Family Rhodobacteraceae Research Articles

Antarctobacter jejuensis sp. nov., isolated from seawater in Jeju, Korea.

A novel bacterium, designated strain 13-2-B6(T), was isolated from seawater adjacent to Songak Mountain on Jeju Island, South Korea. The novel strain was observed to be Gram-negative, aerobic, rod-shaped and motile with a single polar flagellum. On the basis of 16S rRNA gene sequence similarity, strain 13-2-B6(T) was determined to be phylogenetically closely related to the type strain of Antarctobacter heliothermus, currently the sole species of the genus Antarctobacter (family Rhodobacteraceae). Sequence similarity between the 16S rRNA genes of strain 13-2-B6(T) and A. heliothermus EL-219(T) is 96.9 %. Strain 13-2-B6(T) was found to grow optimally at 25-30 °C, pH 7.0-8.0 and 3 % (w/v) NaCl. The predominant isoprenoid quinone in strain 13-2-B6(T) was identified as ubiquinone Q-10 and the major fatty acids were identified as C18:1 ω7c and/or C18:1 ω6c. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two unknown aminolipids, two unknown phospholipids, an unknown glycolipid and an unknown lipid were found to be components of the polar lipid profile. The G + C content of strain 13-2-B6(T) was determined to be 62 mol %. On the basis of its phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain 13-2-B6(T) is considered to represent a novel species of the genus Antarctobacter, for which the name Antarctobacter jejuensis sp. nov. is proposed. The type strain is 13-2-B6(T) (=KCTC 42009(T) =JCM 19898(T)).

Confluentimicrobium lipolyticum gen. nov., sp. nov., a novel lipolytic alphaproteobacterium isolated from the junction between the ocean and a freshwater spring, and emended description of Actibacterium mucosum Lucena et al. 2012.

A Gram-negative, aerobic, non-flagellated and coccoid, ovoid or rod-shaped bacterial strain, designated SSK1-4(T), was isolated from the junction between the ocean and a freshwater spring at Jeju island, South Korea. Strain SSK1-4(T) was found to grow optimally at 30°C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. In the neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences, strain SSK1-4(T) was found to form an evolutionary lineage independent of those of other genera within the family Rhodobacteraceae. Strain SSK1-4(T) exhibited the highest 16S rRNA gene sequence similarity values to the type strains of Ruegeria lacuscaerulensis (94.99%), Ruegeria atlantica (94.98%) and Rhodovulum marinum (94.97%). Sequence similarities to the type strains of other recognized species were less than 94.87%. Strain SSK1-4(T) was found to contain Q-10 as the predominant ubiquinone and C18:1 ω7c and cyclo-C19:0 ω8c as the major fatty acids. The polar profile of strain SSK1-4(T) was found to contain phosphatidylglycerol, sulfoquinovosyldiacylglycerol, an unidentified lipid and an unidentified aminolipid as major components, which distinguish it from those of the phylogenetically related taxa. The DNA G+C content of strain SSK1-4(T) was determined to be 58.4mol%. On the basis of the phylogenetic data and the chemotaxonomic and other phenotypic properties, strain SSK1-4(T) is considered to represent a new genus and species within the class Alphaproteobacteria, for which the name Confluentimicrobium lipolyticum gen. nov., sp. nov. is proposed. The type strain of C. lipolyticum is SSK1-4(T) (=KCTC 42136(T)=CECT 8621(T)). In addition, an emended description of Actibacterium mucosum Lucena et al. 2012 is also proposed.

Pelagibaca abyssi sp. nov., of the family Rhodobacteraceae, isolated from deep-sea water.

A Gram-stain negative, oval-shaped, aerobic, catalase and oxidase-positive bacterium, designated JLT2014(T), was isolated from a deep-seawater sample (obtained at a 2,000 m depth) of the Southeastern Pacific Ocean. The dominant fatty acids were identified as C18:1ω7c/C18:1ω6c, C16:0 and C10:0 3-OH, which altogether represented 60.1 % of the total. The predominant respiratory quinone was identified as Q-10. The G+C content of genomic DNA was determined to be 66.4 mol %. The major polar lipids were identified as phosphatidylethanolamine and diphosphatidylglycerol. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the novel isolate can be affiliated with the Roseobacter clade within the family Rhodobacteraceae. Strain JLT2014(T) exhibited highest 16S rRNA gene sequence similarity value to Pelagibaca bermudensis HTCC2601(T) (sequence similarity value: 97.6 %). The DNA-DNA relatedness value between strain JLT2014(T) and P. bermudensis HTCC2601(T) was 46.9 ± 2 %. Based on phenotypic properties and phylogenetic analysis, the name Pelagibaca abyssi sp. nov. is proposed, with JLT2014(T)(=LMG 27363(T)=CGMCC 1.12376(T)) as the type strain.

Genome sequence of the Wenxinia marina type strain (DSM 24838(T)), a representative of the Roseobacter group isolated from oilfield sediments.

Wenxinia marina Ying et al. 2007 is the type species of the genus Wenxinia, a representative of the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae, isolated from oilfield sediments of the South China Sea. This family was shown to harbor the most abundant bacteria especially from coastal and polar waters, but was also found in microbial mats, sediments and attached to different kind of surfaces.Here we describe the features of W. marina strain HY34T together with the genome sequence and annotation of strain DSM 24838T and novel aspects of its phenotype. The 4,181,754 bp containing genome sequence encodes 4,047 protein-coding genes and 59 RNA genes. The genome of W. marina DSM 24838T was sequenced as part of the activities of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project funded by the DoE and the Transregional Collaborative Research Centre 51 (TRR51) funded by the German Research Foundation (DFG).

Complete genome sequence of the bacteriochlorophyll a-containing Roseibacterium elongatum type strain (DSM 19469(T)), a representative of the Roseobacter group isolated from Australian coast sand.

Roseibacterium elongatum Suzuki et al. 2006 is a pink-pigmented and bacteriochlorophyll a-producing representative of the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae. Representatives of the marine ‘Roseobacter group’ were found to be abundant in the ocean and play an important role in global and biogeochemical processes. In the present study we describe the features of R. elongatum strain OCh 323T together with its genome sequence and annotation. The 3,555,102 bp long genome consists of one circular chromosome with no extrachromosomal elements and is one of the smallest known Roseobacter genomes. It contains 3,540 protein-coding genes and 59 RNA genes. Genome analysis revealed the presence of a photosynthetic gene cluster, which putatively enables a photoheterotrophic lifestyle. Gene sequences associated with quorum sensing, motility, surface attachment, and thiosulfate and carbon monoxide oxidation could be detected. The genome was sequenced as part of the activities of the Transregional Collaborative Research Centre 51 (TRR51) funded by the German Research Foundation (DFG).

Genome sequence of the pink to light reddish-pigmented Rubellimicrobium mesophilum type strain (DSM 19309(T)), a representative of the Roseobacter group isolated from soil, and emended description of the species.

Rubellimicrobium mesophilum Dastager et al. 2008 is a mesophilic and light reddish-pigmented representative of the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae. Representatives of the Roseobacter group play an important role in the marine biogeochemical cycles and were found in a broad variety of marine environments associated with algal blooms, different kinds of sediments, and surfaces of invertebrates and vertebrates. Roseobacters were shown to be widely distributed, especially within the total bacterial community found in coastal waters, as well as in mixed water layers of the open ocean. Here we describe the features of R. mesophilum strain MSL-20T together with its genome sequence and annotation generated from a culture of DSM 19309T. The 4,927,676 bp genome sequence consists of one chromosome and probably one extrachromosomal element. It contains 5,082 protein-coding genes and 56 RNA genes. As previously reported, the G+C content is significantly different from the actual genome sequence-based G+C content and as the type strain tests positively for oxidase, the species description is emended accordingly. The genome was sequenced as part of the activities of the Transregional Collaborative Research Centre 51 (TRR51) funded by the German Research Foundation (DFG).

Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome.

Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.

Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (DSM 16094(T)), a moderately halophilic member of the Roseobacter clade.

Salipiger mucosus Martínez-Cànovas et al. 2004 is the type species of the genus Salipiger, a moderately halophilic and exopolysaccharide-producing representative of the Roseobacter lineage within the alphaproteobacterial family Rhodobacteraceae. Members of this family were shown to be the most abundant bacteria especially in coastal and polar waters, but were also found in microbial mats and sediments. Here we describe the features of the S. mucosus strain DSM 16094T together with its genome sequence and annotation. The 5,689,389-bp genome sequence consists of one chromosome and several extrachromosomal elements. It contains 5,650 protein-coding genes and 95 RNA genes. The genome of S. mucosus DSM 16094T was sequenced as part of the activities of the Transregional Collaborative Research Center 51 (TRR51) funded by the German Research Foundation (DFG).

Seohaeicola westpacificensis sp. nov., A Novel Member of Genera Seohaeicola Isolated from Deep West Pacific Sea Water

Strain JL2247(T), an aerobic, Gram-negative, gliding motile bacterium, was isolated from the western Pacific at the depth of 2,000 m. The cell was spindle-shaped with two narrow poles, and flagella were not observed. The colony was circular, translucent, and milky. This strain showed catalase-positive and oxidase-negative reactions. Its optimal growth conditions were at 32 °C, pH 7.3, and 3 % NaCl. The predominant polar lipids were phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylmonomethylethanolamine. The major fatty acids were summed feature 8 (18:1 w7c and/or 18:1 w6c) and Cyclo C19:0 ω8c and the major respiratory quinone was Q-10. The DNA G+C content of strain JL2247(T) was 72.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JL2247(T) fell into the genus Seohaeicola, family Rhodobacteraceae, order Rhodobacterales, class Alphaproteobacteria, sharing the highest similarity with the only species Seohaeicola saemankumensis SD-15(T) (96.4 % similarity). From the phenotypic, genotypic, and chemotaxonomic data, strain JL2247(T) represents a novel species of the genus Seohaeicola and the name is proposed as Seohaeicola westpacificensis sp. nov. The type strain is JL2247(T) (=CGMCC 1.12198(T) = JCM18883).

Halocynthiibacter namhaensis gen. nov., sp. nov., a novel alphaproteobacterium isolated from sea squirt Halocynthia roretzi

A Gram-negative, non-motile and rod-shaped bacterial strain, designated RA2-3(T), was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain RA2-3(T) was observed to grow optimally at 25°C, at pH 7.0-7.5 and in the presence of 2% (w/v) NaCl. Strain RA2-3(T) exhibited the highest 16S rRNA gene sequence similarity values to the type strains of Litoreibacter meonggei (95.7%), Planktotalea frisia (95.6%), Thalassobius gelatinovorus (95.5%) and Pelagicola litoralis (95.4%). A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain RA2-3(T) clustered with the type strains of Planktotalea frisia, Pelagicola litoralis, Pacificibacter maritimus and Roseovarius marinus. Strain RA2-3(T) was found to contain Q-10 as the predominant ubiquinone and C18:1 ω7c as the major fatty acid. The major polar lipids detected in strain RA2-3(T) were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain RA2-3(T) was 52.9mol%. On the basis of the phylogenetic, chemotaxonomic and phenotypic properties, strain RA2-3(T) is considered to represent a new genus and species within the family Rhodobacteraceae, for which the name Halocynthiibacter namhaensis gen. nov., sp. nov. is proposed. The type strain of H. namhaensis is RA2-3(T) (=KCTC 32362(T)=NBRC 109999(T)).

Roseovarius albus sp. nov., a new Alphaproteobacterium isolated from the Mediterranean Sea

Strain 4SM10(T), an aerobic marine, Gram-negative, heterotrophic and non pigmented bacterium isolated from seawater from Vinaroz in Castellón, Spain, was characterized using a polyphasic approach. Analysis of the 16S rRNA gene sequence placed the strain within the Roseobacter clade in the family Rhodobacteraceae. Phylogenetic analyses also showed that strain 4SM10(T) forms a stable clade with species of the genus Roseovarius, being related to Roseovarius nubinhibens ISM(T) and Roseovarius aestuarii SMK-122(T) at 97.5 and 97.4 % 16S rRNA sequence similarity, respectively. Average Nucleotide Identity (ANI) values, determined as a measure of overall genomic resemblance, confirmed that strain 4SM10(T) does not belong to the same species as R. aestuarii CECT 7745(T) and Roseovarius nubinhibens CECT 7750(T) displaying ANI values well below the 95 % boundary for genomic species. Strain 4SM10(T) requires Na(+) plus a divalent cation (either Mg(2+) or Ca(2+)) to grow, reduces nitrate to nitrite and uses a large number of amino acids and organic acids (but no carbohydrates) as sole carbon sources. Enzymatic activities displayed in API ZYM tests are alkaline phosphatase, leucine arylamidase and acid phosphatase. The major cellular fatty acids were identified as C18:1 ω7c and/or C18:1 ω6c (67.1 %). The DNA G+C content was determined to be 54.27 mol%. Based on the genotypic and phenotypic data obtained, the name Roseovarius albus sp. nov. is proposed for this novel taxon, with the type strain 4SM10(T) (=CECT 7450(T) = KCTC 22653(T)).

Combination of Culture-Dependent and -Independent Methods Reveals Diverse Acyl Homoserine Lactone-Producers from Rhizosphere of Wetland Plants

The culture-dependent method and a degenerate primer-based culture-independent method were combined in an effort to identify N-acyl homoserine lactone (AHL) producers in rhizosphere of wetland plants, Salix babylonica (willow) and Phragmites australis (reed). Overall, eight potential AHL-producing genera were found, which were Aeromonas, Pseudomonas, Polymorphum, Agrobacterium, Rhizobium, Sinorhizobium, Ensifer, and Pectobacterium. Thin layer chromatograph assay revealed various AHL profiles from cultivable AHL-producers. The degenerate primer pair RAHL352F and RAHL461R was found to cover AHL synthetase genes from families Rhizobiaceae and Rhodobacteraceae. Little overlap was found in taxa of potential AHL-producers obtained by the two methods, indicating that they were well complement to each other. This is the first survey for AHL-producers that employed combined culture-dependent and -independent methods.

Comparing Bacterial Community Composition between Healthy and White Plague-Like Disease States in Orbicella annularis Using PhyloChip™ G3 Microarrays

Coral disease is a global problem. Diseases are typically named or described based on macroscopic changes, but broad signs of coral distress such as tissue loss or discoloration are unlikely to be specific to a particular pathogen. For example, there appear to be multiple diseases that manifest the rapid tissue loss that characterizes ‘white plague.’ PhyloChip™ G3 microarrays were used to compare the bacterial community composition of both healthy and white plague-like diseased corals. Samples of lobed star coral (Orbicella annularis, formerly of the genus Montastraea [1]) were collected from two geographically distinct areas, Dry Tortugas National Park and Virgin Islands National Park, to determine if there were biogeographic differences between the diseases. In fact, all diseased samples clustered together, however there was no consistent link to Aurantimonas coralicida, which has been described as the causative agent of white plague type II. The microarrays revealed a large amount of bacterial heterogeneity within the healthy corals and less diversity in the diseased corals. Gram-positive bacterial groups (Actinobacteria, Firmicutes) comprised a greater proportion of the operational taxonomic units (OTUs) unique to healthy samples. Diseased samples were enriched in OTUs from the families Corynebacteriaceae, Lachnospiraceae, Rhodobacteraceae, and Streptococcaceae. Much previous coral disease work has used clone libraries, which seem to be methodologically biased toward recovery of Gram-negative bacterial sequences and may therefore have missed the importance of Gram-positive groups. The PhyloChip™data presented here provide a broader characterization of the bacterial community changes that occur within Orbicella annularis during the shift from a healthy to diseased state.

Tabrizicola aquatica gen. nov. sp. nov., a novel alphaproteobacterium isolated from Qurugöl Lake nearby Tabriz city, Iran

A novel Gram-negative, aerobic, non-motile and rod-shaped bacterium was isolated from Qurugöl Lake near Tabriz city. The bacterium grew chemoorganolheterotrophically and chemolithoautotrophically. However, photo-organoheterotrophic, photo-lithoautotrophic and fermentative growth could not be demonstrated. The presence of photosynthesis genes pufL and pufM was not shown and photosynthesis pigments were not formed. Strain RCRI19(T) grew without NaCl and tolerated up to 3 % NaCl. Growth occurred at pH 6-9 (optimum, pH 7) and 15-55 °C (optimum 40-45 °C). Vitamins were not required for growth. The major fatty acids are C18:1 ω7C, 11-methyl C18:1 ω7C, C18:0 3-OH. The predominant respiratory quinone is ubiquinone Q-10. The G+C content of genomic DNA is 65.9 mol%. Analysis of 16S rRNA sequences showed that strain RCRI19(T) has the highest similarities with uncultured environmental sequences followed by members of the genera Rhodobacter (≤95.75 %), Haematobacter (≤95.53 %), Gemmobacter (≤95.17 %) and Falsirhodobacter (94.60 %) in the family Rhodobacteraceae. DNA-DNA relatedness between strain RCRI19(T) and the closest phylogenetically related strain, Rhodobacter blasticus LMG 4305(T), was 20 %. Based on its phenotypic and chemotaxonomic characteristics and considering that it does not form photosynthetic pigments and is unable to grow phototrophically, it is concluded that strain RCRI19(T) cannot be included into the genus Rhodobacter and any of the other related genera. Therefore, we propose to place the new bacterium into a new genus and species for which the name Tabrizicola aquatica gen. nov. and sp. nov. is proposed. The type strain is RCRI19(T) (=BCCM/LMG 25773(T )= JCM 17277(T )= KCTC 23724(T)).

Sinorhodobacter ferrireducens gen. nov., sp. nov., a non-phototrophic iron-reducing bacterium closely related to phototrophic Rhodobacter species

An Fe(III) oxide-reducing bacterium designated as SgZ-3(T), which could couple glucose oxidation to Fe(III) oxide reduction for energy conservation, was isolated from an electrochemical biofilm. The isolate was Gram-negative, catalase-positive and oxidase-negative, and facultative anaerobic. NaCl was not required for growth, but NaCl concentrations up to 5% (w/v) were tolerated. Growth occurred in TSB (tryptic soy broth) at 20-40°C (optimum 30°C) and at pH 6.0-7.5 (optimum 7.0). Phototrophic growth could not be demonstrated. No vesicular photosynthetic membrane was observed. Bacteriochlorophyll α and carotenoids were absent. Biotin and thiamine were required as growth factors for the isolate. Phylogenetic analysis of the 16S rRNA gene sequence placed strain SgZ-3(T) within the family Rhodobacteraceae and affiliated with an phototrophic genera Rhodobacter. The G+C content of the genomic DNA was 68.6mol%. Strain SgZ-3(T) contained Q-10 as the predominant quinone. The major cellular fatty acids were C18:1 ω6c and/or C18:1 ω7c (66.9%) and C16:0 (9.5%). Based on its phenotypic and phylogenetic properties, chemotaxonomic analysis and the results of physiological and biochemical tests, strain SgZ-3(T) (=KACC 16603(T)=CCTCC AB2012026(T)) was designated as the type strain of a new genus and a novel species of the family Rhodobacteraceae, for which the name Sinorhodobacter ferrireducens sp. nov. was proposed.

Genome sequence of the Leisingera aquimarina type strain (DSM 24565(T)), a member of the marine Roseobacter clade rich in extrachromosomal elements.

Leisingera aquimarina Vandecandelaere et al. 2008 is a member of the genomically well characterized Roseobacter clade within the family Rhodobacteraceae. Representatives of the marine Roseobacter clade are metabolically versatile and involved in carbon fixation and biogeochemical processes. They form a physiologically heterogeneous group, found predominantly in coastal or polar waters, especially in symbiosis with algae, in microbial mats, in sediments or associated with invertebrates. Here we describe the features of L. aquimarina DSM 24565T together with the permanent-draft genome sequence and annotation. The 5,344,253 bp long genome consists of one chromosome and an unusually high number of seven extrachromosomal elements and contains 5,129 protein-coding and 89 RNA genes. It was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2010 and of the activities of the Transregional Collaborative Research Centre 51 funded by the German Research Foundation (DFG).

Description of Tropicibacter mediterraneus sp. nov. and Tropicibacter litoreus sp. nov.

Four strains (M15∅_3, M17T, M49 and R37T) were isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. Together with an older preserved isolate (strain 2OM6) from cultured oysters at Vinaroz, Castellón, Spain, the strains were thoroughly characterized in a polyphasic study and were placed phylogenetically within the Roseobacter clade in the family Rhodobacteraceae. Highest 16S rRNA sequence similarities of the five strains to the types of any established species corresponded to Tropicibacter multivorans (95.8–96.4%), Phaeobacter inhibens (95.9–96.3%) and Phaeobacter gallaeciensis (95.9–96.2%). On the other hand, whole genome (ANI) and protein fingerprinting (MALDI-TOF) data proved: (i) non clonality among the strains, and (ii) the existence of two genospecies, one consisting of strains M15∅_3, M17T, M49 and 2OM6 and another one consisting of strain R37T. Phenotypic traits determined allow differentiating both genospecies from each other and from closely related taxa. In view of all data collected we propose to accommodate these isolates in two species as members of the genus Tropicibacter, Tropicibacter mediterraneus sp. nov. (type strain M17T=CECT 7615T=KCTC 23058T) and Tropicibacter litoreus sp. nov. (type strain R37T=CECT 7639T=KCTC 23353T).

Temperature-driven shifts in the epibiotic bacterial community composition of the brown macroalga Fucus vesiculosus.

The thallus surface of the brown macroalga Fucus vesiculosus is covered by a specific biofilm community. This biofilm supposedly plays an important role in the interaction between host and environment. So far, we know little about compositional or functional shifts of this epibiotic bacterial community under changing environmental conditions. In this study, the response of the microbiota to different temperatures with respect to cell density and community composition was analyzed by nonculture-based methods (denaturing gradient gel electrophoresis and 454 pyrosequencing of the 16S rRNA gene). Redundancy analysis showed that despite high variability among host individuals temperature accounted for 20% of the variation in the bacterial community composition, whereas cell density did not differ between groups. Across all samples, 4341 bacterial operational taxonomic units (OTUs) at a 97% similarity level were identified. Eight percent of OTUs were significantly correlated with low, medium, and high temperatures. Notably, the family Rhodobacteraceae increased in relative abundance from 20% to 50% with increasing temperature. OTU diversity (evenness and richness) was higher at 15°C than at the lower and higher temperatures. Considering their known and presumed ecological functions for the host, change in the epibacterial community may entail shifts in the performance of the host alga.

Marine Rhodobacteraceae l‐haloacid dehalogenase contains a novel His/Glu dyad that could activate the catalytic water

The putative L-haloacid dehalogenase gene (DehRhb) from a marine Rhodobacteraceae family was cloned and overexpressed in Escherichia coli. The DehRhb protein was shown to be an L-haloacid dehalogenase with highest activity towards brominated substrates with short carbon chains (≤ C3). The optimal temperature for enzyme activity was 55 °C, and the Vmax and Km were 1.75 μm·min(-1) ·mg(-1) of protein and 6.72 mm, respectively, when using monobromoacetic acid as a substrate. DehRhb showed moderate thermal stability, with a melting temperature of 67 °C. The enzyme demonstrated high tolerance to solvents, as shown by thermal shift experiments and solvent incubation assays. The DehRhb protein was crystallized and structures of the native, reaction intermediate and substrate-bound forms were determined. The active site of DehRhb had significant differences from previously studied L-haloacid dehalogenases. The asparagine and arginine residues shown to be essential for catalytic activity in other L-haloacid dehalogenases are not present in DehRhb. The histidine residue which replaces the asparagine residue in DehRhb was coordinated by a conformationally strained glutamate residue that replaces a conserved glycine. The His/Glu dyad is positioned for deprotonation of the catalytic water which attacks the ester bond in the reaction intermediate. The catalytic water in DehRhb is shifted by ~ 1.5 Å from its position in other L-haloacid dehalogenases. A similar His/Glu or Asp dyad is known to activate the catalytic water in haloalkane dehalogenases. The DehRhb enzyme represents a novel member within the L-haloacid dehalogenase family and it has potential to be used as a commercial biocatalyst.

Genome of the R-body producing marine alphaproteobacterium Labrenzia alexandrii type strain (DFL-11(T)).

Labrenzia alexandrii Biebl et al. 2007 is a marine member of the family Rhodobacteraceae in the order Rhodobacterales, which has thus far only partially been characterized at the genome level. The bacterium is of interest because it lives in close association with the toxic dinoflagellate Alexandrium lusitanicum. Ultrastructural analysis reveals R-bodies within the bacterial cells, which are primarily known from obligate endosymbionts that trigger “killing traits” in ciliates (Paramecium spp.). Genomic traits of L. alexandrii DFL-11T are in accordance with these findings, as they include the reb genes putatively involved in R-body synthesis. Analysis of the two extrachromosomal elements suggests a role in heavy-metal resistance and exopolysaccharide formation, respectively. The 5,461,856 bp long genome with its 5,071 protein-coding and 73 RNA genes consists of one chromosome and two plasmids, and has been sequenced in the context of the Marine Microbial Initiative.