Environmental and plant community drivers of plant pathogen composition and richness

Makiola, Andreas; Holdaway, Robert J.; Wood, Jamie R.; Orwin, Kate H.; Glare, Travis R.; Dickie, Ian A.

doi:10.1111/nph.17797

Cited by 14 publications

(16 citation statements)

References 37 publications

(72 reference statements)

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“…Seven out of the nine ecological variables sharing top SNPs with more than 10% of microbiota/pathobiota traits correspond to the presence/absence of companion plant species (fig. 2B), which is in line with the neighborhood effects (also known as associational effects) on microbial transmission (Worrich et al 2019; Meyer et al 2022), particularly well-documented for bacterial pathogens (Parker et al 2015; Makiola et al 2022). For instance, a neat association peak located on chromosome 3 was common between the presence/absence of OTU6 - the Plant-Growth Promoting Bacteria (PGPB) Pseudomonas siliginis (Ramirez-Sanchez et al 2022a) - in the root compartment in fall and the presence/absence of Cardamine hirsuta , a closely related to A. thaliana (Hay and Tsiantis 2016) (fig.…”

Section: Resultssupporting

confidence: 76%

The genetic architecture of adaptation to leaf and root bacterial microbiota inArabidopsis thaliana

Roux

Frachon

Bartoli

2022

Preprint

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Understanding the role of host genome in modulating microbiota variation is a need to shed light into the holobiont theory and overcome the current limits on the description of host-microbiota interactions at the genomic and molecular levels. However, the host genetic architecture structuring microbiota is only partly described in plants. In addition, most association genetic studies on microbiota are often carried out outside the native habitats where the host evolve and the identification of signatures of local adaptation on the candidate genes has been overlooked. To fill these gaps and dissect the genetic architecture driving adaptive plant-microbiota interactions, we adopted a Genome-Environmental-Association (GEA) analysis on 141 whole-genome sequenced natural populations of Arabidopsis thaliana characterized in situ for their leaf and root bacterial communities and a large range of environmental descriptors (i.e. climate, soil and plant communities). Across 194 microbiota traits, a much higher fraction of among-population variance was explained by the host genetics than by ecology, with the plant neighborhood as the main ecological driver of microbiota variation. Importantly, the relative importance of host genetics and ecology expressed a phylogenetic signal at the family and genus level. In addition, the polygenic architecture of adaptation to bacterial communities was highly flexible between plant compartments and seasons. Relatedly, signatures of local adaptation were stronger on QTLs of the root microbiota in spring. Finally, we provide evidence that plant immunity, in particular the FLS2 gene, is a major source of adaptive genetic variation structuring bacterial assemblages in A. thaliana.

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Section: Resultssupporting

confidence: 76%

The genetic architecture of adaptation to leaf and root bacterial microbiota inArabidopsis thaliana

Roux

Frachon

Bartoli

2022

Preprint

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“…Symbiotic fungi were able to adjust richness by themselves and with the help of plants to counteract the detrimental effects of salinity, while saprophytic fungi could only adapt to high salt stress by adjusting their richness by themselves [ 105 ]. Inconsistent with the findings of Du et al [ 106 ], there was a weak relationship between SOC and α-diversity of pathogenic fungi in our study, suggesting that other ecological factors may have a greater effect on α-diversity of pathogenic fungi [ 107 ].…”

Section: Discussionsupporting

confidence: 62%

Altitudinal Variation Influences Soil Fungal Community Composition and Diversity in Alpine–Gorge Region on the Eastern Qinghai–Tibetan Plateau

Chen

Shi

Liu

et al. 2022

JoF

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Soil fungi play an integral and essential role in maintaining soil ecosystem functions. The understanding of altitude variations and their drivers of soil fungal community composition and diversity remains relatively unclear. Mountains provide an open, natural platform for studying how the soil fungal community responds to climatic variability at a short altitude distance. Using the Illumina MiSeq high-throughput sequencing technique, we examined soil fungal community composition and diversity among seven vegetation types (dry valley shrub, valley-mountain ecotone broadleaved mixed forest, subalpine broadleaved mixed forest, subalpine coniferous-broadleaved mixed forest, subalpine coniferous forest, alpine shrub meadow, alpine meadow) along a 2582 m altitude gradient in the alpine–gorge region on the eastern Qinghai–Tibetan Plateau. Ascomycota (47.72%), Basidiomycota (36.58%), and Mortierellomycota (12.14%) were the top three soil fungal dominant phyla in all samples. Soil fungal community composition differed significantly among the seven vegetation types along altitude gradients. The α-diversity of soil total fungi and symbiotic fungi had a distinct hollow pattern, while saprophytic fungi and pathogenic fungi showed no obvious pattern along altitude gradients. The β-diversity of soil total fungi, symbiotic fungi, saprophytic fungi, and pathogenic fungi was derived mainly from species turnover processes and exhibited a significant altitude distance-decay pattern. Soil properties explained 31.27−34.91% of variation in soil fungal (total and trophic modes) community composition along altitude gradients, and the effects of soil nutrients on fungal community composition varied by trophic modes. Soil pH was the main factor affecting α-diversity of soil fungi along altitude gradients. The β-diversity and turnover components of soil total fungi and saprophytic fungi were affected by soil properties and geographic distance, while those of symbiotic fungi and pathogenic fungi were affected only by soil properties. This study deepens our knowledge regarding altitude variations and their drivers of soil fungal community composition and diversity, and confirms that the effects of soil properties on soil fungal community composition and diversity vary by trophic modes along altitude gradients in the alpine–gorge region.

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“…As reported, palaeoclimate, current climate, soil development, soil chemistry, topography, and vegetation account for a large variation in the structure of microbial communities 9 , 10 , 35 – 37 . However, micronutrients were demonstrated to explain a unique and significant part of variation in our study.…”

Section: Discussionmentioning

confidence: 64%

“…fungi, the composition of protists is dominated by consumers and is found to be jointly structured by climate, soil physicochemical properties, macronutrients, micronutrients and its prey 20,34 . As reported, palaeoclimate, current climate, soil development, soil chemistry, topography, and vegetation account for a large variation in the structure of microbial communities 9,10,[35][36][37] . However, micronutrients were demonstrated to explain a unique and significant part of variation in our study.…”

Section: Discussionmentioning

confidence: 69%

The neglected role of micronutrients in predicting soil microbial structure

Peng

Liang

Gao

et al. 2022

npj Biofilms Microbiomes

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Predicting the distribution patterns of soil microbial communities requires consideration of more environmental drivers. The effects of soil micronutrients on composition of microbial communities are largely unknown despite micronutrients closely relating to soil fertility and plant communities. Here we used data from 228 agricultural fields to identify the importance of micronutrients (iron, zinc, copper and manganese) in shaping structure of soil microbial communities (bacteria, fungi and protist) along latitudinal gradient over 3400 km, across diverse edaphic conditions and climatic gradients. We found that micronutrients explained more variations in the structure of microbial communities than macronutrients in maize soils. Moreover, micronutrients, particularly iron and copper, explained a unique percentage of the variation in structure of microbial communities in maize soils even after controlling for climate, soil physicochemical properties and macronutrients, but these effects were stronger for fungi and protist than for bacteria. The ability of micronutrients to predict the structure of soil microbial communities declined greatly in paddy soils. Machine learning approach showed that the addition of micronutrients substantially increased the predictive power by 9–17% in predicting the structure of soil microbial communities with up to 69–78% accuracy. These results highlighted the considerable contributions of soil micronutrients to microbial community structure, and advocated that soil micronutrients should be considered when predicting the structure of microbial communities in a changing world.

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Environmental and plant community drivers of plant pathogen composition and richness

Cited by 14 publications

References 37 publications

The genetic architecture of adaptation to leaf and root bacterial microbiota inArabidopsis thaliana

The genetic architecture of adaptation to leaf and root bacterial microbiota inArabidopsis thaliana

Altitudinal Variation Influences Soil Fungal Community Composition and Diversity in Alpine–Gorge Region on the Eastern Qinghai–Tibetan Plateau

The neglected role of micronutrients in predicting soil microbial structure

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