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Azoxystrobin, a quinone outside inhibitor fungicide, reduced tobacco target spot caused by Rhizoctonia solani by 62%, but also affected the composition and diversity of other microbes on the surface and interior of treated tobacco leaves. High-throughput sequencing showed that the dominant bacteria prior to azoxystrobin treatment were Methylobacterium on healthy leaves and Pseudomonas on diseased leaves, and the dominant fungi were Thanatephorous (teleomorph of Rhizoctonia ) and Symmetrospora on healthy leaves and Thanatephorous on diseased leaves. Both bacterial and fungal diversity significantly increased 1 to 18 days post treatment (dpt) with azoxystrobin for healthy and diseased leaves. For bacteria on healthy leaves, the relative abundance of Pseudomonas , Sphingomonas, Unidentified-Rhizobiaceae and Massilia declined, while Methylobacterium and Aureimonas increased. On diseased leaves, the relative abundance of Sphingomonas and Unidentified-Rhizobiaceae declined, while Methylobacterium, Pseudomonas and Pantoea increased. For fungi on healthy leaves, the relative abundance of Thanatephorous declined, while Symmetrospora , Sampaiozyma , Plectosphaerella , Cladosporium and Cercospora increased. On diseased leaves, the relative abundance of Thanatephorous declined, while Symmetrospora , Sampaiozyma , Plectosphaerella , Cladosporium , Phoma , Pantospora and Fusarium , increased. Compared to healthy leaves, azoxystrobin treatment of diseased leaves resulted in greater reductions in Thanatephorous , Sphingomonas and Unidentified-Rhizobiaceae , a greater increase in Methylobacterium , and similar changes in Phoma, Fusarium , Plectosphaerella and Cladosporium . Azoxystrobin had a semi-selective effect altering the microbial diversity of the tobacco leaf microbiome, which could be due to factors, such as differences among bacterial and fungal species in sensitivity to quinone outside inhibitors, ability to use nutrients and niches as certain microbes are affected, and metabolic responses to azoxystrobin.

Leaf microbial communities possess a large panel of enzymes permitting the breakdown of leaf polymers as well as the transformation of organic xenobiotic compounds present in stream waters. This study aims to assess the potential of leaf microbial communities, exhibiting different exposure histories to pesticides (upstream versus downstream), to biotransform three maize herbicides (mesotrione, S-metolachlor, and nicosulfuron) in single and cocktail molecule exposures. The results showed a high dissipation of nicosulfuron (sulfonylurea herbicide) (from 29.1 ± 10.8% to 66 ± 16.2%, day 40) in both single and cocktail exposures, respectively, but not of mesotrione and S-metolachlor. The formation of nicosulfuron metabolites such as ASDM (2-(aminosulfonyl)-N,N-dimethyl-3-pyridinecarboxamide) and ADMP (2-amino-4,6-dimethoxypyrimidine) and the weak sorption (<0.4%) on the leaf matrix confirmed the transformation of this molecule by leaf microorganisms. In addition, the downstream communities showed a greater ability to transform nicosulfuron than the upstream communities suggesting that the exposure history to pesticides is an important parameter and can enhance the biotransformation potential of leaf microorganisms. After 40-day single exposure to nicosulfuron, the downstream communities were also those experiencing the greatest shifts in fungal and bacterial community diversity suggesting a potential adaptation of microorganisms to this herbicide. Our study emphasizes the importance of leaf microbial communities for herbicide biotransformation in polluted stream ecosystems where fungi could play a crucial role.

Background It is well established that the functioning of terrestrial ecosystems depends on biophysical and biogeochemical feedbacks occurring at the soil-plant-atmosphere (SPA) interface. However, dynamic biophysical and biogeochemical processes that operate at local scales are seldom studied in conjunction with structural ecosystem properties that arise from broad environmental constraints. As a result, the effect of SPA interactions on how ecosystems respond to, and exert influence on, the global environment remains difficult to predict. Scope We review recent findings that link structural and functional SPA interactions and evaluate their potential for predicting ecosystem responses to chronic environmental pressures. Specifically, we propose a quantitative framework for the integrated analysis of three major plant functional groups (evergreen conifers, broadleaf deciduous, and understory shrubs) and their distinct mycorrhizal symbionts under rising levels of carbon dioxide, changing climate, and disturbance regime. First, we explain how symbiotic and competitive strategies involving plants and soil microorganisms influence scale-free patterns of carbon, nutrient, and water use from individual organisms to landscapes. We then focus on the relationship between those patterns and structural traits such as specific leaf area, leaf area index, and soil physical and chemical properties that constrain root connectivity and canopy gas exchange. Finally, we use those relationships to predict how changes in ecosystem structure may affect processes that are important for climate stability. Conclusions On the basis of emerging ecological theory and empirical biophysical and biogeochemical knowledge, we propose ten interpretive hypotheses that serve as a primary set of hierarchical relationships (or scaling rules), by which local SPA interactions can be spatially and temporally aggregated to inform broad climate change mitigation efforts. To this end, we provide a series of numerical formulations that simplify the net outcome of complex SPA interactions as a first step towards anticipating shifts in terrestrial carbon, water, and nutrient cycles.

Elemental stoichiometry constitutes an inherent link between biogeochemistry and the structure and processes within food webs, and thus is at the core of ecosystem functioning. Stoichiometry allows for spanning different levels of biological organization, from cellular metabolism to ecosystem structure and nutrient cycling, and is therefore particularly useful for establishing links between different ecosystem compartments. We review elemental carbon : nitrogen : phosphorus (C:N:P) ratios in terrestrial ecosystems (from vegetation, leaf litter, woody debris, and dead roots, to soil microbes and organic matter). While the stoichiometry of the plant, litter, and soil compartments of ecosystems is well understood, heterotrophic microbial communities, which dominate the soil food web and drive nutrient cycling, have received increasing interest in recent years. This review highlights the effects of resource stoichiometry on soil microorganisms and decomposition, specifically on the structure and function of heterotrophic microbial communities and suggests several general patterns. First, latitudinal gradients of soil and litter stoichiometry are reflected in microbial community structure and function. Second, resource stoichiometry may cause changes in microbial interactions and community dynamics that lead to feedbacks in nutrient availability. Third, global change alters the C:N, C:P, and N:P ratios of primary producers, with repercussions for microbial decomposer communities and critical ecosystem services such as soil fertility. We argue that ecological stoichiometry provides a framework to analyze and predict such global change effects at various scales.

Bacteria and fungi drive decomposition, a fundamental process in the carbon cycle, yet the importance of microbial community composition for decomposition remains elusive. Here, we used an 18-month reciprocal transplant experiment along a climate gradient in Southern California to disentangle the effects of the microbial community versus the environment on decomposition. Specifically, we tested whether the decomposition response to climate change depends on the microbial community. We inoculated microbial decomposers from each site onto a common, irradiated leaf litter within “microbial cages” that prevent microbial exchange with the environment. We characterized fungal and bacterial composition and abundance over time and investigated the functional consequences through litter mass loss and chemistry. After 12 months, microbial communities altered both decomposition rate and litter chemistry. Further, the functional measurements depended on an interaction between the community and its climate in a manner not predicted by current theory. Moreover, microbial ecologists have traditionally considered fungi to be the primary agents of decomposition and for bacteria to play a minor role. Our results indicate that not only does climate change and transplantation have differential legacy effects among bacteria and fungi, but also that bacterial communities might be less functionally redundant than fungi with regards to decomposition. Thus, it may be time to reevaluate both the role of microbial community composition in its decomposition response to climate and the relative roles of bacterial and fungal communities in decomposition.

Microbial community responses to environmental change are largely associated with ecological processes; however, the potential for microbes to rapidly evolve and adapt remains relatively unexplored in natural environments. To assess how ecological and evolutionary processes simultaneously alter the genetic diversity of a microbiome, we conducted two concurrent experiments in the leaf litter layer of soil over 18 mo across a climate gradient in Southern California. In the first experiment, we reciprocally transplanted microbial communities from five sites to test whether ecological shifts in ecotypes of the abundant bacterium, Curtobacterium, corresponded to past adaptive differentiation. In the transplanted communities, ecotypes converged toward that of the native communities growing on a common litter substrate. Moreover, these shifts were correlated with community-weighted mean trait values of the Curtobacterium ecotypes, indicating that some of the trait variation among ecotypes could be explained by local adaptation to climate conditions. In the second experiment, we transplanted an isogenic Curtobacterium strain and tracked genomic mutations associated with the sites across the same climate gradient. Using a combination of genomic and metagenomic approaches, we identified a variety of nonrandom, parallel mutations associated with transplantation, including mutations in genes related to nutrient acquisition, stress response, and exopolysaccharide production. Together, the field experiments demonstrate how both demographic shifts of previously adapted ecotypes and contemporary evolution can alter the diversity of a soil microbiome on the same timescale.

1. Land-use intensification drives changes in microbial communities and the soil functions they regulate, but the mechanisms underlying these changes are poorly understood as land use can affect soil communities both directly (e.g. via changes in soil fertility) and indirectly (e.g. via changes in plant inputs). 2. The speed of microbial responses is also poorly understood. For instance, whether it is long-term legacies or short-term changes in land-use intensity that drive changes in microbial communities. 3. To address these topics, we measured multiple microbial functions, bacterial and fungal biomass and abiotic soil properties at two time intervals 3 years apart. This was performed in 150 grassland sites differing greatly in management intensity across three German regions. 4. Observed changes in microbial soil properties were related to both long-term means and short-term changes in: abiotic soil properties, land-use intensity, community abundance-weighted means of plant functional traits and plant biomass properties in regression and structural equation models. Plant traits, particularly leaf phosphorus, and soil pH were the best predictors of change in soil microbial function, as well as fungal and bacterial biomass, while land-use intensity showed weaker effects. 5. Indirect legacy effects, in which microbial change was explained by the effects of long-term land-use intensity on plant traits, were important, thus indicating a time lag between plant community and microbial change. Whenever the effects of short-term changes in land-use intensity were present, they acted directly on soil microorganisms. 6. Synthesis. The results provide new evidence that soil communities and their functioning respond to short-term changes in land-use intensity, but that both rapid and longer time-scale responses to changes in plant functional traits are at least of equal importance. This suggests that management which shapes plant communities may be an effective means of managing soil communities and the functions and services they provide.

Plants emit a plethora of volatile organic compounds in response to biotic and abiotic stresses. These compounds act as infochemicals for ecological communication in the phytobiome. This study reviews the role of microbe-induced plant volatiles (MIPVs) in plant–microbe interactions. MIPVs are affected by the taxonomic position of the microbe, the identity of the plant and the type of interaction. Plants also emit exclusive blends of volatiles in response to nonhost and host interactions, as well as to beneficial microbes and necrotrophic/biotrophic pathogens. These MIPVs directly inhibit pathogen growth and indirectly promote resistance/susceptibility to subsequent plant pathogen attack. Viruses and phloem-limiting bacteria modify plant volatiles to attract insect vectors. Susceptible plants can respond to MIPVs from resistant plants and become resistant. Recent advances in our understanding of the molecular mechanisms of MIPV synthesis in plants and how plant pathogen effectors manipulate their biosynthesis are discussed. This knowledge will help broaden our understanding of plant–microbe interactions and should facilitate the development of new emerging techniques for sustainable plant disease management.

Global forests are experiencing rising temperatures and more severe droughts, with consistently dire forecasts for negative future impacts. Current research on the physiological mechanisms underlying drought impacts is focused on the water- and carbon-associated mechanisms. The role of nutrients is notably missing from this research agenda. Here, we investigate what role, if any, forest nutrition plays for survival and recovery of forests during and after drought. High nutrient availability may play a detrimental role in drought survival due to preferential biomass allocation aboveground that (1) predispose plants to hydraulic constraints limiting photosynthesis and promoting hydraulic failure, (2) increases carbon costs during periods of carbon starvation, and (3) promote biotic attack due to low tissue carbon: nitrogen (C: N). When nutrient uptake occurs during drought, high nutrient availability can increase water use efficiency thus minimizing negative feedbacks between carbon and nutrient balance. Nutrients are released after drought ceases, which might promote faster recovery but the temporal dynamics of microbial immobilization and nutrient leaching have a significant impact on nutrient availability. We provide a framework for understanding nutrient impacts on drought survival that allows a more complete analysis of forest ecosystem responses.

Litter decomposition is a key ecosystem process, relevant for the release and storage of nutrients and carbon in soil. Soil fungi are one of the dominant drivers of organic matter decomposition, but fungal taxa differ substantially in their functional ability to decompose plant litter. Knowledge is mostly based on observational data and subsequent molecular analyses and in vitro studies have been limited to forest ecosystems. In order to better understand functional traits of saprotrophic soil fungi in grassland ecosystems, we isolated 31 fungi from a natural grassland and performed several in vitro studies testing for i) leaf and wood litter decomposition, ii) the ability to use carbon sources of differing complexity, iii) the enzyme repertoire. Decomposition strongly varied among phyla and isolates, with Ascomycota decomposing the most and Mucoromycota decomposing the least. The phylogeny of the fungi and their ability to use complex carbon were the most important predictors for decomposition. Our findings show that it is crucial to understand the role of individual members and functional groups within the microbial community. This is an important way forward to understand the role of microbial community composition for the prediction of litter decomposition and subsequent potential carbon storage in grassland soils.