Ubiquity and Diversity of Cold Adapted Denitrifying Bacteria Isolated From Diverse Antarctic Ecosystems

Nitrogen cycle has been poorly investigated in Antarctic ecosystems. In particular, how extreme conditions of low temperature, dryness, and high radiation select the microorganisms involved in the cycle is not yet understood. Denitrification is an important step in the nitrogen cycle in which nitrate is reduced stepwise to the gases NO, N2O, and N2. Denitrification is carried out by a wide group of microorganisms spread in the phylogenetic tree. The aim of this work was to isolate and characterize denitrifying bacteria present in different cold environments from Antarctica. Bacterial isolates were obtained from lake, meltwater, sea, glacier ice, ornithogenic soil, and penguin feces samples from King George Island, Fildes peninsula in the Antarctic. Samples were taken during the deicing season in five sampling campaigns. From all the samples we were able to isolate denitrifying strains. A total of 199 bacterial isolates with the capacity to grow in anaerobic mineral media reducing nitrate at 4°C were obtained. The characterization of the isolates by 16S rRNA gene sequence analysis showed a high predominance of the genus Pseudomonas, followed by Janthinobacterium, Flavobacterium, Psychrobacter, and Yersinia. Other minor genera detected were Cryobacterium, Iodobacter, Kaistella, and Carnobacterium. The capacity to denitrify was not previously described for most of the bacteria related to our isolates and in many of them denitrifying genes were not present suggesting the presence of new genes in this extreme environment. Our work demonstrates the ubiquity of denitrification in the Maritime Antarctica and gives important information linking denitrification at cold temperature with taxa in an unequivocal way.

Flavobacterium solisilvae sp. nov. and Flavobacterium silvaticum sp. nov., isolated from forest soil

Two Gram-stain-negative, yellow-pigmented and strictly aerobic bacteria, designated strains SE-s27^T and SE-s28^T, were isolated from forest soil. Both strains were non-motile rods that were catalase-positive and oxidase-negative and grew optimally at 25-30 °C, pH 8.0 and with 0 % (w/v) NaCl. Strain SE-s28^T produced flexirubin-type pigments, but strain SE-s27^T did not produce them. Both strains contained menaquinone-6 as the sole respiratory quinone and phosphatidylethanolamine as a major polar lipid. As the major cellular fatty acids (>10 %), SE-s27^T contained iso-C_15 : 1 and iso-C_15 : 1G, whereas SE-s28^T contained iso-C_15 : 0 and summed feature 3 comprising C_16 : 1ω7c and/or C_16 : 1ω6c and/or iso-C_15 : 0 2-OH. The DNA G+C contents of strains SE-s27^T and SE-s28^T were 33.1 and 44.3 mol%, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that SE-s27^T and SE-s28^T formed respective distinct phylogenetic lineages within the genus Flavobacterium. Strains SE-s27^T and SE-s28^T were most closely related to Flavobacterium macrobrachii an-8^T and Flavobacterium piscinae ICH-30^T with 98.0 and 94.5 % 16S rRNA gene sequence similarities, respectively. In conclusion, strains SE-s27^T and SE-s28^T represent novel species of the genus Flavobacterium, for which the names Flavobacterium solisilvae sp. nov. and Flavobacterium silvaticum sp. nov. are proposed. The type strains of F. solisilvae and F. silvaticum are SE-s27^T (=KACC 18802^T=JCM 31544^T) and SE-s28^T (=KACC 18803^T=JCM 31545^T), respectively.

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.

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

The Gram-stain-negative, rod-shaped, facultative anaerobic, motile bacterial strain, designated TP390^T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain TP390^T was related to the genus Flavobacterium and had highest 16S rRNA gene sequence identity with the type strain of Flavobacterium jejuense EC11^T (97.8 %). Sequence similarities to all other type strains of current species of the genus Flavobacterium were below 97 %. The predominant cellular fatty acids were iso-C_15 : 0 and iso-C_15 : 1G. The quinone system for strain TP390^T comprised predominantly menaquinone MK-6 and the polar lipid profile contained phosphatidylethanolamine, four unknown aminolipids, one glycolipid and six unknown polar lipids. The genomic DNA G+C content of strain TP390^T was 31.2 mol%. In addition, the maximum values of in silico DNA-DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain TP390^T with F. jejuense KCTC 42149^T were 22.60 and 80.01% respectively. Combined data from phenotypic, phylogenetic, isDDH and ANI data demonstrated that the strain TP390^T is representative of a novel species of the genus Flavobacterium, for which we propose the name Flavobacterium profundi sp. nov. (type strain TP390^T=KACC 18559^T=CGMCC 1.15398^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).

Flavobacterium parvum sp. nov., isolated from soil polluted by sewer water

A novel Gram-stain-negative, motile by means of gliding, and short rod-shaped bacterium, designated HS916T, was isolated from soil polluted by sewer water in Cheonan-si, South Korea. Growth occurred at 10-35°C (optimum 30°C), pH 6.0-8.0 (optimum pH 7.0), and 0-1% sodium chloride (NaCl, w/v). Based on similarities of 16S rRNA gene sequences, strain HS916^T was closely related to members of the genus Flavobacterium, exhibiting the highest sequence similarities with Flavobacterium glycines Gm-149^T (96.4%), followed by F. granuli Kw05^T (96.3%), F. fluminis 3R17^T (96.3%), F. aquicola TMd3a3^T (96.2%), and F. nitratireducens N1^T (96.2%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HS916T was placed in a monophyletic cluster with F. nitratireducens N1^T and F. fluminis 3R17^T. The predominant fatty acids (> 5% of the total) of strain HS916^T were iso-C_15:0, anteiso-C_15:0, iso-C_15:0 3-OH, C_17:1ω6с, C_16:0 3-OH, iso-C_17:0 3-OH, and summed feature 3 (C_16:1ω7с and/or C_16:1ω6с). The major polar lipids of the strain comprised phosphatidylethanolamine, unidentified aminolipids, and five unidentified lipids. The predominant respiratory quinone and the major polyamine were menaquinone-6 (MK-6) and symhomospermidine, respectively. The DNA G + C content of strain HS916^T was 34.9 mol%. Based on polyphasic analyses, strain HS916^T represents a novel species belonging to the genus Flavobacterium, for which the name Flavobacterium parvum sp. nov. is proposed. The type strain is HS916T (= KACC 19448^T = JCM 32368^T).