Draft genome of Thermomonospora sp. CIT 1 (Thermomonosporaceae) and in silico evidence of its functional role in filter cake biomass deconstruction

Abstract The filter cake from sugar cane processing is rich in organic matter and nutrients, which favors the proliferation of microorganisms with potential to deconstruct plant biomass. From the metagenomic data of this material, we assembled a draft genome that was phylogenetically related to Thermomonospora curvata DSM 43183, which shows the functional and ecological importance of this bacterium in the filter cake. Thermomonospora is a gram-positive bacterium that produces cellulases in compost, and it can survive temperatures of 60 ºC. We identified a complete set of biomass depolymerizing enzymes in the draft genome of Thermomonospora sp. CIT 1, such as α-amylase, catalase-peroxidases, β-mannanase, and arabinanase, demonstrating the potential of this bacterium to deconstruct the components of starch, lignin, and hemicellulose. In addition, the draft genome of Thermomonospora sp. CIT 1 contains 18 genes that do not share identity with five other species of Thermomonospora, suggesting that this bacterium has different genetic characteristics than those present in genomes reported so far for this genus. These findings add a new dimension to the current understanding of the functional profile of this microorganism that inhabits agro-industrial waste, which may boost new gene discoveries and be of importance for application in the production of bioethanol.

摘要 甘蔗加工过程中产生的滤饼（filter cake）富含有机质与营养成分，可促进具备降解植物生物质潜力的微生物增殖。基于该样品的宏基因组（metagenomic）数据，我们组装得到一株与弯曲热单孢菌（Thermomonospora curvata）DSM 43183系统发育相关的草图基因组（draft genome），证实了该细菌在蔗滤饼中具有重要的功能与生态价值。热单孢菌属（Thermomonospora）为革兰氏阳性菌，可在堆肥环境中合成纤维素酶（cellulases），且能耐受60℃的高温。我们在热单孢菌属菌株CIT 1（Thermomonospora sp. CIT 1）的草图基因组中，鉴定得到一套完整的生物质解聚酶（biomass depolymerizing enzymes）体系，包括α-淀粉酶（α-amylase）、过氧化氢酶-过氧化物酶（catalase-peroxidases）、β-甘露聚糖酶（β-mannanase）与阿拉伯聚糖酶（arabinanase），证明该菌具备降解淀粉、木质素（lignin）与半纤维素（hemicellulose）组分的潜力。此外，热单孢菌属菌株CIT 1的草图基因组中包含18个与该属其他5个已报道物种均无序列同源性的基因，提示该菌株具有该属已公开基因组中尚未发现的独特遗传特征。上述研究结果拓展了当前对栖息于农业工业废弃物中的该类微生物功能谱的认知，可为新型功能基因发掘提供新思路，并有望在生物乙醇（bioethanol）生产领域获得重要应用价值。