Distinct biogeographic patterns in Glomeromycotinian and Mucoromycotinian arbuscular mycorrhizal fungi across China: A meta-analysis

Fine root endophytes, recently reclassified as Mucoromycotinian arbuscular mycorrhizal fungi (M-AMF), are now recognized as functionally important as Glomeromycotinian AMF (G-AMF). However, little is known about the biogeography and ecology of M-AMF and G-AMF communities, particularly on a large scale, preventing a systematic assessment of ecosystem diversity and functioning. Here, we investigated the biogeographic assemblies and ecological diversity patterns of both G-AMF and M-AMF, using published 18S rDNA amplicon datasets and associated metadata from 575 soil samples in six ecosystems across China. Contrasting with G-AMF, putative M-AMF were rare in natural/semi-natural sites, where their communities were a subset of those in agricultural sites characterized by intensive disturbances, suggesting different ecological niches that they could occupy. Spatial and environmental factors (e.g., vegetation type) significantly influenced both fungal communities, with soil total‑nitrogen and mean-annual-precipitation being the strongest predictors for G-AMF and M-AMF richness, respectively. Both groups exhibited a strong spatial distance-decay relationship, shaped more by environmental filtering than spatial effects for M-AMF, and the opposite for G-AMF, presumably because stochasticity (e.g., drift) dominantly structured G-AMF communities; while the narrower niche breadth (at community-level) of M-AMF compared to G-AMF suggested its more susceptibility to environmental differences. Furthermore, co-occurrence network links between G-AMF and M-AMF were prevalent across ecosystems, and were predicted to play a key role in stabilizing overall communities harboring both fungi. Based on the macroecological spatial scale datasets, this study provides solid evidence that the two AMF groups have distinct ecological preferences at the continental scale in China, and also highlights the potential impacts of anthropogenic activities on distributions of AMF. These results advance our knowledge of the ecological differences between the two fungal groups in terrestrial ecosystems, suggesting the need for further field-based investigation that may lead to a more sophisticated understanding of ecosystem function and sustainable management.

Quantifying microplastic dispersion due to density effects

An experimental study was conducted on how polymer density affects the transport and fate of microplastics in aquatic flows. For the first time, polypropylene (PP), polyethylene (PE), polymethyl methacrylate (PMMA), polyetheretherketone (PEEK), and polyvinyl chloride (PVC) were chemically stained and tested using solute transport techniques and velocities found among rivers in the natural environment (0.016 - 0.361 m/s). The movement of 3D-polymers with densities ranging from 0.9 - 1.4 g/cm³ was quantified in a laboratory flume scaled to simulate open-channel flows in fluvial systems. Except for PP, in most conditions microplastics exhibited similar transport characteristics to solutes regardless of density and established solute transport models were successfully implemented to predict their transport and fate. Mass recoveries and ADE routing model demonstrated microplastic deposition and resuspension was associated with polymer density below critical velocity thresholds ≤ 0.1 m/s. When density becomes the dominant force at these slower velocities, concentrations of denser than water microplastics will be momentarily or permanently deposited in channel beds and microplastics follow the classical Shields sediment transport methodology. This data is the first to provide microplastic suspension and deposition thresholds based on river velocity and polymer density, making a key contribution to research predicting microplastic fate and organismal exposure.

Viral metagenomics reveals diverse virus-host interactions throughout the soil depth profile

IMPORTANCE

Soil viruses can moderate the roles that their host microbes play in global carbon cycling. However, given that most studies investigate the surface layer (i.e., top 20 cm) of soil, the extent to which this occurs in subsurface soil (i.e., below 20 cm) is unknown. Here, we leveraged public sequencing data to investigate the interactions between viruses and their hosts at soil depth intervals, down to 115 cm. While most viruses were detected throughout the soil depth profile, their adaptation to host microbes varied. Nonetheless, we uncovered evidence for the potential of soil viruses to encourage their hosts to recycle plant-derived carbon in both surface and subsurface soils. This work reasons that our understanding of soil viral functions requires us to continue to dig deeper and compare viruses existing throughout soil ecosystems.

Microplastic transport dynamics in surcharging and overflowing manholes

The transport of microplastics within urban water systems remains poorly understood, with little prior research on their behaviour within manhole configurations. This study represents the first to measure and model the transport dynamics of microplastics within circular and square manholes under different hydraulic scenarios. The transport and fate of polyethylene (PE) was quantified and compared to solutes (Rhodamine WT dye) using energy losses, residence time distributions (RTDs), and mixing models within surcharging and overflowing manholes. The bulk mass of solute and PE concentrations followed similar flow paths across all conditions except for 17.3 ± 7.9 % of PE mass that was immobilized in a dead zone above the inlet pipe for manholes with a surcharge to pipe diameter ratio ≥2. Consequently, these microplastics only exit after a significant change in hydraulic regime occurs, causing microplastics to be at risk of being contaminated over a prolonged duration. No significant mixing differences for PE and solutes were found between manhole geometries. The deconvolution method outperformed the ADZ model with goodness of fit (Rt2) values of 0.99 (0.60) and 1.00 (0.89) for PE and solute mixing, respectively. This establishes the deconvolution method as the most accurate and appropriate model to accurately predict microplastic mixing in manholes and urban drainage systems.

Spatiotemporal Variations of Soil Reactive Nitrogen Oxide Fluxes across the Anthropogenic Landscape

Volatile reactive nitrogen oxides (NOy) are significant atmospheric pollutants, including NOx (nitric oxide [NO] + nitrogen dioxide [NO2]) and NOz (nitrous acid [HONO] + nitric acid [HNO3] + nitrogen trioxide [NO3] + ...). NOy species are products of nitrogen (N) cycle processes, particularly nitrification and denitrification. Biogenic sources, including soil, account for over 50% of natural NOy emissions to the atmosphere, yet emissions from soils are generally not included in atmospheric models as a result of a lack of mechanistic data. This work is a unique investigation of NOy fluxes on a landscape scale, taking a comprehensive set of land-use types, human influence, and seasonality into account to determine large-scale heterogeneity to provide a basis for future modeling and hypothesis generation. By coupling 16S rRNA amplicon sequencing and quantitative polymerase chain reaction, we have linked significant differences in functional potential and activity of nitrifying and denitrifying soil microbes to NOy emissions from soils. Further, we have identified soils subject to increased N deposition that are less microbially active despite increased available N, potentially as a result of poor soil health from anthropogenic pollution. Structural equation modeling suggests human influence on soils to be a more significant effector of soil NOy emissions than land-use type.

Niche differentiation of Mucoromycotinian and Glomeromycotinian arbuscular mycorrhizal fungi along a 2-million-year soil chronosequence

Current literature suggests ecological niche differentiation between co-occurring Mucoromycotinian arbuscular mycorrhizal fungi (M-AMF) and Glomeromycotinian AMF (G-AMF), but experimental evidence is limited. We investigated the influence of soil age, water availability (wet and dry), and plant species (native Microlaena stipoides and exotic Trifolium subterraneum) on anatomical root colonisation and DNA profiles of M-AMF and G-AMF under glasshouse conditions. We grew seedlings of each species in soils collected from the four stages of a soil chronosequence, where pH decreases from the youngest to oldest stages, and phosphorus (P) is low in the youngest and oldest, but high in the intermediate stages. We scored the percentage of root length colonised and used DNA metabarcoding to profile fungal richness and community composition associated with treatment combinations. Soil age, water availability, and plant species were important influencers of root colonisation, although no M-AMF were visible following staining of M. stipoides roots. Soil age and host plant influenced fungal richness and community composition. However, response to soil age, potential host species, and water availability differed between M-AMF and G-AMF. Root colonisation of T. subterraneum by M-AMF and G-AMF was inversely correlated with soil P level. Community composition of M-AMF and G-AMF was structured by soil age and, to a lesser extent, plant species. Richness of M-AMF and G-AMF was negatively, and positively, correlated with available P, respectively. These findings are experimental evidence of ecological niche differentiation of M-AMF and G-AMF and invite further exploration into interactive effects of abiotic and biotic factors on their communities along successional trajectories.

Water flow plays a key role in determining chemical biodegradation in water-sediment systems

Before agrochemicals can be registered and sold, the chemical industry is required to perform regulatory tests to assess their environmental persistence, using defined guidelines. Aquatic fate tests (e.g. OECD 308) lack environmental realism as they are conducted under dark conditions and in small-scale static systems, which can affect microbial diversity and functionality. In this study, water-sediment microflumes were used to investigate the impact of these deficiencies in environmental realism on the fate of the fungicide, isopyrazam. Although on a large-scale, these systems aimed to retain the key aspects of OECD 308 tests. Tests were carried out under both a non-UV light-dark cycle and continuous darkness and under both static and flowing water conditions, to investigate how light and water flow affect isopyrazam biodegradation pathways. In static systems, light treatment played a significant role, with faster dissipation in illuminated compared to dark microflumes (DT50s = 20.6 vs. 47.7 days). In flowing systems (DT50s = 16.8 and 15.3 days), light did not play a significant role in dissipation, which was comparable between the two light treatments, and faster than in dark static microflumes. Microbial phototroph biomass was significantly reduced by water flow in the illuminated systems, thereby reducing their contribution to dissipation. Comprehensive analysis of bacterial and eukaryotic community composition identified treatment specific changes following incubation, with light promoting relative abundance of Cyanobacteria and eukaryotic algae, and flow increasing relative abundance of fungi. We conclude that both water velocity and non-UV light increased isopyrazam dissipation, but the contribution of light depended on the flow conditions. These differences may have resulted from impacts on microbial communities and via mixing processes, particularly hyporheic exchange. Inclusion of both light and flow in studies could improve the extent they mimic natural environments and predict chemical environmental persistence, thus bridging the gap between laboratory and field studies.

Integrated Probe System for Measuring Soil Carbon Dioxide Concentrations

This article outlines the design and implementation of an internet-of-things (IoT) platform for the monitoring of soil carbon dioxide (CO₂) concentrations. As atmospheric CO₂ continues to rise, accurate accounting of major carbon sources, such as soil, is essential to inform land management and government policy. Thus, a batch of IoT-connected CO₂ sensor probes were developed for soil measurement. These sensors were designed to capture spatial distribution of CO₂ concentrations across a site and communicate to a central gateway using LoRa. CO₂ concentration and other environmental parameters, including temperature, humidity and volatile organic compound concentration, were logged locally and communicated to the user through a mobile (GSM) connection to a hosted website. Following three field deployments in summer and autumn, we observed clear depth and diurnal variation of soil CO₂ concentration within woodland systems. We determined that the unit had the capacity to log data continuously for a maximum of 14 days. These low-cost systems have great potential for better accounting of soil CO₂ sources over temporal and spatial gradients and possibly flux estimations. Future testing will focus on divergent landscapes and soil conditions.

Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere

BACKGROUND

The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions.

RESULTS

Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots, and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming," which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation.

CONCLUSIONS

Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability. Video Abstract.

Circadian rhythms in the plant host influence rhythmicity of rhizosphere microbiota

Background

Recent studies demonstrated that microbiota inhabiting the plant rhizosphere exhibit diel changes in abundance. To investigate the impact of plant circadian rhythms on bacterial and fungal rhythms in the rhizosphere, we analysed temporal changes in fungal and bacterial communities in the rhizosphere of Arabidopsis plants overexpressing or lacking function of the circadian clock gene LATE ELONGATED HYPOCOTYL (LHY).

Results

Under diel light–dark cycles, the knock-out mutant lhy-11 and the gain-of-function mutant lhy-ox both exhibited gene expression rhythms with altered timing and amplitude compared to wild-type plants. Distinct sets of bacteria and fungi were found to display rhythmic changes in abundance in the rhizosphere of both of these mutants, suggesting that abnormal patterns of rhythmicity in the plant host caused temporal reprogramming of the rhizosphere microbiome. This was associated with changes in microbial community structure, including changes in the abundance of fungal guilds known to impact on plant health. Under constant environmental conditions, microbial rhythmicity persisted in the rhizosphere of wild-type plants, indicating control by a circadian oscillator. In contrast, loss of rhythmicity in lhy-ox plants was associated with disrupted rhythms for the majority of rhizosphere microbiota.

Conclusions

These results show that aberrant function of the plant circadian clock is associated with altered rhythmicity of rhizosphere bacteria and fungi. In the long term, this leads to changes in composition of the rhizosphere microbiome, with potential consequences for plant health. Further research will be required to understand the functional implications of these changes and how they impact on plant health and productivity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01430-z.

Landscape scale ecology of Tetracladium spp. fungal root endophytes

BACKGROUND

The genus Tetracladium De Wild. (Ascomycota) has been traditionally regarded as a group of Ingoldian fungi or aquatic hyphomycetes-a polyphyletic group of phylogenetically diverse fungi which grow on decaying leaves and plant litter in streams. Recent sequencing evidence has shown that Tetracladium spp. may also exist as root endophytes in terrestrial environments, and furthermore may have beneficial effects on the health and growth of their host. However, the diversity of Tetracladium spp. communities in terrestrial systems and the factors which shape their distribution are largely unknown.

RESULTS

Using a fungal community internal transcribed spacer amplicon dataset from 37 UK Brassica napus fields we found that soils contained diverse Tetracladium spp., most of which represent previously uncharacterised clades. The two most abundant operational taxonomic units (OTUs), related to previously described aquatic T. furcatum and T. maxilliforme, were enriched in roots relative to bulk and rhizosphere soil. For both taxa, relative abundance in roots, but not rhizosphere or bulk soil was correlated with B. napus yield. The relative abundance of T. furcatum and T. maxilliforme OTUs across compartments showed very similar responses with respect to agricultural management practices and soil characteristics. The factors shaping the relative abundance of OTUs homologous to T. furcatum and T. maxilliforme OTUs in roots were assessed using linear regression and structural equation modelling. Relative abundance of T. maxilliforme and T. furcatum in roots increased with pH, concentrations of phosphorus, and increased rotation frequency of oilseed rape. It decreased with increased soil water content, concentrations of extractable phosphorus, chromium, and iron.

CONCLUSIONS

The genus Tetracladium as a root colonising endophyte is a diverse and widely distributed part of the oilseed rape microbiome that positively correlates to crop yield. The main drivers of its community composition are crop management practices and soil nutrients.

Building soil sustainability from root-soil interface traits

Great potential exists to harness plant traits at the root-soil interface, mainly rhizodeposition and root hairs, to 'build' soils with better structure that can trap more carbon and resources, resist climate stresses, and promote a healthy microbiome. These traits appear to have been preserved in modern crop varieties, but scope exists to improve them further because they vary considerably between genotypes and respond to environmental conditions. From emerging evidence, rhizodeposition can act as a disperser, aggregator, and/or hydrogel in soil, and root hairs expand rhizosheath size. Future research should explore impacts of selecting these traits on plants and soils concurrently, expanding from model plants to commercial genotypes, and observing whether impacts currently limited to glasshouse studies occur in the field.

2-aminoethylphosphonate utilisation in Pseudomonas putida BIRD-1 is controlled by multiple master regulators

Bacteria possess various regulatory mechanisms to detect and coordinate a response to elemental nutrient limitation. In pseudomonads, the two‐component system regulators CbrAB, NtrBC and PhoBR, are responsible for regulating cellular response to carbon (C), nitrogen (N) and phosphorus (P) respectively. Phosphonates are reduced organophosphorus compounds produced by a broad range of biota and typified by a direct C‐P bond. Numerous pseudomonads can use the environmentally abundant phosphonate species 2‐aminoethylphosphonate (2AEP) as a source of C, N, or P, but only PhoBR has been shown to play a role in 2AEP utilization. On the other hand, utilization of 2AEP as a C and N source is considered substrate inducible. Here, using the plant‐growth‐promoting rhizobacterium Pseudomonas putida BIRD‐1 we present evidence that 2AEP utilization is under dual regulation and only occurs upon depletion of C, N, or P, controlled by CbrAB, NtrBC, or PhoBR respectively. However, the presence of 2AEP was necessary for full gene expression, i.e. expression was substrate inducible. Mutation of a LysR‐type regulator, termed AepR, upstream of the 2AEP transaminase‐phosphonatase system (PhnWX), confirmed this dual regulatory mechanism. To our knowledge, this is the first study identifying coordination between global stress response and substrate‐specific regulators in phosphonate metabolism.

Diversity and Ecological Guild Analysis of the Oil Palm Fungal Microbiome Across Root, Rhizosphere, and Soil Compartments

The rhizosphere microbiome is a major determinant of plant health, which can interact with the host directly and indirectly to promote or suppress productivity. Oil palm is one of the world’s most important crops, constituting over a third of global vegetable oil production. Currently there is little understanding of the oil palm microbiome and its contribution to plant health and productivity, with existing knowledge based almost entirely on culture dependent studies. We investigated the diversity and composition of the oil palm fungal microbiome in the bulk soil, rhizosphere soil, and roots of 2-, 18-, and 35-year old plantations in Selangor, Malaysia. The fungal community showed substantial variation between the plantations, accounting for 19.7% of community composition, with compartment (root, rhizosphere soil, and bulk soil), and soil properties (pH, C, N, and P) contributing 6.5 and 7.2% of community variation, respectively. Rhizosphere soil and roots supported distinct communities compared to the bulk soil, with significant enrichment of Agaricomycetes, Glomeromycetes, and Lecanoromycetes in roots. Several putative plant pathogens were abundant in roots in all the plantations, including taxa related to Prospodicola mexicana and Pleurostoma sp. The mycorrhizal status and dependency of oil palm has yet to be established, and using 18S rRNA primers we found considerable between-site variation in Glomeromycotinian community composition, accounting for 31.2% of variation. There was evidence for the selection of Glomeromycotinian communities in oil palm roots in the older plantations but compartment had a weak effect on community composition, accounting for 3.9% of variation, while soil variables accounted for 9% of community variation. While diverse Mucoromycotinian fungi were detected, they showed very low abundance and diversity within roots compared to bulk soil, and were not closely related to taxa which have been linked to fine root endophyte mycorrhizal morphology. Many of the fungal sequences showed low similarity to established genera, indicating the presence of substantial novel diversity with significance for plant health within the oil palm microbiome.

Agricultural land-use favours Mucoromycotinian, but not Glomeromycotinian, arbuscular mycorrhizal fungi across ten biomes

Globally, agricultural land-use negatively affects soil biota that contribute to ecosystem functions such as nutrient cycling, yet arbuscular mycorrhizal fungi (AMF) are promoted as essential components of agroecosystems. Arbuscular mycorrhizal fungi include Glomeromycotinian AMF (G-AMF) and the arbuscule-producing fine root endophytes, recently re-classified into the Endogonales order within Mucoromycotina. The correct classification of Mucoromycotinian AMF (M-AMF) and the availability of new molecular tools can guide research to better the understanding of their diversity and ecology. To investigate the impact on G-AMF and M-AMF of agricultural land-use at a continental scale, we sampled DNA from paired farm and native sites across 10 Australian biomes. Glomeromycotinian AMF were present in both native and farm sites in all biomes. Putative M-AMF were favoured by farm sites, rare or absent in native sites, and almost entirely absent in tropical biomes. Temperature, rainfall, and soil pH were strong drivers of richness and community composition of both groups, and plant richness was an important mediator. Both fungal groups occupy different, but overlapping, ecological niches, with M-AMF thriving in temperate agricultural landscapes. Our findings invite exploration of the origin and spread of M-AMF and continued efforts to resolve the phylogeny of this newly reclassified group of AMF.

Natural attenuation of legacy hydrocarbon spills in pristine soils is feasible despite difficult environmental conditions in the monsoon tropics

The Kimberley region of Western Australia is a National Heritage listed region that is internationally recognised for its environmental and cultural significance. However, petroleum spills have been reported at a number of sites across the region, representing an environmental concern. The region is also characterised as having low soil nutrients, high temperatures and monsoonal rain - all of which may limit the potential for natural biodegradation of petroleum. Therefore, this work evaluated the effect of legacy petroleum hydrocarbons on the indigenous soil microbial community (across the domains Archaea, Bacteria and Fungi) at three sites in the Kimberley region. At each site, soil cores were removed from contaminated and control areas and analysed for total petroleum hydrocarbons, soil nutrients, pH and microbial community profiling (using16S rRNA and ITS sequencing on the Illumina MiSeq Platform). The presence of petroleum hydrocarbons decreased microbial diversity across all kingdoms, altered the structure of microbial communities and increased the abundance of putative hydrocarbon degraders (e.g. Mycobacterium, Acremonium, Penicillium, Bjerkandera and Candida). Microbial community shifts from contaminated soils were also associated with an increase in soil nutrients (notably Colwell P and S). Our study highlights the long-term effect of legacy hydrocarbon spills on soil microbial communities and their diversity in remote, infertile monsoonal soils, but also highlights the potential for natural attenuation to occur in these environments.

Tree phyllospheres are a habitat for diverse populations of CO-oxidizing bacteria

Carbon monoxide (CO) is both a ubiquitous atmospheric trace gas and an air pollutant. While aerobic CO-degrading microorganisms in soils and oceans are estimated to remove ~370 Tg of CO per year, the presence of CO-degrading microorganisms in above-ground habitats, such as the phyllosphere, and their potential role in CO cycling remains unknown. CO-degradation by leaf washes of two common British trees, Ilex aquifolium and Crataegus monogyna, demonstrated CO uptake in all samples investigated. Based on the analyses of taxonomic and functional genes, diverse communities of candidate CO-oxidizing taxa were identified, including members of Rhizobiales and Burkholderiales which were abundant in the phyllosphere at the time of sampling. Based on predicted genomes of phyllosphere community members, an estimated 21% of phyllosphere bacteria contained CoxL, the large subunit of CO-dehydrogenase. In support of this, data mining of publicly available phyllosphere metagenomes for genes encoding CO-dehydrogenase subunits demonstrated that, on average, 25% of phyllosphere bacteria contained CO-dehydrogenase gene homologues. A CO-oxidizing Phyllobacteriaceae strain was also isolated from phyllosphere samples which contains genes encoding both CO-dehydrogenase as well as a ribulose-1,5-bisphosphate carboxylase-oxygenase. These results suggest that the phyllosphere supports diverse and potentially abundant CO-oxidizing bacteria, which are a potential sink for atmospheric CO.

A Novel Signaling Pathway Required for Arabidopsis Endodermal Root Organization Shapes the Rhizosphere Microbiome

The Casparian strip (CS) constitutes a physical diffusion barrier to water and nutrients in plant roots, which is formed by the polar deposition of lignin polymer in the endodermis tissue. The precise pattern of lignin deposition is determined by the scaffolding activity of membrane-bound Casparian Strip domain proteins (CASPs), but little is known of the mechanism(s) directing this process. Here, we demonstrate that Endodermis-specific Receptor-like Kinase 1 (ERK1) and, to a lesser extent, ROP Binding Kinase1 (RBK1) are also involved in regulating CS formation, with the former playing an essential role in lignin deposition as well as in the localization of CASP1. We show that ERK1 is localized to the cytoplasm and nucleus of the endodermis and that together with the circadian clock regulator, Time for Coffee (TIC), forms part of a novel signaling pathway necessary for correct CS organization and suberization of the endodermis, with their single or combined loss of function resulting in altered root microbiome composition. In addition, we found that other mutants displaying defects in suberin deposition at the CS also display altered root exudates and microbiome composition. Thus, our work reveals a complex network of signaling factors operating within the root endodermis that establish both the CS diffusion barrier and influence the microbial composition of the rhizosphere.

Evidence for Niche Differentiation in the Environmental Responses of Co-occurring Mucoromycotinian Fine Root Endophytes and Glomeromycotinian Arbuscular Mycorrhizal Fungi

Fine root endophytes (FRE) were traditionally considered a morphotype of arbuscular mycorrhizal fungi (AMF), but recent genetic studies demonstrate that FRE belong within the subphylum Mucoromycotina, rather than in the subphylum Glomeromycotina with the AMF. These findings prompt enquiry into the fundamental ecology of FRE and AMF. We sampled FRE and AMF in roots of Trifolium subterraneum from 58 sites across temperate southern Australia. We investigated the environmental drivers of composition, richness, and root colonization of FRE and AMF by using structural equation modelling and canonical correspondence analyses. Root colonization by FRE increased with increasing temperature and rainfall but decreased with increasing phosphorus (P). Root colonization by AMF increased with increasing soil organic carbon but decreased with increasing P. Richness of FRE decreased with increasing temperature and soil pH. Richness of AMF increased with increasing temperature and rainfall but decreased with increasing soil aluminium (Al) and pH. Aluminium, soil pH, and rainfall were, in decreasing order, the strongest drivers of community composition of FRE; they were also important drivers of community composition of AMF, along with temperature, in decreasing order: rainfall, Al, temperature, and soil pH. Thus, FRE and AMF showed the same responses to some (e.g. soil P, soil pH) and different responses to other (e.g. temperature) key environmental factors. Overall, our data are evidence for niche differentiation among these co-occurring mycorrhizal associates.

Contrasting Responses of Rhizosphere Bacterial, Fungal, Protist, and Nematode Communities to Nitrogen Fertilization and Crop Genotype in Field Grown Oilseed Rape (Brassica napus)

The rhizosphere microbiome is considered to play a key role in determining crop health. However, current understanding of the factors which shape assembly and composition of the microbiome is heavily biased toward bacterial communities, and the relevance for other microbial groups is unclear. Furthermore, community assembly is determined by a variety of factors, including host genotype, environment and agricultural management practices, and their relative importance and interactions remain to be elucidated. We investigated the impact of nitrogen fertilization on rhizosphere bacterial, fungal, nematode and protist communities of 10 contrasting oilseed rape genotypes in a field experiment. We found significant differences in the composition of bacteria, fungi, protist and nematode communities between the rhizosphere and bulk soil. Nitrogen application had a significant but weak effect on fungal, bacterial, and protist community composition, and this was associated with increased relative abundance of a complex of fungal pathogens in the rhizosphere and soil, including Mycosphaerella sp. and Leptosphaeria sp. Network analysis showed that nitrogen application had different effects on microbial community connectivity in the soil and rhizosphere. Crop genotype significantly affected fungal community composition, with evidence for a degree of genotype specificity for a number of pathogens, including L. maculans, Alternaria sp., Pyrenopeziza brassicae, Olpidium brassicae, and L. biglobosa, and also potentially beneficial Heliotales root endophytes. Crop genotype had no significant effect on assembly of bacteria, protist or nematode communities. There was no relationship between genetic distance of crop genotypes and the extent of dissimilarity of rhizosphere microbial communities. Field disease assessment confirmed infection of crops by Leptosphaeria sp., P. brassicae, and Alternaria sp., indicating that rhizosphere microbiome sequencing was an effective indicator of plant health. We conclude that under field conditions soil and rhizosphere nutrient stoichiometry and crop genotype are key factors determining crop health by influencing the infection of roots by pathogenic and mutualistic fungal communities, and the connectivity and stability of rhizosphere microbiome interaction networks.

Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale

BACKGROUND

The plant microbiome plays a vital role in determining host health and productivity. However, we lack real-world comparative understanding of the factors which shape assembly of its diverse biota, and crucially relationships between microbiota composition and plant health. Here we investigated landscape scale rhizosphere microbial assembly processes in oilseed rape (OSR), the UK's third most cultivated crop by area and the world's third largest source of vegetable oil, which suffers from yield decline associated with the frequency it is grown in rotations. By including 37 conventional farmers' fields with varying OSR rotation frequencies, we present an innovative approach to identify microbial signatures characteristic of microbiomes which are beneficial and harmful to the host.

RESULTS

We show that OSR yield decline is linked to rotation frequency in real-world agricultural systems. We demonstrate fundamental differences in the environmental and agronomic drivers of protist, bacterial and fungal communities between root, rhizosphere soil and bulk soil compartments. We further discovered that the assembly of fungi, but neither bacteria nor protists, was influenced by OSR rotation frequency. However, there were individual abundant bacterial OTUs that correlated with either yield or rotation frequency. A variety of fungal and protist pathogens were detected in roots and rhizosphere soil of OSR, and several increased relative abundance in root or rhizosphere compartments as OSR rotation frequency increased. Importantly, the relative abundance of the fungal pathogen Olpidium brassicae both increased with short rotations and was significantly associated with low yield. In contrast, the root endophyte Tetracladium spp. showed the reverse associations with both rotation frequency and yield to O. brassicae, suggesting that they are signatures of a microbiome which benefits the host. We also identified a variety of novel protist and fungal clades which are highly connected within the microbiome and could play a role in determining microbiome composition.

CONCLUSIONS

We show that at the landscape scale, OSR crop yield is governed by interplay between complex communities of both pathogens and beneficial biota which is modulated by rotation frequency. Our comprehensive study has identified signatures of dysbiosis within the OSR microbiome, grown in real-world agricultural systems, which could be used in strategies to promote crop yield. Video abstract.

Bedform characteristics and biofilm community development interact to modify hyporheic exchange

The physical and biological attributes of riverine ecosystems interact in a complex manner which can affect the hydrodynamic behaviour of the system. This can alter the mixing characteristics of a river at the sediment-water interface. Research on hyporheic exchange has increased in recent years driven by a greater appreciation for the importance of this dynamic ecotone in connecting and regulating river systems. An understanding of process-based interactions driving hyporheic exchange is still limited, specifically the feedbacks between the physical and biological controlling factors. The interplay between bed morphology and sediment size on biofilm community development and the impact on hyporheic exchange mechanisms, was experimentally considered. Purpose built recirculating flume systems were constructed and three profiles of bedform investigated: i) flat, ii) undulating λ = 1 m, ii) undulating λ = 0.2 m, across two different sized sediments (0.5 mm and 5 mm). The influence of biofilm growth and bedform interaction on hyporheic exchange was explored, over time, using discrete repeat injections of fluorescent dye into the flumes. Hyporheic exchange rates were greatest in systems with larger sediment sizes (5 mm) and with more bedforms (undulating λ = 0.2). Sediment size was a dominant control in governing biofilm growth and hyporheic exchange in systems with limited bedform. In systems where bedform was prevalent, sediment size and biofilm appeared to no longer be a control on exchange due to the physical influence of advective pumping. Here, exchange rates within these environments were more consistent overtime, despite greater microbial growth. As such, bedform has the potential to overcome the rate limiting effects of biotic factors on hyporheic exchange and sediment size on microbial penetration. This has implications for pollutant and nutrient penetration; bedforms increase hydrological connectivity, generating the opportunity to support microbial communities at depth and as such, improve the self-purification ability of river systems.

First Cryo-Scanning Electron Microscopy Images and X-Ray Microanalyses of Mucoromycotinian Fine Root Endophytes in Vascular Plants

AIMS

Arbuscule-producing fine root endophytes (FRE) (previously incorrectly Glomus tenue) were recently placed within subphylum Mucoromycotina; the first report of arbuscules outside subphylum Glomeromycotina. Here, we aimed to estimate nutrient concentrations in plant and fungal structures of FRE and to test the utility of cryo-scanning electron microscopy (cryoSEM) for studying these fungi.

METHODS

We used replicated cryoSEM and X-ray microanalysis of heavily colonized roots of Trifolium subterraneum.

RESULTS

Intercellular hyphae and hyphae in developed arbuscules were consistently very thin; 1.35 ± 0.03 μm and 0.99 ± 0.03 μm in diameter, respectively (mean ± SE). Several intercellular hyphae were often adjacent to each other forming "hyphal ropes." Developed arbuscules showed higher phosphorus concentrations than senesced arbuscules and non-colonized structures. Senesced arbuscules showed greatly elevated concentrations of calcium and magnesium.

CONCLUSION

While uniformly thin hyphae and hyphal ropes are distinct features of FRE, the morphology of fully developed arbuscules, elevated phosphorus in fungal structures, and accumulation of calcium with loss of structural integrity in senesced arbuscules are similar to glomeromycotinian fungi. Thus, we provide evidence that FRE may respond to similar host-plant signals or that the host plant may employ a similar mechanism of association with FRE and AMF.

Inclusion of seasonal variation in river system microbial communities and phototroph activity increases environmental relevance of laboratory chemical persistence tests

Regulatory tests assess crop protection product environmental fate and toxicity before approval for commercial use. Although globally applied laboratory tests can assess biodegradation, they lack environmental complexity. Microbial communities are subject to temporal and spatial variation, but there is little consideration of these microbial dynamics in the laboratory. Here, we investigated seasonal variation in the microbial composition of water and sediment from a UK river across a two-year time course and determined its effect on the outcome of water-sediment (OECD 308) and water-only (OECD 309) biodegradation tests, using the fungicide isopyrazam. These OECD tests are performed under dark conditions, so test systems incubated under non-UV light:dark cycles were also included to determine the impact on both inoculum characteristics and biodegradation. Isopyrazam degradation was faster when incubated under non-UV light at all collection times in water-sediment microcosms, suggesting that phototrophic communities can metabolise isopyrazam throughout the year. Degradation rate varied seasonally between inoculum collection times only in microcosms incubated in the light, but isopyrazam mineralisation to ¹⁴CO₂ varied seasonally under both light and dark conditions, suggesting that heterotrophic communities may also play a role in degradation. Bacterial and phototroph communities varied across time, but there was no clear link between water or sediment microbial composition and variation in degradation rate. During the test period, inoculum microbial community composition changed, particularly in non-UV light incubated microcosms. Overall, we show that regulatory test outcome is not influenced by temporal variation in microbial community structure; however, biodegradation rates from higher tier studies with improved environmental realism, e.g. through addition of non-UV light, may be more variable. These data suggest that standardised OECD tests can provide a conservative estimate of pesticide persistence end points and that additional tests including non-UV light could help bridge the gap between standard tests and field studies.

Longitudinal dispersion of microplastics in aquatic flows using fluorometric techniques

Microplastics are an emerging environmental contaminant. Existing knowledge on the precise transport processes involved in the movement of microplastics in natural water bodies is limited. Microplastic fate-transport models rely on numerical simulations with limited empirical data to support and validate these models. We adopted fluorometric principles to track the movement of both fluorescent dye and florescent stained microplastics (polyethylene) in purpose-built laboratory flumes with standard fibre-optic fluorometers. Neutrally buoyant microplastics behaved in the same manner as a solute (Rhodamine) and more importantly displayed classical fundamental dispersion theory in uniform open channel flow. This suggests Rhodamine, a fluorescent tracer, can be released into the natural environment with the potential to mimic microplastic movement in the water column.

Urban meadows as an alternative to short mown grassland: effects of composition and height on biodiversity

There are increasing calls to provide greenspace in urban areas, yet the ecological quality, as well as quantity, of greenspace is important. Short mown grassland designed for recreational use is the dominant form of urban greenspace in temperate regions but requires considerable maintenance and typically provides limited habitat value for most taxa. Alternatives are increasingly proposed, but the biodiversity potential of these is not well understood. In a replicated experiment across six public urban greenspaces, we used nine different perennial meadow plantings to quantify the relative roles of floristic diversity and height of sown meadows on the richness and composition of three taxonomic groups: plants, invertebrates, and soil microbes. We found that all meadow treatments were colonized by plant species not sown in the plots, suggesting that establishing sown meadows does not preclude further locally determined grassland development if management is appropriate. Colonizing species were rarer in taller and more diverse plots, indicating competition may limit invasion rates. Urban meadow treatments contained invertebrate and microbial communities that differed from mown grassland. Invertebrate taxa responded to changes in both height and richness of meadow vegetation, but most orders were more abundant where vegetation height was longer than mown grassland. Order richness also increased in longer vegetation and Coleoptera family richness increased with plant diversity in summer. Microbial community composition seems sensitive to plant species composition at the soil surface (0-10 cm), but in deeper soils (11-20 cm) community variation was most responsive to plant height, with bacteria and fungi responding differently. In addition to improving local residents' site satisfaction, native perennial meadow plantings can produce biologically diverse grasslands that support richer and more abundant invertebrate communities, and restructured plant, invertebrate, and soil microbial communities compared with short mown grassland. Our results suggest that diversification of urban greenspace by planting urban meadows in place of some mown amenity grassland is likely to generate substantial biodiversity benefits, with a mosaic of meadow types likely to maximize such benefits.

Extreme rainfall affects assembly of the root-associated fungal community

Global warming is resulting in increased frequency of weather extremes. Root-associated fungi play important roles in terrestrial biogeochemical cycling processes, but the way in which they are affected by extreme weather is unclear. Here, we performed long-term field monitoring of the root-associated fungus community of a short rotation coppice willow plantation, and compared community dynamics before and after a once in 100 yr rainfall event that occurred in the UK in 2012. Monitoring of the root-associated fungi was performed over a 3-yr period by metabarcoding the fungal internal transcribed spacer (ITS) region. Repeated soil testing and continuous climatic monitoring supplemented community data, and the relative effects of environmental and temporal variation were determined on the root-associated fungal community. Soil saturation and surface water were recorded throughout the early growing season of 2012, following extreme rainfall. This was associated with a crash in the richness and relative abundance of ectomycorrhizal fungi, with each declining by over 50%. Richness and relative abundance of saprophytes and pathogens increased. We conclude that extreme rainfall events may be important yet overlooked determinants of root-associated fungal community assembly. Given the integral role of ectomycorrhizal fungi in biogeochemical cycles, these events may have considerable impacts upon the functioning of terrestrial ecosystems.

Plant Rhizosphere Selection of Plasmodiophorid Lineages from Bulk Soil: The Importance of "Hidden" Diversity

Microbial communities closely associated with the rhizosphere can have strong positive and negative impacts on plant health and growth. We used a group-specific amplicon approach to investigate local scale drivers in the diversity and distribution of plasmodiophorids in rhizosphere/root and bulk soil samples from oilseed rape (OSR) and wheat agri-systems. Plasmodiophorids are plant- and stramenopile-associated protists including well known plant pathogens as well as symptomless endobiotic species. We detected 28 plasmodiophorid lineages (OTUs), many of them novel, and showed that plasmodiophorid communities were highly dissimilar and significantly divergent between wheat and OSR rhizospheres and between rhizosphere and bulk soil samples. Bulk soil communities were not significantly different between OSR and wheat systems. Wheat and OSR rhizospheres selected for different plasmodiophorid lineages. An OTU corresponding to Spongospora nasturtii was positively selected in the OSR rhizosphere, as were two genetically distinct OTUs. Two novel lineages related to Sorosphaerula veronicae were significantly associated with wheat rhizosphere samples, indicating unknown plant-protist relationships. We show that group-targeted eDNA approaches to microbial symbiont-host ecology reveal significant novel diversity and enable inference of differential activity and potential interactions between sequence types, as well as their presence.

Converting highly productive arable cropland in Europe to grassland: -a poor candidate for carbon sequestration

Sequestration of atmospheric CO2 as organic carbon by agricultural soils (SOC) is promoted as a climate change mitigation option. IPCC provides guidelines for determining carbon stocks and sequestration potential, incentivising policy changes towards management of farmland for carbon sequestration. However, the basis of the assumption that agricultural soils can sequester significant atmospheric CO2 has been questioned. We sought to determine the potential for conversion of arable cropland to grassland to sequester carbon in the short to medium term and potential limiting factors. There were no differences in SOC stocks in the top 30 cm between grassland up to 17 years old and arable cropland at 14 sites across the UK. However, SOC showed different distribution patterns, being concentrated in the top 10 cm under grassland. Soil microbial communities were significantly different between arable and grassland, with higher biomass and lesser dominance by bacteria in grassland soils. A land use conversion experiment showed these changes occurred within one year of land use change. Failure of grassland soils to accumulate SOC was attributed to reduced available soil nitrogen, resulting in low productivity. The implications of these results for carbon sequestration in soils as a climate change mitigation strategy are discussed.

The 'known' genetic potential for microbial communities to degrade organic phosphorus is reduced in low-pH soils

In soil, bioavailable inorganic orthophosphate is found at low concentrations and thus limits biological growth. To overcome this phosphorus scarcity, plants and bacteria secrete numerous enzymes, namely acid and alkaline phosphatases, which cleave orthophosphate from various organic phosphorus substrates. Using profile hidden Markov modeling approaches, we investigated the abundance of various non specific phosphatases, both acid and alkaline, in metagenomes retrieved from soils with contrasting pH regimes. This analysis uncovered a marked reduction in the abundance and diversity of various alkaline phosphatases in low-pH soils that was not counterbalanced by an increase in acid phosphatases. Furthermore, it was also discovered that only half of the bacterial strains from different phyla deposited in the Integrated Microbial Genomes database harbor alkaline phosphatases. Taken together, our data suggests that these 'phosphatase lacking' isolates likely increase in low-pH soils and future research should ascertain how these bacteria overcome phosphorus scarcity.

Identification of extracellular glycerophosphodiesterases in Pseudomonas and their role in soil organic phosphorus remineralisation

In soils, phosphorus (P) exists in numerous organic and inorganic forms. However, plants can only acquire inorganic orthophosphate (Pi), meaning global crop production is frequently limited by P availability. To overcome this problem, rock phosphate fertilisers are heavily applied, often with negative environmental and socio-economic consequences. The organic P fraction of soil contains phospholipids that are rapidly degraded resulting in the release of bioavailable Pi. However, the mechanisms behind this process remain unknown. We identified and experimentally confirmed the function of two secreted glycerolphosphodiesterases, GlpQI and GlpQII, found in Pseudomonas stutzeri DSM4166 and Pseudomonas fluorescens SBW25, respectively. A series of co-cultivation experiments revealed that in these Pseudomonas strains, cleavage of glycerolphosphorylcholine and its breakdown product G3P occurs extracellularly allowing other bacteria to benefit from this metabolism. Analyses of metagenomic and metatranscriptomic datasets revealed that this trait is widespread among soil bacteria with Actinobacteria and Proteobacteria, specifically Betaproteobacteria and Gammaproteobacteria, the likely major players.

Spatial and temporal variability in the potential of river water biofilms to degrade p-nitrophenol

In order to predict the fate of chemicals in the environment, a range of regulatory tests are performed with microbial inocula collected from environmental compartments to investigate the potential for biodegradation. The abundance and distribution of microbes in the environment is affected by a range of variables, hence diversity and biomass of inocula used in biodegradation tests can be highly variable in space and time. The use of artificial or natural biofilms in regulatory tests could enable more consistent microbial communities be used as inocula, in order to increase test consistency. We investigated spatial and temporal variation in composition, biomass and chemical biodegradation potential of bacterial biofilms formed in river water. Sampling time and sampling location impacted the capacity of biofilms to degrade p-nitrophenol (PNP). Biofilm bacterial community structure varied across sampling times, but was not affected by sampling location. Degradation of PNP was associated with increased relative abundance of Pseudomonas syringae. Partitioning of the bacterial metacommunity into core and satellite taxa revealed that the P. syringae could be either a satellite or core member of the community across sampling times, but this had no impact on PNP degradation. Quantitative PCR analysis of the pnpA gene showed that it was present in all samples irrespective of their ability to degrade PNP. River biofilms showed seasonal variation in biomass, microbial community composition and PNP biodegradation potential, which resulted in inconsistent biodegradation test results. We discuss the results in the context of the mechanisms underlying variation in regulatory chemical degradation tests.

Comparative genomic, proteomic and exoproteomic analyses of three Pseudomonas strains reveals novel insights into the phosphorus scavenging capabilities of soil bacteria

Bacteria that inhabit the rhizosphere of agricultural crops can have a beneficial effect on crop growth. One such mechanism is the microbial-driven solubilization and remineralization of complex forms of phosphorus (P). It is known that bacteria secrete various phosphatases in response to low P conditions. However, our understanding of their global proteomic response to P stress is limited. Here, exoproteomic analysis of Pseudomonas putida BIRD-1 (BIRD-1), Pseudomonas fluorescens SBW25 and Pseudomonas stutzeri DSM4166 was performed in unison with whole-cell proteomic analysis of BIRD-1 grown under phosphate (Pi) replete and Pi deplete conditions. Comparative exoproteomics revealed marked heterogeneity in the exoproteomes of each Pseudomonas strain in response to Pi depletion. In addition to well-characterized members of the PHO regulon such as alkaline phosphatases, several proteins, previously not associated with the response to Pi depletion, were also identified. These included putative nucleases, phosphotriesterases, putative phosphonate transporters and outer membrane proteins. Moreover, in BIRD-1, mutagenesis of the master regulator, phoBR, led us to confirm the addition of several novel PHO-dependent proteins. Our data expands knowledge of the Pseudomonas PHO regulon, including species that are frequently used as bioinoculants, opening up the potential for more efficient and complete use of soil complexed P.

Spatio-Temporal Variation of Core and Satellite Arbuscular Mycorrhizal Fungus Communities in Miscanthus giganteus

Arbuscular mycorrhizal fungi (AMF) are a group of obligate plant symbionts which can promote plant nutrition. AMF communities are diverse, but the factors which control their assembly in space and time remain unclear. In this study, the contributions of geographical distance, environmental heterogeneity and time in shaping AMF communities associated with Miscanthus giganteus (a perennial grass originating from south-east Asia) were determined over a 13 months period. In particular, the community was partitioned into core (abundant and persistent taxa) and satellite (taxa with low abundance and persistence) constituents and the drivers of community assembly for each determined. β-diversity was exceptionally low across the 140 m line transects, and there was limited evidence of geographical scaling effects on the composition of the core, satellite or combined communities. However, AMF richness and community composition changed over time associated with fluctuation within both the core and satellite communities. The degree to which AMF community variation was explained by soil properties was consistently higher in the core community than the combined and satellite communities, suggesting that the satellite community had considerable stochasticity associated with it. We suggest that the partitioning of communities into their core and satellite constituents could be employed to enhance the variation explained within microbial community analyses.

Temporally Variable Geographical Distance Effects Contribute to the Assembly of Root-Associated Fungal Communities

Root-associated fungi are key contributors to ecosystem functioning, however, the factors which determine community assembly are still relatively poorly understood. This study simultaneously quantified the roles of geographical distance, environmental heterogeneity and time in determining root-associated fungal community composition at the local scale within a short rotation coppice (SRC) willow plantation. Culture independent molecular analyses of the root-associated fungal community suggested a strong but temporally variable effect of geographical distance among fungal communities in terms of composition at the local geographical level. Whilst these distance effects were most prevalent on October communities, soil pH had an effect on structuring of the communities throughout the sampling period. Given the temporal variation in the effects of geographical distance and the environment for shaping root-associated fungal communities, there is clearly need for a temporal component to sampling strategies in future investigations of fungal ecology.

Evidence for functional redundancy in arbuscular mycorrhizal fungi and implications for agroecosystem management

Arbuscular mycorrhizal (AM) fungi provide benefits to host plants and show functional diversity, with evidence of functional trait conservation at the family level. Diverse communities of AM fungi ought therefore to provide increased benefits to the host, with implications for the management of sustainable agroecosystems. However, this is often not evident in the literature, with diversity saturation at low species number. Growth and nutrient uptake were measured in onions in the glasshouse on AM-free phosphorus (P)-poor soil, inoculated with between one and seven species of AM fungi in all possible combinations. Inoculation with AM fungi increased shoot dry weight as well as P and copper concentrations in shoots but reduced the concentration of potassium and sulphur. There was little evidence of increased benefit from high AM fungal diversity, and increasing diversity beyond three species did not result in significantly higher shoot weight or P or Cu concentrations. Species of Glomeraceae had the greatest impact on growth and nutrient uptake, while species of Acaulospora and Racocetra did not have a significant impact. Failure to show a benefit from high AM fungal diversity in this and other studies may be the result of experimental conditions, with the benefits of AM fungal diversity only becoming apparent when the host plant is faced with multiple stress factors. Replicating the complex interactions between AM fungi, the host plant and their environment in the laboratory in order to fully understand these interactions is a major challenge to AM research.

Resistance and resilience responses of a range of soil eukaryote and bacterial taxa to fungicide application

The application of plant protection products has the potential to significantly affect soil microbial community structure and function. However, the extent to which soil microbial communities from different trophic levels exhibit resistance and resilience to such compounds remains poorly understood. The resistance and resilience responses of a range of microbial communities (bacteria, fungi, archaea, pseudomonads, and nematodes) to different concentrations of the strobilurin fungicide, azoxystrobin were studied. A significant concentration-dependent decrease, and subsequent recovery in soil dehydrogenase activity was recorded, but no significant impact on total microbial biomass was observed. Impacts on specific microbial communities were studied using small subunit (SSU) rRNA terminal restriction fragment length polymorphism (T-RFLP) profiling using soil DNA and RNA. The application of azoxystrobin significantly affected fungal and nematode community structure and diversity but had no impact on other communities. Community impacts were more pronounced in the RNA-derived T-RFLP profiles than in the DNA-derived profiles. qPCR confirmed that azoxystrobin application significantly reduced fungal, but not bacterial, SSU rRNA gene copy number. Azoxystrobin application reduced the prevalence of ascomycete fungi, but increased the relative abundance of zygomycetes. Azoxystrobin amendment also reduced the relative abundance of nematodes in the order Enoplia, but stimulated a large increase in the relative abundance of nematodes from the order Araeolaimida.

Root traits and microbial community interactions in relation to phosphorus availability and acquisition, with particular reference to Brassica

Brassicas are among the most widely grown and important crops worldwide. Phosphorus (P) is a key mineral element in the growth of all plants and is largely supplied as inorganic rock-phosphate, a dwindling resource, which is likely to be an increasingly significant factor in global agriculture. In order to develop crops which can abstract P from the soil, utilize it more efficiently, require less of it or obtain more from other sources such as soil organic P reservoirs, a detailed understanding the factors that influence P metabolism and cycling in plants and associated soil is required. This review focuses on the current state of understanding of root traits, rhizodeposition and rhizosphere community interaction as it applies to P solubilization and acquisition, with particular reference to Brassica species. Physical root characteristics, exudation of organic acids (particularly malate and citrate) and phosphatase enzymes are considered and the potential mechanisms of control of these responses to P deficiency examined. The influence of rhizodeposits on the development of the rhizosphere microbial community is discussed and the specific features of this community in response to P deficiency are considered; specifically production of phosphatases, phytases and phosphonate hydrolases. Finally various potential approaches for improving overall P use efficiency in Brassica production are discussed.

Distribution and diversity of Paraglomus spp. in tilled agricultural soils

Understanding of the ecology of arbuscular mycorrhizal fungi comes primarily from the order Glomerales, and relatively little is known of the ecology of other orders including the Paraglomerales. We investigated the distribution of the Paraglomerales across the English agricultural landscape under different management systems. Soils were collected from 11 tilled agricultural sites. Presence of Paraglomerales was assessed using PCR amplification of 18S/ITS region ribosomal DNA isolated from trap plants, terminal restriction fragment length polymorphism and cloning. Paraglomus spp. were detected in all samples from one location and sporadically in six more, but not at the other locations. Distribution was not related to soil physiochemical characteristics, but the Paraglomaceae were significantly more common in soils under organic management. Cloning of samples from three sites produced sequences closely related to Paraglomus laccatum but only distantly related to Paraglomus brasilianum and Paraglomus occultum. Individual sites had between 10 and 27 separate terminal restriction fragments (T-RFs). The large number of T-RFs reflected a significant sequence diversity in the ITS region. Paraglomerales were, therefore, widely distributed across the agricultural landscape, though with patchy distribution and low diversity. More intensive agricultural management appeared to impact negatively on Paraglomus spp.

Isolation and characterisation of azoxystrobin degrading bacteria from soil

The first strobilurin fungicides were introduced in 1996, and have since been used in a vast array of disease/plant systems worldwide. The strobilurins now consist of 16 compounds and represent the 2nd most important fungicide group worldwide with 15% of the total fungicide market share. Strobilurins are moderately persistent in soil, and some degradation products (e.g. azoxystrobin acid) have been detected as contaminants of freshwater systems. Little is currently known about the transformation processes involved in the biodegradation of strobilurins or the microbial groups involved. Using sequential soil and liquid culture enrichments, we isolated two bacterial strains which were able to degrade the most widely used strobilurin, azoxystrobin, when supplied as a sole carbon source. 16S rRNA showed that the strains showed homology to Cupriavidus sp. and Rhodanobacter sp. Both isolated strains were also able to degrade the related strobilurin compounds trifloxystrobin, pyraclostrobin, and kresoxim-methyl. An additional nitrogen source was required for degradation to occur, but the addition of a further carbon source reduced compound degradation by approximately 50%. However, (14)C radiometric analysis showed that full mineralisation of azosxystrobin to (14)CO2 was negligible for both isolates. 16S rRNA T-RFLP analysis using both DNA and RNA extracts showed that degradation of azoxystrobin in soil was associated with shifts in bacterial community structure. However, the phylotypes which proliferated during degradation could not be attributed to the isolated degraders.

Impact of black carbon on the bioaccessibility of organic contaminants in soil

The ability of carbonaceous geosorbents (CGs) such as black carbon (BC) to extensively sorb many common environmental contaminants suggests that they potentially possesses qualities useful to the sequestration of harmful xenobiotics within contaminated land. Presently, however, there is limited understanding of the implications for the bioaccessibility, mobility and environmental risk of organic contaminants while sorbed to BC in soil and sediment, in addition to the inherent toxicity of BC itself to terrestrial flora and fauna. We review both the processes involved in and factors influencing BC sorption characteristics, and ultimately consider the impacts BC will have for bioavailability/bioaccessibility, toxicity and risk assessment/remediation of contaminated land. We conclude that while the application of BC is promising, additional work on both their toxicity effects and long-term stability is required before their full potential as a remediation agent can be safely exploited.

Non-UV light influences the degradation rate of crop protection products

Crop protection products (CPPs) are subject to strict regulatory evaluation, including laboratory and field trials, prior to approval for commercial use. Laboratory tests lack environmental realism, while field trials are difficult to control. Addition of environmental complexity to laboratory systems is therefore desirable to mimic a field environment more effectively. We investigated the effect of non-UV light on the degradation of eight CPPs (chlorotoluron, prometryn, cinosulfuron, imidacloprid, lufenuron, propiconazole, fludioxonil, and benzovindiflupyr) by addition of non-UV light to standard OECD 307 guidelines. Time taken for 50% degradation of benzovindiflupyr was halved from 373 to 183 days with the inclusion of light. Similarly, time taken for 90% degradation of chlorotoluron decreased from 79 to 35 days under light conditions. Significant reductions in extractable parent compound occurred under light conditions for prometryn (4%), imidacloprid (8%), and fludioxonil (24%) compared to dark controls. However, a significantly slower rate of cinosulfuron (14%) transformation was observed under light compared to dark conditions. Under light conditions, nonextractable residues were significantly higher for seven of the CPPs. Soil biological and chemical analyses suggest that light stimulates phototroph growth, which may directly and/or indirectly impact CPP degradation rates. The results of this study strongly suggest that light is an important parameter affecting CPP degradation, and inclusion of light into regulatory studies may enhance their environmental realism.

Light structures phototroph, bacterial and fungal communities at the soil surface

The upper few millimeters of soil harbour photosynthetic microbial communities that are structurally distinct from those of underlying bulk soil due to the presence of light. Previous studies in arid zones have demonstrated functional importance of these communities in reducing soil erosion, and enhancing carbon and nitrogen fixation. Despite being widely distributed, comparative understanding of the biodiversity of the soil surface and underlying soil is lacking, particularly in temperate zones. We investigated the establishment of soil surface communities on pasture soil in microcosms exposed to light or dark conditions, focusing on changes in phototroph, bacterial and fungal communities at the soil surface (0–3 mm) and bulk soil (3–12 mm) using ribosomal marker gene analyses. Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus. The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes. However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere.

Increased hyphal branching and growth of ectomycorrhizal fungus Lactarius rufus by the helper bacterium Paenibacillus sp

Paenibacillus sp. EJP73 has been previously demonstrated as a mycorrhization helper bacterium (MHB) for the Lactarius rufus-Pinus sylvestris symbiosis in both laboratory and glasshouse experiments. In the present study, the effect of Paenibacillus sp. EJP73 metabolites on L. rufus EO3 pre-symbiotic growth was tested in two agar plate-based systems. Specifically, volatile metabolites were investigated using a dual plate system, in which the presence of strain EJP73 resulted in a significant negative effect on L. rufus EO3 hyphal radial growth but enhanced hyphal branching and reduced internode distance. Soluble metabolites produced by strain EJP73 were tested on L. rufus EO3 growth in single-agar plate assays by incorporating bacterial cell-free whole or molecular weight fraction spent broth into the agar. Whole spent broth had a negative effect on hyphal growth, whereas a low molecular weight fraction (100-1,000) promoted colony radial growth. Headspace and spent broth analysis of strain EJP73 cultures revealed 2,5-diisopropylpyrazine to be the most significant component. Synthesised 2,5-diisopropylpyrazine and elevated CO2 (2,000 ppm) were tested as specific volatile metabolites in the dual plate system, but neither produced the response shown when strain EJP73 was present. Increased pre-symbiotic hyphal branching leading to increased likelihood of plant infection may be an important MHB mechanism for strain EJP73. Although the precise signal molecules could not be identified, the work suggests a number of metabolites may work synergistically to increase L. rufus root colonisation.

Impacts of biochar on bioavailability of the fungicide azoxystrobin: a comparison of the effect on biodegradation rate and toxicity to the fungal community

There is great interest in using biochar (BC) as a soil amendment to provide a long-term repository of carbon to mitigate climate change. BC can have major impacts on soil biogeochemical cycling processes, largely by the sorption and protection of organic matter from microbial turnover. Application of BC to agricultural soil could also affect the efficacy, fate and environmental impact of pesticides. In the current study we investigated the effect of BC on bioavailability of the fungicide azoxystrobin in soil. We found that application of BC had no effect on sorption or degradation of azoxystrobin, even at a rate of 2% w/w. While azoxystrobin reduced dehydrogenase activity, BC addition greatly increased dehydrogenase, although the inhibitory effect of azoxystrobin was still evident in BC amended soil. Using Terminal Restriction Fragment Length Polymorphism of fungal SSU rRNA gene ITS regions it was found that azoxystrobin altered the structure of the soil fungal community, although this effect was dampened by BC addition. BC application had minor effects on fungal community structure. We conclude that measurement of the effect of BC on pesticide bioavailability by analysis of biodegradation rate and non-target effects on fungal community structure gave contrasting conclusions.

Contrasting arbuscular mycorrhizal communities colonizing different host plants show a similar response to a soil phosphorus concentration gradient

High soil phosphorus (P) concentration is frequently shown to reduce root colonization by arbuscular mycorrhizal (AM) fungi, but the influence of P on the diversity of colonizing AM fungi is uncertain. We used terminal restriction fragment length polymorphism (T-RFLP) of 18S rDNA and cloning to assess diversity of AM fungi colonizing maize (Zea mays), soybean (Glycene max) and field violet (Viola arvensis) at three time points in one season along a P gradient of 10-280 mg l(-1) in the field. Percentage AM colonization changed between sampling time points but was not reduced by high soil P except in maize. There was no significant difference in AM diversity between sampling time points. Diversity was reduced at concentrations of P > 25 mg l(-1), particularly in maize and soybean. Both cloning and T-RFLP indicated differences between AM communities in the different host species. Host species was more important than soil P in determining the AM community, except at the highest P concentration. Our results show that the impact of soil P on the diversity of AM fungi colonizing plants was broadly similar, despite the fact that different plants contained different communities. However, subtle differences in the response of the AM community in each host were evident.

Impact of shortened crop rotation of oilseed rape on soil and rhizosphere microbial diversity in relation to yield decline

Oilseed rape (OSR) grown in monoculture shows a decline in yield relative to virgin OSR of up to 25%, but the mechanisms responsible are unknown. A long term field experiment of OSR grown in a range of rotations with wheat was used to determine whether shifts in fungal and bacterial populations of the rhizosphere and bulk soil were associated with the development of OSR yield decline. The communities of fungi and bacteria in the rhizosphere and bulk soil from the field experiment were profiled using terminal restriction fragment length polymorphism (TRFLP) and sequencing of cloned internal transcribed spacer regions and 16S rRNA genes, respectively. OSR cropping frequency had no effect on rhizosphere bacterial communities. However, the rhizosphere fungal communities from continuously grown OSR were significantly different to those from other rotations. This was due primarily to an increase in abundance of two fungi which showed 100% and 95% DNA identity to the plant pathogens Olpidium brassicae and Pyrenochaeta lycopersici, respectively. Real-time PCR confirmed that there was significantly more of these fungi in the continuously grown OSR than the other rotations. These two fungi were isolated from the field and used to inoculate OSR and Brassica oleracea grown under controlled conditions in a glasshouse to determine their effect on yield. At high doses, Olpidium brassicae reduced top growth and root biomass in seedlings and reduced branching and subsequent pod and seed production. Pyrenochaeta sp. formed lesions on the roots of seedlings, and at high doses delayed flowering and had a negative impact on seed quantity and quality.