Raphaël Wittwer

Cover crops support ecological intensification of arable cropping systems

A major challenge for agriculture is to enhance productivity with minimum impact on the environment. Several studies indicate that cover crops could replace anthropogenic inputs and enhance crop productivity. However, so far, it is unclear if cover crop effects vary between different cropping systems, and direct comparisons among major arable production systems are rare. Here we compared the short-term effects of various cover crops on crop yield, nitrogen uptake, and weed infestation in four arable production systems (conventional cropping with intensive tillage and no-tillage; organic cropping with intensive tillage and reduced tillage). We hypothesized that cover cropping effects increase with decreasing management intensity. Our study demonstrated that cover crop effects on crop yield were highest in the organic system with reduced tillage (+24%), intermediate in the organic system with tillage (+13%) and in the conventional system with no tillage (+8%) and lowest in the conventional system with tillage (+2%). Our results indicate that cover crops are essential to maintaining a certain yield level when soil tillage intensity is reduced (e.g. under conservation agriculture), or when production is converted to organic agriculture. Thus, the inclusion of cover crops provides additional opportunities to increase the yield of lower intensity production systems and contribute to ecological intensification.

Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

BackgroundHarnessing beneficial microbes presents a promising strategy to optimize plant growth and agricultural sustainability. Little is known to which extent and how specifically soil and plant microbiomes can be manipulated through different cropping practices. Here, we investigated soil and wheat root microbial communities in a cropping system experiment consisting of conventional and organic managements, both with different tillage intensities.ResultsWhile microbial richness was marginally affected, we found pronounced cropping effects on community composition, which were specific for the respective microbiomes. Soil bacterial communities were primarily structured by tillage, whereas soil fungal communities responded mainly to management type with additional effects by tillage. In roots, management type was also the driving factor for bacteria but not for fungi, which were generally determined by changes in tillage intensity. To quantify an “effect size” for microbiota manipulation, we found that about 10% of variation in microbial communities was explained by the tested cropping practices. Cropping sensitive microbes were taxonomically diverse, and they responded in guilds of taxa to the specific practices. These microbes also included frequent community members or members co-occurring with many other microbes in the community, suggesting that cropping practices may allow manipulation of influential community members.ConclusionsUnderstanding the abundance patterns of cropping sensitive microbes presents the basis towards developing microbiota management strategies for smart farming. For future targeted microbiota management—e.g., to foster certain microbes with specific agricultural practices—a next step will be to identify the functional traits of the cropping sensitive microbes.

Sebacinales, but not total root associated fungal communities, are affected by land‐use intensity

There is great scientific and societal interest in the ecology and functioning of the immense diversity of microorganisms associated with plant roots (Mendes et al., 2011; Porras-Alfaro & Bayman, 2011). In particular, research into plant–soil interactions has unveiled a pivotal role of root-associated fungi in influencing plant growth and community structure (van der Heijden et al., 2008; Schnitzer et al., 2011; Wagg et al., 2014). So far, knowledge on the identity of fungi associated with plant roots, and forces structuring the communities they form, is still scarce. This extends to agricultural systems, where communities of belowground fungi are a largely unknown but potentially important driver of plant productivity akin to natural systems, and display a considerably high diversity (Orgiazzi et al., 2012). So far, most research has focused on plant pathogens (e.g.Xu et al., 2012) and on arbuscularmycorrhizal fungi (AMF). AMF are an important group of plant symbionts, and we know that these generally increase in diversity in response to reduced agricultural management intensity (Oehl et al., 2004; Verbruggen et al., 2012). For other groups of root endophytes little is known about responses to agricultural management, even though they may be of high ecological significance (Rodriguez et al., 2009). Apart from potential effects on plants, there is great interest in identifying taxa that may serve as bio-markers for sustainable agricultural practices, as has recently been explored for AMF by Jansa et al. (2014). So far this has not been attempted for other root inhabiting fungi, likely because it is unknown whether root-colonizing fungi are sensitive to changes in land-use intensity. In this study we have sampled wheat roots in agricultural fields that were either managed conventionally (seven sites) or had been converted to organic farming recently (2–4 yr; eight sites), moderately long ago (10– 14 yr; six sites), or had been subjected to long-term organic farming (16–33 yr; eight sites). We analyzed the fungal community in roots using next generation sequencing of fungi and ask how different biotic and abiotic aspects drive fungal communities inhabiting wheat roots.

Community Profiling of Fusarium in Combination with Other Plant-Associated Fungi in Different Crop Species Using SMRT Sequencing

Fusarium head blight, caused by fungi from the genus Fusarium, is one of the most harmful cereal diseases, resulting not only in severe yield losses but also in mycotoxin contaminated and health-threatening grains. Fusarium head blight is caused by a diverse set of species that have different host ranges, mycotoxin profiles and responses to agricultural practices. Thus, understanding the composition of Fusarium communities in the field is crucial for estimating their impact and also for the development of effective control measures. Up to now, most molecular tools that monitor Fusarium communities on plants are limited to certain species and do not distinguish other plant associated fungi. To close these gaps, we developed a sequencing-based community profiling methodology for crop-associated fungi with a focus on the genus Fusarium. By analyzing a 1600 bp long amplicon spanning the highly variable segments ITS and D1–D3 of the ribosomal operon by PacBio SMRT sequencing, we were able to robustly quantify Fusarium down to species level through clustering against reference sequences. The newly developed methodology was successfully validated in mock communities and provided similar results as the culture-based assessment of Fusarium communities by seed health tests in grain samples from different crop species. Finally, we exemplified the newly developed methodology in a field experiment with a wheat-maize crop sequence under different cover crop and tillage regimes. We analyzed wheat straw residues, cover crop shoots and maize grains and we could reveal that the cover crop hairy vetch (Vicia villosa) acts as a potent alternative host for Fusarium (OTU F.ave/tri) showing an eightfold higher relative abundance compared with other cover crop treatments. Moreover, as the newly developed methodology also allows to trace other crop-associated fungi, we found that vetch and green fallow hosted further fungal plant pathogens including Zymoseptoria tritici. Thus, besides their beneficial traits, cover crops can also entail phytopathological risks by acting as alternative hosts for Fusarium and other noxious plant pathogens. The newly developed sequencing based methodology is a powerful diagnostic tool to trace Fusarium in combination with other fungi associated to different crop species.

Roots of symptom-free leguminous cover crop and living mulch species harbor diverse Fusarium communities that show highly variable aggressiveness on pea (Pisum sativum)

Leguminous cover crop and living mulch species show not only great potential for providing multiple beneficial services to agro-ecosystems, but may also present pathological risks for other crops in rotations through shared pathogens, especially those of the genus Fusarium. Disease severity on roots of subterranean clover, white clover, winter and summer vetch grown as cover crop and living mulch species across five European sites as well as the frequency, distribution and aggressiveness to pea of Fusarium spp. recovered from the roots were assessed in 2013 and 2014. Disease symptoms were very low at all sites. Nevertheless, out of 1480 asymptomatic roots, 670 isolates of 14 Fusarium spp. were recovered. The most frequently isolated species in both years from all hosts were F. oxysporum and F. avenaceum accounting for 69% of total isolation percentage. They were common at the Swiss, Italian and German sites, whereas at the Swedish site F. oxysporum dominated and F. avenaceum occurred only rarely. The agressiveness and effect on pea biomass were tested in greenhouse assays for 72 isolates of six Fusarium species. Isolates of F. avenaceum caused severe root rot symptoms with mean severity index (DI) of 82 and 74% mean biomass reduction compared to the non-inoculated control. Fusarium oxysporum and F. solani isolates were higly variable in agressiveness and their impact on pea biomass. DI varied between 15 and 50 and biomass changes relative to the non-inoculated control -40% to +10%. Isolates of F. tricinctum, F. acuminatum and F. equiseti were non to weakly agressive often enhancing pea biomass. This study shows that some of the major pea pathogens are characterized by high ecological plasticity and have the ability to endophytically colonize the hosts studied that thus may serve as inoculum reservoir for susceptible main legume grain crops such as pea.

Correction to: Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

Following publication of the original article [1], the authors reported that while the ordination graphs are all correct, the symbols in the legend are wrong.

Conservation tillage and organic farming induce minor variations in Pseudomonas abundance, their antimicrobial function and soil disease resistance

Conservation tillage and organic farming are strategies used worldwide to preserve the stability and fertility of soils. While positive effects on soil structure have been extensively reported, the effects on specific root- and soil-associated microorganisms are less known. The aim of this study was to investigate how conservation tillage and organic farming influence the frequency and activity of plant-beneficial pseudomonads. Amplicon sequencing using the 16S rRNA gene revealed that Pseudomonas is among the most abundant bacterial taxa in the root microbiome of field-grown wheat, independent of agronomical practices. However, pseudomonads carrying genes required for the biosynthesis of specific antimicrobial compounds were enriched in samples from conventionally farmed plots without tillage. In contrast, disease resistance tests indicated that soil from conventional no tillage plots is less resistant to the soilborne pathogen Pythium ultimum compared to soil from organic reduced tillage plots, which exhibited the highest resistance of all compared cropping systems. Reporter strain-based gene expression assays did not reveal any differences in Pseudomonas antimicrobial gene expression between soils from different cropping systems. Our results suggest that plant-beneficial pseudomonads can be favoured by certain soil cropping systems, but soil resistance against plant diseases is likely determined by a multitude of biotic factors in addition to Pseudomonas.