Azotosporobacter soli gen. nov., sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil.

A nitrogen-fixing strain designated SG130T was isolated from paddy soil in Fujian Province, China. Strain SG130T was Gram-staining-negative, rod-shaped, and strictly anaerobic. Strain SG130T showed the highest 16S rRNA gene sequence similarities with the type strains Dendrosporobacter quercicolus DSM 1736T (91.7%), Anaeroarcus burkinensis DSM 6283T (91.0%) and Anaerospora hongkongensis HKU 15T (90.9%). Furthermore, the phylogenetic and phylogenomic analysis also suggested strain SG130T clustered with members of the family Sporomusaceae and was distinguished from other genera within this family. Growth of strain SG130T was observed at 25-45 °C (optimum 30 °C), pH 6.0-9.5 (optimum 7.0) and 0-1% (w/v) NaCl (optimum 0.1%). The quinones were Q-8 and Q-9. The polar lipids were phosphatidylserine (PS), phosphatidylethanolamine (PE), glycolipid (GL), phospholipid (PL) and an unidentified lipid (UL). The major fatty acids (> 10%) were iso-C13:0 3OH (26.6%), iso-C17:1 (15.6%) and iso-C15:1 F (11.4%). The genomic DNA G + C content was 50.7%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T (ANI 68.0% and dDDH 20.3%) were both below the cut-off level for species delineation. The average amino acid identity (AAI) between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T was 63.2%, which was below the cut-off value for bacterial genus delineation (65%). Strain SG130T possessed core genes (nifHDK) involved in nitrogen fixation, and nitrogenase activity (106.38 µmol C2H4 g-1 protein h-1) was examined using the acetylene reduction assay. Based on the above results, strain SG130T is confirmed to represent a novel genus of the family Sporomusaceae, for which the name Azotosporobacter soli gen. nov., sp. nov. is proposed. The type strain is SG130T (= GDMCC 1.3312T = JCM 35641T).

Two novel Fe(III)-reducing bacteria, Geothrix campi sp. nov. and Geothrix mesophila sp. nov., isolated from paddy soils.

In this research, two novel Fe(III)-reducing bacteria, SG10T and SG198T of genus Geothrix, were isolated from the rice field of Fujian Agriculture and Forestry University in Fuzhou, Fujian Province, China. Strains SG10T and SG198T were strictly anaerobic, rod-shaped and Gram-stain-negative. The two novel strains exhibited iron reduction ability, utilizing various single organic acid as the elector donor and Fe(III) as a terminal electron acceptor. Strains SG10T and SG198T showed the highest 16S rRNA sequences similarities to the type strains of Geothrix oryzisoli SG189T (99.0-99.5%) and Geothrix paludis SG195T (99.0-99.7%), respectively. The phylogenetic trees based on the 16S rRNA gene and genome 120 conserved core genes showed that strains SG10T and SG198T belong to the genus Geothrix. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the phylogenetic neighbors and the two isolated strains were 86.1-94.3% and 30.7-59.5%, respectively. The major fatty acids were iso-C15:0, anteiso-C15:0, C16:0 and iso-C13:0 3OH, and MK-8 was the main respiratory quinone. According to above results, the two strains were assigned to the genus Geothrix with the names Geothrix campi sp. nov. and Geothrix mesophila sp. nov. Type strains are SG10T (= GDMCC 1.3406 T = JCM 39331 T) and SG198T (= GDMCC 62910 T = KCTC 25635 T), respectively.

Three Fe(III)-reducing and nitrogen-fixing bacteria, Anaeromyxobacter terrae sp. nov., Anaeromyxobacter oryzisoli sp. nov. and Anaeromyxobacter soli sp. nov., isolated from paddy soil.

Three microaerophilic bacterial strains, designated SG22T, SG63T and SG29T were isolated from paddy soils in PR China. Cells of these strains were Gram-staining-negative and long rod-shaped. SG22T, SG63T and SG29T showed the highest 16S rRNA gene sequence similarities with the members of the genus Anaeromyxobacter. The results of phylogenetic and phylogenomic analysis also indicated that these strains clustered with members of the genus Anaeromyxobacter. The main respiratory menaquinone of SG22T, SG63T and SG29T was MK-8 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 and C16 : 0. SG22T, SG29T and SG63T not only possessed iron reduction ability but also harboured genes (nifHDK) encoding nitrogenase. The genomic DNA G+C contents of SG22T, SG63T and SG29T ranged from 73.3 to 73.5 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values between SG22T, SG63T and SG29T and the closely related species of the genus Anaeromyxobacter were lower than the cut-off values (dDDH 70 % and ANI 95-96 %) for prokaryotic species delineation. On the basis of these results, strains SG22T, SG63T and SG29T represent three novel species within the genus Anaeromyxobacter, for which the names Anaeromyxobacter terrae sp. nov., Anaeromyxobacter oryzisoli sp. nov. and Anaeromyxobacter soli sp. nov., are proposed. The type strains are SG22T (= GDMCC 1.3185T = JCM 35581T), SG63T (= GDMCC 1.2914T = JCM 35124T) and SG29T (= GDMCC 1.2911T = JCM 35123T).

Nitrogen fixation and transcriptome of a new diazotrophic Geomonas from paddy soils.

Nitrogen gas (N2) fixation driven by diazotrophs is a crucial process for supplying nitrogen to paddy soil ecosystems. The genus Geomonas has been considered to be an important potential diazotroph in paddy soils, but direct experimental evidence of the nitrogen-fixing ability of Geomonas in pure culture is still lacking. Hence, we aimed to demonstrate this nitrogen-fixing capability and shed light on how this process was regulated in response to ammonium (NH4 +) in Geomonas. In this study, we determined that a key nitrogenase gene (nifH) was present in 50 isolates from paddy soils. Members of Geomonas contained the minimum nitrogen fixation gene cluster (nifBHDKEN) based on genomic analysis, implying Geomonas species had the potential to fix nitrogen. Acetylene reduction assay (ARA), 15N2 isotope labeling, and total nitrogen accumulation assays validated that Geomonas was, indeed, able to fix nitrogen in pure culture. Under nitrogen-fixing conditions, the cell morphology of Geomonas changed from short rod-shaped (with NH4 +) to long rod-shaped and flagella became longer and thicker. The expression of genes correlated to nitrogen fixation in the Geomonas transcriptome was quantified in response to NH4 +. Expression of genes associated with nitrogenase, flavin-based electron bifurcation complexes (such as the FixAB system), NH4 + uptake, and transformation (e.g., glutamine and glutamate synthetases) were significantly upregulated under nitrogen-fixing conditions, suggesting these mechanisms might be involved in N2 fixation in Geomonas. These results were verified by RT-qPCR. Taken together, our results demonstrate that Geomonas species possess the ability to fix N2 and expand our understanding on the ecological significance and potential applications of Geomonas in paddy soil ecosystems. IMPORTANCE The ability of Geomonas species to fix nitrogen gas (N2) is an important metabolic feature for its application as a plant growth-promoting rhizobacterium. This research is of great importance as it provides the first comprehensive direct experimental evidence of nitrogen fixation by the genus Geomonas in pure culture. We isolated a number of Geomonas strains from paddy soils and determined that nifH was present in these strains. This study demonstrated that these Geomonas species harbored genes encoding nitrogenase, as do Geobacter and Anaeromyxobacter in the same class of Deltaproteobacteria. We demonstrated N2-dependent growth of Geomonas and determined regulation of gene expression associated with nitrogen fixation. The research establishes and advances our understanding of nitrogen fixation in Geomonas.

Isolation and genomics of ten novel Shewanella species from mangrove wetland.

Mangrove bacteria largely compose the microbial community of the coastal ecosystem and are directly associated with nutrient cycling. In the present study, 12 Gram-negative and motile strains were isolated from a mangrove wetland in Zhangzhou, China. Pairwise comparisons (based on 16S rRNA gene sequences) and phylogenetic analysis indicated that these 12 strains belong to the genus Shewanella. The 16S rRNA gene sequence similarities among the 12 Shewanella strains and their related type strains ranged from 98.8 to 99.8 %, but they still could not be considered as known species. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the 12 strains and their related type strains were below the cut-off values (ANI 95-96% and dDDH 70 %) for prokaryotic species delineation. The DNA G+C contents of the present study strains ranged from 44.4 to 53.8 %. The predominant menaquinone present in all strains was MK-7. The present study strains (except FJAT-53532T) also contained ubiquinones (Q-8 and Q-7). The polar lipid phosphatidylglycerol and fatty acid iso-C15 : 0 was noticed in all strains. Based on phenotypic, chemotaxonomic, phylogenetic and genomic comparisons, we propose that these 12 strains represent 10 novel species within the genus Shewanella, with the names Shewanella psychrotolerans sp. nov. (FJAT-53749T=GDMCC 1.2398T=KCTC 82649T), Shewanella zhangzhouensis sp. nov. (FJAT-52072T=MCCC 1K05363T=KCTC 82447T), Shewanella rhizosphaerae sp. nov. (FJAT-53764T=GDMCC 1.2349T=KCTC 82648T), Shewanella mesophila sp. nov. (FJAT-53870T=GDMCC 1.2346T= KCTC 82640T), Shewanella halotolerans sp. nov. (FJAT-53555T=GDMCC 1.2344T=KCTC 82645T), Shewanella aegiceratis sp. nov. (FJAT-53532T=GDMCC 1.2343T=KCTC 82644T), Shewanella alkalitolerans sp. nov. (FJAT-54031T=GDMCC 1.2347T=KCTC 82642T), Shewanella spartinae sp. nov. (FJAT-53681T=GDMCC 1.2345T=KCTC 82641T), Shewanella acanthi sp. nov. (FJAT-51860T=GDMCC 1.2342T=KCTC 82650T) and Shewanella mangrovisoli sp. nov. (FJAT-51754T=GDMCC 1.2341T= KCTC 82647T).

Lederbergia citrea sp. nov., isolated from citrus rhizosphere.

Three Gram-positive-staining strains FJAT-49754T, FJAT-49682 and FJAT-49731 were isolated from the citrus rhizosphere soil sample. These strains showed the highest 16S rRNA gene sequence similarity with the type strain of Lederbergia panacisoli (97.8-97.9 %). The 16S rRNA gene sequence similarities between strains FJAT-49754T, FJAT-49682, and FJAT-49731 were 99.9 %. The average nucleotide identity (ANI) values between strains FJAT-49754T, FJAT-49682 and FJAT-49731 were above 96 %, while the ANI values with the members of the genus Lederbergia were below 95 %, which were below the cut-off level for prokaryotic species delineation. The above results suggest that strains FJAT-49754T, FJAT-49682 and FJAT-49731 belong to a novel species of the genus Lederbergia. Growth of strain FJAT-49754T was observed at 10-40 °C (optimum at 30 °C, pH 6.0-10.0 (optimum at pH 8.0), and NaCl tolerance up to 7 % (w/v) (optimum at 1 %). MK-7 was the only menaquinone detected in strain FJAT-49754T, and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids of strain FJAT-49754T were anteiso-C15 : 0, iso-C15 : 0, and C16 : 0. The genomic DNA G+C content of strain FJAT-49754T was 38.7 %. Based on the above results, strain FJAT-49754T represents a novel species of the genus Lederbergia, for which the name Lederbergia citrea sp. nov., is proposed. The type strain is FJAT-49754T (=CCTCC AB 2019211T=LMG 31589T).

Geothrix fuzhouensis sp. nov. and Geothrix paludis sp. nov., two novel Fe(III)-reducing bacteria isolated from paddy soil.

Two anaerobic, Fe(III)-reducing and Gram-stain-negative strains, designated SG12T and SG195T, were isolated from paddy soils in Fujian Province, PR China. Phylogenetic trees based on 16S rRNA genes and conserved core genes from genomes indicated that strains SG12T and SG195T clustered with members of the genus Geothrix. The two strains showed the highest 16S rRNA sequences similarities to the type strains of 'Geothrix terrae' SG184T (98.4-99.6 %), 'Geothrix alkalitolerans' SG263T (98.4-99.6 %) and Geothrix fermentans DSM 14018T (98.2-98.8 %). The average nucleotide identity and digital DNA-DNA hybridization values between the two strains and the closely related Geothrix species were 85.1-93.5 % and 29.8-52.9 %, respectively, lower than the cut-off level for prokaryotic species delineation. The menaquinone was MK-8 in both strains. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and C16 : 0. Additionally, the two strains possessed iron reduction ability and could utilize organics such as benzene and benzoic acid as electron donors to reduce ferric citrate to ferrous iron. Based on the morphological, biochemical, chemotaxonomic and genome data, the two isolated strains represent two novel species of the genus Geothrix, for which the names Geothrix fuzhouensis sp. nov. and Geothrix paludis sp. nov. are proposed. The type strains are SG12T (=GDMCC 1.3407T=JCM 39330T) and SG195T (= GDMCC 1.3308T=JCM 39327T), respectively.

Sulfurospirillum oryzae sp. nov., A Novel Nitrogen-Fixing Bacterium Isolated from Paddy Soil.

An anaerobic, Gram-staining-negative, rod shaped, nitrogen-fixing strain designed SG202T, was isolated from paddy soil collected from Fujian Province in China. Strain SG202T showed the highest 16S rRNA gene sequence similarity with the type strain Sulfurospirillum multivorans DSM 12446T (98.5%). Phylogenetic trees based on 16S rRNA gene sequences and conserved core genes from genomes indicated that strain SG202T branched with members of the genus Sulfurospirillum. Growth was observed at 25-37 °C (optimum 30 °C), pH 6.0-10.5 (optimum 7.5), and 0-0.6% (w/v) NaCl (optimum 0.2%). Strain SG202T contained MK-6 as the menaquinone and C16:1ω7c (40.6%), C16:0 (33.3%), C18:1ω7c (13.6%) and C14:0 (9.0%) as the major fatty acids. The genomic DNA G+C content was 39.0%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG202T and its closely related species S. multivorans DSM 12446T, Sulfurospirillum halorespirans DSM 13726T, Sulfurospirillum arsenophilum DSM 10659T and Sulfurospirillum diekertiae ACSDCET were 81.3, 81.5, 84.4, 82.2% and 24.5, 24.5, 27.9, 25.2%, respectively. All these values were lower than the recommended species delineation thresholds of ANI (95-96%) and dDDH (70%). Strain SG202T possessed core genes (nifHDK) of nitrogen fixation, and nitrogenase activities (3470.45 µmol C2H4 g-1 protein h-1) was examined using the acetylene reduction assay. Based on the observed physiological properties, chemotaxonomic characteristics and genome analysis, strain SG202T is recognized as a novel species of the genus Sulfurospirillum, for which the name Sulfurospirillum oryzae sp. nov. is proposed. The type strain is SG202T (= GDMCC 1.3379T= JCM 35596T).

A novel strictly anaerobic sulfate-reducing diazotrophic bacterium Fundidesulfovibrio terrae sp. nov., isolated from paddy soil.

A strictly anaerobic sulfate-reducing strain, designated SG127T, was isolated from paddy soil. SG127T showed the highest 16S rRNA gene sequence similarity to the type strain of Fundidesulfovibrio magnetotacticus (98.2 %). A phylogenetic tree based on 16S rRNA gene sequences indicated that SG127T clustered with members of the genus Fundidesulfovibrio. Growth of SG127T was observed at 20-37 °C (optimum, 30 °C), pH 5.5-9.0 (optimum, 7.0-8.0) and with 0-0.2 % (w/v) NaCl (optimally without NaCl). SG127T contained MK-7 as the only menaquinone and anteiso-C15 : 0, anteiso-C17 : 1ω9c, C18 : 0, iso-C14 : 0, iso-C15 : 0, iso-C16:0, iso-C16 : 1H, iso-C18 : 1H and summed feature nine as the major fatty acids. The genomic DNA G+C content of SG127T was 64.6 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between SG127T and the closely related Fundidesulfovibrio magnetotacticus were 78.5% and 23.2 %, respectively, which were lower than the cut-off values (ANI 95-96% and dDDH 70 %) for prokaryotic species delineation. SG127T had desulfoviridin, possessed nitrogen fixation genes (nifHDK) and actively fixed nitrogen according to the acetylene reduction assay. On the basis of these results, strain SG127T represents a novel species of the genus Fundidesulfovibrio, for which the name Fundidesulfovibrio terrae sp. nov. is proposed. The type strain is SG127T (= GDMCC 1.3137T = JCM 35589T).

Geothrix oryzisoli sp. nov., a ferric iron-reducing bacterium isolated from paddy soil.

An anaerobic, Gram-staining-negative, rod-shaped, Fe(III)-reducing strain, designated SG189T, was isolated from paddy soil in Fujian Province, China. Growth occurred at 20-35 ℃ (optimum 30 ℃), pH 6.5-8.0 (optimum 7.0) and 0-0.2% (w/v) NaCl (optimum 0%). The strain SG189T showed the highest 16S rRNA sequences similarities to the type strains of Geothrix fermentans DSM 14018T (98.9%), "Geothrix terrae" SG184T (99.0%) and "Geothrix alkalitolerans" SG263T (99.3%). ANI and dDDH values between strain SG189T and the most closely related Geothrix species were 86.5-87.1% and 31.5-32.9%, which lower than the cut-off values (ANI 95-96% and dDDH 70%) for prokaryotic species delineation. Further, genome-based phylogenomic trees constructed using 81 core genes (UBCG2) and 120 conserved genes (GTDB) showed that strain SG189T formed a clade with members of the genus Geothrix. The menaquinone was shown to be MK-8, and the major fatty acids were iso-C15:0 and iso-C13:0 3OH. The genomic DNA G + C content was 68.2%. Additionally, we found that strain SG189T possessed ability to reduce ferric iron, and strain SG189T could reduce 10 mM of ferric citrate in 10 days with lactate as the sole electron donor. Based on the observed physiological and biochemical properties, chemotaxonomic characteristics, ANI and dDDH values, SG189T represents a novel species of the genus Geothrix, for which the name Geothrix oryzisoli sp. nov. is proposed. The type strain is SG189T (= GDMCC 1.3408T = JCM 39324T).

Shouchella tritolerans sp. nov., a facultative anaerobic bacterium isolated from marine sediments.

An alkali, salt, and thermo-tolerant strain designated FJAT-45399T was isolated from marine sediment in Fujian Province, China. Strain FJAT-45399T was Gram-stain-positive, rod-shaped, and facultatively aerobic. It shared high 16S rRNA gene sequence similarities with the members of the genus Shouchella. Further, the phylogenetic and phylogenomic analysis also suggested strain FJAT-45399T clustered with the members of the genus Shouchella. Growth of strain FJAT-45399T was observed at 15-55 °C (optimum 45-50 °C), pH 7.0-13.0 (optimum 9.0) and 0-15% (w/v) NaCl (optimum 2%). It contained MK-7 as the menaquinone. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and an unidentified glycolipid (UGL) and lipid (UL). The major fatty acids (> 10%) were C16:0 (22.8%), iso-C15:0 (21.3%), and anteiso-C15:0 (14.0%). The genomic DNA G + C content was 44.5%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain FJAT-45399T and the most closely related type strain Shouchella clausii DSM 8716T (ANI 94.1% and dDDH 55.4%) were both below the cut-off level for species delineation. Based on the above results, strain FJAT-45399T represents a novel species of the genus Shouchella, for which the name Shouchella tritolerans sp. nov., is proposed. The type strain is FJAT-45399T (= GDMCC 1.3098T = JCM 35613T).

A novel sulfate-reducing and nitrogen-fixing bacterium Fundidesulfovibrio soli sp. nov., isolated from paddy soils.

A strictly anaerobic sulfate-reducing strain, designated SG60T, was isolated from paddy soil collected in Fujian Province, China. Growth of strain SG60T was observed at 20-37 °C, pH 5.5-10.0 and 0-0.7% (w/v) NaCl. Strain SG60T showed the highest 16S rRNA sequence similarities to the type strains of Fundidesulfovibrio magnetotacticus FSS-1T (97.2%) and Fundidesulfovibrio putealis DSM 16056T (96.4%). Phylogenetic trees based on the16S rRNA sequence and genome-based phylogenomic tree constructed using 120 core genes showed that strain SG60T clustered with members of the genus Fundidesulfovibrio. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG60T and the most closely related type strain F. magnetotacticus were 78.2% and 21.6%, respectively. Strain SG60T contained MK-7 as the main respiratory quinone and anteiso-C15:0, anteiso-C17:1 ω9c, iso-C16:0 and iso-C16:1 H as the major fatty acids. Strain SG60T produced desulfoviridin and possessed genes (nifHDK) encoding functions involved in nitrogen fixation. The genomic DNA G + C content was 65.5%. Based on the observed physiological properties, chemotaxonomic characteristics and ANI and dDDH values, strain SG60T represents a novel species of the genus Fundidesulfovibrio, for which the name Fundidesulfovibrio soli sp. nov. is proposed. The type strain is SG60T (= GDMCC 1.3310T = JCM 35676T).

Bacillus litorisediminis sp. nov., a Thermophilic Bacterium Isolated from Mangrove Sediment.

Two aerobic, Gram-staining-positive, rod-shaped, endospore-forming, thermophilic bacterial strains, designated FJAT-47801T and FJAT-47835, were isolated from the sediment collected from Zhangjiang Estuary Mangrove National Nature Reserve in Fujian Province, China. Growth was observed at 25-55 °C (optimum, 50 °C) and pH 7.0-9.0 (optimum, pH 7.0), with up to 4.0% (w/v) NaCl (optimum, without NaCl). Strains FJAT-47801T and FJAT-47835 showed the highest 16S rRNA gene sequence similarity to Bacillus oleivorans (98.5%). The 16S rRNA gene sequence similarity between FJAT-47801T and FJAT-47835 was 99.9% indicating they were the same species. Phylogenetic (based on 16S rRNA gene sequences) and phylogenomic (based on 120 conserved bacterial single-copy genes) trees showed that strains FJAT-47801T and FJAT-47835 should be affiliated to the genus Bacillus. The of menaquinone of strain FJAT-47801T was MK-7. The major fatty acids of strain FJAT-47801T were iso-C15:0, anteiso-C15:0, iso-C17:0, and C16:0. The major polar lipids strain FJAT-47801T were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), and phosphatidylglycerol (PG). The genomic DNA G+C content of strain FJAT-47801T was 39.3%. The average nucleotide identity (84.3%) and the digital DNA-DNA hybridization value (28.1%) between strain FJAT-47801T and B. oleivorans CCTCC AB 2013353T were below the cut-off level for species delineation. Based on the above results, strain FJAT-47801T represents a novel species of the genus Bacillus, for which the name Bacillus litorisediminis sp. nov., is proposed. The type strain is FJAT-47801T (=GDMCC 1.2712T = JCM 34875T).

Fundidesulfovibrio agrisoli sp. nov., A Nitrogen-Fixing Bacterium Isolated from Rice Field.

A strictly anaerobic nitrogen-fixing strain, designated SG106T, was isolated from rice field. The 16S rRNA gene sequence analysis showed that strain SG106T was closely related to the type strain of Fundidesulfovibrio magnetotacticus (97.3%). In phylogenetic (based on 16S rRNA gene sequences) and phylogenomic (constructed using a concatenated alignment of 117 conserved bacterial single-copy genes with GTDB-Tk) trees, strain SG106T clustered with members of the genus Fundidesulfovibrio. Strain SG106T grew at 20-40 °C and 0-0.4% (w/v) NaCl. Desulfoviridin was found in the strain SG106T. The genomic DNA G + C content of strain SG106T was 66.0%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG106T and the closely related F. magnetotacticus were 78.4% and 21.7%, respectively. Genome analysis showed that strain SG106T encodes genes for nitrogen fixation (nifHDK). Acetylene reduction experiments showed that the nitrogenase activity of strain SG106T could reach 224.7 µmol C2H4 g-1 protein h-1. Based on the above results, strain SG106T represents a novel species of the genus Fundidesulfovibrio, for which the name Fundidesulfovibrio agrisoli sp. nov. is proposed. The type strain is SG106T (= GDMCC 1.3136T = JCM 35588T).

A novel nitrogen-fixing bacterium, Propionivibrio soli sp. nov. isolated from paddy soil.

A facultative anaerobic nitrogen-fixing bacterium, designated SG131T, was isolated from paddy soil. Strain SG131T showed high 16S rRNA gene sequence similarities with type strains Propionivibrio limicola DSM 6832T (96.9%), Propionivibrio pelophilus asp 66T (96.0%) and Propionivibrio dicarboxylicus DSM 5885T (95.7%). The phylogenetic trees (based on 16S rRNA gene sequences and 120 conserved genes from genomes, respectively) indicated that strain SG131T clustered with members of the genus Propionivibrio. Growth of strain SG131T was observed at 25-40 °C, pH 5.5-10.5 and 0-0.5% (w/v) NaCl. The quinone was Q-7, and the main fatty acids were C16:1 ω6c and/or C16:1 ω7c (25.9%), C16:0 (23.3%), C17:0-cyclo (11.7%), C12:0 (6.0%) and C17:0 (5.9%). The genomic DNA G + C content of strain SG131T was 60.3%. The average nucleotide identity (ANI) values between strain SG131T and its most closely related species P. limicola DSM 6832T, P. pelophilus DSM 12018T and P. dicarboxylicus DSM 5885T were 74.4%, 74.9% and 75.6%, respectively. The digital DNA-DNA hybridization (dDDH) values between strain SG131T and its most closely related species P. limicola DSM 6832T, P. pelophilus DSM 12018T and P. dicarboxylicus DSM 5885T were 19.9%, 20.6% and 20.5%, respectively. All these values were lower than the recommended species delineation thresholds of ANI (95-96%) and dDDH (70%). Strain SG131T possessed core genes (nifHDK) of nitrogen fixation and was confirmed its nitrogen-fixing ability by the ARA method. According to the above-described analysis, strain SG131T represents a novel species of the genus Propionivibrio, for which the name Propionivibrio soli sp. nov. is proposed. The type strain is SG131T (= GDMCC 1.3313T = JCM 35595T).

Two ferric-reducing bacteria Geothrix terrae sp. nov. and Geothrix alkalitolerans sp. nov., isolated from paddy soil.

Two Gram-staining-negative strains, designated SG184T and SG263T were isolated from paddy soils in Fujian Province, China. The 16S rRNA gene sequence similarities between strains SG184T, SG263T, and the related type strain Geothrix fermentans DSM 14018T were 98.6% and 99.1%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between the two strains and G. fermentans DSM 14018T were below the cut-off level (95% for ANI and 70% for dDDH) recommended as the criterion for interspecies taxon affiliation. Further, phylogenetic and phylogenomic trees indicated that strains SG184T and SG263T clustered with the member of the genus Geothrix. The menaquinone was MK-8, and the main fatty acids were iso-C15:0 and iso-C13:0 3OH. The genomic DNA G + C content of SG184T and SG263T was 68.07% and 68.05%, respectively. Additionally, two strains had iron reduction ability and could reduce ferrihydrite to ferrous iron. Based on the morphological, biochemical, chemotaxonomic and genome analysis, the two isolated strains represent two novel species of the genus Geothrix, for which the names Geothrix terrae sp. nov. and Geothrix alkalitolerans sp. nov. are proposed. The type strains are SG184T (= GDMCC1.3134 T = JCM39321T) and SG263T (= GDMCC 1.3316 T = JCM 39325T), respectively.

Description of two nitrogen-fixing bacteria, Geomonas fuzhouensis sp. nov. and Geomonas agri sp. nov., isolated from paddy soils.

Two strictly anaerobic nitrogen-fixing strains, designated RG17T and RG53T, were isolated from paddy soils in China. Strains RG17T and RG53T showed the highest 16S rRNA gene sequence similarities to the type strain Geomonas paludis (97.9-98.4%). Phylogenetic tree based on 16S rRNA gene sequences showed that two strains clustered with members of the genus Geomonas. Growth of strain RG17T was observed at 20-42 °C, pH 5.5-8.5 and 0-0.3% (w/v) NaCl while strain RG53T growth was observed at 20-42 °C, pH 5.5-9.5 and 0-0.7% (w/v) NaCl. Strains RG17T and RG53T contained MK-8 as main menaquinone and C15:1 ω6c, iso-C15:0, and Summed Feature 3 as the major fatty acids. The genomic DNA G + C content of strains RG17T and RG53T were 61.6 and 60.7%, respectively. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the isolated strains and the closely related Geomonas species were lower than the cut-off value (dDDH 70% and ANI 95-96%) for prokaryotic species delineation. Both strains possessed nif genes nifHDK and nitrogenase activities. Based on the above results, the two strains represent two novel species of the genus Geomonas, for which the names Geomonas fuzhouensis sp. nov. and Geomonas agri sp. nov., are proposed. The type strains are RG17T (= GDMCC 1.2687T = KTCC 25332T) and RG53T (= GDMCC 1.2630T = KCTC 25331T), respectively.

Genome Analysis and Description of Three Novel Diazotrophs Geomonas Species Isolated From Paddy Soils.

Five strictly anaerobic strains, designated RG2T, RG3, RG10T, RF4T, and RG29, were isolated from paddy soils in China. Strains RG2T, RF4T, RG10T, RG3, and RG29 grew at temperatures ranging 5-42°C and pH ranging 5.5-8.5. Strains RG2T, RF4T, RG3, and RG29 could tolerate NaCl up to 0-0.7% (w/v) while strain RG10T could tolerate NaCl up to 0-0.8% (w/v). The isolated strains showed the highest 16S rRNA gene sequence similarities to the type strains of Geomonas terrae Red111T and Geomonas paludis Red736T. In phylogenetic (based on 16S rRNA gene sequence) and phylogenomic trees, strains clustered with the members of the genus Geomonas. Menaquinone-8 was the predominant quinone present in all strains. The major fatty acid profiles of all strains were C15:1 ω6c, C16:0, iso-C15:0, and Summed Feature 3. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the isolated strains and the closely related Geomonas species were lower than the cutoff value (ANI 95-96% and dDDH 70%) for prokaryotic species delineation. Based on physiological, biochemical, and chemotaxonomic properties, strains RG2T, RG10T, and RF4T could easily be differentiated with the members of the genus Geomonas. Additionally, all the isolated strains possessed nifHDK clusters and catalytic compartments of nitrogenase. Based on the above results, the isolated five strains represent three novel species of the genus Geomonas, for which the names Geomonas oryzisoli sp. nov., Geomonas subterranea sp. nov., and Geomonas nitrogeniifigens sp. nov. are proposed. The type strains are RG10T (= GDMCC1.2537T = KCTC 26318T), RG2T (= GDMCC1.2536T = KCTC 25317T), and RF4T (= GDMCC 1.2547T = KCTC 25316T).

[Meta analysis of association between TNF-α-308 polymorphism and periodontitis in Chinese Han population].

PURPOSE: To assess the association between TNF-α-308 polymorphism and periodontitis in Chinese Han population. METHODS: Articles published between 1994 and 2011 were searched in the fulltext database of CNKI, Chinese Biomedical Literature Database, Wanfang Database and PubMed. Case-control studies on TNF-α-308 polymorphism and periodontitis were searched up to Feb.,2011, including articles in Chinese and in English. Meta analysis was performed to evaluate the prevalence of Allele 2 between case group and control group. RESULTS: Five studies were entered into Meta analysis,with 494 cases and 501 controls . No significant heterogeneity was found among the studies(P=0.38); the pooled OR value of allele 2 was 2.12(95% CI 1.57-2.86), with significant difference(P<0.01). CONCLUSION: Meta analysis showed that TNF-α-308 polymorphism was associated with periodontitis in Chinese Han population.