Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov., Two Acidophilic Bacteria Isolated from Decaying Wood, Hydrolyzing Cellulose and Producing Poly-3-hydroxybutyrate

Abstract

Two novel strains, HW T2.11T and HW T5.17T, were isolated from decaying wood (forest of Champenoux, France). Study of the 16S rRNA sequence similarity indicated that the novel strains belong to the genus Acidisoma. The sequence similarity of the 16S rRNA gene of HW T2.11T with the corresponding sequences of A. tundrae and A. sibiricum was 97.30% and 97.25%, while for HW T5.17T it was 96.85% and 97.14%, respectively. The DNA G+C contents of the strains were 62.32–62.50%. Cells were Gram-negative coccobacilli that had intracellular storage granules (poly-3-hydroxybutyrate (P3HB)) that confer resistance to environmental stress conditions. They were mesophilic and acidophilic organisms growing at 8–25 °C, at a pH of 2.0–6.5, and were capable of using a wide range of organic compounds and complex biopolymers such as starch, fucoidan, laminarin, pectin and cellulose, the latter two being involved in wood composition. The major cellular fatty acid was cyclo C19:0ω8c and the major quinone was Q-10. Overall, genome relatedness indices between genomes of strains HW T2.11T and HW T5.17T (Orthologous Average Nucleotide Identity (OrthoANI) value = 83.73% and digital DNA-DNA hybridization score = 27.5%) confirmed that they belonged to two different species. Genetic predictions indicate that the cyclopropane fatty acid (CFA) pathway is present, conferring acid-resistance properties to the cells. The two novel strains might possess a class IV polyhydroxyalcanoate (PHA) synthase operon involved in the P3HB production pathway. Overall, the polyphasic taxonomic analysis shows that these two novel strains are adapted to harsh environments such as decaying wood where the organic matter is difficult to access, and can contribute to the degradation of dead wood. These strains represent novel species of the genus Acidisoma, for which the names Acidisoma silvae sp. nov. and Acidisoma cellulosilytica sp. nov. are proposed. The type strains of Acidisoma silvae and Acidisoma cellulosilytica are, respectively, HW T2.11T (DSM 111006T; UBOCC-M-3364T) and HW T5.17T (DSM 111007T; UBOCC-M-3365T).

Comparative metagenomic study unveils bacterial communities and their putative involvement in ecological success of two pine-feedingIpsbeetle holobionts

“…These bacteria genera can also recycle uric acid from beetle faeces, helping the beetles meet the crucial nitrogen requirement (23,85) and producing antifungal compounds to suppress pathogenic fungal growth, aiding the beetle survival (86). Other core members such as Dyella, Pseudoxanthomonas, Sphingomonas, Saccharomonospora, Acidisoma have the enzymatic competency to help the beetle metabolize complex carbohydrates found in the conifer cell wall (21,69,(87)(88)(89)(90). Therefore, such microbes belonging to the core bacteriome can be further evaluated in beetlo for potential benefits and targeted for future microbesmediated sustainable beetle management practices (91).…”

The phylogeny of Acetobacteraceae : photosynthetic traits and deranged respiratory enzymes

“…It is intriguing that Acidocella genomes combine early branching forms of the cytochrome bd and bo 3 ubiquinol oxidases with clearly derived features of other components of the respiratory chain ( 19 , 20 ). These features, and the recent report of a new group of Antarctic Acetobacteraceae ( 21 ), stimulated an in-depth analysis of the phylogenomics of all Acetobacteraceae , expanding previous studies ( 4 , 5 , 22 , 23 ) and niches ( 21 , 24 ).…”

Scleromatobacter humisilvae gen. nov., sp. nov., a novel bacterium isolated from oak forest soil

“…These tests were completed with liquid or solid cultures allowing to determine: (i) mannitol fermentation and presence of nitrate reductase (MMN agar medium); (ii) fermentative pathways (mixed acids or butane-2,3-diol pathways; Clark and Lubs liquid medium); (iii) glucose and lactose fermentation, gas and H 2 S production (Kligler-Hajna agar medium); and (iv) citrate utilization (Simmons citrate agar medium). For these assays, culture media, cell cultures and washes and preparation of bacterial suspensions were performed as described above and by Mieszkin et al [9]. Strain BS-T2-15 T is chemoorganoheterotrophic and grows by aerobic respiration.…”