Oak decaying wood harbors taxonomically and functionally different bacterial communities in sapwood and heartwood

Mieszkin, Sophie; Richet, P.; Bach, Cyrille; Lambrot, Catherine; Augusto, Laurent; Buée, Marc; Uroz, Stéphane

doi:10.1016/j.soilbio.2021.108160

Cited by 20 publications

(29 citation statements)

References 70 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Luteibacter displayed the highest chitinase activity in this study, and its mycolytic and cellulolytic activity was described previously (López-Mondéjar et al, 2016;Mieszkin et al, 2021); Luteibacter additionally showed a generally high activity of membrane-bound enzymes (Lasa et al, 2019).…”

Section: Discussionsupporting

confidence: 77%

“…The ability to fix N 2 might explain the association of Alphaproteobacteria with low-N conditions and their positive correlation with the C:N ratio (Rinta-Kanto et al, 2016;Mieszkin et al, 2021). Previous studies detected the order Rhizobiales (Alphaproteobacteria) as one of the abundant members in the deadwood community (Hervé et al, 2013) and showed the presence of nitrogenase genes assigned to this group (Hoppe et al, 2015).…”

Section: Discussionmentioning

confidence: 94%

“…As a result of fungal modulation and changing conditions in the substrate, the composition and abundance of the bacterial community in deadwood change over time showing an increase of bacterial biomass and taxa succession toward community similar to that in soil (Rinta-Kanto et al, 2016;Tláskal et al, 2017). Among the factors influencing bacterial community composition in deadwood, the most often reported are pH, the C:N ratio, and water content (Folman et al, 2008;Hoppe et al, 2015;Tláskal et al, 2017;Moll et al, 2018;Mieszkin et al, 2021), but the biopolymer composition and fungal abundance are also important (Rinta-Kanto et al, 2016;Odriozola et al, 2021). Due to limited knowledge of the functional traits of deadwood bacteria, it is unclear how exactly these factors influence the members of the bacterial community or vice versa and which adaptations make bacterial species successful at various stages of deadwood decomposition.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Deadwood-Inhabiting Bacteria Show Adaptations to Changing Carbon and Nitrogen Availability During Decomposition

Tláskal

Baldrián

2021

Front. Microbiol.

View full text Add to dashboard Cite

Deadwood decomposition is responsible for a significant amount of carbon (C) turnover in natural forests. While fresh deadwood contains mainly plant compounds and is extremely low in nitrogen (N), fungal biomass and N content increase during decomposition. Here, we examined 18 genome-sequenced bacterial strains representing the dominant deadwood taxa to assess their adaptations to C and N utilization in deadwood. Diverse gene sets for the efficient decomposition of plant and fungal cell wall biopolymers were found in Acidobacteria, Bacteroidetes, and Actinobacteria. In contrast to these groups, Alphaproteobacteria and Gammaproteobacteria contained fewer carbohydrate-active enzymes and depended either on low-molecular-mass C sources or on mycophagy. This group, however, showed rich gene complements for N2 fixation and nitrate/nitrite reduction—key assimilatory and dissimilatory steps in the deadwood N cycle. We show that N2 fixers can obtain C independently from either plant biopolymers or fungal biomass. The succession of bacteria on decomposing deadwood reflects their ability to cope with the changing quality of C-containing compounds and increasing N content.

show abstract

Section: Discussionsupporting

confidence: 77%

Section: Discussionmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Deadwood-Inhabiting Bacteria Show Adaptations to Changing Carbon and Nitrogen Availability During Decomposition

Tláskal

Baldrián

2021

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

“…Concerning decaying wood, an important biomass and a broad diversity of bacteria have been reported across the wood decomposition process, suggesting that the involvement of bacteria in this process does not seem negligible [2]. Dominance of bacteria belonging to Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes has been reported considering different wood species [5,[14][15][16][17]. If these phyla are representative of the bacterial communities colonizing deadwood, it is important to note that the related bacterial classes or genera differ according to the tree species, the decay stage, and the type of wood [5,[17][18][19][20].…”

Section: Introductionmentioning

confidence: 99%

“…Dominance of bacteria belonging to Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes has been reported considering different wood species [5,[14][15][16][17]. If these phyla are representative of the bacterial communities colonizing deadwood, it is important to note that the related bacterial classes or genera differ according to the tree species, the decay stage, and the type of wood [5,[17][18][19][20]. While bacteria are poorly effective at decomposing dead wood compared to fungi, a few studies have shown that they are primarily involved in the decomposition of cellulose and pectin as well as in N fixation [21][22][23][24].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

View full text Add to dashboard Cite

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).

show abstract

Changes and driving factors of microbial community composition and functional groups during the decomposition of Pinus massoniana deadwood

Shi,

Wang,

Yang

et al. 2024

Ecology and Evolution

View full text Add to dashboard Cite

Clarifying changes in the microbial community in deadwood at different stages of decomposition is crucial for comprehending the role of deadwood in the biogeochemical processes and the sustainability of forest development. However, there have been no reports on the dynamics of microbial community during the decomposition of Pinus massoniana. We used the “space‐for‐time” substitution to analyze the characteristics of microbial community changes and the key influencing factors in the P. massoniana deadwood during different decomposition stages by 16S and ITS rRNA gene sequencing. The results suggest that the microbial community structure of the early decomposition (decay class I) was significantly different from the other decay classes, while the diversity and richness of the microbial community were the highest in the late decomposition (decay class V). The Linear Discriminant Analysis Effect Size analysis revealed that most bacterial and fungal taxa were significantly enriched in decay classes I and V deadwood. During the initial stages of decomposition, the relative abundance of the bacterial functional group responsible for carbohydrate metabolism was greater than the later stages. As decomposition progressed, the relative abundance of saprophytic fungi gradually decreased, and there was a shift in the comparative abundance of mixed saprophytic‐symbiotic fungi from low to high before eventually decreasing. Total organic carbon, total nitrogen, carbon‐to‐nitrogen ratio, total potassium, total phenol, condensed tannin, lignin, and cellulose were significantly correlated with microbial community structure, with the carbon‐to‐nitrogen ratio having the greatest effect. Our results indicate that the physicochemical properties of deadwood, microbial community structural composition and functional group changes were related to the decay class, among which the carbon‐to‐nitrogen ratio may be an important factor affecting the composition and diversity of microbial communities.

show abstract

Oak decaying wood harbors taxonomically and functionally different bacterial communities in sapwood and heartwood

Cited by 20 publications

References 70 publications

Deadwood-Inhabiting Bacteria Show Adaptations to Changing Carbon and Nitrogen Availability During Decomposition

Deadwood-Inhabiting Bacteria Show Adaptations to Changing Carbon and Nitrogen Availability During Decomposition

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

Changes and driving factors of microbial community composition and functional groups during the decomposition of Pinus massoniana deadwood

Contact Info

Product

Resources

About