Metagenomic analysis of a thermophilic bacterial consortium and its use in the bioremediation of a petroleum-contaminated soil

Biodegradation is difficult at high temperatures due to the limited capacity of microorganisms to survive and function outside their optimum temperature range. Here, a thermophilic petroleum-degrading consortium was enriched from compost at a temperature of 55 °C. 16S rDNA and metagenomic techniques were used to analyze the composition of the consortium and the mechanisms of degradation. The consortium degraded 17000 mg total petroleum hydrocarbons (TPHs) L-1 with a degradation efficiency of 81.5% in 14 days. The consortium utilized a range of substrates such as n-hexadecane, n-docosane, naphthalene and pyrene and grew well over a wide range of pH (4-10) and salinity (0-90 g L-1). The hydrocarbon-degrading extremophilic consortium contained, inter alia, (relative abundance >1%) Caldibacillus, Geobacillus, Mycolicibacterium, Bacillus, Chelatococcus, and Aeribacillus spp. Metagenomic analysis was conducted to discover the degradation and environmental tolerance functional genes of the consortium. Two alkane hydroxylase genes, alkB and ladA, were found. A microcosm study shows that the consortium promoted the bioremediation of soil TPHs. The results indicate that the consortium may be a good candidate for the high-temperature bioremediation of petroleum-contaminated soils.

Chelatococcus albus sp. nov., a bacterium isolated from hot spring microbial mat

A Gram-stain-negative, non-endospore-forming, motile, short rod-shaped strain, designated SYSU G07232T, was isolated from a hot spring microbial mat, sampled from Rehai National Park, Tengchong, Yunnan Province, south-western China. Strain SYSU G07232T grew at 25-50 °C (optimum, 37 °C), at pH 5.5-9.0 (optimum, pH 6.0) and tolerated NaCl concentrations up to 1.0 % (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SYSU G07232T showed closest genetic affinity with Chelatococcus daeguensis K106T. The genomic features and taxonomic status of this strain were determined through whole-genome sequencing and a polyphasic approach. The predominant quinone of this strain was Q-10. Major cellular fatty acids comprised C19 : 0 cyclo ω8c and summed feature 8. The whole-genome length of strain SYSU G07232T was 4.02 Mbp, and the DNA G+C content was 69.26 mol%. The average nucleotide identity (ANIm ≤84.85 % and ANIb ≤76.08  %) and digital DNA-DNA hybridization (≤ 21.9 %) values between strain SYSU G07232T and the reference species were lower than the threshold values recommended for distinguishing novel prokaryotic species. Thus, based on the provided phenotypic, phylogenetic, and genetic data, it is proposed that strain SYSU G07232T (=KCTC 8141T=GDMCC 1.4178T) be designated as representing a novel species within the genus Chelatococcus, named Chelatococcus albus sp. nov.

Seasonal shift of water quality in China Yangtze River and its impacts on membrane fouling development during the drinking water supply by membrane distillation system

Membrane distillation (MD) technique is increasingly regarded as a promising process for drinking water supply and wastewater treatment owing to its great water purification and usage of renewable energy. Like other membrane separation processes, the membrane fouling issue is widely considered as the main obstacle for real applications of large-scale MD systems. Feedwater characteristics, as the predominant factors for membrane fouling layer formation, mostly determined the membrane fouling trend of MD. Thus the impacts of seasonal shifts of initial feedwater quality on the MD membrane fouling were detailedly researched in this study, and the biofilm development mechanism was especially explored. The bacterial community structure of membrane biofilms was clearly clarified in MD runs of Yangtze River waters that collected in four seasons. The results revealed that the winter run posed a quite sharp flux drop, while a relatively milder flux decline behaviour was seen for other groups despite of the higher bacteria concentration of initial feedwaters. The poorer water quality in winter induced the establishment of a rather thick biofilm on the MD membrane, in which the biofilm-forming bacteria (Gammaproteobacteria and Alphaproteobacteria) and organic matters (EPS) were remarkably observed. Comparatively, a relatively thin biofilm containing abundant live cells and fewer organics finally formed in summer and autumn runs, causing a mitigated flux decline trend. Hence, it can be inferred that the membrane flux decline of MD was likely to be more sensitive to the organic attachment on the membrane in comparison with the bacteria adhesion. Finally, a three-phase pretreatment method was suggested for MD fouling control, including heating course, sterilization course, and filtration course.

Genomic plasticity and antibody response of Bordetella bronchiseptica strain HT200, a natural variant from a thermal spring

Classical Bordetella species are primarily isolated from animals and humans causing asymptomatic infection to lethal pneumonia. However, isolation of these bacteria from any extra-host environmental niche has not been reported so far. Here, we have characterized the genomic plasticity and antibody response of Bordetella bronchiseptica strain HT200, isolated from a thermal spring. Genomic ANI value and SNPs-based phylogenetic tree suggest a divergent evolution of strain HT200 from a human-adapted lineage of B. bronchiseptica. Growth and survivability assay showed strain HT200 retained viability for more than 5 weeks in the filter-sterilized spring water. In addition, genes or loci encoding the Bordetella virulence factors such as DNT, ACT and LPS O-antigen were absent in strain HT200, while genes encoding other virulence factors were highly divergent. Phenotypically, strain HT200 was non-hemolytic and showed weak hemagglutination activity, but was able to colonize in the respiratory organs of mice. Further, both infection and vaccination with strain HT200 induced protective antibody response in mouse against challenge infection with virulent B. bronchiseptica strain RB50. In addition, genome of strain HT200 (DSM 26023) showed presence of accessory genes and operons encoding predicted metabolic functions pertinent to the ecological conditions of the thermal spring.

A Novel Moderately Thermophilic Facultative Methylotroph within the Class Alphaproteobacteria

Methylotrophic bacteria (non-methanotrophic methanol oxidizers) consuming reduced carbon compounds containing no carbon–carbon bonds as their sole carbon and energy source have been found in a great variety of environments. Here, we report a unique moderately thermophilic methanol-oxidising bacterium (strain LS7-MT) that grows optimally at 55 °C (with a growth range spanning 30 to 60 °C). The pure isolate was recovered from a methane-utilizing mixed culture enrichment from an alkaline thermal spring in the Ethiopia Rift Valley, and utilized methanol, methylamine, glucose and a variety of multi-carbon compounds. Phylogenetic analysis of the 16S rRNA gene sequences demonstrated that strain LS7-MT represented a new facultatively methylotrophic bacterium within the order Hyphomicrobiales of the class Alphaproteobacteria. This new strain showed 94 to 96% 16S rRNA gene identity to the two methylotroph genera, Methyloceanibacter and Methyloligella. Analysis of the draft genome of strain LS7-MT revealed genes for methanol dehydrogenase, essential for methanol oxidation. Functional and comparative genomics of this new isolate revealed genomic and physiological divergence from extant methylotrophs. Strain LS7-MT contained a complete mxaF gene cluster and xoxF1 encoding the lanthanide-dependent methanol dehydrogenase (XoxF). This is the first report of methanol oxidation at 55 °C by a moderately thermophilic bacterium within the class Alphaproteobacteria. These findings expand our knowledge of methylotrophy by the phylum Proteobacteria in thermal ecosystems and their contribution to global carbon and nitrogen cycles.

Identification of a solo acylhomoserine lactone synthase from the myxobacterium Archangium gephyra

Considered a key taxon in soil and marine microbial communities, myxobacteria exist as coordinated swarms that utilize a combination of lytic enzymes and specialized metabolites to facilitate predation of microbes. This capacity to produce specialized metabolites and the associated abundance of biosynthetic pathways contained within their genomes have motivated continued drug discovery efforts from myxobacteria. Of all myxobacterial biosynthetic gene clusters deposited in the antiSMASH database, only one putative acylhomoserine lactone (AHL) synthase, agpI, was observed, in genome data from Archangium gephyra. Without an AHL receptor also apparent in the genome of A. gephyra, we sought to determine if AgpI was an uncommon example of an orphaned AHL synthase. Herein we report the bioinformatic assessment of AgpI and discovery of a second AHL synthase from Vitiosangium sp. During axenic cultivation conditions, no detectible AHL metabolites were observed in A. gephyra extracts. However, heterologous expression of each synthase in Escherichia coli provided detectible quantities of 3 AHL signals including 2 known AHLs, C8-AHL and C9-AHL. These results suggest that A. gephyra AHL production is dormant during axenic cultivation. The functional, orphaned AHL synthase, AgpI, is unique to A. gephyra, and its utility to the predatory myxobacterium remains unknown.

Effect of salt and metal accumulation on performance of membrane distillation system and microbial community succession in membrane biofilms

Membrane distillation (MD) works as a potential technology for the "zero liquid discharge" water treatment owing to its high concentration brine tolerance. The continuous accumulation of salts and metals in the MD system during the "zero liquid discharge" water treatment inevitably posed remarkable impacts on the biofilm formation as well as the MD performance. Hence, the biofouling mechanism of MD was deeply researched in this study with an emphasis on the roles of salt-stress (NaCl) and metal-stress (Zn and Fe) in biofilm development. The membrane flux decline of MD was effectively mitigated by the appearance of NaCl and ZnO, while that was significantly aggravated under the metal-stress of Fe. Considering the serious membrane scaling caused by NaCl crystals, a sharp flux decline was seen for the NaCl group during the later stage of MD operation. Basing on the 16S rDNA and 16S rRNA analysis, heat-stress, salt-stress, and metal-stress all posed certain impacts on the biofouling development in the MD system, and a more remarkable influence was observed for metal-stress. Under the salt-stress from NaCl, a thin biofilm containing high biovolume of dead cells finally formed, in which the bacterial community mainly consisted of halotolerant and thermophile species. Owing to the Zn²⁺-stress and oxidation-stress mechanisms of ZnO, the bacteria in the MD system were largely dead and live bacterial community in biofilms was dominated by some gram-negative species. Under the metal-stress from Fe, a rather thick biofilm containing higher biovolume of live cells clearly developed, in which the prevailing species could secret large amounts of EPS and accumulate metabolites around cells as biological surfactants, inducing aggravated membrane biofouling and high risk of membrane wetting.

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.

Corrigendum: Saliniramus fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from Hot Lake, Washington, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae

There was an error in the proposed genus name in the published article, in that the genus 'Salinivirga' was effectively published while this article was in review. Therefore, the genus 'Salinivirga' should be replaced with 'Saliniramus'. For the convenience of future readers, we have included the complete corrected article below, in which all occurrences of the incorrect genus name have been amended: A halophilic bacterial strain, HL-109^T, was isolated from the unicyanobacterial consortium UCC-O, which was obtained from the photosynthetic mat of Hot Lake (Washington, USA). A polyphasic approach using phenotypic, genotypic and chemotaxonomic data was used to classify the strain within the order Rhizobiales. The organism stained Gram-negative and was a moderate thermophile with a growth optimum of 45 °C. It was obligately aerobic, heterotrophic and halophilic, growing in both NaCl and MgSO4 brines. The novel isolate had a polymorphic cellular morphology of short rods with occasional branching, and cells were monotrichous. The major fatty acids detected were C18 : 1, C18 : 0, C16 : 0 and C18 : cyc. Phylogenetic analysis of the 16S rRNA gene placed the strain in the order Rhizobiales and it shared 94 % identity with the type strain of its nearest relative, Salinarimonas ramus. Morphological, chemotaxonomic and phylogenetic results did not affiliate the novel organism with any of the families in the Rhizobiales; therefore, HL-109^T is representative of a new lineage, for which the name Saliniramus fredricksonii gen. nov., sp. nov. is proposed, with the type strain HL-109^T (=JCM 31876^T=DSM 102886^T). In addition, examination of the phylogenetics of strain HL-109^T and its nearest relatives, Salinarimonas ramus and Salinarimonasrosea, demonstrates that these halophiles form a clade distinct from the described families of the Rhizobiales. We further propose the establishment of a new family, Salinarimonadaceae fam. nov., to accommodate the genera Saliniramus and Salinarimonas (the type genus of the family).

Microbiological studies of hot springs in India: a review

The earliest microbiological studies on hot springs in India date from 2003, a much later date compared to global attention in this striking field of study. As of today, 28 out of 400 geothermal springs have been explored following both culturable and non-culturable approaches. The temperatures and pH of the springs are 37-99 °C and 6.8-10, respectively. Several studies have been performed on the description of novel genera and species, characterization of different bio-resources, metagenomics of hot spring microbiome and whole genome analysis of few isolates. 17 strains representing novel species and many thermostable enzymes, including lipase, protease, chitinase, amylase, etc. with potential biotechnological applications have been reported by several authors. Influence of physico-chemical conditions, especially that of temperature, on shaping the hot spring microbiome has been established by metagenomic investigations. Bacteria are the predominant life forms in all the springs with an abundance of phyla Firmicutes, Proteobacteria, Actinobacteria, Thermi, Bacteroidetes, Deinococcus-Thermus and Chloroflexi. In this review, we have discussed the findings on all microbiological studies that have been carried out to date, on the 28 hot springs. Further, the possibilities of extrapolating these studies for practical applications and environmental impact assessment towards protection of natural ecosystem of hot springs have also been discussed.

Chelatococcus composti sp. nov., isolated from penicillin fermentation fungi residue with pig manure co-compost

A novel Gram-stain-negative bacterium, designated strain PC-2^T, was isolated from penicillin fermentation fungi residue with pig manure co-compost in China. Phylogenetic analysis, based on 16S rRNA gene sequence comparisons, revealed that strain PC-2^T should be assigned to the genus Chelatococcus and that it had 98.9 % similarity with Chelatococcus daeguensis, 98.8 % with Chelatococcus sambhunathii, 98.4 %, with Chelatococcus caeni and 96.0 % with Chelatococcus asaccharovorans. The G+C content of genomic DNA was 70.9 mol%. On the basis of the phylogenetic analysis, DNA-DNA relatedness values, phenotypic characteristics and chemotaxonomic data, strain PC-2 ^T represents a novel species of the genus Chelatococcus, for which the name Chelatococcus composti sp. nov. is proposed. The type strain is PC-2^T (=DSM 101465^T=CGMCC 1.15283^T).

Chelatococcus thermostellatus sp. nov., a new thermophile for bioplastic synthesis: comparative phylogenetic and physiological study

The poly(3-hydroxybutyrate), PHB, accumulating thermophilic strain MW9^T, isolated from an aerobic organic waste treatment plant, was characterized by detailed physiological and phylogenetic studies. The strain is a Gram-stain-negative, rod shaped, non-spore forming member of Alphaproteobacteria. It shows optimum growth at 50 °C. Based on 16S rRNA gene sequence similarity, the strain together with five very similar isolates, was affiliated to the genus Chelatococcus (Ibrahim et al. in J Appl Microbiol 109:1579–1590, 2010). Rep-PCR genomic fingerprints and partial dnaK gene sequence also revealed that these isolates are very similar, but differ from other Chelatococcus type strains. The major fatty acids were similar to those of other strains of the genus Chelatococcus. DNA–DNA hybridization of strain MW9^T with Chelatococcus species type strains revealed 11.0–47.7 % relatedness. G+C content of DNA was 67.1 mol%, which is comparable with the other strains of Chelatococcus species. The physiological and phenotypic characteristics of the new strain MW9^T are sufficient to differentiate it from previously described species in the genus Chelatococcus. Strain MW9^T is considered to represent a novel species of the genus Chelatococcus, for which the name Chelatococcus thermostellatus is proposed. The type strain is MW9^T (=LMG 27009^T = DSM 28244^T). Compared to known Chelatococcus strains, strain MW9^T could be a potent candidate for bioplastic production at elevated temperature.

Draft Genome Sequence of Chelatococcus sambhunathii Strain HT4T (DSM 18167T) Isolated from a Hot Spring in India

The moderately thermophilic bacterium Chelatococcus sambhunathii strain HT4^T was isolated from hot spring sediment. Based upon the draft genome sequence, the genome is 4.4 Mb and encodes 4,147 proteins.

Chelatococcus reniformis sp. nov., isolated from a glacier

A Gram-stain-negative, non-motile, reniform bacterial strain, B2974T, was isolated from an ice core of the Muztagh Glacier, on the Tibetan Plateau, China. Strain B2974T grew optimally at pH 7.0-7.5 and 25-30 °C in the presence of 0-2.0 % (w/v) NaCl. 16S rRNA gene sequence similarity analysis indicated that strain B2974T was closely related to Chelatococcus asaccharovorans LMG 25503T at a level of 97.1 %. The major quinone of strain B2974T was ubiquinone Q10. The predominant fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C19 : 0 cyclo ω8c. sym-Homospermidine was the major polyamine. The genomic DNA G+C content of the strain was 64 mol%. In DNA-DNA hybridization tests, strain B2974T shared 49.32 % DNA-DNA relatedness with the type strain of Chelatococcus asaccharovorans LMG 25503T. Based on the results of phenotypic and chemotaxonomic characteristics, strain B2974T was considered as a novel species of the genus Chelatococcus, for which the name Chelatococcus reniformis sp. nov. is proposed. The type strain is B2974T (=JCM 30308T=CGMCC 1.12919T).

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India

This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40–58°C; pH: 7.2–7.4) with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate), total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis, and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria.

Qingshengfania soli gen. nov., sp. nov., a member of the order Rhizobiales isolated from the soil of a pesticide factory

Two Gram-stain negative, coccoid to oval-shaped, non-spore-forming bacteria (LR4T and LR4-1), isolated from the soil of a pesticide factory in Nanjing, China, were investigated for their taxonomic allocation by using a polyphasic approach. Both strains grew optimally at pH 7.0, 30 °C and in the absence of NaCl. Both strains were positive for catalase and oxidase activities. Q-10 was the predominant respiratory ubiquinone. The major polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and two unknown aminolipids. The major fatty acids (>10 % of the total fatty acids) were C18:1ω7c/C18:1ω6c (summed feature 8) and C17:1 iso I/C17:1 anteiso B (summed feature 4). Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the two isolates formed a distinct line within a clade containing the genera Chelatococcus, Bosea, Camelimonas, Salinarimonas, Psychroglaciecola, Microvirga, Methylobacterium, Albibacter, Hansschlegelia and Methylopila in the order Rhizobiales, with the highest 16S rRNA gene sequence similarity to Chelatococcus asaccharovorans TE2T (94.12 %), followed by Bosea thiooxidans DSM 9653T (93.25 %). Strains LR4T and LR4-1 were closely related on the basis of DNA-DNA reassociation and therefore represent a single novel species. Based on phenotypic, chemotaxonomic and phylogenetic data, strains LR4T and LR4-1 represent a novel species of a new genus in the order Rhizobiales, for which the name Qingshengfania soli gen. nov., sp. nov. is proposed. The type strain of the type species is LR4T ( = CCTCC AB 2015036T = KCTC 42463T).

Chelatococcus caeni sp. nov., isolated from a biofilm reactor sludge sample

A polyphasic taxonomic study was carried out on strain EBR-4-1T, which was isolated from a biofilm reactor in the Republic of Korea. The cells of the strain were Gram-stain-negative, non-spore-forming, motile and rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of this strain to the Alphaproteobacteria , and it was most closely related to Chelatococcus daeguensis CCUG 54519T, Chelatococcus sambhunathii HT4T, and Chelatococcus asaccharovorans DSM 6462T with 16S rRNA gene sequence similarities to the type strains of these species of 98.8 %, 98.7 %, and 96.3 %, respectively. The G+C content of the genomic DNA of strain EBR-4-1T was 68.7 mol%. Phenotypic and chemotaxonomic data [Q-10 as the major ubiquinone; C19 : 0cycloω8c, C18 : 1 2-OH, and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acids] supported the affiliation of strain EBR-4-1T to the genus Chelatococcus . On the basis of the polyphasic evidence, it is proposed that strain EBR-4-1T should be assigned to a new species, Chelatococcus caeni sp. nov. The type strain is EBR-4-1T ( = KCTC 32487T = JCM 30181T).

Marinomonas fungiae sp. nov., isolated from the coral Fungia echinata from the Andaman Sea

A novel aerobic marine bacterium, strain AN44T, was isolated from the coral Fungia echinata sampled from the Andaman Sea, India. Cells were Gram-negative, motile and rod-shaped. Oxidase and catalase tests were positive. Heterotrophic growth was observed at pH 5.5–10 and at 16–42 °C, with optimum growth at pH 7–8 and 28 °C. Strain AN44T grew in the presence of 0.5–11 % (w/v) NaCl; the optimal NaCl concentration for growth was 3–5 %. The DNA G+C content was 47.8 mol%. Predominant cellular fatty acids of strain AN44T were C18 : 1ω7c, C16 : 1ω7c/C16 : 1ω6c, C16 : 0, C10 : 0 3-OH, C12 : 0, C10 : 0, C14 : 0 and C18 : 0. The sole isoprenoid ubiquinone was Q-8. The polar lipids were an unidentified phospholipid, an unidentified aminophospholipid and two unidentified glycolipids. 16S rRNA gene sequence comparisons revealed that strain AN44T clustered within the radiation of the genus Marinomonas and showed similarity of 97.9 % with Marinomonas ostreistagni UST010306-043T, 97.8 % with Marinomonas aquimarina 11SM4T, 97.1 % with Marinomonas brasilensis R-40503T and 97.0 % with Marinomonas communis 8T. However, DNA–DNA relatedness between strain AN44T and closely related type strains was well below 70 %. On the basis of the data from the present polyphasic taxonomic study, strain AN44T is considered to represent a novel species of the genus Marinomonas , for which the name Marinomonas fungiae sp. nov. is proposed. The type strain is AN44T ( = JCM 18476T = LMG 27065T).

Anoxybacillus suryakundensis sp. nov, a moderately thermophilic, alkalitolerant bacterium isolated from hot spring at Jharkhand, India

Four closely related facultative anaerobe, moderately thermophilic, Gram positive rods (JS1(T), JS5, JS11, and JS15) were isolated from sediment samples from a hot spring at Suryakund, Jharkhand, India. Colonies were pale yellow, rough surface with uneven edges on TSA after 72 h incubation. Heterotrophic growth was observed at 40-60°C and pH 5.5-11.5; optimum growth occurred at 55°C and pH 7.5. 16S rRNA gene sequence analysis revealed the strains belong to genus Anoxybacillus. DNA-DNA homology values among strains were above 70% and showed distinct ERIC and REP PCR profile. On the basis of morphology and biochemical characteristics, strain JS1(T) was studied further. Strain JS1(T) showed 99.30% sequence similarity with A. flavithermus subsp. yunnanensis, 99.23% with A. mongoliensis, 99.16% with A. eryuanensis, 98.74% with A. flavithermus subsp. flavithermus, 98.54% with A. tengchongensis, 98.51% with A. pushchinoensis, 97.91% with A. thermarum, 97.82% with A. kaynarcensis, 97.77% with A. ayderensis and A. kamchatkensis, 97.63% with A. salavatliensis, 97.55% with A. kestanbolensis, 97.48% with A. contaminans, 97.27% with A. gonensis and 97.17% with A. voinovskiensis. In 16S rRNA secondary structure based phylogenetic comparison, strain JS1(T) was clustered with Anoxybacillus eryuanensis, A. mongoliensis, and A. flavithermus subsp. yunnanensis and showed 15 species specific base substitutions with maximum variability in helix 6. Moreover, DNA-DNA relatedness between JS1(T) and the closely related type strains were well below 70%. The DNA G+C content was 42.1 mol%. The major fatty acids were C(15:0 iso), C(16:0 iso) and C(17:0iso). The polar lipids were a phosphatidylgylycerol, a diphosphatidylglycerol, a phosphatidylethnolamine, a phosphatidylcholine, a phosphatidyl monomethylethanolamine and four unknown lipids. Based on polyphasic approach, strain JS1(T) represent a novel species of the genus Anoxybacillus for which Anoxybacillus suryakundensis sp. nov. is proposed. The type strain is JS1(T) (= DSM 27374(T) = LMG 27616(T) =JCM19211(T)).

Taxonomic study of the genus Tepidiphilus: transfer of Petrobacter succinatimandens to the genus Tepidiphilus as Tepidiphilus succinatimandens comb. nov., emended description of the genus Tepidiphilus and description of Tepidiphilus thermophilus sp. nov., isolated from a terrestrial hot spring

Comparative phenotypic, chemotaxonomic and genetic analysis revealed significant similarities among strains of the genera Tepidiphilus and Petrobacter. Analysis of 16S rRNA gene sequences and DNA-DNA relatedness of the type strains Tepidiphilus margaritifer N2-214(T) and Petrobacter succinatimandens 4BON(T) showed sequence similarity of 98.9 % and less than 40 % relatedness, indicating that these strains represent different species of same genus. Both strains had phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol as major polar lipids. Their fatty acid profiles were almost identical, with the predominant fatty acids C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. In view of this, we propose to transfer the member of the genus Petrobacter to the genus Tepidiphilus as Tepidiphilus succinatimandens comb. nov. and to emend the description of the genus Tepidiphilus. Further, a novel bacterium, strain JHK30(T), was isolated from a terrestrial hot spring located at Jharkhand, India, and was identified following a polyphasic approach. Cells were non-sporulating, aerobic, Gram-stain-negative rods and motile by a single polar flagellum. Optimum temperature for growth was 50-55 °C at pH 6.5-7.0. 16S rRNA gene sequence analysis revealed 99.71 % similarity with P. succinatimandens 4BON(T) ( = DSM 15512(T)) and 98.71 % with T. margaritifer N2-214(T) ( = DSM 15129(T)). However, DNA-DNA relatedness of strain JHK30(T) with these two type strains was well below 70 %. The DNA G+C base composition was 66.1 mol%. Strain JHK30(T) represents a novel species of the genus Tepidiphilus for which the name Tepidiphilus thermophilus sp. nov. is proposed. The type strain is JHK30(T) ( = JCM 19170(T) = LMG 27587(T)= DSM 27220(T)).

Microbacterium oryzae sp. nov., an actinobacterium isolated from rice field soil

A novel aerobic soil actinobacterium (strain MB10T) belonging to the genus Microbacterium was isolated from rice field soil samples collected from Jagatpur, Orissa, India. Cells were Gram-stain positive, short rod-shaped and motile. The strain was oxidase-negative and catalase-positive. Heterotrophic growth was observed at pH 5.0–11.0 and at 16–37 °C; optimum growth was observed at 28 °C and pH 7.0–9.0. The DNA G+C content was 71.6 mol%. Predominant cellular fatty acids of strain MB10T were iso-C14 : 0, anteiso-C15 : 0, C16 : 0, iso-C16 : 0 and anteiso-C17 : 0. Cell wall sugars were galactose, glucose and rhamnose. The major isoprenoid quinones were MK-9 (10 %), MK-10 (43 %) and MK-11 (36 %). The peptidoglycan represents the peptidoglycan type B2β. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid and unknown glycolipids. 16S rRNA gene sequence identity revealed the strain MB10T clustered within the radiation of the genus Microbacterium and showed 99.2 % similarity with Microbacterium barkeri DSM 20145T. However, DNA–DNA similarity study was 37.0 % with Microbacterium barkeri DSM 20145T, the nearest phylogenetic relative. On the basis of phenotypic and chemotaxonomic properties, 16S rRNA gene sequence analysis and DNA–DNA reassociation studies, it is proposed that strain MB10T represents a novel species of the genus Microbacterium , for which the name Microbacterium oryzae sp. nov. is proposed; the type strain is MB10T ( = JCM 16837T = DSM 23396 T ).

Rhizobium pusense sp. nov., isolated from the rhizosphere of chickpea (Cicer arietinum L.)

A novel bacterial strain, designated NRCPB10T, was isolated from rhizosphere soil of chickpea (Cicer arietinum L.) in Pusa, New Delhi, India. The 16S rRNA gene sequence of strain NRCPB10T showed highest similarity (98.9 %) to that of Rhizobium radiobacter NCPPB 2437T, followed by Rhizobium larrymoorei AF3-10T (97.7 %) and Rhizobium rubi IFO 13261T (97.4 %). Phylogenetic analysis of strain NRCPB10T based on the housekeeping genes recA and atpD confirmed its position as distinct from recognized Rhizobium species. Levels of DNA–DNA relatedness between strain NRCPB10T and R. radiobacter ICMP 5785T, R. larrymoorei LMG 21410T and R. rubi ICMP 6428T were 51.0, 32.6 and 27.3 %, respectively. Cellular fatty acids of strain NRCPB10T were C18 : 1ω7c (58.9 %), C16 : 0 (15.5 %), C19 : 0 cyclo ω8c (11.5 %), iso-C16 : 1 (5.8 %), C16 : 0 3-OH (4.5 %), C16 : 1ω7c (2.1 %) and C18 : 0 (1.3 %). The G+C content of the genomic DNA of strain NRCPB10T was 59.0 mol%. Strain NRCPB10T did not nodulate chickpea plants or induce tumours in tobacco plants. Phenotypic and physiological properties along with SDS-PAGE of whole-cell soluble proteins differentiated strain NRCPB10T from its closest phylogenetic neighbours. On the basis of data from the present polyphasic taxonomic study, strain NRCPB10T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium pusense sp. nov. is proposed. The type strain is NRCPB10T ( = LMG 25623T = JCM 16209T = NCIMB 14639T).

Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction

Thermophilic microbial communities that are active in a high-solids environment offer great potential for the discovery of industrially relevant enzymes that efficiently deconstruct bioenergy feedstocks. In this study, finished green waste compost was used as an inoculum source to enrich microbial communities and associated enzymes that hydrolyze cellulose and hemicellulose during thermophilic high-solids fermentation of the bioenergy feedstocks switchgrass and corn stover. Methods involving the disruption of enzyme and plant cell wall polysaccharide interactions were developed to recover xylanase and endoglucanase activity from deconstructed solids. Xylanase and endoglucanase activity increased by more than a factor of 5, upon four successive enrichments on switchgrass. Overall, the changes for switchgrass were more pronounced than for corn stover; solids reduction between the first and second enrichments increased by a factor of four for switchgrass while solids reduction remained relatively constant for corn stover. Amplicon pyrosequencing analysis of small-subunit ribosomal RNA genes recovered from enriched samples indicated rapid changes in the microbial communities between the first and second enrichment with the simplified communities achieved by the third enrichment. The results demonstrate a successful approach for enrichment of unique microbial communities and enzymes active in a thermophilic high-solids environment.