Maribacter luteus sp. nov., a marine bacterium isolated from intertidal sand of the Yellow Sea

A novel rod-shaped and Gram-stain-negative bacterium, designated strain RZ05^T, was isolated from a sand sample collected from the intertidal zone of the Yellow Sea, PR China. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain RZ05^T clusters within the genus Maribacter, a member of the family Flavobacteriaceae, and has the highest sequence similarity to Maribacter polysiphoniae KCTC 22021^T (97.8 %), followed by Maribacter arenosus KCTC 52191^T (97.2 %). Cells of this strain were observed to be aerobic, oxidase- and catalase-positive, motile by gliding and formed yellow colonies. Growth occurred at 7-40 °C (optimum, 30 °C), at pH 6.5-9.5 (optimum, pH 7.0) and with 0.5-6 % (optimum, 2 %) NaCl. Its polar lipid profile included phosphatidylethanolamine, two unidentified glycolipids, one unidentified aminolipid and four unidentified lipids. The major cellular fatty acids were iso-C_15 : 0, iso-C_15 : 1 G, iso-C_17 : 0 3-OH, iso-C_16 : 0 3-OH, iso-C_15 : 0 3-OH, summed feature 9 (10-methyl C_16 : 0/iso-C_17 : 1  ω9c) and summed feature 3 (iso-C_15 : 0 2-OH/C_16 : 1  ω7c/C_16 : 1  ω6c). The only respiratory quinone was menaquinone 6 (MK-6). The genome of strain RZ05^T was 4.65 Mbp with a G+C content of 38.9 mol%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain RZ05^T and its most closely related type strain M. polysiphoniae KCTC 22021^T were 80.3 and 26.3  %, respectively. The results of phylogenetic, phenotypic and chemotaxonomic analyses indicated that strain RZ05^T represents a novel species of the genus Maribacter, for which the name Maribacter luteus sp. nov. is proposed. The type strain is RZ05^T (=KCTC 62834^T=MCCC 1K03617^T).

Seonamhaeicola maritimus sp. nov., isolated from coastal sediment

A Gram-stain-negative, facultatively anaerobic, non-motile, rod-shaped and orange-pigmented bacterium, designated 1505^T, was isolated from marine sediment that was obtained off the coast of Weihai, PR China. Strain 1505^T was found to grow at 10-35 °C (optimum, 28 °C), at pH 6.0-9.0 (optimum, 7.5) and in the presence of 1-4 % (w/v) NaCl (optimum, 2 %). Cells were positive for oxidase and catalase activity. The 16S rRNA gene based phylogenetic analysis revealed that the nearest phylogenetic neighbours of strain 1505^T were Seonamhaeicola algicola Gy8^T (97.1 %), Seonamhaeicola marinus B011^T (96.3 %) and Seonamhaeicola aphaedonensis KCTC 32578^T (95.6 %). Based on phylogenomic analysis, the average nucleotide identity values between strain 1505^T and S. algicola Gy8^T, S. marinus B011^T and S. aphaedonensis KCTC 32578^T were 75.9, 76.0 and 77.7 %, respectively; the digital DNA-DNA hybridization values based on the draft genomes between strain 1505^T and S. algicola Gy8^T, S. marinus B011^T and S. aphaedonensis KCTC 32578^T were 20.0, 20.7 and 21.4 %, respectively. Menaquinone-6 (MK-6) was detected as the major respiratory quinone. The dominant cellular fatty acids were iso-C_15 : 1 G and C_18 : 1ω9c. The DNA G+C content of strain 1505^T was 33.3 mol%. The polar lipids included phosphatidylethanolamine, six aminolipids and four unidentified lipids. Based on its phylogenetic and phenotypic characteristics, strain 1505^T is considered to represent a novel species of the genus Seonamhaeicola, for which the name Seonamhaeicola maritimus sp. nov. is proposed. The type strain is 1505^T (=KCTC 72528^T=MCCC 1H00389^T).

Seonamhaeicola sediminis sp. nov., isolated from marine sediment

A novel Gram-stain-negative, orange, rod or curved rod, facultatively anaerobic, gliding bacterial strain, designated strain W255^T, was isolated from Xiaoshi Island, Weihai, China. The strain W255^T grows optimally at a 28 °C, pH 7.5, and 3.0% (w/v) NaCl environment. Its colonies are circular, orange, non-transparent, smooth, and approximately 0.2-0.8 mm in diameter, after being cultured for 72 h on marine agar 2216. Cells of the strain W255^T are 0.3-0.8 µm wide and 1.0-4.0 µm long, catalase-positive and oxidase-positive. The major cellular fatty acids are iso-C_15:0, iso-C_15:1 G, and iso-C_15:0 3-OH. The sole respiratory quinone is MK-6. The major polar lipids include phosphatidylethanolamine, one unidentified amino lipid, one amino glycolipid, and two unidentified lipids (L1 and L2). The phylogenetic analysis based on 16S rRNA gene sequences indicated that strain W255^T has the highest similarities with the type strain of the type species of the genus Seonamhaeicola, S. aphaedonensis KCTC 32578^T (97.2%), and moderate with 'S. acroporae' KCTC 62713^T (96.5%), S. algicola Gy8^T (95.4%) and S. marinus B011^T (94.5%). The ANI and dDDH values between strain W255^T and S. aphaedonensis KCTC 32578^T are 86.6% and 31.3%, respectively. The genomic DNA G + C content is 33.5 mol%. On the basis of gene annotation, it was observed that strain W255^T have the abilities of nitrate reduction and utilizing various carbon sources, suggesting that this strain might be an important participant in the nitrogen cycle and carbon cycle in the marine environment. Based on the phenotypic, chemotaxonomic and phylogenetic analysis, strain W255^T has been considered as a novel species of the genus Seonamhaeicola, for which the name Seonamhaeicola sediminis sp. nov. is proposed. The type strain is W255^T (= MCCC 1H00377^T = KCTC 72085^T).

Flavobacterium cellulosilyticum sp. nov., a novel psychrophilic bacterium isolated from Arctic soil

A novel psychrophilic, light-yellow-coloured, aerobic, Gram-stain-negative, rod-shaped, non-motile bacterium, designated strain AR-3-4^T was isolated from a sample of Arctic soil. Strain AR-3-4^T grew at 0-25 °C, pH 6.0-9.0 and 0-1.0 % (w/v) NaCl concentration. The 16S rRNA gene sequence analysis showed that strain AR-3-4^T belonged to the genus Flavobacterium, with nearest phylogenetic neighbour being Flavobacterium fluvii H7^T (97.5 % sequence similarity). The strain comprised phosphatidylethanolamine as the main polar lipid, MK-6 as predominant respiratory quinone, and summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c), anteiso-C_15 : 0 and iso-C_15 : 0 as the major fatty acids. The average nucleotide identity and in silico DNA-DNA hybridization values between strain AR-3-4^T and closest members were below the threshold values of 95 % and 70 %, respectively. The DNA G+C content was 33.0 mol%. Based on the polyphasic taxonomic data, the novel species Flavobacterium cellulosilyticum sp. nov. is proposed with the type strain AR-3-4^T (=KEMB 9005-740^T=KACC 21171^T=NBRC 113787^T).

Robertkochia solimangrovi sp. nov., isolated from mangrove soil, and emended description of the genus Robertkochia

To date, there is sparse information for the genus Robertkochia with Robertkochia marina CC-AMO-30D^T as the only described member. We report here a new species isolated from mangrove soil collected at Malaysia Tanjung Piai National Park and perform polyphasic characterization to determine its taxonomic position. Strain CL23^T is a Gram-negative, yellow-pigmented, strictly aerobic, catalase-positive and oxidase-positive bacterium. The optimal growth conditions were determined to be at pH 7.0, 30–37 °C and in 1–2 % (w/v) NaCl. The major respiratory quinone was menaquinone-6 (MK-6) and the highly abundant polar lipids were four unidentified lipids, a phosphatidylethanolamine and two unidentified aminolipids. The 16S rRNA gene similarity between strain CL23^T and R. marina CC-AMO-30D^T is 96.67 %. Strain CL23^T and R. marina CC-AMO-30D^T clustered together and were distinguished from taxa of closely related genera in 16S rRNA gene phylogenetic analysis. Genome sequencing revealed that strain CL23^T has a genome size of 4.4 Mbp and a G+C content of 40.72 mol%. Overall genome related indexes including digital DNA–DNA hybridization value and average nucleotide identity are 17.70 % and approximately 70%, below the cutoffs of 70 and 95%, respectively, indicated that strain CL23^T is a distinct species from R. marina CC-AMO-30D^T. Collectively, based on the phenotypic, chemotaxonomic, phylogenetic and genomic evidences presented here, strain CL23^T is proposed to represent a new species with the name Robertkochia solimangrovi sp. nov. (KCTC 72252^T=LMG 31418^T). An emended description of the genus Robertkochia is also proposed.

Formosa maritima sp. nov., isolated from coastal sediment

A Gram-stain-negative, strictly aerobic, gliding-motile, rod-shaped and orange-pigmented bacterium, designated 1494^T, was isolated from marine sediment collected off the coast of Weihai, PR China. Strain 1494^T was found to grow at 4-37 °C (optimum, 30 °C), at pH 6.0-9.0 (pH 7.0) and in the presence of 0-8 % (w/v) NaCl (2 %). Cells were positive for oxidase and catalase activity. The results of 16S rRNA gene based phylogenetic analysis revealed that strain 1494^T belonged to the genus Formosa and exhibited the highest sequence similarity to Formosa spongicola KCTC 22662 ^T (98.4 %). Menaquinone-6 (MK-6) was detected as the major respiratory quinone. The dominant cellular fatty acids were iso-C_15 : 1 G and iso-C_15 : 0. The DNA G+C content of strain 1494^T was 31.1 mol%. The major polar lipids included phosphatidylethanolamine, one unidentified phospholipid and one unidentified lipid. Based on its phylogenetic and phenotypic characteristics, strain 1494^T is considered to represent a novel species from the genus Formosa, for which the name Formosa maritima sp. nov. is proposed. The type strain is 1494^T (=KCTC 72531^T=MCCC 1H00385^T).

Flavobacterium sangjuense sp. nov. isolated from sediment

A yellow-pigmented bacterial strain, GS03^T, was isolated from sediment in a branch of the Nackdong River in Sangju, Korea. Cells were observed to be Gram-negative, aerobic and rod-shaped with gliding motility, and to be positive for catalase and oxidase. Growth was found to occur at 4-30 °C (optimum 25 °C), at pH 7.0-8.5 (optimum pH 7.5) and at NaCl 0% (optimum NaCl 0%, w/v). The major cellular fatty acids (> 10% of the total) were identified as iso C_15:0, iso C_15:1 G, C_15:1ω6c, iso C_15: 0 3-OH and iso C_17: 0 3-OH. The major respiratory quinone was found to be menaquinone MK-6. The genome sequence of GS03^T is 3.1 Mb with G+C content of 36.1 mol%. The major polar lipids of the isolate were identified as phosphatidylethanolamine, three unidentified aminolipids, two unidentified phospholipids, an unidentified lipid and an unidentified aminophospholipid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GS03^T clusters with Flavobacterium paronense KNUS1T^T, with similarity of 96.8%. The phenotypic, phylogenetic, and chemotaxonomic characteristics indicate that strain GS03^T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium sangjuense sp. nov. is proposed. The type strain is GS03^T (= FBCC 502459^T = KCTC 62568^T = JCM 32764^T).

Flavobacterium silvisoli sp. nov., isolated from forest soil

During a study of the Kyonggi University soil bacterial diversity, an aerobic, non-motile, Gram-stain-negative, non-spore-forming, rod-shaped, yellow pigmented bacterium, designated strain RD-2-33^T was isolated. Strain RD-2-33^T grew optimally at 28-35 °C and pH 7.0-7.5; hydrolysed gelatin and DNA; and tolerated 1 % of NaCl. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain RD-2-33^T clustered with the genus Flavobacterium. The closest member was Flavobacterium dankookense ARSA-19^T (97.1 % sequence similarity) and Flavobacterium cheonhonense ARSA-15^T (96.7 %). Sole respiratory quinone was MK-6. The major polar lipids were phosphatidylethanolamine and an unidentified polar lipid. The major cellular fatty acids were iso-C_15 : 0, iso-C_17 : 0 3-OH, and iso-C_15 : 1 G. The DNA G+C content was 38.6 mol%. The average nucleotide identity (ANI) and in silico DNA-DNA hybridisation relatedness between strain RD-2-33^T and Flavobacterium dankookense DSM 25687^T were 75.2 and 19.3 %, respectively. Based on the polyphasic and phylogenetic data, strain RD-2-33^T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium silvisoli sp. nov. is proposed. The type strain is RD-2-33^T (=KEMB 9005-742^T=KACC 21178^T=NBRC 113789^T).

Amniculibacterium aquaticum gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from a stream

Strain KYPW7^T, isolated from the Funglin Stream in Taiwan, was characterized using a polyphasic taxonomy approach. Cells of strain KYPW7^T were Gram-stain-negative, aerobic, non-spore forming, non-motile rods and formed white colonies. Growth occurred at 15-30 °C (optimum 25 °C), at pH 6-8 (optimum pH 6.5) and with 0-1% NaCl (optimum 0%). Phylogenetic analyses based on 16S rRNA and coding sequences of 92 protein clusters showed that strain KYPW7^T represents a novel genus in the family Flavobacteriaceae. The 16S rRNA gene sequence of strain KYPW7^T was related to the species of the genera Chryseobacterium (91.8-96.0% sequence similarity), Bergeyella (95.1-95.8%), Cloacibacterium (94.5-95.7%), Daejeonia (95.6%) and Riemerella (94.0-95.0%). Strain KYPW7^T showed less than 72% average nucleotide identity and less than 24% digital DNA-DNA hybridization identity compared to the type strains of related genera within the family Flavobacteriaceae. The predominant fatty acids were iso-C_15:0 and iso-C_17:0 3-OH. The major isoprenoid quinone was MK-6 and the DNA G + C content was 36.8 mol%. The polar lipids had phosphatidylethanolamine, three uncharacterized aminophospholipids and an uncharacterized phospholipid. The polyamines contained homospermidine, putrescine and spermidine. On the basis of the genotypic and phenotypic data, strain KYPW7^T represents a novel species of a new genus in the family Flavobacteriaceae, for which the name Amniculibacterium aquaticum gen. nov., sp. nov. is proposed. The type strain is KYPW7^T (= BCRC 81123^T = LMG 30598^T = KCTC 62512^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.

Phylogenetic insights into the diversity of Chryseobacterium species

The genus Chryseobacterium was formally established in 1994 and contains 112 species with validly published names. Most of these species are yellow or orange coloured, and contain a flexirubin-type pigment. The genomes of 83 of these 112 species have been sequenced in view of their importance in clinical microbiology and potential applications in biotechnology. The National Center for Biotechnology Information taxonomy browser lists 1415 strains as members of the genus Chryseobacterium, of which the genomes of 94 strains have been sequenced. In this study, by comparing the 16S rDNA and the deduced proteome sequences, at least 20 of these strains have been proposed to represent novel species of the genus Chryseobacterium. Furthermore, a yellow-coloured bacterium isolated from dry soil in the USA (and identified as Flavobacterium sp. strain B-14859) has also been reconciled as a novel member of the genus Chryseobacterium based on the analysis of 16S rDNA sequences and the presence of flexirubin. Yet another bacterium (isolated from a water sample collected in the Western Ghats of India and identified as Chryseobacterium sp. strain WG4) was also found to represent a novel species. These proposals need to be validated using polyphasic taxonomic approaches.

Nonlabens xiamenensis sp. nov., isolated from coastal seawater

A Gram-stain negative, rod-shaped and non-flagellated bacterium, designated strain 1Q3^T, was isolated from coastal seawater in Xiamen Island, China, and subjected to taxonomic characterisation using a polyphasic approach. Strain 1Q3^T was found to be aerobic, non-gliding and to lack flexirubin-type pigments. Catalase activity was found to be negative and oxidase positive. The strain has the ability to degrade protein. The nearly complete 16S rRNA gene sequence of strain 1Q3^T shows high sequence similarities with Nonlabens aestuariivivens OITF-31^T (96.1%), Nonlabens halophilus CAU 1131^T and Nonlabens spongiae UST030701-156^T (95.7% and 95.5%, respectively). Phylogenetic analysis based on 16S rRNA gene sequences and phylogenomic analysis based on a 92 bacterial core gene set indicated that strain 1Q3^T should be affiliated to the genus Nonlabens, but forms a distinct monophyletic branch, which is separated from the other members within the genus Nonlabens. The predominant fatty acids (> 10%) were identified as iso-C_17:0 3-OH, iso-C_15:0 and anteiso-C_15:0. The predominant respiratory quinone was found to be MK-6. The polar lipids were identified as phosphatidylethanolamine, a phospholipid, an aminolipid and three unidentified polar lipids. The draft genome size of strain 1Q3^T is 3.7 Mb with genomic G + C content of 41.1 mol%. Based on these results, strain 1Q3^T is concluded to represent a novel species within the genus Nonlabens, for which the name Nonlabens xiamenensis sp. nov. is proposed with the type strain 1Q3^T (= MCCC 1A14023^T = KCTC 62889^T).

Large-Scale Analysis of Flavobacterium psychrophilum Multilocus Sequence Typing Genotypes Recovered from North American Salmonids Indicates that both Newly Identified and Recurrent Clonal Complexes Are Associated with Disease

Flavobacterium psychrophilum, the etiological agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome (RTFS), causes significant economic losses in salmonid aquaculture, particularly in rainbow trout (Oncorhynchus mykiss). Prior studies have used multilocus sequence typing (MLST) to examine genetic heterogeneity within F. psychrophilum At present, however, its population structure in North America is incompletely understood, as only 107 isolates have been genotyped. Herein, MLST was used to investigate the genetic diversity of an additional 314 North American F. psychrophilum isolates that were recovered from ten fish host species from 20 U.S. states and 1 Canadian province over nearly four decades. These isolates were placed into 66 sequence types (STs), 47 of which were novel, increasing the number of clonal complexes (CCs) in North America from 7 to 12. Newly identified CCs were diverse in terms of host association, distribution, and association with disease. The largest F. psychrophilum CC identified was CC-ST10, within which 10 novel genotypes were discovered, most of which came from O. mykiss experiencing BCWD. This discovery, among others, provides evidence for the hypothesis that ST10 (i.e., the founding ST of CC-ST10) originated in North America. Furthermore, ST275 (in CC-ST10) was recovered from wild/feral adult steelhead and marks the first recovery of CC-ST10 from wild/feral fish in North America. Analyses also revealed that at the allele level, the diversification of F. psychrophilum in North America is driven three times more frequently by recombination than random nucleic acid mutation, possibly indicating how new phenotypes emerge within this species.IMPORTANCE Flavobacterium psychrophilum is the causative agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome (RTFS), both of which cause substantial losses in farmed fish populations worldwide. To better prevent and control BCWD and RTFS outbreaks, we sought to characterize the genetic diversity of several hundred F. psychrophilum isolates that were recovered from diseased fish across North America. Results highlighted multiple F. psychrophilum genetic strains that appear to play an important role in disease events in North American aquaculture facilities and suggest that the practice of trading fish eggs has led to the continental and transcontinental spread of this bacterium. The knowledge generated herein will be invaluable toward guiding the development of future disease prevention techniques.

Tamlana carrageenivorans sp. nov., a carrageenan-degrading bacterium isolated from seawater

A Gram-stain-negative, aerobic, non-motile, rod-shaped, agarolytic and carrageenolytic bacterial strain, designated UJ94^T, was isolated from seawater of Uljin in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain UJ94^T shared sequence similarities of 98.4, 96.1 and 95.4 % with Tamlana agarivorans JW-26^T, Tamlana sedimentorum KMM 9545^T and Tamlana crocina HST1-43^T, respectively. Growth of strain UJ94^T was observed at 4-37 °C and pH 6.5-8.0 in the presence of 2-9 % (w/v) NaCl. The major fatty acids of strain UJ94^T were iso-C15 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and iso-C17 : 0 3-OH; MK-6 was the predominant menaquinone. Phosphatidylethanolamine, two unidentified aminolipids and five unidentified lipids were detected as major polar lipids. The whole circular genome comprised 4 116 543 bp and had a G+C content of 35.2 mol%. The ranges of average nucleotide identity and in silico DNA-DNA hybridization estimated by genome-to-genome distance were 90.6-74.2 % and 47.6-14.6 %, respectively, with the type strains of T. agarivorans and T. sedimentorum. The present polyphasic study, including phylogenetic, chemotaxonomic, biochemical and genomic data, suggested that strain UJ94^T represents a novel species of the genus Tamlana, for which the name Tamlana carrageenivorans sp. nov. is proposed. The type strain is UJ94^T (=KCTC 62451^T=NBRC 113234^T).

Phylogenetic relationship of Ornithobacterium rhinotracheale isolated from poultry and diverse avian hosts based on 16S rRNA and rpoB gene analyses

BACKGROUND

Ornithobacterium (O.) rhinotracheale is an emerging bacterial pathogen in poultry and not fully understood to date. Because of its importance particularly for the global turkey meat industry, reliable diagnostic and characterization methods are needed for early treatment and in future for better vaccine production. The host range of birds infected by O. rhinotracheale or carrying the bacterium in their respiratory tract has constantly increased raising important epidemiological and taxonomic questions for a better understanding of its diversity, ecology and transmission cycles. The purpose of this study was to introduce partial rpoB gene sequencing for O. rhinotracheale into routine diagnostics to differentiate strains isolated from poultry and more diverse avian hosts (i.e., birds of prey, corvids and pigeons) and to compare phylogenetic relationships with results from 16S rRNA gene analysis and multilocus sequence typing (MLST).

RESULTS

Partial 16S rRNA gene analysis revealed a high level of homogeneity among the 65 investigated O. rhinotracheale sequences with similarity values ranging from 98.6 to 100% between sequences from non-galliform and poultry species. The corresponding rpoB gene sequences were heterogeneous and ranged in their similarity values from 85.1 to 100%. The structure of the rpoB tree was in strong correlation with previous MLST results revealing three main clusters A (poultry and birds of prey), B (poultry, birds of prey and corvids) and C (pigeons), which were clearly separated from each other.

CONCLUSIONS

By using partial sequences from a single gene, the rpoB gene analysis is in good agreement with MLST results with a slight decrease in resolution to distinguish more similar strains. The present results provide strong evidence that traditional phenotypic and genetic methods may not properly represent the heterogeneous group of bacteria classified as O. rhinotracheale. From housekeeping gene analyses, it is very likely that the genus Ornithobacterium includes additional species and partial rpoB gene sequencing can be recommended as fast, cost-effective and readily available method to identify strains and differentiate between O. rhinotracheale and Ornithobacterium-like bacteria.

Flavobacterium hydrophilum sp. nov. and Flavobacterium cheongpyeongense sp. nov., isolated from freshwater

Two Gram-stain-negative, non-motile, yellow-pigmented bacterial strains, designated IMCC34758^T and IMCC34759^T, were isolated from freshwater. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains formed a distinct clade within the genus Flavobacterium and they shared 97.9 % sequence similarity. The average nucleotide identity (ANI) and digital DNA-DNA hybridization values (dDDH) between the two strains were 85.5 and 30.2 %, respectively, indicating that they are separate species. The two strains showed ≤98.5 % 16S rRNA gene sequence similarities, 80.6-81.3 % of ANI and 24.7-25.1 % of dDDH values to closely related species of the genus Flavobacterium, indicating that the two strains each represent novel Flavobacteriumspecies. The respiratory quinone detected in both strains was menaquinone-6 (MK-6). The major polar lipids of the two strains were phosphatidylethanolamine, an unidentified aminolipid, an unidentified aminophospholipid and an unidentified polar lipid. The DNA G+C contents of strains IMCC34758^T and IMCC34759^T were 34.0 and 34.1 mol%, respectively. The major fatty acids of the two strains were very similar to each other, comprising iso-C15 : 0, iso-C15 : 1 G, anteiso-C15 : 0 and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). Phenotypic characteristics including enzyme activities and carbon source utilization differentiated the two strains from other Flavobacteriumspecies. Based on these results, strains IMCC34758^T and IMCC34759^T were considered to represent novel species in the genus Flavobacterium, for which the names Flavobacterium hydrophilum (IMCC34758^T=KACC 19591^T=NBRC 113423^T) and Flavobacterium cheongpyeongense (IMCC34759^T=KACC 19592^T=NBRC 113424^T) are proposed, respectively.

Effect of Acidic Industrial Effluent Release on Microbial Diversity and Trace Metal Dynamics During Resuspension of Coastal Sediment

Both industrial effluent discharge and the resuspension of contaminated marine sediments are important sources of trace metals in seawater which potentially affect marine ecosystems. The aim of this study was to evaluate the impact of the industrial wastewaters having acidic pH (2–3) and containing trace metals on microbial diversity in the coastal ecosystem of the Gulf of Gabès (Tunisia, southern Mediterranean Sea) subjected to resuspension events of marine sediments. Four trace elements (As, Cd, U, and V) were monitored during 10-day sediment resuspension experiments. The highest enrichment in the seawater dissolved phase was observed for Cd followed by U, V, and As. Cd remobilization was improved by indigenous microbial community, while U release was mainly abiotic. Acidic effluent addition impacted both trace metal distribution and microbial diversity, particularly that of the abundant phylum Bacteroidetes. Members of the order Saprospirales were enriched from sediment in natural seawater (initial pH > 8), while the family Flavobacteriaceae was favored by acidified seawater (initial pH < 8). Some Flavobacteriaceae members were identified as dominant species in both initial sediment and experiments with acidic wastewater, in which their relative abundance increased with increasing dissolved Cd levels. It could be therefore possible to consider them as bioindicators of metal pollution and/or acidification in marine ecosystems.

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).

Seonamhaeicola acroporae sp. nov., a marine species of the family Flavobacteriaceae isolated from the hard coral Acropora formosa

A novel marine flavobacterial species, designated 3KA7-17^T, was isolated from the hard coral Acropora formosa D. collected in Japan. The strain was pale-orange pigmented, Gram-stain negative, strictly aerobic, coccus shaped, and non-motile. Preliminary analysis based on the 16S rRNA gene sequence revealed an affiliation with the family Flavobacteriaceae of the phylum Bacteroidetes, and it had the greatest sequence similarity (96.0%) to Seonamhaeicola algicola Gy8^T. The DNA G + C content was 34.3 mol%. MK-6 was the major menaquinone, with iso-C15:1 H and/or C13:0 3-OH (24.3%), iso-C15:0 (19.5%), iso-C15:0 3-OH (14.2%), and iso-C17:0 3-OH (15.9%) as the main (> 10%) cellular fatty acids. The major polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminolipids, and two unidentified lipids. Based on distinct phylogenetic and phenotypic evidence, the strain represents a novel species of the genus Seonamhaeicola, for which the name Seonamhaeicola acroporae sp. nov. is proposed and the type strain is 3KA7-17^T (= KCTC 62713^T = NBRC 113410^T).

Zunongwangia flava sp. nov., belonging to the family Flavobacteriaceae, isolated from Salicornia europaea

A yellow pigmented bacterium designated strain MBLN094^T within the family Flavobacteriaceae was isolated from a halophyte Salicornia europaea on the coast of the Yellow Sea. This strain was a Gram-stain negative, aerobic, non-spore forming, rod-shaped bacterium. Phylogenetic analysis of the 16S rRNA gene sequence of strain MBLN094^T was found to be related to the genus Zunongwangia, exhibiting 16S rRNA gene sequence similarity values of 97.0, 96.8, 96.4, and 96.3% to Zunongwangia mangrovi P2E16^T, Z. profunda SM-A87^T, Z. atlantica 22II14-10F7^T, and Z. endophytica CPA58^T, respectively. Strain MBLN094^T grew at 20‒37°C (optimum, 25‒30°C), at pH 6.0‒10.0 (optimum, 7.0‒8.0), and with 0.5‒15.0% (w/v) NaCl (optimum, 2.0‒5.0%). Menaquinone MK-6 was the sole respiratory quinone. The polar lipids were phosphatidylethanolamine, two unidentified aminolipids, and four unidentified lipids. Major fatty acids were iso-C_17:0 3-OH, summed feature 3 (C_16:1ω6c and/or C16:1 ω7c), and iso-C_15:0. The genomic DNA G + C content was 37.4 mol%. Based on these polyphasic taxonomic data, strain MBLN094^T is considered to represent a novel species of the genus Zunongwangia, for which the name Zunongwangia flava sp. nov. is proposed. The type strain is MBLN094^T (= KCTC 62279^T = JCM 32262^T).

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).

Flavobacterium effusum sp. nov., isolated from a freshwater river

A yellowish-orange-coloured bacterial strain, PSI-22^T, was isolated from a freshwater river in Taiwan. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain PSI-22^T belonged to the genus Flavobacterium and showed the highest identity with respect to Flavobacterium dispersum MVW-23^T (98.0 %), Flavobacterium tistrianum GB 56.1^T (97.1 %), Flavobacterium denitrificans ED5^T (97.1 %) and Flavobacterium daemonense THG-DJ7^T (97.0 %) and less than 97 % to other members of the genus. Cells of strain PSI-22^T were Gram-negative, strictly aerobic, motile by gliding and rod-shaped. Optimal growth occurred at 30 °C, pH 6 and in the presence of 0.5 % NaCl. Strain PSI-22^T contained iso-C15 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, one uncharacterized aminophospholipid, one uncharacterized aminophosphoglycolipid, two uncharacterized aminolipids, one uncharacterized phospholipid and one uncharacterized lipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6 and the DNA G+C content of the genomic DNA was 41.4 mol%. The DNA-DNA hybridization value for strain PSI-22^T with F. dispersum BCRC 80978^T, F. tistrianum KCTC 42679^T, F. denitrificans DSM 15936^T and F. daemonense KACC 17651^T was less than 30 %. On the basis of the phylogenetic inference and phenotypic data, strain PSI-22^T should be classified as a novel species, for which the name Flavobacterium effusum sp. nov. is proposed. The type strain is PSI-22^T (=BCRC 80973^T=LMG 29553^T=KCTC 52233^T).

Spongiibacterium fuscum sp. nov., a marine Flavobacteriaceae isolated from the hard coral Galaxea fascicularis

A novel marine bacterium, designated 04OKA-3-218^T, was isolated from the hard coral Galaxea fascicularis L. collected in Japan. The strain was dark-brown-pigmented, Gram-negative, strictly aerobic, curved-rod-shaped and non-motile. Phylogenetic analysis based on the 16S rRNA gene sequence showed the affiliation of the isolate with members of the family Flavobacteriaceae of the phylum Bacteroidetes, with the highest sequence similarity (95.2%) to Spongiibacterium pacificum SW169^T. The DNA G+C content was 42.9 mol%; MK-6 was the major menaquinone; with iso-C17:0 3-OH (28.8%), iso-C15:0 (26.8%) and iso-C15:1 H and/or C13:0 3-OH (21.2%) as the main (>  10%) cellular fatty acids. The major polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminolipids, two unidentified phosphoaminolipids and three unidentified lipids. On the basis of distinct phylogenetic and phenotypic evidences, the strain represents a novel species of the genus Spongiibacterium, for which the name Spongiibacterium fuscum sp. nov. is proposed. The type strain of S. fuscum sp. nov. is 04OKA-3-218^T (= KCTC 62504^T = NBRC 113248^T).

Thalassorhabdus aurantiaca gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from seawater in South Korea

A novel Gram-negative, orange pigmented, strictly aerobic bacterium, designated strain IP9^T, was isolated from seawater at the sea shore of Incheon Eulwang-ri beach, South Korea. Cells of strain IP9^T were observed to be straight or slightly curved rods and colonies to be round and convex. Strain IP9^T was found to be catalase and oxidase positive, and non-motile. Growth was observed in the temperature range of 10-37 °C (optimum at 30 °C), pH range of 6-10 (optimum at pH 7-8) and salt concentration range of 0-7% (w/v) NaCl (optimum at 0-1%). On the basis of 16S rRNA gene sequence similarity and phylogenetic analysis, strain IP9^T was found to be related to the members of the family Flavobacteriaceae, being closely related to Hwangdonia seohaensis KCTC 32177^T (95.3% sequence similarity). The DNA G + C content of the novel strain was determined to be 39.1 mol%. The major polar lipids were found to be phosphatidylethanolamine, three unidentified aminoglycolipids and two unidentified glycolipids. The major fatty acids (> 10%) were identified as iso-C_15:0 and iso-C_17:0 3-OH. The predominant quinone was found to be menaquinone 6 (MK-6). Based on the biochemical, phylogenetic and physiological data, we conclude that strain IP9^T (= KCTC 52523^T = JCM 31732^T) represents the type species of a novel genus of the family Flavobacteriaceae for which the name Thalassorhabdus aurantiaca gen. nov., sp. nov. is proposed.

Description of Lacinutrix salivirga sp. nov., a marine member of the family Flavobacteriaceae isolated from seawater

A novel marine bacterium, designated KMU-57^T, was isolated from seawater collected from the Republic of Korea, and it was characterized using polyphasic taxonomic methods. Strain KMU-57^T was Gram-stain-negative, strictly aerobic, rod-shaped, motile and dark-yellow-pigmented. Comparative analysis based on the 16S rRNA gene sequence showed the affiliation of the isolate with members of the family Flavobacteriaceae of the phylum Bacteroidetes, and it had the greatest sequence similarity (97.6%) to Lacinutrix jangbogonensis PAMC 27137^T. The DNA-DNA relatedness value between strain KMU-57^T and L. jangbogonensis PAMC 27137^T was 37.8 ± 2.2%. The DNA G + C content of strain KMU-57^T was 29.9 mol%; MK-6 was the major menaquinone with; iso-C15:1 G (18.6%) and C16:1 ω7c and/or C16:1 ω6c (15.8%) as the major (> 10%) cellular fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, three unidentified aminolipids, and five unidentified lipids. The strain represents a novel species of the genus Lacinutrix for which the name Lacinutrix salivirga sp. nov. is proposed. The type strain of L. salivirga sp. nov. is KMU-57^T (= KCTC 52878^T = NBRC 112845^T).

Flavobacterium ureilyticum sp. nov., a novel urea hydrolysing bacterium isolated from stream bank soil

A novel bacterium designated S-42^T was isolated from stream bank soil. Cells were found to be aerobic, Gram staining-negative, oxidase-positive, catalase-negative, non-motile, non-spore-forming, rod-shaped, and yellow-pigmented. The strain can grow at 15-35 °C, pH 6.0-10.0, and at 0.5% (w/v) NaCl concentration. Urea was hydrolysed. Flexirubin-type pigments were absent. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain S-42^T formed a lineage within the family Flavobacteriaceae of the phylum Bacteroidetes that is distinct from various species of the genus Flavobacterium, including Flavobacterium maotaiense T9^T (97.6% sequence similarity), Flavobacterium hibernum ATCC 51468^T (97.4%), and Flavobacterium granuli Kw05^T (97.1%). The 16S rRNA gene sequences identity between strain S-42^T and other members of the genus Flavobacterium were < 97.0%. Strain S-42^T contains MK-6 as sole respiratory quinone. The major polar lipids were identified as phosphatidylethanolamine and an unidentified aminolipid. The major cellular fatty acids were identified as iso-C_15:0, summed feature 3 (C_16:1ω7c and/or C_{16: 1}ω6c), C_16:0, anteiso-C_15:0, iso-C_17:0 3-OH, iso-C_15:0 3-OH, and iso-C_15:1 G. The DNA G + C content of the strain was 35.8 mol%. The polyphasic characterization indicated that strain S-42^T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium ureilyticum sp. nov. is proposed. The type strain is S-42^T (= KEMB 9005-537^T = KACC 19115^T = NBRC 112683^T).

Gramella antarctica sp. nov., isolated from marine surface sediment

A Gram-stain-negative, aerobic, yellow-coloured, motile by gliding, rod-shaped bacterial strain, designated R17H11^T, was isolated from surface sediment collected from the Ross Sea, Antarctica. Growth optimally occurred at 25-30 °C, at pH 7.0-7.5 and in the presence of 3 % NaCl (w/v). Phylogenetic trees based on 16S rRNA gene sequences indicated that strain R17H11^T clustered together with Gramella flava JLT2011^T and fell within the genus Gramella. Strain R17H11^T shared the highest 16S rRNA gene similarities (96.1 and 96.0 %) with the type strains of Gramella forsetii and G. flava, and 92.6-95.5 % similarities with those of other known Gramella species. Strain R17H11^T contained menaquinone-6 as the only isoprenoid quinone. The major fatty acids (>5 %) were summed feature 3 (17.5 %, comprising C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 (14.0 %), summed feature 9 (11.8 %, comprising 10-methyl C16 : 0 and/or iso-C17 : 1ω9c), iso-C17 : 0 3-OH (11.8 %), iso-C16 : 0 (7.4 %), C17 : 1ω6c (6.9 %) and anteiso-C15 : 0 (5.1 %). The major polar lipids were phosphatidylethanolamine, four unidentified lipids, an unidentified aminolipid, an unidentified aminophospholipid and an unidentified glycolipid. The DNA G+C content of strain R17H11^T was 38.6 mol%. On the basis of the phylogenetic, physiological and chemotaxonomic characteristics, strain R17H11^T represents a novel species in the genus Gramella, for which the name Gramellaantarctica sp. nov. is proposed. The type strain of the novel species is R17H11^T (=GDMCC 1.1208^T=KCTC 52925^T).

Antarcticibacterium flavum gen. nov., sp. nov., isolated from marine sediment

A Gram-stain-negative, strictly aerobic, yellow-pigmented, non-gliding, oval to rod-shaped bacterial strain, designated JB01H24^T, belonging to the family Flavobacteriaceae, was isolated from marine surface sediment collected from the Ross Sea, Antarctica. Strain JB01H24^T grew at 4-40 °C (optimum 25-30 °C), pH 7.0-9.0 (optimum 7.5-8.0), and in the presence of 0-8 % NaCl (optimum 3 %, w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JB01H24^T formed an independent linkage within the family Flavobacteriaceae and was closely related with the genus Gillisia. Strain JB01H24^T exhibited 16S rRNA gene sequence similarities of 95.3-91.5 % and 94.9-94.0 % to the type strains of the genera Gillisia and Salinimicrobium, respectively. The major fatty acids (>5 %) were iso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), anteiso-C15 : 0, iso-C15 : 1 G and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0). The major polar lipids were phosphatidylethanolamine, seven unidentified lipids, two unidentified aminolipids and an unidentified aminophospholipid. Strain JB01H24^T contained menaquinone-6 as the only ubiquinone. The DNA G+C content was 42.4 mol%. On the basis of phylogenetic, physiological and chemotaxonomic properties, strain JB01H24^T is considered to represent a novel species of a new genus within the family Flavobacteriaceae, for which the name Antarcticibacterium flavum gen. nov., sp. nov. is proposed. The type strain of Antarcticibacterium flavum is JB01H24^T (=GDMCC 1.1229^T=KCTC 52984^T).

Aquaticitalea lipolytica gen. nov., sp. nov., isolated from Antarctic seawater

A Gram-stain-negative, rod-shaped bacterium, designated Ar-125^T, was isolated from Antarctic seawater. It produced carotenoid-like pigments and did not produce Bchl a. Ar-125^T was positive for hydrolysis of DNA, aesculin, gelatin, starch, Tween 40 and Tween 60. The sole respiratory quinone was MK-6. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid, one unidentified glycolipid and two unidentified lipids. The principal fatty acids were branched-chain fatty acids, including iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C16 : 0, iso-C17 : 0 3-OH, iso-C16 : 0 3-OH and iso-C15 : 0 3-OH, as well as C15 : 0. The genomic DNA G+C content was 31.8 mol%. On the basis of 16S rRNA gene sequence analysis, Ar-125^T is closely related to the species of the genera Bizionia(with 16S rRNA gene pairwise sequence similarity of 93.7-96.5 %), Formosa(94.3-95.8 %), Gaetbulibacter(94.2-95.7 %), Geojedonia(95.5 %), Gelidibacter (93.3-95.4 %), Meridianimaribacter(95.3 %) and Psychroserpens (94.8-95.3 %), of the family Flavobacteriaceae. Phylogenetic analysis indicated that it represented an independent lineage and that the closest relatives were members of the genus Gelidibacter. Differential phenotypic properties and chemotaxonomic differences, together with phylogenetic distinctiveness, revealed that Ar-125^T could be differentiated from members of closely related genera. Therefore, it is proposed that Ar-125^T represents a novel species in a new genus, for which the name Aquaticitalea lipolytica gen. nov., sp. nov. (type strain Ar-125^T =CGMCC 1.15295^T =JCM 30876^T) is proposed.

Citreibacter salsisoli gen. nov., sp. nov., a bacterium isolated from marine soil

A Gram-stain-negative, strictly aerobic, yellow-colored, rod-shaped, chemoheterotrophic bacterium, designated SNA426^T, was isolated from marine soil in the Republic of Korea. Preliminary analysis based on the 16S rRNA gene sequence revealed that the novel marine isolate was affiliated with the family Flavobacteriaceae of phylum Bacteroidetes and that it shared the highest (96.2%) sequence similarity with Gillisia mitskevichiae KMM 6034^T. The strain could be differentiated phenotypically from related members of the family Flavobacteriaceae. The major fatty acids of strain SNA426^T were iso-C15:0, C16:1 ω7c and/or C16:1 ω6c and iso-C17:0 3-OH. The DNA G+C content of the strain was 39.6 mol% and the major respiratory quinone was menaquinone 6 (MK-6). Strain SNA426^T had phosphatidylethanolamine, phosphatidylcholine, three unidentified aminolipids and nine unidentified lipids as polar lipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus in the family Flavobacteriaceae, for which the name Citreibacter gen. nov. is proposed. The type species is Citreibacter salsisoli sp. nov., with the type strain SNA426^T (= KCCM 90269^T = CGMCC 1.16129^T).

Flavobacterium amniphilum sp. nov., isolated from a stream

Strain KYPY10^T, isolated from a water sample taken from the Funglin Stream in Taiwan, was characterized using a polyphasic taxonomic approach. Cells of strain KYPY10^T were Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped surrounded by a thick capsule, and formed light-yellow colonies. Growth occurred at 20-30 °C (optimum, 25 °C), at pH 6-7 (optimum, pH 6) and with 0-0.2 % NaCl (optimum, 0 % w/v). Phylogenetic analyses, based on 16S rRNA gene sequences, showed that strain KYPY10^T belonged to the genus Flavobacterium and was most closely related to Flavobacterium brevivitae TTM-43^T (98.4 % sequence similarity) and Flavobacterium vireti THG-SM1^T (98.0 %). Strain KYPY10^T contained iso-C15 : 0, iso-C15 : 1 G, summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0), iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and iso-C16 : 0 as the predominant fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids, five uncharacterized phospholipids and one uncharacterized lipid. The major polyamines were homospermidine and putrescine. The genomic DNA G+C content of strain KYPY10^T was 41.0 mol%. The DNA-DNA relatedness of strain KYPY10^T with respect to recognized species of the genus Flavobacterium was less than 70 %. On the basis of the phylogenetic inference and phenotypic data, strain KYPY10^T was recognized as a representative of a novel species within the genus Flavobacterium. The name Flavobacterium amniphilum sp. nov. is proposed, with strain KYPY10^T (=BCRC 81006^T=LMG 29727^T=KCTC 52443^T) as the type strain.

Arenibacter antarcticus sp. nov., isolated from marine sediment

A strictly aerobic, Gram-stain-negative, pale-golden, rod-shaped bacterium, designated as R18H21^T, was isolated from marine sediment collected from the Ross Sea, Antarctica. Strain R18H21^T grew at 4-40 °C (optimum 25 °C), at pH 6.3-9.2 (optimum 7.5-8.5) and in 0.5-6 % (w/v) NaCl (optimum 2 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain R18H21^T belonged to the genus Arenibacter, with the highest similarity to two type strains, Arenibacter latericius KMM 426^T (96.6 %) and Arenibacter certesii KMM 3941^T (96.6 %), and lower similarities (95.2-95.9 %) to five other members of the genus Arenibacter. The major fatty acids were iso-C17 : 0 3-OH, Summed Feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0, iso-C15 : 1 G. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and an unidentified phospholipid. The respiratory quinone of strain R18H21^T was menaquinone-6. The DNA G+C content was 40.0 mol%. Based on phylogenetic, physiological and chemotaxonomic features, strain R18H21^T has been classified as a novel species in the genus Arenibacter, for which the name Arenibacterantarcticus sp. nov. is proposed. The type strain of the novel species is R18H21^T (=GDMCC 1.1159^T=KCTC 52924^T).

Flavimarina flava sp. nov., isolated from Salicornia herbacea

A Gram-stain-negative, motile-by-gliding, aerobic, non-spore-forming, rod-shaped and yellow-pigmented bacterium was isolated from Salicornia herbacea in the Yellow Sea and designated as strain MBLN091^T. It belonged to the family Flavobacteriaceae. The 16S rRNA gene sequence of this isolated strain was similar to that of Flavimarina pacifica IDSW-73^T with 94.8 % similarity, and with 92.3-92.8 % similarities to those of other closely related species of the genus Leeuwenhoekiella. The similarities of the RNA polymerase subunit B gene between this strain and F. pacifica KCTC 32466^T and Leeuwenhoekiella marinoflava DSM 3653^T were 80.5 and 80.2 %, respectively. Growth of strain MBLN091^T was observed in the presence of 0.5‒15.0 % (w/v) NaCl at 4‒35 °C and pH 6.0-8.0, with optimal growth in the presence of 2.5‒5.0 % (w/v) NaCl at 20‒25 °C and pH 7.0. This isolate was able to hydrolyse gelatin. The only respiratory quinone was MK-6. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and two unidentified lipids. Major fatty acids of the isolate were iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C17 : 0 3-OH and iso-C15 : 1 G. The genomic DNA G+C content was 39.6 mol%. The physiological features were closely related to F. pacifica. Therefore, strain MBLN091^T is considered to represent a novel species within the genus Flavimarina, for which the name Flavimarina flava sp. nov. is proposed. The type strain is MBLN091^T (=KCTC 52527^T=JCM 31731^T).

Flavobacterium dispersum sp. nov., isolated from a freshwater spring

A novel bacterial strain MVW-23^T was isolated from a freshwater spring in Taiwan. The strain was Gram-staining-negative, strictly aerobic, motile by gliding, rod-shaped and formed translucent yellow colonies. Optimal growth occurred at 20-30 °C, pH 7.0, and in the presence of 0.5-1 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain MVW-23^T belonged to the genus Flavobacterium and showed the highest levels of sequence similarity with respect to Flavobacterium denitrificans ED5^T (97.3 %), Flavobacterium kyungheense THG-107^T (97.2 %) and Flavobacterium defluvii EMB117^T (97.0 %). Strain MVW-23^T contained iso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, three uncharacterized aminophospholipids and one uncharacterized phospholipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 39.9 mol%. The DNA-DNA hybridization value for strain MVW-23^T with F. denitrificans DSM 15936^T, F. kyungheense LMG 26575^T and F. defluvii DSM 17963^T was less than 35 %. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain MVW-23^T should be classified as a novel species of the genus Flavobacterium, for which the name Flavobacterium dispersum sp. nov. is presented. The type strain is MVW-23^T (=BCRC 80978^T=LMG 29558^T=KCTC 52234^T).

Maribacter pelagius sp. nov., isolated from seawater

A Gram-stain-negative, gliding, non-endospore-forming and slightly halophilic bacterial strain, CBA3204^T, was isolated from seawater and characterized by polyphasic taxonomic analysis. Phylogenetic analysis based on 16S rRNA sequences revealed that strain CBA3204^T formed a distinct lineage within the family Flavobacteriaceae. The 16S rRNA sequences of strain CBA3204^T had a sequence similarity level of 96.96 % to Maribacter arcticus KOPRI 20941^T as the nearest phylogenetic neighbour. The strain grew optimally at 25-30 °C and in the presence of 2-4 % (w/v) NaCl. The dominant menaquinone was MK-6 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The DNA G+C content was 35.1 mol%. There were some differences in phenotypic properties among strain CBA3204^T and other Maribacter species. On the basis of polyphasic analysis containing phenotypic, phylogenetic and chemotaxonomic data, strain CBA3204^T (=KACC 17671^T=JCM 19533^T) is proposed as a novel species Maribacter pelagius sp. nov.

Tomato root microbiota and Phytophthora parasitica-associated disease

BACKGROUND

Interactions between pathogenic oomycetes and microbiota residing on the surface of the host plant root are unknown, despite being critical to inoculum constitution. The nature of these interactions was explored for the polyphagous and telluric species Phytophthora parasitica.

RESULTS

Composition of the rhizospheric microbiota of Solanum lycopersicum was characterized using deep re-sequencing of 16S rRNA gene to analyze tomato roots either free of or partly covered with P. parasitica biofilm. Colonization of the host root surface by the oomycete was associated with a shift in microbial community involving a Bacteroidetes/Proteobacteria transition and Flavobacteriaceae as the most abundant family. Identification of members of the P. parasitica-associated microbiota interfering with biology and oomycete infection was carried out by screening for bacteria able to (i) grow on a P. parasitica extract-based medium (ii), exhibit in vitro probiotic or antibiotic activity towards the oomycete (iii), have an impact on the oomycete infection cycle in a tripartite interaction S. lycopersicum-P. parasitica-bacteria. One Pseudomonas phylotype was found to exacerbate disease symptoms in tomato plants. The lack of significant gene expression response of P. parasitica effectors to Pseudomonas suggested that the increase in plant susceptibility was not associated with an increase in virulence. Our results reveal that Pseudomonas spp. establishes commensal interactions with the oomycete. Bacteria preferentially colonize the surface of the biofilm rather than the roots, so that they can infect plant cells without any apparent infection of P. parasitica.

CONCLUSIONS

The presence of the pathogenic oomycete P. parasitica in the tomato rhizosphere leads to a shift in the rhizospheric microbiota composition. It contributes to the habitat extension of Pseudomonas species mediated through a physical association between the oomycete and the bacteria.

High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk

Chryseobacterium bovis DSM 19482^T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The C. bovis genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.

Aquimarina seongsanensis sp. nov., isolated from sea water

An orange, rod-shaped, gliding bacterium, designated strain CBA3208^T, was isolated from sea water of Jeju Island, Republic of Korea. Cells were observed to be Gram-stain negative, strictly aerobic, catalase positive and oxidase negative and to hydrolyse starch, gelatin, and Tweens 40 and 80. The major fatty acids were identified as iso-C_15:0, iso-C_17:0 3-OH, and iso-C_15:1 G. The only isoprenoid quinone was found to be menaquinone-6 (MK-6) and the major polar lipids were identified as phosphatidylethanolamine, two aminolipids and four unidentified polar lipids. The DNA G+C content of strain CBA3208^T was determined to be 34.9 mol%. Strain CBA3208^T is considered to represent a novel species of the genus Aquimarina, for which the name Aquimarina seongsanensis sp. nov. is proposed based on this polyphasic taxonomic analysis. The type strain is CBA3208^T (=KACC 17667^T =JCM 19529^T).

Cell Membrane Fatty Acid Composition of Chryseobacterium frigidisoli PB4T, Isolated from Antarctic Glacier Forefield Soils, in Response to Changing Temperature and pH Conditions

Microorganisms in Antarctic glacier forefields are directly exposed to the hostile environment of their habitat characterized by extremely low temperatures and changing geochemical conditions. To survive under those stress conditions microorganisms adapt, among others, their cell membrane fatty acid inventory. However, only little is known about the adaptation potential of microorganisms from Antarctic soil environments. In this study, we examined the adaptation of the cell membrane polar lipid fatty acid inventory of Chryseobacterium frigidisoli PB4T in response to changing temperature (0°C to 20°C) and pH (5.5 to 8.5) regimes, because this new strain isolated from an Antarctic glacier forefield showed specific adaptation mechanisms during its detailed physiological characterization. Flavobacteriaceae including Chryseobacterium species occur frequently in extreme habitats such as ice-free oases in Antarctica. C. frigidisoli shows a complex restructuring of membrane derived fatty acids in response to different stress levels. Thus, from 20°C to 10°C a change from less iso-C15:0 to more iso-C17:1ω7 is observed. Below 10°C temperature adaptation is regulated by a constant increase of anteiso-FAs and decrease of iso-FAs. An anteiso- and bis-unsaturated fatty acid, anteiso-heptadeca-9,13-dienoic acid, shows a continuous increase with decreasing cultivation temperatures underlining the particular importance of this fatty acid for temperature adaptation in C. frigidisoli. Concerning adaptation to changing pH conditions, most of the dominant fatty acids reveal constant relative proportions around neutral pH (pH 6-8). Strong variations are mainly observed at the pH extremes (pH 5.5 and 8.5). At high pH short chain saturated iso- and anteiso-FAs increase while longer chain unsaturated iso- and anteiso-FAs decrease. At low pH the opposite trend is observed. The study shows a complex interplay of different membrane components and provides, therefore, deep insights into adaptation strategies of microorganisms from extreme habitats to changing environmental conditions.

Description of Gramella forsetii sp. nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of Gramella gaetbulicola Cho et al. 2011

Strain KT0803^T was isolated from coastal eutrophic surface waters of Helgoland Roads near the island of Helgoland, North Sea, Germany. The taxonomic position of the strain, previously known as 'Gramella forsetii' KT0803, was investigated by using a polyphasic approach. The strain was Gram-stain-negative, chemo-organotrophic, heterotrophic, strictly aerobic, oxidase- and catalase-positive, rod-shaped, motile by gliding and had orange-yellow carotenoid pigments, but was negative for flexirubin-type pigments. It grew optimally at 22-25 °C, at pH 7.5 and at a salinity between 2-3 %. Strain KT0803^T hydrolysed the polysaccharides laminarin, alginate, pachyman and starch. The respiratory quinone was MK-6. Polar lipids comprised phosphatidylethanolamine, six unidentified lipids and two unidentified aminolipids. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and iso-C17 : 1ω7c, with smaller amounts of iso-C15 : 0 2-OH, C15 : 0, anteiso-C15 : 0 and C17 : 1ω6c. The G+C content of the genomic DNA was 36.6 mol%. The 16S rRNA gene sequence identities were 98.6 % with Gramella echinicola DSM 19838^T, 98.3 % with Gramella gaetbulicola DSM 23082^T, 98.1 % with Gramella aestuariivivens BG-MY13^T and Gramella aquimixticola HJM-19^T, 98.0 % with Gramella lutea YJ019^T, 97.9 % with Gramella portivictoriae DSM 23547^T and 96.9 % with Gramella marina KMM 6048^T. The DNA-DNA relatedness values were <35 % between strain KT0803^T and type strains with >98.2 % 16S rRNA gene sequence identity. Based on the chemotaxonomic, phenotypic and genomic characteristics, strain KT0803^T has been assigned to the genus Gramella, as Gramella forsetii sp. nov. The type strain is KT0803^T (=DSM 17595^T=CGMCC 1.15422^T). An emended description of Gramella gaetbulicolaCho et al. 2011 is also proposed.

Complete genome sequence of Lutibacter profundi LP1T isolated from an Arctic deep-sea hydrothermal vent system

Lutibacter profundi LP1T within the family Flavobacteriaceae was isolated from a biofilm growing on the surface of a black smoker chimney at the Loki's Castle vent field, located on the Arctic Mid-Ocean Ridge. The complete genome of L. profundi LP1T is the first genome to be published within the genus Lutibacter. L. profundi LP1T consists of a single 2,966,978 bp circular chromosome with a GC content of 29.8%. The genome comprises 2,537 protein-coding genes, 40 tRNA species and 2 rRNA operons. The microaerophilic, organotrophic isolate contains genes for all central carbohydrate metabolic pathways. However, genes for the oxidative branch of the pentose-phosphate-pathway, the glyoxylate shunt of the tricarboxylic acid cycle and the ATP citrate lyase for reverse TCA are not present. L. profundi LP1T utilizes starch, sucrose and diverse proteinous carbon sources. In accordance, the genome harbours 130 proteases and 104 carbohydrate-active enzymes, indicating a specialization in degrading organic matter. Among a small arsenal of 24 glycosyl hydrolases, which offer the possibility to hydrolyse diverse poly- and oligosaccharides, a starch utilization cluster was identified. Furthermore, a variety of enzymes may be secreted via T9SS and contribute to the hydrolytic variety of the microorganism. Genes for gliding motility are present, which may enable the bacteria to move within the biofilm. A substantial number of genes encoding for extracellular polysaccharide synthesis pathways, curli fibres and attachment to surfaces could mediate adhesion in the biofilm and may contribute to the biofilm formation. In addition to aerobic respiration, the complete denitrification pathway and genes for sulphide oxidation e.g. sulphide:quinone reductase are present in the genome. sulphide:quinone reductase and denitrification may serve as detoxification systems allowing L. profundi LP1T to thrive in a sulphide and nitrate enriched environment. The information gained from the genome gives a greater insight in the functional role of L. profundi LP1T in the biofilm and its adaption strategy in an extreme environment.

"Vaginella massiliensis" gen. nov., sp. nov., a new genus cultivated from human female genital tract

We relate the main characteristics of "Vaginella massiliensis" strain Marseille P2517 (= DSM 102346 = CSUR P2517), a new member of the Flavobacteriaceae family. The strain Marseille P2517 was cultivated from a vaginal swab from a healthy 22-year-old woman.

Taxonogenomics and description of Vaginella massiliensis gen. nov., sp. nov., strain Marseille P2517T, a new bacterial genus isolated from the human vagina

An obligate aerobic, Gram-negative, nonmotile and nonsporulating rod designated Marseille P2517 was isolated from the vaginal flora. We describe its features, annotate the genome and compare it to the closest species. The 16S rRNA analysis shows 93.03% sequence similarity with Weeksella virosa, the phylogenetically closest species. Its genome is 2 434 475 bp long and presents 38.16% G+C. On the basis of these data, it can be considered as a new genus in the Flavobacteriaceae family, for which we proposed the name Vaginella massiliensis gen. nov., sp. nov. The type strain is Marseille P2517T.

Aurantibacter crassamenti gen. nov., sp. nov., a bacterium isolated from marine sediment

A Gram-stain-negative, strictly aerobic, orange-colored, rod-shaped, chemoheterotrophic bacterium, designated HG732^T, was isolated from marine sediment in Japan. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the novel marine strain was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it shared the highest (94.1 %) sequence similarity with Kriegella aquimaris KMM 3665^T. The strain could be differentiated phenotypically from related members of the family Flavobacteriaceae. Major fatty acids of strain HG732^T were iso-C15:1 G, iso-C15:0 and iso-C17:0 3-OH. The polar lipid profile consisted of phosphatidylglycerol, three unidentidied aminolipids and two unidentified lipids. The DNA G+C content of the strain was determined to be 35.2 mol%, and the major respiratory quinone was identified as menaquinone 6 (MK-6). From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus in the family Flavobacteriaceae, for which the name Aurantibacter crassamenti gen. nov., sp. nov. is proposed. The type strain of A. crassamenti gen. nov., sp. nov. is HG732^T (= KCTC 52207^T = NBRC 112211^T).

High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T)

Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5^T (DSM 17707^T) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5^T is part of the GenomicEncyclopedia ofBacteria andArchaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5^T has 117 genes encoding peptidases but a small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo and serine peptidases were found most frequently. Among CAZymes, eight glycoside hydrolase families, nine glycosyl transferase families, two carbohydrate binding module families and four carbohydrate esterase families were identified. Suprisingly, polysaccharides utilization loci (PULs) were not found in strain GH29-5^T. Based on the coherent physiological and genomic characteristics we suggest that F. suncheonense GH29-5^T feeds rather on proteins than saccharides and lipids.

Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005

Strains of the genus Gramella (family Flavobacteriacae, phylum Bacteroidetes) were isolated from marine habitats such as tidal flat sediments, coastal surface seawater and sea urchins. Flavobacteriaceae have been shown to be involved in the decomposition of plant and algal polysaccharides. However, the potential to decompose polysaccharides may differ tremendously even between species of the same genus. Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)) have genomes of similar lengths, similar numbers of protein coding genes and RNA genes. Both genomes encode for a greater number of peptidases compared to 'G. forsetii'. In contrast to the genome of 'G. forsetii', both genomes comprised a smaller set of CAZymes. Seven polysaccharide utilization loci were identified in the genomes of DSM 19838(T) and DSM 23547(T). Both Gramella strains hydrolyzed starch, galactomannan, arabinoxylan and hydroxyethyl-cellulose, but not pectin, chitosan and cellulose (Avicel). Galactan and xylan were hydrolyzed by strain DSM 19838(T), whereas strain DSM 23547(T) hydrolyzed pachyman and carboxy-methyl cellulose. Conclusively, both Gramella type strains exhibit characteristic physiological, morphological and genomic differences that might be linked to their habitat. Furthermore, the identified enzymes mediating polysaccharide decomposition, are of biotechnological interest.

Feifantangia zhejiangensis gen. nov., sp. nov., a marine bacterium isolated from seawater of the East China Sea

A marine bacterium, NMD7(T), was isolated from seawater of the East China Sea. The cells were found to be aerobic, Gram-stain negative, non-motile rods. Growth of strain NMD7(T) could be observed in the medium without Na(+). Flexirubin-type pigments were observed to be produced. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NMD7(T) is an authentic member of the Cytophaga-Flavobacterium-Bacteroides phylum, forming a monophyletic clade as retrieved in neighbor-joining, maximum-likelihood and maximum-parsimony phylogenetic trees, and is closely related to Formosa spongicola A2(T) (96.0 %). The predominant respiratory quinone was determined to be MK-6. Major cellular fatty acids were identified as iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH. The main polar lipids were found to consist of phosphatidylethanolamine, one aminophospholipid, three aminolipids and five unidentified lipids. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, it is proposed that strain NMD7(T) be classified as representing a new genus, Feifantangia gen. nov. and a new species, Feifantangia zhejiangensis sp. nov. The type strain is NMD7(T) (=KCTC 42445T =MCCC 1K00458T).

Jejuia marina nov., isolated from gravel adjacent to Geommeolle beach on Udo Island, South Korea

A bacterial strain, JH03(T), was isolated from gravel adjacent to Geommeolle beach on Udo Island, South Korea. The cells were Gram-stain-negative, aerobic, non-motile and rod shaped. The ranges of temperature, pH and NaCl concentration for growth of the bacterium were 10-45 °C, pH 6.0-9.5 and 0.5-5.0 % (w/v), respectively. The major fatty acids of the bacterium were iso-C(15:0) (15.4 %), iso-C(15:1) G (14.1 %), iso-C(16:0) 3-OH (14.1 %), iso-C(17:0) 3-OH (11.5 %) and anteiso-C(15:0) (11.3 %). The major isoprenoid quinone was MK-6. The polar lipids included phosphatidylethanolamine, two unidentified amino lipids and three unidentified lipids. The DNA G+C content was 34.2 mol%. The phylogenetic analysis of the 16S rRNA gene sequences showed that strain JH03(T) was most closely related to Jejuia pallidilutea EM39(T) (96.5 % sequence similarity). Based on the polyphasic analysis, strain JH03(T) is a novel species of the genus Jejuia, for which the name Jejuia marina sp. nov. is proposed. The type strain is JH03(T) (= KCTC 42342(T) = JCM 30601(T)).

High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes

Flavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013 is one of about 100 species in the genus Flavobacterium (family Flavobacteriacae, phylum Bacteroidetes) with a validly published name, and has been isolated from the spring of a hard water rivulet in Northern Germany. Including all type strains of the genus Myroides and Flavobacterium into the 16S rRNA gene sequence phylogeny revealed a clustering of members of the genus Myroides as a monophyletic group within the genus Flavobacterium. Furthermore, F. rivuli WB 3.3-2^T and its next relatives seem more closely related to the genus Myroides than to the type species of the genus Flavobacterium, F. aquatile. The 4,489,248 bp long genome with its 3,391 protein-coding and 65 RNA genes is part of the GenomicEncyclopedia ofBacteria andArchaea project. The genome of F. rivuli has almost as many genes encoding carbohydrate active enzymes (151 CAZymes) as genes encoding peptidases (177). Peptidases comprised mostly metallo (M) and serine (S) peptidases. Among CAZymes, 30 glycoside hydrolase families, 10 glycosyl transferase families, 7 carbohydrate binding module families and 7 carbohydrate esterase families were identified. Furthermore, we found four polysaccharide utilization loci (PUL) and one large CAZy rich gene cluster that might enable strain WB 3.3-2^T to decompose plant and algae derived polysaccharides. Based on these results we propose F. rivuli as an interesting candidate for further physiological studies and the role of Bacteroidetes in the decomposition of complex polymers in the environment.

Obligate insect endosymbionts exhibit increased ortholog length variation and loss of large accessory proteins concurrent with genome shrinkage

Extreme genome reduction has been observed in obligate intracellular insect mutualists and is an assumed consequence of fixed, long-term host isolation. Rapid accumulation of mutations and pseudogenization of genes no longer vital for an intracellular lifestyle, followed by deletion of many genes, are factors that lead to genome reduction. Size reductions in individual genes due to small-scale deletions have also been implicated in contributing to overall genome shrinkage. Conserved protein functional domains are expected to exhibit low tolerance for mutations and therefore remain relatively unchanged throughout protein length reduction while nondomain regions, presumably under less selective pressures, would shorten. This hypothesis was tested using orthologous protein sets from the Flavobacteriaceae (phylum: Bacteroidetes) and Enterobacteriaceae (subphylum: Gammaproteobacteria) families, each of which includes some of the smallest known genomes. Upon examination of protein, functional domain, and nondomain region lengths, we found that proteins were not uniformly shrinking with genome reduction, but instead increased length variability and variability was observed in both the functional domain and nondomain regions. Additionally, as complete gene loss also contributes to overall genome shrinkage, we found that the largest proteins in the proteomes of nonhost-restricted bacteroidetial and gammaproteobacterial species often were inferred to be involved in secondary metabolic processes, extracellular sensing, or of unknown function. These proteins were absent in the proteomes of obligate insect endosymbionts. Therefore, loss of genes encoding large proteins not required for host-restricted lifestyles in obligate endosymbiont proteomes likely contributes to extreme genome reduction to a greater degree than gene shrinkage.