The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera

Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera

Genus Pseudomonas is a large assemblage of diverse microorganisms, not sharing a common evolutionary history. To clarify their evolutionary relationships and classification, we have conducted comprehensive phylogenomic and comparative analyses on 388 Pseudomonadaceae genomes. In phylogenomic trees, Pseudomonas species formed 12 main clusters, apart from the "Aeruginosa clade" containing its type species, P. aeruginosa. In parallel, our detailed analyses on protein sequences from Pseudomonadaceae genomes have identified 98 novel conserved signature indels (CSIs), which are uniquely shared by the species from different observed clades/groups. Six CSIs, which are exclusively shared by species from the "Aeruginosa clade," provide reliable demarcation of this clade corresponding to the genus Pseudomonas sensu stricto in molecular terms. The remaining 92 identified CSIs are specific for nine other Pseudomonas species clades and the genera Azomonas and Azotobacter which branch in between them. The identified CSIs provide strong independent evidence of the genetic cohesiveness of these species clades and offer reliable means for their demarcation/circumscription. Based on the robust phylogenetic and molecular evidence presented here supporting the distinctness of the observed Pseudomonas species clades, we are proposing the transfer of species from the following clades into the indicated novel genera: Alcaligenes clade - Aquipseudomonas gen. nov.; Fluvialis clade - Caenipseudomonas gen. nov.; Linyingensis clade - Geopseudomonas gen. nov.; Oleovorans clade - Ectopseudomonas gen. nov.; Resinovorans clade - Metapseudomonas gen. nov.; Straminea clade - Phytopseudomonas gen. nov.; and Thermotolerans clade - Zestomonas gen. nov. In addition, descriptions of the genera Azomonas, Azotobacter, Chryseomonas, Serpens, and Stutzerimonas are emended to include information for the CSIs specific for them. The results presented here should aid in the development of a more reliable classification scheme for Pseudomonas species.

Comparative genomics and informational content analysis uncovered internal regions of the core genes rpoD, pepN and gltX for an MLSA with genome-level resolving power within the genus Pseudomonas

In the field of prokaryotic taxonomy, there has been a recent transition towards phylogenomics as the gold standard approach. However, genome-based phylogenetics is still restrictive for its cost when managing large amounts of isolates. Fast, cheap, and taxonomically competent alternatives, like multilocus sequence analysis (MLSA) are thus recommendable. Nevertheless, the criteria for selecting the conserved genes for MLSA have not been explicit for different bacterial taxa, including the broadly diverse Pseudomonas genus. Here, we have carried out an unbiased and rational workflow to select internal sequence regions of Pseudomonas core genes (CG) for a MLSA with the best phylogenetic power, and with a resolution comparable to the genome-based ANI approach. A computational workflow was established to inspect 126 complete genomes of representatives from over 60 Pseudomonas species and subspecies, in order to identify the most informative CG internal regions and determine which combinations in sets of three partial CG sequences have comparable phylogenetic resolution to that of the current ANI standard. We found that the rpoD^346-1196-pepN^1711-2571-gltX^86-909 concatenated sequences were the best performing in terms of phylogenetic robustness and resulted highly sensitive and specific when contrasted with ANI. The rpoD-pepN-gltX MLSA was validated in silico and in vitro. Altogether, the results presented here supports the proposal of the rpoD-pepN-gltX MLSA as a fast, affordable, and robust phylogenetic tool for members of the Pseudomonas genus.

Leclercia Adecarboxylata and Pseudomonas Oryzihabitans Infection after Achilles Tendon Repair: A Case Report and Literature Review

Leclercia adecarboxylata and Pseudomonas oryzihabitans are two bacteria rarely seen in human infections. We present an unusual case of a patient who developed a localized infection with these bacteria after repair of a ruptured Achilles tendon. We also present a review of the literature regarding infection with these bacteria within the lower extremity.

Genome analysis of Pseudomonas species reveals that Pseudomonas panacis Park et al. 2005 is a later heterotypic synonym of Pseudomonas marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980)

We described the comparative genomic analysis of Pseudomonas panacis DSM 18529T and Pseudomonas marginalis DSM 13124T of the genus Pseudomonas to define the taxonomic assignment. When conducting this analysis, genomic information for 203 type strains was available in the NCBI genome database. The ANI, AAI and isDDH data were higher than the threshold values between Pseudomonas panacis DSM 18529T and Pseudomonas marginalis DSM 13124T. Whole-genome comparisons show 97 % average nucleotide identity, 98 % average amino acid identity and 75 % in silico DNA–DNA hybridization values. Pseudomonas marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980) have priority over the name Pseudomonas panacis Park et al. 2005, therefore nomenclatural authorities propose that Pseudomonas panacis Park et al. 2005 is a later heterotypic synonym of Pseudomonas marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980). The type strain is ATCC 10844T (=DSM 13124T=NCPPB 667T).

Hymenobacter piscis sp. nov., isolated from a fish pond

Bacterial strain NST-14T, isolated from a freshwater fish pond in Taiwan, was characterized using a polyphasic taxonomy approach. The strain was Gram-stain-negative, strictly aerobic, non-motile, rod-shaped and formed pink colonies. Optimal growth occurred at 30 °C, pH 7 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain NST-14T formed a phylogenetic lineage in the genus Hymenobacter . Analysis of 16S rRNA gene sequences showed that strain NST-14T had the highest similarity to Hymenobacter actinosclerus CCUG 39621T (97.7%), Hymenobacter amundsenii P5136T (97.3%) and Hymenobacter humicola P6312T (96.9%). Strain NST-14T showed 75.1–85.3 % average nucleotide identity, 73.7–89.8 % average amino acid identity and 14.5–26.0 % digital DNA–DNA hybridization with the type strains of other closely related Hymenobacter species. Strain NST-14T contained iso-C15 : 0, C16 : 1  ω5c and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) as the predominant fatty acids. The major hydroxyl fatty acids were iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The polar lipids were phosphatidylethanolamine, one unidentified glycolipid, four unidentified aminophospholipids, one unidentified aminolipid, two unidentified phospholipids and three unidentified lipids. The major polyamine was homospermidine. The major isoprenoid quinone was MK-7. The DNA G+C content of the genomic DNA was 62.4 mol%. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain NST-14T should be classified as a novel species of the genus Hymenobacter , for which the name Hymenobacter piscis sp. nov. is proposed. The type strain is NST-14T (=BCRC 81249T=LMG 31686T).

Rhodobacter amnigenus sp. nov. and Rhodobacter ruber sp. nov., isolated from freshwater habitats

Two bacterial strains, designated HSP-20^T and CCP-1^T, isolated from freshwater habitats in Taiwan, were characterized by polyphasic taxonomy. Both strains were Gram-stain-negative, aerobic, non-motile and rod-shaped. Cells of strains HSP-20^T and CCP-1^T formed pink and dark red coloured colonies, respectively. Both strains contained bacteriochlorophyll a, and showed optimum growth under anaerobic conditions by photoheterotrophy, but no growth by photoautotrophy. Phylogenetic analyses based on 16S rRNA gene and whole-genome sequences indicated that both strains belonged to the genus Rhodobacter. Analysis of 16S rRNA gene sequences showed that strains HSP-20^T and CCP-1^T shared 98.3 % sequence similarity and were closely related to Rhodobacter tardus CYK-10^T (96.0 %) and Rhodobacter flagellatus SYSU G03088^T (96.0 %), respectively. Both strains shared common chemotaxonomic characteristics including Q-10 as the major isoprenoid quinone, C_18 : 1  ω7c as the predominant fatty acid, and phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as the main polar lipids. The DNA G+C content of both strains was 66.2 mol%. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between these two novel isolates and their closest relatives were below the cut-off values of 95-96, 90 and 70 %, respectively, used for species demarcation. On the basis of phenotypic and genotypic properties and phylogenetic inference, both strains should be classified as novel species within the genus Rhodobacter, for which the names Rhodobacter amnigenus sp. nov. (=BCRC 81193^T=LMG 31334^T) and Rhodobacter ruber sp. nov. (=BCRC 81189^T=LMG 31335^T) are proposed.

Past, present and future of the boundaries of the Pseudomonas genus: Proposal of Stutzerimonas gen. Nov

Pseudomonas is one the best studied bacterial genera, and it is the genus with the highest number of species among the gram-negative bacteria. Pseudomonas spp. are widely distributed and play relevant ecological roles; several species are commensal or pathogenic to humans, animals and plants. The main aim of the present minireview is the discussion of how the Pseudomonas taxonomy has evolved with the development of bacterial taxonomy since the first description of the genus in 1894. We discuss how the successive implementation of novel methodologies has influenced the taxonomy of the genus and, vice versa, how the taxonomic studies developed in Pseudomonas have introduced novel tools and concepts to bacterial taxonomy. Current phylogenomic analyses of the family Pseudomonadaceae demonstrate that a considerable number of named Pseudomonas spp. are not monophyletic with P. aeruginosa, the type species of the genus, and that a reorganization of several genera can be foreseen. Phylogenomics of Pseudomonas, Azomonas and Azotobacter within the Pseudomonadaceae is presented as a case study. Five new genus names are delineated to accommodate five well-defined phylogenetic branches that are supported by the shared genes in each group, and two of them can be differentiated by physiological and ecological properties: the recently described genus Halopseudomonas and the genus Stutzerimonas proposed in the present study. Five former Pseudomonas species are transferred to Halopseudomonas and 10 species to Stutzerimonas.

Commensal microbe-derived acetate suppresses NAFLD/NASH development via hepatic FFAR2 signalling in mice

BACKGROUND

Non-alcoholic liver disease (NAFLD) is the hepatic manifestation of metabolic syndrome, and it can progress to non-alcoholic steatohepatitis (NASH). Alterations in the gut microbiome have been implicated in the development of NAFLD/NASH, although the underlying mechanisms remain unclear.

RESULTS

We found that the consumption of the prebiotic inulin markedly ameliorated the phenotype of NAFLD/NASH, including hepatic steatosis and fibrosis, in mice. Inulin consumption resulted in global changes in the gut microbiome, including concomitant enrichment of the genera Bacteroides and Blautia, and increased concentrations of short-chain fatty acids, particularly acetate, in the gut lumen and portal blood. The consumption of acetate-releasing resistant starch protected against NAFLD development. Colonisation by Bacteroides acidifaciens and Blautia producta in germ-free mice resulted in synergetic effects on acetate production from inulin. Furthermore, the absence of free fatty acid receptor 2 (FFAR2), an acetate receptor, abolished the protective effect of inulin, as indicated by the more severe liver hypertrophy, hypercholesterolaemia and inflammation. These effects can be attributed to an exacerbation of insulin resistance in the liver, but not in muscle or adipose tissue.

CONCLUSION

These findings demonstrated that the commensal microbiome-acetate-FFAR2 molecular circuit improves insulin sensitivity in the liver and prevents the development of NAFLD/NASH. Video abstract.

Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera

Pseudomonas is a large and diverse genus broadly distributed in nature. Its species play relevant roles in the biology of earth and living beings. Because of its ubiquity, the number of new species is continuously increasing although its taxonomic organization remains quite difficult to unravel. Nowadays the use of genomics is routinely employed for the analysis of bacterial systematics. In this work, we aimed to investigate the classification of species of the genus Pseudomonas on the basis of the analyses of the type strains whose genomes are currently available. Based on these analyses, we propose the creation of three new genera (Denitrificimonas gen nov. comb. nov., Neopseudomonas gen nov. comb. nov. and Parapseudomonas gen nov. comb. nov) to encompass several species currently included within the genus Pseudomonas and the reclassification of several species of this genus in already described taxa.

Flavobacterium difficile sp. nov., isolated from a freshwater waterfall

A bacterial strain designated KDG-16 ^T is isolated from a freshwater waterfall in Taiwan and characterized to determine its taxonomic affiliation. Cells of strain KDG-16 ^T are Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and form light yellow colonies. Optimal growth occurs at 20-25 °C, pH 6-7, and with 0% NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set reveal that strain KDG-16 ^T is affiliated with species in the genus Flavobacterium. Analysis of 16S rRNA gene sequences shows that strain KDG-16 ^T shares the highest similarity with Flavobacterium terrigena DSM 17934 ^T (97.7%). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain KDG-16 ^T and the closely related Flavobacterium species are below the cut-off values of 95-96, 90 and 70%, respectively, used for species demarcation. Strain KDG-16 ^T contains iso-C_15:0, iso-C_15:1 G and iso-C_17:0 3-OH as the predominant fatty acids. The polar lipid profile consists of phosphatidylethanolamine, one uncharacterized aminophospholipid, one uncharacterized phospholipid, two uncharacterized aminolipids and two uncharacterized lipids. The major polyamine is homospermidine. The major isoprenoid quinone is MK-6. Genomic DNA G + C content of strain KDG-16 ^T is 31.6%. Based on the polyphasic taxonomic data obtained, strain KDG-16 ^T is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium difficile sp. nov. is proposed. The type strain is KDG-16 ^T (= BCRC 81194 ^T = LMG 31332 ^T).

Flavobacterium lotistagni sp. nov. and Flavobacterium celericrescens sp. nov., isolated from freshwater habitats

This study presents taxonomic descriptions of strains CYK-4^T and TWA-26^T isolated from freshwater habitats in Taiwan. Both strains were Gram-stain-negative, strictly aerobic, motile by gliding and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that both strains belonged to the genus Flavobacterium. Analysis of 16S rRNA gene sequences showed that strains CYK-4^T and TWA-26^T shared 92.7 % sequence similarity and were most closely related to Flavobacterium ovatum W201E^T (95.6 %) and Flavobacterium aquaticum JC164^T (96.7 %), respectively. Both strains shared common chemotaxonomic characteristics comprising MK-6 as the main isoprenoid quinone, iso-C_15 : 0 and iso-C_15 : 1 G as the predominant fatty acids, phosphatidylethanolamine as the principal polar lipid, and homospermidine as the major polyamine. The DNA G+C contents of strains CYK-4^T and TWA-26^T were 41.5 and 31.8 mol%, respectively. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between these two novel isolates and their closest relatives were below the cut-off values of 95-96, 90 and 70 %, respectively, used for species demarcation. On the basis of phenotypic and genotypic properties and phylogenetic inference, both strains should be classified as novel species within the genus Flavobacterium, for which the names Flavobacterium lotistagni sp. nov. (type strain CYK-4^T=BCRC 81192^T=LMG 31330^T) and Flavobacterium celericrescens sp. nov. (type strain TWA-26^T=BCRC 81200^T=LMG 31333^T) are proposed.

Tabrizicola oligotrophica sp. nov. and Rhodobacter tardus sp. nov., two new species of bacteria belonging to the family Rhodobacteraceae

Two Gram-stain-negative, aerobic, non-motile bacteria, designated KMS-5^T and CYK-10^T, were isolated from freshwater environments. 16S rRNA gene sequence similarity results indicated that these two novel strains belong to the family Rhodobacteraceae. Strain KMS-5^T is closely related to species within the genus Tabrizicola (96.1-96.8 % sequence similarity) and Cypionkella (96.5-97.0 %). Strain CYK-10^T is closest to Rhodobacter thermarum YIM 73036^T with 96.6 % sequence similarity. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set showed that strain KMS-5^T is affiliated with species in the genus Tabrizicola and strain CYK-10^T is placed in a distinct clade with Rhodobacter blasticus ATCC 33485^T, Rhodobacter thermarum YIM 73036^T and Rhodobacter flagellatus SYSU G03088^T. These two strains shared common chemotaxonomic features comprising Q-10 as the major quinone, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as the principal polar lipids, and C_18 : 1  ω7c as the main fatty acid. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between these two novel isolates and their closest relatives were below the cut-off values of 95-96, 90 and 70 %, respectively, used for species demarcation. The obtained polyphasic taxonomic data suggested that strain KMS-5^T represents a novel species within the genus Tabrizicola, for which the name Tabrizicola oligotrophica sp. nov. is proposed with KMS-5^T (=BCRC 81196^T=LMG 31337^T) as the type strain, and strain CYK-10^T should represent a novel species of the genus Rhodobacter, for which the name Rhodobacter tardus sp. nov. is proposed with CYK-10^T (=BCRC 81191^T=LMG 31336^T) as the type strain.

Orrella amnicola sp. nov., isolated from a freshwater river, reclassification of Algicoccus marinus as Orrella marina comb. nov., and emended description of the genus Orrella

A novel Gram-negative, aerobic, non-motile, ovoid to rod-shaped bacterium, designated NBD-18^T, was isolated from a freshwater river in Taiwan. Optimal growth occurred at 30 °C, at pH 6 and in the absence of NaCl. The predominant fatty acids of strain NBD-18^T were C_16 : 0, summed feature 3 (C_16 : 1 ω7c and/or C_16 : 1 ω6c), C_17 : 0 cyclo and summed feature 8 (C_18 : 1 ω7c and/or C_18 : 1 ω6c). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidyldimethylethanolamine. The major polyamine was putrescine. The major isoprenoid quinone was Q-8. The genomic DNA G+C content of strain NBD-18^T was 50.9 %. Strain NBD-18^T was most closely related to Orrella dioscoreae LMG 29303^T and Algicoccus marinus HZ20^T at a 16S rRNA gene sequence similarity of 97.7 %. 16S rRNA gene sequence similarity between O. dioscoreae LMG 29303^T and A. marinus HZ20^T was 97.7 %. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set indicated that strain NBD-18^T, O. dioscoreae LMG 29303^T and A. marinus HZ20^T are affiliated with the same genus. Digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values among these three strains supported that they belong to the same genus and that strain NBD-18^T represents a novel species. Thus, A. marinus HZ20^T should be reclassified as Orrella marina comb. nov. based on the rules for priority of publication and validation. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain NBD-18^T represents a novel species in the genus Orrella, for which the name Orrella amnicola sp. nov. is proposed. The type strain is NBD-18^T (=BCRC 81197^T=LMG 31338^T).

Flavobacterium undicola sp. nov., isolated from a freshwater lake

Bacterial strain BBQ-18^T, isolated from a freshwater lake in Taiwan, is characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicate that strain BBQ-18^T forms a phylogenetic lineage in the genus Flavobacterium. Strain BBQ-18^T is most closely related to Flavobacterium alvei HR-AY^T with 98.5% 16S rRNA gene sequence similarity. Strain BBQ-18^T shows 70.5-89.5% average nucleotide identity and 13.7-38.2% digital DNA-DNA hybridization identity with the type strains of other closely related Flavobacterium species. The strain is Gram-stain negative, strictly aerobic, motile by gliding, rod shaped and formed yellow colonies. Optimal growth occurs at 25 °C, pH 6, and in the absence of NaCl. Strain BBQ-18^T contains iso-C_15:0, summed feature 3 (C_16:1ω6c and/or C_16:1ω7c) and anteiso-C_15:0 as the predominant fatty acids. The polar lipid profile consists of phosphatidylethanolamine, four uncharacterized aminophospholipids and two uncharacterized phospholipids. The major polyamine is homospermidine. The major isoprenoid quinone is MK-6. The DNA G+C content of the genomic DNA is 33.8%. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain BBQ-18^T should be classified as a novel species of the genus Flavobacterium, for which the name Flavobacterium undicola sp. nov. is proposed. The type strain is BBQ-18^T (= BCRC 81050^T = LMG 30052^T = KCTC 52810^T).

Rhodovarius crocodyli sp. nov., isolated from a crocodile pond

Bacterial strain CCP-6^T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain CCP-6^T is affiliated with species in the genus Rhodovarius. Strain CCP-6^T was most closely related to Rhodovarius lipocyclicus CCUG 44693^T with a 98.9% 16S rRNA gene sequence similarity. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed light pink-coloured colonies. Optimal growth occurred at 30 °C, pH 6 and in the absence of NaCl. The major fatty acids of strain CCP-6^T were C_{18 : 1} ω7c, C_{16 : 0} and C_{19 : 0} cyclo ω8c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, three unidentified aminophospholipids and an unidentified phospholipid. The predominant polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content of the genomic DNA was 69.3 mol%. Strain CCP-6^T showed 85.8% average nucleotide identity and 14.5% digital DNA-DNA hybridization identity with Rhodovarius lipocyclicus CCUG 44693^T. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain CCP-6^T represents a novel species in the genus Rhodovarius, for which the name Rhodovarius crocodyli sp. nov. is proposed. The type strain is CCP-6^T (=BCRC 81095^T=LMG 30310^T=KCTC 62188^T).

Sphingomonas lacunae sp. nov., isolated from a freshwater pond

A novel bacterial strain, designated CSW-10^T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed yellow-coloured colonies. Optimal growth occurred at 30 °C, pH 7, and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain CSW-10^T formed a phylogenetic lineage in the genus Sphingomonas. The 16S rRNA gene sequence similarity indicated that strain CSW-10^T was most closely related to Sphingomonas fonticola TNR-2^T (97.6%). Strain CSW-10^T showed 69.8-70.7% average nucleotide identity and 19.0-23.0% digital DNA-DNA hybridization identity with the strains of other related Sphingomonas species. The major fatty acids of strain CSW-10^T were summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c) and C_17:1 ω6c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylcholine, one uncharacterized sphingoglycolipid, five uncharacterized aminophospholipids, one uncharacterized phospholipid and one uncharacterized lipid. The predominant polyamines were homospermidine and spermidine. The major isoprenoid quinone was Q-10. Genomic DNA G+C content of strain CSW-10^T was 62.0 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain CSW-10^T should represent a novel species of the genus Sphingomonas, for which the name Sphingomonas lacunae sp. nov. is proposed. The type strain is CSW-10^T (=BCRC 81190^T =LMG 31340^T).

Novosphingobium ovatum sp. nov., isolated from a freshwater mesocosm

A bacterial strain, designated FSY-8^T, was isolated from a freshwater mesocosm in Taiwan and characterized using the polyphasic taxonomy approach. Cells of strain FSY-8^T were aerobic, Gram-stain-negative, rod-shaped, non-motile and formed yellow coloured colonies on Reasoner's 2A agar. Growth occurred at 20-40 °C (optimum, 30-37 °C) and pH 5-7 (optimum, pH 6) and in the presence of 0-0.5 % NaCl (optimum, 0 %, w/v). The major fatty acids (>10 %) of strain FSY-8^T were summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c) and summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c). The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, diphosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized lipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 64.8 mol %. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-8^T formed a phylogenetic lineage in the genus Novosphingobium. Strain FSY-8^T showed 71.6-77.2 % average nucleotide identity and 19.9-22.8 % digital DNA-DNA hybridization identity with the strains of other Novosphingobium species. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain FSY-8^T should be classified in a novel species of the genus Novosphingobium, for which the name Novosphingobium ovatum sp. nov. is proposed. The type strain is FSY-8^T (=BCRC 81051^T=LMG 30053^T=KCTC 52812^T).

Flavobacterium ichthyis sp. nov., isolated from a fish pond

Bacterial strain NST-5T, isolated from a fish pond in Taiwan, was characterized using a polyphasic taxonomy approach. Results of phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain NST-5T formed a phylogenetic lineage in the genus Flavobacterium . Analysis of 16S rRNA gene sequences showed that strain NST-5T showed the highest similarity to Flavobacterium enshiense DK69T (94.9 %), Flavobacterium ahnfeltiae 10Alg 130T (94.8 %) and Flavobacterium vireti THG-SM1T (94.8 %). Strain NST-5T showed 68.9–72.5% average nucleotide identity and 19.1–23.7% digital DNA–DNA hybridization identity with the type strains of other close related Flavobacterium species. Cells of the strain were Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and formed yellow colonies. Optimal growth occurred at 30 °C, pH 7 and with 0.5% NaCl. Strain NST-5T contained iso-C15:0, C15:0 and iso-C16:0 as the predominant fatty acids. The major hydroxyl fatty acids were iso-C16:0 3-OH and iso-C17:0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, three uncharacterized aminophospholipids, two uncharacterized phospholipids and one uncharacterized aminolipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 35.5 mol%. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain NST-5T should be classified as a novel species of the genus Flavobacterium , for which the name Flavobacterium ichthyis sp. nov. is proposed. The type strain is NST-5T (=BCRC 81198T=LMG 31341T).

Ideonella livida sp. nov., isolated from a freshwater lake

A novel bacterial strain, designated TBM-1^T, isolated from a freshwater lake in Taiwan, was characterized using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain TBM-1^T formed a phylogenetic lineage in the genus Ideonella. Analysis of 16S rRNA gene sequences showed that strain TBM-1^T was most closely related to Ideonella dechloratans CCUG 30898^T with 98.4 % sequence similarity. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain TBM-1^T and closely related strains of the genus Ideonella were 74.4-77.5 %, 69.7-75.4 % and 19.8-21.8 %, respectively, supporting that strain TBM-1^T represents a novel species of the genus Ideonella. Cells were Gram-stain-negative, motile by means of a single polar flagellum, rod-shaped and formed blue colonies. Optimal growth occurred at 30 °C, pH 6 and 0 % NaCl. The predominant fatty acids of strain TBM-1^T were summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), C_18 : 1  ω7c and C_16 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two uncharacterized aminophospholipids and two uncharacterized phospholipids. The main polyamine was putrescine. The major isoprenoid quinone was Q-8. The estimated genome size was 5.26 Mb, with an average G+C content of 70.0 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TBM-1^T should be classified in a novel species of the genus Ideonella, for which the name Ideonella livida sp. nov. is proposed. The type strain is TBM-1^T (=BCRC 81199^T =LMG 31339^T).

Pseudomonas neustonica sp. nov., isolated from the sea surface microlayer of the Ross Sea (Antarctica)

Gram-stain-negative, aerobic and rod-shaped bacterial strains, designated SSM26^T and SSM44, were isolated from a sea surface microlayer sample from the Ross Sea, Antarctica. Analysis of the 16S rRNA gene sequences of strains SSM26^T and SSM44 revealed a clear affiliation with the genus Pseudomonas. Based on the results of phylogenetic analysis, strains SSM26^T and SSM44 showed the closest phylogenetic relationship with the species Pseudomonas sabulinigri KCTC 22137^T with the 16S rRNA gene sequence similarity level of 98.5 %. Strains SSM26^T and SSM44 grew optimally at 30 °C, pH 7.0-7.5 and 0.5-10.0 % NaCl (w/v). The major cellular fatty acids were C_18 : 1  ω7c (31.3-34.9 %), C_16 : 0 (15.5-20.2 %), summed feature 3 (C_16 : 1  ω7c/C_16 : 1  ω6c; 19.5-25.4 %) and C_12 : 0 (6.0-9.3 %). The genomic DNA G+C content of each strain was 56.2 mol%. Genomic relatedness analyses based on the average nucleotide identity and the genome-to-genome distance showed that strains SSM26^T and SSM44 constituted a single species that was clearly distinguishable from its phylogenetically close relatives. The combined phenotypic, chemotaxonomic, genomic and phylogenetic data also showed that strains SSM26^T and SSM44 could be distinguished from validly published members of the genus Pseudomonas. Thus, these strains should be classified as representing a novel species in the genus Pseudomonas, for which the name Pseudomonas neustonica sp. nov. is proposed with the type strain SSM26^T (=KCCM 43193^T=JCM 31284^T=PAMC 28426^T) and a sister strain SSM44 (=KCCM 43194=JCM 31285=PAMC 28427).

Oleiharenicola lentus sp. nov., isolated from irrigation water

Bacterial strain TWA-58^T, isolated from irrigation water in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain TWA-58^T formed a phylogenetic lineage in the genus Oleiharenicola of the family Opitutaceae. Strain TWA-58^T was most closely related to Oleiharenicola alkalitolerans NVT^T with a 96.7 % 16S rRNA gene sequence similarity. Strain TWA-58^T showed 75.2 % average nucleotide identity, 70.9 % average amino acid identity and 21.0 % digital DNA-DNA hybridization identity with O. alkalitolerans NVT^T. Cells were Gram-stain-negative, aerobic, motile, coccoid-shaped and formed transparent colonies. Optimal growth occurred at 25 °C, pH 6, and 0 % NaCl. The major fatty acids of strain TWA-58^T were iso-C_15 : 0 and anteiso-C_15 : 0. The predominant hydroxy fatty acid was iso-C_13 : 0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified aminophospholipids. The major isoprenoid quinone was MK-7. Genomic DNA G+C content of strain TWA-58^T was 65.3 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TWA-58^T should be classified in a novel species of the genus Oleiharenicola, for which the name Oleiharenicola lentus sp. nov. is proposed. The type strain is TWA-58^T (=BCRC 81161^T=LMG 31019^T=KCTC 62872^T).

Aquirufa rosea sp. nov., isolated from a freshwater lake

A bacterial strain designated CAR-16^T was isolated from a freshwater lake in Taiwan and characterized using the polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, motile by gliding, rod-shaped and formed rose-colored colonies. Optimal growth occurred at 30 °C, pH 7 and with 0 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that CAR-16^T represented a member of the family Cytophagaceae and formed a phylogenetic lineage in the genus Aquirufa. CAR-16^T was most closely related to Aquirufa nivalisilvae 59G-WUEMPEL^T with a 99.7 % 16S rRNA gene sequence similarity. CAR-16^T showed 71.2-79.5 % average nucleotide identity and 17.8-21.7 % digital DNA-DNA hybridization identity with the strains of other species of the genus Aquirufa. The major fatty acids of strain CAR-16^T were iso-C_15 : 0, iso-C_15 : 0 3-OH, C_16 : 1ω5c and summed feature 3 (C_16 : 1ω7c/C_16 : 1ω6c and/or iso-C_15 : 0 2-OH). The polar lipid profile consisted of a mixture of phosphatidylethanolamine and several uncharacterized aminophospholipids, phospholipids and lipids. The major isoprenoid quinone was MK-7. The genomic DNA G+C content of CAR-16^T was 38.8 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, CAR-16^T should be classified as representing a novel species of the genus Aquirufa, for which the name Aquirufa rosea sp. nov. is proposed. The type strain is CAR-16^T (=BCRC 81153^T=LMG 30923^T=KCTC 62869^T).

Aquabacterium lacunae sp. nov., isolated from a freshwater pond

A novel bacterial strain, designated KMB7^T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomic approach. Cells were Gram-stain-negative, motile by means of a single polar flagellum, rod-shaped and formed cream colonies. Optimal growth occurred at 25 °C, pH 7, and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain KMB7^T is affiliated with species in the genus Aquabacterium. The 16S rRNA gene sequence similarity indicated that strain KMB7^T is closely related to species within the genus Aquabacterium (95.2-97.6 % sequence similarity) and is most similar to A. fontiphilum CS-6^T (97.6 %), followed by A. parvum B6^T (97.5 %). The average nucleotide identity and digital DNA-DNA hybridization identity between strain KMB7^T and the closely related strains were 74.6-78.0 % and 19.0-21.2 %, respectively. The major fatty acids of strain KMB7^T were summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), C_18 : 1  ω7c and C_16 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, diphosphatidylglycerol and four unidentified phospholipids. The sole isoprenoid quinone was ubiquinone-8 (Q-8). Genomic DNA G+C content of strain KMB7^T was 65.4 %. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain KMB7^T should be classified in a novel species of the genus Aquabacterium, for which the name Aquabacterium lacunae sp. nov. is proposed. The type strain is KMB7^T (=BCRC 81156^T=LMG 30924^T=KCTC 62867^T).

Rubrivivax albus sp. nov., isolated from a freshwater pond

Strain ICH-3^T, isolated from a freshwater pond in Taiwan 9ROC), was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that ICH-3^T is affiliated with the species in the genus Rubrivivax. ICH-3^T was most closely related to Rubrivivax benzoatilyticus JA2^T and Rubrivivax gelatinosus NCIB 8290^T with 97.5 and 97.4 % 16S rRNA gene sequence similarity. The average nucleotide identity and digital DNA-DNA hybridization identity between ICH-3^T and the two closely related strains were 77.3 and 20.9-21.0 %, respectively, indicating that ICH-3^T represents a novel species of the genus Rubrivivax. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed white colonies. Optimal growth occurred at 30 °C, pH 7.5-8.0 and with 0.5 % NaCl. The major fatty acids (>20 %) of ICH-3^T were summed feature 3 (comprising C_16 : 1ω7c and/or C_16 : 1ω6c) and C_16 : 0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid and two uncharacterized phospholipids. The major isoprenoid quinone was Q-8. The genomic DNA G+C content of ICH-3^T was 70.3 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain ICH-3^T should be classified as representing a novel species of the genus Rubrivivax, for which the name Rubrivivax albus sp. nov. is proposed. The type strain is ICH-3^T (=BCRC 81155^T=LMG 30930^T=KCTC 62866^T).

Filimonas effusa sp. nov., isolated from a freshwater river

Strain TTM-71^T, isolated from a freshwater river in Taiwan, was characterized using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain TTM-71^T is affiliated with species in the genus Filimonas. The 16S rRNA gene sequence similarity indicated that strain TTM-71^T is closely related to species within the genus Filimonas (94.7-95.5 % sequence similarity) and had a high sequence similarity with Filimonas endophytica SR 2-06^T (95.5 %). Strain TTM-71^T showed 70.3 % average nucleotide identity and 24.9 % digital DNA-DNA hybridization identity with Filimonas lacunae YT21^T. Cells were Gram-stain-negative, aerobic, motile by gliding, rod-shaped and formed beige-colored colonies. Optimal growth occurred at 20 °C, pH 8, and in the presence of 0.5 % NaCl. The major fatty acids of strain TTM-71^T were iso-C_15 : 0, iso-C_15 : 1 G and summed feature 3 (comprising C_16 : 1  ω7c and/or C_16 : 1  ω6c). The predominant hydroxy fatty acid was iso-C_17 : 0 3-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, four uncharacterized aminophospholipids, one uncharacterized aminolipid, one uncharacterized phospholipid and one uncharacterized lipid. The predominant polyamine was homospermidine. The only isoprenoid quinone was MK-7. Genomic DNA G+C content was 45.6 mol%. On the basis of the polyphasic evidence presented, strain TTM-71^T is considered to represent a novel species of the genus Filimonas, for which the name Filimonas effusa sp. nov. is proposed. The type strain is TTM-71^T (=BCRC 81160^T=LMG 31017^T=KCTC 62871^T).

Methylobacterium oryzihabitans sp. nov., isolated from water sampled from a rice paddy field

Strain TER-1^T was isolated from water sampled from a rice paddy field in Taiwan. Cells were Gram-negative, aerobic, motile, rod-shaped and formed pink-coloured colonies. Optimal growth occurred at 25-30 °C, pH 6-7 and in the presence of 0.5 % NaCl. Strain TER-1^T could grow on C1 compounds such as methanol, formic acid, methylamine and dimethylamine as sole carbon source, and carry methanol dehydrogenase gene, which supports its methylotrophic metabolism. The results of phylogenetic analyses based on the 16S rRNA gene sequence, methanol dehydrogenase gene sequence and coding sequences of 92 protein clusters indicated that strain TER-1^T formed a phylogenetic lineage in the genus Methylobacterium. Strain TER-1^T was most closely related to Methylobacterium isbiliense AR24^T with 96.8 % 16S rRNA gene sequence similarity. Strain TER-1^T showed 77.1-82.8 % average nucleotide identity and 16.4-20.2 % digital DNA-DNA hybridization identity with the strains of other Methylobacterium species. The major fatty acid of strain TER-1^T was C_18 : 1ω7c. The predominant hydroxy fatty acid was C_18 : 0 3-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and two uncharacterized lipids. The only isoprenoid quinone was Q-10. The genomic DNA G+C content of strain TER-1^T was 71.9 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TER-1^T should be classified in a novel species of the genus Methylobacterium, for which the name Methylobacterium oryzihabitans sp. nov. is proposed. The type strain is TER-1^T (=BCRC 81157^T=LMG 30931^T=KCTC 62864^T).

Lacibacter luteus sp. nov., isolated from a freshwater river

An isolate, designated TTM-7^T, recovered from a freshwater river in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain TTM-7^T is affiliated with species in the genus Lacibacter. Strain TTM-7^T was most closely related to Lacibacter cauensis NJ-8^T with a 98.2 % 16S rRNA gene sequence similarity, followed by Lacibacter daechungensis H32-4^T (97.4 %) and Lacibacter nakdongensis SS2-56^T (96.3 %). Cells were Gram-stain-negative, aerobic, motile by gliding, rod-shaped and formed orange colonies. Optimal growth occurred at 25 °C, pH 7 and 0 % NaCl. The major fatty acids of strain TTM-7^T were iso-C_15 : 0, summed feature 3 (comprising C_16 : 1ω7c/C_16 : 1ω6c and/or iso-C_15 : 0 2-OH) and iso-C_15 : 1 G. The predominant hydroxy fatty acid was iso-C_17 : 0 3-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, two unidentified aminoglycolipids, five unidentified aminophospholipids and one unidentified lipid. The major isoprenoid quinone was MK-7. Genomic DNA G+C content of strain TTM-7^T was 40.6 mol%. Strain TTM-7^T showed 83.6 % average nucleotide identity and 16.0 % digital DNA-DNA hybridization identity with Lacibacter cauensis NJ-8^T. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TTM-7^T should be classified in a novel species of the genus Lacibacter, for which the name Lacibacter luteus sp. nov. is proposed. The type strain is TTM-7^T (=BCRC 81159^T=LMG 30926^T=KCTC 62870^T).

Novosphingobium umbonatum sp. nov., isolated from a freshwater mesocosm

A bacterial strain designated FSY-9^T was isolated from a freshwater mesocosm in Taiwan and characterized to determine its taxonomic affiliation. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-9^T formed a phylogenetic lineage in the genus Novosphingobium. Strain FSY-9^T was most closely related to Novosphingobium humi R1-4^T with a 97.2 % 16S rRNA gene sequence similarity. Strain FSY-9^T showed 71.3-72.6 % average nucleotide identity and 17.7-23.0 % digital DNA-DNA hybridization identity with the strains of other Novosphingobium species. Cells of strain FSY-9^T were facultatively anaerobic, Gram-negative, rod-shaped, non-motile and formed light yellow coloured colonies. Growth occurred at 15-37 °C and pH 5.5-7, and in the presence of 0-0.5 % NaCl. The major fatty acids (>10 %) of strain FSY-9^T were summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c), C_18 : 1ω7c and C_16 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, sphingoglycolipid, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized lipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 61.5 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain FSY-9^T should be classified as a novel species of the genus Novosphingobium, for which the name Novosphingobium umbonatum sp. nov. is proposed. The type strain is FSY-9^T (=BCRC 81052^T=LMG 30054^T=KCTC 52813^T).

Phenotypic and genotypic characterization of endophytic bacteria associated with transgenic and non-transgenic soybean plants

Endophytic bacteria isolated from non-transgenic and transgenic Roundup Ready® glyphosate-resistant (GR) soybean plants were investigated to analyze the correspondence between phenotypic and genotypic characteristics and to determine whether or not the strains could be grouped based on the source of isolation in transgenic or non-transgenic plants, respectively. Most of the strains recovered from GR plants have shown the ability for plant growth promotion (PGP) by means of IAA production and inorganic phosphate solubilization, and 100% of the strains showed great motility (swarm or swim); in addition, 90% of the strains were able to metabolize the majority of carbon sources tested. GR soybean fields showed higher endophytes abundance than non-transgenic; however, analyzing the phylogenetic trees constructed using the partial 16SrRNA gene sequences, higher diversity was observed in non-transgenic soybean fields. Overall the majority of isolated endophytes could utilize multiple patterns of carbon sources and express resistance to antibiotics, while isolates varied widely in the PGP ability. The greater pattern and frequency of utilization of carbon sources and frequency and intensity of antibiotic resistance compared with PGP ability within the soybean endophytes community suggest that carbon sources metabolism and antibiotic resistance confer a greater relative fitness benefit than PGP ability. In conclusion, cluster analysis of the phenotypes and 16SrRNA gene sequences reveals lack of correspondence between the pattern of bacterial isolates and the transgenic character of plants, and the heterogeneity of clustering suggested that various adaptive processes, such as stress response, could have contributed to generate phenotypic variability to enhance endophytes overall fitness.

Nocardioides sambongensis sp. nov., isolated from Dokdo Islands soil

Strain KUDC5002^T was isolated from soil sampled on the Dokdo Islands, Republic of Korea. This bacterial strain was Gram stain-positive, non-motile, rod-shaped, capable of growing at 25-37°C and pH 5.0-12.0, and showed optimal growth at 30 °C and pH 7.0-8.0. Strain KUDC5002^T could be grown in tryptic soy broth containing less than 7.0 % NaCl (w/v). The cell width ranged from 0.5 to 0.6 µm and length ranged from 0.8 to 1.0 µm. Strain KUDC5002^T was catalase- and oxidase-positive. Its genomic G+C content was 72.2 mol%. Its major fatty acids were C_18 : 1 ω9c (17.3 %), iso-C_16 : 0 (16.0 %) and iso-C_17 : 0 (11.4 %). Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain KUDC5002^T belongs to the genus Nocardioides and is most closely related to strain Nocardioides humi DCY24^T (97.0 %). Based on its phenotypic, phylogenetic, genetic and chemotaxonomic features, strain KUDC5002^T should be considered a novel species in the genus Nocardioides, for which we have proposed the name Nocardioides sambongensis sp. nov. The type strain is KUDC5002^T (=KCTC 39855^T=DSM 106604^T).

Sandaracinomonas limnophila gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from a freshwater mesocosm

A bacterial strain designated FSY-15^T was isolated from a freshwater mesocosm in Taiwan and characterised using a polyphasic taxonomic approach. Cells of strain FSY-15^T were Gram-negative, aerobic, non-spore forming, non-motile rods and formed orange coloured colonies. Growth occurred at 20-30 °C (optimum, 25 °C), at pH 6-7.5 (optimum, pH 7) and with 0-0.5 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-15^T formed a phylogenetic lineage in the the family Cytophagaceae. Strain FSY-15^T was most closely related to the genera Pseudarcicella and Arcicella, and the levels of 16S rRNA gene sequence identity with respect to members of related genera are less than 94.1 %. Strain FSY-15^T showed less than 68.8 % average nucleotide identity and less than 24.7 % digital DNA-DNA hybridisation identity compared to the type strains of related genera within the family Cytophagaceae. The predominant fatty acids were iso-C_15 : 0, C_16 : 1ω5c and the major hydroxyl fatty acid was iso-C_15 : 0 3-OH. The major isoprenoid quinone was MK-7 and the DNA G+C content was 35.8 mol%. The major polar lipids were phosphatidylethanolamine and several uncharacterised aminophospholipid, aminolipid, phospholipid and lipid. The major polyamine was spermidine. On the basis of the genotypic and phenotypic data, strain FSY-15^T represents a novel species of a new genus in the family Cytophagaceae, for which the name Sandaracinomonas limnophila gen. nov., sp. nov. is proposed. The type strain is FSY-15^T (=BCRC 81011^T =LMG 29732^T =KCTC 52445^T).

Inhella crocodyli sp. nov., isolated from a crocodile pond

Strain CCP-18^T, isolated from a freshwater pond in Taiwan, was characterized by using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CCP-18^T belongs to the genus Inhella and has the highest levels of sequence similarity with respect to Inhella inkyongensis IMCC1713^T (98.9 %) and Inhella fonticola TNR-25^T (98.0 %). Cells were Gram-stain-negative, aerobic, motile, rod-shaped and formed white-coloured colonies. Optimal growth occurred at 25 °C, pH 6 and in the absence of NaCl. The major fatty acids of strain CCP-18^T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids, an unidentified phospholipid, an unidentified aminolipid and an unidentified lipid. The predominant polyamine was putrescine. The major isoprenoid quinone was Q-8. The draft genome was approximately 3.76 Mb in size with a G+C content of 68.9 mol%. The DNA-DNA hybridization values for strain CCP-18^Twith I.inkyongensis IMCC1713^T and I.nhella fonticola TNR-25^T were less than 40 %. Based on the phylogenetic and phenotypic data, strain CCP-18^T should be classified within the genus Inhella as a representative of a novel species, named Inhella crocodyli sp. nov. The type strain is CCP-18^T (=BCRC 81120^T=LMG 30595^T=KCTC 62511^T).

Sphingomonas crocodyli sp. nov., isolated from a crocodile pond

Strain CCP-7^T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain CCP-7^T formed a phylogenetic lineage in the genus Sphingomonas. Strain CCP-7^T was most closely related to Sphingomonas starnbergensis 382^T and Sphingomonas naphthae DKC-5-1^T with 96.2 % 16S rRNA gene sequence similarity. Strain CCP-7^T showed 65.5-76.7 % average nucleotide identity and 20.2-22.5 % digital DNA-DNA hybridization identity with the strains of other related Sphingomonas species. Cells were Gram-stain-negative, aerobic, motile, rod-shaped and formed light orange-coloured colonies. Optimal growth occurred at 30 °C, pH 6 and in the absence of NaCl. The major fatty acid of strain CCP-7^T was C18 : 1ω7c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, three uncharacterized sphingoglycolipids, two uncharacterized phospholipids and six uncharacterized lipids. The predominant polyamine was homospermidine. The only isoprenoid quinone was Q-10. Genomic DNA G+C content of strain CCP-7^T was 64.5 %. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain CCP-7^T should be classified in a novel species of the genus Sphingomonas, for which the name Sphingomonas crocodyli sp. nov. is proposed. The type strain is CCP-7^T (=BCRC 81096^T=LMG 30311^T=KCTC 62190^T).

Flavobacterium amnicola sp. nov., isolated from a sub-tropical stream

Strain LLJ-11^T, isolated from water sampled from a freshwater stream in Taiwan, was characterized using a polyphasic taxonomy approach. Cells of strain LLJ-11^T were Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and formed translucent yellow colonies. Optimal growth occurred at 25 °C, pH 7 and 0 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain LLJ-11^T is affiliated with species in the genus Flavobacterium. Strain LLJ-11^T was most closely related to Flavobacterium amniphilum KYPY10^T with 98.0 % 16S rRNA gene sequence identity. The DNA-DNA relatedness of strain LLJ-11^T with respect to Flavobacterium species was less than 35 %. Average nucleotide identity and digital DNA-DNA hybridization values between strain LLJ-11^T and the type strains of other closely related Flavobacterium species were 70.0-76.3 % and 21.1-23.9 %, respectively. Strain LLJ-11^T contained iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0) as the predominant fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of phosphatidylethanolamine, three uncharacterized aminophospholipids and two uncharacterized phospholipids. The major polyamine was homospermidine. The DNA G+C content was 34.8 mol%. On the basis of the phylogenetic inference and phenotypic data, strain LLJ-11^T is considered a representative of a novel species within the genus Flavobacterium. The name Flavobacterium amnicola sp. nov. is proposed, with strain LLJ-11^T (=BCRC 81124^T=LMG 30599^T=KCTC 62514^T) as the type strain.

Aquincola rivuli sp. nov., isolated from a freshwater stream

Strain KYPY4^T, isolated from a water sample taken from the Funglin stream in Taiwan, was characterized using a polyphasic taxonomic approach. The 16S rRNA gene sequence of strain KYPY4^T was closely related to Ideonella dechloratans CCUG 30898^T (97.1 %) followed by Aquincola tertiaricarbonis L10^T (96.9 %) and Kinneretia asaccharophila KIN192^T (96.8 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KYPY4^T belonged to the genus Aquincola and formed a distinct phyletic line with A. tertiaricarbonis L10^T and Aquincola amnicola TTM-94^T. The draft genome of strain KYPY4^T was approximately 4.93 Mb in size with a G+C content of 70.1 mol%. Strain KYPY4^T showed 73.4-76.9 % average nucleotide identity and 21.3-22.5 % digital DNA-DNA hybridization identity with the strains of other related species in the Rubrivivax-Roseateles-Leptothrix-Ideonella-Aquabacterium group. Cells of strain KYPY4^T were Gram-stain-negative, aerobic, motile, surrounded by a thick capsule and formed light orange colonies. Optimal growth occurred at 30 °C, pH 7 and 0 % NaCl. Strain KYPY4^T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized polar lipids. The major respiratory quinone was Q-8. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain KYPY4^T should be classified as a novel species of the genus Aquincola, for which the name Aquincola rivuli sp. nov. is proposed. The type strain is KYPY4^T (=BCRC 81010^T=KCTC 52441^T).

Rheinheimera riviphila sp. nov., isolated from a freshwater stream

Strain KYPC3^T, isolated from a freshwater stream in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KYPC3^T belonged to the genus Rheinheimera. Strain KYPC3^T exhibited 16S rRNA gene sequence similarity values of 94.8-97.9% to the type strains of species of the genus Rheinheimera. Strain KYPC3^T was most closely related to Rheinheimera chironomi K19414^T with 16S rRNA gene sequence similarity of 97.9%. Cells of strain KYPC3^T were Gram-stain negative, aerobic, motile by means of a single-polar flagellum, non-spore forming, coccoid or short rods surrounded by a thick capsule and forming off-white coloured colonies. Growth occurred at 15-30 °C (optimum, 20-25 °C), at pH 6-8 (optimum, pH 7) and with 0-0.5% NaCl (optimum, 0%). The major fatty acids (> 10%) of strain KYPC3^T were C_12:0 3-OH, summed feature 3 (C_16:1ω7c and/or C_16:1ω6c) and C_16:0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized phospholipid and an uncharacterized lipid. The major isoprenoid quinone was Q-8. The draft genome was approximately 4.75 Mb in size with a G + C content of 49.8 mol%. The DNA-DNA relatedness of strain KYPC3^T with respect to recognized species of the genus Rheinheimera was significantly less than 70%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain KYPC3^T should be classified as a novel species of the genus Rheinheimera, for which the name Rheinheimera riviphila sp. nov. is presented. The type strain is KYPC3^T (= BCRC 81008^T = LMG 29729^T = KCTC 52440^T).

Stagnimonas aquatica gen. nov., sp. nov., a new member of the family Nevskiaceae isolated from a freshwater mesocosm

A novel bacterial strain, designated THS-13^T, isolated from a freshwater mesocosm in Taiwan, was characterized by taking a polyphasic taxonomic approach. Cells of strain THS-13^T were Gram-stain-negative, aerobic, rod-shaped, motile by means of a single polar flagellum and formed translucent white coloured colonies. Growth occurred at 20-35 °C (optimum, 25 °C), at pH 5-8 (pH 6) and with 0-2 % NaCl (1 %). Phylogenetic analyses based on 16S rRNA gene and coding sequences of 92 protein clusters revealed that the strain belonged to the family Nevskiaceae in the class Gammaproteobacteria and represented an independent taxon separated from other genera. Strain THS-13^T shared low level of 16S rRNA gene sequence similarity (less than 93.0 %) to members of other genera in the family Nevskiaceae and was most closely related to Nevskia aquatilis F2-63^T (92.9 %). Strain THS-13^T showed less than 73.4 % average nucleotide identity and less than 23.8 % digital DNA-DNA hybridization identity compared to the type strains of related genera within the family Nevskiaceae. The predominant fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C16 : 0. The major isoprenoid quinone was Q-8 and the DNA G+C content was 67.6 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized phospholipid and an uncharacterized aminolipid. On the basis of the genotypic and phenotypic data, strain THS-13^T represents a novel species of a new genus in the family Nevskiaceae, for which we propose the name Stagnimonas aquatica gen. nov., sp. nov. The type strain is THS-13^T (=BCRC 81158^T=LMG 30925^T=KCTC 62868^T).

Flavobacterium niveum sp. nov., isolated from a freshwater creek

Strain TAPW14^T was isolated from a freshwater creek in Taiwan. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TAPW14^T belonged to the genus Flavobacterium and was most closely related to Flavobacterium akiainvivens IK-1^T (96.6 % sequence identity) and Flavobacterium hauense BX12^T (96.0 %) and less than 96 % sequence similarity to other members of the genus. Cells of strain TAPW14^T were Gram-negative, strictly aerobic, motile by gliding, rod-shaped and formed white colonies. Optimal growth occurred at 20 °C, pH 7 and in the presence of 0.5 % NaCl. Strain TAPW14^T contained summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0 and C16 : 0 as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, three uncharacterized aminophospholipids, one uncharacterized phospholipid and one uncharacterized lipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 46.0 mol%. On the basis of the phylogenetic inference and phenotypic data, strain TAPW14^T should be classified as a novel species, for which the name Flavobacteriumniveum sp. nov. is proposed. The type strain is TAPW14^T (=BCRC 81055^T=LMG 30057^T=KCTC 52808^T).

Screening of bacterial endophytes as potential biocontrol agents against soybean diseases

AIMS

This research was aimed at identifying and characterizing endophytic micro-organisms associated with soybean that have antimicrobial activity towards soybean pathogens.

METHODS AND RESULTS

Soybean plants were collected from field trials in four locations of southern Brazil that were cultivated with conventional (C) and transgenic glyphosate-resistant (GR) soybeans. Endophytic bacteria isolated from roots, stems and leaves of soybeans were evaluated for their capacity to inhibit fungal and bacterial plant pathogens and 13 micro-organisms were identified with antagonistic activity. Approximately 230 bacteria were isolated and identified based on the 16S rRNA and rpoN gene sequences. Bacteria isolated from conventional and transgenic soybeans were significantly different not only in population diversity but also in their antagonistic capacity. Thirteen isolates showed in vitro antagonism against Sclerotinia sclerotiorum, Phomopsis sojae and Rhizoctonia solani. Bacillus sp. and Burkholderia sp. were the most effective isolates in controlling bacterial and fungal pathogens in vitro. Extracts and precipitates from culture supernatants of isolates showed different patterns of inhibitory activity on growth of fungal and bacterial pathogens.

CONCLUSIONS

Bacillus sp. and Burkholderia sp. were the most effective isolates in controlling fungal pathogens in vitro, and the activity is mainly due to peptides. However, most of the studied bacteria showed the presence of antimicrobial compounds in the culture supernatant, either peptides, bacteriocins or secondary metabolites.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results could be significant to develop tools for the biological control of soybean diseases. The work brought to the identification of micro-organisms such as Bacillus sp. and Burkholderia sp. that have the potential to protect crops in order to enhance a sustainable management system of crops. Furthermore, the study provides the first evidences of the influence of management as well as the genetics of glyphosate-resistant soybean on the diversity of bacterial endophytes of soybean phytobiome.

Flavobacterium riviphilum sp. nov., isolated from a freshwater creek

A novel bacterium, designated strain TAPY6^T, was isolated from a freshwater creek in Taiwan. The strain was Gram-stain-negative, strictly aerobic, motile-by-gliding, rod-shaped and formed translucent yellow colonies. Optimal growth occurred at 20-30 °C, pH 6 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TAPY6^T belonged to the genus Flavobacterium and was most closely related to Flavobacterium succinicans LMG 10402^T (97.3 % sequence similarity) and Flavobacterium glycines Gm-149^T (96.3 %). Strain TAPY6^T contained C15 : 0 and iso-C15 : 0 as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, five uncharacterized aminophospholipids, two uncharacterized phospholipids and one uncharacterized aminolipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 39.8 mol%. Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Flavobacterium. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain TAPY6^T represents a novel species in the genus Flavobacterium, for which the name Flavobacterium riviphilum sp. nov. is proposed. The type strain is TAPY6^T (=BCRC 81007^T=LMG 29728^T=KCTC 52444^T).