Long-Term Chemical-Only Fertilization Induces a Diversity Decline and Deep Selection on the Soil Bacteria

Abstract

Fertilization regimes are known to drive succession of the soil microbial community, whereas the assembly rules involved remain elusive. Moreover, the ecological roles of microbial “generalists” and “specialists” in soils with contrasting fertilization regimes have not been characterized. We explored how long-term fertilization regimes (i.e., treatments conducted for at least 30 years) impact the soil bacteria by modifying species richness, diversity, bacterial assembly, and niche breadth. Compared with long-term organic fertilizer input, the soils having undergone chemical-only fertilization contained smaller amounts of carbon resources and had a more acidic environment. This strong environmental constraint lowered the soil bacterial reservoir and resulted in a detectable ecoevolutionary transformation, with both a higher proportion of specialists and a stronger signature of deterministic processes. Overall, this study provided a new comprehensive understanding of the assembly rules of bacterial generalists and specialists under long-term fertilization regimes. This study also highlighted that chemical-only fertilization, a ubiquitous agricultural practice of current conventional agriculture, induced a strong and similar environmental force that transformed the soil microbiota from 28°N to 46°N included in this study. IMPORTANCE Chemical-only fertilization is ubiquitous in contemporary conventional agriculture despite the fact that sustainability of this agricultural practice is increasingly being questioned because of the current observed soil degradation. We explored how long-term chemical-only versus organic-only fertilizations impacted the soil microbiota reservoir in terms of both diversity and induced assembly processes. The results showed that long-term chemical-only fertilization resulted in deep selection pressure on the soil microbial community reservoir, with both a higher proportion of specialists and a stronger signature of deterministic processes. The soil microbiota has clearly changed as a consequence of the fertilization regime. The diagnoses of the functional consequences of these ecoevolutionary changes in relation to agricultural practices are key to imagining agriculture in the time ahead and especially regarding future efforts for the conservation, restoration, and management of the soil microbiota reservoir which is key to the fertility of the ecosystem.

Seed‐borne, endospheric and rhizospheric core microbiota as predictors of plant functional traits across rice cultivars are dominated by deterministic processes

“…The generalists and specialists in each plant microhabitat were classified as previously described (Sriswasdi et al ., 2017; Xu et al ., 2020). Herein, each individual variety of rice was considered a unique environment.…”

“…The OTUs were classified as generalists or specialists when the number of observed OTUs exceeds the expected distribution. Complementarily, the identities of generalists and specialists were verified by using niche breadth, as generalists are distributed across a wider range of environments and have a higher niche breadth value than specialists (Xu et al ., 2020).…”

“…Current research suggests that transient associations should be filtered out to refine the focus on the core microbiota, which comprise stable and persistent microbial taxa and have a greater likelihood of influencing host‐plant phenotype (Vandenkoornhuyse et al ., 2015; Busby et al ., 2017; Lemanceau et al ., 2017). From an ecological perspective, generalist species can be defined as taxa that are able to adapt to diverse habitats or environments (Sriswasdi et al ., 2017; Xu et al ., 2020). Thus, the wide and stably distributed generalist species could be considered as members of the core microbiota, with high occupancy, that persist across multiple hosts and microhabitats (Kokou et al ., 2019).…”

Distinct Community Assembly Processes of Abundant and Rare Soil Bacteria in Coastal Wetlands along an Inundation Gradient

“…To assess the difference between AT and RT subpopulations, Spearman’s rank correlation ρ was used to assess the abundance-occupancy relationship of bacterial taxa between the log-transformed mean relative abundance of bacteria and the number of sites they occupied ( 85 ). The relationship between taxa’s niche width and their log-transformed mean relative abundance was also determined ( 86 , 87 ). In addition, to better understand the biodiversity patterns and to explore their causes, compositional dissimilarities (beta diversity) among sites were subdivided into replacement and richness difference components (Podani family, Sørensen dissimilarities) using the adespatial package.…”

Microbiome of the Rhizosphere: from Structure to Functions

“…Herein, to clarify the general differences, we collected the 16s rRNA amplicon-based sequencing data from all available gene banks, and then synthetically analyzed the data using state-of-the-art bioinformatic methods. Bulk soil serves as a microbial reservoir for the rhizo-microbiome 16 and harbors considerable microbial diversities that are distinctly shaped by the environmental factors of the respective microhabitats 17,18 . We thus hypothesized that i) as the rhizobacterial assemblages are predominantly recruited from the corresponding bulk soil, but are preselected by an excess of released root carbon, the bacterial diversity is generally lower and bacterial network displays less complexity in the rhizosphere.…”