Isolation of Cellulolytic Bacillus subtilis Strains from Agricultural Environments

Contribution of Aerobic Cellulolytic Gut Bacteria to Cellulose Digestion in Fifteen Coastal Grapsoid Crabs Underpins Potential for Mineralization of Mangrove Production

Grapsoid crabs (Decapoda: Grapsoidea) inhabiting along the land-sea transition provided various amounts and quality of vascular plant carbon (e.g., fresh mangrove leaf, leaf litter, and mangrove-derived organic carbon) and perform differing levels of herbivory. Other than endogenous cellulase, symbiotic cellulolytic bacteria could also contribute to the crabs' vascular plant carbon assimilation and mineralization. In this study, we isolated culturable cellulolytic bacteria from three gut regions (i.e., stomach, midgut, and hindgut) of 15 species of grapsoid crabs that inhabit in various coastal habitats (i.e., land margin, mangrove forest, tidal flat, and subtidal area). Bacillus, which was isolated from 11 out of the 15 grapsoid crabs, was the most common genus of culturable prominently cellulolytic bacteria among the target species. Seventy to ninety nine percent of culturable cellulolytic bacteria were removed, and the endoglucanase activity of five species was significantly reduced by 14.4-27.7% after antibiotic treatment. These results suggest that cellulolytic bacteria play a role in assisting mangrove carbon utilization in coastal grapsoid crabs, especially those inhabiting mangrove, mudflat, and subtidal areas. The significantly higher abundance of cellulolytic bacteria and the generally higher hydrolytic capacity of the bacteria in mangrove crab species suggest that they receive more contribution from symbionts for mangrove carbon utilization, while semi-terrestrial crabs seem to depend little on symbiotic cellulase due to the lower abundances.

The Succession of the Cellulolytic Microbial Community from the Soil during Oat Straw Decomposition

The process of straw decomposition is dynamic and is accompanied by the succession of the microbial decomposing community, which is driven by poorly understood interactions between microorganisms. Soil is a complex ecological niche, and the soil microbiome can serve as a source of potentially active cellulolytic microorganisms. Here, we performed an experiment on the de novo colonization of oat straw by the soil microbial community by placing nylon bags with sterilized oat straw in the pots filled with chernozem soil and incubating them for 6 months. The aim was to investigate the changes in decomposer microbiota during this process using conventional sequencing techniques. The bacterial succession during straw decomposition occurred in three phases: the early phase (first month) was characterized by high microbial activity and low diversity, the middle phase (second to third month) was characterized by low activity and low diversity, and the late phase (fourth to sixth months) was characterized by low activity and high diversity. Analysis of amplicon sequencing data revealed three groups of co-changing phylotypes corresponding to these phases. The early active phase was abundant in the cellulolytic members from Pseudomonadota, Bacteroidota, Bacillota, and Actinobacteriota for bacteria and Ascomycota for fungi, and most of the primary phylotypes were gone by the end of the phase. The second intermediate phase was marked by the set of phylotypes from the same phyla persisting in the community. In the mature community of the late phase, apart from the core phylotypes, non-cellulolytic members from Bdellovibrionota, Myxococcota, Chloroflexota, and Thermoproteota appeared. Full metagenome sequencing of the microbial community from the end of the middle phase confirmed that major bacterial and fungal members of this consortium had genes of glycoside hydrolases (GH) connected to cellulose and chitin degradation. The real-time analysis of the selection of these genes showed that their representation varied between phases, and this occurred under the influence of the host, and not the GH family factor. Our findings demonstrate that soil microbial community may act as an efficient source of cellulolytic microorganisms and that colonization of the cellulolytic substrate occurs in several phases, each characterized by its own taxonomic and functional profile.

Medium for the Production of Bacillus-Based Biocontrol Agent Effective against Aflatoxigenic Aspergillus flavus: Dual Approach for Modelling and Optimization

One of the leading limiting factors for wider industrial production and commercialization of microbial biopesticides refers to the high costs of cultivation media. The selection of alternative sources of macronutrients crucial for the growth and metabolic activity of the producing microorganism is a necessary phase of the bioprocess development. Gaining a better understanding of the influence of the medium composition on the biotechnological production of biocontrol agents is enabled through bioprocess modelling and optimization. In the present study, after the selection of optimal carbon and nitrogen sources, two modelling approaches were applied to mathematically describe the behavior of the examined bioprocess—the production of biocontrol agents effective against aflatoxigenic Aspergillus flavus strains. The modelling was performed using four independent variables: cellulose, urea, ammonium sulfate and dipotassium phosphate, and the selected response was the inhibition-zone diameter. After the comparison of the results generated by the Response Surface Methodology (RSM) and the Artificial Neural Network (ANN) approach, the first model was chosen for the further optimization step due to the better fit of the experimental results. As the final investigation step, the optimal cultivation medium composition was defined (g/L): cellulose 5.0, ammonium sulfate 3.77, dipotassium phosphate 0.3, magnesium sulfate heptahydrate 0.3.

Indigenous cellulolytic aerobic and facultative anaerobic bacterial community enhanced the composting of rice straw and chicken manure with biochar addition

Microbial degradation of organic matters is crucial during the composting process. In this study, the enhancement of the composting of rice straw and chicken manure with biochar was evaluated by investigating the indigenous cellulolytic bacterial community structure during the composting process. Compared with control treatment, composting with biochar recorded higher temperature (74 °C), longer thermophilic phase (> 50 °C for 18 days) and reduced carbon (19%) with considerable micro- and macronutrients content. The bacterial community succession showed that composting with biochar was dominated by the cellulolytic Thermobifida and Nocardiopsis genera, which play an important role in lignocellulose degradation. Twenty-three cellulolytic bacterial strains were successfully isolated at different phases of the composting with biochar. The 16S rRNA gene sequencing similarity showed that they were related to Bacilluslicheniformis, Bacillussubtilis,Bacillusaerius, and Bacillushaynesii, which were known as cellulolytic bacteria and generally involved in lignocellulose degradation. Of these isolated bacteria, Bacilluslicheniformis, a facultative anaerobe, was the major bacterial strain isolated and demonstrated higher cellulase activities. The increase in temperature and reduction of carbon during the composting with biochar in this study can thus be attributed to the existence of these cellulolytic bacteria identified.

Complete Genome Sequence of Kluyvera sp. CRP, a Cellulolytic Strain Isolated from Red Panda Feces (Ailurus fulgens)

The enterobacterium genus Kluyvera is widely distributed in the environment and a rare source of infection in humans. Kluyvera sp. strain CRP was isolated from feces of a healthy, captive Chinese red panda (Ailurus fulgens), and its complete genome (5,157,963 bp, 54.80% GC content) was established through hybrid assembly.

Bacillus subtilis PS-216 Antagonistic Activities against Campylobacter jejuni NCTC 11168 Are Modulated by Temperature, Oxygen, and Growth Medium

As the incidence of Campylobacter jejuni and campylobacteriosis grows, so does the need for a better understanding and control of this pathogen. We studied the interactions of C. jejuni NCTC 11168 and a potential probiotic, Bacillus subtilis PS-216, in cocultures at different starting ratios and temperatures (20 °C, 37 °C, 42 °C), under different atmospheres (aerobic, microaerobic), and in different growth media (Mueller–Hinton, chicken litter medium, chicken intestinal-content medium). Under microaerobic conditions, B. subtilis effectively inhibited the growth of C. jejuni at 42 °C (log reduction, 4.19), even when C. jejuni counts surpassed B. subtilis by 1000-fold in the starting inoculum. This inhibition was weaker at 37 °C (log reduction, 1.63), while no impact on CFUs was noted at 20 °C, which is a temperature nonpermissive of C. jejuni growth. Under aerobic conditions, B. subtilis supported C. jejuni survival. B. subtilis PS-216 inhibited the growth of C. jejuni in sterile chicken litter (4.07 log reduction) and in sterile intestinal content (2.26 log reduction). In nonsterile intestinal content, B. subtilis PS-216 was able to grow, to a lesser extent, compared to Mueller–Hinton media, still showing potential as a chicken probiotic that could be integrated into the chicken intestinal microbiota. This study showed the strong influence of environmental parameters on the variability of C. jejuni and B. subtilis interactions. Furthermore, B. subtilis PS-216 antagonism was strongest against C. jejuni NCTC 11168 under conditions that might represent conditions in the chicken environment (42 °C, microaerobic atmosphere, chicken litter medium).

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.

Use of Industrial Wastes as Sustainable Nutrient Sources for Bacterial Cellulose (BC) Production: Mechanism, Advances, and Future Perspectives

A novel nanomaterial, bacterial cellulose (BC), has become noteworthy recently due to its better physicochemical properties and biodegradability, which are desirable for various applications. Since cost is a significant limitation in the production of cellulose, current efforts are focused on the use of industrial waste as a cost-effective substrate for the synthesis of BC or microbial cellulose. The utilization of industrial wastes and byproduct streams as fermentation media could improve the cost-competitiveness of BC production. This paper examines the feasibility of using typical wastes generated by industry sectors as sources of nutrients (carbon and nitrogen) for the commercial-scale production of BC. Numerous preliminary findings in the literature data have revealed the potential to yield a high concentration of BC from various industrial wastes. These findings indicated the need to optimize culture conditions, aiming for improved large-scale production of BC from waste streams.

Culture-Independent and Culture-Dependent Characterization of the Black Soldier Fly Gut Microbiome Reveals a Large Proportion of Culturable Bacteria with Potential for Industrial Applications

Black soldier fly larvae (BSFL) are fast-growing, resilient insects that can break down a variety of organic substrates and convert them into valuable proteins and lipids for applications in the feed industry. Decomposition is mediated by an abundant and versatile gut microbiome, which has been studied for more than a decade. However, little is known about the phylogeny, properties and functions of bacterial isolates from the BSFL gut. We therefore characterized the BSFL gut microbiome in detail, evaluating bacterial diversity by culture-dependent methods and amplicon sequencing of the 16S rRNA gene. Redundant strains were identified by genomic fingerprinting and 105 non-redundant isolates were then tested for their ability to inhibit pathogens. We cultivated representatives of 26 genera, covering 47% of the families and 33% of the genera detected by amplicon sequencing. Among these isolates, we found several representatives of the most abundant genera: Morganella, Enterococcus, Proteus and Providencia. We also isolated diverse members of the less-abundant phylum Actinobacteria, and a novel genus of the order Clostridiales. We found that 15 of the isolates inhibited at least one of the tested pathogens, suggesting a role in helping to prevent colonization by pathogens in the gut. The resulting culture collection of unique BSFL gut bacteria provides a promising resource for multiple industrial applications.

Enzyme biotechnology development for treating polymers in hydraulic fracturing operations

Carboxymethyl cellulose (CMC) is a polymer used in many different industrial sectors. In the oil and gas industry, CMC is often used during hydraulic fracturing (fracking) operations as a thickening agent for effective proppant delivery. Accumulations of CMC at fracture faces (known as filter cakes) can impede oil and gas recovery. Although chemical oxidizers are added to disrupt these accumulations, there is industrial interest in developing alternative, enzyme-based treatments. Little is known about CMC biodegradation under fracking conditions. Here, we enriched a methanogenic CMC-degrading culture and demonstrated its ability to enzymatically utilize CMC under the conditions that typify oil fields. Using the extracellular enzyme fraction from the culture, significant CMC viscosity reduction was observed between 50 and 80˚C, at salinities up to 20% (w/v) and at pH 5-8 compared to controls. Similar levels of viscosity reduction by extracellular enzymes were observed under oxic and anoxic conditions. This proof-of-concept study demonstrates that enzyme biotechnology holds great promise as a viable approach to treating CMC filter cakes under oilfield conditions.

Optimization of the cultivation conditions of Bacillus licheniformis BCLLNF-01 for cellulase production

The objective of this study was to optimize the production of CMCase by Bacillus licheniformis BCLLNF-01, a strain associated with the mucus of the zoanthid Palythoa caribaeorum (Cnidaria, Anthozoa). Production of total cellulase and CMCase was investigated in the supernatant, intracellular content and wall content. Cultivation was carried out in BLM medium supplemented with 1.5 % (w/v) CMC, 5.5 % (v/v) inoculum, 40 °C, pH 6.5, 500 rpm for 72 h, and the highest activity was recorded in the supernatant. A Rotational Central Composite Design (RCCD) 2³ was used to investigate the influence of the carbon source concentration (CMC-0.5 to 1.5 % w/v), inoculum concentration (1-10 % v/v) and temperature (35-45 °C) on CMCase production. The maximum enzyme activity was achieved for a CMC concentration of 1.5 % w/v at 40 °C, attaining 0.493 IU/mL after 96 h of cultivation.

Determining Cellulolytic Activity of Microorganisms

Decomposition of cellulose to glucose requires complex cooperation of glycoside hydrolase enzymes. As a result of glycoside β-1,4 bonds hydrolysis, shorter chains of cellulose, oligodextrin, cellobiose and glucose are created. A number of bacteria and fungi demonstrate the capacity to degrade cellulose. Their activity can be assessed with the use of qualitative and quantitative methods. Qualitative methods with the use of e.g. Congo red, are used in screening studies, however, they do not provide information about the quantity of the produced enzyme. Spectrophotometric methods are more accurate and they measure the quantities of reducing sugars with the use of appropriate substrates, e.g. carboxymethylcellulose is used to determine endoglucanases, avicel cellulose to determine exoglucanases and Whatman filter paper to determine total cellulolytic activity. Activity of microorganisms depends not only on their species or type but also, among others, on substratum composition, cultivation conditions and the appropriate selection of parameters of the carried out enzymatic reactions.

Soluble expression of recombinant active cellulase in E.coli using B.subtilis (natto strain) cellulase gene

BACKGROUND

Cellulases are well known for their various industrial applications. They are naturally produced by different species of bacteria and fungi. Fermentation process of cellulase producers has limitation due to the high substrate cost required for cellulase induction and challenges to maintain the suitable condition for the respective cellulase production. Recombinant cellulase production could be the potential solution to these problems. In the current study, we investigated recombinant cellulase expression in Escherichia coli using cellulase gene from Bacillus subtilis.

RESULTS

Extracellular cellulase production from B. subtilis strain was first confirmed on CMC agar and then the cellulase gene (1500 bp) was amplified from this strain and was further cloned in pET21a expression vector. In initial experimental studies, recombinant cellulase expression was achieved in inclusion bodies through shake flask level fermentation of transformed E. coli expression host BL21DE3. Attempts were made to express this 55 KDa His tagged recombinant cellulase into soluble form by modifications in fermentation conditions. Partially purified recombinant cellulase was obtained using Ni-NTA affinity chromatography. The activity of the purified enzyme was confirmed by 3,5-dinitrosalicylic acid (DNS) qualitative assay.

CONCLUSION

Soluble expression of active recombinant cellulase can be achieved by subtle alteration in the upstream process.

Production and partial characterization of a crude cold-active cellulase (CMCase) from Bacillus mycoides AR20-61 isolated from an Alpine forest site

Purpose

To evaluate the production of a cold-active CMCase (endoglucanase) by Bacillus mycoides AR20-61 isolated from Alpine forest soil and to characterize the crude enzyme.

Methods

After studying the effect of cultivation parameters (medium composition, temperature, NaCl concentration, pH) on bacterial growth and enzyme production, the crude enzyme was characterized with regard to the effect of pH, temperature, and inhibitors on enzyme activity and stability.

Result

Optimum growth and enzyme production occurred at 20–25 °C, pH 7, and 1–1.5% (w/v) CMC. Despite high biomass production over the whole growth temperature range (10–35 °C), enzyme production was low at 10 and 35 °C. CMC concentration had a minor effect on growth, independent of the growth temperature, but a significant effect on CMCase production at temperatures ≥ 20 °C. The crude enzyme was active over a broad temperature range (0–60 °C); the apparent optimum temperature for activity was at 40–50 °C. The cultivation temperature influenced the effect of temperature on enzyme activity and stability. A significantly higher thermosensitivity of the enzyme produced at a cultivation temperature of 10 °C compared to that produced at 25 °C was noted at 50 and 65 °C. The enzyme was highly active over a pH range of 4–6 and showed optimum activity at pH 5. No activity was lost after 60 min of incubation at 30 °C and pH 4–9. The CMCase was resistant against a number of monovalent and divalent metal ions, metal-chelating agents, and phenol.

Conclusion

The CMCase produced by the studied strain is characterized by high activities in the low temperature range (down to 0 °C) and acidic pH range, high stability over a broad pH range, and high resistance against a number of effectors. Our results also demonstrate the different, independent roles of temperature in bacterial growth, enzyme production, nutrient requirements during enzyme production, and enzyme characteristics regarding thermosensitivity, which has not yet been described for cellulases.

Tannin-Tolerant and Extracellular Tannase Producing Bacillus Isolated from Traditional Fermented Tea Leaves and Their Probiotic Functional Properties

A total of 117 Bacillus strains were isolated from Miang, a culture relevant fermented tea of northern Thailand. These strains were collected from 16 sampling sites in north Thailand. In this collection 95 isolates were tannin-tolerant Bacillus capable of growth on nutrient agar supplemented with 0.5% (w/v) total tannins from tea leaves extract (TE). The strains were also positive for pectinase, xylanase and amylase activity, while 91 and 86 isolates were positive for cellulase and β-mannanase, respectively. Only 21 isolates producing extracellular tannase were selected for further characterization. Identification by 16S rRNA gene sequence analysis revealed that more than 50% (11 of 21 isolates) were Bacillustequilensis, whereas the remaining were B. siamensis (3), B. megaterium (3), B. aryabhattai (3) and B. toyonensis (1). B. tequilensis K34.2 produced the highest extracellular tannase activity of 0.60 U/mL after cultivation at 37 °C for 48 h. In addition, all 21 isolates were resistant to 0.3% (w/v) bile salt, sensitive to gentamicin, erythromycin, vancomycin and kanamycin and also tolerant to acidic condition. Cell hydrophobicity varied from 9.4 to 80.4% and neutralized culture supernatants of some Bacillus isolates showed bacteriocin producing potentiality against Samonella enterica serovar Typhimurium TISTR 292. All tested probiotic properties indicated that B. tequilensis K19.3, B. tequilensis K34.2 and B. siamensis K19.1 had high probiotic potential. This is the first report describing tannin-tolerant Bacillus and their extracellular tannase producing capability in Miang, a traditional fermented tea of Thailand.

Structural diversity and efficacy of culturable cellulose decomposing bacteria isolated from rice-pulse resource conservation practices

The diversity of cellulolytic bacteria from the rice-pulse system can be sourced for identification of efficient cellulose decomposing microbial strains. In the present study, the abundance, structural diversity, and cellulolytic potential of the culturable bacterial community were studied in 5-year old rice-pulse system under different resource conservation technologies. Higher cellulose (68% more) and xylanase (35% more) activities were observed under zero tilled soil. The populations of cellulolytic bacteria were significantly higher (44%) in zero tillage (ZT) treatment than those of conventional practice. Results revealed that the cellulolytic bacterial diversity was found to be significantly higher under ZT practice, but the present population may not be sufficient for effective recycling of organic wastes in this system. Out of 290 bacterial isolates, 20 isolates had significantly higher cellulolytic activities, of which the top three superior isolates were received from ZT practice. The cellulolytic bacterial diversity based on 16S rDNA sequencing data revealed that the Firmicutes was the most dominant phyla and the Bacillus spp. were the common genus, the observation also showed that there were 17 different haplotypes were recorded among 20 isolates of cellulolytic bacteria. The present findings indicated that long-term ZT in the rice-pulse system could be a unique source for efficient cellulose decomposing bacteria and further the efficient bacterial strains isolated from this system can be used as efficient bioinoculants for in situ as well as ex-situ decomposition of rice straw particularly in conservation agriculture.

Enzyme production by solid-state fermentation on soybean meal: A comparative study of conventional and ultrasound-assisted extraction methods

Protease, cellulase, and α-amylase producing Bacillus subtilis strain was cultivated by solid-state fermentation technique using soybean meal as a substrate. The aim of the present study was to establish a highly efficient enzymes' extraction method as a first stage in downstream processing. The conventional extraction procedure was optimized by determining pH, stirring rate, solid/liquid ratio, and time of extraction on enzymes' recoveries from fermented soybean meal. Yields of leached enzymes were compared to the amounts of enzymes that are achieved with ultrasound-assisted extraction (UAE). UAE was established to be superior method for obtaining higher yields of proteases (up to 330 IU) and α-amylases (825 IU), under significantly shorter extraction time and gaining more concentrated product. However, the obtained model predicts that conventional process led to a product with a higher cellulolytic activity (≥7.5 IU).

Prospecting Agro-waste Cocktail: Supplementation for Cellulase Production by a Newly Isolated Thermophilic B. licheniformis 2D55

Bacteria isolated from thermophilic environment that can produce cellulase as well as utilise agro-waste biomass have a high potential for developing thermostable cellulase required in the biofuel industry. The cost for cellulase represents a significant challenge in converting lignocellulose to fermentable sugars for biofuel production. Among three potential bacteria examined, Bacillus licheniformis 2D55 (accession no. KT799651) was found to produce the highest cellulolytic activity (CMCase 0.33 U/mL and FPase 0.09 U/mL) at 18–24 h fermentation when grown on microcrystalline cellulose (MCC) as a carbon source in shake flask at 50 °C. Cellulase production process was further conducted on the untreated and NaOH pretreated rice straw (RS), rice husk (RH), sugarcane bagasse (BAG) and empty fruit bunch (EFB). Untreated BAG produced the highest FPase (0.160 U/mL), while the highest CMCase (0.150 U/mL) was supported on the pretreated RH. The mixture of untreated BAG and pretreated RH as agro-waste cocktail has remarkably improved CMCase (3.7- and 1.4-fold) and FPase (2.5- and 11.5-fold) compared to the untreated BAG and pretreated RH, respectively. The mechanism of cellulase production explored through SEM analysis and the location of cellulase enzymes of the isolate was also presented. Agro-waste cocktail supplementation provides an alternative method for an efficient production of cellulase.

Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia

Microbial communities (MCs) create complex metabolic networks in natural habitats and respond to environmental changes by shifts in the community structure. Although members of MCs are often not amenable for cultivation in pure culture, it is possible to obtain a greater diversity of species in the laboratory setting when microorganisms are grown as mixed cultures. In order to mimic the environmental conditions, an appropriate growth medium must be applied. Here, we examined the hypothesis that a greater diversity of microorganisms can be sustained under nutrient-limited conditions. Using a 16 S rRNA amplicon metagenomic approach, we explored the structure of a compost-derived MC. During a five-week time course the MC grown in minimal medium with sugarcane bagasse (SCB) as a sole carbon source showed greater diversity and enrichment in lignocellulose-degrading microorganisms. In contrast, a MC grown in nutrient rich medium with addition of SCB had a lower microbial diversity and limited number of lignocellulolytic species. Our approach provides evidence that factors such as nutrient availability has a significant selective pressure on the biodiversity of microorganisms in MCs. Consequently, nutrient-limited medium may displace bacterial generalist species, leading to an enriched source for mining novel enzymes for biotechnology applications.

New combination of xylanolytic bacteria isolated from the lignocellulose degradation microbial consortium XDC-2 with enhanced xylanase activity

Three bacterial strains with extracellular xylanase activity were isolated from the microbial consortium XDC-2. The aerobic strain A7, belonging to Bacillus sp., was combined with the anaerobe Clostridium sp. strain AA3 and/or Bacteroides sp. strain AA4 to obtain an efficient natural xylanolytic complex enzyme. The synthetic microbial community M1 consisting of strains Bacillus and Clostridium showed enhanced extracellular xylanase activity and production, and higher lignocelluloses degradation capability than any of the pure cultures and other synthetic microbial communities. Neither corn straw degradation nor extracellular xylanase activity was enhanced in the other synthetic microbial communities, Bacillus, Bacteroides with or without Clostridium. Quantitative polymerase chain reaction showed that the aerobic strain Bacillus enabled the growth of the anaerobic strain Clostridium, but not that of the anaerobic strain Bacteroides. These findings suggest that strains Bacillus and Clostridium can coexist well and have a positive synergistic interaction for extracellular xylanase secretion and lignocellulose degradation.

Phylogenetic relationships of fluorescent pseudomonads deduced from the sequence analysis of 16S rRNA, Pseudomonas-specific and rpoD genes

Phylogenetic relationship of 22 FLPs was revealed on the basis of polymorphism in three genes namely 16S rDNA, Pseudomonas-specific and rpoD gene regions. The primers for 16S rDNA, Pseudomonas-specific region and rpoD gene region were amplifying a region of 1492, 990 and 760 bp, respectively, from all the isolates investigated. The RFLP analysis of the PCR products resulted in a classification of these fluorescent pseudomonads which was best answered by rpoD-based RFLP analysis. The 22 FLPs were placed in two major clusters and seven subclusters suggesting that these were genotypically heterogenous and might belong to several species within Pseudomonas sensu stricto. Sequence analysis of these three genes for three selected isolates AS5, AS7 and AS15 showed 16S rDNA and Pseudomonas-specific gene region phylogenies were generally similar, but rpoD gene phylogeny was somewhat different from these two genes. These results were also congruent with the results of RFLP of these three genes. rpoD provided comparable phylogenetic resolution to that of the 16S rRNA and Pseudomonas-specific genes at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoD could complement and better justify the information provided by the 16S rRNA gene. Hence rpoD can be used further as an evolutionary chronometer for species-level identification.

Experimental Evolution of Trichoderma citrinoviride for Faster Deconstruction of Cellulose

Engineering faster cellulose deconstruction is difficult because it is a complex, cooperative, multi-enzyme process. Here we use experimental evolution to select for populations of Trichoderma citrinoviride that deconstruct up to five-fold more cellulose. Ten replicate populations of T. citrinoviride were selected for growth on filter paper by serial culture. After 125 periods of growth and transfer to fresh media, the filter paper deconstruction increased an average of 2.5 fold. Two populations were examined in more detail. The activity of the secreted cellulase mixtures increased more than two-fold relative to the ancestor and the largest increase was in the extracellular β-glucosidase activity. qPCR showed at least 16-fold more transcribed RNA for egl4 (endoglucanase IV gene), cbh1 (cellobiohydrolase I gene) and bgl1 (extracellular β-glucosidase I gene) in selected populations as compared to the ancestor, and earlier peak expressions of these genes. Deep sequencing shows that the regulatory strategies used to alter cellulase secretion differ in the two strains. The improvements in cellulose deconstruction come from earlier expression of all cellulases and increased relative amount of β-glucosidase, but with small increases in the total secreted protein and therefore little increase in metabolic cost.

Droplet-based microfluidics platform for ultra-high-throughput bioprospecting of cellulolytic microorganisms

Discovery of microorganisms producing enzymes that can efficiently hydrolyze cellulosic biomass is of great importance for biofuel production. To date, however, only a miniscule fraction of natural biodiversity has been tested because of the relatively low throughput of screening systems and their limitation to screening only culturable microorganisms. Here, we describe an ultra-high-throughput droplet-based microfluidic system that allowed the screening of over 100,000 cells in less than 20 min. Uncultured bacteria from a wheat stubble field were screened directly by compartmentalization of single bacteria in 20 pl droplets containing a fluorogenic cellobiohydrolase substrate. Sorting of droplets based on cellobiohydrolase activity resulted in a bacterial population with 17- and 7-fold higher cellobiohydrolase and endogluconase activity, respectively, and very different taxonomic diversity than when selected for growth on medium containing starch and carboxymethylcellulose as carbon source.

Application of a new xylanase activity from Bacillus amyloliquefaciens XR44A in brewer's spent grain saccharification

BACKGROUND

Cellulases and xylanases are the key enzymes involved in the conversion of lignocelluloses into fermentable sugars. Western Ghat region (India) has been recognized as an active hot spot for the isolation of new microorganisms. The aim of this work was to isolate new microorganisms producing cellulases and xylanases to be applied in brewer's spent grain saccharification.

RESULTS

93 microorganisms were isolated from Western Ghat and screened for the production of cellulase and xylanase activities. Fourteen cellulolytic and seven xylanolytic microorganisms were further screened in liquid culture. Particular attention was focused on the new isolate Bacillus amyloliquefaciens XR44A, producing xylanase activity up to 10.5 U mL^-1. A novel endo-1,4-beta xylanase was identified combining zymography and proteomics and recognized as the main enzyme responsible for B. amyloliquefaciens XR44A xylanase activity. The new xylanase activity was partially characterized and its application in saccharification of brewer's spent grain, pretreated by aqueous ammonia soaking, was investigated.

CONCLUSION

The culture supernatant of B. amyloliquefaciens XR44A with xylanase activity allowed a recovery of around 43% xylose during brewer's spent grain saccharification, similar to the value obtained with a commercial xylanase from Trichoderma viride, and a maximum arabinose yield of 92%, around 2-fold higher than that achieved with the commercial xylanase. © 2014 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Exploring the microbiota dynamics related to vegetable biomasses degradation and study of lignocellulose-degrading bacteria for industrial biotechnological application

The aims of this study were to evaluate the microbial diversity of different lignocellulosic biomasses during degradation under natural conditions and to isolate, select, characterise new well-adapted bacterial strains to detect potentially improved enzyme-producing bacteria. The microbiota of biomass piles of Arundo donax, Eucalyptus camaldulensis and Populus nigra were evaluated by high-throughput sequencing. A highly complex bacterial community was found, composed of ubiquitous bacteria, with the highest representation by the Actinobacteria, Proteobacteria, Bacteroidetes and Firmicutes phyla. The abundances of the major and minor taxa retrieved during the process were determined by the selective pressure produced by the lignocellulosic plant species and degradation conditions. Moreover, cellulolytic bacteria were isolated using differential substrates and screened for cellulase, cellobiase, xylanase, pectinase and ligninase activities. Forty strains that showed multienzymatic activity were selected and identified. The highest endo-cellulase activity was seen in Promicromonospora sukumoe CE86 and Isoptericola variabilis CA84, which were able to degrade cellulose, cellobiose and xylan. Sixty-two percent of bacterial strains tested exhibited high extracellular endo-1,4-ß-glucanase activity in liquid media. These approaches show that the microbiota of lignocellulosic biomasses can be considered an important source of bacterial strains to upgrade the feasibility of lignocellulose conversion for the ‘greener' technology of second-generation biofuels.

Isolation, screening, and identification of cellulolytic bacteria from natural reserves in the subtropical region of China and optimization of cellulase production by Paenibacillus terrae ME27-1

From different natural reserves in the subtropical region of China, a total of 245 aerobic bacterial strains were isolated on agar plates containing sugarcane bagasse pulp as the sole carbon source. Of the 245 strains, 22 showed hydrolyzing zones on agar plates containing carboxymethyl cellulose after Congo-red staining. Molecular identification showed that the 22 strains belonged to 10 different genera, with the Burkholderia genus exhibiting the highest strain diversity and accounting for 36.36% of all the 22 strains. Three isolates among the 22 strains showed higher carboxymethyl cellulase (CMCase) activity, and isolate ME27-1 exhibited the highest CMCase activity in liquid culture. The strain ME27-1 was identified as Paenibacillus terrae on the basis of 16S rRNA gene sequence analysis as well as physiological and biochemical properties. The optimum pH and temperature for CMCase activity produced by the strain ME27-1 were 5.5 and 50°C, respectively, and the enzyme was stable at a wide pH range of 5.0–9.5. A 12-fold improvement in the CMCase activity (2.08 U/mL) of ME27-1 was obtained under optimal conditions for CMCase production. Thus, this study provided further information about the diversity of cellulose-degrading bacteria in the subtropical region of China and found P. terrae ME27-1 to be highly cellulolytic.

Isolation of Paenibacillus sp. and Variovorax sp. strains from decaying woods and characterization of their potential for cellulose deconstruction

Prospection of cellulose-degrading bacteria in natural environments allows the identification of novel cellulases and hemicellulases that could be useful in second-generation bioethanol production. In this work, cellulolytic bacteria were isolated from decaying native forest soils by enrichment on cellulose as sole carbon source. There was a predominance of Gram positive isolates that belonged to the phyla Proteobacteria and Firmicutes. Many primary isolates with cellulolytic activity were not pure cultures. From these consortia, isolation of pure constituents was attempted in order to test the hypothesis whether microbial consortia are needed for full degradation of complex substrates. Two isolates, CB1-2-A-5 and VG-4-A-2, were obtained as the pure constituents of CB1-2 and VG-4 consortia, respectively. Based on 16S RNA sequence, they could be classified as Variovorax paradoxus and Paenibacillus alvei. Noteworthy, only VG-4 consortium showed measurable xylan degrading capacity and signs of filter paper degradation. However, no xylan or filter paper degrading capacities were observed for the pure cultures isolated from it, suggesting that other members of this consortium were necessary for these hydrolyzing activities. Our results indicated that Paenibacillus sp. and Variovorax sp. as well as VG-4 consortium, might be a useful source of hydrolytic enzymes. Moreover, although Variovorax sp. had been previously identified in metagenomic studies of cellulolytic communities, this is the first report on the isolation and characterization of this microorganism as a cellulolytic genus.

Industrial waste based compost as a source of novel cellulolytic strains and enzymes

Ninety bacteria isolated from raw composting materials were screened for their cellulolytic activity on solid medium containing carboxymethylcellulose. The bacteria producing the highest cellulolytic activity levels were identified by 16S rRNA sequencing as Bacillus licheniformis strain 1, Bacillus subtilis subsp. subtilis strain B7B, Bacillus subtilis subsp. spizizenii strain 6, and Bacillus amyloliquefaciens strain B31C. Cellulase activity production by the most productive strain B. amyloliquefaciens B31C was optimized in liquid culture varying the carbon source. Comparison of growth curves of B. amyloliquefaciens B31C at temperatures from 28 to 47 °C indicated its thermotolerant nature. Moreover, analysis of time courses of cellulase activity production in this thermal range showed that increase of temperature from 28 to 37 °C causes an increase of cellulase activity levels. Investigating the enzymes responsible for cellulase activity produced by B. amyloliquefaciens B31C by proteomic analyses, an endoglucanase was identified. It was shown that the purified enzyme catalyzes carboxymethylcellulose's hydrolysis following Michaelis-Menten kinetics with a K(M) of 9.95 mg ml(-1) and a v(max) of 284 μM min(-1) . It shows a retention of 90% of its activity for at least 144 h of incubation at 40 °C and exhibits a range of optimum temperatures from 50 to 70 °C.