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利用稳定同位素探测技术鉴定地理和土壤条件不同的土壤中对纤维素有响应的细菌和真菌群落。

Identification of cellulose-responsive bacterial and fungal communities in geographically and edaphically different soils by using stable isotope probing.

机构信息

Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.

出版信息

Appl Environ Microbiol. 2012 Apr;78(7):2316-27. doi: 10.1128/AEM.07313-11. Epub 2012 Jan 27.

Abstract

Many bacteria and fungi are known to degrade cellulose in culture, but their combined response to cellulose in different soils is unknown. Replicate soil microcosms amended with [(13)C]cellulose were used to identify bacterial and fungal communities responsive to cellulose in five geographically and edaphically different soils. The diversity and composition of the cellulose-responsive communities were assessed by DNA-stable isotope probing combined with Sanger sequencing of small-subunit and large-subunit rRNA genes for the bacterial and fungal communities, respectively. In each soil, the (13)C-enriched, cellulose-responsive communities were of distinct composition compared to the original soil community or (12)C-nonenriched communities. The composition of cellulose-responsive taxa, as identified by sequence operational taxonomic unit (OTU) similarity, differed in each soil. When OTUs were grouped at the bacterial order level, we found that members of the Burkholderiales, Caulobacteriales, Rhizobiales, Sphingobacteriales, Xanthomonadales, and the subdivision 1 Acidobacteria were prevalent in the (13)C-enriched DNA in at least three of the soils. The cellulose-responsive fungi were identified as members of the Trichocladium, Chaetomium, Dactylaria, and Arthrobotrys genera, along with two novel Ascomycota clusters, unique to one soil. Although similarities were identified in higher-level taxa among some soils, the composition of cellulose-responsive bacteria and fungi was generally unique to a certain soil type, suggesting a strong potential influence of multiple edaphic factors in shaping the community.

摘要

许多细菌和真菌已知可在培养物中降解纤维素,但它们对不同土壤中纤维素的综合反应尚不清楚。本研究使用重复的土壤微宇宙,用 [(13)C]纤维素处理,以鉴定对五种在地理和土壤上具有差异的土壤中的纤维素具有响应性的细菌和真菌群落。通过 DNA-稳定同位素探测结合细菌和真菌群落的小亚基和大亚基 rRNA 基因的 Sanger 测序,评估了纤维素响应性群落的多样性和组成。在每种土壤中,与原始土壤群落或 (12)C-非富集群落相比,(13)C 富集的纤维素响应群落的组成明显不同。通过序列操作分类单元(OTU)相似性鉴定的纤维素响应分类群的组成在每种土壤中均有所不同。当 OTUs 按细菌目水平分组时,我们发现伯克霍尔德氏菌目、柄杆菌目、根瘤菌目、鞘氨醇单胞菌目、黄单胞菌目和 1 亚酸杆菌门的成员在至少三种土壤中的(13)C 富集 DNA 中普遍存在。纤维素响应真菌被鉴定为 Trichocladium、Chaetomium、Dactylaria 和 Arthrobotrys 属的成员,以及两个独特的土壤特有新的子囊菌门簇。尽管在某些土壤中鉴定出了较高分类群的相似性,但纤维素响应细菌和真菌的组成通常是特定土壤类型所特有的,这表明多种土壤因素在塑造群落方面具有很强的潜在影响。

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