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.

Spatial variability and environmental drivers of cassava-arbuscular mycorrhiza fungi (AMF) associations across Southern Nigeria.

Cassava, forming starch-rich, tuberous roots, is an important staple crop in smallholder farming systems in sub-Saharan Africa. Its relatively good tolerance to drought and nutrient-poor soils may be partly attributed to the crop's association with arbuscular mycorrhiza fungi (AMF). Yet insights into AMF-community composition and richness of cassava, and knowledge of its environmental drivers are still limited. Here, we sampled 60 cassava fields across three major cassava-growing agro-ecological zones in Nigeria and used a DNA meta-barcoding approach to quantify large-scale spatial variation and evaluate the effects of soil characteristics and common agricultural practices on AMF community composition, richness and Shannon diversity. We identified 515 AMF operational taxonomic units (OTUs), dominated by Glomus, with large variation across agro-ecological zones, and with soil pH explaining most of the variation in AMF community composition. High levels of soil available phosphorus reduced OTU richness without affecting Shannon diversity. Long fallow periods (> 5 years) reduced AMF richness compared with short fallows, whereas both zero tillage and tractor tillage reduced AMF diversity compared with hoe tillage. This study reveals that the symbiotic relationship between cassava and AMF is strongly influenced by soil characteristics and agricultural management and that it is possible to adjust cassava cultivation practices to modify AMF diversity and community structure.

The role of genetic diversity and arbuscular mycorrhizal fungal diversity in population recovery of the semi-natural grassland plant species Succisa pratensis.

BACKGROUND: Ecosystem restoration is as a critical tool to counteract the decline of biodiversity and recover vital ecosystem services. Restoration efforts, however, often fall short of meeting their goals. Although functionally important levels of biodiversity can significantly contribute to the outcome of ecosystem restoration, they are often overlooked. One such important facet of biodiversity is within-species genetic diversity, which is fundamental to population fitness and adaptation to environmental change. Also the diversity of arbuscular mycorrhizal fungi (AMF), obligate root symbionts that regulate nutrient and carbon cycles, potentially plays a vital role in mediating ecosystem restoration outcome. In this study, we investigated the relative contribution of intraspecific population genetic diversity, AMF diversity, and their interaction, to population recovery of Succisa pratensis, a key species of nutrient poor semi natural grasslands. We genotyped 180 individuals from 12 populations of S. pratensis and characterized AMF composition in their roots, using microsatellite markers and next generation amplicon sequencing, respectively. We also investigated whether the genetic makeup of the host plant species can structure the composition of root-inhabiting AMF communities. RESULTS: Our analysis revealed that population allelic richness was strongly positively correlated to relative population growth, whereas AMF richness and its interaction with population genetic diversity did not significantly contribute. The variation partitioning analysis showed that, after accounting for soil and spatial variables, the plant genetic makeup explained a small but significant part of the unique variation in AMF communities. CONCLUSIONS: Our results confirm that population genetic diversity can contribute to population recovery, highlighting the importance of within-species genetic diversity for the success of restoration. We could not find evidence, however, that population recovery benefits from the presence of more diverse AMF communities. Our analysis also showed that the genetic makeup of the host plant structured root-inhabiting AMF communities, suggesting that the plant genetic makeup may be linked to genes that control symbiosis development.

Improved genotypes and fertilizers, not fallow duration, increase cassava yields without compromising arbuscular mycorrhizal fungus richness or diversity.

Arbuscular mycorrhizal fungi (AMF) are ubiquitous in agroecosystems, but their role in mediating agricultural yield remains contested. Field experiments testing effects of realistic agronomic practices of intensification on AM fungus composition and yields are scarce, especially in the low-input systems of sub-Saharan Africa. A large, full-factorial field experiment was conducted in South-Kivu (DR Congo), testing effects of fallow duration (6 vs. 12 months), genotype (landrace vs. improved), and fertilizer management (control vs. five combinations omitting N, P, K, and/or secondary macro- and micronutrients) on yields of cassava, an important staple crop strongly colonized by AMF. Furthermore, we used DNA-metabarcoding to evaluate effects of these agronomic practices on the AM fungal communities on the roots. The shorter fallow duration strongly increased diversity and richness of AMF, but this did not correspond with increased yields. Cassava yield was mainly determined by genotype, being largest for the improved genotype, which coincided with a significantly higher sum of AM fungal sequences. Effects of fertilizer or genotype on community composition were minor to absent. We found no evidence that increased AMF richness and diversity enhanced cassava yields. In contrast, the use of the improved genotype and mineral fertilizers strongly benefitted yields, without compromising richness or diversity of AMF. Cassava-AMF associations in this work appear robust to fertilizer amendments and modern genotype improvement.

Diversity and community structure of ericoid mycorrhizal fungi in European bogs and heathlands across a gradient of nitrogen deposition.

Despite the ecological significance of ericoid mycorrhizal fungi, little is known about the abiotic and biotic factors driving their diversity and community composition. To determine the relative importance of abiotic and biotic filtering in structuring ericoid mycorrhizal fungal communities, we established 156 sampling plots in two highly contrasting environments but dominated by the same Ericaceae plant species: waterlogged bogs and dry heathlands. Plots were located across 25 bogs and 27 dry heathlands in seven European countries covering a gradient in nitrogen deposition and phosphorus availability. Putatively ericoid mycorrhizal fungal communities in the roots of 10 different Ericaceae species were characterized using high-throughput amplicon sequencing. Variation in ericoid mycorrhizal fungal communities was attributed to both habitat and soil variables on the one hand and host plant identity on the other. Communities differed significantly between bogs and heathlands and, in a given habitat, communities differed significantly among host plant species. Fungal richness was negatively related to nitrogen deposition in bogs and phosphorus availability in bogs and heathlands. Our results demonstrate that both abiotic and biotic filtering shapes ericoid mycorrhizal fungal communities and advocate an environmental policy minimizing excess nutrient input in these nutrient-poor ecosystems to avoid loss of ericoid mycorrhizal fungal taxa.

Soil organic matter rather than ectomycorrhizal diversity is related to urban tree health.

Urban trees provide many ecosystem services, including carbon sequestration, air quality improvement, storm water attenuation and energy conservation, to people living in cities. Provisioning of ecosystem services by urban trees, however, may be jeopardized by the typically poor quality of the soils in urban areas. Given their well-known multifunctional role in forest ecosystems, ectomycorrhizal fungi (EcM) may also contribute to urban tree health and thus ecosystem service provisioning. Yet, no studies so far have directly related in situ EcM community composition to urban tree health indicators. Here, two previously collected datasets were combined: i) tree health data of 175 Tilia tomentosa trees from three European cities (Leuven, Strasbourg and Porto) estimated using a range of reflectance, chlorophyll fluorescence and physical leaf indicators, and ii) ectomycorrhizal diversity of these trees as characterized by next-generation sequencing. Tree health indicators were related to soil characteristics and EcM diversity using canonical redundancy analysis. Soil organic matter significantly explained variation in tree health indicators whereas no significant relation between mycorrhizal diversity variables and the tree health indicators was found. We conclude that mainly soil organic matter, through promoting soil aggregate formation and porosity, and thus indirectly tree water availability, positively affects the health of trees in urban areas. Our results suggest that urban planners should not overlook the importance of soil quality and its water holding capacity for the health of urban trees and potentially also for the ecosystem services they deliver. Further research should also study other soil microbiota which may independently, or in interaction with ectomycorrhiza, mediate tree performance in urban settings.

Variation in ectomycorrhizal fungal communities associated with Silver linden (Tilia tomentosa) within and across urban areas.

Trees in urban areas face harsh environmental conditions. Ectomycorrhizal fungi (EcM) form a symbiosis with many tree species and provide a range of benefits to their host through their extraradical hyphal network. Although our understanding of the environmental drivers and large scale geographical variation of EcM communities in natural ecosystems is growing, our knowledge of EcM communities within and across urban areas is still limited. Here, we characterized EcM communities using Illumina miseq sequencing on 175 root samples of the urban tree Tilia tomentosa from three European cities, namely Leuven (Belgium), Strasbourg (France) and Porto (Portugal). We found strong differences in EcM richness and community composition between cities. Soil acidity, organic matter and moisture content were significantly associated with EcM community composition. In agreement, the explained variability in EcM communities was mostly attributed to general soil characteristics, whereas very little variation was explained by city and heavy metal pollution. Overall, our results suggest that EcM communities in urban areas are significantly associated with soil characteristics, while heavy metal pollution and biogeography had little or no impact. These findings deliver new insights into EcM distribution patterns in urban areas and contribute to specific inoculation strategies to improve urban tree vitality.

Abiotic rather than biotic filtering shapes the arbuscular mycorrhizal fungal communities of European seminatural grasslands.

Although it is well known that arbuscular mycorrhizal fungi (AMF) play a key role in the functioning of natural ecosystems, the underlying drivers determining the composition of AMF communities remain unclear. In this study, we established 138 sampling plots at 46 grassland sites, consisting of 26 acidic grasslands and 20 calcareous grasslands spread across eight European countries, to assess the relative importance of abiotic and biotic filtering in driving AMF community composition and structure in both the grassland soils and in the roots of 13 grassland plant species. Soil AMF communities differed significantly between acidic and calcareous grasslands. In root AMF communities, most variance was attributable to soil variables while very little variation was explained by host plant identity. Root AMF communities in host plant species occurring in only one grassland type closely resembled the soil AMF communities of that grassland type and the root AMF communities of other host plant species occurring in the same grassland type. The observed AMF-host plants networks were not modular but nested. Our results indicate that abiotic conditions, rather than biotic filtering through host plant specificity, are the most important drivers in shaping AMF communities in European seminatural grasslands.

Phosphorus resource partitioning shapes phosphorus acquisition and plant species abundance in grasslands.

Species diversity is commonly hypothesized to result from trade-offs for different limiting resources, providing separate niches for coexisting species1-4. As soil nutrients occur in multiple chemical forms, plant differences in acquisition of the same element derived from different compounds may represent unique niche dimensions5,6. Because plant productivity of ecosystems is often limited by phosphorus7, and because plants have evolved diverse adaptations to acquire soil phosphorus6,8, a promising yet untested hypothesis is phosphorus resource partitioning6,9,10. Here, we provided two different chemical forms of phosphorus to sown grassland mesocosms to investigate phosphorus acquisition of eight plant species that are common in European grasslands, and to identify subsequent patterns of plant abundance. For the first time, we show that the relative abundance of grassland plant species can be influenced by soil phosphorus forms, as higher abundance was linked to higher acquisition of a specific form of phosphorus. These results were supported by a subsequent isotope dilution experiment using intact grassland sods that were treated with different inorganic or organic phosphorus forms. Here, 5 out of 14 species showed greater phosphorus acquisition in the inorganic phosphorus treatment, and 4 in the organic phosphorus treatments. Furthermore, for the species used in both experiments we found similar acquisition patterns. Our results support the hypothesis of phosphorus resource partitioning and may provide a new mechanistic framework to explain high plant diversity in phosphorus-poor ecosystems6,11-13. As world biodiversity hotspots are almost invariably related to phosphorus limitation8,11,12, our results may thus also be key to understanding biodiversity loss in an era of ever-increasing nutrient enrichment14.