Arundinibacter roseus gen. nov., sp. nov., a new member of the family Cytophagaceae

Arcicella gelida sp. nov. and Arcicella lustrica sp. nov., isolated from streams in China and re-examining the taxonomic status of all the genera within the families Spirosomataceae and Cytophagaceae

Three Gram-stain-negative, aerobic, rod-shaped, non-motile strains (DC2WT, DC25WT, and LKC2W) were isolated from streams in China. Comparisons based on the 16S rRNA gene sequences showed that these three strains share 16S rRNA gene sequence similarity values over 97.0 % with the species of genus Arcicella. There was confusion due to the fact that all species of genera Flectobacillus, Aquirufa, and Sandaracinomonas show 16S rRNA gene sequence similarity of over 90.0 % to the above three strains, but the genus Flectobacillus belongs to the family Spirosomataceae and the genera Aquirufa and Sandaracinomonas belong to the family Cytophagaceae. Observing the phylogenetic trees, strains DC2WT, DC25WT, and LKC2W cluster closely with the species of genus Arcicella, but some species within the families Spirosomataceae and Cytophagaceae are not monophyletic. The phylogenomic tree also showed a confused phylogenetic relationships among these non-monophyletic species. Combining the phylogenetic relationships and average nucleotide identity values, the current taxonomic status of all the genera within the families Spirosomataceae and Cytophagaceae were re-examined. The genera 'Chryseosolibacter', 'Dawidia', and Chryseotalea should belong to the new family Chryseotaleaceae fam. nov., the genera Arcicella, Flectobacillus, Pseudarcicella, Aquirufa, and Sandaracinomonas should belong to the new family Flectobacillaceae fam. nov., the genera Fluviimonas, Taeseokella, Arcticibacterium, Emticicia, Jiulongibacter, Marinilongibacter, Lacihabitans, and Leadbetterella should belong to the new family Leadbetterellaceae fam. nov., the genus Litoribacter should be reassigned to the family Cyclobacteriaceae, and the genera Arundinibacter and Tellurirhabdus should be reassigned to the family Spirosomataceae. Strains DC2WT and DC25WT are reported to represent two novel species of the genus Arcicella, for which the names Arcicella gelida sp. nov. (type strain DC2WT=GDMCC 1.3209T=KCTC 92559T) and Arcicella lustrica sp. nov. (type strain DC25WT=GDMCC 1.3210T=KCTC 92557T) are proposed.

Description of Xanthocytophaga agilis sp. nov. and Xanthocytophaga flavus sp. nov. of the new genus Xanthocytophaga gen. nov and the proposal of Rhodocytophagaceae fam. nov. within the order Cytophagales

Four Gram-staining-negative, aerobic, yellow-pigmented and rod-shaped bacteria, named strains BD1B2-1T, NT2B1T, YF14B1 and DM2B3-1, were isolated from four rhizosphere soil samples of banana in China. Comparison of the 16S rRNA gene sequences showed that all these strains were most closely related to an invalidly published species, 'Rhodocytophaga rosea' 172606-1, with similarities ranging from 87.7 to 88.0%. According to the phylogenomic analysis, the four strains were clustered in an independent lineage and closely related to the genus Rhodocytophaga. The genomic sizes of these strains were approximately 9.49-9.77 Mbp with the DNA G + C contents of 38.8-39.0 mol%. They all contained C16:1 ω5c, iso-C15:0 and iso-C17:0 3-OH as the major fatty acids and menaquinone 7 as the only respiratory quinone. They all had phosphatidylethanolamine as the major polar lipids. Based on phenotypic and phylogenomic characteristics, the four strains should represent two novel species within a novel genus, for which the names Xanthocytophaga agilis gen. nov., sp. nov. (BD1B2-1T = GDMCC 1.2890T = JCM 35374T) and Xanthocytophaga flavus sp. nov. (NT2B1T = GDMCC 1.2889T = JCM 35375T) are proposed; the former is assigned as the type species of the novel genus Xanthocytophaga gen. nov. In addition, based on the phenotypic and phylogenomic data, we proposed to reclassify the existing genus Rhodocytophaga in the family Cytophagaceae into a novel family Rhodocytophagaceae fam. nov. The novel family consists of the type genus Rhodocytophaga and the novel genus Xanthocytophaga.

Flavobacterium hungaricum sp. nov. a novel soil inhabitant, cellulolytic bacterium isolated from plough field

A Gram-negative bacterial strain, named Kb82, was isolated from agricultural soil and a polyphasic approach was used for characterisation and to determine its taxonomic position. Based on 16S rRNA gene sequence analysis, the highest similarity was found with Flavobacterium artemisiae SYP-B1015 (98.2%). The highest ANI (83.3%) and dDDH (26.5%) values were found with Flavobacterium ginsenosidimutans THG 01 and Flavobacterium fluviale HYN0086^T, respectively. The isolate is aerobic with rod-shaped cells, positive for catalase and negative for oxidase tests. The DNA G+C content is 34.7 mol%. The only isoprenoid quinone is menaquinone 6 (MK-6). The major fatty acids are iso-C_15:0, summed feature 3 (C_16:1ω7c/C_16:1ω6c) and iso-C_17:0 3OH. The major polar lipid is phosphatidylethanolamine. On the bases of phenotypic characteristics and analysis of 16S rRNA gene sequences, it is concluded that strain Kb82^T represents a novel species in the Flavobacterium genus, for which the name Flavobacterium hungaricum sp. nov. is proposed. The type strain of the species is strain Kb82^T (= LMG 31576^T = NCAIM B.02635^T).

Sphingobacterium hungaricum sp. nov. a novel species on the borderline of the genus Sphingobacterium

A Gram-reaction-negative bacterial strain, designated Kb22^T, was isolated from agricultural soil and characterized using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, the strain shows highest similarity (94.39 %) to Sphingobacterium nematocida M-SX103^T. The highest average nucleotide identity value (71.83 %) was found with Sphingobacterium composti T5-12^T, and the highest amino acid identity value (66.65 %) was found with Sphingobacterium olei HAL-9^T. Cells are aerobic, non-motile rods. The isolate was found to be positive for catalase and oxidase tests. The assembled genome of strain Kb22^T has a total length of 4,06 Mb, the DNA G+C content is 38.1 mol%. The only isoprenoid quinone is menaquinone 7 (MK-7). The major fatty acids are iso-C_15:0 (28.4%), summed feature 3 (C_16:1 ω7c and/or iso-C_15:0 2-OH) (25.7 %) and iso-C_17:0 3-OH (19.7 %). Based on phenotypic characteristics and phylogenetic results, it is concluded that strain Kb22^T is a member of the genus Sphingobacterium and represents a novel species for which the name Sphingobacterium hungaricum sp. nov. is proposed. The type strain of the species is strain Kb22^T (=LMG 31574^T=NCAIM B.02638^T).

Microbial communities of soda lakes and pans in the Carpathian Basin: a review

In this review, I would like to summarize the current knowledge on the microbiology of soda lakes and pans of the Carpathian Basin. First, the characteristic physical and chemical features of these sites are described. Most of the microbiological information presented deals with prokaryotes and algae, but protists and viruses are also mentioned. Planktonic bacterial communities are dominated by members of the phyla Actinobacteria, Bacteroidetes and Proteobacteria; small-sized trebouxiophycean green algae and Synechococcus/Cyanobium picocyanobacteria are the most important components of phytoplankton. Based on the current knowledge, it seems that mainly temperature, salinity, turbidity and grazing pressure regulate community composition and the abundance of individual microbial groups, but the external nutrient load from birds also has a significant impact on the ecological processes.

Sphingobacterium pedocola sp. nov. a novel halotolerant bacterium isolated from agricultural soil

A Gram-reaction-negative halotolerant bacterial strain, designated Ka21^T, was isolated from agricultural soil and characterised using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, highest similarity was found with Sphingobacterium alkalisoli Y3L14^T (96.72%). Cells were observed to be aerobic, non-motile rods. The isolate was found to be able to grow between 0 and 10% of NaCl concentration. The assembled genome of strain Ka21^T has a total length of 5.2 Mb with a G + C content of 41.0 mol%. According to the genome analysis, Ka21^T encodes several glycoside hydrolases that may play a role in the degradation of accumulated plant biomass in the soil. Based on phenotypic characteristics and phylogenetic analysis, it is concluded that strain Ka21^T represents a novel species in the Sphingobacterium genus for which the name Sphingobacterium pedocola sp. nov. is proposed. The type strain of the species is strain Ka21^T (= LMG 31575^T = NCAIM B.02636^T).

Cellvibrio polysaccharolyticus sp. nov., a cellulolytic bacterium isolated from agricultural soil

A novel Gram-reaction-negative bacterial strain, designated Ka43^T, was isolated from agricultural soil and characterised using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, the strain shows highest similarity (97.1 %) to Cellvibrio diazotrophicus E50^T. Cells of strain Ka43^T are aerobic, motile, short rods. The major fatty acids are summed feature 3 (C_16 : 1 ω7c and/or iso-C_15 : 0 2-OH), C_18 : 1  ω7c and C_16 : 0. The only isoprenoid quinone is Q-8. The polar lipid profile includes phosphatidylethanolamine, phosphatidylglycerol, four phospholipids, two lipids and an aminolipid. The assembled genome of strain Ka43^T has a total length of 4.2 Mb and the DNA G+C content is 51.6 mol%. Based on phenotypic data, including chemotaxonomic characteristics and analysis of the 16S rRNA gene sequences, it was concluded that strain Ka43^T represents a novel species in the genus Cellvibrio, for which the name Cellvibrio polysaccharolyticus sp. nov. is proposed. The type strain of the species is strain Ka43^T (=LMG 31577^T=NCAIM B.02637^T).

Prokaryotic community composition in a great shallow soda lake covered by large reed stands (Neusiedler See/Lake Fertő) as revealed by cultivation- and DNA-based analyses

Little is known about the detailed community composition of heterotrophic bacterioplankton in macrophyte-dominated littoral systems, where a considerable amount of dissolved organic carbon originates from aquatic macrophytes instead of phytoplankton. The aim of the present study was to reveal the effect of macrophytes on the microbial community and to elucidate their role in a macrophyte-dominated shallow soda lake, which can be characterised by a mosaic of open waters and reed marsh. Therefore, 16S rRNA gene amplicon sequencing, the most probable number method, cultivation of bacterial strains, EcoPlate and cultivation-based substrate utilisation techniques were applied. Differences in the structures of microbial communities were detected between the water and the sediment samples and between vegetated and unvegetated water samples. Planktonic bacterial communities of an inner pond and a reed-covered area showed significant similarities to each other. Woesearchaeia was the dominant archaeal taxon in the water samples, while Bathyarchaeia, 'Marine Benthic Group D' and 'DHVEG-1' were abundant in the sediment samples. The most probable number of heterotrophic bacteria was lower in the open water than in the reed-associated areas. The vast majority (83%) of the isolated bacterial strains from the water samples of the reed-covered area were able to grow on a medium containing reed extract as the sole source of carbon.

Whole genome sequence analysis of Cupriavidus campinensis S14E4C, a heavy metal resistant bacterium

Cupriavidus sp. are model organisms for heavy metal(loid) resistance and aromatic compound's degradation studies and these characteristics make them a perfect candidate for biotechnological purposes. Bacterial strain S14E4C (identified as Cupriavidus campinensis) was isolated from a playground by enrichment method in a 0.25 mM containing medium. The analysis revealed that this bacterium is able to tolerate high concentrations of heavy metal(loid)s: Cd up to 19.5 mM, Pb to 9 mM, Hg to 5.5 mM and As to 2 mM in heavy metal(loid) salt containing nutrient medium. The whole genome data and analysis of the type strain of C. campinensis CCUG:44526T have not been available so far, thus here we present the genome sequencing results of strain S14E4C of the same species. Analysis was carried out to identify possible mechanisms for the heavy metal resistance and to map the genetic data of C. campinensis. The annotation pipelines revealed that the total genome of strain S14E4C is 6,375,175 bp length with a GC content of 66.3% and contains 2 plasmids with 295,460 bp (GC content 59.9%) and 50,483 bp (GC content 63%). In total 4460 coding sequences were assigned to known functions and 1508 to hypothetical proteins. Analysis proved that strain S14E4C is having gene clusters such as czc, mer, cus, chr, ars to encode various heavy metal resistance mechanisms that play an important role to survive in extreme environments.

Phragmitibacter flavus gen. nov., sp. nov. a new member of the family Verrucomicrobiaceae

The Gram-stain-negative, aerobic, non-motile, oxidase- and catalase-positive, rod-shaped yellow-coloured bacterial strain MG-N-17T was isolated from a water sample of Lake Fertő/Neusiedler See (Hungary). Results of phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain forms a distinct linage within the family Verrucomicrobiaceae of the phylum Verrucomicrobia , and its closest relatives are Verrucomicrobium spinosum DSM 4136T (94.38 %) and Roseimicrobium gellanilyticum DC2a-G7T (91.55 %). The novel bacterial strain prefers a weak alkaline environment and grows optimally between 22–28 °C in the absence of NaCl. The major isoprenoid quinones are MK-10, MK-11, MK-12 and MK-9. The major cellular fatty acids are anteiso-C15 : 0, C16 : 0, C16 : 1ω5c and iso-C14 : 0. The polar lipid profile contains phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and four unidentified glycolipids. The assembled draft genome of strain MG-N-17T had 44 contigs with an N50 value 348255 nt, 56.5× genome coverage, total length of 5 910 933 bp and G+C content of 56.9 mol%. Strain MG-N-17T (=DSM 106674T=NCAIM B.02643T) is proposed as the type strain of a new genus and species in the family Verrucomicrobiaceae , for which the name Phragmitibacter flavus gen. nov., sp. nov. is proposed.