Sculpting the soil microbiota

Custódio, Valéria; Gonin, Mathieu; Stabl, Georg; Bakhoum, Niokhor; Oliveira, M. Margarida; Gutjahr, Caroline; Castrillo, Gabriel

doi:10.1111/tpj.15568

Cited by 53 publications

(28 citation statements)

References 147 publications

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“…Strict hygrophiles are principally associated with Acidobacteriota , Bacteroidota , and Proteobacteria . In ecological and biological terms, it is not surprising that a soil without water restriction presents a variety of microorganisms ( 88 ). However, a study focusing on fungi (internal transcribed spacer [ITS]) could provide more information on the diversity and soil pressure associated with strict hygrophiles as these appear to be more sensitive indicators of soil water content than bacteria ( 89 ).…”

Section: Discussionmentioning

confidence: 99%

Study of Wetland Soils of the Salar de Atacama with Different Azonal Vegetative Formations Reveals Changes in the Microbiota Associated with Hygrophile Plant Type on the Soil Surface

et al. 2022

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The study of the composition and diversity of the wetland soil microbiota associated with hygrophilous plants in a desert ecosystem of the high Puna in northern Chile makes it an ideal approach to search for novel extremophilic microorganisms with unique properties. These microorganisms are adapted to survive in ecological niches, such as those with high UV irradiation, extreme drought, and high salt concentration; they can be applied in various fields, such as biotechnology and astrobiology, and industries, including the pharmaceutical, food, agricultural, biofuel, cosmetic, and textile industries.

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Section: Discussionmentioning

confidence: 99%

Study of Wetland Soils of the Salar de Atacama with Different Azonal Vegetative Formations Reveals Changes in the Microbiota Associated with Hygrophile Plant Type on the Soil Surface

et al. 2022

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“…In this study, it was observed that soil water content showed a significant negative correlation with the fungal Chao1 index ( Figure S3 ). Similarly, the effect of SWC on fungal diversity was also reported in other forest ecosystems, such as the forests in western Canada [ 57 ] and eastern China [ 58 , 59 ] This may be because soil water content influences the O 2 level in the soil and affects soil nutrient availability and transportation [ 29 ], which in turn structures soil fungal metabolic pathways and community composition [ 60 ].…”

Section: Discussionmentioning

confidence: 85%

Does Forest Soil Fungal Community Respond to Short-Term Simulated Nitrogen Deposition in Different Forests in Eastern China?

Liu

Tian

et al. 2022

JoF

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Nitrogen (N) deposition has changed plants and soil microbes remarkably, which deeply alters the structures and functions of terrestrial ecosystems. However, how forest fungal diversity, community compositions, and their potential functions respond to N deposition is still lacking in exploration at a large scale. In this study, we conducted a short-term (4–5 years) experiment of artificial N addition to simulated N deposition in five typical forest ecosystems across eastern China, which includes tropical montane rainforest, subtropical evergreen broadleaved forest, temperate deciduous broadleaved forest, temperate broadleaved and conifer mixed forest, and boreal forest along a latitudinal gradient from tropical to cold temperature zones. Fungal compositions were identified using high-throughput sequencing at the topsoil layer. The results showed that fungal diversity and fungal community compositions among forests varied apparently for both unfertilized and fertilized soils. Generally, soil fungal diversity, communities, and their potential functions responded sluggishly to short-term N addition, whereas the fungal Shannon index was increased in the tropical forest. In addition, environmental heterogeneity explained most of the variation among fungal communities along the latitudinal gradient. Specifically, soil C: N ratio and soil water content were the most important factors driving fungal diversity, whereas mean annual temperature and microbial nutrient limitation mainly shaped fungal community structure and functional compositions. Topsoil fungal communities in eastern forest ecosystems in China were more sensitive to environmental heterogeneity rather than short-term N addition. Our study further emphasized the importance of simultaneously evaluating soil fungal communities in different forest types in response to atmospheric N deposition.

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“…Soil microbial communities are considered essential for maintaining soil health and promoting healthy plant growth [ 75 – 77 ], but agricultural intensification and modern agriculture management practices can have lasting effects on the soil microbiome [ 5 , 17 , 78 ]. In this study, the legacy effects of metam sodium (MS) on soil microbial communities and their response to MS application were examined.…”

Section: Discussionmentioning

confidence: 99%

Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application

Skillman

Dung

et al. 2022

Environmental Microbiome

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Background Soil microorganisms are integral to maintaining soil health and crop productivity, but fumigation used to suppress soilborne diseases may affect soil microbiota. Currently, little is known about the legacy effects of soil fumigation on soil microbial communities and their response to fumigation at the production scale. Here, 16S rRNA gene and internal transcribed spacer amplicon sequencing was used to characterize the bacterial and fungal communities in soils from intensively managed crop fields with and without previous exposure to metam sodium (MS) fumigation. The effect of fumigation history, soil series, and rotation crop diversity on microbial community variation was estimated and the response of the soil microbiome to MS application in an open microcosm system was documented. Results We found that previous MS fumigation reduced soil bacterial diversity but did not affect microbial richness and fungal diversity. Fumigation history, soil series, and rotation crop diversity were the main contributors to the variation in microbial β-diversity. Between fumigated and non-fumigated soils, predominant bacterial and fungal taxa were similar; however, their relative abundance varied with fumigation history. In particular, the abundance of Basidiomycete yeasts was decreased in fumigated soils. MS fumigation also altered soil bacterial and fungal co-occurrence network structure and associations. In microcosms, application of MS reduced soil microbial richness and bacterial diversity. Soil microbial β-diversity was also affected but microbial communities of the microcosm soils were always similar to that of the field soils used to establish the microcosms. MS application also induced changes in relative abundance of several predominant bacterial and fungal genera based on a soil’s previous fumigation exposure. Conclusions The legacy effects of MS fumigation are more pronounced on soil bacterial diversity, β-diversity and networks. Repeated fumigant applications shift soil microbial compositions and may contribute to differential MS sensitivity among soil microorganisms. Following MS application, microbial richness and bacterial diversity decreases, but microbial β-diversity was similar to that of the field soils used to establish the microcosms in the short-term (< 6 weeks). The responses of soil microbiome to MS fumigation are context dependent and rely on abiotic, biotic, and agricultural management practices.

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Sculpting the soil microbiota

Cited by 53 publications

References 147 publications

Study of Wetland Soils of the Salar de Atacama with Different Azonal Vegetative Formations Reveals Changes in the Microbiota Associated with Hygrophile Plant Type on the Soil Surface

Study of Wetland Soils of the Salar de Atacama with Different Azonal Vegetative Formations Reveals Changes in the Microbiota Associated with Hygrophile Plant Type on the Soil Surface

Does Forest Soil Fungal Community Respond to Short-Term Simulated Nitrogen Deposition in Different Forests in Eastern China?

Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application

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