Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity

Romdhane, Sana; Spor, Aymé; Banerjee, Samiran; Breuil, Marie-Christine; Bru, David; Chabbi, Abad; Hallin, Sara; Heijden, Marcel G. A. van der; Saghaï, Aurélien; Philippot, Laurent

doi:10.1186/s40793-021-00396-9

Cited by 68 publications

(29 citation statements)

References 93 publications

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“…Organic fertilizer amendment increased the relative abundance of bacterivorous and omnivorous protists but reduced plant pathogenic protists (Xiong et al, 2018). Additionally, recent study in a long-term field experiment under different levels of land-use intensity has shown that land management not only had a major impact on the structure and composition of bacterial, protistan and fungal communities but also affected microbiome network complexity (Romdhane et al, 2022). In a recent study, Bazany et al (2022) found that water deficit stress can significantly influence inter-kingdom microbial connections in the rhizospheres of corn and sugar beet.…”

Section: Microbial Interactions and Keystone Taxa Of Crop-associated ...mentioning

confidence: 99%

Microbiomes in agroecosystem: Diversity, function and assembly mechanisms

Xiong

2022

Environ Microbiol Rep

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Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop‐associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil–plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co‐occurrence patterns, and crop‐microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.

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Section: Microbial Interactions and Keystone Taxa Of Crop-associated ...mentioning

confidence: 99%

Microbiomes in agroecosystem: Diversity, function and assembly mechanisms

Xiong

2022

Environ Microbiol Rep

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“…Co-occurrence analysis was used to inspect the association between core apicomplexan and metazoan taxa. Although co-occurrence analysis might not reflect the true complexity of host-parasite interactions, this integrative approach can help to better understand how taxonomic identity and land-use change affect the associations between host and parasite taxa 41 . Specifically, we calculated Spearman's correlations between the abundance of the top 20% abundant apicomplexan OTUs and the top 20% abundant OTUs of Arthropoda, Nematoda and Annelida.…”

Section: Statisticsmentioning

confidence: 99%

Land-use effects on parasite-metazoan host association in soils at a continental scale

Geisen

Shangguan

et al. 2022

Preprint

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Soils harbor a large number of unicellular eukaryotic parasites. These parasites, such as Apicomplexa, inhabit a wide range of soil metazoans. However, the distribution of these apicomplexan parasites, their links with hosts and the impact of human-dominated land use remain unknown across larger spatial scales. In this study, we used metabarcoding to investigate the biogeography of and links between Apicomplexa and soil metazoa in three human-dominated ecosystem types (farmlands, residential areas and parks) and more natural forests across subtropical, warm-temperate and mid-temperate climatic regions in China. Our results showed that human-dominated land use indirectly reduced apicomplexan taxon richness by reducing metazoan taxon richness. However, the richness reduction of the parasites was more pronounced in the subtropical region than in temperate regions, with the underlying mechanisms also differing among climate regions. While annual precipitation positively linked with apicomplexan richness in forests through increasing metazoan richness, climatic factors were of minor importance in human-dominated ecosystems, because of a decoupling between apicomplexan and metazoan biodiversity. Our study extends the understanding of the biodiversity of soil metazoan parasites from natural to managed systems. We conclude that land use threatens both soil animals and their parasites, with particularly strong effects on parasites in high biodiversity regions. In addition, the parasite-host association is often decoupled due to the anthropogenic modification of ecosystems. Further studies are needed to decipher the functional importance of soil parasites as their reduction in highly managed systems might indirectly affect metazoan functioning.

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“…Manipulating the soil microbiota is an effective way to alleviate GRP ( Lee et al., 2015 ; Dong et al., 2018 ; Seo et al., 2019 ). Several agricultural practices can shape the soil microbial structure ( Romdhane et al., 2022 ), which can result in either positive ( Qi et al., 2020 ) or negative outcomes on plant health ( Bziuk et al., 2021 ). For example, continuous cropping of ginseng affects the taxonomic and functional diversity of the soil microbial population and the potential pathogenic genera, increasing the risk of soil conduciveness ( Zhang et al., 2020 ; Tong et al., 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Soil amendment with cow dung modifies the soil nutrition and microbiota to reduce the ginseng replanting problem

et al. 2023

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Ginseng is a profitable crop worldwide; however, the ginseng replanting problem (GRP) is a major threat to its production. Soil amendment is a non-chemical method that is gaining popularity for alleviating continuous cropping obstacles, such as GRP. However, the impact of soil amendment with either cow dung or canola on GRP reduction and the associated soil microbiota remains unclear. In the present study, we evaluated the effect of soil amendment with cow dung, canola seed powder, and without amendment (control), on the survival of ginseng seedling transplants, the soil bacterial and fungal communities, and their associated metabolic functions. The results showed that cow dung increased ginseng seedling survival rate by 100 percent and had a remarkable positive effect on ginseng plant growth compared to control, whereas canola did not. Cow dung improved soil nutritional status in terms of pH, electrical conductivity, NO3−, total carbon, total phosphorus, and available phosphorus. The amplicon sequencing results using Illumina MiSeq showed that canola had the strongest negative effect in reducing soil bacterial and fungal diversity. On the other hand, cow dung stimulated beneficial soil microbes, including Bacillus, Rhodanobacter, Streptomyces, and Chaetomium, while suppressing Acidobacteriota. Community-level physiological profiling analysis using Biolog Ecoplates containing 31 different carbon sources showed that cow dung soil had a different metabolic activity with higher utilization rates of carbohydrates and polymer carbon sources, mainly Tween 40 and beta-methyl-d-glucoside. These carbon sources were most highly associated with Bacillota. Furthermore, predicted ecological function analyses of bacterial and fungal communities showed that cow dung had a higher predicted function of fermentation and fewer functions related to plant pathogens and fungal parasites, signifying its potential to enhance soil suppressiveness. Co-occurrence network analysis based on random matrix theory (RMT) revealed that cow dung transformed the soil microbial network into a highly connected and complex network. This study is the first to report the alleviation of GRP using cow dung as a soil amendment, and the study contributes significantly to our understanding of how the soil microbiota and metabolic alterations via cow dung can aid in GRP alleviation.

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Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity

Cited by 68 publications

References 93 publications

Microbiomes in agroecosystem: Diversity, function and assembly mechanisms

Microbiomes in agroecosystem: Diversity, function and assembly mechanisms

Land-use effects on parasite-metazoan host association in soils at a continental scale

Soil amendment with cow dung modifies the soil nutrition and microbiota to reduce the ginseng replanting problem

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