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.

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.

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.

Imaging spectroscopy reveals the effects of topography and logging on the leaf chemistry of tropical forest canopy trees.

Logging, pervasive across the lowland tropics, affects millions of hectares of forest, yet its influence on nutrient cycling remains poorly understood. One hypothesis is that logging influences phosphorus (P) cycling, because this scarce nutrient is removed in extracted timber and eroded soil, leading to shifts in ecosystem functioning and community composition. However, testing this is challenging because P varies within landscapes as a function of geology, topography and climate. Superimposed upon these trends are compositional changes in logged forests, with species with more acquisitive traits, characterized by higher foliar P concentrations, more dominant. It is difficult to resolve these patterns using traditional field approaches alone. Here, we use airborne light detection and ranging-guided hyperspectral imagery to map foliar nutrient (i.e. P, nitrogen [N]) concentrations, calibrated using field measured traits, over 400 km2 of northeastern Borneo, including a landscape-level disturbance gradient spanning old-growth to repeatedly logged forests. The maps reveal that canopy foliar P and N concentrations decrease with elevation. These relationships were not identified using traditional field measurements of leaf and soil nutrients. After controlling for topography, canopy foliar nutrient concentrations were lower in logged forest than in old-growth areas, reflecting decreased nutrient availability. However, foliar nutrient concentrations and specific leaf area were greatest in relatively short patches in logged areas, reflecting a shift in composition to pioneer species with acquisitive traits. N:P ratio increased in logged forest, suggesting reduced soil P availability through disturbance. Through the first landscape scale assessment of how functional leaf traits change in response to logging, we find that differences from old-growth forest become more pronounced as logged forests increase in stature over time, suggesting exacerbated phosphorus limitation as forests recover.

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).

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.

Logging and soil nutrients independently explain plant trait expression in tropical forests.

Plant functional traits regulate ecosystem functions but little is known about how co-occurring gradients of land use and edaphic conditions influence their expression. We test how gradients of logging disturbance and soil properties relate to community-weighted mean traits in logged and old-growth tropical forests in Borneo. We studied 32 physical, chemical and physiological traits from 284 tree species in eight 1 ha plots and measured long-term soil nutrient supplies and plant-available nutrients. Logged plots had greater values for traits that drive carbon capture and growth, whilst old-growth forests had greater values for structural and persistence traits. Although disturbance was the primary driver of trait expression, soil nutrients explained a statistically independent axis of variation linked to leaf size and nutrient concentration. Soil characteristics influenced trait expression via nutrient availability, nutrient pools, and pH. Our finding, that traits have dissimilar responses to land use and soil resource availability, provides robust evidence for the need to consider the abiotic context of logging when predicting plant functional diversity across human-modified tropical forests. The detection of two independent axes was facilitated by the measurement of many more functional traits than have been examined in previous studies.

Canopy structure and topography jointly constrain the microclimate of human-modified tropical landscapes.

Local-scale microclimatic conditions in forest understoreys play a key role in shaping the composition, diversity and function of these ecosystems. Consequently, understanding what drives variation in forest microclimate is critical to forecasting ecosystem responses to global change, particularly in the tropics where many species already operate close to their thermal limits and rapid land-use transformation is profoundly altering local environments. Yet our ability to characterize forest microclimate at ecologically meaningful scales remains limited, as understorey conditions cannot be directly measured from outside the canopy. To address this challenge, we established a network of microclimate sensors across a land-use intensity gradient spanning from old-growth forests to oil-palm plantations in Borneo. We then combined these observations with high-resolution airborne laser scanning data to characterize how topography and canopy structure shape variation in microclimate both locally and across the landscape. In the processes, we generated high-resolution microclimate surfaces spanning over 350 km2 , which we used to explore the potential impacts of habitat degradation on forest regeneration under both current and future climate scenarios. We found that topography and vegetation structure were strong predictors of local microclimate, with elevation and terrain curvature primarily constraining daily mean temperatures and vapour pressure deficit (VPD), whereas canopy height had a clear dampening effect on microclimate extremes. This buffering effect was particularly pronounced on wind-exposed slopes but tended to saturate once canopy height exceeded 20 m-suggesting that despite intensive logging, secondary forests remain largely thermally buffered. Nonetheless, at a landscape-scale microclimate was highly heterogeneous, with maximum daily temperatures ranging between 24.2 and 37.2°C and VPD spanning two orders of magnitude. Based on this, we estimate that by the end of the century forest regeneration could be hampered in degraded secondary forests that characterize much of Borneo's lowlands if temperatures continue to rise following projected trends.

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.

Land use not litter quality is a stronger driver of decomposition in hyperdiverse tropical forest.

In hyperdiverse tropical forests, the key drivers of litter decomposition are poorly understood despite its crucial role in facilitating nutrient availability for plants and microbes. Selective logging is a pressing land use with potential for considerable impacts on plant-soil interactions, litter decomposition, and nutrient cycling. Here, in Borneo's tropical rainforests, we test the hypothesis that decomposition is driven by litter quality and that there is a significant "home-field advantage," that is positive interaction between local litter quality and land use. We determined mass loss of leaf litter, collected from selectively logged and old-growth forest, in a fully factorial experimental design, using meshes that either allowed or precluded access by mesofauna. We measured leaf litter chemical composition before and after the experiment. Key soil chemical and biological properties and microclimatic conditions were measured as land-use descriptors. We found that despite substantial differences in litter quality, the main driver of decomposition was land-use type. Whilst inclusion of mesofauna accelerated decomposition, their effect was independent of land use and litter quality. Decomposition of all litters was slower in selectively logged forest than in old-growth forest. However, there was significantly greater loss of nutrients from litter, especially phosphorus, in selectively logged forest. The analyses of several covariates detected minor microclimatic differences between land-use types but no alterations in soil chemical properties or free-living microbial composition. These results demonstrate that selective logging can significantly reduce litter decomposition in tropical rainforest with no evidence of a home-field advantage. We show that loss of key limiting nutrients from litter (P & N) is greater in selectively logged forest. Overall, the findings hint at subtle differences in microclimate overriding litter quality that result in reduced decomposition rates in selectively logged forests and potentially affect biogeochemical nutrient cycling in the long term.

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.