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\"This book introduces readers to second-generation biofuels obtained from non-food biomass, such as forest residue, agricultural residue, switch grass, and corn stover\"--Provided by publisher.

Filamentous fungi, such as Neurospora crassa, are very efficient in deconstructing plant biomass by the secretion of an arsenal of plant cell wall-degrading enzymes, by remodeling metabolism to accommodate production of secreted enzymes, and by enabling transport and intracellular utilization of plant biomass components. Although a number of enzymes and transcriptional regulators involved in plant biomass utilization have been identified, how filamentous fungi sense and integrate nutritional information encoded in the plant cell wall into a regulatory hierarchy for optimal utilization of complex carbon sources is not understood. Here, we performed transcriptional profiling of N. crassa on 40 different carbon sources, including plant biomass, to provide data on how fungi sense simple to complex carbohydrates. From these data, we identified regulatory factors in N. crassa and characterized one (PDR-2) associated with pectin utilization and one with pectin/hemicellulose utilization (ARA-1). Using in vitro DNA affinity purification sequencing (DAP-seq), we identified direct targets of transcription factors involved in regulating genes encoding plant cell wall-degrading enzymes. In particular, our data clarified the role of the transcription factor VIB-1 in the regulation of genes encoding plant cell wall-degrading enzymes and nutrient scavenging and revealed a major role of the carbon catabolite repressor CRE-1 in regulating the expression of major facilitator transporter genes. These data contribute to a more complete understanding of cross talk between transcription factors and their target genes, which are involved in regulating nutrient sensing and plant biomass utilization on a global level.

Fungi play a major role in the global carbon cycle because of their ability to utilize plant biomass (polysaccharides, proteins, and lignin) as carbon source. Due to the complexity and heterogenic composition of plant biomass, fungi need to produce a broad range of degrading enzymes, matching the composition of (part of) the prevalent substrate. This process is dependent on a network of regulators that not only control the extracellular enzymes that degrade the biomass, but also the metabolic pathways needed to metabolize the resulting monomers. This review will summarize the current knowledge on regulation of plant biomass utilization in fungi and compare the differences between fungal species, focusing in particular on the presence or absence of the regulators involved in this process.

Background and aims One means of reducing nitrate leaching in temperate farming is to include catch crops in crop rotations, which immobilize residual nitrogen (N) in their biomass. For an accurate quantification of the N stored in catch crops and subsequently released from residues, their total biomass, including roots and rhizodeposits has to be assessed. Methods In a pot experiment under controlled conditions, oil and forage radish (Raphanus sativus L. var. oleiformis Pers.) and winter turnip rape (Brassica rapa L. var. silvestris [Lam.] Briggs) plants were leaf-labelled every five to seven days with 15N–urea (99at%) five times during the vegetation. At harvest, plants were separated into shoot, coarse, medium and fine roots by hand picking and wet sieving, respectively. The amount of N derived from rhizodeposition (NdfR) was calculated using two different calculation approaches. In addition to the pot experiment, a field experiment with unlabelled plants was set up to extrapolate the results from the pot experiment to the field scale, at the same time evaluating the influence of additional mineral N fertilization on biomass distribution. The contribution of rhizodeposition to total N in the field was estimated by extrapolating the root-N-to-rhizodeposition-N ratio of the pot experiment to the field experiment. Results In the pot trial, between 4.6 and 10.3% of the total assimilated nitrogen of the catch crops was found as rhizodeposits, which is at the lower end of values from other studies on legumes and non-legumes. In the field experiment the shoot-to-root ratio was lower compared to the pot experiment. Thus, the contribution of rhizodeposition to total N under field conditions is substantially higher. Fertilization in the field trial mostly influenced the formation of above-ground plant biomass. Conclusions Considering the rhizodeposition reveals, that the investigated catch crops store more N than previously assumed. As a consequence, catch crops have to be evaluated with a stronger focus on below-ground biomass to make sure the right amounts of N are considered for fertilization schemes in crop rotations.

Over the past three decades, the view of nutrient limitation has transferred from single-nutrient limitation to multiple-nutrient limitation. On the Qinghai-Tibetan Plateau (QTP), many nitrogen (N) and phosphorus (P) addition experiments have revealed different N- or P-limited patterns at many alpine grassland sites, whereas it is not clear what the general patterns of N and P limitation across the QTP grasslands. We performed a meta-analysis, containing 107 publications, to assess how N and P constrained plant biomass and diversity in alpine grasslands across the QTP. We also tested how mean annual precipitation (MAP) and mean annual temperature (MAT) influence N and P limitations. The findings show that plant biomass in QTP grasslands is co-limited by N and P. Single N limitation is stronger than single P limitation, and the combined positive effect of N and P addition is stronger than that of single nutrient additions. The response of biomass to N fertilization rate shows an increase firstly and then declines, and peaks at approximately 25 g N·m ·year . MAP promotes the effect of N limitation on plant aboveground biomass and diminishes the effect of N limitation on belowground biomass. Meanwhile, N and P addition generally decline plant diversity. Moreover, the negative response of plant diversity to N and P co-addition is strongest than that of single nutrient additions. Our results highlight that N and P co-limitation is more prevalent than N- or P-limitation alone in alpine grasslands on the QTP. Our findings provide a better understanding of nutrient limitation and management for alpine grasslands on the QTP.

Background The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of plant biomass substrates. Which genes need to be activated in certain environmental conditions depends on the composition of the available substrate. Previous studies have demonstrated the involvement of a number of transcriptional regulators in plant biomass degradation and have identified sets of target genes for each regulator. In this study, a broad transcriptional analysis was performed of the A. niger genes encoding (putative) plant polysaccharide degrading enzymes. Microarray data focusing on the initial response of A. niger to the presence of plant biomass related carbon sources were analyzed of a wild-type strain N402 that was grown on a large range of carbon sources and of the regulatory mutant strains Δ xlnR , Δ araR , Δ amyR , Δ rhaR and Δ galX that were grown on their specific inducing compounds. Results The cluster analysis of the expression data revealed several groups of co-regulated genes, which goes beyond the traditionally described co-regulated gene sets. Additional putative target genes of the selected regulators were identified, based on their expression profile. Notably, in several cases the expression profile puts questions on the function assignment of uncharacterized genes that was based on homology searches, highlighting the need for more extensive biochemical studies into the substrate specificity of enzymes encoded by these non-characterized genes. The data also revealed sets of genes that were upregulated in the regulatory mutants, suggesting interaction between the regulatory systems and a therefore even more complex overall regulatory network than has been reported so far. Conclusions Expression profiling on a large number of substrates provides better insight in the complex regulatory systems that drive the conversion of plant biomass by fungi. In addition, the data provides additional evidence in favor of and against the similarity-based functions assigned to uncharacterized genes.

Aims Vegetation restoration has been widely implemented to achieve carbon (C) sequestration and prevent land degradation, and this study aims to evaluate the ecosystem C pools and C sequestration effectiveness of different land-use types. Methods In this study, the plant biomass C stock, litter C stock, soil organic C (SOC) stock and ecosystem C sequestration in Zanthoxylum bungeanum plantations (with stand ages of 28, 20, 15 and 8 years, abbreviated as ZB28, ZB20, ZB15 and ZB8, respectively), abandoned land (AL) and farmland (FL) were estimated. Results (1) the plant biomass and biomass C stock of above-and below-ground increased after farmland conversion, and all of them ranked as ZB28 > ZB20 > ZB15 > AL > ZB8 > FL; (2) the litter stock and C stock, and SOC concentration and stock of different land-use types ranked as AL >  Z. bungeanum plantations > FL, and these indices increased with the stand age; (3) the C stock of the ecosystem in FL was 115.4 Mg C ha −1 , and the C stock of the ecosystem increased by 8.9–66.6 Mg C ha −1 and 52.4 Mg C ha −1 after the conversion of FL to Z. bungeanum plantations and AL, respectively; (4) and soil C sequestration accounts for 55.6–83.6% of ecosystem C sequestration after farmland conversion. Conclusions This implies that the conversion of farmland to Z. bungeanum plantations was the best approach in the arid valley area when the ecosystem C sequestration and economic benefits were considered.

Aims Carbon stocks in alpine meadows on the Qinghai-Tibetan Plateau are being threatened by increases in livestock herding practices. However, the extent to which current fast-growing disturbance by Tibetan pig rooting alters carbon stocks in these meadows and the underlying processes are still unclear. Methods We conducted a 3-year study in meadows with three different plant communities on the southeast Qinghai-Tibetan Plateau to explore the effects of rooting by Tibetan pigs on carbon stocks. Results Rooting by Tibetan pigs decreased plant biomass carbon (PBC), soil organic carbon (SOC), microbial biomass carbon (MBC), and ecosystem carbon (EC) by 91.25%, 30.57%, 28.94%, and 40.47%, respectively. Soil moisture (SM) was the most significant factor negatively associated with PBC, SOC, and EC. Additionally, a decreased SM by rooting also exerted an indirect effect on MBC by directly reducing plant biomass. Conclusions Rooting by Tibetan pigs diminishes carbon stocks by decreasing SM, threatening carbon stocks stored in alpine meadows. Thus, caging or reducing the breeding number of Tibetan pigs combined with restoring soil water levels would be effective ways to recover and maintain carbon stocks in alpine meadows on the Qinghai-Tibetan Plateau.

Studies of plant resource‐use strategies along environmental gradients often assume that dry matter partitioning represents an individual's energy investment in foraging for above‐ versus below‐ground resources. However, ecosystem‐level studies of total below‐ground carbon allocation (TBCA) in forests do not support the equivalency of energy (carbon) and dry matter partitioning, in part because allocation of carbon to below‐ground pools and fluxes that are not accounted for by root biomass (e.g., mycorrhizal hyphae, rhizodeposition; root and soil respiration) can be substantial. Here, we apply this reasoning to individual plants in controlled environments and ask whether dry matter partitioning below‐ground (root mass fraction, RMF) accurately reflects TBCA in studies of optimal partitioning theory. We quantified the relationship between RMF and TBCA in individual plants, using 311 observations from 51 studies that simultaneously measured both allocation variables. Our analysis included tests of whether the RMF‐TBCA relationship depended on mutualist soil microbes, plant growth form, age and study methodology including isotopic pulse–chase duration. We found that RMF was a poor proxy for below‐ground energy investment. This disconnect of RMF and TBCA was driven in part by plants of low RMF (<0.4) exhibiting significantly higher rates of root and soil respiration per unit root mass than plants of high RMF. Root colonization by mutualist microbes, including arbuscular mycorrhizal fungi and nitrogen‐fixing bacteria, increased TBCA by 5%–7%, and TBCA was lower in grasses than other species by 9%–16%. These patterns were evident for relationships assessed both within and between species. We conclude that optimal partitioning studies of plants along environmental gradients are likely to underestimate plant energy allocation below‐ground if the C costs of root and soil respiration are ignored, especially under conditions favouring low RMF. Because energy rather than biomass better reflects how assimilated C supports fitness, this omission of respired C suggests existing studies misrepresent the significance of below‐ground processes to plant function. A free Plain Language Summary can be found within the Supporting Information of this article. A free Plain Language Summary can be found within the Supporting Information of this article.

Metagenomic and bioinformatic approaches were used to characterize plant biomass conversion within the foregut microbiome of Australia's \"model\" marsupial, the Tammar wallaby (Macropus eugenii). Like the termite hindgut and bovine rumen, key enzymes and modular structures characteristic of the \"free enzyme\" and \"cellulosome\" paradigms of cellulose solubilization remain either poorly represented or elusive to capture by shotgun sequencing methods. Instead, multigene polysaccharide utilization loci-like systems coupled with genes encoding β-1,4-endoglucanases and β-1,4-endoxylanases—which have not been previously encountered in metagenomic datasets—were identified, as were a diverse set of glycoside hydrolases targeting noncellulosic polysaccharides. Furthermore, both rrs gene and other phylogenetic analyses confirmed that unique clades of the Lachnospiraceae, Bacteroidales, and Gammaproteobacteria are predominant in the Tammar foregut microbiome. Nucleotide composition-based sequence binning facilitated the assemblage of more than two megabase pairs of genomic sequence for one of the novel Lachnospiraceae clades (WG-2). These analyses show that WG-2 possesses numerous glycoside hydrolases targeting noncellulosic polysaccharides. These collective data demonstrate that Australian macropods not only harbor unique bacterial lineages underpinning plant biomass conversion, but their repertoire of glycoside hydrolases is distinct from those of the microbiomes of higher termites and the bovine rumen.