Soil organic carbon significantly increases when perennial biomass plantations are reverted back to annual arable crops

Funding: This research was supported by funding from the Rural Developing Program (measure 16.01) of the Emilia Romagna region that financed the “FarmCO2Sink” EIP-AGRI operational group (grant number 5015651). Acknowledgments: The authors thank Mike Martin for his support in the modification of the ECOSSE source code.Peer reviewedPublisher PD

Perennial rhizomatous grasses: Can they really increase species richness and abundance in arable land?—A meta-analysis

AbstractPerennial 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

A novel framework for chimeric transcript detection based on accurate gene fusion model

Next generation sequencing plays a key role in the detection of structural variations. Chimeric transcripts are relevant examples of such variations, as they are involved in several diseases. In this work, we propose an effective methodology for the detection of fused transcripts in RNA-Seq paired-end data. The proposed methodology is based on an accurate fusion model implemented by a set of filters reducing the impact of artifacts. Moreover, the methodology accounts for transcripts consistently expressing in the sample under study even if they are not annotated. The effectiveness of the proposed solution has been experimentally validated on of Chronic Myelogenous Leukemia (CML) samples, providing both the genes involved in the fusion and the exact chimeric sequence. \ua9 2011 IEEE

Moisture content estimation and senescence phenotyping of novel Miscanthus hybrids combining UAV-based remote sensing and machine learning

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

An updated portrait of monocyte-macrophages in classical Hodgkin lymphoma

Classical Hodgkin lymphoma (cHL) is a unique neoplastic ecosystem characterized by a heterogeneous immune infiltrate surrounding the rare malignant Hodgkin Reed-Sternberg cells. Though less abundant than T-cells, tumor-infiltrating macrophages play a pivotal role in supporting HRS survival through cell-to-cell and paracrine interactions. Traditional immunohistochemistry based upon the M1-M2 dichotomy yielded controversial results about the composition, functional role and prognostic impact of macrophages in cHL. More recent studies exploiting single-cell technologies and image analyses have highlighted the heterogeneity and the peculiar spatial arrangement of the macrophagic infiltrate, with the most immunosuppressive subpopulations lying in close proximity of HRS cells and the most tumor-hostile subsets kept far away from the neoplastic niches. High-throughput analysis of peripheral blood mononuclear cells in cHL patients have also identified a novel, potentially cytotoxic, subpopulation predicting better response to PD-1 blockade. This review examines the phenotypic profile, spatial localization and clinical impact of tumor-infiltrating macrophages and circulating monocytes in cHL, providing an up-do-date portrait of these innate immune cells with possible translational applications

Chronic Lymphocytic Leukemia B Cells Can Undergo Somatic Hypermutation and Intraclonal Immunoglobulin VHDJH Gene Diversification

Chronic lymphocytic leukemia (CLL) arises from the clonal expansion of a CD5+ B lymphocyte that is thought not to undergo intraclonal diversification. Using VHDJH cDNA single strand conformation polymorphism analyses, we detected intraclonal mobility variants in 11 of 18 CLL cases. cDNA sequence analyses indicated that these variants represented unique point-mutations (1–35/patient). In nine cases, these mutations were unique to individual submembers of the CLL clone, although in two cases they occurred in a large percentage of the clonal submembers and genealogical trees could be identified. The diversification process responsible for these changes led to single nucleotide changes that favored transitions over transversions, but did not target A nucleotides and did not have the replacement/silent nucleotide change characteristics of antigen-selected B cells. Intraclonal diversification did not correlate with the original mutational load of an individual CLL case in that diversification was as frequent in CLL cells with little or no somatic mutations as in those with considerable mutations. Finally, CLL B cells that did not exhibit intraclonal diversification in vivo could be induced to mutate their VHDJH genes in vitro after stimulation. These data indicate that a somatic mutation mechanism remains functional in CLL cells and could play a role in the evolution of the clone

Biomass production and energy balance of herbaceous and woody crops on marginal soils in the Po valley

A wealth of data and information on the cultivation of perennial biomass crops has been collected, but direct comparisons between herbaceous and woody crops are rare. The main objective of this research was to compare the biomass yield, the energy balance and the biomass quality of six perennial bioenergy crops: Populus spp., Robinia pseudoacacia, Salix spp., Arundo donax, Miscanthus 9 giganteus, and Panicum virgatum, grown in two marginal environments. For giant reed and switchgrass, two levels of nitrogen fertilization were applied annually (0–100 kg ha 1). Nitrogen fertilization did not affect biomass or energy production of giant reed; thus, it significantly reduced the energy return on investment (EROI) (from 73 to 27). In switchgrass, nitrogen fertiliza- tion significantly increased biomass production and the capacity of this crop to respond to water availability, making it a favorable option when only biomass production is a target. Net energy gain (NEG) was higher for herbaceous crops than for woody crops. In Casale, EROI calculated for poplar and willow (7, on average) was significantly lower than that of the other crops (14, on average). In Gariga, the highest EROI was calculated for miscanthus (98), followed by nonfertilized giant reed and switchgrass (82 and 73, respectively). Growing degree days10 during the cropping season had no effect on biomass production in any of the studied species, although water availability from May to August was a major factor affecting biomass yield in herbaceous crops. Overall, herbaceous crops had the highest ranking for bioenergy production due to their high biomass yield, high net energy gain (NEG), and biomass quality that renders them suitable to both biochemical and thermochemical conversion. Miscanthus in particular had the highest EROI in both locations (16 and 98, in Casale and Gariga), while giant reed had the highest NEG on the silty-loam soil of Gariga

Impacts of willow and miscanthus bioenergy buffers on biogeochemical N removal processes along the soil-groundwater continuum

In this paper the below- and above-ground biomass production in bioenergy buffers and biogeochemical N removal processes along the soil-groundwater continuum were assessed. In a sandy loam soil with shallow groundwater, bioenergy buffers of miscanthus and willow (5 and 10 m wide) were planted along a ditch of an agricultural field (AF) located in the Po valley (Italy). Mineral N forms and dissolved organic C (DOC) were monitored monthly over an 18 month period in groundwater before and after the bioenergy buffers. Soil samples were measured for inorganic N, DOC, microbial biomass C (MBC) and N (MBN), and potential nitrate reductase activity (NAR). The results indicated that bioenergy buffers are able to efficiently remove from groundwater the incoming NO3-N (62%-5 m and 80%-10 m). NO3-N removal rate was higher when nitrate input from AF increased due to N fertilization. Willow performed better than miscanthus in terms of biomass production (17 Mg DM ha-1 y-1), fine root biomass (5.3 Mg ha-1) and N removal via harvesting (73 kg N ha-1). The negative nonlinear relationship found between NO3-N and DOC along the soil-groundwater continuum from AF to bioenergy buffers indicates that DOC:NO3-N ratio is an important controlling factor for promoting denitrification in bioenergy buffers. Bioenergy buffers promoted soil microbial functioning as they stimulated plant\u2013microbial linkages by increasing the easily available C sources for microorganisms (as DOC). First, willow and miscanthus promoted high rates of biological removal of nitrate (NAR) along the soil profile. Second, rhizosphere processes activated the soil microbial community leading to significant increases in MBC and microbial N immobilization. Herbaceous and woody bioenergy crops have been confirmed as providing good environmental performances when cultivated as bioenergy buffers by mitigating the disservices of agricultural activities such as groundwater N pollution

Site impacts nutrient translocation efficiency in intraspecies and interspecies miscanthus hybrids on marginal lands

Miscanthus, a C4 perennial rhizomatous grass, is capable of growing in varied climates and soil types in Europe, including on marginal lands. It can produce high yields with low nutrient inputs when harvested after complete senescence. Senescence induction and rate depend on complex genetic, environmental, and management interactions. To explore these interactions, we analysed four miscanthus hybrids (two novel seed-based hybrids, GRC 3 [Miscanthus sinensis × sinensis] and GRC 14 [M. sacchariflorus × sinensis]; GRC 15, a novel M. sacchariflorus × sinensis clone; and GRC 9, a standard Miscanthus × giganteus clone) in Italy, Croatia, Germany and the UK. Over all trial locations and hybrids, the average aboveground biomass of the 3-year-old stands in August 2020 was 15 t DM ha−1 with nutrient contents of 7.6 mg N g−1 and 14.6 mg K g−1. As expected, delaying the harvest until spring reduced overall yield and nutrient contents (12 t DM ha−1, 3.3 mg N g−1, and 5.5 mg K g−1). At lower latitudes, the late-ripening M. sacchariflorus × sinensis GRC 14 and GRC 15 combined high yields with low nutrient contents. At the most elevated latitude location (UK), the early-ripening M. sinensis × sinensis combined high biomass yields with low nutrient offtakes. The clonal Miscanthus × giganteus with intermediate flowering and senescence attained similar low nutrient contents by spring harvest at all four locations. Seasonal changes in yield and nutrient levels analysed in this study provide: (1) a first step towards recommending hybrids for specific locations and end uses in Europe; (2) crucial data for determination of harvest time and practical steps in the valorization of biomass; and (3) key sustainability data for life cycle assessments. Identification of trade-offs resulting from genetic × environment × management interactions is critical for increasing sustainable biomass supply from miscanthus grown on marginal lands