Multispecies Consortia Research Articles

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

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.

Plant Growth-Promoting Bacteria of Soil: Designing of Consortia Beneficial for Crop Production.

Plant growth-promoting bacteria are commonly used in agriculture, particularly for seed inoculation. Multispecies consortia are believed to be the most promising form of these bacteria. However, designing and modeling bacterial consortia to achieve desired phenotypic outcomes in plants is challenging. This review aims to address this challenge by exploring key antimicrobial interactions. Special attention is given to approaches for developing soil plant growth-promoting bacteria consortia. Additionally, advanced omics-based methods are analyzed that allow soil microbiomes to be characterized, providing an understanding of the molecular and functional aspects of these microbial communities. A comprehensive discussion explores the utilization of bacterial preparations in biofertilizers for agricultural applications, focusing on the intricate design of synthetic bacterial consortia with these preparations. Overall, the review provides valuable insights and strategies for intentionally designing bacterial consortia to enhance plant growth and development.

Microbial Interactions in Oral Biofilm: Evaluating Therapeutic Interventions and the Emergence of Resistance: A Narrative Review.

The oral cavity comprises numerous anatomical surfaces that are inhabited by a diverse array of bacteria, collectively forming a bacterial biofilm. Within this complex microbial community, certain bacterial species are etiologically linked to the development of common oral pathologies, such as dental caries and periodontitis, which stand as prominent instances of bacterial infections frequently encountered in clinical settings. Most biofilms are believed to be multispecies consortia. While single-species biofilms have been well-researched, mixed-species biofilms and their interactions amongst themselves have not drawn interest. The aim of the current review was to assess the various interactions of dual-species microorganisms in oral biofilm formation. Farnesol given exogenously for the treatment of biofilm can enhance or inhibit the growth of certain organisms, as seen in Candida albicans. In the age of antibiotic resistance, it is imperative to develop and uncover drugs capable of simultaneously targeting multiple species in order to mitigate antimicrobial resistance.

Dual-Species Biofilms Formed by Escherichia coli and Salmonella Enhance Chlorine Tolerance.

In this research, mono- and dual-species biofilms of Escherichia coli (O45:H2 and O121:H19) and Salmonella enterica serovar Typhimurium formed on stainless-steel coupons were treated with 100 mg/L NaClO for 1 min. Confocal laser scanning microscopy (CLSM) was applied to investigate the spatial structural dynamics of mono- and dual-species biofilms, and nuclear magnetic resonance (NMR) spectroscopy was employed to further investigate their metabolic responses toward chlorine. CLSM results indicated that mixed-species biofilms (total biovolume, 148,000 to 167,000 μm3) stimulated the growth of biomass 2 to 6 times that of single-species biofilms. Upon chlorine treatment, E. coli O45 and S. Typhimurium achieved less reduction (P < 0.05) when coexisting in mixed biofilms (0.70 and 1.17 log CFU/coupon reductions, respectively) compared with their corresponding single-species biofilms (1.97 and 2.01 log CFU/coupon reductions, respectively), while for E. coli O121, more reduction (P < 0.05) was achieved in a mixed biofilm (1.37 log CFU/coupon reductions) compared with its single-species biofilm (0.59 log CFU/coupon reductions). Moreover, NMR results suggested that the increase of putrescine (antioxidation regulator) and the decrease of glucose (enhanced glycolysis for energy replenishment) might contribute to the improved chlorine tolerance in mixed biofilms. Overall, dual-species biofilms promoted biofilm growth and their chlorine tolerance. This study improved our knowledge of the metabolic difference of single- and mixed-species biofilms of E. coli and Salmonella to chlorine sanitization and raised an urgency to investigate the effectiveness of common disinfectants against multispecies consortia. IMPORTANCE Outbreaks of Escherichia coli and Salmonella in food might be associated with the cross-contamination of biofilms on food-contact surfaces. The knowledge of the sanitization of mono-species biofilm on the food-contact surface is well established, while mixed-species biofilm occurs more naturally, which could profoundly affect the efficacy of sanitizer. Therefore, this research aims to evaluate the efficacy of using chlorine against single- and dual-species biofilms of E. coli and Salmonella along with the underlying bacterial metabolic responses. The responses of a mixed biofilm of E. coli and Salmonella to chlorine sanitization were clarified, providing insights to develop a targeted and green sanitization strategy against specific pathogens by perturbing their most susceptible metabolism pathway without sanitizer residue.

Machine-assisted cultivation and analysis of biofilms

Biofilms are the natural form of life of the majority of microorganisms. These multispecies consortia are intensively studied not only for their effects on health and environment but also because they have an enormous potential as tools for biotechnological processes. Further exploration and exploitation of these complex systems will benefit from technical solutions that enable integrated, machine-assisted cultivation and analysis. We here introduce a microfluidic platform, where readily available microfluidic chips are connected by automated liquid handling with analysis instrumentation, such as fluorescence detection, microscopy, chromatography and optical coherence tomography. The system is operable under oxic and anoxic conditions, allowing for different gases and nutrients as feeding sources and it offers high spatiotemporal resolution in the analysis of metabolites and biofilm composition. We demonstrate the platform’s performance by monitoring the productivity of biofilms as well as the spatial organization of two bacterial species in a co-culture, which is driven by chemical gradients along the microfluidic channel.

Bacteria Associated With a Commercial Mycorrhizal Inoculum: Community Composition and Multifunctional Activity as Assessed by Illumina Sequencing and Culture-Dependent Tools.

The implementation of sustainable agriculture encompasses practices enhancing the activity of beneficial soil microorganisms, able to modulate biogeochemical soil cycles and to affect soil fertility. Among them, arbuscular mycorrhizal fungi (AMF) establish symbioses with the roots of most food crops and play a key role in nutrient uptake and plant protection from biotic and abiotic stresses. Such beneficial services, encompassing improved crop performances, and soil resources availability, are the outcome of the synergistic action of AMF and the vast communities of mycorrhizospheric bacteria living strictly associated with their mycelium and spores, most of which showing plant growth promoting (PGP) activities, such as the ability to solubilize phosphate and produce siderophores and indole acetic acid (IAA). One of the strategies devised to exploit AMF benefits is represented by the inoculation of selected isolates, either as single species or in a mixture. Here, for the first time, the microbiota associated with a commercial AMF inoculum was identified and characterized, using a polyphasic approach, i.e., a combination of culture-dependent analyses and metagenomic sequencing. Overall, 276 bacterial genera were identified by Illumina high-throughput sequencing, belonging to 165 families, 107 orders, and 23 phyla, mostly represented by Proteobacteria and Bacteroidetes. The commercial inoculum harbored a rich culturable heterotrophic bacterial community, whose populations ranged from 2.5 to 6.1 × 106 CFU/mL. The isolation of functional groups allowed the selection of 36 bacterial strains showing PGP activities. Among them, 14 strains showed strong IAA and/or siderophores production and were affiliated with Actinomycetales (Microbacterium trichotecenolyticum, Streptomyces deccanensis/scabiei), Bacillales (Bacillus litoralis, Bacillus megaterium), Enterobacteriales (Enterobacter), Rhizobiales (Rhizobium radiobacter). This work demonstrates for the first time that an AMF inoculum, obtained following industrial production processes, is home of a large and diverse community of bacteria with important functional PGP traits, possibly acting in synergy with AMF and providing additional services and benefits. Such bacteria, available in pure culture, could be utilized, individually and/or in multispecies consortia with AMF, as biofertilizers and bioenhancers in sustainable agroecosystems, aimed at minimizing the use of chemical fertilizers and pesticides, promoting primary production, and maintaining soil health and fertility.

Parvimonas micra stimulates expression of gingipains from Porphyromonas gingivalis in multi-species communities

Dental biofilms are complex ecosystems containing many bacterial species that live in mutualistic relationships. These interactions can profoundly affect the virulence properties of the community. In this study we investigated how the production of gingipains, virulence factors from Porphyromonas gingivalis important in periodontal disease, was affected by other commonly found members of the sub-gingival microbiome.To mimic the subgingival microbiome, multispecies consortia (P. gingivalis, Fusobacterium nucleatum, Actinomyces naeslundii, Streptococus oralis, Streptococcus mitis, Streptococcus gordonii and Streptococcus cristatus, with or without Parvimonas micra) as well as dual species consortia (P. gingivalis with P. micra, S. oralis or F. nucleatum) were constructed and maintained anaerobically in 10% serum for up to seven days. The number of P. gingivalis was determined by plating on Brucella agar and the gingipain specific fluorogenic substrate BikKam-10 was used to investigate gingipain activity. The effect of secreted products from P. micra on gingipain activity was investigated by adding supernatants from P. micra to P. gingivalis cultures. The most prominent secreted proteins in the supernatant were identified using mass spectrometry.P. gingivalis was unable to grow in serum, either alone or in the presence of S. oralis or F. nucleatum. In contrast, with P. micra growth was significantly enhanced and this was associated with an increase in gingipain activity. In the multi-species consortia, the presence of P. micra caused a 13-fold increase in gingipain activity. Exposure of P. gingivalis to supernatants from P. micra for 24 h caused a 3-fold increase in gingipain activity. This effect was reduced by 43% after heat-treatment of the supernatant. Two dimensional gel electrophoresis revealed that several of the most prominent proteins in the P. micra supernatant were glycolytic enzymes. The results from this study suggests that gingipains are produced in response to a P. micra derived signalling molecule that is most likely a protein.This is the first time it has been shown that P. micra can affect P. gingivalis virulence properties. This is likely to be of significance for the development of be of periodontitis since these two microorganisms are often found together in the subgingival biofilm.

Synergistic Interactions within a Multispecies Biofilm Enhance Individual Species Protection against Grazing by a Pelagic Protozoan.

Biofilm formation has been shown to confer protection against grazing, but little information is available on the effect of grazing on biofilm formation and protection in multispecies consortia. With most biofilms in nature being composed of multiple bacterial species, the interactions and dynamics of a multispecies bacterial biofilm subject to grazing by a pelagic protozoan predator were investigated. To this end, a mono and multispecies biofilms of four bacterial soil isolates, namely Xanthomonas retroflexus, Stenotrophomonas rhizophila, Microbacterium oxydans and Paenibacillus amylolyticus, were constructed and subjected to grazing by the ciliate Tetrahymena pyriformis. In monocultures, grazing strongly reduced planktonic cell numbers in P. amylolyticus and S. rhizophila and also X. retroflexus. At the same time, cell numbers in the underlying biofilms increased in S. rhizophila and X. retroflexus, but not in P. amylolyticus. This may be due to the fact that while grazing enhanced biofilm formation in the former two species, no biofilm was formed by P. amylolyticus in monoculture, either with or without grazing. In four-species biofilms, biofilm formation was higher than in the best monoculture, a strong biodiversity effect that was even more pronounced in the presence of grazing. While cell numbers of X. retroflexus, S. rhizophila, and P. amylolyticus in the planktonic fraction were greatly reduced in the presence of grazers, cell numbers of all three species strongly increased in the biofilm. Our results show that synergistic interactions between the four-species were important to induce biofilm formation, and suggest that bacterial members that produce more biofilm when exposed to the grazer not only protect themselves but also supported other members which are sensitive to grazing, thereby providing a “shared grazing protection” within the four-species biofilm model. Hence, complex interactions shape the dynamics of the biofilm and enhance overall community fitness under stressful conditions such as grazing. These emerging inter- and intra-species interactions could play a vital role in biofilm dynamics in natural environments like soil or aquatic systems.

Developing a model for cystic fibrosis sociomicrobiology based on antibiotic and environmental stress

Cystic fibrosis (CF) infections are invariably biofilm-mediated and polymicrobial, being safe to assume that a myriad of factors affects the sociomicrobiology within the CF infection site and modulate the CF community dynamics, by shaping their social activities, overall functions, virulence, ultimately affecting disease outcome. This work aimed to assess changes in the dynamics (particularly on the microbial composition) of dual-/three-species biofilms involving CF-classical (Pseudomonas aeruginosa) and unusual species (Inquilinus limosus and Dolosigranulum pigrum), according to variable oxygen conditions and antibiotic exposure.Low fluctuations in biofilm compositions were observed across distinct oxygen environments, with dual-species biofilms exhibiting similar relative proportions and P. aeruginosa and/or D. pigrum populations dominating three-species consortia. Once exposed to antibiotics, biofilms displayed high resistance profiles, and microbial compositions, distributions, and microbial interactions significantly challenged. The antibiotic/oxygen environment supported such fluctuations, which enhanced for three-species communities.In conclusion, antibiotic therapy hugely disturbed CF communities’ dynamics, inducing significant compositional changes on multispecies consortia. Clearly, multiple perturbations may disturb this dynamic, giving rise to various microbiological scenarios in vivo, and affecting disease phenotype. Therefore, an appreciation of the ecological/evolutionary nature within CF communities will be useful for the optimal use of current therapies and for newer breakthroughs on CF antibiotherapy.

All together now: experimental multispecies biofilm model systems.

Studies of microorganisms have traditionally focused on single species populations, which have greatly facilitated our understanding of the genetics and physiology that underpin microbial growth, adaptation and biofilm development. However, given that most microorganisms exist as multispecies consortia, the field is increasingly exploring microbial communities using a range of technologies traditionally limited to populations, including meta-omics based approaches and high resolution imaging. The experimental communities currently being explored range from relatively low diversity, for example, two to four species, to significantly more complex systems, comprised of several hundred species. Results from both defined and undefined communities have revealed a number of emergent properties, including improved stress tolerance, increased biomass production, community level signalling and metabolic cooperation. Based on results published to date, we submit that community-based studies are timely and increasingly reveal new properties associated with multispecies consortia that could not be predicted bystudies of the individual component species. Here, we review a range of defined and undefined experimental systems used to study microbial community interactions.

Adaptation potential of naturally occurring cynaobacterial biofilms dominated by Phormidium spp.

The effect of copper ions on physiological and biochemical parameters of naturally occurring biofilms has been studied. Biofilms are multispecies consortia of phototrophic microorganisms dominated by Phormidium spp. We have found that, at 1 h of exposure in the presence of Cu2+ ions (20 mg/dm3), chlorophyll a degraded to give pheophytin accompanied by lipid peroxidation. At 24 h the microorganisms show adaptive response, as is evidenced by the increase in catalase activity, reduced lipid peroxidation, and return of chlorophyll a to normal levels. One hour of exposure of suspended cells (0.031 g/100 cm3 solution) reduces the concentration of copper (II) MPC level, with the purification rate being 99%. This feature of biofilms holds potential for use as biosorbents.

An Engineered Community Approach for Industrial Cultivation of Microalgae.

Although no species lives in isolation in nature, efforts to grow organisms for use in biotechnology have generally focused on a single-species approach, particularly where a product is required at high purity. In such scenarios, preventing the establishment of contaminants requires considerable effort that is economically justified. However, for some applications in biotechnology where the focus is on lower-margin biofuel production, axenic culture is not necessary, provided yields of the desired strain are unaffected by contaminants. In this article, we review what is known about interspecific interactions of natural algal communities, the dynamics of which are likely to parallel contamination in industrial systems. Furthermore, we discuss the opportunities to improve both yields and the stability of cultures by growing algae in multi-species consortia.

Successions of zooperiphyton in a small river

In the small Latka River, which is characterized by a high heterogeneity of abiotic characteristics and a rich fauna composition, a high diversity of developing zooperiphyton structures was recorded consisting of invertebrates with short life cycles: the larvae of chironomids, caddisflies, mayflies, oligochaetes, nematodes, and other animals. One distinctive feature of seasonal and interannual zooperiphyton succession is the annual prevalence in abundance of spreading chironomid larvae of age I, which belong to the most representative dominating group of amphibiotic invertebrates, including species adapted to different saprobic conditions. The taxonomic and quantitative domination of chironomids make it possible to consider the family Chironomidae a key group in the formation of the zoocenosis structure. Under disturbed habitat conditions (pollution, rainfall floods, and the press of omnivorous invertebrates), the restoration of typical structures occurs rather quickly due to the particular features of biology in species short life cycles. However, no relative stabilization in communities was observed. This is the main difference between the sequence of succession processes in the Latka River and that observed in large water bodies (lakes and water reservoirs), where there are no strict limitations on living-space volume or food availability and abiotic conditions are more stable, thus allowing filter-feeding sessile animals (sponges, bryozoans, and zebra mussels) to develop on solid substrates. These species are able to develop multispecies consortia and form relatively stable long-term communities.

Competition Triggers Plasmid-Mediated Enhancement of Substrate Utilisation in Pseudomonas putida

Competition between species plays a central role in the activity and structure of communities. Stable co-existence of diverse organisms in communities is thought to be fostered by individual tradeoffs and optimization of competitive strategies along resource gradients. Outside the laboratory, microbes exist as multispecies consortia, continuously interacting with one another and the environment. Survival and proliferation of a particular species is governed by its competitive fitness. Therefore, bacteria must be able to continuously sense their immediate environs for presence of competitors and prevailing conditions. Here we present results of our investigations on a novel competition sensing mechanism in the rhizosphere-inhabiting Pseudomonas putida KT2440, harbouring gfpmut3b-modified KanR TOL plasmid. We monitored benzyl alcohol (BA) degradation rate, along with GFP expression profiling in mono species and dual species cultures. Interestingly, enhanced plasmid expression (monitored using GFP expression) and consequent BA degradation were observed in dual species consortia, irrespective of whether the competitor was a BA degrader (Pseudomonas aeruginosa) or a non-degrader (E. coli). Attempts at elucidation of the mechanistic aspects of induction indicated the role of physical interaction, but not of any diffusible compounds emanating from the competitors. This contention is supported by the observation that greater induction took place in presence of increasing number of competitors. Inert microspheres mimicking competitor cell size and concentration did not elicit any significant induction, further suggesting the role of physical cell-cell interaction. Furthermore, it was also established that cell wall compromised competitor had minimal induction capability. We conclude that P. putida harbouring pWW0 experience a competitive stress when grown as dual-species consortium, irrespective of the counterpart being BA degrader or not. The immediate effect of this stress is a marked increase in expression of TOL, leading to rapid utilization of the available carbon source and massive increase in its population density. The plausible mechanisms behind the phenomenon are hypothesised and practical implications are indicated and discussed.

Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments.

No microorganism capable of anaerobic growth on methane as the sole carbon source has yet been cultivated. Consequently, information about these microbes has been inferred from geochemical and microbiological observations of field samples. Stable isotope analysis of lipid biomarkers and rRNA gene surveys have implicated specific microbes in the anaerobic oxidation of methane (AOM). Here we use combined fluorescent in situ hybridization and secondary ion mass spectrometry analyses, to identify anaerobic methanotrophs in marine methane-seep sediments. The results provide direct evidence for the involvement of at least two distinct archaeal groups (ANME-1 and ANME-2) in AOM at methane seeps. Although both archaeal groups often occurred in direct physical association with bacteria, they also were observed as monospecific aggregations and as single cells. The ANME-1 archaeal group more frequently existed in monospecific aggregations or as single filaments, apparently without a bacterial partner. Bacteria associated with both archaeal groups included, but were not limited to, close relatives of Desulfosarcina species. Isotopic analyses suggest that monospecific archaeal cells and cell aggregates were active in anaerobic methanotrophy, as were multispecies consortia. In total, the data indicate that the microbial species and biotic interactions mediating anaerobic methanotrophy are diverse and complex. The data also clearly show that highly structured ANME-2/Desulfosarcina consortia are not the sole entities responsible for AOM at marine methane seeps. Other microbial groups, including ANME-1 archaea, are capable of anaerobic methane consumption either as single cells, in monospecific aggregates, or in multispecies consortia.