The potential to increase grassland soil C stocks by extending reseeding intervals is dependent on soil texture and depth.

Grasslands account for ∼30% of global terrestrial carbon (C), of which most is stored in soils and provide important ecosystem services including livestock and forage production. Reseeding of temporary grasslands on a 5-year cycle is a common management practice to rejuvenate sward productivity and reduce soil compaction, but is physically disruptive and may reduce soil organic carbon (SOC) stocks. However, research to date is limited, which impacts on the ability to optimise grassland management for climate change mitigation. To determine whether extending the time interval up to 20 years between grassland reseeding can increase stable SOC stocks, a soil survey was conducted across three UK grassland chrono-sequences comprising 24 fields on contrasting soil types. We found that grassland SOC stocks (39.8-114.8 Mg C ha-1) were higher than co-located fields in arable rotations (29.3-83.2 Mg C ha-1) and the relationship with grassland age followed a curvilinear relationship with rapid SOC stock accumulation in the year following reseeding (2.69-18.3 Mg C ha-1 yr-1) followed by progressively slower SOC accumulation up to 20 years. Contrary to expectation, all grasslands had similar soil bulk densities and sward composition questioning the need for traditional 5-year reseeding cycles. Fractionation of soils into stable mineral associated fractions revealed that coarse textured grassland topsoils (0-15 cm) were near-saturated in C irrespective of grassland age whilst loam soils reached saturation ∼10 years after reseeding. Fine-textured topsoils and subsoils (15-30 cm) of all textures were under saturated and thus appear to hold the most potential to accrue additional stable C. However, the lack of a relationship between C saturation deficit and grassland age in subsoils suggests that more innovative management to promote SOC redistribution to depth, such as a switch to diverse leys or full inversion tillage may be required to maximise subsoil SOC stocks. Taken together our findings suggest that extending the time between grassland reseeding could temporarily increase SOC stocks without compromising sward composition or soil structure. However, detailed monitoring of the trade-offs with grassland productivity are required. Fine textured soils and subsoils (15-30 cm) have the greatest potential to accrue additional stable C due to under saturation of fine mineral pools.

Interactions between climate warming and land management regulate greenhouse gas fluxes in a temperate grassland ecosystem.

Greenhouse gas (GHG) fluxes from grasslands are affected by climate warming and agricultural management practices including nitrogen (N) fertiliser application and grazing. However, the interactive effects of these factors are poorly resolved in field studies. We used a factorial in situ experiment - combining warming, N-fertiliser and above-ground cutting treatments - to explore their individual and interactive effects on plant-soil properties and GHG fluxes in a temperate UK grassland over two years. Our results showed no interactive treatment effects on plant productivity despite individual effects of N-fertiliser and warming on above- and below-ground biomass. There were, however, interactive treatment effects on GHG fluxes that varied across the two years. In year 1, warming and N-fertiliser increased CO2 and reduced N2O fluxes. N-fertilised also interacted with above-ground biomass (AGB) removal increasing N2O fluxes in year one and reducing CO2 fluxes in year two. The grassland was consistently a sink of CH4; N-fertilised increased the sink by 45% (year 1), AGB removal and warming reduced CH4 consumption by 44% and 43%, respectively (year 2). The majority of the variance in CO2 fluxes was explained by above-ground metrics (grassland productivity and leaf dry matter content), with microclimate (air and soil temperature and soil moisture) and below-ground (root N content) metrics also significant. Soil chemistry (soil mineral N and net mineralisation rate), below-ground (specific root length) and microclimate (soil moisture) metrics explained 49% and 24% of the variance in N2O and CH4 fluxes, respectively. Overall, our work demonstrates the importance of interactions between climate and management as determinants of short-term grassland GHG fluxes. These results show that reduced cutting combined with lower inorganic N-fertilisers would constrain grassland C and N cycling and GHG fluxes in warmer climatic conditions. This has implications for strategic grassland management decisions to mitigate GHG fluxes in a warming world.

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.

Isoprene-degrading bacteria associated with the phyllosphere of Salix fragilis, a high isoprene-emitting willow of the Northern Hemisphere.

BACKGROUND: Isoprene accounts for about half of total biogenic volatile organic compound emissions globally, and as a climate active gas it plays a significant and varied role in atmospheric chemistry. Terrestrial plants are the largest source of isoprene, with willow (Salix) making up one of the most active groups of isoprene producing trees. Bacteria act as a biological sink for isoprene and those bacteria associated with high isoprene-emitting trees may provide further insight into its biodegradation. RESULTS: A DNA-SIP experiment incubating willow (Salix fragilis) leaves with 13C-labelled isoprene revealed an abundance of Comamonadaceae, Methylobacterium, Mycobacterium and Polaromonas in the isoprene degrading community when analysed by 16S rRNA gene amplicon sequencing. Metagenomic analysis of 13C-enriched samples confirmed the abundance of Comamonadaceae, Acidovorax, Polaromonas, Variovorax and Ramlibacter. Mycobacterium and Methylobacterium were also identified after metagenomic analysis and a Mycobacterium metagenome-assembled genome (MAG) was recovered. This contained two complete isoprene degradation metabolic gene clusters, along with a propane monooxygenase gene cluster. Analysis of the abundance of the alpha subunit of the isoprene monooxygenase, isoA, in unenriched DNA samples revealed that isoprene degraders associated with willow leaves are abundant, making up nearly 0.2% of the natural bacterial community. CONCLUSIONS: Analysis of the isoprene degrading community associated with willow leaves using DNA-SIP and focused metagenomics techniques enabled recovery of the genome of an active isoprene-degrading Mycobacterium species and provided valuable insight into bacteria involved in degradation of isoprene on the leaves of a key species of isoprene-emitting tree in the northern hemisphere.

Diurnal variability in soil nitrous oxide emissions is a widespread phenomenon.

Manual measurements of nitrous oxide (N2 O) emissions with static chambers are commonly practised. However, they generally do not consider the diurnal variability of N2 O flux, and little is known about the patterns and drivers of such variability. We systematically reviewed and analysed 286 diurnal data sets of N2 O fluxes from published literature to (i) assess the prevalence and timing (day or night peaking) of diurnal N2 O flux patterns in agricultural and forest soils, (ii) examine the relationship between N2 O flux and soil temperature with different diurnal patterns, (iii) identify whether non-diurnal factors (i.e. land management and soil properties) influence the occurrence of diurnal patterns and (iv) evaluate the accuracy of estimating cumulative N2 O emissions with single-daily flux measurements. Our synthesis demonstrates that diurnal N2 O flux variability is a widespread phenomenon in agricultural and forest soils. Of the 286 data sets analysed, ~80% exhibited diurnal N2 O patterns, with ~60% peaking during the day and ~20% at night. Contrary to many published observations, our analysis only found strong positive correlations (R > 0.7) between N2 O flux and soil temperature in one-third of the data sets. Soil drainage property, soil water-filled pore space (WFPS) level and land use were also found to potentially influence the occurrence of certain diurnal patterns. Our work demonstrated that single-daily flux measurements at mid-morning yielded daily emission estimates with the smallest average bias compared to measurements made at other times of day, however, it could still lead to significant over- or underestimation due to inconsistent diurnal N2 O patterns. This inconsistency also reflects the inaccuracy of using soil temperature to predict the time of daily average N2 O flux. Future research should investigate the relationship between N2 O flux and other diurnal parameters, such as photosynthetically active radiation (PAR) and root exudation, along with the consideration of the effects of soil moisture, drainage and land use on the diurnal patterns of N2 O flux. The information could be incorporated in N2 O emission prediction models to improve accuracy.

The importance of nitrogen for net carbon sequestration when considering natural climate solutions.

To store substantial amounts of carbon in natural climate solutions the strong interlinkages between carbon and nitrogen cycling must be considered. There are many agricultural management options for increasing soil organic carbon stocks but each approach must be evaluated in context of the full, net greenhouse gas balance. This requires a detailed understanding of the implications of increased nitrogen demand to store organic forms of carbon in soil, on potential nitrous oxide emissions in particular.

Diversity of isoprene-degrading bacteria in phyllosphere and soil communities from a high isoprene-emitting environment: a Malaysian oil palm plantation.

BACKGROUND: Isoprene is the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, with annual global emissions almost equal to those of methane. Despite its importance in atmospheric chemistry and climate, little is known about the biological degradation of isoprene in the environment. The largest source of isoprene is terrestrial plants, and oil palms, the cultivation of which is expanding rapidly, are among the highest isoprene-producing trees. RESULTS: DNA stable isotope probing (DNA-SIP) to study the microbial isoprene-degrading community associated with oil palm trees revealed novel genera of isoprene-utilising bacteria including Novosphingobium, Pelomonas, Rhodoblastus, Sphingomonas and Zoogloea in both oil palm soils and on leaves. Amplicon sequencing of isoA genes, which encode the α-subunit of the isoprene monooxygenase (IsoMO), a key enzyme in isoprene metabolism, confirmed that oil palm trees harbour a novel diversity of isoA sequences. In addition, metagenome-assembled genomes (MAGs) were reconstructed from oil palm soil and leaf metagenomes and putative isoprene degradation genes were identified. Analysis of unenriched metagenomes showed that isoA-containing bacteria are more abundant in soils than in the oil palm phyllosphere. CONCLUSION: This study greatly expands the known diversity of bacteria that can metabolise isoprene and contributes to a better understanding of the biological degradation of this important but neglected climate-active gas. Video abstract.

Changes in soil organic carbon under perennial crops.

This study evaluates the dynamics of soil organic carbon (SOC) under perennial crops across the globe. It quantifies the effect of change from annual to perennial crops and the subsequent temporal changes in SOC stocks during the perennial crop cycle. It also presents an empirical model to estimate changes in the SOC content under crops as a function of time, land use, and site characteristics. We used a harmonized global dataset containing paired-comparison empirical values of SOC and different types of perennial crops (perennial grasses, palms, and woody plants) with different end uses: bioenergy, food, other bio-products, and short rotation coppice. Salient outcomes include: a 20-year period encompassing a change from annual to perennial crops led to an average 20% increase in SOC at 0-30 cm (6.0 ± 4.6 Mg/ha gain) and a total 10% increase over the 0-100 cm soil profile (5.7 ± 10.9 Mg/ha). A change from natural pasture to perennial crop decreased SOC stocks by 1% over 0-30 cm (-2.5 ± 4.2 Mg/ha) and 10% over 0-100 cm (-13.6 ± 8.9 Mg/ha). The effect of a land use change from forest to perennial crops did not show significant impacts, probably due to the limited number of plots; but the data indicated that while a 2% increase in SOC was observed at 0-30 cm (16.81 ± 55.1 Mg/ha), a decrease in 24% was observed at 30-100 cm (-40.1 ± 16.8 Mg/ha). Perennial crops generally accumulate SOC through time, especially woody crops; and temperature was the main driver explaining differences in SOC dynamics, followed by crop age, soil bulk density, clay content, and depth. We present empirical evidence showing that the FAO perennialization strategy is reasonable, underscoring the role of perennial crops as a useful component of climate change mitigation strategies.

Influence of temperature on the δ13 C values and distribution of methanotroph-related hopanoids in Sphagnum-dominated peat bogs.

Methane emissions from peat bogs are mitigated by methanotrophs, which live in symbiosis with peat moss (e.g. Sphagnum). Here, we investigate the influence of temperature and resultant changes in methane fluxes on Sphagnum and methanotroph-related biomarkers, evaluating their potential as proxies in ancient bogs. A pulse-chase experiment using 13 C-labelled methane in the field clearly showed label uptake in diploptene, a biomarker for methanotrophs, demonstrating in situ methanotrophic activity in Sphagnum under natural conditions. Peat cores containing live Sphagnum were incubated at 5, 10, 15, 20 and 25°C for two months, causing differences in net methane fluxes. The natural δ13 C values of diploptene extracted from Sphagnum showed a strong correlation with temperature and methane production. The δ13 C values ranged from -34‰ at 5°C to -41‰ at 25°C. These results are best explained by enhanced expression of the methanotrophic enzymatic isotope effect at higher methane concentrations. Hence, δ13 C values of diploptene, or its diagenetic products, potentially provide a useful tool to assess methanotrophic activity in past environments. Increased methane fluxes towards Sphagnum did not affect δ13 C values of bulk Sphagnum and its specific marker, the C23 n-alkane. The concentration of methanotroph-specific bacteriohopanepolyols (BHPs), aminobacteriohopanetetrol (aminotetrol, characteristic for type II and to a lesser extent type I methanotrophs) and aminobacteriohopanepentol (aminopentol, a marker for type I methanotrophs) showed a non-linear response to increased methane fluxes, with relatively high abundances at 25°C compared to those at 20°C or below. Aminotetrol was more abundant than aminopentol, in contrast to similar abundances of aminotetrol and aminopentol in fresh Sphagnum. This probably indicates that type II methanotrophs became prevalent under the experimental conditions relative to type I methanotrophs. Even though BHP concentrations may not directly reflect bacterial activity, they may provide insight into the presence of different types of methanotrophs.

Soil & Water Assessment Tool (SWAT) simulated hydrological impacts of land use change from temperate grassland to energy crops: A case study in western UK.

When considering the large-scale deployment of bioenergy crops, it is important to understand the implication for ecosystem hydrological processes and the influences of crop type and location. Based on the potential for future land use change (LUC), the 10,280 km2 West Wales Water Framework Directive River Basin District (UK) was selected as a typical grassland dominated district, and the Soil & Water Assessment Tool (SWAT) hydrology model with a geographic information systems interface was used to investigate implications for different bioenergy deployment scenarios. The study area was delineated into 855 sub-basins and 7,108 hydrological response units based on rivers, soil type, land use, and slope. Changes in hydrological components for two bioenergy crops (Miscanthus and short rotation coppice, SRC) planted on 50% (2,192 km2) or 25% (1,096 km2) of existing improved pasture are quantified. Across the study area as a whole, only surface run-off with SRC planted at the 50% level was significantly impacted, where it was reduced by up to 23% (during April). However, results varied spatially and a comparison of annual means for each sub-basin and scenario revealed surface run-off was significantly decreased and baseflow significantly increased (by a maximum of 40%) with both Miscanthus and SRC. Evapotranspiration was significantly increased with SRC (at both planting levels) and water yield was significantly reduced with SRC (at the 50% level) by up to 5%. Effects on streamflow were limited, varying between -5% and +5% change (compared to baseline) in the majority of sub-basins. The results suggest that for mesic temperate grasslands, adverse effects from the drying of soil and alterations to streamflow may not arise, and with surface run-off reduced and baseflow increased, there could, depending on crop location, be potential benefits for flood and erosion mitigation.

Measured and modelled effect of land-use change from temperate grassland to Miscanthus on soil carbon stocks after 12 years.

Soil organic carbon (SOC) is an important carbon pool susceptible to land-use change (LUC). There are concerns that converting grasslands into the C4 bioenergy crop Miscanthus (to meet demands for renewable energy) could negatively impact SOC, resulting in reductions of greenhouse gas mitigation benefits gained from using Miscanthus as a fuel. This work addresses these concerns by sampling soils (0-30 cm) from a site 12 years (T12) after conversion from marginal agricultural grassland into Miscanthus x giganteus and four other novel Miscanthus hybrids. Soil samples were analysed for changes in below-ground biomass, SOC and Miscanthus contribution to SOC (using a 13C natural abundance approach). Findings are compared to ECOSSE soil carbon model results (run for a LUC from grassland to Miscanthus scenario and continued grassland counterfactual), and wider implications are considered in the context of life cycle assessments based on the heating value of the dry matter (DM) feedstock. The mean T12 SOC stock at the site was 8 (±1 standard error) Mg C/ha lower than baseline time zero stocks (T0), with assessment of the five individual hybrids showing that while all had lower SOC stock than at T0 the difference was only significant for a single hybrid. Over the longer term, new Miscanthus C4 carbon replaces pre-existing C3 carbon, though not at a high enough rate to completely offset losses by the end of year 12. At the end of simulated crop lifetime (15 years), the difference in SOC stocks between the two scenarios was 4 Mg C/ha (5 g CO2-eq/MJ). Including modelled LUC-induced SOC loss, along with carbon costs relating to soil nitrous oxide emissions, doubled the greenhouse gas intensity of Miscanthus to give a total global warming potential of 10 g CO2-eq/MJ (180 kg CO2-eq/Mg DM).

Microbial responses to warming enhance soil carbon loss following translocation across a tropical forest elevation gradient.

Tropical soils contain huge carbon stocks, which climate warming is projected to reduce by stimulating organic matter decomposition, creating a positive feedback that will promote further warming. Models predict that the loss of carbon from warming soils will be mediated by microbial physiology, but no empirical data are available on the response of soil carbon and microbial physiology to warming in tropical forests, which dominate the terrestrial carbon cycle. Here we show that warming caused a considerable loss of soil carbon that was enhanced by associated changes in microbial physiology. By translocating soils across a 3000 m elevation gradient in tropical forest, equivalent to a temperature change of ± 15 °C, we found that soil carbon declined over 5 years by 4% in response to each 1 °C increase in temperature. The total loss of carbon was related to its original quantity and lability, and was enhanced by changes in microbial physiology including increased microbial carbon-use-efficiency, shifts in community composition towards microbial taxa associated with warmer temperatures, and increased activity of hydrolytic enzymes. These findings suggest that microbial feedbacks will cause considerable loss of carbon from tropical forest soils in response to predicted climatic warming this century.

Zones of influence for soil organic matter dynamics: A conceptual framework for data and models.

Soil organic matter (SOM) is an indicator of sustainable land management as stated in the global indicator framework of the United Nations Sustainable Development Goals (SDG Indicator 15.3.1). Improved forecasting of future changes in SOM is needed to support the development of more sustainable land management under a changing climate. Current models fail to reproduce historical trends in SOM both within and during transition between ecosystems. More realistic spatio-temporal SOM dynamics require inclusion of the recent paradigm shift from SOM recalcitrance as an 'intrinsic property' to SOM persistence as an 'ecosystem interaction'. We present a soil profile, or pedon-explicit, ecosystem-scale framework for data and models of SOM distribution and dynamics which can better represent land use transitions. Ecosystem-scale drivers are integrated with pedon-scale processes in two zones of influence. In the upper vegetation zone, SOM is affected primarily by plant inputs (above- and belowground), climate, microbial activity and physical aggregation and is prone to destabilization. In the lower mineral matrix zone, SOM inputs from the vegetation zone are controlled primarily by mineral phase and chemical interactions, resulting in more favourable conditions for SOM persistence. Vegetation zone boundary conditions vary spatially at landscape scales (vegetation cover) and temporally at decadal scales (climate). Mineral matrix zone boundary conditions vary spatially at landscape scales (geology, topography) but change only slowly. The thicknesses of the two zones and their transport connectivity are dynamic and affected by plant cover, land use practices, climate and feedbacks from current SOM stock in each layer. Using this framework, we identify several areas where greater knowledge is needed to advance the emerging paradigm of SOM dynamics-improved representation of plant-derived carbon inputs, contributions of soil biota to SOM storage and effect of dynamic soil structure on SOM storage-and how this can be combined with robust and efficient soil monitoring.

Soil N2O emissions with different reduced tillage methods during the establishment of Miscanthus in temperate grassland.

An increase in renewable energy and the planting of perennial bioenergy crops is expected in order to meet global greenhouse gas (GHG) targets. Nitrous oxide (N2O) is a potent greenhouse gas, and this paper addresses a knowledge gap concerning soil N2O emissions over the possible "hot spot" of land use conversion from established pasture to the biofuel crop Miscanthus. The work aims to quantify the impacts of this land use change on N2O fluxes using three different cultivation methods. Three replicates of four treatments were established: Miscanthus x giganteus (Mxg) planted without tillage; Mxg planted with light tillage; a novel seed-based Miscanthus hybrid planted with light tillage under bio-degradable mulch film; and a control of uncultivated established grass pasture with sheep grazing. Soil N2O fluxes were recorded every 2 weeks using static chambers starting from preconversion in April 2016 and continuing until the end of October 2017. Monthly soil samples were also taken and analysed for nitrate and ammonium. There was no significant difference in N2O emissions between the different cultivation methods. However, in comparison with the uncultivated pasture, N2O emissions from the cultivated Miscanthus plots were 550%-819% higher in the first year (April to December 2016) and 469%-485% higher in the second year (January to October 2017). When added to an estimated carbon cost for production over a 10 year crop lifetime (including crop management, harvest, and transportation), the measured N2O conversion cost of 4.13 Mg CO2-eq./ha represents a 44% increase in emission compared to the base case. This paper clearly shows the need to incorporate N2O fluxes during Miscanthus establishment into assessments of GHG balances and life cycle analysis and provides vital knowledge needed for this process. This work therefore also helps to support policy decisions regarding the costs and benefits of land use change to Miscanthus.

Vinasse application and cessation of burning in sugarcane management can have positive impact on soil carbon stocks.

Bioenergy crops, such as sugarcane, have the potential to mitigate greenhouse gas emissions through fossil fuel substitution. However, increased sugarcane propagation and recent management changes have raised concerns that these practices may deplete soil carbon (C) stocks, thereby limiting the net greenhouse gas benefit. In this study, we use both a measured and modelled approach to evaluate the impacts of two common sugarcane management practices on soil C sequestration potential in Brazil. We explore how transitions from conventional (mineral fertiliser/burning) to improved (vinasse application/unburned) practices influence soil C stocks in total and in physically fractionated soil down to one metre. Results suggest that vinasse application leads to an accumulation of soil C of 0.55 Mg ha-1yr-1 at 0-30 cm depth and applying unburned management led to gains of ∼0.7 Mg ha-1yr-1 at 30-60 cm depth. Soil C concentration in the Silt+Clay fraction of topsoil (0-20 cm) showed higher C content in unburned management but it did not differ under vinasse application. The CENTURY model was used to simulate the consequences of management changes beyond the temporal extent of the measurements. Simulations indicated that vinasse was not the key factor driving increases in soil C stocks but its application may be the most readily available practice to prevent the soil C losses under burned management. Furthermore, cessation of burning may increase topsoil C by 40% after ∼50 years. These are the first data comparing different sugarcane management transitions within a single area. Our findings indicate that both vinasse application and the cessation of burning can play an important role in reducing the time required for sugarcane ethanol production to reach a net C benefit (payback time).

Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes.

More than 200 years ago, Alexander von Humboldt reported that tropical plant species richness decreased with increasing elevation and decreasing temperature. Surprisingly, coordinated patterns in plant, bacterial, and fungal diversity on tropical mountains have not yet been observed, despite the central role of soil microorganisms in terrestrial biogeochemistry and ecology. We studied an Andean transect traversing 3.5 km in elevation to test whether the species diversity and composition of tropical forest plants, soil bacteria, and fungi follow similar biogeographical patterns with shared environmental drivers. We found coordinated changes with elevation in all three groups: species richness declined as elevation increased, and the compositional dissimilarity among communities increased with increased separation in elevation, although changes in plant diversity were larger than in bacteria and fungi. Temperature was the dominant driver of these diversity gradients, with weak influences of edaphic properties, including soil pH. The gradients in microbial diversity were strongly correlated with the activities of enzymes involved in organic matter cycling, and were accompanied by a transition in microbial traits towards slower-growing, oligotrophic taxa at higher elevations. We provide the first evidence of coordinated temperature-driven patterns in the diversity and distribution of three major biotic groups in tropical ecosystems: soil bacteria, fungi, and plants. These findings suggest that interrelated and fundamental patterns of plant and microbial communities with shared environmental drivers occur across landscape scales. These patterns are revealed where soil pH is relatively constant, and have implications for tropical forest communities under future climate change.

Consensus, uncertainties and challenges for perennial bioenergy crops and land use.

Perennial bioenergy crops have significant potential to reduce greenhouse gas (GHG) emissions and contribute to climate change mitigation by substituting for fossil fuels; yet delivering significant GHG savings will require substantial land-use change, globally. Over the last decade, research has delivered improved understanding of the environmental benefits and risks of this transition to perennial bioenergy crops, addressing concerns that the impacts of land conversion to perennial bioenergy crops could result in increased rather than decreased GHG emissions. For policymakers to assess the most cost-effective and sustainable options for deployment and climate change mitigation, synthesis of these studies is needed to support evidence-based decision making. In 2015, a workshop was convened with researchers, policymakers and industry/business representatives from the UK, EU and internationally. Outcomes from global research on bioenergy land-use change were compared to identify areas of consensus, key uncertainties, and research priorities. Here, we discuss the strength of evidence for and against six consensus statements summarising the effects of land-use change to perennial bioenergy crops on the cycling of carbon, nitrogen and water, in the context of the whole life-cycle of bioenergy production. Our analysis suggests that the direct impacts of dedicated perennial bioenergy crops on soil carbon and nitrous oxide are increasingly well understood and are often consistent with significant life cycle GHG mitigation from bioenergy relative to conventional energy sources. We conclude that the GHG balance of perennial bioenergy crop cultivation will often be favourable, with maximum GHG savings achieved where crops are grown on soils with low carbon stocks and conservative nutrient application, accruing additional environmental benefits such as improved water quality. The analysis reported here demonstrates there is a mature and increasingly comprehensive evidence base on the environmental benefits and risks of bioenergy cultivation which can support the development of a sustainable bioenergy industry.

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.

Soil nitrous oxide flux following land-use reversion from Miscanthus and SRC willow to perennial ryegrass.

Decarbonization of the world's energy supply is essential to meet the targets of the 2016 Paris climate change agreement. One promising opportunity is the utilization of second generation, low input bioenergy crops such as Miscanthus and Short Rotation Coppice (SRC) willow. Research has previously been carried out on the greenhouse gas (GHG) balance of growing these feedstocks and land-use changes involved in converting conventional cropland to their production; however, there is almost no body of work understanding the costs associated with their end of life transitions back to conventional crops. It is likely that it is during crop interventions and land-use transitions that significant GHG fluxes might occur. Therefore, in this study, we investigated soil GHG fluxes over 82 weeks during transition from Miscanthus and SRC willow into perennial ryegrass in west Wales, UK. This study captured soil GHG fluxes at a weekly time step, alongside monthly changes in soil nitrogen and labile carbon and reports the results of regression modelling of suspected drivers. Methane fluxes were typically trivial; however, nitrous oxide (N2O) fluxes were notably affected, reverted plots produced significantly more N2O than retained controls and Miscanthus produced significantly higher fluxes overall than willow plots. N2O costs of reversion appeared to be contained within the first year of reversion when the Miscanthus plots produced an average pregrass flux of 0.13 mg N2O m-2 hr-1 while for willow, this was 0.03 mg N2O m-2 hr-1. Total N2O emission from reversion increased the carbon cost over the lifetime of the Miscanthus from 6.50 to 9.91 Mg CO2 eq. ha-1 while for the willow, this increase was from 9.61 to 10.42 Mg CO2 eq. ha-1. Despite these significant increases, the carbon cost of energy contained in these perennial crops remained far lower than the equivalent carbon cost of energy in coal.

Predicting future biomass yield in Miscanthus using the carbohydrate metabolic profile as a biomarker.

In perennial energy crop breeding programmes, it can take several years before a mature yield is reached when potential new varieties can be scored. Modern plant breeding technologies have focussed on molecular markers, but for many crop species, this technology is unavailable. Therefore, prematurity predictors of harvestable yield would accelerate the release of new varieties. Metabolic biomarkers are routinely used in medicine, but they have been largely overlooked as predictive tools in plant science. We aimed to identify biomarkers of productivity in the bioenergy crop, Miscanthus, that could be used prognostically to predict future yields. This study identified a metabolic profile reflecting productivity in Miscanthus by correlating the summer carbohydrate composition of multiple genotypes with final yield 6 months later. Consistent and strong, significant correlations were observed between carbohydrate metrics and biomass traits at two separate field sites over 2 years. Machine-learning feature selection was used to optimize carbohydrate metrics for support vector regression models, which were able to predict interyear biomass traits with a correlation (R) of >0.67 between predicted and actual values. To identify a causal basis for the relationships between the glycome profile and biomass, a 13C-labelling experiment compared carbohydrate partitioning between high- and low-yielding genotypes. A lower yielding and slower growing genotype partitioned a greater percentage of the 13C pulse into starch compared to a faster growing genotype where a greater percentage was located in the structural biomass. These results supported a link between plant performance and carbon flow through two rival pathways (starch vs. sucrose), with higher yielding plants exhibiting greater partitioning into structural biomass, via sucrose metabolism, rather than starch. Our results demonstrate that the plant metabolome can be used prognostically to anticipate future yields and this is a method that could be used to accelerate selection in perennial energy crop breeding programmes.