Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses

Enhancing the carbon content of coal gangue for composting through sludge amendment: A feasibility study

Cocomposting coal gangue and sludge eliminates the challenge of utilizing coal gangue. However, there is limited understanding about the feasibility of cocomposting sludge and coal gangue, as well as the composting indicators, functional microorganisms, and safety risks involved. Therefore, this study evaluated the feasibility of enhancing carbon composting in coal gangue by incorporating sludge along with sawdust as a conditioner. Three laboratory-scale reactors were designed and labeled as T1 (20 % coal gangue, 60 % sludge, and 20 % sawdust), T2 (40 % coal gangue, 40 % sludge, and 20 % sawdust), and T3 (60 % coal gangue, 20 % sludge, and 20 % sawdust). Seed germination and plant growth assessments were conducted to ensure compost stability and assess phytotoxicity to cabbage (Brassica rapa chinensis L.) in terms of growth and biomass. The results indicated that the temperature, pH, EC and ammonia nitrogen of all three reactor conditions met the requirements for product decomposition. Composting was successfully achieved when the sludge proportion was 20 % (T3). However, when the sludge proportion was markedly high (T1), the harmlessness of the compost was reduced. The germination indices of T1, T2, and T3 reached 95 %, 122 %, and 119 % at maturity, respectively. This confirmed that the harmless cycle, which involved promoting condensation and aromatization, enhancing decay, and reducing composting time, was shorter in T2 and T3 than in T1. Coal gangue can also serve as a beneficial habitat for microorganisms, promoting an increase in their population and activity. Potting experiments in sandy soil revealed that the mechanism of action of compost products in soil included not only the enhancement of soil nutrients but also the improvement of soil texture. The results of this study suggest that using coal gangue as a raw material for composting is an efficient and environmentally friendly approach for producing organic fertilizers.

Integrating bioprocess and metagenomics studies to enhance humic acid production from rice straw

Rice straw burning annually (millions of tons) leads to greenhouse gas emissions, and an alternative solution is producing humic acid with high added-value. This study aimed to examine the influence of a microbial consortium and other additives (chicken manure, urea, olive mill waste, zeolite, and biochar) on the composting process of rice straw and the subsequent production of humic acid. Results showed that among the fungal species, Thermoascus aurantiacus exhibited the most prominent impact in expediting maturation and improving compost quality, and Bacillus subtilis was the most abundant bacterial species based on metagenomics analysis. The highest temperature, C/N ratio reduction, and amount of humic acid production (Respectively in lab 61 °C, 54.67%, 298 g kg-1 and in pilot level 65 °C, 72.11%, 310 g kg-1) were related to treatments containing these microorganisms and other additives except urea. Consequently, T. aurantiacus and B. subtilis can be employed on an industrial scale as compost additives to further elevate quality. Functional analysis showed that the bacterial enzymes in the treatments had the highest metabolic activities, including carbohydrate and amino acid metabolism compared to the control. The maximum enzymatic activities were in the thermophilic phase in treatments which were significantly higher than that in the control. The research emphasizes the importance of identifying and incorporating enzymatically active strains that are suitable for temperature conditions, alongside the native strains in decomposing materials. This strategy significantly improves the composting process and yields high-quality humic acid during the thermophilic phase.

Straw Addition Enhances Crop Yield, Soil Aggregation, and Soil Microorganisms in a 14-Year Wheat-Rice Rotation System in Central China

Straw return utilizes waste resources to reduce the use of chemical fertilizers worldwide. However, information is still lacking on the relative impact of straw return on soil fertility, the nutrient composition of different soil aggregates, and soil microbial communities. Therefore, this study aimed to understand the effects of different management practices on the crop yield, soil fertility, and soil community composition in a 14-year wheat-rice rotation system. The treatments included a control (without fertilizer and straw addition), chemical fertilization (NPK), straw return without fertilizer (S), and straw addition with chemical fertilizer (NPKS). The results showed that NPKS improved the wheat and rice yield by 185.12% and 88.02%, respectively, compared to the CK treatment. Additionally, compared to the CK treatment, the N, P, and K contents of the wheat stem were increased by 39.02%, 125%, and 20.23% under the NPKS treatment. Compared to the CK treatment, SOM, TN, TP, AN, AP, AK, CEC, AFe, AMn, ACu, and AZn were increased by 49.12%, 32.62%, 35.06%, 22.89%, 129.36%, 48.34%, 13.40%, 133.95%, 58.98%, 18.26% and 33.33% under the NPKS treatment, respectively. Moreover, straw addition promoted the creation and stabilization of macro-aggregates in crop soils. The relative abundance of macro-aggregates (0.25-2 mm) increased from 37.49% to 52.97%. Straw addition was associated with a higher proportion of aromatic and carbonyl carbon groups in the soil, which, in turn, promoted the formation of macro-aggregates. Redundancy analysis showed that straw return significantly increased the microbial community diversity. These findings demonstrate that straw addition together with chemical fertilizer could increase the crop yield by improving soil fertility, soil aggregate stability, and the diversity of fungi.

Dynamics of Methane-Consuming Biomes from Wieliczka Formation: Environmental and Enrichment Studies

The rocks surrounding Wieliczka salt deposits are an extreme, deep subsurface ecosystem that as we studied previously harbors many microorganisms, including methanotrophs. In the presented research bacterial community structure of the Wieliczka Salt Mine was determined as well as the methanotrophic activity of the natural microbiome. Finally, an enrichment culture of methane-consuming methanotrophs was obtained. The research material used in this study consisted of rocks surrounding salt deposits in the Wieliczka Salt Mine. DNA was extracted directly from the pristine rock material, as well as from rocks incubated in an atmosphere containing methane and mineral medium, and from a methanotrophic enrichment culture from this ecosystem. As a result, the study describes the composition of the microbiome in the rocks surrounding the salt deposits, while also explaining how biodiversity changes during the enrichment culture of the methanotrophic bacterial community. The contribution of methanotrophic bacteria ranged from 2.614% in the environmental sample to 64.696% in the bacterial culture. The methanotrophic enrichment culture was predominantly composed of methanotrophs from the genera Methylomonas (48.848%) and Methylomicrobium (15.636%) with methane oxidation rates from 3.353 ± 0.105 to 4.200 ± 0.505 µmol CH4 mL-1 day-1.

Dynamic variation of bacterial community assemblage and functional profiles during rice straw degradation

Bacteria is one of the most important drivers of straw degradation. However, the changes in bacterial community assemblage and straw-decomposing profiles during straw decomposition are not well understood. Based on cultivation-dependent and independent technologies, this study revealed that the "common species" greatly contributed to the dynamic variation of bacterial community during straw decomposition. Twenty-three functional strains involved in straw decomposition were isolated, but only seven were detected in the high-throughput sequencing data. The straw decomposers, including the isolated strains and the agents determined by functional prediction, constituted only 0.024% (on average) of the total bacterial community. The ecological network showed that most of the identified decomposers were self-existent without associations with other species. These results showed that during straw composition, community assembly might be greatly determined by the majority, but straw decomposition functions might be largely determined by the minority and emphasized the importance of the rare species in community-specific functions.

Prospects of soil microbiome application for lignocellulosic biomass degradation: An overview

Sustainable and practically viable biofuels production technology using lignocellulosic biomass is still seeking its way of implementation owing to some major issues involved therein. Unavailability of efficient microbial sources for the degradation of cellulosic biomass is one of the major roadblocks in biomass to biofuels production technology. In this context, utilization of microbiomes to degrade lignocellulaosic biomass is emerging as a rapid and effective approach that can fulfill the requirements of biomass based biofuels production technology. Therefore, the present review is targeted to explore soil metagenomic approach to improve the lignocellulosic biomass degradation processing for the cost-effective and eco-friendly application. Soil microbiomes consist of rich microbial community along with high probability of cellulolytic microbes, and can be identified by culture independent metagenomics method which can be structurally and functionally explored via genomic library. Therefore, in depth analysis and discussion have also been made via structural & functional metagenomics tools along with their contribution to genomic library. Additionally, the present review highlights currently existing bottlenecks along with their feasible solutions. This review will help to understand the basic research as well as industrial concept for the process improvement based on soil microbiome mediated lignocellulosic biomass degradation, and this may likely to implement for the low-cost commercial biofuels production technology.

Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids

Economically viable production of cellulosic biofuels requires operation at high solids loadings—on the order of 15 wt%. To this end we characterize Nature’s ability to deconstruct and utilize mid-season switchgrass at increasing solid loadings using an anaerobic methanogenic microbiome. This community exhibits undiminished fractional carbohydrate solubilization at loadings ranging from 30 g/L to 150 g/L. Metaproteomic interrogation reveals marked increases in the abundance of specific carbohydrate-active enzyme classes. Significant enrichment of auxiliary activity family 6 enzymes at higher solids suggests a role for Fenton chemistry. Stress-response proteins accompanying these reactions are similarly upregulated at higher solids, as are β-glucosidases, xylosidases, carbohydrate-debranching, and pectin-acting enzymes—all of which indicate that removal of deconstruction inhibitors is important for observed undiminished solubilization. Our work provides insights into the mechanisms by which natural microbiomes effectively deconstruct and utilize lignocellulose at high solids loadings, informing the future development of defined cultures for efficient bioconversion.

Long-Term Cellulose Enrichment Selects for Highly Cellulolytic Consortia and Competition for Public Goods

The complexity of microbial communities hinders our understanding of how microbial diversity and microbe-microbe interactions impact community functions. Here, using six independent communities originating from the refuse dumps of leaf-cutter ants and enriched using the plant polymer cellulose as the sole source of carbon, we examine how changes in bacterial diversity and interactions impact plant biomass decomposition. Over up to 60 serial transfers (∼8 months) using Whatman cellulose filter paper, cellulolytic ability increased and then stabilized in four enrichment lines and was variable in two lines. Bacterial community characterization using 16S rRNA gene amplicon sequencing showed community succession differed between the highly cellulolytic enrichment lines and those that had slower and more variable cellulose degradation rates. Metagenomic and metatranscriptomic analyses revealed that Cellvibrio and/or Cellulomonas dominated each enrichment line and produced the majority of cellulase enzymes, while diverse taxa were retained within these communities over the duration of transfers. Interestingly, the less cellulolytic communities had a higher diversity of organisms competing for the cellulose breakdown product cellobiose, suggesting that cheating slowed cellulose degradation. In addition, we found competitive exclusion as an important factor shaping all of the communities, with a negative correlation of Cellvibrio and Cellulomonas abundance within individual enrichment lines and the expression of genes associated with the production of secondary metabolites, toxins, and other antagonistic compounds. Our results provide insights into how microbial diversity and competition affect the stability and function of cellulose-degrading communities. IMPORTANCE Microbial communities are a key driver of the carbon cycle through the breakdown of complex polysaccharides in diverse environments including soil, marine systems, and the mammalian gut. However, due to the complexity of these communities, the species-species interactions that impact community structure and ultimately shape the rate of decomposition are difficult to define. Here, we performed serial enrichment on cellulose using communities inoculated from leaf-cutter ant refuse dumps, a cellulose-rich environment. By concurrently tracking cellulolytic ability and community composition and through metagenomic and metatranscriptomic sequencing, we analyzed the ecological dynamics of the enrichment lines. Our data suggest that antagonism is prevalent in these communities and that competition for soluble sugars may slow degradation and lead to community instability. Together, these results help reveal the relationships between competition and polysaccharide decomposition, with implications in diverse areas ranging from microbial community ecology to cellulosic biofuels production.

Characterization of three bacterial glycoside hydrolase family 9 endoglucanases with different modular architectures isolated from a compost metagenome

BACKGROUND

Environmental bacteria express a wide diversity of glycoside hydrolases (GH). Screening and characterization of GH from metagenomic sources provides an insight into biomass degradation strategies of non-cultivated prokaryotes.

METHODS

In the present report, we screened a compost metagenome for lignocellulolytic activities and identified six genes encoding enzymes belonging to family GH9 (GH9a-f). Three of these enzymes (GH9b, GH9d and GH9e) were successfully expressed and characterized.

RESULTS

A phylogenetic analysis of the catalytic domain of pro- and eukaryotic GH9 enzymes suggested the existence of two major subgroups. Bacterial GH9s displayed a wide variety of modular architectures and those harboring an N-terminal Ig-like domain, such as GH9b and GH9d, segregated from the remainder. We purified and characterized GH9 endoglucanases from both subgroups and examined their stabilities, substrate specificities and product profiles. GH9e exhibited an original hydrolysis pattern, liberating an elevated proportion of oligosaccharides longer than cellobiose. All of the enzymes exhibited processive behavior and a synergistic action on crystalline cellulose. Synergy was also evidenced between GH9d and a GH48 enzyme identified from the same metagenome.

CONCLUSIONS

The characterized GH9 enzymes displayed different modular architectures and distinct substrate and product profiles. The presence of a cellulose binding domain was shown to be necessary for binding and digestion of insoluble cellulosic substrates, but not for processivity.

GENERAL SIGNIFICANCE

The identification of six GH9 enzymes from a compost metagenome and the functional variety of three characterized members highlight the importance of this enzyme family in bacterial biomass deconstruction.

A thermostable bacterial lytic polysaccharide monooxygenase with high operational stability in a wide temperature range

BACKGROUND

Lytic polysaccharide monooxygenases (LPMOs) are oxidative, copper-dependent enzymes that function as powerful tools in the turnover of various biomasses, including lignocellulosic plant biomass. While LPMOs are considered to be of great importance for biorefineries, little is known about industrial relevant properties such as the ability to operate at high temperatures. Here, we describe a thermostable, cellulose-active LPMO from a high-temperature compost metagenome (called mgLPMO10).

RESULTS

MgLPMO10 was found to have the highest apparent melting temperature (83 °C) reported for an LPMO to date, and is catalytically active up to temperatures of at least 80 °C. Generally, mgLPMO10 showed good activity and operational stability over a wide temperature range. The LPMO boosted cellulose saccharification by recombinantly produced GH48 and GH6 cellobiohydrolases derived from the same metagenome, albeit to a minor extent. Cellulose saccharification studies with a commercial cellulase cocktail (Celluclast®) showed that the performance of this thermostable bacterial LPMO is comparable with that of a frequently utilized fungal LPMO from Thermoascus aurantiacus (TaLPMO9A).

CONCLUSIONS

The high activity and operational stability of mgLPMO10 are of both fundamental and applied interest. The ability of mgLPMO10 to perform oxidative cleavage of cellulose at 80 °C and the clear synergy with Celluclast® make this enzyme an interesting candidate in the development of thermostable enzyme cocktails for use in lignocellulosic biorefineries.

Almond by-product composition impacts the rearing of black soldier fly larvae and quality of the spent substrate as a soil amendment

BACKGROUND

Insect biomass is a sustainable alternative to traditional animal feeds, particularly when insects are produced on low-value high-volume agricultural by-products. Seven samples of almond by-product (hulls and shells) were obtained from processors in California and investigated for larvae production. Experiments were completed with and without larvae and spent substrate samples were assessed for their potential as soil amendments based on standard compost quality indicators.

RESULTS

On average, specific larvae growth and average larval harvest weight were 158% and 109% higher, respectively, when larvae were reared on Monterey and pollinator hulls compared to nonpareil hulls and mixed shells. Larvae methionine and cystine contents were highest when larvae were reared on Monterey hulls and mixed shells, respectively. Available phytonutrients in spent substrate were affected by feedstock sample and larvae rearing. Spent nonpareil substrate without larvae had the highest NH₄ -N levels and spent pollinator substrate incubated without larvae had the highest PO₄ -P levels. Spent mixed shell substrate had the lowest availability of phytonutrients.

CONCLUSION

The findings demonstrate that by-product composition has a significant impact on larvae growth and the properties of the spent substrate, and that spent substrate from larvae rearing requires further stabilization before application as a soil amendment. © 2020 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Cloning of novel bacterial xylanases from lignocellulose-enriched compost metagenomic libraries

Xylanases are in important class of industrial enzymes that are essential for the complete hydrolysis of lignocellulosic biomass into fermentable sugars. In the present study, we report the cloning of novel xylanases with interesting properties from compost metagenomics libraries. Controlled composting of lignocellulosic materials was used to enrich the microbial population in lignocellulolytic organisms. DNA extracted from the compost samples was used to construct metagenomics libraries, which were screened for xylanase activity. In total, 40 clones exhibiting xylanase activity were identified and the thermostability of the discovered xylanases was assayed directly from the library clones. Five genes, including one belonging to the more rare family GH8, were selected for subcloning and the enzymes were expressed in recombinant form in E. coli. Preliminary characterization of the metagenome-derived xylanases revealed interesting properties of the novel enzymes, such as high thermostability and specific activity, and differences in hydrolysis profiles. One enzyme was found to perform better than a standard Trichoderma reesei xylanase in the hydrolysis of lignocellulose at elevated temperatures.

Marine prebiotics: Polysaccharides and oligosaccharides obtained by using microbial enzymes

Utilization of marine algae has increased considerably over the past decades, since biodiversity within brown, red and green marine algae offers possibilities of finding a variety of bioactive compounds. Marine algae are rich sources of dietary fibre. The remarkable positive effects of seaweed dietary fibre on human body are related to their prebiotic activity over the gastrointestinal tract (GIT) microbiota. However, dietary modulation of microorganisms present in GIT can be influenced by different factors such as type and source of the dietary fibre, their molecular weight, type of extraction and purification methods employed, composition and modification of polysaccharide and oligosaccharide. This review will demonstrate evidence that polysaccharides and oligosaccharides from marine algae can be used as prebiotics, emphasizing their use in human health, their application as food and other possible applications. Furthermore, an important approach of microbial enzymes employment during extraction, modification or production of those prebiotics is highlighted.

High Performance Bacteria Anchored by Nanoclay to Boost Straw Degradation

Generally, crop straw degrades slowly in soil, which is unfavorable for tillage and next crop growth. Thus, it is important to develop a promising technology to boost degradation of straw. Herein, a nanobiosystem has been developed by loading bacterial mixture in nanostructured attapulgite (ATP) and using it as a straw returning agent (SRA). Therein, ATP could effectively anchor bacteria to the surface of straw and greatly facilitate the adhesion and growth of bacteria. Consequently, this technology could effectively accelerate the degradation and transformation of straw into nutrients, including nitrogen (N), phosphorus (P), potassium (K), and organic matters (OM). Pot and field tests indicated that SRA displayed significant positive effects on the growth of the next crop. Importantly, SRA could effectively decrease greenhouse gas emissions from farmland, which is beneficial for the environment. Therefore, this work provides a facile and promising method to facilitate the degradation of straw, which might have a potential application value.

The initial soil microbiota impacts the potential for lignocellulose degradation during soil solarization

AIMS

Soil biosolarization (SBS) is a pest control technology that includes the incorporation of organic matter into soil prior to solarization. The objective of this study was to measure the impact of the initial soil microbiome on the temporal evolution of genes encoding lignocellulose-degrading enzymes during SBS.

METHODS AND RESULTS

Soil biosolarization field experiments were completed using green waste (GW) as a soil amendment and in the presence and absence of compost activating inoculum. Samples were collected over time and at two different soil depths for measurement of the microbial community and the predicted lignocellulosic-degrading microbiome. Compost inoculum had a significant positive effect on several predicted genes encoding enzymes involved in cellulose, hemicellulose and lignin degradation. These included beta-glucosidase, endo-1,3(4)-beta-glucanase, alpha-galactosidase and laccase.

CONCLUSION

Amendment of micro-organisms found in compost to soil prior to SBS enhanced the degradation potential of cellulose, hemicellulose and lignin found in GW.

SIGNIFICANCE AND IMPACT OF THE STUDY

The type of organic matter amended and its biotransformation by soil micro-organisms impact the efficacy of SBS. The results suggest that co-amending highly recalcitrant biomass with micro-organisms found in compost improves biomass conversion during SBS.

Witches' broom resistant genotype CCN51 shows greater diversity of symbiont bacteria in its phylloplane than susceptible genotype catongo

Background

Theobroma cacao L. (cacao) is a perennial tropical tree, endemic to rainforests of the Amazon Basin. Large populations of bacteria live on leaf surfaces and these phylloplane microorganisms can have important effects on plant health. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated studies of the phylloplane microbiome. In this study, we characterized the bacterial microbiome of the phylloplane of the catongo genotype (susceptible to witch’s broom) and CCN51 (resistant). Bacterial microbiome was determined by sequencing the V3-V4 region of the bacterial 16S rRNA gene.

Results

After the pre-processing, a total of 1.7 million reads were considered. In total, 106 genera of bacteria were characterized. Proteobacteria was the predominant phylum in both genotypes. The exclusive genera of Catongo showed activity in the protection against UV radiation and in the transport of substrates. CCN51 presented genus that act in the biological control and inhibition in several taxonomic groups. Genotype CCN51 presented greater diversity of microorganisms in comparison to the Catongo genotype and the total community was different between both. Scanning electron microscopy analysis of leaves revealed that on the phylloplane, many bacterial occur in large aggregates in several regions of the surface and isolated nearby to the stomata.

Conclusions

We describe for the first time the phylloplane bacterial communities of T. cacao. The Genotype CCN51, resistant to the witch’s broom, has a greater diversity of bacterial microbioma in comparison to Catongo and a greater amount of exclusive microorganisms in the phylloplane with antagonistic action against phytopathogens.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1339-9) contains supplementary material, which is available to authorized users.

Comparison of thermophilic anaerobic and aerobic treatment processes for stabilization of green and food wastes and production of soil amendments

The management of organic wastes is an environmental and social priority. Aerobic digestion (AED) or composting and anaerobic digestion (AD) are two organic waste management practices that produce a value-added final product. Few side-by-side comparisons of both technologies and their digestate products have been performed. The objective of this study was to compare the impact of initial feedstock properties (moisture content and/or C/N ratio) on stabilization rate by AED and AD and soil amendment characteristics of the final products. Green and food wastes were considered as they are two of the main contributors to municipal organic waste. Stabilization rate was assessed by measurement of CH₄ and CO₂ evolution for AD and AED, respectively. For AD, CH₄ yield showed a second-order relationship with the C/N content (P < 0.05); the optimal C/N ratio indicated by the relationship was 25.5. For AED, cumulative CO₂ evolution values were significantly affected by the C/N ratio and moisture content of the initial feedstock (P < 0.05). A response surface model showed optimal AED stabilization for a C/N of 25.6 and moisture of 64.9% (wet basis). AD final products presented lower soluble chemical oxygen demand (COD) but lower humification degree and aromaticity than the products from AED. This lower stability may lead to further degradation when amended to soil. The results suggest that composting feedstocks with higher C/N produces an end-product with higher suitability for soil amendment. The instability of end products from AD could be leveraged in pest control techniques that rely on organic matter degradation to produce compounds with pesticidal properties.

Discovery and characterization of a thermostable two-domain GH6 endoglucanase from a compost metagenome

Enzymatic depolymerization of recalcitrant polysaccharides plays a key role in accessing the renewable energy stored within lignocellulosic biomass, and natural biodiversities may be explored to discover microbial enzymes that have evolved to conquer this task in various environments. Here, a metagenome from a thermophilic microbial community was mined to yield a novel, thermostable cellulase, named mgCel6A, with activity on an industrial cellulosic substrate (sulfite-pulped Norway spruce) and a glucomannanase side activity. The enzyme consists of a glycoside hydrolase family 6 catalytic domain (GH6) and a family 2 carbohydrate binding module (CBM2) that are connected by a linker rich in prolines and threonines. MgCel6A exhibited maximum activity at 85°C and pH 5.0 on carboxymethyl cellulose (CMC), but in prolonged incubations with the industrial substrate, the highest yields were obtained at 60°C, pH 6.0. Differential scanning calorimetry (DSC) indicated a T_m(app) of 76°C. Both functional data and the crystal structure, solved at 1.88 Å resolution, indicate that mgCel6A is an endoglucanase. Comparative studies with a truncated variant of the enzyme showed that the CBM increases substrate binding, while not affecting thermal stability. Importantly, at higher substrate concentrations the full-length enzyme was outperformed by the catalytic domain alone, underpinning previous suggestions that CBMs may be less useful in high-consistency bioprocessing.

Uncovering the Potential of Termite Gut Microbiome for Lignocellulose Bioconversion in Anaerobic Batch Bioreactors

Termites are xylophages, being able to digest a wide variety of lignocellulosic biomass including wood with high lignin content. This ability to feed on recalcitrant plant material is the result of complex symbiotic relationships, which involve termite-specific gut microbiomes. Therefore, these represent a potential source of microorganisms for the bioconversion of lignocellulose in bioprocesses targeting the production of carboxylates. In this study, gut microbiomes of four termite species were studied for their capacity to degrade wheat straw and produce carboxylates in controlled bioreactors. All of the gut microbiomes successfully degraded lignocellulose and up to 45% w/w of wheat straw degradation was observed, with the Nasutitermes ephratae gut-microbiome displaying the highest levels of wheat straw degradation, carboxylate production and enzymatic activity. Comparing the 16S rRNA gene diversity of the initial gut inocula to the bacterial communities in lignocellulose degradation bioreactors revealed important changes in community diversity. In particular, taxa such as Spirochaetes and Fibrobacteres that were highly abundant in the initial gut inocula were replaced by Firmicutes and Proteobacteria at the end of incubation in wheat straw bioreactors. Overall, this study demonstrates that termite-gut microbiomes constitute a reservoir of lignocellulose-degrading bacteria that can be harnessed in artificial conditions for biomass conversion processes that lead to the production of useful molecules.

Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community

BACKGROUND

Degradation of pectin in lignocellulosic materials is one of the key steps for biofuel production. Biological hydrolysis of pectin, i.e., degradation by pectinolytic microbes and enzymes, is an attractive paradigm because of its obvious advantages, such as environmentally friendly procedures, low in energy demand for lignin removal, and the possibility to be integrated in consolidated process. In this study, a metagenomics sequence-guided strategy coupled with enrichment culture technique was used to facilitate targeted discovery of pectinolytic microbes and enzymes. An apple pomace-adapted compost (APAC) habitat was constructed to boost the enrichment of pectinolytic microorganisms.

RESULTS

Analyses of 16S rDNA high-throughput sequencing revealed that microbial communities changed dramatically during composting with some bacterial populations being greatly enriched. Metagenomics data showed that apple pomace-adapted compost microbial community (APACMC) was dominated by Proteobacteria and Bacteroidetes. Functional analysis and carbohydrate-active enzyme profiles confirmed that APACMC had been successfully enriched for the targeted functions. Among the 1756 putative genes encoding pectinolytic enzymes, 129 were predicted as novel (with an identity <30% to any CAZy database entry) and only 1.92% were more than 75% identical with proteins in NCBI environmental database, demonstrating that they have not been observed in previous metagenome projects. Phylogenetic analysis showed that APACMC harbored a broad range of pectinolytic bacteria and many of them were previously unrecognized.

CONCLUSIONS

The immensely diverse pectinolytic microbes and enzymes found in our study will expand the arsenal of proficient degraders and enzymes for lignocellulosic biofuel production. Our study provides a powerful approach for targeted mining microbes and enzymes in numerous industries.

Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia

Plant biomass (PB) is an important resource for biofuel production. However, the frequent lack of efficiency of PB saccharification is still an industrial bottleneck. The use of enzyme cocktails produced from PB-degrading microbial consortia (PB-dmc) is a promising approach to optimize this process. Nevertheless, the proper use and manipulation of PB-dmc depends on a sound understanding of the ecological processes and mechanisms that exist in these communities. This Opinion article provides an overview of arguments as to how spatiotemporal nutritional fluxes influence the successional dynamics and ecological interactions (synergism versus competition) between populations in PB-dmc. The themes of niche occupancy, 'sugar cheaters', minimal effective consortium, and the Black Queen Hypothesis are raised as key subjects that foster our appraisal of such systems. Here we provide a conceptual framework that describes the critical topics underpinning the ecological basis of PB-dmc, giving a solid foundation upon which further prospective experimentation can be developed.

Polysaccharide Degradation Capability of Actinomycetales Soil Isolates from a Semiarid Grassland of the Colorado Plateau

Among the bacteria, members of the order Actinomycetales are considered quintessential degraders of complex polysaccharides in soils. However, studies examining complex polysaccharide degradation by Actinomycetales (other than Streptomyces spp.) in soils are limited. Here, we examine the lignocellulolytic and chitinolytic potential of 112 Actinomycetales strains, encompassing 13 families, isolated from a semiarid grassland of the Colorado Plateau in Utah. Members of the Streptomycetaceae, Pseudonocardiaceae, Micromonosporaceae, and Promicromonosporaceae families exhibited robust activity against carboxymethyl cellulose, xylan, chitin, and pectin substrates (except for low/no pectinase activity by the Micromonosporaceae). When incubated in a hydrated mixture of blended Stipa and Hilaria grass biomass over a 5-week period, Streptomyces and Saccharothrix (a member of the Pseudonocardiaceae) isolates produced high levels of extracellular enzyme activity, such as endo- and exocellulase, glucosidase, endo- and exoxylosidase, and arabinofuranosidase. These characteristics make them well suited to degrade the cellulose and hemicellulose components of grass cell walls. On the basis of the polysaccharide degradation profiles of the isolates, relative abundance of Actinomycetales sequences in 16S rRNA gene surveys of Colorado Plateau soils, and analysis of genes coding for polysaccharide-degrading enzymes among 237 Actinomycetales genomes in the CAZy database and 5 genomes from our isolates, we posit that Streptomyces spp. and select members of the Pseudonocardiaceae and Micromonosporaceae likely play an important role in the degradation of hemicellulose, cellulose, and chitin substances in dryland soils.IMPORTANCE Shifts in the relative abundance of Actinomycetales taxa have been observed in soil microbial community surveys during large, manipulated climate change field studies. However, our limited understanding of the ecophysiology of diverse Actinomycetales taxa in soil systems undermines attempts to determine the underlying causes of the population shifts or their impact on carbon cycling in soil. This study combines a systematic analysis of the polysaccharide degradation potential of a diverse collection of Actinomycetales isolates from surface soils of a semiarid grassland with analysis of genomes from five of these isolates and publicly available Actinomycetales genomes for genes encoding polysaccharide-active enzymes. The results address an important gap in knowledge of Actinomycetales ecophysiology-identification of key taxa capable of facilitating lignocellulose degradation in dryland soils. Information from this study will benefit future metagenomic studies related to carbon cycling in dryland soils by providing a baseline linkage of Actinomycetales phylogeny with lignocellulolytic functional potential.

Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis

Pretreatment using ionic liquids (IL) is a promising approach for the conversion of lignocellulose to biofuels. Because IL can be inhibitory to enzymes and microorganisms involved in downstream hydrolysis and fermentation steps, discovery of IL-tolerant organisms and enzymes is critical for advancing this technology. Employing metatranscriptomics in the analysis of IL-enriched cultures facilitated tracking of dynamic changes in a complex microbial community at the level of gene transcription and doing so with genome resolution. Specific organisms were discovered that could simultaneously tolerate a moderate IL concentration and transcribe a diverse array of cellulolytic enzymes. Gene sequences of cellulolytic enzymes and efflux pumps from those same organisms were also identified, providing important resources for future research on engineering IL-tolerant organisms and enzymes.

Ionic liquid (IL) pretreatment is a promising approach for the conversion of lignocellulose to biofuels. The toxicity of residual IL, however, negatively impacts the performance of industrial enzymes and microorganisms in hydrolysis and fermentation. In this study, a thermophilic microbial community was cultured on switchgrass amended with various levels of the ionic liquid 1-ethyl-3-methylimidazolium acetate. Changes in the microbial community composition and transcription of genes relevant to IL tolerance and lignocellulose hydrolysis were quantified. Increasing the level of IL to 0.1% (wt) led to increased levels of relative abundance and transcription in organisms of the phylum Firmicutes. Interestingly, IL concentrations of up to 1% (wt) also resulted in greater xylanase transcription and enzyme activity as well as increased transcription of endoglucanase, beta-glucosidase, and IL tolerance genes compared to communities without IL. IL levels above 1% (wt) resulted in decreased enzyme activity and transcription of genes involved in lignocellulose hydrolysis. The results indicate that moderate levels of IL select for thermophilic microorganisms that not only tolerate IL but also effectively hydrolyze lignocellulose from switchgrass. Discovery of IL-tolerant organisms and enzymes is critical for the development of biological processes that convert IL-pretreated biomass to biofuels and chemicals. Employing metatranscriptomic analysis of enrichment cultures can facilitate the discovery of microorganisms and enzymes that may be active in the presence of toxic compounds such as ionic liquids.

IMPORTANCE Pretreatment using ionic liquids (IL) is a promising approach for the conversion of lignocellulose to biofuels. Because IL can be inhibitory to enzymes and microorganisms involved in downstream hydrolysis and fermentation steps, discovery of IL-tolerant organisms and enzymes is critical for advancing this technology. Employing metatranscriptomics in the analysis of IL-enriched cultures facilitated tracking of dynamic changes in a complex microbial community at the level of gene transcription and doing so with genome resolution. Specific organisms were discovered that could simultaneously tolerate a moderate IL concentration and transcribe a diverse array of cellulolytic enzymes. Gene sequences of cellulolytic enzymes and efflux pumps from those same organisms were also identified, providing important resources for future research on engineering IL-tolerant organisms and enzymes.

Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures

Cost-effective biofuel production from lignocellulosic biomass depends on efficient degradation of the plant cell wall. One of the major obstacles for the development of a cost-efficient process is the lack of resistance of currently used fungal enzymes to harsh conditions such as high temperature. Adapted, thermophilic microbial communities provide a huge reservoir of potentially interesting lignocellulose-degrading enzymes for improvement of the cellulose hydrolysis step. In order to identify such enzymes, a leaf and wood chip compost was enriched on a mixture of thermo-chemically pretreated wheat straw, poplar and Miscanthus under thermophile conditions, but in two different set-ups. Unexpectedly, metagenome sequencing revealed that incubation of the lignocellulosic substrate with compost as inoculum in a suspension culture resulted in an impoverishment of putative cellulase- and hemicellulase-encoding genes. However, mimicking composting conditions without liquid phase yielded a high number and diversity of glycoside hydrolase genes and an enrichment of genes encoding cellulose binding domains. These identified genes were most closely related to species from Actinobacteria, which seem to constitute important players of lignocellulose degradation under the applied conditions. The study highlights that subtle changes in an enrichment set-up can have an important impact on composition and functions of the microcosm. Composting-like conditions were found to be the most successful method for enrichment in species with high biomass degrading capacity.

Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts

Chemical and physical pretreatment of biomass is a critical step in the conversion of lignocellulose to biofuels and bioproducts. Ionic liquid (IL) pretreatment has attracted significant attention due to the unique ability of certain ILs to solubilize some or all components of the plant cell wall. However, these ILs inhibit not only the enzyme activities but also the growth and productivity of microorganisms used in downstream hydrolysis and fermentation processes. While pretreated biomass can be washed to remove residual IL and reduce inhibition, extensive washing is costly and not feasible in large-scale processes. IL-tolerant microorganisms and microbial communities have been discovered from environmental samples and studies begun to elucidate mechanisms of IL tolerance. The discovery of IL tolerance in environmental microbial communities and individual microbes has lead to the proposal of molecular mechanisms of resistance. In this article, we review recent progress on discovering IL-tolerant microorganisms, identifying metabolic pathways and mechanisms of tolerance, and engineering microorganisms for IL tolerance. Research in these areas will yield new approaches to overcome inhibition in lignocellulosic biomass bioconversion processes and increase opportunities for the use of ILs in biomass pretreatment.

Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition

BACKGROUND

Compost 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.

RESULTS

Analyses 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.

CONCLUSION

These 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.

Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin

Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.

Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions

BACKGROUND

Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methods included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions.

RESULTS

High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms.

CONCLUSIONS

A stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.

EBI metagenomics in 2016--an expanding and evolving resource for the analysis and archiving of metagenomic data

EBI metagenomics (https://www.ebi.ac.uk/metagenomics/) is a freely available hub for the analysis and archiving of metagenomic and metatranscriptomic data. Over the last 2 years, the resource has undergone rapid growth, with an increase of over five-fold in the number of processed samples and consequently represents one of the largest resources of analysed shotgun metagenomes. Here, we report the status of the resource in 2016 and give an overview of new developments. In particular, we describe updates to data content, a complete overhaul of the analysis pipeline, streamlining of data presentation via the website and the development of a new web based tool to compare functional analyses of sequence runs within a study. We also highlight two of the higher profile projects that have been analysed using the resource in the last year: the oceanographic projects Ocean Sampling Day and Tara Oceans.

Metagenomics for the development of new biocatalysts to advance lignocellulose saccharification for bioeconomic development

The world economy is moving toward the use of renewable and nonedible lignocellulosic biomasses as substitutes for fossil sources in order to decrease the environmental impact of manufacturing processes and overcome the conflict with food production. Enzymatic hydrolysis of the feedstock is a key technology for bio-based chemical production, and the identification of novel, less expensive and more efficient biocatalysts is one of the main challenges. As the genomic era has shown that only a few microorganisms can be cultured under standard laboratory conditions, the extraction and analysis of genetic material directly from environmental samples, termed metagenomics, is a promising way to overcome this bottleneck. Two screening methodologies can be used on metagenomic material: the function-driven approach of expression libraries and sequence-driven analysis based on gene homology. Both techniques have been shown to be useful for the discovery of novel biocatalysts for lignocellulose conversion, and they enabled identification of several (hemi)cellulases and accessory enzymes involved in (hemi)cellulose hydrolysis. This review summarizes the latest progress in metagenomics aimed at discovering new enzymes for lignocellulose saccharification.

Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw

BACKGROUND

New lignocellulolytic enzymes are needed that maintain optimal activity under the harsh conditions present during industrial enzymatic deconstruction of biomass, including high temperatures, the absence of free water, and the presence of inhibitors from the biomass. Enriching lignocellulolytic microbial communities under these conditions provides a source of microorganisms that may yield robust lignocellulolytic enzymes tolerant to the extreme conditions needed to improve the throughput and efficiency of biomass enzymatic deconstruction. Identification of promising enzymes from these systems is challenging due to complex substrate-enzyme interactions and requirements to assay for activity. In this study, metatranscriptomes from compost-derived microbial communities enriched on rice straw under thermophilic and mesophilic conditions were sequenced and analyzed to identify lignocellulolytic enzymes overexpressed under thermophilic conditions. To determine differential gene expression across mesophilic and thermophilic treatments, a method was developed which pooled gene expression by functional category, as indicated by Pfam annotations, since microbial communities performing similar tasks are likely to have overlapping functions even if they share no specific genes.

RESULTS

Differential expression analysis identified enzymes from glycoside hydrolase family 48, carbohydrate binding module family 2, and carbohydrate binding module family 33 domains as significantly overexpressed in the thermophilic community. Overexpression of these protein families in the thermophilic community resulted from expression of a small number of genes not currently represented in any protein database. Genes in overexpressed protein families were predominantly expressed by a single Actinobacteria genus, Micromonospora.

CONCLUSIONS

Coupling measurements of deconstructive activity with comparative analyses to identify overexpressed enzymes in lignocellulolytic communities provides a targeted approach for discovery of candidate enzymes for more efficient biomass deconstruction. Glycoside hydrolase family 48 cellulases and carbohydrate binding module family 33 polysaccharide monooxygenases with carbohydrate binding module family 2 domains may improve saccharification of lignocellulosic biomass under high-temperature and low moisture conditions relevant to industrial biofuel production.

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

BACKGROUND

Recovering individual genomes from metagenomic datasets allows access to uncultivated microbial populations that may have important roles in natural and engineered ecosystems. Understanding the roles of these uncultivated populations has broad application in ecology, evolution, biotechnology and medicine. Accurate binning of assembled metagenomic sequences is an essential step in recovering the genomes and understanding microbial functions.

RESULTS

We have developed a binning algorithm, MaxBin, which automates the binning of assembled metagenomic scaffolds using an expectation-maximization algorithm after the assembly of metagenomic sequencing reads. Binning of simulated metagenomic datasets demonstrated that MaxBin had high levels of accuracy in binning microbial genomes. MaxBin was used to recover genomes from metagenomic data obtained through the Human Microbiome Project, which demonstrated its ability to recover genomes from real metagenomic datasets with variable sequencing coverages. Application of MaxBin to metagenomes obtained from microbial consortia adapted to grow on cellulose allowed genomic analysis of new, uncultivated, cellulolytic bacterial populations, including an abundant myxobacterial population distantly related to Sorangium cellulosum that possessed a much smaller genome (5 MB versus 13 to 14 MB) but has a more extensive set of genes for biomass deconstruction. For the cellulolytic consortia, the MaxBin results were compared to binning using emergent self-organizing maps (ESOMs) and differential coverage binning, demonstrating that it performed comparably to these methods but had distinct advantages in automation, resolution of related genomes and sensitivity.

CONCLUSIONS

The automatic binning software that we developed successfully classifies assembled sequences in metagenomic datasets into recovered individual genomes. The isolation of dozens of species in cellulolytic microbial consortia, including a novel species of myxobacteria that has the smallest genome among all sequenced aerobic myxobacteria, was easily achieved using the binning software. This work demonstrates that the processes required for recovering genomes from assembled metagenomic datasets can be readily automated, an important advance in understanding the metabolic potential of microbes in natural environments. MaxBin is available at https://sourceforge.net/projects/maxbin/.