Structure and function of the global topsoil microbiome.

Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities1-4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.

Arbuscular mycorrhizal fungi trigger danger-associated peptide signaling and inhibit carbon-phosphorus exchange with nonhost plants.

In soil, arbuscular mycorrhizal fungi (AMF) meet the roots of both host and presumed nonhost plants, but the interactional mechanisms of AMF with and functional relevance for nonhost plants is little known. Here we show AMF can colonize an individually grown nonhost plant, Arabidopsis thaliana, and suppress the growth of Arabidopsis and two nonhost Brassica crops. This inhibitory effect increased with increasing AMF inoculum density, and was independent of AMF species or nutrient availability. 13 C isotope labeling and physiological analyses revealed no significant carbon-phosphorus exchange between Arabidopsis and AMF, indicating a lack of nutritional function in this interaction. AMF colonization activated the danger-associated peptide Pep-PEPR signaling pathway, and caused clear defense responses in Arabidopsis. The impairment of Pep-PEPR signaling in nonhost plants greatly compromised AMF-triggered defensive responses and photosynthesis suppression, leading to higher colonization rates and reduced growth suppression upon AMF inoculation. Pretreatment with Pep peptide decreased AMF colonization, and largely substituted for AMF-induced growth suppression in nonhosts, confirming that the Pep-PEPR pathway is a key participant in resistance to AMF colonization and in mediating growth suppression of nonhost plants. This work greatly increases our knowledge about the functional relevance of AMF and their mechanisms of interactions with nonhost plants.

Phosphorus addition increased carbon partitioning to autotrophic respiration but not to biomass production in an experiment with Zea mays.

Plant carbon (C) partitioning-the relative use of photosynthates for biomass production, respiration, and other plant functions-is a key but poorly understood ecosystem process. In an experiment with Zea mays, with or without arbuscular mycorrhizal fungi (AMF), we investigated the effect of phosphorus (P) fertilization and AMF on plant C partitioning. Based on earlier studies, we expected C partitioning to biomass production (i.e., biomass production efficiency; BPE) to increase with increasing P addition due to reduced C partitioning to AMF. However, although plant growth was clearly stimulated by P addition, BPE did not increase. Instead, C partitioning to autotrophic respiration increased. These results contrasted with our expectations and with a previous experiment in the same set-up where P addition increased BPE while no effect on autotropic respiration was found. The comparison of both experiments suggests a key role for AMF in explaining these contrasts. Whereas in the previous experiment substantial C partitioning to AMF reduced BPE under low P, in the current experiment, C partitioning to AMF was too low to directly influence BPE. Our results illustrate the complex influence of nutrient availability and mycorrhizal symbiosis on plant C partitioning.

Positive effects of co-inoculation with Rhizophagus irregularis and Serendipita indica on tomato growth under saline conditions, and their individual colonization estimated by signature lipids.

Tomato roots can be colonized by both mycorrhizal fungi and the endophytic fungus Serendipita indica. This study was aimed at assessment of the impact of single or dual inoculation with R. irregularis and S. indica on tomato growth under saline conditions. We used signature compounds to estimate the abundance of each of these two fungi (fatty acid 16:1ω5 for R. irregularis and ergosterol for S. indica) in roots. A randomized block design was applied with four types of inoculation (no fungus, R. irregularis, S. indica or S. indica + R. irregularis) at different levels of salinity (1.2, 5, and 10 dS/m) with four replications per treatment. The plant dry weight was slightly higher in R. irregularis- than S. indica-inoculated plants, and the highest plant biomass was achieved with dual inoculation. R. irregularis increased the content of the neutral lipid fatty acid 16:1ω5 from 97 to 5300 nmol/g and phospholipid fatty acid 16:1ω5 from 8 to 141 nmol/g in roots (at a salinity level of 1.2 dS m-1), but the increases were lower at higher levels of salinity. Moreover, both these arbuscular mycorrhizal fungal markers were slightly decreased in the presence of S. indica. Root ergosterol increased from 7 to 114 µg g-1 with S. indica inoculation. With increasing salinity, the concentration of ergosterol in roots decreased. Inoculation with R. irregularis caused a decrease in root ergosterol. Increasing salinity resulted in an increase of Cl and Na in tomato shoots, but the increase was significantly lower in single- or dual-inoculated plants in contrast to the control plants.

The responses of microbial temperature relationships to seasonal change and winter warming in a temperate grassland.

Microorganisms dominate the decomposition of organic matter and their activities are strongly influenced by temperature. As the carbon (C) flux from soil to the atmosphere due to microbial activity is substantial, understanding temperature relationships of microbial processes is critical. It has been shown that microbial temperature relationships in soil correlate with the climate, and microorganisms in field experiments become more warm-tolerant in response to chronic warming. It is also known that microbial temperature relationships reflect the seasons in aquatic ecosystems, but to date this has not been investigated in soil. Although climate change predictions suggest that temperatures will be mostly affected during winter in temperate ecosystems, no assessments exist of the responses of microbial temperature relationships to winter warming. We investigated the responses of the temperature relationships of bacterial growth, fungal growth, and respiration in a temperate grassland to seasonal change, and to 2 years' winter warming. The warming treatments increased winter soil temperatures by 5-6°C, corresponding to 3°C warming of the mean annual temperature. Microbial temperature relationships and temperature sensitivities (Q10 ) could be accurately established, but did not respond to winter warming or to seasonal temperature change, despite significant shifts in the microbial community structure. The lack of response to winter warming that we demonstrate, and the strong response to chronic warming treatments previously shown, together suggest that it is the peak annual soil temperature that influences the microbial temperature relationships, and that temperatures during colder seasons will have little impact. Thus, mean annual temperatures are poor predictors for microbial temperature relationships. Instead, the intensity of summer heat-spells in temperate systems is likely to shape the microbial temperature relationships that govern the soil-atmosphere C exchange.

Climate warming and land-use changes drive broad-scale floristic changes in Southern Sweden.

Land-use changes, pollution and climate warming during the 20th century have caused changes in biodiversity across the world. However, in many cases, the environmental drivers are poorly understood. To identify and rank the drivers currently causing broad-scale floristic changes in N Europe, we analysed data from two vascular plant surveys of 200 randomly selected 2.5 × 2.5 km grid-squares in Scania, southernmost Sweden, conducted 1989-2006 and 2008-2015, respectively, and related the change in frequency (performance) of the species to a wide range of species-specific plant traits. We chose traits representing all plausible drivers of recent floristic changes: climatic change (northern distribution limit, flowering time), land-use change (light requirement, response to grazing/mowing, response to soil disturbance), drainage (water requirement), acidification (pH optimum), nitrogen deposition and eutrophication (N requirement, N fixation ability, carnivory, parasitism, mycorrhizal associations), pollinator decline (mode of reproduction) and changes in CO2 levels (photosynthetic pathway). Our results suggest that climate warming and changes in land-use were the main drivers of changes in the flora during the last decades. Climate warming appeared as the most influential driver, with northern distribution limit explaining 30%-60% of the variance in the GLMM models. However, the relative importance of the drivers differed among habitat types, with grassland species being affected the most by cessation of grazing/mowing and species of ruderal habitats by on-going concentration of both agriculture and human population to the most productive soils. For wetland species, only pH optimum was significantly related to species performance, possibly an effect of the increasing humification of acidic water bodies. An observed relative decline of mycorrhizal species may possibly be explained by decreasing nitrogen deposition resulting in less competition for phosphorus. We found no effect of shortage or decline of pollinating lepidopterans and bees.

A phosphorus threshold for mycoheterotrophic plants in tropical forests.

The majority of terrestrial plants associate with arbuscular mycorrhizal (AM) fungi, which typically facilitate the uptake of limiting mineral nutrients by plants in exchange for plant carbon. However, hundreds of non-photosynthetic plant species-mycoheterotrophs-depend entirely on AM fungi for carbon as well as mineral nutrition. Mycoheterotrophs can provide insight into the operation and regulation of AM fungal relationships, but little is known about the factors, fungal or otherwise, that affect mycoheterotroph abundance and distribution. In a lowland tropical forest in Panama, we conducted the first systematic investigation into the influence of abiotic factors on the abundance and distribution of mycoheterotrophs, to ask whether the availability of nitrogen and phosphorus altered the occurrence of mycoheterotrophs and their AM fungal partners. Across a natural fertility gradient spanning the isthmus of Panama, and also in a long-term nutrient-addition experiment, mycoheterotrophs were entirely absent when soil exchangeable phosphate concentrations exceeded 2 mg P kg-1 Experimental phosphorus addition reduced the abundance of AM fungi, and also reduced the abundance of the specific AM fungal taxa required by the mycoheterotrophs, suggesting that the phosphorus sensitivity of mycoheterotrophs is underpinned by the phosphorus sensitivity of their AM fungal hosts. The soil phosphorus concentration of 2 mg P kg-1 also corresponds to a marked shift in tree community composition and soil phosphatase activity across the fertility gradient, suggesting that our findings have broad ecological significance.

Long-term agricultural fertilization alters arbuscular mycorrhizal fungal community composition and barley (Hordeum vulgare) mycorrhizal carbon and phosphorus exchange.

Agricultural fertilization significantly affects arbuscular mycorrhizal fungal (AMF) community composition. However, the functional implications of community shifts are unknown, limiting understanding of the role of AMF in agriculture. We assessed AMF community composition at four sites managed under the same nitrogen (N) and phosphorus (P) fertilizer regimes for 55 yr. We also established a glasshouse experiment with the same soils to investigate AMF-barley (Hordeum vulgare) nutrient exchange, using carbon (13 C) and 33 P isotopic labelling. N fertilization affected AMF community composition, reducing diversity; P had no effect. In the glasshouse, AMF contribution to plant P declined with P fertilization, but was unaffected by N. Barley C allocation to AMF also declined with P fertilization. As N fertilization increased, C allocation to AMF per unit of P exchanged increased. This occurred with and without P fertilization, and was concomitant with reduced barley biomass. AMF community composition showed no relationship with glasshouse experiment results. The results indicate that plants can reduce C allocation to AMF in response to P fertilization. Under N fertilization, plants allocate an increasing amount of C to AMF and receive relatively less P. This suggests an alteration in the terms of P-C exchange under N fertilization regardless of soil P status.

Arbuscular mycorrhizal fungal community composition is altered by long-term litter removal but not litter addition in a lowland tropical forest.

Tropical forest productivity is sustained by the cycling of nutrients through decomposing organic matter. Arbuscular mycorrhizal (AM) fungi play a key role in the nutrition of tropical trees, yet there has been little experimental investigation into the role of AM fungi in nutrient cycling via decomposing organic material in tropical forests. We evaluated the responses of AM fungi in a long-term leaf litter addition and removal experiment in a tropical forest in Panama. We described AM fungal communities using 454-pyrosequencing, quantified the proportion of root length colonised by AM fungi using microscopy, and estimated AM fungal biomass using a lipid biomarker. AM fungal community composition was altered by litter removal but not litter addition. Root colonisation was substantially greater in the superficial organic layer compared with the mineral soil. Overall colonisation was lower in the litter removal treatment, which lacked an organic layer. There was no effect of litter manipulation on the concentration of the AM fungal lipid biomarker in the mineral soil. We hypothesise that reductions in organic matter brought about by litter removal may lead to AM fungi obtaining nutrients from recalcitrant organic or mineral sources in the soil, besides increasing fungal competition for progressively limited resources.

Warmer winters increase the rhizosphere carbon flow to mycorrhizal fungi more than to other microorganisms in a temperate grassland.

A decisive set of steps in the terrestrial carbon (C) cycle is the fixation of atmospheric C by plants and the subsequent C-transfer to rhizosphere microorganisms. With climate change winters are expected to become milder in temperate ecosystems. Although the rate and pathways of rhizosphere C input to soil could be impacted by milder winters, the responses remain unknown. To address this knowledge-gap, a winter-warming experiment was established in a seminatural temperate grassland to follow the C flow from atmosphere, via the plants, to different groups of soil microorganisms. In situ 13 CO2 pulse labelling was used to track C into signature fatty acids of microorganisms. The winter warming did not result in any changes in biomass of any of the groups of microorganisms. However, the C flow from plants to arbuscular mycorrhizal (AM) fungi, increased substantially by winter warming. Saprotrophic fungi also received large amounts of plant-derived C-indicating a higher importance for the turnover of rhizosphere C than biomass estimates would suggest-still, this C flow was unaffected by winter warming. AM fungi was the only microbial group positively affected by winter warming-the group with the closest connection to plants. Winter warming resulted in higher plant productivity earlier in the season, and this aboveground change likely induced plant nutrient limitation in warmed plots, thus stimulating the plant dependence on, and C allocation to, belowground nutrient acquisition. The preferential C allocation to AM fungi was at the expense of C flow to other microbial groups, which were unaffected by warming. Our findings imply that warmer winters may shift rhizosphere C-fluxes to become more AM fungal-dominated. Surprisingly, the stimulated rhizosphere C flow was matched by increased microbial turnover, leading to no accumulation of soil microbial biomass.

Community dynamics of arbuscular mycorrhizal fungi in high-input and intensively irrigated rice cultivation systems.

Application of a mycorrhizal inoculum could be one way to increase the yield of rice plants and reduce the application of fertilizer. We therefore studied arbuscular mycorrhizal fungi (AMF) in the roots of wetland rice (Oryza sativa L.) collected at the seedling, tillering, heading, and ripening stages in four paddy wetlands that had been under a high-input and intensively irrigated rice cultivation system for more than 20 years. It was found that AMF colonization was mainly established in the heading and ripening stages. The AMF community structure was characterized in rhizosphere soils and roots from two of the studied paddy wetlands. A fragment covering the partial small subunit (SSU), the whole internal transcribed spacer (ITS), and the partial large subunit (LSU) rRNA operon regions of AMF was amplified, cloned, and sequenced from roots and soils. A total of 639 AMF sequences were obtained, and these were finally assigned to 16 phylotypes based on a phylogenetic analysis, including 12 phylotypes from Glomeraceae, one phylotype from Claroideoglomeraceae, two phylotypes from Paraglomeraceae, and one unidentified phylotype. The AMF phylotype compositions in the soils were similar between the two surveyed sites, but there was a clear discrepancy between the communities obtained from root and soil. The relatively high number of AMF phylotypes at the surveyed sites suggests that the conditions are suitable for some species of AMF and that they may have an important function in conventional rice cultivation systems. The species richness of root-colonizing AMF increased with the growth of rice, and future studies should consider the developmental stages of this crop in the exploration of AMF function in paddy wetlands.

Phosphorus and carbon availability regulate structural composition and complexity of AM fungal mycelium.

The regulation of the structural composition and complexity of the mycelium of arbuscular mycorrhizal (AM) fungi is not well understood due to their obligate biotrophic nature. The aim of this study was to investigate the structure of extraradical mycelium at high and low availability of carbon (C) to the roots and phosphorus (P) to the fungus. We used monoxenic cultures of the AM fungus Rhizophagus irregularis (formerly Glomus intraradices) with transformed carrot roots as the host in a cultivation system including a root-free compartment into which the extraradical mycelium could grow. We found that high C availability increased hyphal length and spore production and anastomosis formation within individual mycelia. High P availability increased the formation of branched absorbing structures and reduced spore production and the overall length of runner hyphae. The complexity of the mycelium, as indicated by its fractal dimensions, increased with both high C and P availability. The results indicate that low P availability induces a growth pattern that reflects foraging for both P and C. Low C availability to AM roots could still support the explorative development of the mycelium when P availability was low. These findings help us to better understand the development of AM fungi in ecosystems with high P input and/or when plants are subjected to shading, grazing or any management practice that reduces the photosynthetic ability of the plant.

Soil disturbance alters plant community composition and decreases mycorrhizal carbon allocation in a sandy grassland.

We have studied how disturbance by ploughing and rotavation affects the carbon (C) flow to arbuscular mycorrhizal (AM) fungi in a dry, semi-natural grassland. AM fungal biomass was estimated using the indicator neutral lipid fatty acid (NLFA) 16:1ω5, and saprotrophic fungal biomass using NLFA 18:2ω6,9. We labeled vegetation plots with (13)CO(2) and studied the C flow to the signature fatty acids as well as uptake and allocation in plants. We found that AM fungal biomass in roots and soil decreased with disturbance, while saprotrophic fungal biomass in soil was not influenced by disturbance. Rotavation decreased the (13)C enrichment in NLFA 16:1ω5 in soil, but (13)C enrichment in the AM fungal indicator NLFA 16:1ω5 in roots or soil was not influenced by any other disturbance. In roots, (13)C enrichment was consistently higher in NLFA 16:1ω5 than in crude root material. Grasses (mainly Festuca brevipila) decreased as a result of disturbance, while non-mycorrhizal annual forbs increased. This decreases the potential for mycorrhizal C sequestration and may have been the main reason for the reduced mycorrhizal C allocation found in disturbed plots. Disturbance decreased the soil ammonium content but did not change the pH, nitrate or phosphate availability. The overall effect of disturbance on C allocation was that more of the C in AM fungal mycelium was directed to the external phase. Furthermore, the functional identity of the plants seemed to play a minor role in the C cycle as no differences were seen between different groups, although annuals contained less AM fungi than the other groups.

Mechanical soil disturbance as a determinant of arbuscular mycorrhizal fungal communities in semi-natural grassland.

While the effect of disturbance on overall abundance and community composition of arbuscular mycorrhizal (AM) fungi has been researched in agricultural fields, less is known about the impact in semi-natural grasslands. We sampled two AM plant species, Festuca brevipila and Plantago lanceolata, from an ongoing grassland restoration experiment that contained replicated plowed and control plots. The AM fungal community in roots was determined using nested PCR and LSU rDNA primers. We identified 38 phylotypes within the Glomeromycota, of which 29 belonged to Glomus A, six to Glomus B, and three to Diversisporaceae. Only three phylotypes were closely related to known morphospecies. Soil disturbance significantly reduced phylotype richness and changed the AM fungal community composition. Most phylotypes, even closely related ones, showed little or no overlap in their distribution and occurred in either the control or disturbed plots. We found no evidence of host preference in this system, except for one phylotype that preferentially seemed to colonize Festuca. Our results show that disturbance imposed a stronger structuring force for AM fungal communities than did host plants in this semi-natural grassland.

Elemental composition of arbuscular mycorrhizal fungi at high salinity.

We investigated the elemental composition of spores and hyphae of arbuscular mycorrhizal fungi (AMF) collected from two saline sites at the desert border in Tunisia, and of Glomus intraradices grown in vitro with or without addition of NaCl to the medium, by proton-induced X-ray emission. We compared the elemental composition of the field AMF to those of the soil and the associated plants. The spores and hyphae from the saline soils showed strongly elevated levels of Ca, Cl, Mg, Fe, Si, and K compared to their growth environment. In contrast, the spores of both the field-derived AMF and the in vitro grown G. intraradices contained lower or not elevated Na levels compared to their growth environment. This resulted in higher K:Na and Ca:Na ratios in spores than in soil, but lower than in the associated plants for the field AMF. The K:Na and Ca:Na ratios of G. intraradices grown in monoxenic cultures were also in the same range as those of the field AMF and did not change even when those ratios in the growth medium were lowered several orders of magnitude by adding NaCl. These results indicate that AMF can selectively take up elements such as K and Ca, which act as osmotic equivalents while they avoid uptake of toxic Na. This could make them important in the alleviation of salinity stress in their plant hosts.

Organic and conservation agriculture promote ecosystem multifunctionality.

Ecosystems provide multiple services to humans. However, agricultural systems are usually evaluated on their productivity and economic performance, and a systematic and quantitative assessment of the multifunctionality of agroecosystems including environmental services is missing. Using a long-term farming system experiment, we evaluated and compared the agronomic, economic, and ecological performance of the most widespread arable cropping systems in Europe: organic, conservation, and conventional agriculture. We analyzed 43 agroecosystem properties and determined overall agroecosystem multifunctionality. We show that organic and conservation agriculture promoted ecosystem multifunctionality, especially by enhancing regulating and supporting services, including biodiversity preservation, soil and water quality, and climate mitigation. In contrast, conventional cropping showed reduced multifunctionality but delivered highest yield. Organic production resulted in higher economic performance, thanks to higher product prices and additional support payments. Our results demonstrate that different cropping systems provide opposing services, enforcing the productivity-environmental protection dilemma for agroecosystem functioning.

Phosphorus availability influences elemental uptake in the mycorrhizal fungus Glomus intraradices, as revealed by particle-induced X-ray emission analysis.

We investigated element accumulation in the arbuscular mycorrhizal fungus Glomus intraradices. Fungal spores and mycelia growing in monoxenic cultures were analyzed. The elemental composition was quantified using particle-induced X-ray emission (PIXE) in combination with scanning transmission ion microscopy. In the spores, Ca and Fe were associated mainly with the spore wall, while P and K showed patchy distributions and their concentrations were correlated. Excess of P in the hyphal growth medium increased the P and Si concentrations in spores and increased the K/Ca ratio in spores. Increased P availability decreased the concentration of Zn and Mn in spores. We concluded that the availability of P influences the uptake and accumulation of several elements in spores. It is demonstrated that PIXE analysis is a powerful tool for quantitative analysis of elemental accumulation in fungal mycelia.

Absence of carbon transfer between Medicago truncatula plants linked by a mycorrhizal network, demonstrated in an experimental microcosm.

Carbon transfer between plants via a common extraradical network of arbuscular mycorrhizal (AM) fungal hyphae has been investigated abundantly, but the results remain equivocal. We studied the transfer of carbon through this fungal network, from a Medicago truncatula donor plant to a receiver (1) M. truncatula plant growing under decreased light conditions and (2) M. truncatula seedling. Autotrophic plants were grown in bicompartmented Petri plates, with their root systems physically separated, but linked by the extraradical network of Glomus intraradices. A control Myc-/Nod- M. truncatula plant was inserted in the same compartment as the receiver plant. Following labeling of the donor plant with 13CO2, 13C was recovered in the donor plant shoots and roots, in the extraradical mycelium and in the receiver plant roots. Fatty acid analysis of the receiver's roots further demonstrated 13C enrichment in the fungal-specific lipids, while almost no label was detected in the plant-specific compounds. We conclude that carbon was transferred from the donor to the receiver plant via the AM fungal network, but that the transferred carbon remained within the intraradical AM fungal structures of the receiver's root and was not transferred to the receiver's plant tissues.