Screening of a microbial consortium for highly simultaneous degradation of lignocellulose and chlorophenols

The impact of Ricinus straw on tomato growth and soil microbial community

Returning straw can alter the soil microbial community, reduce the occurrence of soilborne diseases, and promote plant growth. In this study, we aimed to evaluate the effects of Ricinus straw on tomato growth and rhizosphere microbial community. We carried out microcosm experiments to investigate the effects of Ricinus straw with different dosages (0, 1, and 3%) on tomato dry biomass and rhizosphere bacterial and fungal communities. The results indicated that the dry biomass of tomato seedlings with 1% addition of Ricinus straw increased by 53.98%. In addition, Ricinus straw also changed the abundance, diversities, and composition of tomato rhizosphere microbial communities. In detail, the addition of 1% Ricinus straw increased the relative abundance of putative beneficial bacteria and fungi in straw decomposition, such as Ramlibacter sp., Azohydromonas sp., Schizothecium sp., and Acaulium sp., and decreased the relative abundance of Fusarium sp. Meanwhile, Ricinus straw inhibited the growth of putative pathogenic microorganisms. The correlation analysis showed that the changes in fungal community operational taxonomic units stimulated by the addition of Ricinus straw may play a crucial positive regulatory role in tomato growth. Finally, the representative fungal strain Fusarium oxysporum f. sp. Lycopersici (FOL), named TF25, was isolated and cultured. We found that Ricinus straw extract inhibited the growth of TF25 in an in vitro experiment with an inhibition rate of 34.95-51.91%. Collectively, Ricinus straw promoted plant growth by changing the rhizosphere microbial community composition and inhibiting FOL growth, which provides new evidence for understanding the improvement of key microorganism composition in improving crop growth and the sustainability of agriculture.

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.

Exploring the optimization of aerobic food waste digestion efficiency through the engineering of functional biofilm Bio-carriers

The possibility of breaking down cellulose-rich food waste through biofilm engineering was investigated. Six previously isolated strains from naturally degrading fruits and vegetables, screened for biofilm-forming ability and cellulolytic activity, were selected to enrich a biocarrier seeding microbial consortium. The food waste model used in this study was cabbage which was aerobically digested under repeated water rinsing and regular effluent drainage. The engineered biocarrier biofilm's functionality was evaluated by tracing microbial succession following metagenomic sequencing, quantitative PCR, scanning electron microscopy, and cellulolytic activity before and after the digestion processes. The engineered microbial consortium demonstrated superior biofilm-forming ability on biocarriers than the original microbial consortium and generally displayed a higher cellulolytic activity. The presented study provides one of the few studies of food waste aerobic digestion using engineered biofilms. Insights presented in this study could help further optimize aerobic food waste digestion.

Challenges and opportunities for the biodegradation of chlorophenols: Aerobic, anaerobic and bioelectrochemical processes

Chlorophenols (CPs) are highly toxic and refractory contaminants which widely exist in various environments and cause serious harm to human and environment health and safety. This review provides comprehensive information on typical CPs biodegradation technologies, the most green and benign ones for CPs removal. The known aerobic and anaerobic degradative bacteria, functional enzymes, and metabolic pathways of CPs as well as several improving methods and critical parameters affecting the overall degradation efficiency are systematically summarized and clarified. The challenges for CPs mineralization are also discussed, mainly including the dechlorination of polychlorophenols (poly-CPs) under aerobic condition and the ring-cleavage of monochlorophenols (MCPs) under anaerobic condition. The coupling of functional materials and degraders as well as the operation of sequential anaerobic-aerobic bioreactors and bioelectrochemical system (BES) are promising strategies to overcome some current limitations. Future perspective and research gaps in this field are also proposed, including the further understanding of microbial information and the specific role of materials in CPs biodegradation, the potential application of innovative biotechnologies and new operating modes to optimize and maximize the function of the system, and the scale-up of bioreactors towards the efficient biodegradation of CPs.

Enhanced anaerobic digestion performance by two artificially constructed microbial consortia capable of woody biomass degradation and chlorophenols detoxification

Catalpa sawdust (CSW) is a promising biomass-based biofuel. However, the complex lignocellulosic structure limits its efficient utilization in biorefinery applications. It is even more so when chlorophenols (CPs), highly toxic organic substances widely used as wood preservatives, are present. Hence, it is crucial to develop effective and eco-friendly approaches to attain deconstruction of lignocellulose and chlorophenols simultaneously as well as to improve methane (CH4) production efficiently. This study might be the first to explore the performance of the novel constructed microbial consortia CS-5 and BC-4 on woody biomass degradation and CPs detoxification simultaneously with CH4 production. After the degradation of CSW and CPs for 15 days by C5-5 or BC-4, significant reduction in lignocellulosic components and CPs mixture was realized with a total weight loss of 69.2 and 56.3 % and CPs degradation of 89 and 95 %, respectively. The toxicity of individual or mixed CPs after 15 days of degradation was reduced by approximately 90 %. The synergistic action of CS-5 and BC-4 enhanced biogas and CH4 yields over 76 and 64 % respectively, higher than control. Furthermore, CH4 production increased by 113.7 % at the peak phase of AD process. Methanosataceae represented 45.1 % of the methanogenic Archaea in digester G-III.

Construction of novel microbial consortia CS-5 and BC-4 valued for the degradation of catalpa sawdust and chlorophenols simultaneously with enhancing methane production

This study might be the first to explore the novel constructed microbial consortia CS-5 and BC-4 for enhancing methane (CH₄) production during anaerobic digestion (AD) with simultaneous degradation of catalpa sawdust and chlorophenols (CPs). Significant reduction in cellulose, hemicellulose and lignin contents was achieved after the biodegradation of catalpa sawdust for 15 days by CS-5 and BC-4, with a total weight loss of 69.2 and 56.3%, respectively. The synergistic microbial consortia enhanced cumulative biogas and CH₄ yields by 76.3 and 64.3%, respectively higher than the corresponding control at the end of AD. More than 90% of CH₄ was produced within 18 days of AD as a result of microbial pretreatment of catalpa sawdust. These consortia resulted in remarkably higher energy conversion efficiency of 44.3% (218.1 L_N CH₄/kg TS) over the control. CS-5 and BC-4 removed more than 69 and 77% of the total amount of CPs tested after 15 days.

Validation of effective roles of non-electroactive microbes on recalcitrant contaminant degradation in bioelectrochemical systems

Bioelectrochemical systems (BESs) have been widely investigated for recalcitrant waste treatment mainly because of their waste removal effectiveness. Electroactive microbes (EMs) have long been thought to contribute to the high effectiveness by interacting with electrodes via electron chains. However, this work demonstrated the dispensable role of EMs for enhanced recalcitrant contamination degradation in BESs. We revealed enhanced p-fluoronitrobenzene (p-FNB) degradation in a BES by observing a defluorination efficiency that was three times higher than that in biodegradation or electrochemical processes. Such an improvement was achieved by the collaborative roles of electrode biofilms and planktonic microbes, as their individual contributions to p-FNB degradation were found to be similarly stimulated by electricity. However, no bioelectrochemical activity was found in either the electrode biofilms or the planktonic microbes during stimulated p-FNB degradation; because no biocatalytically reductive or oxidative turnovers were observed on cyclic voltammetry curves. The non-involvement of EMs was further proven by the similar microbial community evolution for biofilms and planktonic microbes. In summary, we proposed a mechanism for indirect electrical stimulation of microbial metabolism by electrochemically generating the active mediator p-fluoroaniline (p-FA) and further degradation by a sequential combination of electrochemical p-FNB reduction and biological p-FA oxidation by non-EMs.

Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation

Enriched microbial communities, obtained from environmental samples through selective processes, can effectively contribute to lignocellulose degradation. Unfortunately, fully controlled industrial degradation processes are difficult to reach given the intrinsically dynamic nature and complexity of the microbial communities, composed of a large number of culturable and unculturable species. The use of less complex but equally effective microbial consortia could improve their applications by allowing for more controlled industrial processes. Here, we combined ecological theory and enrichment principles to develop an effective lignocellulose-degrading minimal active microbial Consortia (MAMC). Following an enrichment of soil bacteria capable of degrading lignocellulose material from sugarcane origin, we applied a reductive-screening approach based on molecular phenotyping, identification, and metabolic characterization to obtain a selection of 18 lignocellulose-degrading strains representing four metabolic functional groups. We then generated 65 compositional replicates of MAMC containing five species each, which vary in the number of functional groups, metabolic potential, and degradation capacity. The characterization of the MAMC according to their degradation capacities and functional diversity measurements revealed that functional diversity positively correlated with the degradation of the most complex lignocellulosic fraction (lignin), indicating the importance of metabolic complementarity, whereas cellulose and hemicellulose degradation were either negatively or not affected by functional diversity. The screening method described here successfully led to the selection of effective MAMC, whose degradation potential reached up 96.5% of the degradation rates when all 18 species were present. A total of seven assembled synthetic communities were identified as the most effective MAMC. A consortium containing Stenotrophomonas maltophilia, Paenibacillus sp., Microbacterium sp., Chryseobacterium taiwanense, and Brevundimonas sp. was found to be the most effective degrading synthetic community.

Dynamic succession of substrate-associated bacterial composition and function during Ganoderma lucidum growth

Background

Ganoderma lucidum, a valuable medicinal fungus, is widely distributed in China. It grows alongside with a complex microbial ecosystem in the substrate. As sequencing technology advances, it is possible to reveal the composition and functions of substrate-associated bacterial communities.

Methods

We analyzed the bacterial community dynamics in the substrate during the four typical growth stages of G. lucidum using next-generation sequencing.

Results

The physicochemical properties of the substrate (e.g. acidity, moisture, total nitrogen, total phosphorus and total potassium) changed between different growth stages. A total of 598,771 sequences from 12 samples were obtained and assigned to 22 bacterial phyla. Proteobacteria and Firmicutes were the dominant phyla. Bacterial community composition and diversity significantly differed between the elongation stage and the other three growth stages. LEfSe analysis revealed a large number of bacterial taxa (e.g. Bacteroidetes, Acidobacteria and Nitrospirae) with significantly higher abundance at the elongation stage. Functional pathway prediction uncovered significant abundance changes of a number of bacterial functional pathways between the elongation stage and other growth stages. At the elongation stage, the abundance of the environmental information processing pathway (mainly membrane transport) decreased, whereas that of the metabolism-related pathways increased.

Discussion

The changes in bacterial community composition, diversity and predicted functions were most likely related to the changes in the moisture and nutrient conditions in the substrate with the growth of G. lucidum, particularly at the elongation stage. Our findings shed light on the G. lucidum-bacteria-substrate relationships, which should facilitate the industrial cultivation of G. lucidum.

A new screened microbial consortium OEM2 for lignocellulosic biomass deconstruction and chlorophenols detoxification

Recalcitrance limits biomass application in biorefinery. It is even more so when toxic chlorophenols are present. In this study, we screened a microbial consortium, OEM2, for lignocellulose deconstruction and chlorophenols detoxification through a short-term and efficient screening process. Microbial consortium OEM2 had a good buffer capability in the cultivation process and exhibited a high xylanase activity, with over 85% hemicellulose degradation within 12 days. Throughout the treatment process, 41.5% rice straw decomposition on day 12 and around 75% chlorophenols (MCP, 2,4-DCP, 2,4,6-TCP) removal on day 9, were recorded. Moreover, Fourier translation infrared spectroscopy (FTIR) analysis indicated that chemical bonds and groups (eg. hydrogen-bond, β-1,4 glycosidic bond, lignin-carbohydrate cross-linking) in the rice straw were broken. Cuticle and silica layer destruction and subsequent exposed cellulose fibers were observed by scanning electron microscopy (SEM). Microbial consortium OEM2 diversity analysis by 16S rRNA gene sequencing indicated that Proteobacteria (41.3%) was the most abundant phylum and the genera Paenibacillus and Pseudomonas played an important role in the lignocellulose decomposition and chlorophenols detoxification. This study developed a faster and more efficient strategy to screen a specific microbial consortium. And the new microbial consortium, OEM2, makes lignocellulose more accessible and complex pollutants unproblematic in the further biorefinery process.

Screening of a microbial consortium for selective degradation of lignin from tree trimmings

To acquire microbial consortia with effectively precedent degradation of lignin, samples obtained from rotten trunks, rotten stumps and soil near it were screened and isolated after generations of subculture. The dynamic change illustrated that their community structures were affected by pH and tended to be stable after 6 days' cultivation. The desired one, named DM-1, was gained through successive cultivation for over 5 generations, whose high selectivity in lignin degradation was observed within 16 days' cultivation (SV = 2.78). Meanwhile, a remarkable reduction in the fiber crystallinity of tree trimmings (10.35%) resulted from the bio-degradation of DM-1, displayed a greater exposure of cellulose by selective removal of lignin. The diversity analysis of DM-1 was investigated by PCR amplification and 16S rDNA sequencing, indicated that mesorhizobium, cellulosimicrobium, pandoraea, achromobacter and stenotrophomones were the predominant genera. Furthermore, fungi (3 strains), bacteria (4 strains) and actinomycetes (5 strains) constituted 12 strains in total were gained by plate isolation from DM-1.

Microbial consortium OEM1 cultivation for higher lignocellulose degradation and chlorophenol removal

Herein, microbial consortium OEM1 that could simultaneously decompose lignocellulose and chlorophenols was screened from spent mushroom substrates.

Eichhornia crassipes: Agro-waster for a novel thermostable laccase production by Pycnoporus sanguineus SYBC-L1

The aim of this study was to explore the utilization of an intractable waster of Eichhornia crassipes in laccase production by Pycnoporus sanguineus SYBC-L1. E. crassipes as the sole carbon and nitrogen source was confirmed to produce laccase (7.26 U/g dry substrate). The fermentation medium for the maximum enzyme production was optimized and the laccase was then purified and characterized. The optimized culture medium was 25.1% E. crassipes, 13.9% sawdust, 1.5 mM CuSO₄, 40 μM gallic acid, 65% moisture content and initial pH 6.0. A maximum laccase activity of 32.02 U/g dry substrate was detected at 9th day, which was 4.5-fold compared to the initial medium. The molecular mass of the purified Lac-S was 58.4 kDa. The optimum activity of Lac-S for DMP was at pH 3.0 and 70°C. Lac-S showed not only high catalytic activities at low temperature, but also good stabilities toward pH and temperature. The residual catalytic activities of Lac-S were 30%, 40% and 50% at 0°C, 10°C and 20°C, and the half-lives at 50°C, 60°C and 70°C were 21.7, 9.7 and 1.5 h, respectively. The results provide a significant basis for E. crassipes further utilization and Lac-S specific application in harsh industry.