Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting.
Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting.
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DOI：
10.3389/fmicb.2017.00644
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发表时间：
2017
影响因子：
5.2
通讯作者：
Setubal JC
中科院分区：
文献类型：
--
作者：
Lemos LN;Pereira RV;Quaggio RB;Martins LF;Moura LMS;da Silva AR;Antunes LP;da Silva AM;Setubal JC
从复杂的木质纤维素分解微生物群落中选择的微生物群落是解构植物废物的有希望的替代品，因为在生物精炼应用中，需要不同酶的协同作用才能完全降解植物生物量。培养富集还有助于研究财团成员之间的相互作用，并且可以成为新微生物物种的良好来源。在这里，我们使用来自<s:1>圣保罗动物园（巴西）的植物废物堆肥操作的样品作为接种物，以羧甲基纤维素为唯一碳源，在60°C下经过多次传代富集的嗜热好氧联盟。采用散弹枪宏基因组学和基因组中心分析对该联合体的微生物群落组成进行了研究。重建了6个接近完整（超过90%）的基因组。相似性和系统发育分析表明，这6个基因组中有4个是新的，具有以下假设鉴定：一个新的热芽孢杆菌物种；第一个热玉米芽孢杆菌基因组（目前只有16S序列可用），或者是芽孢杆菌目新家族的第一个代表；芽孢杆菌科新属的首个代表；也是梭菌纲中一个新的深分支家族的第一个代表。重建的基因组来自已知物种，鉴定为热葡萄糖酸菌地杆菌和弱钙杆菌。基于COG和CAZy分析的这些基因组的代谢潜力表明，这些基因组编码几种糖苷水解酶（GHs）以及其他与木质纤维素分解相关的基因。新发现的热芽孢杆菌属是GHs多样性和丰度最丰富的，具有最大的生物量降解潜力。我们还使用先前研究中生成的堆肥宏基因组和元转录组数据集，研究了与这些基因组相对应的生物在堆肥操作中的存在和活性。我们获得了强有力的证据，证明六个恢复的基因组中有五个确实存在并活跃在堆肥过程中。因此，我们发现了三种（也许四种）新的嗜热细菌，增加了已知木质纤维素降解物的数量，其生物技术潜力现在可以在进一步的研究中进行调查。
Microbial consortia selected from complex lignocellulolytic microbial communities are promising alternatives to deconstruct plant waste, since synergistic action of different enzymes is required for full degradation of plant biomass in biorefining applications. Culture enrichment also facilitates the study of interactions among consortium members, and can be a good source of novel microbial species. Here, we used a sample from a plant waste composting operation in the São Paulo Zoo (Brazil) as inoculum to obtain a thermophilic aerobic consortium enriched through multiple passages at 60°C in carboxymethylcellulose as sole carbon source. The microbial community composition of this consortium was investigated by shotgun metagenomics and genome-centric analysis. Six near-complete (over 90%) genomes were reconstructed. Similarity and phylogenetic analyses show that four of these six genomes are novel, with the following hypothesized identifications: a new Thermobacillus species; the first Bacillus thermozeamaize genome (for which currently only 16S sequences are available) or else the first representative of a new family in the Bacillales order; the first representative of a new genus in the Paenibacillaceae family; and the first representative of a new deep-branching family in the Clostridia class. The reconstructed genomes from known species were identified as Geobacillus thermoglucosidasius and Caldibacillus debilis. The metabolic potential of these recovered genomes based on COG and CAZy analyses show that these genomes encode several glycoside hydrolases (GHs) as well as other genes related to lignocellulose breakdown. The new Thermobacillus species stands out for being the richest in diversity and abundance of GHs, possessing the greatest potential for biomass degradation among the six recovered genomes. We also investigated the presence and activity of the organisms corresponding to these genomes in the composting operation from which the consortium was built, using compost metagenome and metatranscriptome datasets generated in a previous study. We obtained strong evidence that five of the six recovered genomes are indeed present and active in that composting process. We have thus discovered three (perhaps four) new thermophillic bacterial species that add to the increasing repertoire of known lignocellulose degraders, whose biotechnological potential can now be investigated in further studies.