Effect of tillage and static abiotic soil properties on microbial diversity

Legrand, Fabienne; Picot, Adeline; Cobo‐Díaz, José F.; Carof, Matthieu; Chen, Wen; Floch, Gaétan Le

doi:10.1016/j.apsoil.2018.08.016

Cited by 106 publications

(71 citation statements)

References 71 publications

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“…Shifts in the environmental factors can strongly affect the microbial diversity and composition and influence the ecosystem and its functionality. For example, crop rotation has been related with a diminished bacterial diversity of soils (Ashworth et al 2017), whereas reduced tillage and organic fertilizers increase microbial diversity (Wang et al 2017;Legrand et al 2018).…”

Section: Resultsmentioning

confidence: 99%

Diversity ofSaccharomyces cerevisiaeyeasts associated to spontaneous and inoculated fermenting grapes from Spanish vineyards

Celis

Ruíz

Martín-Santamaría

et al. 2019

Lett Appl Microbiol

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The use of commercial yeast strains is a common practice in winemaking leading to a predictable quality in wine production, avoiding stuck or sluggish fermentations. However, the use of commercial yeasts leads to a consequent reduction in autochthonous microbial diversity. In this study, 1047 isolates from three Spanish appellations of origin were checked for fingerprinting on interdelta polymorphisms and the strain composition and diversity analysed using an extensible open‐source platform for processing and analysis of an in‐house polymorphism database developed for this study. Ancient vineyards managed with organic practices showed intermediate to low levels of strains diversity indicating the existence of stable populations of Saccharomyces cerevisiae strains. A drastic reduction in the number of different S. cerevisiae strains was observed in vineyards with cellars using a selected autochthonous S. cerevisiae strain for winemaking. Contrary, the use of allochthonous commercial strains in wineries did not seem to affect the native S. cerevisiae strain composition and diversity. Significance and Impact of the Study The aim of this study was to compare different viticulture and oenological practices to determine their influence on the composition and diversity of Saccharomyces cerevisiae strains in wine fermentations. The study shows that the use of autochthonous strains of S. cerevisiae as starters for wine fermentation could have an important incidence on S. cerevisiae strains diversity in surrounding vineyards. The use of autochthonous strains of S. cerevisiae reduced the detected number of S. cerevisiae strains, a fact that was not observed when allochthonous commercial strains were used. Furthermore, vineyards managed with organic practices showed intermediate to low levels of S. cerevisiae strain diversity, whereas conventional practices showed higher levels.

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Section: Resultsmentioning

confidence: 99%

Diversity ofSaccharomyces cerevisiaeyeasts associated to spontaneous and inoculated fermenting grapes from Spanish vineyards

Celis

Ruíz

Martín-Santamaría

et al. 2019

Lett Appl Microbiol

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“…The diversity of the soil microbial community was reduced iIn a short time by the conversion, and the relative abundance of bacterial and fungal microbial communities was affected to varying degrees. Forthe bacteria, the dominant bacterial community was Proteobacteria [63], with an abundance of greater than 30%, with similar levels being found in most farmland soils. For instance, Jangid reported that Proteobacteria was found, with a prevalence of 30.6-43.2% [64], irrespective of farming patterns.…”

Section: Changes In Microbial Community Structure After Dryland-to-pamentioning

confidence: 70%

“…The results implied that waterlogging stress in paddy fields changed the soil pH, water and nutrients in different level, as well as affecting the development of soil bacterial communities. Previous studies proved that the evolution of microbial community structure and function was closely related to the levels of carbon and nitrogen in the soil, and the level of one element might limit the uptake and utilization of other elements by microorganisms [28,63,72]. The dryland-to-paddy conversion could improve the availability of soil nutrients through changing the physical and chemical properties of the soil, and thus changed the network structure of the microorganisms.…”

Section: Changes In the Structure Of Microbial Molecular Ecological Nmentioning

confidence: 99%

Flooding Irrigation Weakens the Molecular Ecological Network Complexity of Soil Microbes during the Process of Dryland-to-Paddy Conversion

Zhang

et al. 2020

IJERPH

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Irrigation has been applied on a large scale for the improvement of grain yield per hectare and production stability. However, the dryland-to-paddy conversion affects the ecological environment of areas of long-term dry farming, especially soil microorganisms. Little attention has been paid to the changes in microbial communities and the interactions between their populations in this process. Therefore, in this paper, the compositions and diversity of soil bacterial and fungal communities were explored through a combination of high-throughput sequencing technology and molecular ecological network methods using bacterial 16S rRNA and fungal ITS. The results showed that: (1) both the abundance and diversity of soil bacteria and fungi decreased in a short time, and the abundance of Actinobacteria, Firmicutes and Olpidiomycota varied greatly. (2) Compared to dry land, the modular structure of interaction networks and interspecific relationships of bacterial and fungal communities in paddy soil were simpler, and the network became more unstable. A cooperative relationship dominated in the molecular ecological network of bacteria, while a competitive relationship was dominant in the network of fungi. Actinobacteria and Firmicutes were the dominant bacterial species in dry land and paddy field, respectively. Ascomycota was dominant in the fungal communities of both dry land and paddy field. (3) The change in soil environmental factors, such as pH, electrical conductivity (EC), organic matter (OM) and available potassium (AK), directly affected the soil microbial community structure, showing a significant correlation (p < 0.05). These environmental factors also influenced the dominant microbial species. Microorganisms are the most important link in the carbon and nitrogen cycles of soil, and a large-scale dryland-to-paddy conversion may reduce the ecological stability of regional soil.

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“…Coffee samples came from perennial plantations, grown under agroforestry systems, holding several tree shade species and with minor use of fertilizers and pesticides (Gordon et al, 2007;González-Zamora et al, 2016). Moreover, tillage is not employed, leading to the establishment of many soil microbiota species (Legrand et al, 2018;Dube et al, 2019). By contrast, tomato, an annual crop with short cycle, is known by its intensive cropping systems, with high demand of agrochemicals (both fertilizers and pesticides), applied before and during the growing cycle (Pérez-Olvera et al, 2011;Pratt and Ortega, 2019).…”

Section: Discussionmentioning

confidence: 99%

The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and Tomato

et al. 2020

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The Meloidogyne-based disease complexes (MDCs) are caused by the interaction of different root-knot nematode species and phytopathogenic fungi. These complexes are devastating several important crops worldwide including tomato and coffee. Despite their relevance, little is known about the role of the bacterial communities in the MDCs. In this study 16s rDNA gene sequencing was used to analyze the bacterial microbiome associated with healthy and infested roots, as well with females and eggs of Meloidogyne enterolobii and M. paranaensis, the causal agents of MDC in tomato and coffee, respectively. Each MDC pathosystems displayed a specific taxonomic diversity and relative abundances constituting a very complex system. The main bacterial drivers of the MDC infection process were identified for both crops at order level. While corky-root coffee samples presented an enrichment of Bacillales and Burkholderiales, the corckyroot tomato samples presented an enrichment on Saprospirales, Chthoniobacterales, Alteromonadales, and Xanthomonadales. At genus level, Nocardia was common to both systems, and it could be related to the development of tumor symptoms by altering both nematode and plant systems. Furthermore, we predicted the healthy metabolic profile of the roots microbiome and a shift that may result in an increment of activity of central metabolism and the presence of pathogenic genes in both crops.

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Effect of tillage and static abiotic soil properties on microbial diversity

Cited by 106 publications

References 71 publications

Diversity ofSaccharomyces cerevisiaeyeasts associated to spontaneous and inoculated fermenting grapes from Spanish vineyards

Diversity ofSaccharomyces cerevisiaeyeasts associated to spontaneous and inoculated fermenting grapes from Spanish vineyards

Flooding Irrigation Weakens the Molecular Ecological Network Complexity of Soil Microbes during the Process of Dryland-to-Paddy Conversion

The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and Tomato

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