The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity

Lignin-derived compounds assisted with Kocuria marina H-2 and Pseudomonas putida B6-2 co-culture enhanced naphthalene biodegradation

The implementation of environmentally friendly and sustainable remediation strategies positively impacts solid waste management. In this study, the Kocuria marina H-2 and Pseudomonas putida B6-2 co-culture system demonstrated enhanced naphthalene biodegradation efficiency compared to single-strain cultures. Under optimal conditions of 35 °C, 200 rpm/min, and a 1:1 ratio of the co-culture system, the naphthalene biodegradation potential was further increased. Notably, the addition of both ethylenediamine-pretreated lignin and p-hydroxybenzoic acid significantly elevated naphthalene degradation rates to 68.5 %. In addition, the oil-liquid surface tension decreased, while cell surface hydrophobicity and colony-forming units increased with the addition of lignin-derived compounds. The modification of naphthalene bioavailability by ethylenediamine-pretreated lignin would accelerate the uptake and transport of hydrocarbons via ABC transporters and flagellar assembly. Importantly, genes related to bacterial chemotaxis and fatty acid biosynthesis were upregulated during the co-metabolism of naphthalene and p-hydroxybenzoic acid, further enhancing naphthalene bioconversion.

Developing defined starter culture for reproducible profile of flavour compound in Chinese xiaoqu baijiu fermentation

Defined starter cultures, containing selected microbes could reduce the complexity of natural starter, are beneficial for controllable food fermentations. However, there are challenges in identifying key microbiota and constructing synthetic microbiota for traditional food fermentations. Here, we aimed to develop a defined starter culture for reproducible profile of flavour compounds, using Chinese Xiaoqu Baijiu fermentation as a case. We classified all microbes into 4 modules using weighted correlation network analysis. Module 3 presented significant correlations with flavour compounds (P < 0.05) and the highest gene abundance related with flavour compound production. 13 dominant species in module 3 were selected for mixed culture fermentation, and each species was individually deleted to analyse the effect on flavour compound production. Ten species, presenting significant effects (P < 0.05) on flavour compound production, were selected for developing the starter culture, including Rhizopus oryzae, Rhizopus microsporus, Saccharomyces cerevisiae, Pichia kudriavzevii, Wickerhamomyces anomalus, Lactobacillus acetotolerans, Levilactobacillus brevis, Weissella paramesenteroides, Pediococcus acidilactici, and Leuconostoc pseudomesenteroides. After optimising the structure of the starter culture, the profile similarity of flavour compounds produced by the starter culture reached 81.88% with that by the natural starter. This work indicated feasibility of reproducible profile of flavour compounds with defined starter culture for food fermentations.

Lippia graveolens Essential Oil to Enhance the Effect of Imipenem against Axenic and Co-Cultures of Pseudomonas aeruginosa and Acinetobacter baumannii

This research focuses on assessing the synergistic effects of Mexican oregano (Lippia graveolens) essential oil or carvacrol when combined with the antibiotic imipenem, aiming to reduce the pathogenic viability and virulence of Acinetobacter baumannii and Pseudomonas aeruginosa. The study highlighted the synergistic effect of combining L. graveolens essential oil or carvacrol with imipenem, significantly reducing the required doses for inhibiting bacterial growth. The combination treatments drastically lowered the necessary imipenem doses, highlighting a potent enhancement in efficacy against A. baumannii and P. aeruginosa. For example, the minimum inhibitory concentrations (MIC) for the essential oil/imipenem combinations were notably low, at 0.03/0.000023 mg/mL for A. baumannii and 0.0073/0.000023 mg/mL for P. aeruginosa. Similarly, the combinations significantly inhibited biofilm formation at lower concentrations than when the components were used individually, demonstrating the strategic advantage of this approach in combating antibiotic resistance. For OXA-51, imipenem showed a relatively stable interaction during 30 ns of dynamic simulation of their interaction, indicating changes (<2 nm) in ligand positioning during this period. Carvacrol exhibited similar fluctuations to imipenem, suggesting its potential inhibition efficacy, while thymol showed significant variability, particularly at >10 ns, suggesting potential instability. With IMP-1, imipenem also displayed very stable interactions during 38 ns and demonstrated notable movement and positioning changes within the active site, indicating a more dynamic interaction. In contrast, carvacrol and thymol maintained their position within the active site only ~20 and ~15 ns, respectively. These results highlight the effectiveness of combining L. graveolens essential oil and carvacrol with imipenem in tackling the difficult-to-treat pathogens A. baumannii and P. aeruginosa.

Alleviation of cotton growth suppression caused by salinity through biochar is strongly linked to the microbial metabolic potential in saline-alkali soil

Biochar is a typical soil organic amendment; however, there is limited understanding of its impact on the metabolic characteristics of microorganisms in saline-alkaline soil microenvironment, as well as the advantages and disadvantages of plant-microorganism interactions. To elucidate the mechanisms underlying the impact of saline-alkali stress on cotton, a 6-month pot experiment was conducted, involving the sowing of cotton seedlings in saline-alkali soil. Three different biochar application levels were established: 0 % (C0), 1 % (C1), and 2 % (C2). Results indicated that biochar addition improved the biomass of cotton plants, especially under C2 treatment; the dry weight of cotton bolls were 8.15 times that of C0. Biochar application led to a rise in the accumulation of photosynthetic pigments by 8.30-51.89 % and carbohydrates by 7.4-10.7 times, respectively. Moreover, peroxidase (POD) activity, the content of glutathione (GSH), and ascorbic acid (ASA) were elevated by 23.97 %, 118.39 %, and 48.30 % under C2 treatment, respectively. Biochar caused a reduction in Na+ uptake by 8.21-39.47 %, relative electrical conductivity (REC) of plants, and improved K+/Na+ and Ca2+/Na+ ratio indicating that biochar alleviated salinity-caused growth reduction. Additionally, the application of biochar enhanced the absorption intensity of polysaccharide fingerprints in cotton leaves and roots. Two-factor co-occurrence analysis indicated that the key differential metabolites connected to several metabolic pathways were L-phenylalanine, piperidine, L-tryptophan, and allysine. Interestingly, biochar altered the metabolic characteristics of saline-alkali soil, especially related to the biosynthesis and metabolism of amino acids and purine metabolism. In conclusion, this study demonstrates that biochar may be advantageous in saline soil microenvironment; it has a favorable impact on how plants and soil microbial metabolism interact.

Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition

Understanding the organizational principles of microbial communities is essential for interpreting ecosystem stability. Previous studies have investigated the formation of bacterial communities under nutrient-poor conditions or obligate relationships to observe cooperative interactions among different species. How microorganisms form stabilized communities in nutrient-rich environments, without obligate metabolic interdependency for growth, is still not fully disclosed. In this study, three bacterial strains isolated from the Populus deltoides rhizosphere were co-cultured in complex medium, and their growth behavior was tracked. These strains co-exist in mixed culture over serial transfer for multiple growth-dilution cycles. Competition is proposed as an emergent interaction relationship among the three bacteria based on their significantly decreased growth levels. The effects of different initial inoculum ratios, up to three orders of magnitude, on community structure were investigated, and the final compositions of the mixed communities with various starting composition indicate that community structure is not dependent on the initial inoculum ratio. Furthermore, the competitive relationships within the community were not altered by different initial inoculum ratios. The community structure was simulated by generalized Lotka-Volterra and dynamic flux balance analysis to provide mechanistic predictions into emergence of community structure under a nutrient-rich environment. Metaproteomic analyses provide support for the metabolite exchanges predicted by computational modeling and for highly altered physiologies when microbes are grown in co-culture. These findings broaden our understanding of bacterial community dynamics and metabolic diversity in higher-order interactions and could be significant in the management of rhizospheric bacterial communities.

IMPORTANCE

Bacteria naturally co-exist in multispecies consortia, and the ability to engineer such systems can be useful in biotechnology. Despite this, few studies have been performed to understand how bacteria form a stable community and interact with each other under nutrient-rich conditions. In this study, we investigated the effects of initial inoculum ratios on bacterial community structure using a complex medium and found that the initial inoculum ratio has no significant impact on resultant community structure or on interaction patterns between community members. The microbial population profiles were simulated using computational tools in order to understand intermicrobial relationships and to identify potential metabolic exchanges that occur during stabilization of the bacterial community. Studying microbial community assembly processes is essential for understanding fundamental ecological principles in microbial ecosystems and can be critical in predicting microbial community structure and function.

Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium

Synthetic microbial communities have emerged as an attractive route for chemical bioprocessing. They are argued to be superior to single strains through microbial division of labor (DOL), but the exact mechanism by which DOL confers advantages remains unclear. Here, we utilize a synthetic Saccharomyces cerevisiae consortium along with mathematical modeling to achieve tunable mixed sugar fermentation to overcome the limitations of single-strain fermentation. The consortium involves two strains with each specializing in glucose or xylose utilization for ethanol production. By controlling initial community composition, DOL allows fine tuning of fermentation dynamics and product generation. By altering inoculation delay, DOL provides additional programmability to parallelly regulate fermentation characteristics and product yield. Mathematical models capture observed experimental findings and further offer guidance for subsequent fermentation optimization. This study demonstrates the functional potential of DOL in bioprocessing and provides insight into the rational design of engineered ecosystems for various applications.

Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization

IMPORTANCE

Synthetic communities (SynComs) are an invaluable tool to characterize and model plant-microbe interactions. Multimember SynComs approximate intricate real-world interactions between plants and their microbiome, but the complexity and time required for their construction increase enormously for each additional member added to the SynCom. Therefore, researchers who study a diversity of microbiomes using SynComs are looking for ways to simplify the use of SynComs. In this manuscript, we evaluate the feasibility of creating ready-to-use freezer stocks of a well-studied seven-member SynCom for maize roots. The frozen ready-to-use SynCom stocks work according to the principle of "just add buffer and apply to sterilized seeds or seedlings" and thus can save time applied in multiple days of laborious growing and combining of multiple microorganisms. We show that ready-to-use SynCom stocks provide comparable results to those of freshly constructed SynComs and thus allow for significant time savings when working with SynComs.

Metabolic interactions affect the biomass of synthetic bacterial biofilm communities

IMPORTANCE

Co-occurrence network analysis is an effective tool for predicting complex networks of microbial interactions in the natural environment. Using isolates from a rhizosphere, we constructed multi-species biofilm communities and investigated co-occurrence patterns between microbial species in genome-scale metabolic models and in vitro experiments. According to our results, metabolic exchanges and resource competition may partially explain the co-occurrence network analysis results found in synthetic bacterial biofilm communities.

Control points for design of taxonomic composition in synthetic human gut communities

Microbial communities offer vast potential across numerous sectors but remain challenging to systematically control. We develop a two-stage approach to guide the taxonomic composition of synthetic microbiomes by precisely manipulating media components and initial species abundances. By combining high-throughput experiments and computational modeling, we demonstrate the ability to predict and design the diversity of a 10-member synthetic human gut community. We reveal that critical environmental factors governing monoculture growth can be leveraged to steer microbial communities to desired states. Furthermore, systematically varied initial abundances drive variation in community assembly and enable inference of pairwise inter-species interactions via a dynamic ecological model. These interactions are overall consistent with conditioned media experiments, demonstrating that specific perturbations to a high-richness community can provide rich information for building dynamic ecological models. This model is subsequently used to design low-richness communities that display low or high temporal taxonomic variability over an extended period. A record of this paper's transparent peer review process is included in the supplemental information.

Detection of micro-plasma-induced exosomes secretion in a fibroblast-melanoma co-culture model

BACKGROUND

Melanoma is a highly aggressive tumor and a significant cause of skin cancer-related death. Timely diagnosis and treatment require identification of specific biomarkers in exosomes secreted by melanoma cells. In this study, label-free surface-enhanced Raman spectroscopy (SERS) method with size-matched selectivity was used to detect membrane proteins in exosomes released from a stimulated environment of fibroblasts (L929) co-cultured with melanoma cells (B16-F10). To promote normal secretion of exosomes, micro-plasma treatment was used to gently induce the co-cultured cells and slightly increase the stress level around the cells for subsequent detection using the SERS method.

RESULTS AND DISCUSSION

Firstly, changes in reactive oxygen species/reactive nitrogen species (ROS/RNS) concentrations in the cellular microenvironment and the viability and proliferation of healthy cells are assessed. Results showed that micro-plasma treatment increased extracellular ROS/RNS levels while modestly reducing cell proliferation without significantly affecting cell survival. Secondly, the particle size of secreted exosomes isolated from the culture medium of L929, B16-F10, and co-cultured cells with different micro-plasma treatment time did not increase significantly under single-cell conditions at short treatment time but might be changed under co-culture condition or longer treatment time. Third, for SERS signals related to membrane protein biomarkers, exosome markers CD9, CD63, and CD81 can be assigned to significant Raman shifts in the range of 943-1030 and 1304-1561 cm-1, while the characteristics SERS peaks of L929 and B16-F10 cells are most likely located at 1394/1404, 1271 and 1592 cm-1 respectively.

SIGNIFICANCE AND NOVELTY

Therefore, this micro-plasma-induced co-culture model provides a promising preclinical approach to understand the diagnostic potential of exosomes secreted by cutaneous melanoma/fibroblasts. Furthermore, the label-free SERS method with size-matched selectivity provides a novel approach to screen biomarkers in exosomes secreted by melanoma cells, aiming to reduce the use of labeling reagents and the processing time traditionally required.

The effective of bacterial community dynamics driven by different starter cultures on the flavor development of Chinese fermented sausages

This study aimed to understand the community successions driven by different starters and their effects on the flavor development of Chinese fermented sausages. The results showed that the bacterial genus (67.6%) and pH (32.4%) were the key factors influencing the volatile profile. Inoculated the starters composed of Pediococcus and staphylococci maintained the stable community succession patterns dominated by staphylococci (samples T and S). Although the highly acidic environment (pH < 5.2) caused the community to exhibit a fluctuation in succession pattern, the inoculation of Latilactobacillus paracasei (sample Y) maintained microbial diversity and was conducive to the accumulation of aldehydes and esters. In sample P, inoculated the starter with Latilactobacillus and Staphylococcus also maintained microbial diversity, the moderately acidic environment (pH > 5.4) resulted in a stable succession pattern of the microbial community, and it was not conducive to the accumulation of aldehydes, alcohols and esters.

Selection of initial microbial community for the alcoholic fermentation of sesame flavor-type baijiu

The initial microbial community is critical for the production of volatile metabolites during traditional food fermentations. Selection of the initial community plays an important role in improving the quality of fermented foods. Here, we used high-throughput amplicon sequencing combined with multivariate statistical methods to explore the microbial succession in stacking and alcoholic fermentation stages in sesame flavor-type baijiu making. We proposed a selection strategy for the initial microbial community in the alcoholic fermentation stage, which determined the quality of baijiu. Results suggested that the microbial composition statistically differed between stacking and alcoholic fermentation stages (ANOSIM, Bacteria: R = 0.60, P = 0.001; Fungi: R = 0.53, P = 0.001). Microbial succession drove metabolic succession (Bacteria: r = 0.87, P < 0.05; Fungi: r = 0.56, P < 0.05) in alcoholic fermentation. The fermentation time of stacking fermentation determined the initial community for alcoholic fermentation, and it can be used as a criterion for selection of the initial microbial community for alcoholic fermentation. The succession distance of the microbial community was varied and reached the highest (Bacteria: 0.048, Fungi: 0.064) at 30 h in stacking fermentation. When we selected 30 h as stacking fermentation time, the concentration (4.58 mg/kg) and diversity (0.61) of volatile metabolites were highest at the end of alcoholic fermentation. This work developed a succession distance-guided approach to select the initial microbial community for the alcoholic fermentation of sesame flavor-type baijiu. This approach can be used to improve the quality of baijiu.

Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview

Co-cultivation is an effective method of inducing the production of specialized metabolites (SMs) in microbial strains. By mimicking the ecological interactions that take place in natural environment, this approach enables to trigger the biosynthesis of molecules which are not formed under monoculture conditions. Importantly, microbial co-cultivation may lead to the discovery of novel chemical entities of pharmaceutical interest. The experimental efforts aimed at the induction of SMs are greatly facilitated by computational techniques. The aim of this overview is to highlight the relevance of computational methods for the investigation of SM induction via microbial co-cultivation. The concepts related to the induction of SMs in microbial co-cultures are briefly introduced by addressing four areas associated with the SM induction workflows, namely the detection of SMs formed exclusively under co-culture conditions, the annotation of induced SMs, the identification of SM producer strains, and the optimization of fermentation conditions. The computational infrastructure associated with these areas, including the tools of multivariate data analysis, molecular networking, genome mining and mathematical optimization, is discussed in relation to the experimental results described in recent literature. The perspective on the future developments in the field, mainly in relation to the microbiome-related research, is also provided.

Cooperative microbial interactions drive spatial segregation in porous environments

The role of microbial interactions and the underlying mechanisms that shape complex biofilm communities are poorly understood. Here we employ a microfluidic chip to represent porous subsurface environments and show that cooperative microbial interactions between free-living and biofilm-forming bacteria trigger active spatial segregation to promote their respective dominance in segregated microhabitats. During initial colonization, free-living and biofilm-forming microbes are segregated from the mixed planktonic inoculum to occupy the ambient fluid and grain surface. Contrary to spatial exclusion through competition, the active spatial segregation is induced by cooperative interactions which improves the fitness of both biofilm and planktonic populations. We further show that free-living Arthrobacter induces the surface colonization by scavenging the biofilm inhibitor, D-amino acids and receives benefits from the public goods secreted by the biofilm-forming strains. Collectively, our results reveal how cooperative microbial interactions may contribute to microbial coexistence in segregated microhabitats and drive subsurface biofilm community succession.

Enhancing fengycin production in the co-culture of Bacillus subtilis and Corynebacterium glutamicum by engineering proline transporter

Fengycin possesses antifungal activity but has limited application due to its low yields. Amino acid precursors play a crucial role in fengycin synthesis. Herein, the overexpression of alanine, isoleucine, and threonine transporter-related genes in Bacillus subtilis increased fengycin production by 34.06%, 46.66%, and 7.83%, respectively. Particularly, fengycin production in B. subtilis reached 871.86 mg/L with the addition of 8.0 g/L exogenous proline after enhancing the expression of the proline transport-related gene opuE. To overcome the metabolic burden caused by excessive enhancement of gene expression for supplying precursors, B. subtilis and Corynebacterium glutamicum which produced proline, were co-cultured, which further improved fengycin production. Fengycin production in the co-culture of B. subtilis and C. glutamicum in shake flasks reached 1554.74 mg/L after optimizing the inoculation time and ratio. The fengycin level in the fed-batch co-culture was 2309.96 mg/L in a 5.0-L bioreactor. These findings provide a new strategy for improving fengycin production.

Consolidated bioprocessing of plant biomass to polyhydroxyalkanoate by co-culture of Streptomyces sp. SirexAA-E and Priestia megaterium

Polyhydroxyalkanoate (PHA) production from plant biomass is an ideal way to realize sustainable PHA-based bioplastic. The present study demonstrated consolidated bioconversion of plant biomass to PHA by co-culturing two specialized bacteria, cellulolytic Streptomyces sp. SirexAA-E and PHA producing Priestia megaterium. In monoculture, S. sp. SirexAA-E does not produce PHA, while P. megaterium did not grow on plant polysaccharides. The co-culture showed poly(3-hydroxybutyrate) (PHB) production using purified polysaccharides, including cellulose, xylan, mannan and their combinations, and plant biomass (Miscanthus, corn stalk and corn leaves) as sole carbon sources, confirmed by GC-MS. The co-culture inoculated with 1:4 (v/v) ratio of S. sp. SirexAA-E to P. megaterium produced 40 mg PHB/g Miscanthus using 0.5% biomass loading. Realtime PCR showed ∼85% S. sp. SirexAA-E and ∼15% P. megaterium in the co-culture. Thus, this study provides a concept of proof for one-pot bioconversion of plant biomass into PHB without separate saccharification processes.

The cAMP receptor protein (CRP) enhances the competitive nature of Salmonella Typhimurium

The cAMP receptor protein (CRP) is a global regulatory protein. We evaluated the role of CRP in starvation physiology in Salmonella Typhimurium. The Δcrp mutant survived 10 days of starvation. However, in a co-culture with the wild type in nutrient-rich medium, Δcrp died within 48 h. Similar co-culture results were observed with Escherichia coli and Staphylococcus aureus. Our study showed that the Δcrp mutant was not killed by toxins and the Type IV secretion system of the WT. The possibility of viable but non-culturable cells (VBNC) was also ruled out. However, when the overall metabolism of the co-culture was slowed down (anaerobic condition, inhibition by antibiotics and low temperature) that improved the survival of Δcrp in co-culture. But one more significant observation was that the Δcrp mutant survived in nutrient-free co-culture conditions. These two observations suggest that CRP protein is essential for efficient nutrient assimilation in a competitive environment. The cells without CRP protein are unable to evaluate the energy balance within the cell, and the cell spends energy to absorb nutrients. But the wild type cell absorbs nutrients at a faster rate than Δcrp mutant. This leads to a situation wherein the Δcrp is spending energy to absorb the nutrients but is unable to compete with the wild type. This futile metabolism leads to death. Hence, this study shows that CRP is a metabolism modulator in a complex nutrient environment. This study also highlights the need for innovative growth conditions to understand the unique function of a gene.

Microbial coexistence in the rhizosphere and the promotion of plant stress resistance: A review

Plants can recruit soil microorganisms into the rhizosphere when experiencing various environmental stresses, including biotic (e.g., insect pests) and abiotic (e.g., heavy metal pollution, droughts, floods, and salinity) stresses. However, species coexistence in plant resistance has not received sufficient attention. Current research on microbial coexistence is only at the community scale, and there is a limited understanding of the interaction patterns between species, especially microbe‒microbe interactions. The relevant interaction patterns are limited to a few model strains. The coexisting microbial communities form a stable system involving complex nutritional competition, metabolic exchange, and even interdependent interactions. This pattern of coexistence can ultimately enhance plant stress tolerance. Hence, a systematic understanding of the coexistence pattern of rhizosphere microorganisms under stress is essential for the precise development and utilization of synthetic microbial communities and the achievement of efficient ecological control. Here, we integrated current analytical methods and introduced several new experimental methods to elucidate rhizosphere microbial coexistence patterns. Some advancements (e.g., network analysis, coculture experiments, and synthetic communities) that can be applied to plant stress resistance are also updated. This review aims to summarize the key role and potential application prospects of microbial coexistence in the resistance of plants to environmental stresses. Our suggestions, enhancing plant resistance with coexisting microbes, would allow us to gain further knowledge on plant-microbial and microbial-microbial functions, and facilitate translation to more effective measures.

Metabolic profiling of bacterial co-cultures reveals intermicrobiome interactions and dominant species

In animal production, the use of probiotic microorganisms has increased since the ban on antibiotic growth promoters in 2006. The added microorganisms interact with the microbiome of the animals, whereby the probiotic activity is not fully understood. Several microorganisms of the genus Bacillus are already known for their probiotic activity and are applied as feed supplements to increase the health status of the animals. They are thought to interact with Escherichia coli, one of the most abundant bacteria in the animal gut. In biotechnological applications, co-culturing enables the regulation of bacterial interaction or the production of target metabolites. The basic principles of multi-imaging high-performance thin-layer chromatography (HPTLC) with upstream cultivation were further developed to analyze the metabolic profiles of three axenic bacilli cultures compared to their co-cultures with E. coli DSM 18039 (K12). The comparative profiling visualized bacteria's metabolic interactions and showed how the presence of E. coli affects the metabolite formation of bacilli. The characteristic metabolic profile images showed not only the influence of microbiomes but also of inoculation, cultivation and nutrients on the commercial probiotic. The formation of antimicrobially active metabolites, detected via three different planar bioassays, was influenced by the presence of other microorganisms, especially in the probiotic. This first application of multi-imaging HPTLC in the field of co-culturing enabled visualization of metabolic interactions of bacteria via their produced chemical as well as bioactive metabolite profiles. The metabolic profiling provided evidence of bacterial interactions, intermicrobiome influences and dominant species in the co-culture.

Metabolomic profiles of the liquid state fermentation in co-culture of Eurotium amstelodami and Bacillus licheniformis

As an important source of new drug molecules, secondary metabolites (SMs) produced by microorganisms possess important biological activities, such as antibacterial, anti-inflammatory, and hypoglycemic effects. However, the true potential of microbial synthesis of SMs has not been fully elucidated as the SM gene clusters remain silent under laboratory culture conditions. Herein, we evaluated the inhibitory effect of Staphylococcus aureus by co-culture of Eurotium amstelodami and three Bacillus species, including Bacillus licheniformis, Bacillus subtilis, and Bacillus amyloliquefaciens. In addition, a non-target approach based on ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS) was used to detect differences in extracellular and intracellular metabolites. Notably, the co-culture of E. amstelodami and Bacillus spices significantly improved the inhibitory effect against S. aureus, with the combination of E. amstelodami and B. licheniformis showing best performance. Metabolomics data further revealed that the abundant SMs, such as Nummularine B, Lucidenic acid E2, Elatoside G, Aspergillic acid, 4-Hydroxycyclohexylcarboxylic acid, Copaene, and Pipecolic acid were significantly enhanced in co-culture. Intracellularly, the differential metabolites were involved in the metabolism of amino acids, nucleic acids, and glycerophospholipid. Overall, this work demonstrates that the co-culture strategy is beneficial for inducing biosynthesis of active metabolites in E. amstelodami and B. licheniformis.

Enhanced Bioremediation of Aged Polycyclic Aromatic Hydrocarbons in Soil Using Immobilized Microbial Consortia Combined with Strengthening Remediation Strategies

Microbial biodegradation is considered as one of the most effective strategies for the remediation of soil contaminated with polycyclic aromatic hydrocarbons (PAHs). To improve the degradation efficiency of PAHs, PAH-degrading consortia combined with strengthening remediation strategies was used in this study. The PAH biodegrading performance of seven bacterial consortia constructed by different ratios of Mycobacterium gilvum MI, Mycobacterium sp. ZL7 and Rhodococcus rhodochrous Q3 was evaluated in an aqueous system containing phenanthrene, pyrene, benzo[a]pyrene and benzo[b]fluoranthene. Bacterial consortium H6 (Q3:ZL7:MI = 1:2:2) performed a high degrading efficiency of 59% in 8 days. The H6 was subsequently screened to explore its potential ability and performance to degrade aged PAHs in soils from a coking plant and the effects of strengthening strategies on the aged PAH degradation, including the addition of glucose or sodium dodecyl benzene sulfonate (SDBS) individually or as a mixture along immobilization of the inoculant on biochar. The highest degradation efficiencies, which were 15% and 60% for low-molecular-weight (LMW) PAHs and high-molecular-weight (HMW) PAHs, respectively, were observed in the treatment using immobilized microbial consortium H6 combined with the addition of glucose and SDBS after 24 days incubation. This study provides new insights and guidance for future remediation of aged PAH contaminated soils.

Integrated analysis of potential microbial consortia, soil nutritional status, and agro-climatic datasets to modulate P nutrient uptake and yield effectiveness of wheat under climate change resilience

Climate change has a devastating effect on wheat production; therefore, crop production might decline by 2030. Phosphorus (P) nutrient deficiency is another main limiting factor of reduced yield. Hence, there is a dire need to judiciously consider wheat yield, so that human requirements and nutrition balance can be sustained efficiently. Despite the great significance of biostimulants in sustainable agriculture, there is still a lack of integrated technology encompassing the successful competitiveness of inoculated phosphate-solubilizing bacteria (PSB) in agricultural systems in the context of climatic conditions/meteorological factors and soil nutritional status. Therefore, the present study reveals the modulation of an integrated P nutrient management approach to develop potential PSB consortia for recommended wheat varieties by considering the respective soil health and agro-climatic conditions. The designed consortia were found to maintain adequate viability for up to 9 months, verified through field emission scanning electron microscopy and viable count. Furthermore, a significant increase in grain yield (5%-8%) and seed P (4%) content was observed in consortia-inoculated wheat plants with 20% reduced Diammonium phosphate (DAP) application under net house conditions. Fluorescence in situ hybridization analysis of roots and amplification of the gcd gene of Ochrobactrum sp. SSR indicated the survival and rhizosphere competency of the inoculated PSB. Categorical principal component analysis (CAT-PCA) showed a positive correlation of inoculated field-grown wheat varieties in native soils to grain yield, soil P content, and precipitation for sites belonging to irrigated plains and seed P content, soil organic matter, and number of tillers for sites belonging to Northern dry mountains. However, the impact of inoculation at sites belonging to the Indus delta was found significantly correlated to soil potassium (K) content, electrical conductivity (EC), and temperature. Additionally, a significant increase in grain yield (15%) and seed P (14%) content was observed in inoculated wheat plants. Thus, the present study demonstrates for the first time the need to integrate soil biological health and agro-climatic conditions for consistent performance of augmented PSB and enhanced P nutrient uptake to curtail soil pollution caused by the extensive use of agrochemicals. This study provides innovative insights and identifies key questions for future research on PSB to promote its successful implementation in agriculture.

Comparing the hierarchy of inter- and intra-species interactions with population dynamics of wine yeast cocultures

In winemaking, the development of new fermentation strategies, such as the use of mixed starter cultures with Saccharomyces cerevisiae (Sc) yeast and non-Saccharomyces (NS) species, requires a better understanding of how yeasts interact, especially at the beginning of fermentation. Despite the growing knowledge on interactions between Sc and NS, few data are available on the interactions between different species of NS. It is furthermore still unclear whether interactions are primarily driven by generic differences between yeast species or whether individual strains are the evolutionarily relevant unit for biotic interactions. This study aimed at acquiring knowledge of the relevance of species and strain in the population dynamics of cocultures between five yeast species: Hanseniaspora uvarum, Lachancea thermotolerans, Starmerella bacillaris, Torulaspora delbrueckii and Sc. We performed cocultures between 15 strains in synthetic grape must and monitored growth in microplates. Both positive and negative interactions were identified. Based on an interaction index, our results showed that the population dynamics seemed mainly driven by the two species involved. Strain level was more relevant in modulating the strength of the interactions. This study provides fundamental insights into the microbial dynamics in early fermentation and contribute to the understanding of more complex consortia encompassing multiple yeasts trains.

Facing Resistant Bacteria with Plant Essential Oils: Reviewing the Oregano Case

Antibiotic resistance is a serious global threat, and the misuse of antibiotics is considered its main cause. It is characterized by the expression of bacterial defense mechanisms, e.g., β-lactamases, expulsion pumps, and biofilm development. Acinetobacter baumannii and Pseudomonas aeruginosa are antibiotic-resistant species that cause high morbidity and mortality. Several alternatives are proposed to defeat antibiotic resistance, including antimicrobial peptides, bacteriophages, and plant compounds. Terpenes from different plant essential oils have proven antimicrobial action against pathogenic bacteria, and evidence is being generated about their effect against antibiotic-resistant species. That is the case for oregano essential oil (Lippia graveolens), whose antibacterial effect is widely attributed to carvacrol, its main component; however, minor constituents could have an important contribution. The analyzed evidence reveals that most antibacterial evaluations have been performed on single species; however, it is necessary to analyze their activity against multispecies systems. Hence, another alternative is using plant compounds to inactivate hydrolytic enzymes and biofilms to potentiate antibiotics' effects. Despite the promising results of plant terpenes, more extensive and deep mechanistic studies are needed involving antibiotic-resistant multispecies to understand their full potential against this problem.

The Effect of Dekkera bruxellensis Concentration and Inoculation Time on Biochemical Changes and Cellulose Biosynthesis by Komagataeibacter intermedius

Bacterial Cellulose (BC) is a biopolymer with numerous applications. The growth of BC-producing bacteria, Komagataeibacter intermedius, could be stimulated by Dekkera bruxellensis, however, the effect on BC yield needs further investigation. This study investigates BC production and biochemical changes in the K. intermedius-D. bruxellensis co-culture system. D. bruxellensis was introduced at various concentrations (103 and 106 CFU/mL) and inoculation times (days 0 and 3). BC yield was ~24% lower when D. bruxellensis was added at 103 CFU/mL compared to K. intermedius alone (0.63 ± 0.11 g/L). The lowest BC yield was observed when 103 CFU/mL yeast was added on day 0, which could be compromised by higher gluconic acid production (10.08 g/L). In contrast, BC yields increased by ~88% when 106 CFU/mL D. bruxellensis was added, regardless of inoculation time. High BC yield might correlate with faster sugar consumption or increased ethanol production when 106 CFU/mL D. bruxellensis was added on day 0. These results suggest that cell concentration and inoculation time have crucial impacts on species interactions in the co-culture system and product yield.

Tunable population dynamics in a synthetic filamentous coculture

Microbial cocultures are used as a tool to stimulate natural product biosynthesis. However, studies often empirically combine different organisms without a deeper understanding of the population dynamics. As filamentous organisms offer a vast metabolic diversity, we developed a model filamentous coculture of the cellulolytic fungus Trichoderma reesei RUT-C30 and the noncellulolytic bacterium Streptomyces coelicolor A3(2). The coculture was set up to use α-cellulose as a carbon source. This established a dependency of S. coelicolor on hydrolysate sugars released by T. reesei cellulases. To provide detailed insight into coculture dynamics, we applied high-throughput online monitoring of the respiration rate and fluorescence of the tagged strains. The respiration rate allowed us to distinguish the conditions of successful cellulase formation. Furthermore, to dissect the individual strain contributions, T. reesei and S. coelicolor were tagged with mCherry and mNeonGreen (mNG) fluorescence proteins, respectively. When evaluating varying inoculation ratios, it was observed that both partners outcompete the other when given a high inoculation advantage. Nonetheless, adequate proportions for simultaneous growth of both partners, cellulase, and pigment production could be determined. Finally, population dynamics were also tuned by modulating abiotic factors. Increased osmolality provided a growth advantage to S. coelicolor. In contrast, an increase in shaking frequency had a negative effect on S. coelicolor biomass formation, promoting T. reesei. This comprehensive analysis fills important knowledge gaps in the control of complex cocultures and accelerates the setup of other tailor-made coculture bioprocesses.

Metabolite-Based Mutualistic Interaction between Two Novel Clostridial Species from Pit Mud Enhances Butyrate and Caproate Production

Pit mud microbial consortia play crucial roles in the formation of Chinese strong-flavor baijiu's key flavor-active compounds, especially butyric and caproic acids. Clostridia, one of the abundant bacterial groups in pit mud, were recognized as important butyric and caproic acid producers. Research on the interactions of the pit mud microbial community mainly depends on correlation analysis at present. Interaction between Clostridium and other microorganisms and its involvement in short/medium-chain fatty acid (S/MCFA) metabolism are still unclear. We previously found coculture of two clostridial strains isolated from pit mud, Clostridium fermenticellae JN500901 (C.901) and Novisyntrophococcus fermenticellae JN500902 (N.902), could enhance S/MCFA accumulation. Here, we investigated their underlying interaction mechanism through the combined analysis of phenotype, genome, and transcriptome. Compared to monocultures, coculture of C.901 and N.902 obviously promoted their growth, including shortening the growth lag phase and increasing biomass, and the accumulation of butyric acid and caproic acid. The slight effects of inoculation ratio and continuous passage on the growth and metabolism of coculture indicated the relative stability of their interaction. Transwell coculture and transcriptome analysis showed the interaction between C.901 and N.902 was accomplished by metabolite exchange, i.e., formic acid produced by C.901 activated the Wood-Ljungdahl pathway of N.902, thereby enhancing its production of acetic acid, which was further converted to butyric acid and caproic acid by C.901 through reverse β-oxidation. This work demonstrates the potential roles of mutually beneficial interspecies interactions in the accumulation of key flavor compounds in pit mud. IMPORTANCE Microbial interactions played crucial roles in influencing the assembly, stability, and function of the microbial community. The metabolites of pit mud microbiota are the key to flavor formation of Chinese strong-flavor baijiu. So far, researches on the interactions of the pit mud microbial community have been mainly based on the correlation analysis of sequencing data, and more work needs to be performed to unveil the complicated interaction patterns. Here, we identified a material exchange-based mutualistic interaction system involving two fatty acid-producing clostridial strains (Clostridium fermenticellae JN500901 and Novisyntrophococcus fermenticellae JN500902) isolated from pit mud and systematically elucidated their interaction mechanism for promoting the production of butyric acid and caproic acid, the key flavor-active compounds of baijiu. Our findings provide a new perspective for understanding the complicated interactions of pit mud microorganisms.

Engineering of Yarrowia lipolytica for producing pyruvate from glycerol

The present study aims to increase pyruvate production by engineering Yarrowia lipolytica through modifying the glycerol metabolic pathway. Results: Wild-type Yarrowia lipolytica (Po1d) was engineered to produce six different strains, namely ZS099 (by over-expressing PYK1), ZS100 (by deleting DGA2), ZS101 (by over-expressing DAK1, DAK2, and GCY1), ZS102 (by over-expressing GUT1 and GUT2), ZS103 (by over-expressing GUT1) and ZSGP (by over-expressing POS5 and deleting GPD2). Production of pyruvate from engineered and control strains was determined using high-performance liquid chromatography (HPLC). Subsequently, the fermentation conditions for producing pyruvate were optimized, including the amount of initial inoculation, the addition of calcium carbonate (CaCO₃), thiamine and glycerol. Finally, for scaled-up purposes, a 20-L fermentor was used. It was observed that pyruvate production increased by 136% (8.55 g/L) in ZSGP strain compared to control (3.62 g/L). Furthermore, pyruvate production by ZSGP reached up to 110.4 g/L in 96 h in the scaled-up process. We conclude that ZSGP strain of Y. lipolytica can be effectively used for pyruvate production at the industrial level.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03158-7.

Cellulosic ethanol production by consortia of Scheffersomyces stipitis and engineered Zymomonas mobilis

BACKGROUND

As one of the clean and sustainable energies, lignocellulosic ethanol has achieved much attention around the world. The production of lignocellulosic ethanol does not compete with people for food, while the consumption of ethanol could contribute to the carbon dioxide emission reduction. However, the simultaneous transformation of glucose and xylose to ethanol is one of the key technologies for attaining cost-efficient lignocellulosic ethanol production at an industrial scale. Genetic modification of strains and constructing consortia were two approaches to resolve this issue. Compared with strain improvement, the synergistic interaction of consortia in metabolic pathways should be more useful than using each one separately.

RESULTS

In this study, the consortia consisting of suspended Scheffersomyces stipitis CICC1960 and Zymomonas mobilis 8b were cultivated to successfully depress carbon catabolite repression (CCR) in artificially simulated 80G40XRM. With this strategy, a 5.52% more xylose consumption and a 6.52% higher ethanol titer were achieved by the consortium, in which the inoculation ratio between S. stipitis and Z. mobilis was 1:3, compared with the Z. mobilis 8b mono-fermentation. Subsequently, one copy of the xylose metabolic genes was inserted into the Z. mobilis 8b genome to construct Z. mobilis FR2, leading to the xylose final-consumption amount and ethanol titer improvement by 15.36% and 6.81%, respectively. Finally, various corn stover hydrolysates with different sugar concentrations (glucose and xylose 60, 90, 120 g/L), were used to evaluate the fermentation performance of the consortium consisting of S. stipitis CICC1960 and Z. mobilis FR2. Fermentation results showed that a 1.56-4.59% higher ethanol titer was achieved by the consortium compared with the Z. mobilis FR2 mono-fermentation, and a 46.12-102.14% higher ethanol titer was observed in the consortium fermentation when compared with the S. stipitis CICC1960 mono-fermentation. Furthermore, qRT-PCR analysis of xylose/glucose transporter and other genes responsible for CCR explained the reason why the initial ratio inoculation of 1:3 in artificially simulated 80G40XRM had the best fermentation performance in the consortium.

CONCLUSIONS

The fermentation strategy used in this study, i.e., using a genetically modified consortium, had a superior performance in ethanol production, as compared with the S. stipitis CICC1960 mono-fermentation and the Z. mobilis FR2 mono-fermentation alone. This result showed that this strategy has potential for future lignocellulosic ethanol production.

Enhancing the retention of phosphorus through bacterial oxidation of iron or sulfide in the eutrophic sediments of Lake Taihu

Microbial activity can enhance the sequestration of phosphorus (P) in sediments, but little is known about the mechanisms behind it. In this study, sediment cores were sampled from the most eutrophic Meiliang Bay of Lake Taihu, and three treatments were set up in a laboratory incubation experiment, involving (a) the non-treated sediment cores, (b) inoculation, and (c) sterilization. The dissolved and labile iron (Fe) and P were obtained by high-resolution dialysis and the diffusive gradients in thin films (DGT) technique, respectively. AgI-based DGT was used for measuring the 2D distribution of labile sulfide. The bacterial community was investigated using a scanning electron microscope and 16S rRNA high throughput sequencing technique. The results showed that sterilization reduced the capacity of sediment to immobilize P, and that the critical sediment depth layer for microbial P sequestration was 0-10 mm. In addition, sterilization or inoculation significantly changes the structure of bacterial communities. Fe or S oxidation under micro-aerobic or anaerobic conditions played an important role in bacterial retention of P in the sediments. Nitrate-reducing coupling Fe(II)-oxidizing bacteria (Acidovorax) in the inoculated sediment and electrogenic sulfur-oxidizing bacteria (Candidatus Electronema) in the non-treated sediment were identified as the key bacterial genera responsible for the retention of P in sediments. This implies that bacterial communities could quickly establish the ability for negative feedback regulation by inoculation once the function and structure of indigenous sediment bacteria are seriously impaired, although this needs further validation in the field.

Emergent transcriptional adaption facilitates convergent succession within a synthetic community

Taxonomic convergence is common in bacterial communities but its underlying molecular mechanism remains largely unknown. We thus conducted a time-series transcriptional analysis of a convergent two-species synthetic community that grew in a closed broth-culture system. By analyzing the gene expression and monitoring the community structure, we found that gene expression mainly changed in the early stage, whereas community structure significantly changed in the late stage. The significant change of gene expression occurred even at the very beginning, which was designated as "0 h effect", suggesting the effect of species interaction on gene expression was inevitable. Besides, the effect of interaction on gene expression has a "population effect", which means that majority species have greater impact on gene expressions of minority species than vice versa. Furthermore, gene set enrichment analysis revealed that among a total of 63 unique pathways (occupying about 50% of all the metabolic pathways in both species), 40 (63%) were consistently suppressed, 16 (25%) were conditionally expressed, and only 7 (11%) were consistently activated. Overall, they were strictly regulated by both time and initial structures. Therefore, we proposed that microorganism responses and the induced gene expression changes play important roles in the process of community succession.

Design and engineering of artificial microbial consortia for biohydrogen production

In natural microbial ecosystems the metabolic diversity of the organisms enables interaction among the community members and allows them to engage in syntrophic interactions. With regard to biotechnology, artificial microbial consortium engineering is used to improve productivities and yields of bioprocesses. However, to achieve supreme productivity or efficiency at industrial scale, defined ecosystems must be physiologically well-selected to meet eco-biotechnological demands. Here, we present an artificial microbial consortia design and engineering pipeline for developing dark fermentative biohydrogen production processes. The proposed pipeline might be considered as a blue-print for enhancing other bioprocesses that fundamentally face metabolic restrictions or kinetic limitations.

Untargeted Metabolomics Reveals Species-Specific Metabolite Production and Shared Nutrient Consumption by Pseudomonas aeruginosa and Staphylococcus aureus

While bacterial metabolism is known to impact antibiotic efficacy and virulence, the metabolic capacities of individual microbes in cystic fibrosis lung infections are difficult to disentangle from sputum samples. Here, we show that untargeted metabolomic profiling of supernatants of multiple strains of Pseudomonas aeruginosa and Staphylococcus aureus grown in monoculture in synthetic cystic fibrosis media (SCFM) reveals distinct species-specific metabolic signatures despite intraspecies metabolic variability. We identify a set of 15 metabolites that were significantly consumed by both P. aeruginosa and S. aureus, suggesting that nutrient competition has the potential to impact community dynamics even in the absence of other pathogen-pathogen interactions. Finally, metabolites that were uniquely produced by one species or the other were identified. Specifically, the virulence factor precursor anthranilic acid, as well as the quinoline 2,4-quinolinediol (DHQ), were robustly produced across all tested strains of P. aeruginosa. Through the direct comparison of the extracellular metabolism of P. aeruginosa and S. aureus in a physiologically relevant environment, this work provides insight toward the potential for metabolic interactions in vivo and supports the development of species-specific diagnostic markers of infection. IMPORTANCE Interactions between P. aeruginosa and S. aureus can impact pathogenicity and antimicrobial efficacy. In this study, we aim to better understand the potential for metabolic interactions between P. aeruginosa and S. aureus in an environment resembling the cystic fibrosis lung. We find that S. aureus and P. aeruginosa consume many of the same nutrients, suggesting that metabolic competition may play an important role in community dynamics during coinfection. We further identify metabolites uniquely produced by either organism with the potential to be developed into species-specific biomarkers of infection in the cystic fibrosis lung.

Intraspecies heterogeneity in microbial interactions

Microbial interactions are increasingly recognized as an integral part of microbial physiology. Cell-cell communication mediated by quorum sensing and metabolite exchange is a formative element of microbial interactions. However, loss-of-function mutations in quorum-sensing components are common across diverse species. Furthermore, quorum sensing is modulated by small molecules and environmental conditions that may be altered in the presence of other microbial species. Recent evidence highlights how strain heterogeneity impacts microbial interactions. There is great potential for microbial interactions to act as selective pressures that influence the emergence of common mutations in quorum-sensing genes across the bacterial and fungal domains.