Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleic acid

Actinomyces marmotae sp. nov. and Actinomyces procaprae sp. nov. isolated from wild animals and reclassification of Actinomyces liubingyangii and Actinomyces tangfeifanii as Boudabousia liubingyangii comb. nov. and Boudabousia tangfeifanii comb. nov., respectively

Four Gram-stain-positive, catalase-negative, non-spore-forming, rod-shaped bacterial strains (zg-325^T, zg329, dk561^T and dk752) were isolated from the respiratory tract of marmot (Marmota himalayana) and the faeces of Tibetan gazelle (Procapra picticaudata) from the Qinghai-Tibet Plateau of PR China. The results of 16S rRNA gene sequence-based phylogenetic analyses indicated that strains zg-325^T and dk561^T represent members of the genus Actinomyces, most similar to Actinomyces denticolens DSM 20671^T and Actinomyces ruminicola B71^T, respectively. The DNA G+C contents of strains zg-325^T and dk561^T were 71.6 and 69.3 mol%, respectively. The digital DNA-DNA hybridization values of strains zg-325^T and dk561^T with their most closely related species were below the 70 % threshold for species demarcation. The four strains grew best at 35 °C in air containing 5 % CO₂ on brain heart infusion (BHI) agar with 5 % sheep blood. All four strains had C_18:1ω9c and C_16:0 as the major cellular fatty acids. MK-8 and MK-9 were the major menaquinones in zg-325^T while MK-10 was predominant in dk561^T. The major polar lipids included diphosphatidylglycerol and phosphatidylinositol. On the basis of several lines of evidence from phenotypic and phylogenetic analyses, zg-325^T and dk561^T represent novel species of the genus Actinomyces, for which the name Actinomyces marmotae sp. nov. and Actinomyces procaprae sp. nov. are proposed. The type strains are zg-325^T (=GDMCC 1.1724^T=JCM 34091^T) and dk561^T (=CGMCC 4.7566^T=JCM 33484^T). We also propose, on the basis of the phylogenetic results herein, the reclassification of Actinomyces liubingyangii and Actinomyces tangfeifanii as Boudabousia liubingyangii comb. nov. and Boudabousia tangfeifanii comb. nov., respectively.

Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens

The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species (Chryseobacterium arachidiradicis, Chryseobacterium bovis, Chryseobacterium caeni, Chryseobacterium hispanicum, Chryseobacterium hominis, Chryseobacterium hungaricum,, Chryseobacterium pallidum and Chryseobacterium zeae) to the genus Epilithonimonas and eleven (Chryseobacterium anthropi, Chryseobacterium antarcticum, Chryseobacterium carnis, Chryseobacterium chaponense, Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum, Chryseobacterium palustre, Chryseobacterium solincola, Chryseobacterium treverense and Chryseobacterium yonginense) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.

Nocardioides yefusunii sp. nov., isolated from Equus kiang (Tibetan wild ass) faeces

Two Gram-stain-positive, irregular rod-shaped (0.2-0.5×1.3-2.5 um) strains, HY056^T and HY057, were isolated from the faeces of Equus kiang (the largest of the wild asses) collected at different regions from the Qinghai-Tibetan Plateau of PR China. Phylogenetic analyses indicated that strains HY056^T and HY057 belong to the genus Nocardioides by sharing a similarity ranging from 96.3 to 97.0 % in the 16S rRNA gene sequence and forming a distinct cluster with Nocardioides daphniae JCM 16608^T, Nocardioides houyundeii 78^T, Nocardioides solisilvae Ka25^T and Nocardioides gilvus XZ17^T. The digital DNA-DNA hybridization value of strain HY056^T was 96.9 % with strain HY057, but less than 30.0 % with the above four closest relatives. MK-8(H₄) was the predominant (91.6 %) respiratory quinone. The cell wall contained ll-2,6-diaminopimelic acid as the diamino acid of the peptidoglycan. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phospholipid. The predominant fatty acids (>10.0 %) were C_18 : 1ω9c and iso-C_16:0. The DNA G+C contents of strains HY056^T and HY057 were 68.9 and 69.1 mol%, respectively. β-Glucosidase expression was positive, and acid was produced from d-fructose. Strain HY056^T (=CGMCC 4.7563^T=JCM 33399^T) is assigned as the type strain of a novel species within the genus Nocardioides, for which the name Nocardioidesyefusunii sp. nov is proposed.

Roseomonas wenyumeiae sp. nov., isolated from faeces of Tibetan antelopes (Pantholops hodgsonii) on the Qinghai-Tibet Plateau

Two Gram-stain-negative, catalase- and oxidase-positive, non-spore-forming, aerobic, motile, flagellated, and coccus-shaped strains (Z23^T and Z24) were isolated from faeces of Tibetan antelopes (Pantholops hodgsonii) on the Qinghai-Tibet Plateau, PR China. Results of the morphological, biochemical, and phylogenetic studies indicated that they were similar to each other, but distinct from existing species of the genus Roseomonas. The proposed type strain, Z23^T, had 97.8, 97.1 and 96.8 % 16S rRNA similarity to Roseomonas ludipueritiae DSM 14915^T, Roseomonas aerofrigidensis JCM 31878^T and Roseomonas aerophila KACC 16529^T. Results from further phylogenetic analyses based on the 16S rRNA gene and 857 core genes indicated that the two strains were members of Roseomonas, but clearly separated from the currently recognized species. Strains Z23^T had 43.8 %, 25.0 % DNA-DNA relatedness and 91.2, 81.3 % ANI values with R. ludipueritiae DSM 14915^T and R. aerophila KACC 16529^T. The genomic DNA G+C content of strain Z23^T was 68.6 mol%. The major cellular fatty acids of strain Z23^T were C_18 : 1ω7c and/or C_18 : 1ω6c and C_19 : 0cyclo ω8c. The cell-wall sugars included glucose, rhamnose and ribose. Q-10 was the sole respiratory quinone, and spermidine was the major polyamine component. Polar lipids present in strain Z23^T were phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, three aminolipids, two phospholipids and two unidentified lipids. Based on the distinct differences from other Roseomonas species judged from the genotypic and phenotypic data, a novel species represented by Z23^T and Z24, Roseomonas wenyumeiae sp. nov., is proposed. The type strain is Z23^T (=CGMCC 1.16540^T=DSM 106207^T).

Streptococcus chenjunshii sp. nov. isolated from feces of Tibetan antelopes

Three Gram-stain-positive, catalase-negative, α-haemolytic, chain-forming and coccus-shaped microorganisms (strains Z15^T, Z1 and Z2) were isolated from feces of Tibetan antelopes collected from the Qinghai-Tibet plateau, PR China. The results of 16S rRNA gene sequence studies indicated that Z15^T shared 94.5, 93.1 and 92.2 % similarity with Streptococcus pantholopis DSM 102135^T, Streptococcus ursoris NUM 1615^T and Streptococcus dentapri NUM 1529^T, respectively. rpoB and groEL-based sequence analysis of our three novel isolates revealed interspecies divergence of 16.7 and 14.3 % from Streptococcus pantholopis DSM 102135^T. The genomic DNA G+C content of Z15^T is 42.48 mol%. Z15^T has an average nucleotide identity (ANI) value of 81.19 % with S. pantholopis DSM 102135^T and a DNA-DNA relatedness value of less than 70 % in the in-silico DNA-DNA hybridization (isDDH) with other species of genus Streptococcus deposited in the GenBank database. A whole-genome phylogenetic tree based on 246 core genes of 78 genomes of members of the genus Streptococcusindicated that Z15^T represents a member of genus Streptococcus but one well separated from the currently recognized species. Z15^T contains C18 : 1ω7c (25.5 %), C18 : 1ω9c (19.6 %), C16 : 0 (17.5 %) and C16 : 1ω9c (13.3 %) as its major cellular fatty acids. According to the morphological, biochemical and molecular phylogenetic features of the three novel isolates, they represent a novel species of the genus Streptococcus, and Streptococcus chenjunshii sp. nov. is thus proposed. The type strain is Z15^T (=CGMCC 1.16529=DSM 106182).

Flavobacterium phocarum sp. nov., isolated from soils of a seal habitat in Antarctica

A Gram-stain-negative, yellow-pigmented, non-flagellated, gliding, rod-shaped, oxidase-negative and catalase-positive bacterium, designated SE14^T, was isolated from soil on King George Island, South Shetland Islands, Antarctica. Strain SE14^T grew at 4-25 °C (optimum, 20 °C), at pH 6.0-9.0 (optimum, pH 7.0-7.5) and with 0-3.0 % NaCl (optimum, 1.0-1.5 %), and could not produce flexirubin-type pigments. 16S rRNA gene sequence analysis showed the the isolate belonged to the genus Flavobacterium. Strain SE14^T had the highest 16S rRNA gene sequence similarity to Flavobacterium antarcticum, F. tegetincola and F. degerlachei with 95.8, 95.5 and 95.2 %, respectively. The strain SE14^T consisted of a clade with Flavobacteriumnoncentrifugens (16S rRNA gene sequence similarity 94.9 %) and F. qiangtangense (16S rRNA gene sequence similarity 94.2 %) and simultaneously formed a distinct phyletic lineage in the neighbour-joining phylogenetic tree. Polar lipids of the strain included phosphatidylethanolamine and four unidentified aminolipids. Strain SE14^T contained anteiso-C15 : 0, iso-C15 : 0 and a mixture of iso-C15 : 0 2-OH and/or C16 : 1ω7c as the main fatty acids, and the only respiratory quinone was menaquinone-6. The genomic DNA G+C content was 42.3 mol%. The polyphasic taxonomic study revealed that strain SE14^T belongs to a novel species within the genus Flavobacterium , and the name Flavobacterium phocarum sp. nov. is proposed. The type strain is SE14^T (=CCTCC AB 2017225^T=KCTC 52612^T).

VICTOR: genome-based phylogeny and classification of prokaryotic viruses

MOTIVATION

Bacterial and archaeal viruses are crucial for global biogeochemical cycles and might well be game-changing therapeutic agents in the fight against multi-resistant pathogens. Nevertheless, it is still unclear how to best use genome sequence data for a fast, universal and accurate taxonomic classification of such viruses.

RESULTS

We here present a novel in silico framework for phylogeny and classification of prokaryotic viruses, in line with the principles of phylogenetic systematics, and using a large reference dataset of officially classified viruses. The resulting trees revealed a high agreement with the classification. Except for low resolution at the family level, the majority of taxa was well supported as monophyletic. Clusters obtained with distance thresholds chosen for maximizing taxonomic agreement appeared phylogenetically reasonable, too. Analysis of an expanded dataset, containing >4000 genomes from public databases, revealed a large number of novel species, genera, subfamilies and families.

AVAILABILITY AND IMPLEMENTATION

The selected methods are available as the easy-to-use web service 'VICTOR' at https://victor.dsmz.de.

CONTACT

jan.meier-kolthoff@dsmz.de.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine-seawater interface at Erba Deep in the Red Sea

Two moderately halophilic marine bacterial strains of the family Rhodobacteraceae, designated ZGT108^T and ZGT118^T, were isolated from the brine-seawater interface at Erba Deep in the Red Sea (Saudi Arabia). Cells of both strains were aerobic, rod-shaped, non-motile, and Gram-stain-negative. The sequence similarity of the 16S rRNA genes of strains ZGT108^T and ZGT118^T was 94.9 %. The highest 16S rRNA gene sequence similarity of strain ZGT108^T to its closest relative, Ruegeria conchae JCM 17315^T, was 98.9 %, while the 16S rRNA gene of ZGT118^T was most closely related to that of Ruegeria intermedia LMG 25539^T (97.7 % similarity). The sizes of the draft genomes as presented here are 4 258 055 bp (strain ZGT108^T) and 4 012 109 bp (strain ZGT118^T), and the G+C contents of the draft genomes are 56.68 mol% (ZGT108^T) and 62.94 mol% (ZGT108^T). The combined physiological, biochemical, phylogenetic and genotypic data supported placement of both strains in the genus Ruegeria and indicated that the two strains are distinct from each other as well as from all other members in the genus Ruegeria. This was also confirmed by low DNA-DNA hybridization values (<43.6 %) and low ANI values (<91.8 %) between both strains and the most closely related Ruegeria species. Therefore, we propose two novel species in the genus Ruegeria to accommodate these novel isolates: Ruegeriaprofundi sp. nov. (type strain ZGT108^T=JCM 19518^T=ACCC 19861^T) and Ruegeriamarisrubri sp. nov. (type strain ZGT118^T=JCM 19519^T=ACCC 19862^T).

Ponticoccus marisrubri sp. nov., a moderately halophilic marine bacterium of the family Rhodobacteraceae

Strain SJ5A-1^T, a Gram-stain-negative, coccus-shaped, non-motile, aerobic bacterium, was isolated from the brine-seawater interface of the Erba Deep in the Red Sea, Saudi Arabia. The colonies of strain SJ5A-1^T have a beige to pale-brown pigmentation, are approximately 0.5-0.7 µm in diameter, and are catalase and oxidase positive. Growth occurred optimally at 30-33 °C, pH 7.0-7.5, and in the presence of 9.0-12.0 % NaCl (w/v). Phylogenetic analysis of the 16S rRNA gene indicates that strain SJ5A-1^T is a member of the genus Ponticoccus within the family Rhodobacteraceae. Ponticoccus litoralis DSM 18986^T is the most closely related described species based on 16S rRNA gene sequence identity (96.7 %). The DNA-DNA hybridization value between strain SJ5A-1^T and P. litoralis DSM 18986^T was 36.7 %. The major respiratory quinone of strain SJ5A-1^T is Q-10; it predominantly uses the fatty acids C18 : 1 (54.2 %), C18 : 0 (11.2 %), C16 : 0 (8.6 %), 11-methyl C18 : 1ω7c (7.7 %), C19 : 0cyclo ω8c (3.3 %), and C12 : 1 3-OH (3.5 %), and its major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, phosphocholine, an unknown aminolipid, an unknown phospholipid and two unknown lipids. The genome draft of strain SJ5A-1^T as presented here is 4 562 830 bp in size and the DNA G+C content is 68.0 mol%. Based on phenotypic, phylogenetic and genotypic data, strain SJ5A-1^T represents a novel species in the genus Ponticoccus, for which we propose the name Ponticoccus marisrubri sp. nov. The type strain of P. marisrubri is SJ5A-1^T (=JCM 19520^T=ACCC19863^T).

Rhizobium oryziradicis sp. nov., isolated from rice roots

Two Gram-stain-negative, aerobic, rod-shaped endophytic bacterial strains, N19T and N11-2, were isolated from fresh rice (Oryza sativa) roots during investigation of the rice endophytic bacterial diversity. The 16S rRNA gene sequence results indicated that the similarity between strains N19T and N11-2 was 100 %. Both of them belong to the genus Rhizobium, with close similarity to Rhizobium taibaishanense CCNWSX 0483T (97.7 %), followed by Rhizobium vitis NCPPB 3554T (97.5 %). The sequence similarities of the housekeeping genes recA, gyrB and glnA between the novel isolates and members of the established species of the genus Rhizobium were less than 87 %. The DNA-DNA hybridization rates between strains N19T and N11-2 were 87.9 % using the initial renaturation rate method. Based on draft genome sequences, strain N19T showed 18.2 % and 19.6 % DNA-DNA hybridization values to R. taibaishanense CCNWSX 0483T and R. vitis S4, which demonstrated that these new isolates represent a novel species in the genus Rhizobium. The main cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content of strain N19T was 58.7 mol% (Tm). The polar lipid profile of N19T consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unknown lipid, two unknown aminolipids and an unidentified aminophospholipid. According to physiological and biochemical characteristics and genotypic data, strains N19T and N11-2 are considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium oryziradicis sp. nov. is proposed, with N19T (=ACCC 19962T=KCTC 52413T) as the type strain.

Microbacterium zeae sp. nov., an endophytic bacterium isolated from maize stem

A novel Gram-stain positive, aerobic, non-motile, non-spore-forming and rod-shaped strain designated 1204^T was isolated from surface-sterilised stem tissue of maize planted in Fangshan District of Beijing, People's Republic of China. A polyphasic taxonomic study was performed on the new isolate. On the basis of 16S rRNA gene sequence similarity studies, this isolate belongs to the genus Microbacterium. High levels of 16S rRNA gene sequence similarity were found between strain 1204^T and Microbacterium enclense NIO-1002^T (98.8%) and Microbacterium proteolyticum RZ36^T (98.4%) respectively. However, the DNA-DNA hybridization values between strain 1204^T and its closely related species M. proteolyticum DSM 27100^T and M. enclense DSM 25125^T were 53.9 ± 1.6 and 20.9 ± 1.5% respectively. The DNA G+C content of strain 1204^T was determined to be 68.0 mol%. The major fatty acids were found to consist of anteiso-C_15:0 (37.6%), iso-C_16:0 (28.6%) and anteiso-C_17:0 (16.6%). The predominant menaquinone was MK-11 and the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid and an unidentified lipid. The results of physiological and biochemical tests and minor differences in the fatty acid profiles allowed a clear phenotypic differentiation of strain 1204^T from the closely related species in the genus Microbacterium. Thus, it was concluded that strain 1204^T represents a novel species within the genus Microbacterium, for which the name Microbacterium zeae sp. nov. is proposed, with the type strain 1204^T (= CGMCC 1.15289 = DSM 100750).

Rhizobium rhizosphaerae sp. nov., a novel species isolated from rice rhizosphere

Two novel, Gram-negative, motile, rod-shaped, aerobic bacterial strains, MH17^T and RD15, were isolated from the sterilized root and rhizosphere soil of rice, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that the similarity between strains MH17^T and RD15 was 100%. The isolates exhibit high sequence similarities to Rhizobium oryzae CGMCC 1.7048^T (98.7%) and Rhizobium petrolearium SL-1^T (97.0% and 97.1%), which supports that they belong to a novel species in the genus Rhizobium. Strains MH17^T and RD15 exhibited growth at 15-45 °C, pH 5.0-11.0, 0-2.0% sodium chloride (w/v). Sequence analysis of housekeeping genes gyrB, recA, atpD, ropB, gltA showed that these two novel strains had less than 94% similarity with the known species, indicating the distinct position of MH17^T and RD15 in the genus Rhizobium. The major cellular fatty acids were identified as summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). Type strain MH17^T had 87.5% DNA-DNA relatedness with RD15 by using the initial renaturation rate method. Based on draft genome sequences, strain MH17^T showed 30.1% DNA-DNA hybridization values to R. oryzae CGMCC 1.7048^T, the closely related strain, which supported that MH17^T represents a novel species in the genus Rhizobium. Average nucleotide identity (ANI) between strains MH17^T and RD15 were 97.8%, and strain MH17^T showed 82.2% ANI value with R. oryzae CGMCC 1.7048^T. The DNA G+C content was 60.4 mol% (T_m). Based on physiological, biochemical characteristic, genotypic data, strains MH17^T and RD15 are concluded to represent a new species within the genus Rhizobium, for which the name Rhizobium rhizosphaerae sp. nov. is proposed. The type strain is MH17^T (=ACCC 19963^T = KCTC 52414^T).

Dyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root

A novel Gram-stain-negative, aerobic and rod-shaped bacterial strain, designated 65T, was isolated from surface-sterilized root tissue of maize, collected from Fangshan District of Beijing, People's Republic of China, and was subjected to a taxonomic study by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 65T belonged to the genus Dyadobacter and had highest 16S rRNA gene sequence similarity to Dyadobacter jiangsuensis CGMCC 1.12969T (99.1 %), Dyadobacter beijingensis CGMCC 1.6375T (98.8 %), Dyadobacter fermentans DSM 18053T (98.6 %) and Dyadobacter soli KCTC 22481T (98.6 %). However, the new isolate exhibited relatively low levels of DNA-DNA relatedness with respect to D. jiangsuensis CGMCC 1.12969T (18.2±1.3 %), D. beijingensis CGMCC 1.6375T (14.2±2.0 %), D. fermentans DSM 18053T (14.1±2.0 %) and D. soli KCTC 22481T (13.8±0.6 %). The predominant respiratory quinone was menaquinone-7 (MK-7) and the major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω5c, iso-C15 : 0 3-OH, C16 : 0 3-OH and C16 : 0. The polar lipid profile of strain 65T revealed the presence of phosphatidylethanolamine, four aminolipids and two unidentified phospholipids. The DNA G+C content was 46.6 mol%. The results of physiological and biochemical tests and the differences in the fatty acid profiles allowed the clear phenotypic differentiation of strain 65T from closely related species of the genus Dyadobacter. Strain 65T thus represents a novel species within the genus Dyadobacter, for which the name Dyadobacterendophyticus sp. nov. is proposed. The type strain is 65T (=CGMCC 1.15288T=DSM 100786T).

Streptococcuspantholopis sp. nov., isolated from faeces of the Tibetan antelope (Pantholops hodgsonii)

Two bacterial strains were isolated from faecal samples of Tibetan antelopes. The isolates were Gram-stain-positive, catalase-negative, coccus-shaped organisms that were tentatively identified as representing a novel streptococcal species based on their morphological features, biochemical test results and phylogenomic findings. Comparative 16S rRNA gene sequencing studies confirmed that the organisms were members of the genus Streptococcus, but they did not correspond to any recognized species of the genus. The nearest phylogenetic relative of the unknown coccus was Streptococcus ursoris NUM 1615T (93.4 % 16S rRNA gene sequence similarity). Analysis of groEL and rpoB gene sequences of the novel isolates showed interspecies divergence of 27.0 and 22.2 %, respectively, from the type strain of its closest 16S rRNA gene phylogenetic relative, S. ursoris. The complete genome of strain TA 26T has been sequenced. Digital DNA-DNA hybridization studies between strain TA 26T and other species of the genus Streptococcus deposited in the GenBank database showed less than 70 % DNA-DNA relatedness, supporting a novel species status of the strain. On the basis of their genotypic and phenotypic differences from recognized Streptococcus species, the two isolates represent a novel species of the genus Streptococcus, for which the nameStreptococcus pantholopis sp. nov. (type strain TA 26T=CGMCC 1.15667T=DSM 102135T) is proposed.

Paenibacillus wenxiniae sp. nov., a nifH gene -harbouring endophytic bacterium isolated from maize

A novel Gram-positive, aerobic, motile, endospore-forming, rod-shaped bacterium, designated 373(T) was isolated from surface-sterilised root tissue of a maize planted in Fangshan District of Beijing, Peopole's Republic of China. A polyphasic taxonomic study was performed on the new isolate. On the basis of 16S rRNA gene sequence similarity studies, this isolate belongs to the genus Paenibacillus. The highest 16S rRNA gene sequence similarity was found between strain 373(T) and Paenibacillus hunanensis (98.1%), meanwhile the 16S rRNA gene sequence similarity between strain 373(T) and the type strains of other recognised members of the genus Paenibacillus were all below 95.6%. However, the DNA-DNA hybridization values between strain 373(T) and the type strain P. hunanensis DSM 22170(T) was 30.2%. The DNA G+C content of strain 373(T) was determined to be 46.0 mol%. The predominant respiratory quinone was identified as menaquinone-7 and the polar lipid profile was found to be composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were found to consist of anteiso-C15: 0 (59.6%), anteiso-C17: 0 (12.8%) and C16: 0 (6.7%). The results of physiological and biochemical tests and minor differences in the fatty acid profiles allowed a clear phenotypic differentiation of strain 373(T) from the closely related species in this genus Paenibacillus. Strain 373(T) is concluded to represent a novel species within the genus Paenibacillus, for which the name Paenibacillus wenxiniae sp. nov. is proposed, with the type strain 373(T) (= CGMCC 1.15007 (T) = DSM100576 ).

Diaphorobacter polyhydroxybutyrativorans sp. nov., a novel poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-degrading bacterium isolated from biofilms

A novel Gram-stain-negative, facultatively aerobic and rod-shaped strain, designated SL-205T, was isolated from the biofilms of a denitrifying reactor using poly(3-hydoxybutyrate-co-3-hydroxyvalerate) as the sole carbon source in Beijing, PR China. A polyphasic taxonomic characterization was performed on the novel isolate. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain SL-205T is a member of the genus Diaphorobacter. High levels of 16S rRNA gene sequence similarity were found between strain SL-205T and Diaphorobacter nitroreducens NA10BT (99.4 %) and Diaphorobacter oryzae RF3T (98.5 %), respectively. However, the DNA–DNA relatedness values between strain SL-205T and D. nitroreducens NA10BT and D. oryzae RF3T were 57 ± 1 % and 45 ± 1.5 %, respectively. The G+C content of the genomic DNA of strain SL-205T was 66.8 mol%. The major fatty acids consisted of summed feature 3 (including C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. Ubiquinone Q-8 was the only respiratory quinone; the polar lipid profile comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one uncharacterized phospholipid. We conclude that strain SL-205T represents a novel species of the genus Diaphorobacter for which the name Diaphorobacter polyhydroxybutyrativorans is proposed; the type strain is SL-205T ( = ACCC 19739T = DSM 29460T).

Rhizobium oryzicola sp. nov., potential plant-growth-promoting endophytic bacteria isolated from rice roots

Bacterial strains ZYY136(T) and ZYY9 were isolated from surface-sterilized rice roots from a long-term experiment of rice-rice--Astragalus sinicus rotation. The 16S rRNA gene sequences of strains ZYY136(T) and ZYY9 showed the highest similarity, of 97.0%, to Rhizobium tarimense PL-41(T). Sequence analysis of the housekeeping genes recA, thrC and atpD clearly differentiated the isolates from currently described species of the genus Rhizobium. The DNA-DNA relatedness value between ZYY136(T) and ZYY9 was 82.3%, and ZYY136(T) showed 34.0% DNA-DNA relatedness with the most closely related type strain, R. tarimense PL-41(T). The DNA G+C content of strain ZYY136(T) was 58.1 mol%. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C16 : 0 3-OH. Strains ZYY136(T) and ZYY9 could be differentiated from the previously defined species of the genus Rhizobium by several phenotypic characteristics. Therefore, we conclude that strains ZYY136(T) and ZYY9 represent a novel species of the genus Rhizobium, for which the name Rhizobium oryzicola sp. nov. is proposed (type strain ZYY136(T) = ACCC 05753(T) = KCTC 32088(T)).

Rhizobium metallidurans sp. nov., a symbiotic heavy metal resistant bacterium isolated from the Anthyllis vulneraria Zn-hyperaccumulator

A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming bacterium (ChimEc512T) was isolated from 56 host seedlings of the hyperaccumulating Anthyllis vulneraria legume, which was on an old zinc mining site at Les Avinières, Saint-Laurent-Le-Minier, Gard, South of France. On the basis of 16S rRNA gene sequence similarities, strain ChimEc512T was shown to belong to the genus Rhizobium and to be most closely related to Rhizobium endophyticum CCGE 2052T (98.4 %), Rhizobium tibeticum CCBAU 85039T (98.1 %), Rhizobium grahamii CCGE 502T (98.0 %) and Rhizobium mesoamericanum CCGE 501T (98.0 %). The phylogenetic relationships of ChimEc512T were confirmed by sequencing and analyses of recA and atpD genes. DNA–DNA relatedness values of strain ChimEc512T with R. endophyticum CCGE 2052T, R. tibeticum CCBAU 85039T, R. mesoamericanum CCGE 52T, Rhizobium grahamii CCGE 502T, Rhizobium etli CCBAU 85039T and Rhizobium radiobacter KL09-16-8-2T were 27, 22, 16, 18, 19 and 11 %, respectively. The DNA G+C content of strain ChimEc512T was 58.9 mol%. The major cellular fatty acid was C18 : 1ω7c, characteristic of the genus Rhizobium . The polar lipid profile included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine and moderate amounts of aminolipids, phospholipid and sulfoquinovosyl diacylglycerol. Although ChimEc512T was able to nodulate A. vulneraria, the nodC and nifH genes were not detected by PCR. The rhizobial strain was tolerant to high concentrations of heavy metals: up to 35 mM Zn and up to 0.5 mM Cd and its growth kinetics was not impacted by Zn. The results of DNA–DNA hybridizations and physiological tests allowed genotypic and phenotypic differentiation of strain ChimEc512T from species of the genus Rhizobium with validly published names. Strain ChimEc512T, therefore, represents a novel species, for which the name Rhizobium metallidurans sp. nov. is proposed, with the type strain ChimEc512T ( = DSM 26575 = CIP 110550T).

Chryseobacterium takakiae sp. nov., a member of the phylum Bacteroidetes isolated from Takakia lepidozioides

A Gram-stain-negative, rod-shaped and non-endospore-forming bacterium, designated strain AG1-2T, was isolated from Takakia lepidozioides collected from the Gawalong glacier in Tibet, China and characterized using a polyphasic taxonomic approach. The predominant fatty acids of strain AG1-2T were iso-C15 : 0 (36.0 %), iso-C17 : 0 3-OH (20.2 %), summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl, 16.4 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 11.1 %). The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. Strain AG1-2T contained MK-6 as the dominant menaquinone, and the genomic DNA G+C content was 37.3 mol%. The phylogenetic analysis based on the 16S rRNA gene sequences showed that strain AG1-2T was affiliated to species of the genus Chryseobacterium , and its closest related species were Chryseobacterium taiwanense Soil-3-27T, Chryseobacterium hispalense AG13T, Chryseobacterium camelliae THG C4-1T and Chryseobacterium taeanense PHA3-4T with a sequence similarity of 98.0, 97.8, 97.3 and 97.1 %, respectively. However, the DNA–DNA relatedness values between these strains and strain AG1-2T were 29, 21, 21 and 45 %, respectively. Based on phylogenetic inference and phenotypic data, strain AG1-2T is considered to represent a novel species of the genus Chryseobacterium , for which the name Chryseobacterium takakiae sp. nov. is proposed. The type strain is AG1-2T ( = CGMCC 1.12488T = DSM 26898T).

Microbial taxonomy in the post-genomic era: rebuilding from scratch?

Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, we will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.

Variovorax guangxiensis sp. nov., an aerobic, 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from banana rhizosphere

A 1-aminocyclopropane-1-carboxylate deaminase producing bacterium, designated GXGD002(T), was isolated from the rhizosphere of banana plants cultivated in Guangxi province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GXGD002(T) is a member of the genus Variovorax. High levels of 16S rRNA gene sequence similarity are found between strain GXGD002(T) and Variovorax paradoxus DSM 30034(T) (99.4 %), Variovorax ginsengisoli KCTC 12583(T) (99.1 %), Variovorax boronicumulans KCTC 22010(T) (99.0 %), Variovorax soli DSM18216(T) (98.7 %), Variovorax defluvii DSM 27259(T) (98.1 %) and Variovorax dokdonensis KCTC 12544(T) (97.4 %) respectively. However, the DNA-DNA hybridization values between strain GXGD002(T) and its closely related species V. paradoxus DSM 30034(T), V. ginsengisoli KCTC 12583(T) and V. boronicumulans KCTC 22010(T) were found to be 40.7, 30.9 and 23.7 %, respectively. The DNA G + C content of strain GXGD002(T) was found to be 67.8 mol%. The major fatty acids of strain GXGD002(T) are C16:0 (20.3 %), C10:0 3OH (18.4 %), C17:0 cyclo (18.9 %), C18:1w7c (12.3 %) and summed feature 3 (13.9 %). The predominant respiratory quinone was identified as ubiquinone-8 (Q-8) and the major polar lipids as phosphatidylethanolamine and phosphatidylglycerol. The results of polyphasic taxonomic study including physiological and biochemical tests, whole-cell SDS-PAGE profiles and chemotaxonomic analysis allowed a clear differentiation of strain GXGD002(T) from the other species in the genus Variovorax. Based on these results, a new species, Variovorax guangxiensis, is proposed. The type strain is GXGD002(T) (=DSM 27352(T) = ACCC 05911(T)).

Enterobacter xiangfangensis sp. nov., isolated from Chinese traditional sourdough, and reclassification of Enterobacter sacchari Zhu et al. 2013 as Kosakonia sacchari comb. nov

A Gram-stain-negative bacterial strain, 10-17(T), was isolated from traditional sourdough in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, RNA polymerase β subunit (rpoB) gene sequence analysis, DNA gyrase (gyrB) gene sequence analysis, initiation translation factor 2 (infB) gene sequence analysis, ATP synthase β subunit (atpD) gene sequence analysis, fatty acid methyl ester analysis, determination of DNA G+C content, DNA-DNA hybridization and an analysis of phenotypic features. Strain 10-17(T) was phylogenetically related to Enterobacter hormaechei CIP 103441(T), Enterobacter cancerogenus LMG 2693(T), Enterobacter asburiae JCM 6051(T), Enterobacter mori LMG 25706(T), Enterobacter ludwigii EN-119(T) and Leclercia adecarboxylata LMG 2803(T), having 99.5%, 99.3%, 98.7%, 98.5%, 98.4% and 98.4% 16S rRNA gene sequence similarity, respectively. On the basis of polyphasic characterization data obtained in the present study, a novel species, Enterobacter xiangfangensis sp. nov., is proposed and the type strain is 10-17(T) ( = LMG 27195(T) = NCIMB 14836(T) = CCUG 62994(T)). Enterobacter sacchari Zhu et al. 2013 was reclassified as Kosakonia sacchari comb. nov. on the basis of 16S rRNA, rpoB, gyrB, infB and atpD gene sequence analysis and the type strain is strain SP1(T)( = CGMCC 1.12102(T) = LMG 26783(T)).

Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov

The genus Rhizorhapis gen. nov. (to replace the illegitimate genus name Rhizomonas) is proposed for strains of Gram-negative bacteria causing corky root of lettuce, a widespread and important lettuce disease worldwide. Only one species of the genus Rhizomonas was described, Rhizomonas suberifaciens, which was subsequently reclassified as Sphingomonas suberifaciens based on 16S rRNA gene sequences and the presence of sphingoglycolipid in the cell envelope. However, the genus Sphingomonas is so diverse that further reclassification was deemed necessary. Twenty new Rhizorhapis gen. nov.- and Sphingomonas-like isolates were obtained from lettuce or sow thistle roots, or from soil using lettuce seedlings as bait. These and previously reported isolates were characterized in a polyphasic study including 16S rRNA gene sequencing, DNA-DNA hybridization, DNA G+C content, whole-cell fatty acid composition, morphology, substrate oxidation, temperature and pH sensitivity, and pathogenicity to lettuce. The isolates causing lettuce corky root belonged to the genera Rhizorhapis gen. nov., Sphingobium, Sphingopyxis and Rhizorhabdus gen. nov. More specifically, we propose to reclassify Rhizomonas suberifaciens as Rhizorhapis suberifaciens gen. nov., comb. nov. (type strain, CA1(T) = LMG 17323(T) = ATCC 49355(T)), and also propose the novel species Sphingobium xanthum sp. nov., Sphingobium mellinum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. with the type strains NL9(T) ( = LMG 12560(T) = ATCC 51296(T)), WI4(T) ( = LMG 11032(T) = ATCC 51292(T)) and SP1(T) ( = LMG 12581(T) = ATCC 51289(T)), respectively. Several strains isolated from lettuce roots belonged to the genus Sphingomonas, but none of them were pathogenic.

Mucilaginibacter polytrichastri sp. nov., isolated from a moss (Polytrichastrum formosum), and emended description of the genus Mucilaginibacter

A Gram-staining-negative, rod-shaped, non-spore-forming bacterium, designated strain RG4-7T, was isolated from the moss Polytrichastrum formosum collected from Gawalong glacier in Tibet, China, and characterized by using a polyphasic taxonomic approach. The predominant fatty acids of strain RG4-7T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, two unidentified aminolipids and one unidentified lipid. Strain RG4-7T contained MK-7 as the dominant menaquinone and the G+C content of its genomic DNA was 39.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RG4-7T was affiliated to species of the genus Mucilaginibacter , and its closest relative was Mucilaginibacter jinjuensis YC7004T (97.0 % sequence similarity). However, the DNA–DNA relatedness between this strain and strain RG4-7T was only 49.1±3.7 %. Based on phylogenetic inference and phenotypic data, strain RG4-7T is considered to represent a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter polytrichastri sp. nov. is proposed. The type strain is RG4-7T ( = CGMCC 1.12493T = DSM 26907T). An emended description of the genus Mucilaginibacter is also proposed.

Hepatoprotective effects of kombucha tea: identification of functional strains and quantification of functional components

BACKGROUND

Kombucha tea (KT), a traditional health beverage containing potential hepatoprotective agents, is fermented from sugared tea by a symbiotic culture of yeast and bacteria for 8 days. However, the functional strains that produce components for the hepatoprotective property of KT remain unclear. Multiple strains are involved in traditional KT production. Therefore, KT has not been standardized or produced commercially. This study aimed to identify the functional strains and quantify the functional components with hepatoprotective effects in kombucha tea.

RESULTS

Gluconacetobacter sp. A4 was one of the microorganisms in KT in which the D-saccharic acid-1,4-lactone (DSL) produced by G. sp. A4 was significantly higher than that produced by original tea fungus at 8 days of fermentation. Traditional KT (TKT, tea broth fermented by mixed tea fungus), modified KT (MKT, fermented by single G. sp. A4), and DSL significantly inhibited the acetaminophen-induced increase of alanine aminotransferase, alkaline phosphatase, triglyceride and malondialdehyde, as well as facilitating the reduction of total antioxidant capacity in mice. Furthermore, MKT and TKT are both similar to DSL in terms of protection against acetaminophen-induced liver injury in mice. These results suggested a positive relationship between DSL content and the hepatoprotective effect of TKT, MKT and DSL groups.

CONCLUSION

G. sp. A4 was concluded to be a potential functional strain and DSL might be the key functional component for the hepatoprotective property in KT. The stronger capability of G. sp. A4 in producing DSL makes it a better choice for the commercial production of KT.

Rhizobium rhizoryzae sp. nov., isolated from rice roots

Two strains (J3-AN59(T) and J3-N84) of Gram-stain-negative, aerobic and rod-shaped bacteria were isolated from the roots of fresh rice plants. The 16S rRNA gene sequence similarity results showed that the similarity between strains J3-AN59(T) and J3-N84 was 100 %. Both strains were phylogenetically related to members of the genus Rhizobium, and they were most closely related to Rhizobium tarimense ACCC 06128(T) (97.43 %). Similarities in the sequences of housekeeping genes between strains J3-AN59(T) and J3-N84 and those of recognized species of the genus Rhizobium were less than 90 %. The polar lipid profiles of both strains were predominantly composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unknown aminophospholipid. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C contents of J3-AN59(T) and J3-N84 were 55.7 and 57.1 mol%, respectively. The DNA-DNA relatedness value between J3-AN59(T) and J3-N84 was 89 %, and strain J3-AN59(T) showed 9 % DNA-DNA relatedness to R. tarimense ACCC 06128(T), the most closely related strain. Based on this evidence, we found that J3-AN59(T) and J3-N84 represent a novel species in the genus Rhizobium and we propose the name Rhizobium rhizoryzae sp. nov. The type strain is J3-AN59(T) ( = ACCC 05916(T) = KCTC 23652(T)).

Enterococcus xiangfangensis sp. nov., isolated from Chinese pickle

A Gram-stain-positive bacterial strain, 11097(T), was isolated from traditional pickle in Heilongjiang Province, China. The bacterium was characterized using a polyphasic approach, including 16S rRNA gene sequence analysis, phenylalanyl-tRNA synthase (pheS) gene sequence analysis, RNA polymerase α subunit (rpoA) gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA-DNA hybridization and an analysis of phenotypic features. Strain 11097(T) was phylogenetically related to Enterococcus devriesei, E. pseudoavium, E. viikkiensis, E. avium, E. malodoratus, E. gilvus and E. raffinosus. Strain 11097(T) had 99.1-99.9% 16S rRNA gene sequence similarities, 78.2-83.2% pheS gene sequence similarities and 93.8-96.6% rpoA gene sequence similarities with type strains of phylogenetically related species. Based upon polyphasic characterization data obtained in the present study, a novel species of the genus Enterococcus, Enterococcus xiangfangensis sp. nov., is proposed with the type strain 11097(T) ( = LMG 27495(T) = NCIMB 14834(T)).

Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., isolated from Chinese traditional pickle and sourdough

Three Gram-stain-positive bacterial strains, 11050T, 7-19T and 11102T, were isolated from traditional pickle and sourdough in Heilongjiang Province, China. These bacteria were characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, dnaK gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Strain 11050T belonged to the Lactobacillus plantarum species group and shared 98.0–98.4 % 16S rRNA gene sequence similarities and 84.7–88.9 % dnaK gene sequence similarities with type strains of Lactobacillus plantarum subsp. plantarum , Lactobacillus plantarum subsp. argentoratensis , Lactobacillus pentosus , Lactobacillus paraplantarum , Lactobacillus fabifermentans and Lactobacillus xiangfangensis and had 75.9–80.7 % pheS gene sequence similarities and 90.7–92.5 % rpoA gene sequence similarities with Lactobacillus plantarum subsp. plantarum LMG 6907T, Lactobacillus plantarum subsp. argentoratensis LMG 9205, Lactobacillus pentosus LMG 10755T, Lactobacillus paraplantarum LMG 16673T, Lactobacillus fabifermentans LMG 24284T and Lactobacillus xiangfangensis 3.1.1T, respectively. Strain 7-19T was phylogenetically related to Lactobacillus thailandensis , Lactobacillus pantheris and Lactobacillus sharpeae , having 94.1–96.7 % 16S rRNA gene sequence similarities, 71.5–82.3 % pheS gene sequence similarities and 71.2–83.4 % rpoA gene sequence similarities with type strains of Lactobacillus thailandensis , Lactobacillus pantheris and Lactobacillus sharpeae , respectively. Strain 11102T was phylogenetically related to Lactobacillus oligofermentans , Lactobacillus suebicus , Lactobacillus vaccinostercus and Lactobacillus hokkaidonensis . Strain 11102T had 99.2 % 16S rRNA gene sequence similarity, 81.3 % pheS gene sequence similarity and 96.1 % rpoA gene sequence similarity with Lactobacillus oligofermentans LMG 22743T, respectively. Strain 11102T shared 96.0–96.8 % 16S rRNA gene sequence similarities, 73.3–81.0 % pheS gene sequence similarities and 74.6–76.9 % rpoA gene sequence similarities with type strains of Lactobacillus suebicus , Lactobacillus vaccinostercus and Lactobacillus hokkaidonensis , respectively. Based upon the data from polyphasic characterization obtained in the present study, three novel species, Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., are proposed and the type strains are 11050T ( = LMG 27194T = CCUG 62991T), 7-19T ( = LMG 27191T = NCIMB 14832T = CCUG 62990T) and 11102T ( = LMG 27192T = NCIMB 14833T), respectively.

Lactobacillus heilongjiangensis sp. nov., isolated from Chinese pickle

A Gram-stain-positive bacterial strain, S4-3T, was isolated from traditional pickle in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, dnaK gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Strain S4-3T showed 97.9–98.7 % 16S rRNA gene sequence similarities, 84.4–94.1 % pheS gene sequence similarities and 94.4–96.9 % rpoA gene sequence similarities to the type strains of Lactobacillus nantensis , Lactobacillus mindensis , Lactobacillus crustorum , Lactobacillus futsaii , Lactobacillus farciminis and Lactobacillus kimchiensis . dnaK gene sequence similarities between S4-3T and Lactobacillus nantensis LMG 23510T, Lactobacillus mindensis LMG 21932T, Lactobacillus crustorum LMG 23699T, Lactobacillus futsaii JCM 17355T and Lactobacillus farciminis LMG 9200T were 95.4, 91.5, 90.4, 91.7 and 93.1 %, respectively. Based upon the data obtained in the present study, a novel species, Lactobacillus heilongjiangensis sp. nov., is proposed and the type strain is S4-3T ( = LMG 26166T = NCIMB 14701T).

Hansschlegelia beijingensis sp. nov., an aerobic, pink-pigmented, facultatively methylotrophic bacterium isolated from watermelon rhizosphere soil

A novel Gram-stain-negative, aerobic, rod-shaped strain designated PG04T was isolated from the rhizosphere of watermelon plants cultivated in Beijing, China. A polyphasic taxonomic study was performed on the new isolate. On the basis of 16S rRNA gene sequence similarity studies, isolate PG04T belonged clearly to the genus Hansschlegelia and was most closely related to Hansschlegelia zhihuaiae (97.3 % similarity to the type strain). The predominant respiratory quinone was ubiquinone 10 (Q-10) and the polar lipid profile was composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major fatty acids were C18 : 1ω7c (41.3 %), C19 : 0 cyclo ω8c (30.6 %) and C16 : 0 (19.1 %). The G+C content of the DNA was about 64.4 mol%. DNA–DNA hybridization experiments showed 34.4 % relatedness between strain PG04T and H. zhihuaiae DSM 18984T. The results of physiological and biochemical tests and differences in fatty acid profiles allowed clear phenotypic differentiation of strain PG04T from the most closely related species in the genus, H. zhihuaiae . Strain PG04T therefore represents a novel species within the genus Hansschlegelia , for which the name Hansschlegelia beijingensis sp. nov. is proposed, with the type strain PG04T ( = DSM 25481T = ACCC 05759T).

Partial characterization of an exopolysaccharide secreted by a marine bacterium, Vibrio neocaledonicus sp. nov., from New Caledonia

AIMS

Exopolysaccharides (EPS) are industrially valuable molecules with numerous useful properties. This study describes the techniques used for the identification of a novel Vibrio bacterium and preliminary characterization of its EPS.

METHODS AND RESULTS

Bioprospection in marine intertidal areas of New Caledonia followed by screening for EPS producing brought to selection of the isolate NC470. Phylogenetic analysis (biochemical tests, gene sequencing and DNA-DNA relatedness) permitted to identify NC470 as a new member of the Vibrio genus. The EPS was produced in batch fermentation, purified using the ultrafiltration process and analysed by colorimetry, Fourier Transform Infrared spectroscopy, gas chromatography, Nuclear Magnetic Resonance and HPLC-size exclusion chromatography. This EPS exhibits a high N-acetyl-hexosamines and uronic acid content with a low amount of neutral sugar. The molecular mass was 672 × 10(3)  Da. These data are relevant for possible technological exploitation.

CONCLUSIONS

We propose the name Vibrio neocaledonicus sp. nov for this isolate NC470, producing an EPS with an unusual sugar composition. Comparison with other known polymers permitted to select applications for this polymer.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study contributes to evaluate the marine biodiversity of New Caledonia. It also highlights the biotechnological potential of New Caledonia marine bacteria.

Sporosarcina halophila sp. nov., an Obligate, Slightly Halophilic Bacterium from Salt Marsh Soils

Twenty-two strains of endospore-forming sarcinae have been isolated from salt marsh soils. The isolates differ phenotypically from Sporosarcina ureae, the only species of the genus Sporosarcina which has been validly described, and are distinct from S. ureae in the composition of the cell walls of their vegetative cells. Lysine, found in the tetrapeptide of the murein of S. ureae, is replaced by ornithine in the new isolates. The interpeptide bridge consists of an aspartic acid residue instead of D-glutamylglycine as is found in S. ureae. The mol% G + C of the DNA of the new isolates is in the range of 40.1-40.9 (S. ureae 40.0-41.5). DNA hybridization studies revealed a high DNA-DNA homology within the new isolates but only a low relationship to S. ureae. The main menaquinone is of the MK-7 type as in S. ureae and other aerobic sporeformers. The spores of the new isolates are very similar to spores of S. ureae and Bacillus species in respect of their heat resistance, composition and ultrastructure. None of the new isolates grows on complex media unless supplemented with sodium, magnesium and chloride ions. Strains are slight halophiles as they grow best in the presence of 30 to 50 g NaCl/1 and 5 g MgCl(2)/l. The new isolates thus belong to a new species, for which the name Sporosarcina halophila is proposed. Strain DSM 2266 (= strain 3) is the type strain.

Mesorhizobium silamurunense sp. nov., isolated from root nodules of Astragalus species

Four rhizobial strains representing a previously defined novel group in the genus Mesorhizobium and isolated from Astragalus species in China were further characterized using a polyphasic approach. Phylogenetic analysis of 16S rRNA gene sequences showed that these Gram-negative bacteria belonged to the genus Mesorhizobium , with Mesorhizobium plurifarium LMG 11892T as the closest neighbour sharing a sequence similarity of 99.8 %. Comparative sequence analysis of the atpD, recA, glnII, rpoB, nodC and nifH genes, SDS-PAGE of whole-cell soluble proteins, DNA–DNA hybridization, fatty acid profiles and a series of phenotypic and physiological tests differentitated the novel group from all recognized species of the genus Mesorhizobium . Based on the data obtained in the present and previous studies, this group represents a novel species within the genus Mesorhizobium , for which the name Mesorhizobium silamurunense sp. nov. is proposed. The type strain is CCBAU 01550T ( = HAMBI 3029T = LMG 24822T), and could form effective nodules on Astragalus membranaceus, Astragalus adsurgens and Caragana intermedia, and ineffective nodules on Phaseolus vulgaris in cross-nodulation tests.

Pseudacidovorax intermedius NH-1, a novel marine nitrogen-fixing bacterium isolated from the South China Sea

We have taxonomically and phylogenetically characterized a novel nitrogen-fixing bacterial strain, NH-1, which was recently isolated from surface sediments of the South China Sea. The presence of the nifH gene was determined by PCR amplification. The strain NH-1 was found to belong to the genus Pseudacidovorax based on phenotypic characterization, 16S rDNA sequencing, G+C content and DNA-DNA hybridization. Isolate NH-1 was identified as Pseudacidovorax intermedius. In addition, we investigated the links between environmental factors and the nitrogenase activity of NH-1. We found that the nitrogen fixation capacity of NH-1 varied strongly when cells were grown with different ammonium ion and oxygen concentrations, amino acids and carbohydrates. This is the first report of the isolation of Pseudacidovorax from the ocean and the first study to explore the effects of different culture conditions on the nitrogenase activities of the isolate. This study provides evidence that marine nitrogen-fixing microorganisms are far more diverse than currently recognized.

Lactobacillus xiangfangensis sp. nov., isolated from Chinese pickle

A Gram-positive bacterial strain, 3.1.1T, was isolated from traditional pickle in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, dnaK gene sequence analysis, fatty acid methyl ester analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Based upon the data obtained in the present study, a novel species, Lactobacillus xiangfangensis sp. nov., is proposed with the type strain 3.1.1T ( = LMG 26013T  = NCIMB 14687T).

Bacillus endoradicis sp. nov., an endophytic bacterium isolated from soybean root

A gram-positive, aerobic, motile rod, designated strain CCBAU 05776(T), was isolated from the inner tissues of a healthy soybean (Glycine max L.) root collected from an agricultural field in the countryside of Shijiazhuang city, Hebei Province, China. Phylogenetic analysis of the 16S rRNA gene indicated that this strain was most closely related to Bacillus muralis LMG 20238(T) and Bacillus simplex NBRC 15720(T) with similarity of 96.5 % and 96.3 %, respectively, lower than the suggested threshold (97.0 %) for separating bacterial species. In phenotypic characterization, the novel strain differed from the two most related species in that it did not hydrolyse casein or starch but could grow on MacConkey agar. It grew between 15 and 45 °C and tolerated up to 7 % NaCl (w/v). Strain CCBAU 05776(T) grew in media with pH 5.5 to 10 (optimal growth at pH 7.0-8.0). The predominant cellular fatty acids were iso-C(15 : 0) (40.81 %) and C(16 : 1)ω7c alcohol (10.61 %). The predominant isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C was 40.8 mol% (T(m)). DNA-DNA relatedness of the novel isolate with B. muralis and B. simplex was 42.4 % and 32.7 %, respectively. Based upon the consensus of phylogenetic and phenotypic analyses, strain CCBAU 05776(T) represents a novel species within the genus Bacillus, for which the name Bacillus endoradicis sp. nov. is proposed. The type strain is CCBAU 05776(T) ( = LMG 25492(T)  = HAMBI 3097(T)).

Measurements of genomic GC content in plant genomes with flow cytometry: a test for reliability

• Knowledge of the phylogenetic pattern and biological relevance of the base composition of large eukaryotic genomes (including those of plants) is poor. With the use of flow cytometry (FCM), the amount of available data on the guanine + cytosine (GC) content of plants has nearly doubled in the last decade. However, skepticism exists concerning the reliability of the method because of uncertainty in some input parameters. • Here, we tested the reliability of FCM for estimating GC content by comparison with the biochemical method of DNA temperature melting analysis (TMA). We conducted measurements in 14 plant species with a maximum currently known GC content range (33.6-47.5% as measured by FCM). We also compared the estimations of the GC content by FCM with genomic sequences in 11 Oryza species. • FCM and TMA data exhibited a high degree of correspondence which remained stable over the relatively wide range of binding lengths (3.39-4.09) assumed for the base-specific dye used. A high correlation was also observed between FCM results and the sequence data in Oryza, although the latter GC contents were consistently lower. • Reliable estimates of the genomic base composition in plants by FCM are comparable with estimates obtained using other methods, and so wider application of FCM in future plant genomic research, although it would pose a challenge, would be supported by these findings.

Rhizobium petrolearium sp. nov., isolated from oil-contaminated soil

Two Gram-negative, aerobic, rod-shaped bacteria, designated strains SL-1(T) and F11, which had the ability to decompose polycyclic aromatic hydrocarbons (PAHs), were isolated from soil samples contaminated by oil. The cells were motile by polar or lateral flagella. According to comparison of 16S rRNA gene sequences, strains SL-1(T) and F11 were identical and showed the greatest degree of similarity (96.8%) to both Rhizobium oryzae Alt505(T) and Rhizobium mesosinicum CCBAU 25010(T); however, only Rhizobium oryzae with SL-1(T) and F11 formed a separate clade. There were low similarities (<90%) between the atpD and recA sequences of the two strains and those of the genus of Rhizobium. The bacteria grew at temperatures of 10-40 °C with an optimum of 30 °C. The pH range for growth was 6.0-10.0 and optimum pH was 7.0-8.0. Growth occurred at NaCl concentrations up to 3.0% (w/v). They were catalase- and oxidase-positive. The main cellular fatty acids were summed feature 8 (18:1ω7c and/or 18:1ω6c) and 16:0. The DNA G+C content was 62.2 mol%. Strain SL-1(T) showed 29 and 0% DNA-DNA relatedness, respectively, with the most related strains R. oryzae Alt505(T) and R. mesosinicum CCBAU 25010(T) according to phylogenic analysis of the 16S rRNA gene. According to physiological and biochemical characteristics and genotypic data obtained in this work, the bacteria represent a novel species of the genus Rhizobium, and the name Rhizobium petrolearium is proposed. The type strain is SL-1(T) ( = ACCC 11238(T) = KCTC 23288(T)) and it could nodulate Medicago sativa in nodulation tests.

Hansschlegelia zhihuaiae sp. nov., isolated from a polluted farmland soil

A novel Gram-negative, aerobic, coccoid-shaped strain designated S 113T was isolated from a polluted-soil sample collected in Jiangsu Province, China. A polyphasic taxonomic study including phylogenetic analysis based on the 16S rRNA gene sequence and determination of phenotypic characteristics was performed on the new isolate. The highest 16S rRNA gene sequence similarity was 96.8 %, with Hansschlegelia plantiphila S1 T. The predominant respiratory quinone was ubiquinone 10 (Q-10). The major fatty acids were C18 : 1ω7c and C16 : 0. The G+C content of the DNA was about 65.7 mol%. DNA–DNA hybridization experiments showed 44.9 % relatedness for strain S 113T with its closest relative, H. plantiphila NCIMB 14035T. The dominant phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and phosphatidylcholine. The results of our polyphasic taxonomic analysis indicate that strain S 113T represents a novel species within the genus Hansschlegelia, for which the name Hansschlegelia zhihuaiae sp. nov. is proposed. The type strain is S 113T ( = DSM 18984T  = CCTCC AB 206143T  = KCTC 12880T).

Rhizobium tubonense sp. nov., isolated from root nodules of Oxytropis glabra

Four rhizobial strains, designated CCBAU 85046T, CCBAU 85051, CCBAU 85048 and CCBAU 85049, isolated from root nodules of Oxytropis glabra grown in Tibet, China, were previously defined, using amplified 16S rRNA gene restriction analysis, as a novel group within the genus Rhizobium. To clarify their taxonomic position, these strains were further analysed and compared with reference strains of related bacteria using a polyphasic approach. The 16S rRNA gene analysis showed that the four isolates formed a distinct phylogenetic lineage in the genus Rhizobium. The isolates showed highest sequence similarity (97.8 %) to Rhizobium indigoferae CCBAU 71042T. Phenotypic and physiological tests, DNA–DNA hybridization, phylogenetic analyses of housekeeping genes recA, atpD and glnII and fatty acid profiles also indicated that these four strains constitute a novel group distinct from recognized species of the genus Rhizobium. Based on this evidence, strains CCBAU 85046T, CCBAU 85051, CCBAU 85048 and CCBAU 85049 represent a novel species in the genus Rhizobium, for which the name Rhizobium tubonense sp. nov. is proposed. The type strain is CCBAU 85046T (=LMG 25225T =HAMBI 3066T) and its DNA G+C content is 59.52 mol% (T m). Strain CCBAU 85046T could form effective nodules on plant species Vigna unguiculata and Medicago sativa but not on its host of origin Oxytropis glabra.