Degradation of rice straw at low temperature using a novel microbial consortium LTF-27 with efficient ability

Isolation, Enrichment and Analysis of Aerobic, Anaerobic, Pathogen-Free and Non-Resistant Cellulose-Degrading Microbial Populations from Methanogenic Bioreactor

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.

Efficient degradation of corn straw at low temperature using a novel co-cultured consortium LHWA

Straw degradation was slow under low temperature environments. A cold-tolerant consortium LHWA was constructed by Bacillus cereus, Acinetobacter lwoffii, Penicillium griseofulvum, and Talaromyces funiculosus. The consortium and culture conditions were optimized. Under 4 °C cultivation, liquid fermentation showed a 55.52 % straw weight loss rate after 30 days with inoculum (8.4 %, w/v), peptone (0.4 %, w/v) and Fe2+ concentration (0.06 %, w/v); solid fermentation showed 58.36 % straw weight loss rate after 60 days. According to transcriptomic analysis, the mechanism of cold resistance in B. cereus is to improve the fluidity of the cell membrane, including changing the composition of fatty acids, increasing the expression of cold stress response proteins and cold shock proteins. The constructed consortium LHWA significantly improved the straw degradation efficiency under cold environments.

Assembly of a lignocellulose-degrading synthetic community from the strong-flavor Daqu by a stepwise method

The lignocellulose in Daqu plays an important role during the Baijiu fermentation, such as providing energy for microbial metabolism and precursors for flavor compounds. However, due to the complexity of the Daqu microbial community and the fermentation environment, the regulation of lignocellulose degradation efficiency is limited. In such cases, artificial intervention can be achieved through the application of synthetic communities. Here, we studied the structure of the lignocellulose-degrading microbial communities in Daqu. Based on the characteristics of lignocellulose composition, we developed three high-throughput screening methods and used a stepwise assembly approach to construct a synthetic community composed of Bacillus stercori, Bacillus paramycoides, Klebsiella pneumoniae, and Cyberlindnera fabianii. After fermentation, 54.71 % of the bran was degraded and 11 substances were uniquely produced. 4-vinylguaiacol and 2-ethyl-3,5(6)-dimethylpyrazine were considered to be the key aroma compounds of the synthetic community. This synthetic community offers a new approach to control Daqu fermentation.

Efficient conversion of corn straw to feed protein through solid-state fermentation using a thermophilic microbial consortium

Solid-state fermentation of lignocellulosic waste to produce feed protein is a means of realising solid waste. However, low efficiency and susceptibility to microbial contamination remain significant challenges in feed protein production through room-temperature solid-state fermentation. In this study, thermophilic microbiomes were enriched. After adaptive and nitrogen acclimation, microbiomes with the combined functions of 'thermophilic-rapid decomposition-nitrogen conversion' were obtained and used for feed protein production. High-throughput sequencing and Kyoto Encyclopedia of Genes and Genomes metabolic pathway prediction techniques were used to assess the mechanisms underlying microbial involvement in substance conversion. The results showed that the microbiomes decomposed 78.21 %-81.73 % of straw within 7 days. After nitrogen acclimation, the nitrogen utilisation rate and the true protein content of the microbiomes improved by 19.22 %-26.96 % and 56.14 %-71.99 %, respectively. Fed-batch enzymatic saccharification and fermentation reduced the fermentation time by 28.5 %. Domesticated microbiomes increased the abundance of bacteria and fungi in the fermentation system, enhancing carbon metabolism and the urea cycle. This study presents a novel approach for the high-value utilisation of lignocellulose waste.

Characterization and degradation mechanism of a newly isolated hydrolyzed polyacrylamide-degrading bacterium Alcaligenes faecalis EPDB-5 from the oilfield sludge

Hydrolyzed polyacrylamide (HPAM) is posing serious threats to ecosystems. However, biodegradation is an effective method to remove HPAM owing to its low cost and environmental friendliness. In this study, Alcaligenes faecalis EPDB-5 was isolated as a highly efficient HPAM degrading strain from sludge contaminated with polymerized produced water from Daqing oilfield. Under the optimal conditions, the strain EPDB-5 demonstrated an impressive HPAM degradation rate of 86.05%, the total nitrogen (TN) removal of 71.96% and chemical oxygen demand (COD) removal of 67.98%. Meanwhile, it can maintain a stable degradation rate higher than 75% under different pH and temperature conditions. 27 genes that play a key role in HPAM degradation were annotated by metagenomics sequencing. The key genes were involved in multiple KEGG pathways, including biofilm formation, biosynthesis secondary metabolites, and metabolic pathways. SEM, GPC, and FTIR analyses revealed that the structure of HPAM after biodegradation showed pores, a significant decrease in molecular weight, -NH2 detachment, and carbon chain breakage. Particularly, we propose a possible mechanism of biofilm formation - HPAM degradation - biofilm disappearance and reorganization. Moreover, the degradation rate of strain EPDB-5 on real wastewater containing HPAM was 29.97% in only three days. This work expands our knowledge boundary about the HPAM degradation mechanism at the functional gene level, and supports the potential of strain EPDB-5 as a novel auxiliary microbial resource for the practical application of HPAM.

Outstanding enhancement of caproate production with microwave pyrolyzed highly reductive biochar addition

The integration of biochar into microbial Chain Elongation (CE) proves to be an effective tool of producing high-value bio-based products. This study innovatively applied biochar fabricated under microwave irradiation with carbon fiber cloth assistance into CE system. Results highlighted that microwave biochar achieved maximal CE efficiency yielding 8 g COD/L, with 3-fold increase to the blank group devoid of any biochar. Microwave biochar also obtained the highest substrate utilization rate of 94 %, while conventional biochar group recorded 90 % and the blank group was of 74 %. Mechanistic insights revealed that the reductive surface properties facilitated CE performance, which is relevant to fostering dominant genera of Parabacteroides, Bacteroides, and Macellibacteroides. By metagenomics, microwave biochar up-regulated functional genes and enzymes involved in CE process including ethanol oxidation, the reverse β-oxidation pathway, and the fatty acid biosynthesis pathway. This study effectively facilitated caproate production by utilizing a new microwave biochar preparation strategy.

Building microbial consortia to enhance straw degradation, phosphorus solubilization, and soil fertility for rice growth

Straw pollution and the increasing scarcity of phosphorus resources in many regions of China have had severe impacts on the growing conditions for crop plants. Using microbial methods to enhance straw decomposition rate and phosphorus utilization offers effective solutions to address these problems. In this study, a microbial consortium 6 + 1 (consisting of a straw-degrading bacterium and a phosphate-solubilizing bacterium) was formulated based on their performance in straw degradation and phosphorus solubilization. The degradation rate of straw by 6 + 1 microbial consortium reached 48.3% within 7 days (The degradation ability was 7% higher than that of single bacteria), and the phosphorus dissolution rate of insoluble phosphorus reached 117.54 mg·L- 1 (The phosphorus solubilization ability was 29.81% higher than that of single bacteria). In addition, the activity of lignocellulosic degrading enzyme system was significantly increased, the activities of endoglucanase, β-glucosidase and xylanase in the microbial consortium were significantly higher than those in the single strain (23.16%, 28.02% and 28.86%, respectively). Then the microbial consortium was processed into microbial agents and tested in rice pots. The results showed that the microbial agent significantly increased the content of organic matter, available phosphorus and available nitrogen in the soil. Ongoing research focuses on the determination of the effects and mechanisms of a functional hybrid system of straw degradation and phosphorus removal. The characteristics of the two strains are as follows: Straw-degrading bacteria can efficiently degrade straw to produce glucose-based carbon sources when only straw is used as a carbon source. Phosphate-solubilizing bacteria can efficiently use glucose as a carbon source, produce organic acids to dissolve insoluble phosphorus and consume glucose at an extremely fast rate. The analysis suggests that the microbial consortium 6 + 1 outperformed individual strains in terms of both performance and application effects. The two strains within the microbial consortium promote each other during their growth processes, resulting in a significantly higher rate of carbon source consumption compared to the individual strains in isolation. This increased demand for carbon sources within the growth system facilitates the degradation of straw by the strains. At the same time, the substantial carbon consumption during the metabolic process generated a large number of organic acids, leading to the solubilization of insoluble phosphorus. It also provides a basis for the construction of this type of microbial consortium.

Straw Incorporation with Exogenous Degrading Bacteria (ZJW-6): An Integrated Greener Approach to Enhance Straw Degradation and Improve Rice Growth

Rice straw is an agricultural waste, the disposal of which through open burning is an emerging challenge for ecology. Green manufacturing using straw returning provides a more avant-garde technique that is not only an effective management measure to improve soil fertility in agricultural ecosystems but also nurtures environmental stewardship by reducing waste and the carbon footprint. However, fresh straw that is returned to the field cannot be quickly decomposed, and screening microorganisms with the capacity to degrade straw and understanding their mechanism of action is an efficient approach to solve such problems. This study aimed to reveal the potential mechanism of influence exerted by exogenous degradative bacteria (ZJW-6) on the degradation of straw, growth of plants, and soil bacterial community during the process of returning rice straw to the soil. The inoculation with ZJW-6 enhanced the driving force of cellulose degradation. The acceleration of the rate of decomposition of straw releases nutrients that are easily absorbed by rice (Oryza sativa L.), providing favorable conditions for its growth and promoting its growth and development; prolongs the photosynthetic functioning period of leaves; and lays the material foundation for high yields of rice. ZJW-6 not only directly participates in cellulose degradation as degrading bacteria but also induces positive interactions between bacteria and fungi and enriches the microbial taxa that were related to straw degradation, enhancing the rate of rice straw degradation. Taken together, ZJW-6 has important biological potential and should be further studied, which will provide new insights and strategies for the appropriate treatment of rice straw. In the future, this degrading bacteria may provide a better opportunity to manage straw in an ecofriendly manner.

Synergistic analysis of lignin degrading bacterial consortium and its application in rice straw fiber film

Fiber film have received widespread attention due to its green friendliness. We can use microorganisms to degrade lignin in straw to obtain cellulose and make fiber films. Herein, a group of high-temperature (50 °C) lignin degrading bacterial consortium (LDH) was enriched and culture conditions for lignin degradation were optimized. Combined with high-throughput sequencing technology, the synergistic effect of LDH-composited bacteria was analyzed. Then LDH was used to treat rice straw for the bio-pulping experiment. The results showed that the lignin of rice straw was degraded 32.4 % by LDH at 50 °C for 10 d, and after the optimization of culture conditions, lignin degradation rate increased by 9.05 % (P < 0.001). The bacteria that compose in LDH can synergistically degrade lignin. Paenibacillus can encode all lignin-degrading enzymes present in the LDH. Preliminary tests of LDH in the pulping industry have been completed. This study is the first to use high temperature lignin degrading bacteria to fabricate fiber film.

Dominant factors analyses and challenges of anaerobic digestion under cold environments

With the development of fermentation technology and the improvement of efficiency, anaerobic digestion (AD) has been playing an increasingly primary role in waste treatment and resource recovery. Temperature is undoubtedly the most important factor because it shapes microbial habitats, changes the composition of the microbial community structure, and even affects the expression of related functional genes. More than half of the biosphere is in a long-term or seasonal low-temperature environment (<20 °C), which makes psychrophilic AD have broad application prospects. Therefore, this review discusses the influencing factors and enhancement strategies of psychrophilic AD, which may provide a corresponding reference for future research on low-temperature fermentation. First, the occurrence of AD has been discussed. Then, the adaptation of microorganisms to the low-temperature environment was analyzed. Moreover, the challenges of psychrophilic AD have been reviewed. Meanwhile, the strategies for improving psychrophilic AD are presented. Further, from technology to application, the current situation of psychrophilic AD in pilot-scale tests is described. Finally, the economic and environmental feasibility of psychrophilic AD has been highlighted. In summary, psychrophilic AD is technically feasible, while economic analysis shows that the output benefits cannot fully cover the input costs, and the large-scale practical application of psychrophilic AD is still in its infancy. More research should focus on how to improve fermentation efficiency and reduce the investment cost of psychrophilic AD.

Straw mulch improves soil carbon and nitrogen cycle by mediating microbial community structure and function in the maize field

This study was conducted to investigate the capability of the microbial community characteristics and soil variables to promote carbon and nitrogen cycles in maize fields under straw mulch. We covered the surface soil of the maize field with different amounts of wheat straw (0 kg/ha, 2,250 kg/ha, and 4,500 kg/ha) and used 16S rRNA and ITS sequencing, Biology ECO-plate, traditional enzymology, TOC analyzer, and HPLC to measure bacterial and fungal community composition and functions, characteristics of microbial carbon source metabolism, carbon and nitrogen fraction, enzyme activity, and organic acid content in the maize rhizosphere and non-rhizosphere. The results indicated that short-term straw mulch insignificantly affected the alpha diversity of bacterial and fungal communities whereas significantly influenced their beta diversity. The results of functional prediction revealed that straw mulch considerably boosted the relative abundances of bacteria belonging to chemoheterotrophy, aerobic chemoheterotrophy, ureolysis, and nitrogen fixation and inhibited fermentation and nitrate reduction in maize rhizosphere soil. These processes primarily drove the C and N cycles in soil. Straw mulch also improved fungal saprotrophs by raising the proportion of Chaetomiaceae and Chaetosphaeriaceae. The Biology ECO-plate results illustrated that straw mulch weakened the metabolism capacity of microbial labile carbon resources. As a result, the labile C and N fractions were raised under straw mulch. Our results also showed that straw mulch primarily regulated the microbial community structure in rhizosphere soil by significantly decreasing Firmicutes and Ascomycota relative abundance while increasing Basidiomycota. The fungal community structure is more than bacterial for affecting soil microbial biomass carbon, readily oxidizable organic carbon, dissolved organic carbon, available nitrogen, ammonium, and nitrate directly and indirectly through malic acid content and cellulase, protease, and amylase activity. Overall, our findings imply that straw mulch might influence the bacterial and fungal community structures, thereby boosting the production of labile C and N components and accelerating the C and N cycle in maize fields.

Mining of key genes for cold adaptation from Pseudomonas fragi D12 and analysis of its cold-adaptation mechanism

The psychrotroph Pseudomonas fragi D12, which grew strongly under low temperatures, was screened from tundra soil collected from the permanent alpine zone on Changbai Mountain. To mine the genes critical for cold tolerance and to investigate the cold-adaptation mechanism, whole-genome sequencing, comparative genomic analysis, and transcriptome analysis were performed with P. fragi. A total of 124 potential cold adaptation genes were identified, including nineteen unique cold-adaptive genes were detected in the genome of P. fragi D12. Three unique genes associated with pili protein were significantly upregulated at different degrees of low temperature, which may be the key to the strong low-temperature adaptability of P. fragi D12. Meanwhile, we were pleasantly surprised to find that Pseudomonas fragi D12 exhibited different cold-adaptation mechanisms under different temperature changes. When the temperature declined from 30°C to 15°C, the response included maintenance of the fluidity of cell membranes, increased production of extracellular polymers, elevation in the content of compatibility solutes, and reduction in the content of reactive oxygen species, thereby providing a stable metabolic environment. When the temperature decreased from 15°C to 4°C, the response mainly included increases in the expression of molecular chaperones and transcription factors, enabling the bacteria to restore normal transcription and translation. The response mechanism of P. fragi D12 to low-temperature exposure is discussed. The results provide new ideas for the cold-adaptation mechanism of cold-tolerant microorganisms.

Low-temperature corn straw-degrading bacterial agent and moisture effects on indigenous microbes

While the in situ return of corn straw can improve soil fertility and farmland ecology, additional bacterial agents are required in low-temperature areas of northern China to accelerate straw degradation. Moisture is an important factor affecting microbial activity; however, owing to a lack of bacterial agents adapted to low-temperature complex soil environments, the effects of soil moisture on the interaction between exogenous bacterial agents and indigenous soil microorganisms remain unclear. To this end, we explored the effect of the compound bacterial agent CFF constructed using Pseudomonas putida and Acinetobacter lwoffii, developed to degrade corn straw in low-temperature soils (15 °C), on indigenous bacterial and fungal communities under dry (10% moisture content), slightly wet (20%), and wet (30%) soil-moisture conditions. The results showed that CFF application significantly affected the α-diversity of bacterial communities and changed both bacterial and fungal community structures, enhancing the correlation between microbial communities and soil-moisture content. CFF application also changed the network structure and the species of key microbial taxa, promoting more linkages among microbial genera. Notably, with an increase in soil moisture, CFF enhanced the rate of corn straw degradation by inducing positive interactions between bacterial and fungal genera and enriching straw degradation-related microbial taxa. Overall, our study demonstrates the alteration of indigenous microbial communities using bacterial agents (CFF) to overcome the limitations of indigenous microorganisms for in situ straw-return agriculture in low-temperature areas. KEY POINTS: • Low-temperature and variable moisture conditions (10-30%) were compared • Soil microbial network structure and linkages between genera were altered • CFF improves straw degradation via positive interactions between soil microbes.

Response characteristics of indigenous microbial community in polycyclic aromatic hydrocarbons (PAHs) contaminated aquifers under polyethylene microplastics stress: A microcosmic experimental study

To understand the response characteristics of indigenous microbial community in PAH-contaminated aquifers to the coexistence of microplastics. In this paper, we constructed a groundwater microecosystem using lithologic media collected from the field and subjected it to the stress of a polyethylene microplastics (PE-MPs) concentration gradient. By conducting adsorption experiments and 16S rRNA sequencing, we revealed the growth, structure, metabolism, and resistance mechanisms of the indigenous microbial community in the aquifer lithologic media exposed to varying levels of co-stress from PE-MPs and phenanthrene. Our findings suggest that the adsorption capacity of aquifer lithologic media for phenanthrene is significantly weaker than that of PE-MPs. Additionally, our observations indicated that small particle lithologic media had a greater adsorption capacity for phenanthrene than large particle lithologic media. The presence of PE-MPs was found to increase both the abundance and diversity of microbial communities, although the relationship was not linear with the content of PE-MPs. When exposed to the combined stress of PE-MPs and phenanthrene, the relative abundance of Proteobacteria decreased while that of Bacteroidetes increased. Several genera belonging to Proteobacteria (Aeromonas, Desulfovibrio, Klebsiella, Pantoea, and Microvirgula) and Bacteroidetes (Macellibacteroides and Bacteroides) occupied a central position in the microbial community interaction network and showed significant correlations with other genera. Furthermore, an increase in the proportion of genera capable of degrading various refractory organics was observed. The presence of PE-MPs increased the phenanthrene content in the aquifer lithologic media, thereby intensifying the inhibitory effect on indigenous microbial community in this environment. Despite an increase in the phenanthrene content of aquifer lithologic media due to the presence of PE-MPs, indigenous microbial community in this environment exhibited resistance to the combined inhibition of PE-MPs and phenanthrene through a series of resistance mechanisms. These mechanisms included strengthening the N-cycle process, enhancing metabolic capacity for phenanthrene, improving perception, response, and adaptation to changes in the external environment or intracellular state, modifying the transmembrane transport of the cell membrane to the substrate, and regulating life processes.

Efficient degradation of rice straw through a novel psychrotolerant Bacillus cereus at low temperature

BACKGROUND

Rice straw (RS) is one of the largest sources of lignocellulosic, which is an abundant raw material for biofuels and chemicals. However, the natural degradation of RS under a low temperature environment is the biggest obstacle to returning straw to the field.

RESULTS

In the present study, one bacillus strain W118 was isolated. Strain W118 was identified as Bacillus cereus through morphological and physiological characterization and 16S rDNA sequencing. The optimum growth temperature and pH of strain W118 were 20 °C and 6.5, respectively. Simultaneously, it was found that the strain W118 grew well at low temperature, even at a temperature of 4 °C (OD₆₀₀  = 1.40 ± 0.01). The decrease of various compositions of RS after the fermentation process at a temperature of 20 °C and 4 °C for 14 days was 27.00 ± 0.02% and 23.70 ± 0.04%, respectively. The composition of RS decreased to 50.71 ± 0.02% after being fermented at 4 °C for 25 days. The results of scanning electron microscopy, Fourier transform infrared spectroscopy and X-ray diffraction of RS showed that the compositions of RS were significant decreased.

CONCLUSION

This test suggests that the strain W118 is efficient for degrading RS at low temperature, which has great application potential for straw degradation in a low temperature area. © 2022 Society of Chemical Industry.

Assembly strategies for polyethylene-degrading microbial consortia based on the combination of omics tools and the "Plastisphere"

Numerous microorganisms and other invertebrates that are able to degrade polyethylene (PE) have been reported. However, studies on PE biodegradation are still limited due to its extreme stability and the lack of explicit insights into the mechanisms and efficient enzymes involved in its metabolism by microorganisms. In this review, current studies of PE biodegradation, including the fundamental stages, important microorganisms and enzymes, and functional microbial consortia, were examined. Considering the bottlenecks in the construction of PE-degrading consortia, a combination of top-down and bottom-up approaches is proposed to identify the mechanisms and metabolites of PE degradation, related enzymes, and efficient synthetic microbial consortia. In addition, the exploration of the plastisphere based on omics tools is proposed as a future principal research direction for the construction of synthetic microbial consortia for PE degradation. Combining chemical and biological upcycling processes for PE waste could be widely applied in various fields to promote a sustainable environment.

Lignocellulose dissociation with biological pretreatment towards the biochemical platform: A review

Lignocellulose utilization has been gaining great attention worldwide due to its abundance, accessibility, renewability and recyclability. Destruction and dissociation of the cross-linked, hierarchical structure within cellulose hemicellulose and lignin is the key procedure during chemical utilization of lignocellulose. Of the pretreatments, biological treatment, which can effectively target the complex structures, is attractive due to its mild reaction conditions and environmentally friendly characteristics. Herein, we report a comprehensive review of the current biological pretreatments for lignocellulose dissociation and their corresponding degradation mechanisms. Firstly, we analyze the layered, hierarchical structure of cell wall, and the cross-linked network between cellulose, hemicellulose and lignin, then highlight that the cracking of β-aryl ether is considered the key to lignin degradation because of its dominant position. Secondly, we explore the effect of biological pretreatments, such as fungi, bacteria, microbial consortium, and enzymes, on substrate structure and degradation efficiency. Additionally, combining biological pretreatment with other methods (chemical methods and catalytic materials) may reduce the time necessary for the whole process, which also help to strengthen the lignocellulose dissociation efficiency. Thirdly, we summarize the related applications of lignocellulose, such as fuel production, chemicals platform, and bio-pulping, which could effectively alleviate the energy pressure through bioconversion into high value-added products. Based on reviewing of current progress of lignocellulose pretreatment, the challenges and future prospects are emphasized. Genetic engineering and other technologies to modify strains or enzymes for improved biotransformation efficiency will be the focus of future research.

Community succession and functional prediction of microbial consortium with straw degradation during subculture at low temperature

To systematically explore and analyze the microbial composition and function of microbial consortium M44 with straw degradation in the process of subculture at low temperature. In this study, straw degradation characteristics of samples in different culture stages were determined. MiSeq high-throughput sequencing technology was used to analyze the evolution of community structure and its relationship with degradation characteristics of microbial consortium in different culture periods, and the PICRUSt function prediction analysis was performed. The results showed that straw degradation rate, endoglucanase activity, and filter paper enzyme activity of M44 generally decreased with increasing culture algebra. The activities of xylanase, laccase, and lignin peroxidase, as well as VFA content, showing a single-peak curve change with first an increase and then decrease. In the process of subculture, Proteobacteria, Bacteroidetes, and Firmicutes were dominant in different culture stages. Pseudomonas, Flavobacterium, Devosia, Brevundimonas, Trichococcus, Acinetobacter, Dysgonomonas, and Rhizobium were functional bacteria in different culture stages. It was found by PICRUSt function prediction that the functions were concentrated in amino acid transport and metabolism, carbohydrate transship and metabolism related genes, which may contain a large number of fibers and lignin degrading enzyme genes. In this study, the microbial community succession and the gene function in different culture periods were clarified and provide a theoretical basis for screening and rational utilization of microbial consortia.

Dynamic changes in community structure and degradation performance of a bacterial consortium MMBC-1 during the subculturing revival reveal the potential decomposers of lignocellulose

Bacterial consortium is an important source of lignocellulolytic strains, but it is still a challenge to distinguish the direct decomposers of lignocellulose from other bacteria in such a complex community. This study aims at addressing this issue by focusing on the dynamic changes in community structure and degradation activity of MMBC-1, an established and stable lignocellulolytic bacterial consortium, during its subculturing revival. MMBC-1 was cryopreserved with glycerol as a protective agent and then inoculated for revival. Its enzyme activities for degradation recovered to the maximum level after two rounds of subculturing. Correspondingly, the cellulose and hemicellulose in lignocellulosic carbon source were gradually decomposed during the revival. Meanwhile, the initial dominant bacteria represented by genus Clostridium were replaced by the bacteria belonging to Lachnospira, Enterococcus, Bacillus, Haloimpatiens genera and family Lachnospiraceae. However, only three high-abundance (> 1%) operational taxonomic units (OTUs) (Lachnospira, Enterococcus and Haloimpatiens genera) were suggested to directly engage in lignocellulose degradation according to correlation analysis. By comparison, many low-abundance OTUs, such as the ones belonging to Flavonifractor and Anaerotruncus genera, may play an important role in degradation. These findings showed the dramatic changes in community structure that occurred during the subculturing revival, and paved the way for the discovery of direct decomposers in a stable consortium.

Potential and mechanism for bioremediation of papermaking black liquor by a psychrotrophic lignin-degrading bacterium, Arthrobacter sp. C2

To meet the challenge of bioremediation of black liquor in pulp and paper mills at low temperatures, a psychrotrophic lignin-degrading bacterium was employed in black liquor treatment for the first time. In this study, Arthrobacter sp. C2 exhibited excellent cold adaptability and lignin degradation ability, with a lignin degradation rate of 65.5% and a mineralization rate of 43.9% for 3 g/L lignin at 15 °C. Bioinformatics analysis and multiple experiments confirmed that cold shock protein 1 (Csp1) was the dominant cold regulator of strain C2, and dye-decolorizing peroxidase (DyP) played a crucial role in lignin degradation. Moreover, structural equation modeling (SEM), mRNA monitoring, and phenotypic variation analysis demonstrated that Csp1 not only mediated cold adaptation but also modulated DyP activity by controlling dyp gene expression, thus driving lignin depolymerization for strain C2 at low temperatures. Furthermore, 96.4% of color, 64.2% of chemical oxygen demand (COD), and 100% of nitrate nitrogen (NO₃--N) were removed from papermaking black liquor by strain C2 within 15 days at 15 °C. This study provides insights into the association between the cold regulator and catalytic enzyme of psychrotrophic bacteria and offers a feasible alternative strategy for the bioremediation of papermaking black liquor in cold regions.

Enrichment culture combined with microbial electrochemical enhanced low-temperature anaerobic digestion of cow dung

Enrichment culture combined with the microbial electrochemical system was used to co-enhance the low-temperature (20 °C) anaerobic digestion. The results showed that enrichment culture combined with microbial electrochemical system increased the cumulative methane production in low-temperature anaerobic digestion system by 39.64 % and 133.29 % compared to single and no enrichment culture, respectively. Enrichment culture combined with microbial electrochemical system increased the relative abundance of methanogenic archaea (Methanomassiliicoccus, Methanocorpusculum, unclassified Methanomicrobiaceae, Methanobacterium, Methanoculleus, Methanocalculus) and the relative abundance of cold-tolerant hydrolytic acidifying bacteria (unclassified Bacteroidetes, Treponema). The expressions of specific enzyme genes in the methanogenesis pathway were enhanced, including acetyl-CoA synthetase, formylmethanofuran dehydrogenase, methanol cobalamin methyltransferase, etc. These results indicated that enrichment culture combined with microbial electrochemical system enhanced low-temperature anaerobic digestion methanogenesis by altering microbial communities and stimulating enzyme gene expression to affect volatile fatty acids, pH, redox potential, and reducing sugar parameters.

Community succession and straw degradation characteristics using a microbial decomposer at low temperature

This study explored changes in the microbial community structure during straw degradation by a microbial decomposer, M44. The microbial community succession at different degradation periods was analyzed using MiSeq high-throughput sequencing. The results showed that 14 days after inoculation, the filter paper enzyme and endoglucanase activities increased to 2.55 U·mL^-1 and 2.34 U·mL^-1. The xylanase, laccase, and lignin peroxidase activities rose to 9.86 U·mL^-1, 132.16 U·L^-1, and 85.43 U·L^-1 after 28 d, which was consistent with changes in the straw degradation rate. The degradation rates of straw, lignin, cellulose, and hemicellulose were 31.43%, 13.67%, 25.04%, and 21.69%, respectively, after 28 d of fermentation at 15°C. Proteobacteria, Firmicutes, and Bacteroidetes were the main bacterial species in samples at different degradation stages. The dominant genera included Pseudomonas, Delftia, and Paenibacillus during the initial stage (1 d, 7 d) and the mid-term stage (14 d). The key functional microbes during the late stage (21 d, 28 d) were Rhizobium, Chryseobacterium, Sphingobacterium, Brevundimonas, and Devosia. Changes in the bacterial consortium structure and straw degradation characteristics during different degradation periods were clarified to provide a theoretical basis for the rational utilization of microbial decomposer M44.

Augmentation characteristics and microbial community dynamics of low temperature resistant composite strains LTF-27

Biogas production in the cold regions of China is hindered by low temperatures, which led to slow lignocellulose biotransformation. Cold-adapted lignocellulose degrading microbial complex community LTF-27 was used to investigate the influence of hydrolysis on biogas production. After 5 days of hydrolysis at 15 ± 1 °C, the hydrolysis conversion rate of the corn straw went up to 22.64%, and the concentration of acetic acid increased to 2596.56 mg/L. The methane production rates of total solids (TS) inoculated by LTF-27 reached 204.72 mL/g, which was higher than the biogas (161.34 mL/g), and the control group (CK) inoculated with cultural solution (121.19 mL/g), the methane production rate of volatile solids (VS) increased by 26.88% and 68.92%, respectively. Parabacteroides, Lysinibacillus, and Citrobacter were the main organisms that were responsible for hydrolysis. While numerous other bacteria genera in the gas-producing phase, Macellibacteroides were the most commonly occurring one. Methanosarcina and Methanobacteriaceae contributed 86.25% and 11.80% of the total Archaea abundance during this phase. This study proves the psychrotrophic LTF-27's applicability in hydrolysis and biomass gas production in low temperatures.

The Unexplored Wealth of Microbial Secondary Metabolites: the Sphingobacteriaceae Case Study

Research on secondary metabolites (SMs) has been mostly focused on Gram-positive bacteria, especially Actinobacteria. The association of genomics with robust bioinformatics tools revealed the neglected potential of Gram-negative bacteria as promising sources of new SMs. The family Sphingobacteriaceae belongs to the phylum Bacteroidetes having representatives in practically all environments including humans, rhizosphere, soils, wastewaters, among others. Some genera of this family have demonstrated great potential as plant growth promoters, bioremediators and producers of some value-added compounds such as carotenoids and antimicrobials. However, to date, Sphingobacteriaceae's SMs are still poorly characterized, and likewise, little is known about their chemistry. This study revealed that Sphingobacteriaceae pangenome encodes a total of 446 biosynthetic gene clusters (BGCs), which are distributed across 85 strains, highlighting the great potential of this bacterial family to produce SMs. Pedobacter, Mucilaginibacter and Sphingobacterium were the genera with the highest number of BGCs, especially those encoding the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), terpenes, polyketides and nonribosomal peptides (NRPs). In Mucilaginibacter and Sphingobacterium genera, M. lappiensis ATCC BAA-1855, Mucilaginibacter sp. OK098 (both with 11 BGCs) and Sphingobacterium sp. 21 (6 BGCs) are the strains with the highest number of BGCs. Most of the BGCs found in these two genera did not have significant hits with the MIBiG database. These results strongly suggest that the bioactivities and environmental functions of these compounds, especially RiPPs, PKs and NRPs, are still unknown. Among RiPPs, two genera encoded the production of class I and class III lanthipeptides. The last are associated with LanKC proteins bearing uncommon lyase domains, whose dehydration mechanism deserves further investigation. This study translated genomics into functional information that unveils the enormous potential of environmental Gram-negative bacteria to produce metabolites with unknown chemistries, bioactivities and, more importantly, unknown ecological roles.

Coconut Mesocarp-Based Lignocellulosic Waste as a Substrate for Cellulase Production from High Promising Multienzyme-Producing Bacillus amyloliquefaciens FW2 without Pretreatments

Facing the crucial issue of high cost in cellulase production from commercial celluloses, inexpensive lignocellulosic materials from agricultural wastes have been attractive. Therefore, several studies have focused on increasing the efficiency of cellulase production by potential microorganisms capable of secreting a high and diversified amount of enzymes using agricultural waste as valuable substrates. Especially, extremophilic bacteria play an important role in biorefinery due to their high value catalytic enzymes that are active even under harsh environmental conditions. Therefore, in this study, we aim to investigate the ability to produce cellulase from coconut-mesocarp of the potential bacterial strain FW2 that was isolated from kitchen food waste in South Korea. This strain was tolerant in a wide range of temperature (−6–75 °C, pH range (4.5–12)) and at high salt concentration up to 35% NaCl. The molecular weight of the purified cellulase produced from strain FW2 was estimated to be 55 kDa. Optimal conditions for the enzyme activity using commercial substrates were found to be 40–50 °C, pH 7.0–7.5, and 0–10% NaCl observed in 920 U/mL of CMCase, 1300 U/mL of Avicelase, and 150 U/mL of FPase. It was achieved in 650 U/mL, 720 U/mL, and 140 U/mL of CMCase, Avicelase, and FPase using coconut-mesocarp, respectively. The results revealed that enzyme production by strain FW2 may have significant commercial values for industry, argo-waste treatment, and other potential applications.

Contemporary proteomic research on lignocellulosic enzymes and enzymolysis: A review

This review overviewed the current researches on the isolation of novel strains, the development of novel identification protocols, the key enzymes and their synergistic interactions with other functional enzyme systems, and the strategies for enhancing enzymolysis efficiencies. The main obstacle for realizing biorefinery of lignocellulosic biomass to biofuels or biochemicals is the high cost of enzymolysis stage. Therefore, research prospects to reduce the costs for lignocellulose hydrolysis were outlined.

Distribution patterns of functional microbial community in anaerobic digesters under different operational circumstances: A review

Anaerobic digestion (AD) processes are promising to effectively recover resources from organic wastes or wastewater. As a microbial-driven process, the functional anaerobic species played critical roles in AD. However, the lack of effective understanding of the correlations of varying microbial communities with different operational factors hinders the microbial regulation to improve the AD performance. In this paper, the main anaerobic functional microorganisms involved in different stages of AD processes were first demonstrated. Then, the response of anaerobic microbial community to different operating parameters, exogenous interfering substances and digestion substrates, as well as the digestion efficiency, were discussed. Finally, the research gaps and future directions on the understanding of functional microorganisms in AD were proposed. This review provides insightful knowledge of distribution patterns of functional microbial community in anaerobic digesters, and gives critical guidance to regulate and enrich specific functional microorganisms to accumulate certain AD products.

Degradation of lignocelluloses in straw using AC-1, a thermophilic composite microbial system

In composting, the degradation of lignocellulose in straw is problematic due to its complex structures such as lignin. A common solution to this problem is the addition of exogenous inoculants. AC-1, a stable thermophilic microbial composite, was isolated from high temperature compost samples that can decompose lignocellulose at 50–70 °C. AC-1 had a best degradation efficiency of rice straw at 60 °C (78.92%), of hemicellulose, cellulose and lignin were 82.49%, 97.20% and 20.12%, respectively. It showed degrad-ability on both simple (filter paper, absorbent cotton) and complex (rice straw) cellulose materials. It produced acetic and formic acid during decomposition process and the pH had a trend of first downward then upward. High throughput sequencing revealed the main bacterial components of AC-1 were Tepidimicrobium, Haloplasma, norank-f-Limnochordaceae, Ruminiclostridium and Rhodothermus which provides major theoretical basis for further application of AC-1.

Structure-function elucidation of a microbial consortium in degrading rice straw and producing acetic and butyric acids via metagenome combining 16S rDNA sequencing

The characterized microbial consortium can efficiently degrade rice straw to produce acetic and butyric acids in high yields. The rice straw lost 86.9% in weight and degradation rates of hemicellulose, cellulose, and lignin attained were 97.1%, 86.4% and 70.3% within 12 days, respectively. During biodegradation via fermentation of rice straw, average concentrations of acetic and butyric acids reached 1570 mg/L and 1270 mg/L, accounting for 47.2% and 35.4% of the total volatile fatty acids, respectively. The consortium mainly composed of Prevotella, Cellulosilyticum, Pseudomonas, Clostridium and Ruminococcaceae, etc. Metagenomic analyses indicated that glycoside hydrolases (GHs) were the largest enzyme group with a relative abundance of 54.5%. Various lignocellulose degrading enzymes were identified in the top 30 abundant GHs, and were primarily distributed in the dominant genera (Prevotella, Cellulosilyticum and Clostridium). These results provide a new route for the commercial recycling of rice straw to produce organic acids.

Microbial communities and their enzymes facilitate degradation of recalcitrant polymers in anaerobic digestion

Microbial consortia efficiently degrade complex biopolymers found in the organic fraction of municipal solid waste (OFMSW). Through enzyme production and division of labor during anaerobic digestion, microbial communities break down recalcitrant polymers and make fermentation products, including methane. However, microbial communities remain underutilized for waste degradation as it remains difficult to characterize and predict microbial interactions during waste breakdown, especially as cultivation conditions change drastically throughout anaerobic digestion. This review discusses recent progress and opportunities in cultivating natural and engineered consortia for OFMSW hydrolysis, including how recalcitrant substrates are degraded by enzymes as well as the critical factors that govern microbial interactions and culture stability. Methods to measure substrate degradation are also reviewed, and we demonstrate the need for increased standardization to enable comparisons across different environments.

A Review on Bacterial Contribution to Lignocellulose Breakdown into Useful Bio-Products

Discovering novel bacterial strains might be the link to unlocking the value in lignocellulosic bio-refinery as we strive to find alternative and cleaner sources of energy. Bacteria display promise in lignocellulolytic breakdown because of their innate ability to adapt and grow under both optimum and extreme conditions. This versatility of bacterial strains is being harnessed, with qualities like adapting to various temperature, aero tolerance, and nutrient availability driving the use of bacteria in bio-refinery studies. Their flexible nature holds exciting promise in biotechnology, but despite recent pointers to a greener edge in the pretreatment of lignocellulose biomass and lignocellulose-driven bioconversion to value-added products, the cost of adoption and subsequent scaling up industrially still pose challenges to their adoption. However, recent studies have seen the use of co-culture, co-digestion, and bioengineering to overcome identified setbacks to using bacterial strains to breakdown lignocellulose into its major polymers and then to useful products ranging from ethanol, enzymes, biodiesel, bioflocculants, and many others. In this review, research on bacteria involved in lignocellulose breakdown is reviewed and summarized to provide background for further research. Future perspectives are explored as bacteria have a role to play in the adoption of greener energy alternatives using lignocellulosic biomass.

Zerovalent Iron Effectively Enhances Medium-Chain Fatty Acids Production from Waste Activated Sludge through Improving Sludge Biodegradability and Electron Transfer Efficiency

A novel zerovalent iron (ZVI) technique to simultaneously improve the production of medium-chain fatty acids (MCFAs) from waste activated sludge (WAS) and enhance WAS degradation during anaerobic WAS fermentation was proposed in this study. Experimental results showed that the production and selectivity of MCFAs were effectively promoted when ZVI was added at 1-20 g/L. The maximum MCFAs production of 15.4 g COD (Chemical Oxygen Demand)/L and MCFAs selectivity of 71.7% were both achieved at 20 g/L ZVI, being 5.3 and 4.8 times that without ZVI (2.9 g COD/L and 14.9%). Additionally, ZVI also promoted WAS degradation, which increased from 0.61 to 0.96 g COD/g VS when ZVI increased from 0 to 20 g/L. The microbial community analysis revealed that the ZVI increased the populations of key anaerobes related to hydrolysis, acidification, and chain elongation. Correspondingly, the solubilization, hydrolysis, and acidification processes of WAS were revealed to be improved by ZVI, thereby providing more substrates (short-chain fatty acids (SCFAs)) for producing MCFAs. The mechanism studies showed that ZVI declined the oxidation-reduction potential (ORP), creating a more favorable environment for the anaerobic biological processes. More importantly, ZVI with strong conductivity could act as an electron shuttle, contributing to increasing electron transfer efficiency from electron donor to acceptor. This strategy provides a new paradigm of transforming waste sludge into assets by a low-cost waste to bring significant economic benefits to sludge disposal and wastewater treatment.