Unravelling the cellulolytic and hemicellulolytic potential of Streptomyces griseoincarnatus SSPJ4 from semi-arid agricultural region: genome analysis and saccharification studies
Aug 2026· Iranian Journal of Microbiology· Vol 18, pp. 561 - 573· 0 citations· 41 references
Medicine
TL;DR
The findings demonstrate the considerable potential of S. griseoincarnatus SSPJ4 as a source of accessory lignocellulolytic enzymes for improving biomass saccharification and could be exploited to develop cost-effective and efficient enzymatic formulations for second-generation bioethanol production.
Abstract
Background and Objectives: Second-generation bioethanol, a sustainable and environmentally friendly alternative to fossil fuels, can significantly contribute to the economy. However, saccharification accounts for approximately 20–25% of total bioethanol production costs, which can be reduced by using the improved enzyme cocktails. Therefore, the present study aimed to isolate and characterize potent cellulolytic Streptomyces strains capable of enhancing the hydrolytic conversion of lignocellulosic biomass. Materials and Methods: Degraded wood and soil samples were collected and enriched with paddy straw. The isolates were obtained using standard methods and characterized by 16S rRNA sequencing. The best isolate was subjected to whole-genome sequencing to identify hydrolytic genes involved in agro-waste degradation. Saccharification assays were performed using crude culture filtrate in combination with the commercial cellulase cocktail Celluclast® to evaluate sugar release from alkali-pretreated paddy straw. Results: Among the 38 isolates obtained, five were identified as potential cellulolytic Streptomyces strains based on 16S rRNA gene sequencing: Streptomyces tunisiensis SSPJ1, Streptomyces griseoincarnatus SSPJ4, Streptomyces werraensis SSPJ14, Streptomyces ardesiacus SSPJ32, and Streptomyces tendae SSPJ48. S. griseoincarnatus SSPJ4 emerged as the most promising isolate, demonstrating significantly higher enzyme activities. S. griseoincarnatus SSPJ4 was subjected to whole-genome sequencing using the GALAXY tool for assembly and annotation, with an assembled genome of 7.3 Mb, 72.38% G+C content, and 6678 genes. Biosynthetic gene clusters (23) were identified using antiSMASH, and 226 proteins were annotated with CAZy domains, of which 121 belonged to the glycoside hydrolase (GH) family. Supplementation of Celluclast® with the crude enzyme preparation from S. griseoincarnatus SSPJ4 enhanced the saccharification of alkali-pretreated paddy straw, resulting in a 1.55-fold higher sugar yield compared with Celluclast® alone. Conclusion: The findings demonstrate the considerable potential of S. griseoincarnatus SSPJ4 as a source of accessory lignocellulolytic enzymes for improving biomass saccharification. Its enzyme repertoire could be exploited to develop cost-effective and efficient enzymatic formulations for second-generation bioethanol production.
The sustainable valorization of agricultural waste, such as chili pepper straw, is often challenged by the absence of effective microbes that can degrade cell wall components. In this study, metagenomic analysis found that Pseudomonadota was the dominant phylum in the carboxymethyl cellulose (CMC)-enriched microbial communities. In addition, a cellulolytic bacterial strain, designated as Cellulomonas iranensis 7–12, was isolated from naturally decayed chili pepper straw and identified by colony morphology, Gram staining, 16 S rRNA gene sequencing, and genome-based average nucleotide identity (ANI) analysis. Within 30 h, C. iranensis 7–12 displayed robust cellulolytic activity, causing nearly complete disintegration of filter paper, a cellulose model substrate. In contrast, chili pepper straw, a structurally more complex lignocellulosic substrate, was only partially degraded, with dry-weight loss increasing from 11.98% in the uninoculated control to 32.63% after 4 d of fermentation with C. iranensis 7–12. C. iranensis 7–12 exhibited a predominantly extracellular cellulase–xylanase activity profile, with extracellular xylanase activity reaching 3.41 U/mL and exceeding the measured cellulase activities. Whole-genome sequencing of C. iranensis 7–12 identified a complete 3.79-Mb circular chromosome and a diverse CAZyme repertoire, including glycoside hydrolase families related to cellulose and hemicellulose degradation, carbohydrate-binding modules, carbohydrate esterases, and secretion-associated proteins. Moreover, scanning electron microscopy (SEM) examination revealed that the surface and internal microstructure of chili pepper straw were disrupted. Similarly, Fourier-transform infrared (FTIR) spectroscopy analysis showed marked changes in the characteristic absorption bands associated with cellulose, hemicellulose, and lignin-containing structures, indicating partial degradation of polysaccharide components and lignin-associated structural alteration. Collectively, C. iranensis 7–12 shows great potential for the bioconversion of chili pepper straw and the high-performance microbes will be further developed for the effective use of biomass resources.
Crop straw is an abundant lignocellulosic resource, but its efficient bioconversion is hindered by the recalcitrant structure of plant cell walls. This study integrated degradation phenotyping, enzyme activity assays, whole-genome analysis, and comparative transcriptomics to link the wheat-straw degradation performance of strain XH2 with its enzymatic and molecular responses. Strain XH2 was isolated from fully decomposed compost collected in Anhui Province, China, selected based on the formation of a distinct hydrolysis halo on CMC-Congo red agar, and deposited in the China Center for Type Culture Collection (CCTCC) under accession number CCTCC M 2025519. Morphological, cultural, phylogenetic, and genomic analyses identified strain XH2 as Streptomyces thermocarboxydus. Its degradation capacity was evaluated during 28 days of cultivation by measuring straw degradation, lignocellulosic components, scanning electron microscopy (SEM), and extracellular enzyme activities. S. thermocarboxydus XH2 caused marked disruption of the wheat-straw surface and achieved a degradation rate of 31.45%. Cellulose and hemicellulose contents decreased from 41.10% to 28.87% and from 30.72% to 16.85%, respectively, whereas lignin decreased from 8.28% to 6.30%. Endoglucanase activity, filter paper activity (FPase, an indicator of total cellulase activity), and xylanase activity peaked on day 7, reaching 35.99, 17.68, and 37.01 U/mL, respectively. Genome analysis revealed multiple genes encoding cellulases and hemicellulases. Comparative transcriptomic analysis after 72 h of cultivation in wheat-straw medium identified 1614 differentially expressed genes relative to Gause No. 1 medium, with major enrichment in ABC transporters and fructose and mannose metabolism. Most genes associated with polysaccharide degradation were upregulated. These findings link the degradation phenotype of S. thermocarboxydus XH2 to its enzymatic and molecular responses and support its further evaluation as a candidate for wheat-straw bioconversion under greenhouse and field conditions.
Tingyao Lv, Yushuo Zhang, Chao Wang et al.· Microorganisms· 0 citations
Cellulolytic and lignocellulolytic microbes play an important role in the decomposition of plant biomass, but their isolation in tropical rainforest soil is often hindered by microbial competition, fungal growth dominance, and variations in pH and nutrient content that affect the viability of the isolates. This study aimed to isolate and characterize lignocellulose-degrading microorganisms from the HPPB soil of Andalas University, while also evaluating their relationship with environmental parameters. Isolation was carried out using CMC Agar and Tanat Agar on three soil composites, accompanied by soil chemical analysis. The results show a clear fertility gradient, with nitrogen decreasing from 34-15 mg/kg, phosphorus from 38-19 mg/kg, and potassium from 88-42 mg/kg. Microbial populations exhibit functional specialization: Composite B has the highest population of cellulolytic bacteria (26.9 × 104 CFU/g), while Composite C is dominated by lignocellulolytic bacteria (50.0 × 104 CFU/g). Based on colony diameter, bacteria SP2 (84.1 mm) and SP3 (69.7 mm) are the most active cellulolytic isolates, while fungi SP6 (90.0 mm) and SP8 (80.2 mm) are the dominant lignin decomposers. Enzyme dynamics over 28 days showed a sequential pattern: bacteria reached peak cellulase activity earlier, with SP1 increasing from 1.13-2.64 U/mL on day 7, while fungi worked more intensively in the later phase, marked by LiP activity of isolate SP6 reaching 0.1172 U/mL on day 28. Molecular analysis of the five selected isolates confirmed that bacteria SP1, SP2, and SP3 belong to the genus Bacillus, while fungal isolates JSP8 and JSP6 are closely related to Trichoderma and Penicillium, which are three key genera in the lignocellulosic decomposers of tropical ecosystems. Overall, these results affirm the close relationship between soil conditions, substrate composition, and the functional specialization of microbes, while also demonstrating the applicative potential of the isolates as bioactivators for biomass decomposition and organic waste processing.
Santi Diana Putri, H. Hermansah, A. Agustian et al.· Journal of Pure and Applied...· 0 citations
Bioenergy biorefineries generate lignocellulosic by-products rich in fermentable sugars that can serve as renewable feedstocks for the production of high-value bioproducts, including microbial pigments with promising bioactive properties (antioxidant, antimicrobial, and anticancer). Therefore, this study aimed to identify a suitable inoculum preparation strategy, to optimize the culture medium, and to evaluate biopigment production using xylose-based media derived from sugarcane bagasse hemicellulosic hydrolysate (SBHH). Different inoculation strategies were evaluated (cell suspension, whole mycelial discs, and fractionated mycelial discs) and supplementation with Tween 80 (TW80). The medium composition was optimized using a Box–Behnken design, with xylose, yeast extract, and TW80 as variables, and fermentations were then conducted under selected inoculum conditions in semi-defined media and SBHH. The mycelial disc inoculation strategy was selected due to its high biopigment production and lower operational complexity, yielding 8.99, 8.48, and 11.78 AU of yellow, orange, and red biopigments, respectively. The optimized culture composition consisted of 55.65 g/L of xylose, 4.18 g/L of yeast extract, and 15.38 g/L of Tween 80. The cultivation of M. ruber in SBHH resulted in 12.73, 10.75, and 14.56 AU of yellow, orange, and red biopigments, respectively. Thus, the strategy of inoculum preparation associated with non-ionic surfactant proved promising for application in bioenergy biorefineries.
Willian de S. M. Reis, G. L. de Arruda, S. D. da Silva et al.· Fermentation· 0 citations
Findings demonstrates that optimized pretreatment coupled with selected indigenous bacterial isolates enhanced conversion of WB into protein-enriched microbial biomass, providing a basis for further development of lignocellulosic biomass valorization for SCP production.
Sharda Devi Rajput, S. Keshavkant· Biomass Conversion and Biore...· 0 citations
The untapped microbial diversity of the Amazon region represents a strategic frontier for biotechnological applications. This study screened, identified, and evaluated the potential of yeasts isolated from Amazonian environments to bioconvert sugarcane bagasse hydrolysate into ethanol and xylitol. The lignocellulosic hydrolysate was obtained by thermochemical treatment using H2SO4 (0.78% v/v) at 121 °C for 68 min, with a 20% solid loading. The yeast-like isolates were identified by sequencing the internal transcribed spacer (ITS) region (5.8S rDNA) and the D1/D2 domain of the 26S rDNA. Fifteen strains belonging to the genera Pichia, Debaryomyces, Meyerozyma, and Cyberlindnera exhibited the native capacity to convert xylose into xylitol and/or ethanol, achieving product yields (YP/S) of up to 0.20 g g− 1 for ethanol and 0.25 g g− 1 for xylitol in synthetic medium. Although initial fermentation in the acid hydrolysate (28.9 g L− 1 xylose, 5.0 g L− 1 arabinose, 1.2 g L− 1 glucose, and 5.9 g L− 1 acetic acid) supported cell growth, product synthesis was strongly inhibited by the high concentration of byproducts. The use of a biomass deacetylation strategy reduced acetic acid levels to 1.0 g L− 1, enabling the conversion of sugars into the desired alcohols. Cyberlindnera saturnus strains achieved YP/S of up to 0.10 g g− 1 for ethanol and 0.14 g g− 1 for xylitol on deacetylated hydrolysate, while simultaneously performing the bioabatement of furans and residual acetic acid. These findings highlight unconventional Amazonian yeasts that, pending bioprocess optimization, exhibit promising metabolic traits for lignocellulosic biorefineries, including potential new yeast taxa.
Leissandra Nascimento Castelo, Filipe Soares de Freitas, Raphael Ferreira Rocha et al.· Systems Microbiology and Bio...· 0 citations
