Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil

We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13C-incorporation into DNA from 13C-xylose and 13C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated 13C in the 13C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi and Planctomycetes.

本研究采用DNA稳定同位素示踪（DNA Stable Isotope Probing, SIP）这一精密实验方法，探究微生物对土壤有机质分解过程的贡献。本实验针对土壤中代谢易变性碳与结构性碳的功能类微生物群系，系统解析其动态变化与生态特征。我们向土壤基质中添加两类复合改良底物，分别以¹³C-木糖（¹³C-xylose）与¹³C-纤维素（¹³C-cellulose）进行标记，以模拟植物生物质中常见组分来源的易变性碳库与结构性碳库。研究结果显示，分别有49个与63个操作分类单元（operational taxonomic units, OTUs）从¹³C-木糖与¹³C-纤维素中摄取¹³C并将其整合至自身DNA中。在¹³C-木糖处理组中，摄取¹³C的微生物类群随培养时间发生显著演替：培养第1天以厚壁菌门（Firmicutes）为绝对优势类群，第3天转为拟杆菌门（Bacteroidetes），第7天则以放线菌门（Actinobacteria）为主导类群。此类¹³C标记动态表明，易变性碳可通过不同营养层级进行传递与周转。与之形成鲜明对比的是，纤维素碳的微生物代谢普遍发生于培养14天之后，且其系统发育组成随时间未发生显著程度的改变。参与代谢纤维素碳的微生物类群隶属于若干研究程度较低但广泛分布于土壤的演化支系，包括疣微菌门（Verrucomicrobia）、绿弯菌门（Chloroflexi）与浮霉菌门（Planctomycetes）。