Distinct effects of abundant and rare microbial communities on ecosystem multifunctionality across the soil profiles in agricultural Isohumosols

Highlights

	● Microbial taxa living in deep soil cooperated closely with each other to cope with environmental stress.
	● Rare microbial taxa occupy more central positions within ecological networks.
	● Rare microbial community assembly was predominantly governed by deterministic processes.
	● The impact of rare microbial taxa on ecosystem multifunctionality was greater than that of abundant taxa.

Abstract

Elucidating the intricate dynamics of microbial communities across soil profiles is essential for deciphering the mechanisms by which microorganisms regulate ecosystem functions. However, previous studies on soil microorganisms have predominantly centered on abundant taxa, neglecting the significant role of rare taxa in maintaining ecosystem functions. This study comprehensively analyzed the diversity and assembly processes of both rare and abundant microbial taxa in the profiles of Udic and Ustic Isohumosols in northeast China. We also explored the relative contribution of rare and abundant microbial taxa in maintaining ecosystem multifunctionality. Results showed that rare microbial taxa exhibited a higher diversity compared to abundant taxa, and rare microbial taxa occupied more central positions within networks. Furthermore, rare taxa displayed narrower ecological niche breadths and stronger phylogenetic signals, and their community assembly was predominantly governed by deterministic processes. In contrast, stochastic processes exert more pronounced influences on the assemblage of abundant taxa. Ecosystem multifunctionality was significantly reduced in deep soil horizons relative to the surface soil horizons. This is accompanied by close cooperation of microorganisms to cope with environmental stress in deep soils. This study highlights the pivotal role of rare microbial communities in shaping multifunctionality of ecosystems across the entire soil profiles.

Graphical abstract

Keywords

assembly processes / ecosystem functions / microbial interactions / rare taxa / soil profiles

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Author contributions

Haidong Gu: Investigation, formal analysis, data curation. Zhuxiu Liu: Investigation, formal analysis, writing – original draft. Qin Yao: Investigation, visualization. Feng Jiao: Formal analysis, investigation. Junjie Liu: Supervision, fund acquisition, experiment design, writing – reviewing & editing. Jian Jin: Conceptualization, methodology. Xiaobing Liu: Conceptualization, methodology. Guanghua Wang: Supervision, fund acquisition, experiment design, writing – reviewing & editing.

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgements

This work was supported by the National Natural Science Foundation of China (Grant No. 41977202), the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDA28020201), and the Heilongjiang Provincial Natural Science Foundation of China (Grant No. ZD2022D001).

Data availability

All raw sequences were deposited in the Genome Sequence Archive (GSA) (see the website of bigd.big.ac.cn/gsa) with the accession numbers, PRJCA007978, PRJCA007990, and PRJCA007975, respectively. The full code is available from the corresponding author upon reasonable request.

Electronic supplementary material

Supplementary material is available in the online version of this article at https://doi.org/10.1007/s42832-024-0289-4 and is accessible for authorized users.

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