| genetic tools for the investigation of roseobacter clade bacteria. | the roseobacter clade represents one of the most abundant, metabolically versatile and ecologically important bacterial groups found in marine habitats. a detailed molecular investigation of the regulatory and metabolic networks of these organisms is currently limited for many strains by missing suitable genetic tools. | 2009 | 20021642 |
| complete genome sequence of roseophage vb_dshp-r1, which infects dinoroseobacter shibae dfl12. | the roseophages, a group of marine viruses that uniquely infect the roseobacter clade of bacteria, play a significant role in marine ecosystems. here we present a complete genomic sequence of an n4 phage 'vb_dshp-r1', which infects dinoroseobacter shibae dfl12, together with its structural and genomic features. vb_dshp-r1 has an ~ 75 nm diameter icosahedral structure and a complete genome of 75,028 bp. this is the first genome sequence of a lytic phage of the genus dinoroseobacter. | 2015 | 26380630 |
| oxidative stress and starvation in dinoroseobacter shibae: the role of extrachromosomal elements. | aerobic anoxygenic phototrophic bacteria (aap) are abundant in the photic zone of the marine environment. dinoroseobacter shibae, a representative of the roseobacter group, converts light into additional energy that enhances its survival especially under starvation. however, light exposure results in the production of cytotoxic reactive oxygen species in aaps. here we investigated the response of d. shibae to starvation and oxidative stress, focusing on the role of extrachromosomal elements (ecr ... | 2015 | 25859246 |
| erratum to: 'complete genome sequence of roseophage vb_dshp-r1, which infects dinoroseobacter shibae dfl12'. | [this corrects the article doi: 10.1186/1944-3277-10-6.]. | 2015 | 26413198 |
| dealing with salinity extremes and nitrogen limitation - an unexpected strategy of the marine bacterium dinoroseobacter shibae. | having the right coping strategy for changes in osmolarity or desiccation is essential for the survival of every cell. so far, nothing is known about compatible solutes and the salt adaptation of the marine rhodobacteraceae. the family member dinoroseobacter shibae dfl12(t) is shown here to form the compatible solutes α-glucosylglycerol (gg) and α-glucosylglycerate (gga). to our knowledge, this is the first experimental evidence for gga formation within the α-proteobacteria. together with glutam ... | 2017 | 26914854 |
| complete genome sequence of roseophage vb_dshp-r1, which infects dinoroseobacter shibae dfl12. | the roseophages, a group of marine viruses that uniquely infect the roseobacter clade of bacteria, play a significant role in marine ecosystems. here we present a complete genomic sequence of an n4 phage 'vb_dshp-r1', which infects dinoroseobacter shibae dfl12, together with its structural and genomic features. vb_dshp-r1 has an ~ 75 nm diameter icosahedral structure and a complete genome of 75,028 bp. this is the first genome sequence of a lytic phage of the genus dinoroseobacter. | 2014 | 25685262 |
| open source approaches to establishing roseobacter clade bacteria as synthetic biology chassis for biogeoengineering. | 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 ... | 2016 | 27441104 |
| fixation of co2 using the ethylmalonyl-coa pathway in the photoheterotrophic marine bacterium dinoroseobacter shibae. | the ability of aerobic anoxygenic photoheterotrophs (aaps) to gain additional energy from sunlight represents a competitive advantage, especially in conditions where light has easy access or under environmental conditions may change quickly, such as those in the world's oceans. however, the knowledge about the metabolic consequences of aerobic anoxygenic photosynthesis is very limited. combining transcriptome and metabolome analyses, isotopic labeling techniques, measurements of growth, oxygen u ... | 2017 | 28371065 |
| acyl-homoserine lactone quorum sensing in the roseobacter clade. | members of the roseobacter clade are ecologically important and numerically abundant in coastal environments and can associate with marine invertebrates and nutrient-rich marine snow or organic particles, on which quorum sensing (qs) may play an important role. in this review, we summarize current research progress on roseobacterial acyl-homoserine lactone-based qs, particularly focusing on three relatively well-studied representatives, phaeobacter inhibens dsm17395, the marine sponge symbiont r ... | 2014 | 24402124 |
| gene flow across genus barriers - conjugation of dinoroseobacter shibae's 191-kb killer plasmid into phaeobacter inhibens and ahl-mediated expression of type iv secretion systems. | rhodobacteraceae harbor a conspicuous wealth of extrachromosomal replicons (ecrs) and therefore the exchange of genetic material via horizontal transfer has been supposed to be a major evolutionary driving force. many plasmids in this group encode type iv secretion systems (t4ss) that are expected to mediate transfer of proteins and/or dna into host cells, but no experimental evidence of either has yet been provided. dinoroseobacter shibae, a species of the roseobacter group within the rhodobact ... | 2016 | 27303368 |
| identification of genetic modules mediating the jekyll and hyde interaction of dinoroseobacter shibae with the dinoflagellate prorocentrum minimum. | the co-cultivation of the alphaproteobacterium dinoroseobacter shibae with the dinoflagellate prorocentrum minimum is characterized by a mutualistic phase followed by a pathogenic phase in which the bacterium kills aging algae. thus it resembles the "jekyll-and-hyde" interaction that has been proposed for other algae and roseobacter. here, we identified key genetic components of this interaction. analysis of the transcriptome of d. shibae in co-culture with p. minimum revealed growth phase depen ... | 2015 | 26617596 |
| respiratory kinetics of marine bacteria exposed to decreasing oxygen concentrations. | during aerobic respiration, microorganisms consume oxygen (o2) through the use of different types of terminal oxidases which have a wide range of affinities for o2. the km values for o2 of these enzymes have been determined to be in the range of 3 to 200 nmol liter(-1). in this study, we examined the time course of development of aerobic respiratory kinetics of four marine bacterial species (dinoroseobacter shibae, roseobacter denitrificans, idiomarina loihiensis, and marinobacter daepoensis) du ... | 2016 | 26682857 |
| transposon mutagenesis identified chromosomal and plasmid genes essential for adaptation of the marine bacterium dinoroseobacter shibae to anaerobic conditions. | anaerobic growth and survival are integral parts of the life cycle of many marine bacteria. to identify genes essential for the anoxic life of dinoroseobacter shibae, a transposon library was screened for strains impaired in anaerobic denitrifying growth. transposon insertions in 35 chromosomal and 18 plasmid genes were detected. the essential contribution of plasmid genes to anaerobic growth was confirmed with plasmid-cured d. shibae strains. a combined transcriptome and proteome approach ident ... | 2013 | 23974024 |
| you are what you talk: quorum sensing induces individual morphologies and cell division modes in dinoroseobacter shibae. | dinoroseobacter shibae, a member of the roseobacter clade abundant in marine environments, is characterized by a pronounced pleomorphism. cell shapes range from variable-sized ovoid rods to long filaments with a high copy number of chromosomes. time-lapse microscopy shows cells dividing either by binary fission or by budding from the cell poles. here we demonstrate that this morphological heterogeneity is induced by quorum sensing (qs). d. shibae utilizes three acylated homoserine lactone (ahl) ... | 2013 | 23823498 |
| structure and function of a short lov protein from the marine phototrophic bacterium dinoroseobacter shibae. | light, oxygen, voltage (lov) domains are widely distributed in plants, algae, fungi, bacteria, and represent the photo-responsive domains of various blue-light photoreceptor proteins. their photocycle involves the blue-light triggered adduct formation between the c(4a) atom of a non-covalently bound flavin chromophore and the sulfur atom of a conserved cysteine in the lov sensor domain. lov proteins show considerable variation in the structure of n- and c-terminal elements which flank the lov co ... | 2015 | 25887755 |
| the ctra phosphorelay integrates differentiation and communication in the marine alphaproteobacterium dinoroseobacter shibae. | dinoroseobacter shibae, a member of the roseobacter clade abundant in marine environments, maintains morphological heterogeneity throughout growth, with small cells dividing by binary fission and large cells dividing by budding from one or both cell poles. this morphological heterogeneity is lost if the quorum sensing (qs) system is silenced, concurrent with a decreased expression of the ctra phosphorelay, a regulatory system conserved in alphaproteobacteria and the master regulator of the caulo ... | 2014 | 24524855 |
| Formation of polyhydroxyalkanoate in aerobic anoxygenic phototrophic bacteria and its relationship to carbon source and light availability. | Aerobic anoxygenic phototrophic bacteria (AAPB) are unique players in carbon cycling in the ocean. Cellular carbon storage is an important mechanism regulating the nutrition status of AAPB but is not yet well understood. In this paper, six AAPB species (Dinoroseobacter sp. JL1447, Roseobacter denitrificans OCh 114, Roseobacter litoralis OCh 149, Dinoroseobacter shibae DFL 12(T), Labrenzia alexandrii DFL 11(T), and Erythrobacter longus DSMZ 6997) were examined, and all of them demonstrated the ab ... | 2011 | 21908634 |
| transcriptional response of the photoheterotrophic marine bacterium dinoroseobacter shibae to changing light regimes. | bacterial aerobic anoxygenic photosynthesis (aap) is an important mechanism of energy generation in aquatic habitats, accounting for up to 5% of the surface ocean's photosynthetic electron transport. we used dinoroseobacter shibae, a representative of the globally abundant marine roseobacter clade, as a model organism to study the transcriptional response of a photoheterotrophic bacterium to changing light regimes. continuous cultivation of d. shibae in a chemostat in combination with time serie ... | 2011 | 21654848 |
| hasllibacter halocynthiae gen. nov., sp. nov., a nutriacholic acid-producing bacterium isolated from the marine ascidian halocynthia roretzi. | the gram-negative, aerobic, ovoid to rod-shaped bacterial strain kme 002(t) was isolated from a marine ascidian, halocynthia roretzi, off the coast of gangneung, korea. phylogenetic analyses based on the 16s rrna gene sequence showed that this strain belongs to the family rhodobacteraceae in the class alphaproteobacteria and is closely related to species dinoroseobacter shibae, roseovarius crassostreae and pseudoruegeria aquimaris with 95.0, 94.7 and 94.5% 16s rrna gene similarity, respectively. ... | 2011 | 21551335 |
| influence of light and anoxia on chemiosmotic energy conservation in dinoroseobacter shibae. | in the present study we have investigated the influence of light and anoxia on the energetic state of the aerobic anoxygenic phototroph (aap) dinoroseobacter shibae. respiration, chemiosmotic proton translocation and the adenylate energy charge (aec) of the cells were measured comparing light versus dark and oxic versus anoxic conditions. light caused a decrease of the respiration rates of washed cells. this might be a substitution rather than a direct inhibitory effect, because both photosynthe ... | 2011 | 21461053 |
| an alphaproteobacterium capable of both aerobic and anaerobic anoxygenic photosynthesis but incapable of photoautotrophy: charonomicrobium ambiphototrophicum, gen. nov., sp. nov. | a facultatively aerobic deep brown coccoid to ovoid bacterium, strain eg17(t), was isolated from a saline effluent stream in the nacl-dominated brine spring system known as east german creek in the province of manitoba, canada. the strain produced bchl a incorporated into a functional reaction center and two light-harvesting complexes with absorption peaks at 802, 850, and 879 nm. eg17(t) is the first reported anoxygenic phototroph capable of photoheterotrophic growth under both oxic and anoxic ... | 2011 | 21308412 |
| pathways and substrate specificity of dmsp catabolism in marine bacteria of the roseobacter clade. | the volatiles released by phaeobacter gallaeciensis, oceanibulbus indolifex and dinoroseobacter shibae have been investigated by gc-ms, and several mesh-derived sulfur volatiles have been identified. an important sulfur source in the oceans is the algal metabolite dimethylsulfoniopropionate (dmsp). labelled [2h6]dmsp was fed to the bacteria to investigate the production of volatiles from this compound through the lysis pathway to [2h6]dimethylsulfide or the demethylation pathway to [2h3]-3-(meth ... | 2010 | 20043308 |
| metabolic fluxes in the central carbon metabolism of dinoroseobacter shibae and phaeobacter gallaeciensis, two members of the marine roseobacter clade. | in the present work the central carbon metabolism of dinoroseobacter shibae and phaeobacter gallaeciensis was studied at the level of metabolic fluxes. these two strains belong to the marine roseobacter clade, a dominant bacterial group in various marine habitats, and represent surface-associated, biofilm-forming growth (p. gallaeciensis) and symbiotic growth with eukaryotic algae (d. shibae). based on information from recently sequenced genomes, a rich repertoire of pathways has been identified ... | 2009 | 19788729 |
| the complete genome sequence of the algal symbiont dinoroseobacter shibae: a hitchhiker's guide to life in the sea. | dinoroseobacter shibae dfl12(t), a member of the globally important marine roseobacter clade, comprises symbionts of cosmopolitan marine microalgae, including toxic dinoflagellates. its annotated 4 417 868 bp genome sequence revealed a possible advantage of this symbiosis for the algal host. d. shibae dfl12(t) is able to synthesize the vitamins b(1) and b(12) for which its host is auxotrophic. two pathways for the de novo synthesis of vitamin b(12) are present, one requiring oxygen and the other ... | 2010 | 19741735 |
| wenxinia marina gen. nov., sp. nov., a novel member of the roseobacter clade isolated from oilfield sediments of the south china sea. | an aerobic and heterotrophic, gram-negative bacterial isolate, strain hy34(t), was isolated from sediment of an oilfield in the south china sea, china. the taxonomy of strain hy34(t) was studied by phenotypic and phylogenetic methods. strain hy34(t) formed faint-pink colonies on marine agar 2216. cells of strain hy34(t) were non-motile, ovoid or short rods. strain hy34(t) was positive for catalase and oxidase, and nitrate was reduced to nitrite. the nearly complete 16s rrna gene sequence of stra ... | 2007 | 17684242 |
| discovery of complex mixtures of novel long-chain quorum sensing signals in free-living and host-associated marine alphaproteobacteria. | more than 100 bacterial isolates from various marine habitats were screened for ahl production by using gfp reporter constructs based on the lasr system of pseudomonas aeruginosa and the luxr system of vibrio fischeri. of the 67 alphaproteobacteria tested, most of which belonged into the so-called roseobacter clade, 39 induced fluorescence in either one or both sensor strains up to 103-fold compared to controls. acylated homoserine lactones were identified by gc-ms analysis and shown to have cha ... | 2005 | 16283687 |
| the chafer pheromone buibuilactone and ant pyrazines are also produced by marine bacteria. | headspace extracts obtained from agar plate cultures of two marine bacteria from the north sea (germany), loktanella strain bio-204 and dinoroseobacter shibae strain dfl-27, were analyzed by gc-ms. several gamma-lactones and one delta-lactone were identified, besides pyrazines and some sulfur compounds. the absolute configuration of the major lactone (r,z)-dodec-5-en-4-olide, known as buibuilactone, a pheromone of several scarab beetles, was determined by a new catalytic enantioselective synthes ... | 2005 | 16124260 |
| dinoroseobacter shibae gen. nov., sp. nov., a new aerobic phototrophic bacterium isolated from dinoflagellates. | a novel group of aerobic anoxygenic phototrophic bacteria was isolated from marine dinoflagellates, and two strains were characterized in detail. cells were gram-negative cocci or ovoid rods and were motile by means of a single, polarly inserted flagellum. they were obligate aerobes requiring 1-7 % salinity. the optimal ph range for growth was 6.5-9.0 and the temperature optimum was 33 degrees c. the bacteria contained bacteriochlorophyll a and spheroidenone as the only carotenoid. the in vivo a ... | 2005 | 15879238 |
| complete genome sequence of vb_dshp-r2c, a n4-like lytic roseophage. | vb_dshp-r2c, a lytic phage that infects the marine bacterium dinoroseobacter shibae dfl12(t), one of the model organisms of the roseobacter clade, was isolated. here we report the overall genome architecture of r2c. genome analysis revealed that r2c is an n4-like phage with a 74.8 kb genome that contains 85 putative gene products. | 2015 | 25795023 |
| "you produce while i clean up", a strategy revealed by exoproteomics during synechococcus-roseobacter interactions. | most of the energy that is introduced into the oceans by photosynthetic primary producers is in the form of organic matter that then sustains the rest of the food web, from micro to macro-organisms. however, it is the interactions between phototrophs and heterotrophs that are vital to maintaining the nutrient balance of marine microbiomes that ultimately feed these higher trophic levels. the primary produced organic matter is mostly remineralized by heterotrophic microorganisms but, because most ... | 2015 | 25728650 |
| plasmid curing and the loss of grip--the 65-kb replicon of phaeobacter inhibens dsm 17395 is required for biofilm formation, motility and the colonization of marine algae. | surface colonization is characteristic for a broad range of marine roseobacters and many strains have been isolated from biofilms, microbial mats and dinoflagellates. phaeobacter inhibens dsm 17395, one of the best-studied representatives of the roseobacter group, is an effective colonizer of marine surfaces, but the genetic basis of this trait is unknown. based on the composition of its 65-kb repa-i type plasmid that contains more than 20 genes for polysaccharide metabolism, including a rhamnos ... | 2015 | 25595869 |
| discovery of the first light-dependent protochlorophyllide oxidoreductase in anoxygenic phototrophic bacteria. | in all photosynthetic organisms, chlorophylls function as light-absorbing photopigments allowing the efficient harvesting of light energy. chlorophyll biosynthesis recurs in similar ways in anoxygenic phototrophic proteobacteria as well as oxygenic phototrophic cyanobacteria and plants. here, the biocatalytic conversion of protochlorophyllide to chlorophyllide is catalysed by evolutionary and structurally distinct protochlorophyllide reductases (pors) in anoxygenic and oxygenic phototrophs. it i ... | 2014 | 25039543 |
| a dual-species co-cultivation system to study the interactions between roseobacters and dinoflagellates. | some microalgae in nature live in symbiosis with microorganisms that can enhance or inhibit growth, thus influencing the dynamics of phytoplankton blooms. in spite of the great ecological importance of these interactions, very few defined laboratory systems are available to study them in detail. here we present a co-cultivation system consisting of the toxic phototrophic dinoflagellate prorocentrum minimum and the photoheterotrophic alphaproteobacterium dinoroseobacter shibae. in a mineral mediu ... | 2014 | 25009539 |
| gene regulatory and metabolic adaptation processes of dinoroseobacter shibae dfl12t during oxygen depletion. | metabolic flexibility is the key to the ecological success of the marine roseobacter clade bacteria. we investigated the metabolic adaptation and the underlying changes in gene expression of dinoroseobacter shibae dfl12(t) to anoxic life by a combination of metabolome, proteome, and transcriptome analyses. time-resolved studies during continuous oxygen depletion were performed in a chemostat using nitrate as the terminal electron acceptor. formation of the denitrification machinery was found enh ... | 2014 | 24648520 |
| light enhances survival of dinoroseobacter shibae during long-term starvation. | aerobic anoxygenic phototrophs (aaps) as being photoheterotrophs require organic substrates for growth and use light as a supplementary energy source under oxic conditions. we hypothesized that aaps benefit from light particularly under carbon and electron donor limitation. the effect of light was determined in long-term starvation experiments with dinoroseobacter shibae dfl 12(t) in both complex marine broth and defined minimal medium with succinate as the sole carbon source. the cells were sta ... | 2013 | 24386315 |
| identification of new n-acylhomoserine lactone signalling compounds of dinoroseobacter shibae dfl-12(t) by overexpression of luxi genes. | bacteria of the roseobacter clade are widespread in the ocean and occur in many different habitats. in the genome of dinoroseobacter shibae dfl-12, luxi homologous genes that encode synthases responsible for the formation of n-acylhomoserine lactones (ahls) have been described. these compounds are known autoinducers that regulate several biological traits-namely, flagella formation and cell differentiation-in d. shibae through quorum sensing. the ahls produced by d. shibae mainly consisted of n- ... | 2013 | 24218333 |
| swimming in light: a large-scale computational analysis of the metabolism of dinoroseobacter shibae. | the roseobacter clade is a ubiquitous group of marine α-proteobacteria. to gain insight into the versatile metabolism of this clade, we took a constraint-based approach and created a genome-scale metabolic model (idsh827) of dinoroseobacter shibae dfl12t. our model is the first accounting for the energy demand of motility, the light-driven atp generation and experimentally determined specific biomass composition. to cover a large variety of environmental conditions, as well as plasmid and single ... | 2013 | 24098096 |
| roseibacterium beibuensis sp. nov., a novel member of roseobacter clade isolated from beibu gulf in the south china sea. | a novel aerobic, bacteriochlorophyll-containing bacteria strain jlt1202r(t) was isolated from beibu gulf in the south china sea. cells were gram-negative, non-motile, and short-ovoid to rod-shaped with two narrower poles. strain jlt1202r(t) formed circular, opaque, wine-red colonies, and grew optimally at 3-4 % nacl, ph 7.5-8.0 and 28-30 °c. the strain was catalase, oxidase, onpg, gelatin, and voges-proskauer test positive. in vivo absorption spectrum of bacteriochlorophyll a presented two peaks ... | 2012 | 22847226 |