Site-Specific Conditions Change the Response of Bacterial Producers of Soil Structure-Stabilizing Agents Such as Exopolysaccharides and Lipopolysaccharides to Tillage Intensity.

Agro-ecosystems experience huge losses of land every year due to soil erosion induced by poor agricultural practices such as intensive tillage. Erosion can be minimized by the presence of stable soil aggregates, the formation of which can be promoted by bacteria. Some of these microorganisms have the ability to produce exopolysaccharides and lipopolysaccharides that "glue" soil particles together. However, little is known about the influence of tillage intensity on the bacterial potential to produce these polysaccharides, even though more stable soil aggregates are usually observed under less intense tillage. As the effects of tillage intensity on soil aggregate stability may vary between sites, we hypothesized that the response of polysaccharide-producing bacteria to tillage intensity is also determined by site-specific conditions. To investigate this, we performed a high-throughput shotgun sequencing of DNA extracted from conventionally and reduced tilled soils from three tillage system field trials characterized by different soil parameters. While we confirmed that the impact of tillage intensity on soil aggregates is site-specific, we could connect improved aggregate stability with increased absolute abundance of genes involved in the production of exopolysaccharides and lipopolysaccharides. The potential to produce polysaccharides was generally promoted under reduced tillage due to the increased microbial biomass. We also found that the response of most potential producers of polysaccharides to tillage was site-specific, e.g., Oxalobacteraceae had higher potential to produce polysaccharides under reduced tillage at one site, and showed the opposite response at another site. However, the response of some potential producers of polysaccharides to tillage did not depend on site characteristics, but rather on their taxonomic affiliation, i.e., all members of Actinobacteria that responded to tillage intensity had higher potential for exopolysaccharide and lipopolysaccharide production specifically under reduced tillage. This could be especially crucial for aggregate stability, as polysaccharides produced by different taxa have different "gluing" efficiency. Overall, our data indicate that tillage intensity could affect aggregate stability by both influencing the absolute abundance of genes involved in the production of exopolysaccharides and lipopolysaccharides, as well as by inducing shifts in the community of potential polysaccharide producers. The effects of tillage intensity depend mostly on site-specific conditions.

Enhanced soil quality with reduced tillage and solid manures in organic farming - a synthesis of 15 years.

Demands upon the sustainability of farming are increasing in step with climate change and diversity loss. Organic farming offers a viable approach. To further improve organic management, three strategies with potential to enhance soil quality are being tested in a long-term trial since 2002 on a clay loam in temperate Switzerland: reduced tillage vs. ploughing, solid vs. liquid manures and biodynamic preparations. A synthesis of 15 years reveals an increase in topsoil organic carbon (SOC, +25%), microbial biomass (+32%) and activity (+34%) and a shift in microbial communities with conversion from ploughing to reduced tillage. Soils under reduced tillage are more stratified in SOC and nutrients. Additional application of composted manure has increased SOC by 6% compared to pure slurry application, with little impact on soil microbes. Biodynamic preparations have had a minor impact on soil quality. Fertilisation and biodynamic preparations did not affect yields. Both higher and lower yields were harvested in the reduced tillage system in relation to ploughing. The main yield determinants were N supply and higher weed infestation under reduced tillage. Continuously reduced tillage in organic farming has been proven to enhance soil quality at this site, while also presenting more challenges in management.

The impact of long-term organic farming on soil-derived greenhouse gas emissions.

Agricultural practices contribute considerably to emissions of greenhouse gases. So far, knowledge on the impact of organic compared to non-organic farming on soil-derived nitrous oxide (N2O) and methane (CH4) emissions is limited. We investigated N2O and CH4 fluxes with manual chambers during 571 days in a grass-clover- silage maize - green manure cropping sequence in the long-term field trial "DOK" in Switzerland. We compared two organic farming systems - biodynamic (BIODYN) and bioorganic (BIOORG) - with two non-organic systems - solely mineral fertilisation (CONMIN) and mixed farming including farmyard manure (CONFYM) - all reflecting Swiss farming practices-together with an unfertilised control (NOFERT). We observed a 40.2% reduction of N2O emissions per hectare for organic compared to non-organic systems. In contrast to current knowledge, yield-scaled cumulated N2O emissions under silage maize were similar between organic and non-organic systems. Cumulated on area scale we recorded under silage maize a modest CH4 uptake for BIODYN and CONMIN and high CH4 emissions for CONFYM. We found that, in addition to N input, quality properties such as pH, soil organic carbon and microbial biomass significantly affected N2O emissions. This study showed that organic farming systems can be a viable measure contributing to greenhouse gas mitigation in the agricultural sector.

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.

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.

Restricting the nonlinearity parameter in soil greenhouse gas flux calculation for more reliable flux estimates.

The static chamber approach is often used for greenhouse gas (GHG) flux measurements, whereby the flux is deduced from the increase of species concentration after closing the chamber. Since this increase changes diffusion gradients between chamber air and soil air, a nonlinear increase is expected. Lateral gas flow and leakages also contribute to non linearity. Several models have been suggested to account for this non linearity, the most recent being the Hutchinson-Mosier regression model (hmr). However, the practical application of these models is challenging because the researcher needs to decide for each flux whether a nonlinear fit is appropriate or exaggerates flux estimates due to measurement artifacts. In the latter case, a flux estimate from the linear model is a more robust solution and introduces less arbitrary uncertainty to the data. We present the new, dynamic and reproducible flux calculation scheme, kappa.max, for an improved trade-off between bias and uncertainty (i.e. accuracy and precision). We develop a tool to simulate, visualise and optimise the flux calculation scheme for any specific static N2O chamber measurement system. The decision procedure and visualisation tools are implemented in a package for the R software. Finally, we demonstrate with this approach the performance of the applied flux calculation scheme for a measured flux dataset to estimate the actual bias and uncertainty. The kappa.max method effectively improved the decision between linear and nonlinear flux estimates reducing the bias at a minimal cost of uncertainty.

Impact of reduced tillage on greenhouse gas emissions and soil carbon stocks in an organic grass-clover ley - winter wheat cropping sequence.

Organic reduced tillage aims to combine the environmental benefits of organic farming and conservation tillage to increase sustainability and soil quality. In temperate climates, there is currently no knowledge about its impact on greenhouse gas emissions and only little information about soil organic carbon (SOC) stocks in these management systems. We therefore monitored nitrous oxide (N2O) and methane (CH4) fluxes besides SOC stocks for two years in a grass-clover ley - winter wheat - cover crop sequence. The monitoring was undertaken in an organically managed long-term tillage trial on a clay rich soil in Switzerland. Reduced tillage (RT) was compared with ploughing (conventional tillage, CT) in interaction with two fertilisation systems, cattle slurry alone (SL) versus cattle manure compost and slurry (MC). Median N2O and CH4 flux rates were 13 µg N2O-N m-2 h-1 and -2 µg CH4C m-2 h-1, respectively, with no treatment effects. N2O fluxes correlated positively with nitrate contents, soil temperature, water filled pore space and dissolved organic carbon and negatively with ammonium contents in soil. Pulse emissions after tillage operations and slurry application dominated cumulative gas emissions. N2O emissions after tillage operations correlated with SOC contents and collinearly to microbial biomass. There was no tillage system impact on cumulative N2O emissions in the grass-clover (0.8-0.9 kg N2O-N ha-1, 369 days) and winter wheat (2.1-3.0 kg N2O-N ha-1, 296 days) cropping seasons, with a tendency towards higher emissions in MC than SL in winter wheat. Including a tillage induced peak after wheat harvest, a full two year data set showed increased cumulative N2O emissions in RT than CT and in MC than SL. There was no clear treatment influence on cumulative CH4 uptake. Topsoil SOC accumulation (0-0.1 m) was still ongoing. SOC stocks were more stratified in RT than CT and in MC than SL. Total SOC stocks (0-0.5 m) were higher in RT than CT in SL and similar in MC. Maximum relative SOC stock difference accounted for +8.1 Mg C ha-1 in RT-MC compared to CT-SL after 13 years which dominated over the relative increase in greenhouse gas emissions. Under these site conditions, organic reduced tillage and manure compost application seems to be a viable greenhouse gas mitigation strategy as long as SOC is sequestered.