Maximizing microbial perchlorate degradation using a genetic algorithm: consortia optimization

Microorganisms in consortia perform many tasks more effectively than individual organisms and in addition grow more rapidly and in greater abundance. In this work, experimental datasets were assembled consisting of all possible selected combinations of perchlorate reducing strains of microorganisms and their perchlorate degradation rates were evaluated. A genetic algorithm (GA) methodology was successfully applied to define sets of microbial strains to achieve maximum rates of perchlorate degradation. Over the course of twenty generations of optimization using a GA, we saw a statistically significant 2.06 and 4.08-fold increase in average perchlorate degradation rates by consortia constructed using solely the perchlorate reducing bacteria (PRB) and by consortia consisting of PRB and accompanying organisms that did not degrade perchlorate, respectively. The comparison of kinetic rates constant in two types of microbial consortia additionally showed marked increases.     

人工电活性微生物菌群的设计与应用

包括产电菌群和噬电菌群的人工电活性微生物菌群(synthetic electroactive microbial consortia)通过菌种间的物质能量级联反应介导化学能与(光)电能间的相互转化，其可利用底物来源广泛、双向电子传递速率快、环境稳定性强，在清洁电能开发、废水处理、环境修复、生物固碳固氮以及生物燃料、无机纳米材料、高聚物等高值化学品合成等多个领域具有广泛的应用前景。针对人工电活性微生物菌群设计、构建与应用，本文总结电活性微生物菌群界面电子传递和种间电子传递机制，概括基于“劳力分工”原理设计构建人工电活性微生物菌群物质能量级联反应基本架构，总结菌群关系与菌群生态位优化等人工电活性微生物菌群工程化策略，分类列举人工电活性微生物菌群在利用廉价生物质产电、生物光伏固碳产电，光驱噬电生物菌群固氮等相关应用。最后对人工电活性微生物菌群未来研究方向进行了展望。     

Culturable and metagenomic approaches of wheat bran and wheat straw phyllosphere’s highlight new lignocellulolytic microorganisms

The phyllosphere, defined as the aerial parts of plants, is one of the most prevalent microbial habitats on earth. The microorganisms present on the phyllosphere can have several interactions with the plant. The phyllosphere represents then a unique niche where microorganisms have evolved through time in that stressful environment and may have acquired the ability to degrade lignocellulosic plant cell walls in order to survive to oligotrophic conditions. The dynamic lignocellulolytic potential of two phyllospheric microbial consortia (wheat straw and wheat bran) has been studied. The microbial diversity rapidly changed between the native phyllospheres and the final degrading microbial consortia after 48 h of culture. Indeed, the initial microbial consortia was dominated by the Ralstonia (35·8%) and Micrococcus (75·2%) genera for the wheat bran and wheat straw whereas they were dominated by Candidatus phytoplasma (59%) and Acinetobacter (31·8%) in the final degrading microbial consortia respectively. Culturable experiments leading to the isolation of several new lignocellulolytic isolates (belonging to Moraxella and Atlantibacter genera) and metagenomic reconstruction of the microbial consortia highlighted the existence of an unpredicted microbial diversity involved in lignocellulose fractionation but also the existence of new pathways in known genera (presence of CE2 for Acinetobacter, several AAs for Pseudomonas and several GHs for Bacillus in different metagenomes-assembled genomes). The phyllosphere from agricultural co-products represents then a new niche as a lignocellulolytic degrading ecosystem.     

Composition and dynamics of biostimulated indigenous oil-degrading microbial consortia from the Irish, North and Mediterranean Seas: a mesocosm study

Diversity of indigenous microbial consortia and natural occurrence of obligate hydrocarbon-degrading bacteria (OHCB) are of central importance for efficient bioremediation techniques. To investigate the microbial population dynamics and composition of oil-degrading consortia, we have established a series of identical oil-degrading mesocosms at three different locations, Bangor (Menai Straits, Irish Sea), Helgoland (North Sea) and Messina (Messina Straits, Mediterranean Sea). Changes in microbial community composition in response to oil spiking, nutrient amendment and filtration were assessed by ARISA and DGGE fingerprinting and 16Sr RNA gene library analysis. Bacterial and protozoan cell numbers were quantified by fluorescence microscopy. Very similar microbial population sizes and dynamics, together with key oil-degrading microorganisms, for example, Alcanivorax borkumensis, were observed at all three sites; however, the composition of microbial communities was largely site specific and included variability in relative abundance of OHCB. Reduction in protozoan grazing had little effect on prokaryotic cell numbers but did lead to a decrease in the percentage of A.?borkumensis 16S rRNA genes detected in clone libraries. These results underline the complexity of marine oil-degrading microbial communities and cast further doubt on the feasibility of bioaugmentation practices for use in a broad range of geographical locations.     

Biosolubilization of Low-Grade Rock Phosphate by Native Microbial Consortia from Phosphate Mines: Effect of Sampling Sources and Culture Media

Abstract

Two native microbial consortia were isolated from the soil and drainage in the phosphate mines, and their abilities to solubilize low-grade rock phosphate (RP) in two different culture media, namely Pikovskaya (PKV) and National Botanical Research Institute’s phosphate (NBRIP) medium, respectively, were estimated. Results showed that the two microbial consortia could grow steadily in the solution and continuously released soluble phosphate from the RP during 14?d of experiments. This process was accompanied by a drop in pH of the solution. The microbial consortium isolated from the soil achieved the largest release of soluble phosphate and pH reduction in the PKV medium among the four microbial consortia named PS, NS, PD, and ND, respectively. Fourier transform infrared spectroscopy (FTIR) analysis of RP indicated that hydroxyl, alkyl C-H bond, amide, and carboxyl were involved in the RP solubilization, and significant changes of them were observed after the experiments. The four microbial consortia were sampled before and after the experiments for the analysis of their bacterial and fungal community structures by Illumina MiSeq sequencing. Results showed that the relative diversities and abundances of the dominant bacteria and fungi varied with different sampling sources (soil and drainage) and culture media (PKV and NBRIP medium).     

Isolation and characterization of pyrene metabolizing microbial consortia from the plant rhizoplane

Most research on the ecology of PAH degrading bacteria in the rhizosphere has focused on individual strains that grow on specific PAHs. Thus, there are fundamental questions as to importance of microbial consortia for PAH degradation in the plant rhizosphere. The study reported here characterized cultivable pyrene degrading rhizoplane microbial communities from two different plant species using a root printing technique on agar plates. Colonies were revealed by formation of clearing zones on medium containing a thin film of pyrene on the surface of a mineral nutrient agar. Prints of the rhizoplane colonies were obtained from roots of Melilotus officinalis (sweet yellow clover) and Andropogon gerardii (big bluestem) plants. Phylogenetic characterizations of selected pyrene degrading colonies were assessed by PCR-DGGE and DNA sequencing. Results showed that different populations of cultivable pyrene degraders were obtained from representative consortia that were examined. Many of the PAH degrading consortia consisted of mixtures of bacterial species that were unable to degrade pyrene by themselves. While this study focused on culturable PAH degraders, the results suggest that pyrene degradation in the rhizosphere commonly involves the activity of bacterial consortia in which various species of bacteria interact to achieve PAH degradation.     

Optimization of field scale biopiles for bioremediation of petroleum hydrocarbon contaminated soil at low temperature conditions by response surface methodology (RSM)

Ex-Situ Bioremediation has been increasingly viewed as an appropriate remediation technology for hydrocarbon contaminated soils under cold climates conditions in countries like Canada. A response surface methodology (RSM) based on a factorial design was performed to investigate and optimize the effects of the microbial consortia application rate and amount of mature compost amendment on the TPH removal (964 μg g⁻¹ initial concentration). 18 field-scale biopiles (16 m³ each) were constructed, maintained and subjected to different microbial consortium and mature compost application rates under cold climate conditions over a period of 94 days. TPHs removal rates in the range of 74–82% was observed in the treatments setups where mature compost and microbial consortia were used simultaneously, compared to an average 48% of TPHs removal in control setup.The interaction between these two factors were studied and modelled using a statistical regression model, which showed that the microbial consortia application rate, the mature compost amendment and their interactions had a significant effect on TPHs degradation with a coefficient of determination (R²) of 0.88. Furthermore, using a numerical optimization approach, the optimum rates predicted via RSM were estimated at 4.1 ml m⁻³ and 7% for microbial consortia and compost application rates to obtain a maximum TPH removal of 90.7%.     

Enrichment of microbial cultures able to degrade 1,3-dichloro-2-propanol: a comparison between batch and continuous methods

Microbial cultures able to degrade xenobiotic compounds are the key element for biological treatment of waste effluents and are obtained from enrichment processes. In this study, two common enrichment methods, suspension batch and immobilized continuous, were compared. The main selection factor was the presence of 1,3-dichloro-2-propanol (1,3-DCP) as the single carbon source. Both methods have successfully enriched microbial consortia able to degrade 1,3-DCP. When tested in batch culture, the degradation rates of 1,3-DCP by the two consortia were different, with the consortia obtained by batch enrichment presenting slightly higher rates. A preliminary morphological and biochemical analysis of the predominant colonial types present in each degrading consortia revealed the presence of different constituting strains. Three bacterial isolates capable of degrading 1,3-DCP as single strains were obtained from the batch enrichments. These strains were classified by 16S rRNA analysis as belonging to the Rhizobiaceae group. Degradation rates of 1,3-DCP were lower when single species were used, reaching 45 mg l^-1 d^-1, as compared to 74 mg l^-1 d^-1 of the consortia enriched on the batch method. Mutualistic interactions may explain the better performance of the enriched consortia.     

New approaches in bioprocess‐control: Consortium guidance by synthetic cell‐cell communication based on fungal pheromones

Bioconversions in industrial processes are currently dominated by single‐strain approaches. With the growing complexity of tasks to be carried out, microbial consortia become increasingly advantageous and eventually may outperform single‐strain fermentations. Consortium approaches benefit from the combined metabolic capabilities of highly specialized strains and species, and the inherent division of labor reduces the metabolic burden for each strain while increasing product yields and reaction specificities. However, consortium‐based designs still suffer from a lack of available tools to control the behavior and performance of the individual subpopulations and of the entire consortium. Here, we propose to implement novel control elements for microbial consortia based on artificial cell–cell communication via fungal mating pheromones. Coupling to the desired output is mediated by pheromone‐responsive gene expression, thereby creating pheromone‐dependent communication channels between different subpopulations of the consortia. We highlight the benefits of artificial communication to specifically target individual subpopulations of microbial consortia and to control e.g. their metabolic profile or proliferation rate in a predefined and customized manner. Due to the steadily increasing knowledge of sexual cycles of industrially relevant fungi, a growing number of strains and species can be integrated into pheromone‐controlled sensor‐actor systems, exploiting their unique metabolic properties for microbial consortia approaches.     

Characterization of Thermophilic Consortia from Two Souring Oil Reservoirs

The microbial consortia from produced water at two different oil fields in Alaska (Kuparuk) and the North Sea (Ninian) were investigated for sulfate-reducing and methanogenic activity over a range of temperatures and for a variety of substrates. The consortia were sampled on site, and samples were either incubated on site at 60(deg)C with various substrates or frozen for later incubation and analyses. Temperature influenced the rates of sulfate reduction, hydrogen sulfide production, and substrate oxidation, as well as the cell morphology. The highest rates of sulfate reduction and substrate oxidation were found between 50 and 60(deg)C. Formate and n-butyrate were the most favorable electron donors at any tested temperature. Acetate was utilized at 35(deg)C but not at 50 or 70(deg)C and was produced at 60(deg)C. This indicates that the high levels of acetate found in produced water from souring oil formations are due mainly to an incomplete oxidation of volatile fatty acids to acetate. The cell size distribution of the microbial consortium indicated a nonuniform microbial composition in the original sample from the Kuparuk field. At different temperatures, different microbial morphologies and physiologies were observed. Methane-producing activity at thermophilic temperatures (60(deg)C) was found only for the Kuparuk consortium when hydrogen and carbon dioxide were present. No methane production from acetate was observed. Suppression of methanogenic activity in the presence of sulfate indicated a competition with sulfate-reducing bacteria for hydrogen.     

Changes in composition and microbial communities in excess sludge after heat-alkaline treatment and acclimation

This study examined the effects of combining heat-alkaline treatment (HAT) with an acclimation process on sludge reduction. Changes in sludge components and microbial communities in both the mixed liquor suspended solids (MLSS) and supernatant fractions were monitored throughout the process. HAT was performed under different pH conditions (pH 7, pH 11 and pH 13) at 60 °C. Approximately 42–62% of the released materials were proteins. After an 8-day acclimation of sludge, the protein concentration in the supernatant had significantly decreased under all conditions. Treatment conditions at pH 11 were optimal for sludge reduction due to the increased efficiency and reduced consumption of chemicals to adjust the pH. A molecular analysis showed that the microbial consortia in both fractions after the cell lysis differed depending on the pH and temperature, and only a few types of bacteria were resistant under extreme conditions. The microbial communities in the MLSS under different conditions were similar after the 8-day acclimation.     

Fermentation Enhancement of Methanogenic Archaea Consortia from an Illinois Basin Coalbed via DOL Emulsion Nutrition

Microbially enhanced coalbed methane technology must be used to increase the methane content in mining and generate secondary biogenic gas. In this technology, the metabolic processes of methanogenic consortia are the basis for the production of biomethane from some of the organic compounds in coal. Thus, culture nutrition plays an important role in remediating the nutritional deficiency of a coal seam. To enhance the methane production rates for microorganism consortia, different types of nutrition solutions were examined in this study. Emulsion nutrition solutions containing a novel nutritional supplement, called dystrophy optional modification latex, increased the methane yield for methanogenic consortia. This new nutritional supplement can help methanogenic consortia form an enhanced anaerobic environment, optimize the microbial balance in the consortia, and improve the methane biosynthesis rate.     

Bacterial communities in full-scale wastewater treatment systems

Bacterial metabolism determines the effectiveness of biological treatment of wastewater. Therefore, it is important to define the relations between the species structure and the performance of full-scale installations. Although there is much laboratory data on microbial consortia, our understanding of dependencies between the microbial structure and operational parameters of full-scale wastewater treatment plants (WWTP) is limited. This mini-review presents the types of microbial consortia in WWTP. Information is given on extracellular polymeric substances production as factor that is key for formation of spatial structures of microorganisms. Additionally, we discuss data on microbial groups including nitrifiers, denitrifiers, Anammox bacteria, and phosphate- and glycogen-accumulating bacteria in full-scale aerobic systems that was obtained with the use of molecular techniques, including high-throughput sequencing, to shed light on dependencies between the microbial ecology of biomass and the overall efficiency and functional stability of wastewater treatment systems. Sludge bulking in WWTPs is addressed, as well as the microbial composition of consortia involved in antibiotic and micropollutant removal.     

Emerging strategies for engineering microbial communities

From biosynthesis to bioremediation, microbes have been engineered to address a variety of biotechnological applications. A promising direction in these endeavors is harnessing the power of designer microbial consortia that consist of multiple populations with well-defined interactions. Consortia can accomplish tasks that are difficult or potentially impossible to achieve using monocultures. Despite their potential, the rules underlying microbial community maintenance and function (i.e. the task the consortium is engineered to carry out) are not well defined, though rapid progress is being made. This limited understanding is in part due to the greater challenges associated with increased complexity when dealing with multi-population interactions. Here, we review key features and design strategies that emerge from the analysis of both natural and engineered microbial communities. These strategies can provide new insights into natural consortia and expand the toolbox available to engineers working to develop novel synthetic consortia.     

微生物菌群发酵生产化学品的研究进展

廉价生物质资源的利用是工业生物技术领域研究的热点,复杂的成分和较多的杂质使传统的单菌发酵方式难以应对,成为产业化的关键问题。文中从微生物菌群的工业应用、微生物菌群发酵与纯种发酵的比较、微生物细胞间的相互作用等方面综述了微生物菌群发酵技术的最新研究进展,并对微生物菌群的设计和应用进行了展望。微生物菌群发酵可以充分利用廉价生物质基质、生产多个产品或减少副产物的生成,在生物基化学品和燃料的生产中将是一种有前景的发酵技术。     

Biogeography, evolution, and diversity of epibionts in phototrophic consortia

Motile phototrophic consortia are highly regular associations in which numerous cells of green sulfur bacteria surround a flagellated colorless beta-proteobacterium in the center. To date, seven different morphological types of such consortia have been described. In addition, two immotile associations involving green sulfur bacteria are known. By employing a culture-independent approach, different types of phototrophic consortia were mechanically isolated by micromanipulation from 14 freshwater environments, and partial 16S rRNA gene sequences of the green sulfur bacterial epibionts were determined. In the majority of the lakes investigated, different types of phototrophic consortia were found to co-occur. In all cases, phototrophic consortia with the same morphology from the same habitat contained only a single epibiont phylotype. However, morphologically indistinguishable phototrophic consortia collected from different lakes contained different epibionts. Overall, 19 different types of epibionts were detected in the present study. Whereas the epibionts within one geographic region were very similar (Dice coefficient, 0.582), only two types of epibionts were found to occur on both the European and North American continents (Dice coefficient, 0.190). None of the epibiont 16S rRNA gene sequences have been detected so far in free-living green sulfur bacteria, suggesting that the interaction between epibionts and chemotrophic bacteria in the phototrophic consortia is an obligate interaction. Based on our phylogenetic analysis, the epibiont sequences are not monophyletic. Thus, the ability to form symbiotic associations either arose independently from different ancestors or was present in a common ancestor prior to the radiation of green sulfur bacteria and the transition to the free-living state in independent lineages. The present study thus demonstrates that there is great diversity and nonrandom geographical distribution of phototrophic consortia in the natural environment.     

Microbial characterization of toluene-degrading denitrifying consortia obtained from terrestrial and marine ecosystems

The degradation characteristics of toluene coupled to nitrate reduction were investigated in enrichment culture and the microbial communities of toluene-degrading denitrifying consortia were characterized by denaturing gradient gel electrophoresis (DGGE) technique. Anaerobic nitrate-reducing bacteria were enriched from oil-contaminated soil samples collected from terrestrial (rice field) and marine (tidal flat) ecosystems. Enriched consortia degraded toluene in the presence of nitrate as a terminal electron acceptor. The degradation rate of toluene was affected by the initial substrate concentration and co-existence of other hydrocarbons. The types of toluene-degrading denitrifying consortia depended on the type of ecosystem. The clone RS-7 obtained from the enriched consortium of the rice field was most closely related to a toluene-degrading and denitrifying bacterium, Azoarcus denitrificians (A. tolulyticus sp. nov.). The clone TS-11 detected in the tidal flat enriched consortium was affiliated to Thauera sp. strain S2 (T. aminoaromatica sp. nov.) that was able to degrade toluene under denitrifying conditions. This indicates that environmental factors greatly influence microbial communities obtained from terrestrial (rice field) and marine (tidal flat) ecosystems.     

Growth of Chlorinated Solvent‐Degrading Consortia in Fed‐Batch Bioreactors and Development of a Double‐Substrate High‐Performing Microbial Inoculum

The long‐term growth process of two microbial consortia effective in the aerobic cometabolic biodegradation of a mixture of 6‐chlorinated aliphatic hydrocarbons (CAHs), the effectiveness of these consortia as inocula for the bio‐augmentation of different types of microcosms and the development of a double‐substrate, high‐performing consortium is presented. The propane‐utilizing consortium generally proved to be the most effective one, being able to biodegrade vinyl chloride, cis‐ and trans‐1,2‐dichloroethylene, trichloroethylene, 1,1,2‐trichloroethane and 1,1,2,2‐tetrachloroethane at all the CAH concentrations tested (0–4 μM). Both consortia maintained unaltered CAH degradation capacities over a 300‐day growth period in the absence of the CAHs and were effective in inducing the rapid onset of CAH depletion upon inoculation in slurry microcosms set up with five types of aquifer materials. A consortium supplied with both methane and propane combined the best degradation capacities of the two single‐substrate consortia, and maintained stable performances for 150 days under slurry conditions. The degree of conversion of the organic Cl to chloride ions was equal to 90 %.     

Combinational quorum sensing devices for dynamic control in cross-feeding cocultivation

Quorum sensing (QS) offers cell density dependent dynamic regulations in cell culture through devices such as synchronized lysis circuit (SLC) and metabolic toggle switch (MTS). However, there is still a lack of studies on cocultivation with a combination of different QS-based devices. Taking the production of isopropanol and salidroside as case studies, we have mathematically modeled a comprehensive set of QS-regulated cocultivation schemes and constructed experimental combinations of QS devices, respectively, to evaluate their feasibility and optimality for regulating growth competition and corporative production. Glucose split ratio is proposed for the analysis of competition between cell growth and targeted production. Results show that the combination of different QS devices across multiple members offers a new tool with the potential to effectively coordinate synthetic microbial consortia for achieving high product titer in cross-feeding cocultivation. It is also evident that the performance of such systems is significantly affected by dynamic characteristics of chosen QS devices, carbon source control and the operational settings. This study offers insights for future applications of combinational QS devices in synthetic microbial consortia.