Abundant fungi adapt to broader environmental gradients than rare fungi in agricultural fields

Jiao, Shuo; Lu, Yahai

doi:10.1111/gcb.15130

Cited by 287 publications

(241 citation statements)

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“…Both stochastic and deterministic components are embedded in four ecological processes, including selection, dispersal, diversi cation, and drift [27]. The balance between stochastic and deterministic assembly processes is mediated by environmental factors [28]. Several recent studies have provided an excellent overview of the ecological processes controlling microbial community structure and biogeographic patterns in general [29][30][31][32][33].…”

Section: Introductionmentioning

confidence: 99%

Microbiota community assembly in wild rice (Oryza longistaminata) in response to drought stress shows phylogenetic conservation, stochasticity, and aboveground-belowground patterns

Ding

Peng

Chen

et al. 2020

Preprint

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Abstract Background Drought is a global environmental stress that limits crop yields. Microbial communities control many biogeochemical processes, and a predictive understanding of how crop microbial communities assemble in response to drought stress is central to addressing the challenges caused by drought. Little is known about the microbiome assembly processes in rice-ecosystems, particularly with regard to their environmental adaptation. Wild rice may serve as a source of superior drought tolerance candidate for rice breeding. There is an urgent need to explore wild rice resistance mechanisms to drought stress. Here, we evaluated the effect of drought stress on the microbial community recruitment and assembly in the endosphere (leaf, stem, and root) and rhizosphere of Oryza longistaminata. Results Species replacement was the dominant process shaping microbial community composition under drought stress. O. longistaminata recruited the phyla Actinobacteria and Fusobacteria, the genus Streptomyces, and phototrophic prokaryotes to improve its fitness. The host exerted strong effects on microbiome assembly, and the responses of the microbial community structure to the drought environment showed above- and belowground patterns. Drought reduced taxonomic α-diversity and destabilized co-occurrence network properties in the leaves and stems, but not in the roots and rhizosphere. Drought promoted the restructuring and strengthening of belowground network links to more strongly interconnect network properties. The drought response of the microbiome was phylogenetically conserved. Stochastic (neutral) processes acted on microbial community reassembly in response to drought stress across all four compartments. Conclusions Our results provide new insight into the mechanisms through which drought alters microbial community assembly in drought-tolerant wild rice and reveal a potential strategy for manipulating plant microbiomes to improve crop fitness.

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Section: Introductionmentioning

confidence: 99%

Microbiota community assembly in wild rice (Oryza longistaminata) in response to drought stress shows phylogenetic conservation, stochasticity, and aboveground-belowground patterns

Ding

Peng

Chen

et al. 2020

Preprint

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“…Microbial β-diversity varies along environmental gradients (e.g., pH and salinity) [14,15]. Many ecological theories that attempt to explain diversity-environment interconnections mainly consider species interaction models (e.g., competition and cooperation) and its in-situ resource (e.g., space and nutrient availability) [13,16,17]. Heterogeneity in substrate preference and environmental stress adaptations of microorganisms results in differences in microbial growth and biomass yield [14,15,18].…”

Section: Introductionmentioning

confidence: 99%

“…Heterogeneity in substrate preference and environmental stress adaptations of microorganisms results in differences in microbial growth and biomass yield [14,15,18]. This can lead to a skewed abundance distribution in a local microbial community, with relatively few dominant and a large number of rare species (alternatively known as a "rare biosphere") [17,19,20]. Previous studies have reported that rare and abundant species often show different distribution patterns and functional traits [21][22][23].…”

Section: Introductionmentioning

confidence: 99%

“…Recent studies have described the biogeography of rare and abundant microbial taxa in various environments [17,20], with both spatial effects and environmental factors in uencing soil microbial diversity [17,20,24]. For instance, local physicochemical properties have greater effects on both rare and abundant bacterial β-diversity compared to geospatial factors [20].…”

Section: Introductionmentioning

confidence: 99%

“…For instance, local physicochemical properties have greater effects on both rare and abundant bacterial β-diversity compared to geospatial factors [20]. However, most studies investigate the biogeography of rare and abundant bacterial communities in agricultural soils [17,22,24,25], and little is known about rare and abundant bacterial and fungal taxa in natural wetlands.…”

Section: Introductionmentioning

confidence: 99%

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Stronger Environmental Adaption of Abundant than Rare Microbes in Wetland Soils from the Qinghai-Tibet Plateau

Wan

Gadd

Yang

et al. 2020

Preprint

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Background: Disentangling the biogeographic patterns of rare and abundant microbial sub-communities is essential in order to understand the generation and maintenance of microbial diversity with respect to the functions they provide. However, little is known about ecological assembly processes and environmental adaptation of rare and abundant microbial sub-communities across large spatial-scale wetlands. Using Illumina sequencing, we investigated the taxonomic and phylogenetic β-diversity of rare and abundant bacterial and fungal sub-communities in Qinghai-Tibet Plateau wetland soils. Additionally, we determined environmental breadths and phylogenetic signals of ecological preferences of rare and abundant microbial sub-communities, and investigated community assembly processes of microbial taxa. Results: We found that both taxonomic and phylogenetic similarities of rare and abundant microbial sub-communities attenuated with geographical distance. Based on threshold indicator taxa analysis and Blomberg’s K statistic, abundant microbial taxa exhibited broader environmental thresholds and stronger phylogenetic signals for ecological traits than rare microbial taxa. The strong correlations between community compositional dissimilarity and phylogenetic distance of rare microbial sub-communities also revealed that rare taxa may be more sensitive to environmental changes. In addition, the rare microbial sub-communities exhibited closer phylogenetic clustering compared with abundant microbial sub-communities. The null model analysis revealed that dispersal limitation belonging to stochastic process dominated ecological assembly of abundant bacterial sub-community, and rare and abundant fungal sub-communities; variable selection belonging to deterministic process governed community assembly of rare bacterial taxa. Neutral model analysis and variation partitioning analysis further confirmed that abundant microbial sub-communities were less environmentally constrained. Soil ammonia nitrogen was the crucial factor in mediating the balance between stochasticity and determinism of both rare and abundant microbial sub-communities, as reflected by distinct differences in stochastic process with higher ammonia nitrogen content.Conclusions: Abundant microbial sub-communities may have better environmental adaptation potential and are less dispersed by environmental changes compared with rare microbial sub-communities. Our findings extend knowledge of the adaptation of rare and abundant microbial taxa to ongoing environmental change and could facilitate prediction of biodiversity loss caused by global climate change and increasing human activity in wetlands of the Qinghai-Tibet Plateau.

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Biogeography and assembly processes of abundant and rare soil microbial taxa in the southern part of the Qilian Mountain National Park, China

Feng,

Li,

Deng

et al. 2024

Ecology and Evolution

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Soil microorganisms play vital roles in regulating multiple ecosystem functions. Recent studies have revealed that the rare microbial taxa (with extremely low relative abundances, which are still largely ignored) are also crucial in maintaining the health and biodiversity of the soil and may respond differently to environmental pressure. However, little is known about the soil community structures of abundant and rare taxa and their assembly processes in different soil layers on the Qinghai‐Tibet Plateau (QTP). The present study investigated the community structure and assembly processes of soil abundant and rare microbial taxa on the northeastern edge of the QTP. Soil microbial abundance was defined by abundant taxa, whereas rare taxa contributed to soil microbial diversity. The results of null model show that the stochastic process ruled the assembly processes of all sub‐communities. Dispersal limitation contributed more to the assembly of abundant microbial taxa in the different soil layers. In contrast, drift played a more critical role in the assembly processes of the rare microbial taxa. In addition, in contrast to previous studies, the abundant taxa played more important roles in co‐occurrence networks, most likely because of the heterogeneity of the soil, the sparsity of amplicon sequencing, the sampling strategy, and the limited samples in the present study. The results of this study improve our understanding of soil microbiome assemblies on the QTP and highlight the role of abundant taxa in sustaining the stability of microbial co‐occurrence networks in different soil layers.

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Abundant fungi adapt to broader environmental gradients than rare fungi in agricultural fields

Abstract: Revealing the fundamental mechanisms for maintaining and generating species diversity is critical to determine the links between community stability and ecosystem function (Hanson, Fuhrman,

Cited by 287 publications

References 102 publications

Microbiota community assembly in wild rice (Oryza longistaminata) in response to drought stress shows phylogenetic conservation, stochasticity, and aboveground-belowground patterns

Microbiota community assembly in wild rice (Oryza longistaminata) in response to drought stress shows phylogenetic conservation, stochasticity, and aboveground-belowground patterns

Stronger Environmental Adaption of Abundant than Rare Microbes in Wetland Soils from the Qinghai-Tibet Plateau

Biogeography and assembly processes of abundant and rare soil microbial taxa in the southern part of the Qilian Mountain National Park, China

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