Distinct responses of rare and abundant microbial taxa to long-term soil acidification

Abstract

Global agricultural soils are experiencing rapid acidification due to atmospheric deposition and excessive fertilizer applications. Soil acidification deteriorates soil health and disrupts dynamics of soil microorganisms, threatening soil ecosystem function. However, the underlying mechanisms of acidification impacting community assembly of soil abundant and rare microbial taxa remain elusive. Here, we investigated the soil bacterial and fungal community compositions, functions, and assemblies of both abundant and rare taxa in agricultural soil that has undergone 16 years of acidification, spanning three pH gradients (pH 4.0, 6.5, and 8.0). Our results indicated that soil acidification differentially altered the co-occurrence patterns and driving factors of bacterial and fungal communities. In acidic soils, the assembly of bacterial communities was primarily governed by deterministic processes, whereas fungal communities were predominantly influenced by stochastic processes. Acidification increased the prevalence of deterministic processes among rare taxa compared to abundant taxa within bacterial and fungal communities. This significantly diminished the complexity and stability of soil microbial interactions, resulting in an imbalance within soil microbiomes under acidification. Additionally, acidification significantly impaired bacterial functions related to carbon and nitrogen metabolism. Overall, these findings provide insights into microbial population succession in long-term acidifying soils, and into our understanding of biological amelioration strategies for soil acidification.

Graphical abstract

Keywords

soil acidification / bacterial community / fungal community / rare biosphere / microbial function

Highlight

	● Responses of abundant and rare microbial taxa to soil acidification were investigated.
	● Bacterial and fungal communities exhibited distinct assembly patterns.
	● Rare taxa were more vulnerable to acidification compared to abundant taxa.
	● Acidification modified the composition of dominant species within soil bacterial communities.
	● pH is a critical predictor of microbial community assembly.

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