Diversity and assembly of active bacteria and their potential function along soil aggregates in a paddy field

放线菌门 细菌 芽单胞菌门 蛋白质细菌 拟杆菌 生物 微生物种群生物学 相对物种丰度 稳定同位素探测 群落结构 微生物 丰度(生态学) 16S核糖体RNA 生态学 遗传学
作者
Chenxiao Ding,Xinji Xu,Yaowei Liu,Xing Huang,MengYuan Xi,Haiyang Liu,Elizabeth Deyett,Marc G. Dumont,Hongjie Di,Marcela Hernández,Jianming Xu,Yong Li
出处
期刊:Science of The Total Environment [Elsevier BV]
卷期号:866: 161360-161360 被引量:8
标识
DOI:10.1016/j.scitotenv.2022.161360
摘要

Numerous studies have found that soil microbiomes differ at the aggregate level indicating they provide spatially heterogeneous habitats for microbial communities to develop. However, an understanding of the assembly processes and the functional profile of microbes at the aggregate level remain largely rudimentary, particularly for those active members in soil aggregates. In this study, we investigated the diversity, co-occurrence network, assembly process and predictive functional profile of active bacteria in aggregates of different sizes using H218O-based DNA stable isotope probing (SIP) and 16S rRNA gene sequencing. Most of the bacterial reads were active with 91 % of total reads incorporating labelled water during the incubation. The active microbial community belonged mostly of Proteobacteria and Actinobacteria, with a relative abundance of 55.32 % and 28.12 %, respectively. Assembly processes of the active bacteria were more stochastic than total bacteria, while the assembly processes of total bacteria were more influenced by deterministic processes. Furthermore, many functional profiles such as environmental information processing increased in active bacteria (19.39 %) compared to total bacteria (11.22 %). After incubation, the diversity and relative abundance of active bacteria of certain phyla increased, such as Proteobacteria (50.70 % to 59.95 %), Gemmatimonadetes (2.63 % to 4.11 %), and Bacteroidetes (1.50 % to 2.84 %). In small macroaggregates (SMA: 0.25-2 mm), the active bacterial community and its assembly processes differed from that of other soil aggregates (MA: microaggregates, <0.25 mm; LMA: large macroaggregates, 2-4 mm). For functional profiles, the relative abundance of important functions, such as amino acid metabolism, signal transduction and cell motility, increased with incubation days and/or in SMA compared to other aggregates. This study provides robust evidence that the community of active bacteria and its assembly processes in soil aggregates differed from total bacteria, and suggests the importance of dominant active bacteria (such as Proteobacteria) for the predicted functional profiles in the soil ecosystem.
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