Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas

Abstract

Three bacterial strains, designated Red330T, Red736T and Red745T, were isolated from forest and paddy soils in Japan. Strains Red330T, Red736T and Red745T are flagella-harbouring and strictly anaerobic bacteria forming red colonies. A 16S rRNA gene sequence-based phylogenetic tree showed that all three strains were located in a cluster, including the type strains of Geomonas species, which were recently separated from the genus Geobacter within the family Geobacteraceae . Similarities of the 16S rRNA gene sequences among the three strains and Geomonas oryzae S43T, the type species of the genus Geomonas , were 96.3–98.5 %. The genome-related indexes, average nucleotide identity, digital DNA–DNA hybridization, and average amino acid identity, among the three strains and G. oryza e S43T were 74.7–86.8 %, 21.2–33.3 % and 70.4–89.8 %, respectively, which were lower than the species delineation thresholds. Regarding the phylogenetic relationships based on genome sequences, the three strains clustered with the type strains of Geomonas species, which were independent from the type strains of Geobacter species. The distinguishableness of the three isolated strains was supported by physiological and chemotaxonomic properties, with the profile of availability of electron donors and cellular fatty acids composition being particularly different among them. Based on genetic, phylogenetic and phenotypic properties, the three isolates represent three novel independent species in the genus Geomonas , for which the names Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov. are proposed. The type strains are Red330T (=NBRC 114028T=MCCC 1K03949T), Red736T (=NBRC 114029T=MCCC 1K03950T) and Red745T (=NBRC 114030T=MCCC 1K03951T), respectively.

Genome-Based Taxonomic Rearrangement of the Order Geobacterales Including the Description of Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov.

“…Moreover, in contrast to strain Red51 T , strain Red69 T showed more similar fatty acid profiles with the type species G. oryzae S43 T , because they both contain iso-C 15:0 , C 16:1 ω7c, and iso-C 15:0 3-OH as the top three fatty acids (Table 3). was characterized as the predominant quinone for the two novel strains, which is consistent with other type strains in the genus Geomonas (Xu et al, 2019;Itoh et al, 2021).…”

“… Strains: 1, Geomonas azotofigens Red51 T (this study); 2, Geomonas diazotrophica Red69 T (this study); 3, Geomonas paludis Red736 T ( Itoh et al, 2021 ); 4, Geomonas oryzae S43 T ( Xu et al, 2019 ); 5, Geomonas edaphica Red53 T ( Xu et al, 2019 ); 6, Geomonas ferrireducens S62 T ( Xu et al, 2019 ); 7, Geomonas terrae Red111 T ( Xu et al, 2019 ); 8, Geomonas silvestris Red330 T ( Itoh et al, 2021 ); 9, Geomonas limicola Red745 T ( Itoh et al, 2021 ); 10, Geomonas bemidjiensis Bem T ( Nevin et al, 2005 ; Xu et al, 2019 ); 11, Geomonas bremensis Dfr1 T ( Straub and Buchholz-Cleven, 2001 ). +, Positive; −, negative.…”

“…Strains Red51 T and Red69 T were recovered from anaerobic enrichment cultures containing microbe-harboring paddy soils collected from Yukuhashi, Fukuoka, Kanzaki, and Saga, Japan, respectively. The detailed enrichment method by using the soil slurry incubation was the same as that introduced in our previous studies ( Xu et al, 2020 ; Itoh et al, 2021 ). After isolation and purification processes, the two strains were routinely cultured on R2A agar (Difco, NJ, United States) plates supplemented with 5mM fumarate (modified R2A agar) or R2A broth (Wako, Japan) supplemented with 5mM fumarate (modified R2A broth).…”

“…The temperature range and optimum temperature for bacterial growth were examined on modified R2A agar plates and in modified R2A broth at 10, 13, 16, 20, 25, 30, 33, 37, 40, and 45°C. The pH ranges and optimum pH for growth were assayed between 5.0 and 9.0 (in increments of 0.5 pH units) in modified R2A broth gassed with He at 30°C supplemented with 20mM pH buffer solutions as described previously ( Itoh et al, 2021 ). Bacterial growth on the broth conditions was quantified using a spectrophotometer (Jasco V550, Tokyo, Japan) at 600nm wavelength (OD 600 ) after 3days of incubation.…”

“…The bacterial mean generation time was calculated according to Todar’s Online Textbook of Bacteriology, 4 and the growth curves were generated based on the OD 600 values of biomass over time, using 50ml modified R2A broth in 100ml serum bottles (N 2 /CO 2 ) at 30°C with 1/100 inoculation scale ( Supplementary Figure 1 ). Electron acceptor and donor utilization tests were carried out as described previously using MFM with Fe(III)-NTA (10mM) as the electron acceptor for all electron donor tests and acetate (10mM) as the electron donor for all electron acceptor tests ( Itoh et al, 2021 ). The final concentrations of the tested electron donors and acceptors were the same as those described by Nevin et al (2005) .…”