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Priority pollutants such as polyethylene (PE) microplastic, lead (Pb 2+ ), and cadmium (Cd 2+ ) have attracted the interest of environmentalists due to their ubiquitous nature and toxicity to all forms of life. In this study, periphytic biofilms (epiphyton and epixylon) were used to bioremediate heavy metals (HMs) and to biodegrade PE under high (120,000 ppm) methane (CH 4 ) doses. Both periphytic biofilms were actively involved in methane oxidation, HMs accumulation and PE degradation. Epiphyton and epixylon both completely removed Pb 2+ and Cd 2+ at concentrations of 2 mg L -1 and 50 mg L -1 , respectively, but only partially removed these HMs at a relatively higher concentration (100 mg L -1 ). Treatment containing 12% 13 CH 4 proved to be most effective for biodegradation of PE. A synergistic effect of HMs and PE drastically changed microbial biota and methanotrophic communities. High-throughput 16S rRNA gene sequencing revealed that Cyanobacteria was the most abundant class, followed by Gammaproteobacteria and Alphaproteobacteria in all high-methane-dose treatments. DNA stable-isotope probing was used to label 13 C in a methanotrophic community. A biomarker for methane-oxidizing bacteria, pmoA gene sequence of a 13 C-labeled fraction, revealed that Methylobacter was most abundant in all high-methane-dose treatments compared to near atmospheric methane (NAM) treatment, followed by Methylococcus . Methylomonas , Methylocystis , Methylosinus, and Methylocella were also found to be increased by high doses of methane compared to NAM treatment. Overall, Cd +2 had a more determinantal effect on methanotrophic activity than Pb 2+ . Epiphyton proved to be more effective than epixylon in HMs removal and PE biodegradation. The findings proved that both epiphyton and epixylon can be used to bioremediate HMs and biodegrade PE as an efficient ecofriendly technique under high methane concentrations.

Marine sponges are sources of various bioactive metabolites, including several anticancer drugs, produced mainly by sponge-associated microbes. Palk Bay, on the south-east coast of India, is an understudied, highly disturbed reef environment exposed to various anthropogenic and climatic stresses. In recent years, Palk Bay suffered from pollution due to the dumping of untreated domestic sewage, effluents from coastal aquaculture, tourism, salt pans, cultivation of exotic seaweeds, and geogenic heavy-metal pollution, especially arsenic, mercury, cadmium, and lead. Low microbial-abundant sponge species, such as Gelliodes pumila and Cliona lobata, were found to be ubiquitously present in this reef environment. Triplicate samples of each of these sponge species were subjected to Illumina MiSeq sequencing using V3-V4 region-specific primers. In both C. lobata and G. pumila, there was an overwhelming dominance (98 and 99%) of phylum Candidatus Saccharibacteria and Proteobacteria, respectively. The overall number of operational taxonomic units (OTUs) was 68 (40 and 13 OTUs unique to G. pumila and C. lobata, respectively; 15 shared OTUs). Alphaproteobacteria was the most abundant class in both the sponge species. Unclassified species of phylum Candidatus Saccharibacteria from C. lobata and Chelotivorans composti from G. pumila were the most abundant bacterial species. The predominance of Alphaproteobacteria also revealed the occurrence of various xenobiotic-degrading, surfactant-producing bacterial genera in both the sponge species, indirectly indicating the possible polluted reef status of Palk Bay. Studies on sponge microbiomes at various understudied geographical locations might be helpful in predicting the status of reef environments.

A Gram-stain-negative bacterium, designated strain 40Bstr34 T , isolated from a sediment sample from the West Pacific Ocean, was taxonomically characterized by using a polyphasic approach. The strain was phylogenetically close to Jiella aquimaris LZB041 T and Jiella endophytica CBS5Q-3 T , with 16S rRNA gene sequence similarities of 98.5 and 97.1 %, respectively. The genome of strain 40Bstr34 T featured a G+C content of 65.7 % for a 5.8 Mb chromosome. Up-to-date bacterial core gene set analysis revealed that strain 40Bstr34 T represents one independent lineage with J.aquimaris LZB041 T . In silico DNA-DNA hybridization values between strain 40Bstr34 T and its phylogenetic neighbours ranged from 30.3-34.2 %, below the cutoff of 70 %. In addition, the corresponding average nucleotide identity values were between 81.8-83.7 %, which are lower than 95 % threshold. The predominant cellular fatty acids of strain 40Bstr34 T were summed feature 8 (C 18 : 1   ω 6c and/or C 18 : 1   ω 7c ), cyclo-C 19 : 0   ω8 c and iso-C 17 : 0 3-OH, and ubiquinone-10 as the predominant respiratory quinone. The major polar lipids included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and two unidentified lipids. Based on the results of phenotypic, chemotaxonomic and genetic analyses, strain 40Bstr34 T is identified as representing a novel species of the genus Jiella for which the name Jiella pacifica sp. nov. is proposed. The type strain is 40Bstr34 T (=JCM 33903 T =MCCC 1K04569 T ).

A novel marine bacterium, designated strain 216LB-ZA1-12 T , was isolated from a Penaeus vannamei aquaculture seawater sample. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 216LB-ZA1-12 T belonged to the genus Sneathiella , with the highest sequence similarity to Sneathiella glossodoripedis MKT133 T (97.7 %), followed by Sneathiella limimaris GH1-24 T (97.0 %), Sneathiella chungangensis CAU 1294 T (96.6 %) and Sneathiella chinensis LMG 23452 T (96.1 %). The average nucleotide identity and the DNA-DNA hybridization estimate values between strain 216LB-ZA1-12 T and four close type strains were between 69.2-71.3% and 16.7-17.8 %, respectively. The bacterium was Gram-stain-negative, facultatively anaerobic, oxidase and catalase positive, oval- to rod-shaped, and motile. Growth was observed at pH 7-9, salinities of 1-15% and temperatures of 4-42 °C. The G+C content of the chromosomal DNA was 48.50 mol%. The major respiratory quinone was determined to be Q-10. The principal fatty acids were summed feature 8 (C 18 : 1   ω 7c/ ω 6c ) and C 16 : 0 . The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and aminophospholipid. The combined genotypic and phenotypic data show that strain 216LB-ZA1-12 T represents a novel species within the genus Sneathiella , for which the name Sneathiella aquimaris sp. nov. is proposed, with the type strain 216LB-ZA1-12 T (=MCCC 1A14570 T =KCTC 72144 T ).

Here we investigated the diversity of bacterial communities from deep-sea surface sediments under influence of asphalt seeps at the Sao Paulo Plateau using next-generation sequencing method. Sampling was performed at North São Paulo Plateau using the human occupied vehicle Shinkai 6500 and her support vessel Yokosuka. The microbial diversity was studied at two surficial sediment layers (0-1 and 1-4 cm) of five samples collected in cores in water depths ranging from 2456 to 2728 m. Bacterial communities were studied through sequencing of 16S rRNA gene on the Ion Torrent platform and clustered in operational taxonomic units. We observed high diversity of bacterial sediment communities as previously described by other studies. When we considered community composition, the most abundant classes were Alphaproteobacteria (27.7%), Acidimicrobiia (20%), Gammaproteobacteria (11.3%) and Deltaproteobacteria (6.6%). Most abundant OTUs at family level were from two uncultured bacteria from Actinomarinales (5.95%) and Kiloniellaceae (3.17%). The unexpected high abundance of Alphaproteobacteria and Acidimicrobiia in our deep-sea microbial communities may be related to the presence of asphalt seep at North São Paulo Plateau, since these bacterial classes contain bacteria that possess the capability of metabolizing hydrocarbon compounds.

Kiloniella laminariae is a true marine bacterium and the first member of the family and order, the Kiloniellaceae and Kiloniellales. K. laminariae LD81 T (= DSM 19542 T ) was isolated from the marine macroalga Saccharina latissima and is a mesophilic, typical marine chemoheterotrophic aerobic bacterium with antifungal activity. Phylogenetic analysis of 16S rRNA gene sequence revealed the similarity of K. laminariae LD81 T not only with three validly described species of the genus Kiloniella, but also with undescribed isolates and clone sequences from marine samples in the range of 93.6-96.7%. We report on the analysis of the draft genome of this alphaproteobacterium and describe some selected features. The 4.4 Mb genome has a G + C content of 51.4%, contains 4213 coding sequences including 51 RNA genes as well as 4162 protein-coding genes, and is a part of the Genomic Encyclopaedia of Bacteria and Archaea (GEBA) project. The genome provides insights into a number of metabolic properties, such as carbon and sulfur metabolism, and indicates the potential for denitrification and the biosynthesis of secondary metabolites. Comparative genome analysis was performed with K. laminariae LD81 T and the animal-associated species Kiloniella majae M56.1 T from a spider crab, Kiloniella spongiae MEBiC09566 T from a sponge as well as Kiloniella litopenai P1-1 from a white shrimp, which all inhabit quite different marine habitats. The analysis revealed that the K. laminariae LD81 T contains 1397 unique genes, more than twice the amount of the other species. Unique among others is a mixed PKS/NRPS biosynthetic gene cluster with similarity to the biosynthetic gene cluster responsible for the production of syringomycin.

Estuaries being the connecting link between terrestrial and marine environment, experience spatial variations in the hydrographic variables as well as concentrations of pollutants. The present study reports a contrasting difference in the metal tolerance and enzyme activity of particle-associated bacteria (PAB) isolated from the upstream and downstream reaches of a tropical estuary [Cochin Estuary (CE) in the southwest coast of India], exposed to different levels of heavy metal contamination. The upstream of the estuary has been overloaded with heavy metals in the last few decades, while the downstream is less polluted. There were only 25% of culturable PAB phylogenetically common in both upstream and downstream. The PAB isolated from the upstream were dominated by γ-proteobacteria (48.1%) followed by α-proteobacteria (25.0%), while it was in the reverse order of α-proteobacteria (45.9%) and γ-proteobacteria (36.1%) in the downstream. More number of PAB from the upstream showed tolerance to higher concentrations of Zn and Cd. The Acinetobacter sp. MMRF1051 isolated from the upstream showed tolerance up to 250 mM Zn, 100 mM Cd, and 250 mM Ni. The enzyme expression profile of PAB from downstream was in the order of lipase > phosphatase > β-glucosidase > aminopeptidase, while it was in the order of β-glucosidase > lipase > aminopeptidase > phosphatase in the upstream of the estuary. The present study shows the selective pressure exerted by heavy metal pollution on the diversity of culturable bacteria associated with particulate matter in a tropical estuary. Also, the variation in their enzyme activities may impinge the remineralization of particulate organic matter (POM) in the system and may impart adverse impacts on ecosystem functioning.

With the increase in iron/steel production, the higher volume of by-products (slag) generated necessitates its efficient recycling. Because the Linz-Donawitz (LD) slag is rich in silicon (Si) and other fertilizer components, we aim to evaluate the impact of the LD slag amendment on soil quality (by measuring soil physicochemical and biological properties), plant nutrient uptake, and strengthens correlations between nutrient uptake and soil bacterial communities. We used 16 S rRNA illumine sequencing to study soil bacterial community and APIZYM assay to study soil enzymes involved in C, N, and P cycling. The LD slag was applied at 2 Mg ha -1 to Japonica and Indica rice cultivated under flooded conditions. The LD slag amendment significantly improved soil pH, plant photosynthesis, soil nutrient availability, and the crop yield, irrespective of cultivars. It significantly increased N, P, and Si uptake of rice straw. The slag amendment enhanced soil microbial biomass, soil enzyme activities and enriched certain bacterial taxa featuring copiotrophic lifestyles and having the potential role for ecosystem services provided to the benefit of the plant. The study evidenced that the short-term LD slag amendment in rice cropping systems is useful to improve soil physicochemical and biological status, and the crop yield.

A coccobacilli-shaped proteobacterium, designated strain SYSU XM001 T , was isolated from an activated sludge sample collected from JiMei sewage treatment plant, Xiamen, PR China. Cells were Gram-stain-negative, catalase-positive and oxidase-negative. The 16S rRNA gene sequence of strain SYSU XM001 T shared less than 92 % sequence identities with members of the class Alphaproteobacteria , with highest sequence similarity to Aquidulcibacter paucihalophilus TH1-2 T (91.6 %; family Hyphomonadaceae , order Rhodobacterales ). The strain exhibited growth at 25-37 °C, pH 7.0-9.0 and in the presence of up to 1 % (w/v) NaCl. Its chemotaxonomic features included ubiquinone-10 as the respiratory isoprenologue, iso-C 16 : 0 , 10-methyl C 16 : 0 TSBA and anteiso-C 17 : 0 as major cellular fatty acids and monoglycosyldiglyceride, glucuronopyranosyldiglyceride and two unidentified glycolipids as the main polar lipids. The DNA G+C content was determined to be 62.9 % (draft genome). Analyses of the phylogenetic data and differences in the chemotaxonomic and biochemical features from related genera in the family Hyphomonadaceae indicated that strain SYSU XM001 T merits representation of a novel species of a novel genus, for which the name Vitreimonas flagellata gen. nov., sp. nov. is proposed. The type strain of Vitreimonas flagellata is SYSU XM001 T (=CGMCC 1.16661 T =KCTC 62915 T ).

A novel thermotolerant bacterial strain was isolated from a hot spring in a Tibetan geothermal field. Phylogenetic analysis of the 16S rRNA gene sequence of the novel strain showed that it belongs to a distinct lineage far from any known taxa. The new isolate shared the highest pairwise sequence identity with Phreatobacter cathodiphilus S-12 T (92.8 % similarity) according to the 16S rRNA gene sequences. Cells were Gram-stain-negative, aerobic, rod-shaped and formed white round colonies. The strain grew at the ranges of 28-45 °C (optimum, 37 °C), pH 5.0-7.0 (optimum, pH 6.0) and 0-2 % NaCl. The strain was positive for catalase and oxidase. The major respiratory quinone was ubiquinone Q-10. Polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The major fatty acids were summed feature 8 (C 18 : 1   ω7 c and/or C 18 : 1   ω6 c ). The DNA G+C content was 68.3 mol%. Based on these distinguishing properties, this strain is proposed to represent a new species of a new genus Rhabdaerophilum calidifontis gen. nov., sp. nov., within a new family Rhabdaerophilaceae fam. nov. The type strain of the type species of Rhabdaerophilum calidifontis is SYSU G02060 T (=KCTC 72351 T =CGMCC 1.17070 T ).

This study of lichens in the subarctic zone of the northern hemisphere has resulted in the detection of new representatives of the order Rhizobiales. The16S rRNA gene sequence phylogeny placed the strains as a separate branch inside the Rhizobiales clade. Strain RmlP001 T exhibits 91.85% similarity to Roseiarcus fermentans strain Pf56 T and 91.76% to Beijerinckia doebereinerae strain LMG 2819 T , whilst strain RmlP026 T is closely related to B. doebereinerae strain LMG 2819 T (91.85%) and Microvirga pakistanensis strain NCCP-1258 T (91.39%). A whole-genome phylogeny of the strains confirmed their taxonomic positions. The cells of both strains were observed to be Gram-negative, motile rods that multiplied by binary fission. The cells were found to contain poly-β-hydroxybutyrate and polyphosphate, to grow at pH 3.5-8.0 and 10-30 °C, and could not fix atmospheric nitrogen. Their major cellular fatty acid identified was C 18:1 ω7c (68-71%) and their DNA G + C contents determined to be 70.5-70.8%. Beta-carotene was identified as their major carotenoid pigment; Q-10 was the only ubiquinone detected. Strains RmlP001 T and RmlP026 T are distinguishable from related species by the presence of β-carotene, the absence of C1 metabolism and the ability to grow in the presence of 3.5% NaCl. Based on their phylogenetic, phenotypic and chemotaxonomic features, we propose a novel genus Lichenibacterium and two novel species, Lichenibacterium ramalinae (the type species of the genus) and Lichenibacterium minor, to accommodate these bacteria within the family Lichenibacteriaceae fam. nov. of the order Rhizobiales. The L. ramalinae type strain is RmlP001 T (= KCTC 72076 T  = VKM B-3263 T ) and the L. minor type strain is RmlP026 T (= KCTC 72077 T  = VKM B-3277 T ).

Recent developments in the legume rhizobium symbiotic interaction particularly those related to the emergence of novel strains of bacteria that nodulate and fix nitrogen in legumes is gaining momentum. These novel strains of bacteria were mostly isolated from the root nodules of indigenous and invasive legumes belonging to the sub families Papilionoideae and Mimosoideae in South Africa, South America and South East China. These rhizobia are phylogenetically and taxonomically different from the traditional 'alpha rhizobia' and are termed 'β-rhizobia' as they belong to the β-sub class of Proteobacteria. There are also new reports of novel species of root nodulating bacteria from the α-Proteobacteria, not known for several decades since the discovery of rhizobia. However, in this review focus is given to the emerging β-rhizobia isolated from the indigenous Papilionoid legumes in the Cape Floristic regions in South Africa and the indigenous and invasive Mimosoid legumes in South America and South East Asia respectively. The nodulation of the indigenous South African Papilionoid legumes including that of Aspalathus linearis (rooibos) is discussed in a bit detail. Previous reports indicated that A. linearis is very specific in its rhizobium requirement and was reported to be nodulated by the slow growing Bradyrhizobium spp. This review however summarizes that the bacteria associated with the root nodules of A. linearis belong to members of both the alpha (α) Proteobacteria that include Mesorhizobium, Rhizobium and Bradyrhizobium spp. and the beta (β) Proteobacteria represented by the genus Burkholderia (now reclassified as Paraburkholderia). In addition, the occurrence of Paraburkholderia as the newly emerging root nodule symbionts of various other legumes has been discussed. In doing so, the review highlights that nodulation is no longer restricted to the traditional 'rhizobia' group following the emergence of the new beta rhizobia as potential nodulators of various indigenous legumes. It thus provides some insights on the status of the legume-rhizobium host specificity concept and the loss of this specificity in several symbiotic associations that puts the long held dogma of host specificity of the legume rhizobium symbiosis in a dilemma.

A bacterial strain, designated Sp-1 T , was isolated from the heterotrich ciliate Spirostomum yagiui collected from a reservoir located in Ulsan, Republic of Korea. Cells of Sp-1 T were Gram stain-negative, rod-shaped, non-spore-forming, non-motile and contained poly-β-hydroxybutyrate granules. Phylogenetic analyses based on 16S rRNA gene sequences indicated that Sp-1 T constituted a distinct phylogenetic lineage within different families in the order Rhizobiales with a pairwise sequence similarity of 95 % to the species of the genus Ochrobactrum: Ochrobactrum anthropi ATCC 49188 T and Ochrobactrum cytisi ESC1 T (family Brucellaceae ). The major cellular fatty acids were C 19 : 0 cyclo ω8 c (44.4 %) and C 16 : 0 (32.1 %). The identified sole isoprenoid quinone was ubiquinone-10 (Q-10). The major polar lipids produced were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid, two unidentified phospholipids and three unidentified lipids. The genome size was about 5.4 Mbp and the DNA G+C content was 68.2 mol%. Sp-1 T exhibited the highest average nucleotide identity value of 76.6 % and in silico DNA-DNA hybridization value of 22.1 % with Pseudoxanthobacter soli DSM 19599 T (family Xanthobacteraeae ). This strain is distinguishable from closely related members of the order Rhizobiales by its differential phenotypic, chemotaxonomic, genomic and phylogenetic characteristics. On the basis of evidence from polyphasic taxonomic analysis, we concluded that Sp-1 T represents a novel species in a novel genus within the order Rhizobiales , for which the name Segnochrobactrum spirostomi gen. nov., sp. nov. is proposed. The type strain is Sp-1 T (=KCTC 62036 T =JCM 32162 T ). We also describe a novel family, Segnochrobactraceae fam. nov., to encompass the proposed novel genus and species.

A novel piezophilic alphaproteobacterium, strain D4M1 T , was isolated from deep seawater of the Mariana Trench. 16S rRNA gene analysis showed that strain D4M1 T was most closely related to Oceanicella actignis PRQ-67 T (94.2%), Oceanibium sediminis O448 T (94.2%), and Thioclava electrotropha ElOx9 T (94.1%). Phylogenetic analyses based on both 16S rRNA gene and genome sequences showed that strain D4M1 T formed an independent monophyletic branch paralleled with the genus Oceanicella in the family Rhodobacteraceae. Cells were Gram-stain-negative, aerobic short rods, and grew optimally at 37°C, pH 6.5, and 3.0% (w/v) NaCl. Strain D4M1 T was piezophilic with the optimum pressure of 10 MPa. The principal fatty acids were C 18:1 ω7c/C 18:1 ω6c and C 16:0 , major respiratory quinone was ubiquinone-10, and predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminophospholipid. The complete genome contained 5,468,583-bp with a G + C content of 70.2 mol% and contained 4,855 protein-coding genes and 78 RNA genes. Genomic analysis revealed abundant clues on bacterial high-pressure adaptation and piezophilic lifestyle. The combined evidence shows that strain D4M1 T represents a novel species of a novel genus in the family Rhodobacteraceae, for which the name Paraoceanicella profunda gen. nov., sp. nov. is proposed (type strain D4M1 T  = MCCC 1K03820 T  = KCTC 72285 T )., (© 2019 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

A Gram-staining-negative, aerobic, curved rod-shaped and thermophilic bacterial strain, designated YIM 72297 T , was isolated from a sediment sample collected from a hot spring in Tengchong county, Yunnan province, south-west China. Growth was observed at pH 5.0-9.0 with an optimum of pH 7.0-7.5, and at 45-60 °C with an optimum of 55 °C. Positive for catalase and oxidase. The 16S rRNA gene sequence comparison indicated that strain YIM 72297 T was most closely related to Elioraea tepidiphila DSM 17972 T (96.9 %) and showed <91 % sequence similarities to members of the order Rhodospirillales . Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 72297 T formed a distinct lineage within the genus Elioraea , and revealed that the genus Elioraea formed a novel family-level clade in the order Rhodospirillales . The ANI and the dDNA-DNA hybridization estimate values between strains YIM 72297 T and Elioraea tepidiphila DSM 17972 T were 70.8 and 20.1 %, respectively. Strain YIM 72297 T contained Q-10 as the predominant ubiquinone. The major fatty acids (>5 %) were summed C 18 : 0 (35.8 %), summed feature 8 (30.1 %), C 16 : 0 (12.6 %), C 18 : 1 2OH (5.6 %) and C 16 : 0 2OH (5.4 %). The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, diphosphosphatidylglycerol and phosphatidylglycerol in addition to two unidentified aminolipids. The DNA G+C content of YIM 72297 T was 70.8 mol% (draft genome). On the basis of the polyphasic taxonomic evidence presented in this study, strain YIM 72297 T should be classified as representing a novel species of the genus Elioraea , for which the name Elioraea thermophila sp. nov. is proposed, with the type strain YIM 72297 T (=CCTCC AB 2017169 T =KCTC 62323 T ). In addition, a novel family, Elioraeaceae fam. nov., is proposed to accommodate the genus Elioraea .

A Gram-stain-negative, cocci or short rod-shaped, yellow-pigmented bacterium, designated strain S2-4-2 T , was isolated from coastal sediment of Spartina alterniflora in Quanzhou Bay, PR China. Growth was observed at 15-40 °C (optimum, 30 °C) and pH 6.0-8.0 (optimum, pH 7.0). Strain S2-4-2 T tolerated 0-10 % NaCl (optimum, 1 %). The 16S rRNA gene of strain S2-4-2 T showed highest sequence similarity to Croceicoccus pelagius Ery9 T (98.2 %), followed by Croceicoccus naphthovorans PQ-2 T , Croceicoccus marinus E4A9 T and Croceicoccus mobilis Ery22 T (97.6%, 96.3 and 96.3 %, respectively). Phylogenetic analysis based on 16S rRNA gene sequences and phylogenomic analysis based on 92 up-to-date bacterial core gene sets indicated that strain S2-4-2 T forms a distinct monophyletic branch affiliated to the genus Croceicoccus . The average nucleotide identity value between strain S2-4-2 T and its close relatives were estimated to be 74.8-85.7 %. The respiratory quinone was found to be Q-10. The predominant fatty acids (>10 %) were identified as summed feature 8 (C 18 : 1 ω7 c and/or C 18 : 1 ω6 c ) and summed feature 3 (C 16 : 1 ω7 c and C 16 : 1 ω6 c ). The polar lipids were identified as phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and an unidentified phospholipid. The draft genome size of strain S2-4-2 T was 3.5 Mb with a genomic G+C content of 63.0 mol%. Based on these results, strain S2-4-2 T is concluded to represent a novel species within the genus Croceicoccus , for which the name Croceicoccus sediminis sp. nov. is proposed with the type strain S2-4-2 T (=MCCC 1K03706 T =KCTC 72146 T ).

A Gram-stain-negative, strictly aerobic, rod-shaped bacterium, without flagellum and designated ZYF765 T , was isolated from seawater sampled at a depth of 4000 m in the Mariana Trench. Strain ZYF765 T grew with 1-15 % (w/v) NaCl (optimum, 4 %), at 16-37 °C (28 °C) and at pH 6.0-10.0 (pH 7.0-8.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain ZYF765 T formed a lineage within the family Hyphomonadaceae , and was distinct from the most closely related species Glycocaulis abyssi , Glycocaulis albus and Glycocaulis alkaliphilus with 16S rRNA gene sequences similarities ranging from 98.42 to 98.63 %. The major respiratory quinone was ubiquinone-10 (Q-10). The polar lipids comprised three unidentified glycolipids, one unidentified aminophospholipid, one unidentified phospholipid and one unidentified aminolipid. The predominant fatty acids (more than 10 % of total fatty acids) were C 18 : 1 ω7 c (46.2 %) and C 18 : 0 (14.1 %). The DNA G+C content was 67.7 mol%. On the basis of the results of polyphasic taxonomic analysis, strain ZYF765 T is considered to represent a novel species within the genus Glycocaulis , for which the name Glycocaulis profundi sp. nov. is proposed. The type strain is ZYF765 T (=JCM 33028 T =MCCC 1K03554 T ).

A Gram-negative, motile, aerobic and coccoid rod-shaped bacterium, designated strain YIM132180 T , was isolated from a Lepraria sp. lichen collected from Pu'er, Yunnan Province, China. The strain grew at 15-35 °C (optimum, 25-28 °C), at 0-2% (w/v) NaCl (optimum, 0-1%) and at pH 6.0-9.0 (optimum, pH 7.0). The 16S rRNA gene sequence showed that strain YIM132180 T had highest similarity (96.4%) with Aureimonas endophytica 2T4P-2-4 T , followed by Aureimonas ureilytica NBRC 106430 T (95.7%) and Aureimonas rubiginis CC-CFT034 T (95.6%). Phylogenetic analysis showed that the strain grouped with species of the genus Aureimonas. The genomic sequence was 4,779,519 bp and contained 4584 coding sequences (CDSs), 54 RNA genes, 3 complete rRNA genes and 47 tRNA genes. The major fatty acids (>10%) of strain YIM132180 T were C 18:1 ω7c, C- 16:0 and C 19:0 cyclo ω8c. The predominant menaquinone was ubiquinone 10 (Q-10). The polar lipid profile comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, unidentified phospholipid, amino lipid, lipid and most importantly sulfoquinovosyldiacylglycerol (SQDG). Based on the draft genome sequence, the G +C content of strain YIM132180 T was 68.4 mol%. The results of the polyphasic taxonomic study, including phenotypic, chemotaxonomic, and phylogenetic analyses, showed that strain YIM132180 T represents a novel species of the genus Aureimonas, for which the name Aureimonas leprariae sp. nov. is proposed. The type strain is YIM 132180 T (=KCTC 72462 T  = CGMCC 1.17389 T ).

A salt-tolerant, Gram-negative, rod-shaped and yellow-pigmented bacterium, designated strain AY-3R T , was isolated from rhizosphere soil of a desert xerophyte, Haloxylon ammodendron , sampled at Badain Jaran Desert, Alxa region, Inner Mongolia, PR China. Growth of this strain was observed at 20-42 °C (optimum, 28-30 °C), at pH 6.0-9.0 (optimum, pH 6.0-7.0) and at 0-8 % (w/v) NaCl (optimum, 3 %). Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain AY-3R T was a member of the genus Altererythrobacter , with the highest similarity to Altererythrobacter aerophilus Ery1 T (97.6 %), followed by Altererythrobacter xinjiangensis S3-63 T (96.9 %). The predominant fatty acids (>10.0 %) were C 18 : 1 ω7 c , C 17 : 1 ω6 c and summed feature 3 (C 16 : 1 ω7 c and/or C 16 : 1 ω6 c ). The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and one unknown polar lipid. The predominant respiratory quinone was ubiquinone-10. The G+C content of the genomic DNA of strain AY-3R T was 66.3 mol%. On the basis of the data from this polyphasic taxonomic study, strain AY-3R T represents a novel species of the genus Altererythrobacter , named Altererythrobacter rhizovicinus sp. nov. (=MCCC 1K03572 T =KCTC 72280 T ).

The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI-B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI-C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations., (© 2019 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.)

The present study aimed to examine the taxonomic relationship between two alphaproteobacterial species, Mabikibacter ruber Choi et al . 2017 and Notoacmeibacter marinus Huang et al . 2017. Comparison of the 16S rRNA gene sequences revealed that they shared 99.9 % sequence similarity. Digital DNA-DNA hybridization (dDDH) estimate (79.8 %) and average nucleotide identity (ANI) value (97.8 %) compared between M. ruber YP382-1-A and N. marinus XMTR2A4 T , were both greater than the threshold for bacterial species delineation, strongly supporting the hypothesis that they represented a single species. Moreover, M. ruber YP382-1-A and N. marinus XMTR2A4 T shared similar physiological and biochemical properties and fatty acid profiles though they displayed distinct colony colours and other minor different properties, including genome size and ability to degrade cellulose, which were presumably due to the presence of a megaplasmid in the genome of M. ruber YP382-1-A. On the basis of the results of genomic analysis, phenotypic and physiological properties, and fatty acid composition, Mabikibacter ruber Choi et al . 2017 is a later heterotypic synonym of Notoacmeibacter marinus Huang et al . 2017 according to the priority of names determined by the date of original publication.

An oval- to rod-shaped, motile, Gram-stain-negative, oxidase-positive, catalase-negative, pink-coloured phototrophic bacterium (designated as strain JA968 T ) was isolated from an estuary near Pata, Gujarat, India. Cells had an intracytoplasmic membrane architecture as lamellae and divided by budding. Strain JA968 T had bacteriochlorophyll- a and spirilloxanthin series carotenoids as photosynthetic pigments. The strain exhibited photolithoautotrophic, photoorganoheterotrophic and chemoorganoheterotrophic growth modes and required thiamine as a growth factor. Strain JA968 T had C 18 : 1 ω7 c /C 18  : 1 ω6 c as the predominant fatty acid with ubiquinone-10 (Q-10) and menaquinone-10 (MK-10) forming the quinone composition. The genomic DNA G+C content of the strain was 63.5 mol%. Pairwise comparison of 16S rRNA gene sequences showed that strain JA968 T was highly similar to Afifella marina DSM 2698 T (99.9 %) and Afifella pfennigii DSM 17143 T (98.4 %). The average nucleotide identity values were 92 % between strain JA968 T and A. marina DSM 2698 T , and 78 % between strain JA968 T and A. pfennigii DSM 17143 T . The digital DNA-DNA hybridization values between strain JA968 T and A. marina and A. pfennigii were 49 and 19 %, respectively. The genomic distinction was also supported by differences in phenotypic and chemotaxonomic characteristics. We propose that strain JA968 T represents a new species of the genus Afifella with the name Afifella aestuarii sp. nov. The type strain is JA968 T (=KCTC 15634 T =NBRC 113338 T ).

Microbial communities in natural ecosystems are subject to strong ecological rules. The study of local communities along a regional metacommunity can reveal patterns of community assembly, and disentangle the underlying ecological processes. In particular, we seek drivers of community assembly at the regional scale using a large lacustrine dataset (>300 lakes) along the geographical, limnological and physico-chemical gradients in the Pyrenees. By using high throughput amplicon sequencing of the 16S rRNA gene, and inferring environmental sources of bacterial immigrants, we showed that surface aquatic bacterial assemblages were strongly influenced by terrestrial populations from soil, biofilms or sediments, and primarily selected by a pH-alkalinity gradient. Indeed, source proportions explained 27% of the community variation, and chemistry 15% of the total variation, half of it shared with the sources. Major taxonomic groups such as Verrucomicrobia, Actinobacteria and Bacteroidetes showed higher aquatic affinities than Parcubacteria, Gammaproteobacteria, Alphaproteobacteria or Betaproteobacteria, which may be recruited and selected through different hydrographic habitats. A regional fingerprint was observed with lower alpha diversity and higher beta diversity in the central Pyrenees than in both ends. We suggest an ecological succession process, likely influenced by complex interactions of environmental source dispersal and environmental filtering along the mountain range geography., (© 2019 Society for Applied Microbiology and John Wiley & Sons Ltd.)

A novel alphaproteobacterium, strain WS11 T , was isolated from a deep-sea sediment sample collected from the New Britain Trench. The full-length 16S rRNA gene of strain WS11 T had the highest sequence similarity of 97.6 % to Rhizobium subbaraonis JC85 T , followed by Mycoplana ramosa DSM 7292 T (96.9 %) and Rhizobium azooxidifex Po 20/26 T (96.8 %). Phylogenetic analysis of concatenated 16S rRNA, atpD and recA gene sequences showed that strain WS11 T was deeply separated from the species within the family Rhizobiaceae . Phylogenomic analysis based on the whole-genome protein sequences showed that strain WS11 T formed an independent monophyletic branch in the family Rhizobiaceae , paralleled with the species in the families Brucellaceae and Phyllobacteriaceae within the order Rhizobial es. Cells were Gram-stain-negative, oxidase- and catalase-positive, and aerobic short rods (1.5-2.4×0.9-1.0 µm). Growth was observed at salinities ranging from 0 to 5% (optimum, 1 %), from pH 6.5 to 9 (optimum, pH 7) and at temperatures between 20 and 30 °C (optimum, 28 °C). Strain WS11 T was piezotolerant, growing optimally at 0.1 MPa (range 0.1-70 MPa). The main fatty acid was summed feature 8 (C 18 : 1 ω 7 c /C 18  : 1 ω 6c ). The sole respiratory quinone was ubiquinone-10 (Q-10). The predominant polar lipids were phosphatidylcholine, two unidentified aminophospholipids and an unidentified phospholipid. The genome size was about 4.36 Mbp and the G+C content was 62.3 mol%. The combined genotypic and phenotypic data show that strain WS11 T represents a novel species of a novel genus in the family Rhizobiaceae , for which the name Georhizobium profundi gen. nov., sp. nov. is proposed (type strain WS11 T =MCCC 1K03498 T =KCTC 62439 T ).

Phagocytosis is a key eukaryotic feature, conserved from unicellular protists to animals, that enabled eukaryotes to feed on other organisms. It could also be a driving force behind endosymbiosis, a process by which α-proteobacteria and cyanobacteria evolved into mitochondria and plastids, respectively. Here we describe a planctomycete bacterium, 'Candidatus Uab amorphum', which is able to engulf other bacteria and small eukaryotic cells through a phagocytosis-like mechanism. Observations via light and electron microscopy suggest that this bacterium digests prey cells in specific compartments. With the possible exception of a gene encoding an actin-like protein, analysis of the 'Ca. Uab amorphum' genomic sequence does not reveal any genes homologous to eukaryotic phagocytosis genes, suggesting that cell engulfment in this microorganism is probably not homologous to eukaryotic phagocytosis. The discovery of this "phagotrophic" bacterium expands our understanding of the cellular complexity of prokaryotes, and may be relevant to the origin of eukaryotic cells.

A Gram-stain-negative, non-spore-forming, non-motile, short-rod-shaped and aerobic bacterial strain (designated lm1 T ) was isolated from propylene oxide saponification wastewater activated sludge obtained from a wastewater treatment facility in Binzhou (Shandong province, PR China). Strain lm1 T grew between 15 and 45 °C (optimum, 40 °C). The pH range for growth was at pH 4.0-10.0 (optimum growth at pH 8.0). The range of NaCl concentration for the growth of strain lm1 T was 0-4.0 % (w/v), with optimum growth at 1.0-2.0 % (w/v). Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain lm1 T belonged to the genus Rhodoligotrophos and was closely related to Rhodoligotrophos appendicifer JCM 16873 T (96.7 % 16S rRNA gene sequence similarity) and Rhodoligotrophosjinshengii CCTCC AB2013083 T (96.2 %). The average nucleotide identity value and the digital DNA-DNA hybridization value between strain lm1 T and R. appendicifer JCM 16873 T were 73.4 and 14.3 %, respectively. The major cellular fatty acids of strain lm1 T were C 19 : 0 cyclo ω8 c , C 18 : 1 ω7 c and C 16 : 0 . Strain lm1 T contained Q-10 as the predominant respiratory quinone. The polar lipid profile was composed of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, three unidentified aminolipids, one unidentified glycolipid and five unknown lipids. The G+C content of the genomic DNA was 64.4 mol%. Based on polyphasic taxonomic data, strain lm1 T could be classified as a representative of a novel species of the genus Rhodoligotrophos , for which the name Rhodoligotrophosdefluvii sp. nov. is proposed. The type strain is lm1 T (=CCTCC AB2019071 T =KCTC 72156 T ).

A Gram-stain-negative, rod-shaped, non-motile, aerobic, catalase-negative and oxidase-positive bacterium, designated strain Sn-9-2 T , was isolated from a cave soil sample collected from Tiandong cave, Guizhou Province, south-west PR China. Growth occurred at 15-40 °C (optimum, 30 °C), at pH 5.0-9.0 (optimum, pH 7.0-8.0) and with 0-1 % NaCl (w/v). The predominant respiration quinone was ubiquinone-10 (Q-10). The major cellular fatty acids were summed feature 8 (C 18 : 1 ω7 c or C 18 : 1 ω6 c ; 83.9 %) and C 16 : 0 (5.8 %). The major polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, three unidentified phospholipids, two unidentified glycolipids, two unidentified polar lipids and one unidentified aminolipid. The DNA G+C content of strain Sn-9-2 T was 67.5 mol%. Based on the results of 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain Sn-9-2 T (MF958452) were identified as Aquabacter spiritensis (FR733686) DSM 9035 T (97.5 %), Xanthobacter autorophicus (jgi.1053054) DSM 432 T (97.2 %) and Xanthobacter tagetidis ATCC 700314 T RCTF01000015 (96.9 %). The average nucleotide identity values were 78.0, 77.4 and 77.6 % and the digital DNA-DNA hybridization values were 21.8, 22.0 and 18.8 % between strain Sn-9-2 T and A. spiritensis DSM 9035 T , X. autotrophicus DSM 432 T and X. tagetidis DSM 11105 T , respectively. The DNA-DNA hybridization data indicated that strain Sn-9-2 T represented a novel genomic species. On the basis of the results of phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA-DNA hybridization data, strain Sn-9-2 T should represent a novel species of the genus Aquabacter , for which the name Aquabactercavernae sp. nov. is proposed. The type strain is Sn-9-2 T (=KCTC 62308 T =CCTCC AB 2018270 T ).

Two Gram-stain-negative, facultative anaerobic chemoheterotrophic, pink-coloured, rod-shaped and non-motile bacterial strains, PAMC 29128 and PAMC 29148 T , were isolated from lichen. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strains PAMC 29128 and PAMC 29148 T belong to lichen-associated Rhizobiales -1 (LAR1), an uncultured phylogenetic lineage of the order Rhizobiales and the most closely related genera were Methylocapsa (<93.9 %) and Methylosinus (<93.8 %). The results of phylogenomic and genomic relatedness analyses also showed that strains PAMC 29128 and PAMC 29148 T were clearly distinguished from other species in the order Rhizobiales with average nucleotide identity values of <71.4 % and genome-to-genome distance values of <22.7 %. Genomic analysis revealed that strains PAMC 29128 and PAMC 29148 T did not contain genes involved in atmospheric nitrogen fixation or utilization of carbon compounds such as methane and methanol. Strains PAMC 29128 and PAMC 29148 T were able to utilize certain monosaccharides, disaccharides, sugar alcohols and other organic compounds as a sole carbon source. The major fatty acids (>10 %) were summed feature 8 (C 18 : 1  ω7 c and/or C 18 : 1  ω6 c ; 33.7-39.7 %), summed feature 3 (C 16 : 1 ω7 c and/or C 16:1 ω 6c ; 25.2-25.4 %) and C 19 :0 cyclo ω8 c (11.9-15.4 %). The major respiratory quinone was Q-10. The genomic DNA G+C contents of PAMC 29128 and PAMC 29148 T were 63.0 and 63.1 mol%, respectively. Their distinct phylogenetic position and some physiological characteristics support the proposal of Lichenihabitans gen. nov., with the type species Lichenihabitans psoromatis sp. nov. (type strain, PAMC 29148 T =KCCM 43293 T =JCM 33311 T ). Lichenihabitantaceae fam. nov. is also proposed.

A number of anaerobic ciliates, unicellular eukaryotes, intracellularly possess methanogenic archaea and bacteria as symbiotic partners. Although this tripartite relationship is of interest in terms of the fact that each participant is from a different domain, the difficulty in culture and maintenance of those host species with symbiotic partners has disturbed both ecological and functional studies so far. In this study, we obtained a stable culture of a small anaerobic scuticociliate, strain GW7. By transmission electron microscopic observation and fluorescent in situ hybridization with domain-specific probes, we demonstrate that GW7 possesses both archaeal and bacterial endosymbionts in its cytoplasm. These endosymbionts are in dependently associated with hydrogenosomes, which are organelle producing hydrogen and ATP under anaerobic conditions. Clone library analyses targeting prokaryotic 16S rRNA genes, fluorescent in situ hybridization with endosymbiont-specific probes, and molecular phylogenetic analyses revealed the phylogenetic affiliations and intracellular localizations of these endosymbionts. The endosymbiotic archaeon is a methanogen belonging to the genus Methanoregula (order Methanomicrobiales ); a member of this genus has previously been described as the endosymbiont of an anaerobic ciliate from the genus Metopus (class Armophorea), which is only distantly related to strain GW7 (class Oligohymenophorea). The endosymbiotic bacterium belongs to the family Holosporaceae of the class Alphaproteobacteria , which also comprises several endosymbionts of various aerobic ciliates. For this endosymbiotic bacterium, we propose a novel candidate genus and species, " Candidatus Hydrogenosomobacter endosymbioticus." IMPORTANCE Tripartite symbioses between anaerobic ciliated protists and their intracellular archaeal and bacterial symbionts are not uncommon, but most reports have been based mainly on microscopic observations. Deeper insights into the function, ecology, and evolution of these fascinating symbioses involving partners from all three domains of life have been hampered by the difficulties of culturing anaerobic ciliates in the laboratory and the frequent loss of their prokaryotic partners during long-term cultivation. In the present study, we report the isolation of an anaerobic scuticociliate, strain GW7, which has been stably maintained in our laboratory for more than 3 years without losing either of its endosymbionts. Unexpectedly, molecular characterization of the endosymbionts revealed that the bacterial partner of GW7 is phylogenetically related to intranuclear endosymbionts of aerobic ciliates. This strain will enable future genomic, transcriptomic, and proteomic analyses of the interactions in this tripartite symbiosis and a comparison with endosymbioses in aerobic ciliates., (Copyright © 2019 American Society for Microbiology.)

The low temperature and elevated hydrostatic pressure in hadal trenches at water depths below 6000 m render sample collection difficult. Here, in situ hadal water microbial samples were collected from the Mariana Trench and analysed. The hadal microbial communities at different depths were revealed to be consistent and were dominated by heterotrophic Marinimicrobia. Thirty high-quality metagenome-assembled genomes (MAGs) were retrieved to represent the major hadal microbes affiliated with 12 prokaryotic phyla. Most of the MAGs were newly reported and probably derived from novel hadal inhabitants as exemplified by a potentially new candidate archaeal phylum in the DPANN superphylum. Metabolic reconstruction indicated that a great number of the MAGs participated in nitrogen and sulfur cycling, in which the nitrification process was driven sequentially by Thaumarchaeota and Nitrospirae and sulfur oxidization by Rhodospirillales in the Alphaproteobacteria class. Moreover, several groups of hadal microbes were revealed to be potential carbon monoxide oxidizers. Metatranscriptomic result highlighted the contribution of Chloroflexi in degrading recalcitrant dissolved organic matter and Marinimicrobia in extracellular protein decomposition. The present work provides an in-depth view on the hadal microbial communities regarding their endemism and element cycles., (© 2019 Society for Applied Microbiology and John Wiley & Sons Ltd.)

A novel, Gram-stain-negative marine bacterium, designated GH2-6 T , was isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia) collected in Gangwha Island, the Republic of Korea. The cells of the organism were strictly aerobic, oxidase- and catalase-positive, non-flagellated rods. Growth occurred at 20-45°C, pH 5-10, and 0.5-9 (w/v) NaCl. The requirement of Na + for growth (0.5-3%) was observed. The major respiratory quinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an aminolipid and a glycolipid. The predominant fatty acids were C 18:1 ω7c, C 18:0 , C 16:0 , C 19:0 cyclo ω8c, C 18:1 ω7c 11-methyl and summed feature 2 (C 14:0 3-OH and/or C 16:1 iso I). The genome size was 4.45 Mb and the G+C content of the genomic DNA was 61.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GH2-6 T belonged to genus Martelella and formed a tight cluster with M. radicis BM5-7 T and M. endophytica YC6887 T . Levels of 16S rRNA gene sequence similarity between the novel isolate and members of the genus were 99.3-95.5%, but strain GH2-6 T possessed an extended loop (49 nucleotides in length) between positions 187 and 213 of the 16S rRNA gene sequence (E. coli numbering). DDH values in vitro between the novel isolate and the closest relatives were 23.2±12.8-46.3±5.2%. On the basis of polyphasic data presented in this study, the type strain GH2-6 T (= KACC 19403 T = KCTC 62125 T = NBRC 113212 T ) represents a novel species of the genus Martelella for which the name Martelella lutilitoris sp. nov. is proposed.

Many of the sequenced bacterial and archaeal genomes encode regions of viral provenance. Yet, not all of these regions encode bona fide viruses. Gene transfer agents (GTAs) are thought to be former viruses that are now maintained in genomes of some bacteria and archaea and are hypothesized to enable exchange of DNA within bacterial populations. In Alphaproteobacteria, genes homologous to the "head-tail" gene cluster that encodes structural components of the Rhodobacter capsulatus GTA (RcGTA) are found in many taxa, even if they are only distantly related to Rhodobacter capsulatus. Yet, in most genomes available in GenBank RcGTA-like genes have annotations of typical viral proteins, and therefore are not easily distinguished from their viral homologs without additional analyses. Here, we report a "support vector machine" classifier that quickly and accurately distinguishes RcGTA-like genes from their viral homologs by capturing the differences in the amino acid composition of the encoded proteins. Our open-source classifier is implemented in Python and can be used to scan homologs of the RcGTA genes in newly sequenced genomes. The classifier can also be trained to identify other types of GTAs, or even to detect other elements of viral ancestry. Using the classifier trained on a manually curated set of homologous viruses and GTAs, we detected RcGTA-like "head-tail" gene clusters in 57.5% of the 1,423 examined alphaproteobacterial genomes. We also demonstrated that more than half of the in silico prophage predictions are instead likely to be GTAs, suggesting that in many alphaproteobacterial genomes the RcGTA-like elements remain unrecognized., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

A Gram-negative, aerobic, short rodshaped, asporogenous bacterium, designated CBS5Q-3 T , was isolated from a surface-sterilised root of Ficus microcarpa Linn. f. collected from Guangxi, China and investigated by a polyphasic approach to determine its taxonomic position. Strain CBS5Q-3 T was found to grow optimally with 2% (w/v) NaCl at 30 °C, pH 7.0-8.0. Substrate mycelia and aerial mycelia were not formed, and no diffusible pigments were observed on the media tested. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBS5Q-3 T is closely related to species of genus Jiella and shares high 16S rRNA gene sequence similarity of 98.1% with Jiella aquimaris JCM 30119 T . The average nucleotide identity and in silico DNA-DNA hybridization values between strain CBS5Q-3 T and J. aquimaris JCM 30119 T were 82.8% and 26.0%, respectively. The DNA G + C content of strain CBS5Q-3 T was determined to be 66.5 mol %. The cell wall peptidoglycan was found to contain meso-diaminopimelic acid and ubiquinone Q-10 identified as the respiratory lipoquinone. The polar lipids were found to be comprised of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and three unidentified aminolipids, while the major fatty acids were identified as C 18:1 ω7c and cyclo-C 19:0 ω8c. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain CBS5Q-3 T can be concluded to represent a novel species of the genus Jiella, for which the name Jiella endophytica sp. nov. is proposed. The type strain is CBS5Q-3 T (= JCM 33167 T  = CGMCC 1.13863 T ).

A Gram-stain-negative, rod-shaped and facultative anaerobic strain named YE-B6 T was isolated from the intestine of abalone, Haliotis discus hannai . The reactions of oxidase and catalase were both positive. Strain YE-B6 T could grow at 10-37 °C (optimum, 28-33 °C), at pH 7-9 (optimum, pH 7) and in salinity of 0-8 % NaCl (w/v; optimum, 2 %). The 16S rRNA gene sequence of strain YE-B6 T had maximum sequence similarities to Cohaesibacter celericrescens H1304 T (98.0 %), Cohaesibacter marisflavi DQHS21 T (97.4 %), Cohaesibacter haloalkalitolerans JC131 T (97.4 %) and Cohaesibacter gelatinilyticus CL-GR15 T (97.3 %). Results of phylogenetic analysis showed that it was affiliated to the genus Cohaesibacter within the order Rhizobiales in the Alphaproteobacteria . The respiratory quinone of strain YE-B6 T was Q-10. The cellular fatty acids mainly comprised C 18 : 1 ω 7 c and summed feature 3 (C 16 : 1 ω6 c and/or C 16 : 1 ω7 c ). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, two unidentified aminolipids, two unidentified polar lipids and one unidentified phospholipid. The G+C content of strain YE-B6 T was 55.6 mol%. Based on its genotypic, physiological and biochemical characteristics, strain YE-B6 T represented a novel species within the genus Cohaesibacter , for which the name Cohaesibacterintestini sp. nov. is proposed. The type strain of the new species is YE-B6 T (=MCCC 1A13131 T =KCTC 62716 T ).

Members of the SAR11 order Pelagibacterales dominate the surface oceans. Their extensive diversity challenges emerging operational boundaries defined for microbial 'species' and complicates efforts of population genetics to study their evolution. Here, we employed single-amino acid variants (SAAVs) to investigate ecological and evolutionary forces that maintain the genomic heterogeneity within ubiquitous SAR11 populations we accessed through metagenomic read recruitment using a single isolate genome. Integrating amino acid and protein biochemistry with metagenomics revealed that systematic purifying selection against deleterious variants governs non-synonymous variation among very closely related populations of SAR11. SAAVs partitioned metagenomes into two main groups matching large-scale oceanic current temperatures, and six finer proteotypes that connect distant oceanic regions. These findings suggest that environmentally-mediated selection plays a critical role in the journey of cosmopolitan surface ocean microbial populations, and the idea 'everything is everywhere but the environment selects' has credence even at the finest resolutions., Competing Interests: TD, EK, OK, OE, IU, MR, SG, AE No competing interests declared, (© 2019, Delmont et al.)

Qipengyuania sediminis CGMCC 1.12928 T , a family member of Erythrobacteraceae, the class of Alphaproteobacteria, was isolated from a borehole sediment sample collected from Qiangtang Basin in Qinghai-Tibetan Plateau, the largest permafrost in China. Understanding bacterial molecular feature may shed light on the ecological strategy in the extreme environment. Here we describe the complete genome sequence and annotation of strain CGMCC 1.12928 T , including the complete genome sequence and annotation. The genome of strain CGMCC 1.12928 T consist of a single-circular chromosome, comprises 2,416,000 bp with an average G + C content of 66.7 mol%, and contains 2414 genes; including 2367 CDSs, 44 tRNA genes, as well as one operon of 16S-23S-5S rRNA genes. Genomic properties indicated that strain CGMCC 1.12928 T has a relatively smaller genome size and higher G + C content within the family Erythrobacteraceae. In addition, genomic analysis revealed its genome contains multiple function genes responsible for nitrogen, sulfur and phosphorus cycles and explained the cold adaption mechanism. Thus, this strain plays an active role in the biogeochemical cycle in cold niche. The whole-genome of this isolate will widen our understanding of the ecological role of the genus Qipengyuania in permafrost.

Rickettsiales are a lineage of obligate intracellular Alphaproteobacteria, encompassing important human pathogens, manipulators of host reproduction, and mutualists. Here we report the discovery of a novel Rickettsiales bacterium associated with Paramecium, displaying a unique extracellular lifestyle, including the ability to replicate outside host cells. Genomic analyses show that the bacterium possesses a higher capability to synthesise amino acids, compared to all investigated Rickettsiales. Considering these observations, phylogenetic and phylogenomic reconstructions, and re-evaluating the different means of interaction of Rickettsiales bacteria with eukaryotic cells, we propose an alternative scenario for the evolution of intracellularity in Rickettsiales. According to our reconstruction, the Rickettsiales ancestor would have been an extracellular and metabolically versatile bacterium, while obligate intracellularity would have evolved later, in parallel and independently, in different sub-lineages. The proposed new scenario could impact on the open debate on the lifestyle of the last common ancestor of mitochondria within Alphaproteobacteria.

A Gram-stain-negative, aerobic, flagellated, rod-shaped bacterial strain, SM1705 T , was isolated from a surface seawater sample collected from the South China Sea. The strain grew at 10-40 °C and with 0.5-13.0 % (w/v) NaCl. It hydrolysed Tweens 20, 40 and 60, but did not hydrolyse starch or Tween 80 nor reduce nitrate to nitrite. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM1705 T was affiliated with the genus Parvularcula, sharing the highest sequence similarity (96.0 %) with type strain of Parvularcula bermudensis and forming a coherent branch together with the latter within the clade of Parvularcula. The major cellular fatty acids were identified as summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C18 : 0. Polar lipids included three unidentified glycolipids and one unidentified lipid. The major respiratory quinone of strain SM1705 T was Q10. The genomic DNA G+C content of strain SM1705 T was 59.3 mol%. Based on the polyphasic evidence presented in this paper, strain SM1705 T represents a novel Parvularcula species, for which the name Parvularcula marina sp. nov. is proposed. The type strain is SM1705 T (=KCTC 62795 T =MCCC 1K03505 T =CCTCC AB 2018345 T ).

A novel Gram-stain-negative, aerobic, oxidase-positive, motile, dimorphic rod bacterium, with a polar flagellum or a polar prostheca, designated as strain WD6-1 T , was isolated from a sediment sample collected from a marine solar saltern located in Weihai, PR China. Growth of strain WD6-1 T was observed at 15-45 °C (optimum, 37-40 °C). The pH range for growth was pH 6.0-9.5 (optimum, pH 7.0-7.5) while the NaCl concentration was 1.0-16.0 % (w/v; optimum, 5.0 %). The most closely related species was Marinicauda algicola (97.0 % 16S rRNA gene sequence similarity). The DNA G+C content of strain WD6-1 T was 69.5 mol% and the sole respiratory quinone was ubiquinone 10 (Q-10). The major cellular fatty acids (>10 %) of strain WD6-1 T included summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C18 : 0 and C17 : 0, and the major polar lipids were glucuronopyranosyldiglyceride, monoglycosyldiglyceride and sulfo-quinovosyl diacylglycerol. Based on the results of phylogenetic, genotypic and phenotypic analyses, the isolate is representative of a new member of the genus Marinicauda, for which the name Marinicaudasalina sp. nov. is proposed. The type strain is WD6-1 T (=KCTC 62348 T =MCCC 1H00282 T ).

A novel endophytic bacterium, designated strain SX2RGS8 T , was isolated from the surface-sterilized roots of an endangered medicinal plant (Ferula sinkiangensis K. M. Shen) collected from Xinjiang, north-western PR China. The taxonomic position of the candidate was investigated using a polyphasic approach. Strain SX2RGS8 T was found to be aerobic, Gram-stain-negative, oxidase-negative, catalase-positive and axiolitic-shaped. Strain SX2RGS8 T grew at 4-45 °C (optimum, 28 °C), pH 4.0-10.0 (pH 7.0) and in the presence of 0-5 % (w/v) NaCl. The polar lipids detected for strain SX2RGS8 T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, unidentified phosphoglycolipids, an unidentified phospholipid and unidentified lipids. The major respiratory quinone of strain SX2RGS8 T was ubiquinone 10 and the major fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content was determined to be 66.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate belonged to the family Erythrobacteraceae and showed 99.2 % (Porphyrobacter mercurialis), 95.5 % (Porphyrobacter donghaensisi) and 95.4 % (Porphyrobacter colymbi) similarities to its closest relatives. The isolate contained carotenoids, but no bacteriochlorophyll a. On the basis of phenotypic, genotypic and phylogenetic data, strain SX2RGS8 T represents a novel species of a novel genus in the family Erythrobacteraceae, for which the name Croceibacterium ferulae gen. nov., sp. nov. is proposed. The type strain is SX2RGS8 T (=CGMCC 1.16402 T =KCTC 62090 T ). In addition, Porphyrobacter mercurialis Coil et al. 2016 is proposed to be transferred to this new genus as Croceibacterium mercuriale comb. nov.

A Gram-negative, aerobic, short-rod-shaped, motile (with a terminal flagellum), non-spore-forming bacterium, designated strain 85 T , was isolated from a surface-sterilized bark of Sonneratia caseolaris collected from Qinzhou in Guangxi, China and was analyzed using a polyphasic approach to determine its taxonomic position. Strain 85 T grew optimally in the presence of 1-2% (w/v) NaCl at 30°C and pH 6.0-7.0. Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain 85 T belonged to the genus Fulvimarina and shared the highest 16S rRNA gene sequence similarity with Fulvimarina pelagi HTCC2506 T (96.16%). The cell-wall peptidoglycan contained meso-diaminopimelic acid and ubiquinone Q-10 was the predominant respiratory lipoquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified amino lipid, three unidentified phospholipids and six unidentified lipids. The major fatty acid was C 18:1 ω7c. The DNA G+C content of strain 85 T was 65.4 mol%, and the average nucleotide identity and estimated DDH values between strain 85 T and the type strain of Fulvimarina pelagi HTCC2506 T were 77.3% and 21.7%, respectively. Based on the phylogenetic, phenotypic, and chemotaxonomic analyses, strain 85 T should be considered as a novel species of the genus Fulvimarina with the proposed name Fulvimarina endophytica sp. nov., and its type strain is 85 T (= KCTC 62717 T = CGMCC 1.13665 T ).

Strain IMCC1322 was isolated from a surface water sample from the East Sea of Korea. Based on 16S rRNA analysis, IMCC1322 was found to belong to the OCS28 sub-clade of SAR116. The cells appeared as short vibrioids in logarithmic-phase culture, and elongated spirals during incubation with mitomycin or in aged culture. Growth characteristics of strain IMCC1322 were further evaluated based on genomic information; proteorhodopsin (PR), carbon monoxide dehydrogenase, and dimethylsulfoniopropionate (DMSP)-utilizing enzymes. IMCC1322 PR was characterized as a functional retinylidene protein that acts as a light-driven proton pump in the cytoplasmic membrane. However, the PR-dependent phototrophic potential of strain IMCC1322 was only observed under CO-inhibited and nutrient-limited culture conditions. A DMSP-enhanced growth response was observed in addition to cultures grown on C 1 compounds like methanol, formate, and methane sulfonate. Strain IMCC1322 cultivation analysis revealed biogeochemical processes characteristic of the SAR116 group, a dominant member of the microbial community in euphotic regions of the ocean. The polyphasic taxonomy of strain IMCC1322 is given as Candidatus Puniceispirillum marinum, and was confirmed by chemotaxonomic tests, in addition to 16S rRNA phylogeny and cultivation analyses.

A taxonomic study was carried out on strain HN-Y73 T , which was isolated from sponge collected from Yangpu Bay, Hainan, PR China. Strain HN-Y73 T was Gram-stain-negative, non-motile, ovoid- to rod-shaped, yellow-pigmented and could grow at 10-42 °C (optimum, 28 °C), at pH 5.0-9.0 (pH 8.0) and in 0.5-16 % (w/v) NaCl (3-4 %). This isolate was positive for oxidase, catalase and the hydrolysis of aesculin and xylan, but negative for the hydrolysis of casein and gelatin. Strain HN-Y73 T shared the highest 16S rRNA gene sequence similarity with Altererythrobacter endophyticus BR75 T (96.9 %), followed by Altererythrobacter estronivorus MH-B5 T (96.0 %), Altererythrobacter indicus MSSRF26 T (95.9 %) and Altererythrobacter mangrovi C9-11 T (95.7 %). The phylogenetic tree showed that strain HN-Y73 T forms a clade with A. endophyticus BR75 T , A. indicus MSSRF26 T and A. estronivorus MH-B5 T within the genus Altererythrobacter. The dominant fatty acids were summed feature 8 (C18 : 1ω7c/ω6c) and C19 : 0cyclo ω8c. The major polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, sphingoglycolipid phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, one unidentified glycolipid, two unidentified phospholipids and four unidentified lipids. The respiratory lipoquinone was identified as Q-10. The G+C content of the genomic DNA was 57.6 mol%. Based on the phenotypic and phylogenetic data, strain HN-Y73 T represents a novel species of the genus Altererythrobacter, for which the name Altererythrobacter spongiae sp. nov. is proposed. The type strain is HN-Y73 T (=MCCC 1K03324 T =LMG 30461 T ).

A marine proteobacterium, designated strain GH1-16 T , was isolated from a sample of tidal mudflat collected at the seashore of Gangwha Island, Republic of Korea and the taxonomic status was examined by a polyphasic approach. The isolate was Gram-reaction-negative, strictly aerobic, catalase- and oxidase-positive, non-motile, short-rod-shaped and produced yellow-coloured colonies. An absolute requirement for Na + was observed. The major respiratory quinone was ubiquinone-10. The major polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. The dominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C17 : 1ω6c. The DNA G+C content was 60.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GH1-16 T was closely related to members of the genus Altererythrobacter. The closest relative was Altererythrobacter marensis MSW-14 T (97.3 % sequence similarity) followed by Altererythrobacter aquaemixtae JSSK-8 T (96.8 %) and Altererythrobacter epoxidivorans JCS350 T (96.7 %). The DNA relatedness of strain GH1-16 T against its closest relative was 21.8-25.0 %. On the basis of data obtained by a polyphasic taxonomic approach, strain GH1-16 T (=KCTC 52845 T =NBRC 113275 T ) is considered to represent a novel species of the genus Altererythrobacter, for which the name Altererythrobacter lutipelagi sp. nov. is proposed.

The ubiquitous alpha-proteobacteria of the order "Candidatus Pelagibacterales" (SAR11) are highly abundant in aquatic environments, and among them, members of the monophyletic lineage LD12 (also known as SAR11 clade IIIb) are specifically found in lacustrine ecosystems. Clade IIIb bacteria are some of the most prominent members of freshwater environments, but little is known about their biology due to the lack of genome representatives. Only recently, the first non-marine isolate was cultured and described as "Candidatus Fonsibacter ubiquis". Here, we expand the collection of freshwater IIIb representatives and describe a new IIIb species of the genus "Ca. Fonsibacter". Specifically, we assembled a collection of 67 freshwater metagenomic datasets from the interconnected lakes of the Chattahoochee River basin (GA, USA) and obtained nearly complete metagenome-assembled genomes (MAGs) representing 5 distinct IIIb subclades, roughly equivalent to species based on genomic standards, including the previously described "Ca. F. ubiquis". Genomic comparisons between members of the IIIb species revealed high similarity in gene content. However, when comparing their abundance profiles in the Chattahoochee basin and various aquatic environments, differences in temporal and spatial distributions among the distinct species were observed implying niche differentiation might be underlying the coexistence of the highly functionally similar representatives. The name Ca. Fonsibacter lacus sp. nov. is proposed for the most abundant and widespread species in the Chattahoochee River basin and various freshwater ecosystems., (Copyright © 2019 Elsevier GmbH. All rights reserved.)

Marine bacterioplankton face stiff competition for limited nutrient resources. SAR11, a ubiquitous clade of very small and highly abundant Alphaproteobacteria, are known to devote much of their energy to synthesizing ATP-binding cassette periplasmic proteins that bind substrates. We hypothesized that their small size and relatively large periplasmic space might enable them to outcompete other bacterioplankton for nutrients. Using uptake experiments with 14 C-glycine betaine, we discovered that two strains of SAR11, Candidatus Pelagibacter sp. HTCC7211 and Cand. P. ubique HTCC1062, have extraordinarily high affinity for glycine betaine (GBT), with half-saturation (K s ) values around 1 nM and specific affinity values between 8 and 14 L mg cell -1  h -1 . Competitive inhibition studies indicated that the GBT transporters in these strains are multifunctional, transporting multiple substrates in addition to GBT. Both strains could use most of the transported compounds for metabolism and ATP production. Our findings indicate that Pelagibacter cells are primarily responsible for the high affinity and multifunctional GBT uptake systems observed in seawater. Maximization of whole-cell affinities may enable these organisms to compete effectively for nutrients during periods when the gross transport capacity of the heterotrophic plankton community exceeds the supply, depressing ambient concentrations., (© 2019 Society for Applied Microbiology and John Wiley & Sons Ltd.)

A novel marine bacterium, designated strain GH1-24 T , was isolated from a tidal mudflat sample collected at Gangwha Island, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequence comparison exhibited that the novel isolate was most closely related to Sneathiella and formed a tight cluster with Sneathiella glossodoripedis JCM 23214 T with 98.1 % sequence similarity. The 16S rRNA gene sequence similarities to other Sneathiella species were low: Sneathiella chinensis LMG 23452 T (96.1 %) and Sneathiellachungangensis CAU 1294 T (95.8 %). Cells of the organism were Gram-reaction-negative, strictly aerobic, catalase- and oxidase-positive, motile rods and showed growth at 0.5-6 % NaCl, 20-42 °C and pH 6.0-8.0. The G+C content of the DNA was 54.9 mol%. The major isoprenoid quinone was Q-10. The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and C19 : 0cyclo ω8c. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The results of phenotypic and phylogenetic analyses and DNA-DNA relatedness studies suggest that the isolate can be a member of a novel species of the genus Sneathiella, for which the name Sneathiellalimimaris sp. nov. is proposed. The type strain is GH1-24 T (=KCTC 52846 T =NBRC 113276 T ).

A Gram-stain negative, aerobic, coccus-shaped bacterium, designated strain M2BS9Y-3-1 T , was isolated from a surface-sterilized leaf of Rhizophora stylosa. It grew in the pH range 5.0-9.0 (optimum, 7.0) and at temperatures between 20 and 37 °C (optimum, 30 °C). Growth was possible at concentrations of 1-10% (w/v) NaCl (optimum, 2%). The phylogenetic trees based on 16S rRNA gene sequences indicated that strain M2BS9Y-3-1 T clustered together with Notoacmeibacter marinus XMTR2A4 T (98.44% similarity) and separated from other species of the family Notoacmeibacteraceae. The average nucleotide identity and in silico DNA-DNA hybridization values between strain M2BS9Y-3-1 T and N. marinus XMTR2A4 T were 76.8%, 19.8%, respectively. The G+C content of the genomic DNA was 60.0 mol%. The cell wall peptidoglycan contained meso-diaminobutyric acid and ubiquinone Q-10 was the respiratory lipoquinone. The major fatty acid was C 18:1 ω7c. The lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, an unidentified aminophospholipid and three unidentified lipids. The results of taxonomic analysis suggested that strain M2BS9Y-3-1 T represents a novel species of the genus Notoacmeibacter for which the name Notoacmeibacter ruber sp. nov. is proposed. The type strain is M2BS9Y-3-1 T (KCTC 62838 T  = CGMCC 1.13746 T ).

A new aerobic alphaproteobacterium, strain SA-279 T , was isolated from a water sample of a crater lake. The 16S rRNA gene sequence analysis revealed that strain SA-279 T formed a distinct lineage within the family Ancalomicrobiaceae and shared the highest pairwise similarity values with Pinisolibacterravus E9 T (96.4 %) and Ancalomicrobiumadetum NBRC 102456 T (94.2 %). Cells of strain SA-279 T were rod-shaped, motile, oxidase and catalase positive, and capable of forming rosettes. Its predominant fatty acids were C18 : 1ω7c (69.0 %) and C16 : 1ω7c (22.7 %), the major respiratory quinone was Q-10, and the main polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified aminophospholipid and an unidentified lipid. The G+C content of the genomic DNA of strain SA-279 T was 69.2 mol%. On the basis of the phenotypic, chemotaxonomic and molecular data, strain SA-279 T is considered to represent a new genus and species within the family Ancalomicrobiaceae, for which the name Siculibacillus lacustris gen. nov., sp. nov. is proposed. The type strain is SA-279 T (=DSM 29840 T =JCM 31761 T ).