Search Results (93)

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

Gut microbes are important for saproxylophagous insects, but little is known about the specific types of microbes that we can grow in the lab and how their diet affects them. We characterized aerobic culturable microbes from the superworm Zophobas atratus larvae reared on a standard diet (SD) and a fungal-based diet (FD) using the selective plating and 16S rRNA sequencing of isolates. Five functional groups were cultured: amino acid autotrophs, enterobacteria, yeasts, cellulolytic bacteria, and molds. A quantitative assessment revealed distinct diet-dependent patterns: SD-fed larvae showed the dominance of enterobacteria and amino acid autotrophs, while FD-fed larvae exhibited a higher abundance of enterobacteria and yeasts. Mold populations remained minimal under both diets. A phylogenetic analysis of bacterial isolates showed four core bacterial phyla (Pseudomonadota, Actinobacteria, Bacillota, and Bacteroidota) with diet-sensitive genus-level variations. Pseudomonadota dominated both diets, but certain genera were associated with different diets: Micrococcus and Brucella in the SD versus Citrobacter and Pseudomonas in the FD. Shared genera (Klebsiella, Enterobacter, and Bacillus) may represent a core culturable community. These findings demonstrate the influence of diet on culturable gut microbes while highlighting the need for complementary molecular approaches to study unculturable taxa. The isolated strains provide resources for investigating microbial functions in insect nutrition. Full article

Annually, a considerable amount of agricultural waste is produced leading to serious environmental pollution if not managed effectively. A wide range of bio-decomposers, including fungi, bacteria, and actinomycetes may break down the complex agro-residues in an eco-friendly way through secreting many cellulolytic and amylolytic enzymes. The present study aimed at exploring the ability of Frankia to degrade cellulose and starch and identifying the cellulase and α-amylase genes in Frankia genomes for potential agricultural waste degradation. Frankia alni ACN14a and Frankia casuarinae CcI₃ produced clear zones around growing hyphae on carboxymethyl cellulose (CMC) and starch substrates. The hydrolytic index (HI) ranged from 1 to 2.14 reflecting variation in their degradation efficacy. Quantification of CMCase (carboxymethyl cellulase) production in strain ACN14a presented the maximum activity (0.504 U/mL) under 1% CMC after 16 days whereas strain CcI₃ produced a weak activity after 6 days from incubation. Besides, amylase activity in strain ACN14a reached the highest value (3.215 U/mL) after 4 days of growing with 1% starch, while strain CcI₃ had the superior production (3.04 U/mL) after 12 days from 1% starch condition. Data mining and genome blasting led to the identification of multiple genes related to cellulose and starch degradation. Two endoglucanases (celA1, FRAAL4955 and celA2, FRAAL4956), two glycosyl hydrolase family 16 (FRAAL6120 and FRAAL2663), and one glycosyl hydrolase family 16 (Francci3_3843) were predicted in the two genomes. Likewise, the α-amylase genes (FRAAL5900) from Frankia alni ACN14a and (Francci3_3679) from strain CcI₃ were identified. The gene expression of endo-1, 4-beta-glucanase (celA2, FRAAL4956) revealed the maximum increment in its mRNA abundance under 0.25% CMC exposure and showed a 3.3-fold increase. Frankia capability to degrade cellulose and starch represents a critical process in nutrient cycling and environment protection. Full article

The biochemical degradation of abundant cellulosic biomass for industrial use and energy production has been extensively researched in recent years. Some elaborate cellulose digestion approaches have been developed based on specialized bacteria, which possess sophisticated mechanisms to efficiently degrade recalcitrant natural carbohydrates. In this study, we assembled catalytic domains from multiple cellulolytic enzymes onto a scaffold along with a cellulose-binding module (CBM), specifically targeting crystalline cellulose. The catalytic domains of endoglucanase and cellobiohydrolase from Acetivibrio thermocellus were linked to a heterotrimeric protein scaffold that assembles in a specific order. The bicatalytic complex failed to show the anticipated synergistic effect in cooperative cellulolysis, presumably because the catalytic domains only serve as weak anchors for each other in binding to the substrate. On the other hand, cellulose digestion was remarkably promoted by incorporating a CBM into a stable complex with a catalytic domain. Interestingly, the reversible association of catalytic domains and excess CBM proved more advantageous than fixed association. This suggests that the dynamic incorporation of CBM units enhances the accessibility of cellulose-degrading catalytic modules to the polysaccharide strand by preventing overly strong binding. This finding could have interdisciplinary applications for enzymes converting polymeric substrates other than cellulose. 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

This research investigated the effects of hydrothermal depolymerization with Fe/Ni loaded C catalysts on the anaerobic digestion (AD) performance of corn stover (CS). CS was depolymerized at 140 °C for 20 min with Fe/C or Ni/C catalysts, and then anaerobically digested. The results showed that the biomethane yield with Fe/C-600 increased by 36.6% compared to that of the control. This increase could be attributed to effective CS depolymerization with catalysts (DC), indicated by modified structures of solid fraction and enriched available components of liquid fraction. SEM analyses showed that CS microphysical structure after DC was obviously disrupted, resulting in more accessibility of cellulose and hemicellulose. The crystallinity index (CrI) of depolymerized CS was significantly reduced from 32.5% to 23.5%, allowing for a more easily biodegradable non-crystalline area to be available for enzymes. Meanwhile, the DC group produced 4.7 times more reducing sugar (RS), and a 3.4 times increase in total volatile fatty acids (VFAs) as compared to the control. Furthermore, these enhancements in DC led to an increased relative abundance of cellulolytic bacteria (Hydrogenispora and Fermentimonas) and anaerobic methanogenic archaea (Methanosarcina) in following the AD process. This could explain the reason for the biomethane yield increase with DC from microbial perspectives. This study demonstrated that hydrothermal depolymerization with Fe/C or Ni/C could provide an effective approach for obtaining more biomethane from CS via AD. Full article

The impact of macroalgae species on rumen function remains largely unexplored. This present study aimed to identify the biocompounds of the three types of marine macroalgae described: Macrocystis pyrifera (Brown), Ulva spp. (Lettuce), Mazzaella spp. (Red) and their effect on species-specific modulations of the rumen microbiome. The macroalgae were characterized using GC-MS. Twelve Rambouillet lambs were randomly assigned to one of four experimental diets (n = 3 per treatment): (a) control diet (CD); (b) CD + 5 g of Red algae; (c) CD + 5 g of Brown algae; and (d) CD + 5 g of Lettuce algae. After the lambs ended their fattening phase, they donated ruminal fluid for DNA extraction and 16S rRNA gene V3 amplicon sequencing. Results: The tagged 16S rRNA amplicon sequencing and statistical analysis revealed that the dominant ruminal bacteria shared by all four sample groups belonged to phyla Firmicutes and Bacteroidota. However, the relative abundance of these bacterial groups was markedly affected by diet composition. In animals fed with macroalgae, the fibrinolytic and cellulolytic bacteria Selenomonas was found in the highest abundance. The diversity in chemical composition among macroalgae species introduces a range of bioactive compounds, particularly VOCs like anethole, beta-himachalene, and 4-ethylphenol, which demonstrate antimicrobial and fermentation-modulating properties. Full article

Raw potato fries are a type of potato by-product (PBP), and they have great potential as a partial replacement of grain in animal feeds to improve the environmental sustainability of food production. This study aimed to investigate the effects of replacing corn with different levels of PBP (0%, 12.84%, 25.65%, and 38.44%) in the total mixed ration (TMR) of Angus bull. Sixty 16-month-old Angus bulls (548.5 ± 15.0 kg, mean ± SD) were randomly assigned to four treatments. The results indicated that with the increase in the substitution amount of PBP, the body weight decreased significantly. The dry matter apparent digestibility and starch apparent digestibility linearly decreased as PBP replacement increased. The feed ingredient composition in the TMR varied, leading to a corresponding change in the rumen microbiota, especially in cellulolytic bacteria and amylolytic bacteria. The abundance of Succiniclasticum in the 12.84% PBP and 38.44% PBP diets was significantly higher than that in the 0% PBP and 25.65% PBP diets. The abundance of Ruminococcus linearly increased. In conclusion, using PBP to replace corn for beef cattle had no negative impact on rumen fermentation, and the decrease in apparent digestibility explained the change in growth performance. Its application in practical production is highly cost-effective and a strategy to reduce food waste. 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

Honey and pollen from Tetragonisca fiebrigi and Scaptotrigona jujuyensis, stingless bees from northern Argentina, presented a particular microbiological profile and associated enzymatic activities. The cultured bacteria were mostly Bacillus spp. (44%) and Escherichia spp. (31%). The phylogenetic analysis showed a taxonomic distribution according to the type of bee that was similar in both species. Microbial enzymatic activities were studied using hierarchical clustering. Bacillus spp. was the main bacterium responsible for enzyme production. Isolates with xylanolytic activity mostly presented cellulolytic activity and, in fewer cases, lipolytic activity. Amylolytic activity was associated with proteolytic activity. None of the isolated strains produced multiple hydrolytic enzymes in substantial amounts, and bacteria were classified according to their primary hydrolytic activity. These findings add to the limited knowledge of microbiological diversity in honey and pollen from stingless bees and also provide a physiological perspective of this community to assess its biotechnological potential in the food industry. Full article

This review provides insights into cellulolytic bacteria present in global forest and agricultural soils over a period of 11 years. It delves into the study of soil-dwelling cellulolytic bacteria and the enzymes they produce, cellulases, which are crucial in both soil formation and the carbon cycle. Forests and agricultural activities are significant contributors to the production of lignocellulosic biomass. Forest ecosystems, which are key carbon sinks, contain 20–30% cellulose in their leaf litter. Concurrently, the agricultural sector generates approximately 998 million tons of lignocellulosic waste annually. Predominant genera include Bacillus, Pseudomonas, Stenotrophomonas, and Streptomyces in forests and Bacillus, Streptomyces, Pseudomonas, and Arthrobacter in agricultural soils. Selection of cellulolytic bacteria is based on their hydrolysis ability, using artificial cellulose media and dyes like Congo red or iodine for detection. Some studies also measure cellulolytic activity in vitro. Notably, bacterial cellulose hydrolysis capability may not align with their cellulolytic enzyme production. Enzymes such as GH1, GH3, GH5, GH6, GH8, GH9, GH10, GH12, GH26, GH44, GH45, GH48, GH51, GH74, GH124, and GH148 are crucial, particularly GH48 for crystalline cellulose degradation. Conversely, bacteria with GH5 and GH9 often fail to degrade crystalline cellulose. Accurate identification of cellulolytic bacteria necessitates comprehensive genomic analysis, supplemented by additional proteomic and transcriptomic techniques. Cellulases, known for degrading cellulose, are also significant in healthcare, food, textiles, bio-washing, bleaching, paper production, ink removal, and biotechnology, emphasizing the importance of discovering novel cellulolytic strains in soil. 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