Microbial communities in crop phyllosphere and root endosphere are more resistant than soil microbiota to fertilization

Zheng

et al. 2022

Preprint

Self Cite

Background Deciphering the local diversity and community assembly of plant-associated microorganisms is crucial to better predict the ecological functioning in forest ecosystems. The differences in microbial diversity and community assembly pattern between plant aboveground and belowground compartments, however, are less documented. Here, we examined the bacterial communities in the leaf- (endophytic and epiphytic) and root- (root and rhizospheric soil) associated habitats of 13 tree species in a subtropical forest ecosystem. Results The bacterial α-diversity (phylotype richness) substantially differed across the four habitats, with the highest and lowest values observed in soil and leaf endophytic compartments, respectively. The variations of α-diversity amongst the 13 tree species were more obvious in leaf endophytic and epiphytic habitats than in their corresponding roots and soils. The bacterial community compositions were different across the four habitats and were significantly more divergent in leaf- than in root-associated habitats. Moreover, deterministic processes dominated the endophytic and epiphytic community assembly, whereas stochastic processes primarily affected community assembly in root and rhizospheric soils. Leaf nutrients (nitrogen and phosphorus) and soil pH were the main factors influencing leaf- and root-related community compositions, respectively. Conclusions This study highlights the contrasting diversity and community assembly patterns between leaf- and root-inhabiting bacteria. Our findings contribute to a better understanding of the maintenance mechanisms of microbial diversity in the subtropical forest ecosystem.

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Contrasting diversity and community assembly of leaf- and root-associated bacterial communities from 13 tree species in a subtropical forest

Zheng

et al. 2022

Preprint

Self Cite

“…Plant‐associated microbiomes can be either positively or negatively influenced by agricultural management practices, resulting in taxonomic and functional alternations of the microbiomes 20 . A number of recent studies have investigated how common agricultural management practices (e.g., inorganic and organic fertilization regimes) and abiotic factors (e.g., climatic and edaphic factors) impacted the structure and functions of soil‐ and plant‐associated microbiomes and crop productivity 13,21,22 . A majority of them, however, merely focused on bacteria, fungi and protists, 21,23,24 and we have limited knowledge of the impact of agricultural management practices on fungal plant pathogens across various plant compartments.…”

Section: Introductionmentioning

confidence: 99%

“…20 A number of recent studies have investigated how common agricultural management practices (e.g., inorganic and organic fertilization regimes) and abiotic factors (e.g., climatic and edaphic factors) impacted the structure and functions of soil-and plant-associated microbiomes and crop productivity. 13,21,22 A majority of them, however, merely focused on bacteria, fungi and protists, 21,23,24 and we have limited knowledge of the impact of agricultural management practices on fungal plant pathogens across various plant compartments. Agricultural management practices often influence the dynamics of microbial communities through modulating trophic biological interactions and change the relative abundances of beneficial and pathogenic microorganisms predicted to impact plant pathogenesis.…”

mentioning

confidence: 99%

Organic fertilization regimes suppress fungal plant pathogens through modulating the resident bacterial and protistan communities

Sun

Jiao

Ren

et al. 2022

J of Sust Agri & Env

Self Cite

Introduction Fungal plant pathogens are an emerging threat to economically important crop production worldwide and a significant risk to global food security. However, we have limited knowledge of how agricultural management practices drive the emergence and spread of pathogens within crop microbiomes and the underlying ecological mechanisms. Materials and Methods We characterized the profiles of potential fungal plant pathogens, as well as bacterial and protistan communities, in sorghum phyllosphere, root endosphere, and rhizosphere and bulk soils collected from a long‐term experiment with multiple inorganic and organic fertilization regimes. Results We found contrasting patterns of fungal plant pathogens across the four sorghum–soil compartments and that organic fertilization regime significantly reduced the diversity and proportions of fungal plant pathogens in rhizosphere and bulk soils. We further found that the changes in fungal plant pathogens were driven more by resident bacterial and protistan communities than by soil physicochemical parameters. There was a significantly negative relationship between the diversity of fungal plant pathogens in the rhizosphere and bulk soils with sorghum yield and protein contents. Structural equation modeling revealed that long‐term organic fertilization regimes contributed to the suppression of fungal plant pathogens mainly through modulating the resident bacterial and protistan communities. Conclusion These findings advance our understanding of the responses of fungal plant pathogens in crop microbiomes to fertilization regimes, with implications for more targeted strategies to manage the impacts of fungal pathogens on plant health and economic losses.

Are plant traits drivers of endophytic communities in seasonally flooded tropical forests?

Boisseaux,

Troispoux,

Bordes

et al. 2024

American J of Botany

PremiseIn the Amazon basin, seasonally flooded (SF) forests offer varying water constraints, providing an excellent way to investigate the role of habitat selection on microbial communities within plants. However, variations in the microbial community among host plants cannot solely be attributed to environmental factors, and how plant traits contribute to microbial assemblages remains an open question.MethodsWe described leaf‐ and root‐associated microbial communities using ITS2 and 16 S high‐throughput sequencing and investigated the stochastic‐deterministic balance shaping these community assemblies using two null models. Plant ecophysiological functioning was evaluated by focusing on 10 leaf and root traits in 72 seedlings, belonging to seven tropical SF tree species in French Guiana. We then analyzed how root and leaf traits drove the assembly of endophytic communities.ResultsWhile both stochastic and deterministic processes governed the endophyte assembly in the leaves and roots, stochasticity prevailed. Discrepancies were found between fungi and bacteria, highlighting that these microorganisms have distinct ecological strategies within plants. Traits, especially leaf traits, host species and spatial predictors better explained diversity than composition, but they were modest predictors overall.ConclusionsThis study widens our knowledge about tree species in SF forests, a habitat sensitive to climate change, through the combined analyses of their associated microbial communities with functional traits. We emphasize the need to investigate other plant traits to better disentangle the drivers of the relationship between seedlings and their associated microbiomes, ultimately enhancing their adaptive capacities to climate change.