Reclassification of Cellulosimicrobium variabile Bakalidou et al. 2002 as Isoptericola variabilis gen. nov., comb. nov

Genomic analysis of Isoptericola halotolerans SM2308 reveals its potential involved in fucoidan degradation

Marine bacteria play important roles in the degradation and recycling of algal polysaccharides. However, the marine bacteria involved in fucoidan degradation and their degradation pathways remain poorly understood. Here, we report the complete genome sequence of Isoptericola halotolerans SM2308, isolated from a brown algal sample collected from an intertidal zone of the Yellow Sea in China. The genome of strain SM2308 consists of a single circular chromosome of 4,011,455 bp with a high GC content of 72.70 %. Strain SM2308 exhibited rapid growth on fucoidan as the sole carbon source, indicating its capacity to degrade fucoidan. Gene annotation and metabolic pathway analyses showed that strain SM2308 possesses a complete pathway for utilizing fucoidan, including the extracellular breakdown of polymeric fucoidan into smaller fucooligosaccharides/fucose by fucoidanases, the transmembrane transport of fucooligosaccharides/fucose into the cytoplasm by an ABC transporter, and the intracellular fucose catabolism via a non-phosphorylative pathway. This represents the first genome of an actinobacterium from the order Micrococcales with fucoidan-degrading ability. The genome of Isoptericola halotolerans SM2308 provides insights into the role of actinobacteria in the biogeochemical cycling of fucoidan in marine ecosystems.

Assessing hydrocarbon degradation capacity of Isoptericola peretonis sp. nov. and related species: a comparative study

Since the beginning of their production and use, fossil fuels have affected ecosystems, causing significant damage to their biodiversity. Bacterial bioremediation can provide solutions to this environmental problem. In this study, the new species Isoptericola peretonis sp. nov. 4D.3T has been characterized and compared to other closely related species in terms of hydrocarbon degradation and biosurfactant production by in vitro and in silico analyses. Biosurfactants play an important role in microbial hydrocarbon degradation by emulsifying hydrocarbons and making them accessible to the microbial degradation machinery. The tests performed showed positive results to a greater or lesser degree for all strains. In the synthesis of biosurfactants, all the strains tested showed biosurfactant activity in three complementary assays (CTAB, hemolysis and E24%) and rhamnolipid synthesis genes have been predicted in silico in the majority of Isoptericola strains. Regarding hydrocarbon degradation, all the Isoptericola strains analyzed presented putative genes responsible for the aerobic and anaerobic degradation of aromatic and alkane hydrocarbons. Overall, our results highlight the metabolic diversity and the biochemical robustness of the Isoptericola genus which is proposed to be of interest in the field of hydrocarbon bioremediation.

Isoptericola haloaureus sp. nov., a dimorphic actinobacterium isolated from mangrove sediments of southeast India, implicating biosaline agricultural significance through nitrogen fixation and salt tolerance genes

Strain MP-1014T, an obligate halophilic actinobacterium, was isolated from the mangrove soil of Thandavarayancholanganpettai, Tamil Nadu, India. A polyphasic approach was utilized to explore its phylogenetic position completely. The isolate was Gram-positive, filamentous, non-motile, and coccoid in older cultures. Ideal growth conditions were seen at 30 °C and pH 7.0, with 5% NaCl (W/V), and the DNA G + C content was 73.3%. The phylogenic analysis of this strain based upon 16S rRNA gene sequence revealed 97-99.8% similarity to the recognized species of the genus Isoptericola. Strain MP-1014T exhibits the highest similarity to I. sediminis JC619T (99.7%), I. chiayiensis KCTC19740T (98.9%), and subsequently to I. halotolerans KCTC19646T (98.6%), when compared with other members within the Isoptericola genus (< 98%). ANI scores of strain MP-1014T are 86.4%, 84.2%, and 81.5% and dDDH values are 59.7%, 53.6%, and 34.8% with I. sediminis JC619T, I. chiayiensis KCTC19740T and I. halotolerans KCTC19646T respectively. The major polar lipids of the strain MP-1014T were phosphatidylinositol, phosphatidylglycerol, diphosphotidylglycerol, two unknown phospholipids, and glycolipids. The predominant respiratory menaquinones were MK9 (H4) and MK9 (H2). The major fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C14:0, C15:0, and C16:0. Also, initial genome analysis of the organism suggests it as a biostimulant for enhancing agriculture in saline environments. Based on phenotypic and genetic distinctiveness, the strain MP-1014 T represents the novel species of the genus Isoptericola assigned Isoptericola haloaureus sp. nov., is addressed by the strain MP-1014 T, given its phenotypic, phylogenetic, and hereditary uniqueness. The type strain is MP-1014T [(NCBI = OP672482.1 = GCA_036689775.1) ATCC = BAA 2646T; DSMZ = 29325T; MTCC = 13246T].

Isoptericola luteus sp. nov., a novel yellow bacterium isolated from soil

An aerobic, non-motile, Gram-stain-positive bacterium, designated strain NEAU-Y5T, was isolated from a soil sample collected from Northeast Agricultural University, Heilongjiang province. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-Y5T belonged to the genus and showed high 16S rRNA sequence similarity to Isoptericola variabilis (98.9 %), Isoptericola nanjingensis (98.9 %), Isoptericola cucumis (98.5 %), Isoptericola hypogeus (98.5 %), Isoptericola dokdonensis (98.5 %), Isoptericola jiangsuensis (98.3 %), and Isoptericola halalbus (98.1 %), followed by other members of the genus Isoptericola (<98 %), and phylogenetically clustered with I. dokdonensis and I. jiangsuensis. Strain NEAU-Y5T was found to grow at 4-40 °C (optimum, 28 °C), pH 6.0-12.0 (optimum, pH 7.0), and tolerated 0-6 % NaCl (w/v). The cell-wall peptidoglycan type was l-Lys-d-Asp. The whole-cell hydrolysates contained glucose, galactose, and ribose. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, and glucosamine unknown phospholipid. Major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-9(H4). The DNA G+C content was 73.4 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between strain NEAU-Y5T and the type strains of the genus Isoptericola ranged from 18.6 to 23.5 % and from 77.3 to 81.6 %, respectively. Based on morphological, physiological, chemotaxonomic, and phylogenetic data, as well as digital DNA-DNA hybridization and average nucleotide identity values, the novel strain NEAU-Y5T could be differentiated from its closest relatives. Therefore, the strain represents a novel species of the genus Isoptericola, for which the name Isoptericola luteus sp. nov. is proposed. The type strain is NEAU-Y5T (=CCTCC AA 2019087T=DSM 110637T).

Termite Microbial Symbiosis as a Model for Innovative Design of Lignocellulosic Future Biorefinery: Current Paradigms and Future Perspectives

The hunt for renewable and alternative fuels has driven research towards the biological conversion of lignocellulosic biomass (LCB) into biofuels, including bioethanol and biohydrogen. Among the natural biomass utilization systems (NBUS), termites represent a unique and easy-to-access model system to study host–microbe interactions towards lignocellulose bioconversion/valorization. Termites have gained significant interest due to their highly efficient lignocellulolytic systems. The wood-feeding termites apply a unique and stepwise process for the hydrolysis of lignin, hemicellulose, and cellulose via biocatalytic processes; therefore, mimicking their digestive metabolism and physiochemical gut environments might lay the foundation for an innovative design of nature-inspired biotechnology. This review highlights the gut system of termites, particularly the wood-feeding species, as a unique model for future biorefinery. The gut system of termites is a treasure-trove for prospecting novel microbial species, including protists, bacteria, and fungi, having higher biocatalytic efficiencies and biotechnological potentials. The significance of potential bacteria and fungi for harnessing the enzymes appropriate for lignocellulosic biorefinery is also discussed. Termite digestomes are rich sources of lignocellulases and related enzymes that could be utilized in various industrial processes and biomass-related applications. Consideration of the host and symbiont as a single functioning unit will be one of the most crucial strategies to expedite developments in termite-modeled biotechnology in the future.

Isoptericola croceus sp. nov., a novel actinobacterium isolated from saline-alkali soil

A novel actinomycete, designated strain q2^T, was isolated from the saline-alkaline soil, collected from Daqing, Heilongjiang province, China. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain q2^T belongs to the genus Isoptericola, and showed the highest sequence similarity to Isoptericola halotolerans KCTC 19046^T (98.48%) and Isoptericola chiayiensis KCTC 19740^T (98.13%), respectively. The average nucleotide identity values between strain q2^T and other members of the genus Isoptericola were lower than 95% recommended for distinguishing novel prokaryotic species. Cells of strain q2^T were Gram-staining-positive, aerobic, non-motile, rod-shaped and non-spore-forming. Colonies of strain q2^T were golden-yellow pigmented, tidy edged and smooth surfaced. Growth occurred at 15-37 °C (optimum, 29 °C), pH 7.0-10.0 (optimum, pH 8.0). The predominant respiratory quinones were MK-9(H₄) and MK-9(H₂). The main detected polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and phosphatidylinositol mannoside. The peptidoglycan compositions were L-alanine, D-aspartic, L-glutamic acid and L-lysine (type A4α). The major cellular fatty acids (> 10%) were anteiso-C_15:0, iso-C_15:0, and anteiso-C_17:0. The G+C content of the genomic DNA was determined to be 69.7%. Based on the phenotypic, physiological, genotypic, and phylogenetic data, strain q2^T represents a novel species of the genus Isoptericola, for which the name Isoptericola croceus sp. nov. is proposed. The type strain is q2^T (= GDMCC 1.2923^T = KCTC 49759^T).

The car tank lid bacteriome: a reservoir of bacteria with potential in bioremediation of fuel

Bioprospecting of microorganisms suitable for bioremediation of fuel or oil spills is often carried out in contaminated environments such as gas stations or polluted coastal areas. Using next-generation sequencing (NGS) we analyzed the microbiota thriving below the lids of the fuel deposits of diesel and gasoline cars. The microbiome colonizing the tank lids differed from the diversity found in other hydrocarbon-polluted environments, with Proteobacteria being the dominant phylum and without clear differences between gasoline or diesel-fueled vehicles. We observed differential growth when samples were inoculated in cultures with gasoline or diesel as the main carbon source, as well as an increase in the relative abundance of the genus Pseudomonas in diesel. A collection of culturable strains was established, mostly Pseudomonas, Stenotrophomonas, Staphylococcus, and Bacillus genera. Strains belonging to Bacillus, Pseudomonas, Achromobacter, and Isoptericola genera showed a clear diesel degradation pattern when analyzed by GC-MS, suggesting their potential use for bioremediation and a possible new species of Isoptericola was further characterized as hydrocarbon degrader.

Cellulosimicrobium protaetiae sp. nov., isolated from the gut of the larva of Protaetia brevitarsis seulensis

A Gram-stain-positive, non-spore-forming, yellow-pigmented, non-motile, non-flagellated, facultative anaerobic and rod-shaped bacterial strain, designated BI34T, was isolated from the gut of the larva of Protaetia brevitarsis seulensis. Strain BI34T grew at 15–40 °C (optimum, 37 °C), at pH 6.5–9.0 (optimum, pH 7.5) and in the presence of 0–7 % (w/v) NaCl (optimum, 2 %). Based on the results of 16S rRNA gene sequence analysis, strain BI34T belonged to the phylum Actinobacteria and was closely related to Cellulosimicrobium funkei NBRC 104118T (99.3 %), Cellulosimicrobium cellulans NBRC 15516T (99.1 %), Cellulosimicrobium composti BIT-GX5T (99.0 %), Cellulosimicrobium fucosivorans SE3T (99.0 %), Cellulosimicrobium marinum NBRC 110994T (98.4 %) and Cellulosimicrobium terreum DS-61T (97.0 %). The genome to genome relatedness of the average nucleotide identity (ANI) and the digital DNA–DNA hybridization (dDDH) values calculated by the Genome-to-Genome Distance Calculator between strain BI34T and its related species mentioned above were lower than the threshold of 95 and 70 % for speciation, respectively. The predominant menaquinone of strain BI34T contained MK-9(H4), and the major fatty acids were anteiso-C15 : 0, C16 : 0 and anteiso-C17 : 0. Strain BI34T had diphosphatidylglycerol and phosphatidylglycerol as major polar lipids. The whole-cell sugars were galactose, glucose and ribose, and the cell-wall peptidoglycan contained lysine, alanine, aspartic acid and glutamic acid. The DNA G+C content of strain BI34T was 73.8 mol%. The difference in physiological and biochemical characteristics and the below-threshold values of genome-to-genome relatedness indicate that strain BI34T represents a novel species in the genus Cellulosimicrobium , for which the name Cellulosimicrobium protaetiae sp. nov. is proposed. The type strain is BI34T (=KCTC 49302T=NBRC 114073T).

Functional and Taxonomic Effects of Organic Amendments on the Restoration of Semiarid Quarry Soils

The application of organic amendments to mining soils has been shown to be a successful method of restoration, improving key physicochemical soil properties. However, there is a lack of a clear understanding of the soil bacterial community taxonomic and functional changes that are brought about by these treatments. We present further metagenomic sequencing (MGS) profiling of the effects of different restoration treatments applied to degraded, arid quarry soils in southern Spain which had previously been profiled only with 16S rRNA gene (16S) and physicochemical analyses. Both taxonomic and functional MGS profiles showed clear separation of organic treatment amendments from control samples, and although taxonomic differences were quite clear, functional redundancy was higher than expected and the majority of the latter signal came from the aggregation of minor (<0.1%) community differences. Significant taxonomic differences were seen with the presumably less-biased MGS-for example, the phylum Actinobacteria and the two genera Chloracidobacterium (Acidobacteria) and Paenibacillus (Firmicutes) were determined to be major players by the MGS and this was consistent with their potential functional roles. The former phylum was much less present, and the latter two genera were either minor components or not detected in the 16S data. Mapping of reads to MetaCyc/BioCyc categories showed overall slightly higher biosynthesis and degradation capabilities in all treatments versus control soils, with sewage amendments showing highest values and vegetable-based amendments being at intermediate levels, matching higher nutrient levels, respiration rates, enzyme activities, and bacterial biomass previously observed in the treated soils. IMPORTANCE The restoration of soils impacted by human activities poses specific challenges regarding the reestablishment of functional microbial communities which will further support the reintroduction of plant species. Organic fertilizers, originating from either treated sewage or vegetable wastes, have shown promise in restoration experiments; however, we still do not have a clear understanding of the functional and taxonomic changes that occur during these treatments. We used metagenomics to profile restoration treatments applied to degraded, arid quarry soils in southern Spain. We found that the assortments of individual functions and taxa within each soil could clearly identify treatments, while at the same time they demonstrated high functional redundancy. Functions grouped into higher pathways tended to match physicochemical measurements made on the same soils. In contrast, significant taxonomic differences were seen when the treatments were previously studied with a single marker gene, highlighting the advantage of metagenomic analysis for complex soil communities.

Genome information of the cellulolytic soil actinobacterium Isoptericola dokdonensis DS-3 and comparative genomic analysis of the genus Isoptericola

The actinobacterial group is regarded as a reservoir of biologically active natural products and hydrolytic enzymes with the potential for biomedical and industrial applications. Here, we present the complete genome sequence of Isoptericola dokdonensis DS-3 isolated from soil in Dokdo, small islets in the East Sea of Korea. This actinomycete harbors a large number of genes encoding carbohydrate-degrading enzymes, and its activity to degrade carboxymethyl cellulose into glucose was experimentally evaluated. Since the genus Isoptericola was proposed after reclassification based on phylogenetic analysis, strains of Isoptericola have been continuously isolated from diverse environments and the importance of this genus in the ecosystem has been suggested by recent culturomic or metagenomic studies. The phylogenic relationships of the genus tended to be closer among strains that had been isolated from similar habitats. By analyzing the properties of published genome sequences of seven defined species in the genus, a large number of genes for carbohydrate hydrolysis and utilization, as well as several biosynthetic gene clusters for secondary metabolites, were identified. Genomic information of I. dokdonensis DS-3 together with comparative analysis of the genomes of Isoptericola provides insights into understanding this actinobacterial group with a potential for industrial applications.

Cellulosimicrobium composti sp. nov., a thermophilic bacterium isolated from compost

A Gram-stain-positive, yellow-pigmented, non-motile actinobacterial strain, designated as BIT-GX5^T, was isolated from a sesame husks compost collected in Beijing, PR China. This bacterium was found to be able to grow in the temperature range from 16 to 50 °C and had an optimal growth temperature at 45 °C. Its taxonomic position was analysed using a polyphasic approach. The 16S rRNA gene sequence (1482 bp) of strain BIT-GX5^T was most similar to Cellulosimicrobium funkei ATCC BAA-886^T (99.45%), Cellulosimicrobium cellulans LMG 16121^T (99.17%) and Cellulosimicrobium marinum RS-7-4^T (98.75%). The results of phylogenetic analyses, based on the 16S rRNA gene, concatenated sequences of five housekeeping genes (gyrB, rpoB, recA, atpD and trpB) and genome sequences, placed strain BIT-GX5^T in a separate lineage among the genus Cellulosimicrobium within the family Promicromonosporaceae. The major polar lipids of strain BIT-GX5^T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid and aminolipid. The major isoprenoid quinone was MK-9(H₄), while the cell-wall sugars were galactose, rhamnose, glucose and mannose. The peptidoglycan type was A4α l-Lys-d-Ser-d-Asp. The major fatty acids were anteiso-C_15:0 and iso-C_15: 0, which were similar to other members in the genus Cellulosimicrobium. Results of in silico DNA-DNA hybridization and average nucleotide identity calculations plus physiological and biochemical tests exhibited the genotypic and phenotypic differentiation of strain BIT-GX5^T from the other members of the genus Cellulosimicrobium. Therefore, strain BIT-GX5^T is considered to represent a novel species within the genus Cellulosimicrobium, for which the name Cellulosimicrobium composti sp. nov. is proposed. The type strain is BIT-GX5^T (= CGMCC 1.17687^T = KCTC 49391^T).

Isoptericola sediminis sp. nov., Isolated from Chilika Lagoon

A yellow-colored, Gram-stain-positive, rod shaped, non-motile bacterium, designated as strain JC619^T, was isolated from the sediment of Chilika lagoon, India. Strain JC619^T shows highest 16S rRNA gene sequence similarity (99.08%) with Isoptericola chiayiensis KCTC 19740^T followed by Isoptericola halotolerans KCTC 19046^T (98.6%) and other members of the genus Isoptericola (< 98%). NaCl is required for growth of strain JC619^T and tolerates up to 18% (w/v) and pH up to 10. Strain JC619^T grows optimally at temperature 30 °C, NaCl concentration of 3% (w/v), and at pH 7.5. The genome size of strain JC619^T is 3.2 Mb with G+C content of 73.0 mol%. ANI scores of strain JC619^T are 81.9% and 80.1% and dDDH values are 24.4% and 22.7% with I. chiayiensis KCTC 19740^T and I. halotolerans KCTC 19046^T, respectively. Respiratory quinones are MK-9(H4) and MK-9(H2). Predominant fatty acids (> 10%) are anteiso-C_15:0, iso-C_16:0, and iso-C_15:0. Major polar lipids of strain JC619^T are phosphatidylglycerol, phosphatidylinositolmannoside, diphosphatidylglycerol, and phosphatidylinositol. Strain JC619^T is catalase positive but cytochrome oxidase negative and reduces nitrate. The genomic distinction of strain JC619^T with its nearest related species of the genus Isoptericola is well supported with chemotaxonomic characteristics and differential physiological properties. Therefore, strain JC619^T represents a new species under the genus Isoptericola for which Isoptericola sediminis sp. nov. is proposed. Type strain is JC619^T (=KCTC 49244^T =NBRC 114063^T).

Puerhibacterium puerhi gen. nov., sp. nov., a novel member of the family Promicromonosporaceae, isolated from Pu-erh tea pile-fermentation

A Gram-staining positive aerobic bacterium, designated TLY-12^T, was isolated from the Pu-erh tea pile-fermentation process in Pu'er city, Yunnan, China. Strain TLY-12^T grew at 15-37 °C (optimum, 30 °C), pH 6.0-11.0 (optimum, pH 9.0) and 0-9.0% (w/v) NaCl (optimum, 3.0%). The major cellular fatty acids were anteiso-C_15:0, C_16:0 and iso-C_16:0. The respiratory quinone were menaquinones MK-9 (H₂) and MK-9 (H₄). The polar lipids were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylinositol (PI), phosphoglycolipid (PGL), glycolipid (GL) and an unidentified phospholipid (PL). The peptidoglycan contained glutamic acid, aspartic acid, alanine and lysine, with the last named being the diagnostic diamino acid. Whole-cell sugars of the isolate were ribose, galactose and glucose. Phylogenetic analyses of 16S rRNA gene showed that this strain belonged to the family Promicromonosporaceae, and was most closely related to Isoptericola cucumis DSM 101603 ^T, which gave sequence similarity of 97.9%. Genome sequencing revealed a genome size of 3.91 Mbp and a G + C content of 75.0%. Average nucleotide identity and digital DNA-DNA hybridization values were all below the species threshold of described Promicromonosporaceae species. Genome phylogenetic analysis showed that strain TLY-12^T formed a separate evolutionary branch, and was parallel to other related genera of Promicromonosporaceae. Based on the phylogenetic, phenotypic, chemotaxonomic and genome pairwise data, strain TLY-12^T is considered to represent a novel species in a new genus in the family Promicromonosporaceae, for which the name Puerhibacterium puerhi gen. nov, sp. nov. is proposed. The type strain is TLY-12^T (= CGMCC 1.17157^T = KCTC 49467^T).

Statistical augmentation of polyhydroxybutyrate production by Isoptericola variabilis: Characterization, moulding, in vitro cytocompatibility and biodegradability evaluation

This study aimed to explore the production of polyhydroxybutyrate (PHB), a polyhydroxyalkanoate (PHA), which has been widely considered as a potential substitute for the synthetic polymers. Among 53 actinomycete isolates, 11 of them were found to be PHB positive and the quantity of PHB from the positive isolates varied from 10.5 to 29.82 wt% on a dry cell weight basis. A strain designated as PPLAT 012, accumulated relatively higher PHB and has been identified as Isoptericola variabilis by 16S rRNA gene sequence analysis. An effort has also been made to optimize the PHB production by the hyper-producing strain using the conventional, one-factor-at-a-time, and statistical response surface methodologies and the maximum PHB production (46.18%) in DSMZ medium, amended with 12% glucose and 9% potassium nitrate with a pH of 7.0. Further, the characteristic properties such as processability, cytocompatibility and biodegradability of the extracted PHB was also demonstrated. The physical properties of the recovered PHB was further improved by blending with PLA and the resultant blends were characterized. The present investigation has demonstrated that the isolate, Isoptericola variabilis, could be utilized as a potential source for the production of PHB with desirable characteristics, suitable for biomedical applications.

Isoptericola halalbus sp. nov., a halotolerant actinobacterium isolated from saline lake sediment

A novel Gram-stain-positive bacterium, designated CFH 91151^T, was isolated from sediment collected from a saline lake in Yuncheng, Shanxi Province, PR China. Cells of strain CFH 91151^T were rod-or v-shaped, aerobic, non-motile, non-spore-forming and halotolerant. Results of 16S rRNA gene sequence analysis revealed that strain CFH 91151^T was closely related to Isoptericola variabilis MX5^T and Isoptericola nanjingensis H17^T (98.7 and 98.4% sequence similarity, respectively). The strain grew at 4-45 °C, pH 5.0-9.0 and with 0-14.0 % (w/v) NaCl. Cells were positive for catalase, nitrate was not used and H₂S was not produced. Major cellular fatty acids were anteiso-C_15 : 0 (62.76 %), anteiso-C_17 : 0 (12.09 %) and iso-C_15 : 0 (9.46 %). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified phospholipids and three unidentified glycolipids. The menaquinone was MK-9 (H4). The genome size was 4.10 Mbp with a G+C content of 72.4 mol%. The average amino acid identity (ANI) and in silico DNA-DNA hybridization (DDH) values between CFH 91151^T and the other species of the genus Isoptericola were found to be low (ANIm <87.19 %, ANIb <84.38 % and DDH <29.30 %). Based on physiological properties, chemotaxonomic characteristics and low ANI and DDH results, strain CFH 91151^T is considered to represent a novel species, for which the name Isoptericola halalbus sp. nov. is proposed. The type strain is CFH 91151^T (=DSM 105976^T=KCTC 49061^T).

Biodegradation of biodiesel-oil by Cellulosimicrobium sp. Isolated from Colombian Caribbean soils

Biodiesel is considered to be a natural substitute for fossil fuel. The comparatively low toxicity of biodiesel and its susceptibility to microbial biodegradation could reduce its environmental impact. Currently, biodiesel is sold previously mixed with petroleum-based hydrocarbons. The aim of this work was to measure the biodegradation potential of commercially available biodiesel, using bacterial strains (BBCOL-001, BBCOL-002, and BBCOL-003) isolated from a tropical forest soils in the Colombian Caribbean. According to nucleotide sequencing of the gene encoding for 16S rRNA, the strains belong to members of the genus Cellulosimicrobium. GC-MS analysis showed that biodiesel-oil alkanes were degraded by an average of 81.5% with optical density reaching 0.2-0.3 in minimal salt media at 37°C for 5 days. Individual diesel-oil alkanes were degraded by the strains at rates between 64.9% to 100%. The increase in bacterial biomass confirmed the use of the substrates by the microorganisms, suggesting these hydrocarbons are a carbon source. Changes in the biochemical behaviour of the strains suggested their capacity to adapt to environmental conditions might be an important resource for bioremediation.

Xylanimonas allomyrinae sp. nov. isolated from the gut of larva of Allomyrina dichotoma, reclassification of Xylanibacterium ulmi as Xylanimonas ulmi comb. nov. and Xylanimicrobium pachnodae as Xylanimonas pachnodae comb. nov., and emendation of the genus Xylanimonas

A bacterium that was Gram-staining-positive, facultatively anaerobic, non-motile, rod- or filamentous-shaped, designated as strain 2JSPR-7T, was isolated from a gut of larvae of Allomyrina dichotoma which were raised at the National Institute of Agricultural Sciences, Wanju-gun, Republic of Korea. 2JSPR-7T had the highest 16S rRNA gene sequence similarity to Xylanibacterium ulmi XIL08T (98.1 %), Xylanimicrobium pachnodae NBRC 107786T (97.8 %) and Xylanimonas cellulosilytica DSM 15894T (97.5 %). Optimum growth conditions were at 28–30 °C, pH 7–8 and 0 % salt concentration. The cellular fatty acids mainly consisted of anteiso-C15 : 0, C14 : 0 and C16 : 0. The polar lipids were diphosphatidylglycerol, four unidentified phospholipids and two unidentified glycophospholipids. The major menaquinones were MK-8(H4) and MK-9(H4). The peptidoglycan structure was suggested to be the type A3α (A11.14) l-Lys–l-Ser with the presence of d-Ala, l-Ala, d-Glu, l-Ser and l-Lys. Whole cell sugars were rhamnose, ribose and glucose. The DNA G+C content was 72.7 mol%. We encountered difficulty in selecting a suitable genus to accommodate strain 2JSPR-7T from any of the genera Xylanimonas , Xylanimicrobium and Xylanibacterium based on the polyphasic approach including phylogenetic and phenotypic characterization. Therefore, it is proposed to combine the genera Xylanimicrobium and Xylanibacterium with the genus Xylanimonas considering the priority of publication and to classify strain 2JSPR-7T in the genus as Xylanimonas allomyrinae sp. nov. The type strain of the novel species is 2JSPR-7T (=KACC 19330T=NBRC 113052T). In addition, the description of the genus Xylanimonas is emended, and Xylanibacterium ulmi and Xylanimicrobium pachnodae are reclassified as Xylanimonas ulmi comb. nov. and Xylanimonas pachnodae comb. nov., respectively.

Antribacter gilvus gen. nov., sp. nov., a new member of the family Promicromonosporaceae from a karstic cavern

A novel actinobacterium, designated strain CFH 30434^T, was isolated from a soil sample collected from a karst cave in Luoyang, Henan Province, PR China. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive, non-motile and coccoid or short rods. The strain was found to be oxidase-positive and weakly catalase-positive. Strain CFH 30434^T grew optimally at 28 °C, pH 7.0-9.0 and in the presence of up to 0-1.5 % NaCl (w/v). The whole-cell sugars were glucose, mannose and rhamnose. The major isoprenoid quinone was MK-9(H₈) and the major fatty acids (>10 % of the total fatty acids compositions) were anteiso-C_15 : 0, iso-C_15:0 and iso-C_14 : 0. The polar lipids detected were diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified phosphoglycolipid, an unidentified phospholipid and an unidentified glycolipid. The genomic DNA G+C content was determined to be 72.3 mol%. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that CFH 30434^T clustered within the family Promicromonosporaceae, and closely with the type strains of Xylanimicrobium pachnodae DSM 12657^T, Myceligenerans crystallogenes DSM 17134^T and Promicromonospora xylanilytica CCTCC AA 208046^T (97.3 %, 96.2 and 95.9 % sequence similarities, respectively). Phylogenetic analysis showed that strain CFH 30434^T formed a separate evolutionary branch, and was parallel to other related genera of Promicromonosporaceae. Its phylogenetic distinctiveness and distinguishing phenotypic characteristics supported that strain CFH 30434^T represents a novel genus of the family Promicromonosporaceae, for which the name Antribacter gilvus gen. nov., sp. nov. is proposed. The type strain is CFH 30434^T (=CGMCC 1.13856^T=KCTC 49093^T).

Promicromonospora kermanensis sp. nov., an actinobacterium isolated from soil

A novel strain belonging to the genus Promicromonospora, designated HM 533T, was isolated from soil in Kerman Province, Iran. It produced long and branched hyphae on ISP 2 medium that developed into a large number of irregular-shaped spores. It showed optimal growth at 25-30 °C and pH 5.0-8.0 with 0-4 % (w/v) NaCl. The peptidoglycan type of strain HM 533T was A4α l-Lys-l-Ala-d-Glu. Whole-cell hydrolysates of strain HM 533T contained the sugars ribose, glucose and galactose. The main phospholipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, two unknown glycolipids and an unknown phospholipid. MK-9(H4) and MK-9(H2) were the predominant menaquinones. The fatty acids pattern was mainly composed of the saturated branched-chain acids anteiso-C15 : 0 and iso-C15 : 0. The 16S rRNA gene sequence analysis showed the highest pairwise sequence identity (99.5-97.1 %) with the members of the genus Promicromonospora. Based on phenotypic and genotypic features, strain HM 533T is considered to represent a novel species of the genus Promicromonospora, for which the name Promicromonospora kermanensis is proposed with strain HM 533T (=DSM 45485T=UTMC 00533T=CECT 8709T) as the type strain.

Krasilnikoviella muralis gen. nov., sp. nov., a member of the family Promicromonosporaceae, isolated from the Takamatsuzuka Tumulus stone chamber interior and reclassification of Promicromonospora flava as Krasilnikoviella flava comb. nov

A Gram-stain-positive, facultatively anaerobic actinomycete, designated strain T6220-5-2bT, was isolated from a sample taken from a mouldy spot on the surface of a mural painting (the white tiger, Byakko) inside the stone chamber of Takamatsuzuka Tumulus in Asuka village, Nara Prefecture, Japan. Based on 16S rRNA gene sequence analysis of the isolate, it was closely related to the genus Promicromonospora, but formed of a novel lineage within the family Promicromonosporaceae. The closest related species to strain T6220-5-2bT was Promicromonospora flava, with which it shared 99.1 % 16S rRNA gene sequence similarity. The isoprenoid quinone systems were menaquinones MK-9(H2), MK-9(H0) and MK-9(H4). The predominant cellular fatty acids for the isolate were anteiso-C15 : 0 and iso-C15 : 0. The peptidoglycan contained glutamic acid, aspartic acid, alanine and lysine, with the last named being the diagnostic diamino acid. The cell-wall acyl type was acetyl. The major polar lipids of the isolate were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositolmannoside, two unknown phospholipids and an unknown phosphoglycolipid. Whole-cell sugars of the isolate were galactose, glucose and ribose. The DNA G+C content of the genomic DNA was 75.2 mol%. Based on the results of phylogenetic, physiological and biochemical analyses and DNA-DNA hybridization experiments, the isolate was considered to represent a novel species of a new genus in the family Promicromonosporaceae, for which the name Krasilnikoviella muralis gen. nov., sp. nov. is proposed. The type strain of Krasilnikoviella muralis is T6220-5-2bT (=JCM 28789T=NCIMB 15040T). The reclassification of Promicromonospora flava as Krasilnikoviella flava comb. nov. is also proposed with the emended description of this species.

Isoptericola cucumis sp. nov., isolated from the root tissue of cucumber (Cucumis sativus)

A Gram-stain-positive, aerobic organism, showing an irregular cell morphology, was isolated from the root tissue of cucumber (Cucumis sativus) and investigated in detail for its taxonomic position. On the basis of the 16S rRNA gene sequence analysis, strain AP-38T was shown to be most closely related to Isoptericola variabilis (99.1 %) and Isoptericola nanjingensis (98.9 %). The 16S rRNA gene sequence similarity to all other species of the genus Isoptericola was ≤98.5 %. DNA-DNA relatedness to Isoptericola variablis DSM 10177T and Isoptericola nanjingensis DSM 24300T was 31(reciprocal 41 %) and 34 (reciprocal 34 %), respectively. The diagnostic diamino acid of the peptidoglycan was l-lysine. The quinone system contained predominantly menaquinones MK-9(H4) and MK-9(H2). In the polar lipid profile, major compounds were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two phosphatidylinositol mannosides. The polyamine pattern contained the major components spermidine and spermine and significant amounts of tyramine. In the fatty acid profile, anteiso-C15 : 0 and iso-C15 : 0 were present in major amounts. These data support the allocation of the strain to the genus Isoptericola. The results of physiological and biochemical characterization additionally provide phenotypic differentiation of strain AP-38T from I. variabilis and I. nanjingensis. AP-38T represents a novel species of the genus Isoptericola, for which we propose the name Isoptericola cucumis sp. nov., with AP-38T (= LMG 29223T=CCM 8653T) as the type strain.

Cellulosimicrobium aquatile sp. nov., isolated from Panagal reservoir, Nalgonda, India

A Gram-stain positive, non-spore forming, non-motile, yellow-pigmented, rod shaped and coccoid aerobic strain designated 3bp(T) was isolated from Panagal reservoir, at Nalgonda, Telangana, India. Based on 16S rRNA gene sequence analysis it was identified that strain 3bp(T) belongs to the class Actinobacteria and is closely related to Cellulosimicrobium funkei VTT E-072700(T), Cellulosimicrobium cellulans LMG16221(T) and Cellulosimicrobium terreum KCTC 19206(T). The DNA-DNA relatedness data demonstrated that strain 3bp(T) is distinguishable from the above three species of the genus. Further, the chemotaxonomic properties of strain 3bp(T) were consistent with those of the genus Cellulosimicrobium: MK-9(H4) was the predominant menaquinone, anteiso-C15 : 0, iso-C15:0,  anteiso-C17 : 0 and iso- C16:0 were the predominant cellular fatty acids and the cell-wall peptidoglycan contains L-lysine. The DNA G+C content of strain 3bp(T) was 73.8 mol%. The results of the polyphasic analysis allowed a clear differentiation of strain 3bp(T) from all other members of the genus Cellulosimicrobium. Strain 3bp(T) is thus considered to represent a novel member of the genus Cellulosimicrobium, for which the name Cellulosimicrobium aquatile sp. nov. is proposed. The type strain is 3bp(T) (=KCTC 39527(T) = MCC 2761(T) = LMG 28646(T)).

Promicromonospora iranensis sp. nov., an actinobacterium isolated from rhizospheric soil

A novel strain of the genus Promicromonospora, designated HM 792(T), was isolated from soil in Fars Province, Iran. On ISP 2 medium, the yellow-pigmented isolate produced long and branched hyphae that developed into a large number of irregularly shaped spores. It showed growth at 25-30 °C and pH 6.0-9.0 with 0-8 % (w/v) NaCl. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Promicromonospora. Whole-cell hydrolysates of strain HM 792(T) contained the amino acids d-glutamic acid, l-alanine and l-lysine along with the sugars glucose and ribose. The main polar lipids were diphosphatidylglycerol, two unknown phospholipids, two unknown glycolipids and two unknown phosphoglycolipids, complemented by minor concentrations of phosphatidylinositol and phosphatidylglycerol. MK-9(H4) was the predominant menaquinone. The fatty-acid pattern was composed mainly of the saturated branched-chain acids anteiso-C15 : 0 and iso-C15 : 0. 16S rRNA gene sequence analysis showed the highest pairwise sequence identity (96.6-99.0 %) with the members of the genus Promicromonospora. Based on phenotypic and genotypic features, strain HM 792(T) is considered to represent a novel species of the genus Promicromonospora, for which the name Promicromonospora iranensis sp. nov. is proposed. Strain HM 792(T) ( = DSM 45554(T) = UTMC00792(T) = CCUG 63022(T)) is the type strain.

Oceanitalea nanhaiensis gen. nov., sp. nov., an actinobacterium isolated from seawater

A Gram-positive, motile, short-rod-shaped bacterium, designated strain JLT1488T, was isolated from the South China Sea and investigated in a taxonomic study using a polyphasic approach. The peptidoglycan type determined for strain JLT1488T was A4α with lysine as the diagnostic cell-wall diamino acid and an interpeptide bridge of l-Lys–l-Glu. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, an unknown glycolipid and an unknown phospholipid. The only detected menaquinone was MK-8(H4), and the major fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) , C16 : 0 and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c); significant amounts of C12 : 0 3-OH, C10 : 0 and C19 : 0 cyclo ω8c were also present. The G+C content of the genomic DNA was 62.3 mol%. Comparison of the 16S rRNA gene sequence of strain JLT1488T with those of related type strains demonstrated that it represented a novel lineage within the family Bogoriellaceae , suborder Micrococcineae , being closely related to species of the genera Georgenia , Bogoriella and Cellulomonas (94.6–96.8 % sequence similarity). These results demonstrate that strain JLT1488T is a member of a new genus, for which the name Oceanitalea nanhaiensis gen. nov., sp. nov. is proposed. The type strain of the type species is JLT1488T ( = JCM 17755T = CGMCC 1.10826T).

Isoptericola chiayiensis sp. nov., isolated from mangrove soil

A novel actinomycete, designated strain 06182M-1T, was isolated from a mangrove soil sample collected from Chiayi County in Taiwan. Phylogenetic analysis based on 16S rRNA gene sequences revealed levels of similarity of 97.0–98.8 % to the type strains of recognized species of the genus Isoptericola. Chemotaxonomic data also supported the placement of strain 06182M-1T within the genus Isoptericola. However, the low levels of DNA–DNA relatedness between the novel strain and the type strains of recognized species of the genus Isoptericola, in combination with differential phenotypic data, demonstrate that strain 06182M-1T represents a novel species of the genus Isoptericola, for which the name Isoptericola chiayiensis sp. nov. is proposed. The type strain is 06182M-1T ( = BCRC 16888T  = KCTC 19740T).

Isoptericola nanjingensis sp. nov., a mineral-weathering bacterium

A Gram-positive-staining, non-motile, rod- or coccoid-shaped actinobacterium, designated strain H17T, was isolated from a soil sample from Nanjing, Jiangsu Province, PR China. The organism grew optimally at 30 °C, pH 7.0 and with 3 % NaCl (w/v). Strain H17T contained L-Lys-D-Asp as the cell-wall peptidoglycan type and galactose, xylose and mannose as the whole-cell sugars. The major fatty acids were anteiso-C15:0 and iso-C15:0. The total polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipids, phosphatidylinositol, phosphoglycolipid, one unidentified glycolipid and one unidentified lipid. The menaquinone was MK9(H4). Mycolic acids were not detected. The DNA G+C content was 72.4 mol%. Phylogenetic analysis of this strain based on 16S rRNA gene sequences revealed 97.8-99.6 % similarity to recognized species of the genus Isoptericola. The low level of DNA-DNA relatedness to other species of the genus Isoptericola and the many phenotypic properties that distinguished strain H17T from recognized species of this genus demonstrated that isolate H17T should be classified as representing a novel species of the genus Isoptericola. The name Isoptericola nanjingensis sp. nov. is proposed for this novel species. The type strain is H17T (=DSM 24300T=CCTCC AB 2011005T).

Koreibacter algae gen. nov., sp. nov., isolated from seaweed

A Gram-positive, aerobic, non-motile, rod-shaped actinomycete, designated strain DSW-2T, was isolated from a seaweed sample collected around Mara Island, Jeju, Republic of Korea. Comparative 16S rRNA gene sequence analysis showed that strain DSW-2T belongs to the suborder Micrococcineae and forms a distinct clade separated from representatives of the several families of this order. Levels of 16S rRNA gene sequence similarity between the novel strain and members of this suborder were lower than 96.4 %. The peptidoglycan type is A3α with Lys–Ser as the interpeptide bridge. Whole-cell sugars are glucose and galactose. The major menaquinone is MK-9(H4). The predominant fatty acid is ai-C15 : 0. The polar lipids are phosphatidylglycerol and phosphatidylinositol. The DNA G+C content was 68.3 mol%. On the basis of the chemotaxonomic markers and phylogenetic distinctiveness presented here, it is evident that the isolate represents a novel taxon within the suborder Micrococcineae. The name Koreibacter algae gen. nov., sp. nov. is proposed, with the type strain DSW-2T (=KCTC 13436T =DSM 22126T).

Isoptericola jiangsuensis sp. nov., a chitin-degrading bacterium

A Gram-positive-staining, non-motile, rod- or coccoid-shaped bacterium, strain CLGT, was isolated from beach sand from Lianyungang, Jiangsu Province, PR China. The organism grew optimally at 30 °C and pH 7.0. Strain CLGT contained l-Lys–d-Asp as the peptidoglycan type and galactose, rhamnose and xylose as the whole-cell sugars. It contained anteiso-C15 : 0 and iso-C15 : 0 as the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid, phosphatidylinositol, three phosphoglycolipids and one unidentified lipid. The DNA G+C content was 70.3 mol%. The 16S rRNA gene sequence similarity of strain CLGT with Isoptericola dokdonensis DS-3T was 99.4 % but the DNA–DNA relatedness between strain CLGT and I. dokdonensis DS-3T was 58.7 %. There were also many phenotypic properties that distinguished strain CLGT from recognized species of the genus Isoptericola. The results showed that strain CLGT represents a novel species of the genus Isoptericola, for which the name Isoptericola jiangsuensis sp. nov. is proposed. The type strain is CLGT (=DSM 21863T=CCTCC AB208287T).

Luteimicrobium subarcticum gen. nov., sp. nov., a new member of the suborder Micrococcineae

A novel Gram-stain-positive bacterium, designated R19-04T, was isolated from a soil sample from Rishiri Island, Japan, and its taxonomic position was investigated by a polyphasic approach. Cells of strain R19-04T exhibited a rod–coccus cycle. The peptidoglycan type of the isolate was A4α; lysine was the diagnostic diamino acid. The predominant menaquinone was MK-8(H2) and the major fatty acid was anteiso-C15 : 0. The polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content was 72.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain R19-04T represented a novel member of the suborder Micrococcineae. Its nearest phylogenetic neighbours were the members of the genus Oerskovia, with 16S rRNA gene sequence similarity of 97.0–97.1 %. However, strain R19-04T was clearly distinguishable from members of the genus Oerskovia and phylogenetically related genera in terms of chemotaxonomic characteristics. On the basis of the chemotaxonomic and phylogenetic characteristics, a novel genus and species are proposed, Luteimicrobium subarcticum gen. nov., sp. nov. The type strain of Luteimicrobium subarcticum is R19-04T (=NBRC 105647T =DSM 22413T).

An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa

The higher ranks of the class Actinobacteria were proposed and described in 1997. At each rank, the taxa were delineated from each other solely on the basis of 16S rRNA gene sequence phylogenetic clustering and taxon-specific 16S rRNA signature nucleotides. In the past 10 years, many novel members have been assigned to this class while, at the same time, some members have been reclassified. The new 16S rRNA gene sequence information and the changes in phylogenetic positions of some taxa influence decisions about which 16S rRNA nucleotides to define as taxon-specific. As a consequence, the phylogenetic relationships of Actinobacteria at higher levels may need to be reconstructed. Here, we present new 16S rRNA signature nucleotide patterns of taxa above the family level and indicate the affiliation of genera to families. These sets replace the signatures published in 1997. In addition, Actinopolysporineae subord. nov. and Actinopolysporaceae fam. nov. are proposed to accommodate the genus Actinopolyspora, Kineosporiineae subord. nov. and Kineosporiaceae fam. nov. are proposed to accommodate the genera Kineococcus, Kineosporia and Quadrisphaera, Beutenbergiaceae fam. nov. is proposed to accommodate the genera Beutenbergia, Georgenia and Salana and Cryptosporangiaceae fam. nov. is proposed to accommodate the genus Cryptosporangium. The families Nocardiaceae and Gordoniaceae are proposed to be combined in an emended family Nocardiaceae. Emended descriptions are also proposed for most of the other higher taxa.

Cellulosimicrobium terreum sp. nov., isolated from soil

A Gram-positive, yellow-pigmented, non-motile and rod-shaped or coccoid bacterial strain, DS-61T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. The strain grew optimally at pH 6.5-7.5 and 25 degrees C in the presence of 1.0% (w/v) NaCl. Strain DS-61T had peptidoglycan of the type based on L-Lys-L-Thr-D-Asp and contained galactose as the only whole-cell sugar. MK-9(H4) was the predominant menaquinone and anteiso-C15:0 and iso-C15:0 were the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid. The DNA G+C content was 72.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-61T is most closely affiliated to the genus Cellulosimicrobium, clustering with Cellulosimicrobium cellulans and Cellulosimicrobium funkei. The levels of 16S rRNA gene sequence similarity between strain DS-61T and the type strains of Cellulosimicrobium cellulans and Cellulosimicrobium funkei were 97.4-97.6%. DNA-DNA relatedness data and differential phenotypic properties demonstrated that strain DS-61T is distinguishable from these two recognized Cellulosimicrobium species. On the basis of phenotypic, phylogenetic and genetic data, strain DS-61T represents a novel species of the genus Cellulosimicrobium, for which the name Cellulosimicrobium terreum sp. nov. is proposed. The type strain is DS-61T (=KCTC 19206T=DSM 18665T). An emended description of the genus is given.

Demequina aestuarii gen. nov., sp. nov., a novel actinomycete of the suborder Micrococcineae, and reclassification of Cellulomonas fermentans Bagnara et al. 1985 as Actinotalea fermentans gen. nov., comb. nov

An actinobacterial strain containing demethylmenaquinone DMK-9(H4) as the diagnostic isoprenoid quinone was isolated from a tidal flat sediment sample, from South Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JC2054T represents a distinct phyletic line within the suborder Micrococcineae of the order Actinomycetales. The closest phylogenetic neighbour was Cellulomonas fermentans, with 94.7 % 16S rRNA gene sequence similarity. The novel isolate was strictly aerobic and slightly halophilic, with optimum growth occurring in 2–4 % (w/v) NaCl. Cells were non-motile, non-sporulating and rod-shaped. The peptidoglycan type was of the A-type of cross-linkage. l-ornithine was the diamino acid and d-glutamate represented the N-terminus of the interpeptide bridge. The predominant fatty acids were anteiso-branched and straight-chain fatty acids. The major polar lipids were phosphatidylinositol, diphosphatidylglycerol and an unknown phospholipid. The menaquinone composition of C. fermentans was determined to be MK-10(H4), MK-9(H4) and MK-8(H4) in the ratio 56 : 2 : 1. On the basis of the polyphasic evidence presented in this study, it is proposed that strain JC2054T should be classified as representing a novel genus and species of the suborder Micrococcineae, with the name Demequina aestuarii gen. nov., sp. nov. The type strain is JC2054T (=IMSNU 14027T=KCTC 9919T=JCM 12123T). In addition, it was clear from the phylogenetic analysis and chemotaxonomic data that C. fermentans does not belong to the genus Cellulomonas or any other recognized genera. Therefore, C. fermentans should be reclassified as representing a novel genus, for which the name Actinotalea fermentans gen. nov., comb. nov. is proposed, with strain DSM 3133T (=ATCC 43279T=CFBP 4259T=CIP 103003T=NBRC 15517T=JCM 9966T=LMG 16154T) as the type strain.

Isoptericola dokdonensis sp. nov., isolated from soil

A Gram-positive, non-motile, rod- or coccoid-shaped Isoptericola-like bacterium, strain DS-3T, was isolated from a soil sample from Dokdo, Korea, and its taxonomic position was investigated by a polyphasic approach. The organism grew optimally at 30 °C and pH 7.0–8.0. Strain DS-3T had the peptidoglycan type based on l-lys–d-Asp, and galactose, glucose, rhamnose and ribose as the whole-cell sugars. It contained MK-9(H4) as the predominant menaquinone and anteiso-C15 : 0 and iso-C15 : 0 as the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unidentified glycolipids. The DNA G+C content was 74.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-3T was most closely related to members of the genus Isoptericola. Similarity values between the 16S rRNA gene sequences of strain DS-3T and the type strains of Isoptericola species ranged from 98.0 to 98.4 %. DNA–DNA relatedness values (11–23 %) and differential phenotypic properties demonstrated that strain DS-3T was distinguishable from recognized Isoptericola species. On the basis of phenotypic properties and phylogenetic and genetic distinctiveness, strain DS-3T represents a novel species in the genus Isoptericola, for which the name Isoptericola dokdonensis sp. nov. is proposed. The type strain is DS-3T (=KCTC 19128T=CIP 108921T).

Characterization of clinical isolates previously identified as Oerskovia turbata: proposal of Cellulosimicrobium funkei sp. nov. and emended description of the genus Cellulosimicrobium

Taxonomic studies were performed on 13 clinical isolates (ten of which were epidemiologically related) that had been previously identified as Oerskovia turbata. Comparative phylogenetic analysis, based on 16S rRNA gene sequences, indicated that the isolates are closely related to Cellulosimicrobium cellulans with sequence similarity values ranging from 99.5 to 99.8 %. Chemotaxonomic results (fatty acid profiles and menaquinones) supported the inclusion of these isolates in the genus Cellulosimicrobium. The DNA G+C content was 74.5 mol%. The results of DNA-DNA reassociation, whole-cell sugars (with galactose as the characteristic whole sugar) and phenotypic properties, including antimicrobial resistance, indicated that these isolates are representatives of a novel species of the genus Cellulosimicrobium. The name Cellulosimicrobium funkei sp. nov. is proposed for the novel strains, with strain W6122T (=ATCC BAA-886T = DSM 16025T = CCUG 50705T) as the type strain. The definition of this novel Cellulosimicrobium species will assist in the understanding of the epidemiology and clinical significance of these micro-organisms.

Isoptericola halotolerans sp. nov., a novel actinobacterium isolated from saline soil from Qinghai Province, north-west China

A Gram-positive, non-motile actinobacterium, designated strain YIM 70177T, was isolated from a saline soil sample from Qinghai Province, north-west China. Phylogenetic analysis of this organism based on 16S rRNA gene sequences revealed 98·3 % similarity toIsoptericola variabilisDSM 10177T. Chemotaxonomic data determined for the isolate, such as the peptidoglycan type A4α, variationl-lys–d-Asp, supported the placement of strain YIM 70177Twithin the genusIsoptericola. Galactose was detected as cell wall sugar. Phospholipids identified were phosphatidylinositol, phosphatidylglycerol and diphosphatidylglycerol, and the predominant menaquinones were MK-9(H4) and MK-9(H2). The major fatty acids were ai-C15 : 0, C16 : 0, ai-C17 : 0and i-C15 : 0. The DNA G+C content was 72·8 mol%. The low level of DNA–DNA relatedness (27·4 %) toI. variabilisDSM 10177Tin combination with differentiating chemotaxonomic and physiological data demonstrated that the isolate YIM 70177Tshould be classified as representing a novel species of the genusIsoptericola. The nameIsoptericola halotoleranssp. nov. is proposed, with strain YIM 70177T(=DSM 16376T=KCTC 19046T) as the type strain.

Isoptericola hypogeus sp. nov., isolated from the Roman catacomb of Domitilla

In order to clarify the taxonomic position of an actinobacterium from the Roman catacomb of Domitilla, a combination of phenotypic characterization, phylogenetic analysis based on the 16S rRNA gene sequence and DNA–DNA relatedness studies was used. The results from the polyphasic taxonomic study of this organism showed that strain HKI 0342T (=DSM 16849T=NCIMB 14033T) should be considered as the type strain of a novel species of the genus Isoptericola, for which the name Isoptericola hypogeus sp. nov. is proposed.

Reclassification of Promicromonospora pachnodae Cazemier et al. 2004 as Xylanimicrobium pachnodae gen. nov., comb. nov

The recently described facultatively anaerobic Promicromonospora pachnodae is phylogenetically only moderately related to authentic members of Promicromonospora. P. pachnodae is closely related to Xylanibacterium ulmi and slightly less closely related to Xylanimonas cellulosilytica and Isoptericola variabilis (basonym Cellulosimicrobium variabile). Members of the different genera of Promicromonosporaceae have similar chemotaxonomic properties; they share the same peptidoglycan type (A4α) and have similar profiles of polar lipids, menaquinones, fatty acids and whole cell sugars. However, they differ from each other in the detailed amino acid composition of peptidoglycan, a taxonomically significant character that has previously been used in the delineation of actinobacterial genera. Recognized Promicromonospora species and Xylanibacterium ulmi exhibit the l-lys–l-ala–d-Glu type, Xylanimonas cellulosilytica and I. variabilis show the l-lys–d-Asp type, whereas P. pachnodae has the l-lys–l-ser–d-Glu type. This property, together with the distinct phylogenetic position of Promicromonospora pachnodae, suggests a novel genus for the xylanolytic organism Xylanimicrobium pachnodae (Cazemier et al. 2004) gen. nov., comb. nov.

Myceligenerans xiligouense gen. nov., sp. nov., a novel hyphae-forming member of the family Promicromonosporaceae

Strain XLG9A10.2T was isolated from an alkaline salt marsh soil in western China. 16S rRNA gene sequence analysis indicated that strain XLG9A10.2T constitutes a distinct lineage within the family Promicromonosporaceae, sharing 94·8–95·1 % gene similarity with members of the genus Promicromonospora and 94·4–95·7 % similarity with those of Xylanimonas and related genera. The general colony and cell morphology of strain XLG9A10.2T is similar to that of members of Promicromonospora, but differs from members of the genus Xylanimonas in forming a well-developed branching mycelium and production of coccoid spores. Strain XLG9A10.2T shows the peptidoglycan type A4α (l-lys←l-thr←d-Glu), contains glucose, mannose and galactose as whole cell sugars and has MK-9(H4) and MK-9(H6) as major menaquinones, while phospholipids are phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, three unidentified phospholipids and one unidentified glycolipid. The DNA base composition is 71·9 mol% G+C. On the basis of morphological, chemotaxonomic, metabolic and phylogenetic differences from other species of Promicromonosporaceae, a new genus and species, Myceligenerans xiligouense gen. nov., sp. nov., is proposed. The type strain is XLG9A10.2T (=DSM 15700T=CGMCC 1.3458T.)