Stable Microbial Consortium Research Articles

Genomic analysis and assessment of pathogenic (toxicogenic) potential of Staphylococcus haemolyticus and Bacillus paranthracis consortia isolated from bovine mastitis in Russia

Three stable microbial consortia, each composed of Bacillusparanthracis and Staphylococcushaemolyticus strains, were isolated from milk of cows diagnosed with mastitis in three geographically remote regions of Russia. The composition of these consortia remained stable following multiple passages on culture media. Apparently, this stability is due to the structure of the microbial biofilms formed by the communities. The virulence of the consortia depended on the B. paranthracis strains. It seems plausible that the ability of the consortia to cause mastitis in cattle was affected by mutations of the cytK gene of B. paranthracis.

Engineering complex communities by directed evolution.

Directed evolution has been used for decades to engineer biological systems at or below the organismal level. Above the organismal level, a small number of studies have attempted to artificially select microbial ecosystems, with uneven and generally modest success. Our theoretical understanding of artificial ecosystem selection is limited, particularly for large assemblages of asexual organisms, and we know little about designing efficient methods to direct their evolution. Here, we have developed a flexible modeling framework that allows us to systematically probe any arbitrary selection strategy on any arbitrary set of communities and selected functions. By artificially selecting hundreds of in-silico microbial metacommunities under identical conditions, we first show that the main breeding methods used to date, which do not necessarily let communities to reach their ecological equilibrium, are outperformed by a simple screen of sufficiently mature communities. We then identify a range of alternative directed evolution strategies that, particularly when applied in combination, are well suited for the top-down engineering of large, diverse, and stable microbial consortia. Our results emphasize that directed evolution allows an ecological structure-function landscape to be navigated in search for dynamically stable and ecologically resilient communities with desired quantitative attributes.

Enrichment of Mesophilic and Thermophilic Mixed Microbial Consortia for Syngas Biomethanation: The Role of Kinetic and Thermodynamic Competition

Mixed culture-based syngas biomethanation is a robust bioconversion process with high versatility in terms of exploitable feedstocks and potential applications, as it could be operated independently, or coupled to anaerobic digestion systems and in-situ biogas upgrading processes. Typically, the syngas biomethanation consists in the stepwise conversion of syngas into methane through a number of catabolic routes, which may vary considerably depending on the operating conditions. In this study, two enrichments were performed at 37 °C and 60 °C to investigate the effect of the incubation temperature on the microbial selection process and the dominant catabolic routes followed. This was carried out through the characterization of the catabolic routes and the microbial composition of the enriched cultures, and a thermodynamic feasibility study on their metabolic networks. The enrichments resulted in two stable microbial consortia with different patterns of activity. The mesophilic enriched consortium presented a more intricate metabolic network composed by four microbial trophic groups, where aceticlastic methanogenesis contributed to 64.9 ± 8.3% of the CH4 production. The metabolic network of the thermophilic enriched consortium was much simpler, consisting in the syntrophic association of carboxydotrophic hydrogenogens and hydrogenotrophic methanogens. This led to significant differences in methane productivity, corresponding to 1.83 ± 0.27 and 33.48 ± 0.90 mmol CH4/g VSS/h for the mesophilic and the thermophilic enriched consortium, respectively, which would potentially make the thermophilic consortium more suited for industrial applications. 16S rRNA gene amplicon analysis indicated the presence of strains with similarity to Acetobacterium sp., Methanospirillum hungateii, Methanospirillum stamsii and Methanothrix sp. at mesophilic conditions, and Thermincola carboxydiphila and Methanothermobacter sp. at thermophilic conditions, implying a role in the conversion of syngas. The thermodynamic feasibility study demonstrated that the microbial selection was not driven solely by kinetic competition, since thermodynamic limitations also played a significant role defining the dominant catabolic routes.

Screening and construction of a novel microbial consortium SSA-6 enriched from the gut symbionts of wood-feeding termite, Coptotermes formosanus and its biomass-based biorefineries

Biorefinery industry from lignocellulose faces one major obstacle which lies in the inefficient degradation of biomass. Lignocellulosic processes in wood-feeding termites are considered to be a very efficient biodegradation reaction due to a significant contribution from gut symbionts. In the present study, high degradation ratio of sawdust (84.3%) was achieved by the stable microbial consortium Cf-S, enriched from the termite gut symbionts of Coptotermes formosanus, within 120 h at 35 °C and pH 7. Molecular identification and phylogenetic analysis of Cf-S indicated that two yeasts and four bacterial candidates were identified for new species. Clustering and ordination analyses of Cf-S revealed that six strains Cf-S-2, Cf-S-6, Cf-S-11, Cf-S-20, Cf-S-22 and Cf-S-17 exhibited metabolic activities and physiological capabilities compared with other strains. These six strains were selected to construct a novel microbial consortium, designated SSA-6 that could make SSA-6 potentially consortium suitable for a wide variety of applications. The synergistic interaction of SSA-6 candidates led to significant higher cellulolytic, xylanolytic and ligninolytic activities than that produced by either strain alone (P = 0.003, 0.003 and 0.004, respectively). The consortium SSA-6 showed significant lower time for dye removal (Remazol Brilliant Blue R, Azure B, and Methylene Blue) together with higher dye concentration and decolorization ratio when compared with each individual strain (P < 0.001). The co-culture SSA-6 candidates produced 84.3, 203.6 and 168.4% more ethanol than that produced by Cf-S-2, Cf-S-17 and Cf-S-22 alone, respectively. This study shows the potential of constructing a novel microbial consortium valued for biomass-based biorefineries.

Characterization of an Anaerobic, Thermophilic, Alkaliphilic, High Lignocellulosic Biomass-Degrading Bacterial Community, ISHI-3, Isolated from Biocompost

The generation of a complex microbial consortium is a promising approach for efficient biomass decomposition. An anaerobic thermophilic alkaliphilic microbial consortium with efficient degradation ability was screened from bovine manure compost using non-pretreated milling corn stover (CS) and rice straw (RS). A stable microbial consortium ISHI-3 with high degradation ability for CS and RS was isolated by the roll tube technique. ISHI-3 comprised Herbivorax saccincola and bacteria belonging to the classes Pelotomaculum, Tepidanaerobacter, and Tepidimicrobium, as determined by DGGE of the PCR-generated 16S rRNA genes. Furthermore, metagenomics analysis using a 16S rRNA library was carried out to determine the bacterial distribution during degradation of CS and RS. H. saccincola and bacteria belonging to Pelotomaculum were relatively abundant in the beginning to middle periods of culture with CS and RS whereas bacteria belonging to Tepidanaerobacter and Tepidimicrobium gradually increased in the population during the later stages. To understand the role of non-cellulolytic bacteria in the consortium, novel strains ET1 and GL4, which were most closely related to Tepidimicrobium ferriphilum and Tepidanaerobacter acetatoxydans, were isolated from ISHI-3. Based on their carbon source usage, morphology, and phylogenetic analysis, we propose that strains ET1 and GL4 should be classified as a novel genus or species. Bacteria ET1 and GL4 can utilize different organic compounds as carbon and energy sources such as organic acids, alcohols, sugars, and amino acids, showing a preference for organic acids and alcohols rather than sugars such as glucose and cellobiose. These results indicated that ET1 and GL4 help to accelerate efficient lignocellulose degradation of H. saccincola.

Microbial detoxification of eleven food and feed contaminating trichothecene mycotoxins

BackgroundContamination of agricultural commodities with multiple trichothecene mycotoxins, produced by toxigenic Fusarium species, is a food safety issue, which greatly affects grain production and marketing worldwide. Importantly, exposure to multiple trichothecenes may increase toxicity in animals due to their synergistic and/or additive effects. To address the problem this study aimed to achieve a novel biological trait capable of detoxifying various food and feed contaminating trichothecenes under aerobic and anaerobic conditions and wide range of temperatures.ResultsA highly enriched microbial consortium (called DX100) capable of transforming eleven trichothecenes to significantly less toxic de-epoxy forms was achieved after prolonged incubation of soil microbial culture with 200 μg/mL deoxynivalenol (DON). DX100 demonstrated de-epoxidation activity under aerobic and anaerobic conditions, a greater range of temperatures and around neutral pH. The consortium contains 70% known and 30% unknown bacterial species, dominated by Stenotrophomonas species. Probably novel bacteria including strains of Stenotrophomonas and Alkaliphilus-Blautia species complex could be involved in aerobic and anaerobic de-epoxidation of trichothecenes, respectively. DX100 showed rapid and stable activity by de-epoxidizing 100% of 50 μg/mL deoxynivalenol at 48 h of incubation and retaining de-epoxidation ability after 100 subcultures in mineral salts broth (MSB). It was able to de-epoxidize high concentration of DON (500 μg/mL), and transformed ten more food contaminating trichothecenes into de-epoxy forms and/or other known/unknown compounds. Microbial de-epoxidation rate increased with increasing trichothecene concentrations in the broth media, suggesting that DX100 maintains a robust trichothecene detoxifying mechanism. Furthermore, the nature of microbial de-epoxidation reaction and inhibition of the reaction by sodium azide and the finding that bacterial cell culture lysate retained activity suggests that certain cytoplasmic reductases may be responsible for the de-epoxidation activity.ConclusionsThis study reports the enrichment procedure for obtaining an effective and stable microbial consortium DX100 capable of de-epoxidizing several food contaminating trichothecene mycotoxins. DX100, which has de-epoxidation ability under wide range of conditions, represents a unique enzymatic source which has great industrial potential for reducing contamination of foods/feeds with multiple trichothecenes, and minimizing their synergistic/additive cytotoxic effects on consumer health.

Characterization of Enrichment Cultures Involved in the Carbon, Sulfur and Iron Biogeochemical Cycles in French Guiana Mobile Muds

ABSTRACTThe fluidized sediment ecosystem off French Guiana is characterized by active physical reworking, diversity of electron acceptors and highly variable redox regime. It is well studied geochemically but little is known about specific microorganisms involved in its biogeochemistry. Based on the biogeochemical profiles and rate kinetics, several possible biotically mediated pathways of the carbon, sulfur and iron cycles were hypothesized. Enrichment studies were set up with a goal to culture microorganisms responsible for these pathways. Stable microbial consortia potentially capable of the following chemolithoautotrophic types were enriched from the environment and characterized: elemental sulfur/thiosulfate disproportionators, thiosulfate-oxidizing ferrihydrite and nitrate reducers, sulfide/ferrous sulfide oxidizers coupled with nitrate and microaerophilic iron oxidizers. Attempts to generate several enrichments (anoxic ammonia oxidation, and sulfide oxidizers with ferric iron or manganese oxide) were not successful. Heterotrophic sulfate and elemental sulfur reduction bacteria are prominent and dominate reductive sulfur transformations. We hypothesize that carbon dioxide fixation coupled with synthesis of organic matter happens mostly via sulfur disproportionation and sulfur species oxidation with iron oxidation playing a minor role.

A novel lab-scale two-stage reactor for biogas production through the use of efficient and stable microbial consortia

A novel lab-scale two-stage reactor for biogas production through the use of efficient and stable microbial consortia

Synergistic microbial consortium for bioenergy generation from complex natural energy sources.

Microbial species have evolved diverse mechanisms for utilization of complex carbon sources. Proper combination of targeted species can affect bioenergy production from natural waste products. Here, we established a stable microbial consortium with Escherichia coli and Shewanella oneidensis in microbial fuel cells (MFCs) to produce bioenergy from an abundant natural energy source, in the form of the sarcocarp harvested from coconuts. This component is mostly discarded as waste. However, through its usage as a feedstock for MFCs to produce useful energy in this study, the sarcocarp can be utilized meaningfully. The monospecies S. oneidensis system was able to generate bioenergy in a short experimental time frame while the monospecies E. coli system generated significantly less bioenergy. A combination of E. coli and S. oneidensis in the ratio of 1 : 9 (v : v) significantly enhanced the experimental time frame and magnitude of bioenergy generation. The synergistic effect is suggested to arise from E. coli and S. oneidensis utilizing different nutrients as electron donors and effect of flavins secreted by S. oneidensis. Confocal images confirmed the presence of biofilms and point towards their importance in generating bioenergy in MFCs.

Biodegradation of di-n-butyl phthalate by a stable bacterial consortium, HD-1, enriched from activated sludge

HD-1, a stable microbial consortium capable of mineralizing di-n-butyl phthalate (DBP), was developed from activated sludge. The dominant microorganisms in the consortium, Gordonia sp., Burkholderia sp. and Achromobacter sp., were identified by denaturing gradient gel electrophoresis (DGGE). The consortium could mineralize approximately 90% of 1200mg/L DBP after 48h of cultivation. The optimal DBP degradation conditions were 25–30°C and pH 8.0–9.0. The addition of yeast (0.5g/L), sodium acetate (0.5g/L, 1.0g/L), Brij 35 (0.2%, 0.5%, 1.0%), or Triton X-100 (0.2%) enhanced DBP degradation. The DBP degradation rate was influenced by the presence of dimethyl phthalate (DMP) and diethyl phthalate (DEP). Only one main intermediate, phthalic acid, could be monitored by gas chromatography–mass spectrometry (GC–MS) during the degradation process. The HD-1 consortium also utilized phenol, o-dihydroxybenzene as the sole carbon and energy source. The results indicate the consortium may represent a promising application for DBP bioremediation.

Isolation and Description of a Stable Carbazole-Degrading Microbial Consortium Consisting of Chryseobacterium sp. NCY and Achromobacter sp. NCW

A stable microbial consortium, separated from a refinery wastewater sample, was able to utilize carbazole as the sole source of carbon, nitrogen, and energy, and liberated ammonia from excess nitrogen. Two bacterial strains (NCY and NCW) were isolated from the microbial consortium using a nutrient agar plate. Based on the 16S rDNA sequence analysis, the two bacteria were identified as Chryseobacterium sp. NCY and Achromobacter sp. NCW, respectively. No intermediates of carbazole degradation were detected by high-performance liquid chromatography. The substrate specificity assay showed that the consortium could utilize compounds similar to carbazole, such as phenanthrene, naphthalene, and imidazole. Neither the pure strain NCY nor NCW could degrade carbazole after domestication for several times. It was suggested that the two bacteria formed a microbial consortium capable of metabolizing carbazole.

Molecular analysis of a sulphate-reducing consortium used to treat metal-containing effluents

A sulphate-reducing consortium used in a bioprocess to remove toxic metals from solution as insoluble sulphides, was characterised using molecular (PCR-based) and traditional culturing techniques. After prolonged cultivation under anoxic biofilm-forming conditions, the mixed culture contained a low diversity of sulphate-reducing bacteria, dominated by one strain closely related to Desulfomicrobium norvegicum, identified by three independent PCR-based analyses. The genetic targets used were the 16S rRNA gene, the 16S-23S rRNA gene intergenic spacer region and the disulfite reductase (dsr) gene, which is conserved amongst all known sulphate-reducing bacteria. This organism was also isolated by conventional anaerobic techniques, confirming its presence in the mixed culture. A surprising diversity of other non-sulphate-reducing facultative and obligate anaerobes were detected, supporting a model of the symbiotic/commensal nature of carbon and energy fluxes in such a mixed culture while suggesting the physiological capacity for a wide range of biotransformations by this stable microbial consortium.

Removal of nitrobenzene vapors by a trickling air biofilter

A stable microbial consortium that grew on nitrobenzene (NB) as its sole source of carbon, nitrogen and energy and liberated excess nitrogen as ammonia, was immobilized on a perlite-packed trickling air biofilter. On a sustained basis, the biofilter removed 50 g NB m−3 packing h−1 and its operation at pH 8.7 resulted in ammonia stripping, making pH and salinity controls unnecessary. Low maintenance and stable performance during 4 months of continuous operation invite the scale-up of this biofilter for control of NB emissions.