Phosphorus limitation promotes soil carbon storage in a boreal forest exposed to long-term nitrogen fertilization.

Forests play a crucial role in global carbon cycling by absorbing and storing significant amounts of atmospheric carbon dioxide. Although boreal forests contribute to approximately 45% of the total forest carbon sink, tree growth and soil carbon sequestration are constrained by nutrient availability. Here, we examine if long-term nutrient input enhances tree productivity and whether this leads to carbon storage or whether stimulated microbial decomposition of organic matter limits soil carbon accumulation. Over six decades, nitrogen, phosphorus, and calcium were supplied to a Pinus sylvestris-dominated boreal forest. We found that nitrogen fertilization alone or together with calcium and/or phosphorus increased tree biomass production by 50% and soil carbon sequestration by 65% compared to unfertilized plots. However, the nonlinear relationship observed between tree productivity and soil carbon stock across treatments suggests microbial regulation. When phosphorus was co-applied with nitrogen, it acidified the soil, increased fungal biomass, altered microbial community composition, and enhanced biopolymer degradation capabilities. While no evidence of competition between ectomycorrhizal and saprotrophic fungi has been observed, key functional groups with the potential to reduce carbon stocks were identified. In contrast, when nitrogen was added without phosphorus, it increased soil carbon sequestration because microbial activity was likely limited by phosphorus availability. In conclusion, the addition of nitrogen to boreal forests may contribute to global warming mitigation, but this effect is context dependent.

Accumulation of pathogens in soil microbiome can explain long-term fluctuations of legumes in a grassland community.

All plant populations fluctuate in time. Apart from the dynamics imposed by external forces such as climate, these fluctuations can be driven by endogenous processes taking place within the community. In this study, we aimed to identify potential role of soil-borne microbial communities in driving endogenous fluctuations of plant populations. We combined a unique, 35-yr long abundance data of 11 common plant species from a species-rich mountain meadow with development of their soil microbiome (pathogenic fungi, arbuscular mycorrhizal fungi and oomycetes) observed during 4 yr of experimental cultivation in monocultures. Plant species which abundance fluctuated highly in the field (particularly legumes) accumulated plant pathogens in their soil mycobiome. We also identified increasing proportion of mycoparasitic fungi under highly fluctuating legume species, which may indicate an adaptation of these species to mitigate the detrimental effects of pathogens. Our study documented that long-term fluctuations in the abundance of plant species in grassland communities can be explained by the accumulation of plant pathogens in plant-soil microbiome. By contrast, we found little evidence of the role of mutualists in plant population fluctuations. These findings offer new insights for understanding mechanisms driving both long-term vegetation dynamics and patterns of species coexistence and richness.

Beyond the rootzone: Unveiling soil property and biota gradients around plants.

Although the effects of plants on soil properties are well known, the effects of distance from plant roots to root-free soil on soil properties and associated soil organisms are much less studied. Previous research on the effects of distance from a plant explored specific soil organisms and properties, however, comparative studies across a wide range of plant-associated organisms and multiple model systems are lacking. We conducted a controlled greenhouse experiment using soil from two contrasting habitats. Within each soil type, we cultivated two plant species, individually and in combination, studying soil organisms and properties in the root centre, the root periphery, and the root-free zones. We showed that the distance from the cultivated plant (representing decreasing amount of plant roots) had a significant impact on the abiotic properties of the soil (pH and available P and N) and also on the composition of the fungal, bacterial, and nematode communities. The specific patterns, however, did not always match our expectations. For example, there was no significant relationship between the abundance of fungal pathogens and the distance from the cultivated plant compared to a strong decrease in the abundance of arbuscular mycorrhizal fungi. Changes in soil chemistry along the distance from the cultivated plant were probably one of the important drivers that affected bacterial communities. The abundance of nematodes also decreased with distance from the cultivated plant, and the rate of their responses reflected the distribution of their food sources. The patterns of soil changes along the gradient from plant to root-free soil were largely similar in two contrasting soil types and four plant species or their mixtures. This suggests that our results can be generalised to other systems and contribute to a better understanding of the mechanisms of soil legacy formation.

Effect of plant communities on bacterial and fungal communities in a Central European grassland.

BACKGROUND: Grasslands provide fundamental ecosystem services that are supported by their plant diversity. However, the importance of plant taxonomic diversity for the diversity of other taxa in grasslands remains poorly understood. Here, we studied the associations between plant communities, soil chemistry and soil microbiome in a wooded meadow of Certoryje (White Carpathians, Czech Republic), a European hotspot of plant species diversity. RESULTS: High plant diversity was associated with treeless grassland areas with high primary productivity and high contents of soil nitrogen and organic carbon. In contrast, low plant diversity occurred in grasslands near solitary trees and forest edges. Fungal communities differed between low-diversity and high-diversity grasslands more strongly than bacterial communities, while the difference in arbuscular mycorrhizal fungi (AMF) depended on their location in soil versus plant roots. Compared to grasslands with low plant diversity, high-diversity plant communities had a higher diversity of fungi including soil AMF, a different fungal and soil AMF community composition and higher bacterial and soil AMF biomass. Root AMF composition differed only slightly between grasslands with low and high plant diversity. Trees dominated the belowground plant community in low-diversity grasslands, which influenced microbial diversity and composition. CONCLUSIONS: The determinants of microbiome abundance and composition in grasslands are complex. Soil chemistry mainly influenced bacterial communities, while plant community type mainly affected fungal (including AMF) communities. Further studies on the functional roles of microbial communities are needed to understand plant-soil-microbe interactions and their involvement in grassland ecosystem services.

Fungal communities are passengers in community development of dune ecosystems, while bacteria are not.

An increasing number of studies of above-belowground interactions provide a fundamental basis for our understanding of the coexistence between plant and soil communities. However, we lack empirical evidence to understand the directionality of drivers of plant and soil communities under natural conditions: 'Are soil microorganisms driving plant community functioning or do they adapt to the plant community?' In a field experiment in an early successional dune ecosystem, we manipulated soil communities by adding living (i.e., natural microbial communities) and sterile soil inocula, originating from natural ecosystems, and examined the annual responses of soil and plant communities. The experimental manipulations had a persistent effect on the soil microbial community with divergent impacts for living and sterile soil inocula. The plant community was also affected by soil inoculation, but there was no difference between the impacts of living and sterile inocula. We also observed an increasing convergence of plant and soil microbial composition over time. Our results show that alterations in soil abiotic and biotic conditions have long-term effects on the composition of both plant and soil microbial communities. Importantly, our study provides direct evidence that soil microorganisms are not "drivers" of plant community dynamics. We found that soil fungi and bacteria manifest different community assemblies in response to treatments. Soil fungi act as "passengers," that is, soil microorganisms reflect plant community dynamics but do not alter it, whereas soil bacteria are neither "drivers" nor "passengers" of plant community dynamics in early successional ecosystems. These results are critical for understanding the community assembly of plant and soil microbial communities under natural conditions and are directly relevant for ecosystem management and restoration.

Plant effects on microbiome composition are constrained by environmental conditions in a successional grassland.

BACKGROUND: Below-ground microbes mediate key ecosystem processes and play a vital role in plant nutrition and health. Understanding the composition of the belowground microbiome is therefore important for maintaining ecosystem stability. The structure of the belowground microbiome is largely determined by individual plants, but it is not clear how far their influence extends and, conversely, what the influence of other plants growing nearby is. RESULTS: To determine the extent to which a focal host plant influences its soil and root microbiome when growing in a diverse community, we sampled the belowground bacterial and fungal communities of three plant species across a primary successional grassland sequence. The magnitude of the host effect on its belowground microbiome varied among microbial groups, soil and root habitats, and successional stages characterized by different levels of diversity of plant neighbours. Soil microbial communities were most strongly structured by sampling site and showed significant spatial patterns that were partially driven by soil chemistry. The influence of focal plant on soil microbiome was low but tended to increase with succession and increasing plant diversity. In contrast, root communities, particularly bacterial, were strongly structured by the focal plant species. Importantly, we also detected a significant effect of neighbouring plant community composition on bacteria and fungi associating with roots of the focal plants. The host influence on root microbiome varied across the successional grassland sequence and was highest in the most diverse site. CONCLUSIONS: Our results show that in a species rich natural grassland, focal plant influence on the belowground microbiome depends on environmental context and is modulated by surrounding plant community. The influence of plant neighbours is particularly pronounced in root communities which may have multiple consequences for plant community productivity and stability, stressing the importance of plant diversity for ecosystem functioning.

GlobalAMFungi: a global database of arbuscular mycorrhizal fungal occurrences from high-throughput sequencing metabarcoding studies.

Arbuscular mycorrhizal (AM) fungi are crucial mutualistic symbionts of the majority of plant species, with essential roles in plant nutrient uptake and stress mitigation. The importance of AM fungi in ecosystems contrasts with our limited understanding of the patterns of AM fungal biogeography and the environmental factors that drive those patterns. This article presents a release of a newly developed global AM fungal dataset (GlobalAMFungi database, https://globalamfungi.com) that aims to reduce this knowledge gap. It contains almost 50 million observations of Glomeromycotinian AM fungal amplicon DNA sequences across almost 8500 samples with geographical locations and additional metadata obtained from 100 original studies. The GlobalAMFungi database is built on sequencing data originating from AM fungal taxon barcoding regions in: i) the small subunit rRNA (SSU) gene; ii) the internal transcribed spacer 2 (ITS2) region; and iii) the large subunit rRNA (LSU) gene. The GlobalAMFungi database is an open source and open access initiative that compiles the most comprehensive atlas of AM fungal distribution. It is designed as a permanent effort that will be continuously updated by its creators and through the collaboration of the scientific community. This study also documented applicability of the dataset to better understand ecology of AM fungal taxa.

Improved recovery and annotation of genes in metagenomes through the prediction of fungal introns.

Metagenomics provides a tool to assess the functional potential of environmental and host-associated microbiomes based on the analysis of environmental DNA: assembly, gene prediction and annotation. While gene prediction is straightforward for most bacterial and archaeal taxa, it has limited applicability in the majority of eukaryotic organisms, including fungi that contain introns in gene coding sequences. As a consequence, eukaryotic genes are underrepresented in metagenomics datasets and our understanding of the contribution of fungi and other eukaryotes to microbiome functioning is limited. Here, we developed a machine intelligence-based algorithm that predicts fungal introns in environmental DNA with reasonable precision and used it to improve the annotation of environmental metagenomes. Intron removal increased the number of predicted genes by up to 9.1% and improved the annotation of several others. The proportion of newly predicted genes increased with the share of eukaryotic genes in the metagenome and-within fungal taxa-increased with the number of introns per gene. Our approach provides a tool named SVMmycointron for improved metagenome annotation, especially of microbiomes with a high proportion of eukaryotes. The scripts described in the paper are made publicly available and can be readily utilized by microbiome researchers analysing metagenomics data.

Symbiotic status alters fungal eco-evolutionary offspring trajectories.

Despite host-fungal symbiotic interactions being ubiquitous in all ecosystems, understanding how symbiosis has shaped the ecology and evolution of fungal spores that are involved in dispersal and colonization of their hosts has been ignored in life-history studies. We assembled a spore morphology database covering over 26,000 species of free-living to symbiotic fungi of plants, insects and humans and found more than eight orders of variation in spore size. Evolutionary transitions in symbiotic status correlated with shifts in spore size, but the strength of this effect varied widely among phyla. Symbiotic status explained more variation than climatic variables in the current distribution of spore sizes of plant-associated fungi at a global scale while the dispersal potential of their spores is more restricted compared to free-living fungi. Our work advances life-history theory by highlighting how the interaction between symbiosis and offspring morphology shapes the reproductive and dispersal strategies among living forms.

Climate-driven shifts in plant and fungal communities can lead to topsoil carbon loss in alpine ecosystems.

Alpine tundra ecosystems suffer from ongoing warming-induced tree encroachment and vegetation shifts. While the effects of tree line expansion on the alpine ecosystem receive a lot of attention, there is also an urgent need for understanding the effect of climate change on shifts within alpine vegetation itself, and how these shifts will consequently affect soil microorganisms and related ecosystem characteristics such as carbon storage. For this purpose, we explored relationships between climate, soil chemistry, vegetation, and fungal communities across seven mountain ranges at 16 alpine tundra locations in Europe. Among environmental factors, our data highlighted that plant community composition had the most important influence on variation in fungal community composition when considered in combination with other factors, while climatic factors had the most important influence solely. According to our results, we suggest that rising temperature, associated with a replacement of ericoid-dominated alpine vegetation by non-mycorrhizal or arbuscular mycorrhizal herbs and grasses, will induce profound changes in fungal communities toward higher dominance of saprotrophic and arbuscular mycorrhizal fungi at the expense of fungal root endophytes. Consequently, topsoil fungal biomass and carbon content will decrease.

Forest microbiome and global change.

Forests influence climate and mitigate global change through the storage of carbon in soils. In turn, these complex ecosystems face important challenges, including increases in carbon dioxide, warming, drought and fire, pest outbreaks and nitrogen deposition. The response of forests to these changes is largely mediated by microorganisms, especially fungi and bacteria. The effects of global change differ among boreal, temperate and tropical forests. The future of forests depends mostly on the performance and balance of fungal symbiotic guilds, saprotrophic fungi and bacteria, and fungal plant pathogens. Drought severely weakens forest resilience, as it triggers adverse processes such as pathogen outbreaks and fires that impact the microbial and forest performance for carbon storage and nutrient turnover. Nitrogen deposition also substantially affects forest microbial processes, with a pronounced effect in the temperate zone. Considering plant-microorganism interactions would help predict the future of forests and identify management strategies to increase ecosystem stability and alleviate climate change effects. In this Review, we describe the impact of global change on the forest ecosystem and its microbiome across different climatic zones. We propose potential approaches to control the adverse effects of global change on forest stability, and present future research directions to understand the changes ahead.

Defending Earth's terrestrial microbiome.

Microbial life represents the majority of Earth's biodiversity. Across disparate disciplines from medicine to forestry, scientists continue to discover how the microbiome drives essential, macro-scale processes in plants, animals and entire ecosystems. Yet, there is an emerging realization that Earth's microbial biodiversity is under threat. Here we advocate for the conservation and restoration of soil microbial life, as well as active incorporation of microbial biodiversity into managed food and forest landscapes, with an emphasis on soil fungi. We analyse 80 experiments to show that native soil microbiome restoration can accelerate plant biomass production by 64% on average, across ecosystems. Enormous potential also exists within managed landscapes, as agriculture and forestry are the dominant uses of land on Earth. Along with improving and stabilizing yields, enhancing microbial biodiversity in managed landscapes is a critical and underappreciated opportunity to build reservoirs, rather than deserts, of microbial life across our planet. As markets emerge to engineer the ecosystem microbiome, we can avert the mistakes of aboveground ecosystem management and avoid microbial monocultures of single high-performing microbial strains, which can exacerbate ecosystem vulnerability to pathogens and extreme events. Harnessing the planet's breadth of microbial life has the potential to transform ecosystem management, but it requires that we understand how to monitor and conserve the Earth's microbiome.

Bacterial community in soil and tree roots of Picea abies shows little response to clearcutting.

Clearcutting represents a standard management practice in temperate forests with dramatic consequences for the forest ecosystem. The removal of trees responsible for the bulk of primary production can result in a complex response of the soil microbiome. While studies have shown that tree root-symbiotic ectomycorrhizal fungi disappear from soil and decomposing fine roots of trees become a hotspot for fungal decomposition, the fate of the bacterial component of the soil microbiome following clearcutting is unclear. Here, we investigated the response of bacterial community composition for 2 years following clearcutting of a Picea abies stand in soil, rhizosphere and tree roots, by 16S rRNA amplicon sequencing. While in the first few months after clearcutting there was no significant response of bacterial community composition in the rhizosphere and soil, bacterial communities associated with tree roots underwent more profound changes over time. Acidobacteria were abundant in rhizosphere and soil, while Firmicutes were strongly represented in the roots. In addition, bacterial communities on decomposing roots were significantly different from those on pre-clearcut live roots. Compared with fungi, the response of bacterial communities to clearcutting was much less pronounced, indicating independent development of the two microbial domains.

Asymmetric Interaction Between Two Mycorrhizal Fungal Guilds and Consequences for the Establishment of Their Host Plants.

Arbuscular mycorrhiza (AM) and ectomycorrhiza (EcM) are the most abundant and widespread types of mycorrhizal symbiosis, but there is little and sometimes conflicting information regarding the interaction between AM fungi (AMF) and EcM fungi (EcMF) in soils. Their competition for resources can be particularly relevant in successional ecosystems, which usually present a transition from AM-forming herbaceous vegetation to EcM-forming woody species. The aims of this study were to describe the interaction between mycorrhizal fungal communities associated with AM and EcM hosts naturally coexisting during primary succession on spoil banks and to evaluate how this interaction affects growth and mycorrhizal colonization of seedlings of both species. We conducted a greenhouse microcosm experiment with Betula pendula and Hieracium caespitosum as EcM and AM hosts, respectively. They were cultivated in three-compartment rhizoboxes. Two lateral compartments contained different combinations of both host plants as sources of fungal mycelia colonizing the middle compartment, where fungal biomass, diversity, and community composition as well as the growth of each host plant species' seedlings were analyzed. The study's main finding was an asymmetric outcome of the interaction between the two plant species: while H. caespitosum and associated AMF reduced the abundance of EcMF in soil, modified the composition of EcMF communities, and also tended to decrease growth and mycorrhizal colonization of B. pendula seedlings, the EcM host did not have such effects on AM plants and associated AMF. In the context of primary succession, these findings suggest that ruderal AM hosts could hinder the development of EcM tree seedlings, thus slowing the transition from AM-dominated to EcM-dominated vegetation in early successional stages.

Soil microbial communities following 20 years of fertilization and crop rotation practices in the Czech Republic.

BACKGROUND: Although fertilization and crop rotation practices are commonly used worldwide in agriculture to maximize crop yields, their long-term effect on the structures of soil microorganisms is still poorly understood. This study investigated the long-term impact of fertilization and crop rotation on soil microbial diversity and the microbial community structure in four different locations with three soil types. Since 1996, manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and NPK (NPK; 330 kg N/ha) fertilizers were periodically applied to the soils classified as chernozem, luvisol and cambisol, which are among the most abundant or fertile soils used for agricultural purposes in the world. In these soils, potato (Solanum tuberosum L.), winter wheat (Triticum aestivum L.), and spring barley (Hordeum vulgare L.) were rotated every three years. RESULTS: Soil chemistry, which was significantly associated with location, fertilization, crop rotation, and the interaction of fertilization and location, was the dominant driver of soil microbial communities, both prokaryotic and fungal. A direct effect of long-term crop rotation and fertilization on the structure of their communities was confirmed, although there was no evidence of their influence on microbial diversity. Fungal and bacterial communities responded differently to fertilization treatments; prokaryotic communities were only significantly different from the control soil (CF) in soils treated with MF and SF3x, while fungal communities differed across all treatments. Indicator genera were identified for different treatments. These taxa were either specific for their decomposition activities or fungal plant pathogens. Sequential rotation of the three crops restricted the growth of several of the indicator plant pathogens. CONCLUSIONS: Long-term fertilization and crop rotation significantly altered microbial community structure in the soil. While fertilization affected soil microorganisms mainly through changes in nutrient profile, crop rotations lead to the attraction and repulsion of specific plant pathogens. Such changes in soil microbial communities need to be considered when planning soil management.

Temporal turnover of the soil microbiome composition is guild-specific.

Although spatial and temporal variation are both important components structuring microbial communities, the exact quantification of temporal turnover rates of fungi and bacteria has not been performed to date. In this study, we utilised repeated resampling of bacterial and fungal communities at specific locations across multiple years to describe their patterns and rates of temporal turnover. Our results show that microbial communities undergo temporal change at a rate of 0.010-0.025 per year (in units of Sorensen similarity), and the change in soil is slightly faster in fungi than in bacteria, with bacterial communities changing more rapidly in litter than soil. Importantly, temporal development differs across fungal guilds and bacterial phyla with different ecologies. While some microbial guilds show consistent responses across regional locations, others show site-specific development with weak general patterns. These results indicate that guild-level resolution is important for understanding microbial community assembly, dynamics and responses to environmental factors.

PacBio sequencing of Glomeromycota rDNA: a novel amplicon covering all widely used ribosomal barcoding regions and its applicability in taxonomy and ecology of arbuscular mycorrhizal fungi.

There is no consensus barcoding region for determination of arbuscular mycorrhizal fungal (AMF) taxa. To overcome this obstacle, we have developed an approach to sequence an AMF marker within the ribosome-encoding operon (rDNA) that covers all three widely applied variable molecular markers. Using a nested PCR approach specific to AMF, we amplified a part (c. 2.5 kb) of the rDNA spanning the majority of the small subunit rRNA (SSU) gene, the complete internal transcribed spacer (ITS) region and a part of the large subunit (LSU) rRNA gene. The PCR products were sequenced on the PacBio platform utilizing Single Molecule Real Time (SMRT) sequencing. Employing this method for selected environmental DNA samples, we were able to describe complex AMF communities consisting of various glomeromycotan lineages. We demonstrate the applicability of this new 2.5 kb approach to provide robust phylogenetic assignment of AMF lineages without known sequences from pure cultures and to consolidate information about AMF taxon distributions coming from three widely used barcoding regions into one integrative dataset.

Forest Microhabitat Affects Succession of Fungal Communities on Decomposing Fine Tree Roots.

Belowground litter derived from tree roots has been shown as a principal source of soil organic matter in coniferous forests. Fate of tree root necromass depends on fungal communities developing on the decaying roots. Local environmental conditions which affect composition of tree root mycobiome may also influence fungal communities developing on decaying tree roots. Here, we assessed fungal communities associated with decaying roots of Picea abies decomposing in three microhabitats: soil with no vegetation, soil with ericoid shrubs cover, and P. abies deadwood, for a 2-year period. Forest microhabitat showed stronger effect on structuring fungal communities associated with decaying roots compared to living roots. Some ericoid mycorrhizal fungi showed higher relative abundance on decaying roots in soils under ericoid shrub cover, while saprotrophic fungi had higher relative abundance in roots decomposing inside deadwood. Regardless of the studied microhabitat, we observed decline of ectomycorrhizal fungi and increase of endophytic fungi during root decomposition. Interestingly, we found substantially more fungal taxa with unknown ecology in late stages of root decomposition, indicating that highly decomposed roots may represent so far overlooked niche for soil fungi. Our study shows the importance of microhabitats on the fate of the decomposing spruce roots.