Tessaracoccus lacteus sp. nov., Isolated from the Sludge of a Wastewater Treatment Plant

A bacterium, designated strain T21T, that is non-motile, rod-shaped, and formed pale white colonies, was isolated from the sludge of a wastewater treatment plant's secondary sedimentation tank in China. Strain T21T could grow at 20-40 °C (optimum growth at 30 °C), pH 3.0-10.0 (optimum growth at pH 5.0) and in the presence of 0-8.0% (w/v) NaCl (optimum growth at 2.0%). Based on phylogenetic analysis of 16S rRNA gene sequences and genome sequences, the isolate belongs to the genus Tessaracoccus in the phylum Actinomycetota. It exhibited a close relationship with Tessaracoccus palaemonis J1M15T, Tessaracoccus defluvii LNB-140T, Tessaracoccus flavescens SST-39T, and Tessaracoccus coleopterorum HDW20T. The 16S rRNA gene sequence similarities are 99.8%, 97.9%, 97.9%, and 97.8%, respectively. The major cellular fatty acids were anteiso-C15:0 and C16:0. The main respiratory quinone was MK-9(H4). The polar lipids included phosphatidylglycerol, diphosphatidylglycerol, glycolipid, and phospholipid. Genome annotation of strain T21T predicted the presence of 2829 genes, of which 2754 are coding proteins and 59 are RNA genes. The genomic DNA G+C content was 69.2%. Based on the results of phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses, we propose the name Tessaracoccus lacteus sp. nov. for this novel species within the genus Tessaracoccus. The type strain is T21T (=CCTCC AB 2023031T = KCTC 49936T).

Metabolomics analysis of flavor differences in Shuixian (Camellia sinensis) tea from different production regions and their microbial associations

Shuixian is renowned for its "rock flavor". However, the variations in Shuixian flavor are unclear, as the discussion mainly considers regional factors and overlooks the role of microorganisms. Sensory evaluation of Shuixian from three different regions (Zhengyan, Banyan, and Waishan) revealed that each had unique flavor characteristics: a woody aroma with slight acidity, a strong floral and fruity aroma with good freshness, and a distinct sweet aroma and sourness. Metabolomic analyses have revealed that 2-methylpyrazine was a crucial component of the woody aroma, whereas other metabolites contributed to sweet aroma, freshness, and acidity. Moreover, examinations of the relationship between flavor metabolites and microorganisms revealed that fungi had a more pronounced influence on the metabolite content of Shuixian. The study evaluated the role of fermentation microorganisms in shaping the flavor based on Shuixian flavor analyses, contributing to further research into the "rock flavor", as well as potential microbial interventions.

Terrirubrum flagellatum gen. nov., sp. nov. of Terrirubraceae fam. nov. and Lichenibacterium dinghuense sp. nov. from forest soil and proposal of Rhodoblastaceae fam. nov

Two Gram-negative, aerobic, rod-shaped bacterial strains, 7MK25T and 6Y81T, were isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Based on the results of 16S rRNA gene sequence analysis, strain 7MK25T showed the highest similarity (93.6 %) to Methyloferula stellata AR4T, followed by Bosea thiooxidans DSM 9653T (93.3 %). Strain 6Y81T had the highest similarity of 97.9 % to Lichenibacterium minor RmlP026T, followed by Lichenibacterium ramalinae RmlP001T (97.2 %). Phylogenomic analysis using the UBCG and PhyloPhlAn methods consistently showed that strain 7MK25T formed a sister clade to Boseaceae, while strain 6Y81T formed an independent clade within the genus Lichenibacterium, both in the order Hyphomicrobiales. The digital DNA-DNA hybridization and average nucleotide identity values between strains 7MK25T, 6Y81T and their close relatives were in the ranges of 19.1-29.9 % and 72.5-85.5 %, respectively. The major fatty acids of 7MK25T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C19 : 0 cyclo ω8c, C16 : 0 and C17 : 0 cyclo, while those of 6Y81T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C16 : 0 and C16 : 0 3-OH. Strains 7MK25T and 6Y81T took diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as their dominant polar lipids, and Q-10 as their major respiratory quinone. On the basis of phenotypic and phylogenetic data, strain 7MK25T is proposed to represent a novel species of a novel genus with name Terrirubrum flagellatum gen. nov., sp. nov., within a novel family Terrirubraceae fam. nov., with 7MK25T (=KCTC 62738T=GDMCC 1.1452T) as its type strain. Strain 6Y81T represents a novel species in the genus Lichenibacterium, for which the name Lichenibacterium dinghuense sp. nov. (type strain 6Y81T=KACC 21 727T=GDMCC 1.2176T) is proposed. Rhodoblastaceae fam. nov. with Rhodoblastus as the type genus is also proposed to solve the non-monophylectic problem of the family Roseiarcaceae.

Improved anaerobic sludge fermentation mediated by a tryptophan-degrading consortium: Effectiveness assessment and mechanism deciphering

The hydrolysis of extracellular polymeric substances (EPS) represents a critical bottleneck in the anaerobic fermentation of waste activated sludge (WAS), while tryptophan is identified as an underestimated constituent of EPS. Herein, we harnessed a tryptophan-degrading microbial consortium (TDC) to enhance the hydrolysis efficiency of WAS. At TDC dosages of 5%, 10%, and 20%, a notable increase in SCOD was observed by factors of 1.13, 1.39, and 1.88, respectively. The introduction of TDC improved both the yield and quality of short chain fatty acids (SCFAs), the maximum SCFA yield increased from 590.6 to 1820.2, 1957.9 and 2194.9 mg COD/L, whilst the acetate ratio within SCFAs was raised from 34.1% to 61.2-70.9%. Furthermore, as TDC dosage increased, the relative activity of protease exhibited significant increments, reaching 116.3%, 168.0%, and 266.1%, respectively. This enhancement facilitated WAS solubilization and the release of organic substances from bound EPS into soluble EPS. Microbial analysis identified Tetrasphaera and Soehngenia as key participants in WAS solubilization and the breakdown of protein fraction. Metabolic analysis revealed that TDC triggered the secretion of enzymes associated with amino acid metabolism and fatty acid biosynthesis, thereby fostering the decomposition of proteins and production of SCFAs.

Growth of microalgae and cyanobacteria consortium in a photobioreactor treating liquid anaerobic digestate from vegetable waste

This research examines the biological treatment of undiluted vegetable waste digestate conducted in a bubble column photobioreactor. Initially, the bioreactor containing 3N-BBM medium was inoculated with Microglena sp., Tetradesmus obliquus, and Desmodesmus subspicatus mixture with a density of 1.0 × 104 cells/mL and the consortium was cultivated for 30 days. Then, the bioreactor was semi-continuously fed with liquid digestate with hydraulic retention time (HRT) of 30 days, and the treatment process was continued for the next 15 weeks. The change in the microalgal and cyanobacterial species domination was measured in regular intervals using cell counting with droplet method on a microscope slide. At the end of the experiment, Desmonostoc sp. cyanobacteria (identified with 16S ribosomal RNA genetical analysis) as well as Tetradesmus obliquus green algae along with Rhodanobacteraceae and Planococcaceae bacteria (determined with V3-V4 16sRNA metagenomic studies) dominated the microbial community in the photobioreactor. The experiment demonstrated high treatment efficiency, since nitrogen and soluble COD were removed by 89.3 ± 0.5% and 91.2 ± 1.6%, respectively, whereas for phosphates, 72.8 ± 2.1% removal rate was achieved.

Chryseobacterium pyrolae sp. nov., isolated from the rhizosphere soil of Pyrola calliantha H

A novel Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated pc2-12T, was isolated from the rhizosphere soil of the herb Pyrola calliantha collected from arid areas of Tibet. The strain grew most vigorously with 1 % (w/v) NaCl, at pH 7.0 and at 25 °C. According to the results of 16S rRNA gene sequence analysis, pc2-12T was closely related to the members of the genus Chryseobacterium, with highest levels of sequence similarity to Chryseobacterium viscerum 687B-08T (98.42 %), Chryseobacterium oncorhynchi 701B-08T (98.11 %) and Chryseobacterium ureilyticum DSM 18017T (97.98 %). The average nucleotide identity values between pc2-12T and C. viscerum 687B-08T, C. oncorhynchi 701B-08T and C. ureilyticum DSM 18017T were 79.71, 79.49 and 79.26 %, respectively. The in silico DNA-DNA hybridisation values between pc2-12T and C. viscerum 687B-08T, C. oncorhynchi 701B-08T and C. ureilyticum DSM 18017T were 23.30, 23.00 and 22.90 %, respectively. The draft genome sequence of pc2-12T was 4.64 Mb long, with DNA G+C content of 37.0 mol%. The fatty acids contained in the cells of pc2-12T were mainly composed of iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The main polar lipid was phosphatidylethanolamine. MK-6 was the sole respiratory quinone. On the basis of the results of analysis of all the data described, pc2-12T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium pyrolae sp. nov., is proposed. The type strain is pc2-12T (=GDMCC 1.3256T= JCM 35712T).

Tessaracoccus caeni sp. nov., a novel member of Propionibacteriaceae isolated from activated sludge in Hefei, PR China

A floc-forming bacterial strain, designated HF-7T, was isolated from the activated sludge of an industrial wastewater treatment plant in Hefei, PR China. Cells of this strain were Gram-stain-positive, catalase- and oxidase-negative, facultatively anaerobic, and rod-shaped. Growth occurred at 20-42 °C (optimum, 28 °C), at pH 5.5-10.5 (optimum, pH 7.5) and with 0-8.0 % (w/v) NaCl (optimum, 1 %). The major fatty acid was anteiso-C15 : 0. The polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol. The DNA G+C content was 67 mol% from whole genomic sequence analysis. Based on the results of 16S rRNA gene sequence analysis, this strain should be assigned to the genus Tessaracoccus and is closely related to Tessaracoccus arenae CAU 1319T (95.87 % similarity), Tessaracoccus lapidicaptus IPBSL-7T (95.19 %) and Tessaracoccus bendigoensis Ben 106T (94.63 %) but separated from them by large distances in different phylogenetic trees. Based on whole genome analysis, the orthologous average nucleotide identity and in silico DNA-DNA hybridization values against two of the closest relatives were 75.21-76.50 % and 14.2-24.4 %, respectively. The phylogenetic, genotypic, phenotypic and chemotaxonomic data demonstrated that strain HF-7T could be distinguished from its phylogenetically related species and represents a novel species within the genus Tessaracoccus, for which the name Tessaracoccus caeni sp. nov. is proposed. The type strain is HF-7T (=KCTC 49959T=CCTCC AB 2023019T).

Eukaryotes inherited inositol lipids from bacteria: implications for the models of eukaryogenesis

The merger of two very different microbes, an anaerobic archaeon and an aerobic bacterium, led to the birth of eukaryotic cells. Current models hypothesize that an archaeon engulfed bacteria through external protrusions that then fused together forming the membrane organelles of eukaryotic cells, including mitochondria. Images of cultivated Lokiarchaea sustain this concept, first proposed in the inside-out model which assumes that the membrane traffic system of archaea drove the merging with bacterial cells through membrane expansions containing inositol lipids, considered to have evolved first in archaea. This assumption has been evaluated here in detail. The data indicate that inositol lipids first emerged in bacteria, not in archaea. The implications of this finding for the models of eukaryogenesis are discussed.

Vertical organization of microbial communities in Salineta hypersaline wetland, Spain

Microbial communities inhabiting hypersaline wetlands, well adapted to the environmental fluctuations due to flooding and desiccation events, play a key role in the biogeochemical cycles, ensuring ecosystem service. To better understand the ecosystem functioning, we studied soil microbial communities of Salineta wetland (NE Spain) in dry and wet seasons in three different landscape stations representing situations characteristic of ephemeral saline lakes: S1 soil usually submerged, S2 soil intermittently flooded, and S3 soil with halophytes. Microbial community composition was determined according to different redox layers by 16S rRNA gene barcoding. We observed reversed redox gradient, negative at the surface and positive in depth, which was identified by PERMANOVA as the main factor explaining microbial distribution. The Pseudomonadota, Gemmatimonadota, Bacteroidota, Desulfobacterota, and Halobacteriota phyla were dominant in all stations. Linear discriminant analysis effect size (LEfSe) revealed that the upper soil surface layer was characterized by the predominance of operational taxonomic units (OTUs) affiliated to strictly or facultative anaerobic halophilic bacteria and archaea while the subsurface soil layer was dominated by an OTU affiliated to Roseibaca, an aerobic alkali-tolerant bacterium. In addition, the potential functional capabilities, inferred by PICRUSt2 analysis, involved in carbon, nitrogen, and sulfur cycles were similar in all samples, irrespective of the redox stratification, suggesting functional redundancy. Our findings show microbial community changes according to water flooding conditions, which represent useful information for biomonitoring and management of these wetlands whose extreme aridity and salinity conditions are exposed to irreversible changes due to human activities.

Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov., isolated from the gastrointestinal tract of lake prawn

Two novel Gram-stain-positive, non-motile and non-spore-forming bacterial strains, designated J2M5^T and J1M15^T, were isolated from the gastrointestinal tract of a lake prawn Palaemon paucidens. Strain J2M5^T was an obligately aerobic bacterium that formed milky-coloured colonies and showed a rod-coccus cell cycle, while strain J1M15^T was a facultatively aerobic bacterium that formed orangish-yellow-coloured colonies and showed rod-shaped cells. Strains J2M5^T and J1M15^T showed the highest 16S rRNA gene sequence similarity to Nocardioides ganghwensis JC2055^T (98.63 %) and Tessaracoccus flavescens SST-39^T (98.08 %), respectively. The whole-genome sequence of strain J2M5^T was 4.52 Mbp in size and the genomic G+C content directly calculated from the genome sequence of strain J2M5^T was 72.5 mol%. The whole-genome sequence of strain J1M15^T was 3.20 Mbp in size and the genomic G+C content directly calculated from the genome sequence of strain J1M15^T was 69.6mol %. Strains J2M5^T and J1M15^T showed high OrthoANI similarity to N. ganghwensis JC2055^T (83.6 %) and T. flavescens (77.2 %), respectively. We analysed the genome sequences of strains J2M5^T and J1M15^T in terms of carbohydrate-active enzymes, antibiotic resistance genes and virulence factor genes. Strains J2M5^T and J1M15^T contained MK-8 (H₄) and MK-9 (H₄) as the predominant respiratory quinones, respectively. The major polar lipids of both strains were phosphatidylglycerol and diphosphatidylglycerol. Additionally, strain J2M5^T possessed phosphatidylcholine, phosphatidylserine and phosphatidylethanolamine. The cellular sugar components of strain J2M5^T were ribose, mannose, glucose and galactose, and its cellular amino acid components were l-alanine and l-lysine. The cellular sugar components of strain J1M15^T were rhamnose, ribose, mannose and glucose, and its cellular amino acid component was l-alanine. The major cellular fatty acids of strains J2M5^T and J1M15^T were iso-C_{16 : 0} and anteiso-C_15 : 0, respectively. The multiple taxonomic analyses indicated that strains J2M5^T and J1M15^T represent novel species of the genus Nocardioides and Tessaracoccus, respectively. We propose the names Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov. for strain J2M5^T (=KCTC 49461^T=CCUG 74767^T) and strain J1M15^T (=KCTC 49462^T=CCUG 74766^T), respectively.

Effect of external carbon addition and enrofloxacin on the denitrification and microbial community of sequencing batch membrane reactor treating synthetic mariculture wastewater

The effect of sequencing batch membrane bioreactor (SMBR) on external carbon addition and enrofloxacin was investigated to treat synthetic mariculture wastewater. Anoxic/anaerobic and low COD/TN can improve the ammonia oxidation of the system, and the NH₄⁺-N removal efficiency above 99%. External carbon was added and an anoxic environment was set to provide a suitable environment for denitrifying bacteria. When the external carbon source was 50-207 mg/L, the TN removal efficiency (31.82%-37.73%) and the COD of the effluent (28.85-36.58 mg/L) had little change. The partition resistance model showed that cake deposition resistance (R_C,irr) and irreversible resistance (R_PB) were the main components. And with the increase in cleaning times, the fouling rate of membrane components accelerated. Enrofloxacin can promote the TN removal efficiency (45.66%-93.74%) and had a significant effect on TM7a, Cohaesibacter, Vibrio and Phaeobacter.

Devosia ureilytica sp. nov., isolated from Kuche River in China

Two novel strains, designated XJ19-45^T and XJ19-1, were isolated from water of Kuche River in Xinjiang Uygur Autonomous Region, China. Their cells were Gram-stain-negative, aerobic and motile rods. The phylogenetic analyses based on 16S rRNA genes and genomes showed that the two isolates belonged to the genus Devosia and the closest relative was Devosia subaequoris HST3-14^T. The 16S rRNA genes sequences pairwise similarities, average nucleotide identities, digital DNA-DNA hybridizations and average amino acid identities between type strain XJ19-45^T and other relatives were all less than 98.3, 80.3, 23.6 and 85.7 %, respectively, all below the species delineation thresholds. Pan-genomic analysis indicated that the novel isolate XJ19-45^T shared 1594 core gene clusters with the 11 closely related type strains in Devosia, and the number of strain-specific clusters was 390. The major cellular fatty acids (>10 %) of the two isolates were summed feature 8, C_18 : 1 ω7c 11-methyl and C_16 : 0. Diphosphatidylglycerol, phosphatidylglycerol and glycolipids were the major polar lipids, and Q10 was the detected respiratory quinone. Based on the results of phenotypic, physiological, chemotaxonomic and genotypic characterizations, we propose that the isolates represent a novel species, for which the name Devosia ureilytica sp. nov. is proposed. The type strain is XJ19-45^T (=CGMCC 1.19388^T=KCTC 92263^T).

Salinarimonas soli sp. nov., isolated from soil

A light pink coloured bacterium, designated strain BN140002T, was isolated from a soil sample collected in Goesan-gun, Chungcheongbuk-do, Republic of Korea. Cells of strain BN140002T were Gram-stain-negative, aerobic, motile and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed 94.7, 94.7, 93.9, 93.3, 93.4 and 93.0% similarities to Salinarimonas rosea KCTC 22346T, Salinarimonas ramus DSM 22962T, Saliniramus fredricksonii HL-109T, Microvirga soli R491T, Chelatococcus caeni EBR-4-1T and Chelatococcus composti PC-2T, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine. The major cellular fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and summed feature 1 (C12 : 0 aldehyde and/or unknown 10.98) and the predominant ubiquinone was Q-10. The genomic DNA G+C content of strain BN140002T was 70.1 mol%. The genomic orthoANI values between strain BN140002T and Salinarimonas rosea KCTC 22346T and Salinarimonas ramus DSM 22962T were 75.0 and 74.8 %, respectively. Strain BN140002T had a class I-C type CRISPR-Cas system (CRISPR-associated helicase Cas3, CRISPR-associated protein Cas8c, CRISPR-associated protein Cas7, CRISPR-associated RecB family exonuclease Cas4, CRISPR-associated protein 1, 2). Based on phenotypic, chemotaxonomic and phylogenetic data, strain BN140002T should be assigned as a novel species of the genus Salinarimonas , for which the name Salinarimonas soli sp. nov. is proposed. The type strain is BN140002T (=KCTC 42643T=CCTCC AB 2017173T).

Roseomonas oleicola sp. nov., isolated from an oil production mixture in Yumen Oilfield, and emended description of Roseomonas frigidaquae

A pink, ovoid-shaped, Gram-stain-negative, strictly aerobic and motile bacterial strain, designated ROY-5-3^T, was isolated from an oil production mixture from Yumen Oilfield in PR China. The strain grew at 4-42 °C (optimum, 30 °C), at pH 5-10 (optimum, 7) and with 0-5 % (w/v) NaCl (optimum, 0%). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that ROY-5-3^T belongs to the genus Roseomonas and shared the highest pairwise similarities with Roseomonas frigidaquae CW67^T (98.1%), Roseomonas selenitidurans BU-1^T (97.8%), Roseomonas tokyonensis K-20^T (97.7%) and Roseomonas stagni HS-69^T (97.3%). The average nucleotide identity and digital DNA-DNA hybridization values between ROY-5-3^T and other related type strains of Roseomonas species were less than 84.08 and 28.60 %, respectively, both below the species delineation threshold. Pan-genomic analysis showed that the novel isolate ROY-5-3^T shared 3265 core gene families with the four closely related type strains in Roseomonas, and the number of strain-specific gene families was 513. The major fatty acids were identified as summed feature 8 (C_{18 : 1} ω6c/C_{18 : 1} ω7c), summed feature 3 (C_{16 : 1} ω6c/C_{16 : 1} ω7c) and C_{16 : 0}. Strain ROY-5-3^T contained Q-10 as the main ubiquinone and the genomic DNA G+C content was 69.8 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. Based on the phylogenetic, morphological, physiological, chemotaxonomic and genome analyses, strain ROY-5-3^T represents a novel species of the genus Roseomonas for which the name Roseomonas oleicola sp. nov. is proposed. The type strain is ROY-5-3^T (=CGMCC 1.13459^T =KCTC 82484^T).

Basalt-Hosted Microbial Communities in the Subsurface of the Young Volcanic Island of Surtsey, Iceland

The island of Surtsey was formed in 1963–1967 on the offshore Icelandic volcanic rift zone. It offers a unique opportunity to study the subsurface biosphere in newly formed oceanic crust and an associated hydrothermal-seawater system, whose maximum temperature is currently above 120°C at about 100m below surface. Here, we present new insights into the diversity, distribution, and abundance of microorganisms in the subsurface of the island, 50years after its creation. Samples, including basaltic tuff drill cores and associated fluids acquired at successive depths as well as surface fumes from fumaroles, were collected during expedition 5059 of the International Continental Scientific Drilling Program specifically designed to collect microbiological samples. Results of this microbial survey are investigated with 16S rRNA gene amplicon sequencing and scanning electron microscopy. To distinguish endemic microbial taxa of subsurface rocks from potential contaminants present in the drilling fluid, we use both methodological and computational strategies. Our 16S rRNA gene analysis results expose diverse and distinct microbial communities in the drill cores and the borehole fluid samples, which harbor thermophiles in high abundance. Whereas some taxonomic lineages detected across these habitats remain uncharacterized (e.g., Acetothermiia, Ammonifexales), our results highlight potential residents of the subsurface that could be identified at lower taxonomic rank such as Thermaerobacter, BRH-c8a (Desulfallas-Sporotomaculum), Thioalkalimicrobium, and Sulfurospirillum. Microscopy images reveal possible biotic structures attached to the basaltic substrate. Finally, microbial colonization of the newly formed basaltic crust and the metabolic potential are discussed on the basis of the data.

Capnocytophaga periodontitidis sp. nov., isolated from subgingival plaque of periodontitis patient

Two carbon dioxide-requiring, gliding, Gram-stain-negative strains, designated p1a2^T and 051621, were isolated from subgingival plaque in association with severe periodontitis. The 16S rRNA gene sequence analysis revealed that they represented members of the genus Capnocytophaga and had less than 96.4 % pairwise similarity with species with validly published names in this genus. The whole-genome sequences of those strains had less than 91.9 % average nucleotide identity and 48.4 % digital DNA-DNA hybridization values with the other type strains of species of the genus Capnocytophaga, both below the species delineation threshold. The results of pan-genomic analysis indicated that p1a2^T and 051621 shared 765 core gene families with the other ten species in this genus, and the numbers of strain-specific gene families were 493 and 455, respectively. The major fatty acids were iso-C_15 : 0 and C_16 : 0. A combination of phenotypic, chemotaxonomic, phylogenetic and genotypic data clearly indicate that p1a2^T and 051621 should be considered to represent a novel species of the genus Capnocytophaga, for which the name Capnocytophaga periodontitidis sp. nov. is proposed. The type strain is p1a2^T (=CGMCC 1.17337^T=JCM 34126^T).

The oil spill and the use of chemical surfactant reduce microbial corrosion on API 5L steel buried in saline soil

In order to evaluate the biocorrosion of API 5L metal buried in saline soils, three different conditions in microcosms were evaluated. The control microcosm contained only saline soil, the second had the addition of petroleum, and the third contained the addition of both petroleum and surfactant. The corrosion rate of the metals was measured by loss of mass after 30 days, and the microbial communities were delineated using 16S rRNA gene sequencing techniques. The species were dominated by halophiles in all samples analyzed. Among the bacteria, the predominant group was Proteobacteria, with emphasis on the Alphaproteobacteria and Gammaproteobacteria. Betaproteobacteria and Deltaproteobacteria members were also identified in a smaller number in all conditions. Firmicutes were especially abundant in the control system, although it was persistently present in other conditions evaluated. Bacteroidetes and Actinobacteria were also present in a considerable number of OTUs in the three microcosms. Halobacteria were predominant among archaea and were present in all conditions. The analysis pointed to a conclusion that in the control microcosm, the corrosion rate was higher, while the microcosm containing only oil had the lowest corrosion rate. These results suggest that, under these conditions, the entry of other carbon sources favors the presence of petroleum degraders, rather than samples involved in the corrosion of metals.

Microbacterium karelineae sp. nov. isolated from a halophyte plant in the Taklamakan desert

A bacterial strain, designated TRM 80801^T, was isolated from the Karelinea in Taklamakan desert, Xinjiang Uygur Autonomous Region, north-west China. Cells were Gram-stain-positive, aerobic, non-motile, short rods. Strain TRM 80801^T grew at 4-50 °C, with optimum growth at 28 °C, and grew at pH 6.0-11.0 and 1-15 % (w/v) NaCl. Phylogenetic analyses of the 16S rRNA gene sequences placed strain TRM 80801^T within the genus Microbacterium with the highest similarities to Microbacterium suaedae YZYP 306^T (98.97 %) and Microbacterium indicum BBH6^T (98.17 %), respectively. The DNA G+C content of TRM 80801^T is 69.38 mol%. The cell-wall peptidoglycan contained the amino acids ornithine, glutamic acid, glycine and alanine, the diagnostic diamino acid was ornithine. The acyl type of the peptidoglycan was glycolyl. Whole-cell sugars were ribose, mannose, glucose, rhamnose and galactose. The major cellular fatty acids were anteiso-C_15 : 0, anteiso-C_17 : 0 and iso-C_16 : 0. The predominant menaquinones were MK-10, MK-11 and MK-12. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol. The whole-genome average nucleotide identity (ANI) value between strain TRM 80801^T and Microbacterium suaedae YZYP 306^T is 70.2 %. On the basis of the evidence presented in this study, strain TRM 80801^T is representative of a novel species in the genus Microbacterium, for which the name Microbacterium karelineae sp. nov. is proposed. The type strain is TRM 80801^T (=CCTCC AB 2019248^T=KCTC 49357^T).

Tessaracoccus coleopterorum sp. nov., isolated from the intestine of the dark diving beetle, Hydrophilus acuminatus

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated as strain HDW20^T, isolated from the intestine of the dark diving beetle Hydrophilus acuminatus. The isolate was Gram-stain-positive, facultatively anaerobic, non-motile, coccus-shaped, and formed pale orange colonies. Phylogenetic analysis based on 16S rRNA gene sequences and genome sequences showed that the isolate belonged to the genus Tessaracoccus in the phylum Actinobacteria and was closely related to T. flavescens SST-39^T, T. defluvii JCM 17540^T, and T. aquimaris NSG39^T, with the highest 16S rRNA gene sequence similarity of 98.5 % and a highest average nucleotide identity (ANI) value of 80.6 %. The major cellular fatty acids were C_18 : 1  ω9c and anteiso-C_15 : 0. The main respiratory quinone was MK-9 (H₄). The major polar lipid components were phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content was 69.0 %. The isolate contains ʟʟ-diaminopimelic acid, ʟ-alanine, and ʟ-lysine as amino acid components, and ribose, glucose, and galactose as sugar components of the cell wall peptidoglycan. The results of phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses suggested that strain HDW20^T represents a novel species within the genus Tessaracoccus. We propose the name Tessaracoccus coleopterorum sp. nov. The type strain is HDW20^T (=KACC 21348^T=KCTC 49324^T=JCM 33674^T).

Azospirillum oleiclasticum sp. nov, a nitrogen-fixing and heavy oil degrading bacterium isolated from an oil production mixture of Yumen Oilfield

Two nitrogen-fixing and heavy oil degrading strains, designated RWY-5-1-1^T and ROY-1-1-2, were isolated from an oil production mixture from Yumen Oilfield in China. The 16S rRNA gene sequence showed they belong to Azospirillum and have less than 96.1 % pairwise similarity with each species in this genus. The average nucleotide identity and digital DNA-DNA hybridization values between them and other type strains of Azospirillum species were less than 75.69 % and 22.0 %, respectively, both below the species delineation threshold. Pan-genomic analysis showed that the novel isolate RWY-5-1-1^T shared 2145 core gene families with other type strains in Azospirillum, and the number of strain-specific gene families was 1623, almost two times more than the number known from other species. Furthermore, genes related to nitrogenase, hydrocarbon degradation and biosurfactant production were found in the isolates' genomes. Also, this strain was capable of reducing acetylene to ethylene at a rate of 22nmol ethylene h^-1 (10⁸ cells) and degrading heavy oil at a rate of 36.2 %. The major fatty acids and polar lipids were summed feature 8 (C_18:1ω7c/C_18:1ω6c), and phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylcholine. Furthermore, a combination of phenotypic, chemotaxonomic, phylogenetic and genotypic data clearly indicated that strains RWY-5-1-1^T and ROY-1-1-2 represent a novel species, for which the name Azospirillum oleiclasticum sp. nov. is proposed. The type strain is RWY-5-1-1^T (=CGMCC 1.13426^T =KCTC 72259 ^T). Azospirillum novel strains with the ability of heavy oil degradation associated with the promotion of plant growth has never been reported to date.

Crenobacter caeni sp. nov. Isolated from Sludge

Strain HX-7-9^T was isolated from the activated sludge collected from the outlet of the biochemical treatment facility of agricultural chemical plant in Nanjing, Jiangsu province, PR China. Strain HX-7-9^T is Gram staining-negative, rod-shaped, non-spore-forming and flagellated. The 16S rRNA gene-based phylogenetic analysis indicate that strain HX-7-9^T belongs to the genus Crenobacter, moderately related to Crenobacter luteus YIM-78141^T (94.8% similarity). The genomic DNA G+C content of the strain was 67.5 mol%. Strain HX-7-9^T was able to grow at 16-45 °C (optimum at 37 °C), at pH 6.0-8.0 (optimum at pH 7.0) and with 0-1% (w/v) NaCl (optimum at 0). Predominant fatty acid constituents were C_16:0 and summed feature 3 (C_16:1ω7c and/or C_16:1ω6c). The respiratory ubiquinone was Q-8. The polar lipid profile is composed of diphosphatidylglycerol (DPG), phosphatidylmonomethylethanolamine (PME), phosphatidylethanolamine (PE), phospholipids (PL), glycolipid (GL) and aminophospholipid (APL). The ANI and dDDH values obtained between the genomes of HX-7-9^T and C. luteus YIM-78141^T were 79.8 and 19.1%, respectively. On the basis of data from phenotypic, chemotaxonomic and genotypic analysis, strain HX-7-9^T represents a novel species of the genus Crenobacter, for which the name Crenobacter caeni sp. nov. is proposed. The type strain is HX-7-9^T (= KCTC 72654^T = CCTCC AB 2019349^T).

Azoarcus halotolerans sp. nov., a novel member of Rhodocyclaceae isolated from activated sludge collected in Hong Kong

A floc-forming bacterial strain, designated HKLI-1^T, was isolated from the activated sludge of a municipal sewage treatment plant in Hong Kong SAR, PR China. Cells of this strain were Gram-stain-negative, strictly aerobic, catalase- and oxidase-positive, rod-shaped and motile by means of a single polar flagellum. Growth occurred at 18-37 °C (optimum, 28 °C), pH 5.5-9.0 (optimum, pH 7.5) and with 0-8.0 % (w/v) NaCl (optimum, 1-1.5 %) concentration. The major fatty acids of strain HKLI-1^T were C_16 : 0 and summed feature 3 (C_16 : 1 ω7c and/or C_16 : 1 ω6c). The polar lipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and three unidentified lipids. The DNA G+C content was 63.5 mol% from whole genomic sequence analysis. Based on the results of 16S rRNA gene sequences analysis, this strain should be assigned to the genus Azoarcus and is closely related to Azoarcus olearius DQS-4^T (94.93 % 16S rRNA gene sequence pairwise similarity), Azoarcus toluclasticus MF63^T (94.91 %) and Azoarcus communis SWub3^T (94.01 %), but separate from them by large distances in different phylogenetic trees. Based on whole genome analysis, the orthologous average nucleotide identity and in silico DNA-DNA hybridization values against four of the closest relatives were 73.03-74.83 and 17.2-23.0 %, respectively. The phylogenetic, genotypic, phenotypic and chemotaxonomic data demonstrated that strain HKLI-1^T could be distinguished from its phylogenetically related species, and that this strain represented a novel species within the genus Azoarcus, for which the name Azoarcus halotolerans sp. nov. is proposed. The type strain is HKLI-1^T (= 72659^T=CCTCC AB 2019312^T).

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.

Tessaracoccus antarcticus sp. nov., a rhodopsin-containing bacterium from an Antarctic environment and emended description of the genus Tessaracoccus

A Gram-stain-positive, facultatively anaerobic bacterium, strain JDX10T, was isolated from a soil sample of Fildes Peninsula, Antarctica. Cells of the strain were irregular rod-shaped and non-motile. Cells grew at 4–40 °C (optimum, 28 °C), at pH 6.0–9.0 (optimum, 7.5) and with 0.0–3.0 % (w/v) NaCl (optimum, 1.0 %). According to phylogenetic analysis based on 16S rRNA gene sequences, strain JDX10T was associated with the genus Tessaracoccus , and showed highest similarities to Tessaracoccus rhinocerotis CCTCC AB 2013217T (97.2 %), Tessaracoccus flavescens SST-39T (96.9 %) and Tessaracoccus terricola JCM 32157T (96.9 %). The average nucleotide identity scores of strain JDX10T to T. rhinocerotis CCTCC AB 2013217T and T. bendigoensis JCM 13525T were 74.8 and 73.3 %, respectively and the Genome-to-Genome Distance Calculator scores were 19.2 and 18.7 %, respectively. The major (>10.0 %) cellular fatty acid was anteiso-C15 : 0. The predominant isoprenoid quinone was MK-10(H4). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The phylogenetic analysis and physiological and biochemical data showed that strain JDX10T should be classified as representing a novel species in the genus Tessaracoccus , for which the name Tessaracoccus antarcticus sp. nov. is proposed. The type strain is JDX10T (=MCCC 1H00351T=KCTC 49242T).

Application of humic acid changes the microbial communities and inhibits the expression of tetracycline resistance genes in 4-chlorophenol wastewater treatment

The occurrence and spread of antibiotic resistance genes (ARGs) are concerns that have threatened public health for many years. However, the effects of humic acid (HA) application on the expression of ARGs in chlorophenols wastewater treatment are rarely reported. In this study, we investigated the sludge performance, including the removal of pollutants, changes in the microbial communities, and the expression of tetracycline resistance genes (TRGs), to explore the function of HA in 4-chlorophenol (4-CP) wastewater treatment at different HA concentrations. The results showed that HA application did not significantly stimulate the removal of pollutants, other than the removal of PO₄^3--P. High-throughput sequencing analysis indicated that the application of HA influenced the microbial communities and changed the expression level of TRGs. Quantitative real-time PCR analysis showed that the expression of numerous TRGs (tetC, tetG, tetW, tetX, and intI1) was significantly inhibited by the application of HA (25 mg L^-1) during 4-CP wastewater treatment. In summary, HA application played an important role in treating chlorophenols wastewater and reducing the expression of TRGs. This work aimed to provide an efficient method of reducing the expression level of ARGs in industrial wastewater treatment, which has inevitable environmental significance.

Genomic and phenotypic insights point to diverse ecological strategies by facultative anaerobes obtained from subsurface coal seams

Microbes in subsurface coal seams are responsible for the conversion of the organic matter in coal to methane, resulting in vast reserves of coal seam gas. This process is important from both environmental and economic perspectives as coal seam gas is rapidly becoming a popular fuel source worldwide and is a less carbon intensive fuel than coal. Despite the importance of this process, little is known about the roles of individual bacterial taxa in the microbial communities carrying out this process. Of particular interest is the role of members of the genus Pseudomonas, a typically aerobic taxa which is ubiquitous in coal seam microbial communities worldwide and which has been shown to be abundant at early time points in studies of ecological succession on coal. The current study performed aerobic isolations of coal seam microbial taxa generating ten facultative anaerobic isolates from three coal seam formation waters across eastern Australia. Subsequent genomic sequencing and phenotypic analysis revealed a range of ecological strategies and roles for these facultative anaerobes in biomass recycling, suggesting that this group of organisms is involved in the degradation of accumulated biomass in coal seams, funnelling nutrients back into the microbial communities degrading coal to methane.

Chitiniphilus eburneus sp. nov., a novel chitinolytic bacterium isolated from sludge

A novel Gram-stain-negative, curved rod-shaped, motile and non-endospore-forming strain, designated HX-2-15^T, was isolated from activated sludge of agricultural chemical plant in Nanjing, Jiangsu province, PR China (32° 03' N, 118° 46' E) . Growth was observed at 15-37 °C (optimum between 25 and 30 °C), at pH 6.0-8.0 (optimum at pH 7.0) and with 0-3.0 % (w/v) NaCl (optimum at 0.5 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain showed closest affiliation to Chitiniphilus shinanonensis SAY3^T, with a sequence similarity of 99.0 %. The predominant cellular fatty acids were C_16:0, C_17:0 cyclo and summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c). The major quinone was ubiquinone Q-8 . The polar lipid profile was composed of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, one unidentified lipid and one unidentified aminophosphoglycolipid . The genomic DNA G+C content of the strain was 63.6 mol%. The ANI and dDDH values obtained between the genomes of HX-2-15^T and C. shinanonensis SAY3^T were 85.3 and 29.3 % respectively. On the basis of data from phenotypic, chemotaxonomic and genotypic analysis, strain HX-2-15^T represents a novel species of the genus Chitiniphilus, for which the name Chitiniphilus eburneus sp. nov. is proposed. The type strain is HX-2-15^T (=KCTC 72286^T=CCTCC AB 2019178^T).

Bacteria isolated from Bengal cat (Felis catus × Prionailurus bengalensis) anal sac secretions produce volatile compounds potentially associated with animal signaling

In social animals, scent secretions and marking behaviors play critical roles in communication, including intraspecific signals, such as identifying individuals and group membership, as well as interspecific signaling. Anal sacs are an important odor producing organ found across the carnivorans (species in the mammalian Order Carnivora). Secretions from the anal sac may be used as chemical signals by animals for behaviors ranging from defense to species recognition to signaling reproductive status. In addition, a recent study suggests that domestic cats utilize short-chain free fatty acids in anal sac secretions for individual recognition. The fermentation hypothesis is the idea that symbiotic microorganisms living in association with animals contribute to odor profiles used in chemical communication and that variation in these chemical signals reflects variation in the microbial community. Here we examine the fermentation hypothesis by characterizing volatile organic compounds (VOC) and bacteria isolated from anal sac secretions collected from a male Bengal cat (Felis catus × Prionailurus bengalensis), a cross between the domestic cat and the leopard cat. Both left and right anal sacs of a male Bengal cat were manually expressed (emptied) and collected. Half of the material was used to culture bacteria or to extract bacterial DNA and the other half was used for VOC analysis. DNA was extracted from the anal sac secretions and used for a 16S rRNA gene PCR amplification and sequencing based characterization of the microbial community. Additionally, some of the material was plated out in order to isolate bacterial colonies. Three taxa (Bacteroides fragilis, Tessaracoccus, and Finegoldia magna) were relatively abundant in the 16S rRNA gene sequence data and also isolated by culturing. Using Solid Phase Microextraction (SPME) gas chromatography-mass spectrometry (GC-MS), we tentatively identified 52 compounds from the Bengal cat anal sac secretions and 67 compounds from cultures of the three bacterial isolates chosen for further analysis. Among 67 compounds tentatively identified from bacterial isolates, 51 were also found in the anal sac secretion. We show that the bacterial community in the anal sac consists primarily of only a few abundant taxa and that isolates of these taxa produce numerous volatiles that are found in the combined anal sac volatile profile. Several of these volatiles are found in anal sac secretions from other carnivorans, and are also associated with known bacterial biosynthesis pathways. This is consistent with the fermentation hypothesis and the possibility that the anal sac is maintained at least in part to house bacteria that produce volatiles for the host.

Extant microbial communities in the partially desiccated Rincon de Parangueo maar crater lake in Mexico

Rincon de Parangueo is a maar where a perennial lake was present until the 1980s. A conspicuous feature of the lake’s sediments is the presence of bioherms and organo-sedimentary deposits produced by microbial communities. The gradual lake desiccation during the last 40 years has produced dramatic environmental changes inside the maar basin, which resulted in the formation of a highly saline-alkaline system with extant microorganisms. In this paper we succinctly describe the geologic setting where the microbial communities have developed inside of the maar crater and the results obtained from high-throughput sequencing methods to characterize the microbial component (Bacteria, Eukarya and Archaea) in endolithic mats of calcareous sediments, and microbial mats and free-living microorganisms in the soda ponds. The studied sites displayed different microbial communities with a diverse number of phylotypes belonging to Bacteria and Eukarya, contrasting with a much less diverse component in Archaea. The sequences here detected were related to environmental sequences from sites with extreme life conditions such as high alkalinity (alkaliphiles), high salinity (halophiles) and high temperature (thermophiles). Moreover, our results indicate an important unexplored endemic microbial biodiversity in the vestiges of the former lake that need to be studied.

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

Functional Genetic Diversity and Culturability of Petroleum-Degrading Bacteria Isolated From Oil-Contaminated Soils

In this study, we compared the culturability of aerobic bacteria isolated from long-term oil-contaminated soils via enrichment and direct-plating methods; bacteria were cultured at 30°C or ambient temperatures. Two soil samples were collected from two sites in the Shengli oilfield located in Dongying, China. One sample (S0) was close to the outlet of an oil-production water treatment plant, and the other sample (S1) was located 500 m downstream of the outlet. In total, 595 bacterial isolates belonging to 56 genera were isolated, distributed in Actinobacteria, Firmicutes, Bacterioidetes, and Proteobacteria. It was interesting that Actinobacteria and Firmicutes were not detected from the 16S rRNA gene clone library. The results suggested the activation of rare species during culture. Using the enrichment method, 239 isolates (31 genera) and 96 (22 genera) isolates were obtained at ambient temperatures and 30°C, respectively, from S0 soil. Using the direct-plating method, 97 isolates (15 genera) and 163 isolates (20 genera) were obtained at ambient temperatures and 30°C, respectively, from two soils. Of the 595 isolates, 244 isolates (41.7% of total isolates) could degrade n-hexadecane. A greater number of alkane-degraders was isolated at ambient temperatures using the enrichment method, suggesting that this method could significantly improve bacterial culturability. Interestingly, the proportion of alkane degrading isolates was lower in the isolates obtained using enrichment method than that obtained using direct-plating methods. Considering the greater species diversity of isolates obtained via the enrichment method, this technique could be used to increase the diversity of the microbial consortia. Furthermore, phenol hydroxylase genes (pheN), medium-chain alkane monooxygenases genes (alkB and CYP153A), and long-chain alkane monooxygenase gene (almA) were detected in 60 isolates (11 genotypes), 91 isolates (27 genotypes) and 93 isolates (24 genotypes), and 34 isolates (14 genotypes), respectively. This study could provide new insights into microbial resources from oil fields or other environments, and this information will be beneficial for bioremediation of petroleum contamination and for other industrial applications.

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).

Study of methanogenic enrichment cultures of rock cores from the deep subsurface of the Iberian Pyritic Belt

Two deep boreholes were drilled at 320 and 620 meters below surface in the Iberian Pyritic Belt (IPB) at Peña de Hierro (Huelva, Southwestern Spain). Cores were sampled and used for the establishment of enrichment cultures with methanogenic activity. The cultivable diversity of these enrichments was accessed using different cultivation techniques and several isolates were recovered in pure culture from various depths in both boreholes. Although no archaeal isolates were obtained in pure culture, strict anaerobes and facultative anaerobic bacteria belonging to the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were isolated and identified using the 16S rRNA gene sequence. Analysis of three selected enrichment cultures by amplification of both bacterial and archaeal 16S rRNA gene followed by pyrosequencing revealed further information on the populations enriched. The archaeal sequences obtained from the methanogenic enrichment cultures belonged to the orders Methanosarcinales and Methanocellales. To best of our knowledge this is the first report of enrichment in members of the Methanocellales in a deep terrestrial subsurface ecosystem. Several bacterial populations, predominantly consisting of Firmicutes and Proteobacteria, were also enriched. The prevalent microbial populations enriched as detected by pyrosequencing analysis, as well as the bacterial isolates cultivated were affiliated with known fermentative, sulfate reducing and acetogenic bacteria or methanogenic archaea. Our results show a great diversity in the microbial communities of the IPB deep subsurface.

Complete Genome Sequence of Tessaracoccus sp. Strain T2.5-30 Isolated from 139.5 Meters Deep on the Subsurface of the Iberian Pyritic Belt

Here, we report the complete genome sequence of Tessaracoccus sp. strain T2.5-30, which consists of a chromosome with 3.2 Mbp, 70.4% G+C content, and 3,005 coding DNA sequences. The strain was isolated from a rock core retrieved at a depth of 139.5 m in the subsurface of the Iberian Pyritic Belt (Spain).

Soda pans of the Pannonian steppe harbor unique bacterial communities adapted to multiple extreme conditions

Soda pans of the Pannonian steppe are unique environments regarding their physical and chemical characteristics: shallowness, high turbidity, intermittent character, alkaline pH, polyhumic organic carbon concentration, hypertrophic condition, moderately high salinity, sodium and carbonate ion dominance. The pans are highly productive environments with picophytoplankton predominance. Little is known about the planktonic bacterial communities inhabiting these aquatic habitats; therefore, amplicon sequencing and shotgun metagenomics were applied to reveal their composition and functional properties. Results showed a taxonomically complex bacterial community which was distinct from other soda lakes regarding its composition, e.g. the dominance of class Alphaproteobacteria was observed within phylum Proteobacteria. The shotgun metagenomic analysis revealed several functional gene components related to the harsh and at the same time hypertrophic environmental conditions, e.g. proteins involved in stress response, transport and hydrolase systems targeting phytoplankton-derived organic matter. This is the first detailed report on the indigenous planktonic bacterial communities coping with the multiple extreme conditions present in the unique soda pans of the Pannonian steppe.

Tessaracoccus massiliensis sp. nov., a new bacterial species isolated from the human gut

A new Actinobacterium, designated Tessaracoccus massiliensis type strain SIT-7(T) (= CSUR P1301 = DSM 29060), have been isolated from a Nigerian child with kwashiorkor. It is a facultative aerobic, Gram positive, rod shaped, non spore-forming, and non motile bacterium. Here, we describe the genomic and phenotypic characteristics of this isolate. Its 3,212,234 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 67.81% and contains 3,058 protein-coding genes and 49 RNA genes.

Characterization of the transcriptome of Achromobacter sp. HZ01 with the outstanding hydrocarbon-degrading ability

Microbial remediation has become one of the most important strategies for eliminating petroleum pollutants. Revealing the transcript maps of microorganisms with the hydrocarbon-degrading ability contributes to enhance the degradation of hydrocarbons and further improve the effectiveness of bioremediation. In this study, we characterized the transcriptome of hydrocarbon-degrading Achromobacter sp. HZ01 after petroleum treatment for 16h. A total of 38,706,280 and 38,954,413 clean reads were obtained by RNA-seq for the petroleum-treated group and control, respectively. By an effective de novo assembly, 3597 unigenes were obtained, including 3485 annotated transcripts. Petroleum treatment had significantly influenced the transcriptional profile of strain HZ01, involving 742 differentially expressed genes. A part of genes were activated to exert specific physiological functions, whereas more genes were down-regulated including specific genes related to cell motility, genes associated with glycometabolism, and genes coding for ribosomal proteins. Identification of genes related to petroleum degradation revealed that the fatty acid metabolic pathway and a part of monooxygenases and dehydrogenases were activated, whereas the TCA cycle was inactive. Additionally, terminal oxidation might be a major aerobic pathway for the degradation of n-alkanes in strain HZ01. The newly obtained data contribute to better understand the gene expression profiles of hydrocarbon-degrading microorganisms after petroleum treatment, to further investigate the genetic characteristics of strain HZ01 and other related species and to develop cost-effective and eco-friendly strategies for remediation of crude oil-polluted environments.

Multiwall carbon nanotubes increase the microbial community in crude oil contaminated fresh water sediments

Since crude oil contamination is one of the biggest environmental concerns, its removal from contaminated sites is of interest for both researchers and industries. In situ bioremediation is a promising technique for decreasing or even eliminating crude oil and hydrocarbon contamination. However, since these compounds are potentially toxic for many microorganisms, high loads of contamination can inhibit the microbial community and therefore reduce the removal rate. Therefore, any strategy with the ability to increase the microbial population in such circumstances can be of promise in improving the remediation process. In this study, multiwall carbon nanotubes were employed to support microbial growth in sediments contaminated with crude oil. Following spiking of fresh water sediments with different concentrations of crude oil alone and in a mixture with carbon nanotubes for 30days, the microbial profiles in these sediments were obtained using FLX-pyrosequencing. Next, the ratios of each member of the microbial population in these sediments were compared with those values in the untreated control sediment. This study showed that combination of crude oil and carbon nanotubes can increase the diversity of the total microbial population. Furthermore, these treatments could increase the ratios of several microorganisms that are known to be effective in the degradation of hydrocarbons.