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Soil organisms are a crucial part of the terrestrial biosphere. Despite their importance for ecosystem functioning, few quantitative, spatially explicit models of the active belowground community currently exist. In particular, nematodes are the most abundant animals on Earth, filling all trophic levels in the soil food web. Here we use 6,759 georeferenced samples to generate a mechanistic understanding of the patterns of the global abundance of nematodes in the soil and the composition of their functional groups. The resulting maps show that 4.4 ± 0.64 × 10 20 nematodes (with a total biomass of approximately 0.3 gigatonnes) inhabit surface soils across the world, with higher abundances in sub-Arctic regions (38% of total) than in temperate (24%) or tropical (21%) regions. Regional variations in these global trends also provide insights into local patterns of soil fertility and functioning. These high-resolution models provide the first steps towards representing soil ecological processes in global biogeochemical models and will enable the prediction of elemental cycling under current and future climate scenarios. High-resolution spatial maps of the global abundance of soil nematodes and the composition of functional groups show that soil nematodes are found in higher abundances in sub-Arctic regions, than in temperate or tropical regions.

Population growth and climate change challenge our food and farming systems and provide arguments for an increased intensification of agriculture. A promising option is eco-functional intensification through organic farming, an approach based on using and enhancing internal natural resources and processes to secure and improve agricultural productivity, while minimizing negative environmental impacts. In this concept an active soil microbiota plays an important role for various soil based ecosystem services such as nutrient cycling, erosion control and pest and disease regulation. Several studies have reported a positive effect of organic farming on soil health and quality including microbial community traits. However, so far no systematic quantification of whether organic farming systems comprise larger and more active soil microbial communities compared to conventional farming systems was performed on a global scale. Therefore, we conducted a meta-analysis on current literature to quantify possible differences in key indicators for soil microbial abundance and activity in organic and conventional cropping systems. All together we integrated data from 56 mainly peer-reviewed papers into our analysis, including 149 pairwise comparisons originating from different climatic zones and experimental duration ranging from 3 to more than 100 years. Overall, we found that organic systems had 32% to 84% greater microbial biomass carbon, microbial biomass nitrogen, total phospholipid fatty-acids, and dehydrogenase, urease and protease activities than conventional systems. Exclusively the metabolic quotient as an indicator for stresses on microbial communities remained unaffected by the farming systems. Categorical subgroup analysis revealed that crop rotation, the inclusion of legumes in the crop rotation and organic inputs are important farming practices affecting soil microbial community size and activity. Furthermore, we show that differences in microbial size and activity between organic and conventional farming systems vary as a function of land use (arable, orchards, and grassland), plant life cycle (annual and perennial) and climatic zone. In summary, this study shows that overall organic farming enhances total microbial abundance and activity in agricultural soils on a global scale.

Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered. Effects of habitat restoration on belowground organisms and ecosystem processes are poorly understood. Morriën and colleagues show that changes in the composition and network interactions of soil biota lead to improved carbon uptake efficiency when formerly cultivated land is restored.

Plants release a wide set of secondary metabolites including volatile organic compounds (VOCs). Many of those compounds are considered to function as defense against herbivory, pests, and pathogens. However, little knowledge exists about the role of belowground plant VOCs for attracting beneficial soil microorganisms. We developed an olfactometer system to test the attraction of soil bacteria by VOCs emitted by Carex arenaria roots. Moreover, we tested whether infection of C. arenaria with the fungal pathogen Fusarium culmorum modifies the VOCs profile and bacterial attraction. The results revealed that migration of distant bacteria in soil towards roots can be stimulated by plant VOCs. Upon fungal infection, the blend of root VOCs changed and specific bacteria with antifungal properties were attracted. Tests with various pure VOCs indicated that those compounds can diffuse over long distance but with different diffusion abilities. Overall, this work highlights the importance of plant VOCs in belowground long-distance plant–microbe interactions.

Global crop yields are limited by water and nutrient availability. Soil mulching (with plastic or straw) reduces evaporation, modifies soil temperature and thereby affects crop yields. Reported effects of mulching are sometimes contradictory, likely due to differences in climatic conditions, soil characteristics, crop species and also water and nitrogen (N) input levels. Here we report on a meta-analysis of the effects of mulching on wheat and maize, using 1310 yield observations from 74 studies conducted in 19 countries. Our results indicate that mulching significantly increased yields, WUE (yield per unit water) and NUE (yield per unit N) by up to 60%, compared with no-mulching. Effects were larger for maize than wheat and larger for plastic mulching than straw mulching. Interestingly, plastic mulching performed better at relatively low temperature while straw mulching showed the opposite trend. Effects of mulching also tended to decrease with increasing water input. Mulching effects were not related to soil organic matter content. In conclusion, soil mulching can significantly increase maize and wheat yields, WUE and NUE and thereby may contribute to closing the yield gap between attainable and actual yields, especially in dryland and low nutrient input agriculture. The management of soil mulching requires site-specific knowledge.

The extent to which pre-Columbian societies altered Amazonian landscapes is hotly debated. We performed a basin-wide analysis of pre-Columbian impacts on Amazonian forests by overlaying known archaeological sites in Amazonia with the distributions and abundances of 85 woody species domesticated by pre-Columbian peoples. Domesticated species are five times more likely than nondomesticated species to be hyperdominant. Across the basin, the relative abundance and richness of domesticated species increase in forests on and around archaeological sites. In southwestern and eastern Amazonia, distance to archaeological sites strongly influences the relative abundance and richness of domesticated species. Our analyses indicate that modern tree communities in Amazonia are structured to an important extent by a long history of plant domestication by Amazonian peoples.

Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soil communities caused by agricultural management affect the extended plant phenotype. In the current study, we performed shotgun metagenome sequencing of the rhizosphere microbiome of the peanut ( Arachis hypogaea ) and metatranscriptome analysis of the roots of peanut plants grown in the soil with different management histories, peanut monocropping and crop rotation. We found that the past planting record had a significant effect on the assembly of the microbial community in the peanut rhizosphere, indicating a soil memory effect. Monocropping resulted in a reduction of the rhizosphere microbial diversity, an enrichment of several rare species, and a reduced representation of traits related to plant performance, such as nutrients metabolism and phytohormone biosynthesis. Furthermore, peanut plants in monocropped soil exhibited a significant reduction in growth coinciding with a down-regulation of genes related to hormone production, mainly auxin and cytokinin, and up-regulation of genes related to the abscisic acid, salicylic acid, jasmonic acid, and ethylene pathways. These findings suggest that land use history affects crop rhizosphere microbiomes and plant physiology.

Seasonal freezing induces large thaw emissions of nitrous oxide, a trace gas that contributes to stratospheric ozone destruction and atmospheric warming. Cropland soils are by far the largest anthropogenic source of nitrous oxide. However, the global contribution of seasonal freezing to nitrous oxide emissions from croplands is poorly quantified, mostly due to the lack of year-round measurements and difficulty in capturing short-lived pulses of nitrous oxide with traditional measurement methods. Here we present measurements collected with half-hourly resolution at two contrasting cropland sites in Ontario and Manitoba, Canada, over 14 and 9 years, respectively. We find that the magnitude of freeze–thaw-induced nitrous oxide emissions is related to the number of days with soil temperatures below 0 °C, and we validate these findings with emissions data from 11 additional sites from cold climates around the globe. Based on an estimate of cropland area experiencing seasonal freezing, reanalysis model estimates of soil temperature, and the relationship between cumulative soil freezing days and emissions that we derived from the cropland sites, we estimate that seasonally frozen cropland contributes 1.07 ± 0.59 Tg of nitrogen as nitrous oxide annually. We conclude that neglecting freeze–thaw emissions would lead to an underestimation of global agricultural nitrous oxide emissions by 17 to 28%. Large fluxes of nitrous oxide occur when frozen soils thaw. Field measurements and mathematical models suggest that freeze–thaw events are responsible for 17 to 28% of nitrous oxide emitted from agricultural soils globally.

The abundance of species is assumed to depend on their life history traits, such as growth rate and resource specialization. However, this assumption has not been tested for bacteria. Here we investigate how abundance of soil bacteria relates to slow growth and substrate specialization (oligotrophy) vs. fast growth and substrate generalization (copiotrophy). We collected 47 saprotrophic soil bacterial isolates of differing abundances and measured their growth rate and the ability to use a variety of single carbon sources. Opposite to our expectation, there was no relationship between abundance in soil and the measured growth rate or substrate utilization profile (SUP). However, isolates with lower growth rates used fewer substrates than faster growing ones supporting the assumption that growth rate may relate to substrate specialization. Interestingly, growth rate and SUP were correlated with phytogeny, rather than with abundance in soil. Most markedly, Gammaproteobacteria on average grew significantly faster and were able to use more substrates than other bacterial classes, whereas Alphaproteobacteria were growing relatively slowly and used fewer substrates. This finding suggests that growth and substrate utilization are phylogenetically deeply conserved. We conclude that growth rate and substrate utilization of soil bacteria are not general determinants of their abundance. Future studies on explaining bacterial abundance need to determine how other factors, such as competition, prédation and abiotic factors may contribute to rarity or abundance in soil bacteria.

Activities of rhizosphere microbes are key to the functioning of terrestrial ecosystems. It is commonly believed that bacteria are the major consumers of root exudates and that the role of fungi in the rhizosphere is mostly limited to plant-associated taxa, such as mycorrhizal fungi, pathogens and endophytes, whereas less is known about the role of saprotrophs. In order to test the hypothesis that the role of saprotrophic fungi in rhizosphere processes increases with increased time after abandonment from agriculture, we determined the composition of fungi that are active in the rhizosphere along a chronosequence of ex-arable fields in the Netherlands. Intact soil cores were collected from nine fields that represent three stages of land abandonment and pulse labeled with 13 CO 2 . The fungal contribution to metabolization of plant-derived carbon was evaluated using phospholipid analysis combined with stable isotope probing (SIP), whereas fungal diversity was analyzed using DNA-SIP combined with 454-sequencing. We show that in recently abandoned fields most of the root-derived 13 C was taken up by bacteria but that in long-term abandoned fields most of the root-derived 13 C was found in fungal biomass. Furthermore, the composition of the active functional fungal community changed from one composed of fast-growing and pathogenic fungal species to one consisting of beneficial and slower-growing fungal species, which may have essential consequences for the carbon flow through the soil food web and consequently nutrient cycling and plant succession.