Distinct and Temporally Stable Assembly Mechanisms Shape Bacterial and Fungal Communities in Vineyard Soils

Abstract

Microbial communities in agricultural soils are fundamental for plant growth and in vineyard ecosystems contribute to defining regional wine quality. Managing soil microbes towards beneficial outcomes requires knowledge of how community assembly processes vary across taxonomic groups, spatial scales, and through time. However, our understanding of microbial assembly remains limited. To quantify the contributions of stochastic and deterministic processes to bacterial and fungal assembly across spatial scales and through time, we used 16 s rRNA gene and ITS sequencing in the soil of an emblematic wine-growing region of Italy.Combining null- and neutral-modelling, we found that assembly processes were consistent through time, but bacteria and fungi were governed by different processes. At the within-vineyard scale, deterministic selection and homogenising dispersal dominated bacterial assembly, while neither selection nor dispersal had clear influence over fungal assembly. At the among-vineyard scale, the influence of dispersal limitation increased for both taxonomic groups, but its contribution was much larger for fungal communities. These null-model-based inferences were supported by neutral modelling, which estimated a dispersal rate almost two orders-of-magnitude lower for fungi than bacteria.This indicates that while stochastic processes are important for fungal assembly, bacteria were more influenced by deterministic selection imposed by the biotic and/or abiotic environment. Managing microbes in vineyard soils could thus benefit from strategies that account for dispersal limitation of fungi and the importance of environmental conditions for bacteria. Our results are consistent with theoretical expectations whereby larger individual size and smaller populations can lead to higher levels of stochasticity.

Physicochemical Properties and Microbiome of Vineyard Soils from DOP Ribeiro (NW Spain) Are Influenced by Agricultural Management

“…In this research, for most of the evaluated soil properties, no significant differences were detected between the sampling dates, as also reported in other studies [ 58 ]. Therefore, the data from both sampling campaigns were treated as replicates.…”

Fungal diversities and community assembly processes show different biogeographical patterns in forest and grassland soil ecosystems

“…However, some investigations have highlighted the implication of neutrality for certain fungal communities, arbuscular mycorrhizal (AM) and ectomycorrhizal fungi (EM) in soil and roots ( Caruso et al, 2012 ; Davison et al, 2016 ; Schröter et al, 2019 ). Our observation in the context of different habitats is in line with the results of recent large-scale studies in natural soil from different habitats across Scotland ( Powell et al, 2015 ), suburban agricultural districts of Shanghai, China ( Li et al, 2021 ), and a wine-growing region of Italy ( Larsen et al, 2022 ). In contrast to our finding, however, Birch et al (2022) , who reported that deterministic processes, particularly homogenizing selection, dominated fungal communities along an 1,800 km transect of North America across Pseudotsuga forests.…”

“…Our results indicate a greater tendency toward stochastic processes, which is inconsistent with the seminal work of Zheng et al (2021) , who highlighted a substantial divergence among whole fungal communities and the AM and EM fungal community subsets within and among 12 forest ecosystems along a large latitudinal gradient. These findings might provide new evidence for the size-dispersal hypothesis that organisms with larger body sizes, like fungi, are more dispersal-limited than those with smaller body sizes, like bacteria ( Zhang et al, 2021 ; Larsen et al, 2022 ). The more substantial dispersal limitation in fungal community assembly also supplied a conceivable illustration for the more elevated beta diversities (heterogeneity in species composition; Galiana et al, 2018 ).…”

Lettuce seedlings rapidly assemble their microbiome from the environment through deterministic processes

“…The beta Nearest Taxon Index (βNTI, quantifying the deviation of Mean Nearest Taxon Distances from null expectations) was calculated using the package picante and used to test whether microbial communities assembled following deterministic or stochastic assembly processes [62, 63]. The RCbray index was estimated using the package iCAMP [28].…”