Four new Microbacterium species isolated from seaweeds and reclassification of five Microbacterium species with a proposal of Paramicrobacterium gen. nov. under a genome-based framework of the genus Microbacterium

The taxonomic relationships of 10 strains isolated from seaweeds collected from two beaches in Republic of Korea were studied by sequencing and analyses of 16S rRNA genes and whole genomes. For the construction of a more reliable and robust 16S rRNA gene phylogeny, the authentic and nearly complete 16S rRNA gene sequences of all the Microbacterium type strains were selected through pairwise comparison of the sequences contained in several public databases including the List of Prokaryotic names with Standing in Nomenclature (LPSN). The clustering of the ten study strains into five distinct groups was apparent in this single gene-based phylogenetic tree. In addition, the 16S rRNA gene sequences of a few type strains were shown to be incorrectly listed in LPSN. An overall phylogenomic clustering of the genus Microbacterium was performed with a total of 113 genomes by core genome analysis. As a result, nine major (≥ three type strains) and eight minor (two type strains) clusters were defined mostly at gene support index of 92 and mean intra-cluster OrthoANIu of >80.00%. All of the study strains were assigned to a Microbacterium liquefaciens clade and distributed further into four subclusters in the core genome-based phylogenetic tree. In vitro phenotypic assays for physiological, biochemical, and chemotaxonomic characteristics were also carried out with the ten study strains and seven closely related type strains. Comparison of the overall genomic relatedness indices (OGRI) including OrthoANIu and digital DNA-DNA hybridization supported that the study strains constituted four new species of the genus Microbacterium. In addition, some Microbacterium type strains were reclassified as members of preexisting species. Moreover, some of them were embedded in a new genus of the family Microbacteriaceae based on their distinct separation in the core genome-based phylogenetic tree and amino acid identity matrices. Based on the results here, four new species, namely, Microbacterium aurugineum sp. nov., Microbacterium croceum sp. nov., Microbacterium galbinum sp. nov., and Microbacterium sufflavum sp. nov., are described, along with the proposal of Paramicrobacterium gen. nov. containing five reclassified Microbacterium species from the "Microbacterium agarici clade", with Paramicrobacterium agarici gen. nov., comb. nov. as the type species.

Microbacterium paulum sp. nov., isolated from microfiltered milk

A novel Gram-stain-positive, strictly aerobic, short rod-shaped bacterium, designated 2C^T, was isolated from freshly packaged microfiltered milk. This strain was able to grow within the NaCl concentration range of 0-5 % (w/v), temperature range of 8-37 °C (optimally at 30 °C) and at pH 6.0-10.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 2C^T was closely related to species of the genus Microbacterium, with the highest sequence similarity (99.2 %) to Microbacterium lacticum DSM 20427^T as well as Microbacterium flavum DSM 18909^T (=YM18-098^T). The phylogenetic tree based on 16S rRNA genes showed that strain 2C^T clustered with M. flavum DSM 18909^T. However, the phylogenetic tree based on concatenated 16S rRNA and four housekeeping genes showed that strain 2C^T clustered with M. lacticum DSM 20427^T. Furthermore, the phylogenomic tree showed that strain 2C^T clustered with M. lacticum DSM 20427^T and M. flavum DSM 18909^T. The major respiratory quinones were MK-10, MK-11 and MK-12. The predominant cellular fatty acids were anteiso-C_15 : 0, iso-C_16 : 0 and anteiso-C_17 : 0. The polar lipid composition of strain 2C^T consisted of diphosphatidylglycerol, phosphatidylglycerol, three unidentified glycolipids and two unidentified lipids. The cell-wall peptidoglycan type was a variant of B1α {Gly} [l-Lys] d-Glu-l-Lys, with the amino acids lysine, glycine, alanine and glutamic acid. The whole-cell sugars consisted of galactose, glucose, ribose and minor amounts of rhamnose. In addition, strain 2C^T showed a glycolyl-type cell wall. The genomic DNA G+C content was 69.8mol%, while the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with the closely related Microbacterium species were below the recognized thresholds of 95-96 % ANI and 70 % DDH for species definition. Based on the phenotypic and genotypic data, strain 2C^T (=LMG 32277^T=CECT 30329^T) is considered to represent a new species, for which the name Microbacterium paulum sp. nov. is proposed.

Microbacterium helvum sp. nov., a novel actinobacterium isolated from cow dung

A Gram-positive, aerobic, non-motile, non-spore-forming, short rod-shaped strain, NEAU-LLC^T, was isolated from cow dung in Shangzhi City, Heilongjiang Province, Northeast China and identified by a polyphasic taxonomic study. Colonies was light yellow, round, with entire margin. Strain NEAU-LLC^T was grown at 15-45 ℃ and pH 6.0-10.0. NaCl concentration ranged from 0 to 5% (W/V). The 16S rRNA gene sequence of NEAU-LLC^T showed the high similarities with Microbacterium kyungheense JCM 18735^T (98.5%), Microbacterium trichothecenolyticum JCM 1358^T (98.3%) and Microbacterium jejuense JCM 18734^T (98.2%). The whole-cell sugars were glucose, rhamnose and ribose. The menaquinones contained MK-12 and MK-13. Ornithine, glutamic acid, lysine and a small amount of alanine and glycine were the amino acids in the hydrolyzed products of the cell wall. The major fatty acids were iso-C_16:0, iso-C_18:0, anteiso-C_15:0 and anteiso-C_17:0. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The genome of NEAU-LLC^T was 4,369,375 bp and G + C content is 70.28 mol%. A combination of DNA-DNA hybridization result and some phenotypic characteristics demonstrated that strain NEAU-LLC^T could be distinguished from its closely related strains. Therefore, the strain NEAU-LLC^T was considered to represent a novel species, which was named Microbacterium helvum sp. (Type strain NEAU-LLC^T = CCTCC AA 2018026^T = JCM 32661^T).

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

A Gram-stain-positive, strictly aerobic, polar flagellated, short rod-shaped bacterium, designated DFW100M-13T, was isolated from gut of the larva of Protaetia brevitarsis seulensis collected from Wanju-gun, South Korea. The growth range of NaCl concentration was 0–3 % (w/v) (optimally 0 % (w/v)), the temperature range for growth was 10–40 °C (optimally 28–30 °C), and the pH range for growth was pH 6.0–9.0 (optimally pH 7.0–8.0). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain DFW100M-13T had a high sequence similarity to members of the genus Microbacterium , having the highest similarity with Microbacterium luticocti DSM 19459T (97.7 %), Microbacterium rhizosphaerae CHO1T (97.1 %), and Microbacterium immunditiarum SK 18T (97.0 %), and formed a distinct lineage with Microbacterium luticocti DSM 19459T within the genus Microbacterium . A phylogenetic tree based on house-keeping genes also showed the result similar to the 16S rRNA gene-based tree. The main respiratory quinone (>10 %) was MK-11, MK-12 and MK-10, and the predominant cellular fatty acids (>10 %) were iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, an inidentified glycolipid and an unidnetified lipid. The peptidoglycan type was supposed to be the B2ß with amino acids d-alanine, d-glutamic acid, glycine, l-homoserine and d-ornithine. The genomic DNA G+C content was 68.0 mol%. Based on the polyphasic taxonomic data, strain DFW100M-13T is considered to represent a novel species, for which the name Microbacterium protaetiae sp. nov. is proposed. The type strain is DFW100M-13T (=KACC 19323T=NBRC 113120T).

Microbacterium wangchenii sp. nov., isolated from faeces of Tibetan gazelles (Procapra picticaudata) on the Qinghai-Tibet Plateau

Two strains of Gram-stain-positive, aerobic, non-spore-forming, non-motile, rod-shaped bacteria (designated dk512^T and dk508) were isolated from the faeces of Tibetan gazelle (Procapra picticaudata) collected from the Qinghai-Tibet Plateau, PR China. The 16S rRNA gene sequences of the strains showed the highest identity to Microbacterium saccharophilum K-1^T (98.0 and 97.9 % similarity, respectively). The phylogenetic analysis based on 16S rRNA gene sequences revealed that dk512^T and dk508 were members of the genus Microbacterium, and most closely related to strains Microbacterium mitrae M4-8^T and Microbacterium hatanonis FCC-01^T. The strains grew optimally on brain-heart infusion (BHI) agar with 5.0 % (v/v) sheep blood at 30 °C, pH 7.0 and with 1.0 % (w/v) NaCl. The genome of type strain dk512^T was 3.8 Mb with a G+C content of 70.6 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain dk512^T and previously characterized Microbacterium species were <95 and <70 %, respectively. In strain dk512^T, the detected primary cellular fatty acids were anteiso-C_15 : 0 and anteiso-C_17 : 0, the main respiratory quinones were MK-9 (37.9 %) and MK-10 (35.7 %), and the polar lipids included diphosphatidylglycerol, phosphatidylglycerol and three unidentified glycolipids. The major cell-wall sugars were rhamnose, ribose and galactose. Alanine, glutamic acid, glycine and ornithine were in the cell-wall peptidoglycan. Based on phenotypic data and phylogenetic inference, these two strains represent a novel species of the genus Microbacterium, named here as Microbacterium wangchenii sp. nov, where dk512^T is designated the type strain (=CGMCC 1.16590^T=JCM 33494^T=KCTC 49313^T).

Fates of intracellular and extracellular antibiotic resistance genes and microbial community structures in typical swine wastewater treatment processes

Swine wastewater is an important reservoir of spread antibiotic resistance to the environment. Intra- and extracellular antibiotic resistance genes (iARGs and eARGs) were quantified during two typical swine wastewater treatment processes including a sequencing membrane bioreactor (SMBR) at pilot-scale and anaerobic-anoxic-oxic (A²O) at full-scale. The concentrations of iARGs and eARGs in raw wastewater were 3.42E+09 and 3.79E+07 copies/mL, respectively. The compositions were different between iARGs and eARGs. SMBR showed 0.63 log higher removals in the concentrations of iARG than A²O, while similar removal effects (3.01-3.44 log copies/mL) of eARGs were performed by the two processes. It suggested that membrane separation had advantages in the concentration removals of iARG rather than eARG. sul1 took the dominance in eARGs in effluent and had positive correlations with intI1, which indicated the risk of horizontal gene transfer of eARGs after wastewater discharge. Microbial community structures were estimated by 16S rRNA gene sequencing with both intra- and extracellular DNA (iDNA and eDNA). Compared between the effluent samples of the two treatment processes, microbial community structures estimated by iDNA had great differences, however which were similar for eDNA. Microbial community and water-quality parameters were the major influencing factors on ARG occurrences during swine wastewater treatment.

Microbacterium halophytorum sp. nov., a novel endophytic actinobacterium isolated from halophytes

Two actinobacterial strains, YJYP 303^T and YZYP 518, were isolated from two species of halophytes collected from the southern edge of the Gurbantunggut Desert. Cells were Gram-stain-positive, aerobic, short rods and without flagella. Growth of the two strains was found to occur at 4-44 °C, pH 6.0-12.0 and in the presence of up to 15 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains are associated with members of the genus Microbacterium. In the phylogenetic tree, the two strains shared a clade with Microbacterium halotolerans YIM 70130^T (97.58 % 16S rRNA gene sequence identity) and Microbacterium populi KCTC 29152^T (96.54 %). The average nucleotide identity values of strain YJYP 303^T and YZYP 518 to M. halotolerans YIM 70130^T were determined to be 79.97 and 80.03 %, respectively. The genomic DNA G+C contents of strains YJYP 303^T and YZYP 518 were 69.72 and 70.57 %, respectively. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The predominant respiratory quinones was MK-11, followed by MK-10 and MK-12. The muramic acid type of peptidoglycan was N-glycolyl. The whole-cell sugars were mannose, ribose, rhamnose, glucose, galactose and two unidentified sugars. The cell-wall amino acids were glutamic acid, ornithine, glycine and alanine. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. On the basis of the evidence presented in this study, strains YJYP 303^T and YZYP 518 are characterized as members of a novel species in the genus Microbacterium, for which the name Microbacteriumhalophytorum sp. nov. is proposed. The type strain is YJYP 303^T (=CGMCC 1.16264^T=KCTC 49100^T).

Microbacterium album sp. nov. and Microbacterium deserti sp. nov., two halotolerant actinobacteria isolated from desert soil

Strains SYSU D8007^T and SYSU D8014^T were isolated from desert soil collected from Saudi Arabia. The two isolates were Gram-stain-positive, non-motile, aerobic and non-spore-forming. These strains were able to grow at 4-45 °C and in the presence of up to 8 % (w/v) NaCl. Strain SYSU D8007^T could grow at pH 6.0-10.0, and strain SYSU D8014^T at pH 5.0-10.0. They shared highest 16S rRNA gene sequence similarities with Microbacterium marinilacus YM11-607^T and Microbacterium paludicola US15^T. Menaquinones MK-11 and MK-12 were detected as the respiratory quinones. The polar lipid profiles of strains SYSU D8007^T and SYSU D8014^T consisted of diphosphatidylglycerol and phosphatidylglycerol, but differed in the number of unidentified glycolipids. Strain SYSU D8007^T contained anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 as the predominant fatty acids, while strain SYSU D8014^T contained anteiso-C15 : 0 and anteiso-C17 : 0 as the major fatty acids (>10 %). While glucose, rhamnose and ribose were detected in strain SYSU D8007^T as the whole-cell sugars, galactose, glucose and rhamnose were present in strain SYSU D8014^T. The genomic DNA G+C content of strains SYSU D8007^T and SYSU D8014^T was 72.2 and 73.6 mol%, respectively. Based on phenotypic, genotypic and phylogenetic characteristics, it can be concluded that strains SYSU D8007^T and SYSU D8014^T represent two novel species of the genus Microbacterium, for which the names Microbacterium album sp. nov. and Microbacterium deserti sp. nov. are proposed, respectively. The type strains are SYSU D8007^T (=CGMCC 1.15794^T=KCTC 39990^T) and SYSU D8014^T (=CPCC 204619^T=KCTC39991^T).

Microbacterium rhizosphaerae sp. nov., isolated from a Ginseng field, South Korea

A novel Gram-stain positive, aerobic, short rod-shaped, non-motile bacterium, designated strain CHO1^T, was isolated from rhizosphere soil from a ginseng agriculture field. Strain CHO1^T was observed to form yellow colonies on R2A agar medium. The cell wall peptidoglycan was found to contain alanine, glycine, glutamic acid, D-ornithine and serine. The cell wall sugars were identified as galactose, mannose, rhamnose and ribose. Strain CHO1^T was found to contain MK-11, MK-12, MK-13 as the predominant menaquinones and anteiso-C_15:0, iso-C_16:0, and anteiso-C_17:0 as the major fatty acids. Diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, an unidentified phospholipid and three unidentified glycolipids were found to be present in strain CHO1^T. Based on 16S rRNA gene sequence analysis, strain CHO1^T was found to be closely related to Microbacterium mangrovi DSM 28240^T (97.81 % similarity), Microbacterium immunditiarum JCM 14034^T (97.45 %), Microbacterium oryzae JCM 16837^T (97.33 %) and Microbacterium ulmi KCTC 19363^T (97.10 %) and to other species of the genus Microbacterium. The DNA G+C content of CHO1^T was determined to be 70.1 mol %. The DNA-DNA hybridization values of CHO1^T with M. mangrovi DSM 28240^T, M. immunditiarum JCM 14034^T, M. oryzae JCM 16837^T and M. ulmi KCTC 19363^T were 46.7 ± 2, 32.4 ± 2, 32.0 ± 2 and 29.2 ± 2 %, respectively. On the basis of genotypic, phenotypic and phylogenetic properties, it is concluded that strain CHO1^T represents a novel species within the genus Microbacterium, for which the name Microbacterium rhizosphaerae sp. nov. is proposed. The type strain of M. rhizosphaerae is CHO1^T (= KEMB 7306-513^T = JCM 31396^T).