Evaluation of simplified ester-linked fatty acid analysis (ELFA) for phospholipid fatty acid (PLFA) analysis of bacterial population.

Phospholipid fatty acid (PLFA) analysis is used for characterizing microbial communities based on their lipid profiles. This method avoids biases from PCR or culture, allowing data collection in a natural state. However, PLFA is labor-intensive due to lipid fractionation. Simplified ester-linked fatty acid analysis (ELFA), which skips lipid fractionation, offers an alternative. It utilizes base-catalyzed methylation to derivatize only lipids, not free fatty acids, and found glycolipid and neutral lipid fractions are scarcely present in most bacteria, allowing lipid fractionation to be skipped. ELFA method showed a high correlation to PLFA data (r = 0.99) and higher sensitivity than the PLFA method by 1.5-2.57-fold, mainly due to the higher recovery of lipids, which was 1.5-1.9 times higher than with PLFA. The theoretical limit of detection (LOD) and limit of quantification (LOQ) for the ELFA method indicated that 1.54-fold less sample was needed for analysis than with the PLFA method. Our analysis of three bacterial cultures and a simulated consortium revealed the effectiveness of the ELFA method by its simple procedure and enhanced sensitivity for detecting strain-specific markers, which were not detected in PLFA analysis. Overall, this method could be easily used for the population analysis of synthetic consortia.

Enhancing Pisum sativum growth and symbiosis under heat stress: the synergistic impact of co-inoculated bacterial consortia and ACC deaminase-lacking Rhizobium.

The 1-aminocyclopropane-1-carboxylate (ACC) deaminase is a crucial bacterial trait, yet it is not widely distributed among rhizobia. Hence, employing a co-inoculation approach that combines selected plant growth-promoting bacteria with compatible rhizobial strains, especially those lacking ACC deaminase, presents a practical solution to alleviate the negative effects of diverse abiotic stresses on legume nodulation. Our objective was to explore the efficacy of three non-rhizobial endophytes, Phyllobacterium salinisoli (PH), Starkeya sp. (ST) and Pseudomonas turukhanskensis (PS), isolated from native legumes grown in Tunisian arid regions, in improving the growth of cool-season legume and fostering symbiosis with an ACC deaminase-lacking rhizobial strain under heat stress. Various combinations of these endophytes (ST + PS, ST + PH, PS + PH, and ST + PS + PH) were co-inoculated with Rhizobium leguminosarum 128C53 or its ΔacdS mutant derivative on Pisum sativum plants exposed to a two-week heat stress period.Our findings revealed that the absence of ACC deaminase activity negatively impacted both pea growth and symbiosis under heat stress. Nevertheless, these detrimental effects were successfully mitigated in plants co-inoculated with ΔacdS mutant strain and specific non-rhizobial endophytes consortia. Our results indicated that heat stress significantly altered the phenolic content of pea root exudates. Despite this, there was no impact on IAA production. Interestingly, these changes positively influenced biofilm formation in consortia containing the mutant strain, indicating synergistic bacteria-bacteria interactions. Additionally, no positive effects were observed when these endophytic consortia were combined with the wild-type strain. This study highlights the potential of non-rhizobial endophytes to improve symbiotic performance of rhizobial strains lacking genetic mechanisms to mitigate stress effects on their legume host, holding promising potential to enhance the growth and yield of targeted legumes by boosting symbiosis.

Bidirectional Enhancement of Nitrogen Removal by Indigenous Synergetic Microalgal-Bacterial Consortia in Harsh Low-C/N Wastewater.

Conventional microalgal-bacterial consortia have limited capacity to treat low-C/N wastewater due to carbon limitation and single nitrogen (N) removal mode. In this work, indigenous synergetic microalgal-bacterial consortia with high N removal performance and bidirectional interaction were successful in treating rare earth tailing wastewaters with low-C/N. Ammonia removal reached 0.89 mg N L-1 h-1, 1.84-fold more efficient than a common microalgal-bacterial system. Metagenomics-based metabolic reconstruction revealed bidirectional microalgal-bacterial interactions. The presence of microalgae increased the abundance of bacterial N-related genes by 1.5- to 57-fold. Similarly, the presence of bacteria increased the abundance of microalgal N assimilation by 2.5- to 15.8-fold. Furthermore, nine bacterial species were isolated, and the bidirectional promotion of N removal by the microalgal-bacterial system was verified. The mechanism of microalgal N assimilation enhanced by indole-3-acetic acid was revealed. In addition, the bidirectional mode of the system ensured the scavenging of toxic byproducts from nitrate metabolism to maintain the stability of the system. Collectively, the bidirectional enhancement system of synergetic microalgae-bacteria was established as an effective N removal strategy to broaden the stable application of this system for the effective treatment of low C/N ratio wastewater.

Fungal-bacterial consortia: A promising strategy for the removal of petroleum hydrocarbons.

Nowadays, petroleum hydrocarbon pollution is one of the most widespread types of contamination that poses a serious threat to both public health and the environment. Among various physicochemical methods, bioremediation is an eco-friendly and cost-effective way to eliminate petroleum hydrocarbon pollutants. The successful degradation of all hydrocarbon components and the achievement of optimal efficiency are necessary for the success of this process. Using potential microbial consortia with rich metabolic networks is a promising strategy for addressing these challenges. Mixed microbial communities, comprising both fungi and bacteria, exhibit diverse synergistic mechanisms to degrade complex hydrocarbon contaminants, including the dissemination of bacteria by fungal hyphae, enhancement of enzyme and secondary metabolites production, and co-metabolism of pollutants. Compared to pure cultures or consortia of either fungi or bacteria, different studies have shown increased bioremediation of particular contaminants when combined fungal-bacterial treatments are applied. However, antagonistic interactions, like microbial competition, and the production of inhibitors or toxins can observed between members. Furthermore, optimizing environmental factors (pH, temperature, moisture, and initial contaminant concentration) is essential for consortium performance. With the advancements in synthetic biology and gene editing tools, it is now feasible to design stable and robust artificial microbial consortia systems. This review presents an overview of using microbial communities for the removal of petroleum pollutants by focusing on microbial degradation pathways, and their interactions. It also highlights the new strategies for constructing optimal microbial consortia, as well as the challenges currently faced and future perspectives of applying fungal-bacterial communities for bioremediation.

Sudden sulfamethoxazole shock leads to nitrite accumulation in microalgae-nitrifying bacteria consortia: Physiological responses and light regulating strategy.

Antibiotic shock may potentially impact the performance of promising microalgae-nitrifying bacteria consortia (MNBC) processes. This study investigated physiological behaviors of MNBC under sulfamethoxazole (SMX) shock (mg/L level) and verified a light regulating strategy for improving process performance. Results showed that SMX shock did not affect ammonium removal but caused nitrite accumulation, resulting from combined effects of excessive reactive oxidative species (ROS) production, inhibited microalgal photosynthetic activity, upregulated expressions of amoA and hao, and downregulated expression of nxrA. Moreover, high ammonium concentration aggravated nitrite accumulation and reduced ammonium removal owing to significantly reduced dissolved oxygen (DO). Increasing light intensity enhanced microalgal photo-oxygenation and promoted expressions of all nitrification-related genes, thus improving ammonium removal and alleviating nitrite accumulation. A central composite design coupled with response surface methodology (CCD-RSM) further demonstrated the negative impacts of SMX shock and high ammonium on MNBC and the effectiveness of the light regulation in maintaining stable process performance. This study provides theoretical basis for physiological responses and regulatory strategy of the MNBC process facing short-term antibiotic shock.

Construction of algal-bacterial consortia using green microalgae Chlorella vulgaris and As(III)-oxidizing bacteria: As tolerance and metabolomic profiling.

Bioremediation became a promising technology to resolve arsenic (As) contamination in aquatic environment. Since monoculture such as microalgae or bacteria was sensitive to environmental disturbance and vulnerable to contamination, green microalgae Chlorella vulgaris and arsenite (As(III)) - oxidizing bacteria Pseudomonas sp. SMS11 were co-cultured to construct algal-bacterial consortia in the current study. The effects of algae-bacteria (A:B) ratio and exposure As(III) concentration on algal growth, As speciation and metabolomic profile were investigated. Algal growth arrested when treated with 100 mg/L As(III) without the co-cultured bacteria. By contrast, co-cultured with strain SMS11 significantly enhanced As tolerance in C. vulgaris especially with A:B ratio of 1:10. All the As(III) in culture media of the consortia were oxidized into As(V) on day 7. Methylation of As was observed on day 14. Over 1% and 0.5% of total As were converted into dimethylarsinic acid (DMA) after 21 days cultivation when the initial concentrations of As(III) were 1 and 10 mg/L, respectively. Metabolomic analysis was further performed to reveal the response of consortia metabolites to external As(III). The enriched metabolomic pathways were associated with carbohydrate, amino acid and energy metabolisms. Tricarboxylic acid cycle and glyoxylate and dicarboxylate metabolism were upregulated under As stress due to their biological functions on alleviating oxidative stress and protecting cells. Both carbohydrate and amino acid metabolisms provided precursors and potential substrates for energy production and cell protection under abiotic stress. Alterations of the pathways relevant to carbohydrate or amino acid metabolism were triggered by energy requirement.

Identification of bacterial community in a rapid composting method using 16SrDNA genes sequencing.

Composting is a process of microbial degradation of organic waste and is commonly applied for waste management. This is a slow process and requires a lot of land and human resources. The present study investigated mechanical augmentation with required microbial culture for composting municipal solid waste (MSW). Thirty isolates were subjected to 16S rDNA PCR amplification and gene sequencing. The isolates' sequencing from the compost samples was processed on BLASTn. Fourteen strains were identified for further experiments. The results divulge that Empedobacter (04), Bacillus (02), Proteus (02), Lactiplantibacillus (01), Klebsiella (01), Citrobacter (01), Brevibacillus (01), E. coli (01) and one unidentified strain were growing during composting. Eleven combinations of bacterial consortium and respective additives were applied for the organic waste decomposition in the next stage, resulting in varied completion periods ranging from 3 to 14 days. Two combinations were completed within 3 days, which are considered ideal combinations for composting. The microbial consortium was significantly diverse, which is a reason for rapid biodegradation. The present study reveals that the technology will be highly feasible for municipal solid waste management in tropical/subtropical countries.

Isolation of bacterial consortia with probiotic potential from the rumen of tropical calves.

Probiotics are live microorganisms that confer health benefits to their animal host by balancing the composition of its gastrointestinal microbiota and modulating its immune response. In this work, we studied bacterial consortia isolated from the rumen of 28- and 42-day-old calves to select those showing probiotic capacity. Consortia were characterized and their growth dynamics were determined in several growth media. The number of viable bacteria was larger in the Man, Rogosa and Sharpe broth (MRS) than in nutritive medium A (MNA) and the largest was for A3D42. Antibiotic susceptibility of bacterial consortia in MRS was higher than in MNA and the most susceptible samples were A1D28 and A3D42. In turn, A3D42 showed the highest tolerance to bile salts in MRS and MNA. Moreover, all bacterial consortia showed optimal growth at pH 5, 5.5, 6 and 7 in both media, while their temperature tolerance was higher in MRS. The antagonistic activity of bacterial consortia in MNA was higher than in MRS with A2D42 showing the best antagonistic activity for Pseudomona aureginosa (ATCC 9027) and Staphylococcus aureus (ATCC 6538) in MNA. Additionally, A1D42 and A2D42 in MRS and A3D42 in MNA had significant adhesion to mucins, and A1D42 in MRS had the highest. Regarding their species composition, all bacterial consortia in MRS belonged to the phylum Firmicutes, and the class Bacilli and bacterial consortia in MNA belonged to three phyla; Proteobacteria, Firmicutes, and Bacteroidetes. Lactobacillus casei, Lactobacillus rhamnosus, Lactobacillus fermentum, and Lactobacillus johnsonii were identified in all bacterial consortia in MRS broth. Based on these results, A1D42 and A3D42 grown in MRS showed the best potential as probiotics for calves, which could result in health benefits and improve their production.

The bacterial consortia promote plant growth and secondary metabolite accumulation in Astragalus mongholicus under drought stress.

Astragalus mongholicus is a widely used Traditional Chinese Medicine. However, cultivated A. mongholicus is often threatened by water shortage at all growth stage, and the content of medicinal compounds of cultivated A. mongholicus is much lower than that of wild plants. To alleviate drought stress on A. mongholicus and improve the accumulation of medicinal components in roots of A. mongholicus, we combined different bacteria with plant growth promotion or abiotic stress resistance characteristics and evaluated the role of bacterial consortium in helping plants tolerate drought stress and improving medicinal component content in roots simultaneously. Through the determination of 429 bacterial strains, it was found that 97 isolates had phosphate solubilizing ability, 63 isolates could release potassium from potash feldspar, 123 isolates could produce IAA, 58 isolates could synthesize ACC deaminase, and 21 isolates could secret siderophore. Eight bacterial consortia were constructed with 25 bacterial isolates with more than three functions or strong growth promoting ability, and six out of eight bacterial consortia significantly improved the root dry weight. However, only consortium 6 could increase the root biomass, astragaloside IV and calycosin-7-glucoside content in roots simultaneously. Under drought challenge, the consortium 6 could still perform these functions. Compared with non-inoculated plants, the root dry weight of consortium inoculated-plants increased by 120.0% and 78.8% under mild and moderate drought stress, the total content of astragaloside IV increased by 183.83% and 164.97% under moderate and severe drought stress, calycosin-7-glucoside content increased by 86.60%, 148.56% and 111.45% under mild, moderate and severe drought stress, respectively. Meanwhile, consortium inoculation resulted in a decrease in MDA level, while soluble protein and proline content and SOD, POD and CAT activities increased. These findings provide novel insights about multiple bacterial combinations to improve drought stress responses and contribute to accumulate more medicinal compounds.

Soot biodegradation by psychrotolerant bacterial consortia.

To probe the bioavailability of soot released into the atmosphere is pivotal to understanding their environmental impacts. Soot aerosol absorbs organic matter, creating a hot spot for biogeochemical transformation and the global carbon cycle. Soot primarily contains condensed aromatics chemically recalcitrant; however, oligotrophic microorganisms might use it as a nutritional source. This study investigated the influence of psychrotolerant bacterial consortia on soot. Significant increase in the bacterial biomass, reduction in water-insoluble organic carbon (OC) and elemental carbon (EC) in soot residues and increase in water-soluble OC in the filtrate signifies the use of soot as a carbon and nutritional source. The influence on morphology and composition of soot was reported using Fourier Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy, and Energy Dispersive X-Ray analysis (EDX). The FTIR analysis showed significant variations in the pattern of soot spectra, suggesting degradation. Elemental analysis and EDX showed a reduction in carbon percentage. Besides, the reduction of optical density with incubation time signifies the OC and EC consumption. This study shows that soot can be a substrate and pivotal factor in the microbial food web. Nowadays, soot emission to the environment is growing; therefore, soot involvement in microbe-mediated processes should be closely focused.

Bioelectricity production and shortcut nitrogen removal by microalgal-bacterial consortia using membrane photosynthetic microbial fuel cell.

Membrane photosynthetic microbial fuel cell (MPMFC) utilizes O2, NO3- and NO2- as cathodic electron acceptors, enabling simultaneous treatment of nitrogen, CO2 and organic carbon in the cathode compartment. In this work, development of a novel cathodic process with in situ nitritation via microalgal photosynthesis during the light period is reported for achieving shortcut nitrogen removal (SNR) from ammonium-rich wastewater. Moreover, a tubular low-cost ceramic membrane was used to separate and recycle the microalgal-bacterial biomass to the cathode compartment during the continuous operation. The influence of NH4+ concentration and ratio of chemical oxygen demand to total nitrogen on the MPMFC performance was examined. Denitritation under dark and anoxic conditions occurred due to denitrifying bacteria (DNB) subsequent to nitritation under light and aerobic conditions by ammonia-oxidizing bacteria (AOB) in the consortia. Final concentrations of NH4+ and NO2- in the effluent of 0.10 mg NH4+-L-1 and 0.02 mg NO2--L-1, respectively, were obtained using MPMFC which resulted in a nitrogen removal efficiency of 99 ± 0.5%. The maximum electricity production achieved using the MPMFC was 56 ± 0.1 mA. This study demonstrated that combining microalgal photosynthesis, nitritation and denitritation in the cathode compartment of MPMFC is advantageous for avoiding the cost due to external aeration and organic carbon source necessary for ammonium removal as well as utilization of NO2- or NO3- as an electron acceptor.

Establishing causality in Salmonella-microbiota-host interaction: The use of gnotobiotic mouse models and synthetic microbial communities.

Colonization resistance (CR), the ability to block infections by potentially harmful microbes, is a fundamental function of host-associated microbial communities and highly conserved between animals and humans. Environmental factors such as antibiotics and diet can disturb microbial community composition and thereby predispose to opportunistic infections. The most prominent is Clostridioides difficile, the causative agent of diarrhea and pseudomembranous colitis. In addition, the risk to succumb to infections with genuine human enteric pathogens like nontyphoidal Salmonella (NTS) is also increased by a low-diverse, diet or antibiotic-disrupted microbiota. Despite extensive microbial community profiling efforts, only a limited set of microorganisms have been causally linked with protection against enteric pathogens. Furthermore, it remains a challenge to predict colonization resistance from complex microbiome signatures due to context-dependent action of microorganisms. In the past decade, the study of NTS infection has led to the description of several fundamental principles of microbiota-host-pathogen interaction. In this review, I will give an overview on the current state of knowledge in this field and outline experimental approaches to gain functional insight to the role of specific microbes, functions and metabolites in Salmonella-microbiota-host interaction. In particular, I will highlight the value of mouse infection models, which, in combination with culture collections, synthetic communities and gnotobiotic models have become essential tools to screen for protective members of the microbiota and establishing causal relationship and mechanisms in infection research.

Bacterial consortium biotransformation of pentachlorophenol contaminated wastewater.

The aims of this study were (i) to compare PCP removal (100 mg L-1) by two bacterial consortia B1 and B2 in sterile wastewater (STWW) and liquid mineral medium (MSM), (ii) PCP effect in biofilm formation and antimicrobial susceptibility. PCP removal was measured by high-performance liquid chromatography (HPLC) during 168 h at 30 °C. Biofilm formation was assessed with two approaches: Congo Red Agar and Microtiter-plate. Antimicrobial susceptibility was determined by the agar disc diffusion technique. The results showed that the PCP removal for consortium B1 and B2 after 168 h was 70 and 97.5% in STWW; 62.2 and 85.5% in MSM, respectively. In addition, PCP addition showed an increase in biofilm development especially for B2 consortium around 3.5 nm in 100 mg L-1 PCP. PCP added in the Muller Hinton (MH) medium and Gentamicin disc showed a clear increase in diameter of cell lysis around 2 to 4.5 cm.

Novel consortia of enterobacter and pseudomonas formulated from cow dung exhibited enhanced biodegradation of polyethylene and polypropylene.

This study prioritizes the biodegradation potential of novel bacterial consortia formulated from cow dung samples towards low-density polyethylene (LDPE) and polypropylene (PP) in comparison with our previous studies. Ten possible consortia were formulated using 10 selected isolates with >10% weight reduction of LDPE and PP, these were pre-treated under UV for 1 h, and their biodegradation potential was studied for 160 days. The isolates present in prioritized consortia were characterized by standard microbiology and 16SrRNA gene sequencing methods. Out of 10 bacterial consortia formulated, potential consortium-CB3 showed greater percentage degradation (weight reduction) of 64.25 ± 2% and 63.00 ± 2% towards LDPE and PP films, respectively (p < 0.05) at 37 °C compared to other consortia. Significant structural variations due to the formation of bacterial biofilm were observed in CB3 treated LDPE and PP films. The three bacteria-IS1, IS2, and IS3-that constituted CB3 were found to be novel strains and designated to be Enterobacter sp nov. bt DSCE01, Enterobacter cloacae nov. bt DSCE02, and Pseudomonas aeruginosa nov. bt DSCE-CD03, respectively. This novel consortium can be scaled up for enhanced degradation of plastic polymers and probably design cost-effective bio-digester for industrial applications using CB3 as potential inoculum.

Optimization of complete RB-5 azo dye decolorization using novel cold-adapted and mesophilic bacterial consortia.

Azo dyes are an important group of recalcitrant xenobiotics, which are difficult to degrade and deteriorate in cold environments. In this study, two microbial consortia consisting of cold-adapted and mesophilic bacteria were developed for effective decolorization of Reactive Black-5 azo dye. These bacteria were isolated from textile wastewater and soil of a cold region. Identification of bacterial isolates using 16s rRNA gene analysis revealed that they belong to genus Pseudoarthrobacter, Gordonia, Stenotrophomonas, and Sphingomonas. Decolorization assay was performed for every strain at dye concentrations of 25, 50 and 100 mg/L and the consortia PsGo consisting of mesophilic bacteria and StSp consisting of cold-adapted bacteria were constructed accordingly. Results showed that the consortia PsGo and StSp were able to decolorize 54 and 34 percent of RB-5 (50 mg/L) during 7 days. To improve the dye removal efficiency of the consortia, several parameters including temperature, pH, carbon and nitrogen sources were optimized. Over longer periods, StSp consortium managed to completely decolorize RB-5 (50 mg/L) at optimized conditions of 25-30 °C, pH 9, and using glucose and NH4H2PO4 as carbon and nitrogen source respectively, whereas PsGo consortium decolorized RB-5 (50 mg/mL) completely at 37 °C, pH 11, and with lactose and NH4H2PO4 used as carbon and nitrogen sources. Kinetic of reactions for StSp and PsGo consortia were found to be 0.05 and 0.13 day-1 respectively, but became 0.71 and 0.9 day-1 after optimization. In general, cold ecosystems are good sources for the isolation of novel bacterial strains with a potential application, especially when used as consortia, in environmental biotechnology such as decolorization of RB-5.

Development of a bacterial consortium comprising oil-degraders and diazotrophic bacteria for elimination of exogenous nitrogen requirement in bioremediation of diesel-contaminated soil.

The purpose of this study was to develop an effective bacterial consortium and determine their ability to overcome nitrogen limitation for the enhanced remediation of diesel-contaminated soils. Towards this, various bacterial consortia were constructed using oil-degrading and nitrogen-fixing microbes. The diesel removal efficiency of various developed consortia was evaluated by delivering the bacterial consortia to the diesel-contaminated soils. The consortium Acinetobacter sp. K-6 + Rhodococcus sp. Y2-2 + NH4NO3 resulted in the highest removal (85.3%) of diesel from the contaminated soil. The consortium containing two different oil-degrading microbes (K-6 + Y2-2) and one nitrogen-fixing microbe Azotobacter vinelandii KCTC 2426 removed 83.1% of the diesel from the soil after 40 days of treatment. The total nitrogen content analysis revealed higher amounts of nitrogen in soil treated with the nitrogen-fixing microbe when compared with that of the soil supplemented with exogenous inorganic nitrogen. The findings in this present study reveal that the consortium containing the nitrogen-fixing microbe degraded similar amounts of diesel to that degraded by the consortium supplemented with exogenous inorganic nitrogen. This suggests that the developed consortium K-6 + Y2-2 + KCTC 2426 compensated for the nitrogen limitation and eliminated the need for exogenous nitrogen in bioremediation of diesel-contaminated soils.

Functional relevance of microbiome signatures: The correlation era requires tools for consolidation.

Compelling research over the past decade identified a fundamental role of the intestinal microbiome on human health. Compositional and functional changes of this microbial ecosystem are correlated with a variety of human pathologies. Metagenomic resolution and bioinformatic tools considerably improved, allowing even strain-level analysis. However, the search for microbial risk patterns in human cohorts is often confounded by environmental factors (eg, medication) and host status (eg, disease relapse), questioning the prognostic and therapeutic value of the currently available information. In addition to a better stratification of human phenotypes, the implementation of standardized protocols for sampling and analysis is needed to improve the reproducibility and comparability of microbiome signatures at a meaningful taxonomic resolution. At the level of mechanistic understanding, the molecular integration of pleiotropic signals coming from this complex and dynamically changing ecosystem is one of the biggest challenges in this field. The first successful attempts to apply reverse genetics based on the available metagenomic information yielded identification of small molecules and metabolites with functional relevance for microbe-host interactions. Further expansion on the isolation of bacteria from the "unculturable biomass" will help characterize microbiome signatures in model systems, finally aiming at the development of clinically relevant synthetic consortia with safe and functionally well-defined strains. In conclusion and beyond reasonable enthusiasm, the mechanistic implementation and clinical relevance of microbiome alterations on disease susceptibility is still in its infancy, but the integration of all the above-mentioned strategies will help overcome the correlation era in microbiome research and lead to a rational evaluation of clinical strategies relevant for targeted microbial intervention.

Contributions of Composition and Interactions to Bacterial Respiration Are Reliant on the Phylogenetic Similarity of the Measured Community.

Bacterial diversity underpins many ecosystem functions; however, the impact of within-species variation on the relationship between diversity and function remains unclear. Processes involving strain differentiation, such as niche radiation, are often overlooked in studies that focus on phylogenetic variation. This study used bacterial isolates assembled in two comparable microcosm experiments to test how species variation affected ecosystem function. We compared the relationship between diversity and activity (CO2 production) in increasingly diverse multispecies microcosms and with multiple ecotypes of a single species. The bacteria used were isolated from a low-diversity environment and are species of potential clinical significance such as Pseudomonas aeruginosa. All isolates were profiled for single carbon source utilisation. These data showed an increased breadth of resource use in the multiple ecotypes when compared to the mixed-species. The study observed significantly increasing respiration in more complex mixed-species assemblages, which was not observed when ecotypes of a single species were combined. We further demonstrate that the variation observed in the bacterial activity was due to the roles of each of the constituent isolates; between different species, the interactions between the isolates drove the variation in activity, whilst in single species, assemblage variation was due to which isolates were present. We conclude that both between- and within-species variations play different roles in community function, although through different mechanisms, and should be included in models of changing diversity and ecosystem functioning.

Assessment of bacterial biodetoxification of herbicide atrazine using Aliivibrio fischeri cytotoxicity assay with prolonged contact time.

In our study, we determined and compared the atrazine-biodetoxification ability of 41 bacterial strains and 21 consortia created of those with over 50% degradation rate in pure cultures. Biodegradation capacity was measured with GC-MS. Detoxification was assessed based on the cytotoxic effect of end-products to Aliivibrio fischeri in chronic bioluminescence inhibition assay with 25 h contact time. Chronic A. fischeri assay adapted to a microplate, which is suitable for examine numerous residues simultaneously, also appeared to be significantly more sensitive to atrazine compared to the standard acute (30 min) test. Due to its sensitivity, the chronic assay could be a valuable tool to provide a more comprehensive view of the ecological risks of atrazine and other chemicals. Thirteen strains were able to degrade more than 50% of 50 ppm atrazine. Four of these belong to Rhodococcus aetherivorans, R. qingshengii, Serratia fonticola and Olivibacter oleidegradans which species' atrazine degrading ability has never been reported before. Four consortia degrading ability was more effective than that of the creating individual strains; moreover, their residues did not show cytotoxic effects to A. fischeri. However, in several cases, the degradation products of sole strains and consortia resulted in significant bioluminescence inhibition. Thus high biodegradation (>90%) does not certainly mean the reduction or cessation of toxicity highlighting the importance of the evaluation of biological effects of degradation residues to improve the efficiency and abate the ecological risks of bioremediation techniques.

Engineering synthetic bacterial consortia for enhanced desulfurization and revalorization of oil sulfur compounds.

The 4S pathway is the most studied bioprocess for the removal of the recalcitrant sulfur of aromatic heterocycles present in fuels. It consists of three sequential functional units, encoded by the dszABCD genes, through which the model compound dibenzothiophene (DBT) is transformed into the sulfur-free 2-hydroxybiphenyl (2HBP) molecule. In this work, a set of synthetic dsz cassettes were implanted in Pseudomonas putida KT2440, a model bacterial "chassis" for metabolic engineering studies. The complete dszB1A1C1-D1 cassette behaved as an attractive alternative - to the previously constructed recombinant dsz cassettes - for the conversion of DBT into 2HBP. Refactoring the 4S pathway by the use of synthetic dsz modules encoding individual 4S pathway reactions revealed unanticipated traits, e.g., the 4S intermediate 2HBP-sulfinate (HBPS) behaves as an inhibitor of the Dsz monooxygenases, and once secreted from the cells it cannot be further taken up. That issue should be addressed for the rational design of more efficient biocatalysts for DBT bioconversions. In this sense, the construction of synthetic bacterial consortia to compartmentalize the 4S pathway into different cell factories for individual optimization was shown to enhance the conversion of DBT into 2HBP, overcome the inhibition of the Dsz enzymes by the 4S intermediates, and enable efficient production of unattainable high added value intermediates, e.g., HBPS, that are difficult to obtain using the current monocultures.