Elioraea tepida, sp. nov., a Moderately Thermophilic Aerobic Anoxygenic Phototrophic Bacterium Isolated from the Mat Community of an Alkaline Siliceous Hot Spring in Yellowstone National Park, WY, USA

Strain MS-P2T was isolated from microbial mats associated with Mushroom Spring, an alkaline siliceous hot spring in Yellowstone National Park, WY, USA. The isolate grows chemoheterotrophically by oxygen-dependent respiration, and light stimulates photoheterotrophic growth under strictly oxic conditions. Strain MS-P2T synthesizes bacteriochlorophyll a and the carotenoid spirilloxanthin. However, photoautotrophic growth did not occur under oxic or anoxic conditions, suggesting that this strain should be classified as an aerobic anoxygenic phototrophic bacterium. Strain MS-P2T cells are motile, curved rods about 0.5 to 1.0 μm wide and 1.0 to 1.5 μm long. The optimum growth temperature is 45-50 °C, and the optimum pH for growth is circum-neutral (pH 7.0-7.5). Sequence analysis of the 16S rRNA gene revealed that strain MS-P2T is closely related to Elioraea species, members of the class Alphaproteobacteria, with a sequence identity of 96.58 to 98%. The genome of strain MS-P2T is a single circular DNA molecule of 3,367,643 bp with a mol% guanine-plus-cytosine content of 70.6%. Based on phylogenetic, physiological, biochemical, and genomic characteristics, we propose this bacteriochlorophyll a-containing isolate is a new species belonging to the genus Elioraea, with the suggested name Elioraeatepida. The type-strain is strain MS-P2T (= JCM33060T = ATCC TSD-174T).

Roseococcus microcysteis sp. nov., isolated from a Microcystis aeruginosa culture sample

Strain NIBR12^T (=KACC 22094^T=HAMBI 3739^T), a novel Gram-stain-negative, obligate aerobic, non-spore-forming, non-motile and coccobacillus-shaped bacterium, was isolated from a cyanobacterial sample culture (Microcysitis aeruginosa NIBRCYC000000452). The newly identified bacterial strain grew optimally in modified Reasoner's 2A medium under the following conditions: 0 % (w/v) NaCl, pH 7.5 and 35 °C. Phylogenetic analysis using the 16S rRNA gene sequence confirmed that strain NIBR12^T belongs to the genus Roseococcus, with its closest neighbours being Roseococcus suduntuyensis SHET^T (98.8%), Roseococcus thiosulfatophilus RB-3^T (97.7%), "Sediminicoccus rosea" R-30^T (95.7 %) and Rubritepida flocculans H-8^T (95.0 %). Genomic comparison of strain NIBR12^T with type species in the genus Roseococcus was conducted using digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity analyses, resulting in values of ≤53.7, ≤93.7 and ≤96.1 %, respectively. The genomic DNA G+C content of strain NIBR12^T was 70.9 mol%. The major fatty acids of strain NIBR12^T were summed feature 8 (C_18 : 1  ω7c and/or C_18:1 ω6c) and summed feature 3 (C_{16 : 1} ω6c/C_{16 : 1} ω7c). Q-9 was its major respiratory quinone. Moreover, the major polar lipids of strain NIBR12^T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Based on our chemotaxonomic, genotypic and phenotype analyses, strain NIBR12^T is identified as represeting a novel species of the genus Roseococcus, for which the name Roseococcus microcysteis sp. nov. is proposed.

Sabulicella rubraurantiaca gen. nov., sp. nov., a new member of the family Acetobacteraceae, isolated from desert soil

Strain SYSU D01096^T was isolated from a sandy soil sample collected from Gurbantunggut Desert in Xinjiang, PR China. Phylogenetic analysis of the nearly full-length 16S rRNA gene sequence revealed that strain SYSU D01096^T belonged to the family Acetobacteraceae and was closest to Rubritepida flocculans DSM 14296^T (96.0% similarity). Cells of strain SYSU D01096^T were observed to be non-motile, short rod-shaped and Gram-staining negative. The colonies were observed to be translucent, reddish orange, circular, convex and smooth. Growth occurred at 15-37 °C (optimum, 28-30 °C), pH 4.0-8.0 (optimum, pH 7.0) and 0-0.5% NaCl (w/v; optimum, 0%) on Reasoner's 2A medium. The predominant ubiquinone was identified as ubiquinone 9 and the major fatty acids were Summed Feature 8 (C_18:1 ω7c and/or C_18:1 ω6c) and C_16:0. The polar lipids consisted of diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylglycerol (PG), one unidentified phospholipid (PL), three unidentified aminolipids (AL1-3) and one unidentified aminophospholipid (APL). The genomic DNA G + C content was 69.1%. Phylogenetic tree based on 16S rRNA gene sequences indicated strain SYSU D01096^T represented an individual lineage in the family Acetobacteraceae, which was supported by 30 core gene-based phylogenomic tree. Based on the multi-analysis including physiological, chemotaxonomic and phylogenetic comparison, strain SYSU D01096^T was proposed to represent a novel species of a novel genus, named Sabulicella rubraurantiaca gen. nov., sp. nov., within the family Acetobacteraceae. The type strain is SYSU D01096^T (= CGMCC 1.8619^T = KCTC 82268^T = MCCC 1K04998^T).

Phylotaxogenomics for the Reappraisal of the Genus Roseomonas With the Creation of Six New Genera

The genus Roseomonas is a significant group of bacteria which is invariably of great clinical and ecological importance. Previous studies have shown that the genus Roseomonas is polyphyletic in nature. Our present study focused on generating a lucid understanding of the phylogenetic framework for the re-evaluation and reclassification of the genus Roseomonas. Phylogenetic studies based on the 16S rRNA gene and 92 concatenated genes suggested that the genus is heterogeneous, forming seven major groups. Existing Roseomonas species were subjected to an array of genomic, phenotypic, and chemotaxonomic analyses in order to resolve the heterogeneity. Genomic similarity indices (dDDH and ANI) indicated that the members were well-defined at the species level. The Percentage of Conserved Proteins (POCP) and the average Amino Acid Identity (AAI) values between the groups of the genus Roseomonas and other interspersing members of the family Acetobacteraceae were below 65 and 70%, respectively. The pan-genome evaluation depicted that the pan-genome was an open type and the members shared 958 core genes. This claim of reclassification was equally supported by the phenotypic and chemotaxonomic differences between the groups. Thus, in this study, we propose to re-evaluate and reclassify the genus Roseomonas and propose six novel genera as Pararoseomonas gen. nov., Falsiroseomonas gen. nov., Paeniroseomonas gen. nov., Plastoroseomonas gen. nov., Neoroseomonas gen. nov., and Pseudoroseomonas gen. nov.

Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics

Soil quality is usually determined by its physical-chemical characteristics without taking into account the bacterial communities that play a fundamental role in the chemical decomposition of plant nutrients. In this context, the objective of the study was to evaluate bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii cultivation under different gradients of use (first, second and third use) and crop development (pre-sowing, hypocotyl development and post-harvest). The sampling was carried out in the Bombón plateau in the central Andes of Peru, during the rainy and low water seasons, by the systematic method based on a specific pattern assigned in a geometric rectangular shape at a depth of 0 - 20 cm. The characterization of the bacterial communities was carried out through the metagenomic sequencing of the 16S rRNA. 376 families of bacteria were reported, of which it was determined that there was a significant change in bacterial composition and distribution in relation to use pressure. There were no major changes due to the development of Lepidium meyenii. The families most sensitive to use pressure and soil poverty indicators were Verrucomicrobiaceae, Acidobacteraceae and Aakkermansiaceae.

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.

Roseicella frigidaeris gen. nov., sp. nov., isolated from an air-conditioning system

A Gram-stain-negative, facultatively aerobic bacterial strain, designated DB1506^T, of the family Acetobacteraceae, was isolated from an air-conditioning system in the Republic of Korea. Colonies were pink- to rosy-coloured and cells were non-motile cocci with catalase- and oxidase-positive activities. Growth of strain DB1506^T was observed at 20-37 °C (optimum, 30 °C), pH 5.5-8.5 (pH 7.0) and in the presence of 0-0.5 % (w/v) NaCl (0 %). Strain DB1506^T contained summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C18 : 1 2-OH as major fatty acids and ubiquinone-10 as the sole isoprenoid quinone. Phosphatidylglycerol, phosphatidylethanolamine, unidentified phospholipids, unidentified aminolipids and unidentified polar lipids were detected as major polar lipids. The G+C content of the genomic DNA calculated from the whole genome sequence was 72.5 mol%. Strain DB1506^T was most closely related to Paracraurococcus ruber NS89^T, Dankookia rubra WS-10^T and Siccirubricoccus deserti SYSU D8009^T with 16S rRNA gene sequence similarities of 96.01, 95.88 and 95.44 %, respectively, but strain DB1506^T formed a clearly distinct phylogenic lineage from them within the family Acetobacteraceae. On the basis of phenotypic, chemotaxonomic and molecular properties, strain DB1506^T represents a novel species of a new genus within the family Acetobacteraceae, for which the name Roseicella frigidaeris gen. nov., sp. nov. is proposed. The type strain is DB1506^T (=KACC 19791^T=JCM 32945^T).

Caldovatus sediminis gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a hot spring

A Gram-stain-negative, ovoid-shaped, aerobic, non-motile, catalase- and oxidase-positive, and moderately thermophilic bacterial strain, designated strain YIM 72346T, was isolated from a sediment sample collected from a hot spring in Tengchong county, Yunnan province, south-west China. Growth occurred at 37-50 °C (optimum, 45 °C), at pH 6.0-9.0 (optimum, pH 6.5-7.0) and in the presence of 0.5-1.0 % (w/v) NaCl (optimum, 0.5 %). The major cellular fatty acids were C18 : 1ω7c, C16 : 0, C19 : 0cyclo ω8c,and C18 : 1 2-OH. The genomic DNA G+C content was determined to be 69.8 mol%. The predominant ubiquinone was Q-10. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid and two unidentified phospholipids. Bacteriochlorophyll α and carotenoic acids were not detected. Strain YIM 72346T was not observed for the accumulation of poly-β-hydroxybutyrate. The strain shared highest 16S rRNA gene sequence identities with Crenalkalicoccus roseus YIM 78023T (93.3 %) and Craurococcus roseus NS130T (92.7 %), but formed a distinct lineage within the family Acetobacteraceae in the phylogenetic trees. On the basis of genotypic, phenotypic, chemotaxonomic and phylogenetic analyses, strain YIM 72346T is considered to represent a novel genus and species of the family Acetobacteraceae, for which the name Caldovatus sediminis gen. nov., sp. nov. is proposed. The type strain of Caldovatus sediminis is YIM 72346T (=KCTC 52714T=CGMCC 1.16330T).

Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae

Clubroot caused by Plasmodiophora brassicae, is a severe disease of cruciferous crops that causes large hypertrophic galls in the roots. The plant microbiome is important for growth promotion and disease suppression. In this study, using 16S rRNA and internal transcribed spacer (ITS) sequencing techniques, we compared the endosphere microbiome of symptomatic and asymptomatic B. napus roots infected with P. brassicae collected from the same natural clubroot field. The results showed that the microbial population and its relative abundance in the asymptomatic roots was far higher than that in the symptomatic roots, and that many microorganisms in asymptomatic roots have biological control and plant growth promotion functions that may be related to clubroot symptoms. These results suggest the importance of the endosphere microbiome in clubroot disease and provide potential bio-control resources for its prevention.

Siccirubricoccus deserti gen. nov., sp. nov., a proteobacterium isolated from a desert sample

Strain SYSU D8009^T was isolated from a desert sample collected from Saudi Arabia. The taxonomic position of the isolate was investigated by a polyphasic approach. The novel isolate was Gram-stain-negative, non-motile, aerobic and non-spore-forming. It was able to grow at 4-45 °C and pH 4.0-8.0, and exhibited NaCl tolerance of up to 1.5 % (w/v). Strain SYSU D8009^T shared the closest 16S rRNA gene sequence similarities with members of the family Acetobacteraceae, with a value of less than 96.0 %. In the phylogenetic dendrograms, the strain clustered with the genera Paracraurococcus, Craurococcus and Crenalkalicoccus within the family Acetobacteraceae but with a distinct lineage, thereby demonstrating that the strain should be classified within the family Acetobacteraceae. The respiratory ubiquinone was found to be Q-10. The polar lipids of the strain comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and four unidentified aminolipids. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The genomic DNA G+C content of strain SYSU D8009^T was determined to be 71.6 mol%. Based on the results of the phylogenetic analyses and differences in the physiological and biochemical characteristics, strain SYSU D8009^T merits representation of a novel species of a new genus within the family Acetobacteraceae, for which the name Siccirubricoccus deserti gen. nov., sp. nov. is proposed. The type strain of Siccirubricoccus deserti sp. nov. is SYSU D8009^T (=CGMCC 1.15936^T=KCTC 62088^T).

Paucibacter oligotrophus sp. nov., isolated from fresh water, and emended description of the genus Paucibacter

A Gram-stain-negative, rod-shaped, non-spore forming, motile and strictly oxidative bacterium, strain CHU3T, was isolated from fresh water in the Daecheong Reservoir, South Korea. A comparison of the 16S rRNA gene sequence showed that the novel bacterium is closely related to Paucibacter toxinivorans 2C20T (=KCTC 42569T) with a sequence similarity value of 97.8 %, Pelomonas saccharophila DSM 654T (=KCTC 52256T) with 97.4 % similarity and Pelomonas aquatica CCUG 52575T (=KCTC 42961T) with 97.3 % similarity, respectively. The major fatty acids (>10 %) of the isolate were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. Ubiquinone-8 was detected as the respiratory quinone. The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine and an unidentified aminolipid. The DNA G+C content was 62.5 mol%. DNA-DNA hybridization experiments with PaucibactertoxinivoransKCTC 42569T (=2C20T), PelomonassaccharophilaKCTC 52256T (=DSM 654T) and PelomonasaquaticaKCTC 42961T (=CCUG 52575T) resulted in relatedness values of 20 % (reciprocal 11 %), 16 % (reciprocal 17 %) and 15 % (reciprocal 19 %), respectively. The phylogenetic analysis, DNA-DNA hybridization value, polar lipids, fatty acid composition and other physiological characteristics confirmed that strain CHU3T represents a novel species in the genus Paucibacter for which the name Paucibacter oligotrophus sp. nov. is proposed. The type strain is CHU3T (=KCTC 42519T=CICC 24092T). An emended description of the genus Paucibacter is also proposed on the basis of new data obtained in this study.

Nitrogen fixing bacteria in the family Acetobacteraceae and their role in agriculture

For centuries, the Acetobacteraceae is known as a family that harbors many species of organisms of biotechnological importance for industry. Nonetheless, since 1988 representatives of this family have also been described as nitrogen fixing bacteria able to plant growth promotion by a variety of mechanisms. Nitrogen fixation is a biological process that guarantees that the atmospheric N2 is incorporated into organic matter by several bacterial groups. Most representatives of this group, also known as diazotrophic, are generally associated with soil rhizosphere of many plants and also establishing a more specific association living inside roots, leaves, and others plants tissues as endophyte. Their roles as plant growth-promoting microorganisms are generally related to increase in plant biomass, phosphate and other mineral solubilization, and plant pathogen control. Here, we report many of these plant growth-promoting processes related to nitrogen fixing species already described in Acetobacteraceae family, especially Gluconacetobacter diazotrophicus and their importance to agriculture. In addition, a brief review of the state of art of the phylogenetics, main physiological and biochemical characteristics, molecular and functional genomic data of this group of Acetobacteraceae is presented.

Gelidibacter sediminis sp. nov., isolated from a sediment sample of the Yellow Sea

The Gram-stain-negative, yellow-pigmented, rod-shaped bacterial strain, designated S11-41T, was isolated from a sediment sample of the Yellow Sea in China. The strain was able to grow well over a wide temperature range (1–35 °C). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S11-41T was related to the members of the genus Gelidibacter, sharing highest sequence similarities with the type strains of Geldibacter salicanalis (98.2 %), Geldibacter algens (97.4 %) and Geldibacter mesophilus (96.9 %). The genomic DNA G+C content of strain S11-41T was 39.2 mol%. The predominant cellular fatty acids were iso-C15 : 0 (13.2 %), iso-C17 : 0 3-OH (12.8 %) and iso-C15 : 1 G (12.2 %). Phosphatidylethanolamine was identified as the major polar lipid. Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain S11-41T is a representative of a novel species of the genus Gelidibacter, for which we propose the name Gelidibacter sediminis sp. nov. (type strain S11-41T = DSM 28135T = LMG 28076T).

P uniceibacterium sediminis sp. nov., from intertidal sediment

The Gram-stain-negative, rod-shaped bacterial strain designated RU-1-R-18T was isolated from intertidal sediment on Sakhalin Island in Russia. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RU-1-R-18T was related to the genus Puniceibacterium and shared highest sequence similarities with the type strain Puniceibacterium antarcticum KACC 16875T (97.9 %). The predominant cellular fatty acid was C18 : 1ω7c. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminophospholipid and seven unidentified polar lipids. The genomic DNA G+C content of strain RU-1-R-18T was 59.1 mol%. Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain RU-1-R-18T represents a novel species of the genus Puniceibacterium , for which the name Puniceibacterium sediminis sp. nov. is proposed (type strain RU-1-R-18T = LMG 28384T = DSM 29052T).

Algibacter amylolyticus sp. nov., isolated from intertidal sediment

A Gram-reaction-negative, rod-shaped, yellow-pigmented, motile by gliding bacterial strain, designated RU-4-M-4T, was isolated from intertidal sediment of Sakhalin Island in Russia. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RU-4-M-4T was related to the genus Algibacter and had highest 16S rRNA gene sequence similarity with Algibacter pectinivorans KACC 14153T (97.2 %). The major cellular fatty acids were iso-C15 : 0 3-OH, C15 : 0 and iso-C15 : 1 G. The predominant menaquinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. The genomic DNA G+C content of strain RU-4-M-4T was 36.4 mol%. Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain RU-4-M-4T is a representative of a novel species of the genus Algibacter , for which we propose the name Algibacter amylolyticus sp. nov. (type strain RU-4-M-4T = LMG 28383T = DSM 29199T).

Characterization of culturable heterotrophic bacteria in hydrocarbon-contaminated soil from an alpine former military site

We characterized the culturable, heterotrophic bacterial community in soil collected from a former alpine military site contaminated with petroleum hydrocarbons. The physiologically active eubacterial community, as revealed by fluorescence-in situ-hybridization, accounted for 14.9 % of the total (DAPI-stained) bacterial community. 4.0 and 1.2 % of the DAPI-stained cells could be attributed to culturable, heterotrophic bacteria able to grow at 20 and 10 °C, respectively. The majority of culturable bacterial isolates (23/28 strains) belonged to the Proteobacteria with a predominance of Alphaproteobacteria. The remaining isolates were affiliated with the Firmicutes, Actinobacteria and Bacteroidetes. Five strains could be identified as representatives of novel species. Characterization of the 28 strains demonstrated their adaptation to the temperature and nutrient conditions prevailing in the studied soil. One-third of the strains was able to grow at subzero temperatures (-5 °C). Studies on the effect of temperature on growth and lipase production with two selected strains demonstrated their low-temperature adaptation.