Reticulibacter mediterranei gen. nov., sp. nov., within the new family Reticulibacteraceae fam. nov., and Ktedonospora formicarum gen. nov., sp. nov., Ktedonobacter robiniae sp. nov., Dictyobacter formicarum sp. nov. and Dictyobacter arantiisoli sp. nov., belonging to the class Ktedonobacteria

Abstract

The aerobic, Gram-positive, mesophilic Ktedonobacteria strains, Uno17T, SOSP1-1T, 1-9T, 1-30T and 150040T, formed mycelia of irregularly branched filaments, produced spores or sporangia, and numerous secondary metabolite biosynthetic gene clusters. The five strains grew at 15–40 °C (optimally at 30 °C) and pH 4.0–8.0 (optimally at pH 6.0–7.0), and had 7.21–12.67 Mb genomes with 49.7–53.7 mol% G+C content. They shared MK9(H2) as the major menaquinone and C16 : 1-2OH and iso-C17 : 0 as the major cellular fatty acids. Phylogenetic and phylogenomic analyses showed that Uno17T and SOSP1-9T were most closely related to members of the genus Dictyobacter , with 94.43–96.21 % 16S rRNA gene similarities and 72.16–81.56% genomic average nucleotide identity. The strain most closely related to SOSP1-1T and SOSP1-30T was Ktedonobacter racemifer SOSP1-21T, with 91.33 and 98.84 % 16S rRNA similarities, and 75.13 and 92.35% average nucleotide identities, respectively. Strain 150040T formed a distinct clade within the order Ktedonobacterales , showing <90.47 % 16S rRNA gene similarity to known species in this order. Based on these results, we propose: strain 150040T as Reticulibacter mediterranei gen. nov., sp. nov. (type strain 150 040T=CGMCC 1.17052T=BCRC 81202T) within the family Reticulibacteraceae fam. nov. in the order Ktedonobacterales ; strain SOSP1-1T as Ktedonospora formicarum gen. nov., sp. nov. (type strain SOSP1-1T=CGMCC 1.17205T=BCRC 81203T) and strain SOSP1-30T as Ktedonobacter robiniae sp. nov. (type strain SOSP1-30T=CGMCC 1.17733T=BCRC 81205T) within the family Ktedonobacteraceae ; strain Uno17T as Dictyobacter arantiisoli sp. nov. (type strain Uno17T=NBRC 113155T=BCRC 81116T); and strain SOSP1-9T as Dictyobacter formicarum sp. nov. (type strain SOSP1-9T=CGMCC 1.17206T=BCRC 81204T) within the family Dictyobacteraceae .

Microbial communities from weathered outcrops of a sulfide-rich ultramafic intrusion, and implications for mine waste management

“…Related organisms in the same class have been isolated from a soil-like granular mass (Tengu-no-mugimeshi) collected from an alpine area in Gunma Prefecture, Japan (Wang et al ., 2019), an ant nest collected in Honduras, soil from a pine wood in Spain, and soil “collected under a bush” in Corsica, France (Cavaletti et al ., 2006). Yabe et al (2021) describe the metabolic capabilities of seven Ktedonobacter isolates, all of which are mesophiles, heterotrophic, and form aerial mycelia, with an optimal growth pH of 5-7. Other members of this class, genus Thermogemmatispora , have been isolated from geothermally heated environments, and can oxidize carbon monoxide in addition to a diversity of carbon sources (Yabe et al ., 2011; King and King, 2014).…”

Identification and screening of enzymatic abilities of Ktedonobacteria from forest soil of Cisolok Geothermal Area, Indonesia

“…All Ktedonobacteria isolates obtained from forest soil in the Cisolok geothermal area are considered as mesophilic bacteria due to the growth temperature of isolation and cultivation occurring at 30°C. Member of Ktedonobacteria consists of mesophilic bacteria which grow optimally at 25 to 30 °C (Cavaletti et al 2006;Wang et al 2019;Yan et al 2020;Yabe et al 2021) and thermophilic bacteria which grow optimally at 50 to 65°C (Yabe et al 2010b;King and King 2014;Zheng et al 2019b). Mesophilic Ktedonobacteria comprises of families Dictyobacteraceae (Wang et al 2019), Ktedonobacteraceae (Cavaletti et al 2006), Ktedonosporobacteraceae (Yan et al 2020), and Reticulibacteraceae (Yabe et al 2021) within order Ktedonobacterales (Cavaletti et al 2006).…”

“…Member of Ktedonobacteria consists of mesophilic bacteria which grow optimally at 25 to 30 °C (Cavaletti et al 2006;Wang et al 2019;Yan et al 2020;Yabe et al 2021) and thermophilic bacteria which grow optimally at 50 to 65°C (Yabe et al 2010b;King and King 2014;Zheng et al 2019b). Mesophilic Ktedonobacteria comprises of families Dictyobacteraceae (Wang et al 2019), Ktedonobacteraceae (Cavaletti et al 2006), Ktedonosporobacteraceae (Yan et al 2020), and Reticulibacteraceae (Yabe et al 2021) within order Ktedonobacterales (Cavaletti et al 2006). A total of 17 ktedonobacterial isolates from forest soil of the Cisolok geothermal area were used in phylogenetic analyses (Figure 3).…”

“…Mount Salak is an active volcano, another geothermal area in West Java. Other known species of Dictyobacter were obtained from the soil in geothermal areas e.g., D. alpinus, D. kobayashii (Wang et al 2019), D. vulcani (Zheng et al 2020), D. fomicarum (Yabe et al 2021), and only one species was not obtained from geothermal sites e.g. D. arantiisoli (Yabe et al 2021).…”

“…This class was predominantly found in extreme acidic oligotrophic environments (Tebo et al 2015), and recorded at low abundances in non-extreme environments, such as sandy soil (Acosta-Martinez et al 2010). Current isolation and cultivation approach resulted in only a few Ktedonobacteria taxa which have been formally proposed since 2006, with 19 species within eight genera (Cavaletti et al 2006;Yabe et al 2021). Therefore, intensive efforts in developing isolation and cultivation methods are urgently required to increase the number of culturable Ktedonobacteria in an attempt to discover new natural products (Zheng et al 2019a).…”