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

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome

BACKGROUND

Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome.

RESULTS

After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments).

CONCLUSION

Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.

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

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.

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

An anaerobic, Gram-staining-negative, rod shaped, nitrogen-fixing strain designed SG202^T, was isolated from paddy soil collected from Fujian Province in China. Strain SG202^T showed the highest 16S rRNA gene sequence similarity with the type strain Sulfurospirillum multivorans DSM 12446^T (98.5%). Phylogenetic trees based on 16S rRNA gene sequences and conserved core genes from genomes indicated that strain SG202^T 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 SG202^T contained MK-6 as the menaquinone and C_16:1ω7c (40.6%), C_16:0 (33.3%), C_18:1ω7c (13.6%) and C_14:0 (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 SG202^T and its closely related species S. multivorans DSM 12446^T, Sulfurospirillum halorespirans DSM 13726^T, Sulfurospirillum arsenophilum DSM 10659^T and Sulfurospirillum diekertiae ACS_DCE^T 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 SG202^T 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 SG202^T is recognized as a novel species of the genus Sulfurospirillum, for which the name Sulfurospirillum oryzae sp. nov. is proposed. The type strain is SG202^T (= GDMCC 1.3379^T= JCM 35596^T).

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

An alkali, salt, and thermo-tolerant strain designated FJAT-45399^T was isolated from marine sediment in Fujian Province, China. Strain FJAT-45399^T 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-45399^T clustered with the members of the genus Shouchella. Growth of strain FJAT-45399^T 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 C_16:0 (22.8%), iso-C_15:0 (21.3%), and anteiso-C_15:0 (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-45399^T and the most closely related type strain Shouchella clausii DSM 8716^T (ANI 94.1% and dDDH 55.4%) were both below the cut-off level for species delineation. Based on the above results, strain FJAT-45399^T represents a novel species of the genus Shouchella, for which the name Shouchella tritolerans sp. nov., is proposed. The type strain is FJAT-45399^T (= GDMCC 1.3098^T = JCM 35613^T).

Lactococcus intestinalis sp. nov., a new lactic acid bacterium isolated from intestinal contents in Alzheimer's disease mice

A gram-positive, facultatively anaerobic, and coccoid or ovoid-shaped bacterium designated M2458^T was isolated from the intestinal contents of APP^swe/PS^ΔE9 mouse model of Alzheimer's disease. With the polyphasic approach, the taxonomic position of the novel isolate was confirmed. Strain M2458^T grew well at 37 °C on YCFA agar. Strain M2458^T belongs to the family Streptococcaceae and class Bacilli, and it is closed to Lactococcus formosensis NBRC 109475^T (97.59% sequence similarity) according to its 16S rRNA gene sequence. In a comparison of two housekeeping genes, rpoA and rpoB, strain M2458^T was found to be well separated from Lactococcus formosensis NBRC 109475^T. On the basis of whole genome sequences, the DNA G+C content was 38.29 mol%. The phylogentic analysis of the whole genome showed that a different branch was clearly formed in the phylogenetic tree of strain M2458^T compared to other strains in the genus Lactococcus. A total of eight genes in strain M2458^T are involved in the 'neurodegenerative disease' pathway, which involves an annotated protein (glyceraldehyde 3-phosphate dehydrogenase) involved in Alzheimer's disease. In terms of average nucleotide identity and digital DNA-DNA hybridization, strain M2458^T was identified as a novel species of the genus Lacococcus. The major fatty acids (> 10% of the total fatty acids) were C18:1ω9c (39.68%), C16:0 (13.26%) and C18:1ω7c (11.52%). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid. As a result of its genotypic and phenotypic characteristics, strain M2458^T was considered to be a new species within the genus Lactococcus; the name Lactococcus intestinalis sp. nov. has been proposed, with type strain M2458^T (=JCM 35706 = CGMCC 1.60066).

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

A facultative anaerobic nitrogen-fixing bacterium, designated SG131^T, was isolated from paddy soil. Strain SG131^T showed high 16S rRNA gene sequence similarities with type strains Propionivibrio limicola DSM 6832^T (96.9%), Propionivibrio pelophilus asp 66^T (96.0%) and Propionivibrio dicarboxylicus DSM 5885^T (95.7%). The phylogenetic trees (based on 16S rRNA gene sequences and 120 conserved genes from genomes, respectively) indicated that strain SG131^T clustered with members of the genus Propionivibrio. Growth of strain SG131^T 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 C_16:1 ω6c and/or C_16:1 ω7c (25.9%), C_16:0 (23.3%), C_17:0-cyclo (11.7%), C_12:0 (6.0%) and C_17:0 (5.9%). The genomic DNA G + C content of strain SG131^T was 60.3%. The average nucleotide identity (ANI) values between strain SG131^T and its most closely related species P. limicola DSM 6832^T, P. pelophilus DSM 12018^T and P. dicarboxylicus DSM 5885^T were 74.4%, 74.9% and 75.6%, respectively. The digital DNA-DNA hybridization (dDDH) values between strain SG131^T and its most closely related species P. limicola DSM 6832^T, P. pelophilus DSM 12018^T and P. dicarboxylicus DSM 5885^T 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 SG131^T 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 SG131^T represents a novel species of the genus Propionivibrio, for which the name Propionivibrio soli sp. nov. is proposed. The type strain is SG131^T (= GDMCC 1.3313^T = JCM 35595^T).