Search Results (53)

Cellulose, the most abundant organic polymer in soil, is degraded by the action of microbial communities. Cellulolytic taxa are widespread in soils, enhancing the biodegradation of cellulose by the synergistic action of different cellulase enzymes. β-glucosidases are the last enzymes responsible for the degradation of cellulose by producing glucose from the conversion of the disaccharide cellobiose. Different soils from the states of Delaware, Maryland, New Jersey, and New York were analyzed by direct DNA extraction, PCR analysis, and next generation sequencing of amplicon sequences coding for β-glucosidase genes. To determine the community structure and diversity of microorganisms carrying β-glucosidase genes, amplicon sequence variant analysis was performed. Results showed that the majority of β-glucosidase genes did not match any known phylum or genera with an average of 84% of sequences identified as unclassified. The forest soil sample from New York showed the highest value with 95.62%. When identification was possible, the bacterial phyla Pseudomonadota, Actinomycetota, and Chloroflexota were found to be dominant microorganisms with β-glucosidase genes in soils. The Delaware soil showed the highest diversity with phyla and genera showing the presence of β-glucosidase gene sequences in bacteria, fungi, and plants. However, the Chloroflexota genus Kallotanue was detected in 3 out of the 4 soil locations. When phylogenetic analysis of unclassified β-glucosidase genes was completed, most sequences aligned with the Chloroflexota genus Kallotenue and the Pseudomonadota species Sphingomonas paucimobilis. Since most sequences did not match known phyla, there is tremendous potential to discover new enzymes for possible biotechnological and pharmaceutical applications. Full article

Background: Nowadays, the microbial degradation of cellulose represents a new perspective for reducing cellulose waste from industry and households and at the same time obtaining energy sources. Methods: We isolated and enriched two aerobic (at 37 °C and 50 °C) and one anaerobic microbial consortium from an anaerobic bioreactor for biogas production by continuous subculturing on peptone cellulose solution (PCS) medium supplemented with 0.3% treated or untreated Whatman filter paper under static conditions. Samples were taken every 7 days until day 21 to determine the percentage of cellulose biodegradation. We determined the antimicrobial resistance of aerobic and anaerobic consortia and some single colonies by disc diffusion method, against 42 clinically applied antibiotics. PCR analyses were performed to search for the presence of eight genes for cellulolytic activity and nine genes for antibiotic resistance. By metagenomics analysis, the bacterial and fungal genus distributions in the studied populations were determined. Results: Aerobes cultured at 50 °C degraded cellulose to the greatest extent (47%), followed by anaerobes (24–38%) and aerobes (8%) cultured at 37 °C. The bacterial sequence analysis showed that the dominant phyla are Bacillota and Bacteroidetes and genera—Paraclostridium, Defluvitalea, Anaerobacillus, Acetivibrio, Lysinibacillus, Paenibacillus, Romboutsia, Terrisporobacter, Clostridium, Sporanaerobacter, Lentimicrobium, etc. in a different ratio depending on the cultivation conditions and the stage of the process. Some of these representatives are cellulolytic and hemicellulolytic microorganisms. We performed lyophilization and proved that it is suitable for long-term storage of the most active consortium, which degrades even after the 10th re-inoculation for a period of one year. We proved the presence of ssrA, ssrA BS and blaTEM genes. Conclusions: Our findings demonstrated the potential utility of the microbial consortium of anaerobes in the degradation of waste lignocellulose biomass. Full article

Slow decomposition rates of cereal crop residues can lead to agronomic challenges, such as nutrient immobilization, delayed soil warming, and increased pest pressures. In this regard, microbial inoculation with efficient strains offers a viable and eco-friendly solution to accelerating the decomposition process of crop residues. However, this solution often focuses mostly on selecting microorganisms based on the appropriate enzymic capabilities and neglects the metabolic versatility required to utilize both structural and non-structural components of residues. Therefore, this study aimed to address these limitations by assessing the metabolic profiles of five previously identified cellulolytic bacterial strains, including Bacillus pumilus 1G17, Micromonospora chalcea 1G49, Bacillus mobilis 5G17, Streptomyces canus 1TG5, and Streptomyces achromogenes 3TG21 using Biolog Phenotype Microarray analysis. Moreover, this study evaluated the impact of wheat straw inoculation with single strains and a bacterial consortium on soil organic carbon and nitrogen content in a pot experiment. Results revealed that, beyond the core subset of 12 carbon sources, the strains exhibited diverse metabolic capacities in utilizing 106 carbon sources. All strains demonstrated effective straw biomass degradation compared to the negative control, with significant differences detected only in oil seed rape straw biodegradation estimations. Furthermore, wheat straw inoculated with a bacterial consortium showed a significant increase in soil organic carbon content after 180 days in the pot experiment. Overall, these findings underscore the critical role of metabolic profiling in gaining a deeper understanding of microbial capabilities and addressing the complexities of residue composition and environmental variability. Full article

The increasing demand for renewable energy sources has led to significant interest in second-generation biofuels derived from lignocellulosic biomass and waste materials. This review underscores the pivotal role of lignocellulosic biomass valorization in meeting global energy needs, mitigating greenhouse gas emissions, and fostering a circular bioeconomy. Key pretreatment methods—including steam explosion, pressure treatment, and chemical pretreatment—are analyzed for their ability to enhance the accessibility of cellulose and hemicellulose in enzymatic saccharification. Advances in cellulolytic enzyme development and fermentation strategies, such as the use of genetically engineered microorganisms capable of fermenting both hexoses and pentoses, are discussed in detail. Furthermore, the potential of biorefinery systems is explored, highlighting their capacity to integrate biomass valorization into biofuel production alongside high-value bioproducts. Case studies and recent trends in bioethanol and biogas production are examined, providing insights into the current state of research and its industrial applications. While lignocellulosic biofuels hold considerable promise for sustainable development and emissions reduction, challenges related to cost optimization, process scalability, and technological barriers must be addressed to enable large-scale implementation. This review serves as a comprehensive foundation for bridging the gap between laboratory research and industrial application, emphasizing the need for continued innovation and interdisciplinary collaboration in biofuel technologies. Full article

For the targeted selection of microbial communities that provide cellulose degradation, soil samples containing cellulolytic microorganisms and specific plant residues as a substrate can be used. The details of this process have not been studied: in particular, whether the use of different soils determines the varying efficiency of communities; whether these established cellulolytic communities will have substrate specificity, and other factors. To answer these questions, four soil microbial communities with different cellulolytic activity (Podzol and the soil of Chernevaya taiga) and substrates (oat straw and hemp shives) with different levels of cellulose availability were used, followed by trained communities that were tested on botrooth substrates (in all possible combinations). Based on the analysis of the taxonomic structure of all communities and their efficiency across all substrates (decomposition level, carbon, and nitrogen content), it was shown that the most important taxa of all trained microbial cellulolytic communities are recruited from secondary soil taxa. The original soil does not affect the efficiency of cellulose decomposition: both soils produce equally active communities. Unexpectedly, the resulting communities trained on oats were more effective on hemp than the communities trained on hemp. In general, the usage of pre-trained microbial communities increases the efficiency of decomposition. Full article

The search for active cellulolytic consortia among soil microorganisms is of significant applied interest, but the dynamics of the formation of such communities remain insufficiently studied. To gain insight into the formation of an active cellulolytic community, the experiment was designed to examine the colonization of a sterile substrate (cellulose) by microorganisms from two soil types: sod-podzolic and chernozem. To achieve this, the substrate was placed in the soil and incubated for six months. To assess microbiome dynamics, the experiment employed sequencing of 16S rRNA gene fragment and ITS2 amplicon libraries at four time points. It was demonstrated that, from the second month of the experiment, the prokaryotic component of the communities reached a state of stability, with a community composition specific to each soil type. The results demonstrated no relationship between changes in community diversity and soil respiration. There also was no significant shift in the community diversity throughout the chronosequence. Furthermore, the taxonomic composition of the community shifted towards a decrease in the proportion of Pseudomonadota and an increase in representatives of the Bacteroidota, Bacillota, and Verrucomicrobiota phyla. The network analysis of the community demonstrated that, in contrast to sod-podzolic soil, chernozem is distinguished by a higher modularity, with the formation of taxon-specific groups of microorganisms at each stage of the chronoseries. These differences are attributed to the alterations in the eukaryotic component of the community, particularly in the prevalence of nematodes and predatory fungi, which in turn influenced the cellulolytic community. Full article

Acute hepatopancreatic necrosis disease, caused by Vibrio parahaemolyticus strains carrying the pirA and pirB toxin genes (VpAHPND), has been causing great economic losses in Asia and America in the shrimp farming industry. Numerous strains are resistant to antibiotics. However, supplementation with probiotic antagonists has become a more desirable treatment alternative. Fourteen strains of microorganisms were assessed for their potential to inhibit VpAHPND in vitro activity. The bacteria with the highest activity were challenged with VpAHPND-infected Pacific white shrimp Litopenaeus vannamei. Furthermore, the genomic characteristics of probiotic bacteria were explored by whole-genome sequencing. We identified the Sonora strain as Bacillus pumilus, which possesses positive proteolytic and cellulolytic activities that may improve shrimp nutrient uptake and digestion. Challenge trials showed a low cumulative mortality (11.1%). B. pumilus Son has a genome of 3,512,470 bp and 3734 coding sequences contained in 327 subsystems. Some of these genes are related to the biosynthesis of antimicrobial peptides (surfactins, fengycin, schizokinen, bacilibactin, and bacilysin), nitrogen and phosphorus metabolism, and stress response. Our in vitro and in vivo findings suggest that B. pumilus Sonora has potential as a functional probiotic. Full article

Enzyme-production microorganisms typically occupy a dominant position in composting, where cellulolytic microorganisms actively engage in the breakdown of lignocellulose. Exploring strains with high yields of cellulose-degrading enzymes holds substantial significance for the industrial production of related enzymes and the advancement of clean bioenergy. This study was inclined to screen cellulolytic bacteria, conduct genome analysis, mine cellulase-related genes, and optimize cellulase production. The potential carboxymethylcellulose-hydrolyzing bacterial strain Z2.6 was isolated from the maturation phase of pig manure-based compost with algae residuals as the feedstock and identified as Bacillus velezensis. In the draft genome of strain Z2.6, 31 related cellulolytic genes were annotated by the CAZy database, and further validation by cloning documented the existence of an endo-1,4-β-D-glucanase (EC 3.2.1.4) belonging to the GH5 family and a β-glucosidase (EC 3.2.1.21) belonging to the GH1 family, which are predominant types of cellulases. Through the exploration of ten factors in fermentation medium with Plackett–Burman and Box–Behnken design methodologies, maximum cellulase activity was predicted to reach 2.98 U/mL theoretically. The optimal conditions achieving this response were determined as 1.09% CMC-Na, 2.30% salinity, and 1.23% tryptone. Validation under these specified conditions yielded a cellulose activity of 3.02 U/mL, demonstrating a 3.43-fold degree of optimization. In conclusion, this comprehensive study underscored the significant capabilities of strain Z2.6 in lignocellulolytic saccharification and its potentialities for future in-depth exploration in biomass conversion. Full article

The industrial processing of coconut to produce valuable foods, such as water and milk, generates large volumes of waste, especially the fruit shell. Despite this, material can be used in bioprocess applications, e.g., the production of enzymes, its recalcitrance hinders the cultivation of microorganisms, and low productivity is usually achieved. In this study, the production of cellulolytic enzymes through solid-state fermentation (SSF) and their extraction was investigated using the green coconut fiber pretreated by steam explosion, followed by alkali. The fungus Trichoderma reesei CCT-2768 was cultivated, using an experimental design, to study the effect of the water activity and the amount of biomass in the reactor. The combination of the pretreatment strategies yielded more porous biomass, with less hemicellulose (5.38%, compared to 10.15% of the raw biomass) and more cellulose (47.77% and 33.96% in the pretreated and raw biomasses, respectively). The water activity significantly affected the production of cellulases, with maximum activity yielded at the highest investigated value (0.995). Lastly, the extraction of the enzymes from the cultivation medium was studied, and a 9 g/L NaCl solution recovered the highest CMCase and FPase activities (5.19 and 1.19 U/g, respectively). This study provides an important contribution to the valorization of the coconut residue through (i) the application of the steam explosion technology to optimize the production of cellulases using the SSF technology and (ii) their extraction using different solvents. Full article

The analysis of the secretome allows us to identify the proteins, especially carbohydrate-active enzymes (CAZymes), secreted by different microorganisms cultivated under different conditions. The CAZymes are divided into five classes containing different protein families. Thermothelomyces thermophilus is a thermophilic ascomycete, a source of many glycoside hydrolases and oxidative enzymes that aid in the breakdown of lignocellulosic materials. The secretome analysis of T. thermophilus LMBC 162 cultivated with submerged fermentation using tamarind seeds as a carbon source revealed 79 proteins distributed between the five diverse classes of CAZymes: 5.55% auxiliary activity (AAs); 2.58% carbohydrate esterases (CEs); 20.58% polysaccharide lyases (PLs); and 71.29% glycoside hydrolases (GHs). In the identified GH families, 54.97% are cellulolytic, 16.27% are hemicellulolytic, and 0.05 are classified as other. Furthermore, 48.74% of CAZymes have carbohydrate-binding modules (CBMs). Observing the relative abundance, it is possible to state that only thirteen proteins comprise 92.19% of the identified proteins secreted and are probably the main proteins responsible for the efficient degradation of the bulk of the biomass: cellulose, hemicellulose, and pectin. Full article

Cellulolytic microorganisms play a crucial role in agricultural waste disposal. Strain QXD-8^T was isolated from soil in northern China. Similarity analyses of the 16S rRNA gene, as well as the 120 conserved genes in the whole-genome sequence, indicate that it represents a novel species within the genus Microbacterium. The Microbacterium sp. QXD-8^T was able to grow on the CAM plate with sodium carboxymethyl cellulose as a carbon source at 15 °C, forming a transparent hydrolysis circle after Congo red staining, even though the optimal temperature for the growth and cellulose degradation of strain QXD-8^T was 28 °C. In the liquid medium, it effectively degraded cellulose and produced reducing sugars. Functional annotation revealed the presence of encoding genes for the GH5, GH6, and GH10 enzyme families with endoglucanase activity, as well as the GH1, GH3, GH39, and GH116 enzyme families with β-glucosidase activity. Additionally, two proteins in the GH6 family, one in the GH10, and two of nine proteins in the GH3 were predicted to contain a signal peptide and transmembrane region, suggesting their potential for extracellularly degrade cellulose. Based on the physiological features of the type strain QXD-8^T, we propose the name Microbacterium psychrotolerans for this novel species. This study expands the diversity of psychrotolerant cellulolytic bacteria and provides a potential microbial resource for straw returning in high-latitude areas at low temperatures. Full article

Excessive agricultural intensification adversely affects soil quality, particularly in hilly terrain, leading to increased erosion. Anthropogenic denudation, intensified by tillage erosion, results in the displacement of soil material from hilltops and shoulders to their bases. The research hypothesis posits that tillage erosion adversely affects the microbiological and chemical properties of soils, especially at the hilltops of intensively cultivated areas. The study aimed to assess the microbiological and chemical properties of Luvisols cultivated under conventional plowing in the moraine region of the Southern Krajna Lakeland, Poland. The evaluation focused on the results of soil sample analyses taken from the hilltops and foothills of eroded mounds. Microbiological investigations included determining the abundance of actinomycetes, filamentous fungi, heterotrophic bacteria, cellulolytic microorganisms, copiotrophs, and oligotrophs. Additionally, pH values and the contents of phosphorus, potassium, magnesium, total organic carbon, and nitrogen were determined. A higher abundance of bacteria, actinomycetes, and copiotrophs was observed at the foothills. Statistically significant differences due to slope effects were noted for all chemical parameters, with higher concentrations of organic carbon, nitrogen, potassium, and phosphorus found in the foothill areas. Understanding denudation processes can contribute to sustainable soil resource use and agrocenosis conservation. Full article

The aim of the study was to determine the impact that three cultivation systems—conventional till (CT), reduced till (RT), and strip-till one-pass (ST-OP)—had on the biological parameters of the soil and their relationships with organic matter properties in the row zone (R) and inter-row zone (IR). For this purpose, a long-term static field experiment was carried out, from which soil samples were taken from a depth of 0–20 cm and the following were determined: TOC; TN content and fractional composition of organic matter; activity of dehydrogenases (DEHs), catalase (CAT), alkaline (AlP), and acid phosphatase (AcP); and the abundances of heterotophic bacteria (B), filamentous fungi (F), actinobacteria (Ac), and cellulolytic microorganisms (Ce). Soil samples for biological parameter tests were collected in summer (July) and autumn (October). RT and ST-OP increase the content of TOC, TN, carbon, and nitrogen in the humic and fulvic acid fractions. For the studied groups of microorganisms, the conditions for development were least favourable under CT cultivation. The results show that in July, the activities of DEH and CAT were the highest in ST-OP, whereas in October, they were the highest under CT. AlP and AcP activity were markedly the highest under ST-OP in both months. Enzyme activity was significantly the highest in the IR zone. The results indicate that, of the calculated multiparametric indicators, (AlP/AcP, GMea, BIF, BA12, and TEI), BA12 is a sensitive biological indicator of soil quality. Full article

Dietary fiber is a substance that cannot be digested by endogenous digestive enzymes but can be digested by the cellulolytic enzymes produced by intestinal microorganisms. In the past, dietary fiber was considered an anti-nutrient component in diets because it could resist digestion by endogenous enzymes secreted by the intestine and has a negative effect on the digestion of energy-producing nutrients. However, due to its functional properties, potential health benefits to animals, and innate fermentability, it has attracted increasing attention in recent years. There are a plethora of studies on dietary fiber. Evidence suggests that dietary fiber can provide energy for pigs through intestinal microbial fermentation and improve sow welfare, reproductive performance, intestinal flora, and immunity. This is a brief overview of the composition and classification of dietary fiber, the mechanism of action and effects of dietary fiber on reproductive performance, intestinal microorganisms, and the immune index of the sow. This review also provides scientific guidance for the application of dietary fiber in sow production. Full article

The phytoremediation of soil contaminated with petroleum depends on the association of plants with rhizosphere bacteria capable of promoting plant growth and destroying petroleum hydrocarbonates. In the present work, we studied the effects of “Lenoil” biological product containing bacteria Pseudomonas turukhanskensis IB 1.1, capable of destroying petroleum hydrocarbons on Secale cereale L plants, which previously proved to be resistant to the weak oil pollution of gray forest soil and to the composition of microorganisms in their rhizosphere. The composition of microorganisms in the rhizosphere of rye roots was studied, morphometric parameters of shoots and roots of rye plants were estimated, and hormone concentration was immunoassayed under conditions of 4% petroleum pollution of the soil. Addition of petroleum to the soil increased the content of oligonitrophilic (by 24%) and hydrocarbon-oxidizing (by 33%) microorganisms; however, the content of cellulolytic (by 12.5 times) microorganisms in the rhizosphere decreased. The use of Lenoil led to a further increase in the number of cellulolytic (by 5.6 times) and hydrocarbon-oxidizing (by 3.8 times) microorganisms and a decrease in the number of oligonitrophilic (by 22.7%) microorganisms in the rhizosphere. Under petroleum pollution, the content of auxins (IAA), zeatin riboside, zeatin nucleotide, and zeatin decreased, while the content of abscisic acid (ABA) increased in the shoots of rye plants. Lenoil treatment led to an eight-fold increase in the IAA content in the roots and a decrease in the ABA content in the aerial part and in the roots. It was shown for the first time that the treatment of petroleum-contaminated soil with “Lenoil” increased root mass due to the development of lateral roots, concurrent with high root IAA content. Petroleum pollution increased the deposition of lignin and suberin in the roots, which strengthened the apoplastic barrier and, thus, reduced the infiltration of toxic components. The deposition of suberin and lignin decreased under ”Lenoil” treatment, indicating a decrease in the concentration of toxic petroleum components in the soil degraded by the bacteria. Thus, the biological preparation reduced the growth-inhibiting effect of petroleum on rye plants by increasing the content of growth-stimulating phytohormones (IAA and cytokinins) and reducing the content of ABA, justifying the importance of further study of relevant hormones for the improvement of phytoremediation. Full article