Mediterranean biomes are biodiversity hotspots, and vineyards are important components of the Mediterranean landscape. Over the last few decades, the amount of land occupied by vineyards has augmented rapidly, thereby increasing threats to Mediterranean ecosystems. Land use change and agricultural management have important effects on soil biodiversity, because they change the physical and chemical properties of soil. These changes may also have consequences on wine production considering that soil is a key component of terroir. Here, we describe the taxonomic diversity and metabolic functions of bacterial and fungal communities present in forest and vineyard soils in Chile. To accomplish this goal, we collected soil samples from organic vineyards in central Chile and employed a shotgun metagenomic approach to sequence the microbial DNA. Additionally, we studied the surrounding native forest to obtain a baseline of the soil conditions in the area prior to the establishment of the vineyard. Our metagenomic analyses revealed that both habitats shared most of the soil microbial species. The most abundant genera in the two habitats were the bacteria Candidatus Solibacter and Bradyrhizobium and the fungus Gibberella. Our results suggest that the soil microbial communities are similar in these forests and vineyards. Therefore, we hypothesize that native forests surrounding the vineyards may be acting as a microbial reservoir buffering the effects of the land conversion. Regarding the metabolic diversity, we found that genes pertaining to the metabolism of amino acids, fatty acids, and nucleotides as well as genes involved in secondary metabolism were enriched in forest soils. On the other hand, genes related to miscellaneous functions were more abundant in vineyard soils. These results suggest that the metabolic function of microbes found in these habitats differs, though differences are not related to taxonomy. Finally, we propose that the implementation of environmentally friendly practices by the wine industry may help to maintain the microbial diversity and ecosystem functions associated with natural habitats.

Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests.

Effect of different tillage systems on aggregate structure and inner distribution of organic carbon

Excessive soil evaporation induced water loss resulting in drought stress is a significant yield-limiting factor in dry-land regions of China. However, the crop yield response to straw mulch and tillage depends on the cumulative rainfall that varies greatly from year to year due to frequent occurrences of extreme weather events. The aim of this study was to investigate the responses of grain yield and water and nitrogen use efficiency to mulch-based no-tillage in both humid and dry climates. The experiment was laid out in split plot design using tillage as a main factor and maize straw mulch as sub-plot with three replications each. Maize straw mulch combined with no-tillage was able to conserve soil moisture (0.348 cm3 cm–3 vs. 0.398 cm3 cm–3) at tillering stage and reduce daily variation of soil temperature in the topsoil layer, and thereby increased the maximum number of wheat tillers and fertile spikes by 51.3% and 72.3%, respectively, compared to the no-mulch control. The favorable soil hydrothermal regime also enhanced the activities of soil urease and neutral phosphatase, which activated the release of plant-available soil N and Olsen–P by 61.4% and 43.2%, respectively, compared to the no-mulch control. Improved plant-available soil N lead to greater root system vigor and root surface area and thus promoted the nitrogen uptake efficiency (NUpE), maximum value of LAI and the plant assimilate accumulation. The grain yield, WUE and nitrogen utilization efficiency (NUtE) in mulch-based no-tillage were 36.8%, 16.0% and 14.8% greater, respectively, than those in no-mulch control, and they were more effective in a dry climate than in a humid climate. These results suggest that maize straw mulch combined with no-tillage can not only conserve soil moisture for wheat tillering but also activate the release of plant-available soil N and plant N acquisition for higher grain yield and water and nitrogen use efficiency.

The combined effects of maize straw mulch and no-tillage on grain yield and water and nitrogen use efficiency of dry-land winter wheat (Triticum aestivum L.)

The continuous cropping of plants can result in the disruption of the soil microbial community and caused significant declines in yields. However, there are few reports on the effects of continuous cropping of sugarcane on the microbial community structure and functional pathway. In the current study, we analyzed the structural and functional changes of microbial community structure in the rhizospheric soil of sugarcane in different continuous cropping years using Illumina Miseq high-throughput sequencing and metagenomics analysis. We collected rhizosphere soils from fields of no continuous cropping history (NCC), 10 years of continuous cropping (CC10), and 30 years of continuous cropping (CC30) periods in the Fujian province. The results demonstrated that continuous sugarcane cropping resulted in significant changes in the physicochemical properties of soil and the composition of soil bacterial and fungal communities. With the continuous cropping, the crop yield dramatically declined from NCC to CC30. Besides, the redundancy analysis (RDA) of the dominant bacterial and fungal phyla and soil physicochemical properties revealed that the structures of the bacterial and fungal communities were mainly driven by pH and TS. Analysis of potential functional pathways during the continuous cropping suggests that different KEGG pathways were enriched in different continuous cropping periods. The significant reduction of bacteria associated with rhizospheric soil nitrogen and sulfur cycling functions and enrichment of pathogenic bacteria may be responsible for the reduction of effective nitrogen and total sulfur content in rhizospheric soil of continuous sugarcane as well as the reduction of sugarcane yield and sugar content. Additionally, genes related to nitrogen and sulfur cycling were identified in our study, and the decreased abundance of nitrogen translocation genes and AprAB and DsrAB in the dissimilatory sulfate reduction pathway could be the cause of declined biomass. The findings of this study may provide a theoretical basis for uncovering the mechanism of obstacles in continuous sugarcane cropping and provide better guidance for sustainable development of the sugarcane.

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Soil Metagenomics Reveals Effects of Continuous Sugarcane Cropping on the Structure and Functional Pathway of Rhizospheric Microbial Community.

Stable soil aggregates are essential for optimal crop growth and preventing soil erosion. However, tillage is often used in agriculture to loosen the soil, which disrupts the integrity of these aggregates. Soil aggregation can be enhanced by bacteria through their ability to produce exopolysaccharides and lipopolysaccharides. These compounds stabilize soil aggregates by “gluing” soil particles together. However, it has yet to be shown how tillage influences the bacterial potential to produce aggregate-stabilizing agents. Therefore, we sampled conventional and reduced tillage treatments at 0–10 cm, 10–20 cm and 20–50 cm from a long-term field trial in Frick, Switzerland. We compared the stable aggregate fraction of the soil and the bacterial potential to produce exopolysaccharides (EPS) and lipopolysaccharides (LPS) under different tillage regimes by employing a shotgun metagenomic approach. We established a method which combines hidden Markov model searches with blasts against sequences derived from the Kyoto Encyclopedia of Genes and Genomes database to analyze genes specific for the biosynthesis of these compounds. Our data revealed that the stable aggregate fraction as well as the bacterial potential to produce EPS and LPS were comparable under both tillage regimes. The highest potential to produce these compounds was found in the upper soil layer, which was disturbed by tillage, but had higher content of organic carbon compared to the layer below the tillage horizon. Additionally, key players of EPS and LPS production differed at different sampling depths. Some families with high potential to produce EPS and LPS, such as Chitinophagaceae and Bradyrhizobiaceae, were more abundant in the upper soil layers, while others, e.g. Nitrospiraceae and Planctomycetaceae, preferred the lowest sampled soil depth. Each family had the potential to form a limited number of different aggregate-stabilizing agents. Our results indicate that conventional tillage and reduced tillage equally promote the bacterial potential to produce EPS and LPS in the tillage horizon. However, as major bacterial groups triggering EPS and LPS formation were not the same, it is likely that gene expression pattern differ in the different treatments due to various pathways of gene induction and transcription in different bacterial species.

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A long-term field experiment demonstrates the influence of tillage on the bacterial potential to produce soil structure-stabilizing agents such as exopolysaccharides and lipopolysaccharides.

This study examined the effect of conversion from a conventional tillage (CT) to a no-tillage (NT) practice and of bagasse mulching (M) on soil microbial community composition and potential functions, using phospholipid fatty acid (PLFA) analysis and shotgun metagenome sequencing. Our results showed that both the NT and the M treatment increased microbial PLFAs. The shotgun sequencing results suggested that the functional profiles are more resistant to agricultural managements than to community compositions, which supports the hypothesis of the functional redundancy of soil microbial communities. However, some metabolism-related sequences were significantly affected by different treatments. The percentage of sequences related to metabolism of carbohydrates, especially saccharide groups, was significantly higher in the CT soils than in NT and M soils, which may be linked to lower carbon (C) availability in CT soils. Compared with CT, the NT had higher alpha diversity and more sequences related to DNA metabolism, which may be associated with higher nutrient availability. On the other hand, the M treatment decreased the percentages of sequences related to the metabolism of amino acids and derivatives, which may be due to the limited nitrogen (N) because of the high C/N ratio of bagasse. We also observed interaction effects of the NT and M treatments; although both the NT and M treatments increased the relative abundance of Proteobacteria, this variable in NT + M soils was not higher than in each single treatment. Overall, our findings suggest that the microbial communities change their composition and functionality in response to the NT and M treatments, and these shifts have the potential to affect important soil processes that sustain crop productivity, such as C sequestration and major nutrient cycles.

Shifts in the composition and potential functions of soil microbial communities responding to a no-tillage practice and bagasse mulching on a sugarcane plantation

Kenta Yamada

Papers

Shifts in the composition and potential functions of soil microbial communities responding to a no-tillage practice and bagasse mulching on a sugarcane plantation