Soil inoculation steers restoration of terrestrial ecosystems

Biological control for One Health

Biological control has been effectively exploited by mankind since 300 CE. By promoting the natural regulation of pests, weeds, and diseases, it produces societal benefits at the food-environment-health nexus. Here we scrutinize biological control endeavours and their social-ecological outcomes through a holistic 'One-Health' lens, recognizing that the health of humans, animals, plants, and the wider environment are linked and interdependent. Evidence shows that biological control generates desirable outcomes within all One Health dimensions, mitigating global change issues such as chemical pollution, biocide resistance, biodiversity loss, and habitat destruction. Yet, its cross-disciplinary achievements remain underappreciated. To remedy this, we advocate a systems-level, integrated approach to biological control research, policy, and practice. Framing biological control in a One Health context helps to unite medical and veterinary personnel, ecologists, conservationists and agricultural professionals in a joint quest for solutions to some of the most pressing issues in planetary health.

Strengthened plant-microorganism interaction after topsoil removal cause more deterministic microbial assembly processes and increased soil nitrogen mineralization

Topsoil removal, among other restoration measures, has been recognized as one of the most successful methods to restore biodiversity and ecosystem functioning in European grasslands. However, knowledge about how removal as well as other restoration methods influence interactions between plant and microbial communities is very limited. The aims of the current study were to understand the impact of topsoil removal on plant-microorganism interactions and on soil nitrogen (N) mineralization, as one example of ecosystem functioning. We examined how three different grassland restoration methods, namely 'Harvest only', 'Topsoil removal' and 'Topsoil removal + Propagules (plant seed addition)', affected i) the interactions between plants and soil microorganisms, ii) soil microbial community assembly processes, and iii) soil N mineralization. We compared the outcome of these three restoration methods to initial degraded and target semi-natural grasslands in the Canton of Zurich, Switzerland. We were able to show that 'Topsoil removal' and 'Topsoil removal + Propagules', but not 'Harvest only', reduced the soil total N pool and available N concentration, but increased soil N mineralization and strengthened the plant-microorganism interactions. Microbial community assembly processes shifted towards more deterministic after both topsoil removal treatments. These shifts could be attributed to an increase in dispersal limitation and selection due to stronger interactions between plants and soil microorganisms. The negative relationship between soil N mineralization and microbial community stochasticity indicated that microbial assembly processes, to some extent, can be incorporated into model predictions of soil functions. Overall, the results suggest that topsoil removal may change the microbial assembly processes and thus the functioning of grassland ecosystems by enhancing the interaction between plants and soil microorganisms.

Unlocking agro-ecosystem sustainability: exploring the bottom-up effects of microbes, plants, and insect herbivores

Agricultural ecosystem formation and evolution depend on interactions and communication between multiple organisms. Within this context, communication occurs between microbes, plants, and insects, often involving the release and perception of a wide range of chemical cues. Unraveling how this information is coded and interpreted is critical to expanding our understanding of how agricultural ecosystems function in terms of competition and cooperation. Investigations examining dual interactions (e.g. plant-microbe, insect-microbe, and insect-plant) have resolved some basic components of this communication. However, there is a need for systematically examining multitrophic interactions that occur simultaneously between microorganisms, insects, and plants. A more thorough understanding of these multitrophic interactions has been made possible by recent advancements in the study of such ecological interactions, which are based on a variety of contemporary technologies such as artificial intelligence sensors, multi-omics, metabarcoding, and others. Frequently, these developments have led to the discovery of startling examples of each member manipulating the other. Here, we review recent advances in the understanding of bottom-up chemical communication between microorganisms, plants, and insects, and their consequences. We discuss the components of these "chemo-languages" and how they modify outcomes of multi-species interactions across trophic levels. Further, we suggest prospects for translating the current basic understanding of multitrophic interactions into strategies that could be applied in agricultural ecosystems to increase food safety and security.

From Microbes to Microbiomes: Applications for Plant Health and Sustainable Agriculture

Plant-microbe interaction research has had a transformative trajectory, from individual microbial isolate studies to comprehensive analyses of plant microbiomes within the broader phytobiome framework. Acknowledging the indispensable role of plant microbiomes in shaping plant health, agriculture, and ecosystem resilience, we underscore the urgent need for sustainable crop production strategies in the face of contemporary challenges. We discuss how the synergies between advancements in 'omics technologies and artificial intelligence can help advance the profound potential of plant microbiomes. Furthermore, we propose a multifaceted approach encompassing translational considerations, transdisciplinary research initiatives, public-private partnerships, regulatory policy development, and pragmatic expectations for the practical application of plant microbiome knowledge across diverse agricultural landscapes. We advocate for strategic collaboration and intentional transdisciplinary efforts to unlock the benefits offered by plant microbiomes and address pressing global issues in food security. By emphasizing a nuanced understanding of plant microbiome complexities and fostering realistic expectations, we encourage the scientific community to navigate the transformative journey from discoveries in the laboratory to field applications. As companies specializing in agricultural microbes and microbiomes undergo shifts, we highlight the necessity of understanding how to approach sustainable agriculture with site-specific management solutions. While cautioning against overpromising, we underscore the excitement of exploring the many impacts of microbiome-plant interactions. We emphasize the importance of collaborative endeavors with societal partners to accelerate our collective capacity to harness the diverse and yet-to-be-discovered beneficial activities of plant microbiomes.

Ecological phage therapy: Can bacteriophages help rapidly restore the soil microbiome?

Soil microbiota underpin ecosystem functionality yet are rarely targeted during ecosystem restoration. Soil microbiota recovery following native plant revegetation can take years to decades, while the effectiveness of soil inoculation treatments on microbiomes remains poorly explored. Therefore, innovative restoration treatments that target soil microbiota represent an opportunity to accelerate restoration outcomes. Here, we introduce the concept of ecological phage therapy-the application of phage for the targeted reduction of the most abundant and dominant bacterial taxa present in degraded ecosystems. We propose that naturally occurring bacteriophages-viruses that infect bacteria-could help rapidly shift soil microbiota towards target communities. Bacteriophages sculpt the microbiome by lysis of specific bacteria, and if followed by the addition of reference soil microbiota, such treatments could facilitate rapid reshaping of soil microbiota. Here, we experimentally tested this concept in a pilot study. We collected five replicate pre-treatment degraded soil samples, then three replicate soil samples 48 hours after phage, bacteria, and control treatments. Bacterial 16S rDNA sequencing showed that phage-treated soils had reduced bacterial diversity; however, when we combined ecological phage therapy with reference soil inoculation, we did not see a shift in soil bacterial community composition from degraded soil towards a reference-like community. Our pilot study provides early evidence that ecological phage therapy could help accelerate the reshaping of soil microbiota with the ultimate aim of reducing timeframes for ecosystem recovery. We recommend the next steps for ecological phage therapy be (a) developing appropriate risk assessment and management frameworks, and (b) focussing research effort on its practical application to maximise its accessibility to restoration practitioners.

Response of Soil Fungal Community to Reforestation on Shifting Sand Dune in the Horqin Sandy Land, Northeast China

Reforestation of native shrub on shifting sand dunes has been widely used for desertification control in semi-arid grassland in Northeast China. Previous studies have confirmed that plantation establishment facilitates fixing sand dunes, restoring vegetation, and improving soil properties, but very few have focused on the response of the soil fungal community. In this study, a chronosequence of Caragana microphylla (CM) shrub sand-fixation plantations (8-, 19-, and 33-year-old), non-vegetated shifting sand dunes (0 years), and adjacent natural CM forests (NCFs; 50-year-old) in the Horqin sandy land were selected as experimental sites. Soil properties including enzymatic activities were determined, and the composition and structure of the soil fungal community were investigated using the Illumina MiSeq sequencing technique based on the internal transcribed spacer (ITS) rDNA. This study aimed to (1) describe the response of the soil fungal community to revegetation onto a moving sand dune by planting a native shrub plantation; (2) determine the main soil factors driving the succession of the fungal community; and (3) discuss whether the soil fungal community can be restored to its original state by reforestation. The reforestation of CM significantly ameliorated soil properties, increased soil fungal diversity, and altered the composition and structure of the soil fungal community. Ascomycota, Basidiomycota, and Zoopagomycota were the dominant phyla in all sites. Ascomycota did not respond to plantation development, whereas the other two dominant phyla linearly increased or decreased with the plantation age. The relative abundance of dominant genera varied with sites and showed a waning and waxing characteristic. The composition and structure of the soil fungal community in the 33-year CM plantation were very close to that of the NCF, indicating the restorability of the soil fungal community. The succession of the soil fungal community was directly driven by soil properties, of which soil moisture, organic matter, total N, urease, and protease were the main affecting factors.

The role of the plant microbiome for forestry, agriculture and urban greenspace in times of environmental change

This Lilliput article provides a literature overview on ecological effects of the plant microbiome with a focus on practical application in forestry, agriculture and urban greenspace under the spectre of climate change. After an overview of the mostly bacterial microbiome of the model plant Arabidopsis thaliana, worldwide data from forests reveal ecological differentiation with respect to major guilds of predominantly fungal plant root symbionts. The plant-microbiome association forms a new holobiont, an integrated unit for ecological adaptation and evolutionary selection. Researchers explored the impact of the microbiome on the capacity of plants to adapt to changing climate conditions. They investigated the impact of the microbiome in reforestation programs, after wildfire, drought, salination and pollution events in forestry, grasslands and agriculture. With increasing temperatures plant populations migrate to higher latitudes and higher altitudes. Ecological studies compared the dispersal capacity of plant seeds with that of soil microbes and the response of soil and root microbes to experimental heating of soils. These studies described a succession of microbiome associations and the kinetics of a release of stored soil carbon into the atmosphere enhancing global warming. Scientists explored the impact of synthetic microbial communities (SynComs) on rice productivity or tea quality; of whole soil addition in grassland restoration; or single fungal inoculation in maize fields. Meta-analyses of fungal inoculation showed overall a positive effect, but also a wide variation in effect sizes. Climate change will be particularly prominent in urban areas ("urban heat islands") where more than half of the world population is living. Urban landscape architecture will thus have an important impact on human health and studies started to explore the contribution of the microbiome from urban greenspace to 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.

Restoration age affects microbial-herbaceous plant interactions in an oak woodland

In degraded ecosystems, soil microbial communities (SMCs) may influence the outcomes of ecological restoration. Restoration practices can affect SMCs, though it is unclear how variation in the onset of restoration activities in woodlands affects SMCs, how those SMCs influence the performance of hard-to-establish woodland forbs, and how different woodland forbs shape SMCs. In this study, we quantified soil properties and species abundances in an oak woodland restoration chronosequence (young, intermediate, and old restorations). We measured the growth of three woodland forb species when inoculated with live whole-soil from young, intermediate, or old restorations. We used DNA metabarcoding to characterize SMCs of each inoculum treatment and the soil after conditioning by each plant species. Our goals were to (1) understand how time since the onset of restoration affected soil abiotic properties, plant communities, and SMCs in a restoration chronosequence, (2) test growth responses of three forb species to whole-soil inoculum from restoration sites, and (3) characterize changes in SMCs before and after conditioning by each forb species. Younger restored woodlands had greater fire-sensitive tree species and lower concentrations of soil phosphorous than intermediate or older restored woodlands. Bacterial and fungal soil communities varied significantly among sites. Forbs exhibited the greatest growth in soil from the young restoration. Each forb species developed a unique soil microbial community. Our results highlight how restoration practices affect SMCs, which can in turn affect the growth of hard-to-establish forb species. Our results also highlight that the choice of forb species can alter SMCs, which could have long-term potential consequences for restoration success.

Tracking arbuscular mycorrhizal fungi to their source: active inoculation and passive dispersal differentially affect community assembly in urban soils

Communities of arbuscular mycorrhizal (AM) fungi assemble passively over time via biotic and abiotic mechanisms. In degraded soils, AM fungal communities can assemble actively when humans manage mycorrhizas for ecosystem restoration. We investigated mechanisms of urban AM fungal community assembly in a 2-yr green roof experiment. We compared AM fungal communities in inoculated and uninoculated trays to samples from two potential sources: the inoculum and air. Active inoculation stimulated more distinct and diverse AM fungal communities, an effect that intensified over time. In the treatment trays, 45% of AM fungal taxa were detected in the inoculum, 2% were detected in aerial samples, 23% were detected in both inoculum and air, and 30% were not detected in either source. Passive dispersal of AM fungi likely resulted in the successful establishment of a small number of species, but active inoculation with native AM fungal species resulted in an immediate shift to a diverse and unique fungal community. When urban soils are constructed or modified by human activity, this is an opportunity for intervention with AM fungi that will persist and add diversity to that system.

Horizontal gene transfer in plant microbiomes: integrons as hotspots for cross-species gene exchange

Plant microbiomes play important roles in plant health and fitness. Bacterial horizontal gene transfer (HGT) can influence plant health outcomes, driving the spread of both plant growth-promoting and phytopathogenic traits. However, community dynamics, including the range of genetic elements and bacteria involved in this process are still poorly understood. Integrons are genetic elements recently shown to be abundant in plant microbiomes, and are associated with HGT across broad phylogenetic boundaries. They facilitate the spread of gene cassettes, small mobile elements that collectively confer a diverse suite of adaptive functions. Here, we analysed 5,565 plant-associated bacterial genomes to investigate the prevalence and functional diversity of integrons in this niche. We found that integrons are particularly abundant in the genomes of Pseudomonadales, Burkholderiales, and Xanthomonadales. In total, we detected nearly 9,000 gene cassettes, and found that many could be involved in plant growth promotion or phytopathogenicity, suggesting that integrons might play a role in bacterial mutualistic or pathogenic lifestyles. The rhizosphere was enriched in cassettes involved in the transport and metabolism of diverse substrates, suggesting that they may aid in adaptation to this environment, which is rich in root exudates. We also found that integrons facilitate cross-species HGT, which is particularly enhanced in the phyllosphere. This finding may provide an ideal opportunity to promote plant growth by fostering the spread of genes cassettes relevant to leaf health. Together, our findings suggest that integrons are important elements in plant microbiomes that drive HGT, and have the potential to facilitate plant host adaptation.

Rewilding soil and litter invertebrates and fungi increases decomposition rates and alters detritivore communities

Habitat degradation and associated reductions in ecosystem functions can be reversed by reintroducing or 'rewilding' keystone species. Rewilding projects have historically targeted restoration of processes such as grazing regimes or top-down predation effects. Few projects focus on restoring decomposition efficiency, despite the pivotal role decomposition plays in global carbon sequestration and nutrient cycling. Here, we tested whether rewilding entire communities of detritivorous invertebrates and fungi can improve litter decomposition efficiency and restore detritivore communities during ecological restoration. Rewilding was conducted by transplanting leaf litter and soil, including associated invertebrate and fungal communities from species-rich remnant sites into species-poor, and geographically isolated, revegetated farmland sites in a temperate woodland region of southeastern Australia. We compared communities in sites under the following treatments: remnant (conservation area and source of litter transplant), rewilded revegetation (revegetated farmland site with litter transplant) and control revegetation (revegetated site, no transplant). In one 'before' and three 'after' sampling periods, we measured litter decomposition and the abundance and diversity of detritivorous invertebrates and fungi. We quantified the effect of detritivores on the rate of litter decomposition using piecewise Structural Equation Modelling. Decomposition was significantly faster in rewilding sites than in both control and remnant areas and was largely driven by a greater abundance of invertebrate detritivores. Similarly, the abundance of invertebrate detritivores in rewilding revegetation sites exceeded the level of remnant communities, whereas there was little difference between control and remnant sites. In contrast, rewilding did not increase saprotrophic fungi relative abundance/diversity and there was no strong relationship between decomposition and fungal diversity. Our findings suggest the relatively simple act of transplanting leaf litter and soil can increase functional efficiency during restoration and alter community composition. Our methods may prove important across a range of contexts where other restoration methods have failed to restore ecosystem processes to pre-degradation levels.

Assembly processes of rhizosphere and phyllosphere bacterial communities in constructed wetlands created via transformation of rice paddies

Constructed wetlands are an efficient and cost-effective method of restoring degraded wetlands, in which the microorganisms present make a significant contribution to the ecosystem. In this study, we comprehensively investigated the patterns of diversity and assembly processes of 7 types of constructed wetlands at the rhizosphere and phyllosphere levels. The results showed that the rhizosphere communities of the constructed wetlands exhibited a more balanced structure than that of paddy fields, and 5 types of constructed wetland demonstrated higher potential diversity than that of paddy fields. However, the opposite trend was observed for the phyllosphere communities. Analysis of mean nearest taxon difference indicated that both deterministic and stochastic processes affected the establishment of the rhizosphere and phyllosphere communities, and stochastic processes may have had a larger effect. An iCAMP model showed that dispersal limitation was the most important factor (67% relative contribution) in the rhizosphere community, while drift was the most important (47% relative contribution) in the phyllosphere community. Mantel tests suggested that sucrase, average height, top height, total biomass, belowground biomass, maximum water-holding capacity, and capillary porosity were significantly correlated with processes in the rhizosphere community, whereas factors such as the deterministic process, average height, top height, and SOC were significantly correlated with deterministic processes in the phyllosphere community. Our results can assist in the evaluation of artificial restorations, and can provide understanding of the ecological processes of microbial communities, as well as new insights into the manipulation of microorganisms in polluted wetland ecosystems.

Soil microbiome analysis supports claims of ineffectiveness of Pseudomonas fluorescens D7 as a biocontrol agent of Bromus tectorum

IMPORTANCE

Cheatgrass is one of North America's most problematic invasive species. Invasion by this annual grass alters ecosystem structure and function and has proven very challenging to remove with traditional approaches. Commercially available bioherbicides, like P. fluorescens D7, are applied with the goal of providing lasting control from a single application. However, experimental results suggest that this bioherbicide has limited efficacy under field conditions. Potential explanations for variable efficacy include a failure of this bioherbicide to establish in the soil microbiome. However, to our knowledge, no data exist to support or refute this hypothesis. Here, we use a deep-sequencing approach to better understand the effects of this bioherbicide on the soil microbiome and screen for P. fluorescens at 18 months post-application.

Above- and belowground fungal biodiversity of Populus trees on a continental scale

Understanding drivers of terrestrial fungal communities over large scales is an important challenge for predicting the fate of ecosystems under climate change and providing critical ecological context for bioengineering plant-microbe interactions in model systems. We conducted an extensive molecular and microscopy field study across the contiguous United States measuring natural variation in the Populus fungal microbiome among tree species, plant niche compartments and key symbionts. Our results show clear biodiversity hotspots and regional endemism of Populus-associated fungal communities explained by a combination of climate, soil and geographic factors. Modelling climate change impacts showed a deterioration of Populus mycorrhizal associations and an increase in potentially pathogenic foliar endophyte diversity and prevalence. Geographic differences among these symbiont groups in their sensitivity to environmental change are likely to influence broader forest health and ecosystem function. This dataset provides an above- and belowground atlas of Populus fungal biodiversity at a continental scale.

New microbial tools to boost restoration and soil organic matter

Anthropogenic activities are causing unprecedented rates of soil and ecosystem degradation, and the current restoration practices take decades and are prone to high rates of failure. Here we propose, the development and application of emerging microbiome tools that can potentially improve the contents and diversity of soil organic matters, enhancing the efficacy and consistency of restoration outcomes.

Are Plant-Soil Feedbacks Caused by Many Weak Microbial Interactions?

We used high-throughput sequencing and multivariate analyses to describe soil microbial community composition in two four-year field plant-soil feedback (PSF) experiments in Minnesota, USA and Jena, Germany. In descending order of variation explained, microbial community composition differed between the two study sites, among years, between bulk and rhizosphere soils, and among rhizosphere soils cultivated by different plant species. To try to identify soil organisms or communities that may cause PSF, we correlated plant growth responses with the microbial community composition associated with different plants. We found that plant biomass was correlated with values on two multivariate axes. These multivariate axes weighted dozens of soil organisms, suggesting that PSF was not caused by individual pathogens or symbionts but instead was caused by 'many weak' plant-microbe interactions. Taken together, the results suggest that PSFs result from complex interactions that occur within the context of a much larger soil microbial community whose composition is determined by factors associated with 'site' or year, such as soil pH, soil type, and weather. The results suggest that PSFs may be highly variable and difficult to reproduce because they result from complex interactions that occur in the context of a larger soil microbial community.

Designing amendments to improve plant performance for mine tailings revegetation

To provide recommendations for establishment of plants on low-pH Formosa Mine tailings, two greenhouse experiments were conducted to evaluate the use of remedial amendments to improve the survival and growth of Douglas fir (Pseudotsuga menziesii) seedlings. A preliminary experiment indicated that 1% lime (by weight) raised tailings pH, permitting seedling survival. However, high rates of biosolid application (BS; 2% by weight) added to supply nutrients were phytotoxic when added with lime. A gasified conifer biochar (BC) added to tailings at 1%, 2.5%, or 5% (by weight), along with lime and BS, caused an additional increase in pH, decreased electrical conductivity (EC), and tended to increase the survival of Douglas fir. The addition of a locally sourced microbial inoculum (LSM) did not affect survival. A subsequent experiment expanded our experimental design by testing multiple levels of amendments that included lime (0.5% and 1% by weight), three application rates (0.2%, 0.5%, and 2%) of two nutrient sources (BS or mineral fertilizer), BC (0% and 2.5%), and with or without LSM. There were many interactions among amendments. In general, Douglas fir survival was enhanced when lime and BC were added. These experiments suggest that amending with lime, a nutrient source, and BC would enhance revegetation on low-pH, metal-contaminated mine tailings.

Understory ferns promote the restoration of soil microbial diversity and function in previously degraded lands

Microorganisms facilitate the recovery of previously degraded soils, such as degraded lands experiencing vegetation restoration and understory expansion, through vital soil functions like nutrient cycling and decomposing organic matter. Despite the role of microorganisms in recovery, little is known about the effects of the process on microbial diversity and function. Here, we performed an understory fern, Dicranopteris dichotoma (Thunb.) Berhn removal treatments nested within three Masson pine (Pinus massoniana L.) plantations with different restoration years in subtropical China. Three ferns treatments including no ferns cover, with ferns cover, and the ferns removal treatments were established to assess the impact of the ferns on soil microbial diversity and function during revegetation and drivers of observed changes. We combined high-throughput sequencing, network structure modeling, and function prediction of soil bacterial and fungal communities to determine microbial diversity and functions. Our results showed that soil bacterial and fungal diversity increased with restoration time. Understory ferns significantly increased soil microbial diversity in the un-restored land but the effect became smaller in two restored sites. Understory ferns significantly increased the relative abundance of bacterial phyla Proteobacteria and Acidobacteria, but decreased that of Chloroflexi and Firmicutes. Furthermore, the presence of ferns increased the abundance of Basidiomycota, but increased the abundance of Ascomycota. Co-occurrence network analysis revealed that the presence of ferns leads to more complex of bacterial networks with more connections, nodes, average degrees, betweenness, and degrees. The functional predictions indicate that aerobic chemoheterotrophy, chemoheterotrophy, and nitrogen fixation functional groups play key roles in the nutrient cycling of soils with ferns cover. The bacterial and fungal community compositions were strongly affected by revegetation and understory ferns as litter biomass and soil nitrogen were identified as the key environmental factors. Our study highlights the role of understory in facilitating microbial diversity and function recovery during degraded lands restoration.

Implications of Soil Microbial Community Assembly for Ecosystem Restoration: Patterns, Process, and Potential

While it is now widely accepted that microorganisms provide essential functions in restoration ecology, the nature of relationships between microbial community assembly and ecosystem recovery remains unclear. There has been a longstanding challenge to decipher whether microorganisms facilitate or simply follow ecosystem recovery, and evidence for each is mixed at best. We propose that understanding microbial community assembly processes is critical to understanding the role of microorganisms during ecosystem restoration and thus optimizing management strategies. We examine how the connection between environment, community structure, and function is fundamentally underpinned by the processes governing community assembly of these microbial communities. We review important factors to consider in evaluating microbial community structure in the context of ecosystem recovery as revealed in studies of microbial succession: (1) variation in community assembly processes, (2) linkages to ecosystem function, and (3) measurable microbial community attributes. We seek to empower restoration ecology with microbial assembly and successional understandings that can generate actionable insights and vital contexts for ecosystem restoration efforts.

Environmental microbiome engineering for the mitigation of climate change

Environmental microbiome engineering is emerging as a potential avenue for climate change mitigation. In this process, microbial inocula are introduced to natural microbial communities to tune activities that regulate the long-term stabilization of carbon in ecosystems. In this review, we outline the process of environmental engineering and synthesize key considerations about ecosystem functions to target, means of sourcing microorganisms, strategies for designing microbial inocula, methods to deliver inocula, and the factors that enable inocula to establish within a resident community and modify an ecosystem function target. Recent work, enabled by high-throughput technologies and modeling approaches, indicate that microbial inocula designed from the top-down, particularly through directed evolution, may generally have a higher chance of establishing within existing microbial communities than other historical approaches to microbiome engineering. We address outstanding questions about the determinants of inocula establishment and provide suggestions for further research about the possibilities and challenges of environmental microbiome engineering as a tool to combat climate change.

Functional substitutability of native herbivores by livestock for soil carbon stock is mediated by microbial decomposers

Grazing by large mammalian herbivores impacts climate as it can favor the size and stability of a large carbon (C) pool in the soils of grazing ecosystems. As native herbivores in the world's grasslands, steppes, and savannas are progressively being displaced by livestock, it is important to ask whether livestock can emulate the functional roles of their native counterparts. While livestock and native herbivores can have remarkable similarity in their traits, they can differ greatly in their impacts on vegetation composition which can affect soil-C. It is uncertain how these similarities and differences impact soil-C via their influence on microbial decomposers. We test competing alternative hypotheses with a replicated, long-term, landscape-level, grazing-exclusion experiment to ask whether livestock in the Trans-Himalayan ecosystem of northern India can match decadal-scale (2005-2016) soil-C stocks under native herbivores. We evaluate multiple lines of evidence from 17 variables that influence soil-C (quantity and quality of C-input from plants, microbial biomass and metabolism, microbial community composition, eDNA, veterinary antibiotics in soil), and assess their inter-relationships. Livestock and native herbivores differed in their effects on several soil microbial processes. Microbial carbon use efficiency (CUE) was 19% lower in soils under livestock. Compared to native herbivores, areas used by livestock contained 1.5 kg C m^-2 less soil-C. Structural equation models showed that alongside the effects arising from plants, livestock alter soil microbial communities which is detrimental for CUE, and ultimately also for soil-C. Supporting evidence pointed toward a link between veterinary antibiotics used on livestock, microbial communities, and soil-C. Overcoming the challenges of sequestering antibiotics to minimize their potential impacts on climate, alongside microbial rewilding under livestock, may reconcile the conflicting demands from food-security and ecosystem services. Conservation of native herbivores and alternative management of livestock is crucial for soil-C stewardship to envision and achieve natural climate solutions.

Experimental community coalescence sheds light on microbial interactions in soil and restores impaired functions

BACKGROUND

Microbes typically live in communities where individuals can interact with each other in numerous ways. However, knowledge on the importance of these interactions is limited and derives mainly from studies using a limited number of species grown in coculture. Here, we manipulated soil microbial communities to assess the contribution of interactions between microorganisms for assembly of the soil microbiome.

RESULTS

By combining experimental removal (taxa depletion in the community) and coalescence (mixing of manipulated and control communities) approaches, we demonstrated that interactions between microorganisms can play a key role in determining their fitness during soil recolonization. The coalescence approach not only revealed the importance of density-dependent interactions in microbial community assembly but also allowed to restore partly or fully community diversity and soil functions. Microbial community manipulation resulted in shifts in both inorganic nitrogen pools and soil pH, which were related to the proportion of ammonia-oxidizing bacteria.

CONCLUSIONS

Our work provides new insights into the understanding of the importance of microbial interactions in soil. Our top-down approach combining removal and coalescence manipulation also allowed linking community structure and ecosystem functions. Furthermore, these results highlight the potential of manipulating microbial communities for the restoration of soil ecosystems. Video Abstract.

Whole-of-community invertebrate rewilding: Leaf litter transplants rapidly increase beetle diversity during restoration

Restoration of degraded areas is now a central tool in humanity's response to continued species-loss. However, restoration projects often report exceedingly slow or failed recolonization of fauna, especially dispersal-constrained groups such as invertebrates. Active interventions via reintroducing or "rewilding" invertebrates may assist recolonization and speed up restoration of communities toward a desired target. However, invertebrate rewilding is rarely implemented during ecological restoration. Here, we studied the efficacy of invertebrate rewilding as a means of reintroducing dispersal-constrained species and improving diversity and compositional similarities to remnant communities during restoration. Rewilding was conducted by transplanting leaf litter and soil, including associated communities of invertebrates from species rich remnant sites into species poor, and geographically isolated, revegetated farmland sites. We sampled pre- and post-rewilding invertebrate communities in remnant, rewilded revegetation, and control revegetation sites. We analyzed morphospecies richness, abundance, community composition, and modeled morphospecies traits (dispersal method/trophic guild) using a Hierarchical Modelling of Species Communities approach to determine which biological properties facilitated establishment. Beetle (Coleoptera) morphospecies richness increased rapidly in rewilded sites and was indistinguishable from remnant communities as early as 7 months post-rewilding. Beetle community similarity in the rewilding sites significantly deviated from the control sites 27 months post-rewilding, however remnant communities remained distinct over the study timeframe. Establishment success varied as other taxa did not respond as consistently as beetles within the study timeframe. Furthermore, there were no discernible shifts in dispersal traits in rewilded sites. However, predatory morphospecies were more likely to establish post-rewilding than other trophic groups. Our results demonstrate that the relatively simple act of transplanting leaf litter can result in comparatively large increases in morphospecies richness during restoration in a short timeframe. We advocate methodologies such as ours should be adopted more frequently to address failed community restoration as they are cost-effective and can be easily applied by practitioners in various restoration settings. However, further efficacy tests (e.g., varying the number of rewilding events) and longer study timeframes are needed to ensure effectiveness for a broader range of invertebrate taxa and ecosystems.

Silva Nova – Restoring soil biology and soil functions to gain multiple benefits in new forests

Afforestation is proposed as one of the most effective climate solutions for carbon sequestration. As a majority of threatened species are linked to forests, afforestation can also contribute to mitigate the biodiversity crisis. There is however a caveat: the agricultural legacy (high nutrient availability, altered soil biota structure and function) of new forests constrains the development of forest-adapted species, affects tree growth and stability, and delays environmental benefits from afforestation.

We hypothesize that inoculation of former arable land with soil (including microbiome, fauna and seeds/rhizomes of understory vegetation) from old forests along with targeted tree species mixtures will improve productivity and more rapidly restore forest-adapted communities. This will ultimately result in diverse, stable and resilient multifunctional forests.

We will test this hypothesis and develop applied inoculation methods by: i) exploring soil biota and benchmarking biodiversity in existing afforestation research Chronosequence platforms (chronosequences and sites with increasing distance to other forests); ii) conducting inoculation experiments in mesocosms to measure seedling performance and, above- and belowground linkages; iii) establishing field-scale inoculation experiments in new and existing afforestations to test short- and long-term inoculation success on forest productivity, biodiversity and soil functioning at the ecosystem scale; iv) incorporating the landscape context into guidelines and tools for spatially explicit prioritization of areas for assisted dispersal.

The aims are to resolve barriers for successful restoration and develop landscape-scale afforestation strategies that optimize productivity and biodiversity for the planning and implementation of green infrastructure; and produce basic knowledge on the tree, understory vegetation, soil fauna and microbiome nexus and its effect on forest productivity, biodiversity and soil functions (N-retention, C-sequestration, methane uptake).

Grass-microbial inter-domain ecological networks associated with alpine grassland productivity

Associations between grasses and soil microorganisms can strongly influence plant community structures. However, the associations between grass productivity and diversity and soil microbes, as well as the patterns of co-occurrence between grass and microbes remain unclear. Here, we surveyed grass productivity and diversity, determined soil physicochemical, and sequenced soil archaea, bacteria and fungi by metabarcoding technology at 16 alpine grasslands. Using the Distance-decay relationship, Inter-Domain Ecological Network (IDEN), and Mantel tests, we investigated the relationship between grass productivity, diversity and microbial diversity, and the patterns of co-occurrence between grass and microbial inter-domain network in alpine grassland. We found the archaea richness, bacteria richness and Shannon, and fungi α-diversity were significantly negatively correlation with grass diversity, but archaea and bacteria diversity were positively correlation with grass productivity. Moreover, an increase in microbial β-diversity was observed along with increased discrepancy in grass diversity and productivity and soil variables. Variance partitioning analysis suggested that the contribution of grass productivity on microbial community was higher than that of soil variables and grass diversity, which implies that microbial community was more related to grass productivity. Inter-Domain Ecological Network showed that the grass species formed complex and stable ecological networks with some bacterial, archaeal, and fungal species, and the grass-fungal ecological networks showed the highest robustness, which indicated that soil fungi could better co-coexist with aboveground grass in alpine grasslands. Besides, the connectivity degrees of the grass-microbial network were significantly positively correlated with grass productivity, suggesting that the coexistence pattern of grasses and microbes had a positive feedback effect on the grass productivity. The results are important for establishing the regulatory mechanisms between plants and microorganisms in alpine grassland ecosystems.

Leveraging microbiome rediversification for the ecological rescue of soil function

BACKGROUND

Global biodiversity losses threaten ecosystem services and can impact important functional insurance in a changing world. Microbial diversity and function can become depleted in agricultural systems and attempts to rediversify agricultural soils rely on either targeted microbial introductions or retaining natural lands as biodiversity reservoirs. As many soil functions are provided by a combination of microbial taxa, rather than outsized impacts by single taxa, such functions may benefit more from diverse microbiome additions than additions of individual commercial strains. In this study, we measured the impact of soil microbial diversity loss and rediversification (i.e. rescue) on nitrification by quantifying ammonium and nitrate pools. We manipulated microbial assemblages in two distinct soil types, an agricultural and a forest soil, with a dilution-to-extinction approach and performed a microbiome rediversification experiment by re-introducing microorganisms lost from the dilution. A microbiome water control was included to act as a reference point. We assessed disruption and potential restoration of (1) nitrification, (2) bacterial and fungal composition through 16S rRNA gene and fungal ITS amplicon sequencing and (3) functional genes through shotgun metagenomic sequencing on a subset of samples.

RESULTS

Disruption of nitrification corresponded with diversity loss, but nitrification was successfully rescued in the rediversification experiment when high diversity inocula were introduced. Bacterial composition clustered into groups based on high and low diversity inocula. Metagenomic data showed that genes responsible for the conversion of nitrite to nitrate and taxa associated with nitrogen metabolism were absent in the low diversity inocula microcosms but were rescued with high diversity introductions.

CONCLUSIONS

In contrast to some previous work, our data suggest that soil functions can be rescued by diverse microbiome additions, but that the concentration of the microbial inoculum is important. By understanding how microbial rediversification impacts soil microbiome performance, we can further our toolkit for microbial management in human-controlled systems in order to restore depleted microbial functions.

Soil legacy effects of plants and drought on aboveground insects in native and range-expanding plant communities

Soils contain biotic and abiotic legacies of previous conditions that may influence plant community biomass and associated aboveground biodiversity. However, little is known about the relative strengths and interactions of the various belowground legacies on aboveground plant-insect interactions. We used an outdoor mesocosm experiment to investigate the belowground legacy effects of range-expanding versus native plants, extreme drought and their interactions on plants, aphids and pollinators. We show that plant biomass was influenced more strongly by the previous plant community than by the previous summer drought. Plant communities consisted of four congeneric pairs of natives and range expanders, and their responses were not unanimous. Legacy effects affected the abundance of aphids more strongly than pollinators. We conclude that legacies can be contained as soil 'memories' that influence aboveground plant community interactions in the next growing season. These soil-borne 'memories' can be altered by climate warming-induced plant range shifts and extreme drought.

Sympatric soil biota mitigate a warmer-drier climate for Bouteloua gracilis

Climate change is altering temperature and precipitation, resulting in widespread plant mortality and shifts in plant distributions. Plants growing in soil types with low water holding capacity may experience intensified effects of reduced water availability as a result of climate change. Furthermore, complex biotic interactions between plants and soil organisms may mitigate or exacerbate the effects of climate change. This 3-year field experiment observed the performance of Bouteloua gracilis ecotypes that were transplanted across an environmental gradient with either sympatric soil from the seed source location or allopatric soil from the location that plants were transplanted into. We also inoculated plants with either sympatric or allopatric soil biotic communities to test: (1) how changes in climate alone influence plant growth, (2) how soil types interact with climate to influence plant growth, and (3) the role of soil biota in mitigating plant migration to novel environments. As expected, plants moved to cooler-wetter sites exhibited enhanced growth; however, plants moved to warmer-drier sites responded variably depending on the provenance of their soil and inoculum. Soil and inoculum provenance had little influence on the performance of plants moved to cooler-wetter sites, but at warmer-drier sites they were important predictors of plant biomass, seed set, and specific leaf area. Specifically, transplants inoculated with their sympatric soil biota and grown in their sympatric soil were as large as or larger than reference plants grown at the seed source locations; however, individuals inoculated with allopatric soil biota were smaller than reference site individuals at warmer, drier sites. These findings demonstrate complicated plant responses to various aspects of environmental novelty where communities of soil organisms may help ameliorate stress. The belowground microbiome of plants should be considered to predict the responses of vegetation more accurately to climate change.

Soil aggregate microbiomes steer plant community overyielding in ungrazed and intensively grazed grassland soils

Plant and soil microbial community composition play a central role in maintaining ecosystem functioning. Most studies have focused on soil microbes in the bulk soil, the rhizosphere and inside plant roots, however, less is known about the soil community that exists within soil aggregates, and how these soil communities influence plant biomass production. Here, using field-conditioned soil collected from experimental ungrazed and grazed grasslands in Inner Mongolia, China, we examined the composition of microbiomes inside soil aggregates of various size classes, and determined their roles in plant-soil feedbacks (PSFs), diversity-productivity relationships, and diversity-dependent overyielding. We found that grazing induced significantly positive PSF effects, which appeared to be mediated by mycorrhizal fungi, particularly under plant monocultures. Despite this, non-additive effects of microbiomes within different soil aggregates enhanced the strength of PSF under ungrazed grassland, but decreased PSF strength under intensively grazed grassland. Plant mixture-related increases in PSF effects markedly enhanced diversity-dependent overyielding, primarily due to complementary effects. Selection effects played far less of a role. Our work suggests that PSF contributes to diversity-dependent overyielding in grasslands via non-additive effects of microbiomes within different soil aggregates. The implication of our work is that assessing the effectiveness of sustainable grassland restoration and management on soil properties requires inspection of soil aggregate size-specific microbiomes, as these are relevant determinants of the feedback interactions between soil and plant performance.

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.

Climate drives rhizosphere microbiome variation and divergent selection between geographically distant Arabidopsis populations

Disentangling the contribution of climatic and edaphic factors to microbiome variation and local adaptation in plants requires an experimental approach to uncouple their effects and test for causality. We used microbial inocula, soil matrices and plant genotypes derived from two natural Arabidopsis thaliana populations in northern and southern Europe in an experiment conducted in climatic chambers mimicking seasonal changes in temperature, day length and light intensity of the home sites of the two genotypes. The southern A. thaliana genotype outperformed the northern genotype in the southern climate chamber, whereas the opposite was true in the northern climate chamber. Recipient soil matrix, but not microbial composition, affected plant fitness, and effects did not differ between genotypes. Differences between chambers significantly affected rhizosphere microbiome assembly, although these effects were small in comparison with the shifts induced by physicochemical differences between soil matrices. The results suggest that differences in seasonal changes in temperature, day length and light intensity between northern and southern Europe have strongly influenced adaptive differentiation between the two A. thaliana populations, whereas effects of differences in soil factors have been weak. By contrast, below-ground differences in soil characteristics were more important than differences in climate for rhizosphere microbiome differentiation.

Microbiome ethics, guiding principles for microbiome research, use and knowledge management

The overarching biological impact of microbiomes on their hosts, and more generally their environment, reflects the co-evolution of a mutualistic symbiosis, generating fitness for both. Knowledge of microbiomes, their systemic role, interactions, and impact grows exponentially. When a research field of importance for planetary health evolves so rapidly, it is essential to consider it from an ethical holistic perspective. However, to date, the topic of microbiome ethics has received relatively little attention considering its importance. Here, ethical analysis of microbiome research, innovation, use, and potential impact is structured around the four cornerstone principles of ethics: Do Good; Don't Harm; Respect; Act Justly. This simple, but not simplistic approach allows ethical issues to be communicative and operational. The essence of the paper is captured in a set of eleven microbiome ethics recommendations, e.g., proposing gut microbiome status as common global heritage, similar to the internationally agreed status of major food crops.

Effects of Commercial Arbuscular Mycorrhizal Inoculants on Plant Productivity and Intra-Radical Colonization in Native Grassland: Unintentional De-Coupling of a Symbiosis?

There has been a surge in industries built on the production of arbuscular mycorrhizal (AM) fungal-based inoculants in the past few decades. This is not surprising, given the positive effects of AM fungi on plant growth and nutritional status. However, there is growing concern regarding the quality and efficacy of commercial inoculants. To assess the potential benefits and negative consequences of commercial AM fungal inoculants in grasslands, we conducted a controlled growth chamber study assessing the productivity and AM fungal root colonization of nine grassland plant species grown in grassland soil with or without one of six commercial AM fungal products. Our research showed no evidence of benefit; commercial inoculants never increased native plant biomass, although several inoculants decreased the growth of native species and increased the growth of invasive plant species. In addition, two commercial products contained excessive levels of phosphorus or nitrogen and consistently reduced AM fungal root colonization, indicating an unintentional de-coupling of the symbiosis. As there is little knowledge of the ecological consequences of inoculation with commercial AM fungal products, it is critical for restoration practitioners, scientists, and native plant growers to assess the presence of local AM fungal communities before investing in unnecessary, or possibly detrimental, AM fungal products.

Soil Biota Adversely Affect the Resistance and Recovery of Plant Communities Subjected to Drought

Climate change predictions indicate that summer droughts will become more severe and frequent. Yet, the impact of soil communities on the response of plant communities to drought remains unclear. Here, we report the results of a novel field experiment, in which we manipulated soil communities by adding soil inocula originating from different successional stages of coastal dune ecosystems to a plant community established from seeds on bare dune sand. We tested if and how the added soil biota from later-successional ecosystems influenced the sensitivity (resistance and recovery) of plant communities to drought. In contrast to our expectations, soil biota from later-successional soil inocula did not improve the resistance and recovery of plant communities subjected to drought. Instead, inoculation with soil biota from later successional stages reduced the post-drought recovery of plant communities, suggesting that competition for limited nutrients between plant community and soil biota may exacerbate the post-drought recovery of plant communities. Moreover, soil pathogens present in later-successional soil inocula may have impeded plant growth after drought. Soil inocula had differential impacts on the drought sensitivity of specific plant functional groups and individual species. However, the sensitivity of individual species and functional groups to drought was idiosyncratic and did not explain the overall composition of the plant community. Based on the field experimental evidence, our results highlight the adverse role soil biota can play on plant community responses to environmental stresses. These outcomes indicate that impacts of soil biota on the stability of plant communities subjected to drought are highly context-dependent and suggest that in some cases the soil biota activity can even destabilize plant community biomass responses to drought.

Microbe Related Chemical Signalling and Its Application in Agriculture

The agriculture sector has been put under tremendous strain by the world’s growing population. The use of fertilizers and pesticides in conventional farming has had a negative impact on the environment and human health. Sustainable agriculture attempts to maintain productivity, while protecting the environment and feeding the global population. The importance of soil-dwelling microbial populations in overcoming these issues cannot be overstated. Various processes such as rhizospheric competence, antibiosis, release of enzymes, and induction of systemic resistance in host plants are all used by microbes to influence plant-microbe interactions. These processes are largely founded on chemical signalling. Producing, releasing, detecting, and responding to chemicals are all part of chemical signalling. Different microbes released distinct sorts of chemical signal molecules which interacts with the environment and hosts. Microbial chemicals affect symbiosis, virulence, competence, conjugation, antibiotic production, motility, sporulation, and biofilm growth, to name a few. We present an in-depth overview of chemical signalling between bacteria-bacteria, bacteria-fungi, and plant-microbe and the diverse roles played by these compounds in plant microbe interactions. These compounds’ current and potential uses and significance in agriculture have been highlighted.

Ancient grasslands guide ambitious goals in grassland restoration

Grasslands, which constitute almost 40% of the terrestrial biosphere, provide habitat for a great diversity of animals and plants and contribute to the livelihoods of more than 1 billion people worldwide. Whereas the destruction and degradation of grasslands can occur rapidly, recent work indicates that complete recovery of biodiversity and essential functions occurs slowly or not at all. Grassland restoration-interventions to speed or guide this recovery-has received less attention than restoration of forested ecosystems, often due to the prevailing assumption that grasslands are recently formed habitats that can reassemble quickly. Viewing grassland restoration as long-term assembly toward old-growth endpoints, with appreciation of feedbacks and threshold shifts, will be crucial for recognizing when and how restoration can guide recovery of this globally important ecosystem.

Legacies at work: plant-soil-microbiome interactions underpinning agricultural sustainability

Agricultural intensification has had long-lasting negative legacies largely because of excessive inputs of agrochemicals (e.g., fertilizers) and simplification of cropping systems (e.g., continuous monocropping). Conventional agricultural management focuses on suppressing these negative legacies. However, there is now increasing attention for creating positive above- and belowground legacies through selecting crop species/genotypes, optimizing temporal and spatial crop combinations, improving nutrient inputs, developing intelligent fertilizers, and applying soil or microbiome inoculations. This can lead to enhanced yields and reduced pest and disease pressure in cropping systems, and can also mitigate greenhouse gas emissions and enhance carbon sequestration in soils. Strengthening positive legacies requires a deeper understanding of plant-soil-microbiome interactions and innovative crop, input, and soil management which can help to achieve agricultural sustainability.

Soil inoculum identity and rate jointly steer microbiomes and plant communities in the field

Inoculation with soil from different ecosystems can induce changes in plant and soil communities and promote the restoration of degraded ecosystems. However, it is unknown how such inoculations influence the plant and soil communities, how much inoculum is needed, and whether inocula collected from similar ecosystems will steer soil and plant communities in different directions. We conducted a three-year soil inoculation experiment at a degraded grassland and used two different soil inocula both from grasslands with three inoculation rates. We measured the development of the soil and plant communities over a period of three years. Our results show that soil inoculation steers the soil microbiome and plant communities at the inoculated site into different directions and these effects were stronger with higher amount of soil used to inoculate. Network analyses showed that inoculation with upland meadow soil introduced more genera occupying the central position in the biotic network and resulted in more complex networks in the soil than inoculation with meadow steppe soil. Our findings emphasize that there are specific effects of donor soil on soil microbiomes as well as plant communities and that the direction and speed of development depend on the origin and the amount of soil inoculum used. Our findings have important implications for the restoration of biodiversity and ecosystem functioning in degraded grassland ecosystems.

Arbuscular Mycorrhizal Fungi Taxa Show Variable Patterns of Micro-Scale Dispersal in Prairie Restorations

Human land use disturbance is a major contributor to the loss of natural plant communities, and this is particularly true in areas used for agriculture, such as the Midwestern tallgrass prairies of the United States. Previous work has shown that arbuscular mycorrhizal fungi (AMF) additions can increase native plant survival and success in plant community restorations, but the dispersal of AMF in these systems is poorly understood. In this study, we examined the dispersal of AMF taxa inoculated into four tallgrass prairie restorations. At each site, we inoculated native plant species with greenhouse-cultured native AMF taxa or whole soil collected from a nearby unplowed prairie. We monitored AMF dispersal, AMF biomass, plant growth, and plant community composition, at different distances from inoculation. In two sites, we assessed the role of plant hosts in dispersal, by placing known AMF hosts in a “bridge” and “island” pattern on either side of the inoculation points. We found that AMF taxa differ in their dispersal ability, with some taxa spreading to 2-m in the first year and others remaining closer to the inoculation point. We also found evidence that AMF spread altered non-inoculated neighboring plant growth and community composition in certain sites. These results represent the most comprehensive attempt to date to evaluate AMF spread.

Biogeochemical dynamics of nutrients and rare earth elements (REEs) during natural succession from biocrusts to pioneer plants in REE mine tailings in southern China

The exploitation of ion-adsorption rare earth element (REE) deposits has resulted in large quantities of abandoned mine tailings, which pose significant risks to the surrounding environment. However, the natural evolutional patterns at early successional stages and related biogeochemical dynamics (e.g. nutrient and REE cycling) on such mine tailings remains poorly understood. To this end, a chronosequence of REE mine tailings abandoned for up to 15 years was investigated in a post-mining site in south China. Our results showed that biocrusts were the earliest colonizers on these tailings, reaching a peak of 10% of surface coverage after 10 years of abandonment. Later on, after 15 years, the biocrusts began to be replaced by pioneer plants (e.g. Miscanthus sinensis), suggesting a rather rapid succession. This ecological succession was accompanied by obvious changes in soil nutrients and microbial community structure. Compared to bulk soils, both the biocrusts and rhizospheric soils favored an accumulation of nutrients (e.g. P, S, N, C). Notably, the autotrophic bacteria (e.g. Chloroflexi and Cyanobacteria) with C and N fixation abilities were preferentially enriched in biocrusts, while heterotrophic plant growth promoting bacteria (e.g. Pseudoocardiaceae and Acidobacteriales) were mainly present in the rhizosphere. Moreover, the biocrusts showed a remarkably high concentration of REEs (up to 1820 mg kg^-1), while the rhizospheric soils tended to decrease REE concentrations (~400 mg kg^-1) in comparison with bulk soils, indicating that the REEs could be redistributed by biological processes. Principal component analysis and mantel tests showed that the concentrations of nutrients and REEs were the most important factors affecting the microbial communities in biocrusts, rhizospheric and bulk soils. In sum, based on the observation of nutrient accumulation and pollutant (i.e. REE) dynamics in the initial successional stages, this work provides a feasible theoretical basis for future restoration practices on REE mine tailings.

Specific Plant Mycorrhizal Responses Are Linked to Mycorrhizal Fungal Species Interactions

Effects of arbuscular mycorrhizal fungi (AMF) on plants span the continuum from mutualism to parasitism due to the plant-AMF specificity, which obscures the utilization of AMF in the restoration of degraded lands. Caragana korshinskii, Hedysarum laeve, Caragana microphylla, and Poa annua are the most frequently used plants for revegetation in Kubuqi Desert, China, and the influence of AMF on their re-establishment remains to be explored further. Herein, using a greenhouse experiment, we tested the plant-AMF feedbacks between the four plant species and their conspecific or heterospecific AMF, retrieved from their rhizosphere in the Kubuqi Desert. AMF showed beneficial effects on plant growth for all these plant-AMF pairs. Generally, AMF increased the biomass of C. korshinskii, H. laeve, C. microphylla, and P. annua by 97.6, 50.6, 46.5, and 381.1%, respectively, relative to control. In addition, the AMF-plant specificity was detected. P. annua grew best, but C. microphylla grew worst with conspecific AMF communities. AMF community from P. annua showed the largest beneficial effect on all the plants (with biomass increased by 63.9-734.4%), while the AMF community from C. microphylla showed the least beneficial effect on all the plants (with biomass increased by 9.9-59.1%), except for P. annua (a 292.4% increase in biomass). The magnitude of AMF effects on plant growth was negatively correlated with the complexity of the corresponding AMF co-occurrence networks. Overall, this study suggests that AMF effects on plant growth vary due to plant-AMF specificity. We also observed the broad-spectrum benefits of the native AMF from P. annua, which indicates its potential utilization in the restoration of the desert vegetation.

Core arbuscular mycorrhizal fungi are predicted by their high abundance-occupancy relationship while host-specific taxa are rare and geographically structured

Habitat restoration may depend on the recovery of plant microbial symbionts such as arbuscular mycorrhizal (AM) fungi, but this requires a better understanding of the rules that govern their community assembly. We examined the interactions of soil and host-associated AM fungal communities between remnant and restored patches of subtropical montane forests. While AM fungal richness did not differ between habitat types, community membership did and was influenced by geography, habitat and host. These differences were largely driven by rare host-specific AM fungi that displayed near-complete turnover between forest types, while core AM fungal taxa were highly abundant and ubiquitous. The bipartite networks in the remnant forest were more specialized and hosts more specific than in the restored forest. Host-associated AM fungal communities nested within soil communities in both habitats, but only significantly so in the restored forest. Our results provide evidence that restored and remnant forests harbour the same core fungal symbionts, while rare host-specific taxa differ, and that geography, host identity and taxonomic resolution strongly affect the observed distribution patterns of these fungi. We suggest that host-specific interactions with AM fungi, as well as spatial processes, should be explicitly considered to effectively re-establish target host and symbiont communities.