Jiménez Diego Javier, Dini-Andreote Francisco, van Elsas Jan Dirk
Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Nijenborgh 7, 9747AG Groningen, The Netherlands.
Biotechnol Biofuels. 2014 Jun 12;7:92. doi: 10.1186/1754-6834-7-92. eCollection 2014.
Mixed microbial cultures, in which bacteria and fungi interact, have been proposed as an efficient way to deconstruct plant waste. The characterization of specific microbial consortia could be the starting point for novel biotechnological applications related to the efficient conversion of lignocellulose to cello-oligosaccharides, plastics and/or biofuels. Here, the diversity, composition and predicted functional profiles of novel bacterial-fungal consortia are reported, on the basis of replicated aerobic wheat straw enrichment cultures.
In order to set up biodegradative microcosms, microbial communities were retrieved from a forest soil and introduced into a mineral salt medium containing 1% of (un)treated wheat straw. Following each incubation step, sequential transfers were carried out using 1 to 1,000 dilutions. The microbial source next to three sequential batch cultures (transfers 1, 3 and 10) were analyzed by bacterial 16S rRNA gene and fungal ITS1 pyrosequencing. Faith's phylogenetic diversity values became progressively smaller from the inoculum to the sequential batch cultures. Moreover, increases in the relative abundances of Enterobacteriales, Pseudomonadales, Flavobacteriales and Sphingobacteriales were noted along the enrichment process. Operational taxonomic units affiliated with Acinetobacter johnsonii, Pseudomonas putida and Sphingobacterium faecium were abundant and the underlying strains were successfully isolated. Interestingly, Klebsiella variicola (OTU1062) was found to dominate in both consortia, whereas K. variicola-affiliated strains retrieved from untreated wheat straw consortia showed endoglucanase/xylanase activities. Among the fungal players with high biotechnological relevance, we recovered members of the genera Penicillium, Acremonium, Coniochaeta and Trichosporon. Remarkably, the presence of peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannases and beta-glucosidases, involved in lignocellulose degradation, was indicated by predictive bacterial metagenome reconstruction. Reassuringly, tests for specific (hemi)cellulolytic enzymatic activities, performed on the consortial secretomes, confirmed the presence of such gene functions.
In an in-depth characterization of two wheat straw degrading microbial consortia, we revealed the enrichment and selection of specific bacterial and fungal taxa that were presumably involved in (hemi) cellulose degradation. Interestingly, the microbial community composition was strongly influenced by the wheat straw pretreatment. Finally, the functional bacterial-metagenome prediction and the evaluation of enzymatic activities (at the consortial secretomes) revealed the presence and enrichment of proteins involved in the deconstruction of plant biomass.
细菌和真菌相互作用的混合微生物培养物已被认为是一种分解植物废料的有效方法。特定微生物群落的特征描述可能是与将木质纤维素高效转化为纤维寡糖、塑料和/或生物燃料相关的新型生物技术应用的起点。在此，基于重复的需氧小麦秸秆富集培养，报告了新型细菌-真菌群落的多样性、组成和预测功能概况。
为了建立生物降解微观世界，从森林土壤中获取微生物群落，并将其引入含有1%（未）处理小麦秸秆的矿物盐培养基中。在每个培养步骤之后，使用1到1000倍的稀释度进行连续传代。通过细菌16S rRNA基因和真菌ITS1焦磷酸测序分析了三个连续批次培养（传代1、3和10）旁边的微生物来源。从接种物到连续批次培养，费思系统发育多样性值逐渐变小。此外，在富集过程中，肠杆菌目、假单胞菌目、黄杆菌目和鞘脂杆菌目的相对丰度有所增加。与约翰逊不动杆菌、恶臭假单胞菌和粪便鞘脂杆菌相关的操作分类单元丰富，并且成功分离出了潜在菌株。有趣的是，发现变栖克雷伯菌（OTU1062）在两个群落中均占主导地位，而从未处理小麦秸秆群落中获取的与变栖克雷伯菌相关的菌株表现出内切葡聚糖酶/木聚糖酶活性。在具有高度生物技术相关性的真菌成员中，我们发现了青霉属、顶孢霉属、附球菌属和丝孢酵母属的成员。值得注意的是，通过预测性细菌宏基因组重建表明存在参与木质纤维素降解的过氧化物酶、α-L-岩藻糖苷酶、β-木糖苷酶、β-甘露糖苷酶和β-葡萄糖苷酶。令人放心的是，对群落分泌蛋白进行的特定（半）纤维素分解酶活性测试证实了此类基因功能的存在。
在对两个降解小麦秸秆的微生物群落进行深入表征时，我们揭示了可能参与（半）纤维素降解的特定细菌和真菌类群的富集和选择。有趣的是，微生物群落组成受小麦秸秆预处理的强烈影响。最后，功能性细菌宏基因组预测和酶活性评估（在群落分泌蛋白水平）揭示了参与植物生物质解构的蛋白质的存在和富集。
