Highlights • Soil bacteria differ in their survival strategies and ability to influence the terrestrial carbon (C) pool. • Omics approaches can characterize microbial system interactions and impact ...terrestrial C sequestration. • Omics-derived data can be incorporated into predictive ecological models. • This integration will aid development of microbe-based strategies for capturing and sequestering atmospheric CO2.
A lack of empirical evidence for the microbial regulation of ecosystem processes, including carbon (C) degradation, hinders our ability to develop a framework to directly incorporate the genetic ...composition of microbial communities in the enzyme-driven Earth system models. Herein we evaluated the linkage between microbial functional genes and extracellular enzyme activity in soil samples collected across three geographical regions of Australia. We found a strong relationship between different functional genes and their corresponding enzyme activities. This relationship was maintained after considering microbial community structure, total C and soil pH using structural equation modelling. Results showed that the variations in the activity of enzymes involved in C degradation were predicted by the functional gene abundance of the soil microbial community (R
>0.90 in all cases). Our findings provide a strong framework for improved predictions on soil C dynamics that could be achieved by adopting a gene-centric approach incorporating the abundance of functional genes into process models.
Agricultural intensification is placing tremendous pressure on the soil's capacity to maintain its functions leading to large-scale ecosystem degradation and loss of productivity in the long term. ...Therefore, there is an urgent need to find early indicators of soil health degradation in response to agricultural management. In recent years, major advances in soil meta-genomic and spatial studies on microbial communities and community-level molecular characteristics can now be exploited as 'biomarker' indicators of ecosystem processes for monitoring and managing sustainable soil health under global change. However, a continental scale, cross biome approach assessing soil microbial communities and their functional potential to identify the unifying principles governing the susceptibility of soil biodiversity to land conversion is lacking. We conducted a meta-analysis from a dataset generated from 102 peer-reviewed publications as well as unpublished data to explore how properties directly linked to soil nutritional health (total C and N; C:N ratio), primary productivity (NPP) and microbial diversity and composition (relative abundance of major bacterial phyla determined by next generation sequencing techniques) are affected in response to agricultural management across the main biomes of Earth (arid, continental, temperate and tropical). In our analysis, we found strong statistical trends in the relative abundance of several bacterial phyla in agricultural (e.g., Actinobacteria and Chloroflexi) and natural (Acidobacteria, Proteobacteria, and Cyanobacteria) systems across all regions and these trends correlated well with many soil properties. However, main effects of agriculture on soil properties and productivity were biome-dependent. Our meta-analysis provides evidence on the predictable nature of the microbial community responses to vegetation type. This knowledge can be exploited in future for developing a new set of indicators for primary productivity and soil health.
Summary
Harnessing plant microbiota can assist in sustainably increasing primary productivity to meet growing global demands for food and biofuel. However, development of rational microbiome‐based ...approaches for improving crop yield and productivity is currently hindered by a lack of understanding of the major biotic and abiotic factors shaping the crop microbiome under relevant field conditions. We examined bacterial and fungal communities associated with both aerial (leaves, stalks) and belowground (roots, soil) compartments of four commercial sugarcane varieties (Saccharum spp.) grown in several growing regions in Australia. We identified drivers of the sugarcane microbiome under field conditions and evaluated whether the plants shared a core microbiome. Sugarcane‐associated microbial assemblages were primarily determined by plant compartment, followed by growing region, crop age, variety and Yellow Canopy Syndrome (YCS). We detected a core set of microbiota and identified members of the core microbiome that were influenced by YCS incidence. Our study revealed key hub microorganisms in the core microbiome networks of sugarcane leaves, stalks, roots and rhizosphere soil despite location and time‐associated shifts in the community assemblages. Elucidating their functional roles and identification of the keystone core microbiota that sustain plant health could provide a technological breakthrough for a sustainable increase in crop productivity.
Our knowledge of host-associated microorganisms and their role in host functions is rapidly evolving. Stress-affected plants assemble beneficial microbes in their rhizosphere to maximize survival and ...growth. Similarly, insects have gut microbiomes that extend their functional repertoire in fighting stress. A strong microbial linkage between soil, plants, and pollinators is emerging and this can influence pollination services and overall ecosystem health. Yet, the nature of microbial interactions between different ecosystem components remains poorly understood. Here we highlight the acquisition pathways of beneficial microbes and their functions in protecting hosts against stress. By adopting a new ‘eco-holobiont’ approach, which explicitly incorporates biotic feedbacks, we can significantly expand our ecological understanding and better develop sustainable environmental management.
Host holobionts extend host capacity for nutrient uptake and stress protection. Stress-affected plants promote the accumulation of beneficial microbes in the rhizosphere, putatively driven by an alteration of root exudates. Such a ‘cry for help’ strategy increases plant survival rates under stress.Gut microbiomes of insect pollinators play multifunctional roles in host growth, development, and immunity. They can be switched to dysbiotic conditions when exposed to agrochemicals, with negative consequences for host health and survival.Recent evidence shows that flowers have a microbiome that both interacts with foraging pollinators and can be inherited by seeds. It provides a microbial link between soil, plants, and pollinators.Adopting a new ‘eco-holobiont’ approach can expand our ecological understanding and help to develop sustainable environmental management.
Ectomycorrhizal (ECM) mycelium is a key component of the ectomycorrhizal symbiosis, yet we know little regarding the fine-scale diversity and distribution of mycelium in ECM fungal communities.
We ...collected four 20 × 20 × 2-cm3 (800-cm3) slices of Scots pine (Pinus sylvestris) forest soil and divided each into 100 2 × 2 × 2-cm3 (8-cm3) cubes. The presence of mycelium of ECM fungi was determined using an internal transcribed spacer (ITS) database terminal restriction fragment length polymorphism (T-RFLP) approach.
As expected, many more ECM fungi were detected as mycelium than as ectomycorrhizas in a cube or slice. More surprisingly, up to one-quarter of the 43 species previously detected as ectomycorrhizas over an area of 400 m2 could be detected in a single 8-cm3 cube, and up to three-quarters in a single 800-cm3 slice. ECM mycelium frequency decreased markedly with depth and there were distinct ‘hotspots’ of mycelium in the moss/F1 layer.
Our data demonstrate a high diversity of ECM mycelium in a small (8-cm3) volume of substrate, and indicate that the spatial scale at which ECM species are distributed as mycelium may be very different from the spatial scale at which they are distributed as tips.
A key component of biodiversity is the number and abundance of individuals (i.e. genotypes), and yet such intraspecific diversity is rarely considered when investigating the effects of biodiversity ...of mycorrhizal plants and fungi on ecosystem processes. Within a species, individuals vary considerably in important reproductive and functional attributes, including carbon fixation, mycelial growth and nutrient utilization, but this is driven by both genetic and environmental (including climatic) factors. The interactions between individual plants and mycorrhizal fungi can have important consequences for the maintenance of biodiversity and regulation of resource transfers in ecosystems. There is also emerging evidence that assemblages of genotypes may affect ecosystem processes to a similar extent as assemblages of species. The application of whole-genome sequencing and population genomics to mycorrhizal plants and fungi will be crucial to determine the extent to which individual variation in key functional attributes is genetically based. We argue the need to unravel the importance of the diversity (especially assemblages of different evenness and richness) of individuals of both mycorrhizal plants and fungi, and the need to take a ‘community genetics’ approach to better understand the functional significance of the biodiversity of mycorrhizal symbioses.
Background and aims Extreme climate events, including flooding and prolonged drought, may establish long-lasting (legacy) effects on soil abiotic and biotic properties, potentially influencing soil ...N-cycling, microbial communities, and plant productivity. Nitrogen (N) fertilizer often stimulates plant growth, but it remains unknown whether N addition can alleviate the impact of legacy drought or waterlogging events on crops. Our aim was to assess the interactive effects of legacy extreme climate events and N-addition on these processes. Methods Using cotton as a model system, soils previously exposed to waterlogging and prolonged drought were used to examine potential legacy impacts of extreme climate on soil N process rates, abundance and structure of associated microbial communities, and cotton growth and productivity under different levels of N fertilizer application (0, 100, 200 and 300 kg N/ha). Results The deleterious legacy effects of prolonged drought on plant productivity were due to negative impacts on microbial abundance and community structure, and soil nutrient availability, thereby negatively influencing the rate of nitrification, and consequently plant available N. The legacy impacts of prolonged drought persisted throughout the experiment despite fertiliser applications of up to 300 kg of N/ha. The only observed legacy impacts of waterlogging were low NO3− levels in soils without N-addition and shifts in the abundance and structure of the N2O-reducing community. Conclusions There were strong legacy impacts of prolonged drought, but minor legacy impacts of waterlogging, on soils and crop yields which could not be fully counteracted by the high rates of N fertilizer application. This study provides critical knowledge contributing to the development of adaptation and soil N management strategies to minimize the loss of farm productivity, within the context of increased frequencies and intensities of extreme weather events.
Small RNAs (sRNAs) are known to regulate pathogenic plant-microbe interactions. Emerging evidence from the study of these model systems suggests that microRNAs (miRNAs) can be translocated between ...microbes and plants to facilitate symbiosis. The roles of sRNAs in mutualistic mycorrhizal fungal interactions, however, are largely unknown. In this study, we characterized miRNAs encoded by the ectomycorrhizal fungus
and investigated their expression during mutualistic interaction with
Using sRNA sequencing data and in situ miRNA detection, a novel fungal miRNA,
, was found to be transported into
roots after interaction with
Further characterization experiments demonstrate that inhibition of
negatively impacts the maintenance of mycorrhizal roots in
, while supplementation of
led to deeper integration of the fungus into plant tissues. Target prediction and experimental testing suggest that
may target the host NB-ARC domain containing transcripts, suggesting a potential role for this miRNA in subverting host signaling to stabilize the symbiotic interaction. Altogether, we provide evidence of previously undescribed cross-kingdom sRNA transfer from ectomycorrhizal fungi to plant roots, shedding light onto the involvement of miRNAs during the developmental process of mutualistic symbioses.
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