Soil Microbiomes in Apple Orchards Are Influenced by the Type of Agricultural Management but Never Match the Complexity and Connectivity of a Semi-natural Benchmark.

Conversion of natural ecosystems into agricultural land may strongly affect the soil microbiome and the functioning of the soil ecosystem. Alternative farming systems, such as organic farming, have therefore been advocated to reduce this impact, yet the outcomes of different agricultural management regimes often remain ambiguous and their evaluations mostly lack a proper more natural benchmark. We used high-throughput amplicon sequencing, linear models, redundancy analyses, and co-occurrence network analyses to investigate the effect of organic and integrated pest management (IPM) on soil fungal and bacterial communities in both the crop and drive rows of apple orchards in Belgium, and we included semi-natural grasslands as a benchmark. Fungi were strongly influenced by agricultural management, with lower diversity indices and distinct communities in IPM compared to organic orchards, whereas IPM orchards had a higher AMF abundance and the most complex and connected fungal communities. Bacterial diversity indices, community composition, and functional groups were less affected by management, with only a higher network connectivity and abundance of keystone taxa in organic drive rows. On the other hand, none of the agricultural soil microbiomes matched the complexity and connectedness of our semi-natural benchmark, demonstrating that even more nature-friendly agricultural management practices strongly affect the soil microbiome and highlighting the essential role of (semi-)natural systems as a harbor of robust and functionally diverse fungal and bacterial communities.

Both organic and integrated pest management of apple orchards maintain soil health as compared to a semi-natural reference system.

Growing concerns about the negative environmental impacts of agriculture have resulted in the increasing adoption of farming systems that try to reconcile crop production with environmental sustainability, such as organic farming. As organic farming refrains from using synthetic inputs, it heavenly relies on maintaining soil health. However, it is still poorly understood how organic management performs in terms of maintaining soil health in real commercial and heterogeneous farm settings as compared to conventional management, and especially as compared to a natural reference system. Here, we compared a set of soil health indicators among 24 commercial apple orchards that were either managed organically or conventionally using Integrated Pest Management (IPM) practices. In addition, we quantified the same indicators in 12 semi-natural grasslands as a benchmark to assess to what extent soil processes and functions have been degraded due to agricultural practices. As soil heath indicators, we quantified soil bulk density, organic matter content, organic carbon content, organic carbon stock, total nitrogen (N), potential heterotrophic respiration, potential net N mineralization, litter decomposition and litter stabilization, and we added the diversity of the herbaceous vegetation and the soil microbiome as covariates in our models. We found no differences between organic and IPM orchards, and neither of the farming systems showed evidence of impaired soil health compared to the semi-natural benchmark, with the exception of higher decomposition rates measured in both orchard types. We observed, however, high spatial variation in soil health between drive and crop rows within the orchards. Especially in the IPM orchards, crop rows showed impaired soil health compared to the adjacent drive rows, indicating that there is still opportunity to improve soil management in the IPM system. In addition, our results show that a considerable part of the variation in soil characteristics can be attributed to the study site, suggesting that both natural heterogeneity and personal management preferences by individual farmers are more important than the management system. Overall, and at least in terms of the soil variables measured in this study, our results suggest that perennial crop systems can be managed in a sustainable way, without jeopardizing soil health.

Nutrient enrichment is associated with altered nectar and pollen chemical composition in Succisa pratensis Moench and increased larval mortality of its pollinator Bombus terrestris L.

Pollinators are declining worldwide and possible underlying causes include disease, invasive pest species and large scale land use changes resulting in habitat loss and degradation. One particular cause of habitat degradation is the increased inflow of nutrients due to anthropogenic combustion processes and large scale application of agricultural fertilizers. This nutrient pollution has been shown to affect pollinators through the loss of nectar and pollen-providing plant species. However, it may also affect pollinators through altering the nectar and pollen chemical composition of plant species, hence influencing pollinator food quality. Here, we experimentally investigated the effect of nutrient enrichment on amino acid and sugar composition of nectar and pollen in the grassland plant Sucissa pratensis, and the subsequent colony size and larval mortality of the pollinating bumblebee Bombus terrestris. We found less of the essential amino acids glycine and arginine in the pollen of fertilized plants, and more arginine, ornithine and threonine in the pollen of control plants. Nectar glucose and pollen fructose levels were lower in fertilized plants as compared to control plants. Furthermore, bumblebee colonies visiting fertilized plants showed more dead larvae than colonies visiting control plants. Our results suggest that the fitness of bumblebees can be negatively affected by changes in their food quality following nutrient pollution. If similar patterns hold for other plant and pollinator species, this may have far reaching implications for the maintenance of pollination ecosystem services, as nutrient pollution continues to rise worldwide.

The role of above-ground competition and nitrogen vs. phosphorus enrichment in seedling survival of common European plant species of semi-natural grasslands.

Anthropogenic activities have severely altered fluxes of nitrogen and phosphorus in ecosystems worldwide. In grasslands, subsequent negative effects are commonly attributed to competitive exclusion of plant species following increased above-ground biomass production. However, some studies have shown that this does not fully account for nutrient enrichment effects, questioning whether lowering competition by reducing grassland productivity through mowing or herbivory can mitigate the environmental impact of nutrient pollution. Furthermore, few studies so far discriminate between nitrogen and phosphorus pollution. We performed a full factorial experiment in greenhouse mesocosms combining nitrogen and phosphorus addition with two clipping regimes designed to relax above-ground competition. Next, we studied the survival and growth of seedlings of eight common European grassland species and found that five out of eight species showed higher survival under the clipping regime with the lowest above-ground competition. Phosphorus addition negatively affected seven plant species and nitrogen addition negatively affected four plant species. Importantly, the negative effects of nutrient addition and higher above-ground competition were independent of each other for all but one species. Our results suggest that at any given level of soil nutrients, relaxation of above-ground competition allows for higher seedling survival in grasslands. At the same time, even at low levels of above-ground competition, nutrient enrichment negatively affects survival as compared to nutrient-poor conditions. Therefore, although maintaining low above-ground competition appears essential for species' recruitment, for instance through mowing or herbivory, these management efforts are likely to be insufficient and we conclude that environmental policies aimed to reduce both excess nitrogen and particularly phosphorus inputs are also necessary.