Microbial Consortium with High Cellulolytic Activity (MCHCA) for Enhanced Biogas Production

Degradation of edible mushroom waste by Hermetia illucens L. and consequent adaptation of its gut microbiota

The edible fungus industry is one of the pillar industries in the Yunnan-Guizhou Plateau, China. The expansion of the planting scale has led to the release of various mushroom residues, such as mushroom feet, and other wastes, which are not treated adequately, resulting in environmental pollution. This study investigated the ability of black soldier fly (Hermetia illucens L.) larvae (BSFL) to degrade mushroom waste. Moreover, this study analyzed changes in the intestinal bacterial community and gene expression of BSFL after feeding on mushroom waste. Under identical feeding conditions, the remaining amount of mushroom waste in Pleurotus ostreatus treatment group was reduced by 18.66%, whereas that in Flammulina velutipes treatment group was increased by 31.08%. Regarding gut microbial diversity, compared with wheat bran-treated control group, Dysgonomonas, Providencia, Enterococcus, Pseudochrobactrum, Actinomyces, Morganella, Ochrobactrum, Raoultella, and Ignatzschineria were the most abundant bacteria in the midgut of BSFL in F. velutipes treatment group. Furthermore, Dysgonomonas, Campylobacter, Providencia, Ignatzschineria, Actinomyces, Enterococcus, Morganella, Raoultella, and Pseudochrobactrum were the most abundant bacteria in the midgut of BSFL in P. ostreatus treatment group. Compared with wheat bran-treated control group, 501 upregulated and 285 downregulated genes were identified in F. velutipes treatment group, whereas 211 upregulated and 43 downregulated genes were identified in P. ostreatus treatment group. Using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment analyses, we identified 14 differentially expressed genes (DEGs) related to amino sugar and nucleotide sugar metabolism in F. velutipes treatment group, followed by 12 DEGs related to protein digestion and absorption. Moreover, in P. ostreatus treatment group, two DEGs were detected for fructose and mannose metabolism, and two were noted for fatty acid metabolism. These results indicate that feeding on edible mushroom waste can alter the intestinal microbial community structure of BSFL; moreover, the larval intestine can generate a corresponding feedback. These changes contribute to the degradation of edible mushroom waste by BSFL and provide a reference for treating edible mushroom waste using BSFL.

Valorization of crop residues and animal wastes: Anaerobic co-digestion technology

To switch the over-reliance on fossil-based resources, curb environmental quality deterioration, and promote the use of renewable fuels, much attention has recently been directed toward the implementation of sustainable and environmentally benign 'waste-to-energy' technology exploiting a clean, inexhaustible, carbon-neutral, and renewable energy source, namely agricultural biomass. From this perspective, anaerobic co-digestion (AcoD) technology emerges as a potent and plausible approach to attain sustainable energy development, foster environmental sustainability, and, most importantly, circumvent the key challenges associated with mono-digestion. This review article provides a comprehensive overview of AcoD as a biochemical valorization pathway of crop residues and livestock manure for biogas production. Furthermore, this manuscript aims to assess the different biotic and abiotic parameters affecting co-digestion efficiency and present recent advancements in pretreatment technologies designed to enhance feedstock biodegradability and conversion rate. It can be concluded that the substantial quantities of crop residues and animal waste generated annually from agricultural practices represent valuable bioenergy resources that can contribute to meeting global targets for affordable renewable energy. Nevertheless, extensive and multidisciplinary research is needed to evolve the industrial-scale implementation of AcoD technology of livestock waste and crop residues, particularly when a pretreatment phase is included, and bridge the gap between small-scale studies and real-world applications.

A concerted enzymatic de-structuring of lignocellulosic materials using a compost-derived microbial consortia favoring the consolidated pretreatment and bio-saccharification

The robustness of microbial consortia isolated from compost habitat encompasses the complementary metabolism that aids in consolidated bioprocessing (CBP) of lignocellulosic biomass (LCB) by division of labor across the symbionts. Composting of organic waste is deemed to be an efficient way of carbon recycling, where the syntrophic microbial population exerts a concerted action of lignin and polysaccharide (hemicellulose and cellulose) component of plant biomass. The potential of this interrelated microorganism could be enhanced through adaptive laboratory evolution (ALE) with LCB for its desired functional capabilities. Therefore, in this study, microbial symbionts derived from organic compost was enriched on saw dust (SD) (woody biomass), aloe vera leaf rind (AVLR) (agro-industrial waste) and commercial filter paper (FP) (pure cellulose) through ALE under different conditions. Later, the efficacy of enriched consortium (EC) on consolidated pretreatment and bio-saccharification was determined based on substrate degradation, endo-enzymes profiling and fermentable sugar yield. Among the treatment sets, AVLR biomass treated with EC-5 has resulted in the higher degradation rate of lignin (47.01 ± 0.66%, w/w) and polysaccharides (45.87 ± 1.82%, w/w) with a total sugar yield of about 60.01 ± 4.24 mg/g. In addition, the extent of structural disintegration of substrate after EC-treatment was clearly deciphered by FTIR and XRD analysis. And the factors of Pearson correlation matrix reinforces the potency of EC-5 by exhibiting a strong positive correlation between AVLR degradation and the sugar release. Thus, a consortium based CBP could promote the feasibility of establishing a sustainable second generation biorefinery framework.

Dairy manure acidogenic fermentation at hyperthermophilic temperature enabled superior activity of thermostable hydrolytic enzymes linked to the genus Caldicoprobacter

In this study, fermentation experiments were conducted under mesophilic, thermophilic, and hyperthermophilic conditions to investigate adaptation of microbial communities and its effect on extracellular enzyme activities toward degradation of cellulose, hemicellulose and proteins in dairy manure. Hyperthermophilic conditions transformed the microbiome structure and stimulated activity of extracellular proteolytic, cellulolytic, and hemicellulolytic enzymes. Specifically, the activities of protease, cellulose 1,4-β-cellobiosidase, and β-glucosidase secreted by hyperthermophilic microbes were higher by 22%, 47% and 49% compared to those produced by mesophilic and thermophilic communities. Enhanced hydrolytic activity of hyperthermophilic microbes enabled improved feedstock solubilization and production of 39% and 22% more soluble COD than mesophilic and thermophilic microbes, respectively. Connections between hydrolytic function and microbial community structure at various temperatures were assessed using the PICRUSt2 computational tool. Genus Caldicoprobacter was identified as the primary candidate responsible for increased production of thermostable endo-1,4-β-glucanase, β-glucosidase and endo-1,4-β-xylanase, and enhanced hydrolytic performance of hyperthermophilic microbial community.

Taxonomic and enzymatic basis of the cellulolytic microbial consortium KKU-MC1 and its application in enhancing biomethane production

Lignocellulosic biomass is a promising substrate for biogas production. However, its recalcitrant structure limits conversion efficiency. This study aims to design a microbial consortium (MC) capable of producing the cellulolytic enzyme and exploring the taxonomic and genetic aspects of lignocellulose degradation. A diverse range of lignocellulolytic bacteria and degrading enzymes from various habitats were enriched for a known KKU-MC1. The KKU-MC1 was found to be abundant in Bacteroidetes (51%), Proteobacteria (29%), Firmicutes (10%), and other phyla (8% unknown, 0.4% unclassified, 0.6% archaea, and the remaining 1% other bacteria with low predominance). Carbohydrate-active enzyme (CAZyme) annotation revealed that the genera Bacteroides, Ruminiclostridium, Enterococcus, and Parabacteroides encoded a diverse set of cellulose and hemicellulose degradation enzymes. Furthermore, the gene families associated with lignin deconstruction were more abundant in the Pseudomonas genera. Subsequently, the effects of MC on methane production from various biomasses were studied in two ways: bioaugmentation and pre-hydrolysis. Methane yield (MY) of pre-hydrolysis cassava bagasse (CB), Napier grass (NG), and sugarcane bagasse (SB) with KKU-MC1 for 5 days improved by 38-56% compared to non-prehydrolysis substrates, while MY of prehydrolysed filter cake (FC) for 15 days improved by 56% compared to raw FC. The MY of CB, NG, and SB (at 4% initial volatile solid concentration (IVC)) with KKU-MC1 augmentation improved by 29-42% compared to the non-augmentation treatment. FC (1% IVC) had 17% higher MY than the non-augmentation treatment. These findings demonstrated that KKU-MC1 released the cellulolytic enzyme capable of decomposing various lignocellulosic biomasses, resulting in increased biogas production.

Arabinan saccharification by biogas reactor metagenome-derived arabinosyl hydrolases

BACKGROUND

Plant cell walls represent the most plentiful renewable organic resource on earth, but due to their heterogeneity, complex structure and partial recalcitrance, their use as biotechnological feedstock is still limited.

RESULTS

In order to identify efficient enzymes for polysaccharide breakdown, we have carried out functional screening of metagenomic fosmid libraries from biogas fermenter microbial communities grown on sugar beet pulp, an arabinan-rich agricultural residue, or other sources containing microbes that efficiently depolymerize polysaccharides, using CPH (chromogenic polysaccharide hydrogel) or ICB (insoluble chromogenic biomass) labeled polysaccharide substrates. Seventy-one depolymerase-encoding genes were identified from 55 active fosmid clones by using Illumina and Sanger sequencing and dbCAN CAZyme (carbohydrate-active enzyme) annotation. An around 56 kb assembled DNA fragment putatively originating from Xylanivirga thermophila strain or a close relative was analyzed in detail. It contained 48 ORFs (open reading frames), of which 31 were assigned to sugar metabolism. Interestingly, a large number of genes for enzymes putatively involved in degradation and utilization of arabinose-containing carbohydrates were found. Seven putative arabinosyl hydrolases from this DNA fragment belonging to glycoside hydrolase (GH) families GH51 and GH43 were biochemically characterized, revealing two with endo-arabinanase activity and four with exo-α-L-arabinofuranosidase activity but with complementary cleavage properties. These enzymes were found to act synergistically and can completely hydrolyze SBA (sugar beet arabinan) and DA (debranched arabinan).

CONCLUSIONS

We screened 32,776 fosmid clones from several metagenomic libraries with chromogenic lignocellulosic substrates for functional enzymes to advance the understanding about the saccharification of recalcitrant lignocellulose. Seven putative X. thermophila arabinosyl hydrolases were characterized for pectic substrate degradation. The arabinosyl hydrolases displayed maximum activity and significant long-term stability around 50 °C. The enzyme cocktails composed in this study fully degraded the arabinan substrates and thus could serve for arabinose production in food and biofuel industries.

The Structure of Stable Cellulolytic Consortia Isolated from Natural Lignocellulosic Substrates

Recycling plant matter is one of the challenges facing humanity today and depends on efficient lignocellulose degradation. Although many bacterial strains from natural substrates demonstrate cellulolytic activities, the CAZymes (Carbohydrate-Active enZYmes) responsible for these activities are very diverse and usually distributed among different bacteria in one habitat. Thus, using microbial consortia can be a solution to rapid and effective decomposition of plant biomass. Four cellulolytic consortia were isolated from enrichment cultures from composting natural lignocellulosic substrates—oat straw, pine sawdust, and birch leaf litter. Enrichment cultures facilitated growth of similar, but not identical cellulose-decomposing bacteria from different substrates. Major components in all consortia were from Proteobacteria, Actinobacteriota and Bacteroidota, but some were specific for different substrates—Verrucomicrobiota and Myxococcota from straw, Planctomycetota from sawdust and Firmicutes from leaf litter. While most members of the consortia were involved in the lignocellulose degradation, some demonstrated additional metabolic activities. Consortia did not differ in the composition of CAZymes genes, but rather in axillary functions, such as ABC-transporters and two-component systems, usually taxon-specific and associated with CAZymes. Our findings show that enrichment cultures can provide reproducible cellulolytic consortia from various lignocellulosic substrates, the stability of which is ensured by tight microbial relations between its components.

A comprehensive review on anaerobic fungi applications in biofuels production

Anaerobic fungi (Neocallimastigomycota) are promising lignocellulose-degrading microorganisms that can be exploited by the biofuel industry. While natural production of ethanol by these microorganisms is very low, there is a greater potential for their use in the biogas industry. More specifically, anaerobic fungi can contribute to biogas production by either releasing holocellulose or reducing sugars from lignocelluloses that can be used as a substrate by bacteria and methanogens involved in the anaerobic digestion (AD) process or by metabolizing acetate and formate that can be directly consumed by methanogens. Despite their great potential, the appropriate tools for engineering anaerobic fungi have not been established yet. The first section of this review justifies how the biofuel industry can benefit from using anaerobic fungi and is followed by their taxonomy. In the third section, the possibility of using anaerobic fungi for the consolidated production of bioethanol is briefly discussed. Nevertheless, the main focus of this review is on the upstream and mainstream effects of bioaugmentation with anaerobic fungi on the AD process. The present review also scrutinizes the constraints on the way of efficient engineering of anaerobic rumen fungi. By providing this knowledge, this review aims to help research in this field with identifying the challenges that must be addressed by future experiments to achieve the full potentials of these promising microorganisms. To sum up, the pretreatment of lignocelluloses by anaerobic fungi can prevent carbohydrate loss due to respiration (compared to white-rot fungi). Following fungal mixed acid fermentation, the obtained slurry containing sugars and more susceptible holocellulose can be directly consumed by AD microorganisms (bacteria, methanogens). The bioaugmentation of anaerobic fungi into the AD process can increase methane biosynthesis by >3.3 times. Despite this, for the commercial AD process, novel genetic engineering techniques and kits must be developed to efficiently improve anaerobic fungi viability throughout the AD process.

Fibrolytic rumen bacteria of camel and sheep and their applications in the bioconversion of barley straw to soluble sugars for biofuel production

Lignocellulosic biomass such as barley straw is a renewable and sustainable alternative to traditional feeds and could be used as bioenergy sources; however, low hydrolysis rate reduces the fermentation efficiency. Understanding the degradation and colonization of barley straw by rumen bacteria is the key step to improve the utilization of barley straw in animal feeding or biofuel production. This study evaluated the hydrolysis of barley straw as a result of the inoculation by rumen fluid of camel and sheep. Ground barley straw was incubated anaerobically with rumen inocula from three fistulated camels (FC) and three fistulated sheep (FR) for a period of 72 h. The source of rumen inoculum did not affect the disappearance of dry matter (DMD), neutral detergent fiber (NDFD). Group FR showed higher production of glucose, xylose, and gas; while higher ethanol production was associated with cellulosic hydrolysates obtained from FC group. The diversity and structure of bacterial communities attached to barley straw was investigated by Illumina Mi-Seq sequencing of V4-V5 region of 16S rRNA genes. The bacterial community was dominated by phylum Firmicutes and Bacteroidetes. The dominant genera were RC9_gut_group, Ruminococcus, Saccharofermentans, Butyrivibrio, Succiniclasticum, Selenomonas, and Streptococcus, indicating the important role of these genera in lignocellulose fermentation in the rumen. Group FR showed higher RC9_gut_group and group FC revealed higher Ruminococcus, Saccharofermentans, and Butyrivibrio. Higher enzymes activities (cellulase and xylanase) were associated with group FC. Thus, bacterial communities in camel and sheep have a great potential to improve the utilization lignocellulosic material in animal feeding and the production of biofuel and enzymes.

Enhancement of the enzymatic hydrolysis efficiency of wheat bran using the Bacillus strains and their consortium

In the downstream process, the bioconversion of lignocellulosic biomass can be improved by applying a biological pretreatment procedure using microorganisms to produce hydrolytic enzymes to modify the recalcitrant structure of lignocellulose. In this study, various Bacillus strains (B. subtilis B.01162 and B.01212, B. coagulans B.01123 and B.01139, B. cereus B.00076 and B.01718, B. licheniformis B.01223 and B.01231) were evaluated for the degrading capacity of wheat bran in the submerged medium using enzymatic activities, reducing sugars and weight loss as indicators. The obtained results revealed that the B. subtilis B.01162, B. coagulans B.01123 and B. cereus B.00076 could be promising degraders for the wheat bran pretreatment. Besides, the application of their consortium (the combination of 2-3 Bacillus species) showed the positive effects on cellulose bioconversion compared with monocultures. Among them, the mixture of B. subtilis B.01162 and B. coagulans B.01123 increased significantly the cellulase, endo-glucanase, and xylanase enzyme activity resulting in accelerating the lignocellulose degradation. Our results served a very good base for the development of microbial consortium for biological pretreatment of lignocellulosic raw materials.

Ensiling pretreatment with two novel microbial consortia enhances bioethanol production in sterile rice straw

The present study extracts and enriches cellulolytic microbial consortia from yak (Bos grunniens) and evaluates their effects on the fermentation profile and bioethanol yield in rice straw silage. Two microbial consortia (CF and PY) with high cellulolytic activity were isolated and observed to be prone to utilize natural carbon sources. Two consortia were introduced with and without combined lactic acid bacteria (CLAB) to rice straw for up to 60 days of ensiling, and their application notably decreased the levels of structural carbohydrates and pH values of rice straw silages. Treatments that combining microbial consortia and CLAB resulted in the highest levels of lactic acid, water soluble carbohydrates, mono- and disaccharides, and lignocellulose degradation, with PY + CLAB group yielding the highest bioethanol production. The microbial consortia identified herein exhibit great potential for degrading fibrous substrates, and their combination with CLAB provides a feasible way to efficiently use rice straw for bioethanol production.

Optimization of biogas yield from lignocellulosic materials with different pretreatment methods: a review

Population increase and industrialization has resulted in high energy demand and consumptions, and presently, fossil fuels are the major source of staple energy, supplying 80% of the entire consumption. This has contributed immensely to the greenhouse gas emission and leading to global warming, and as a result of this, there is a tremendous urgency to investigate and improve fresh and renewable energy sources worldwide. One of such renewable energy sources is biogas that is generated by anaerobic fermentation that uses different wastes such as agricultural residues, animal manure, and other organic wastes. During anaerobic digestion, hydrolysis of substrates is regarded as the most crucial stage in the process of biogas generation. However, this process is not always efficient because of the domineering stableness of substrates to enzymatic or bacteria assaults, but substrates' pretreatment before biogas production will enhance biogas production. The principal objective of pretreatments is to ease the accessibility of the enzymes to the lignin, cellulose, and hemicellulose which leads to degradation of the substrates. Hence, the use of pretreatment for catalysis of lignocellulose substrates is beneficial for the production of cost-efficient and eco-friendly process. In this review, we discussed different pretreatment technologies of hydrolysis and their restrictions. The review has shown that different pretreatments have varying effects on lignin, cellulose, and hemicellulose degradation and biogas yield of different substrate and the choice of pretreatment technique will devolve on the intending final products of the process.

Effects of Bacillus subtilis and its metabolites on corn silage quality

Cellulolytic micro-organisms are potent silage inoculants that decrease the fibrous content in silage and increase the fibre digestibility and nutritional value of silage. This study aimed to evaluate the effects of Bacillus subtilis CCMA 0087 and its enzyme β-glucosidase on the nutritional value and aerobic stability of corn silage after 30 and 60 days of storage. We compared the results among silage without inoculant (SC) and silages inoculated with B. subtilis 8 log₁₀ CFU per kg forage (SB8), 9 log₁₀ CFU per kg forage (SB9) and 9·84 log₁₀ CFU per kg forage + β-glucosidase enzyme (SBE). No differences were observed in the levels of dry matter, crude protein and neutral detergent fibre due to the different treatments or storage times of the silos. Notably, the population of spore-forming bacteria increased in the SB9-treated silage. At 60 days of ensiling, the largest populations of lactic acid bacteria were found in silages treated with SB8 and SBE. Yeast populations were low for all silages, irrespective of the different treatments, and the presence of filamentous fungi was observed only in the SBE-treated silage. Among all silage treatments, SB9 treatment resulted in the highest aerobic stability.

Biodegradation of creosote-treated wood by two novel constructed microbial consortia for the enhancement of methane production

Lignocellulose biodegradation is limited because of its recalcitrant structure particularly when polluted by toxic and carcinogenic compounds such as creosote oil (CRO). As far as we know, this might be the first report that explores the biodegradation of creosote treated wood (CTW) to serve biomethane production. Two novel CTW-degrading microbial consortia, designated as CTW-1 and CTW-2, were screened and constructed to enhance methane production from CRO-treated pine sawdust. After 12 days of biological pretreatment by CTW-1 and CTW-2, a significant reduction in lignocellulosic content of CTW was recorded; estimated as 49 and 43%, respectively. More than 64 and 91% of cumulative biogas and methane yields were obtained from biodegraded CTW over control. Ecotoxicity of treated and untreated CTW was compared by Microtox test. The biodegraded CTW hydrolysates showed a toxicity decrease of more than 80%, suggesting the promising role of constructed microbial consortia for biofuel production and bioremediation.

A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to 'knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

Artificial consortium demonstrates emergent properties of enhanced cellulosic-sugar degradation and biofuel synthesis

Planktonic cultures, of a rationally designed consortium, demonstrated emergent properties that exceeded the sums of monoculture properties, including a >200% increase in cellobiose catabolism, a >100% increase in glycerol catabolism, a >800% increase in ethanol production, and a >120% increase in biomass productivity. The consortium was designed to have a primary and secondary-resource specialist that used crossfeeding with a positive feedback mechanism, division of labor, and nutrient and energy transfer via necromass catabolism. The primary resource specialist was Clostridium phytofermentans (a.k.a. Lachnoclostridium phytofermentans), a cellulolytic, obligate anaerobe. The secondary-resource specialist was Escherichia coli, a versatile, facultative anaerobe, which can ferment glycerol and byproducts of cellobiose catabolism. The consortium also demonstrated emergent properties of enhanced biomass accumulation when grown as biofilms, which created high cell density communities with gradients of species along the vertical axis. Consortium biofilms were robust to oxic perturbations with E. coli consuming O₂, creating an anoxic environment for C. phytofermentans. Anoxic/oxic cycling further enhanced biomass productivity of the biofilm consortium, increasing biomass accumulation ~250% over the sum of the monoculture biofilms. Consortium emergent properties were credited to several synergistic mechanisms. E. coli consumed inhibitory byproducts from cellobiose catabolism, driving higher C. phytofermentans growth and higher cellulolytic enzyme production, which in turn provided more substrate for E. coli. E. coli necromass enhanced C. phytofermentans growth while C. phytofermentans necromass aided E. coli growth via the release of peptides and amino acids, respectively. In aggregate, temporal cycling of necromass constituents increased flux of cellulose-derived resources through the consortium. The study establishes a consortia-based, bioprocessing strategy built on naturally occurring interactions for improved conversion of cellulose-derived sugars into bioproducts.

Role of Microbial Hydrolysis in Anaerobic Digestion

There is a growing need of substrate flexibility for biobased production of energy and value-added products that allows the application of variable biodegradable residues within a circular economy. It can be used to balance fluctuating energy provision of other renewable sources. Hydrolysis presents one of the biggest limitations during anaerobic digestion. Methods to improve it will result in broader process applicability and improved integration into regional material cycles. Recently, one focus of anaerobic digestion research has been directed to systems with a separate hydrolysis–acidogenesis stage as it might be promised to improve process performance. Conditions can be adjusted to each class of microorganisms individually without harming methanogenic microorganisms. Extensive research of separate biomass pretreatment via biological, chemical, physical or mixed methods has been conducted. Nevertheless, several methods lack economic efficiency, have a high environmental impact or focus on specific substrates. Pretreatment via a separate hydrolysis stage as cell-driven biotransformation in a suspension might be an alternative that enables high yields, flexible feeding and production, and a better process control. In this review, we summarize existing technologies for microbial hydrolytic biotransformation in a separate reactor stage and the impacts of substrate, operational parameters, combined methods and process design as well as remaining challenges.

Enhancing the plants growth and arsenic uptake from soil using arsenite-oxidizing bacteria

Plants, that naturally inhabit arsenic-contaminated areas may be used for effective arsenic-uptake from soil. The efficiency of this process may be increased by the reducing arsenic phytotoxicity and stimulating the activity of indigenous soil microbiota. As we showed, it can be achieved by the bioaugmenting of soil with arsenite-oxidizing bacteria (AOB). This study aimed to investigate the influence of soil bioaugmentation with AOB on the structure, quantity, and activity of the indigenous soil microbiota as well as to estimate the effect of such changes on the morphology, growth rate, and arsenic-uptake efficiency of plants. Plants-microbes interactions were investigated using the effective arsenites oxidizer Ensifer sp. M14 and the native plant alfalfa. The experiments were performed both in potted garden soil enriched with arsenic and in highly arsenic polluted, natural soil. The presence of M14 strain in soil contributed to the increase both in plants growth intensity and arsenic-uptake efficiency with regard to the soil without M14. After 40 days of plants culture, their average biomass increased by about 60% compared to non-bioaugmented soil, while the arsenic accumulation increased more than two times. The soil bioaugmentation contributed also to the increase in the quantity and activity of soil microorganisms without disturbing the natural microbial community structure. In the bioaugmented soil, the noticable increase in the quantity of heterotrophic, denitrifying, nitrifying and cellulolytic bacteria as well as in the activity of dehydrogenases and cellulases were observed. Soil bioaugmentation with M14 enables the application of native and commonly occurring plant species for enhancing the treatment of arsenic-contaminated soil. This in situ strategy may constitute a valuable alternative both to the chemical and physical methods of arsenic removal from soil and to the biological ways based on the arsenic hyperaccumulating plants and/or the arsenic mobilizing bacteria.

Enhanced anaerobic digestion performance by two artificially constructed microbial consortia capable of woody biomass degradation and chlorophenols detoxification

Catalpa sawdust (CSW) is a promising biomass-based biofuel. However, the complex lignocellulosic structure limits its efficient utilization in biorefinery applications. It is even more so when chlorophenols (CPs), highly toxic organic substances widely used as wood preservatives, are present. Hence, it is crucial to develop effective and eco-friendly approaches to attain deconstruction of lignocellulose and chlorophenols simultaneously as well as to improve methane (CH4) production efficiently. This study might be the first to explore the performance of the novel constructed microbial consortia CS-5 and BC-4 on woody biomass degradation and CPs detoxification simultaneously with CH4 production. After the degradation of CSW and CPs for 15 days by C5-5 or BC-4, significant reduction in lignocellulosic components and CPs mixture was realized with a total weight loss of 69.2 and 56.3 % and CPs degradation of 89 and 95 %, respectively. The toxicity of individual or mixed CPs after 15 days of degradation was reduced by approximately 90 %. The synergistic action of CS-5 and BC-4 enhanced biogas and CH4 yields over 76 and 64 % respectively, higher than control. Furthermore, CH4 production increased by 113.7 % at the peak phase of AD process. Methanosataceae represented 45.1 % of the methanogenic Archaea in digester G-III.

Full-scale anaerobic reactor samples would be more suitable than lab-scale anaerobic reactor and natural samples to inoculate the wheat straw batch anaerobic digesters

This study evaluated the effects of the inocula from natural wetland, lab-scale and full-scale anaerobic reactors on wheat straw anaerobic digestion. Three replicate batch reactors were constructed for each inoculum to investigate the reactor performances and microbial communities. Reactors seeded with full-scale reactor samples were started up most rapidly, achieved the highest methane production, and were recognized as the higher efficient reactors. The dominance of acetoclastic methanogens, including Methanosaeta and Methanoscrina, was crucial for the higher efficient reactors, whereas hydrogenotrophic methanogens were dominant in other reactors. Genus Treponema, which could enhance the cellulose degradation and conduct homoacetogenesis, was first reported to be dominant in the bacterial communities of high efficient reactors. Inoculum sources and process conditions were suggested to be the deterministic factors in shaping the microbial communities in the higher efficient reactors. These findings contribute to the startup of new anaerobic reactors.

Enzymatic hydrolysis of Opuntia ficus-indica cladode by Acinetobacter pittii and alcohol fermentation by Kluyveromyces marxianus: pH, temperature and microorganism effect

In the present work the effect of three factors: pH, temperature and type of microorganism using a factorial design 3²x2 was evaluated on: growth, total cellulases hydrolytic activity (FPases), endoglucanases hydrolytic activity (CMCases), free reducing sugars (FRS), glucose, sucrose, and alcohol production using a culture medium based on mineral salts added with cladodes flour of Opuntia ficus-indica at 20% as the unique carbon source. Two wild microorganisms were used, Acinetobacter pittii a bacteria isolated from decaying cladodes, and Kluyveromyces marxianus a yeast isolated from termite stomach. The maximum hydrolytic activities were obtained with Acinetobacter pittii at 37 °C and pH 6.5 for total cellulases (0.67 ± 0.02 IU/ml) and for endoglucanases (0.23 ± 0.02 IU/ml) at 24 and 4 h. The maximum production of alcohol was 12.98 ± 0.06 g/L obtained with Kluyveromyces marxianus at 4 h with conditions of 40 °C and pH 5.5.

Thermotolerant cellulolytic Clostridiaceae and Lachnospiraceae rich consortium enhanced biogas production from oil palm empty fruit bunches by solid-state anaerobic digestion

Thermotolerant cellulolytic consortium for improvement biogas production from oil palm empty fruit bunches (EFB) by prehydrolysis and bioaugmentation strategies was investigated via solid-state anaerobic digestion (SS-AD). The prehydrolysis EFB with Clostridiaceae and Lachnospiraceae rich consortium have maximum methane yield of 252 and 349 ml CH₄ g^-1 VS with total EFB degradation efficiency of 62% and 86%, respectively. Clostridiaceae and Lachnospiraceae rich consortium augmentation in biogas reactor have maximum methane yield of 217 and 85.2 ml CH₄ g^-1 VS with degradation efficiency of 42% and 16%, respectively. The best improvement of biogas production was achieved by prehydrolysis EFB with Lachnospiraceae rich consortium with maximum methane production of 113 m³ CH₄ tonne^-1 EFB. While, Clostridiaceae rich consortium was suitable for augmentation in biogas reactor with maximum methane production of 70.6 m³ CH₄ tonne^-1 EFB. Application of thermotolerant cellulolytic consortium into the SS-AD systems could enhance biogas production of 3-11 times.

Microbial community design: methods, applications, and opportunities

Microbial communities can perform a variety of behaviors that are useful in both therapeutic and industrial settings. Engineered communities that differ in composition from naturally occurring communities offer a unique opportunity for improving upon existing community functions and expanding the range of microbial community applications. This has prompted recent advances in various community design approaches including artificial selection procedures, reduction from existing communities, combinatorial evaluation of potential microbial combinations, and model-based in silico community optimization. Computational methods in particular offer a likely avenue toward improved synthetic community development going forward. This review introduces each class of design approach and surveys their recent applications and notable innovations, closing with a discussion of existing design challenges and potential opportunities for advancement.

Genome-Wide and Functional View of Proteolytic and Lipolytic Bacteria for Efficient Biogas Production through Enhanced Sewage Sludge Hydrolysis

In this study, we used a multifaceted approach to select robust bioaugmentation candidates for enhancing biogas production and to demonstrate the usefulness of a genome-centric approach for strain selection for specific bioaugmentation purposes. We also investigated the influence of the isolation source of bacterial strains on their metabolic potential and their efficiency in enhancing anaerobic digestion. Whole genome sequencing, metabolic pathway reconstruction, and physiological analyses, including phenomics, of phylogenetically diverse strains, Rummeliibacillus sp. POC4, Ochrobactrum sp. POC9 (both isolated from sewage sludge) and Brevundimonas sp. LPMIX5 (isolated from an agricultural biogas plant) showed their diverse enzymatic activities, metabolic versatility and ability to survive under varied growth conditions. All tested strains display proteolytic, lipolytic, cellulolytic, amylolytic, and xylanolytic activities and are able to utilize a wide array of single carbon and energy sources, as well as more complex industrial by-products, such as dairy waste and molasses. The specific enzymatic activity expressed by the three strains studied was related to the type of substrate present in the original isolation source. Bioaugmentation with sewage sludge isolates–POC4 and POC9–was more effective for enhancing biogas production from sewage sludge (22% and 28%, respectively) than an approach based on LPMIX5 strain (biogas production boosted by 7%) that had been isolated from an agricultural biogas plant, where other type of substrate is used.

Meta-omics based analyses of microbiome involved in biomethanation of rice straw in a thermophilic anaerobic bioreactor under optimized conditions

Biomethanation of rice straw was performed at 55 °C without thermochemical pretreatment using cattle dung supplemented with Methanothermobacter thermautotrophicus strains. Methane yield of 323 ml g^-1 VS obtained under optimized conditions such as particle size (1 mm), carbon to nitrogen ratio (15:1), substrate to inoculum ratio (1:1), organic loading rate (7.5% w/v) and hydraulic retention time (20 days), was one of the highest ever reported from rice straw. Metagenome analysis revealed several putative novel taxa among resident microbes. The genomes of Clostridium, Hungateiclostridium, Alkaliphilus, Anaerocolumna, Olsenella, Paenibacillus, Pseudoclostridium, Tepidanaerobacter and Turicibacter were recovered as metagenome assisted genomes. Clostridium spp. and M. thermautotrophicus were the dominant hydrolytic and methanogenic microbes, respectively. Syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis was found to be the major pathway for methane production. Efficient thermophilic biomethanation of rice straw without thermochemical pretreatment using cattle dung supplemented with M. thermautotrophicus is reported for the first time.

Long-Term Storage and Use of Artificially Immobilized Anaerobic Sludge as a Powerful Biocatalyst for Conversion of Various Wastes Including Those Containing Xenobiotics to Biogas

The aim of this paper is to demonstrate the possibilities of anaerobic sludge cells immobilized into poly(vinyl alcohol) cryogel for the methanogenic conversion of various lignocellulosic waste and other media containing antibiotics (ampicillin, kanamycin, benzylpenicillin) or pesticides (chlorpyrifos or methiocarb and its derivatives). It was established that the immobilized cells of the anaerobic consortium can be stored frozen for at least three years while preserving a high level of metabolic activity. The cells after the long-term storage in an immobilized and frozen state were applied for the methanogenesis of a wide number of wastes, and an increase in both methane yield and methane portion in the produced biogas as compared to the conventionally used suspended anaerobic sludge cells, was ensured. It was shown that the “additional” introduction of bacterial Clostridium acetobutylicum, Pseudomonas sp., Enterococcus faecalis cells (also immobilized using same support) improves characteristics of methanogenesis catalyzed by immobilized anaerobic sludge.

Genome-Guided Characterization of Ochrobactrum sp. POC9 Enhancing Sewage Sludge Utilization-Biotechnological Potential and Biosafety Considerations

Sewage sludge is an abundant source of microorganisms that are metabolically active against numerous contaminants, and thus possibly useful in environmental biotechnologies. However, amongst the sewage sludge isolates, pathogenic bacteria can potentially be found, and such isolates should therefore be carefully tested before their application. A novel bacterial strain, Ochrobactrum sp. POC9, was isolated from a sewage sludge sample collected from a wastewater treatment plant. The strain exhibited lipolytic, proteolytic, cellulolytic, and amylolytic activities, which supports its application in biodegradation of complex organic compounds. We demonstrated that bioaugmentation with this strain substantially improved the overall biogas production and methane content during anaerobic digestion of sewage sludge. The POC9 genome content analysis provided a deeper insight into the biotechnological potential of this bacterium and revealed that it is a metalotolerant and a biofilm-producing strain capable of utilizing various toxic compounds. The strain is resistant to rifampicin, chloramphenicol and β-lactams. The corresponding antibiotic resistance genes (including bla_OCH and cmlA/floR) were identified in the POC9 genome. Nevertheless, as only few genes in the POC9 genome might be linked to pathogenicity, and none of those genes is a critical virulence factor found in severe pathogens, the strain appears safe for application in environmental biotechnologies.

Biogas production from different lignocellulosic biomass sources: advances and perspectives

The present work summarizes different sources of biomass used as raw material for the production of biogas, focusing mainly on the use of plants that do not compete with the food supply. Biogas obtained from edible plants entails a developed technology and good yield of methane production; however, its use may not be sustainable. Biomass from agricultural waste is a cheap option, but in general, with lower methane yields than those obtained from edible plants. On the other hand, the use of algae or aquatic plants promises to be an efficient and sustainable option with high yields of methane produced, but it necessary to overcome the existing technological barriers. Moreover, these last raw materials have the additional advantage that they can be obtained from wastewater treatment and, therefore, they could be applied to the concept of biorefinery. An estimation of methane yield per hectare per year of the some types of biomass and operational conditions employed is presented as well. In addition, different strategies to improve the yield of biogas, such as physical, chemical, and biological pretreatments, are presented. Other alternatives for enhanced the biogas production such as bioaugmentation and biohythane are showed and finally perspectives are mentioned.

Screening of a microbial consortium for selective degradation of lignin from tree trimmings

To acquire microbial consortia with effectively precedent degradation of lignin, samples obtained from rotten trunks, rotten stumps and soil near it were screened and isolated after generations of subculture. The dynamic change illustrated that their community structures were affected by pH and tended to be stable after 6 days' cultivation. The desired one, named DM-1, was gained through successive cultivation for over 5 generations, whose high selectivity in lignin degradation was observed within 16 days' cultivation (SV = 2.78). Meanwhile, a remarkable reduction in the fiber crystallinity of tree trimmings (10.35%) resulted from the bio-degradation of DM-1, displayed a greater exposure of cellulose by selective removal of lignin. The diversity analysis of DM-1 was investigated by PCR amplification and 16S rDNA sequencing, indicated that mesorhizobium, cellulosimicrobium, pandoraea, achromobacter and stenotrophomones were the predominant genera. Furthermore, fungi (3 strains), bacteria (4 strains) and actinomycetes (5 strains) constituted 12 strains in total were gained by plate isolation from DM-1.

Corn silage fungal-based solid-state pretreatment for enhanced biogas production in anaerobic co-digestion with cow manure

The objective of this research was to use white-rot fungus Trametes versicolor for corn silage pretreatment and to investigate the effect of pretreatment on biogas productivity. Semi-continuous pilot-scale experiment, comprised of two experimental phases, was carried out. In the first phase, operational conditions of the full-scale biogas plant were reproduced at pilot-scale. In that phase, the reactor was daily fed with the mixture of cow manure, digestate from industrial postfermentor, corn grits and ensiled corn silage, and the average methane generation rate was 0.167 m³_CH4 kg_VS^-1. In the second phase, corn grits and ensiled corn silage were replaced with corn silage pretreated with T. versicolor, and the average methane generation rate increased up to 0.236 m³_CH4 kg_VS^-1. The results of this study suggest that application of fungal-based solid-state pretreated corn silage has positive effect on pH stability and increase the biogas productivity.

Importance of inoculum source and initial community structure for biogas production from agricultural substrates

This study evaluated the importance of inoculum source for start-up and operation of biogas processes. Three different inocula with different community structure were used to initiate six laboratory continuous stirred tank reactor (CSTR) processes operated with a grass manure mixture as substrate. The processes were evaluated by chemical and microbiological analysis, by targeting the overall bacterial community and potential cellulose-degrading bacteria. As expected, the results showed a large difference in community structure in the inocula and in process performance during the first hydraulic retention time (HRT). However, the performance and overall microbial community structure became similar in the reactors over time. An inoculum from a high-ammonia process, characterized by low diversity and low degradation efficiency, took the longest time to reach stability and final methane yield. The overall bacterial community was mainly shaped by the operating conditions but, interestingly, potential cellulose-degrading bacteria seemed mainly to originate from the substrate.

Biological strategies for enhanced hydrolysis of lignocellulosic biomass during anaerobic digestion: Current status and future perspectives

Lignocellulosic biomass is the most abundant renewable bioresource on earth. In lignocellulosic biomass, the cellulose and hemicellulose are bound with lignin and other molecules to form a complex structure not easily accessible to microbial degradation. Anaerobic digestion (AD) of lignocellulosic biomass with a focus on improving hydrolysis, the rate limiting step in AD of lignocellulosic feedstocks, has received considerable attention. This review highlights challenges with AD of lignocellulosic biomass, factors contributing to its recalcitrance, and natural microbial ecosystems, such as the gastrointestinal tracts of herbivorous animals, capable of performing hydrolysis efficiently. Biological strategies that have been evaluated to enhance hydrolysis of lignocellulosic biomass include biological pretreatment, co-digestion, and inoculum selection. Strategies to further improve these approaches along with future research directions are outlined with a focus on linking studies of microbial communities involved in hydrolysis of lignocellulosics to process engineering.

Complete Genome Sequence of a New Firmicutes Species Isolated from Anaerobic Biomass Hydrolysis

A new Firmicutes isolate, strain HV4-6-A5C, was obtained from the hydrolysis stage of a mesophilic and anaerobic two-stage lab-scale leach-bed system for biomethanation of fresh grass. It is assumed that the bacterial isolate contributes to plant biomass degradation. Here, we report a draft annotated genome sequence of this organism.

Carbon dioxide (CO2) biofixation by microalgae and its potential for biorefinery and biofuel production

Carbon dioxide (CO₂) using biological process is one of the promising approaches for CO₂ capture and storage. Recently, biological sequestration using microalgae has gained many interest due to its capability to utilize CO₂ as carbon source and biomass produced can be used as a feedstock for other value added product for instance biofuel and chemicals. In this study, the CO₂ biofixation by two microalgae species, Chlorella sp. and Tetraselmis suecica was investigated using different elevated CO₂ concentration. The effect of CO₂ concentration on microalgae growth kinetic, biofixation and its chemical composition were determined using 0.04, 5, 15 and 30% CO₂. The variation of initial pH value and its relationship on CO₂ concentration toward cultivation medium was also investigated. The present study indicated that both microalgae displayed different tolerance toward CO₂ concentration. The maximum biomass production and biofixation for Chlorella sp. of 0.64gL^-1 and 96.89mgL^-1d^-1 was obtained when the cultivation was carried out using 5 and 15% CO_2, respectively. In contrast, the maximum biomass production and CO₂ biofixation for T. suecica of 0.72gL^-1 and 111.26mgL^-1d^-1 were obtained from cultivation using 15 and 5% CO₂. The pH value for the cultivation medium using CO₂ was between 7.5 and 9, which is favorable for microalgal growth. The potential of biomass obtained from the cultivation as a biorefinery feedstock was also evaluated. An anaerobic fermentation of the microalgae biomass by bacteria Clostridium saccharoperbutylacenaticum N1-4 produced various type of value added product such as organic acid and solvent. Approximately 0.27 and 0.90gL^-1 of organic acid, which corresponding to acetic and butyric acid were produced from the fermentation of Chlorella sp. and T. suecica biomass. Overall, this study suggests that Chlorella sp. and T. suecica are efficient microorganism that can be used for CO₂ biofixation and as a feedstock for chemical production.

Design and composition of synthetic fungal-bacterial microbial consortia that improve lignocellulolytic enzyme activity

Microbial interactions are important for metabolism as they can improve or reduce metabolic efficiency. To improve lignocellulolytic enzyme activity, a series of synergistic microbial consortia of increasing diversity and complexity were devised using fungal strains, including Trichoderma reesei, Penicillium decumbens, Aspergillus tubingensis, and Aspergillus niger. However, when a screened microbial community with cellulolytic capacity was added to the consortia to increase the number of strains, it engendered more microbial interactions with the above strains and universally improved the β-glucosidase activity of the consortia. Analysis of the microbial community structure revealed that the bacteria in the consortia are more important for lignocellulolytic enzyme activity than the fungi. One fungal and 16 bacterial genera in the consortia may interact with T. reesei and are potential members of a devised synergistic microbial consortium. Such devised microbial consortia may potentially be applied to effectively and economically degrade lignocellulose.

The application of biotechnology on the enhancing of biogas production from lignocellulosic waste

Anaerobic digestion of lignocellulosic waste is considered to be an efficient way to answer present-day energy crisis and environmental challenges. However, the recalcitrance of lignocellulosic material forms a major obstacle for obtaining maximum biogas production. The use of biological pretreatment and bioaugmentation for enhancing the performance of anaerobic digestion is quite recent and still needs to be investigated. This paper reviews the status and perspectives of recent studies on biotechnology concept and investigates its possible use for enhancing biogas production from lignocellulosic waste with main emphases on biological pretreatment and bioaugmentation techniques.

Biogas Production: Microbiology and Technology

Biogas, containing energy-rich methane, is produced by microbial decomposition of organic material under anaerobic conditions. Under controlled conditions, this process can be used for the production of energy and a nutrient-rich residue suitable for use as a fertilising agent. The biogas can be used for production of heat, electricity or vehicle fuel. Different substrates can be used in the process and, depending on substrate character, various reactor technologies are available. The microbiological process leading to methane production is complex and involves many different types of microorganisms, often operating in close relationships because of the limited amount of energy available for growth. The microbial community structure is shaped by the incoming material, but also by operating parameters such as process temperature. Factors leading to an imbalance in the microbial community can result in process instability or even complete process failure. To ensure stable operation, different key parameters, such as levels of degradation intermediates and gas quality, are often monitored. Despite the fact that the anaerobic digestion process has long been used for industrial production of biogas, many questions need still to be resolved to achieve optimal management and gas yields and to exploit the great energy and nutrient potential available in waste material. This chapter discusses the different aspects that need to be taken into consideration to achieve optimal degradation and gas production, with particular focus on operation management and microbiology.