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Lone Gram - One of the best experts on this subject based on the ideXlab platform.
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Phylogenetic distribution of roseobacticides in the Roseobacter group and their effect on microalgae
Environmental microbiology reports, 2018Co-Authors: Eva C. Sonnenschein, Kristian Fog Nielsen, Mikkel Bentzon-tilia, Christopher B. W. Phippen, Silas Anselm Rasmussen, Lone GramAbstract:The Roseobacter-group species Phaeobacter inhibens produces the antibacterial tropodithietic acid (TDA) and the algaecidal roseobacticides with both compound classes sharing part of the same biosynthetic pathway. The purpose of this study was to investigate the production of roseobacticides more broadly in TDA-producing Roseobacters and to compare the effect of producers and non-producers on microalgae. Of 33 Roseobacters analyzed, roseobacticide production was a unique feature of TDA-producing P. inhibens, P. gallaeciensis and P. piscinae strains. One TDA-producing Phaeobacter, 27-4, did not produce roseobacticides, possibly due to a transposable element. TDA-producing Ruegeria and Pseudovibrio did not produce roseobacticides. Addition of roseobacticide-containing bacterial extracts affected the growth of the microalgae Rhodomonas salina, Thalassiosira pseudonana and Emiliania huxleyi, while growth of Tetraselmis suecica was unaffected. During co-cultivation, growth of E. huxleyi was initially stimulated by the roseobacticide producer DSM 17395, while the subsequent decline in algal cell numbers during senescence was enhanced. Strain 27-4 that does not produce roseobacticides had no effect on algal growth. Both bacterial strains, DSM 17395 and 27-4, grew during co-cultivation presumably utilizing algal exudates. Furthermore, TDA-producing Roseobacters have potential as probiotics in marine larviculture and it is promising that the live feed Tetraselmis was unaffected by roseobacticides-containing extracts.
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Phylogenetic distribution of roseobacticides in the Roseobacter group and their effect on microalgae
2018Co-Authors: Eva C. Sonnenschein, Kristian Fog Nielsen, Mikkel Bentzon-tilia, Christopher B. W. Phippen, Silas Anselm Rasmussen, Lone GramAbstract:The Roseobacter -group species Phaeobacter inhibens produces the antibacterial tropodithietic acid (TDA) and the algaecidal roseobacticides with both compound classes sharing part of the same biosynthetic pathway. The purpose of this study was to investigate the production of roseobacticides more broadly in TDA-producing Roseobacters and to compare the effect of producers and non-producers on microalgae. Of 33 Roseobacters analyzed, roseobacticide production was a unique feature of TDA-producing P. inhibens , P. gallaeciensis and P. piscinae strains. One TDA-producing Phaeobacter strain, 27-4, was unable to produce roseobacticides, possibly due to a transposable element. TDA-producing Ruegeria mobilis and Pseudovibrio did not produce roseobacticides. Addition of roseobacticide-containing bacterial extracts affected the growth of the microalgae Rhodomonas salina , Thalassiosira pseudonana and Emiliania huxleyi , while growth of Tetraselmis suecica was unaffected. During co-cultivation, growth of E. huxleyi was initially stimulated by the roseobacticide producer DSM 17395, while the subsequent decline in algal cell numbers during senescence was enhanced. Strain 27-4 that does not produce roseobacticides had no effect on algal growth. Both bacterial strains, DSM 17395 and 27-4, grew during co-cultivation presumably utilizing algal exudates. Furthermore, TDA-producing Roseobacters have potential as probiotics in marine larviculture and it is promising that the live feed Tetraselmis was unaffected by roseobacticides-containing extracts.
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Biotechnological Applications of the Roseobacter Clade
Bioprospecting, 2016Co-Authors: Mikkel Bentzon-tilia, Lone GramAbstract:The multitude of distinct niches that prevail in the marine environment has facilitated the development of very diverse marine microbiomes. This diversity is, naturally, reflected in their biochemistry and secondary metabolites and, hence, marine microbes represent a virtually untapped source of new bioactive compounds. The Roseobacter clade of marine α-proteobacteria represents some of the most abundant organisms in the marine environment and they may constitute as much as 20–30 % of the prokaryotic community during algal blooms. Often, they exhibit traits suggestive of a lifestyle in close association with phytoplankton; including traits related to surface colonization, iron scavenging, and the production of bioactive secondary metabolites. Despite the fact that relatively few bioactive compounds have been identified in the α-proteobacteria, the Roseobacters are known to produce compounds capable of stimulating algae growth, i.e. auxins, and algaecidal compounds, i.e. the roseobacticides. In addition, the Roseobacters can produce a range of antibacterial products, such as the small tropolone compound tropodithietic acid (TDA) and the nonribosomal peptide indigoidine. TDA targets a broad spectrum of Gram-positive and Gram-negative bacteria in which resistance towards the compound does not arise easily. Mining the genomes of Roseobacters also reveal that they are likely capable of producing other compounds than hitherto discovered by classical bio-assay guided fractionation, since the genomes contain genes/gene clusters probably encoding unknown bioactive secondary metabolites. Therefore, bacteria of the Roseobacter clade may serve as potential sources of novel bioactive compounds, including novel antibiotics, which is of paramount importance in the battle against antibiotic resistant pathogenic bacteria.
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Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage
Nature Microbiology, 2016Co-Authors: Sara Billerbeck, Sonja Voget, Thorsten Brinkhoff, Bernd Wemheuer, Rolf Daniel, Lone Gram, Anja Poehlein, Helge-ansgar Giebel, Wade H. Jeffrey, Meinhard SimonAbstract:Global sampling campaigns show that the CHAB-I-5 Roseobacter cluster is abundant in the marine environment, and found from the poles to the tropics. Analysis of the draft genome of strain SB2 reveals adaptation to an oligotrophic lifestyle. 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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Inactivation of Vibrio anguillarum by attached and planktonic Roseobacter cells.
Applied and environmental microbiology, 2010Co-Authors: Paul D'alvise, Kristian Fog Nielsen, Jette Melchiorsen, Cisse Hedegaard Porsby, Lone GramAbstract:The purpose of the present study was to investigate the inhibition of Vibrio by Roseobacter in a combined liquid-surface system. Exposure of Vibrio anguillarum to surface-attached Roseobacters (107 CFU/cm2) resulted in significant reduction or complete killing of the pathogen inoculated at 102 to 104 CFU/ml. The effect was likely associated with the production of tropodithietic acid (TDA), as a TDA-negative mutant did not affect survival or growth of V. anguillarum.
Mary Ann Moran - One of the best experts on this subject based on the ideXlab platform.
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Evolutionary Ecology of the Marine Roseobacter Clade
Microbiology and molecular biology reviews : MMBR, 2014Co-Authors: Haiwei Luo, Mary Ann MoranAbstract:SUMMARY Members of the Roseobacter clade are equipped with a tremendous diversity of metabolic capabilities, which in part explains their success in so many different marine habitats. Ideas on how this diversity evolved and is maintained are reviewed, focusing on recent evolutionary studies exploring the timing and mechanisms of Roseobacter ecological diversification.
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Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters.
The ISME journal, 2014Co-Authors: Haiwei Luo, Ramunas Stepanauskas, Brandon K. Swan, Austin L. Hughes, Mary Ann MoranAbstract:The vast majority of surface ocean bacteria are uncultivated. Compared with their cultured relatives, they frequently exhibit a streamlined genome, reduced G+C content and distinct gene repertoire. These genomic traits are relevant to environmental adaptation, and have generally been thought to become fixed in marine bacterial populations through selection. Using single-cell genomics, we sequenced four uncultivated cells affiliated with the ecologically relevant Roseobacter clade and used a composition-heterogeneous Bayesian phylogenomic model to resolve these single-cell genomes into a new clade. This lineage has no representatives in culture, yet accounts for ∼35% of Roseobacters in some surface ocean waters. Analyses of multiple genomic traits, including genome size, G+C content and percentage of noncoding DNA, suggest that these single cells are representative of oceanic Roseobacters but divergent from isolates. Population genetic analyses showed that substitution of physicochemically dissimilar amino acids and replacement of G+C-rich to G+C-poor codons are accelerated in the uncultivated clade, processes that are explained equally well by genetic drift as by the more frequently invoked explanation of natural selection. The relative importance of drift vs selection in this clade, and perhaps in other marine bacterial clades with streamlined G+C-poor genomes, remains unresolved until more evidence is accumulated.
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Genome content of uncultivated marine Roseobacters in the surface ocean.
Environmental microbiology, 2011Co-Authors: Haiwei Luo, Ari Löytynoja, Mary Ann MoranAbstract:Summary Understanding of the ecological roles and evolution- ary histories of marine bacterial taxa can be compli- cated by mismatches in genome content between wild populations and their better-studied cultured relatives. We used computed patterns of non- synonymous (amino acid-altering) nucleotide diversity in marine metagenomic data to provide high-confidence identification of DNA fragments from uncultivated members of the Roseobacter clade, an abundant taxon of heterotrophic marine bacteri- oplankton in the world's oceans. Differences in gene stoichiometry in the Global Ocean Survey metage- nomic data set compared with 39 sequenced isolates indicated that natural Roseobacter populations differ systematically in several genomic attributes from their cultured representatives, including fewer genes for signal transduction and cell surface modifications but more genes for Sec-like protein secretion systems, anaplerotic CO2 incorporation, and phos- phorus and sulfate uptake. Several of these trends match well with characteristics previously identified as distinguishing r- versus K-selected ecological strategies in bacteria, suggesting that the r-strategist model assigned to cultured Roseobacters may be less applicable to their free-living oceanic counterparts. The metagenomic Roseobacter DNA fragments revealed several traits with evolutionary histories suggestive of horizontal gene transfer from other marine bacterioplankton taxa or viruses, including pyrophosphatases and glycosylation proteins.
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Analysis of sulfur-related transcription by Roseobacter communities using a taxon-specific functional gene microarray
Environmental microbiology, 2010Co-Authors: Johanna M. Rinta-kanto, Ronald P Kiene, Scott M. Gifford, Shulei Sun, Helmut Bürgmann, Shalabh Sharma, Daniela A. Del Valle, Mary Ann MoranAbstract:Summary The fraction of dissolved dimethylsulfoniopropionate (DMSPd) converted by marine bacterioplankton into the climate-active gas dimethylsulfide (DMS) varies widely in the ocean, with the factors that determine this value still largely unknown. One current hypothesis is that the ratio of DMS formation : DMSP demethylation is determined by DMSP availability, with ‘availability’ in both an absolute sense (i.e. concentration in seawater) and in a relative sense (i.e. proportionally to other labile organic S compounds) proposed as the critical factor. We investigated these models during an experimentally induced phytoplankton bloom using a taxon-specific microarray targeting DMSP-related gene transcription in members of the Roseobacter clade, a group hypothesized to play an important role in the surface ocean sulfur cycle and well represented by genome sequences. The array consisted of 1578 probes to 431 genes and was designed to target diverse Roseobacter communities in natural seawater by using hierarchical probe design based on 13 genome sequences. The prevailing pattern of Roseobacter gene transcription showed relative depletion of DMSP-related transcripts during the peak of the bloom, despite increasing absolute concentrations and flux of DMSP-related compounds. DMSPd thus appeared to be assimilated by Roseobacter populations in proportion to its relative abundance in the organic matter pool (the ‘relative sense’ hypothesis), rather than assimilated in preference to other labile organic sulfur or carbon compounds produced during the bloom. The relative investment of the Roseobacter community in DMSP demethylation was not useful for predicting the formation of DMS, however, suggesting a complex regulatory process that may involve multiple taxa and alternative fates of DMSPd.
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occurrence and expression of gene transfer agent genes in marine bacterioplankton
Applied and Environmental Microbiology, 2008Co-Authors: Erin J Biers, Kui Wang, Feng Chen, Robert Belas, Catherine Pennington, Mary Ann MoranAbstract:Genes with homology to the transduction-like gene transfer agent (GTA) were observed in genome sequences of three cultured members of the marine Roseobacter clade. A broader search for homologs for this host-controlled virus-like gene transfer system identified likely GTA systems in cultured Alphaproteobacteria, and particularly in marine bacterioplankton representatives. Expression of GTA genes and extracellular release of GTA particles (∼50 to 70 nm) was demonstrated experimentally for the Roseobacter clade member Silicibacter pomeroyi DSS-3, and intraspecific gene transfer was documented. GTA homologs are surprisingly infrequent in marine metagenomic sequence data, however, and the role of this lateral gene transfer mechanism in ocean bacterioplankton communities remains unclear.
Robert Belas - One of the best experts on this subject based on the ideXlab platform.
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A Novel Inducer of Roseobacter Motility Is Also a Disruptor of Algal Symbiosis
Journal of bacteriology, 2012Co-Authors: Preeti Sule, Robert BelasAbstract:Silicibacter sp. strain TM1040, a member of the Roseobacter clade, forms a symbiosis with unicellular phytoplankton, which is inextricably linked to the biphasic "swim or stick" lifestyle of the bacteria. Mutations in flaC bias the population toward the motile phase. Renewed examination of the FlaC(-) strain (HG1016) uncovered that it is composed of two different cells: a pigmented type, PS01, and a nonpigmented cell, PS02, each of which has an identical mutation in flaC. While monocultures of PS01 and PS02 had few motile cells (0.6 and 6%, respectively), coculturing the two strains resulted in a 10-fold increase in the number of motile cells. Cell-free supernatants from coculture or wild-type cells were fully capable of restoring motility to PS01 and PS02, which was due to increased fliC3 (flagellin) transcription, FliC3 protein levels per cell, and flagella synthesis. The motility-inducing compound has an estimated mass of 226 Da, as determined by mass spectrometry, and is referred to as Roseobacter Motility Inducer (RMI). Mutations affecting genes involved in phenyl acetic acid synthesis significantly reduced RMI, while defects in tropodithietic acid (TDA) synthesis had marginal or no effect on RMI. RMI biosynthesis is induced by p-coumaric acid, a product of algal lignin degradation. When added to algal cultures, RMI caused loss of motility, cell enlargement, and vacuolization in the algal cells. RMI is a new member of the roseobacticide family of troponoid compounds whose activities affect Roseobacters, by shifting their population toward motility, as well as their phytoplankton hosts, through an algicidal effect.
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molecular mechanisms underlying Roseobacter phytoplankton symbioses
Current Opinion in Biotechnology, 2010Co-Authors: Haifeng Geng, Robert BelasAbstract:Members of the Roseobacter clade of α-proteobacteria are among the most abundant and ecologically relevant marine bacteria. Bacterial isolates and gene sequences derived from this taxonomic lineage have been retrieved from marine environments ranging from sea ice to open ocean mixed layer to tropical coral reefs, and in ecological niches ranging from free-living plankton to sponge symbiont to biofilm pioneer. Although Roseobacters are cosmopolitan in the marine environment, their numbers and activity significantly rise with increases in the population density of phytoplankton [ 1 , 2 ], suggesting that these bacteria are highly adapted to engage in these symbioses. This review examines the molecules and phenotypes of Roseobacters that are important in establishing and maintaining the symbioses between Roseobacters and phytoplankton.
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Molecular mechanisms underlying Roseobacter–phytoplankton symbioses
Current opinion in biotechnology, 2010Co-Authors: Haifeng Geng, Robert BelasAbstract:Members of the Roseobacter clade of α-proteobacteria are among the most abundant and ecologically relevant marine bacteria. Bacterial isolates and gene sequences derived from this taxonomic lineage have been retrieved from marine environments ranging from sea ice to open ocean mixed layer to tropical coral reefs, and in ecological niches ranging from free-living plankton to sponge symbiont to biofilm pioneer. Although Roseobacters are cosmopolitan in the marine environment, their numbers and activity significantly rise with increases in the population density of phytoplankton [ 1 , 2 ], suggesting that these bacteria are highly adapted to engage in these symbioses. This review examines the molecules and phenotypes of Roseobacters that are important in establishing and maintaining the symbioses between Roseobacters and phytoplankton.
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occurrence and expression of gene transfer agent genes in marine bacterioplankton
Applied and Environmental Microbiology, 2008Co-Authors: Erin J Biers, Kui Wang, Feng Chen, Robert Belas, Catherine Pennington, Mary Ann MoranAbstract:Genes with homology to the transduction-like gene transfer agent (GTA) were observed in genome sequences of three cultured members of the marine Roseobacter clade. A broader search for homologs for this host-controlled virus-like gene transfer system identified likely GTA systems in cultured Alphaproteobacteria, and particularly in marine bacterioplankton representatives. Expression of GTA genes and extracellular release of GTA particles (∼50 to 70 nm) was demonstrated experimentally for the Roseobacter clade member Silicibacter pomeroyi DSS-3, and intraspecific gene transfer was documented. GTA homologs are surprisingly infrequent in marine metagenomic sequence data, however, and the role of this lateral gene transfer mechanism in ocean bacterioplankton communities remains unclear.
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Genetic dissection of tropodithietic acid biosynthesis by marine Roseobacters.
Applied and environmental microbiology, 2008Co-Authors: Haifeng Geng, Jesper Bartholin Bruhn, Kristian Fog Nielsen, Lone Gram, Robert BelasAbstract:ABSTRACT The symbiotic association between the Roseobacter Silicibacter sp. strain TM1040 and the dinoflagellate Pfiesteria piscicida involves bacterial chemotaxis to dinoflagellate-produced dimethylsulfoniopropionate (DMSP), DMSP demethylation, and ultimately a biofilm on the surface of the host. Biofilm formation is coincident with the production of an antibiotic and a yellow-brown pigment. In this report, we demonstrate that the antibiotic is a sulfur-containing compound, tropodithietic acid (TDA). Using random transposon insertion mutagenesis, 12 genes were identified as critical for TDA biosynthesis by the bacteria, and mutation in any one of these results in a loss of antibiotic activity (Tda−) and pigment production. Unexpectedly, six of the genes, referred to as tdaA-F, could not be found on the annotated TM1040 genome and were instead located on a previously unidentified plasmid (ca. 130 kb; pSTM3) that exhibited a low frequency of spontaneous loss. Homologs of tdaA and tdaB from Silicibacter sp. strain TM1040 were identified by mutagenesis in another TDA-producing Roseobacter, Phaeobacter sp. strain 27-4, which also possesses two large plasmids (ca. 60 and ca. 70 kb, respectively), and tda genes were found by DNA-DNA hybridization in 88% of a diverse collection of nine Roseobacters with known antibiotic activity. These data suggest that Roseobacters may use a common pathway for TDA biosynthesis that involves plasmid-encoded proteins. Using metagenomic library databases and a bioinformatics approach, differences in the biogeographical distribution between the critical TDA synthesis genes were observed. The implications of these results to Roseobacter survival and the interaction between TM1040 and its dinoflagellate host are discussed.
Alison Buchan - One of the best experts on this subject based on the ideXlab platform.
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Acyl-homoserine lactone-based quorum sensing in the Roseobacter clade: complex cell-to-cell communication controls multiple physiologies
Frontiers in microbiology, 2013Co-Authors: William Nathan Cude, Alison BuchanAbstract:Bacteria have been widely reported to use quorum sensing (QS) systems, which employ small diffusible metabolites to coordinate gene expression in a population density dependent manner. In Proteobacteria, the most commonly described QS signaling molecules are N-acyl-homoserine lactones (AHLs). Recent studies suggest that members of the abundant marine Roseobacter lineage possess AHL-based QS systems and are environmentally relevant models for relating QS to ecological success. As reviewed here, these studies suggest that the roles of QS in Roseobacters are varied and complex. An analysis of the 43 publically available Roseobacter genomes shows conservation of QS protein sequences and overall gene topologies, providing support for the hypothesis that quorum sensing is a conserved and widespread trait in the clade.
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production of the antimicrobial secondary metabolite indigoidine contributes to competitive surface colonization by the marine Roseobacter phaeobacter sp strain y4i
Applied and Environmental Microbiology, 2012Co-Authors: Nathan W Cude, Jason P Mooney, Arash A Tavanaei, Mary K Hadden, Ashley M Frank, Christopher A Gulvik, Alison BuchanAbstract:Members of the Roseobacter lineage of marine bacteria are prolific surface colonizers in marine coastal environments, and antimicrobial secondary metabolite production has been hypothesized to provide a competitive advantage to colonizing Roseobacters. Here, we report that the Roseobacter Phaeobacter sp. strain Y4I produces the blue pigment indigoidine via a nonribosomal peptide synthase (NRPS)-based biosynthetic pathway encoded by a novel series of genetically linked genes: igiBCDFE. A Tn5-based random mutagenesis library of Y4I showed a perfect correlation between indigoidine production by the Phaeobacter strain and inhibition of Vibrio fischeri on agar plates, revealing a previously unrecognized bioactivity of this molecule. In addition, igiD null mutants (igiD encoding the indigoidine NRPS) were more resistant to hydrogen peroxide, less motile, and faster to colonize an artificial surface than the wild-type strain. Collectively, these data provide evidence for pleiotropic effects of indigoidine production in this strain. Gene expression assays support phenotypic observations and demonstrate that igiD gene expression is upregulated during growth on surfaces. Furthermore, competitive cocultures of V. fischeri and Y4I show that the production of indigoidine by Y4I significantly inhibits colonization of V. fischeri on surfaces. This study is the first to characterize a secondary metabolite produced by an NRPS in Roseobacters.
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Development and application of quantitative-PCR tools for subgroups of the Roseobacter clade.
Applied and environmental microbiology, 2009Co-Authors: Alison Buchan, Mary K Hadden, Marcelino T. SuzukiAbstract:Specific SYBR green-based quantitative-PCR assays targeting conserved regions in the 16S-23S rRNA internal transcribed spacer regions were developed for five subgroups of the environmentally abundant and biogeochemically active Roseobacter clade of marine bacteria. The assays were applied to field samples demonstrating their utility in investigations of abundant Roseobacter group phylotypes in the environment.
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Surface Colonization by Marine Roseobacters: Integrating Genotype and Phenotype
Applied and environmental microbiology, 2009Co-Authors: Rachael N. Slightom, Alison BuchanAbstract:The Roseobacter clade is a broadly distributed, abundant, and biogeochemically relevant group of marine bacteria. Representatives are often associated with organic surfaces in disparate marine environments, suggesting that a sessile lifestyle is central to the ecology of lineage members. The importance of surface association and colonization has been demonstrated recently for select strains, and it has been hypothesized that production of antimicrobial agents, cell density-dependent regulatory mechanisms, and morphological features contribute to the colonization success of Roseobacters. Drawing on these studies, insight into a broad representation of strains is facilitated by the availability of a substantial collection of genome sequences that provides a holistic view of these features among clade members. These genome data often corroborate phenotypic data but also reveal significant variation in terms of gene content and synteny among group members, even among closely related strains (congeners and conspecifics). Thus, while detailed studies of representative strains are serving as models for how Roseobacters transition between planktonic and sessile lifestyles, it is becoming clear that additional studies are needed if we are to have a more comprehensive view of how these transitions occur in different lineage members. This is important if we are to understand how associations with surfaces influence metabolic activities contributing to the cycling of carbon and nutrients in the world's oceans.
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Gene transfer agent (GTA) genes reveal diverse and dynamic Roseobacter and Rhodobacter populations in the Chesapeake Bay
ISME Journal, 2009Co-Authors: Yanlin Zhao, Charles Budinoff, Andrew Lang, Alison Buchan, Nianzhi Jiao, Kui Wang, Feng ChenAbstract:Within the bacterial class Alphaproteobacteria, the order Rhodobacterales contains the Roseobacter and Rhodobacter clades. Roseobacters are abundant and play important biogeochemical roles in marine environments. Roseobacter and Rhodobacter genomes contain a conserved gene transfer agent (GTA) gene cluster, and GTA-mediated gene transfer has been observed in these groups of bacteria. In this study, we investigated the genetic diversity of these two groups in Chesapeake Bay surface waters using a specific PCR primer set targeting the conserved Rhodobacterales GTA major capsid protein gene (g5). The g5 gene was successfully amplified from 26 Rhodobacterales isolates and the bay microbial communities using this primer set. Four g5 clone libraries were constructed from microbial assemblages representing different regions and seasons of the bay and yielded diverse sequences. In total, 12 distinct g5 clusters could be identified among 158 Chesapeake Bay clones, 11 fall within the Roseobacter clade, and one falls in the Rhodobacter clade. The vast majority of the clusters (10 out of 12) lack cultivated representatives. The composition of g5 sequences varied dramatically along the bay during the wintertime, and a distinct Roseobacter population composition between winter and summer was observed. The congruence between g5 and 16S rRNA gene phylogenies indicates that g5 may serve as a useful genetic marker to investigate diversity and abundance of Roseobacter and Rhodobacter in natural environments. The presence of the g5 gene in the natural populations of Roseobacter and Rhodobacter implies that genetic exchange through GTA transduction could be an important mechanism for maintaining the metabolic flexibility of these groups of bacteria.
Meinhard Simon - One of the best experts on this subject based on the ideXlab platform.
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Lipidomic analysis of Roseobacters of the pelagic RCA cluster and their response to phosphorus limitation
2020Co-Authors: Eleonora Silvano, Meinhard Simon, Yanlin Zhao, Mathias Wolterink, Helge-a. Giebel, Dave J. Scanlan, Yin Chen, Mingyu YangAbstract:Abstract The marine Roseobacter-clade Affiliated cluster (RCA) represents one of the most abundant groups of bacterioplankton in the global oceans, particularly in temperate and sub-polar regions. They play a key role in the biogeochemical cycling of various elements and are important players in oceanic climate-active trace gas metabolism. In contrast to copiotrophic Roseobacter counterparts such as Ruegeria pomeroyi DSS-3 and Phaeobacter sp. MED193, RCA bacteria are truly pelagic and have smaller genomes. We have previously shown that RCA bacteria do not appear to encode the PlcP-mediated lipid remodelling pathway, whereby marine heterotrophic bacteria remodel their membrane lipid composition in response to phosphorus (P) stress by substituting membrane glycerophospholipids with alternative glycolipids or betaine lipids. In this study, we report lipidomic analysis of six RCA isolates. In addition to the commonly found glycerophospholipids such as phosphatidylglycerol and phosphatidylethanolamine, RCA bacteria synthesise a relatively uncommon phospholipid, acylphosphatidylglycerol, which is not found in copiotrophic Roseobacters. Instead, like the abundant SAR11 clade, RCA bacteria upregulate ornithine lipid biosynthesis in response to P stress, suggesting a key role of this aminolipid in the adaptation of marine heterotrophs to oceanic nutrient limitation.
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Composition of Total and Cell-Proliferating Bacterioplankton Community in Early Summer in the North Sea – Roseobacters Are the Most Active Component
Frontiers in microbiology, 2017Co-Authors: Insa Bakenhus, Sara Billerbeck, Helge-ansgar Giebel, Leon Dlugosch, Felix Milke, Meinhard SimonAbstract:Heterotrophic bacterioplankton communities play an important role in organic matter processing in the oceans worldwide. In order to investigate the significance of distinct phylogenetic bacterial groups it is not only important to assess their quantitative abundance but also their growth dynamics in relation to the entire bacterioplankton. Therefore bacterial abundance, biomass production and the composition of the entire and cell-proliferating bacterioplankton community were assessed in North Sea surface waters between the German Bight and 58°N in early summer by applying catalyzed reporter deposition (CARD-FISH) and bromodeoxyuridine fluorescence in situ hybridization (BrdU-FISH). Bacteroidetes and the Roseobacter group dominated the cell-proliferating fraction with 10-55% and 8-31% of total BrdU-positive cells, respectively. While Bacteroidetes also showed high abundances in the total bacterial fraction, Roseobacters constituted only 1-9% of all cells. Despite abundances of up to 55% of total bacterial cells, the SAR11 clade constituted
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Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats
The ISME Journal, 2017Co-Authors: Meinhard Simon, Carmen Scheuner, Jan P. Meier-kolthoff, Marcus Ulbrich, Hans-peter Klenk, Irene Wagner-döbler, Dietmar Schomburg, Thorsten Brinkhoff, Jörn Petersen, Markus GökerAbstract:Marine Rhodobacteraceae ( Alphaproteobacteria ) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As ‘ Roseobacter clade’, these ‘Roseobacters’ are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations. Our analyses, providing no unequivocal evidence for the monophyly of Roseobacters, indicate several shifts between marine and non-marine habitats that occurred independently and were accompanied by characteristic changes in genomic content of orthologs, enzymes and metabolic pathways. Non-marine Rhodobacteraceae gained high-affinity transporters to cope with much lower sulphate concentrations and lost genes related to the reduced sodium chloride and organohalogen concentrations in their habitats. Marine Rhodobacteraceae gained genes required for fucoidan desulphonation and synthesis of the plant hormone indole 3-acetic acid and the compatible solutes ectoin and carnitin. However, neither plasmid composition, even though typical for the family, nor the degree of oligotrophy shows a systematic difference between marine and non-marine Rhodobacteraceae . We suggest the operational term ‘ Roseobacter group’ for the marine Rhodobacteraceae strains.
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Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage
Nature Microbiology, 2016Co-Authors: Sara Billerbeck, Sonja Voget, Thorsten Brinkhoff, Bernd Wemheuer, Rolf Daniel, Lone Gram, Anja Poehlein, Helge-ansgar Giebel, Wade H. Jeffrey, Meinhard SimonAbstract:Global sampling campaigns show that the CHAB-I-5 Roseobacter cluster is abundant in the marine environment, and found from the poles to the tropics. Analysis of the draft genome of strain SB2 reveals adaptation to an oligotrophic lifestyle. 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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Distinct compositions of free-living, particle-associated and benthic communities of the Roseobacter group in the North Sea
FEMS microbiology ecology, 2015Co-Authors: Saranya Kanukollu, Meinhard Simon, Bernd Wemheuer, Janina Herber, Sara Billerbeck, Judith Lucas, Rolf Daniel, Heribert Cypionka, Bert EngelenAbstract:The Roseobacter group is one of the predominant lineages in the marine environment. While most investigations focus on pelagic Roseobacters, the distribution and metabolic potential of benthic representatives is less understood. In this study, the diversity of the Roseobacter group was characterized in sediment and water samples along the German/Scandinavian North Sea coast by 16S rRNA gene analysis and cultivation-based methods. Molecular analysis indicated an increasing diversity between communities of the Roseobacter group from the sea surface to the seafloor and revealed distinct compositions of free-living and attached fractions. Culture media containing dimethyl sulfide (DMS), dimethyl sulfonium propionate (DMSP) or dimethyl sulfoxide (DMSO) stimulated growth of Roseobacters showing highest most probable numbers (MPN) in DMSO-containing dilutions of surface sediments (2.1 × 10(7) Roseobacters cm(-3)). Twenty Roseobacters (12 from sediments) were isolated from DMSP- and DMS-containing cultures. Sequences of the isolates represented 0.04% of all Bacteria and 4.7% of all Roseobacters in the pyrosequencing dataset from sediments. Growth experiments with the isolate Shimia sp. SK013 indicated that benthic Roseobacters are able to switch between aerobic and anaerobic utilization of organic sulfur compounds. This response to changing redox conditions might be an adaptation to specific environmental conditions on particles and in sediments.
