Balestrini Vitória Pinheiro, Pinto Otávio Henrique Bezerra, Simmons Blake A, Gladden John M, Krüger Ricardo Henrique, Quirino Betania Ferraz
Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasília, DF, 70770-901, Brazil.
Microbial Biology Graduate Program, University of Brasília, Brasília, DF, 70790-900, Brazil.
Curr Res Microb Sci. 2024 Oct 28;7:100302. doi: 10.1016/j.crmicr.2024.100302. eCollection 2024.
Despite recent progress, bacterial degradation of lignin is not completely understood. To address the mechanisms that bacteria from unknown taxonomic groups use to perform lignin-monomer degradation, functional analysis of bacterial metagenome-assembled genomes from soil-derived consortia enriched for microorganisms capable of degrading lignin was performed. A total of 232 metagenome-assembled genomes were recovered. After applying quality criteria of at least 70 % genome completeness and contamination less than or equal to 10 %, 39 genomes were obtained. From these, a total of 14 genomes from bacteria of unknown classification at lower taxonomic levels (i.e., only classified to the order level or higher) were chosen for further functional analysis. A global analysis of the potential ecological functions of these bacteria was performed, followed by a detailed analysis of monolignol degradation pathways. The phylum with the highest number of genomes was Proteobacteria. The genomes presented functions consistent with soil-derived bacteria, like denitrification, with different metabolic capacities related to the sulfur, chlorine, arsenic and carbon cycles, in addition to the degradation of plant cell wall components like cellulose, hemicellulose, and lignin. The Sphingomonadales_OP 08 genome showed the greatest potential to degrade cellulose and hemicellulose, although it does not appear to be able to degrade lignin. The Actinobacteria_BY 70 genome presented the highest number of enzymes and pathways related to the degradation of monolignols; furthermore, it showed the greatest potential for aromatic ring breakage by different fission pathways. The genomes of the two Actinobacteria showed the caffeic acid pathway, an important phenolic compound presenting several biological properties, such as antimicrobial and antioxidant. To our knowledge, this is the first time this pathway has been reported in this class of bacteria.
尽管最近取得了进展，但木质素的细菌降解仍未完全被理解。为了探究未知分类群的细菌用于进行木质素单体降解的机制，对从富含能够降解木质素的微生物的土壤来源菌群中获得的细菌宏基因组组装基因组进行了功能分析。总共获得了232个宏基因组组装基因组。在应用至少70%的基因组完整性和小于或等于10%的污染率的质量标准后，得到了39个基因组。从这些基因组中，总共选择了14个低分类水平（即仅分类到目水平或更高）的未知分类细菌的基因组进行进一步的功能分析。对这些细菌的潜在生态功能进行了全局分析，随后对单木质醇降解途径进行了详细分析。基因组数量最多的门是变形菌门。这些基因组呈现出与土壤来源细菌一致的功能，如反硝化作用，除了降解纤维素、半纤维素和木质素等植物细胞壁成分外，还具有与硫、氯、砷和碳循环相关的不同代谢能力。鞘脂单胞菌目_OP 08基因组显示出降解纤维素和半纤维素的最大潜力，尽管它似乎不能降解木质素。放线菌_BY 70基因组呈现出与单木质醇降解相关的酶和途径数量最多；此外，它通过不同的裂变途径显示出芳香环断裂的最大潜力。这两个放线菌的基因组显示出咖啡酸途径，咖啡酸是一种具有多种生物学特性（如抗菌和抗氧化）的重要酚类化合物。据我们所知，这是首次在这类细菌中报道该途径。
