Molecular phylogenetic analysis
Almost full-length 16S rRNA gene sequence (1442 bp) of strain MSA67T was identified and deposited into the GenBank database (accession number MN006580). MSA67T 16S rRNA gene sequence shared the highest similarity with D. riboflavina IFO13584T (98.0 %) and D. chinhatensis IPL18T (97.0 %). These levels of similarity were below the recently recommended cutoff of 98.65 % (Kim et al. 2014). Maximum-likelihood (Fig. 1), neighbor-joining algorithm (Fig. S1) and maximum-parsimony (Fig. S2) phylogenetic trees revealed that strain MSA67T is a member of a putative novel species of the genus Devosia.
The genome of strain MSA67T has been deposited into the GenBank database (accession number JAEKMH000000000). One 16S rRNA fragment from the genome was detected, and it shared 100 % similarity with that from the PCR, and there are no contaminated sequences in the sample by analyzing the sequencing and GC depth (Fig. S3). The genomic size of strain MSA67T was 4.1 MB. The DNA G+C content of strain MSA67T was 63.6 % from the genomic sequence, which was in line with the genus Devosia range from 59.5 to 66.2 mol % (Table S1). The detailed analysis of the MSA67T genome was presented in Table S2. Table S3 showed the distribution of genes into COG functional categories . Phylogenomic tree showed the relationship between related species (Fig. 2). The ANI and dDDH values between strain MSA67T and members of the genus Devosia were presented in detail in Table S1. Both ANI and dDDH values were below the species delineation thresholds of 95–96 % ANI and 70 % dDDH, respectively. All above data supports that MSA67T represents a novel genomospecies of the genus Devosia.
Physiological properties analysis
MSA67T cells were Gram-negative. They are rod-shaped aerobic bacteria. After incubating for 3 days in MA, colonies were observed as smooth, opaque, convex and circular with cream-color and entire margins. Cells grew well in MA, R2A agar and LB agar media, however, they couldn’t grow in TSA. Growth occurred at 4–40 °C (optimal temperature, 28-30 °C), at pH 5.0–10.0 (optimal pH, 7.0) and in 0–8 % (w/v) NaCl (optimal concentration, 2.0-3.0 %). More phenotypic differences are detailed in Table 1.
The major fatty acids, which represent more than 10 % of the total fatty acids, detected in strain MSA67T were C18:1ω6c and/or C18:1ω7c, 45.2 %, C16:0 (22.1 %) and C18:1ω7c 11-methyl (23.7 %). The MSA67T fatty acid profile was similar to that of the two reference strains. Differences between them are detailed in Table 2. Respiratory quinone of strain MSA67T was identified as Q-10 (100 %), similar to all members of the genus Devosia. The polar lipids of strain MSA67T included diphosphatidylglycerol, phosphatidylglycerol, glycolipids and three unidentified phospholipids (Fig. S4).
According to the phylogenic, phenotypic and chemotaxonomic data, MSA67T is considered to be a member of the genus Devosia within the family Devosiaceae, for which the name Devosia sediminis sp. nov. is proposed.
Description of Devosia sediminis sp. nov.
Devosia sediminis (se.di'mi.nis. L. gen. n. sediminis of sediment).
Cells are Gram-negative, rod-shaped, aerobic, devoid of gliding motility, approximately 0.5–0.7μm wide and 2.1–3.4 μm long. After growing in MA at 28 °C for 3 days, colonies are smooth, opaque, convex and circular with cream-color and entire margins, and approximately 1–2 mm in diameter . Growth occurs at 4–40 °C (optimal temperature, 28-30 °C), at pH 5.0–10.0 (optimal pH, 7.0) and in 0–8 % (w/v) NaCl (optimal concentration, 2.0-3.0 %). Cells grow well in MA, R2A agar and LB agar media, however, they cannot grow in TSA. They are positive for oxidase and catalase; negative for hydrolysis of Tweens 20, 40 and 80, starch, skimmed milk and CM- cellulose.
In API 20NE tests, they are positive for urease activity, β-galactosidase, β-glucosidase (aesculin hydrolysis), L-arabinose, N-acetylglucosamine, D-glucose, D-mannose and maltose. They are negative for nitrate reduction to nitrite, D-glucose fermentation, indole production, arginine dihydrolase, D-mannitol, gelatin hydrolysis, trisodium citrate, potassium gluconate, adipic acid, capric acid, malic acid and phenylacetic acid. In API ZYM tests, they are positive for esterase lipase(C8), esterase (C4), leucine arylamidase, alkaline phosphatase, acid phosphatase, valine arylamidase, naphthol-AS-BI-phosphohydrolase, α-Glucosidase, α-Mannosidase, β-Galactosidase, β-Glucosidase, N-acetyl-β-glucosaminidase and trypsin. They are weakly positive for cystine arylamdase, α-chymotrypsin; and negative for lipase (C14), α-galactosidase, β-glucuronidase and β-fucosidase. In API 50CH tests, they are positive for D-fructose, D-ribose, D-glucose, N-acetylglucosamine, arbutin, aesculin ferric citrate, salicin, D-cellobiose, D-maltose, D-lactose (bovine origin), D-trehalose, starch, glycogen; weakly positive for potassium 5-ketogluconate and glycerol; and negative for erythritol, D-arabinose, D-adonitol, D-xylose, D-galactose, D-arabitol, D-melezitose, D-raffinose, D-melibiose, D-mannose, D-mannitol, D-turanose, D-lyxose, D-tagatose, D-fucose, D-sorbitol, L-arabinose, L-sorbose, L-rhamnose, L-fucose, L-arabitol, L-xylose, methyl-β-D-xylopyranoside, dulcito, inositol, methyl-α-D-mannopyranoside, methyl-α-D-glucopyranoside, amygdalin, inulin, xylitol, gentiobiose, potassium gluconate and potassium 2-ketogluconate. The major fatty acids are C16:0, C18:1ω7c 11-methyl and C18:1ω6c and/or C18:1ω7c. The polar lipids are glycolipids, phosphatidylglycerol, diphosphatidylglycerol, and three unidentified phospholipids. Respiratory quinone is identified to be Q-10. The genomic size of the strain is 4.1 MB. The DNA G+C content of the strain is 63.6 %.
In summary, the type strain, MSA67T (=CGMCC 1.18467T=KCTC 82192T) has been isolated from the sediment of the Mohe Basin in Northeast China. The GenBank/EMBL/DDBJ accession numbers for the genome and 16S rRNA gene sequence of the type strain are JAEKMH000000000 and MN006580, respectively.