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

Numerous studies have found that soil microbiomes differ at the aggregate level indicating they provide spatially het-erogeneous 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 mem-bers in soil aggregates. In this study, we investigated the diversity, co-occurrence network, assembly process and pre-dictive 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 incor-porating 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 bac-teria 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 in-creased 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 abun-dance of important functions, such as amino acid metabolism, signal transduction and cell motility, increased with in-cubation days and/or in SMA compared to other aggregates. This study provides robust evidence that the community active bacteria and its assembly processes in soil aggregates differed from total bacteria, and suggests the importance dominant active bacteria (such as Proteobacteria) for the predicted functional profiles in the soil ecosystem.

Automated summary

Numerous studies have shown that the soil microbiomes differ at the aggregate level, providing heterogeneous habitats for microbial communities. However, the understanding of the assembly processes and functional profiles of active bacteria in soil aggregates is limited. This study used DNA stable isotope probing and gene sequencing to investigate the diversity, assembly processes, and functional profiles of active bacteria in different-sized aggregates. The results revealed that the active bacterial community differed from the total bacterial community in terms of assembly processes and functional profiles. The study emphasizes the importance of dominant active bacteria, such as Proteobacteria, in predicting functional profiles in the soil ecosystem.