Responses of the soil microbial community to nitrogen fertilizer regimes and historical exposure to extreme weather events : flooding or prolonged-drought

Extreme weather events, including flooding and prolonged-drought, may establish long-lasting effects on soil biotic and abiotic properties, thus influencing ecosystem functions including primary productivity in subsequent years. Nitrogen (N) fertilizer addition often improves soil fertility, thereby potentially alleviating legacy effects on soil function and plant productivity. The soil microbial community plays a central role in mediating soil functioning; however, little is known about the legacy impacts of extreme weather events and N fertilizer addition on soil bacterial communities and the key processes involved in carbon (C) cycling. Here, the potential legacy effects of waterlogging, prolonged-drought and N fertilizer addition (0, 100, 200 and 300 kg N/ha) on soil bacteria and microbial respiration were investigated. The abundance, diversity and composition of the bacterial community, and basal and induced-respiration rates, in a farming soil system were examined, using quantitative PCR, high-throughput DNA sequencing, and MicroResp™. Soils previously exposed to short-term waterlogging events and prolonged-drought (by air-drying for 4 months) were used in our study. Prolonged drought, but not waterlogging, had a strong legacy effect on the soil bacterial community and microbial respiration. The addition of N fertilizer up to 300 kg N/ha could not fully counteract the legacy effects of prolonged-drought on soil bacteria. However, N addition did increase bacterial abundance and diversity, and inhibited soil microbial respiration. Significant correlations between microbial respiration and bacterial community structure were observed, but N addition weakened these relationships. Our results suggest that the resilience (rate of recovery) of soil bacterial communities and functions to prolonged-drought is limited in farming systems, and therefore, may take a long time to recover completely. Subsequently, this should be explicitly considered when developing adaptation strategies to alleviate the impacts of extreme weather events

The ectomycorrhizal fungus Pisolithus microcarpusencodes a microRNA involved in cross-kingdom gene silencing during symbiosis

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 Pisolithus microcarpus and investigated their expression during mutualistic interaction with Eucalyptus grandis. Using sRNA sequencing data and in situ miRNA detection, a novel fungal miRNA, Pmic_miR-8, was found to be transported into E. grandis roots after interaction with P. microcarpus. Further characterization experiments demonstrate that inhibition of Pmic_miR-8 negatively impacts the maintenance of mycorrhizal roots in E. grandis, while supplementation of Pmic_miR-8 led to deeper integration of the fungus into plant tissues. Target prediction and experimental testing suggest that Pmic_miR-8 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

Acquisition of host-derived carbon in biomass of the ectomycorrhizal fungus Pisolithus microcarpus is correlated to fungal carbon demand and plant defences

Ectomycorrhizal (ECM) fungi are key players in forest carbon (C) sequestration, receiving a substantial proportion of photosynthetic C from their forest tree hosts in exchange for plant growth-limiting soil nutrients. However, it remains unknown whether the fungus or plant controls the quantum of C in this exchange, nor what mechanisms are involved. Here, we aimed to identify physiological and genetic properties of both partners that influence ECM C transfer. Using a microcosm system, stable isotope tracing, and transcriptomics, we quantified plant-to-fungus C transfer between the host plant Eucalyptus grandis and nine isolates of the ECM fungus Pisolithus microcarpus that range in their mycorrhization potential and investigated fungal growth characteristics and plant and fungal genes that correlated with C acquisition. We found that C acquisition by P. microcarpus correlated positively with both fungal biomass production and the expression of a subset of fungal C metabolism genes. In the plant, C transfer was not positively correlated to the number of colonized root tips, but rather to the expression of defence- and stress-related genes. These findings suggest that C acquisition by ECM fungi involves individual fungal demand for C and defence responses of the host against C drain

Myristate and the ecology of AM fungi : significance, opportunities, applications and challenges

A recent study by Sugiura and coworkers reported the nonsymbiotic growth and spore production of an arbuscular mycorrhizal (AM) fungus, Rhizophagus irregularis, when the fungus received an external supply of certain fatty acids, myristates (C:14). This discovery follows the insight that AM fungi receive fatty acids from their hosts when in symbiosis. If this result holds up and can be repeated under nonsterile conditions and with a broader range of fungi, it has numerous consequences for our understanding of AM fungal ecology, from the level of the fungus, at the plant community level, and to functional consequences in ecosystems. In addition, myristate may open up several avenues from a more applied perspective, including improved fungal culture and supplementation of AM fungi or inoculum in the field. We here map these potential opportunities, and additionally offer thoughts on potential risks of this potentially new technology. Lastly, we discuss the specific research challenges that need to be overcome to come to an understanding of the potential role of myristate in AM ecology

Fine-scale diversity and distribution of ectomycorrhizal fungal mycelium in a Scots pine forest

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 new tool of the trade : plant-trait based approaches in microbial ecology

We view the microbial ecology toolbox as containing many complementary instruments, and how they are used needs to reflect this complementarity. Next generation sequencing has exponentially increased sequencing depth, enhancing descriptions of microbial communities and discovering rare species and lineages that had previously been undetectable (Öpik et al. 2009; Gilbert et al. 2009). Microbial ecologists are also learning how to overcome the bias in ‘culture-dependent’ approaches, using genomics to elucidate functional roles and requirements (Mackelprang et al. 2011). However, by itself, next generation sequencing does little to aid understanding of the ecological drivers of microbial diversity and its consequences for ecosystem functioning and stability. Without the incorporation of complementary tools into these studies, as well as the use of appropriate experimental designs (Prosser 2010), microbial ecology will not move beyond an exercise in natural history and into a more predictive ecological science

Microbial modulators of soil carbon storage : integrating genomic and metabolic knowledge for global prediction

Soil organic carbon performs a number of functions in ecosystems and it is clear that microbial communities play important roles in land-atmosphere carbon (C) exchange and soil C storage. In this review, we discuss microbial modulators of soil C storage, 'omics'-based approaches to characterize microbial system interactions impacting terrestrial C sequestration, and how data related to microbial composition and activities can be incorporated into mechanistic and predictive models. We argue that although making direct linkage of genomes to global phenomena is a significant challenge, many connections at intermediate scales are viable with integrated application of new systems biology approaches and powerful analytical and modelling techniques. This integration could enhance our capability to develop and evaluate microbial strategies for capturing and sequestering atmospheric CO2

A soil fungal metacommunity perspective reveals stronger and more localised interactions above the tree line of an alpine/subalpine ecotone

Dispersal affects community structure by facilitating colonisation and homogenising local communities, while species sorting along environmental gradients contributes to divergent community assembly. Fungi often have widespread distributions and are assumed to be dispersed easily across the landscape, with environmental selection being a primary driver of community assembly. To investigate the influence of spatial and environmental characteristics in shaping fungal community patterns, we characterised 143 communities of soil fungi along an altitudinal transect in Australia transitioning from subalpine to alpine vegetation (approximately 150 m difference in elevation over a distance of 1200 m). First, we inferred drivers of community assembly using canonical analyses including climate, edaphic properties, vegetation and spatial variables, all of which explained a statistically significant but very small amount of variation. We then employed an approach that defines the metacommunity with which each local community interacts via immigration and emigration and then estimates metacommunity characteristics. Using this approach, we inferred scales over which community interactions occurred along spatial, environmental and phylogenetic dimensions and the strength of community interactions based on the similarity of local communities to the metacommunity. Constructed metacommunities above the tree line consisted of local communities that were more clustered in space and more homogeneous than those at or below the tree line. Thus, mixing is likely occurring to a greater degree among fewer communities in the alpine environment. Comparisons of metacommunity estimates suggested that fungal evolutionary histories did not constrain community assembly as strongly as spatial proximity or environmental variation. This work suggests that differences exist in how fungal communities assembly along this altitudinal transect, despite site on its own explaining little compositional variation, and that the rate and the degree of species mixing among communities differs depending on the environmental context

Now you see it, now you don't : the challenge of detecting, monitoring and conserving ectomycorrhizal fungi

Fungi are a vital component of ecosystem biodiversity, but spend most of their lives hidden from view. Monitoring ectomycorrhizal (ECM) fungi has mostly relied on the abundance and distribution of above-ground sporocarps without consideration of their below-ground vegetative mycelium. Molecular methods may provide the means of obtaining this information and allow a more accurate determination of their possible decline and threat of extinction. Stipitate hydnoid sporocarp occurrence was recorded and mapped for 9 yr at two sites in Scotland, UK. Soil samples were collected at locations where sporocarps of Hydnellum aurantiacum, Hydnellum caeruleum, Phellodon niger or Sarcodon glaucopus had occurred 1-4 yr previously. Species-specific DNA was detected at all sporocarp locations and RNA was detected at 75 % of the locations indicating that these species remained below-ground and viable at the majority of locations for at least 4 yr in the absence of sporocarps

Resilience of fungal communities to elevated CO2

Soil filamentous fungi play a prominent role in regulating ecosystem functioning in terrestrial ecosystems. This necessitates understanding their responses to climate change drivers in order to predict how nutrient cycling and ecosystem services will be influenced in the future. Here, we provide a quantitative synthesis of ten studies on soil fungal community responses to elevated CO2. Many of these studies reported contradictory diversity responses. We identify the duration of the study as an influential parameter that determines the outcome of experimentation. Our analysis reconciles the existing globally distributed experiments on fungal community responses to elevated CO2 and provides a framework for comparing results of future CO2 enrichment studies