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

Effect of Thermophilic Microbial Agents on Crude Fiber Content, Carbohydrate-Active Enzyme Genes, and Microbial Communities during Chinese Medicine Residue Composting

The objective of this study was to investigate the impact of thermophilic bacteria on crude fiber content, carbohydrate-active enzyme (CAZyme) genes, and associated microbial communities during Chinese medicine residues composting. The study examines changes over 15 days of composting with (T) and without (CK) thermophilic microbial agents. Results show that the group T compost temperature reached a maximum of 71.0 °C and remained above 70 °C for 2 days, while the group CK maximum temperature was only 60.9 °C. On Day 15, the seed germination index (GI) of group T reached 98.7%, while the group CK GI was only 56.7%. After composting, the degradation rates of cellulose, hemicellulose, and lignin in group T increased by 5.1, 22.5, and 18.5%, respectively, compared to those in group CK. Thermophilic microbial agents changed the microbial communities related to CAZymes, increasing unclassified_o_Myxococcales and Sphaerobacter abundance and reducing Acinetobacter and Sphingobacterium abundance. Thermophilic microbial agents also increased the abundance of the GT4, GT2_Glycos_transf_2, and AA3 gene families. These results show that thermophilic microbial agents can increase composting temperature, accelerate compost maturation, and promote crude fiber degradation. Therefore, they have broad application potential.

Changes in sulfur in soybean rhizosphere soil and the response of microbial flora in a continuous cropping system mediated by Funneliformis mosseae

Soybean is an S-loving crop, and continuous cropping might cause soil sulfur shortage. The primary objectives of this study are to determine whether Funneliformis mosseae (F. mosseae) can enhance the content of available S in S-deficient soil and thereby improve the sulfur utilization rate in soybean. The experiment used Heinong 48 (HN48), a soybean variety with a vast planting area in Heilongjiang Province, and F. mosseae was inoculated in the soil of soybean that had been continuously cropped for 0 and 3 years. The results of the barium sulfur turbidimetric assay show that the sulfur content in the soil and soybean was reduced by continuous cropping and increased by inoculation with F. mosseae; the results of the macro-genome sequencing technology, show that the diversity and abundance of bacteria in the soil was decreased by continuous cropping and increased by inoculation with F. mosseae. The sulfur-oxidizing bacteria (SOB) activity and sulfur-related gene expression levels were lower in the continuous crop group compared to the control group and higher in the F.mosseae-inoculated group compared to the control group. Continuous cropping reduced the sulfur content and ratio of soybean rhizosphere soil, affecting soil flora activity and thus soybean growth; F. mosseae inoculation increased the sulfur content of soybean root-perimeter soil and plants, increased the diversity and abundance of rhizosphere soil microorganisms, increased the expression of genes for sulfur transport systems, sulfur metabolism, and other metabolic functions related to elemental sulfur, and increased the species abundance and metabolic vigor of most SOB. In summary, continuous cropping inhibits soil sulfur uptake and utilization in soybean while the inoculation with F. mosseae can significantly improve this situation. This study offers a theoretical research foundation for using AMF as a bio-fungal agent to enhance soil sulfur use. It also supports the decrease of chemical fertilizers, their substitution, and the protection of native soil.

Exploring Gut Microbiome Variations between Popillia japonica Populations of Azores

Popillia japonica (Coleoptera: Scarabaeidae), is an emerging invasive pest in Europe and America. In the Azores, this pest was first found on Terceira Island during the sixties and soon spread to other islands. The rate of infestation differs between islands, and we hypothesized that microbiome composition could play a role. Therefore, we sampled 3rd instar larvae and soil from sites with high and low infestation rates to analyze the microbiome using next-generation sequencing. We analyzed twenty-four 16S DNA libraries, which resulted in 3278 operational taxonomic units. The alpha and beta diversity of the soil microbiome was similar between sites. In contrast, the larvae from high-density sites presented a higher bacterial gut diversity than larvae from low-density sites, with biomarkers linked to plant digestion, nutrient acquisition, and detoxification. Consequently, larvae from high-density sites displayed several enriched molecular functions associated with the families Ruminococcaceae, Clostridiaceae and Rikenellaceae. These bacteria revealed a supportive function by producing several CAZyme families and other proteins. These findings suggest that the microbiome must be one drive for the increase in P. japonica populations, thus providing a checkpoint in the establishment and spread of this pest.

Genome-Wide Characteristics of GH9B Family Members in Melon and Their Expression Profiles under Exogenous Hormone and Far-Red Light Treatment during the Grafting Healing Process

β-1,4-glucanase can not only promote the wound healing of grafted seedlings but can also have a positive effect on a plant's cell wall construction. As a critical gene of β-1,4-glucanase, GH9B is involved in cell wall remodeling and intercellular adhesion and plays a vital role in grafting healing. However, the GH9B family members have not yet been characterized for melons. In this study, 18 CmGH9Bs were identified from the melon genome, and these CmGH9Bs were located on 15 chromosomes. Our phylogenetic analysis of these CmGH9B genes and GH9B genes from other species divided them into three clusters. The gene structure and conserved functional domains of CmGH9Bs in different populations differed significantly. However, CmGH9Bs responded to cis elements such as low temperature, exogenous hormones, drought, and injury induction. The expression profiles of CmGH9Bs were different. During the graft healing process of the melon scion grafted onto the squash rootstock, both exogenous naphthyl acetic acid (NAA) and far-red light treatment significantly induced the upregulated expression of CmGH9B14 related to the graft healing process. The results provided a technical possibility for managing the graft healing of melon grafted onto squash by regulating CmGH9B14 expression.

Insight into CAZymes of Alicyclobacillus mali FL18: Characterization of a New Multifunctional GH9 Enzyme

In the bio-based era, cellulolytic and hemicellulolytic enzymes are biocatalysts used in many industrial processes, playing a key role in the conversion of recalcitrant lignocellulosic waste biomasses. In this context, many thermophilic microorganisms are considered as convenient sources of carbohydrate-active enzymes (CAZymes). In this work, a functional genomic annotation of Alicyclobacillus mali FL18, a recently discovered thermo-acidophilic microorganism, showed a wide reservoir of putative CAZymes. Among them, a novel enzyme belonging to the family 9 of glycosyl hydrolases (GHs), named AmCel9, was identified; in-depth in silico analyses highlighted that AmCel9 shares general features with other GH9 members. The synthetic gene was expressed in Escherichia coli and the recombinant protein was purified and characterized. The monomeric enzyme has an optimal catalytic activity at pH 6.0 and has comparable activity at temperatures ranging from 40 °C to 70 °C. It also has a broad substrate specificity, a typical behavior of multifunctional cellulases; the best activity is displayed on β-1,4 linked glucans. Very interestingly, AmCel9 also hydrolyses filter paper and microcrystalline cellulose. This work gives new insights into the properties of a new thermophilic multifunctional GH9 enzyme, that looks a promising biocatalyst for the deconstruction of lignocellulose.

Metagenomic Approaches as a Tool to Unravel Promising Biocatalysts from Natural Resources: Soil and Water

Natural resources are considered a promising source of microorganisms responsible for producing biocatalysts with great relevance in several industrial areas. However, a significant fraction of the environmental microorganisms remains unknown or unexploited due to the limitations associated with their cultivation in the laboratory through classical techniques. Metagenomics has emerged as an innovative and strategic approach to explore these unculturable microorganisms through the analysis of DNA extracted from environmental samples. In this review, a detailed discussion is presented on the application of metagenomics to unravel the biotechnological potential of natural resources for the discovery of promising biocatalysts. An extensive bibliographic survey was carried out between 2010 and 2021, covering diverse metagenomic studies using soil and/or water samples from different types and locations. The review comprises, for the first time, an overview of the worldwide metagenomic studies performed in soil and water and provides a complete and global vision of the enzyme diversity associated with each specific environment.

Synergy of Cellulase Systems between Acetivibrio thermocellus and Thermoclostridium stercorarium in Consolidated-Bioprocessing for Cellulosic Ethanol

Anaerobes harbor some of the most efficient biological machinery for cellulose degradation, especially thermophilic bacteria, such as Acetivibrio thermocellus and Thermoclostridium stercorarium, which play a fundamental role in transferring lignocellulose into ethanol through consolidated bioprocessing (CBP). In this study, we compared activities of two cellulase systems under varying kinds of hemicellulose and cellulose. A. thermocellus was identified to contribute specifically to cellulose hydrolysis, whereas T. stercorarium contributes to hemicellulose hydrolysis. The two systems were assayed in various combinations to assess their synergistic effects using cellulose and corn stover as the substrates. Their maximum synergy degrees on cellulose and corn stover were, respectively, 1.26 and 1.87 at the ratio of 3:2. Furthermore, co-culture of these anaerobes on the mixture of cellulose and xylan increased ethanol concentration from 21.0 to 40.4 mM with a high cellulose/xylan-to-ethanol conversion rate of up to 20.7%, while the conversion rates of T. stercorarium and A. thermocellus monocultures were 19.3% and 15.2%. The reason is that A. thermocellus had the ability to rapidly degrade cellulose while T. stercorarium co-utilized both pentose and hexose, the metabolites of cellulose degradation, to produce ethanol. The synergistic effect of cellulase systems and metabolic pathways in A. thermocellus and T. stercorarium provides a novel strategy for the design, selection, and optimization of ethanol production from cellulosic biomass through CBP.

Bioengineered microbial platforms for biomass-derived biofuel production - A review

Global warming issues, rapid fossil fuel diminution, and increasing worldwide energy demands have diverted accelerated attention in finding alternate sources of biofuels and energy to combat the energy crisis. Bioconversion of lignocellulosic biomass has emerged as a prodigious way to produce various renewable biofuels such as biodiesel, bioethanol, biogas, and biohydrogen. Ideal microbial hosts for biofuel synthesis should be capable of using high substrate quantity, tolerance to inhibiting substances and end-products, fast sugar transportation, and amplified metabolic fluxes to yielding enhanced fermentative bioproduct. Genetic manipulation and microbes' metabolic engineering are fascinating strategies for the economical production of next-generation biofuel from lignocellulosic feedstocks. Metabolic engineering is a rapidly developing approach to construct robust biofuel-producing microbial hosts and an important component for future bioeconomy. This approach has been widely adopted in the last decade for redirecting and revamping the biosynthetic pathways to obtain a high titer of target products. Biotechnologists and metabolic scientists have produced a wide variety of new products with industrial relevance through metabolic pathway engineering or optimizing native metabolic pathways. This review focuses on exploiting metabolically engineered microbes as promising cell factories for the enhanced production of advanced biofuels.

Dietary fibre complexity and its influence on functional groups of the human gut microbiota

The aim of this review is to provide an overview of the complex interactions between dietary fibre and the resident microbial community in the human gut. The microbiota influences both health maintenance and disease development. In the large intestine, the microbiota plays a crucial role in the degradation of dietary carbohydrates that remain undigested in the upper gut (non-digestible carbohydrates or fibre). Dietary fibre contains a variety of different types of carbohydrates, and its breakdown is facilitated by many different microbial enzymes. Some microbes, termed generalists, are able to degrade a range of different carbohydrates, whereas others are more specialised. Furthermore, the physicochemical characteristics of dietary fibre, such as whether it enters the gut in soluble or insoluble form, also likely influence which microbes can degrade it. A complex nutritional network therefore exists comprising primary degraders able to attack complex fibre and cross feeders that benefit from fibre breakdown intermediates or fermentation products. This leads predominately to the generation of the short-chain fatty acids (SCFA) acetate, propionate and butyrate, which exert various effects on host physiology, including the supply of energy, influencing glucose and lipid metabolism and anti-carcinogenic and anti-inflammatory actions. In order to effectively modulate the gut microbiota through diet, there is a need to better understand the complex competitive and cooperative interactions between gut microbes in dietary fibre breakdown, as well as how gut environmental factors and the physicochemical state of fibre originating from different types of diets influence microbial metabolism and ecology in the gut.