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

Tláskal, Vojtěch; Baldrián, Petr

doi:10.3389/fmicb.2021.685303

Cited by 31 publications

(27 citation statements)

References 74 publications

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“…In order to understand the deadwood as a dynamic habitat, it is necessary to describe the composition of associated microorganisms with an emphasis on the major groups – fungi and bacteria – whose ecologies are often genus-specific 10 . Further, it is important to link deadwood-associated organisms to processes occurring at different stages of decomposition either by characterization of isolates 7 , 11 or by cultivation-independent techniques.…”

Section: Background and Summarymentioning

confidence: 99%

Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood

et al. 2021

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Deadwood represents significant carbon (C) stock in a temperate forests. Its decomposition and C mobilization is accomplished by decomposer microorganisms – fungi and bacteria – who also supply the foodweb of commensalist microbes. Due to the ecosystem-level importance of deadwood habitat as a C and nutrient stock with significant nitrogen fixation, the deadwood microbiome composition and function are critical to understanding the microbial processes related to its decomposition. We present a comprehensive suite of data packages obtained through environmental DNA and RNA sequencing from natural deadwood. Data provide a complex picture of the composition and function of microbiome on decomposing trunks of European beech (Fagus sylvatica L.) in a natural forest. Packages include deadwood metagenomes, metatranscriptomes, sequences of total RNA, bacterial genomes resolved from metagenomic data and the 16S rRNA gene and ITS2 metabarcoding markers to characterize the bacterial and fungal communities. This project will be of use to microbiologists, environmental biologists and biogeochemists interested in the microbial processes associated with the transformation of recalcitrant plant biomass.

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Section: Background and Summarymentioning

confidence: 99%

Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood

et al. 2021

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“…Members of the genera Stenotrophomonas, Massilia, Rhodanobacter, Luteibacter, Sphingomonas and ANPR were highly represented in the active bacterial communities. While the majority of these dominant bacteria genera are known for their potential function in C cycle such as cellulose degraders (Stenotrophomonas, Massilia, Luteibacter) [33][34][35] and catabolizing aromatic lignin depolymerization (Sphingomonas) [36], some of them are also known to potentially play important roles in N cycling. Majority of members of Sphingomonas and ANPR are able to fix atmospheric N 2 [37], Rhodanobacter spp.…”

Section: Discussionmentioning

confidence: 99%

Cross-kingdom interactions and functional patterns of active microbiota matter in governing deadwood decay

et al. 2022

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Microbial community members are the primary microbial colonizers and active decomposers of deadwood. This study placed sterilized standardized beech and spruce sapwood specimens on the forest ground of 8 beech- and 8 spruce-dominated forest sites. After 370 days, specimens were assessed for mass loss, nitrogen (N) content and 15 N isotopic signature, hydrolytic and lignin-modifying enzyme activities. Each specimen was incubated with bromodeoxyuridine (BrdU) to label metabolically active fungal and bacterial community members, which were assessed using amplicon sequencing. Fungal saprotrophs colonized the deadwood accompanied by a distinct bacterial community that was capable of cellulose degradation, aromatic depolymerization, and N 2 fixation. The latter were governed by the genus Sphingomonas , which was co-present with the majority of saprotrophic fungi regardless of whether beech or spruce specimens were decayed. Moreover, the richness of the diazotrophic Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group was significantly correlated with mass loss, N content and 15 N isotopic signature. By contrast, presence of obligate predator Bdellovibrio spp. shifted bacterial community composition and were linked to decreased beech deadwood decay rates. Our study provides the first account of the composition and function of metabolically active wood-colonizing bacterial and fungal communities, highlighting cross-kingdom interactions during the early and intermediate stages of wood decay.

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“…Substrates targeted by CAZymes show that woodassociated Sodalis members utilize rather labile plant polymers or chitin to obtain C and do not serve as important cellulose degraders. The broader degradation capabilities were described for other deadwood-associated bacterial taxa such as those from the phyla Acidobacteria and Bacteroidetes (Tláskal and Baldrian, 2021). The ecological function of free-living Sodalis strains might be resolved based on the multiplied presence of nifHDK operons expressing nitrogenase, a key enzyme for nitrogen fixation which is dependent on the metal cofactors (e.g., molybdenum).…”

Section: Discussionmentioning

confidence: 99%

“…The obtained sequences were compared by BLASTn with bacterial 16S rRNA gene-based community data from the same habitat (Tláskal et al, 2017). Bacterial strains with high similarity and coverage to the most abundant bacteria recovered by environmental DNA sequencing were selected for further cultivation and genome sequencing (Tláskal and Baldrian, 2021).…”

Section: Sodalis Isolationmentioning

confidence: 99%

Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood

et al. 2021

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The bacterial genus Sodalis is represented by insect endosymbionts as well as free-living species. While the former have been studied frequently, the distribution of the latter is not yet clear. Here, we present a description of a free-living strain, Sodalis ligni sp. nov., originating from decomposing deadwood. The favored occurrence of S. ligni in deadwood is confirmed by both 16S rRNA gene distribution and metagenome data. Pangenome analysis of available Sodalis genomes shows at least three groups within the Sodalis genus: deadwood-associated strains, tsetse fly endosymbionts and endosymbionts of other insects. This differentiation is consistent in terms of the gene frequency level, genome similarity and carbohydrate-active enzyme composition of the genomes. Deadwood-associated strains contain genes for active decomposition of biopolymers of plant and fungal origin and can utilize more diverse carbon sources than their symbiotic relatives. Deadwood-associated strains, but not other Sodalis strains, have the genetic potential to fix N2, and the corresponding genes are expressed in deadwood. Nitrogenase genes are located within the genomes of Sodalis, including S. ligni, at multiple loci represented by more gene variants. We show decomposing wood to be a previously undescribed habitat of the genus Sodalis that appears to show striking ecological divergence.

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

Cited by 31 publications

References 74 publications

Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood

Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood

Cross-kingdom interactions and functional patterns of active microbiota matter in governing deadwood decay

Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood

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