Cellulose degradation potential of Paenibacillus lautus strain BHU3 and its whole genome sequence

Responses of physiological, microbiome and lipid metabolism to lignocellulose wastes in gut of yellow mealworm (Tenebrio molitor)

There is limited research on physiological and degradation mechanisms of yellow mealworm, a novel organic waste converter, in processing lignocellulosic wastes. This study has selected two types of lignocellulosic wastes, distillers' grains (DG) and maize straw (MS), to feed yellow mealworms. This study investigated the effects of lignocellulosic wastes on the growth, antioxidant system, microbiome, and lipidome of yellow mealworms. The relative growth of lignocellulosic waste group was not significantly different from wheat bran. The antioxidant level was elevated in DG. MS was significantly enriched in cellulose-degrading bacteria in the gut and was accompanied by disturbances in lipid metabolism. The correlation coefficients were used to construct a network connecting diet, microbiota, and lipids. The correlation analysis indicated that two sphingolipids, hexylglyceramide and dihydroglyceramide, were strongly and positively linked with the dominating species. This study provides comprehensive information on physiological and mechanism of mealworms in process of treating lignocellulosic waste.

Characterization of Cellulose-Degrading Bacteria Isolated from Silkworm Excrement and Optimization of Its Cellulase Production

An abundance of refractory cellulose is the key limiting factor restricting the resource utilization efficiency of silkworm (Bombyx mori) excrement via composting. Screening for cellulose-degrading bacteria is likely to provide high-quality strains for the safe and rapid decomposition of silkworm excrement. In this study, bacteria capable of degrading cellulose with a high efficiency were isolated from silkworm excrement and the conditions for cellulase production were optimized. The strains were preliminarily screened via sodium carboxymethyl cellulose culture and staining with Congo red, rescreened via a filter paper enzyme activity test, and identified via morphological observation, physiological and biochemical tests, and phylogenetic analysis of the 16S rDNA sequence. Enzyme activity assay was performed using the 3,5-dinitrosalicylic acid method. DC-11, a highly cellulolytic strain, was identified as Bacillus subtilis. The optimum temperature and pH of this strain were 55 °C and 6, respectively, and the filter paper enzyme activity (FPase), endoglucanase activity (CMCase), and exoglucanase activity (CXase) reached 15.40 U/mL, 11.91 U/mL, and 20.61 U/mL. In addition, the cellulose degradation rate of the treatment group treated with DC-11 was 39.57% in the bioaugmentation test, which was significantly higher than that of the control group without DC-11 (10.01%). Strain DC-11 was shown to be an acid-resistant and heat-resistant cellulose-degrading strain, with high cellulase activity. This strain can exert a bioaugmentation effect on cellulose degradation and has the potential for use in preparing microbial inocula that can be applied for the safe and rapid composting of silkworm excrement.

Sulfate reduction behavior in response to changing of pressure coupling with temperature inside landfill

The behavior of sulfate reduction, which was the source of hydrogen sulfide (H2S) odor, was investigated under changing pressure and temperature conditions inside landfills. The results showed that the release of H2S and methyl mercaptan (MM) was significantly inhibited at 25 °C and 50 °C under pressure, and the highest H2S and MM concentrations released were only 0.82 %-1.30 % and 1.87 %-4.32 % of atmospheric pressure, respectively. Analysis of the microbial community structure and identification of sulfate-reducing bacteria (SRB) revealed that temperature significantly altered the microbial community in the landfill environment, while pressure inhibited some bacteria and induced the growth and reproduction of specific bacteria. Key SRB (Desulfosporosinus-ASV212, Desulfitibacter-ASV1744) mediated differentiated sulfate reduction behavior in the pressure-bearing environment at 25 °C, while key SRB (Dethiobacter-ASV177, Desulfitibacter-ASV2355 and ASV316) were involved at 50 °C. This study provides a theoretical basis for the formulation of landfill gas management and control strategies.

Enhanced simultaneous removal of sulfamethoxazole and zinc (II) in the biochar-immobilized bioreactor: Performance, microbial structures and gene functions

Biochar-immobilized functional bacteria Bacillus SDB4 was applied for sulfamethoxazole (SMX) and zinc (Zn2+) simultaneous removal in the bioreactor. Under the optimal operating conditions of HRT of 10 h, pH of 7.0, SMX concentration of 10 mg L-1 and Zn2+ concentration of 50 mg L-1, the removal efficiencies of SMX and Zn2+ by the immobilized reactor (IR) were 97.42% and 96.14%, respectively, 20.39% and 30.15% higher than those by free bioreactor (FR). SEM-EDS and FTIR results revealed that the functional groups and light metals on the carrier promoted the biosorption and biotransformation of SMX and Zn2+ in IR. Moreover, the improvement of SMX and Zn2+ removal might be related to the abundance enhancement of functional bacteria and genes. Bacillus SDB4 responsible for SMX and Zn2+ removal was the main strain in IR and FR. Biochar increased the relative abundance of Bacillus from 32.12% in FR to 38.73% in IR and improved the abundances of functional genes (such as carbohydrate metabolism, replication and repair and membrane transport) by 1.82%-11.04%. The correlations among the physicochemical properties, microbial communities, functional genes and SMX-Zn2+ co-contaminant removal proposed new insights into the mechanisms of biochar enhanced microbial removal of antibiotics and heavy metals in biochar-immobilized bioreactors.

Papermaking wastewater treatment coupled to 2,3-butanediol production by engineered psychrotrophic Raoultella terrigena

The simultaneous bioremediation and bioconversion of papermaking wastewater by psychrotrophic microorganisms holds great promise for developing sustainable environments and economies in cold regions. Here, the psychrotrophic bacterium Raoultella terrigena HC6 presented high endoglucanase (26.3 U/mL), xylosidase (732 U/mL), and laccase (8.07 U/mL) activities for lignocellulose deconstruction at 15 °C. mRNA monitoring and phenotypic variation analyses confirmed that cold-inducible cold shock protein A (CspA) facilitated the expression of the cel208, xynB68, and lac432 genes to increase the enzyme activities in strain HC6. Furthermore, the cspA gene-overexpressing mutant (strain HC6-cspA) was deployed in actual papermaking wastewater and achieved 44.3%, 34.1%, 18.4%, 80.2% and 100% removal rates for cellulose, hemicellulose, lignin, COD, and NO3--N at 15 °C. Simultaneously, 2,3-butanediol (2,3-BD) was produced from the effluent with a titer of 2.98 g/L and productivity of 0.154 g/L/h. This study reveals an association between the cold regulon and lignocellulolytic enzymes and provides a promising candidate for simultaneous papermaking wastewater treatment and 2,3-BD production.

Whole genome sequencing and the lignocellulose degradation potential of Bacillus subtilis RLI2019 isolated from the intestine of termites

BACKGROUND

Lignocellulosic biomass is the most abundant and renewable terrestrial raw material for conversion into bioproducts and biofuels. However, the low utilization efficiency of lignocellulose causes environmental pollution and resource waste, which limits the large-scale application of bioconversion. The degradation of lignocellulose by microorganisms is an efficient and cost-effective way to overcome the challenge of utilizing plant biomass resources. This work aimed to screen valuable cellulolytic bacteria, explore its molecular mechanism from genomic insights, and investigate the ability of the strain to biodegrade wheat straw.

RESULTS

Bacillus subtilis (B. subtilis) RLI2019 was isolated from the intestine of Reticulitermes labralis. The strain showed comprehensive enzyme activities related to lignocellulose degradation, which were estimated as 4.06, 1.97, 4.12, 0.74, and 17.61 U/mL for endoglucanase, β-glucosidase, PASC enzyme, filter paper enzyme, and xylanase, respectively. Whole genome sequencing was performed to better understand the genetic mechanism of cellulose degradation. The genome size of B. subtilis RLI2019 was 4,195,306 bp with an average GC content of 43.54%, and the sequence characteristics illustrated an extremely high probability (99.41%) as a probiotic. The genome contained 4,381 protein coding genes with an average GC content of 44.20%, of which 145 genes were classified into six carbohydrate-active enzyme (CAZyme) families and 57 subfamilies. Eight cellulose metabolism enzyme-related genes and nine hemicellulose metabolism enzyme-related genes were annotated by the CAZyme database. The starch and sucrose metabolic pathway (ko00500) was the most enriched with 46 genes in carbohydrate metabolism. B. subtilis RLI2019 was co-cultured with wheat straw for 7 days of fermentation, the contents of neutral detergent fiber, acid detergent fiber, hemicellulose, and lignin were significantly reduced by 5.8%, 10.3%, 1.0%, and 4.7%, respectively. Moreover, the wheat straw substrate exhibited 664.9 μg/mL of reducing sugars, 1.22 U/mL and 6.68 U/mL of endoglucanase and xylanase activities, respectively. Furthermore, the fiber structures were effectively disrupted, and the cellulose crystallinity was significantly reduced from 40.2% to 36.9%.

CONCLUSIONS

The complex diversity of CAZyme composition mainly contributed to the strong cellulolytic attribute of B. subtilis RLI2019. These findings suggest that B. subtilis RLI2019 has favorable potential for biodegradation applications, thus it can be regarded as a promising candidate bacterium for lignocellulosic biomass degradation.

Screening and genome-wide analysis of lignocellulose-degrading bacteria from humic soil

Crop straw contains huge amounts of exploitable energy, and efficient biomass degradation measures have attracted worldwide attention. Mining strains with high yields of cellulose-degrading enzymes is of great significance for developing clean energy and industrial production of related enzymes. In this study, we reported a high-quality genome sequence of Bacillus velezensis SSF6 strain using high-throughput sequencing technology (Illumina PE150 and PacBio) and assessed its lignocellulose degradation potential. The results demonstrated that the genome of B. velezensis SSF6 was 3.89 Mb and contained 4,015 genes, of which 2,972, 3,831 and 158 genes were annotated in the COGs (Clusters of Orthologous Groups), KEGG (Kyoto Encyclopedia of Genes and Genomes) and CAZyme (Carbohydrate-Active enZymes) databases, respectively, and contained a large number of genes related to carbohydrate metabolism. Furthermore, B. velezensis SSF6 has a high cellulose degradation capacity, with a filter paper assay (FPA) and an exoglucanase activity of 64.48 ± 0.28 and 78.59 ± 0.42 U/mL, respectively. Comparative genomic analysis depicted that B. velezensis SSF6 was richer in carbohydrate hydrolase gene. In conclusion, the cellulose-degrading ability of B. velezensis SSF6 was revealed by genome sequencing and the determination of cellulase activity, which laid a foundation for further cellulose degradation and bioconversion.

Biosynthesis of poly(3-hydroxybutyrate) by N,N-dimethylformamide degrading strain Paracoccus sp. PXZ: A strategy for resource utilization of pollutants

N,N-dimethylformamide is a toxic chemical solvent, which widely exists in industrial wastewater. Nevertheless, the relevant methods merely achieved non-hazardous treatment of N,N-dimethylformamide. In this study, one efficient N,N-dimethylformamide degrading strain was isolated and developed for pollutant removal coupling with poly(3-hydroxybutyrate) (PHB) accumulation. The functional host was characterized as Paracoccus sp. PXZ, which could consume N,N-dimethylformamide as the nutrient substrate for cell reproduction. Whole-genome sequencing analysis confirmed that PXZ simultaneously possesses the essential genes for poly(3-hydroxybutyrate) synthesis. Subsequently, the approaches of nutrient supplementation and various physicochemical variables to strengthen poly(3-hydroxybutyrate) production were investigated. The optimal biopolymer concentration was 2.74 g·L^-1 with a poly(3-hydroxybutyrate) proportion of 61%, showing a yield of 0.29 g-PHB·g^-1-fructose. Furthermore, N,N-dimethylformamide served as the special nitrogen matter that could realize a similar poly(3-hydroxybutyrate) accumulation. This study provided a fermentation technology coupling with N,N-dimethylformamide degradation, offering a new strategy for resource utilization of specific pollutants and wastewater treatment.

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.

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.

A Novel Potent Crystalline Chitin Decomposer: Chitin Deacetylase from Acinetobacter schindleri MCDA01

Chitosan is a functional ingredient that is widely used in food chemistry as an emulsifier, flocculant, antioxidant, or preservative. Chitin deacetylases (CDAs) can catalyze the hydrolysis of acetyl groups, making them useful in the clean production of chitosan. However, the high inactivity of crystalline chitin catalyzed by CDAs has been regarded as the technical bottleneck of crystalline chitin deacetylation. Here, we mined the AsCDA gene from the genome of Acinetobacter schindleri MCDA01 and identified a member of the uraD_N-term-dom superfamily, which was a novel chitin deacetylase with the highest deacetylation activity. The AsCDA gene was expressed in Escherichia coli BL21 by IPTG induction, whose activity to colloidal chitin, α-chitin, and β-chitin reached 478.96 U/mg, 397.07 U/mg, and 133.27 U/mg, respectively. In 12 h, the enzymatic hydrolysis of AsCDA removed 63.05% of the acetyl groups from α-chitin to prepare industrial chitosan with a degree of deacetylation higher than 85%. AsCDA, as a potent chitin decomposer in the production of chitosan, plays a positive role in the upgrading of the chitosan industry and the value-added utilization of chitin biological resources.

Complete genome sequencing and investigation on the fiber-degrading potential of Bacillus amyloliquefaciens strain TL106 from the tibetan pig

Background

Cellulolytic microorganisms are considered a key player in the degradation of feed fiber. These microorganisms can be isolated from various resources, such as animal gut, plant surfaces, soil and oceans. A new strain of Bacillus amyloliquefaciens, TL106, was isolated from faeces of a healthy Tibetan pigs. This strain can produce cellulase and shows strong antimicrobial activity in mice. Thus, in this study, to better understand the strain of B. amyloliquefaciens TL106 on degradation of cellulose, the genome of the strain TL106 was completely sequenced and analyzed. In addition, we also explored the cellulose degradation ability of strain TL106 in vitro.

Results

TL106 was completely sequenced with the third generation high-throughput DNA sequencing. In vitro analysis with enzymatic hydrolysis identified the activity of cellulose degradation. TL106 consisted of one circular chromosome with 3,980,960 bp and one plasmid with 16,916 bp, the genome total length was 3.99 Mb and total of 4,130 genes were predicted. Several genes of cellulases and hemicellulase were blasted in Genbank, including β-glucosidase, endoglucanase, ß-glucanase and xylanase genes. Additionally, the activities of amylase (20.25 U/mL), cellulase (20.86 U/mL), xylanase (39.71 U/mL) and β-glucanase (36.13 U/mL) in the fermentation supernatant of strain TL106 were higher. In the study of degradation characteristics, we found that strain TL106 had a better degradation effect on crude fiber, neutral detergent fiber, acid detergent fiber, starch, arabinoxylan and β-glucan of wheat and highland barley .

Conclusions

The genome of B. amyloliquefaciens TL106 contained several genes of cellulases and hemicellulases, can produce carbohydrate-active enzymes, amylase, cellulase, xylanase and β-glucanase. The supernatant of fermented had activities of strain TL106. It could degrade the fiber fraction and non-starch polysaccharides (arabinoxylans and β-glucan) of wheat and highland barley. The present study demonstrated that the degradation activity of TL106 to crude fiber which can potentially be applied as a feed additive to potentiate the digestion of plant feed by monogastric animals.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02599-7.

Paenibacillus amylolyticus osteomyelitis in a Poodle dog: case report and literature review

Paenibacilli are gram-variable, endospore-forming bacteria that occupy various ecologic niches. These microorganisms have been known to infect humans occasionally at various anatomic sites. However, in humans, as well as in other vertebrate animals, the relationship between disease and isolation of Paenibacillus spp. remains poorly understood. We report here a case of infection in an adult Poodle dog. The animal had nodules in the lungs and multifocal osteolytic expansile bone lesions. From bone, Paenibacillus amylolyticus was recovered by culture and identified by MALDI-TOF mass spectroscopy and 16S rDNA sequencing; pyogranulomatous inflammation was observed in lung and bone specimens. The microorganism was resistant to clindamycin and imipenem. Four-month treatment with amoxicillin–clavulanate resulted in clinical resolution of disease in this dog. Nevertheless, therapy for more prolonged periods should be considered because recurrent infections can occur as a result of the transition of Paenibacillus spores to vegetative cells. Disease caused by a Paenibacillus species has not been reported previously in dogs, to our knowledge.

Whole genome sequencing and analysis of fenvalerate degrading bacteria Citrobacter freundii CD-9

Citrobacter freundii CD-9 is a Gram-negative bacteria sourced from factory sludge that can use fenvalerate as its sole carbon source and has a broad degradation spectrum for pyrethroid pesticides. The whole genome of CD-9 sequenced using Illumina HiSeq PE150 was reported in this study. The CD-9 genome size was 5.33 Mb and the G + C content was 51.55%. A total of 5291 coding genes, 9 5s-rRNA, and 79 tRNA were predicted bioinformatically. 3586 genes annotated to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database that can be involved in 173 metabolic pathways, including various microbial metabolic pathways that degrade exogenous chemicals, especially those that degrade aromatic compounds, and also produce a variety of bioactive substances. Fifty genes related to pyrethroid degradation were identified in the C. freundii CD-9 genome, including 9 dioxygenase, 25 hydrolase, and 16 esterase genes. Notably, RT-qPCR results showed that from the predicted 13 genes related to fenvalerate degradation, the expression of six genes, including esterase, HAD family hydrolase, lipolytic enzyme, and gentisic acid dioxygenase, was induced in the presence of fenvalerate. In this study, the key genes and degradation mechanism of C. freundii CD-9 were analyzed and the results provide scientific evidence to support its application in environmental bioremediation. It can establish application models for different environmental pollution management by constructing genetically engineered bacteria for efficient fenvalerate or developing enzyme formulations that can be industrially produced.

Simultaneous bio-reduction of nitrate and Cr(VI) by mechanical milling activated corn straw

Abundant lignocellulose waste is an ideal energy source for environmental bioremediation, but its recalcitrance to bioavailability makes this a challenging prospect. We hypothesized that the disruption of straw's recalcitrant structure by mechanochemical ball milling would enhance its availability for the simultaneous bioreduction of nitrate and Cr(VI). The results showed that the ball-milling process increased the quantity of water-soluble organic matter released from corn straw and changed the composition of organic matter by strongly disrupting its lignocellulose structure. The increase in ball-milling time increased the specific surface area of the straw and favored the adhesion of microorganisms on the straw surface, which enhanced the bioavailability of the energy in the straw. Substantially increased removal of NO₃^--N (206.47 ± 0.67 mg/g) and Cr(VI) (37.62 ± 0.09 mg/g) was achieved by using straw that was ball milled for 240 min, which validated that ball milling can improve the utilization efficiency of straw by microorganisms. Cellular and molecular biological analyses showed that ball-milled straw increased microbial energy metabolism and cellular activity related to the electron transport chain. This work offers a potential way to achieve the win-win goal of utilizing agricultural wastes and remediating environmental pollution.

Mechanism for biodegradation of sulfamethazine by Bacillus cereus H38

Degradation of sulfonamides (SAs) by microorganisms has become a focus of current research. Sulfamethazine (SMZ) is a type of SA widely used in the livestock and poultry industry. However, understanding the intermediate products, degradation pathways and mechanism of SMZ biodegradation is limited at present. In this study, a SMZ degrading bacterium Bacillus cereus H38, which can use SMZ as its only carbon source, was isolated from farmland soil. The bacterium was gram-positive with rod-shaped cells. The effects of initial SMZ concentration, pH, temperature and amount of inoculation on the biodegradation of SMZ were investigated by a single factor experiment. The results showed that the maximum degradation rate of SMZ was achieved in the environmental conditions at an initial SMZ concentration of 5 mg/L, pH of 7.0, temperature of 25 °C and inoculation amount of 5%. Under these optimum degradation conditions, strain H38 can completely degrade SMZ within 3 days. The effects of intracellular enzymes, extracellular enzymes and periplasmic enzymes on the SMZ degradation process were compared. It was found that intracellular enzymes contributed the most to the biodegradation of SMZ, and the degradation rate approached 70%. Three possible intermediates were identified by LC-MS/MS, and two degradation pathways were proposed. Whole genome sequencing results showed that the genome size of strain H38 was 5,477,631 bp, including 5599 coding sequences (CDSs), and the GC content was 35.21%. In addition, functional annotation of CDSs was performed to analyze the metabolic pathways of nitrogen and sulfur in strain H38 combining genomics and bioinformatics. This study proposes new insights into the mechanism for biodegradation of SAs and will inform future research.

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

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

Chitosan Oligosaccharide Production Potential of Mitsuaria sp. C4 and Its Whole-Genome Sequencing

Chitooligosaccharide is a kind of functional food, which is the degradation product of chitosan (COS) catalyzed by the endo-chitosanase (COSE) enzyme. A COSE with a molecular weight of 34 kDa was purified and characterized from a newly isolated Mitsuaria sp. C4 (C4), and a 38.46% recovery rate and 4.79-fold purification were achieved. The purified C4 COSE exhibited optimum activity at 40°C and pH 7.2 and was significantly inhibited in the presence of Cu²⁺ and Fe³⁺. The K_m and V_min of the COSE toward COS were 2.449 g/L and 0.042 g/min/L, respectively. The highest COSE activity reached 8.344 U/ml after optimizing, which represented a 1.34-fold of increase. Additionally, chitooligosaccharide obtained by COSE hydrolysis of COS was verified by using thin-layer chromatography and high-performance liquid chromatography analysis. Whole-genome sequencing demonstrated that the C4 strain contains 211 carbohydrate enzymes, our purified COSE belonging to GHs-46 involved in carbohydrate degradation. Phylogenetic analysis showed that the novel COSE obtained from the C4 strain was clustered into the degree of polymerization = two to three groups, which can perform catalysis in a similar manner to produce (GlcN)₂ and (GlcN)₃. This work indicates that the C4 strain could be a good resource for enhancing carbohydrate degradation and might represent a useful tool for chitooligosaccharide production in the functional food industry.

Safety Evaluation and Whole Genome Sequencing of Aspergillus japonicas PJ01 Reveal Its Potential to Degrade Citrus Segments in Juice Processing

Aspergillus japonicas PJ01 (A. japonicas PJ01) is a strain isolated from the rotten branches. In previ-ous studies, it was shown that it can produce complex enzymes to degrade polysaccharide com-ponents. In this study, we evaluated the safety of its crude enzyme solution. Acute oral toxicity, subchronic toxicity, micronucleus and sperm malformation tests all validated the high biologi-cal safety for the crude enzymes. Secondly, we carried out the citrus segment degradation ex-periment of crude enzyme solution. Compared with the control group, the crude enzyme solu-tion of A. japonicas PJ01 can completely degrade the segments in 50 min, which provides the basis for enzymatic peeling during juice processing. The whole genome sequencing showed that the genome of A. japonicus PJ01 has a GC content of 51.37% with a size of 36204647 bp, and encoded 10070 genes. GO, COG, KEGG and CAZy databases were used in gene annotation analyses. Pathway enrichment showed many genes related to carbohydrate metabolism, rich in genes re-lated to pectinase, xylanase and carboxylcellulase. Therefore, the complex enzyme produced by A. japonicus PJ01 can be used in gizzard juice processing to achieve efficient enzymatic decapsu-lation.

Isolation and characterization of anaerobic bacteria with fiber degradation potential from faeces of Boselaphus tragocamelus grazing on semi arid Indian conditions

Hindgut of wild ruminants harbours diversified anaerobic bacteria with promising fiber degrading ability. Fibrolytic enzyme activity is strongly influenced by diet and host species which till date remains unexplored for harnessing their optimum benefits. The present study was conducted to isolate and characterize fiber degrading anaerobic bacteria from faeces of wild blue bull (Boselaphus tragocamelus) inhabiting in semiarid regions. A total of 167 isolates were obtained from 85 faecal samples using M-10 medium, on the basis of clear zones formed on Congo red plates 20 isolates were selected and designated as NLG1-20 for microscopic and biochemical characterization. Further, molecular confirmation was done by PCR analysis with universal 16S rDNA primers. All isolates were obligatory anaerobes except, NLG4, NLG19 and NLG20. Majority of the sugars tested were utilized by most of the isolates except arabinose. Fibrolytic enzyme activities revealed that NLG1 had highest endoglucanase activity, NLG13 had highest exoglucanase activity while NLG8 showed maximum xylanase activity. In case of FPase assay, highest and lowest values were observed in isolate NLG11 (8.96 U/mL) and NLG8 (5.58 U/mL), respectively. Phylogenetic analysis of the isolates revealed a highly diverse group of microbes mainly belonging to the family Paenibacillaceae which have not been previously characterized in ruminants for fiber degradation. Therefore, results obtained in the present study indicated that the screened isolates showed promising fiber degrading potential in terms of filter paper assay and fibrolytic enzyme activity which can be explored further for improving lignocellulose digestibility in ruminants as an additive.

Cellulolytic bacterium characterization and genome functional analysis: An attempt to lay the foundation for waste management

Lignocellulosic waste has offered a cost-effective and food security-wise substrate for the generation of biofuels and value-added products. Here, whole-genome sequencing and comparative genomic analyses were performed for Serratia sp. AXJ-M. The results showed that strain AXJ-M contained a high proportion of strain-specific genes related to carbohydrate metabolism. Furthermore, the genetic basis of strain AXJ-M for efficient degradation of cellulose was identified. Cellulase activity tests revealed strong cellulose degradation ability and cellulase activities in strain AXJ-M. mRNA expression indicated that GH1, GH3 and GH8 might determine the strain's cellulose degradation ability. The SWISS-MODEL and Ramachandran Plot were used to predict and evaluate the 3D structure, respectively. High performance liquid chromatography (HPLC) and gas chromatography-mass spectrometer (GC-MS) were used to analyze the cellulose degradation products. Further research is needed to elucidate the cellulose degradation mechanism and to develop industrial applications for lignocellulosic biomass degradation and waste management.

Molecular modeling, docking and simulation dynamics of β-glucosidase reveals high-efficiency, thermo-stable, glucose tolerant enzyme in Paenibacillus lautus BHU3 strain

The enzyme β-glucosidase mediates the rate limiting step of conversion of cellobiose to glucose and thus plays a vital role in the process of cellulose degradation. The present study deals with analysis of the effective novel strain of Paenibacillus lautus BHU3 for identifying high-efficiency thermostable, glucose tolerant β-glucosidases. Seven counterparts with elevated T_m values ranging from 64.6 to 75.8 °C with high thermo-stability, were revealed through this analysis. The blind molecular docking of the model enzymes structures with cellobiose and pNPG gave high negative interaction energies ranging from -11.33 to -13.29 and -6.43 to -9.054 (kcal mol^-1), respectively. The enzyme WP_096774744.1 effectively formed 5 hydrogen bonds with the highest interaction energy (-13.29 kcal mol^-1) with cellobiose at its catalytic site. Molecular dynamics simulation analysis performed for the WP_096774744.1-pNPG complex predicted Glu5, Arg7, Lue68, Gly69 and Phe325 as the major contributing residues for accomplishing hydrolysis of β-1-4-linkage. Further, the molecular docking of WP_096774744.1 enzyme with glucose revealed a distinct glucose-binding site distant from the substrate-binding site, thus confirming the deficient competitive inhibition by glucose. Hence, WP_096774744.1 β-glucosidase appears to be an efficient enzyme with enhanced activity to biodegrade the cellulosic materials and highly relevant for waste management and various industrial applications.

Glycation of gut proteins initiates microbial dysbiosis and can promote establishment of diabetes in experimental animals

Diabetes and obesity is associated with change in the gut microbiota, however, the reason for such transition is still unknown. The secondary complications in diabetes mainly stem from protein glycation, oxidative stress and inflammatory response. It is intended to study the correlation between gut proteins glycation and microbial dysbiosis and thereby progression to diabetes. The study was carried out through feeding high fructose to male Wistar rats and evaluating their gut microbiota. The rate of gut flora excretion via faecal matter was found to decrease on fructose feed for 7 days. Intestinal flora was drastically reduced and pathogenic succession observed. Intestinal fluorescence studies confirmed that there is heavy glycation of gut proteins. Microbes obtained from fructose fed animals could grow on glycated BSA. There was significant increase in level of TNF-α and IFN-γ providing evidence of inflammation. Though microbial dysbiosis was observed in diabetes, the cause for this remained elusive. In the present study we prove that high fructose feed and glycation of the gut proteins probably prevent adherence/survival of the gut microflora in control animals and promotes transition to a changed microflora which is capable of adhering/utilizing glycated proteins as well as high fructose. The changed microbiota, enhanced protein glycation and inflammation help in establishing insulin resistance.

Functional genomics assessment of lytic polysaccharide mono-oxygenase with glycoside hydrolases in Paenibacillus dendritiformis CRN18

Recently discovered Lytic Polysaccharide Mono-Oxygenase (LPMO) enhances the enzymatic deconstruction of complex polysaccharide by oxidation. The present study demonstrates the agricultural waste hydrolyzing capabilities of Paenibacillus dendritiformis CRN18, which exhibits the enzyme activity of exo-glucanase, β-glucosidase, β-glucuronidase, endo-1, 4 β-xylanases, arabinosidase, and α-galactosidase as 0.1U/ml, 0.3U/ml, 0.09U/ml, 0.1U/ml, 0.05U/ml, and 0.41U/ml, respectively. The genome analysis of strain reveals the presence of four LPMO genes, along with lignocellulolytic genes. The gene structure of LPMO and its phylogenetic analysis shows the evolutionary relatedness with the Bacillus LPMO gene. Gene position of LPMOs in the genome of strains shows the close association of two LPMOs with chitin active enzyme GH18, and the other two are associated with hemicellulases (GH39, GH23). Protein-protein interaction and gene networking of LPMO sheds light on the co-occurrence, neighborhood, and interaction of LPMOs with chitinase and xylanase enzymes. Structural prediction of LPMOs unravels the information of the LPMO's binding site. Although the LPMO has been explored for its oxidative mechanism, a little light has been shed on its gene structure. This study provides insights into the LPMO gene structure in P. dendritiformis CRN18 and its potential in lignocellulose hydrolysis.

A Comparative Analysis of Ash Leaf-Colonizing Bacterial Communities Identifies Putative Antagonists of Hymenoscyphus fraxineus

In the last few years, the alarming spread of Hymenoscyphus fraxineus, the causal agent of ash dieback, has resulted in a substantial threat to native ash stands in central and northern Europe. Since leaves and leaf petioles are the primary infection sites, phyllosphere microorganisms are presumed to interact with the pathogen and are discussed as a source of biocontrol agents. We studied compound leaves from susceptible and visible infection-free trees in four ash stands with a high likelihood of infection to assess a possible variation in the bacterial microbiota, depending on the health status of the trees. The bacterial community was analyzed by culture-independent 16S rRNA gene amplicon sequencing and through the isolation and taxonomic classification of 2,589 isolates using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The bacterial community structure did not show significant differences. However, a set of amplicon sequence variants (ASVs) and MALDI groups belonging to Luteimonas, Aureimonas, Pseudomonas, Bacillus, and Paenibacillus were distinctly increased in tolerant trees, which may be associated with the ability of the tree to resist the pathogen. The most obvious differences were observed for Luteimonas, a genus that is also exclusively present in the healthy core microbiome. In a first in vitro screen of antagonists, approximately 11% of total isolates suppressed the growth of H. fraxineus, but a statistical test with two different H. fraxineus strains confirmed only the antagonistic activity of 8% of these isolates. The antagonistic isolates were assigned to Bacillus velezensis, Pantoea vagans, and Pseudomonas caspiana. Overall, our study provides a set of isolates or phylogenetic groups that might be involved in the process that prevents the penetration and spread of H. fraxineus. In the next step, in planta experiments are required with a longer period of exposure to H. fraxineus to evaluate effective isolates or consortia of isolates acting through direct antagonism or competition or indirectly by inducing resistance.

Isolation, characterisation, and genome sequencing of Rhodococcus equi: a novel strain producing chitin deacetylase

Chitin deacetylase (CDA) can hydrolyse the acetamido group of chitin polymers to produce chitosans, which are used in various fields including the biomedical and pharmaceutical industries, food production, agriculture, and water treatment. CDA represents a more environmentally-friendly and easier to control alternative to the chemical methods currently utilised to produce chitosans from chitin; however, the majority of identified CDAs display activity toward low-molecular-weight oligomers and are essentially inactive toward polymeric chitin or chitosans. Therefore, it is important to identify novel CDAs with activity toward polymeric chitin and chitosans. In this study, we isolated the bacterium Rhodococcus equi F6 from a soil sample and showed that it expresses a novel CDA (ReCDA), whose activity toward 4-nitroacetanilide reached 19.20 U/mL/h during fermentation and was able to deacetylate polymeric chitin, colloidal chitin, glycol-chitin, and chitosan. Whole genome sequencing revealed that ReCDA is unique to the R. equi F6 genome, while phylogenetic analysis indicated that ReCDA is evolutionarily distant from other CDAs. In conclusion, ReCDA isolated from the R. equi F6 strain expands the known repertoire of CDAs and could be used to deacetylate polymeric chitosans and chitin in industrial applications.

Genome sequencing of gut symbiotic Bacillus velezensis LC1 for bioethanol production from bamboo shoots

BACKGROUND

Bamboo, a lignocellulosic feedstock, is considered as a potentially excellent raw material and evaluated for lignocellulose degradation and bioethanol production, with a focus on using physical and chemical pre-treatment. However, studies reporting the biodegradation of bamboo lignocellulose using microbes such as bacteria and fungi are scarce.

RESULTS

In the present study, Bacillus velezensis LC1 was isolated from Cyrtotrachelus buqueti, in which the symbiotic bacteria exhibited lignocellulose degradation ability and cellulase activities. We performed genome sequencing of B. velezensis LC1, which has a 3929,782-bp ring chromosome and 46.5% GC content. The total gene length was 3,502,596 bp using gene prediction, and the GC contents were 47.29% and 40.04% in the gene and intergene regions, respectively. The genome contains 4018 coding DNA sequences, and all have been assigned predicted functions. Carbohydrate-active enzyme annotation identified 136 genes annotated to CAZy families, including GH, GTs, CEs, PLs, AAs and CBMs. Genes involved in lignocellulose degradation were identified. After a 6-day treatment, the bamboo shoot cellulose degradation efficiency reached 39.32%, and the hydrolysate was subjected to ethanol fermentation with Saccharomyces cerevisiae and Escherichia coli KO11, yielding 7.2 g/L of ethanol at 96 h.

CONCLUSIONS

These findings provide an insight for B. velezensis strains in converting lignocellulose into ethanol. B. velezensis LC1, a symbiotic bacteria, can potentially degrade bamboo lignocellulose components and further transformation to ethanol, and expand the bamboo lignocellulosic bioethanol production.

Chitin degradation potential and whole-genome sequence of Streptomyces diastaticus strain CS1801

The aim of this study was to evaluate the chitin degradation potential and whole-genome sequence of Streptomyces diastaticus strain CS1801, which had been screened out in our previous work. The results of fermentation revealed that CS1801 can convert the chitin derived from crab shells, colloidal chitin and N-acetylglucosamine to chitooligosaccharide. Additional genome-wide analysis of CS1801 was also performed to explore the genomic basis for chitin degradation. The results showed that CS1801 possesses a chromosome with 5,611,479 bp (73% GC) and a plasmid with 1,388,284 bp (73% GC). The CS1801 genome consists of 7584 protein-coding genes, 90 tRNA and 21 rRNA operons. In addition, the results of genomic CAZyme analysis indicated that CS1801 comprises 103 glycoside hydrolase family genes, which could regulate the glycoside hydrolases that contribute to chitin degradation. The whole-genome information of CS1801 could highlight the mechanism underlying the chitin degradation activity of CS1801, strongly indicating that CS1801 is characterized by a substantial number of genes encoding chitinases and the complete metabolic pathway of chitin, conferring CS1801 with promising potential applicability in chitooligosaccharide production.

An assessment of the genomics, comparative genomics and cellulose degradation potential of Mucilaginibacter polytrichastri strain RG4-7

In this study, whole genome sequencing and comparative genomic analyses were performed for Mucilaginibacter polytrichastri RG4-7 and its carboxymethyl cellulose degradation potential was assessed. The results showed that the genome of strain RG4-7 was 5.84 Mb and contained 5019 predicted genes, in which a high proportion of strain-specific genes were related to carbohydrate metabolism. The carboxymethyl cellulose (CMC) degradation and cellulase activity tests revealed the strong cellulose degradation ability, CMCase and β-glucosidase activity in strain RG4-7. Real-time RT-PCR testing of most cellulose degradation related glycoside hydrolase (GH) families showed that GH9 (OKS85969), GH1 (OKS85832), GH3 (OKS89331 and OKS85615) were significantly up-regulated when strain RG4-7 was inoculated with CMC-Na, which suggested that GH9, GH1 and GH3 might determine its cellulose degradation ability. Certainly, further research need to be done to elucidate cellulose degradation mechanisms in strain RG4-7 in order to develop its industrial application value in lignocellulosic biomass degradation and waste management.

Biodegradation mechanism of tetracycline (TEC) by strain Klebsiella sp. SQY5 as revealed through products analysis and genomics

Although it has been proved that abiotic processes can transform tetracycline (TEC), little is known about how microbial processes may degrade TEC in aquatic environment. The objective of this study is to investigate the biodegradation pathway of TEC by strain Klebsiella sp. SQY5 and molecular mechanism of TEC resistance under the aerobic conditions. Effects of mycelium, intracellular, and extracellular enzyme on TEC degradation process were explored, suggesting that mycelium contributed the most of TEC degradation with a maximum efficiency of 58.64%. Biodegradation characteristic of TEC and its degradation products were studied. The results showed that nine possible biodegradation products were identified, and a potential biodegradation pathway was proposed including the removal of methyl, carbonyl, and amine groups. The functional genes of this bacterium were also determined by genomics, and analysis indicated that functional genes that could be relevant to hydrolysis, ring opening and oxidation played an important role in the process of TEC biodegradation. Results from this study can provide a theoretical basis for better estimating the fate, transportation, and degradation of antibiotics in aquatic environment.

The Diversity and Geographic Distribution of Cultivable Bacillus-Like Bacteria Across Black Soils of Northeast China

Bacillus-like species are gram-positive bacteria that are ubiquitous in soils. Many of Bacillus-like bacteria are demonstrated as beneficial microbes widely used in industry and agriculture. However, the knowledge related to their diversity and distribution patterns in soils is still rudimentary. In this study, we developed a combined research method of using culture-dependent and high-throughput sequencing to investigate the composition and diversity of cultivable Bacillus-like bacterial communities across 26 soil samples obtained from the black soil zone in northeast China. Nearly all bacterial 16S rDNA sequences were classified into the order Bacillales. Fifteen genera were detected, with Bacillus, Paenibacillus, and Brevibacillus being the three most abundant genera. Although more than 2,000 OTUs were obtained across all samples, 33 OTUs were confirmed as the abundant species with a relative abundance over 5% in at least one sample. Pairwise analysis showed that the diversity of Bacillus-like bacterial communities were significantly and positively correlated with soil total carbon contents and soil sampling latitudes, which suggests that a latitudinal gradient diversity of Bacillus-like bacterial communities exists in the black soil zone. The principal coordinates analysis revealed that the Bacillus-like bacterial communities were remarkably affected by soil sampling latitudes and soil total carbon content. In general, this study demonstrated that a distinct biogeographic distribution pattern of cultivable Bacillus-like bacterial communities existed in the black soil zone, which emphasizes that the strategy of local isolation and application of beneficial Bacillus-like strains is rather important in black soil agriculture development.

Depolymerization of lignocellulose of oil palm empty fruit bunch by thermophilic microorganisms from tropical climate

Previous studies on screening of lignin-degrading bacteria mainly focused on the ligninolytic ability of the isolated bacteria for the utilization of lignin monomers. In this study, we focused on the depolymerization of alkali lignin to prove the ability of the isolated thermophilic bacterial strains to utilize and depolymerize more than a monomer of alkali lignin within 7 days of incubation. Indigenous thermophilic bacterial isolates from the palm oil plantation were used to evaluate the depolymerization and utilization of alkali lignin. The confirmation of the bacterium-mediated depolymerization of oil palm empty fruit bunch was achieved through the removal of silica bodies, as observed with scanning electron microscopy. Stenotrophomonas sp. S2 and Bacillus subtilis S11Y were able to reduce approximately 50% and 20% of alkali lignin at 7 days of incubation without the requirement for additional carbon sources.

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

AIMS

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

METHODS AND RESULTS

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

CONCLUSION

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

SIGNIFICANCE AND IMPACT OF THE STUDY

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