Labrenzia suaedae sp. nov., a marine bacterium isolated from a halophyte, and emended description of the genus Labrenzia

Roseibium algae sp. nov., isolated from a marine alga (Grateloupia sp.)

A novel Gram-stain-negative, rod-shaped, non-spore-forming, aerobic, motile bacterium with a single polar or subpolar flagellum, designated strain H3510T, was isolated from marine alga collected on sea shore of Yantai, PR China. The organism grew optimally at 28 °C and pH 7.0 and in presence of 3.0 % (w/v) NaCl. The strain exhibited positive catalase activity but negative oxidase and nitrate reduction activities. The predominant cellular fatty acids were C18 : 1  ω7c and/or C18 : 1  ω6c, 11-methyl C18 : 1  ω7c, and C16 : 0. Additionally, the major polar lipids were phosphatidylglycerol, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, and phosphatidylethanolamine; the respiratory quinone was ubiquinone 10 (Q-10). The genomic DNA G+C content of strain H3510T was 54.2%. The novel strain showed the closest relationship with Roseibium polysiphoniae KMM 9699T with 98.2 % 16S rRNA gene sequence similarity. The calculated values for average nucleotide identity and DNA-DNA hybridization between strain H3510T and the phylogenetically related Roseibium species were in the range of 71.3-74.9 % and 13.7-19.9 %, respectively. Based on polyphasic analyses, strain H3510T was identified as representing a novel species of the genus Roseibium, for which the name Roseibium algae sp. nov. is proposed. The type strain is H3510T (=KCTC 8206T=MCCC 1K04325T). The heterologously expressed inositol 2-dehydrogenase gene from strain H3510T displayed high oxidation activity on myo-inositol and showed potential in the production of rare stereoisomers of inositol, such as scyllo-inositol.

Roseibium algicola sp. nov. and Roseibium porphyridii sp. nov., isolated from marine red algae

Two Gram-stain-negative, strictly aerobic rods, designated as RMAR6-6T and KMA01T, exhibiting catalase- and oxidase-positive activities, were isolated from marine red algae in the Republic of Korea. Cells of strain RMAR6-6T exhibited flagellar motility, while those of strain KMA01T were non-motile. Strain RMAR6-6T exhibited optimal growth at 30-35°C and pH 7.0-8.0 with 4.0-6.0 % (w/v) NaCl, while strain KMA01T grew optimally at 30-35 °C, pH 7.0-8.0 and 2.0-5.0% NaCl. Both strains shared common major respiratory isoprenoid quinone (ubiquinone-10), cellular fatty acids (C18 : 0, C18: 1  ω7c 11-methyl, C20 : 1  ω7c and summed feature 8) and polar lipids (phosphatidylglycerol, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sulphoquinovosyldiacylglycerol). The genomic DNA G+C contents were 59.0 and 55.0 mol% for strains RMAR6-6T and KMA01T, respectively. With 98.5 % 16S rRNA gene similarity, 75.2 % average nucleotide identity (ANI) and 19.8 % digital DNA-DNA hybridization (dDDH) values, strains RMAR6-6T and KMA01T were identified as representing distinct species. Phylogenetic analyses based on both 16S rRNA gene and genome sequences revealed that strains RMAR6-6T and KMA01T formed distinct phylogenic lineages within the genus Roseibium, most closely related to Roseibium aggregatum IAM 12614T and Roseibium album CECT 5094T, respectively. The ANI and dDDH values between strain RMAR6-6T and R. aggregatum IAM 12614T were 87.5 and 33.3 %, respectively. Similarly, the values between KMA01T and R. album CECT 5094T were 74.2 % (ANI) and 19.3 % (dDDH). Based on phenotypic, chemotaxonomic and molecular characteristics, strains RMAR6-6T and KMA01T represent two novel species of the genus Roseibium, for which the names R. algicola sp. nov. (RMAR6-6T=KACC 22482T=JCM 34977T) and R. porphyridii sp. nov. (KMA01T=KACC 22479T=JCM 34597T) are proposed, respectively.

Multiple bacterial partners in symbiosis with the nudibranch mollusk Rostanga alisae

The discovery of symbiotic associations extends our understanding of the biological diversity in the aquatic environment and their impact on the host’s ecology. Of particular interest are nudibranchs that unprotected by a shell and feed mainly on sponges. The symbiotic association of the nudibranch Rostanga alisae with bacteria was supported by ample evidence, including an analysis of cloned bacterial 16S rRNA genes and a fluorescent in situ hybridization analysis, and microscopic observations. A total of 74 clones belonging to the phyla α-, β-, γ-Proteobacteria, Actinobacteria, and Cyanobacteria were identified. FISH confirmed that bacteriocytes were packed with Bradyrhizobium, Maritalea, Labrenzia, Bulkholderia, Achromobacter, and Stenotrophomonas mainly in the foot and notum epidermis, and also an abundance of Synechococcus cyanobacteria in the intestinal epithelium. An ultrastructural analysis showed several bacterial morphotypes of bacteria in epidermal cells, intestine epithelium, and in mucus layer covering the mollusk body. The high proportion of typical bacterial fatty acids in R. alisae indicated that symbiotic bacteria make a substantial contribution to its nutrition. Thus, the nudibranch harbors a high diversity of specific endo- and extracellular bacteria, which previously unknown as symbionts of marine invertebrates that provide the mollusk with essential nutrients. They can provide chemical defense against predators.

Diverse key nitrogen cycling genes nifH, nirS and nosZ associated with Pichavaram mangrove rhizospheres as revealed by culture-dependent and culture-independent analyses

Mangroves are highly productive unique ecosystems harboring diverse unexplored microbial communities that play crucial roles in nutrient cycling as well as in maintaining ecosystem services. The mangrove-associated microbial communities transform the dead vegetation into nutrient sources of nitrogen, phosphorus, potash, etc. To understand the genetic and functional diversity of the bacterial communities involved in nitrogen cycling of this ecosystem, this study explored the diversity and distribution of both the nitrogen fixers and denitrifiers associated with the rhizospheres of Avicennia marina, Rhizophora mucronata, Suaeda maritima, and Salicornia brachiata of the Pichavaram mangroves. A combination of both culturable and unculturable (PCR-DGGE) approaches was adopted to explore the bacterial communities involved in nitrogen fixation by targeting the nifH genes, and the denitrifiers were explored by targeting the nirS and nosZ genes. Across the rhizospheres, Gammaproteobacteria was found to be predominant representing both nitrogen fixers and denitrifiers as revealed by culturable and unculturable analyses. Sequence analysis of soil nifH, nirS and nosZ genes clustered to unculturable, with few groups clustering with culturable groups, viz., Pseudomonas sp. and Halomonas sp. A total of 16 different culturable genera were isolated and characterized in this study. Other phyla like Firmicutes and Actinobacteria were also observed. The PCR-DGGE analysis also revealed the presence of 29 novel nifH sequences that were not reported earlier. Thus, the mangrove ecosystems serve as potential source for identifying unexplored novel microbial communities that contribute to nutrient cycling.

Comparative Genomic Analysis of Labrenzia aggregata (Alphaproteobacteria) Strains Isolated From the Mariana Trench: Insights Into the Metabolic Potentials and Biogeochemical Functions

Hadal zones are marine environments deeper than 6,000 m, most of which comprise oceanic trenches. Microbes thriving at such depth experience high hydrostatic pressure and low temperature. The genomic potentials of these microbes to such extreme environments are largely unknown. Here, we compare five complete genomes of bacterial strains belonging to Labrenzia aggregata (Alphaproteobacteria), including four from the Mariana Trench at depths up to 9,600 m and one reference from surface seawater of the East China Sea, to uncover the genomic potentials of this species. Genomic investigation suggests all the five strains of L. aggregata as participants in nitrogen and sulfur cycles, including denitrification, dissimilatory nitrate reduction to ammonium (DNRA), thiosulfate oxidation, and dimethylsulfoniopropionate (DMSP) biosynthesis and degradation. Further comparisons show that, among the five strains, 85% gene functions are similar with 96.7% of them encoded on the chromosomes, whereas the numbers of functional specific genes related to osmoregulation, antibiotic resistance, viral infection, and secondary metabolite biosynthesis are majorly contributed by the differential plasmids. A following analysis suggests the plasmidic gene numbers increase along with isolation depth and most plasmids are dissimilar among the five strains. These findings provide a better understanding of genomic potentials in the same species throughout a deep-sea water column and address the importance of externally originated plasmidic genes putatively shaped by deep-sea environment.

Roseibium limicola sp. nov., isolated from tidal mudflat

A novel bacterium, designated strain CAU 1637^T, was isolated from a tidal mudflat. Cells of strain CAU 1637^T were Gram-stain-negative, aerobic, motile with single flagellum and rod-shaped. The optimum conditions for growth were observed at 30 °C, pH 6.0 and in the presence of 2 % (w/v) NaCl. The respiratory quinone was ubiquinone-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1637^T was closely related to the genus Roseibium, with the highest similarity to Roseibium aestuarii NRBC 112946^T (97.4 %), followed by Roseibium hamelinense NRBC 16783^T (96.8 %), Roseibium aquae JCM 19310^T (96.4 %), Roseibium sediminis KCTC 52373^T (95.8 %) and Roseibium denhamense JCM 10543^T (95.3 %). The predominant cellular fatty acids were C_18 : 1  ω7c 11-methyl and summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c). The major polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The average nucleotide identity values between the novel isolate and related strains ranged from 71.0 to 76.4 %, and the DNA-DNA hybridization values ranged from 19.3 to 20.3 %. The G+C content was 58.4 mol% and the whole-genome size was 4.6 Mb, which included 17 contigs and 3931 protein-coding genes. Based on the taxonomic data, strain CAU 1637^T represents a novel species of the genus Roseibium, for which the name Roseibium limicola sp. nov. is proposed. The type strain is CAU 1637^T (=KCTC 82429^T=MCCC 1K06080^T).

Roseibium litorale sp. nov., isolated from a tidal flat sediment and proposal for the reclassification of Labrenzia polysiphoniae as Roseibium polysiphoniae comb. nov

A novel Gram-stain-negative, facultatively anaerobic, rod-shaped and non-motile bacterial strain, designated as 4C16A^T, was isolated from a tidal flat sediment and characterized by using a polyphasic taxonomic approach. Strain 4C16A^T was found to grow at 10-40 °C (optimum, 28 °C), at pH 5.0-10.0 (optimum, pH 6.0-7.0) and in 0-6 % (w/v) NaCl (optimum, 1 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 4C16A^T fell into the genus Roseibium, and shared the highest identity of 98.9 % with the closest type strain Roseibium suaedae KACC 13772^T and less than 98.0 % identity with other type strains of recognized species within this genus. The phylogenomic analysis indicated that strain 4C16A^T formed an independent branch within this genus. The 28.6 % digital DNA-DNA hybridization estimate and 85.0 % average nucleotide identity between strains 4C16A^T and R. suaedae KACC 13772^T were the highest, but still far below their respective threshold for species definition, implying that strain 4C16A^T should represent a novel genospecies. The predominant cellular fatty acid was summed feature 8; the polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylmonomethylethanolamine; the respiratory quinones were Q-9 and Q-10. The genomic DNA G+C content was 59.8mol %. Based on phylogenetic analyses and phenotypic and chemotaxonomic characteristics, strain 4C16A^T is concluded to represent a novel species of the genus Roseibium, for which the name Roseibium litorale sp. nov. is proposed. The type strain of the species is 4C16A^T (=GDMCC 1.1932^T=KACC 22078^T). We also propose the reclassification of Labrenzia polysiphoniae as Roseibium polysiphoniae comb. nov. and 'Labrenzia callyspongiae' as Roseibium callyspongiae sp. nov.

Comparative Analysis of Bacterial Diversity and Community Structure in the Rhizosphere and Root Endosphere of Two Halophytes, Salicornia europaea and Glaux maritima, Collected from Two Brackish Lakes in Japan

Microbial community structures associated with halophytes and their compositions among different habitats, particularly natural saline sites, have not yet been investigated in detail. In the present study, we examined the diversity and composition of the rhizosphere and root endosphere bacteria of two halophytes, Salicornia europaea L. and Glaux maritima L., collected from two adjacent brackish lakes, Lake Notoro and Lake Tofutsu, in Japan. The bacterial species richness and diversity indices of the two halophytes collected from both lakes showed no significant differences in the rhizosphere or root endosphere. In contrast, beta diversity and taxonomic analyses revealed significant differences in the bacterial communities from each halophyte between the two lakes even though the two locations were natural saline sites, indicating that the bacterial communities for S. europaea and G. maritima both fluctuated in a manner that depended on the geographical location. Common and abundant genera associated with each halophyte across the two lakes were then identified to verify the bacterial genera specifically inhabiting each plant species. The results obtained showed that the composition of abundant genera inhabiting each halophyte across two lakes was distinct from that reported previously in other saline soil areas. These results suggest that each halophyte in different geographical sites had an individual complex bacterial community.

Hongsoonwoonella zoysiae gen. nov., sp. nov., a new member of the family Stappiaceae isolated from a tidal mudflat

A Gram stain-negative bacterial strain, designated SY4-7^T, was isolated from rhizosphere mudflat of a halophyte (Zoysia sinica) collected around Seonyu Island, Republic of Korea. Cells of the organism were strictly aerobic, non-sporulating, non-motile rods and grew at 20-42 °C, pH 6-8 and 1-6% (w/v) NaCl. The 16S rRNA gene-based phylogenetic analyses revealed that strain SY4-7^T formed an independent cluster separated from the recognized genera of the family Stappiaceae, which was also supported by phylogenomic analysis-based 92-core gene sequences. The type stains of the phylogenetically closest relatives were Stappia indica (95.6% sequence similarity), Stappia stellulata (95.1%) and Roseibium hamelinense (95.1%). The isoprenoid quinone was Q-10. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, an unidentified phosphoglycolipid, an unidentified aminolipid, two unidentified phospholipids and an unidentified lipid. The major cellular fatty acids are C_18:1ω7c and C_19:1 cyclo ω8c. The G + C content of the genomic DNA is 60.7%. Discrimination of the organism from all the recognized genera of the family Stappiaceae was apparent by the chemotaxonomic and phylogenetic features. Based on the results presented here, strain SY4-7^T (= KCTC 72226^T = NBRC 113902^T) represents a novel species of a new genus in the family Stappiaceae, for which the name Hongsoonwoonella zoysiae sp. nov. is proposed.

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Diluted conventional media improve the microbial cultivability from aquarium seawater

The cultivation of microbial species remains a primary challenge in microbiology and obtaining pure cultures is essential for the study of microbial physiology and function. When isolating microorganisms from aquaculture environments, Vibrio are the most dominate isolates on the media that are commonly used. In order to expand our ability to study microbial species, an easy-operation and low-cost medium that can reduce the interference of Vibrio strains and increase the cultivability of other bacteria is urgently needed. We compared viable cell counts on conventional media (CM; including Marine Agar 2216 and LB media) and diluted media (DM; including 1/10-Marine Agar 2216, 1/10-LB). We also assessed the diversity of cultivable microorganisms under high and low nutrient conditions by a plate-wash strategy coupled with high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene. The results show that microbial communities from DM, especially 1/10-Marine Agar 2216, are more diverse than those obtained from CM. Vibrio isolates were reduced on DM. PICRUSt analysis revealed that nutrient composition is a significant contributor to the diversity and function of the cultivable microbial communities. Bacteria grown on CM possess more pathogenic characteristics, whereas DM favors the growth of bacteria that have multiple metabolic functions. Collectively, our data provide strong evidence that dilution of CM influences the cultivability of bacteria from aquaculture seawater. It also supports that DM can expand the range of microbial species that can be cultivated. This study also provides insights for media design in microbial cultivation from aquaculture systems.

Paracoccus sediminilitoris sp. nov., isolated from a tidal flat sediment

A novel marine Gram-stain-negative, non-spore-forming, motile, aerobic, coccoid or ovoid bacterium, designated as strain DSL-16T, was isolated from a tidal flat sediment on the East China Sea and characterized phylogenetically and phenotypically. Optimal growth of the strain occurred at 35 °C (range 4–40 °C), at pH 6 (range 5–11) and with 4 % (w/v) NaCl (range 1–14 %). The nearest phylogenetic neighbour was Paracoccus seriniphilus DSM 14827T (98.2 % 16S rRNA gene sequence similarity). The digital DNA–DNA hybridization value between strain DSL-16T and P. seriniphilus DSM 14827T was 19.5±2.2 %. The average nucleotide identity value between strain DSL-16T and P. seriniphilus DSM 14827T was 83.6 %. The sole respiratory ubiquinone was Q-10. The major polar lipids were phosphatidylmonomethylethanolamine (PME), phosphatidylglycerol (PG), phosphatidylcholine (PC), phosphatidylethanolamine (PE), diphosphatidyglycerol (DPG) and glycolipid (GL). The predominant cellular fatty acids of strain DSL-16T were C18 : 1ω7c, C18 : 0 and 11-methyl C18 : 1ω7c. The G+C content of the genomic DNA was 64.5 mol%. The combined genotypic and phenotypic data indicated that strain DSL-16T represents a novel species of the genus Paracoccus , for which the name Paracoccus sediminilitoris sp. nov. is proposed. The type strain is DSL-16T (=KCTC 62644T=MCCC 1K03534T).

Analysis of marine microbial communities colonizing various metallic materials and rust layers

High-throughput sequencing was used to visualize microbial biocoenoses on different metallic surfaces and rust layers of highly corroded steels after immersion in coastal marine water for 30 months at Sanya, China. Distinct microbial community compositions were observed on these metallic surfaces. The dominant genus was the copper-tolerant, acid-producing Lactobacillus on copper alloys, the common aerobic surface colonizers Bacillus and Ruegeria on aluminum alloys, and aerobic biofilm-forming Pseudomonas on carbon steel. Most of these are copiotrophic microbes compared to planktonic microbes, which are oligotrophic. Additionally, sulfate-reducing prokaryotes (SRP) were detected in the rust layer, but the dominant genera changed from the outer layer to the inner part. The dominant genera detected in the outer, middle and inner rusts layers were Desulfotomaculum, Desulfonatronum (obligate anaerobe) and Desulfovibiro (electroactive), respectively. Further, the coexistence of methanogens with SRP suggests interspecies interactions.

Bacterial Diversity Associated With the Rhizosphere and Endosphere of Two Halophytes: Glaux maritima and Salicornia europaea

Root-associated microbial communities are very important in the adaptation of halophytes to coastal environments. However, little has been reported on microbial community structures related to halophytes, or on comparisons of their compositions among halophytic plant species. Here, we studied the diversity and community structure of both rhizosphere and root endosphere bacteria in two halophytic plants: Glaux maritima and Salicornia europaea. We sampled the rhizosphere, the root endosphere, and bulk control soil samples, and performed bacterial 16S rRNA sequencing using the Illumina MiSeq platform to characterize the bacterial community diversities in the rhizosphere and root endosphere of both halophytes. Among the G. maritima samples, the richness and diversity of bacteria in the rhizosphere were higher than those in the root endosphere but were lower than those of the bulk soil. In contrast for S. europaea, the bulk soil, the rhizosphere, and the root endosphere all had similar bacterial richness and diversity. The number of unique operational taxonomic units within the root endosphere, the rhizosphere, and the bulk soil were 181, 366, and 924 in G. maritima and 126, 416, and 596 in S. europaea, respectively, implying habitat-specific patterns for each halophyte. In total, 35 phyla and 566 genera were identified. The dominant phyla across all samples were Proteobacteria and Bacteroidetes. Actinobacteria was extremely abundant in the root endosphere from G. maritima. Beneficial bacterial genera were enriched in the root endosphere and rhizosphere in both halophytes. Rhizobium, Actinoplanes, and Marinomonas were highly abundant in G. maritima, whereas Sulfurimonas and Coleofasciculus were highly abundant in S. europaea. A principal coordinate analysis demonstrated significant differences in the microbiota composition associated with the plant species and type of sample. These results strongly indicate that there are clear differences in bacterial community structure and diversity between G. maritima and S. europaea. This is the first report to characterize the root microbiome of G. maritima, and to compare the diversity and community structure of rhizosphere and root endosphere bacteria between G. maritima and S. europaea.

Chthonobacter albigriseus gen. nov., sp. nov., isolated from grass-field soil

A novel aerobic, Gram-stain-negative and non-motile bacterial strain, designated ED7T, was isolated from grass-field soil in Cheonan, Korea. Strain ED7T utilized methanol and methylamine, but not formate, as carbon and energy sources. The strain was able to grow at 20-42 °C (optimum 30-35 °C), at pH 7.0-8.5 (optimum pH 7.5-8.0), and in the absence of NaCl. According to the similarities of the 16S rRNA gene sequences, strain ED7T was most closely related to the genera Labrenzia (≤93.3 % 16S rRNA gene sequence similarity), Pleomorphomonas (≤93.1 %) and Prosthecomicrobium (≤93.1 %). A phylogenetic analysis based on the 16S rRNA gene sequence of strain ED7T revealed that it was affiliated with the family Methylocystaceae, being most closely related to the genus Pleomorphomonas. In contrast to Pleomorphomonas koreensis and Pleomorphomonas oryzae, strain ED7T did not contain the nifH gene. The DNA G+C content of the genomic DNA of strain ED7T was 71.8 mol%. The predominant fatty acids of strain ED7T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 2 (C14 : 0 3-OH, and/or C16 : 1 iso I), 11-methyl C18 : 1ω7c and C16 : 0 3-OH. The major isoprenoid quinone was ubiquinone 10 (Q-10). The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unknown aminophospholipid. Based on phenotypic, chemotaxonomic and genotypic characteristic data, strain ED7T could be differentiated from other genera, suggesting that strain ED7T represents a novel species of a new genus in the family Methylocystaceae, for which the name Chthonobacter albigriseus gen. nov., sp. nov. is proposed. The type strain of the type species is ED7T (=JCM 30603T=KCTC 42450T).

Oharaeibacter diazotrophicus gen. nov., sp. nov., a diazotrophic and facultatively methylotrophic bacterium, isolated from rice rhizosphere

A novel facultatively methanol-utilizing bacterial strain, SM30T, was isolated from rice rhizosphere. Strain SM30T was Gram-stain-negative, aerobic, motile, short rods, and grew optimally at pH 7 and at 28 °C. It could tolerate 0 to 2 % (w/v) NaCl. Based on 16S rRNA gene sequence comparisons, strain SM30T was most closely related to Pleomorphomonas oryzae DSM 16300T, with a low similarity of 94.17 %. One of the lanthanide metals, lanthanum, could enhance its growth slightly on methanol. Phylogenetic trees, based on the mxaF, xoxF and cpn60 genes of SM30T showed its distinct phylogenetic position with respect to species with validly published names. Polymerase chain reaction (PCR) amplification of the nifH and growth on nitrogen-free medium indicated that strain SM30T is a diazotroph. The major cellular fatty acids were summed feature 8 (containing 18 : 1ω7c and 18 : 1ω6c) and cyclo 19 : 0ω8c. The major quinone was ubiquinone 10. The DNA G+C content was 74.6 mol%. Based on the genotypic and phenotypic characteristics, strain SM30T represents a novel genus and species, for which the name Oharaeibacter diazotrophicus gen. nov., sp. nov. is proposed with the type strain SM30T (=NBRC 111955T=DSM 102969T).

Labrenzia salina sp. nov., isolated from the rhizosphere of the halophyte Arthrocnemum macrostachyum

A novel, halophilic, motile, rod-shaped, Gram-staining-negative and non-endospore forming bacterium, designated Cs25T, was isolated from the rhizosphere of the halophyte Arthrocnemum macrostachyum growing in a tidal flat. Strain Cs25T was observed to be catalase-negative and oxidase-positive, and to hydrolyse hypoxanthine. Growth occurred from 15 to 40 °C, at pH 7.0-10.0 and with 1-11 % (w/v) NaCl. Q-10 was identified as the dominant ubiquinone, and the major cellular fatty acids were C18 : 1ω7c, 11-methyl C18 : 1ω7c, C20 : 1ω7c and C18 : 0. The polar lipids comprised phosphatidylmonomethylethanolamine, phosphatidylcholine, sulphoquinovosyldiacylglyceride, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The 16S rRNA gene showed 99.19, 98.6 and 98.59 % sequence identity with Labrenzia alba DSM 18320T, L. aggregata DSM 13394T and L. marina DSM 17023T, respectively. Based on the phenotypic and molecular features and DNA-DNA hybridization data, it is concluded that strain Cs25T represents a novel species for which the name Labrenzia salinasp. nov. is proposed. The type strain is Cs25T (=DSM 29163T=CECT 8816T).

Complete Genome Sequence of Labrenzia sp. Strain CP4, Isolated from a Self-Regenerating Biocathode Biofilm

Here, we present the complete genome sequence of Labrenzia sp. strain CP4, isolated from an electricity-consuming marine biocathode biofilm. Labrenzia sp. strain CP4 consists of a circular 5.2 Mbp chromosome and an 88 Kbp plasmid.

Culturable endophytic bacteria from the salt marsh plant Halimione portulacoides: phylogenetic diversity, functional characterization, and influence of metal(loid) contamination

Halimione portulacoides is abundant in salt marshes, accumulates mercury (Hg), and was proposed as useful for phytoremediation and pollution biomonitoring. Endophytic bacteria promote plant growth and provide compounds with industrial applications. Nevertheless, information about endophytic bacteria from H. portulacoides is scarce. Endophytic isolates (n = 665) were obtained from aboveground and belowground plant tissues, from two Hg-contaminated sites (sites E and B) and a noncontaminated site (site C), in the estuary Ria de Aveiro. Representative isolates (n = 467) were identified by 16S rRNA gene sequencing and subjected to functional assays. Isolates affiliated with Proteobacteria (64 %), Actinobacteria (23 %), Firmicutes (10 %), and Bacteroidetes (3 %). Altererythrobacter (7.4 %), Marinilactibacillus (6.4 %), Microbacterium (10.2 %), Salinicola (8.8 %), and Vibrio (7.8 %) were the most abundant genera. Notably, Salinicola (n = 58) were only isolated from site C; Hoeflea (17), Labrenzia (22), and Microbacterium (67) only from belowground tissues. This is the first report of Marinilactibacillus in the endosphere. Principal coordinate analysis showed that community composition changes with the contamination gradient and tissue. Our results suggest that the endosphere of H. portulacoides represents a diverse bacterial hotspot including putative novel species. Many isolates, particularly those affiliated to Altererythrobacter, Marinilactibacillus, Microbacterium, and Vibrio, tested positive for enzymatic activities and plant growth promoters, exposing H. portulacoides as a source of bacteria and compounds with biotechnological applications.

Hartmannibacter diazotrophicus gen. nov., sp. nov., a phosphate-solubilizing and nitrogen-fixing alphaproteobacterium isolated from the rhizosphere of a natural salt-meadow plant

A phosphate-mobilizing, Gram-negative bacterium was isolated from rhizospheric soil of Plantago winteri from a natural salt meadow as part of an investigation of rhizospheric bacteria from salt-resistant plant species and evaluation of their plant-growth-promoting abilities. Cells were rods, motile, strictly aerobic, oxidase-positive and catalase-negative. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain E19T was distinct from other taxa within the class Alphaproteobacteria . Strain E19T showed less than 93.5 % 16S rRNA gene sequence similarity with members of the genera Rhizobium (≤93.5 %), Labrenzia (≤93.1 %), Stappia (≤93.1 %), Aureimonas (≤93.1 %) and Mesorhizobium (≤93.0 %) and was most closely related to Rhizobium rhizoryzae (93.5 % 16S rRNA gene sequence similarity to the type strain). The sole respiratory quinone was Q-10, and the polar lipids comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an aminolipid and an unidentified phospholipid. Major fatty acids were C18 : 1ω7c (71.4 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1; 8.3 %), C20 : 0 (7.9 %) and C16 : 0 (6.1 %). The DNA G+C content of strain E19T was 59.9±0.7 mol%. The capacity for nitrogen fixation was confirmed by the presence of the nifH gene and the acetylene reduction assay. On the basis of the results of our polyphasic taxonomic study, the new isolate represents a novel genus and species, for which the name Hartmannibacter diazotrophicus gen. nov., sp. nov. is proposed. The type strain of Hartmannibacter diazotrophicus is E19T ( = LMG 27460T = KACC 17263T).

Roseibium aquae sp. nov., isolated from a saline lake

A Gram-staining-negative bacterium, strain DSG-S4-2T, was isolated from Dasugan Lake, a saline lake (salinity 3.1 %, w/v) in Qaidam basin, Qinghai, China and its taxonomic position was determined by using a polyphasic approach. Cells of strain DSG-S4-2T were non-spore-forming rods, 0.5–0.8 µm wide and 1.2–3.8 µm long and motile by means of a single polar flagellum. Strain DSG-S4-2T was strictly heterotrophic and aerobic, catalase-positive and oxidase-negative. PufLM and coxL genes were present, bacteriochlorophyll a (BChl a) and a carotenoid pigment were produced. Growth was observed in the presence of 0–8.0 % (w/v) NaCl (optimum, 1.0–2.0 %), at 20–40 °C (optimum, 35 °C) and pH 6.5–10.5 (optimum, pH 7.5–8.0). Strain DSG-S4-2T contained Q-10 as the sole respiratory quinone. The polar lipids contained two aminolipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, sulphoquinovosyldiacylglyceride, phosphatidylcholine and some unknown phospholipids, like the other members of the genus Roseibium . The predominant fatty acid (>70 %) was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content was 61.4 mol% (determined from melting temperature). Phylogenetic trees (neighbour-joining, maximum-likelihood and maximum-parsimony) based on 16S rRNA gene sequences showed that strain DSG-S4-2T was associated with the members of the genus Roseibium , with highest 16S rRNA gene sequence similarity to Roseibium denhamense OCh 254T (96.3 %) and Roseibium hamelinense OCh 368T (96.3 %). Based on the data presented above, it is concluded that strain DSG-S4-2T represents a novel species of the genus Roseibium , for which the name Roseibium aquae sp. nov. is proposed. The type strain is DSG-S4-2T ( = CGMCC 1.12426T = JCM 19310T).