Roseobacter Clade Research Articles

A newly discovered Roseobacter cluster in temperate and polar oceans.

Bacterioplankton phylotypes of alpha-Proteobacteria have been detected in various marine regions, but systematic biogeographical studies of their global distribution are missing. Alpha-Proteobacteria comprise one of the largest fractions of heterotrophic marine bacteria and include two clades, SAR11 and Roseobacter, which account for 26 and 16% of 16S ribosomal RNA gene clones retrieved from marine bacterioplankton. The SAR11 clade attracted much interest because related 16S rRNA gene clones were among the first groups of marine bacteria to be identified by cultivation-independent approaches and appear to dominate subtropical surface bacterioplankton communities. Here we report on the global distribution of a newly discovered cluster affiliated to the Roseobacter clade, comprising only as-yet-uncultured phylotypes. Bacteria of this cluster occur from temperate to polar regions with highest abundance in the Southern Ocean, but not in tropical and subtropical regions. Between the south Atlantic subtropical front and Antarctica, we detected two distinct phylotypes, one north and one south of the polar front, indicating that two adjacent but different oceanic provinces allow the persistence of distinct but closely related phylotypes. These results suggest that the global distribution of major marine bacterioplankton components is related to oceanic water masses and controlled by their environmental and biogeochemical properties.

Jannaschia helgolandensis gen. nov., sp. nov., a novel abundant member of the marine Roseobacter clade from the North Sea.

Heterotrophic bacteria were isolated from a water sample taken from the North Sea, 2 km off the coast of the island of Helgoland, by direct plating of the serially diluted sample on complex marine media. Sixteen of 80 strains from the highest sample dilution belonged to the 'Roseobacter-Sulfitobacter-Silicibacter' group within the 2-subclass of the Proteobacteria on the basis of partial 16S rDNA sequence analysis. Phylogenetic analysis of nearly complete 16S rDNA sequences showed that the closest relative of two strains, Hel 10(T) and Hel 26, was Ketogulonicigenium vulgare (94.4% similarity). These strains were Gram-negative, non-motile rods, obligate aerobes, required sodium ions and 1-7% sea salts for growth and did not produce bacteriochlorophyll. Their optimal growth temperature was 25-30 degrees C. The strains had Q-10 as the dominant respiratory quinone. Chemotaxonomic analysis showed a combination of ester-linked 3-OH 10 : 0, 12 : 1 and amide-linked 3-oxo 14 : 0 (or 3-OH 14 : 1) and 3-OH 14 : 0 fatty acids, which appears to be a unique feature of strains Hel 10(T) and Hel 26 within this subsection of the 2-subclass of the Proteobacteria. Based on 16S rDNA sequence analysis and chemotaxonomic data, the strains are assigned to a new genus and species, Jannaschia helgolandensis gen. nov., sp. nov., with the type strain Hel 10(T) (= DSM 14858(T) = NCIMB 13941(T)).

Seasonal changes in the taxonomic composition of bacterioplankton in a coastal oligotrophic system

The succession of taxa within the bacterioplankton assemblage was followed over a whole seasonal cycle in Blanes Bay, an oligotrophic coastal system (average chl a: 0.5 µg l -1 ) in the NW Mediterranean Sea. Phylogenetic composition of the bacterioplankton was studied by means of DGGE (denaturing gradient gel electrophoresis) and sequencing of predominant bands. Analysis of DGGE fingerprints showed gradual changes in the dominant bacterial members over the sampling period. The time scale during which a single population appeared in significant amounts in the sys- tem ranged between weeks and months. Most of the DGGE bands sequenced showed high similari- ties to sequences of uncultured marine bacteria. The bacterial assemblage appeared to be dominated by members of α -Proteobacteria (mostly from the Roseobacter clade), Cytophaga-Flavobacteria-Bac- teroides (CFB) and cyanobacteria throughout the year. Two bands related to prasinophyte chloro- plasts were detected, whereas no bands related to SAR11 (α -Proteobacteria) or SAR86 (γ-Proteobac- teria) clusters were found. Contrasting with the relative stability of broad phylogenetic groups, examination of bands belonging to α -Proteobacteria, CFB and cyanobacteria revealed a substitution of closely related phylotypes during the seasonal cycle within each one of these 3 groups. Overall, the taxonomic composition of the bacterioplankton in this coastal marine system appeared to be rather stable in time, showing gradual changes throughout the year.

Spatial variability in bacterioplankton community composition at the Skagerrak-Kattegat Front

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 255:1-13 (2003) - doi:10.3354/meps255001 Spatial variability in bacterioplankton community composition at the Skagerrak-Kattegat Front Jarone Pinhassi1,*, Anne Winding2, Svend J. Binnerup2, Ulla Li Zweifel4, Bo Riemann3, Åke Hagström4 1Institut de Ciències del Mar-CMIMA (CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain 2Department of Environmental Chemistry and Microbiology, and 3Department of Marine Ecology, National Environmental Research Institute, Frederiksborgvej 399, 4000 Roskilde, Denmark 4Marine Microbiology, Kalmar University, PO Box 905, 391 82 Kalmar, Sweden *Email: jarone@cmima.csic.es ABSTRACT: The distribution of bacterial heterotrophic production and cell concentrations in the world oceans is well documented. Nevertheless, information on the distribution of specific bacterial taxa and how this is influenced by environmental factors in separate sea areas is sparse. Here we report on bacterial community structure across the Skagerrak-Kattegat front. The front separates North Sea water from water with a Baltic Sea origin. We documented community differences across the front using denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified bacterial 16S ribosomal DNA and whole-genome DNA hybridization towards community DNA. Analysis of the community Œfingerprints¹ by DGGE revealed clustering of samples according to side of the front and depth. Consistent with these results, whole-genome DNA hybridization for 28 bacterial species isolated from the sampling region indicated that bacteria related to the Roseobacter clade and Bacteroidetes as well as prosthecate bacteria (e.g. Hyphomonas) showed distinct distribution patterns on each side of the front, and also with depth. Differences in bacterioplankton species composition across the frontal area were paralleled by differences in quantitative variables such as phytoplankton biomass (chl a), dissolved organic carbon, and bacterial production. Furthermore, we observed differences in more descriptive variables such as salinity range, bacterial growth-limiting nutrients and phytoplankton composition. We suggest that not only quantitative but also qualitative differences in variables that affect bacterial growth are required to cause divergence in bacterioplankton community composition between marine regions. KEY WORDS: Marine bacteria · Plankton · Species distribution · Environmental factors · Denaturing gradient gel electrophoresis · DGGE · DNA hybridization Full text in pdf format NextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 255. Online publication date: June 24, 2003 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2003 Inter-Research.

Characterisation of bacterial communities associated with toxic and non-toxic dinoflagellates: Alexandrium spp. and Scrippsiella trochoidea

Several dinoflagellate species have been shown to produce potent neurotoxins known as paralytic shellfish toxins. Evidence is also accumulating that marine bacteria associated with dinoflagellates play a role in the accumulation of paralytic shellfish toxins. In this study, the diversity of bacteria in cultures of both toxic and non-toxic dinoflagellates, Alexandrium spp. and Scrippsiella trochoidea, were compared using colony morphology, restriction fragment length polymorphisms, denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA genes and, ultimately, sequence determination of the 16S rRNA genes. The results suggest that a number of different bacterial species are associated with dinoflagellates, some of which are common to each of the dinoflagellate cultures examined, whereas others appear to be unique to a particular dinoflagellate. The phylogenetic diversity of the bacteria observed was limited to two bacterial phyla, the Proteobacteria and the Cytophaga-Flavobacter-Bacteroides (CFB). Although phylum level diversity was limited, many distinct phylogenetic clades were recovered, including members of both the α- and γ-subclasses of the Proteobacteria. Additionally, several of the bacterial phylotypes isolated were not closely related to any published bacterial species but, rather, were identical to isolates characterised from Alexandrium cultures 4 years earlier. Finally, many of the bacteria isolated from the dinoflagellate cultures were related to microorganisms with known surface-associated life histories (e.g. the CFB phylum, Hyphomonas, Caulobacter and some members of the Roseobacter clade including Ruegeria algicola).

Characterisation of bacterial communities associated with toxic and non-toxic dinoflagellates: Alexandrium spp. and Scrippsiella trochoidea

Several dinoflagellate species have been shown to produce potent neurotoxins known as paralytic shellfish toxins. Evidence is also accumulating that marine bacteria associated with dinoflagellates play a role in the accumulation of paralytic shellfish toxins. In this study, the diversity of bacteria in cultures of both toxic and non-toxic dinoflagellates, Alexandrium spp. and Scrippsiella trochoidea, were compared using colony morphology, restriction fragment length polymorphisms, denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA genes and, ultimately, sequence determination of the 16S rRNA genes. The results suggest that a number of different bacterial species are associated with dinoflagellates, some of which are common to each of the dinoflagellate cultures examined, whereas others appear to be unique to a particular dinoflagellate. The phylogenetic diversity of the bacteria observed was limited to two bacterial phyla, the Proteobacteria and the Cytophaga-Flavobacter-Bacteroides (CFB). Although phylum level diversity was limited, many distinct phylogenetic clades were recovered, including members of both the α- and γ-subclasses of the Proteobacteria. Additionally, several of the bacterial phylotypes isolated were not closely related to any published bacterial species but, rather, were identical to isolates characterised from Alexandrium cultures 4 years earlier. Finally, many of the bacteria isolated from the dinoflagellate cultures were related to microorganisms with known surface-associated life histories (e.g. the CFB phylum, Hyphomonas, Caulobacter and some members of the Roseobacter clade including Ruegeria algicola).

Quantitative mapping of bacterioplankton populations in seawater: field tests across an upwelling plume in Monterey Bay

Few methods are available for quantifying specific prokaryotic taxa in marine plankton samples. In this study, we report a novel sampling and analysis strategy that circumvents some of the difficulties associated with current methods. This new approach allows for increased spatial, tempo- ral and phylogenetic resolution over what has been achievable in routine bacterioplankton surveys. Picoplankton from small volume samples (30 ml) were collected on polysulfone filters and DNA was extracted with a commercially available DNA purification kit. The contribution of different bacterio- plankton members at the group and subgroup levels was quantified by 5' nuclease assays. Percent- ages of small subunit (SSU) rDNAs from SAR11, SAR86, Roseobacter, Cytophaga and Synechococcus clades in DNA extracted from small samples were compared with SSU rDNA in DNA samples extracted from 6 to 9 l seawater. Only small differences were observed between the methods. The approach was also tested by estimating gene copy numbers in a seawater sample spiked with vary- ing numbers of cells from a cultivated marine Roseobacter strain. Finally we measured SSU rDNAs from the same groups of marine bacterioplankton in samples from a rapid survey of an upwelling plume in Monterey Bay, California, USA. A strong negative correlation between the percentage of Cytophagales and recently upwelled water, and an overlap between higher SAR86 percentages and a chlorophyll a concentration peak was found. The results confirm that rapid mapping of specific bacterioplankton groups is achievable using small samples and 5' nuclease assays.

Development of clade- (Roseobacter and Alteromonas) and taxon-specific oligonucleotide probes to study interactions between toxic dinoflagellates and their associated bacteria

Bacteria associated with toxic algae in culture have been implicated in the enhancement of algal toxin production and auto-toxigenesis. Toxigenic and non-toxigenic bacterial isolates from Alexandrium spp. have been determined to belong predominantly to the α- and γ-subclasses of the class Proteobacteria. Within these subclasses, the isolates were further classified into two clades that were phylogenetically affiliated with (1) the genus Roseobacter, a newly identified group that is of major significance within the α-Proteobacteria and (2) the genus Alteromonas. Specific 16S rRNA sequence signatures were identified for these clades as well as for three pairs of isolates and for one subcluster within the Roseobacter clade and for three clusters representing eight isolates in the Alteromonas clade. Oligonucleotide probes complementary to these regions were designed and their specificities were tested using dot-blot and whole-cell in situ hybridizations of target and non-target strains. The empirically determined dissociation temperatures of the probes ranged between 55 and 65 making them applicable as a set for screening environmental samples. In situ hybridization of bacteria in cultures of Alexandrium spp. with the clade-specific probes showed a loose association of these bacteria within the phycosphere. In addition, the fluorescent signal of the probes was bright and easily distinguishable from autofluorescent bacteria and the dinoflagellates.

Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems

In order to extend previous comparisons between coastal marine bacterioplankton communities and their open ocean and freshwater counterparts, here we summarize and provide new data on a clone library of 105 SSU rRNA genes recovered from seawater collected over the western continental shelf of the USA in the Pacific Ocean. Comparisons to previously published data revealed that this coastal bacterioplankton clone library was dominated by SSU rRNA gene phylotypes originally described from surface waters of the open ocean, but also revealed unique SSU rRNA gene lineages of β Proteobacteria related to those found in clone libraries from freshwater habitats. β Proteobacteria lineages common to coastal and freshwater samples included members of a clade of obligately methylotrophic bacteria, SSU rRNA genes affiliated with Xylophilus ampelinus, and a clade related to the genus Duganella. In addition, SSU rRNA genes were recovered from such previously recognized marine bacterioplankton SSU rRNA gene clone clusters as the SAR86, SAR11, and SAR116 clusters within the class Proteobacteria, the Roseobacter clade of the α subclass of the Proteobacteria, the marine group A/SAR406 cluster, and the marine Actinobacteria clade. Overall, these results support and extend previous observations concerning the global distribution of several marine planktonic prokaryote SSU rRNA gene phylotypes, but also show that coastal bacterioplankton communities contain SSU rRNA gene lineages (and presumably bacterioplankton) shown previously to be prevalent in freshwater habitats.

Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems.

In order to extend previous comparisons between coastal marine bacterioplankton communities and their open ocean and freshwater counterparts, here we summarize and provide new data on a clone library of 105 SSU rRNA genes recovered from seawater collected over the western continental shelf of the USA in the Pacific Ocean. Comparisons to previously published data revealed that this coastal bacterioplankton clone library was dominated by SSU rRNA gene phylotypes originally described from surface waters of the open ocean, but also revealed unique SSU rRNA gene lineages of beta Proteobacteria related to those found in clone libraries from freshwater habitats. beta Proteobacteria lineages common to coastal and freshwater samples included members of a clade of obligately methylotrophic bacteria, SSU rRNA genes affiliated with Xylophilus ampelinus, and a clade related to the genus Duganella. In addition, SSU rRNA genes were recovered from such previously recognized marine bacterioplankton SSU rRNA gene clone clusters as the SAR86, SAR11, and SAR116 clusters within the class Proteobacteria, the Roseobacter clade of the alpha subclass of the Proteobacteria, the marine group A/SAR406 cluster, and the marine Actinobacteria clade. Overall, these results support and extend previous observations concerning the global distribution of several marine planktonic prokaryote SSU rRNA gene phylotypes, but also show that coastal bacterioplankton communities contain SSU rRNA gene lineages (and presumably bacterioplankton) shown previously to be prevalent in freshwater habitats.

The pKNOCK series of broad-host-range mobilizable suicide vectors for gene knockout and targeted DNA insertion into the chromosome of gram-negative bacteria.

The pKNOCK series of broad-host-range mobilizable suicide vectors for gene knockout and targeted DNA insertion into the chromosome of gram-negative bacteria.