Microbial metaproteome data from decayed beech dead wood

Kipping, Lydia; Holzscheck, Nicholas; Maurer, Florian P.; Muszynski, Sarah; Noll, Matthias; Jehmlich, Nico

doi:10.1016/j.dib.2020.105285

Cited by 6 publications

(3 citation statements)

References 7 publications

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“…The collected wood chips were handled according to a previously described procedure [ 44 ] (exhaustively described in the Supplementary Methods ). Briefly, the wood chips were fine milled and extracted using a cell lysis step that included thaw–freeze cycles and ultrasonication.…”

Section: Methodsmentioning

confidence: 99%

Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species

Kipping,

Jehmlich,

Moll

et al. 2024

The ISME Journal

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Deadwood provides habitat for fungi and serves diverse ecological functions in forests. We already have profound knowledge of fungal assembly processes, physiological and enzymatic activities, and resulting physico-chemical changes during deadwood decay. However, in situ detection and identification methods, fungal origins, and a mechanistic understanding of the main lignocellulolytic enzymes are lacking. This study used metaproteomics to detect the main extracellular lignocellulolytic enzymes in 12 tree species in a temperate forest that have decomposed for 8 ½ years. Mainly white-rot (and few brown-rot) Basidiomycota were identified as the main wood decomposers, with Armillaria as the dominant genus; additionally, several soft-rot xylariaceous Ascomycota were identified. The key enzymes involved in lignocellulolysis included manganese peroxidase, peroxide-producing alcohol oxidases, laccase, diverse glycoside hydrolases (cellulase, glucosidase, xylanase), esterases, and lytic polysaccharide monooxygenases. The fungal community and enzyme composition differed among the 12 tree species. Ascomycota species were more prevalent in angiosperm logs than in gymnosperm logs. Regarding lignocellulolysis as a function, the extracellular enzyme toolbox acted simultaneously and was interrelated (e.g. peroxidases and peroxide-producing enzymes were strongly correlated), highly functionally redundant, and present in all logs. In summary, our in situ study provides comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in temperate tree species. These findings will allow us to relate changes in environmental factors to lignocellulolysis as an ecosystem function in the future.

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Section: Methodsmentioning

confidence: 99%

Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species

Kipping,

Jehmlich,

Moll

et al. 2024

The ISME Journal

Self Cite

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“…Greenhouse soils 1DEaN-terminal sequencingGeLC-MS/MS 5 Murase et al (2003) Compost soil GeLC-MS/MS 4 Benndorf et al (2007) River gravel or lava granules 2DE 240 Benndorf et al (2009) Agricultural soil 2DE ∼250 Chen et al 2009± Toluene-amended soil microbial± inoculated cultures 1DMALDI-TOF/TOF MS 47 Williams et al (2010) Grassland soil 2D-LC-MS/MS 333 Chourey et al (2010) Beech leaf litter GeLC-MS/MS Up to 1,724 Schneider et al (2010Schneider et al ( , 2012 Soil microcosms spiked with Cupriavidus metallidurans proteins 2DE 320 Giagnoni et al (2011) Rice Kipping et al (2020) during hemp and flax retting, but they did not identify the proteins responsible for these activities. The astounding advances of the past decade that have led to fast and affordable protein sequencing technologies associated with the increase in database information have led to a rapid increase in the number of protein identifications (Table 6).…”

Section: Matrix Proteome Analysis Methods Number Of Proteins Referencesmentioning

confidence: 99%

Targeted Metagenomics of Retting in Flax: The Beginning of the Quest to Harness the Secret Powers of the Microbiota

et al. 2020

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“…Some bacteria are found to directly decompose complex polymers in wood, such as cellulose, hemicellulose, and even lignin [ 5 ]. Nevertheless, a recent study found that most (~ 90% or more) of identified peptides of deadwood have a fungal origin which infers that fungi are the main producers of extracellular enzymes in deadwood [ 6 ]. Despite the importance of wood-inhabiting fungi on nutrient cycling and many ecosystem functions, their ecological processes are still not fully understood [ 7 , 8 ].…”

Section: Introductionmentioning

confidence: 99%

Community Assembly Processes of Deadwood Mycobiome in a Tropical Forest Revealed by Long-Read Third-Generation Sequencing

Purahong,

Ji,

2024

Microb Ecol

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Despite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still highly unexplored. In this study, we analyzed the wood-inhabiting fungal richness, community composition, and phylogenetics using PacBio sequencing. Opposite to what has been expected that deterministic processes especially environmental filtering through wood-physicochemical properties controls the community assembly of wood-inhabiting fungal communities, here we showed that both deterministic and stochastic processes can highly contribute to the community assembly processes of wood-inhabiting fungi in this tropical forest. We demonstrated that the dynamics of stochastic and deterministic processes varied with wood decomposition stages. The initial stage was mainly governed by a deterministic process (homogenous selection), whereas the early and later decomposition stages were governed by the stochastic processes (ecological drift). Deterministic processes were highly contributed by wood physicochemical properties (especially macronutrients and hemicellulose) rather than soil physicochemical factors. We elucidated that fine-scale fungal-fungal interactions, especially the network topology, modularity, and keystone taxa of wood-inhabiting fungal communities, strongly differed in an initial and decomposing deadwood. This current study contributes to a better understanding of the ecological processes of wood-inhabiting fungi in tropical regions where the knowledge of wood-inhabiting fungi is highly limited.

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Microbial metaproteome data from decayed beech dead wood

Cited by 6 publications

References 7 publications

Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species

Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species

Targeted Metagenomics of Retting in Flax: The Beginning of the Quest to Harness the Secret Powers of the Microbiota

Community Assembly Processes of Deadwood Mycobiome in a Tropical Forest Revealed by Long-Read Third-Generation Sequencing

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