Dynamics of Abundant and Rare Bacteria During Degradation of Lignocellulose from Sugarcane Biomass

Exploring alkali-treated corn cob for high-rate removal of NOX and SO2 from flue gas: Focus on carbon release capacity, removal performance, and comparison with conventional carbon sources

This investigation explored the potential of utilizing alkali-treated corn cob (CC) as a solid carbon source to improve NOX and SO2 removal from flue gas. Leaching experiments unveiled a hierarchy of chemical oxygen demand release capacity: 0.03 mol/L alkali-treated CC > 0.02 mol/L > 0.01 mol/L > 0.005 mol/L > control. In NOX and SO2 removal experiments, as the inlet NOX concentration rose from 300 to 1000 mg/m3, the average NOX removal efficiency increased from 58.56 % to 80.00 %. Conversely, SO2 removal efficiency decreased from 99.96 % to 91.05 %, but swiftly rebounded to 98.56 % by day 18. The accumulation of N intermediates (NH4+, NO3-, NO2-) increased with escalating inlet NOX concentration, while the accumulation of S intermediates (SO42-, SO32-, S0) varied based on shifts in the population of functional bacteria. The elevation in inlet NOX concentration stimulated the growth of denitrifying bacteria, enhancing NOX removal efficiency. Concurrently, the population of nitrate-reducing sulfur-oxidizing bacteria and sulfate-reducing bacteria expanded, aiding in the accumulation of S0 and the removal of SO2. The comparison experiments on carbon sources confirmed the comparable NOX and SO2 removal efficiencies of alkali-treated CC and glucose, yet underscored differences in intermediates accumulation due to distinct genus structures.

Using ozone nanobubbles, and microalgae to promote the removal of nutrients from aquaculture wastewater: Insights from the changes of microbiomes

Integrated aquaculture wastewater treatment systems (IAWTSs) are widely used in treating aquaculture wastewater with the aeration-microalgae unit serving as an important component. In this study, we artificially constructed an IAWTS and applied two aeration-microalgae methods: ordinary aeration or ozone nanobubbles (ONBs) with microalgae (Nannochloropsis oculata). The impact of N.oculata and ONBs on the removal performance of nutrients and the underlying micro-ecological mechanisms were investigated using 16S rRNA gene amplicon sequencing. The results demonstrated that the combined use of ONBs and N.oculata exhibited superior purification effects with 78.25%, 76.59% and 86.71% removal of CODMn, TN and TP. N.oculata played a pivotal role as the primary element in wastewater purification, while ONBs influenced nutrient dynamics by affecting both N.oculata and bacterial communities. N.oculata actively shaped bacterial communities, with a specific focus on nitrogen and phosphorus cycling in the micro-environment remodeled by ONBs. Rare bacterial communities displayed heightened activity in response to the changes in N.oculata, ONBs, and nutrient levels. These findings provide a novel approach to improve the technological processes the IAWTS, contributing to the advancement of sustainable aquaculture practices by offering valuable insights into wastewater purification efficiency and micro-ecological mechanisms.

Andean soil-derived lignocellulolytic bacterial consortium as a source of novel taxa and putative plastic-active enzymes

An easy and straightforward way to engineer microbial environmental communities is by setting up liquid enrichment cultures containing a specific substrate as the sole source of carbon. Here, we analyzed twenty single-contig high-quality metagenome-assembled genomes (MAGs) retrieved from a microbial consortium (T6) that was selected by the dilution-to-stimulation approach using Andean soil as inoculum and lignocellulose as a selection pressure. Based on genomic metrics (e.g., average nucleotide and amino acid identities) and phylogenomic analyses, 15 out of 20 MAGs were found to represent novel bacterial species, with one of those (MAG_26) belonging to a novel genus closely related to Caenibius spp. (Sphingomonadaceae). Following the rules and requirements of the SeqCode, we propose the name Andeanibacterium colombiense gen. nov., sp. nov. for this taxon. A subsequent functional annotation of all MAGs revealed that MAG_7 (Pseudobacter hemicellulosilyticus sp. nov.) contains 20, 19 and 16 predicted genes from carbohydrate-active enzymes families GH43, GH2 and GH92, respectively. Its lignocellulolytic gene profile resembles that of MAG_2 (the most abundant member) and MAG_3858, both of which belong to the Sphingobacteriaceae family. Using a database that contains experimentally verified plastic-active enzymes (PAZymes), twenty-seven putative bacterial polyethylene terephthalate (PET)-active enzymes (i.e., alpha/beta-fold hydrolases) were detected in all MAGs. A maximum of five putative PETases were found in MAG_3858, and two PETases were found to be encoded by A. colombiense. In conclusion, we demonstrate that lignocellulose-enriched liquid cultures coupled with genome-resolved metagenomics are suitable approaches to unveil the hidden bacterial diversity and its polymer-degrading potential in Andean soil ecosystems.

Origin, Selection, and Succession of Coastal Intertidal Zone-Derived Bacterial Communities Associated with the Degradation of Various Lignocellulose Substrates

Terrestrial microbial consortia were reported to play fundamental roles in the global carbon cycle and renewable energy production through the breakdown of complex organic carbon. However, we have a poor understanding of how biotic/abiotic factors combine to influence consortia assembly and lignocellulose degradation in aquatic ecosystems. In this study, we used 96 in situ lignocellulose enriched, coastal intertidal zone-derived bacterial consortia as the initial inoculating consortia and developed 384 cultured consortia under different lignocellulose substrates (aspen, pine, rice straw, and purified Norway spruce lignin) with gradients of salinity and temperature. As coastal consortia, salinity was the strongest driver for assembly, followed by Norway spruce lignin, temperature, and aspen. Moreover, a conceptual model was proposed to demonstrate different succession dynamics between consortia under herbaceous and woody lignocelluloses. The succession of consortium under Norway spruce lignin is greatly related with abiotic factors, while its substrate degradation is mostly correlated with biotic factors. A discrepant pattern was observed in the consortium under rice straw. Finally, we developed four groups of versatile, yet specific consortia. Our study not only reveals that coastal intertidal wetlands are important natural resources to enrich lignocellulolytic degrading consortia but also provides insights into the succession and ecological function of coastal consortium.

Migration of rare and abundant species, assembly mechanisms, and ecological networks of microbiomes in drinking water treatment plants: Effects of different treatment processes

Microorganisms play an important role in the degradation of pollutants. However, they also cause problems in drinking water distribution systems, such as pipe corrosion and biofilm growth. The microbial assembly mechanisms and molecular ecological networks associated with different drinking water treatment processes have not yet been clearly analyzed. Therefore, this study investigated the microbiomes of three processes (coal filtration-activated carbon, ozone-activated carbon and UV, and ozone-activated carbon) during different seasons. The results showed that the microbial composition and diversity among the different processes and during different seasons. Water treatment processes had deterministic effects on the microbial assembly process and significantly changed the composition of rare and abundant species, altering the size and modules of molecular ecology networks. Rare species considered as keystone species play important roles in microbial ecology and microbial community construction. Ozone-activated carbon and UV/chlorination decreased the bacterial concentration, increased the deterministic process of microbial assembly, and significantly reduced the size of the network, which is of great significance to microbial control in drinking water. This research broadens our perspectives on the microbial assembly associated with drinking water treatment processes and contributes to ensuring the safe supply of drinking water.

Revealing the driving synergistic degradation mechanism of Rhodococcus sp. B2 on the bioremediation of pretilachlor-contaminated soil

The pretilachlor has been widely used worldwide and has contaminated the environment for many years. The environmental fate of pretilachlor and its residues removal from the contaminated environment have attracted great concern. Reportedly, pretilachlor could partly be transformed to HECDEPA by Rhodococcus sp. B2. However, the effects of pretilachlor on soil bacterial communities and its complete metabolic pathway remain unknown. Herein, we investigated the mechanism of driving synergistic degradation of pretilachlor by strain B2 in the soil. The results revealed that pretilachlor showed a negative effect on bacterial communities and caused significant variations in the community structure. Strain B2 showed the ability to remediate the pretilachlor-contaminated soils and network analysis revealed that it may drive the enrichment of potential pretilachlor-degrading bacteria from the soil. The soil pretilachlor degradation may be facilitated by the members of the keystone families Comamonadaceae, Caulobacteraceae, Rhodospirillaceae, Chitinophagaceae, and Sphingomonadaceae. Meanwhile, Sphingomonas sp. M6, a member of the Sphingomonadaceae family, has been isolated from the strain B2 inoculation sample soil. The co-culture, comprising strain M6 and B2, could synergistic degrade pretilachlor within 30 h, which is the highest degradation rate. Strain M6 could completely degrade the HECDEPA via CDEPA and DEA. In the soil, a comparable pretilachlor degradation pathway may exist. This study suggested that strain B2 had the potential to drive the remediation of pretilachlor-contaminated soils.

Moss biocrust accelerates the recovery and resilience of soil microbial communities in fire-affected semi-arid Mediterranean soils

After wildfires in Mediterranean ecosystems, ruderal mosses are pioneer species, stabilizing the soil surface previous to the establishment of vascular vegetation. However, little is known about the implication of pioneer moss biocrusts for the recovery and resilience of soils in early post-fire stages in semi-arid areas. Therefore, we studied the effects of the burgeoning biocrust on soil physicochemical and biochemical properties and the diversity and composition of microbial communities after a moderate-to-high wildfire severity. Seven months after the wildfire, the biocrust softened the strong impact of the fire in soils, affecting the diversity and composition of bacteria and fungi community compared to the uncrusted soils exposed to unfavourable environmental stress. Soil moisture, phosphorous, and enzyme activities representing the altered biogeochemical cycles after the fire, were the main explanatory variables for biocrust microbial community composition under the semi-arid conditions. High bacterial diversity was found in soils under mosses, while long-lasting legacies are expected in the fungal community, which showed greater sensitivity to the fire. The composition of bacterial and fungal communities at several taxonomical levels was profoundly altered by the presence of the moss biocrust, showing a rapid successional transition toward the unburned soil community. Pioneer moss biocrust play an important role improving the resilience of soil microbial communities. In the context of increasing fire intensity, studying the moss biocrust effects on the recovery of soils microbiome is essential to understanding the resistance and resilience of Mediterranean forests to wildfires.

Nutrient Removal in Eutrophic Water Promotes Stability of Planktonic Bacterial and Protist Communities

Nutrient (nitrogen and phosphorus) removal by using bioremediation technologies in eutrophic water alters bacterial and protist community structure and function, but how it changes the stability of community remains unclear. To fill this gap, in this study, bacterial and protist communities were investigated using 16S and 18S rRNA gene high-throughput sequencing during the nutrient removal by using ecological floating beds of Canna indica L. Our results showed that both bacterial and protist community compositions in the treatment group were similar to those in the control group at the beginning of the experiment (day 1 to day 11), but then bacterial and protist community compositions became more stable with the removal of nutrients in the treatment group than those in the control group (day 12 to day 18). We further explored the mechanisms for this increased stability and found that the contribution of the stochastic process to bacterial and protist community variations was higher in the control group than that in the treatment group. This suggests that the high nutrient concentration in the control group might increase the random colonization or extinction, and therefore resulted in the high temporal variability (i.e., unstable) of bacterial and protist communities. Our findings suggest that bioremediation for eutrophication can promote the stability of aquatic communities, and therefore potentially maintain aquatic ecosystem functions and services to humanity.

Fusarium oxysporum Disrupts Microbiome-Metabolome Networks in Arabidopsis thaliana Roots

While the plant host metabolome drives distinct enrichment of detrimental and beneficial members of the microbiome, the mechanistic interomics relationships remain poorly understood. Here, we studied microbiome and metabolome profiles of two Arabidopsis thaliana accessions after Fusarium oxysporum f.sp. mathioli (FOM) inoculation, Landsberg erecta (Ler-0) being susceptible and Col-0 being resistant against FOM. By using bacterial and fungal amplicon sequencing and targeted metabolite analysis, we observed highly dynamic microbiome and metabolome profiles across FOM host progression, while being markedly different between FOM-inoculated and noninoculated Col-0 and Ler-0. Co-occurrence network analysis revealed more robust microbial networks in the resistant Col-0 compared to Ler-0 during FOM infection. Correlation analysis revealed distinct metabolite-OTU correlations in Ler-0 compared with Col-0 which could possibly be explained by missense variants of the Rfo3 and Rlp2 genes in Ler-0. Remarkably, we observed positive correlations in Ler-0 between most of the analyzed metabolites and the bacterial phyla Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, and Verrucomicrobia, and negative correlations with Actinobacteria, Firmicutes, and Chloroflexi. The glucosinolates 4-methyoxyglucobrassicin, glucoerucin and indole-3 carbinol, but also phenolic compounds were strongly correlating with the relative abundances of indicator and hub OTUs and thus could be active in structuring the A. thaliana root-associated microbiome. Our results highlight interactive effects of host plant defense and root-associated microbiota on Fusarium infection and progression. Our findings provide significant insights into plant interomic dynamics during pathogen invasion and could possibly facilitate future exploitation of microbiomes for plant disease control. IMPORTANCE Plant health and fitness are determined by plant-microbe interactions which are guided by host-synthesized metabolites. To understand the orchestration of this interaction, we analyzed the distinct interomic dynamics in resistant and susceptible Arabidopsis ecotypes across different time points after infection with Fusarium oxysporum (FOM). Our results revealed distinct microbial profiles and network resilience during FOM infection in the resistant Col-0 compared with the susceptible Ler-0 and further pinpointed specific microbe-metabolite associations in the Arabidopsis microbiome. These findings provide significant insights into plant interomics dynamics that are likely affecting fungal pathogen invasion and could possibly facilitate future exploitation of microbiomes for plant disease control.

Degradation of switchgrass by Bacillus subtilis 1AJ3 and expression of a beta-glycoside hydrolase

Increasing demand for carbon neutrality has led to the development of new techniques and modes of low carbon production. The utilization of microbiology to convert low-cost renewable resources into more valuable chemicals is particularly important. Here, we investigated the ability of a cellulolytic bacterium, Bacillus subtilis 1AJ3, in switchgrass lignocellulose degradation. After 5 days of culture with the strain under 37°C, cellulose, xylan, and acid-insoluble lignin degradation rates were 16.13, 14.24, and 13.91%, respectively. Gas chromatography-mass spectrometry (GC-MS) analysis and field emission scanning electron microscopy (FE-SEM) indicated that the lignin and surface of switchgrass were degraded after incubation with the bacterial strain. Strain 1AJ3 can grow well below 60°C, which satisfies the optimum temperature (50°C) condition of most cellulases; subsequent results emphasize that acid-heat incubation conditions increase the reducing sugar content in a wide range of cellulosic biomass degraded by B. subtilis 1AJ3. To obtain more reducing sugars, we focused on β-glycoside hydrolase, which plays an important role in last steps of cellulose degradation to oligosaccharides. A β-glycoside hydrolase (Bgl-16A) was characterized by cloning and expression in Escherichia coli BL21 and further determined to belong to glycoside hydrolase (GH) 16 family. The Bgl-16A had an enzymatic activity of 365.29 ± 10.43 U/mg, and the enzyme's mode of action was explained by molecular docking. Moreover, the critical influence on temperature (50°C) of Bgl-16A also explained the high-efficiency degradation of biomass by strain under acid-heat conditions. In terms of potential applications, both the strain and the recombinant enzyme showed that coffee grounds would be a suitable and valuable substrate. This study provides a new understanding of cellulose degradation by B. subtilis 1AJ3 that both the enzyme action mode and optimum temperature limitation by cellulases could impact the degradation. It also gave new sight to unique advantage utilization in the industrial production of green manufacturing.

Metagenomic mining of Indian river confluence reveal functional microbial community with lignocelluloytic potential

Microbial carbohydrate-active enzymes (CAZyme) can be harnessed for valorization of Lignocellulosic biomass (LCB) to value-added chemicals/products. The two Indian Rivers Ganges and the Yamuna having different origins and flow, face accumulation of carbon-rich substrates due to the discharge of wastewater from adjoining paper and pulp industries, which could potentially contribute to the natural enrichment of LCB utilizing genes, especially at their confluence. We analyzed CAZyme diversity in metagenomic datasets across the sacred confluence of the Rivers Ganges and Yamuna. Functional annotation using CAZyme database identified a total of 77,815 putative genes with functional domains involved in the catalysis of carbohydrate degradation or synthesis of glycosidic bonds. The metagenomic analysis detected ~ 41% CAZymes catalyzing the hydrolysis of lignocellulosic biomass polymers- cellulose, hemicellulose, lignin, and pectin. The Beta diversity analysis suggested higher CAZyme diversity at downstream region of the river confluence, which could be useful niche for culture-based studies. Taxonomic origin for CAZymes revealed the predominance of bacteria (97%), followed by archaea (1.67%), Eukaryota (0.63%), and viruses (0.7%). Metagenome guided CAZyme diversity of the microflora spanning across the confluence of Ganges-Yamuna River, could be harnessed for biomass and bioenergy applications.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03190-7.

Strengthen "the sustainable farm" concept via efficacious conversion of farm wastes into methane

With escalating global demand for renewable energy, exploitation of farm wastes (i.e., agriculture straw wastes (ASWs), livestock wastewater (LW) and sewage sludge (SS)) has been considered to attain maximum methane yield (MY) via anaerobic digestion (AD). Results pointed that mixture of SS and LW as anaerobes' source with 20 g of ASWs/300 mL of working volume achieved maximum MY and volatile solid (VS) removal efficiency of 0.44 (±0.05) L/gVS and 51.4 (±4.1)%, respectively. This was mainly because of emerging heavy duty bacterial species (i.e., Syntrophorhabdaceae and Synergistaceae) and archaeal community (i.e, Methanosarcina and Methanoculleus) after 70 days of anaerobic incubation. This was acquired along with boosting enzymatic activity, especially xylanase, cellulase and protease up to 71.5(±7.9), 179.3(±14.3) and 207.2(±16.2) U/100 mL, respectively. Furthermore, the digestate contained high concentrations of NH₄⁺ (960.1±(76.8) mg/L), phosphorus (126.3±(10.1) mg/L) and trace metals, making it a good candidate as organic fertilizer.

Hexavalent Chromium Removal and Prokaryotic Community Analysis in Glass Column Reactor Packed with Aspen Wood as Solid Organic Substrate

Microbial hexavalent chromium (Cr(VI)) reduction is a promising method for Cr(VI)-laden wastewater treatment. However, the soluble organic substrate required for heterotrophic microbial Cr(VI) reduction necessitates constant supervision, and an excessive supply of soluble organic substrate can result in deterioration of the quality of the effluent. In this study, we evaluated aspen wood, a low-cost lignocellulose biomass, as a solid organic substrate for heterotrophic Cr(VI) reduction. A laboratory-scale aspen wood-packed glass column reactor inoculated with activated sludge was operated for 148 days for evaluation. Following reactor operation, an effective average dissolved Cr(VI) removal rate of 0.75 mg L^-1 h^-1 was confirmed under an average dissolved Cr(VI) loading rate of 0.90 mg L^-1 h^-1. Subsequently, 16S ribosomal ribonucleic acid gene amplicon sequencing analysis revealed that the dominant prokaryotic operational taxonomic units detected in the reactor were associated with prokaryotic lineages with the capacity for lignocellulose biodegradation, Cr compound resistance, and Cr(VI) reduction. Proteobacteria and Chloroflexi were two major prokaryotic phyla in the reactor. Our data indicate that aspen wood is an effective solid organic substrate for the development of simplified, effective, and low-cost microbial Cr(VI)-removing reactors.

Bacterial diversity dynamics in microbial consortia selected for lignin utilization

Lignin is nature's largest source of phenolic compounds. Its recalcitrance to enzymatic conversion is still a limiting step to increase the value of lignin. Although bacteria are able to degrade lignin in nature, most studies have focused on lignin degradation by fungi. To understand which bacteria are able to use lignin as the sole carbon source, natural selection over time was used to obtain enriched microbial consortia over a 12-week period. The source of microorganisms to establish these microbial consortia were commercial and backyard compost soils. Cultivation occurred at two different temperatures, 30°C and 37°C, in defined culture media containing either Kraft lignin or alkaline-extracted lignin as carbon source. iTag DNA sequencing of bacterial 16S rDNA gene was performed for each of the consortia at six timepoints (passages). The initial bacterial richness and diversity of backyard compost soil consortia was greater than that of commercial soil consortia, and both parameters decreased after the enrichment protocol, corroborating that selection was occurring. Bacterial consortia composition tended to stabilize from the fourth passage on. After the enrichment protocol, Firmicutes phylum bacteria were predominant when lignin extracted by alkaline method was used as a carbon source, whereas Proteobacteria were predominant when Kraft lignin was used. Bray-Curtis dissimilarity calculations at genus level, visualized using NMDS plots, showed that the type of lignin used as a carbon source contributed more to differentiate the bacterial consortia than the variable temperature. The main known bacterial genera selected to use lignin as a carbon source were Altererythrobacter, Aminobacter, Bacillus, Burkholderia, Lysinibacillus, Microvirga, Mycobacterium, Ochrobactrum, Paenibacillus, Pseudomonas, Pseudoxanthomonas, Rhizobiales and Sphingobium. These selected bacterial genera can be of particular interest for studying lignin degradation and utilization, as well as for lignin-related biotechnology applications.

Bacterial Communities in Alkaline Saline Soils Amended with Young Maize Plants or Its (Hemi)Cellulose Fraction

We studied three soils of the former lake Texcoco with different electrolytic conductivity (1.9 dS m-1, 17.3 dS m-1, and 33.4 dS m-1) and pH (9.3, 10.4, and 10.3) amended with young maize plants and their neutral detergent fibre (NDF) fraction and aerobically incubated in the laboratory for 14 days while the soil bacterial community structure was monitored by means of 454-pyrosequencing of their 16S rRNA marker gene. We identified specific bacterial groups that showed adaptability to soil salinity, i.e., Prauseria in soil amended with young maize plants and Marinobacter in soil amended with NDF. An increase in soil salinity (17.3 dS m-1, 33.4 dS m-1) showed more bacterial genera enriched than soil with low salinity (1.9 dS m-1). Functional prediction showed that members of Alfa-, Gamma-, and Deltaproteobacteria, which are known to adapt to extreme conditions, such as salinity and low nutrient soil content, were involved in the lignocellulose degradation, e.g., Marinimicrobium and Pseudomonas as cellulose degraders, and Halomonas and Methylobacterium as lignin degraders. This research showed that the taxonomic annotation and their functional prediction both highlighted keystone bacterial groups with the ability to degrade complex C-compounds, such as lignin and (hemi)cellulose, in the extreme saline-alkaline soil of the former Lake of Texcoco.

Unraveling a Lignocellulose-Decomposing Bacterial Consortium from Soil Associated with Dry Sugarcane Straw by Genomic-Centered Metagenomics

Second-generation biofuel production is in high demand, but lignocellulosic biomass’ complexity impairs its use due to the vast diversity of enzymes necessary to execute the complete saccharification. In nature, lignocellulose can be rapidly deconstructed due to the division of biochemical labor effectuated in bacterial communities. Here, we analyzed the lignocellulolytic potential of a bacterial consortium obtained from soil and dry straw leftover from a sugarcane milling plant. This consortium was cultivated for 20 weeks in aerobic conditions using sugarcane bagasse as a sole carbon source. Scanning electron microscopy and chemical analyses registered modification of the sugarcane fiber’s appearance and biochemical composition, indicating that this consortium can deconstruct cellulose and hemicellulose but no lignin. A total of 52 metagenome-assembled genomes from eight bacterial classes (Actinobacteria, Alphaproteobacteria, Bacilli, Bacteroidia, Cytophagia, Gammaproteobacteria, Oligoflexia, and Thermoleophilia) were recovered from the consortium, in which ~46% of species showed no relevant modification in their abundance during the 20 weeks of cultivation, suggesting a mostly stable consortium. Their CAZymes repertoire indicated that many of the most abundant species are known to deconstruct lignin (e.g., Chryseobacterium) and carry sequences related to hemicellulose and cellulose deconstruction (e.g., Chitinophaga, Niastella, Niabella, and Siphonobacter). Taken together, our results unraveled the bacterial diversity, enzymatic potential, and effectiveness of this lignocellulose-decomposing bacterial consortium.

Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium

The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems.

The engineering of complex communities can be a successful path to understand the ecology of microbial systems and improve biotechnological processes. Here, we developed a strategy to assemble a minimal and effective lignocellulolytic microbial consortium (MELMC) using a sequential combination of dilution-to-stimulation and dilution-to-extinction approaches. The consortium was retrieved from Andean forest soil and selected through incubation in liquid medium with a mixture of three types of agricultural plant residues. After the dilution-to-stimulation phase, approximately 50 bacterial sequence types, mostly belonging to the Sphingobacteriaceae, Enterobacteriaceae, Pseudomonadaceae, and Paenibacillaceae, were significantly enriched. The dilution-to-extinction method demonstrated that only eight of the bacterial sequence types were necessary to maintain microbial growth and plant biomass consumption. After subsequent stabilization, only two bacterial species (Pseudomonas sp. and Paenibacillus sp.) became highly abundant (>99%) within the MELMC, indicating that these are the key players in degradation. Differences in the composition of bacterial communities between biological replicates indicated that selection, sampling, and/or priority effects could shape the consortium structure. The MELMC can degrade up to ∼13% of corn stover, consuming mostly its (hemi)cellulosic fraction. Tests with chromogenic substrates showed that the MELMC secretes an array of endoenzymes able to degrade xylan, arabinoxylan, carboxymethyl cellulose, and wheat straw. Additionally, the metagenomic profile inferred from the phylogenetic composition along with an analysis of carbohydrate-active enzymes of 20 bacterial genomes support the potential of the MELMC to deconstruct plant polysaccharides. This capacity was mainly attributed to the presence of Paenibacillus sp.

IMPORTANCE The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems.

Enrichment and characterization of bacterial consortia for degrading 2-mercaptobenzothiazole in rubber industrial wastewater

Benzothiazoles especially 2-mercaptobenzothiazole (2-MBT) in rubber industrial wastewater can be released into the environment. They can cause adverse health impacts. This study aimed to obtain efficient 2-MBT-degrading bacteria for wastewater application. The bacterial consortia were enriched by incubating rubber wastewater sludge in a medium containing 2-MBT for 28 days. Stepwise acclimatization was conducted with increasing 2-MBT concentrations from 50 to 200 mg L^-1 in nitrogen-containing medium for 76 days. The process significantly increased the bacterial number and changed the dominant populations. Among these consortia, the EN consortium from benzothiazole-containing sludge had the highest specific 2-MBT biodegradation rate of 5.2 ± 0.5 mg L^-1 day^-1 mg protein^-1 and could degrade up to 300 mg L^-1 2-MBT. From 16S rRNA gene analysis, Pseudomonas was the dominant genus at approximately 70 % of the total population. Stenotrophomonas was the second most abundant populations and have never been reported for 2-MBT biodegradation. The EN consortium removed 65-79 % and 90-93 % of 112 mg L^-1 2-MBT and ∼4000 mg L^-1 COD in rubber wastewater, respectively, which were significantly higher than the values of natural attenuation. Therefore, the EN consortium could be an ideal inoculum for the post-treatment of benzothiazoles in rubber industrial wastewater.