DNA stable-isotope probing delineates carbon flows from rice residues into soil microbial communities depending on fertilization.

DNA stable-isotope probing delineates carbon flows from rice residues into soil microbial communities depending on fertilization.

Appl Environ Microbiol. 2020 Jan 17;:

Authors: Kong Y, Kuzyakov Y, Ruan Y, Zhang J, Wang T, Wang M, Guo S, Shen Q, Ling N

Abstract
Decomposition of crop residues in soil is mediated by microorganisms whose activities varied with fertilization. The complexity of active microorganisms and their interactions by utilizing residues is impossible to disentangle without isotope applications. Thus, 13C-labeled rice residues were employed and DNA stable-isotope probing (DNA-SIP) combined with high-throughput sequencing was applied to identify microbes active in assimilating residue carbon (C). Manure addition strongly modified microbial community compositions involved in the C flow from rice-residues. Relative abundances of bacterial genus Lysobacter and fungal genus Syncephalis were increased, but that of bacterial genus Streptomyces and fungal genus Trichoderma were decreased in soils receiving mineral fertilizers plus manure (NPKM) compared to soils receiving only mineral fertilizers (NPK). Microbes involved in the flow of residue-C formed more complex network in NPKM than that in NPK soils, because of necessity to decompose more diverse organic compounds. The fungal species (Jugulospora rotula and Emericellopsis terricola in NPK and NPKM soils, respectively) were identified as keystone species in network and may significantly contribute to residue-C decomposition. Most of fungal genera in NPKM soils, especially Chaetomium, Staphylotrichum, Penicillium and Aspergillus, responded faster to residue addition than those in NPK soils. This is connected with the changes in the composition of the rice residue during the degradation and with fungal adaptation (abundance and activity) to continuous manure input. Our findings provide fundamental information about the roles of key microbial groups in residue decomposition and offer important cue on manipulating the soil microbiome for residue utilization and C sequestration in soil.Importance Identifying and understanding the active microbial communities and interactions involved in plant-residue utilization is a key question to elucidate the transformation of soil organic matter (SOM) in agricultural ecosystems. Microbial community composition responds strongly to management, but little is known about specific microbial groups involved in plant-residue utilization and consequently microbial functions under distinct fertilization. We combined DNA stable-isotope (13C) probing and high-throughput sequencing to identify active fungal and bacterial groups degrading residues in soils after 3-year mineral fertilization with and without manure. Manuring changed the active microbial composition and complexified microbial interactions involved in residue-C flow. Most fungal genera, especially Chaetomium, Staphylotrichum, Penicillium and Aspergillus, responded to residue addition faster in soils historically received manure. We generated a valuable “library of microorganisms” involved in plant residue utilization for future targeted research to exploit specific functions of microbial groups in organic matter utilization and C sequestration.

PMID: 31953339 [PubMed – as supplied by publisher]

Source: Industry