Analysis of microbial utilization of rice straw in paddy soil using a DNA‐SIP approach

Abstract

Considering the close connection between soil microorganisms with carbon (C) cycling, the aim of this study was to identify the specific bacterial and fungal microbes that assimilate 13C from incorporated rice straw and explore their dynamics and characteristics during straw decomposition in paddy soil. Soil microcosms based on 12/13C‐labeled rice straw were incubated with the determination of CO2 production at 1, 3, 7, 14, 28, 56 and 90 days after straw incorporation. Meanwhile, the targeted soil bacterial and fungal communities were characterized using a DNA‐based stable isotope probing (DNA‐SIP) approach combined with Illumina MiSeq sequencing. Rice straw decomposed rapidly in the first 2 weeks, coupled with a large turnover of soil native organic matter. During this process, Actinobacteria including the orders Streptomycetales, Caternulisporales and Corynebacteriales dominated the community utilizing rice straw‐derived C with a succession from Streptomyces, to Kitasatospora, to Catenulispora. At Days 56 to 90, the dominant orders assimilating rice straw‐derived 13C were Micrococcales, Sphingobacteriia, Gammaproteobacteria from phyla Actinobacteria, Bacteroidetes and Proteobacteria, respectively. The fungal orders Onygenales, Capnodiales, Sordariales and Pleosporales showed stronger ability of 13C utilization at late decomposition stage. Taken together, along with stimulation of soil organic matter mineralization after rice straw addition, dynamics of 13C‐assimilating bacterial and fungal groups with various characteristics were identified.

Pairing litter decomposition with microbial community structures using the Tea Bag Index (TBI)

“…3c). Similar increases in relative abundance of Pseudomonadales, Flavobacteriales, Sphingobacteriales, 290 Micrococcales have been observed in straw decomposing soil microcosms (Jiménez et al, 2014;Guo et al, 2020).…”

Pairing litter decomposition with microbial community structures using the Tea Bag Index (TBI)

“…4a). Similar increases in relative abundance of Pseudomonadales, Flavobacteriales, Sphingobacteriales, and Micrococcales have been observed in straw decomposing soil microcosms (Jiménez et al, 2014;Guo et al, 2020). Members of Pseudomonadales, Flavobacteriales, and Rhizobiales are well known to have the capacity to degrade plant lignin, (hemi-)cellulose, or carboxymethyl cellulose (Koga et al, 1999;McBride et al, 2009;Wang et al, 2013;Talia et al, 2012;Jackson et al, 2017).…”

Impact of rice straw management strategies on rice rhizosphere microbiomes

“…The dominance of particular bacterial phyla as found in our study (i. e. Proteobacteria, Bacteroidetes and Firmicutes; Online Resource 5) is consistent with that found in previous studies, in rice and other plants. Such phyla, since long, are considered to be common inhabitants of soil (Edwards et al, 2015(Edwards et al, , 2018Guo et al, 2020). The clear dichotomy between the M and EI treatments was a major finding; it was supported by the differential abundances of Proteobacteria, Epsilonbacteraeota and Bacteroidetes (more abundant in the EI group) and Acidobacteria (most abundant in the M group) (Fig.…”

“…Moreover, they are the key players in most biogeochemical cycles, including the transformations of crop residues, thus affecting SOM status (van Elsas et al, 2019). Soil bacteria like Bacillus, Paenibacillus, Sphingobacterium, Klebsiella, Flavobacterium, Streptomyces, Kitasatospora and others are main players in the degradation of cellulose, hemicellulose, starch, pectin and other plant compounds (Jiménez et al, 2014;Guo et al, 2020). Also, soil fungi, in particular those belonging to the Ascomycota (e.g.…”

“…Also, soil fungi, in particular those belonging to the Ascomycota (e.g. members of Trichoderma and Penicillium), have been reported as key degraders of plant remains, transforming in particular the cellulose moieties of these (Guo et al, 2020).…”