Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov., isolated from paddy soils

Abstract

Three bacterial strains (Red232T, Red267T and Red630T) were isolated from paddy soils sampled in Japan. Cells of these strains were Gram-stain-negative, facultative anaerobic, long rod-shaped with monotrichous flagella or pilus-like structures for motility, and formed red colonies on agar plates. Phylogenetic trees based on 16S rRNA gene and multiple single-copy gene sequences showed that the three strains formed a cluster with the type strains of Anaeromyxobacter species, independent from any other strain genera. Similarity values of the 16S rRNA gene sequences and genomes among the three isolated strains and the type strain of Anaeromyxobacter , Anaeromyxobacter dehalogenans 2CP-1T, were 95.4–97.4% for 16S rRNA gene sequence, 75.3–79.5% for average nucleotide identity, 19.6–21.7% for digital DNA–DNA hybridization and 64.1–72.6% for average amino acid identity, all of which are below the species delineation thresholds. Nitrogenase genes were observed in the genomes of the three novel strains, but not in A. dehalogenans 2CP-1T. Moreover, multiple genomic, physiological and chemotaxonomic features supported the discrimination between these three strains. Based on the evidence in this study, the three isolates represent three novel independent species for which the following names are proposed: Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov. The type strains are Red232T (=NBRC 114074T=MCCC 1K03954T), Red267T (=NBRC 114075T=MCCC 1K04211T), and Red630T (=NBRC 114076T=MCCC 1K03957T), respectively.

Global soil metagenomics reveals ubiquitous yet previously-hidden predominance ofDeltaproteobacteriain nitrogen-fixing microbiome

“…At the end of 2018 (prior to the development of the slurry incubation method), RefSeq contained 23 genomes from Geobacteraceae and 5 from Anaeromyxobacteraceae , whereas these numbers were tripled by September 28, 2022. Approximately 50% of these increases could be attributed to isolates obtained by the slurry incubation method (Table 1) (Itoh et al, 2022, 2021; Liu et al, 2021; Masuda et al, 2020; Xu et al, 2021, 2020, 2019; Yang et al, 2022; Zhang et al, 2021), and all of these isolates bear the core nif genes ( nifHDK ) in their genomes. Apart from these isolates, we obtained two other distinct strains belonging to the genus Geomonas , namely Red32 (isolated from paddy soil in Joetsu, Niigata, Japan) and Red276 (pond sediment in Myoko, Niigata, Japan; Table 1).…”

“…Previous and current efforts to enrich culture collections (Itoh et al, 2022(Itoh et al, , 2021Masuda et al, 2020;Xu et al, 2021Xu et al, , 2020Xu et al, , 2019Zhang et al, 2021) has substantially expanded the available repertoire of Anaeromyxobacteraceae and Geobacteraceae strains. In fact, an average of 55.4% and 25.6% of NifD/K sequences derived from Anaeromyxobacteraceae and Geobacteraceae members, respectively, displayed higher proximity to our novel strains than to any other nitrogenase sequence in KEGG from these families (Fig.…”

“…One potential problem is that genomic information of Anaeromyxobacteraceae and Geobacteraceae has been poorly represented in reference databases because pure isolates of these bacteria have been difficult to obtain. Fortunately, recent studies significantly enriched the reference sequence databases by isolating dozens of novel members within these families using our previously developed slurry incubation method (Itoh et al, 2022(Itoh et al, , 2021Liu et al, 2021;Masuda et al, 2020;Xu et al, 2021Xu et al, , 2020Xu et al, , 2019Yang et al, 2022;Zhang et al, 2021). In addition, it has been reported that diversity analyses based on PCR amplicon sequencing can miss and/or underestimate even major groups in the environmental microbiome because of so-called PCR bias, the poor coverage of target genes by universal primers (Delmont et al, 2018;Jones et al, 2013), calling for extensive analyses of shotgun metagenomic data rather than PCR amplicon-based data.…”

Mesoterricola silvestris gen. nov., sp. nov., Mesoterricola sediminis sp. nov., Geothrix oryzae sp. nov., Geothrix edaphica sp. nov., Geothrix rubra sp. nov., and Geothrix limicola sp. nov., six novel members of Acidobacteriota isolated from soils

“…All genomes were analysed using DDBJ Fast Annotation and Submission Tools (DFAST) ver. 1.2.18 [32] with the same settings as the previous study [20]. BlastKOALA ver.…”

“…Since 2019, we have reported the successful cultivation and isolation of many novel lineages of strict or facultative anaerobic bacteria from various soil environments using the soil slurry incubation method that we developed [15][16][17][18][19][20]. During these experiments, 48 Acidobacteriota strains were isolated from paddy soils, an upland farm soil, freshwater sediments, and forest soils collected in various regions of Japan, which show similarities to the 16S rRNA gene sequence of the type strains of the genus Geothrix.…”