Effective cellulose degradation by a mixed-culture system composed of a cellulolytic Clostridium and aerobic non-cellulolytic bacteria

Isolation and Characterization of a Low-Temperature, Cellulose-Degrading Microbial Consortium from Northeastern China

The lack of efficient ways to dispose of lignocellulosic agricultural residues is a serious environmental issue. Low temperatures greatly impact the ability of organisms to degrade these wastes and convert them into nutrients. Here, we report the isolation and genomic characterization of a microbial consortium capable of degrading corn straw at low temperatures. The microorganisms isolated showed fast cellulose-degrading capabilities, as confirmed by scanning electron microscopy and the weight loss in corn straw. Bacteria in the consortium behaved as three diverse and functionally distinct populations, while fungi behaved as a single population in both diversity and functions overtime. The bacterial genus Pseudomonas and the fungal genus Thermoascus had prominent roles in the microbial consortium, showing significant lignocellulose waste-degrading functions. Bacteria and fungi present in the consortium contained high relative abundance of genes for membrane components, with amino acid breakdown and carbohydrate degradation being the most important metabolic pathways for bacteria, while fungi contained more genes involved in energy use, carbohydrate degradation, lipid and fatty acid decomposition, and biosynthesis.

Artificial selection of microbial communities: what have we learnt and how can we improve?

Microbial communities are capable of performing diverse functions with important bioindustrial and medical applications. One approach to improving community function is to breed new communities by artificially selecting for those displaying high community function ('community selection'). Importantly, community selection can improve the function of interest without needing to understand how the function arises, just like in classical artificial selection of individuals. However, experimental studies of community selection have had varied and largely limited success. Here, we review a conceptual framework to help foster an understanding of community selection and its associated challenges, and provide broad insights for designing effective selection strategies.

The Potential of Wild Yeasts as Promising Biocontrol Agents against Pine Canker Diseases

Native wild yeasts from forest ecosystems represent an interesting potential source of biocontrol organisms in synergy with disease-tolerant forest materials. Yeasts have a combination of competitive mechanisms and low requirements for their biotechnological application as biocontrol agents. The current study aimed to increase the number of biocontrol candidates against Fusarium circinatum and Diplodia sapinea. The enzymatic and antagonistic activities of the biocontrol candidates were evaluated using different screening methods, in which the direct impact on the growth of the pathogen was measured as well as some properties such as cellulose and lignin degradation, tolerance to biocides, volatile compound production, or iron effect, which may be of interest in biotechnological processes related to the management of forest diseases. A total of 58 yeast strains belonging to 21 different species were obtained from oak forest and vineyard ecosystems and evaluated. The application of yeast treatment behaved differently depending on the pathogen and the plant clone. The 2g isolate (Torulaspora delbrueckii) showed the highest inhibitory activity for D. sapinea and 25q and 90q (Saccharomyces paradoxus) for F. circinatum. Clones IN416 and IN216 were the most susceptible and the most tolerant to D. sapinea, respectively, while the opposite was observed for F. circinatum.

Microbiome - based agents can optimize composting of agricultural wastes by modifying microbial communities

Microorganisms that facilitate the decomposition of agricultural wastes are of importance during composting processes. Here, we assessed if microbial agents, comprising Clonostachys rosea, Bacillus amylolyticus and Rhodospirillum photometricum can facilitate the decomposition of a compost mix of vegetable waste, chicken manure, sawdust, and biochar. The results showed that inoculating the compost mix with the microbial agents elevated the compost temperature, increased the thermophilic period, and enhanced cellulose degradation. Microbial agent inoculation also changed the diversity and richness of decomposing microbial communities. Among the microbial agents, the mixture of C. rosea and B. amylolyticus performed better than other mixtures. Taken together, the results confirmed that the microbial agents comprising C. rosea can enhance the composting process by ameliorating the physiochemical conditions of agricultural wastes and promoting the diversity and proliferation of beneficial bacteria involved in the decomposition of cellulose.

Comparative genomic analyses of four novel Ramlibacter species and the cellulose-degrading properties of Ramlibacter cellulosilyticus sp. nov

In this study, four novel bacterial strains, USB13^T, AW1^T, GTP1^T, and HM2^T, were isolated from various environments in Busan and Jeju Island, Republic of Korea. The 16S rRNA sequencing results indicated that the four novel strains belong to the genus Ramlibacter. All four strains were tested for their potential cellulolytic properties, where strain USB13^T was identified as the only novel bacterium and the first within its genus to show cellulolytic activity. When tested, the highest activities of endoglucanase, exoglucanase, β-glucosidase, and filter paper cellulase (FPCase) were 1.91 IU/mL, 1.77 IU/mL, 0.76 IU/mL, and 1.12 IU/mL, respectively at pH 6.0. Comparisons of draft whole genome sequences (WGS) were also made using average nucleotide identity, digital DNA-DNA hybridization values, and average amino acid identity values, while whole genome comparison was visualized using the BLAST Ring Image Generator. The G + C contents of the strains ranged from 67.9 to 69.9%, while genome sizes ranged from 4.31 to 6.15 Mbp. Based on polyphasic evidence, the novel strains represent four new species within the genus Ramlibacter, for which the names Ramlibacter cellulosilyticus sp. nov. (type strain, USB13^T = KACC 21656^T = NBRC 114839^T) Ramlibacter aurantiacus sp. nov. (type strain, AW1^T = KACC 21544^T = NBRC 114862^T), Ramlibacter albus sp. nov. (type strain, GTP1^T = KACC 21702^T = NBRC 114488^T), and Ramlibacter pallidus sp. nov. (type strain, HM2^T = KCTC 82557^T = NBRC 114489^T) are proposed.

Microbial co-occurrence networks driven by low-abundance microbial taxa during composting dominate lignocellulose degradation

Lignocellulose, which contains cellulose, hemicellulose and lignin, is one of the most important factors determining the rate and quality of compost decomposition, and the microbial community composition affects the rate of lignocellulose decomposition. Interactions between microbial taxa contribute significantly to ecosystem energy flow and material cycling. However, it is not clear how interactions between microbial taxa affect the degradation of lignocellulose during the composting process. For this reason we carried out aerobic co-composting experiments with maize straw and cattle manure to explore the contribution of microbial community diversity and the interaction between taxa to lignocellulosic degradation. The results showed that moisture and temperature had the greatest effect on microbial communities during composting and that lignocellulose degradation was dominated by microbial co-occurrence networks rather than microbial community diversity. Overall co-occurrence network and bacterial-fungal interactions explained 23.9-84.1 % of lignocellulosic degradation, whereas microbial diversity only accounted for 24.6-31.5 %. Interestingly, keystone taxa analysis of the microbial co-occurrence networks revealed that low-abundance taxa influenced microbial interactions driving lignocellulose degradation. Our results provide a new perspective for understanding lignocellulose degradation during composting, offering insights into important microbial interaction mechanisms for improving compost quality and efficiency.

Enhancing the Activity of Carboxymethyl Cellulase Enzyme Using Highly Stable Selenium Nanoparticles Biosynthesized by Bacillus paralicheniformis Y4

The inorganic selenium is absorbed and utilized inefficiently, and the range between toxicity and demand is narrow, so the application is strictly limited. Selenium nanoparticles have higher bioactivity and biosafety properties, including increased antioxidant and anticancer properties. Thus, producing and applying eco-friendly, non-toxic selenium nanoparticles in feed additives is crucial. Bacillus paralicheniformis Y4 was investigated for its potential ability to produce selenium nanoparticles and the activity of carboxymethyl cellulases. The selenium nanoparticles were characterized using zeta potential analyses, Fourier transform infrared (FTIR) spectroscopy, and scanning electron microscopy (SEM). Additionally, evaluations of the anti-α-glucosidase activity and the antioxidant activity of the selenium nanoparticles and the ethyl acetate extracts of Y4 were conducted. B. paralicheniformis Y4 exhibited high selenite tolerance of 400 mM and the selenium nanoparticles had an average particle size of 80 nm with a zeta potential value of −35.8 mV at a pH of 7.0, suggesting that the particles are relatively stable against aggregation. After 72 h of incubation with 5 mM selenite, B. paralicheniformis Y4 was able to reduce it by 76.4%, yielding red spherical bio-derived selenium nanoparticles and increasing the carboxymethyl cellulase activity by 1.49 times to 8.96 U/mL. For the first time, this study reports that the carboxymethyl cellulase activity of Bacillus paralicheniforis was greatly enhanced by selenite. The results also indicated that B. paralicheniformis Y4 could be capable of ecologically removing selenite from contaminated sites and has great potential for producing selenium nanoparticles as feed additives to enhance the added value of agricultural products.

Bioaugmentation with methanogens cultured in a micro-aerobic microbial community for overloaded anaerobic digestion recovery

Anaerobic digestion (AD) is widely used for conversion of waste materials into biogas, but inhibition of methane production caused by overloading can be a major problem. The micro-aerobic microbial community MC1 was used to successfully culture methanogens, Methanosarcina acetivorans C2A and Methanosaeta thermophila NBRC 101360. The maximum 16S rRNA gene concentrations of Methanosarcina acetivorans C2A and Methanosaeta thermophila NBRC101360 were 1.06 × 10⁶ and 1.35 × 10³ copies/mL, respectively. The five key bacteria in MC1 were quantified to assess the effect of inoculation on the abundances of the bacteria in the mixed culture. The original MC1 total 16S rRNA gene concentration was 1.93 × 10⁸ copies/mL, and the total 16S rRNA gene concentration had increased to 4.79 × 10⁹ copies/mL on day 9 (p < 0.05). The proportions of the key strains in MC1+MST had changed by day 9. Cells were harvested and used to bioaugment and increase the pH values of the high- and medium-temperature anaerobic systems. After bioaugmentation, thermophilic AD recovered well. The cumulative amounts of gas produced were 44.78% and 28.28% higher in the MC1+MST and MC1 groups, respectively, than the sterilized control. The MC1+MST group gave better results than the chemical addition control group (CaCO₃). There was no clear effect of bioaugmentation in mesophilic AD. When compared with traditional pure culture of methanogens as inoculants, methanogen cultivation in MC1 was simple and there was no need to separate and purify the target strains. This simplified methanogenic bioaugmentation agent was useful to study the mechanism of bioaugmentation for the recovery from low pH inhibition, showing the potential for practical application.

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.

Archaeal and Bacterial Content in a Two-Stage Anaerobic System for Efficient Energy Production from Agricultural Wastes

Anaerobic digestion (AD) is a microbially-driven process enabling energy production. Microorganisms are the core of anaerobic digesters and play an important role in the succession of hydrolysis, acidogenesis, acetogenesis, and methanogenesis processes. The diversity of participating microbial communities can provide new information on digester performance for biomass valorization and biofuel production. In this study anaerobic systems were used, operating under mesophilic conditions that realized biodegradation processes of waste wheat straw pretreated with NaOH-a renewable source for hydrogen and methane production. These processes could be managed and optimized for hydrogen and methane separately but combining them in a two-stage system can lead to higher yields and a positive energy balance. The aim of the study was to depict a process of biohydrogen production from lignocellulosic waste followed by a second one leading to the production of biomethane. Archaeal and bacterial consortia in a two-stage system operating with wheat straw were identified for the first time and the role of the most important representatives was elucidated. The mixed cultures were identified by the molecular-biological methods of metagenomics. The results showed that biohydrogen generation is most probably due to the presence of Proteiniphilum saccharofermentans, which was 28.2% to 45.4% of the microbial community in the first and the second bioreactor, respectively. Archaeal representatives belonging to Methanobacterium formicicum (0.71% of the community), Methanosarcina spelaei (0.03%), Methanothrix soehngenii (0.012%), and Methanobacterium beijingense (0.01%) were proven in the methane-generating reactor. The correlation between substrate degradation and biogas accumulation was calculated, together with the profile of fatty acids as intermediates produced during the processes. The hydrogen concentration in the biogas reached 14.43%, and the Methane concentration was 69%. Calculations of the energy yield during the two-stage process showed 1195.89 kWh·t^-1 compared to a 361.62 kWh·t^-1 cumulative yield of energy carrier for a one-stage process.

Unraveling aerobic cultivable cellulolytic microorganisms within the gastrointestinal tract of sheep (Ovis aries) and their evaluation for cellulose biodegradation

Anaerobic cellulolytic microbes in gastrointestinal tract (GT) of ruminants have been well-documented, however, knowledge of aerobic microbes with cellulolytic activities in ruminant GT is comparably limited. Here, we unraveled aerobic cultivable cellulolytic microbes in GT of Ujimqin sheep (Ovis aries) and evaluated the cellulolytic potential of promising isolates. Twenty-two strains were found to possess cellulose degrading potential by Congo-red staining and phylogenetic analysis of the 16S rDNA/ITS sequence revealed that all strains belonged to nine genera, i.e., Bacillus, Streptomyces, Pseudomonas, Lactobacillus, Brachybacterium, Sanguibacter, Rhizobium, Fusarium, and Aspergillus. Strains with high cellulolytic activities were selected to further evaluate the various enzyme activities on lignocellulosic alfalfa hay (Medicago sativa). Among them, isolate Bacillus subtilis RE2510 showed the highest potential of cellulose degradation considering the high endoglucanase (0.1478 ± 0.0014 IU ml-1), exoglucanase (0.1735 ± 0.0012 IU ml-1) and β-glucosidase (0.3817 ± 0.0031 IU ml-1) after 10-day incubation with alfalfa hay. A significant destruction effect of the cellulose structure and the attachment of B. subtilis RE2510 to the hay were also revealed by using scanning electron microscope. This study expands our knowledge of aerobic cellulolytic isolates from GT of sheep and also highlights their potential application as microbial additive in the aerobic process of cellulose bioconversion.

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.

Steering ecological-evolutionary dynamics to improve artificial selection of microbial communities

Microbial communities often perform important functions that depend on inter-species interactions. To improve community function via artificial selection, one can repeatedly grow many communities to allow mutations to arise, and "reproduce" the highest-functioning communities by partitioning each into multiple offspring communities for the next cycle. Since improvement is often unimpressive in experiments, we study how to design effective selection strategies in silico. Specifically, we simulate community selection to improve a function that requires two species. With a "community function landscape", we visualize how community function depends on species and genotype compositions. Due to ecological interactions that promote species coexistence, the evolutionary trajectory of communities is restricted to a path on the landscape. This restriction can generate counter-intuitive evolutionary dynamics, prevent the attainment of maximal function, and importantly, hinder selection by trapping communities in locations of low community function heritability. We devise experimentally-implementable manipulations to shift the path to higher heritability, which speeds up community function improvement even when landscapes are high dimensional or unknown. Video walkthroughs: https://go.nature.com/3GWwS6j ; https://online.kitp.ucsb.edu/online/ecoevo21/shou2/ .

Meta-fermentation system with a mixed culture for the production of optically pure l-lactic acid can be reconstructed using the minimum isolates with a simplified pH control strategy

Meta-l-lactic acid fermentation from non-treated kitchen refuse was reconstructed using a combination of isolated bacterial strains under several pH control strategies. The meta-fermentation system was successfully reconstructed using a combination of Weizmannia coagulans MN-07, Caldibacillus thermoamylovorans OM55-6, and Caldibacillus hisashii N-11 strains. Additionally, a simplified constant pH control strategy was employed, which decreased fermentation time and increased production. The optimum pH (6.5) for the reconstructed meta-fermentation was favorable for the respective pure cultures of the three selected strains. The l-lactic acid production performance of the reconstructed meta-fermentation system was as follows: concentration, 24.5 g L^-1 ; optical purity, 100%; productivity, 0.341 g L^-1 h^-1 ; yield, 1.06 g g^-1 . These results indicated that constant pH control was effective in the reconstructed meta-fermentation with the best performance of l-lactic acid production at pH optimal for the selected bacterial growth, while the switching from swing pH control would suppress the activities of unfavorable bacterial species in un-isolated meta-fermentation.

Metabolic engineering for the production of butanol, a potential advanced biofuel, from renewable resources

Butanol is an important chemical and potential fuel. For more than 100 years, acetone-butanol-ethanol (ABE) fermentation of Clostridium strains has been the most successful process for biological butanol production. In recent years, other microbes have been engineered to produce butanol as well, among which Escherichia coli was the best one. Considering the crude oil price fluctuation, minimizing the cost of butanol production is of highest priority for its industrial application. Therefore, using cheaper feedstocks instead of pure sugars is an important project. In this review, we summarized butanol production from different renewable resources, such as industrial and food waste, lignocellulosic biomass, syngas and other renewable resources. This review will present the current progress in this field and provide insights for further engineering efforts on renewable butanol production.

A Review on Bacterial Contribution to Lignocellulose Breakdown into Useful Bio-Products

Discovering novel bacterial strains might be the link to unlocking the value in lignocellulosic bio-refinery as we strive to find alternative and cleaner sources of energy. Bacteria display promise in lignocellulolytic breakdown because of their innate ability to adapt and grow under both optimum and extreme conditions. This versatility of bacterial strains is being harnessed, with qualities like adapting to various temperature, aero tolerance, and nutrient availability driving the use of bacteria in bio-refinery studies. Their flexible nature holds exciting promise in biotechnology, but despite recent pointers to a greener edge in the pretreatment of lignocellulose biomass and lignocellulose-driven bioconversion to value-added products, the cost of adoption and subsequent scaling up industrially still pose challenges to their adoption. However, recent studies have seen the use of co-culture, co-digestion, and bioengineering to overcome identified setbacks to using bacterial strains to breakdown lignocellulose into its major polymers and then to useful products ranging from ethanol, enzymes, biodiesel, bioflocculants, and many others. In this review, research on bacteria involved in lignocellulose breakdown is reviewed and summarized to provide background for further research. Future perspectives are explored as bacteria have a role to play in the adoption of greener energy alternatives using lignocellulosic biomass.

Enrichment and characterization of an effective hexavalent chromium-reducing microbial community YEM001

Chromium (Cr) is one of the most widely used heavy metals in industrial processes, resulting in water and soil pollution that seriously threaten environmental safety. In this paper, we have directionally enriched a Cr(VI)-reducing bacterial community YEM001 from no-Cr(VI) polluted pond sedimental sludge by selectively growing it in Cr(VI)-containing media. This community could effectively reduce Cr(VI) in laboratory rich media containing different concentrations of Cr(VI), such as 61% reduction at 435 mg/L Cr(VI), 85% reduction at 355 mg/L Cr(VI), and complete reduction at 269 mg/L Cr(VI) in 93.5 h. It was also able to completely reduce 100 mg/L and 300 mg/L Cr(VI) in landfill leachate and natural sludge in 48 h, respectively. Optimal pH for Cr(VI) reduction of the YEM001 is between 7 and 8 and the best efficiency for Cr(VI) reduction occurs at 30 °C. Metagenomic data demonstrated that the YEM001 community was composed of multiple bacteria, including well-known Cr(VI)-reducing bacteria and non-Cr(VI)-reducing bacteria. Delftia, Comamonas, Alicycliphilus, Acidovorax, Bacillus, and Clostridioides account for 83% of total community abundance. The stability of the composition of the YEM001 community and its Cr(VI)-reducing activity allows for its application in bioremediation of environmental Cr(VI) pollution.

Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil

Microorganisms that degrade cellulose utilize extracellular reactions that yield free by-products which can promote interactions with noncellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We performed comparative genomics with genome bins from a shotgun metagenomic-stable isotope probing experiment to characterize the attributes of cellulolytic and noncellulolytic taxa accessing ¹³C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits that limit access, while noncellulolytic taxa would display greater metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential, and auxotrophy. The most ¹³C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Noncellulolytic taxa that accessed ¹³C from cellulose (Planctomycetales, Verrucomicrobia, and Vampirovibrionales) were also more dependent, as indicated by patterns of auxotrophy and ¹³C labeling (i.e., partial labeling or labeling at later stages). Major ¹³C-labeled cellulolytic microbes (e.g., Sorangium, Actinomycetales, Rhizobiales, and Caulobacteraceae) possessed adaptations for surface colonization (e.g., gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposing particulate organic matter. Our results demonstrated that access to cellulosic C was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion.

Insight into the effect of nitrogen-rich substrates on the community structure and the co-occurrence network of thermophiles during lignocellulose-based composting

Thermophilic microorganisms play vital roles in the composting process. To elucidate how raw materials affect thermophilic microbial community composition and their interactions, the succession of thermophilic bacterial and fungal communities were monitored in reed straw co-composting with four common nitrogen-rich substrates. The results of high-throughput sequencing showed that raw materials and composting process significantly changed bacterial and fungal community composition. Firmicutes and Actinobacteria drove the assembly of bacterial communities, while Ascomycetes drove the assembly of fungal communities. Network analysis indicated that during the composting process, the addition of nitrogen-rich sources abundant in easily degradable substances promoted the complexity of thermophilic microbial network. Moreover, microorganisms mainly exhibited synergistic effects, and inter-kingdom competition was more intense than intra-kingdom competition. Notably, rare species play essential roles in maintaining the network construction. Our findings provided novel insights into thermophilic microbial community assembly and their co-occurrence networks during the composting process.

The difference between cellulolytic 'culturomes' and microbiomes inhabiting two contrasting soil types

High-throughput 16S rRNA sequencing was performed to compare the microbiomes inhabiting two contrasting soil types-sod-podzolic soil and chernozem-and the corresponding culturome communities of potentially cellulolytic bacteria cultured on standard Hutchinson media. For each soil type, soil-specific microorganisms have been identified: for sod-podzolic soil-Acidothermus, Devosia, Phenylobacterium and Tumebacillus, and for chernozem soil-Sphingomonas, Bacillus and Blastococcus. The dynamics of differences between soil types for bulk soil samples and culturomes varied depending on the taxonomic level of the corresponding phylotypes. At high taxonomic levels, the number of common taxa between soil types increased more slowly for bulk soil than for culturome. Differences between soil-specific phylotypes were detected in bulk soil at a low taxonomic level (genus, species). A total of 13 phylotypes were represented both in soil and in culturome. No relationship was shown between the abundance of these phylotypes in soil and culturome.

Prokaryotic community composition in a great shallow soda lake covered by large reed stands (Neusiedler See/Lake Fertő) as revealed by cultivation- and DNA-based analyses

Little is known about the detailed community composition of heterotrophic bacterioplankton in macrophyte-dominated littoral systems, where a considerable amount of dissolved organic carbon originates from aquatic macrophytes instead of phytoplankton. The aim of the present study was to reveal the effect of macrophytes on the microbial community and to elucidate their role in a macrophyte-dominated shallow soda lake, which can be characterised by a mosaic of open waters and reed marsh. Therefore, 16S rRNA gene amplicon sequencing, the most probable number method, cultivation of bacterial strains, EcoPlate and cultivation-based substrate utilisation techniques were applied. Differences in the structures of microbial communities were detected between the water and the sediment samples and between vegetated and unvegetated water samples. Planktonic bacterial communities of an inner pond and a reed-covered area showed significant similarities to each other. Woesearchaeia was the dominant archaeal taxon in the water samples, while Bathyarchaeia, 'Marine Benthic Group D' and 'DHVEG-1' were abundant in the sediment samples. The most probable number of heterotrophic bacteria was lower in the open water than in the reed-associated areas. The vast majority (83%) of the isolated bacterial strains from the water samples of the reed-covered area were able to grow on a medium containing reed extract as the sole source of carbon.

Microorganisms and Enzymes Used in the Biological Pretreatment of the Substrate to Enhance Biogas Production: A Review

The pretreatment of lignocellulosic biomass (LC biomass) prior to the anaerobic digestion (AD) process is a mandatory step to improve feedstock biodegradability and biogas production. An important potential is provided by lignocellulosic materials since lignocellulose represents a major source for biogas production, thus contributing to the environmental sustainability. The main limitation of LC biomass for use is its resistant structure. Lately, biological pretreatment (BP) gained popularity because they are eco-friendly methods that do not require chemical or energy input. A large number of bacteria and fungi possess great ability to convert high molecular weight compounds from the substrate into lower mass compounds due to the synthesis of microbial extracellular enzymes. Microbial strains isolated from various sources are used singly or in combination to break down the recalcitrant polymeric structures and thus increase biogasgeneration. Enzymatic treatment of LC biomass depends mainly on enzymes like hemicellulases and cellulases generated by microorganisms. The articles main purpose is to provide an overview regarding the enzymatic/biological pretreatment as one of the most potent techniques for enhancing biogas production.

Phytoremediation potential of heavy metal accumulator plants for waste management in the pulp and paper industry

The present manuscript has focused on the heavy metal; accumulation potential by common native plants i.e. Chenopodium album L., Ricinus communis, Ranunculus sceleratus, and Rumex dentatus growing on the disposed of pulp and paper mill effluent sludge. The sludge showed the abundance of benzene propanoic acid tert- butyldimethylsilyl ester, Octadecanoic acid, TMS, Hexadecanoic acid, TMS, cinnamic acid-α-phenyl-TMS ester, β-sitosterol TMS, 4-mercaptobenzoic acid as residual complex organic compounds along with heavy metals Fe (98.30 mg/L-1), Zn (51.00 mg/L-1), Cu (3.21 mg/L-1), Cd (9.11 mg/L-1), Mn (18.27 mg/L-1), Ni (5.21 mg/L-1), (Hg 0.014 mg/L-1) which were above the prescribed limit of environmental standard. The complexation of organic compounds with heavy metal restricts the bioavailability of metals to plants. But the metal analysis in various parts of the plant showed a significant amount of metal accumulation. Further, histological observations of root tissue through TEM showed apparent deposition of metal granules near the cell wall and vacuole as adoption features of plants. But the variable concentration of metal accumulation in different parts by various plants indicated the variable potential of tested plants with various metals. This also indicated their metal bio-availability and movement to plant tissue. Further, their bioconcentration factor (BCF) and translocation factor (TF) > 1.0 indicated the hyperaccumulation tendency of plants Mn was accumulated maximum in leaves C. album (69.38 mg/kg-1) followed by Cu (25.75 mg/kg -1), As (23.20 mg/kg -1), Fe (20.90 mg/kg -1) and Pb was maximum accumulated (22.41 mg/kg -1) in R. cummunis leaves. The result revealed that arsenic has been accumulated in higher amount root, shoot and leaves of all tested plants. The metal accumulator plants showed phytoremediation potential also by reducing various pollution parameters after growth on sludge. These potential plants may be used as biotechnological tools for the eco-restoration of polluted sites.

Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data

Modulation of interspecies interactions by the presence of neighbor species is a key ecological factor that governs dynamics and function of microbial communities, yet the development of theoretical frameworks explicit for understanding context-dependent interactions are still nascent. In a recent study, we proposed a novel rule-based inference method termed the Minimal Interspecies Interaction Adjustment (MIIA) that predicts the reorganization of interaction networks in response to the addition of new species such that the modulation in interaction coefficients caused by additional members is minimal. While the theoretical basis of MIIA was established through the previous work by assuming the full availability of species abundance data in axenic, binary, and complex communities, its extension to actual microbial ecology can be highly constrained in cases that species have not been cultured axenically (e.g., due to their inability to grow in the absence of specific partnerships) because binary interaction coefficients - basic parameters required for implementing the MIIA - are inestimable without axenic and binary population data. Thus, here we present an alternative formulation based on the following two central ideas. First, in the case where only data from axenic cultures are unavailable, we remove axenic populations from governing equations through appropriate scaling. This allows us to predict neighbor-dependent interactions in a relative sense (i.e., fractional change of interactions between with versus without neighbors). Second, in the case where both axenic and binary populations are missing, we parameterize binary interaction coefficients to determine their values through a sensitivity analysis. Through the case study of two microbial communities with distinct characteristics and complexity (i.e., a three-member community where all members can grow independently, and a four-member community that contains member species whose growth is dependent on other species), we demonstrated that despite data limitation, the proposed new formulation was able to successfully predict interspecies interactions that are consistent with experimentally derived results. Therefore, this technical advancement enhances our ability to predict context-dependent interspecies interactions in a broad range of microbial systems without being limited to specific growth conditions as a pre-requisite.

Exploring the Relationship Between Clostridium thermocellum JN4 and Thermoanaerobacterium thermosaccharolyticum GD17

Characterizing and engineering microbial communities for lignocellulosic biofuel production has received widespread attention. Previous research has established that Clostridium thermocellum JN4 and Thermoanaerobacterium thermosaccharolyticum GD17 coculture significantly improves overall cellulosic biofuel production efficiency. Here, we investigated this interaction and revealed the mechanism underlying the improved efficiency observed. In contrast to the previously reported mutualistic relationship, a harmful effect toward C. thermocellum JN4 was observed in these microbial consortia. Although T. thermosaccharolyticum GD17 relieves the carbon catabolite repression of C. thermocellum JN4 regarding obtaining more cellobiose or glucose released from lignocellulose, T. thermosaccharolyticum GD17 significantly hampers the growth of C. thermocellum JN4 in coculture. The increased formation of end products is due to the strong competitive metabolic advantage of T. thermosaccharolyticum GD17 over C. thermocellum JN4 in the conversion of glucose or cellobiose into final products. The possibility of controlling and rebalancing these microbial consortia to modulate cellulose degradation was achieved by adding T. thermosaccharolyticum GD17 stimulants into the system. As cellulolytic bacteria are usually at a metabolic disadvantage, these discoveries may apply to a large proportion of cellulosic biofuel-producing microbial consortia. These findings provide a reference for engineering efficient and modular microbial consortia for modulating cellulosic conversion.

Simulations reveal challenges to artificial community selection and possible strategies for success

Multispecies microbial communities often display "community functions" arising from interactions of member species. Interactions are often difficult to decipher, making it challenging to design communities with desired functions. Alternatively, similar to artificial selection for individuals in agriculture and industry, one could repeatedly choose communities with the highest community functions to reproduce by randomly partitioning each into multiple "Newborn" communities for the next cycle. However, previous efforts in selecting complex communities have generated mixed outcomes that are difficult to interpret. To understand how to effectively enact community selection, we simulated community selection to improve a community function that requires 2 species and imposes a fitness cost on one or both species. Our simulations predict that improvement could be easily stalled unless various aspects of selection are carefully considered. These aspects include promoting species coexistence, suppressing noncontributors, choosing additional communities besides the highest functioning ones to reproduce, and reducing stochastic fluctuations in the biomass of each member species in Newborn communities. These considerations can be addressed experimentally. When executed effectively, community selection is predicted to improve costly community function, and may even force species to evolve slow growth to achieve species coexistence. Our conclusions hold under various alternative model assumptions and are therefore applicable to a variety of communities.

Microbial coexistence through chemical-mediated interactions

Many microbial functions happen within communities of interacting species. Explaining how species with disparate growth rates can coexist is important for applications such as manipulating host-associated microbiota or engineering industrial communities. Here, we ask how microbes interacting through their chemical environment can achieve coexistence in a continuous growth setup (similar to an industrial bioreactor or gut microbiota) where external resources are being supplied. We formulate and experimentally constrain a model in which mediators of interactions (e.g. metabolites or waste-products) are explicitly incorporated. Our model highlights facilitation and self-restraint as interactions that contribute to coexistence, consistent with our intuition. When interactions are strong, we observe that coexistence is determined primarily by the topology of facilitation and inhibition influences not their strengths. Importantly, we show that consumption or degradation of chemical mediators moderates interaction strengths and promotes coexistence. Our results offer insights into how to build or restructure microbial communities of interest.

Enrichment and Characterisation of a Mixed-Source Ethanologenic Community Degrading the Organic Fraction of Municipal Solid Waste Under Minimal Environmental Control

The utilisation of the organic fraction of municipal solid waste as feedstock for bioethanol production could reduce the need for disposal of the ever-increasing amounts of municipal solid waste, especially in developing countries, and fits with the integrated goals of climate change mitigation and transport energy security. Mixed culture fermentation represents a suitable approach to handle the complexity and variability of such waste, avoiding expensive and vulnerable closed-control operational conditions. It is widely accepted that the control of pH in these systems can direct the fermentation process toward a desired fermentation product, however, little empirical evidence has been provided in respect of lignocellulosic waste substrates and different environmental inocula sources. We evaluated ethanol production from the organic fraction of municipal solid waste using five different inocula sources where lignocellulose degradation putatively occurs, namely, compost, woodland soil, rumen, cow faeces and anaerobic granular sludge, when incubated in batch microcosms at either initially neutral or acidic pH and under initially aerobic or anaerobic conditions. Although ethanol was produced by all the inocula tested, their performance was different in response to the imposed experimental conditions. Rumen and anaerobic granular sludge produced significantly the highest ethanol concentrations (∼30 mM) under initially neutral and acidic pH, respectively. A mixed-source community formed by mixing rumen and sludge (R + S) was then tested over a range of initial pH. In contrast to the differences observed for the individual inocula, the maximal ethanol production of the mixed community was not significantly different at initial pH of 5.5 and 7. Consistent with this broader functionality, the microbial community analyses confirmed the R + S community enriched comprised bacterial taxa representative of both original inocula. It was demonstrated that the interaction of initial pH and inocula source dictated ethanologenic activity from the organic fraction of municipal solid waste. Furthermore, the ethanologenic mixed-source community enriched, was comprised of taxa belonging to the two original inocula sources (rumen and sludge) and had a broader functionality. This information is relevant when diverse inocula sources are combined for mix culture fermentation studies as it experimentally demonstrates the benefits of diversity and function assembled from different inocula.

Metagenomic Insights Into a Cellulose-Rich Niche Reveal Microbial Cooperation in Cellulose Degradation

Background

Cellulose is the most abundant organic polymer mainly produced by plants in nature. It is insoluble and highly resistant to enzymatic hydrolysis. Cellulolytic microorganisms that are capable of producing a battery of related enzymes play an important role in recycling cellulose-rich plant biomass. Effective cellulose degradation by multiple synergic microorganisms has been observed within a defined microbial consortium in the lab culture. Metagenomic analysis may enable us to understand how microbes cooperate in cellulose degradation in a more complex microbial free-living ecosystem in nature.

Results

Here we investigated a typical cellulose-rich and alkaline niche where constituent microbes survive through inter-genera cooperation in cellulose utilization. The niche has been generated in an ancient paper-making plant, which has served as an isolated habitat for over 7 centuries. Combined amplicon-based sequencing of 16S rRNA genes and metagenomic sequencing, our analyses showed a microbial composition with 6 dominant genera including Cloacibacterium, Paludibacter, Exiguobacterium, Acetivibrio, Tolumonas, and Clostridium in this cellulose-rich niche; the composition is distinct from other cellulose-rich niches including a modern paper mill, bamboo soil, wild giant panda guts, and termite hindguts. In total, 11,676 genes of 96 glucoside hydrolase (GH) families, as well as 1,744 genes of carbohydrate transporters were identified, and modeling analysis of two representative genes suggested that these glucoside hydrolases likely evolved to adapt to alkaline environments. Further reconstruction of the microbial draft genomes by binning the assembled contigs predicted a mutualistic interaction between the dominant microbes regarding the cellulolytic process in the niche, with Paludibacter and Clostridium acting as helpers that produce endoglucanases, and Cloacibacterium, Exiguobacterium, Acetivibrio, and Tolumonas being beneficiaries that cross-feed on the cellodextrins by oligosaccharide uptake.

Conclusion

The analysis of the key genes involved in cellulose degradation and reconstruction of the microbial draft genomes by binning the assembled contigs predicted a mutualistic interaction based on public goods regarding the cellulolytic process in the niche, suggesting that in the studied microbial consortium, free-living bacteria likely survive on each other by acquisition and exchange of metabolites. Knowledge gained from this study will facilitate the design of complex microbial communities with a better performance in industrial bioprocesses.

Effects of amino acids on the lignocellulose degradation by Aspergillus fumigatus Z5: insights into performance, transcriptional, and proteomic profiles

BACKGROUND

As a ubiquitous filamentous fungal, Aspergillus spp. play a critical role in lignocellulose degradation, which was also defined as considerable cell factories for organic acids and industrially relevant enzymes producer. Nevertheless, the production of various extracellular enzymes can be influenced by different factors including nitrogen source, carbon source, cultivation temperature, and initial pH value. Thus, this study aims to reveal how amino acids affect the decomposition of lignocellulose by Aspergillus fumigatus Z5 through transcriptional and proteomics methods.

RESULTS

The activities of several lignocellulosic enzymes secreted by A. fumigatus Z5 adding with cysteine, methionine, and ammonium sulfate were determined with the chromatometry method. The peak of endo-glucanase (7.33 ± 0.03 U mL-1), exo-glucanase (10.50 ± 0.07 U mL-1), β-glucosidase (21.50 ± 0.22 U mL-1), and xylanase (76.43 ± 0.71 U mL-1) were all obtained in the Cys treatment. The secretomes of A. fumigatus Z5 under different treatments were also identified by LC-MS/MS, and 227, 256 and 159 different proteins were identified in the treatments of Cys, Met, and CK (Control, treatment with ammonium sulfate as the sole nitrogen source), respectively. Correlation analysis results of transcriptome and proteome data with fermentation profiles showed that most of the cellulose-degrading enzymes including cellulases, hemicellulases and glycoside hydrolases were highly upregulated when cysteine was added to the growth medium. In particular, the enzymes that convert cellulose into cellobiose appear to be upregulated. This study could increase knowledge of lignocellulose bioconversion pathways and fungal genetics.

CONCLUSIONS

Transcriptome and proteome analyses' results indicated that cysteine could significantly promote the secretion of lignocellulosic enzymes of an efficient lignocellulosic decomposing strain, A. fumigatus Z5. The possible reason for these results is that Z5 preferred to use amino acids such as cysteine to adapt to the external environment through upregulating carbon-related metabolism pathways.

A novel strategy to enhance biohydrogen production using graphene oxide treated thermostable crude cellulase and sugarcane bagasse hydrolyzate under co-culture system

Graphene oxide (GO) treated thermostable crude cellulase has been obtained via fungal co-cultivation of strain Cladosporium cladosporioides NS2 and Emericella variecolor NS3 using mix substrate of orange peel and rice straw under solid state fermentation (SSF). Enzyme activity of 60 IU/gds FP, 300 IU/gds EG and 400 IU/gds BGL are recorded in the presence of 1.0% GO in 96 h. This crude enzyme showed 50 °C as optimum incubation temperature, thermally stable at 55 °C for 600 min and stability in the pH range 4.5-8.0. Further, 70.04 g/L of sugar hydrolyzate is obtained from enzymatic conversion of 3.0% alkali pre-treated baggase using GO treated crude cellulase. Finally, 2870 ml/L cumulative biohydrogen production having bacterial biomass ∼2.2 g/L and the complimentary initial pH 7.0 is recorded from sugar hydrolyzate via dark fermentation using co-culture of Clostridium pasteurianum (MTCC116) and a newly isolated Bacillus subtilis PF_1.

Model Microbial Consortia as Tools for Understanding Complex Microbial Communities

A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.

Organic Amendments in a Long-term Field Trial-Consequences for the Bulk Soil Bacterial Community as Revealed by Network Analysis

This study intended to elucidate the long-term effects of organic soil amendments on bacterial co-occurrence in bulk soil with and without addition of mineral fertiliser. Previous research mostly neglected the bacterial co-occurrence structure and focussed mainly on the parameters species diversity and abundance changes of species. Here we present a systematic comparison of two frequently used soil amendments, manure and straw, with regard to their impact on bacterial co-occurrence in a long-term field trial in Speyer, Germany. The approach involved 16S amplicon sequencing in combination with a bacterial network analysis, comparing the different fertiliser regimes. The results show an increase of bacterial diversity as well as an accumulation of bacteria of the order Bacillales in plots fertilised with manure compared to a control treatment. In the straw-amended plots neither an increase in diversity was found nor were indicative species detectable. Furthermore, network analysis revealed a clear impact of mineral fertiliser addition on bacterial co-occurrence structure. Most importantly, both organic amendments increased network complexity irrespective of mineral fertilisation regime. At the same time, the effects of manure and straw exhibited differences that might be explained by differences in their nutritional/chemical contents. It is concluded that bacterial interactions are a crucial parameter for the assessment of amendment effects regarding soil health and sustainability.

Compost bacteria and fungi that influence growth and development of Agaricus bisporus and other commercial mushrooms

Mushrooms are an important food crop for many millions of people worldwide. The most important edible mushroom is the button mushroom (Agaricus bisporus), an excellent example of sustainable food production which is cultivated on a selective compost produced from recycled agricultural waste products. A diverse population of bacteria and fungi are involved throughout the production of Agaricus. A range of successional taxa convert the wheat straw into compost in the thermophilic composting process. These initially break down readily accessible compounds and release ammonia, and then assimilate cellulose and hemicellulose into compost microbial biomass that forms the primary source of nutrition for the Agaricus mycelium. This key process in composting is performed by a microbial consortium consisting of the thermophilic fungus Mycothermus thermophilus (Scytalidium thermophilum) and a range of thermophilic proteobacteria and actinobacteria, many of which have only recently been identified. Certain bacterial taxa have been shown to promote elongation of the Agaricus hyphae, and bacterial activity is required to induce production of the mushroom fruiting bodies during cropping. Attempts to isolate mushroom growth-promoting bacteria for commercial mushroom production have not yet been successful. Compost bacteria and fungi also cause economically important losses in the cropping process, causing a range of destructive diseases of mushroom hyphae and fruiting bodies. Recent advances in our understanding of the key bacteria and fungi in mushroom compost provide the potential to improve productivity of mushroom compost and to reduce the impact of crop disease.

Characterization of cellulolytic microbial consortium enriched on Napier grass using metagenomic approaches

Energy grass is a promising substrate for production of biogas by anaerobic digestion. However, the conversion efficiency is limited by the enzymatically recalcitrant nature of cellulosic wastes. In this study, an active, structurally stable mesophilic lignocellulolytic degrading microbial consortium (Np-LMC) was constructed from forest compost soil microbiota by successive subcultivation on Napier grass under facultative anoxic conditions. According to tagged 16S rRNA gene amplicon sequencing, increasing abundance of facultative Proteobacteria was found in the middle of batch cycle which was then subsequently replaced by the cellulose degraders Firmicutes and Bacteroidetes along with decreasing CMCase, xylanase, and β-glucanase activity profiles in the supernatant after 5 days of incubation. Anaerobic/facultative bacteria Dysgonomonas and Sedimentibacter and aerobic bacteria Comamonas were the major genera found in Np-LMC. The consortium was active on degradation of the native and delignified grass. Direct shotgun sequencing of the consortium metagenome revealed relatively high abundance of genes encoding for various lignocellulose degrading enzymes in 23 glycosyl hydrolase (GH) families compared to previously reported cellulolytic microbial communities in mammalian digestive tracts. Enzymes attacking cellulose and hemicellulose were dominated by GH2, 3, 5, 9, 10, 26, 28 and 43 in addition to a variety of carbohydrate esterases (CE) and auxiliary activities (AA), reflecting adaptation of the enzyme systems to the native herbaceous substrate. The consortium identified here represents the microcosm specifically bred on energy grass, with potential for enhancing degradation of fibrous substrates in bioenergy industry.

Variation of bacterial communities in water and sediments during the decomposition of Microcystis biomass

The bacterial community composition in water and sediment samples during the decomposition of Microcystis biomass were analyzed using the 454 pyrosequencing technique. We found dramatic shifts in the bacterial community composition of water and sediments after the addition of Microcystis biomass. Among all the detected phyla, only Firmicutes was found to be dominant in both water and sediment samples. The genus Clostridium sensu stricto was the absolutely dominant group in Firmicutes and showed drastic variations with incubation time during the decomposition process. Peak values in relative abundance of Clostridium sensu stricto appeared in the first few days for water and sediment samples. Environmental factors such as pH, dissolved oxygen (DO), and dissolved organic carbon (DOC) in water samples showed drastic variations during the decomposing process, which might be the prominent forces driving the variation of bacterial communities. The abundant genus, Clostridium sensu stricto, were thought to be well adapted to higher DOC and turbidity and lower pH and DO conditions. Compared with the sediment samples, the decomposition of Microcystis biomass had greater influence on the bacterial community composition in water and Clostridium sensu stricto might play important roles in the process of Microcystis biomass decomposition.

Advances in industrial microbiome based on microbial consortium for biorefinery

One of the important targets of industrial biotechnology is using cheap biomass resources. The traditional strategy is microbial fermentations with single strain. However, cheap biomass normally contains so complex compositions and impurities that it is very difficult for single microorganism to utilize availably. In order to completely utilize the substrates and produce multiple products in one process, industrial microbiome based on microbial consortium draws more and more attention. In this review, we first briefly described some examples of existing industrial bioprocesses involving microbial consortia. Comparison of 1,3-propanediol production by mixed and pure cultures were then introduced, and interaction relationships between cells in microbial consortium were summarized. Finally, the outlook on how to design and apply microbial consortium in the future was also proposed.

Environmental Origin of the Genus Bordetella

Members of the genus Bordetella include human and animal pathogens that cause a variety of respiratory infections, including whooping cough in humans. Despite the long known ability to switch between a within-animal and an extra-host lifestyle under laboratory growth conditions, no extra-host niches of pathogenic Bordetella species have been defined. To better understand the distribution of Bordetella species in the environment, we probed the NCBI nucleotide database with the 16S ribosomal RNA (16S rRNA) gene sequences from pathogenic Bordetella species. Bacteria of the genus Bordetella were frequently found in soil, water, sediment, and plants. Phylogenetic analyses of their 16S rRNA gene sequences showed that Bordetella recovered from environmental samples are evolutionarily ancestral to animal-associated species. Sequences from environmental samples had a significantly higher genetic diversity, were located closer to the root of the phylogenetic tree and were present in all 10 identified sequence clades, while only four sequence clades possessed animal-associated species. The pathogenic bordetellae appear to have evolved from ancestors in soil and/or water. We show that, despite being animal-adapted pathogens, Bordetella bronchiseptica, and Bordetella hinzii have preserved the ability to grow and proliferate in soil. Our data implicate soil as a probable environmental origin of Bordetella species, including the animal-pathogenic lineages. Soil may further constitute an environmental niche, allowing for persistence and dissemination of the bacterial pathogens. Spread of pathogenic bordetellae from an environmental reservoir such as soil may potentially explain their wide distribution as well as frequent disease outbreaks that start without an obvious infectious source.

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.

Multi-pollutant treatment of crystalline cellulosic effluent: Function of dissolved oxygen on process control

Treatment of crystalline cellulose based wastewater was carried out in periodic discontinuous batch reactor (PDBR). Specific influence of dissolved oxygen on treatment of crystalline cellulosic (CC) wastewater was evaluated in three different microenvironments such as aerobic, anoxic and anaerobic. PDBR-aerobic biosystem documented relatively higher substrate degradation [2.63kgCOD/m(3)-day (92%)] in comparison to PDBR-anoxic [2.12kgCOD/m(3)-day (71%)] and PDBR-anaerobic [1.81kgCOD/m(3)-day (63%)], which is in accordance with the observed DO levels. Similarly, multipollutants viz., phosphates and nitrates removal was observed to be higher in aerobic followed by anoxic and anaerobic operations. Higher nitrate removal in aerobic operation might be attributed to the efficient denitrification carried out by the biocatalyst, which utilizes both nitrates and oxygen as oxidizing agents. Multiscan spectral profiles depicted reduction in color intensity in all three microenvironments that correlated with the substrate degradation observed. Despite the high organic load, PDBR functioned well without exhibiting process inhibition.

Construction and Characterization of a Cellulolytic Consortium Enriched from the Hindgut of Holotrichia parallela Larvae

Degradation of rice straw by cooperative microbial activities is at present the most attractive alternative to fuels and provides a basis for biomass conversion. The use of microbial consortia in the biodegradation of lignocelluloses could reduce problems such as incomplete synergistic enzymes, end-product inhibition, and so on. In this study, a cellulolytic microbial consortium was enriched from the hindgut of Holotrichia parallela larvae via continuous subcultivation (20 subcultures in total) under static conditions. The degradation ratio for rice straw was about 83.1% after three days of cultivation, indicating its strong cellulolytic activity. The diversity analysis results showed that the bacterial diversity and richness decreased during the consortium enrichment process, and the consortium enrichment process could lead to a significant enrichment of phyla Proteobacteria and Spirochaetes, classes Clostridia, Epsilonproteobacteria, and Betaproteobacteria, and genera Arcobacter, Treponema, Comamonas, and Clostridium. Some of these are well known as typical cellulolytic and hemicellulolytic microorganisms. Our results revealed that the microbial consortium identified herein is a potential candidate for use in the degradation of waste lignocellulosic biomass and further highlights the hindgut of the larvae as a reservoir of extensive and specific cellulolytic and hemicellulolytic microbes.

Pretreatment of non-sterile, rotted silage maize straw by the microbial community MC1 increases biogas production

Using microbial community MC1 to pretreat lignocellulosic materials increased the yield of biogas production, and the substrate did not need to be sterilized, lowering the cost. Rotted silage maize straw carries many microbes. To determine whether such contamination affects MC1, rotted silage maize straw was pretreated with MC1 prior to biogas production. The decreases in the weights of unsterilized and sterilized rotted silage maize straw were similar, as were their carboxymethyl cellulase activities. After 5d pretreatment, denaturing gradient gel electrophoresis and quantitative polymerase chain reaction results indicated that the proportions of five key strains in MC1 were the same in the unsterilized and sterilized groups; thus, MC1 was resistant to microbial contamination. However, its resistance to contamination decreased as the degradation time increased. Following pretreatment, volatile fatty acids, especially acetic acid, were detected, and MC1 enhanced biogas yields by 74.7% compared with the untreated group.

Enhancing anaerobic digestion of cotton stalk by pretreatment with a microbial consortium (MC1)

Microbial pretreatment is beneficial in some anaerobic digestion systems, but the consortia used to date have not been able to effectively increase methane production from cotton stalk. In this study, a thermophilic microbial consortium (MC1) was used for pretreatment in order to enhance biogas and methane production yields. The results indicated that the concentrations of soluble chemical oxygen demand and volatile organic products increased significantly in the early stages of pretreatment. Ethanol, acetic acid, propionic acid, and butyric acid were the predominant volatile organic products in the MC1 hydrolysate. Biogas and methane production yields from cotton stalk were significantly increased following MC1 pretreatment. In addition, the methane production rate from the treated cotton stalk was greater than that from the untreated sample.

Exploration of the key functional proteins from an efficient cellulolytic microbial consortium using dilution-to-extinction approach

In the present study, the cellulose binding proteins (CBPs) secreted by a putative cellulolytic microbial consortium were isolated and purified by affinity digestion. The purified CBPs were subsequently separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Using mass spectrometric analyses, eight CBPs were identified and annotated to be similar to known proteins secreted by Clostridium clariflavum DSM 19732 and Paenibacillus sp. W-61. In addition, in combination with dilution-to-extinction approach and zymogram analysis technique, CBPs 6 (97kDa) and 12 (52kDa) were confirmed to be the key functional proteins that influence cellulolytic activities. Moreover, structural domain analyses and enzymatic activity detection indicated that CBPs 6 and 12 contained glycoside hydrolase families (GH) 9 and 48 catalytic modules, which both revealed endoglucandase and xylanase activities. It was suggested that the coexistence of GH9 and GH48 catalytic domains present in these two proteins could synergistically promote the efficient degradation of cellulose.