Affiliation(s)
- Matthias Wietz
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0204, USA
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Nielsen A, Mansson M, Wietz M, Varming AN, Phipps RK, Larsen TO, Gram L, Ingmer H. Nigribactin, a novel siderophore from Vibrio nigripulchritudo, modulates Staphylococcus aureus virulence gene expression. Mar Drugs 2012. [PMID: 23203279 PMCID: PMC3509537 DOI: 10.3390/md10112584] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Staphylococcus aureus is a serious human pathogen that employs a number of virulence factors as part of its pathogenesis. The purpose of the present study was to explore marine bacteria as a source of compounds that modulate virulence gene expression in S. aureus. During the global marine Galathea 3 expedition, a strain collection was established comprising bacteria that express antimicrobial activity against Vibrio anguillarum and/or Staphylococcus aureus. Within this collection we searched colony material, culture supernatants, and cell extracts for virulence modulating activity showing that 68 out of 83 marine bacteria (affiliated with the Vibrionaceae and Pseudoalteromonas sp.) influenced expression of S. aureus hla encoding α-hemolysin toxin and/or spa encoding Protein A. The isolate that upon initial screening showed the highest degree of interference (crude ethyl acetate extract) was a Vibrio nigripulchritudo. Extraction, purification and structural elucidation revealed a novel siderophore, designated nigribactin, which induces spa transcription. The effect of nigribactin on spa expression is likely to be independent from its siderophore activity, as another potent siderophore, enterobactin, failed to influence S. aureus virulence gene expression. This study shows that marine microorganisms produce compounds with potential use in therapeutic strategies targeting virulence rather than viability of human pathogens.
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Affiliation(s)
- Anita Nielsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark; (A.N.); (A.N.V.)
| | - Maria Mansson
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark; (M.M.); (R.K.P.); (T.O.L.)
| | - Matthias Wietz
- National Food Institute, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark; (M.W.); (L.G.)
- Scripps Institution of Oceanography, Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Anders N. Varming
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark; (A.N.); (A.N.V.)
| | - Richard K. Phipps
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark; (M.M.); (R.K.P.); (T.O.L.)
| | - Thomas O. Larsen
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark; (M.M.); (R.K.P.); (T.O.L.)
| | - Lone Gram
- National Food Institute, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark; (M.W.); (L.G.)
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark; (A.N.); (A.N.V.)
- Author to whom correspondence should be addressed; ; Tel.: +45-35332773; Fax: +45-35332755
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Mansson M, Nielsen A, Kjærulff L, Gotfredsen CH, Wietz M, Ingmer H, Gram L, Larsen TO. Inhibition of virulence gene expression in Staphylococcus aureus by novel depsipeptides from a marine photobacterium. Mar Drugs 2011; 9:2537-2552. [PMID: 22363239 PMCID: PMC3280567 DOI: 10.3390/md9122537] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 11/22/2011] [Accepted: 11/30/2011] [Indexed: 12/15/2022] Open
Abstract
During a global research expedition, more than five hundred marine bacterial strains capable of inhibiting the growth of pathogenic bacteria were collected. The purpose of the present study was to determine if these marine bacteria are also a source of compounds that interfere with the agr quorum sensing system that controls virulence gene expression in Staphylococcus aureus. Using a gene reporter fusion bioassay, we recorded agr interference as enhanced expression of spa, encoding Protein A, concomitantly with reduced expression of hla, encoding α-hemolysin, and rnaIII encoding RNAIII, the effector molecule of agr. A marine Photobacterium produced compounds interfering with agr in S. aureus strain 8325-4, and bioassay-guided fractionation of crude extracts led to the isolation of two novel cyclodepsipeptides, designated solonamide A and B. Northern blot analysis confirmed the agr interfering activity of pure solonamides in both S. aureus strain 8325-4 and the highly virulent, community-acquired strain USA300 (CA-MRSA). To our knowledge, this is the first report of inhibitors of the agr system by a marine bacterium.
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Affiliation(s)
- Maria Mansson
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark;
- Author to whom correspondence should be addressed; ; Tel.: +45-4525-2724; Fax: +45-4588-4148
| | - Anita Nielsen
- Department of Veterinary Disease Biology, Faculty of Life Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark; (A.N.); (H.I.)
| | - Louise Kjærulff
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark; (L.K.); (C.H.G.)
| | - Charlotte H. Gotfredsen
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark; (L.K.); (C.H.G.)
| | - Matthias Wietz
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark; (M.W.); (L.G.)
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Life Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark; (A.N.); (H.I.)
| | - Lone Gram
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark; (M.W.); (L.G.)
| | - Thomas O. Larsen
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark;
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Abstract
Vibrio coralliilyticus is a putative coral pathogen in tropical oceans, but also possesses antagonistic traits. We previously reported antibacterial activity in Vibrio coralliilyticus strain S2052 based upon the antibiotic andrimid. The purpose of the present study was to determine whether V. coralliilyticus S2052 produces the antibiotic under conditions mimicking natural habitats of vibrios. S2052 synthesized andrimid with both chitin and macroalgal extracts as sole nutrient source. With chitin, the biosynthesis of metabolites other than andrimid was largely abolished, and the yield of the antibiotic per cell was twofold higher. In cultures with Artemia as live chitin model system, S2052 reached up to 10(8) cells ml(-1) , produced andrimid and showed attachment to the exoskeleton and chitinous exuviae. The metabolic focus on andrimid production with chitin indicates that the antibiotic could serve an ecophysiological function. S2052 was compared with two related V. coralliilyticus strains (LMG20984(T) and LMG10953). Despite overall similar secondary metabolomes, LMG20984(T) and LMG10953 did not produce andrimid, and their optimum biosynthetic temperature was 30 as compared with 25°C for S2052. In addition, S2052 appeared less pathogenic towards Artemia than reported for the type strain. Different physiologies of S2052 and closely related strains indicated that V. coralliilyticus subspecies may be adapted to different niches.
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Affiliation(s)
- Matthias Wietz
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark. Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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Wietz M, Mansson M, Gotfredsen CH, Larsen TO, Gram L. Antibacterial compounds from marine Vibrionaceae isolated on a global expedition. Mar Drugs 2010; 8:2946-60. [PMID: 21339958 PMCID: PMC3039463 DOI: 10.3390/md8122946] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 12/01/2010] [Accepted: 12/09/2010] [Indexed: 12/19/2022] Open
Abstract
On a global research expedition, over 500 bacterial strains inhibitory towards pathogenic bacteria were isolated. Three hundred of the antibacterial strains were assigned to the Vibrionaceae family. The purpose of the present study was to investigate the phylogeny and bioactivity of five Vibrionaceae strains with pronounced antibacterial activity. These were identified as Vibrio coralliilyticus (two strains), V. neptunius (two strains), and Photobacterium halotolerans (one strain) on the basis of housekeeping gene sequences. The two related V. coralliilyticus and V. neptunius strains were isolated from distant oceanic regions. Chemotyping by LC-UV/MS underlined genetic relationships by showing highly similar metabolite profiles for each of the two V. coralliilyticus and V. neptunius strains, respectively, but a unique profile for P. halotolerans. Bioassay-guided fractionation identified two known antibiotics as being responsible for the antibacterial activity; andrimid (from V. coralliilyticus) and holomycin (from P. halotolerans). Despite the isolation of already known antibiotics, our findings show that marine Vibrionaceae are a resource of antibacterial compounds and may have potential for future natural product discovery.
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Affiliation(s)
- Matthias Wietz
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; E-Mail:
| | - Maria Mansson
- Centre for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; E-Mails: (M.M.); (T.O.L.)
| | - Charlotte H. Gotfredsen
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; E-Mail:
| | - Thomas O. Larsen
- Centre for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; E-Mails: (M.M.); (T.O.L.)
| | - Lone Gram
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +45-4525-2586; Fax: +45-4588-4774
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Abstract
Microbial biofilms developing in aquaculture tanks represent a reservoir for opportunistic bacterial pathogens, and procedures to control formation and bacterial composition of biofilms are important for the development of commercially viable aquaculture industries. This study investigated the effects of seawater ozonation on biofilm development on microscope glass slides placed in small-scale aquaculture tanks containing the live feed organism Artemia. Fluorescence in situ hybridization (FISH) demonstrated that ozonation accelerated the biofilm formation cycle, while it delayed the establishment of filamentous bacteria. Gammaproteobacteria and Alphaproteobacteria were the most abundant bacterial groups in the biofilm for both water types, but ozonation influenced their dynamics. With ozonation, the bacterial community structure was relatively stable and dominated by Gammaproteobacteria throughout the experiment (21-66% of total bacteria). Without ozonation, the community showed larger fluctuations, and Alphaproteobacteria emerged as dominant after 18 days (up to 54% of total bacteria). Ozonation of seawater also affected the dynamics of less abundant populations in the biofilm such as Betaproteobacteria, Planctomycetales and the Cytophaga/Flavobacterium branch of phylum Bacteroidetes. The abundance of Thiothrix, a bacterial genus capable of filamentous growth and fouling of larvae, increased with time for both water types, while no temporal trend could be detected for the genus Vibrio. Denaturing gradient gel electrophoresis (DGGE) demonstrated temporal changes in the dominant bacterial populations for both water types. Sequencing of DGGE bands confirmed the FISH data, and sequences were related to bacterial groups commonly found in biofilms of aquaculture systems. Several populations were closely related to organisms involved in sulfur cycling. Improved Artemia survival rates in tanks receiving ozonated water suggested a positive effect of ozonation on animal health. Although the used ozonation protocol did not hinder biofilm formation, the results suggest ozonation as a promising approach for manipulation of bacterial populations in aquaculture systems, which can prove beneficial for cultured animals.
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Affiliation(s)
- Matthias Wietz
- Australian Institute of Marine Science, PMB 3 Townsville MC, Queensland 4810, Australia
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Abstract
AIMS This study aimed to determine the bacterial community associated with wild-caught, mid-stage larvae of spiny lobsters (Palinuridae) in their native oligotrophic marine environment, and to compare their diversity and composition with communities associated with aquaculture-reared larvae of the tropical rock lobster Panulirus ornatus. METHODS AND RESULTS Bacterial clone libraries constructed from wild P. ornatus (two libraries) and Panulirus penicillatus (one library) larvae (phyllosoma) revealed a dominance of alpha-proteobacterial sequences, with Sulfitobacter spp.-affiliated sequences dominating both P. ornatus libraries and constituting a major portion of the P. penicillatus library. Vibrio-related sequences were rarely detected from wild phyllosoma clone libraries in contrast to similar studies of aquaculture-reared animals. Scanning electron microscopy analysis revealed low levels of bacterial colonization on the external carapace of wild phyllosoma, again in contrast to aquaculture-reared animals, which are often colonized with filamentous bacteria (mainly Thiothrix sp.) that compromise their health. Fluorescence in situ hybridization of sectioned wild phyllosoma tissue displayed low overall abundance of bacteria within the tissue and on external surfaces, with alpha-, beta-, and gamma-Proteobacteria being confirmed as members of this bacterial community. CONCLUSIONS The consistency in predominant clone sequences retrieved from the three libraries indicated a conserved microbiota associated with wild phyllosoma. In addition, the observed differences in the microbial composition and load of reared and wild phyllosoma are indicative of the different environments in which the animals live. SIGNIFICANCE AND IMPACT OF THE STUDY Bacterial disease during early larval stages is a major constraint currently hindering the development of an aquaculture industry for the ornate rock lobster P. ornatus. Knowledge of the microbial community associated with wild animals will be advantageous for the identification of bacteria that may promote animal health.
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Affiliation(s)
- M S Payne
- The Australian Institute of Marine Science, Townsville, Australia
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