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Soil is one of the key elements for supporting life on Earth. It delivers multiple ecosystem services, which are provided by soil processes and functions performed by soil biodiversity. In particular, soil microbiome is one of the fundamental components in the sustainment of plant biomass production and plant health. Both targeted and untargeted management of soil microbial communities appear to be promising in the sustainable improvement of food crop yield, its nutritional quality and safety. –Omics approaches, which allow the assessment of microbial phylogenetic diversity and functional information, have increasingly been used in recent years to study changes in soil microbial diversity caused by agronomic practices and environmental factors. The application of these high-throughput technologies to the study of soil microbial diversity, plant health and the quality of derived raw materials will help strengthen the link between soil well-being, food quality, food safety and human health.

The cultivation of perennial energy crops (PECs) couples the production of ligno‐cellulosic biomass to the provision of multiple ecosystem services, such as the reduction of greenhouse gas emissions and the mitigation of climate change through carbon (C) sequestration in soil. Though C sequestration in soil by PECs has been widely studied, the contribution of their belowground biomass (BGB) to soil C sequestration and their influence on soil nitrogen (N) storage potential has received very little attention. In this study, C and N stocks in soil and BGB fractions (plant belowground organs and fine roots) were measured for six PECs (Populus spp. ‘Poplar’, Robinia pseudoacacia ‘Black locust’, Salix spp. ‘Willow’, Arundo donax ‘Giant reed’, Miscanthus × giganteus ‘Miscanthus’ and Panicum virgatum ‘Switchgrass’) grown on marginal soil, 11 years after establishment. All PECs had a higher soil organic carbon (SOC) stock and soil total nitrogen (STN) stock than arable land in the top (0–10 cm) soil layer. In this same top layer, woody crops had the highest SOC stock. The increase in SOC under PECs led to increased soil porosity in the top‐soil layer. On average, 43% of the belowground C stock of PECs was allocated in the plant belowground organs (PBO; i.e. in the rhizomes of herbaceous PECs and the stump for woody PECs). Giant reed had the highest C stock in PBO, whereas switchgrass the lowest (22.7 vs. 5.9 Mg C ha−1). On the contrary, switchgrass had the highest C stock in fine roots. Giant reed had the highest belowground C stock (sum of soil and BGB contribution) and black locust the highest belowground N stock. After 11 years of PEC cultivation, 68% of the belowground C stock was allocated in the BGB, and 32% was as SOC. Eleven years of perennial energy crops (PECs) cultivation on marginal lands lead to sequester in the first 30 cm of soil 0.48 Mg SOC ha year−1 under herbaceous PECs and of 0.50 Mg C ha year−1 under woody PECs. In the potential re‐convertible layer (0–30 cm), PECs accumulated more C in the belowground biomass (BGB) than in soil while in subsoil (30–100 cm) more C was stored in soil than in the BGB. In subsoil herbaceous PECs stored more C than woody PECs.

The cultivation of perennial biomass crops (PBCs) on marginal lands is necessary to provide feedstock for the bio-based EU economy and accrue environmental benefits through carbon (C) sequestration in soil. Short rotation coppice (SRC) species, e.g., willow, black locust, and poplar, and perennial rhizomatous grasses, e.g., miscanthus, switchgrass, and giant reed, have been tested in many EU projects in the last 10 years to investigate their productive potential and contribution to the mitigation of climate change. A major knowledge gap regarding PBCs is the fate of accumulated soil organic carbon (SOC), once PBC plantations are reverted to arable crops. In this study, the effects of PBCs reversion on SOC and carbon-dioxide emission (CO2) were monitored over a 2-year period in a long-term (11-year) multispecies trial of six PBCs: Three SRC species including poplar (Populus spp.), willow (Salix spp.), and black locust (Robinia pseudoacacia), and three herbaceous rhizomatous grasses including miscanthus (Miscanthus x giganteus), switchgrass (Panicum virgatum), and giant reed (Arundo donax). The SOC change and GHG emissions were then modeled with the ECOSSE model. Two years after the reversion, SOC increased significantly for all PBCs with no significant difference between them. During the PBC cultivation phase, 5.35 Mg SOC ha−1 was sequestered while 10.95 Mg SOC ha−1 was added by reversion, which indicated that 67% of SOC sequestration occurred after the reversion. The ECOSSE model was successfully used to simulate SOC sequestration trajectories (R2 = 0.77) and CO2 emission from soil (R2 = 0.82) after the reversion of the six PBCs. This indicated that the high SOC sequestration rate after the reversion was due to humification of belowground biomass (roots + rhizomes/stumps), which had been mulched and incorporated into the reversion layer (0–30 cm). This occurred in the first 2 months (on average 5.47 Mg SOC ha−1 y−1) and in the first year after the reversion (1.3–1.8 Mg SOC ha−1 y−1). Considering the entire PBCs cultivation cycle (13 years of PBCs + reversion), PBCs showed annual SOC sequestration rates higher than 1 Mg SOC ha−1 y−1, placing PBCs cultivation and reversion as one of the most promising agricultural practices to combine biomass production, with the recovery of marginal lands to agricultural production through increasing the SOC.

Perennial grains provide various ecosystem services compared to the annual counterparts thanks to their extensive root system and permanent soil cover. However, little is known about the evolution and diversification of perennial grains rhizosphere and its ecological functions over time. In this study, a suite of -OMICSs - metagenomics, enzymomics, metabolomics and lipidomics - was used to compare the rhizosphere environment of four perennial wheat lines at the first and fourth year of growth in comparison with an annual durum wheat cultivar and the parental species Thinopyrum intermedium . We hypothesized that wheat perenniality has a greater role in shaping the rhizobiome composition, biomass, diversity, and activity than plant genotypes because perenniality affects the quality and quantity of C input – mainly root exudates – hence modulating the plant-microbes crosstalk. In support of this hypothesis, the continuous supply of sugars in the rhizosphere along the years created a favorable environment for microbial growth which is reflected in a higher microbial biomass and enzymatic activity. Moreover, modification in the rhizosphere metabolome and lipidome over the years led to changes in the microbial community composition favoring the coexistence of more diverse microbial taxa, increasing plant tolerance to biotic and abiotic stresses. Despite the dominance of the perenniality effect, our data underlined that the OK72 line rhizobiome distinguished from the others by the increase in abundance of Pseudomonas spp., most of which are known as potential beneficial microorganisms, identifying this line as a suitable candidate for the study and selection of new perennial wheat lines.

Perennial crops have been proposed as a solution to couple the production of sustainable biomass for multiple uses with several environmental benefits such as soil C storage. Concerns exist that the C sequestered in soil could be lost in a few years after the perennial crops are reverted to arable land. In this study, the current knowledge on the effects of perennial crop reversion on soil C and N was summarized by performing a meta-analysis. One year after the reversion a significant increase of soil C and N stocks (+15% and +12% respectively) were found in the 0–30 cm layer, while in the time interval between the second to fifth year after the reversion, there were no significant increases or decreases of soil C and N. The incorporation of the belowground biomass (BGB) into the soil at reversion plays a key role in the fate of soil C and N stocks after the reversion. In fact, when reverting a multiannual biomass crop there are significant losses of soil C and N. In contrast, when reverting a perennial biomass crop (PBCs) such as rhizomatous herbaceous or SRC woody crops there are no losses of soil C and N. The BGB of perennial grass is mainly composed of root systems and not of a huge amount of belowground organs as in the case of PBCs. The shredding of the BGB and its transformation as particulate organic matter (POM) represent the major pulse C input at the reversion that can undergo further stabilization into a mineral-associated organic matter (MAOM) fraction. Introducing PBCs into crop rotation resulted in an effective carbon farming solution with a potential positive legacy for food crops in terms of achievement of both climate and soil fertility goals.

Miscanthus holds a great potential in the frame of the bioeconomy, and yield prediction can help improve Miscanthus’ logistic supply chain. Breeding programs in several countries are attempting to produce high-yielding Miscanthus hybrids better adapted to different climates and end-uses. Multispectral images acquired from unmanned aerial vehicles (UAVs) in Italy and in the UK in 2021 and 2022 were used to investigate the feasibility of high-throughput phenotyping (HTP) of novel Miscanthus hybrids for yield prediction and crop traits estimation. An intercalibration procedure was performed using simulated data from the PROSAIL model to link vegetation indices (VIs) derived from two different multispectral sensors. The random forest algorithm estimated with good accuracy yield traits (light interception, plant height, green leaf biomass, and standing biomass) using 15 VIs time series, and predicted yield using peak descriptors derived from these VIs time series with root mean square error of 2.3 Mg DM ha−1. The study demonstrates the potential of UAVs’ multispectral images in HTP applications and in yield prediction, providing important information needed to increase sustainable biomass production.

Stresses caused by drought and heavy metals (HMs) adversely affect the establishment and yield potential of Miscanthus plants. These stresses are particularly acute on lower quality ‘contaminated and marginal-lands’ less suitable for food production. In our prior research assessing drought and zinc stress tolerance across seven novel Miscanthus hybrids, a M. sacchariflorus × M. sinensis hybrid ‘GRC10’ exhibited superior stress tolerance and biomass production. This study investigated the effects of drought (D), zinc (Zn) stress, and their combination (D + Zn) on stress tolerance in the Miscanthus GRC10 using untargeted metabolomics to uncover stress tolerance mechanisms. Synchronous measurements of growth parameters, leaf gas exchange parameters, the maximum quantum yield of photosystem II (Fv/Fm), performance index (PI-ABS), antioxidant enzyme activity, proline, and malondialdehyde (MDA) production were made to elucidate associations. Both D, Zn, and combination (D + Zn) stress induced a broad metabolic reprogramming of secondary metabolism and hormone synthesis pathways. Fatty acid derivatives, nitrogen-containing compounds, hormone/signal-related compounds (jasmonate), and secondary metabolites (phenylpropanoids, N-containing compounds, and terpenes) showed significant ( p < 0.05) abundance changes in response to D, Zn, and its combination D + Zn stress. Drought, Zn, and combination D + Zn stress treatments increased proline accumulation ( p < 0.0001), antioxidant enzyme activities ( p < 0.05), including superoxide dismutase (SOD), ascorbate peroxidase (APX), glutathione reductase (GR), and decreased levels of MDA. Overall, these responses indicate that the Miscanthus GRC10 hybrid displays a complex response to drought and Zn stresses that confers growth resilience in Zn-contaminated and drought-prone lands.

Perennial rhizomatous grasses (PRG), such as miscanthus and switchgrass, are considered promising lignocellulosic feedstocks. Their cultivation is expected to experience a significant increase in the near future, as it offers a wide range of benefits. For instance, when PRG replace typical annual crops, positive biodiversity impacts are usually anticipated. However, to date, there is no solid, statistically strong evidence for this hypothesis. This study aims to evaluate its validity through a meta‐analysis based on an extensive systematic literature review of research comparing biodiversity attributes in PRG and common annual crops. Dynamics of species richness and abundance in response to PRG cultivation were quantitatively evaluated drawing on 220 paired comparisons from 25 studies. This includes data on five taxonomic groups—arthropods, birds, earthworms, mammals and plants—and three PRG—miscanthus, switchgrass and reed canary grass. The results indicate that biodiversity tends to be higher in PRG cultivations relative to the reference crops, but the initial hypothesis of significantly beneficial impacts could not be confirmed. Trends were specific to the individual taxonomic groups: significantly higher biodiversity was found for plants and small mammals. Positive but insignificant trends were observed for arthropods and birds, while earthworm response was neutral and insignificant. More substantial conclusions could not be drawn, which is mainly due to the low number of studies conducting biodiversity assessments in PRG cultivations that included a comparison with annual crops. In addition, a detailed analysis of the observed responses was impaired by poor reporting of the parameters influencing biodiversity in the studies reviewed, such as planting and crop density, as well as yields. For this reason, we conclude with a call for improved data reporting in biodiversity assessments of PRG cultivations and detail requirements for future biodiversity research. It is commonly hypothesized that the cultivation of perennial rhizomatous grasses (PRG) benefits biodiversity when replacing typical annual crops. However, to date, there is no solid, statistically strong evidence for this hypothesis. This study aimed to deliver a test of its validity. Based on a systematic literature review, a meta‐analysis was conducted. Data on species richness and abundance were extracted from 25 studies. The analysis indicated positive effects on five taxonomic groups (arthropods, birds, earthworms, mammals, plants). However, the positive effects of the cultivation of PRG were not statistically significant.

Demand for sustainably produced biomass is expected to increase with the need to provide renewable commodities, improve resource security and reduce greenhouse gas emissions in line with COP26 commitments. Studies have demonstrated additional environmental benefits of using perennial biomass crops (PBCs), when produced appropriately, as a feedstock for the growing bioeconomy, including utilisation for bioenergy (with or without carbon capture and storage). PBCs can potentially contribute to Common Agricultural Policy (CAP) (2023–27) objectives provided they are carefully integrated into farming systems and landscapes. Despite significant research and development (R&D) investment over decades in herbaceous and coppiced woody PBCs, deployment has largely stagnated due to social, economic and policy uncertainties. This paper identifies the challenges in creating policies that are acceptable to all actors. Development will need to be informed by measurement, reporting and verification (MRV) of greenhouse gas emissions reductions and other environmental, economic and social metrics. It discusses interlinked issues that must be considered in the expansion of PBC production: (i) available land; (ii) yield potential; (iii) integration into farming systems; (iv) R&D requirements; (v) utilisation options; and (vi) market systems and the socio‐economic environment. It makes policy recommendations that would enable greater PBC deployment: (1) incentivise farmers and land managers through specific policy measures, including carbon pricing, to allocate their less productive and less profitable land for uses which deliver demonstrable greenhouse gas reductions; (2) enable greenhouse gas mitigation markets to develop and offer secure contracts for commercial developers of verifiable low‐carbon bioenergy and bioproducts; (3) support innovation in biomass utilisation value chains; and (4) continue long‐term, strategic R&D and education for positive environmental, economic and social sustainability impacts. Perennial biomass crops (PBCs) can potentially contribute to Common Agricultural Policy (2023–27) objectives provided they are carefully integrated into farming systems and landscapes. Despite significant research and development (R&D) investment over decades in herbaceous and coppiced woody PBCs, deployment has largely stagnated due to social, economic and policy uncertainties. This paper identifies the challenges in creating policies that are acceptable to all actors and discusses the interlinked issues: (i) available land; (ii) yield potential; (iii) integration into farming systems; (iv) R&D requirements; (v) utilisation options; and (vi) market systems and the socio‐economic environment.

Miscanthus is a leading perennial biomass crop that can produce high yields on marginal lands. Moisture content is a highly relevant biomass quality trait with multiple impacts on efficiencies of harvest, transport, and storage. The dynamics of moisture content during senescence and overwinter ripening are determined by genotype × environment interactions. In this paper, unmanned aerial vehicle (UAV)‐based remote sensing was used for high‐throughput plant phenotyping (HTPP) of the moisture content dynamics during autumn and winter senescence of 14 contrasting hybrid types (progeny of M. sinensis x M. sinensis [M. sin x M. sin, eight types] and M. sinensis x M. sacchariflorus [M. sin x M. sac, six types]). The time series of moisture content was estimated using machine learning (ML) models and a range of vegetation indices (VIs) derived from UAV‐based remote sensing. The most important VIs for moisture content estimation were selected by the recursive feature elimination (RFE) algorithm and were BNDVI, GDVI, and PSRI. The ML model transferability was high only when the moisture content was above 30%. The best ML model accuracy was achieved by combining VIs and categorical variables (5.6% of RMSE). This model was used for phenotyping senescence dynamics and identifying the stay‐green (SG) trait of Miscanthus hybrids using the generalized additive model (GAM). Combining ML and GAM modeling, applied to time series of moisture content values estimated from VIs derived from multiple UAV flights, proved to be a powerful tool for HTPP. This study estimated the moisture content of 14 contrasting Miscanthus hybrids combining unmanned aerial vehicle (UAV) remote sensing and machine learning. The random forest (RF) model was trained with moisture content values measured directly from each plot trial, UAV multispectral data (the vegetation indices) and categorical variables of Miscanthus hybrids (material, hybrid code, and genotype). The time series of the moisture content values estimated by RF model from VIs derived from multiple UAV flights were used for phenotyping senescence dynamics and identifying the stay‐green (SG) trait of Miscanthus hybrids using the generalized additive model.