Proposal to reclassify Aquiflexum aquatile into a novel genus as Cognataquiflexum aquatile gen. nov., comb. nov., and description of Cognataquiflexum nitidum sp. nov. and Cognataquiflexum rubidum sp. nov., isolated from freshwater lakes on the Tibetan Plateau

Thousands of lakes harbouring different characteristics (pH, salinity, temperature) are located on the Tibetan Plateau, and the mining of microbial resources inhabited in these lakes has great value. Two Gram-stain-negative, aerobic, rod-shaped, non-motile strains (LQ15W^T and AIY15W^T) were isolated from freshwater lakes on the Tibetan Plateau. Comparisons based on the 16S rRNA gene sequences showed that both strains LQ15W^T and AIY15W^T share 16S rRNA gene sequence similarities 98.4 % with Aquiflexum aquatile Z0201^T, but only about 95.0 % with Aquiflexum balticum DSM 16537^T. The 16S rRNA gene sequence similarity between strains LQ15W^T and AIY15W^T was 98.9 %. The phylogenetic tree reconstructed based on 16S rRNA gene sequences also showed that strains LQ15W^T and AIY15W^T take A. aquatile Z0201^T as their closest neighbour and these three strains form a tight cluster. In the phylogenomic tree, the genus Aquiflexum was splited into two clusters by Mariniradius saccharolyticus. Strains LQ15W^T, AIY15W^T and A. aquatile Z0201^T still formed a close cluster, and A. balticum DSM 16537^T and Aquiflexum lacus CUG 91378^T formed another cluster. The calculated OrthoANIu, average amino acid identity and digital DNA-DNA hybridization values among strains LQ15W^T, AIY15W^T, A. aquatile Z0201^T, A. balticum DSM 16537^T and A. lacus CUG 91378^T were less than 91.0, 92.9 and 42.1 %, respectively. The major respiratory quinones of both strains LQ15W^T and AIY15W^T were MK-7 (32 %) and MK-8 (68 %), and their major fatty acids were iso-C_15 : 0, C_18 : 1  ω9c, summed feature 3 and summed feature 9. The predominant polar lipids of both strains were phosphatidylethanolamine, unidentified aminophospholipids, unidentified phospholipids and lipids. Strain AIY15W^T also contained phosphatidylglycerol and unidentified glycolipid. Considering the distinct phylogenetic relationships and chemotaxonomic characteristics between strains A. aquatile Z0201^T and A. balticum DSM 16537^T, it is proposed to reclassify A. aquatile into a novel genus Cognataquiflexum gen. nov. as Cognataquiflexum aquatile comb. nov., and strains LQ15W^T and AIY15W^T should represent two independent novel species of the genus Cognataquiflexum, for which the names Cognataquiflexum nitidum sp. nov. (type strain: LQ15W^T=CICC 24711^T=JCM 34222^T) and Cognataquiflexum rubidum sp. nov. (type strain: AIY15W^T=CICC 24708^T=JCM 34612^T) are proposed.

Penaeicolahalotolerans gen. nov., sp. nov., a novel bacterium of the family Cyclobacteriaceae isolated from a shrimp pond

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterium (designated as LMIT005^T) was isolated from shrimp ponds in Shantou, China. The new isolate was characterized taxonomically using a polyphasic approach. Based on 16S rRNA gene sequence analysis, strain LMIT005^T was found to be affiliated with the family Cyclobacteriaceae of the order Cytophagales while appearing as a distinct lineage. The 16S rRNA gene sequence similarity between strain LMIT005^T and Algoriphagus yeomjeoni KCTC 12309^T, the closest type strain in the family, was 91.3 %. Strain LMIT005^T grew optimally at 25 °C, pH 7 and in the presence of 2.0 % (w/v) NaCl. The DNA G+C content (data from genome sequence) was 40.5 mol%. Compared with reference strain A. yeomjeoni KCTC 12309^T, the average nucleotide identity (ANI) of LMIT005^T was 70 %. The sole respiratory quinone of LMIT005^T was menaquinone (MK-7), and the major fatty acids were summed feature 3 (C_16 : 1 ω6c / C_16 : 1 ω7c). The polar lipids of strain LMIT005^T were mainly composed of phosphatidylethanolamine, phosphatidylcholine, two unidentified amino lipids, two unidentified lipids, one unidentified glycolipid and one unidentified phospholipid. The draft genome of strain LMIT005^T comprised 3 089 781 bp (3.09 Mb) nucleotides and 2773 genes. Antimicrobial resistant-related genes (blal, mexA, and mexb) were annotated in the genome of strain LMIT005^T, which indicated that it might be able to resist β-lactam antibiotics. This was further verified by antimicrobial resistant test. Given its distinct genomic, morphological, and physiological differences from previously described type strains, strain LMIT005^T is proposed as a representative of a novel genus of the family Cyclobacteriaceae, with the name Penaeicola halotolerans gen. nov., sp. nov. The type strain is LMIT005^T (=KCTC 82616^T=CICC 25047^T).

Pararhodonellum marinum gen. nov., sp. nov., isolated from deep-sea sediment

A Gram-stain-negative, non-motile bacterial strain, designated SW124^T, was isolated from a deep-sea sediment sample collected from the Indian Ocean. SW124^T was aerobic and catalase-positive. The strain grew at 4-40 °C (optimum, 30 °C), at pH 5.0-8.6 (optimum, pH 7.0) and in the presence of 0.5-9.5 % (w/v) NaCl (optimum, 3.0%). The results of comparative analyses of the 16S rRNA gene sequence indicated that SW124^T was grouped in the vicinity of the genus Rhodonellum in the family Cyclobacteriaceae. The quinone system contained menaquinone MK-7. The predominant cellular fatty acids were iso-C_15 : 0, iso-C_17 : 0 3-OH and summed feature 3 (comprising C_16 : 1ω7c and/or C_16 : 1ω6c). SW124^T contained phosphatidylethanolamine (PE) as the major polar lipid. The genomic DNA G+C content of SW124^T was 41.7 mol%. On the basis of its phenotypic characteristics and phylogenetic data, we propose that strain SW124^T (=CGMCC 1.16171^T=KCTC 82235^T) represents a novel species of a novel genus, with the name Pararhodonellum marinum gen. nov., sp. nov.

Lunatibacter salilacus gen. nov., sp. nov., a member of the family Cyclobacteriaceae, isolated from a saline and alkaline lake sediment

A non-motile, Gram-staining negative, catalase- and oxidase-positive, crescent-rod shaped bacterium, designated strain CUG 91308^T, was isolated from a sediment sample of Qinghai Lake, Qinghai Province, China. Colonies on OSM agar were round, smooth, flat and pinkish-orange in colour. Strain CUG 91308^T could grow at 15-37 °C, pH 6-12 and in the presence of up to 7.0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CUG 91308^T belonged to the family Cyclobacteriaceae and formed a clade with the genus Lunatimonas in the phylogenetic tree, but separated from any species of the known genera within the family. The genomic DNA G+C content is about 42.1 %. The predominant fatty acids (>10 %) were iso-C_15 : 0 (21.1 %), summed feature 3 (C_16 : 1  ω7c / C_16 : 1  ω6c / iso-C_15 : 0 2OH) (14.3 %), iso-C_17 : 0 3OH (12.3 %) and summed feature 9 (iso-C_17 : 1  ω9c / C_16 : 0 10-methyl) (10.6 %). The polar lipids of strain CUG 91308^T were phosphatidylethanolamine (PE) and four unidentified polar lipids. Strain CUG 91308^T contained MK-7 as the major respiratory quinone. On the basis of phenotypic, genotypic and phylogenetic data, strain CUG 91308^T represents a novel species of a novel genus in the family Cyclobacteriaceae, for which the name Lunatibacter salilacus gen. nov., sp. nov. is proposed. The type strain of the proposed new isolate is CUG 91308^T (=KCTC 62636^T=CGMCC 1.13593^T).

Pleomorphovibrio marinus gen. nov., sp. nov., isolated from deep-sea sediment

A Gram-stain-negative, non-motile bacterial strain, designated SW125^T, was isolated from a deep-sea vsediment sample collected from the Indian Ocean. Cells were aerobic, catalase-positive and oxidase-positive. The strain grew at 4-42 °C (optimum, 30 °C), at pH 5.0-10.0 (optimum, pH 7.0-7.6) and in the presence of 0.5-9.0 % (w/v) NaCl (optimum, 2.0-3.0 %). Comparative analyses of the 16S rRNA gene sequence showed that strain SW125^T was grouped in the vicinity of the genus Negadavirga with the highest sequence similarity of 91.6 % to the type strain of Negadavirga shengliensis. The quinone system contained menaquinone MK-7 as the predominant component. The predominant cellular fatty acids of strain SW125^T were iso-C_15 : 0, iso-C_17 : 0 3-OH and summed feature 3 (comprising C_16 : 1ω7c and/or C_16 : 1ω6c). Strain SW125^T contained phosphatidylethanolamine as the major polar lipid. The genomic DNA G+C content of strain SW125^T was 43.2 mol%. On the basis of its phenotypic characteristics and phylogenetic data, strain SW125^T represents a novel species of a new genus, for which the name Pleomorphovibrio marinus gen. nov., sp. nov. is proposed. The type strain is SW125^T (=CGMCC 1.16172^T=DSM 107180^T=KCTC 62653^T).

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Negadavirga shengliensis gen. nov., sp. nov., a novel member of the family Cyclobacteriaceae isolated from oil-contaminated saline soil

Four novel Gram-stain-negative, rod-shaped, and non-motile bacterial strains, SLG210-21(T), SLG210-4, SLG210-5 and SLG210-14, were isolated from oil-contaminated saline soil in Shengli Oilfield, China. Growth were observed at 25-42 °C (optimum 37 °C), in the presence of 0-10 % (w/v) NaCl (optimum 0-1 %) and at pH 4.0-10.0 (optimum pH 7.6-8.6). All the strains were positive for catalase and α, β-galactosidase activities and nitrogen reduction, and negative for oxidase activity, glucose fermentation and hydrolysis of agar, starch, gelatin, Tween 40, 60 and 80. The DNA G+C contents of the four strains were 41.3-43.0 mol% and the predominant respiratory quinones were all menaquinone-7. The major fatty acids were iso-C15:0, anteiso-C15:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:1 ω5c and summed feature 9 (iso-C17:1 ω9c and/or 10-methyl C16:0), while the polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, glycolipid, two unidentified phospholipids and two unidentified amino lipids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the four strains clustered together to form a stable branch in the family Cyclobacteriaceae, and were most closely related to the genera Cyclobacterium and Echinicola with the 16S rRNA gene sequence similarities being 88.6-90.3 and 89.6-91.4 %, respectively. DNA-DNA hybridization between SLG210-21(T) and the other three strains showed the relatedness of 93.8 ± 4.5, 96.2 ± 4.2 and 82.3 ± 4.8 %, respectively. Based on the polyphasic analysis, a novel species in a new genus, Negadavirga Shengliensis gen. nov., sp. nov., is proposed with SLG210-21(T) (=LMG 27737(T) = CGMCC1.12768(T)) [corrected] as the type strain.

Mariniradius saccharolyticus gen. nov., sp. nov., a member of the family Cyclobacteriaceae isolated from marine aquaculture pond water, and emended descriptions of the genus Aquiflexum and Aquiflexum balticum

A novel marine, Gram-stain-negative, oxidase- and catalase- positive, rod-shaped bacterium, designated strain AK6T, was isolated from marine aquaculture pond water collected in Andhra Pradesh, India. The fatty acids were dominated by iso-C15 : 0, iso-C17 : 1ω9c, iso-C15 : 1 G, iso-C17 : 0 3-OH and anteiso-C15 : 0. Strain AK6T contained MK-7 as the sole respiratory quinone and phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid and seven unidentified lipids as polar lipids. The DNA G+C content of strain AK6T was 45.6 mol%. Phylogenetic analysis showed that strain AK6T formed a distinct branch within the family Cyclobacteriaceae and clustered with Aquiflexum balticum DSM 16537T and other members of the family Cyclobacteriaceae . 16S rRNA gene sequence analysis confirmed that Aquiflexum balticum DSM 16537T was the nearest neighbour, with pairwise sequence similarity of 90.1 %, while sequence similarity with the other members of the family was <88.5 %. Based on differentiating phenotypic characteristics and phylogenetic inference, strain AK6T is proposed as a representative of a new genus and species of the family Cyclobacteriaceae , as Mariniradius saccharolyticus gen. nov., sp. nov. The type strain of Mariniradius saccharolyticus is AK6T ( = MTCC 11279T = JCM 17389T). Emended descriptions of the genus Aquiflexum and Aquiflexum balticum are also proposed.

Mongoliicoccus roseus gen. nov., sp. nov., an alkaliphilic bacterium isolated from a haloalkaline lake

Two pink, non-motile, aerobic, alkaliphilic, halotolerant, Gram-negative cocci, designated MIM28T and MIM29, were isolated from the surface water of a haloalkaline lake on the Mongolia Plateau. The isolates grew optimally at 30–33 °C, at pH 8–9 and with 3–4 % (w/v) NaCl. The isolates were chemoheterotrophic and could assimilate carbohydrates, organic acids and amino acids. The major respiratory quinone was menaquinone MK-7. The major polar lipids were phosphatidylcholine and phosphatidylethanolamine. The predominant cellular fatty acids were iso-C15 : 0 (13.8–17.5 %), anteiso-C15 : 0 (10.5–11.2 %), iso-C16 : 0 (9.9–13.0 %), C16 : 0 (4.3–4.6 %), iso-C17 : 0 (3.8–5.3 %), anteiso-C17 : 0 (3.7–7.1 %), C17 : 1ω6c (4.6–6.4 %), iso-C17 : 0 3-OH (4.6–5.8 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 4.0–6.4 %) and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl; 10.4–12.5 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates were most closely related to Litoribacter ruber YIM CH208T (93.6 % 16S rRNA gene sequence similarity), the genus Echinicola (90.4–92 %) and other members of the family Cyclobacteriaceae (87.8–90 %). The DNA G+C contents of strains MIM28T and MIM29 were 62.8 and 62.2 mol%. On the basis of morphology, physiology, fatty acid composition, phylogeny and 16S rRNA gene sequence analysis, the isolates are assigned to a novel species of a new genus, for which we propose the name Mongoliicoccus roseus gen. nov., sp. nov.; the type strain of the type species is MIM28T ( = ACCC 05511T  = KCTC 19808T).

Cecembia calidifontis sp. nov., isolated from a hot spring runoff, and emended description of the genus Cecembia

Two red-pigmented isolates, designated RQ-33(T) and TU-13, were recovered from hot spring runoffs on the Island of São Miguel in the Azores, Portugal. These organisms have an optimum growth temperature of approximately 45 °C and an optimum pH for growth between 7.5 and 8.5. Based on 16S rRNA gene sequence analysis, the novel isolates were most closely related to the type strain of Cecembia lonarensis at 96.4 % pairwise similarity. Cells of the two isolates were non-motile, rod-shaped, Gram-stain-negative, strictly aerobic, and oxidase- and catalase-positive. The major fatty acids were iso-C15 : 0 and C15 : 0, phosphatidylethanolamine was the major polar lipid, and menaquinone 7 was the major respiratory quinone. Based on phylogenetic analyses, and physiological and biochemical characteristics, these isolates from the Azores represent a novel species of the genus Cecembia for which the name Cecembia calidifontis is proposed with strain RQ-33(T) ( = DSM 21411(T) = LMG 24596(T)) as the type strain. The description of the genus Cecembia is also emended.

Fontibacter ferrireducens sp. nov., an Fe(III)-reducing bacterium isolated from a microbial fuel cell

A novel, dissimilatory Fe(III)-reducing bacterium, designated strain SgZ-2(T), which could couple glucose oxidation to iron reduction for energy conservation, was isolated from a microbial fuel cell. The isolate was Gram-staining-negative, catalase-positive, oxidase-negative and facultatively anaerobic. The strain was able to grow on tryptic soy agar at 15-37 °C and in the presence of 0-5 % (w/v) NaCl. The predominant cellular fatty acids (>5 %) were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c; the major respiratory quinone was MK-7; the major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and three other unidentified lipids; and the DNA G+C content was 55.3 mol%. Phylogenetic analyses based on 16S rRNA sequences showed that the novel strain was most closely related to Fontibacter flavus CC-GZM-130(T) (99.9 % sequence similarity), and was a member of the family Cyclobacteriaceae. The levels of DNA-DNA relatedness observed between strain SgZ-2(T) and F. flavus CCM 7650(T) (<41 %) indicated that the two strains represented two distinct species. Based on phylogenetic analyses and phenotypic characteristics, strain SgZ-2(T) represents a novel species of the genus Fontibacter, for which the name Fontibacter ferrireducens sp. nov. is proposed. The type strain is SgZ-2(T) ( = CCTCC M 2011498(T)  = KACC 16525(T)).

Litoribacter ruber gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium isolated from a soda lake sediment

A novel alkaliphilic, halotolerant, rod-shaped bacterium, designated strain YIM CH208T, was isolated from a soda lake in Yunnan, south-west China. The taxonomy of strain YIM CH208T was investigated by a polyphasic approach. Strain YIM CH208T was Gram-negative, strictly aerobic and non-motile and formed red colonies. Optimal growth conditions were 28 °C, pH 8.5 and 0.5–2.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genus Echinicola in the phylum Bacteroidetes and was related to the species Echinicola pacifica and Rhodonellum psychrophilum, with sequence similarity of 91.7 and 91.6 % to the respective type strains. The DNA G+C content was 45.1 mol%. The major respiratory quinone was menaquinone-7 (MK-7). The predominant cellular fatty acids were iso-C17 : 1 ω9c (19.9 %), C15 : 0 3-OH (12.1 %), iso-C17 : 0 3-OH (11.3 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 10.7 %) and C17 : 1 ω6c (8.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain YIM CH208T represents a novel species of a new genus, for which the name Litoribacter ruber gen. nov., sp. nov. is proposed. The type strain of Litoribacter ruber is YIM CH208T (=ACCC 05414T =KCTC 22899T).