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Tran DQ, Milke F, Niggemann J, Simon M. The diatom Thalassiosira rotula induces distinct growth responses and colonization patterns of Roseobacteraceae, Flavobacteria and Gammaproteobacteria. Environ Microbiol 2023; 25:3536-3555. [PMID: 37705313 DOI: 10.1111/1462-2920.16506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/03/2023] [Indexed: 09/15/2023]
Abstract
Diatoms as important phytoplankton components interact with and are colonized by heterotrophic bacteria. This colonization has been studied extensively in the past but a distinction between the bacterial colonization directly on diatom cells or on the aggregated organic material, exopolymeric substances (EPS), was little addressed. Here we show that the diatom Thalassiosira rotula and EPS were differently colonized by strains of Roseobacteraceae and Flavobacteriaceae in two and tree partner treatments and an enriched natural bacterial community as inoculum. In two partner treatments, the algae and EPS were generally less colonized than in the three partner treatments. Two strains benefitted greatly from the presence of another partner as the proportions of their subpopulations colonizing the diatom cell and the EPS were much enhanced relative to their two partner treatments. Highest proportions of bacteria colonizing the diatom and EPS occurred in the treatment inoculated with the enriched natural bacterial community. Dissolved organic carbon, amino acids and carbohydrates produced by T. rotula were differently used by the bacteria in the two and three partner treatments and most efficiently by the enriched natural bacterial community. Our approach is a valid model system to study physico-chemical bacteria-diatom interactions with increasing complexity.
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Affiliation(s)
- Den Quoc Tran
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Felix Milke
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jutta Niggemann
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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2
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Beauvais M, Schatt P, Montiel L, Logares R, Galand PE, Bouget FY. Functional redundancy of seasonal vitamin B 12 biosynthesis pathways in coastal marine microbial communities. Environ Microbiol 2023; 25:3753-3770. [PMID: 38031968 DOI: 10.1111/1462-2920.16545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023]
Abstract
Vitamin B12 (cobalamin) is a major cofactor required by most marine microbes, but only produced by a few prokaryotes in the ocean, which is globally B12 -depleted. Despite the ecological importance of B12 , the seasonality of B12 metabolisms and the organisms involved in its synthesis in the ocean remain poorly known. Here we use metagenomics to assess the monthly dynamics of B12 -related pathways and the functional diversity of associated microbial communities in the coastal NW Mediterranean Sea over 7 years. We show that genes related to potential B12 metabolisms were characterized by an annual succession of different organisms carrying distinct production pathways. During the most productive winter months, archaea (Nitrosopumilus and Nitrosopelagicus) were the main contributors to B12 synthesis potential through the anaerobic pathway (cbi genes). In turn, Alphaproteobacteria (HIMB11, UBA8309, Puniceispirillum) contributed to B12 synthesis potential in spring and summer through the aerobic pathway (cob genes). Cyanobacteria could produce pseudo-cobalamin from spring to autumn. Finally, we show that during years with environmental perturbations, the organisms usually carrying B12 synthesis genes were replaced by others having the same gene, thus maintaining the potential for B12 production. Such ecological insurance could contribute to the long-term functional resilience of marine microbial communities exposed to contrasting inter-annual environmental conditions.
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Affiliation(s)
- Maxime Beauvais
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Philippe Schatt
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Lidia Montiel
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Écogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - François-Yves Bouget
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
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3
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Liu Y, Brinkhoff T, Berger M, Poehlein A, Voget S, Paoli L, Sunagawa S, Amann R, Simon M. Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster. MICROBIOME 2023; 11:265. [PMID: 38007474 PMCID: PMC10675870 DOI: 10.1186/s40168-023-01644-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/07/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster. RESULTS The total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44-3.12 Mbp) and higher G + C contents (46.36-53.70%) than the four Pseudoplanktomarina species (2.26-2.72 Mbp, 42.22-43.72 G + C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G + C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species. CONCLUSIONS Our detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches. Video Abstract.
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Affiliation(s)
- Yanting Liu
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China.
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany.
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Sonja Voget
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zurich, Switzerland
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany.
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstr. 231, 26129, Oldenburg, Germany.
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Den TQ, Neu TR, Sultana S, Giebel HA, Simon M, Billerbeck S. Distinct glycoconjugate cell surface structures make the pelagic diatom Thalassiosira rotula an attractive habitat for bacteria. JOURNAL OF PHYCOLOGY 2023; 59:309-322. [PMID: 36471567 DOI: 10.1111/jpy.13308] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/14/2022] [Indexed: 05/28/2023]
Abstract
Interactions between marine diatoms and bacteria have been studied for decades. However, the visualization of physical interactions between these diatoms and their colonizers is still limited. To enhance our understanding of these specific interactions, a new Thalassiosira rotula isolate from the North Sea (strain 8673) was characterized by scanning electron microscopy and confocal laser scanning microscopy (CLSM) after staining with fluorescently labeled lectins targeting specific glycoconjugates. To investigate defined interactions of this strain with bacteria the new strain was made axenic and co-cultivated with a natural bacterial community and in two- or three-partner consortia with different bacteria of the Roseobacter group, Gammaproteobacteria and Bacteroidetes. The CLSM analysis of the consortia identified six out of 78 different lectins as very suitable to characterize glycoconjugates of T. rotula. The resulting images show that fucose-containing threads were the dominant glycoconjugates secreted by the T. rotula cells but chitin and to a lesser extent other glycoconjugates were also identified. Bacteria attached predominantly to the fucose glycoconjugates. The colonizing bacteria showed various attachment patterns such as adhering to the diatom threads in aggregates only or attaching to both the surfaces and the threads of the diatom. Interestingly the colonization patterns of single bacteria differed strikingly from those of bacterial co-cultures, indicating that interactions between two bacterial species impacted the colonization of the diatom. Our observations help to better understand physical interactions and specific colonization patterns of distinct bacterial mono- and co-cultures with an abundant diatom of costal seas.
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Affiliation(s)
- Tran Quoc Den
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thomas R Neu
- Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Sabiha Sultana
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Helge-A Giebel
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Sara Billerbeck
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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5
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Zucker F, Bischoff V, Olo Ndela E, Heyerhoff B, Poehlein A, Freese HM, Roux S, Simon M, Enault F, Moraru C. New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria. Virus Evol 2022; 8:veac070. [PMID: 36533142 PMCID: PMC9753089 DOI: 10.1093/ve/veac070] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/24/2022] [Accepted: 07/28/2022] [Indexed: 10/01/2023] Open
Abstract
The Microviridae family represents one of the major clades of single-stranded DNA (ssDNA) phages. Their cultivated members are lytic and infect Proteobacteria, Bacteroidetes, and Chlamydiae. Prophages have been predicted in the genomes from Bacteroidales, Hyphomicrobiales, and Enterobacteriaceae and cluster within the 'Alpavirinae', 'Amoyvirinae', and Gokushovirinae. We have isolated 'Ascunsovirus oldenburgi' ICBM5, a novel phage distantly related to known Microviridae. It infects Sulfitobacter dubius SH24-1b and uses both a lytic and a carrier-state life strategy. Using ICBM5 proteins as a query, we uncovered in publicly available resources sixty-five new Microviridae prophages and episomes in bacterial genomes and retrieved forty-seven environmental viral genomes (EVGs) from various viromes. Genome clustering based on protein content and phylogenetic analysis showed that ICBM5, together with Rhizobium phages, new prophages, episomes, and EVGs cluster within two new phylogenetic clades, here tentatively assigned the rank of subfamily and named 'Tainavirinae' and 'Occultatumvirinae'. They both infect Rhodobacterales. Occultatumviruses also infect Hyphomicrobiales, including nitrogen-fixing endosymbionts from cosmopolitan legumes. A biogeographical assessment showed that tainaviruses and occultatumviruses are spread worldwide, in terrestrial and marine environments. The new phage isolated here sheds light onto new and diverse branches of the Microviridae tree, suggesting that much of the ssDNA phage diversity remains in the dark.
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Affiliation(s)
- Falk Zucker
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Vera Bischoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Eric Olo Ndela
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, 1 Imp. Amélie Murat, Aubière 63170, Frankreich
| | - Benedikt Heyerhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August-University Göttingen, Institute of Microbiology and Genetics, Grisebachstr. 8, Göttingen D-37077, Germany
| | - Heike M Freese
- Leibniz-Institut DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7 B, Braunschweig D-38124, Germany
| | - Simon Roux
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA 94720, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Francois Enault
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, 1 Imp. Amélie Murat, Aubière 63170, Frankreich
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
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6
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Srinivas S, Berger M, Brinkhoff T, Niggemann J. Impact of Quorum Sensing and Tropodithietic Acid Production on the Exometabolome of Phaeobacter inhibens. Front Microbiol 2022; 13:917969. [PMID: 35801100 PMCID: PMC9253639 DOI: 10.3389/fmicb.2022.917969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/03/2022] [Indexed: 11/29/2022] Open
Abstract
Microbial interactions shape ecosystem diversity and chemistry through production and exchange of organic compounds, but the impact of regulatory mechanisms on production and release of these exometabolites is largely unknown. We studied the extent and nature of impact of two signaling molecules, tropodithietic acid (TDA) and the quorum sensing molecule acyl homoserine lactone (AHL) on the exometabolome of the model bacterium Phaeobacter inhibens DSM 17395, a member of the ubiquitous marine Roseobacter group. Exometabolomes of the wild type, a TDA and a QS (AHL-regulator) negative mutant were analyzed via Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Based on a total of 996 reproducibly detected molecular masses, exometabolomes of the TDA and QS negative mutant were ∼70% dissimilar to each other, and ∼90 and ∼60% dissimilar, respectively, to that of the wild type. Moreover, at any sampled growth phase, 40–60% of masses detected in any individual exometabolome were unique to that strain, while only 10–12% constituted a shared “core exometabolome.” Putative annotation revealed exometabolites of ecological relevance such as vitamins, amino acids, auxins, siderophore components and signaling compounds with different occurrence patterns in the exometabolomes of the three strains. Thus, this study demonstrates that signaling molecules, such as AHL and TDA, extensively impact the composition of bacterial exometabolomes with potential consequences for species interactions in microbial communities.
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Affiliation(s)
- Sujatha Srinivas
- 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
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jutta Niggemann
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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7
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Lu X, Wang K, Mou X. Metagenomes of polyamine-transforming bacterioplankton along a nearshore-open ocean transect. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:268-276. [PMID: 37073219 PMCID: PMC10077212 DOI: 10.1007/s42995-021-00114-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/22/2021] [Indexed: 05/03/2023]
Abstract
Short-chained aliphatic polyamines (PAs) have recently been recognized as an important carbon, nitrogen, and/or energy source for marine bacterioplankton. To study the genes and taxa involved in the transformations of different PA compounds and their potential variations among marine systems, we collected surface bacterioplankton from nearshore, offshore, and open ocean stations in the Gulf of Mexico and examined their metagenomic responses to additions of single PA model compounds (putrescine, spermidine, or spermine). Genes affiliated with PA uptake and all three known PA degradation pathways, i.e., transamination, γ-glutamylation, and spermidine cleavage, were significantly enriched in most PA-treated metagenomes. In addition, identified PA-transforming taxa were mostly the alpha and gamma classes of Proteobacteria, with less important contributions from members of Betaproteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and Planctomycetes. These findings suggest that PA transformations are ubiquitous, have diverse pathways, and are carried out by a broad range of the bacterioplankton taxa in the Gulf of Mexico. Identified PA-transforming bacterial genes and taxa were different among nearshore, offshore, and open ocean sites, but were little different among individual compound-amended metagenomes at any specific site. These observations further indicate that PA-transforming taxa and genes are site-specific and with high similarities among PA compounds. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-021-00114-x.
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Affiliation(s)
- Xinxin Lu
- Department of Biological Sciences, Kent State University, Kent, OH USA
| | - Kai Wang
- Department of Biological Sciences, Kent State University, Kent, OH USA
| | - Xiaozhen Mou
- Department of Biological Sciences, Kent State University, Kent, OH USA
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8
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Francis B, Urich T, Mikolasch A, Teeling H, Amann R. North Sea spring bloom-associated Gammaproteobacteria fill diverse heterotrophic niches. ENVIRONMENTAL MICROBIOME 2021; 16:15. [PMID: 34404489 PMCID: PMC8371827 DOI: 10.1186/s40793-021-00385-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND The planktonic bacterial community associated with spring phytoplankton blooms in the North Sea is responsible for a large amount of carbon turnover in an environment characterised by high primary productivity. Individual clades belonging to the Gammaproteobacteria have shown similar population dynamics to Bacteroidetes species, and are thus assumed to fill competing ecological niches. Previous studies have generated large numbers of metagenome assembled genomes and metaproteomes from these environments, which can be readily mined to identify populations performing potentially important ecosystem functions. In this study we attempt to catalogue these spring bloom-associated Gammaproteobacteria, which have thus far attracted less attention than sympatric Alphaproteobacteria and Bacteroidetes. METHODS We annotated 120 non-redundant species-representative gammaproteobacterial metagenome assembled genomes from spring bloom sampling campaigns covering the four years 2010-2012 and 2016 using a combination of Prokka and PfamScan, with further confirmation via BLAST against NCBI-NR. We also matched these gene annotations to 20 previously published metaproteomes covering those sampling periods plus the spring of 2009. RESULTS Metagenome assembled genomes with clear capacity for polysaccharide degradation via dedicated clusters of carbohydrate active enzymes were among the most abundant during blooms. Many genomes lacked gene clusters with clearly identifiable predicted polysaccharide substrates, although abundantly expressed loci for the uptake of large molecules were identified in metaproteomes. While the larger biopolymers, which are the most abundant sources of reduced carbon following algal blooms, are likely the main energy source, some gammaproteobacterial clades were clearly specialised for smaller organic compounds. Their substrates range from amino acids, monosaccharides, and DMSP, to the less expected, such as terpenoids, and aromatics and biphenyls, as well as many 'unknowns'. In particular we uncover a much greater breadth of apparent methylotrophic capability than heretofore identified, present in several order level clades without cultivated representatives. CONCLUSIONS Large numbers of metagenome assembled genomes are today publicly available, containing a wealth of readily accessible information. Here we identified a variety of predicted metabolisms of interest, which include diverse potential heterotrophic niches of spring bloom-associated Gammaproteobacteria. Features such as those identified here could well be fertile ground for future experimental studies.
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Affiliation(s)
- Ben Francis
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Tim Urich
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Annett Mikolasch
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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9
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Chhalodia AK, Dickschat JS. Breakdown of 3-(allylsulfonio)propanoates in bacteria from the Roseobacter group yields garlic oil constituents. Beilstein J Org Chem 2021; 17:569-580. [PMID: 33727980 PMCID: PMC7934745 DOI: 10.3762/bjoc.17.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/19/2021] [Indexed: 11/24/2022] Open
Abstract
Two analogues of 3-(dimethylsulfonio)propanoate (DMSP), 3-(diallylsulfonio)propanoate (DAllSP), and 3-(allylmethylsulfonio)propanoate (AllMSP), were synthesized and fed to marine bacteria from the Roseobacter clade. These bacteria are able to degrade DMSP into dimethyl sulfide and methanethiol. The DMSP analogues were also degraded, resulting in the release of allylated sulfur volatiles known from garlic. For unknown compounds, structural suggestions were made based on their mass spectrometric fragmentation pattern and confirmed by the synthesis of reference compounds. The results of the feeding experiments allowed to conclude on the substrate tolerance of DMSP degrading enzymes in marine bacteria.
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Affiliation(s)
- Anuj Kumar Chhalodia
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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10
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Liu Y, Blain S, Crispi O, Rembauville M, Obernosterer I. Seasonal dynamics of prokaryotes and their associations with diatoms in the Southern Ocean as revealed by an autonomous sampler. Environ Microbiol 2020; 22:3968-3984. [PMID: 32755055 DOI: 10.1111/1462-2920.15184] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/10/2020] [Accepted: 08/01/2020] [Indexed: 11/29/2022]
Abstract
The Southern Ocean remains one of the least explored marine environments. The investigation of temporal microbial dynamics has thus far been hampered by the limited access to this remote ocean. We present here high-resolution seasonal observations of the prokaryotic community composition during phytoplankton blooms induced by natural iron fertilization. A total of 18 seawater samples were collected by a moored remote autonomous sampler over 4 months at 5-11 day intervals in offshore surface waters (central Kerguelen Plateau). Illumina sequencing of the 16S rRNA gene revealed that among the most abundant amplicon sequence variants, SAR92 and Aurantivirga were the first bloom responders, Pseudomonadaceae, Nitrincolaceae and Polaribacter had successive peaks during the spring bloom decline, and Amylibacter increased in relative abundance later in the season. SAR11 and SUP05 were abundant prior to and after the blooms. Using network analysis, we identified two groups of diatoms representative of the spring and summer bloom that had opposite correlation patterns with prokaryotic taxa. Our study provides the first seasonal picture of microbial community dynamics in the open Southern Ocean and thereby offers biological insights to the cycling of carbon and iron, and to an important puzzling issue that is the modest nitrate decrease associated to iron fertilization.
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Affiliation(s)
- Yan Liu
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France.,College of Marine Life Sciences, Ocean University of China, Qingdao, China.,School of Life Sciences, Ludong University, Yantai, China
| | - Stéphane Blain
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
| | - Olivier Crispi
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
| | - Mathieu Rembauville
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
| | - Ingrid Obernosterer
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
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11
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Stabili L, Rizzo L, Basso L, Marzano M, Fosso B, Pesole G, Piraino S. The Microbial Community Associated with Rhizostoma pulmo: Ecological Significance and Potential Consequences for Marine Organisms and Human Health. Mar Drugs 2020; 18:md18090437. [PMID: 32839397 PMCID: PMC7551628 DOI: 10.3390/md18090437] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/12/2020] [Accepted: 08/18/2020] [Indexed: 01/02/2023] Open
Abstract
Jellyfish blooms are frequent and widespread in coastal areas worldwide, often associated with significant ecological and socio-economic consequences. Recent studies have also suggested cnidarian jellyfish may act as vectors of bacterial pathogens. The scyphomedusa Rhizostoma pulmo is an outbreak-forming jellyfish widely occurring across the Mediterranean basin. Using combination of culture-based approaches and a high-throughput amplicon sequencing (HTS), and based on available knowledge on a warm-affinity jellyfish-associated microbiome, we compared the microbial community associated with R. pulmo adult jellyfish in the Gulf of Taranto (Ionian Sea) between summer (July 2016) and winter (February 2017) sampling periods. The jellyfish-associated microbiota was investigated in three distinct compartments, namely umbrella, oral arms, and the mucus secretion. Actinobacteria, Bacteroidetes, Chlamydiae, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Fusobacteria, Planctomycetes, Proteobacteria, Rhodothermaeota, Spirochaetes, Tenericutes, and Thaumarchaeota were the phyla isolated from all the three R. pulmo compartments in the sampling times. In particular, the main genera Mycoplasma and Spiroplasma, belonging to the class Mollicutes (phylum Tenericutes), have been identified in all the three jellyfish compartments. The taxonomic microbial data were coupled with metabolic profiles resulting from the utilization of 31 different carbon sources by the BIOLOG Eco-Plate system. Microorganisms associated with mucus are characterized by great diversity. The counts of culturable heterotrophic bacteria and potential metabolic activities are also remarkable. Results are discussed in terms of R. pulmo ecology, the potential health hazard for marine and human life as well as the potential biotechnological applications related to the associated microbiome.
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Affiliation(s)
- Loredana Stabili
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Prov.le Lecce Monteroni, 73100 Lecce, Italy; (L.B.); (S.P.)
- Institute of Water Research of the National Research Council, S.S. di Taranto, Via Roma 3, 74123 Taranto, Italy
- Correspondence: (L.S.); (L.R.); (M.M.)
| | - Lucia Rizzo
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
- Correspondence: (L.S.); (L.R.); (M.M.)
| | - Lorena Basso
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Prov.le Lecce Monteroni, 73100 Lecce, Italy; (L.B.); (S.P.)
| | - Marinella Marzano
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari (IBIOM), CNR, 70126 Bari, Italy; (B.F.); (G.P.)
- Correspondence: (L.S.); (L.R.); (M.M.)
| | - Bruno Fosso
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari (IBIOM), CNR, 70126 Bari, Italy; (B.F.); (G.P.)
| | - Graziano Pesole
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari (IBIOM), CNR, 70126 Bari, Italy; (B.F.); (G.P.)
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari “Aldo Moro”, 70121 Bari, Italy
| | - Stefano Piraino
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Prov.le Lecce Monteroni, 73100 Lecce, Italy; (L.B.); (S.P.)
- CoNISMa, Piazzale Flaminio 9, 00196 Rome, Italy
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12
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Cobaviruses - a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. ISME JOURNAL 2019; 13:1404-1421. [PMID: 30718806 PMCID: PMC6775973 DOI: 10.1038/s41396-019-0362-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 01/15/2019] [Accepted: 01/22/2019] [Indexed: 11/13/2022]
Abstract
Bacteriophages are widely considered to influence bacterial communities, however most phages are still unknown or not studied well enough to understand their ecological roles. We have isolated two phages infecting Lentibacter sp. SH36, affiliated with the marine Roseobacter group, and retrieved similar phage genomes from publicly available metagenomics databases. Phylogenetic analysis placed the new phages within the Cobavirus group, in the here newly proposed genus Siovirus and subfamily Riovirinae of the Podoviridae. Gene composition and presence of direct terminal repeats in cultivated cobaviruses point toward a genome replication and packaging strategy similar to the T7 phage. Investigation of the genomes suggests that viral lysis of the cell proceeds via the canonical holin-endolysin pathway. Cobaviral hosts include members of the genera Lentibacter, Sulfitobacter and Celeribacter of the Roseobacter group within the family Rhodobacteraceae (Alphaproteobacteria). Screening more than 5,000 marine metagenomes, we found cobaviruses worldwide from temperate to tropical waters, in the euphotic zone, mainly in bays and estuaries, but also in the open ocean. The presence of cobaviruses in protist metagenomes as well as the phylogenetic neighborhood of cobaviruses in glutaredoxin and ribonucleotide reductase trees suggest that cobaviruses could infect bacteria associated with phototrophic or grazing protists. With this study, we expand the understanding of the phylogeny, classification, genomic organization, biogeography and ecology of this phage group infecting marine Rhodobacteraceae.
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13
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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. THE ISME JOURNAL 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] [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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14
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Barak-Gavish N, Frada MJ, Ku C, Lee PA, DiTullio GR, Malitsky S, Aharoni A, Green SJ, Rotkopf R, Kartvelishvily E, Sheyn U, Schatz D, Vardi A. Bacterial virulence against an oceanic bloom-forming phytoplankter is mediated by algal DMSP. SCIENCE ADVANCES 2018; 4:eaau5716. [PMID: 30397652 PMCID: PMC6200362 DOI: 10.1126/sciadv.aau5716] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/17/2018] [Indexed: 05/12/2023]
Abstract
Emiliania huxleyi is a bloom-forming microalga that affects the global sulfur cycle by producing large amounts of dimethylsulfoniopropionate (DMSP) and its volatile metabolic product dimethyl sulfide. Top-down regulation of E. huxleyi blooms has been attributed to viruses and grazers; however, the possible involvement of algicidal bacteria in bloom demise has remained elusive. We demonstrate that a Roseobacter strain, Sulfitobacter D7, that we isolated from a North Atlantic E. huxleyi bloom, exhibited algicidal effects against E. huxleyi upon coculturing. Both the alga and the bacterium were found to co-occur during a natural E. huxleyi bloom, therefore establishing this host-pathogen system as an attractive, ecologically relevant model for studying algal-bacterial interactions in the oceans. During interaction, Sulfitobacter D7 consumed and metabolized algal DMSP to produce high amounts of methanethiol, an alternative product of DMSP catabolism. We revealed a unique strain-specific response, in which E. huxleyi strains that exuded higher amounts of DMSP were more susceptible to Sulfitobacter D7 infection. Intriguingly, exogenous application of DMSP enhanced bacterial virulence and induced susceptibility in an algal strain typically resistant to the bacterial pathogen. This enhanced virulence was highly specific to DMSP compared to addition of propionate and glycerol which had no effect on bacterial virulence. We propose a novel function for DMSP, in addition to its central role in mutualistic interactions among marine organisms, as a mediator of bacterial virulence that may regulate E. huxleyi blooms.
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Affiliation(s)
- Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miguel José Frada
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
- The Interuniversity Institute for Marine Sciences, Eilat 88103, Israel
- Department of Ecology, Evolution and Behavior, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Chuan Ku
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Peter A. Lee
- Hollings Marine Laboratory, College of Charleston, Charleston, SC 29412, USA
| | - Giacomo R. DiTullio
- Hollings Marine Laboratory, College of Charleston, Charleston, SC 29412, USA
| | - Sergey Malitsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Biological Services, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Stefan J. Green
- DNA Services Facility, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Ron Rotkopf
- Department of Biological Services, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elena Kartvelishvily
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uri Sheyn
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
- Corresponding author.
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15
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Bakenhus I, Voget S, Poehlein A, Brinkhoff T, Daniel R, Simon M. Genome sequence of Planktotalea frisia type strain (SH6-1 T), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton bloom. Stand Genomic Sci 2018; 13:7. [PMID: 29682168 PMCID: PMC5896138 DOI: 10.1186/s40793-018-0311-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/21/2018] [Indexed: 12/15/2022] Open
Abstract
Planktotalea frisia SH6-1T Hahnke et al. (Int J Syst Evol Microbiol 62:1619-24, 2012) is a planktonic marine bacterium isolated during a phytoplankton bloom from the southern North Sea. It belongs to the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae. Here we describe the draft genome sequence and annotation of the type strain SH6-1T. The genome comprises 4,106,736 bp and contains 4128 protein-coding and 38 RNA genes. The draft genome sequence provides evidence for at least three extrachromosomal elements, encodes genes for DMSP utilization, quorum sensing, photoheterotrophy and a type IV secretion system. This indicates not only adaptation to a free-living lifestyle of P. frisia but points also to interactions with prokaryotic or eukaryotic organisms.
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Affiliation(s)
- Insa Bakenhus
- 1Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Sonja Voget
- 2Institute of Microbiology and Genetics, Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- 2Institute of Microbiology and Genetics, Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Thorsten Brinkhoff
- 1Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- 2Institute of Microbiology and Genetics, Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Meinhard Simon
- 1Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
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16
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Wienhausen G, Noriega-Ortega BE, Niggemann J, Dittmar T, Simon M. The Exometabolome of Two Model Strains of the Roseobacter Group: A Marketplace of Microbial Metabolites. Front Microbiol 2017; 8:1985. [PMID: 29075248 PMCID: PMC5643483 DOI: 10.3389/fmicb.2017.01985] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/27/2017] [Indexed: 12/04/2022] Open
Abstract
Recent studies applying Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) showed that the exometabolome of marine bacteria is composed of a surprisingly high molecular diversity. To shed more light on how this diversity is generated we examined the exometabolome of two model strains of the Roseobacter group, Phaeobacter inhibens and Dinoroseobacter shibae, grown on glutamate, glucose, acetate or succinate by FT-ICR-MS. We detected 2,767 and 3,354 molecular formulas in the exometabolome of each strain and 67 and 84 matched genome-predicted metabolites of P. inhibens and D. shibae, respectively. The annotated compounds include late precursors of biosynthetic pathways of vitamins B1, B2, B5, B6, B7, B12, amino acids, quorum sensing-related compounds, indole acetic acid and methyl-(indole-3-yl) acetic acid. Several formulas were also found in phytoplankton blooms. To shed more light on the effects of some of the precursors we supplemented two B1 prototrophic diatoms with the detected precursor of vitamin B1 HET (4-methyl-5-(β-hydroxyethyl)thiazole) and HMP (4-amino-5-hydroxymethyl-2-methylpyrimidine) and found that their growth was stimulated. Our findings indicate that both strains and other bacteria excreting a similar wealth of metabolites may function as important helpers to auxotrophic and prototrophic marine microbes by supplying growth factors and biosynthetic precursors.
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Affiliation(s)
- Gerrit Wienhausen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Beatriz E Noriega-Ortega
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jutta Niggemann
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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17
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Dogs M, Wemheuer B, Wolter L, Bergen N, Daniel R, Simon M, Brinkhoff T. Rhodobacteraceae on the marine brown alga Fucus spiralis are abundant and show physiological adaptation to an epiphytic lifestyle. Syst Appl Microbiol 2017; 40:370-382. [PMID: 28641923 DOI: 10.1016/j.syapm.2017.05.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/05/2017] [Accepted: 05/12/2017] [Indexed: 12/01/2022]
Abstract
Macroalgae harbour specific microbial communities on their surface that have functions related to host health and defence. In this study, the bacterial biofilm of the marine brown alga Fucus spiralis was investigated using 16S rRNA gene amplicon-based analysis and isolation of bacteria. Rhodobacteraceae (Alphaproteobacteria) were the predominant family constituting 23% of the epibacterial community. At the genus level, Sulfitobacter, Loktanella, Octadecabacter and a previously undescribed cluster were most abundant, and together they comprised 89% of the Rhodobacteraceae. Supported by a specific PCR approach, 23 different Rhodobacteraceae-affiliated strains were isolated from the surface of F. spiralis, which belonged to 12 established and three new genera. For seven strains, closely related sequences were detected in the 16S rRNA gene dataset. Growth experiments with substrates known to be produced by Fucus spp. showed that all of them were consumed by at least three strains, and vitamin B12 was produced by 70% of the isolates. Since growth of F. spiralis depends on B12 supplementation, bacteria may provide the alga with this vitamin. Most strains produced siderophores, which can enhance algal growth under iron-deficient conditions. Inhibiting properties against other bacteria were only observed when F. spiralis material was present in the medium. Thus, the physiological properties of the isolates indicated adaption to an epiphytic lifestyle.
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Affiliation(s)
- Marco Dogs
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bernd Wemheuer
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Laura Wolter
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Nils Bergen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
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18
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Bergen B, Endres S, Engel A, Zark M, Dittmar T, Sommer U, Jürgens K. Acidification and warming affect prominent bacteria in two seasonal phytoplankton bloom mesocosms. Environ Microbiol 2016; 18:4579-4595. [PMID: 27690275 DOI: 10.1111/1462-2920.13549] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 08/10/2016] [Accepted: 09/26/2016] [Indexed: 01/05/2023]
Abstract
In contrast to clear stimulatory effects of rising temperature, recent studies of the effects of CO2 on planktonic bacteria have reported conflicting results. To better understand the potential impact of predicted climate scenarios on the development and performance of bacterial communities, we performed bifactorial mesocosm experiments (pCO2 and temperature) with Baltic Sea water, during a diatom dominated bloom in autumn and a mixed phytoplankton bloom in summer. The development of bacterial community composition (BCC) followed well-known algal bloom dynamics. A principal coordinate analysis (PCoA) of bacterial OTUs (operational taxonomic units) revealed that phytoplankton succession and temperature were the major variables structuring the bacterial community whereas the impact of pCO2 was weak. Prokaryotic abundance and carbon production, and organic matter concentration and composition were partly affected by temperature but not by increased pCO2 . However, pCO2 did have significant and potentially direct effects on the relative abundance of several dominant OTUs; in some cases, these effects were accompanied by an antagonistic impact of temperature. Our results suggest the necessity of high-resolution BCC analyses and statistical analyses at the OTU level to detect the strong impact of CO2 on specific bacterial groups, which in turn might also influence specific organic matter degradation processes.
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Affiliation(s)
- Benjamin Bergen
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Biological Oceanography, Seestrasse 15, Rostock, D-18119, Germany
| | - Sonja Endres
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Biological Oceanography, Düsternbrooker Weg 20, Kiel, D-24105, Germany
| | - Anja Engel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Biological Oceanography, Düsternbrooker Weg 20, Kiel, D-24105, Germany
| | - Maren Zark
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Marine Geochemistry, Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 911, Oldenburg, D-26113, Germany
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Marine Geochemistry, Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 911, Oldenburg, D-26113, Germany
| | - Ulrich Sommer
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Biological Oceanography, Düsternbrooker Weg 20, Kiel, D-24105, Germany
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Biological Oceanography, Seestrasse 15, Rostock, D-18119, Germany
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19
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Borg Y, Grigonyte AM, Boeing P, Wolfenden B, Smith P, Beaufoy W, Rose S, Ratisai T, Zaikin A, Nesbeth DN. Open source approaches to establishing Roseobacter clade bacteria as synthetic biology chassis for biogeoengineering. PeerJ 2016; 4:e2031. [PMID: 27441104 PMCID: PMC4941783 DOI: 10.7717/peerj.2031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/20/2016] [Indexed: 11/20/2022] Open
Abstract
Aim. The nascent field of bio-geoengineering stands to benefit from synthetic biologists' efforts to standardise, and in so doing democratise, biomolecular research methods. Roseobacter clade bacteria comprise 15-20% of oceanic bacterio-plankton communities, making them a prime candidate for establishment of synthetic biology chassis for bio-geoengineering activities such as bioremediation of oceanic waste plastic. Developments such as the increasing affordability of DNA synthesis and laboratory automation continue to foster the establishment of a global 'do-it-yourself' research community alongside the more traditional arenas of academe and industry. As a collaborative group of citizen, student and professional scientists we sought to test the following hypotheses: (i) that an incubator capable of cultivating bacterial cells can be constructed entirely from non-laboratory items, (ii) that marine bacteria from the Roseobacter clade can be established as a genetically tractable synthetic biology chassis using plasmids conforming to the BioBrick(TM) standard and finally, (iii) that identifying and subcloning genes from a Roseobacter clade species can readily by achieved by citizen scientists using open source cloning and bioinformatic tools. Method. We cultivated three Roseobacter species, Roseobacter denitrificans, Oceanobulbus indolifexand Dinoroseobacter shibae. For each species we measured chloramphenicol sensitivity, viability over 11 weeks of glycerol-based cryopreservation and tested the effectiveness of a series of electroporation and heat shock protocols for transformation using a variety of plasmid types. We also attempted construction of an incubator-shaker device using only publicly available components. Finally, a subgroup comprising citizen scientists designed and attempted a procedure for isolating the cold resistance anf1 gene from Oceanobulbus indolifexcells and subcloning it into a BioBrick(TM) formatted plasmid. Results. All species were stable over 11 weeks of glycerol cryopreservation, sensitive to 17 µg/mL chloramphenicol and resistant to transformation using the conditions and plasmids tested. An incubator-shaker device, 'UCLHack-12' was assembled and used to cultivate sufficient quantity of Oceanobulbus indolifexcells to enable isolation of the anf1 gene and its subcloning into a plasmid to generate the BioBrick(TM) BBa_K729016. Conclusion.The process of 'de-skilling' biomolecular techniques, particularly for relatively under-investigated organisms, is still on-going. However, our successful cell growth and DNA manipulation experiments serve to indicate the types of capabilities that are now available to citizen scientists. Science democratised in this way can make a positive contribution to the debate around the use of bio-geoengineering to address oceanic pollution or climate change.
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Affiliation(s)
- Yanika Borg
- Department of Biochemical Engineering, University College London, United Kingdom.,Department of Mathematics, University College London, London, United Kingdom
| | | | | | | | | | | | - Simon Rose
- London BioHackspace, London, United Kingdom
| | | | - Alexey Zaikin
- Department of Mathematics, University College London, London, United Kingdom.,Institute for Women's Health, University College London, London, United Kingdom
| | - Darren N Nesbeth
- Department of Biochemical Engineering, University College London, United Kingdom
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20
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Kleist S, Ulbrich M, Bill N, Schmidt-Hohagen K, Geffers R, Schomburg D. Dealing with salinity extremes and nitrogen limitation - an unexpected strategy of the marine bacteriumDinoroseobacter shibae. Environ Microbiol 2016; 19:894-908. [DOI: 10.1111/1462-2920.13266] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/12/2016] [Accepted: 02/12/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Sarah Kleist
- Department of Bioinformatics and Biochemistry, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig; Langer Kamp 19 b D-38106 Braunschweig Germany
| | - Marcus Ulbrich
- Department of Bioinformatics and Biochemistry, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig; Langer Kamp 19 b D-38106 Braunschweig Germany
| | - Nelli Bill
- Department of Bioinformatics and Biochemistry, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig; Langer Kamp 19 b D-38106 Braunschweig Germany
| | - Kerstin Schmidt-Hohagen
- Department of Bioinformatics and Biochemistry, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig; Langer Kamp 19 b D-38106 Braunschweig Germany
| | - Robert Geffers
- Department of Molecular Bacteriology; Helmholtz-Centre for Infection Research (HZI); D-38124 Braunschweig
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig; Langer Kamp 19 b D-38106 Braunschweig Germany
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21
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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] [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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22
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Billerbeck S, Wemheuer B, Voget S, Poehlein A, Giebel HA, Brinkhoff T, Gram L, Jeffrey WH, Daniel R, Simon M. Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage. Nat Microbiol 2016; 1:16063. [PMID: 27572966 DOI: 10.1038/nmicrobiol.2016.63] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/05/2016] [Indexed: 12/13/2022]
Abstract
The identification and functional characterization of microbial communities remains a prevailing topic in microbial oceanography as information on environmentally relevant pelagic prokaryotes is still limited. The Roseobacter group, an abundant lineage of marine Alphaproteobacteria, can constitute large proportions of the bacterioplankton. Roseobacters also occur associated with eukaryotic organisms and possess streamlined as well as larger genomes from 2.2 to >5 Mpb. Here, we show that one pelagic cluster of this group, CHAB-I-5, occurs globally from tropical to polar regions and accounts for up to 22% of the active North Sea bacterioplankton in the summer. The first sequenced genome of a CHAB-I-5 organism comprises 3.6 Mbp and exhibits features of an oligotrophic lifestyle. In a metatranscriptome of North Sea surface waters, 98% of the encoded genes were present, and genes encoding various ABC transporters, glutamate synthase and CO oxidation were particularly upregulated. Phylogenetic gene content analyses of 41 genomes of the Roseobacter group revealed a unique cluster of pelagic organisms distinct from other lineages of this group, highlighting the adaptation to life in nutrient-depleted environments.
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Affiliation(s)
- Sara Billerbeck
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg D-26111, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology &Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen D-37077, Germany
| | - Sonja Voget
- Genomic and Applied Microbiology &Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen D-37077, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology &Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen D-37077, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg D-26111, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg D-26111, Germany
| | - Lone Gram
- Department of Systems Biology, Technical University of Denmark, Lyngby DK-2800 Kgs, Denmark
| | - Wade H Jeffrey
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, Florida 32514, USA
| | - Rolf Daniel
- Genomic and Applied Microbiology &Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen D-37077, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg D-26111, Germany
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23
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Vanucci S, Guidi F, Pistocchi R, Long RA. Phylogenetic structure of bacterial assemblages co-occurring with Ostreopsis cf. ovata bloom. HARMFUL ALGAE 2016; 55:259-271. [PMID: 28073540 DOI: 10.1016/j.hal.2016.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 04/05/2016] [Accepted: 04/06/2016] [Indexed: 06/06/2023]
Abstract
Extensive blooms of the toxic epiphytic/benthic dinoflagellate Ostreopsis cf. ovata are being reported with increasing frequency and spatial distribution in temperate coastal regions including the Mediterranean. These blooms are of human and environmental health concern due to the production of isobaric palytoxin and a wide range of ovatoxins by Ostreopsis cf. ovata. Bacterial-microalgal interactions are important regulators in algal bloom dynamics and potentially toxin dynamics. This study investigated the bacterial assemblages co-occurring with O. cf. ovata (OA) and from ambient seawaters (SW) during the early and peak phases of bloom development in NW Adriatic Sea. Fractions of the bacterial assemblages co-occurring with O. cf. ovata (OA) and more closely associated to the mucilage layer (LA) embedding O. cf. ovata cells were also reported. In total, 14 bacterial phyla were detected by targeted 454 pyrosequencing of the 16S rRNA gene. The dominant bacterial phyla in the OA assemblages were Proteobacteria and Bacteroidetes; while at the class level, Alphaproteobacteria were the most abundant (83 and 66%, relative abundance, early and peak bloom phases), followed by Flavobacteria (7 and 19%, early and peak phases). Actinobacteria and Cyanobacteria were of minor importance (<5% of the relative bacterial abundance each). Gammaproteobacteria showed a notably presence in OA assemblage only at the early phase of the bloom (genus Haliea, 13%). The Alphaproteobacteria were predominately composed by the genera Ruegeria, Jannaschia and Erythrobacter which represented about half of the total phylotypes' contribution of OA at both early and peak phases of the O. cf. ovata bloom, suggesting interactions between this consortium and the microalga. Moreover, the highest contribution of Ruegeria (30% of the total phylotypes) was observed at the early phase of the bloom in LA assemblage. Microbial assemblages associated with the ambient seawaters while being also dominated by Alphaproteobacteria and Flavobacteria were partially distinct from those associated with O. cf. ovata due to the presence of genera almost not retrieved in the latter assemblages.
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Affiliation(s)
- Silvana Vanucci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm), University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 S. Agata, Messina, Italy.
| | - Flavio Guidi
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via S'Alberto 163, 48123 Ravenna, Italy
| | - Rossella Pistocchi
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via S'Alberto 163, 48123 Ravenna, Italy
| | - Richard A Long
- Department of Biological Sciences, Florida A&M University, Tallahassee, FL 32307, United States
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24
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Lutz C, Thomas T, Steinberg P, Kjelleberg S, Egan S. Effect of interspecific competition on trait variation inPhaeobacter inhibensbiofilms. Environ Microbiol 2016; 18:1635-45. [DOI: 10.1111/1462-2920.13253] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/26/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Carla Lutz
- Centre for Marine Bio-Innovation
- School of Biotechnology and Biomolecular Science
| | - Torsten Thomas
- Centre for Marine Bio-Innovation
- School of Biotechnology and Biomolecular Science
| | - Peter Steinberg
- Centre for Marine Bio-Innovation
- School of Biological, Earth and Environmental Science; University of New South Wales; Sydney Australia
- Singapore Centre for Environmental Life Sciences Engineering; Nanyang Technological University; Singapore
- Sydney Institute of Marine Science; Mosman New South Wales Australia
| | - Staffan Kjelleberg
- Centre for Marine Bio-Innovation
- School of Biotechnology and Biomolecular Science
- Singapore Centre for Environmental Life Sciences Engineering; Nanyang Technological University; Singapore
| | - Suhelen Egan
- Centre for Marine Bio-Innovation
- School of Biotechnology and Biomolecular Science
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25
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Isolation of TDA-producing Phaeobacter strains from sea bass larval rearing units and their probiotic effect against pathogenic Vibrio spp. in Artemia cultures. Syst Appl Microbiol 2016; 39:180-188. [PMID: 26922490 DOI: 10.1016/j.syapm.2016.01.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/28/2016] [Accepted: 01/29/2016] [Indexed: 10/22/2022]
Abstract
Fish-pathogenic Vibrio can cause large-scale crashes in marine larval rearing units and, since the use of antibiotics can result in bacterial antibiotic resistance, new strategies for disease prevention are needed. Roseobacter-clade bacteria from turbot larval rearing facilities can antagonize Vibrio anguillarum and reduce mortality in V. anguillarum-infected cod and turbot larvae. In this study, it was demonstrated that antagonistic Roseobacter-clade bacteria could be isolated from sea bass larval rearing units. In addition, it was shown that they not only antagonized V. anguillarum but also V. harveyi, which is the major bacterial pathogen in crustaceans and Mediterranean sea bass larvae cultures. Concomitantly, they significantly improved survival of V. harveyi-infected brine shrimp. 16S rRNA gene sequence homology identified the antagonists as Phaeobacter sp., and in silico DNA-DNA hybridization indicated that they could belong to a new species. The genomes contained genes involved in synthesis of the antibacterial compound tropodithietic acid (TDA), and its production was confirmed by UHPLC-TOFMS. The new Phaeobacter colonized live feed (Artemia) cultures and reduced Vibrio counts significantly, since they reached only 10(4)CFUmL(-1), as opposed to 10(8)CFUmL(-1) in non-Phaeobacter treated controls. Survival of V. anguillarum-challenged Artemia nauplii was enhanced by the presence of wild type Phaeobacter compared to challenged control cultures (89±1.0% vs 8±3.2%). In conclusion, TDA-producing Phaeobacter isolated from Mediterranean marine larviculture are promising probiotic bacteria against pathogenic Vibrio in crustacean live-feed cultures for marine fish larvae.
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26
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 462] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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27
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Gram L, Rasmussen BB, Wemheuer B, Bernbom N, Ng YY, Porsby CH, Breider S, Brinkhoff T. Phaeobacter inhibens from the Roseobacter clade has an environmental niche as a surface colonizer in harbors. Syst Appl Microbiol 2015; 38:483-93. [PMID: 26343311 DOI: 10.1016/j.syapm.2015.07.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 07/06/2015] [Accepted: 07/08/2015] [Indexed: 12/27/2022]
Abstract
Phaeobacter inhibens belongs to the marine Roseobacter clade and is important as a carbon and sulfur metabolizer, a biofilm former and producer of the antibiotic tropodithietic acid (TDA). The majority of cultured strains have been isolated from marine aquaculture sites, however, their niche in the environment is to date unknown. Here, we report on the repeated isolation of Phaeobacter inhibens strains from a marine environment (harbors) not related to aquaculture. Based on phenotype and 16S rRNA gene sequence similarity, a total of 64 P. inhibens strains were identified from 35 samples (eukaryotic organisms or biofilms on inert surfaces) in Jyllinge Harbor during late summer and autumn, but not during winter and spring in 2009, 2011, and 2012. P. inhibens strains were also isolated from biofilms at three other Danish harbors (in 2012), but not from the surrounding seawater. Ten of the 14 samples from which P. inhibens was cultured contained bryozoans. DNA was extracted (in 2012) from 55 out of 74 Jyllinge Harbor samples, and 35 were positive for Phaeobacter using a genus-specific PCR. P. inhibens strains were isolated from nine of these samples. DNA and RNA were isolated from 13 random samples and used for amplification of 16S rRNA. P. inhibens was detected in five of these samples, all of which were biofilm samples, by pyrotag-sequencing at a prevalence of 0.02-0.68% of the prokaryotic community. The results indicated that P. inhibens had a niche in biofilms of fouled surfaces in harbor areas and that the population followed a seasonal fluctuation.
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Affiliation(s)
- Lone Gram
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet Bldg 301, DK-2800 Kgs. Lyngby, Denmark.
| | - Bastian Barker Rasmussen
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet Bldg 301, DK-2800 Kgs. Lyngby, Denmark
| | - Bernd Wemheuer
- Georg-August University Göttingen, Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Nete Bernbom
- National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, DK-2800 Kgs. Lyngby, Denmark
| | - Yoke Yin Ng
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet Bldg 301, DK-2800 Kgs. Lyngby, Denmark
| | - Cisse H Porsby
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet Bldg 301, DK-2800 Kgs. Lyngby, Denmark
| | - Sven Breider
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Germany
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28
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Lidbury I, Kimberley G, Scanlan DJ, Murrell JC, Chen Y. Comparative genomics and mutagenesis analyses of choline metabolism in the marine Roseobacter clade. Environ Microbiol 2015; 17:5048-62. [PMID: 26058574 PMCID: PMC4744692 DOI: 10.1111/1462-2920.12943] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 06/03/2015] [Indexed: 11/30/2022]
Abstract
Choline is ubiquitous in marine eukaryotes and appears to be widely distributed in surface marine waters; however, its metabolism by marine bacteria is poorly understood. Here, using comparative genomics and molecular genetic approaches, we reveal that the capacity for choline catabolism is widespread in marine heterotrophs of the marine Roseobacter clade (MRC). Using the model bacterium Ruegeria pomeroyi, we confirm that the betA, betB and betC genes, encoding choline dehydrogenase, betaine aldehyde dehydrogenase and choline sulfatase, respectively, are involved in choline metabolism. The betT gene, encoding an organic solute transporter, was essential for the rapid uptake of choline but not glycine betaine (GBT). Growth of choline and GBT as a sole carbon source resulted in the re‐mineralization of these nitrogen‐rich compounds into ammonium. Oxidation of the methyl groups from choline requires formyltetrahydrofolate synthetase encoded by fhs in R. pomeroyi, deletion of which resulted in incomplete degradation of GBT. We demonstrate that this was due to an imbalance in the supply of reducing equivalents required for choline catabolism, which can be alleviated by the addition of formate. Together, our results demonstrate that choline metabolism is ubiquitous in the MRC and reveal the role of Fhs in methyl group oxidation in R. pomeroyi.
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Affiliation(s)
- Ian Lidbury
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - George Kimberley
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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29
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Brock NL, Menke M, Klapschinski TA, Dickschat JS. Marine bacteria from the Roseobacter clade produce sulfur volatiles via amino acid and dimethylsulfoniopropionate catabolism. Org Biomol Chem 2015; 12:4318-23. [PMID: 24848489 DOI: 10.1039/c4ob00719k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) is a versatile sulfur source for the production of sulfur-containing secondary metabolites by marine bacteria from the Roseobacter clade. (34)S-labelled DMSP and cysteine, and several DMSP derivatives with modified S-alkyl groups were synthesised and used in feeding experiments that gave insights into the biosynthesis of sulfur volatiles from these bacteria.
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Affiliation(s)
- Nelson L Brock
- Institut für Organische Chemie, Hagenring 30, 38106 Braunschweig, Germany.
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30
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Temporal and vertical distributions of bacterioplankton at the Gray's Reef National Marine Sanctuary. Appl Environ Microbiol 2014; 81:910-7. [PMID: 25416764 DOI: 10.1128/aem.02802-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Large spatial scales and long-term shifts of bacterial community composition (BCC) in the open ocean can often be reliably predicted based on the dynamics of physical-chemical variables. The power of abiotic factors in shaping BCC on shorter time scales in shallow estuarine mixing zones is less clear. We examined the diurnal variation in BCC at different water depths in the spring and fall of 2011 at a station in the Gray's Reef National Marine Sanctuary (GRNMS). This site is located in the transition zone between the estuarine plume and continental shelf waters of the South Atlantic Bight. A total of 234,516 pyrotag sequences of bacterial 16S rRNA genes were recovered; they were taxonomically affiliated with >200 families of 23 bacterial phyla. Nonmetric multidimensional scaling analysis revealed significant differences in BCC between spring and fall samples, likely due to seasonality in the concentrations of dissolved organic carbon and nitrate plus nitrite. Within each diurnal sampling, BCC differed significantly by depth only in the spring and differed significantly between day and night only in the fall. The former variation largely tracked changes in light availability, while the latter was most correlated with concentrations of polyamines and chlorophyll a. Our results suggest that at the GRNMS, a coastal mixing zone, diurnal variation in BCC is attributable to the mixing of local and imported bacterioplankton rather than to bacterial growth in response to environmental changes. Our results also indicate that, like members of the Roseobacter clade, SAR11 bacteria may play an important role in processing dissolved organic material in coastal oceans.
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31
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Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling. ISME JOURNAL 2014; 9:760-9. [PMID: 25148480 DOI: 10.1038/ismej.2014.149] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/03/2014] [Accepted: 07/11/2014] [Indexed: 11/08/2022]
Abstract
Bacteria of the marine Roseobacter clade are characterised by their ability to utilise a wide range of organic and inorganic compounds to support growth. Trimethylamine (TMA) and trimethylamine N-oxide (TMAO) are methylated amines (MA) and form part of the dissolved organic nitrogen pool, the second largest source of nitrogen after N2 gas, in the oceans. We investigated if the marine heterotrophic bacterium, Ruegeria pomeroyi DSS-3, could utilise TMA and TMAO as a supplementary energy source and whether this trait had any beneficial effect on growth. In R. pomeroyi, catabolism of TMA and TMAO resulted in the production of intracellular ATP which in turn helped to enhance growth rate and growth yield as well as enhancing cell survival during prolonged energy starvation. Furthermore, the simultaneous use of two different exogenous energy sources led to a greater enhancement of chemoorganoheterotrophic growth. The use of TMA and TMAO primarily as an energy source resulted in the remineralisation of nitrogen in the form of ammonium, which could cross feed into another bacterium. This study provides greater insight into the microbial metabolism of MAs in the marine environment and how it may affect both nutrient flow within marine surface waters and the flux of these climatically important compounds into the atmosphere.
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33
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Wemheuer B, Güllert S, Billerbeck S, Giebel HA, Voget S, Simon M, Daniel R. Impact of a phytoplankton bloom on the diversity of the active bacterial community in the southern North Sea as revealed by metatranscriptomic approaches. FEMS Microbiol Ecol 2013; 87:378-89. [DOI: 10.1111/1574-6941.12230] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/18/2013] [Accepted: 09/19/2013] [Indexed: 12/18/2022] Open
Affiliation(s)
- Bernd Wemheuer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Institute of Microbiology and Genetics; Georg-August-University Göttingen; Göttingen Germany
| | - Simon Güllert
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Institute of Microbiology and Genetics; Georg-August-University Göttingen; Göttingen Germany
| | - Sara Billerbeck
- Biology of Geological Processes - Aquatic Microbial Ecology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl-von-Ossietzky-University Oldenburg; Oldenburg Germany
| | - Helge-Ansgar Giebel
- Biology of Geological Processes - Aquatic Microbial Ecology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl-von-Ossietzky-University Oldenburg; Oldenburg Germany
| | - Sonja Voget
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Institute of Microbiology and Genetics; Georg-August-University Göttingen; Göttingen Germany
| | - Meinhard Simon
- Biology of Geological Processes - Aquatic Microbial Ecology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl-von-Ossietzky-University Oldenburg; Oldenburg Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Institute of Microbiology and Genetics; Georg-August-University Göttingen; Göttingen Germany
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34
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Christie-Oleza JA, Miotello G, Armengaud J. Proteogenomic definition of biomarkers for the large Roseobacter clade and application for a quick screening of new environmental isolates. J Proteome Res 2013; 12:5331-9. [PMID: 24044462 DOI: 10.1021/pr400554e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Whole-cell, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry has become a routine and reliable method for microbial characterization due to its simplicity, low cost, and high reproducibility. The identification of microbial isolates relies on the spectral resemblance of low-molecular-weight proteins to already-existing isolates within the databases. This is a gold standard for clinicians who have a finite number of well-defined pathogenic strains but represents a problem for environmental microbiologists with an overwhelming number of organisms to be defined. Here we set a milestone for implementing whole-cell MALDI-TOF mass spectrometry to identify isolates from the biosphere. To make this technique accessible for environmental studies, we propose to (i) define biomarkers that will always show up with an intense m/z signal in the MALDI-TOF spectra and (ii) create a database with all the possible m/z values that these biomarkers can generate to screen new isolates. We tested our method with the relevant marine Roseobacter lineage. The use of shotgun nanoLC-MS/MS proteomics on the small proteome fraction of nine Roseobacter strains and the proteogenomic toolbox helped us to identify potential biomarkers in terms of protein abundance and low variability among strains. We show that the DNA binding protein, HU, and the ribosomal proteins, L29 and L30, are the most robust biomarkers within the Roseobacter clade. The molecular weights of these three biomarkers, as for other conserved homologous proteins, vary due to sequence variation above the genus level. Therefore, we calculated the m/z values expected for each one of the known Roseobacter genera and tested our strategy during an extensive screening of natural marine isolates obtained from coastal waters of the Western Mediterranean Sea. The use of this technique versus standard sequencing methods is discussed.
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Hahnke S, Sperling M, Langer T, Wichels A, Gerdts G, Beardsley C, Brinkhoff T, Simon M. Distinct seasonal growth patterns of the bacteriumPlanktotalea frisiain the North Sea and specific interaction with phytoplankton algae. FEMS Microbiol Ecol 2013; 86:185-99. [DOI: 10.1111/1574-6941.12151] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 05/10/2013] [Accepted: 05/21/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Sarah Hahnke
- Institute for Chemistry and Biology of the Marine Environment (ICBM); University of Oldenburg; Oldenburg; Germany
| | - Martin Sperling
- Institute for Chemistry and Biology of the Marine Environment (ICBM); University of Oldenburg; Oldenburg; Germany
| | - Thomas Langer
- Institute for Chemistry and Biology of the Marine Environment (ICBM); University of Oldenburg; Oldenburg; Germany
| | - Antje Wichels
- Alfred Wegener Institute for Polar and Marine Research (AWI); Biologische Anstalt Helgoland; Helgoland; Germany
| | - Gunnar Gerdts
- Alfred Wegener Institute for Polar and Marine Research (AWI); Biologische Anstalt Helgoland; Helgoland; Germany
| | - Christine Beardsley
- Institute for Chemistry and Biology of the Marine Environment (ICBM); University of Oldenburg; Oldenburg; Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICBM); University of Oldenburg; Oldenburg; Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM); University of Oldenburg; Oldenburg; Germany
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Brock NL, Citron CA, Zell C, Berger M, Wagner-Döbler I, Petersen J, Brinkhoff T, Simon M, Dickschat JS. Isotopically labeled sulfur compounds and synthetic selenium and tellurium analogues to study sulfur metabolism in marine bacteria. Beilstein J Org Chem 2013; 9:942-50. [PMID: 23766810 PMCID: PMC3678758 DOI: 10.3762/bjoc.9.108] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 04/26/2013] [Indexed: 11/23/2022] Open
Abstract
Members of the marine Roseobacter clade can degrade dimethylsulfoniopropionate (DMSP) via competing pathways releasing either methanethiol (MeSH) or dimethyl sulfide (DMS). Deuterium-labeled [(2)H6]DMSP and the synthetic DMSP analogue dimethyltelluriopropionate (DMTeP) were used in feeding experiments with the Roseobacter clade members Phaeobacter gallaeciensis DSM 17395 and Ruegeria pomeroyi DSS-3, and their volatile metabolites were analyzed by closed-loop stripping and solid-phase microextraction coupled to GC-MS. Feeding experiments with [(2)H6]DMSP resulted in the incorporation of a deuterium label into MeSH and DMS. Knockout of relevant genes from the known DMSP demethylation pathway to MeSH showed in both species a residual production of [(2)H3]MeSH, suggesting that a second demethylation pathway is active. The role of DMSP degradation pathways for MeSH and DMS formation was further investigated by using the synthetic analogue DMTeP as a probe in feeding experiments with the wild-type strain and knockout mutants. Feeding of DMTeP to the R. pomeroyi knockout mutant resulted in a diminished, but not abolished production of demethylation pathway products. These results further corroborated the proposed second demethylation activity in R. pomeroyi. Isotopically labeled [(2)H3]methionine and (34)SO4 (2-), synthesized from elemental (34)S8, were tested to identify alternative sulfur sources besides DMSP for the MeSH production in P. gallaeciensis. Methionine proved to be a viable sulfur source for the MeSH volatiles, whereas incorporation of labeling from sulfate was not observed. Moreover, the utilization of selenite and selenate salts by marine alphaproteobacteria for the production of methylated selenium volatiles was explored and resulted in the production of numerous methaneselenol-derived volatiles via reduction and methylation. The pathway of selenate/selenite reduction, however, proved to be strictly separated from sulfate reduction.
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Affiliation(s)
- Nelson L Brock
- Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Christian A Citron
- Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Claudia Zell
- Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9–11, 26129 Oldenburg, Germany
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9–11, 26129 Oldenburg, Germany
| | - Irene Wagner-Döbler
- Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Jörn Petersen
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9–11, 26129 Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9–11, 26129 Oldenburg, Germany
| | - Jeroen S Dickschat
- Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
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