BackgroundCompost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are thus important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. Studies have revealed substantial diversity in compost microbiomes, yet how this diversity relates to functions and even to the genes encoding lignocellulolytic enzymes remains obscure. Here, we used a metagenomic analysis of the rice straw-adapted (RSA) microbial consortia enriched from compost ecosystems to decipher the systematic and functional contexts within such a distinctive microbiome.ResultsAnalyses of the 16S pyrotag library and 5 Gbp of metagenomic sequence showed that the phylum Actinobacteria was the predominant group among the Bacteria in the RSA consortia, followed by Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes. The CAZymes profile revealed that CAZyme genes in the RSA consortia were also widely distributed within these bacterial phyla. Strikingly, about 46.1 % of CAZyme genes were from actinomycetal communities, which harbored a substantially expanded catalog of the cellobiohydrolase, β-glucosidase, acetyl xylan esterase, arabinofuranosidase, pectin lyase, and ligninase genes. Among these communities, a variety of previously unrecognized species was found, which reveals a greater ecological functional diversity of thermophilic Actinobacteria than previously assumed.ConclusionThese data underline the pivotal role of thermophilic Actinobacteria in lignocellulose biodegradation processes in the compost habitat. Besides revealing a new benchmark for microbial enzymatic deconstruction of lignocelluloses, the results suggest that actinomycetes found in compost ecosystems are potential candidates for mining efficient lignocellulosic enzymes in the biofuel industry.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0440-2) contains supplementary material, which is available to authorized users.

Experiments in nutrient solution were conducted to investigate the exudation of organic acids (OAs) induced by phosphorus deficiency (-P) and/or aluminium toxicity (1Al) in two contrasting soybean genotypes as related to internal OA concentration and related enzyme activities. Baxi 10 (BX10), a known P-efficient soybean (Glycine max [L] Merr.) genotype, was shown to be more resistant to 1Al than a P-inefficient genotype Bendi 2 (BD2), indicating the potential of selecting soybean cultivars with dual resistance to -P and 1Al. The two contrasting genotypes were further characterized for root exudation and formation of oxalate, malate and citrate and their related enzyme activities in response to -P, 1Al or both combined. -P significantly induced malate and oxalate exudation from both soybean genotypes, although the P-efficient BX10 tended to excrete much more oxalate than the P-inefficient BD2. The 1Al treatment triggered citrate efflux from both genotypes, with BX10 having a much greater efflux rate than BD2. Interestingly, -P did not appear to induce citrate exudation, whereas 1Al had no obvious effect on malate or oxalate exudation from the two genotypes. The exudation of OAs was generally diminished under the coupled stress of -P and 1Al in comparison with either single stress, implying a possible antagonistic effect of the two stresses on OA exudation. Root malate content was negatively correlated with its exudation in BX10 but positively in BD2. A similar tendency was observed for oxalate content and exudation only with less magnitude. Determination of six related enzymes, phosphoenolpyruvate carboxylase (PEPC), phosphoenolpyruvate phosphatase (PEPP), malate enzyme (ME), isocitrate dehydrogenase (ICDH), malate dehydrogenase (MDH), and pyruvate kinase (PK), in the root tips showed that their activities were not significantly altered during the early stage of treatments (2 and 4 days) whereas at 14 days after stress imposition, the activities of PEPC, PEPP, ME and ICDH were generally enhanced for both genotypes. However, the activity of these enzymes did not appear to be correlated with OA exudation or formation. This study clearly demonstrates that OA exudation is differentially induced by -P and 1Al in soybean plants, with specific induction of oxalate and malate by -P and citrate by 1Al. The lack of a close relationship between OA exudation and internal concentration or enzyme activities may suggest that the regulation of OA formation and exudation by -P and/or 1Al could be imposed at different stages.

Although nitrous oxide (N2O) emissions from composting contribute to the accelerated greenhouse effect, it is difficult to implement practical methods to mitigate these emissions. In this study, the effects of biochar amendment during pig manure composting were investigated to evaluate the inter-relationships between N2O emission and the abundance of denitrifying bacteria. Analytical results from two pilot composting treatments with (PWSB, pig manure + wood chips + sawdust + biochar) or without (PWS, pig manure + wood chips + sawdust) biochar (3% w/w) demonstrated that biochar amendment not only lowered NO2(-)-N concentrations but also lowered the total N2O emissions from pig manure composting, especially during the later stages. Quantification of functional genes involved in denitrification and Spearman rank correlations matrix revealed that the N2O emission rates correlated with the abundance of nosZ, nirK, and nirS genes. Biochar-amended pig manure had a higher pH and a lower moisture content. Biochar amendment altered the abundance of denitrifying bacteria significantly; less N2O-producing and more N2O-consuming bacteria were present in the PWSB, and this significantly lowered N2O emissions in the maturation phase. Together, the results demonstrate that biochar amendment could be a novel greenhouse gas mitigation strategy during pig manure composting.