Motile Strain Research Articles

Duganella lactea sp. nov., Duganella guangzhouensis sp. nov., Duganella flavida sp. nov. and Massilia rivuli sp. nov., isolated from a subtropical stream in PR China and proposal to reclassify Duganella ginsengisoli as Massilia ginsengisoli comb. nov.

Five Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (FT50WT, FT80WT, FT92WT, FT94W and FT135WT) were isolated from a subtropical stream in PR China. Comparisons based on 16S rRNA gene sequences showed that strains FT50WT, FT94W and FT135WT take strain Duganella sacchari Sac-22T, and strains FT80WT and FT92WT take strain Duganella ginsengisoli DCY83T as their closest neighbour in the phylogenetic trees, respectively. The G+C contents of strains FT50WT, FT80WT, FT92WT, FT94W and FT135WT were 63.3, 62.4, 62.8, 63.8 and 60.8 %, respectively. The reconstructed phylogenomic tree based on concatenated 92 core genes showed that strains FT50WT, FT80WT, FT94W and FT135WT clustered together with species of the genus Duganella, but strains FT92WT and D. ginsengisoli KCTC 42409T were located in the clades of the genus Massilia. The calculated pairwise average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among strains FT50WT, FT80WT, FT92WT, FT94W, FT135WT and related strains were in the ranges of 75.6-87.8% and 20.3-33.8% except that the values between strains FT50WT and FT94W were 98.7 and 89.2%, respectively. The respiratory quinone of these five strains was Q-8. The major fatty acids were C16 : 1 ω7c, C16 : 0, C18 : 1 ω7c and C12 : 0. The polar lipids included phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. Considering the distinct phylogenetic relationships of D. ginsengisoli with species of the genus Massilia in the phylogenomic tree, it was reasonable to transfer D. ginsengisoli to the genus Massilia as Massilia ginsengisoli comb. nov. Combining the results of phylogenomic analysis, ANI and dDDH data, and a range of physiological and biochemical characteristics together, strains FT50WT and FT94W should belong to the same species and be assigned to genus Duganella with strains FT80WT and FT135WT together, and strain FT92WT should be assigned to the genus Massilia, for which the names Duganella lactea sp. nov. (type strain FT50WT=GDMCC 1.1674T=KACC 21466T), Duganella guangzhouensis sp. nov. (FT80WT=GDMCC 1.1678T=KACC 21470T), Duganella flavida sp. nov. (FT135WT=GDMCC 1.1745T=KACC 21659T) and Massilia rivuli sp. nov. (FT92WT=GDMCC 1.1682T=KACC 21474T) are proposed.

Arthrobacter sedimenti sp. nov., isolated from river sediment in Yuantouzhu park, China.

A Gram-stain positive, motile, aerobic and rod-shaped strain (MIC A30T) was isolated from river sediment in Yuantouzhu park, Wuxi City, China. Growth occurred at 20-40°C, at pH 6.0-9.0 and at 0-5.0% NaCl. Strain MIC A30T was moderately related to Arthrobacter liuii CGMCC 1.12778T (97.9%), Arthrobacter pokkaliiT (97.9%) and Arthrobacter globiformis NBRC 12137T (96.7%) by 16S rRNA analysis. The DNA-DNA relatedness values between strain MIC A30T and these reference strains were below 30%. The DNA G+C content was 63.1mol%. Average nucleotide identity (ANI) and genome-to-genome distance (GGD) values between strain MIC A30T and A. liuii CGMCC 1.12778T were 60.34% and 29.39%, respectively. Quinone was identified as MK-9(H2). Major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. Major fatty acids were iso-C15:0, anteiso-C15:0 and anteiso-C17:0. Whole-cell sugars were galactose, mannose and rhamnose. The cell wall peptidoglycan contained A4α peptidoglycan type with lysine as the diagnostic diamino acid. Based on several taxonomic results, strain MIC A30T is identified as a novel species in genus Arthrobacter, whose name is proposed as Arthrobacter sedimenti sp. nov. The type strain is MIC A30T (= KACC 19599T = CGMCC 1.13474T).

Massilia aquatica sp. nov., Isolated from a Subtropical Stream in China.

A Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strain FT127WT was isolated from a subtropical stream in China. Comparison based on 16S rRNA gene sequences showed that strain FT127WT belongs to genus Massilia and shares 98.5% similarity with Massilia buxea A9T as its closest neighbor. The genome size of strain FT127WT was 6.65 Mbp with G + C content of 65.3%. The calculated pairwise OrthoANIu values and digital DNA-DNA hybridization values between strain FT127WT and each of strains M. buxea KCTC 52429T, Massilia armeniaca ZMN-3T, Massilia plicata DSM 17505T and Massilia namucuonensis CGMCC 1.11014T were less than 83.1% and 26.6%, respectively. The reconstructed phylogenomic tree based on concatenated 92 core genes showed that strain FT127WT clusters closely with M. namucuonensis CGMCC 1.11014T. The respiratory quinone of strain FT127WT was Q-8. The major fatty acids were C16:1 ω7c, C16:0 and C12:0. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. Combining above all characteristics, strain FT127WT should represent a novel species within genus Massilia, for which the name Massilia aquatica sp. nov. (type strain FT127WT = GDMCC 1.1690T = KACC 21482T) is proposed.

Bacillus aerolatus sp. nov., a novel member of the genus Bacillus, isolated from bioaerosols in a school playground.

A Gram-positive, endospore-forming, rod-shaped bacterium with a single flagellum, and a motile strain, designated CX253, was isolated from bioaerosols. The isolate is facultatively anaerobic, is able to grow at 25-45℃ (optimum 37℃) and pH 6.5-10.0 (optimum 7.5), and can tolerate up to 5.0% NaCl (w/v) under aerobic conditions. The diagnostic diamino acid in the cell wall of strain CX253T is meso-diaminopimelic acid, while major isoprenoid quinone is menaquinone 6 (MK-6) along with a smaller amount of MK-7 (20%). The polar lipid profile is composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipids and glycolipids. The major cellular fatty acid is iso-C15:0 and anteiso-C15:0. Phylogenetic analysis based on 16S rRNA gene and genome sequence grouped strain CX253T into the genus Bacillus. The strain was most closely related to Bacillus thermotolerans CCTCC AB 2012108T by comparison of 16S rRNA gene sequence (97.2% similarity) and to Bacillus wudalianchiensis CCTCC AB 2015266T by comparison of gyrB gene sequence (80.1% similarity). The draft genome of strain CX253T comprised 3,929,195bp with a G + C content of 43.3mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain CX253T and phylogenetically related Bacillus species were lower than 95% and 70%, respectively. Thus, the polyphasic evidence generated through phenotypic, chemotaxonomic and genomic methods confirmed that strain CX253T (= GDMCC 1.1608T = KACC 21318T) was a novel species of the genus Bacillus, for which the name Bacillus aerolatus sp. nov. is proposed.

Paenibacillus anseongense sp. nov. a Silver Nanoparticle Producing Bacterium Isolated from Rhizospheric Soil.

A silver nanoparticle (AgNP) producing, Gram stain-positive, aerobic, motile, and rod-shaped novel bacterial strain, designated as MAH-34T was isolated from rhizospheric soil of magnolia tree. The colonies were creamy white, smooth, circular, and 0.9-2.0mm in diameter when grown on R2A agar. Strain MAH-34T was found to be able to grow at 10-37°C, at pH 6.0-9.5, and at 0-1% NaCl. The strain showed activity for both catalase, and oxidase tests, and was able to rapid synthesis of AgNPs. The TEM image revealed the spherical shape of biosynthesized AgNPs, and the size was 5 to 15nm. Based on 16S rRNA gene sequence comparisons, the isolate was shown to be a member of genus Paenibacillus, and the close type strains were Paenibacillus chondroitinus DSM 5051T (98.3%), Paenibacillus aceris KUDC4121T (98.2%), Paenibacillus nebraskensis JJ-59T (97.8%), Paenibacillus alginolyticus DSM 5050T (97.6%), Paenibacillus ferrarius CY1T (97.4%), Paenibacillus frigoriresistens YIM 016T (97.3%), and Paenibacillus pocheonensis Gsoil 1138T (97.3%). Strain MAH-34T had a genome size of 8,647,010bp. The genomic G + C content was 46.0mol %. The major isoprenoid quinone was determined as menaquinone-7 (MK-7). The major cellular fatty acids were determined as C15:0 anteiso, and C16:0 iso. Based on the DNA-DNA hybridization results, genotypic analysis, chemotaxonomic, and physiological data, strain MAH-34T represents a novel species, for which the name Paenibacillus anseongense sp. nov. is proposed, with MAH-34T as the type strain (= KACC 19974T = CGMCC1.16610T).

PCR-based screening, isolation, and partial characterization of motile lactobacilli from various animal feces

BackgroundMost lactobacilli found in animal intestines are generally non-motile, but there are few exceptions. Our previous work showed that Lactobacillus agilis BKN88, which is a highly motile strain originating from a chicken, takes advantage of motility in gut colonization in murine models, and thus motile lactobacilli likely have unique ecological characteristics conferred by motility. However, the ecology and habitat of gut-derived motile lactobacilli are still rarely understood. In addition, the limited availability of motile Lactobacillus isolates is one of the major obstacles for further studies. To gain insight into the ecology and habitat of the motile lactobacilli, we established a routinely applicable detection method for motile lactobacilli using PCR and subsequent selective isolation in semi-solid MRS medium for the collection of additional motile lactobacilli from animal feces.ResultsWe applied the PCR detection using motile lactobacilli-specific primers, based on the motor switch protein gene (fliG) of flagella, to 120 animal feces, followed by selective isolation performed using 45 animal feces. As a result, motile lactobacilli were detected in 44 animal feces. In the selective isolation, 29 isolates of L. agilis and 2 isolates of L. ruminis were obtained from 8 animal species.ConclusionsThese results indicated that motile lactobacilli are distributed in different animal species. Moreover, phylogenetic analysis of the L. agilis isolates suggests co-evolution with the host, and adaptation to a particular environmental niche.

Duganella alba sp. nov., Duganella aquatilis sp. nov., Duganella margarita sp. nov. and Duganella levis sp. nov., isolated from subtropical streams in China.

Six Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (FT9WT, FT25W, FT26WT, FT109WT, FT134W and CY42WT) were isolated from subtropical streams in China. Comparisons based on 16S rRNA gene sequences showed that the six strains shared similarities of less than 98.1 % with other species within the family Oxalobacteraceae and formed two separately distinct clades in phylogenetic trees. The 16S rRNA gene sequence similarities between strains FT9WT and FT25W, and between strains FT109WT and FT134W were both 99.7 %. The genome sizes of strains FT9WT, FT25W, FT26WT, FT109WT, FT134W and CY42WT were 6.45, 6.45, 6.54, 6.43, 6.52 and 6.74 Mbp with G+C contents of 64.0, 64.0, 63.8, 63.2, 63.2 and 62.5 %, respectively. The calculated pairwise average nucleotide (ANI) values among the six strains and other related species were less than 93.9 %, except that the values were 99.9 % between strains FT9WT and FT25W, 98.2 % between strains FT109WT and FT134W, and 95.0 and 95.1 % between strain FT26WT and strains FT9WT and FT25W, respectively. However, strain FT26WT shared 16S rRNA gene sequence similarities of only 98.3 and 98.2 % with FT9WT and FT25W, respectively. The respiratory quinone of the six strains was determined to be Q-8. The major fatty acids were C16 : 1ω7c, C16 : 0 and C12 : 0. The predominant polar lipids included phosphatidylethanolamine and phosphatidylglycerol. Considering the phenotypic, biochemical, genotypic and ANI data, strains FT9WT and FT25W, and FT109WT and FT134W may belong to the same species, respectively. Although the pairwise ANI values between strain FT26WT and each of strains FT9WT and FT25W were located in the transition region of species demarcation, the dissimilarities among them indicated that strain FT26WT could represent an independent novel species. The reconstructed phylogenomic tree based on a concatenation of 92 core genes showed that the six strains clustered closely with Duganella sacchari Sac-22T and Duganella radicis KCTC 22382T, and supported that these six strains belong to the genus Duganella. The names Duganella albus sp. nov. (type strain FT9WT=GDMCC 1.1637T=KACC 21313T), Duganella aquatilis sp. nov. (type strain FT26WT=GDMCC 1.1641T=KACC 21315T), Duganella pernnla sp. nov. (type strain FT109WT=GDMCC 1.1688T=KACC 21480T) and Duganella levis sp. nov. (type strain CY42WT=GDMCC 1.1673T=KACC 21465T) are proposed.

Sphingomonas suaedae sp. nov., a chitin-degrading strain isolated from rhizosphere soil of Suaeda salsa

A Gram-stain-negative, aerobic, chitin-degrading, motile bacterial strain with a single polar flagellum, designated XS-10T, was isolated from saline soil sampled from the rhizosphere of Suaeda salsa, Tumd Right Banner, Inner Mongolia, PR China. Strain XS-10T grew at 10-40 °C (optimum, 35 °C), pH 5.0-9.0 (optimum, pH 8.0) and 0-12.5% NaCl (optimum 2.0 %). The phylogenetic analysis based on both the 16S rRNA gene and the phylogenomic tree revealed that strain XS-10T formed a clade with Sphingomonas turrisvirgatae MCT13T and Sphingomonas koreensis JSS-26T, sharing 98.4 and 97.5 % 16S rRNA gene similarities to S. koreensis JSS-26T and S. turrisvirgatae MCT13T, respectively. Spermidine and Q-10 were the major polyamine and the major respiratory quinone, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, two unidentified lipids and an unidentified aminophospholipid. The major fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and C17 : 1 ω6c. The genome of strain XS-10T consisted of a 4 154 291 bp chromosome with a DNA G+C content of 65.5 mol%. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values of strain XS-10T with S. turrisvirgatae MCT13T and S. koreensis JSS-26T were 77.8 and 78.6 %, 75.9 and 76.3 %, and 22.0 and 22.9 %, respectively. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain XS-10T is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas suaedae sp. nov. is proposed. The type strain is XS-10T (=CGMCC 1.17078T=JCM 33850T).

Aureimonas psammosilene sp. nov., isolated from the roots of Psammosilene tunicoides.

One motile strain designated, YIM DR1026T was isolated from the roots of Psammosilene tunicoides collected from Gejiu, Yunnan province, China. The cells of strain YIM DR1026T were Gram-negative and short-rod shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YIM DR1026T was a member of the genus Aureimonas and closely related to Aureimonas rubiginis (96.7%). DNA-DNA relatedness values between strain YIM 1026T and Aureimonas rubiginis BCRC 80440T was 38.2 ± 1.5%. The ANI value between YIM DR1026T and other Aureimonas members were below the cut-off level (95-96%) recommended as the average nucleotide identity (ANI) criterion for interspecies identity. Strain YIM DR1026T grew at 4-30°C (optimum 28°C), pH 4.0-9.0 (optimum pH 6.0-7.0) and tolerated NaCl (w/v) up to 1% (optimum 0%). Q-10 was sole the respiratory ubiquinone present in YIM DR1026T. Polar lipids of strain YIM DR1026T were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, sulfoquinovosyldiacylglycerol, unidentified aminolipid and unidentified polar lipid. The genomic G + C content was 64.6mol%. The major fatty acids were C18:1ω7c, C16:0 and summed feature 3 (C16:1ω7c/C16:1ω6c). Based on phenotypic, phylogenetic, chemotaxonomic and genome comparison, strain YIM DR1026T represents a novel species of the genus Aureimonas, for which the name Aureimonas psammosilene sp. nov. is proposed. The type strain is YIM DR1026T (= KCTC 42691T = NBRC 112412T).

Flavobacterium profundi sp. nov., isolated from a deep-sea seamount.

The Gram-stain-negative, rod-shaped, facultative anaerobic, motile bacterial strain, designated TP390T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain TP390T was related to the genus Flavobacterium and had highest 16S rRNA gene sequence identity with the type strain of Flavobacterium jejuense EC11T (97.8 %). Sequence similarities to all other type strains of current species of the genus Flavobacterium were below 97 %. The predominant cellular fatty acids were iso-C15 : 0 and iso-C15 : 1G. The quinone system for strain TP390T comprised predominantly menaquinone MK-6 and the polar lipid profile contained phosphatidylethanolamine, four unknown aminolipids, one glycolipid and six unknown polar lipids. The genomic DNA G+C content of strain TP390T was 31.2 mol%. In addition, the maximum values of in silico DNA-DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain TP390T with F. jejuense KCTC 42149T were 22.60 and 80.01% respectively. Combined data from phenotypic, phylogenetic, isDDH and ANI data demonstrated that the strain TP390T is representative of a novel species of the genus Flavobacterium, for which we propose the name Flavobacterium profundi sp. nov. (type strain TP390T=KACC 18559T=CGMCC 1.15398T).

Cold-shock proteins affect desiccation tolerance, biofilm formation and motility in Listeria monocytogenes

Listeria monocytogenes is a foodborne pathogen whose biofilm formation and desiccation tolerance may contribute to its survival in the food industry. L. monocytogenes possesses three cold-shock domain family proteins (CspA, CspB and CspD) known to be essential for adaptation against various food-relevant stress conditions including cold growth. The role of Csps in desiccation tolerance and biofilm formation was investigated in csp mutants as well as twenty-one other wild-type (WT) strains. Mutants with a single (ΔcspA) or multiple (ΔcspAB, ΔcspAD and ΔcspABD) deletions of csp genes, in a desiccation sensitive WT background (L. monocytogenes EGD-e) were immotile and exhibited an elevated desiccation tolerance compared to the parent strain. However, deletion of cspA in the more desiccation resistant food and outbreak related L. monocytogenes strains 568 and 08-5578 had no impact on desiccation tolerance although compared to the parent strains the mutants were also immotile. A correlation between lower motility and higher desiccation tolerance was observed among the 20 WT strains (Spearman rank correlation, rs = −0.56, p = 0.01), although exceptions occurred indicating that multiple factors influence the diverse desiccation tolerance among L. monocytogenes strains. Expression of cspA was upregulated in WT EGD-e, 568 and 08-5578 strains after desiccation for seven days, while the 568 and 08-5578 ΔcspA mutants expressed elevated levels of cspD and cspB (>30 fold higher) compared to their WTs. This indicates that upregulation of the other csps compensates for the deleted cspA gene. Although biofilm formation was improved in all EGDe csp mutants relative to the WT strain, the opposite was observed for 568 and 08-5578 WT strains and their cspA deletion mutants. Only motile strains formed biofilm in the peg lid assay but a significant negative correlation (rs = −0.60, p = 0.01) was seen between higher motility and higher biofilm formation of WT strains. In conclusion, the survival of L. monocytogenes strains in the food processing environment may depend on the control of motility, which is a necessity for biofilm formation but disadvantageous for desiccation survival.

Duganella rivus sp. nov., Duganella fentianensis sp. nov., Duganella qianjiadongensis sp. nov. and Massilia guangdongensis sp. nov., isolated from subtropical streams in China and reclassification of all species within genus Pseudoduganella.

Four Gram-stain-negative, catalase-positive, rod-shaped and motile strains (FT55WT, FT93WT, CY13WT and DS3T) were isolated from subtropical streams in China. Comparisons based on 16S rRNA gene sequences indicated that strains FT55WT, FT93WT and CY13WT take strain Pseudoduganella danionis E3/2T, and strain DS3T takes strain Pseudoduganella eburnea 10R5-21T as their closest neighbour, respectively. The genome sizes of strains FT55WT, FT93WT, CY13WT and DS3T were 6.15, 5.10, 5.31 and 5.72 Mbp with G+C contents of 61.7, 60.9, 60.6 and 64.0%, respectively. The reconstructed phylogenomic tree based on concatenated 92 core genes showed that strain FT55WT clusters closely with Duganella radicis KCTC 22382T and Duganella sacchari Sac-22T, strains FT93WT and CY13WT form a distinct clade with P. danionis DSM 103461T and this clade clusters with the clades of genus Duganella together, and strain DS3T forms a distinct clade with P. eburnea JCM 31587T and Pseudoduganella violaceinigra DSM 15887T and this clade clusters closely with the clades of genus Massilia, respectively. The calculated pairwise OrthoANIu values and digital DNA-DNA hybridization (DDH) values among strains FT55WT, FT93WT, CY13WT, DS3T and related strains were in the ranges of 75.6-94.2% and 20.6-56.2%, respectively. Q-8 was the sole respiratory quinone of these four strains. The major fatty acids were C16:1ω7c, C16:0 and C12:0. The polar lipids included phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid. Considering the similar fatty acids and polar lipids profiles of species within genus Pseudoduganella, Massilia and Duganella, there is currently no justification for assigning the species of genus Pseudoduganella into the Massilia and Duganella clades in the phylogenomic tree. It is reasonable to transfer P. violaceinigra and P. eburnea to the genus Massilia as Massilia violaceinigrum comb. nov. and Massilia eburnea comb. nov., and transfer P. danionis to the genus Duganella as Duganella danionis comb. nov. Considering phylogenomic analysis, OrthoANIu data, digital DDH data and a range of physiological and biochemical characteristics, strains FT55WT, FT93WT and CY13WT should be assigned to genus Duganella, and strain DS3T should be classified as a novel species within genus Massilia, for which the names Duganella rivus sp. nov. (type strain FT55WT = GDMCC 1.1675T = KACC 21467T), Duganella fentianensis sp. nov. (type strain FT93WT = GDMCC 1.1683T = KACC 21475T), Duganella qianjiadongensis sp. nov. (type strain CY13WT = GDMCC 1.1669T = KACC 21461T) and Massilia guangdongensis sp. nov. (type strain DS3T = GDMCC 1.1636T = KACC 21312T) are proposed.

Rugamonas aquatica sp. nov. and Rugamonas rivuli sp. nov., isolated from a subtropical stream in PR China.

Two Gram-stain-negative, catalase- and oxidase-positive, rod-shaped, motile strains (FT29WT and FT103WT) were isolated from a subtropical stream in PR China. Comparisons based on 16S rRNA gene sequences showed that strains FT29WT and FT103WT showed 98.7 and 98.6 % 16S rRNA gene sequence similarities to Rugamonas rubra CCM 3730T as their closest neighbour, respectively. The calculated pairwise OrthoANIu values between strain R. rubra CCM 3730T and strains FT29WT and FT103WT were all 81.4 %. The respiratory quinone of strains FT29WT and FT103WT was determined to be Q-8. The major fatty acids were C16 : 1 ω7c, C16 : 0 and C12 : 0. The polar lipids of strain FT103WT included phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid, but strain FT29WT did not contain phosphatidylglycerol. The genome sizes of strains FT29WT and FT103WT were 7.23 and 6.84 Mbp with G+C contents of 63.8 and 63.9 %, respectively. Although the pairwise OrthoANIu value between strains FT29WT and FT103WT was 95.2 % which located in the transition region of species demarcation, the dissimilarities in the aspects of phenotypic, biochemical and genotypic characteristics supported these two strains should belong to the different species within genus Rugamonas, for which the names Rugamonas aquatica sp. nov. (type strain FT29WT=GDMCC 1.1643T=KACC 21316T) and Rugamonas rivuli sp. nov. (type strain FT103WT=GDMCC 1.1685T=KACC 21477T) are proposed.

Devosia marina sp. nov., isolated from deep seawater of the South China Sea, and reclassification of Devosia subaequoris as a later heterotypic synonym of Devosia soli.

A Gram-stain-negative, aerobic, rod-shaped and motile bacterial strain, designated L53-10-65T, was isolated from deep seawater of the South China Sea. Strain L53-10-65T was found to grow at 4-41 °C (optimum, 28 °C), at pH 5.0-9.0 (pH 7.0-8.0) and in 0-7 % (w/v) NaCl (2 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain L53-10-65T fell within the genus Devosia, with the highest similarity to Devosia indica IO390501T (98.4 %), followed by 'Devosia lucknowensis' L15T (97.7 %) and Devosia riboflavina IFO 13584T (96.8 %). The digital DNA-DNA hybridization (dDDH) values between strain L53-10-65T and the three relatives above were 43.7, 21.5 and 20.9 %, respectively; the average nucleotide identity (ANI) values were 91.3, 78.4 and 76.8 %, respectively. These values were below the 70 % dDDH and 95-96 % ANI thresholds for bacterial species delineation. The major cellular fatty acids of strain L53-10-65T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C18 : 1 ω7c 11-methyl and C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and glycolipids. The respiratory quinone was identified as Q-10. The DNA G+C content of strain L53-10-65T was 61.3 mol%. Based on the results of phylogenetic analysis and distinctive phenotypic characteristics, strain L53-10-65T is concluded to represent a novel species of the genus Devosia, for which the name Devosia marina sp. nov. is proposed. The type strain of the species is L53-10-65T (=MCCC 1A05139T=KCTC 72888T). Moreover, we propose that Devosia subaequoris is a later heterotypic synonym of Devosia soli based on the present results.

Rhodobacter xinxiangensis sp. nov., isolated from pakchoi-cultivated soil contaminated with heavy metal and its potential to reduce Cd and Pb accumulation in pakchoi (Brassica campestris L.).

A Gram-stain-negative, aerobic, and motile strain, TJ48T, was isolated from pakchoi-cultivated soil contaminated with Cd and Pb in Xinxiang (China). Cells of the strain were rod-shaped and colonies on LB agar were faint yellow. Strain TJ48T was positive for catalase and oxidase and the optimal condition for growth was 28°C, with 1% (w/v) NaCl and at pH 7.0. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain TJ48T was closely related to the genus Rhodobacter and the closest relatives were Rhodobacter ovatus JA234T (97.4%, 16S rRNA gene sequence similarity) and Rhodobacter azotoformans KA25T (96.5%). The DNA G + C content of strain TJ48T was 64.7mol%. Genome-to-genome distance calculations (GGDC) and ANIb values from genomic comparison between the genomes of strain TJ48T and the related reference species were less than 70% and 95%, respectively. The major cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C17:0. The only isoprenoid quinone detected was Ubiquinone-10 (Q-10). The polar lipid profile contains diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipids, and three unidentified lipids. Strain TJ48T significantly increased the dry weight of roots (26.2-66.3%) and shoots (16.7-37.8%) of pakchoi and reduced the Cd (50.2-60.1%) and Pb (55.6-60.9%) contents in pakchoi shoots and roots. On the basis of the physiological, genotypic and genomic characteristics, the strain TJ48T represent a novel species of the genus Rhodobacter, and the name Rhodobacter xinxiangensis sp. nov. is proposed (type strain TJ48T = CCTCC AB2019120T = KCTC 72510T).

Halomonas montanilacus sp. nov., isolated from hypersaline Lake Pengyanco on the Tibetan Plateau.

A Gram-stain-negative, catalase- and oxidase-positive, aerobic, rod-shaped, motile strain (PYC7WT) was isolated from Lake Pengyanco on the Tibetan Plateau. Comparisons based on 16S rRNA gene sequences showed that strain PYC7WT belongs to the genus Halomonas, with Halomonas malpeensis YU-PRIM-29T and Halomonas johnsoniae T68687T as its closest neighbours (96.8 and 96.6 % 16S rRNA gene sequence similarity, respectively), and only 93.1 % 16S rRNA gene sequence similarity to Halomonas elongata ATCC 33173T. The predominant respiratory quinone of strain PYC7WT is Q-9, with Q-8 as a minor component. The major fatty acids are C18 : 1 ω6c and / or C18 : 1 ω7c, C16 : 0, C16 : 1 ω6c and/or C16 : 1 ω7c, and C12 : 0 3OH. The polar lipids of strain PYC7WT include phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. Genome sequencing revealed a genome size of 4.79 Mbp and a G+C content of 62.9 mol%. DNA-DNA hybridization values of strain PYC7WT showed 45, 30 and 38 % relatedness with Halomonas johnsoniae DSM 21197T, Halomonas hamiltonii DSM 21196T and Halomonas stevensii DSM 21198T, respectively. Combining phenotypic, biochemical, genotypic and DNA-DNA hybridization data, we propose that strain PYC7WT represents a novel species within the genus Halomonas and to have the name Halomonas montanilacus sp. nov.; PYC7WT (=CICC 24506T= KCTC 62529T) is the type strain.

Mesorhizobium alexandrii sp. nov., isolated from phycosphere microbiota of PSTs-producing marine dinoflagellate Alexandrium minutum amtk4.

An aerobic, Gram-stain-negative, motile and rod-shaped bacterial strain, designated as Z1-4T, was isolated from the phycosphere microbiota of marine dinoflagellate Alexandrium minutum that produces paralytic shellfish poisoning toxins. Phylogenetic analysis based on 16S rRNA gene sequences showed that the new isolate belongs to the genus Mesorhizobium, and it was closely related to Mesorhizobium waimense LMG 28228T and Mesorhizobium amorphae LMG 18977T with both 16S rRNA gene sequence similarities of 97.3%. The values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) relatedness between strain Z1-4T and its relatives are both well below the thresholds used for the delineation of a new species. A genome-based phylogenetic tree constructed by up-to-date bacterial core gene set (UBCG) indicates that strain Z1-4T forms an independent branch within the genus Mesorhizobium. The respiratory quinone of strain Z1-4T was Q-10. The major fatty acids were similar to other members of the genus Mesorhizobium containing the summed feature 8, C16:0, C19:0cycloω8c, C17:0 and summed feature 3. The polar lipids are phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, five glycolipids and seven unknown polar lipids. The DNA G + C content was determined to be 62.1mol% based on its genomic sequence. Combined evidences based on the genotypic, chemotaxonomic and phenotypic characteristics clearly indicates that strain Z1-4T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium alexandrii sp. nov. is proposed. The type strain is Z1-4T (= KCTC72512T = CCTCC AB 2019101T).

Luteimonas cellulosilyticus sp. nov., Cellulose-Degrading Bacterium Isolated from Soil in Changguangxi National Wetland Park, China.

A Gram-negative, motile, aerobic, and rod-shaped strain (MIC 1.5T) was isolated from soil in Changguangxi national wetland park. Growth occurred at 20-45°C, at pH 6.0-8.0, and at 0-4.0% NaCl. Based on 16S rRNA gene sequence analysis, strain MIC 1.5T was related to were identified as Luteimonas dalianensis CGMCC 1.12191T (95.3%), Luteimonas padinae DSM 101536T (94.5%), Luteimonas huabeiensis DSM 26429T (94.1%), and Luteimonas mephitis DSM 12574T (92.5%). The DNA-DNA relatedness values between strain MIC 1.5T , and these strains were well below 31%. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The DNA G+C content of strain MIC 1.5T was 66.3mol%. Average nucleotide identity (ANI) and genome-to-genome distance (GGD) values between strain MIC 1.5T and L. dalianensis CGMCC 1.12191T were 65.39% and 29.52%, respectively. The quinone was identified as Q-8. The major fatty acids were iso-C15:0, iso-C15:0 3OH, and iso-C17:0 3OH and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). Based on the phylogenetic, physiological, and chemotaxonomic results, strain MIC 1.5T represents a novel species of the genus Luteimonas, for which the name Luteimonas cellulosilyticus sp. nov. is proposed. The type strain is MIC 1.5T (= KACC 19469T = CCTCC AB 2017256T).

Identification and characterization of psychrotrophic strain of Planococcus maritimus for glucosylated C30 carotenoid production

Cold-adapted bacteria produce various pigments as their adaptive strategy. Here, we studied an aerobic, gram-positive motile coccoid bacterial strain KK21, isolated from the Siachen, Himalayas and characterized the major pigments present in it. The KK21 strain is capable of growth in a broad range of temperature (-4 to 37°C), pH (6.0-13.0) and salinity (0.5-8%). Phylogenetic analysis based on 16S rRNA gene sequence showed that it belongs to the genus Planococcus and closely related to P. maritimus. Total pigment extraction was best found in polar methanol. Alanine among amino acids, NaCl among inorganic salts and evening primrose amongst oils best supported the pigment production at 10°C after 6 days in BHI at neutral pH of 7.0. Maximum pigment production was recorded at 3% of NaCl concentration. In photoprotection activity, radiation exposed plates showed increased colony forming units and more than 3.5 times of total carotenoid production after 15 min exposure compared to the control group. Detailed characterization of orange pigment was done systematically by TLC, HPLC and MALDI-TOF. Chromatographic and MALDI-TOF data have revealed the exclusive presence of glycosylated C30-carotenoid in P. maritimus KK21 with m/z of 655.871.

Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15

Photobacterium species are widely distributed in the marine environment. The overall metabolism of this genus remains largely unknown. In order to improve our knowledge on this bacterium, the relationship between the genome and phenome of the Photobacterium isolate was analyzed. The cream colored, Gram-negative, rod-shaped and motile bacterial strain, J15, was isolated from marine water of Tanjung Pelepas, Johor, Malaysia. The 5,684,538 bp genome of strain J15 comprised 3 contigs (2 chromosomes and 1 plasmid) with G + C content of 46.39 % and contained 4924 protein-coding genes including 180 tRNAs and 40 rRNAs. The phenotypic microarray (PM) as analyzed using BIOLOG showed the utilization of; i) 93 of the 190 carbon sources tested, where 61 compounds were used efficiently; ii) 41 of the 95 nitrogen sources tested, where 22 compounds were used efficiently; and iii) 3 of the 94 phosphorous and sulphur sources tested. Furthermore, high tolerance to osmotic stress, basic pH and toxic compounds as well as resistance to antibiotics of strain J15 were determined by BIOLOG PM. The ANI and kSNP analyses revealed that strain J15 to be the same species with Photobacterium marinum AK15 with ANI value of 96.93 % and bootstrapping value of 100 in kSNP. Based on the ANI and kSNP analyses, strain J15 was identified as P. marinum J15.