Perennial forages as second generation bioenergy crops

Ecotoxicity of Caffeine as a Bio-Protective Component of Flax-Fiber-Reinforced Epoxy-Composite Building Material

Caffeine is a verified bio-protective substance in the fight against the biodegradation of cellulose materials, but its ecotoxicity in this context has not yet been studied. For this reason, the ecotoxicity of flax-fiber-reinforced epoxy composite with or without caffeine was tested in the present study. Prepared samples of the composite material were tested on freshwater green algal species (Hematococcus pluvialis), yeasts (Saccharomyces cerevisae), and crustacean species (Daphnia magna). Aqueous eluates were prepared from the studied material (with caffeine addition (12%) and without caffeine and pure flax fibers), which were subjected to chemical analysis for the residues of caffeine or metals. The results indicate the presence of caffeine up to 0.001 mg/L. The eluate of the studied material was fully toxic for daphnids and partially for algae and yeasts, but the presence of caffeine did not increase its toxicity statistically significantly, in all cases. The final negative biological effects were probably caused by the mix of heavy metal residues and organic substances based on epoxy resins released directly from the tested composite material.

Changes in soil microbial biomass and organic C pools improve the sustainability of perennial grass and legume system under organic nutrient management

Introduction

The perennial grass-legume cropping system benefits soil because of its high biomass turnover, cover cropping nature, and different foraging behaviors. We investigated the response of soil organic carbon (SOC) pools and their stock to organic and inorganic nutrient management in the Guinea grass and legume (cowpea-Egyptian clover) cropping system.

Methods

Depth-wise soil samples were collected after harvesting the Egyptian clover. Based on the ease of oxidation with chromic acid, different pools of SOC oxidizable using the Walkley-Black C method, very labile, labile, less labile, non-labile; and dissolved organic C (DOC), microbial biomass C (MBC), and total organic C (TOC) in soils were analyzed for computing several indices of SOC.

Result and discussion

After 10 years of crop cycles, FYM and NPKF nutrient management recorded greater DOC, MBC, SOC stocks, and C sequestration than the NPK. Stocks of all SOC pools and carbon management index (CMI) decreased with soil depth. A significant improvement in CMI, stratification ratio, sensitivity indices, and sustainable yield index was observed under FYM and NPKF. This grass-legume intercropping system maintained a positive carbon balance sequestered at about 0.8Mg C ha^-1 after 10 years without any external input. Approximately 44-51% of the applied carbon through manure was stabilized with SOC under this cropping system. The DOC, MBC, and SOC in passive pools were identified for predicting dry fodder yield. This study concludes that the application of organics in the perennial grass-legume inter cropping system can maintain long-term sustainability, enhance the C sequestration, and offset the carbon footprint of the farm enterprises.

Effect of Cultivar, Plant Spacing and Harvesting Age on Yield, Characteristics, Chemical Composition, and Anthocyanin Composition of Purple Napier Grass

Purple Napier grass is a semi-dwarf, purple-leaved Napier grass. The purple color is anthocyanins. Anthocyanin is classified as a group of flavonoids. It has antioxidant properties. The objective of this study was to determine the effect of plant spacing and harvesting age on the forage yield, morphological characteristics, chemical composition, and anthocyanin composition of purple Napier grass. An experiment was conducted to determine the effect of plant spacing and harvesting age on the forage yield, morphological characteristics, chemical composition, and anthocyanin composition of purple Napier grass when grown on a sandy soil. The cultivars were Napier Pakchong 1 (Pennisetum purpureum × Pennisetum americanum cv. Pakchong 1) and purple Napier grass (Pennisetum purpureum “Prince”), with plant spacings of 50 × 50, 50 × 75, and 75 × 75 cm, and the harvesting ages were 45, 60, and 75 days. The experiment was a 2 × 3 × 3 factorial layout in a randomized complete block design with four replications, for a total of 72 plots, each 5 × 5 m. The purple Napier grass had a higher number of tillers per plant than the Napier Pakchong 1 grass. The LSR value (leaf/stem ratio) was influenced by the interaction of cultivar × plant spacing × harvesting age. The purple Napier grass planted at 75 × 75 cm for 45 days had the highest LSR value. The crude protein of the purple Napier grass, the grass planted at 75 × 75 cm, and the grass for 45 days were significantly higher than the other treatments. The purple Napier grass planted at 75 × 75 cm for 45 days had the highest (p < 0.05) anthocyanin content. It was concluded that purple Napier grass planted at 75 × 75 cm for 45 days would contain the proper number of tillers per plant, LSR value, chemical composition for ruminants, and the highest anthocyanin composition.

Deciphering the role of SPL12 and AGL6 from a genetic module that functions in nodulation and root regeneration in Medicago sativa

Our results show that SPL12 plays a crucial role in regulating nodule development in Medicago sativa L. (alfalfa), and that AGL6 is targeted and downregulated by SPL12. Root architecture in plants is critical because of its role in controlling nutrient cycling, water use efficiency and response to biotic and abiotic stress factors. The small RNA, microRNA156 (miR156), is highly conserved in plants, where it functions by silencing a group of SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. We previously showed that transgenic Medicago sativa (alfalfa) plants overexpressing miR156 display increased nodulation, improved nitrogen fixation and enhanced root regenerative capacity during vegetative propagation. In alfalfa, transcripts of eleven SPLs, including SPL12, are targeted for cleavage by miR156. In this study, we characterized the role of SPL12 in root architecture and nodulation by investigating the transcriptomic and phenotypic changes associated with altered transcript levels of SPL12, and by determining SPL12 regulatory targets using SPL12-silencing and -overexpressing alfalfa plants. Phenotypic analyses showed that silencing of SPL12 in alfalfa caused an increase in root regeneration, nodulation, and nitrogen fixation. In addition, AGL6 which encodes AGAMOUS-like MADS box transcription factor, was identified as being directly targeted for silencing by SPL12, based on Next Generation Sequencing-mediated transcriptome analysis and chromatin immunoprecipitation assays. Taken together, our results suggest that SPL12 and AGL6 form a genetic module that regulates root development and nodulation in alfalfa.

Genetic variation in hydrogen cyanide potential of perennial sorghum evaluated by colorimetry

Both annual and perennial sorghum biomass serve as important forage for ruminant animals around the world. Unfortunately, sorghum can produce hydrogen cyanide (HCN), which, if occurring in high enough concentrations, can be toxic or lethal to animals that consume it. The objectives of this study were to develop a fast and inexpensive colorimetric assay to measure the hydrogen cyanide potential (HCN-P) as well as to compare this with existing visual assays while assessing the range of variation for HCN-P among perennial and annual sorghum biomass. The HCN-P of 100 sorghum lines derived from an interspecific hybridization program was determined over 2 years (establishment and regrowth) using both visual and colorimetric assays. Visual assessment underestimated the HCN-P and was less accurate than colorimetry. Repeatability for HCN-P across all sampling dates was functionally zero in the visual assessment and low for the colorimetric assay. This was mostly explained by the significant pedigree × year interaction effects and growth stage. Growth stage substantially influenced HCN-P, which should be considered when feeding animals on fresh forage.

Characteristics of Selected Silphium Species as Alternative Plants for Cultivation and Industry with Particular Emphasis on Research Conducted in Poland: A Review

This article reviews the available research results of selected species of the genus Silphium L. (Asteraceae) as alternative plants for crops and industry. Silphium species have valuable qualities across a wide range of uses, which is very important in considering plant resources as a green alternative to a sustainable future. Species of the genus Silphium are tall perennials found in fields, prairies, open forests, and groves in the central and eastern parts of the United States and Canada. Various tribes of Native North American used Silphium for medicinal purposes. The cup plant Silphium perfoliatum L. is the most popular species of the genus Silphium due to its attractive ornamental, honey−giving, healing, and forage qualities. As the literature review shows, species of the genus Silphium are characterized by a high production potential in terms of yields and contain significant amounts of nutrients, i.e., carbohydrates, proteins, and L-ascorbic acid, as well as minerals and biologically active substances, e.g., terpenoids and essential oils, flavonoids, phenolic acids, and oleanosides. In addition, the research confirmed the possibility of using Silphium for fodder, as honeybee forage, phytoremediation plants, for reclamation of degraded land, as plants for energy purposes (biomass, biogas), and as plants that provide components with antimicrobial activity. This review largely takes into account many years of research experience conducted in Poland.

Comprehensive analysis of MAPK cascade genes in sorghum (Sorghum bicolor L.) reveals SbMPK14 as a potential target for drought sensitivity regulation

The mitogen-activated protein kinase (MAPK) cascade plays a crucial role in regulating many important biological processes in plants. Here, we identified and characterized eight MAPKK and 49 MAPKKK genes in sorghum and analyzed their differential expression under drought treatment; we also characterized 16 sorghum MAPK genes. RNA-seq analysis revealed that 10 MAPK cascade genes were involved in drought stress response at the transcriptome level in sorghum. Overexpression of SbMPK14 in Arabidopsis and maize resulted in hypersensitivity to drought by promoting water loss, indicating that SbMPK14 functions as a negative regulator of the drought response. Subsequent transcriptome analysis and qRT-PCR verification of maize SbMPK14 overexpression lines revealed that SbMPK14 likely increases plant drought sensitivity by suppressing the activity of specific ERF and WRKY transcription factors. This comprehensive study provides valuable insight into the mechanistic basis of MAPK cascade gene function and their responses to drought in sorghum.

Genomic Variation Shaped by Environmental and Geographical Factors in Prairie Cordgrass Natural Populations Collected across Its Native Range in the USA

Prairie cordgrass (Spartina pectinata Link) is a native perennial warm-season (C4) grass common in North American prairies. With its high biomass yield and abiotic stress tolerance, there is a high potential of developing prairie cordgrass for conservation practices and as a dedicated bioenergy crop for sustainable cellulosic biofuel production. However, as with many other undomesticated grass species, little information is known about the genetic diversity or population structure of prairie cordgrass natural populations as compared to their ecotypic and geographic adaptation in North America. In this study, we sampled and characterized a total of 96 prairie cordgrass natural populations with 9315 high quality SNPs from a genotyping-by-sequencing (GBS) approach. The natural populations were collected from putative remnant prairie sites throughout the Midwest and Eastern USA, which are the major habitats for prairie cordgrass. Partitioning of genetic variance using SNP marker data revealed significant variance among and within populations. Two potential gene pools were identified as being associated with ploidy levels, geographical separation, and climatic separation. Geographical factors such as longitude and altitude, and environmental factors such as annual temperature, annual precipitation, temperature of the warmest month, precipitation of the wettest month, precipitation of Spring, and precipitation of the wettest month are important in affecting the intraspecific distribution of prairie cordgrass. The divergence of prairie cordgrass natural populations also provides opportunities to increase breeding value of prairie cordgrass as a bioenergy and conservation crop.

Quantitative trait locus mapping combined with variant and transcriptome analyses identifies a cluster of gene candidates underlying the variation in leaf wax between upland and lowland switchgrass ecotypes

Mapping combined with expression and variant analyses in switchgrass, a crop with complex genetics, identified a cluster of candidate genes for leaf wax in a fast-evolving region of chromosome 7K. Switchgrass (Panicum virgatum L.) is a promising warm-season candidate energy crop. It occurs in two ecotypes, upland and lowland, which vary in a number of phenotypic traits, including leaf glaucousness. To initiate trait mapping, two F₂ mapping populations were developed by crossing two different F₁ sibs derived from a cross between the tetraploid lowland genotype AP13 and the tetraploid upland genotype VS16, and high-density linkage maps were generated. Quantitative trait locus (QTL) analyses of visually scored leaf glaucousness and of hydrophobicity of the abaxial leaf surface measured using a drop shape analyzer identified highly significant colocalizing QTL on chromosome 7K (Chr07K). Using a multipronged approach, we identified a cluster of genes including Pavir.7KG077009, which encodes a Type III polyketide synthase-like protein, and Pavir.7KG013754 and Pavir.7KG030500, two highly similar genes that encode putative acyl-acyl carrier protein (ACP) thioesterases, as strong candidates underlying the QTL. The lack of homoeologs for any of the three genes on Chr07N, the relatively low level of identity with other switchgrass KCS proteins and thioesterases, as well as the organization of the surrounding region suggest that Pavir.7KG077009 and Pavir.7KG013754/Pavir.7KG030500 were duplicated into a fast-evolving chromosome region, which led to their neofunctionalization. Furthermore, sequence analyses showed all three genes to be absent in the two upland compared to the two lowland accessions analyzed. This study provides an example of and practical guide for trait mapping and candidate gene identification in a complex genetic system by combining QTL mapping, transcriptomics and variant analysis.

Changes in phenotype and gene expression under lead stress revealed key genetic responses to lead tolerance in Medicago sativa L

Lead (Pb) is a serious heavy metal soil pollutant. It can be absorbed and accumulated by plant roots and impact plant growth. Medicago sativa L. (alfalfa) is a low-input forage and potential bioenergy crop, and improving its yield and quality has always been a focus of the alfalfa breeding industry. Little is known about the mechanism by which alfalfa responds to Pb stress at the molecular level. In this study, three alfalfa genotypes (a lead-resistant type (LR), a lead-sensitive type (LS) and an intermediate type (IN)) with contrasting abilities to resist lead were exposed to different durations of Pb treatment. Next-generation sequencing (NGS)-based RNA-seq technology was employed to characterize the root transcriptomes of three genotypes of alfalfa and identify differentially expressed genes (DEGs) during Pb stress. Genotypes LR and LS displayed different mechanisms of tolerance. In LR, the accumulation of more resistant substances was induced by the upregulation of sucrose synthase, glucan endo-1,3-beta-glucosidase, beta-amylase 3, probable trehalose-phosphate phosphatase J, 6-phosphofructo-2-kinase delta-1-pyrroline-5-carboxylate synthase (P5CS) and δ-ornithine aminotransferase (δ-OAT). In addition, flavin monooxygenase (YUCCA), 4-coumarate:CoA ligase-like protein (4CL), cinnamoyl-CoA reductase-like protein (CCR), ferulate 5-hydroxylase (F5H) and caffeic acid O-methyltransferase (COMT) were upregulated, leading to root development in a short time under Pb stress. Further study of the expression levels of metal transport-related genes, such as NRAMP (metal transporter), MATE (multidrug and toxin extrusion), HIPPs (heavy metal-associated isoprenylated plant proteins), MTP (metal tolerance protein), and ABC transporter, suggested that these genes were differentially expressed after lead treatment in the three alfalfa genotypes. Our research provides useful information for further studies on the molecular mechanism of Pb resistance in Medicago sativa L.

Life Cycle Assessment Analysis of Alfalfa and Corn for Biogas Production in a Farm Case Study

In the last years the greenhouse effect has been significantly intensified due to human activities, generating large additional amounts of Greenhouse gases (GHG). The fossil fuels are the main causes of that. Consequently, the attention on the composition of the national fuel mix has significantly grown, and the renewables are becoming a more significant component. In this context, biomass is one of the most important sources of renewable energy with a great potential for the production of energy. The study has evaluated, through an LCA (Life Cycle Assessment) study, the attitude of alfalfa (Medicago sativa) as “no food” biomass alternative to maize silage (corn), in the production of biogas from anaerobic digestion. Considering the same functional unit (1 m3 of biogas from anaerobic digestion) and the same time horizon, alfalfa environmental impact was found to be much comparable to that of corn because it has an impact of about 15% higher than corn considering the total score from different categories and an impact of 5% higher of corn considering only greenhouse gases. Therefore, the analysis shows a similar environmental load in the use of alfalfa biomass in energy production compared to maize. Corn in fact, despite a better yield per hectare and yield of biogas, requires a greater amount of energy inputs to produce 1m3 of biogas, while alfalfa, which requires less energy inputs in its life cycle, has a lower performance in terms of yield. The results show the possibility to alternate the two crops for energy production from an environmental perspective.

Engineering of Bioenergy Crops: Dominant Genetic Approaches to Improve Polysaccharide Properties and Composition in Biomass

Large-scale, sustainable production of lignocellulosic bioenergy from biomass will depend on a variety of dedicated bioenergy crops. Despite their great genetic diversity, prospective bioenergy crops share many similarities in the polysaccharide composition of their cell walls, and the changes needed to optimize them for conversion are largely universal. Therefore, biomass modification strategies that do not depend on genetic background or require mutant varieties are extremely valuable. Due to their preferential fermentation and conversion by microorganisms downstream, the ideal bioenergy crop should contain a high proportion of C6-sugars in polysaccharides like cellulose, callose, galactan, and mixed-linkage glucans. In addition, the biomass should be reduced in inhibitors of fermentation like pentoses and acetate. Finally, the overall complexity of the plant cell wall should be modified to reduce its recalcitrance to enzymatic deconstruction in ways that do no compromise plant health or come at a yield penalty. This review will focus on progress in the use of a variety of genetically dominant strategies to reach these ideals. Due to the breadth and volume of research in the field of lignin bioengineering, this review will instead focus on approaches to improve polysaccharide component plant biomass. Carbohydrate content can be dramatically increased by transgenic overexpression of enzymes involved in cell wall polysaccharide biosynthesis. Additionally, the recalcitrance of the cell wall can be reduced via the overexpression of native or non-native carbohydrate active enzymes like glycosyl hydrolases or carbohydrate esterases. Some research in this area has focused on engineering plants that accumulate cell wall-degrading enzymes that are sequestered to organelles or only active at very high temperatures. The rationale being that, in order to avoid potential negative effects of cell wall modification during plant growth, the enzymes could be activated post-harvest, and post-maturation of the cell wall. A potentially significant limitation of this approach is that at harvest, the cell wall is heavily lignified, making the substrates for these enzymes inaccessible and their activity ineffective. Therefore, this review will only include research employing enzymes that are at least partially active under the ambient conditions of plant growth and cell wall development.

Alfalfa response to heat stress is modulated by microRNA156

Heat stress and extreme temperatures negatively affect plant development by disrupting regular cellular and biochemical functions, ultimately leading to reduced crop production. Alfalfa (Medicago sativa) is an important forage crop grown worldwide as forage for livestock feed. Limiting the effects of abiotic stress by developing alfalfa cultivars that are stress tolerant would help mitigate losses to crop production. Members of the microRNA156 (miR156) family regulate the Squamosa Promoter-Binding Protein-Like (SPL) genes that in turn impact plant growth and development by regulating downstream genes in response to various abiotic stresses. In this study, alfalfa with miR156 overexpression and SPL13 RNAi knockdown show increased tolerance to heat stress (40°C). Transgenic plants show high water potential and increased non-enzymatic antioxidant content under heat stress. Moreover, anthocyanin content and chlorophyll abundance were increased under stress. Expression of some important transcription factors and downstream genes involved in abiotic stress response were altered in miR156-overexpressing genotypes under heat. Taken together, our results demonstrate that the miR156/SPL13 network contributes to improving heat stress tolerance in alfalfa.

Implications of Observed and Simulated Soil Carbon Sequestration for Management Options in Corn-based Rotations

Managing cropping systems to sequester soil organic C (SOC) improves soil health and resilience to changing climate. Perennial crops, no-till planting, manure, and cover crops can add SOC; however, their impacts have not been well documented in the northeastern United States. Our objectives were (i) to monitor SOC from a bioenergy cropping study in Pennsylvania that included a corn ( L.)-soybean [ (L.) Merr.]-alfalfa ( L.) rotation, switchgrass ( L.), and reed canarygrass ( L.); (ii) to use the CQESTR model to predict SOC sequestration in the bioenergy crops (with and without projected climate change); and (iii) to use CQESTR to simulate influence of tillage, manure, cover cropping, and corn stover removal in typical dairy forage (silage corn-alfalfa) or grain corn-soybean rotations. Over 8 yr, measured SOC increased 0.4, 1.1, and 0.8 Mg C ha yr in the bioenergy rotation, reed canarygrass, and switchgrass, respectively. Simulated and measured data were significantly correlated ( < 0.001) at all depths. Predicted sequestration (8-14 Mg C ha over 40 yr) in dairy forage rotations was much larger than with corn-soybean rotations (-4.0-0.6 Mg C ha over 40 yr), due to multiple years of perennial alfalfa. No-till increased sequestration in the simulated dairy forage rotation and prevented a net loss of C in corn-soybean rotations. Simulations indicated limited impact of cover crops and manure on long-term SOC sequestration. The low solids content of liquid dairy manure is the likely reason for the less-than-expected impact of manure. Overall, simulations suggest that inclusion of alfalfa provides the greatest potential for SOC sequestration with a typical Pennsylvania crop rotation.

The culturable endophytic fungal communities of switchgrass grown on a coal-mining site and their effects on plant growth

Plants have a diverse endophytic microbiome that is functionally important for their growth, development, and health. In this study, the diversity and specificity of culturable endophytic fungal communities were explored in one of the most important biofuel crops, switchgrass plants (Panicum virgatum L.), which have been cultivated on a reclaimed coal-mining site for more than 20 years. The endophytic fungi were isolated from the surface-sterilized shoot (leaf and stem), root, and seed tissues of switchgrass plants and then cultured for identification. A total of 1339 fungal isolates were found and 22 operational taxonomic units (OTUs) were sequence identified by internal transcribed spacer (ITS) primers and grouped into 7 orders and 4 classes. Although a diverse range of endophytic fungi associated with switchgrass were documented, the most abundant class, order, and species were Sordariomycetes, Hypocreales, and Fusarium spp. respectively. About 86% of the isolated endophytic fungi were able to enhance the heights of the shoots; 69% could increase the shoot fresh weights; and 62% could improve the shoot dry weights after being reintroduced back into the switchgrass plants, which illustrated their functional importance. Through the Shannon Diversity Index analysis, we observed a gradation of species diversity, with shoots and roots having the similar values and seeds having a lesser value. It was observed that the switchgrass plants showing better growth performance displayed higher endophytic fungal species diversity and abundance. It was also discovered that the rhizosphere soil organic matter content was positively correlated with the fungal species diversity. All these data demonstrate the functional association of these beneficial endophytic fungi with switchgrass and their great potential in improving the switchgrass growth and biomass to benefit the biofuel industry by reducing chemical inputs and burden to the environment.

Gene editing by CRISPR/Cas9 in the obligatory outcrossing Medicago sativa

The CRISPR/Cas9 technique was successfully used to edit the genome of the obligatory outcrossing plant species Medicago sativa L. (alfalfa). RNA-guided genome engineering using Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR)/Cas9 technology enables a variety of applications in plants. Successful application and validation of the CRISPR technique in a multiplex genome, such as that of M. sativa (alfalfa) will ultimately lead to major advances in the improvement of this crop. We used CRISPR/Cas9 technique to mutate squamosa promoter binding protein like 9 (SPL9) gene in alfalfa. Because of the complex features of the alfalfa genome, we first used droplet digital PCR (ddPCR) for high-throughput screening of large populations of CRISPR-modified plants. Based on the results of genome editing rates obtained from the ddPCR screening, plants with relatively high rates were subjected to further analysis by restriction enzyme digestion/PCR amplification analyses. PCR products encompassing the respective small guided RNA target locus were then sub-cloned and sequenced to verify genome editing. In summary, we successfully applied the CRISPR/Cas9 technique to edit the SPL9 gene in a multiplex genome, providing some insights into opportunities to apply this technology in future alfalfa breeding. The overall efficiency in the polyploid alfalfa genome was lower compared to other less-complex plant genomes. Further refinement of the CRISPR technology system will thus be required for more efficient genome editing in this plant.

SPL13 regulates shoot branching and flowering time in Medicago sativa

Our results show SPL13 plays a crucial role in regulating vegetative and reproductive development in Medicago sativa L. (alfalfa), and that MYB112 is targeted and downregulated by SPL13 in alfalfa. We previously showed that transgenic Medicago sativa (alfalfa) plants overexpressing microRNA156 (miR156) show a bushy phenotype, reduced internodal length, delayed flowering time, and enhanced biomass yield. In alfalfa, transcripts of seven SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors, including SPL13, are targeted for cleavage by miR156. Thus, association of each target SPL gene to a trait or set of traits is essential for developing molecular markers for alfalfa breeding. In this study, we investigated SPL13 function using SPL13 overexpression and silenced alfalfa plants. Severe growth retardation, distorted branches and up-curled leaves were observed in miR156-impervious 35S::SPL13m over-expression plants. In contrast, more lateral branches and delayed flowering time were observed in SPL13 silenced plants. SPL13 transcripts were predominantly present in the plant meristems, indicating that SPL13 is involved in regulating shoot branch development. Accordingly, the shoot branching-related CAROTENOID CLEAVAGE DIOXYGENASE 8 gene was found to be significantly downregulated in SPL13 RNAi silencing plants. A R2R3-MYB gene MYB112 was also identified as being directly silenced by SPL13 based on Next Generation Sequencing-mediated transcriptome analysis and chromatin immunoprecipitation assays, suggesting that MYB112 may be involved in regulating alfalfa vegetative growth.

Management of native warm-season grasses for beef cattle and biomass production in the Mid-South USA

Native grasses, such as switchgrass (SG; L.), big bluestem (BB; Vitman), indiangrass (IG; Nash), and eastern gamagrass (EG; [L.] L.) may be capable of providing desirable summer forage for cattle as well as a source of biomass for renewable energy. To evaluate that potential, experiments were conducted at 2 locations in Tennessee comparing weaned beef () steers (268 ± 25 kg initial BW) during early-season grazing (Early; 30 d, typically corresponding to May, followed by postdormancy biomass harvest) and full-season grazing (Full, mean duration = 98 d). For Exp. 1, which compared SG, a blend of BB and IG (BBIG), and EG, ADG was greater ( < 0.05) for BBIG (1.02 kg/d) than SG (0.85 kg/d), and both were greater ( < 0.05) than EG (0.66 kg/d). Grazing days for SG and EG were similar (389 and 423 animal unit days [AUD]/ha, respectively) and exceeded ( < 0.05) that of BBIG (233 AUD/ha) during Full. In Exp. 2 (SG and BBIG only), rates of gain were comparable to that of Exp. 1, but AUD were 425 (SG) and 299 (BBIG) AUD/ha. Such rates of gain and grazing days indicate that these grasses can provide desirable summer forage for growing cattle. Early produced 211 to 324 kg BW gain/ha, depending on experiment and forage, followed by dormant-season harvests of 7.5 to 10.5 Mg/ha of biomass, indicating a potential for beef cattle forage and biomass production on the same land resource. Native grasses provided productive summer pasture and good rates of gain on growing cattle and could contribute to forage programs, especially where cool-season grasses currently predominate.

Effect of Phragmites japonicus harvest frequency and timing on dry matter yield and nutritive value

Phragmites is a cosmopolitan perennial emergent macrophyte that is distributed worldwide. In recent years, Phragmites has attracted attention for its potential use as roughage. Given the increasing demand for feed and the number of constructed wetlands (CWs) vegetated with Phragmites, Phragmites is expected to play an important role in roughage production. Thus, it is vital to understand the effects of harvest timing and frequency on dry matter yield, nutritive value, and nitrogen (N) removal to establish appropriate vegetation management. In two CWs in Southwest China, four treatments with different harvesting frequencies were evaluated in monospecific areas of P. japonicus. The four treatments included no harvest, single harvest at 6 months, two harvests at 2 and 4 months, and three harvests at 2, 4, and 6 months. A sharp decline in the total digestible nutrients (TDN) concentration and the rate of increase in dry matter (DM) yield was associated with the heading timings, and the seasonal variations in TDN were likely influenced by carbohydrate accumulation in the stems. The three harvest treatment contributed to substantially improve the N and DM yields without decreasing the nutritive value but negatively affected the growth in the following year. Therefore, not only the combinations of harvest timing and frequency but also other management practices, including partial harvesting, may be needed to optimize CW performance and roughage production.

Comparative transcriptome investigation of global gene expression changes caused by miR156 overexpression in Medicago sativa

Background

Medicago sativa (alfalfa) is a low-input forage and potential bioenergy crop, and improving its yield and quality has always been a focus of the alfalfa breeding industry. Transgenic alfalfa plants overexpressing a precursor of alfalfa microRNA156 (MsmiR156) were recently generated by our group. These plants (miR156OE) showed enhanced biomass yield, reduced internodal length, increased shoot branching and trichome density, and a delay in flowering time. Transcripts of three SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes (MsSPL6, MsSPL12, and MsSPL13) were found to be targeted for cleavage by MsmiR156 in alfalfa.

Results

To further illustrate the molecular mechanisms underlying the effects of miR156 in alfalfa, two miR156OE genotypes (A11a and A17) were subjected to Next Generation RNA Sequencing with Illumina HiSeq. More than 1.11 billion clean reads were obtained from our available sequenced samples. A total of 160,472 transcripts were generated using Trinity de novo assembly and 4,985 significantly differentially expressed genes were detected in miR156OE plants A11a and A17 using the Medicago truncatula genome as reference. A total of 17 genes (including upregulated, downregulated, and unchanged) were selected for quantitative real-time PCR (qRT-PCR) validation, which showed that gene expression levels were largely consistent between qRT-PCR and RNA-Seq data. In addition to the established SPL genes MsSPL6, MsSPL12 and MsSPL13, four new SPLs; MsSPL2, MsSPL3, MsSPL4 and MsSPL9 were also down-regulated significantly in both miR156OE plants. These seven SPL genes belong to genes phylogeny clades VI, IV, VIII, V and VII, which have been reported to be targeted by miR156 in Arabidopsis thaliana. The gene ontology terms characterized electron transporter, starch synthase activity, sucrose transport, sucrose-phosphate synthase activity, chitin binding, sexual reproduction, flavonoid biosynthesis and lignin catabolism correlate well to the phenotypes of miR156OE alfalfa plants.

Conclusions

This is the first report of changes in global gene expression in response to miR156 overexpression in alfalfa. The discovered miR156-targeted SPL genes belonging to different clades indicate miR156 plays fundamental and multifunctional roles in regulating alfalfa plant development.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3014-6) contains supplementary material, which is available to authorized users.

Nitrogen Fertilization Effects on Productivity and Nitrogen Loss in Three Grass-Based Perennial Bioenergy Cropping Systems

Nitrogen (N) fertilization can greatly improve plant productivity but needs to be carefully managed to avoid harmful environmental impacts. Nutrient management guidelines aimed at reducing harmful forms of N loss such as nitrous oxide (N2O) emissions and nitrate (NO3(-)) leaching have been tailored for many cropping systems. The developing bioenergy industry is likely to make use of novel cropping systems, such as polycultures of perennial species, for which we have limited nutrient management experience. We studied how a switchgrass (Panicum virgatum) monoculture, a 5-species native grass mixture and an 18-species restored prairie responded to annual fertilizer applications of 56 kg N ha(-1) in a field-scale agronomic trial in south-central Wisconsin over a 2-year period. We observed greater fertilizer-induced N2O emissions and sub-rooting zone NO3(-) concentrations in the switchgrass monoculture than in either polyculture. Fertilization increased aboveground net primary productivity in the polycultures, but not in the switchgrass monoculture. Switchgrass was generally more productive, while the two polycultures did not differ from each other in productivity or N loss. Our results highlight differences between polycultures and a switchgrass monoculture in responding to N fertilization.

Timing of harvest of Phragmites australis (CAV.) Trin. ex Steudel affects subsequent canopy structure and nutritive value of roughage in subtropical highland

In recent decades, constructed wetlands dominated by common reeds [Phragmites australis (CAV.) Trin. ex Steudel] have been utilized for treating nitrogen-rich wastewaters. Although plant harvest is a vegetation management in constructed wetlands for the purpose of improving nutrient removal, harvested biomass has become a problem in many places. The reed has attracted increasing interest for its potential as high-quality roughage for ruminants. Therefore, it is crucial to understand the effect of reed harvest timing on subsequent regrowth, reconstruction of canopy structure, and nutritive value of regrown biomass for roughage when defining an appropriate vegetation management in constructed wetlands. The shoots of common reeds were harvested in January (winter), March (spring), and May (early summer) in a free-water surface constructed wetland in southwest China. Harvesting in winter enhanced the shoot regrowth and concentrations of total digestible nutrients (TDN), probably due to vigorous translocations of nonstructural carbohydrates from rhizomes. Harvesting in spring and early summer decreased aboveground biomass, nitrogen (N) standing stock, and concentrations of TDN. From fifty to 110 days after harvest, the TDN had sharply declined to values similar to non-harvested stands. Thus, to obtain high-quality roughage, it is recommended that regrown shoots be harvested again within a year in the early growing stage after the first harvest in winter.

Solid-state anaerobic digestion of fungal pretreated Miscanthus sinensis harvested in two different seasons

Solid-state anaerobic digestion of Miscanthus sinensis harvested in fall and spring was compared under different total solids contents and feedstock-to-inoculum ratios. The highest specific methane yields reached 170-175LCH4/kg volatile solids for both harvest seasons. Miscanthus harvested in fall generated a 6% higher methane yield in average than miscanthus harvested in spring. Fungal pretreatment with Ceriporiopsis subvermispora decreased the lignin content of miscanthus harvested in spring by 25.7%, but there was no significant delignification observed for miscanthus harvested in fall. Fungal pretreatment of miscanthus harvested in spring increased the specific methane yield by 25%, but fungal pretreatment caused a slight methane yield reduction for miscanthus harvested in fall. Methane yields for miscanthus were comparable with those from other energy crops.

Towards a carbon-negative sustainable bio-based economy

The bio-based economy relies on sustainable, plant-derived resources for fuels, chemicals, materials, food and feed rather than on the evanescent usage of fossil resources. The cornerstone of this economy is the biorefinery, in which renewable resources are intelligently converted to a plethora of products, maximizing the valorization of the feedstocks. Innovation is a prerequisite to move a fossil-based economy toward sustainable alternatives, and the viability of the bio-based economy depends on the integration between plant (green) and industrial (white) biotechnology. Green biotechnology deals with primary production through the improvement of biomass crops, while white biotechnology deals with the conversion of biomass into products and energy. Waste streams are minimized during these processes or partly converted to biogas, which can be used to power the processing pipeline. The sustainability of this economy is guaranteed by a third technology pillar that uses thermochemical conversion to valorize waste streams and fix residual carbon as biochar in the soil, hence creating a carbon-negative cycle. These three different multidisciplinary pillars interact through the value chain of the bio-based economy.

Effects of nitrogen source and water availability on stem carbohydrates and cellulosic bioethanol traits of alfalfa plants

Symbiotic association of legumes with rhizobia frequently results in higher photosynthesis and soluble carbohydrates in comparison with nitrate-fed plants, which might improve its potential for biomass conversion into bioethanol. A greenhouse experiment was conducted to examine the effects of nitrogen source and water availability on stem characteristics and on relationships between carbohydrates, phenolic metabolism activity and cell wall composition in alfalfa (Medicago sativa L. cv. Aragón). The experiment included three treatments: (1) plants fed with ammonium nitrate (AN); (2) plants inoculated with rhizobia (R); and (3) plants inoculated with rhizobia and amended with sewage sludge (RS). Two levels of irrigation were imposed: (1) well-watered and (2) drought stress. Under well-watered conditions, nitrogen-fixing plants have increased photosynthesis and stem fermentable carbohydrate concentrations, which result in higher potential for biomass conversion to bioethanol than in AN plants. The latter had higher lignin due to enhanced activities of phenolic metabolism-related enzymes. Under drought conditions, the potential for bioethanol conversion decreased to a similar level in all treatments. Drought-stressed nitrogen-fixing plants have high concentrations of fermentable carbohydrates and cell wall cellulose, but ammonium nitrate-fed plants produced higher plant and stem biomass, which might compensate the decreasing stem carbohydrates and cellulose concentrations.

Exploring the plant-associated bacterial communities in Medicago sativa L

Background

Plant-associated bacterial communities caught the attention of several investigators which study the relationships between plants and soil and the potential application of selected bacterial species in crop improvement and protection. Medicago sativa L. is a legume crop of high economic importance as forage in temperate areas and one of the most popular model plants for investigations on the symbiosis with nitrogen fixing rhizobia (mainly belonging to the alphaproteobacterial species Sinorhizobium meliloti). However, despite its importance, no studies have been carried out looking at the total bacterial community associated with the plant. In this work we explored for the first time the total bacterial community associated with M. sativa plants grown in mesocosms conditions, looking at a wide taxonomic spectrum, from the class to the single species (S. meliloti) level.

Results

Results, obtained by using Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis, quantitative PCR and sequencing of 16 S rRNA gene libraries, showed a high taxonomic diversity as well as a dominance by members of the class Alphaproteobacteria in plant tissues. Within Alphaproteobacteria the families Sphingomonadaceae and Methylobacteriaceae were abundant inside plant tissues, while soil Alphaproteobacteria were represented by the families of Hyphomicrobiaceae, Methylocystaceae, Bradyirhizobiaceae and Caulobacteraceae. At the single species level, we were able to detect the presence of S. meliloti populations in aerial tissues, nodules and soil. An analysis of population diversity on nodules and soil showed a relatively low sharing of haplotypes (30-40%) between the two environments and between replicate mesocosms, suggesting drift as main force shaping S. meliloti population at least in this system.

Conclusions

In this work we shed some light on the bacterial communities associated with M. sativa plants, showing that Alphaproteobacteria may constitute an important part of biodiversity in this system, which includes also the well known symbiont S. meliloti. Interestingly, this last species was also found in plant aerial part, by applying cultivation-independent protocols, and a genetic diversity analysis suggested that population structure could be strongly influenced by random drift.

The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species

Major feedstock sources for future biofuel production are likely to be high biomass producing plant species such as poplar, pine, switchgrass, sorghum and maize. One active area of research in these species is genome-enabled improvement of lignocellulosic biofuel feedstock quality and yield. To facilitate genomic-based investigations in these species, we developed the Biofuel Feedstock Genomic Resource (BFGR), a database and web-portal that provides high-quality, uniform and integrated functional annotation of gene and transcript assembly sequences from species of interest to lignocellulosic biofuel feedstock researchers. The BFGR includes sequence data from 54 species and permits researchers to view, analyze and obtain annotation at the gene, transcript, protein and genome level. Annotation of biochemical pathways permits the identification of key genes and transcripts central to the improvement of lignocellulosic properties in these species. The integrated nature of the BFGR in terms of annotation methods, orthologous/paralogous relationships and linkage to seven species with complete genome sequences allows comparative analyses for biofuel feedstock species with limited sequence resources.

Database URL:http://bfgr.plantbiology.msu.edu

Carbon gain, allocation and storage in rhizomes in response to elevated atmospheric carbon dioxide and nutrient supply in a perennial C3 grass, Phalaris arundinacea

Reed canary grass (Phalaris arundinacea L.) is a fast-growing, perennial, rhizomatous C3 grass considered as a model invasive species for its aggressive behaviour. The same traits make it a candidate for bioenergy feedstock. We tested the following hypotheses: (1) elevated atmospheric [CO2] and nutrient supply enhance photosynthetic carbon acquisition of this fructan-accumulating grass with little or no photosynthetic downregulation; (2) elevated [CO2] promotes carbon allocation to growth when nutrients are sufficient and to fructan storage in rhizomes when nutrients are low. Plants were grown at ambient or elevated (+320μmolmol-1) [CO2], and fertilised using full or one-eighth strength modified Hoagland solution. We investigated leaf photosynthesis, whole-plant water use, biomass allocation, and nitrogen and carbon storage in rhizomes. Elevated [CO2] enhanced light-saturated net CO2 assimilation by 61%. It doubled whole-plant, stem and root biomass in summer. Plants grown in elevated [CO2] had a greater rate of CO2 assimilation at higher [CO2], indicating a shift in photosynthetic apparatus for enhanced carbon gain under elevated [CO2]. The majority of belowground biomass was allocated to rhizomes for storage rather than to roots in both seasons. In autumn, elevated [CO2] increased fructan concentration in rhizomes from 8.1 to 11.7% of biomass when nutrients were low (P=0.023). Our results suggest that elevated [CO2] combined with sufficient nutrients is likely to enhance carbon gain and growth of P. arundinacea, and to increase its productivity and competitiveness in summer. Elevated [CO2] is likely to enhance long-term fructan storage in rhizomes, which may benefit overwintering and vegetative spread.

Interactions among bioenergy feedstock choices, landscape dynamics, and land use

Landscape implications of bioenergy feedstock choices are significant and depend on land-use practices and their environmental impacts. Although land-use changes and carbon emissions associated with bioenergy feedstock production are dynamic and complicated, lignocellulosic feedstocks may offer opportunities that enhance sustainability when compared to other transportation fuel alternatives. For bioenergy sustainability, major drivers and concerns revolve around energy security, food production, land productivity, soil carbon and erosion, greenhouse gas emissions, biodiversity, air quality, and water quantity and quality. The many implications of bioenergy feedstock choices require several indicators at multiple scales to provide a more complete accounting of effects. Ultimately, the long-term sustainability of bioenergy feedstock resources (as well as food supplies) throughout the world depends on land-use practices and landscape dynamics. Land-management decisions often invoke trade-offs among potential environmental effects and social and economic factors as well as future opportunities for resource use. The hypothesis being addressed in this paper is that sustainability of bioenergy feedstock production can be achieved via appropriately designed crop residue and perennial lignocellulosic systems. We find that decision makers need scientific advancements and adequate data that both provide quantitative and qualitative measures of the effects of bioenergy feedstock choices at different spatial and temporal scales and allow fair comparisons among available options for renewable liquid fuels.

Plant-Parasitic Nematodes Are Potential Pathogens of Miscanthus × giganteus and Panicum virgatum Used for Biofuels

A survey of Miscanthus × giganteus and switchgrass plots throughout the midwestern and southeastern United States was conducted to determine the occurrence and distribution of plant-parasitic nematodes associated with these biofuel crops. During 2008, rhizosphere soil samples were collected from 24 Miscanthus × giganteus and 38 switchgrass plots in South Dakota, Iowa, and Illinois. Additional samples were collected from 11 Miscanthus × giganteus and 10 switchgrass plots in Illinois, Kentucky, Georgia, and Tennessee the following year. The 11 dominant genera recovered from the samples were Pratylenchus, Helicotylenchus, Xiphinema, Longidorus, Heterodera, Hoplolaimus, Tylenchorhynchus, Criconemella, Paratrichodorus, Hemicriconemoides, and Paratylenchus. Populations of Helicotylenchus, Xiphinema, and Pratylenchus were common and recorded in 90.5, 83.8, and 91.9% of the soil samples from Miscanthus × giganteus, respectively, and in 91.6, 75, and 83.3% of the soil samples from switchgrass, respectively. Prominence value (PV) (PV = population density × √frequency of occurrence/10) was calculated for the nematodes identified. Helicotylenchus had the highest PV (PV = 384) and was followed by Xiphinema (PV = 152) and Pratylenchus (PV = 72). Several of the nematode species associated with the two biofuels crops were plant parasites. Of these, Pratylenchus penetrans, P. scribneri, P. crenatus, Helicotylenchus pseudorobustus, Hoplolaimus galeatus, X. americanum, and X. rivesi are potentially the most damaging pests to Miscanthus × giganteus and switchgrass. Due to a lack of information, the damaging population thresholds of plant-parasitic nematodes to Miscanthus × giganteus and switchgrass are currently unknown. However, damage threshold value ranges have been reported for other monocotyledon hosts. If these damage threshold value ranges are any indication of the population densities required to impact Miscanthus × giganteus and switchgrass, then every state surveyed has potential for yield losses due to plant-parasitic nematodes. Specifically, Helicotylenchus, Xiphinema, Pratylenchus, Hoplolaimus, Tylenchorhynchus, Criconemella, and Longidorus spp. were all found to have population densities within or above the threshold value ranges reported for other monocotyledon hosts.

Application of sequence-independent amplification (SIA) for the identification of RNA viruses in bioenergy crops

Miscanthus x giganteus, energycane, and Panicum virgatum (switchgrass) are three potential biomass crops being evaluated for commercial cellulosic ethanol production. Viral diseases are potentially significant threats to these crops. Therefore, identification of viruses infecting these bioenergy crops is important for quarantine purposes, virus resistance breeding, and production of virus-free planting materials. The application is described of sequence-independent amplification, for the identification of RNA viruses in bioenergy crops. The method involves virus partial purification from a small amount of infected leaf tissue (miniprep), extraction of viral RNA, amplification of randomly primed cDNAs, cloning, sequencing, and BLAST searches for sequence homology in the GenBank. This method has distinct advantage over other virus characterization techniques in that it does not require reagent specific to target viruses. Using this method, a possible new species was identified in the genus Marafivirus in switchgrass related to Maize rayado fino virus, its closest relative currently in GenBank. Sugarcane mosaic virus (SCMV), genus Potyvirus, was identified in M.xgiganteus, energycane, corn (Zea mays), and switchgrass. Other viruses identified were: Maize dwarf mosaic virus (MDMV), genus Potyvirus, in johnsongrass (Sorghum halepense); Soil borne wheat mosaic virus (SBWMV), genus Furovirus, in wheat (Triticum aestivum); and Bean pod mottle virus (BPMV), genus Comovirus, in soybean (Glycine max). The method was as sensitive as conventional RT-PCR. This is the first report of a Marafivirus infecting switchgrass, and SCMV infecting both energycane and M. x giganteus.

Chemical evidence for intrinsic 'Si' within Equisetum cell walls

This contribution provides the first detailed chemical evidence for the association of 'Si' with soluble carbohydrate and proteinaceous components of Equisetum arvense cell walls. For Equisetum telmateia and E. arvense, the presence of intrasilica organics trapped within phytolithic silica deposits and organics packaged within silica coated particles on the outside of spores have previously been identified. The current paper shows that 'Si' is also found intimately associated with cell wall polymers that can be released using mild extraction procedures (CDTA and Na(2)CO(3)/NaBH(4)) that do not solubilise the mineral phase. The isolates comprise both protein and carbohydrate components with increases in 'Si' (up to slightly more than 1% by weight) being particularly linked to increased levels of protein within the extracts. The general composition of the cell wall isolates associated with 'Si' was very different to that previously found for intrasilica and spore related material with much lower levels of charged amino acids, particularly basic amino acids being detected. The range of monosaccharides detected was much wider than for the other silicified materials investigated. It is possible that 'Si' in some form could act to crosslink the cell wall polymers thereby providing a modest improvement in rigidity/stability of the cell wall against biotic and abiotic stresses. This study demonstrates that distinct differences are to be found between extra- and intrasilica organics in the cell wall of E. arvense.