Richy Etienne, Thiago Dobbler Priscila, Tláskal Vojtěch, López-Mondéjar Rubén, Baldrian Petr, Kyselková Martina
Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14200, Prague 4, Czech Republic.
Institute of Soil Biology and Biogeochemistry, Biology Centre of the Czech Academy of Sciences, Na Sádkách 7, 37005, České Budějovice, Czech Republic.
Environ Microbiome. 2024 Dec 3;19(1):99. doi: 10.1186/s40793-024-00639-5.
Deadwood decomposition is an essential ecological process in forest ecosystems, playing a key role in nutrient cycling and carbon sequestration by enriching soils with organic matter. This process is driven by diverse microbial communities encompassing specialized functions in breaking down organic matter, but the specific roles of individual microorganisms in this process are still not fully understood.
Here, we characterized the deadwood microbiome in a natural mixed temperate forest in Central Europe using PacBio HiFi long-read sequencing and a genome-resolved transcriptomics approach in order to uncover key microbial contributors to wood decomposition. We obtained high quality assemblies, which allowed attribution of complex microbial functions such as nitrogen fixation to individual microbial taxa and enabled the recovery of metagenome-assembled genomes (MAGs) from both abundant and rare deadwood bacteria. We successfully assembled 69 MAGs (including 14 high-quality and 7 single-contig genomes) from 4 samples, representing most of the abundant bacterial phyla in deadwood. The MAGs exhibited a rich diversity of carbohydrate-active enzymes (CAZymes), with Myxococcota encoding the highest number of CAZymes and the full complement of enzymes required for cellulose decomposition. For the first time we observed active nitrogen fixation by Steroidobacteraceae, as well as hemicellulose degradation and chitin recycling by Patescibacteria. Furthermore, PacBio HiFi sequencing identified over 1000 biosynthetic gene clusters, highlighting a vast potential for secondary metabolite production in deadwood, particularly in Pseudomonadota and Myxococcota.
PacBio HiFi long-read sequencing offers comprehensive insights into deadwood decomposition processes by advancing the identification of functional features involving multiple genes. It represents a robust tool for unraveling novel microbial genomes in complex ecosystems and allows the identification of key microorganisms contributing to deadwood decomposition.
枯木分解是森林生态系统中一个重要的生态过程，通过向土壤中富集有机物质，在养分循环和碳固存中发挥关键作用。这一过程由多种微生物群落驱动，这些群落具有分解有机物质的特定功能，但单个微生物在这一过程中的具体作用仍未完全了解。
在这里，我们使用PacBio HiFi长读长测序和基因组解析转录组学方法，对中欧一片天然混交温带森林中的枯木微生物组进行了表征，以揭示对木材分解起关键作用的微生物。我们获得了高质量的组装结果，这使得诸如固氮等复杂的微生物功能能够归因于单个微生物分类群，并能够从丰富和稀有的枯木细菌中恢复宏基因组组装基因组（MAG）。我们成功地从4个样本中组装了69个MAG（包括14个高质量和7个单重叠群基因组），代表了枯木中大多数丰富的细菌门。这些MAG表现出丰富多样的碳水化合物活性酶（CAZyme），其中粘球菌门编码的CAZyme数量最多，并且拥有纤维素分解所需的全套酶。我们首次观察到类固醇杆菌科的活跃固氮作用，以及小杆菌门的半纤维素降解和几丁质循环利用。此外，PacBio HiFi测序鉴定出1000多个生物合成基因簇，突出了枯木中次级代谢产物产生的巨大潜力，特别是在假单胞菌门和粘球菌门中。
PacBio HiFi长读长测序通过推进涉及多个基因的功能特征鉴定，为枯木分解过程提供了全面的见解。它是揭示复杂生态系统中新型微生物基因组的强大工具，并能够识别对枯木分解起关键作用的微生物。
