Pyrinomonas methylaliphatogenes gen. nov., sp. nov., a novel group 4 thermophilic member of the phylum Acidobacteria from geothermal soils

Abstract

Pyrinomonas methylaliphatogenes gen. nov., sp. nov., a novel group 4 thermophilic member of the phylum Acidobacteria from geothermal soils An aerobic, thermophilic, moderately acidophilic non-spore-forming bacterium, strain K22 T , was isolated from geothermally heated soil at Mount Ngauruhoe, New Zealand. On the basis of 16S rRNA gene sequence similarity, K22 T was shown to belong to subdivision 4 of the phylum Acidobacteria and to be most closely related to 'Candidatus Chloracidobacterium thermophilum' (86 %) and Blastocatella fastidiosa (86 %). Cells stained Gram-negative and were catalase and oxidase-positive. The major fatty acids detected were iso-C 15 : 0 , iso-C 17 : 0 , iso-C 19 : 0 and iso-C 21 : 0 when standard lipid extraction protocols were employed. Analysis of the total cell lipid acid hydrolysate also detected membrane-spanning and ether lipids, which made up approximately 40 % of the total membrane composition. These lipids included dicarboxylic (iso-diabolic) acid and the glyceryl ether of alkyl analogues of iso-C 15 : 0 and iso-diabolic acid. The G+C content of the genomic DNA was 59.6 mol% and the primary respiratory quinone was MK-8. Strain K22 T grew at 50-69 6C with an optimum temperature of 65 6C and at pH 4.1-7.8 with an optimum growth pH of 6.5. NaCl tolerance was up to 1 % (w/v). Cells displayed a chemoheterotrophic and obligately aerobic metabolism. Cells grew on nutrient broth, alginate, arabinose, Casamino acids, glucose, lactate, formate, mannose, sodium alginate, peptone, sucrose, tryptone, xanthan, xylan, xylose and yeast extract. Nitrogen sources included nitrate, ammonium, urea, yeast extract and Casamino acids, but not dinitrogen gas. The distinct phylogenetic position and the phenotypic characteristics separate strain K22 T from all other members of the class Acidobacteria and indicate that it represents a novel species and genus, for which the name Pyrinomonas methylaliphatogenes gen. nov., sp. nov. is proposed. The type strain of the type species is K22The Acidobacteria are a large and diverse bacterial phylum detected over a range of environments (Barns et al., 1999), particularly in soil ecosystems (Janssen, 2006). There are currently a total of 7734 16S rRNA gene non-redundant phylotypes grouping within the phylum Acidobacteria as per the latest version of the ARB-SILVA (SSU r113 NR) database (Pruesse et al., 2007). However, to date, only 15 genera in five of the approximately 26 subdivisions in this phylum (Barns et al.,

Ether- and Ester-Bound iso -Diabolic Acid and Other Lipids in Members of Acidobacteria Subdivision 4

“…Seven strains of bacteria belonging to Acidobacteria SD 4 were analyzed for their lipid compositions; five are species that have previously been characterized (Blastocatella fastidiosa [42], Pyrinomonas methylaliphatogenes [44], "Ca. Chloracidobacterium thermophilum" [41], Aridibacter famidurans, and Aridibacter kavangonensis [43]), and two are novel strains isolated from soils in Namibia (Table 1).…”

“…Blastocatella fastidosa, an aerobic chemoorganoheterotroph (42), and two Aridibacter species (43) were isolated from semiarid savannah soils. The thermophile Pyrinomonas methylaliphatogenes was isolated from a geothermally heated soil and possesses a chemoheterotrophic and obligately aerobic metabolism (44). Molecular ecological studies based on 16S rRNA genes have indicated that, in wetlands, the most abundant Acidobacteria members fall in SD 1 and 3 (21), whereas in lakes SD 1, 6, and 7 thrive (45).…”

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

“…The abundance of transporters specific for amino acids, polyamines and organocations seemed to be especially high in the genomes stemming from terrestrial strains (Supporting Information Table S6), suggesting their potential to not only use inorganic but also organic N sources via mineralization. Soils have been reported to contain varying types and amounts of free amino acids (Monreal and McGill, 1985;Kielland, 1994), which could serve as a source of N. Although select strains have been reported to grow on ammonia, nitrate, nitrite and/or amino acids (Eichorst, 2007;Koch et al, 2008;Dedysh et al, 2012;Crowe et al, 2014;Tank and Bryant, 2015b;Myers and King, 2016;Vieira et al, 2017;D. Trojan and S.A. Eichorst, unpublished data), a more detailed growth-based study is warranted, as previous work illustrated that while C. thermophilum B harboured putative genes for ammonium uptake, it was unable to grow solely on ammonium (Tank and Bryant, 2015b).…”

“…Based on previous genomic and physiological investigations, many subdivision 1 and 3 strains have been described as versatile heterotrophs that grow optimally at low pH, produce copious amounts of extracellular material, harbour a low rRNA operon copy number suggesting an oligotrophic (more K-selected) lifestyle, and contain both low-specificity major facilitator superfamily and high-affinity ABC-type transporters (Ward et al, 2009;Rawat et al, 2012;Kielak et al, 2016). Some more striking physiologies such as iron reduction and/or fermentative growth (Liesack et al, 1994;Coates et al, 1999), phototrophy (Garcia Costas et al, 2012), along with the ability to grow under thermophilic conditions have been described in select strains from subdivision 4, 8, 10 and 23 (Izumi et al, 2012;Losey et al, 2013;Crowe et al, 2014;Stamps et al, 2014;Tank and Bryant, 2015a). Yet the vast majority of acidobacteria detected in soils based on culture dependent and independent approaches are members of subdivisions 1, 2, 3, 4, 5 and 6 (Janssen, 2006;Jones et al, 2009).…”

“…o. Tank and Bryant (2015a,b); p Crowe et al, 2014;. q. Vieira et al, 2017; r. Liesack et al, 1994; s. Coates et al, 1999; t. Losey et al, 2013.…”