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

Sophie Mieszkin,Karine Alain,Christelle Simon-Colin,Eva Pouder,Stéphane Uroz

doi:10.3390/microorganisms9102053

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).

Highlights

We describe two new representatives of the Acidisoma genus isolated from decaying oak wood, A. silvae HW T2.11T (DSM 111006T ) and A. cellulosilytica
In the neighbor-joining tree based on 16S rRNA gene sequences, strains HW T2.11T and HW T5.17T formed a distinct clade with A. tundrae and A. sibiricum strains (Figure 1)
The level of 16S rRNA gene sequence similarity with the type strains of Acidisoma showed that both novel isolates displayed sufficient molecular differences for a delineation at the species level as these values were below the threshold value (98.70–99%) [46]

Summary

Introduction

Deadwood decomposition plays an essential role in forest ecosystems as it maintains the soil fertility and the physico-chemical balance of the biogeochemical cycles in these ecosystems (e.g., carbon (C) cycle, recycling of nitrogen (N), and micronutrients) [1]. This process is mainly performed by a succession of decomposers including insects, fungi, and bacteria that interact to progressively decompose and recycle the nutrients [2,3,4,5]. Wood consists of complex macromolecules such as cellulose, hemicellulose, and lignin, the latter being

Methods

Results

Conclusion