Compatible rhizosphere microbes mediated alleviation of biotic stress in chickpea through enhanced antioxidant and phenylpropanoid activities

The study was conducted to examine efficacy of a rhizospheric microbial consortium comprising of a fluorescent Pseudomonas (PHU094), Trichoderma (THU0816) and Rhizobium (RL091) strain on activation of physiological defense responses in chickpea against biotic stress caused by the collar rot pathogen Sclerotium rolfsii. Results of individual microbes were compared with dual and triple strain mixture treatments with reduced microbial load (1/2 and 1/3rd, respectively, of individual microbial load compared to single microbe application) in the mixtures. Periodical studies revealed maximum activities of phenylalanine ammonia lyase [E.C. 4.1.3.5] and polyphenol oxidase [E.C. 1.14.18.1] and accumulation of total phenol content in chickpea in the triple microbe consortium treated plants challenged with the pathogen compared to the single microbe and dual microbial consortia. Similarly, the expression of the antioxidant enzymes superoxide dismutase [E.C.1.15.1.1] and peroxidase [E.C.1.11.1.7] was also highest in the triple microbial consortium which was correlated with lesser lipid peroxidation in chickpea under the biotic stress. Histochemical staining clearly showed maximum and uniform lignification in vascular bundles of chickpea stem sections treated with the triple microbes. The physiological responses were directly correlated with the mortality rate as least plant mortality was recorded in the triple microbe consortium treated plants. The results thus suggest an augmented elicitation of stress response in chickpea under S. rolfsii stress by the triple microbial consortium in a synergistic manner under reduced microbial load.     

Microbial consortium-mediated reprogramming of defence network in pea to enhance tolerance against Sclerotinia sclerotiorum

Aims: To evaluate the potentiality of three rhizosphere microorganisms in suppression of Sclerotinia rot in pea in consortia mode and their impact on host defence responses. Methods and Results: Pseudomonas aeruginosa PJHU15, Trichoderma harzianum TNHU27 and Bacillus subtilis BHHU100 from rhizospheric soils were selected based on compatibility, antagonistic and plant growth promotion activities. The microbes were used as consortia to assess their ability to trigger the phenylpropanoid and antioxidant activities and accumulation of proline, total phenol and pathogenesis‐related (PR) proteins in pea under the challenge of the soft‐rot pathogen Sclerotinia sclerotiorum. The triple‐microbe consortium and single‐microbe treatments showed 1·4–2·3 and 1·1–1·7‐fold increment in defence parameters, respectively, when compared to untreated challenged control. Activation of the phenylpropanoid pathway and accumulation of total phenolics were highest at 48 h, whereas accumulation of proline and PR proteins along with activities of the antioxidant enzymes was highest at 72 h. Conclusions: The compatible microbial consortia triggered defence responses in an enhanced level in pea than the microbes alone and provided better protection against Sclerotinia rot. Significance and Impact of the Study: Rhizosphere microbes in consortium can enhance protection in pea against the soft‐rot pathogen through augmented elicitation of host defence responses.     

Artificial microbial consortia for bioproduction processes

The application of artificial microbial consortia for biotechnological production processes is an emerging field in research as it offers great potential for the improvement of established as well as the development of novel processes. In this review, we summarize recent highlights in the usage of various microbial consortia for the production of, for example, platform chemicals, biofuels, or pharmaceutical compounds. It aims to demonstrate the great potential of co-cultures by employing different organisms and interaction mechanisms and exploiting their respective advantages. Bacteria and yeasts often offer a broad spectrum of possible products, fungi enable the utilization of complex lignocellulosic substrates via enzyme secretion and hydrolysis, and microalgae can feature their abilities to fixate CO₂ through photosynthesis for other organisms as well as to form lipids as potential fuelstocks. However, the complexity of interactions between microbes require methods for observing population dynamics within the process and modern approaches such as modeling or automation for process development. After shortly discussing these interaction mechanisms, we aim to present a broad variety of successfully established co-culture processes to display the potential of artificial microbial consortia for the production of biotechnological products.     

Pesticide relevance and their microbial degradation: a-state-of-art

The extensive use of pesticide causes imbalance in properties of soil, water and air environments due to having problem of natural degradation. Such chemicals create diverse environmental problem via biomagnifications. Currently, microbial degradation is one of the important techniques for amputation and degradation of pesticide from agricultural soils. Some studies have reported that the genetically modified microorganism has ability to degrade specific pesticide but problem is that they cannot introduce in the field because they cause some other environmental problems. Only combined microbial consortia of indigenous and naturally occurring microbes isolated from particular contaminated environment have ability to degrade pesticides at faster rate. The bioaugumentation processes like addition of necessary nutrients or organic matter are required to speed up the rate of degradation of a contaminant by the indigenous microbes. The use of indigenous microbial strains having plant growth activities is ecologically superior over the chemical methods. In this review, we have attempted to discuss the recent challenge of pesticide problem in soil environment and their biodegradation with the help of effective indigenous pesticides degrading microorganisms. Further, we highlighted and explored the molecular mechanism for the pesticide degradation in soil with effective indigenous microbial consortium. This review suggests that the use of pesticide degrading microbial consortia which is an eco-friendly technology may be suitable for the sustainable agriculture production.     

Emerging Molecular Tools for Engineering Phytomicrobiome

Microbial plant interaction plays a major role in the sustainability of plants. The understanding of phytomicrobiome interactions enables the gene-editing tools for the construction of the microbial consortia. In this interaction, microbes share several common secondary metabolites and terpenoid metabolic pathways with their host plants that ensure a direct connection between the microbiome and associated plant metabolome. In this way, the CRISPR-mediated gene-editing tool provides an attractive approach to accomplish the creation of microbial consortia. On the other hand, the genetic manipulation of the host plant with the help of CRISPR-Cas9 can facilitate the characterization and identification of the genetic determinants. It leads to the enhancement of microbial capacity for more trait improvement. Many plant characteristics like phytovolatilization, phytoextraction, phytodesalination and phytodegradation are targeted by these approaches. Alternatively, chemical communications by PGPB are accomplished by the exchange of different signal molecules. For example, quorum-sensing is the way of the cell to cell communication in bacteria that lead to the detection of metabolites produced by pathogens during adverse conditions and also helpful in devising some tactics towards understanding plant immunity. Along with quorum-sensing, different volatile organic compounds and N-acyl homoserine lactones play a significant role in cell to cell communication by microbe to plant and among the plants respectively. Therefore, it is necessary to get details of all the significant approaches that are useful in exploring cell to cell communications. In this review, we have described gene-editing tools and the cell to cell communication process by quorum-sensing based signaling. These signaling processes via CRISPR- Cas9 mediated gene editing can improve the microbe-plant community in adverse climatic conditions.     

Enhancement of methane production from cassava residues by biological pretreatment using a constructed microbial consortium

In the study, a stable thermophilic microbial consortium with high cellulose-degradation ability was successfully constructed. That several species of microbes coexisted in this consortium was proved by DGGE (denaturing gradient gel electrophoresis) and sequence analysis. The cooperation and symbiosis of these microbes in this consortium enhanced their cellulose-degradation ability. The pretreatment of cassava residues mixing with distillery wastewater prior to anaerobic digestion was investigated by using this microbial consortium as inoculums in batch bioreactors at 55 °C. The experimental results showed that the maximum methane yield (259.46 mL/g-VS) of cassava residues was obtained through 12 h of pretreatment by this microbial consortium, which was 96.63% higher than the control (131.95 mL/g-VS). In addition, it was also found that the maximum methane yield is obtained when the highest filter paper cellulase (FPase), carboxymethyl cellulase (CMCase) and xylanase activity and soluble COD (sCOD) are produced.     

Dynamics of microbial competition,commensalism, and cooperation and its implications for coculture and microbiome engineering

Microbial consortium is a complex adaptive system with higher‐order dynamic characteristics that are not present by individual members. To accurately predict the social interactions, we formulate a set of unstructured kinetic models to quantitatively capture the dynamic interactions of multiple microbial species. By introducing an interaction coefficient, we analytically derived the steady‐state solutions for the interacting species and the substrate‐depleting profile in the chemostat. We analyzed the stability of the possible coexisting states defined by competition, parasitism, amensalism, commensalism, and cooperation. Our model predicts that only parasitism, commensalism, and cooperation could lead to stable coexisting states. We also determined the optimal social interaction criteria of microbial coculture when sequential metabolic reactions are compartmentalized into two distinct species. Coupled with Luedeking–Piret and Michaelis–Menten equations, accumulation of metabolic intermediates in one species and formation of end‐product in another species could be derived and assessed. We discovered that parasitism consortia disfavor the bioconversion of intermediate to final product; and commensalism consortia could efficiently convert metabolic intermediates to final product and maintain metabolic homeostasis with a broad range of operational conditions (i.e., dilution rates); whereas cooperative consortia leads to highly nonlinear pattern of precursor accumulation and end‐product formation. The underlying dynamics and emergent properties of microbial consortia may provide critical knowledge for us to understand ecological coexisting states, engineer efficient bioconversion process, deliver effective gut therapeutics as well as elucidate probiotic‐pathogen or tumor‐host interactions in general.     

A programmable Escherichia coli consortium via tunable symbiosis

Synthetic microbial consortia that can mimic natural systems have the potential to become a powerful biotechnology for various applications. One highly desirable feature of these consortia is that they can be precisely regulated. In this work we designed a programmable, symbiotic circuit that enables continuous tuning of the growth rate and composition of a synthetic consortium. We implemented our general design through the cross-feeding of tryptophan and tyrosine by two E. coli auxotrophs. By regulating the expression of genes related to the export or production of these amino acids, we were able to tune the metabolite exchanges and achieve a wide range of growth rates and strain ratios. In addition, by inverting the relationship of growth/ratio vs. inducer concentrations, we were able to "program" the co-culture for pre-specified attributes with the proper addition of inducing chemicals. This programmable proof-of-concept circuit or its variants can be applied to more complex systems where precise tuning of the consortium would facilitate the optimization of specific objectives, such as increasing the overall efficiency of microbial production of biofuels or pharmaceuticals.     

Mixed PGPR consortium: an effective modulator of antioxidant network for management of collar rot in cauliflower

Abstract

Sclerotinia sclerotiorum is a cosmopolitan fungal pathogen causing stem and collar watery soft rot of cauliflower. Previous management of this disease with chemical pesticides caused hazardous results which lead to use of more eco-friendly microbial approaches. In the present study, consortia of Trichoderma harzianum TNHU27 and Pseudomonas aeruginosa PJHU15 were assessed for their ability in controlling Sclerotinia rot in cauliflower. The seedlings of cauliflower were challenged singly and in consortium with these two compatible microbes. The plants were evaluated upon challenge inoculation with S. sclerotiorum for changes in total phenolic content, the activity of defense and antioxidative enzymes. The microbial consortium comprising of T. harzianum and P. aeruginosa significantly enhanced the defense responses of the plant in comparison to pathogen challenged and unchallenged control. The study elucidates that plant beneficial microbes in the consortium may provide superior protection by induction of faster and enhanced defense responses in comparison to unchallenged and single microbe challenged plants under pathogen challenged conditions.     

Engineering microbial consortia: a new frontier in synthetic biology

Microbial consortia are ubiquitous in nature and are implicated in processes of great importance to humans, from environmental remediation and wastewater treatment to assistance in food digestion. Synthetic biologists are honing their ability to program the behavior of individual microbial populations, forcing the microbes to focus on specific applications, such as the production of drugs and fuels. Given that microbial consortia can perform even more complicated tasks and endure more changeable environments than monocultures can, they represent an important new frontier for synthetic biology. Here, we review recent efforts to engineer synthetic microbial consortia, and we suggest future applications.     

Biotransformation of 2,4-dinitrotoluene in a phototrophic co-culture of engineered Synechococcus elongatus and Pseudomonas putida

In contrast to the current paradigm of using microbial mono-cultures in most biotechnological applications, increasing efforts are being directed towards engineering mixed-species consortia to perform functions that are difficult to programme into individual strains. In this work, we developed a synthetic microbial consortium composed of two genetically engineered microbes, a cyanobacterium (Synechococcus elongatus PCC 7942) and a heterotrophic bacterium (Pseudomonas putida EM173). These microbial species specialize in the co-culture: cyanobacteria fix CO₂ through photosynthetic metabolism and secrete sufficient carbohydrates to support the growth and active metabolism of P. putida, which has been engineered to consume sucrose and to degrade the environmental pollutant 2,4-dinitrotoluene (2,4-DNT). By encapsulating S. elongatus within a barium–alginate hydrogel, cyanobacterial cells were protected from the toxic effects of 2,4-DNT, enhancing the performance of the co-culture. The synthetic consortium was able to convert 2,4-DNT with light and CO₂ as key inputs, and its catalytic performance was stable over time. Furthermore, cycling this synthetic consortium through low nitrogen medium promoted the sucrose-dependent accumulation of polyhydroxyalkanoate, an added-value biopolymer, in the engineered P. putida strain. Altogether, the synthetic consortium displayed the capacity to remediate the industrial pollutant 2,4-DNT while simultaneously synthesizing biopolymers using light and CO₂ as the primary inputs.     

Consortia of cyanobacteria/microalgae and bacteria: biotechnological potential

Microbial metabolites are of huge biotechnological potential and their production can be coupled with detoxification of environmental pollutants and wastewater treatment mediated by the versatile microorganisms. The consortia of cyanobacteria/microalgae and bacteria can be efficient in detoxification of organic and inorganic pollutants, and removal of nutrients from wastewaters, compared to the individual microorganisms. Cyanobacterial/algal photosynthesis provides oxygen, a key electron acceptor to the pollutant-degrading heterotrophic bacteria. In turn, bacteria support photoautotrophic growth of the partners by providing carbon dioxide and other stimulatory means. Competition for resources and cooperation for pollutant abatement between these two guilds of microorganisms will determine the success of consortium engineering while harnessing the biotechnological potential of the partners. Relative to the introduction of gene(s) in a single organism wherein the genes depend on the regulatory- and metabolic network for proper expression, microbial consortium engineering is easier and achievable. The currently available biotechnological tools such as metabolic profiling and functional genomics can aid in the consortium engineering. The present review examines the current status of research on the consortia, and emphasizes the construction of consortia with desired partners to serve a dual mission of pollutant removal and commercial production of microbial metabolites.     

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.     

Interspecific interactions in mixed microbial cultures in a biodegradation perspective

In recent works, microbial consortia consisting of various bacteria and fungi exhibited a biodegradation performance superior to single microbial strains. A highly efficient biodegradation of synthetic dyes, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, and other organic pollutants can be achieved by mixed microbial cultures that combine degradative enzyme activities inherent to individual consortium members. This review summarizes biodegradation results obtained with defined microbial cocultures and real microbial consortia. The necessity of using a proper strategy for the microbial consortium development and optimization was clearly demonstrated. Molecular genetic and proteomic techniques have revolutionized the study of microbial communities, and techniques such as the denaturing gradient gel electrophoresis, rRNA sequencing, and metaproteomics have been used to identify consortium members and to study microbial population dynamics. These analyses could help to further enhance and optimize the natural activities of mixed microbial cultures.     

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.     

Temporal stability and biodiversity of two complex antilisterial cheese-ripening microbial consortia

The temporal stability and diversity of bacterial species composition as well as the antilisterial potential of two different, complex, and undefined microbial consortia from red-smear soft cheeses were investigated. Samples were collected twice, at 6-month intervals, from each of two food producers, and a total of 400 bacterial isolates were identified by Fourier-transform infrared spectroscopy and 16S ribosomal DNA sequence analysis. Coryneform bacteria represented the majority of the isolates, with certain species being predominant. In addition, Marinolactobacillus psychrotolerans, Halomonas venusta, Halomonas variabilis, Halomonas sp. (10(6) to 10(7) CFU per g of smear), and an unknown, gram-positive bacterium (10(7) to 10(8) CFU per g of smear) are described for the first time in such a consortium. The species composition of one consortium was quite stable over 6 months, but the other consortium revealed less diversity of coryneform species as well as less stability. While the first consortium had a stable, extraordinarily high antilisterial potential in situ, the antilisterial activity of the second consortium was lower and decreased with time. The cause for the antilisterial activity of the two consortia remained unknown but is not due to the secretion of soluble, inhibitory substances by the individual components of the consortium. Our data indicate that the stability over time and a potential antilisterial activity are individual characteristics of the ripening consortia which can be monitored and used for safe food production without artificial preservatives.     

Environments that induce synthetic microbial ecosystems

Interactions between microbial species are sometimes mediated by the exchange of small molecules, secreted by one species and metabolized by another. Both one-way (commensal) and two-way (mutualistic) interactions may contribute to complex networks of interdependencies. Understanding these interactions constitutes an open challenge in microbial ecology, with applications ranging from the human microbiome to environmental sustainability. In parallel to natural communities, it is possible to explore interactions in artificial microbial ecosystems, e.g. pairs of genetically engineered mutualistic strains. Here we computationally generate artificial microbial ecosystems without re-engineering the microbes themselves, but rather by predicting their growth on appropriately designed media. We use genome-scale stoichiometric models of metabolism to identify media that can sustain growth for a pair of species, but fail to do so for one or both individual species, thereby inducing putative symbiotic interactions. We first tested our approach on two previously studied mutualistic pairs, and on a pair of highly curated model organisms, showing that our algorithms successfully recapitulate known interactions, robustly predict new ones, and provide novel insight on exchanged molecules. We then applied our method to all possible pairs of seven microbial species, and found that it is always possible to identify putative media that induce commensalism or mutualism. Our analysis also suggests that symbiotic interactions may arise more readily through environmental fluctuations than genetic modifications. We envision that our approach will help generate microbe-microbe interaction maps useful for understanding microbial consortia dynamics and evolution, and for exploring the full potential of natural metabolic pathways for metabolic engineering applications.     

Metabolomic profiling elucidates community dynamics of the Ketogulonicigenium vulgare–Bacillus megaterium consortium

Many microbial consortia are established upon metabolic interactions. Elucidating such interactions is a priority in understanding the population dynamics of these microbial consortia. In this study, we investigated the interaction dynamics of the vitamin C biosynthesis consortium comprising of Ketogulonicigenium vulgare and Bacillus megaterium. We systematically quantified the dynamic evolution of the ecosystem??s population and metabolism in response to a wide range of seeding concentrations and compositions of the two microorganisms. The consortium population dynamics was determined by quantitative PCR. The metabolomic profile of the community was systematically investigated by gas chromatography coupled with time-of-flight mass spectrometry. Our results showed that B. megaterium was responsible for initiating the reproduction of K. vulgare, meanwhile, K. vulgare could promote the growth of B. megaterium. Principal component analysis of the metabolomic profiling elucidated variations of intermediates in central carbon metabolism, nucleotide and amino acids metabolism in this microbial consortium. These findings provided new insights into the characterization of the community dynamics and the optimization of co-culture fermentation for vitamin C biosynthesis.