Dataset Information

Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health.

ABSTRACT: BACKGROUND: To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known. METHODOLOGY/PRINCIPAL FINDINGS: We studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt). Using a polyphasic methodological approach to analyse microbial communities in soil as well as associated with cultivated plants, drastic effects caused by 30 years of agriculture were detected. Analysing bacterial fingerprints, we found statistically significant differences between agricultural and native desert soil of about 60%. A pyrosequencing-based analysis of the 16S rRNA gene regions showed higher diversity in agricultural than in desert soil (Shannon diversity indices: 11.21/7.90), and displayed structural differences. The proportion of Firmicutes in field soil was significantly higher (37%) than in the desert (11%). Bacillus and Paenibacillus play the key role: they represented 96% of the antagonists towards phytopathogens, and identical 16S rRNA sequences in the amplicon library and for isolates were detected. The proportion of antagonistic strains was doubled in field in comparison to desert soil (21.6%/12.4%); disease-suppressive bacteria were especially enriched in plant roots. On the opposite, several extremophilic bacterial groups, e.g., Acidimicrobium, Rubellimicrobium and Deinococcus-Thermus, disappeared from soil after agricultural use. The N-fixing Herbaspirillum group only occurred in desert soil. Soil bacterial communities were strongly driven by the a-biotic factors water supply and pH. CONCLUSIONS/SIGNIFICANCE: After long-term farming, a drastic shift in the bacterial communities in desert soil was observed. Bacterial communities in agricultural soil showed a higher diversity and a better ecosystem function for plant health but a loss of extremophilic bacteria. Interestingly, we detected that indigenous desert microorganisms promoted plant health in desert agro-ecosystems.

SUBMITTER: Koberl M

PROVIDER: S-EPMC3166316 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health.

Köberl Martina M Müller Henry H Ramadan Elshahat M EM Berg Gabriele G

PloS one 20110902 9

<h4>Background</h4>To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known.<h4>Methodology/principal findings</h4>We studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt). ...[more]

PMID: 21912695

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Project description:Soil is one of the biggest reservoirs of microbial diversity, yet the processes that define the community dynamics are not fully understood. Apart from soil management being vital for agricultural purposes, it is also considered a favorable environment for the evolution and development of antimicrobial resistance, which is due to its high complexity and ongoing competition between the microorganisms. Different approaches to agricultural production might have specific outcomes for soil microbial community composition and antibiotic resistance phenotype. Therefore in this study we aimed to compare the soil microbiota and its resistome in conventional and organic farming systems that are continually influenced by the different treatment (inorganic fertilizers and pesticides vs. organic manure and no chemical pest management). The comparison of the soil microbial communities revealed no major differences among the main phyla of bacteria between the two farming styles with similar soil structure and pH. Only small differences between the lower taxa could be observed indicating that the soil community is stable, with minor shifts in composition being able to handle the different styles of treatment and fertilization. It is still unclear what level of intensity can change microbial composition but current conventional farming in Central Europe demonstrates acceptable level of intensity for soil bacterial communities. When the resistome of the soils was assessed by screening the total soil DNA for clinically relevant and soil-derived antibiotic resistance genes, a low variety of resistance determinants was detected (resistance to β-lactams, aminoglycosides, tetracycline, erythromycin, and rifampicin) with no clear preference for the soil farming type. The same soil samples were also used to isolate antibiotic resistant cultivable bacteria, which were predominated by highly resistant isolates of Pseudomonas, Stenotrophomonas, Sphingobacterium and Chryseobacterium genera. The resistance of these isolates was largely dependent on the efflux mechanisms, the soil Pseudomonas spp. relying mostly on RND, while Stenotrophomonas spp. and Chryseobacterium spp. on RND and ABC transporters.

Project description:Biodiversity-benefits of organic farming have mostly been documented at the field scale. However, these benefits from organic farming to species diversity may not propagate to larger scales because variation in the management of different crop types and seminatural habitats in conventional farms might allow species to cope with intensive crop management. We studied flowering plant communities using a spatially replicated design in different habitats (cereal, ley and seminatural grasslands) in organic and conventional farms, distributed along a gradient in proportion of seminatural grasslands. We developed a novel method to compare the rates of species turnover within and between habitats, and between the total species pools in the two farming systems. We found that the intrahabitat species turnover did not differ between organic and conventional farms, but that organic farms had a significantly higher interhabitat turnover of flowering plant species compared with conventional ones. This was mainly driven by herbicide-sensitive species in cereal fields in organic farms, as these contained 2.5 times more species exclusive to cereal fields compared with conventional farms. The farm-scale species richness of flowering plants was higher in organic compared with conventional farms, but only in simple landscapes. At the interfarm level, we found that 36% of species were shared between the two farming systems, 37% were specific to organic farms whereas 27% were specific to conventional ones. Therefore, our results suggest that that both community nestedness and species turnover drive changes in species composition between the two farming systems. These large-scale shifts in species composition were driven by both species-specific herbicide and nitrogen sensitivity of plants. Our study demonstrates that organic farming should foster a diversity of flowering plant species from local to landscape scales, by promoting unique sets of arable-adapted species that are scarce in conventional systems. In terms of biodiversity conservation, our results call for promoting organic farming over large spatial extents, especially in simple landscapes, where such transitions would benefit plant diversity most.

Dataset Information

Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health.

Publications

Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health.

Similar Datasets

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