Interaction variability shapes succession of synthetic microbial ecosystems

Integrated multi-omics uncover viruses, active fermenting microbes and their metabolic profiles in the Daqu microbiome

The coexistence and coevolution of viruses and fermenting microbes have a significant impact on the structure and function of microbial communities. Although the presence of viruses in Daqu, the fermentation starter for Chinese Baijiu, has been documented, their specific effects on the community composition and metabolic functions of low, medium, and high-temperature Daqu remain unclear. In this study, we employed multi-omics technology to explore the distribution of viruses and active bacteria and fungi in various Daqu and their potential metabolic roles. Viral metagenomic sequencing showed a predominance of Parvoviridae in High-Temperature Daqu (HTQ), while Genomoviridae were dominant in Medium-Temperature Daqu (MTQ) and Low- Temperature Daqu (LTQ). Phages belonging to the Siphoviridae, Podoviridae, Herelleviridae, and Myoviridae families showed significantly different abundances across three Daqu groups. Metatranscriptomic analysis showed that fungal communities were most active in LTQ, whereas bacterial communities were dominant in MTQ and HTQ. By employing the CRISPR-Cas spacer, a higher predicted number of phage-host linkages was identified in LTQ, particularly with hosts including Lactobacillus, Staphylococcus, Acinetobacter, Enterobacter, and Bacillus. Correlation analysis showed that bacteria like Acinetobacter, Lactobacillus, and Streptococcus exhibited the strongest associations with metabolites, particularly amino acids and organic acids. The potential phage-induced metabolic differences in the three Daqu groups were mainly linked to pathways involved in the metabolism of amino acids, sugars, and organic acids. Overall, our study elucidates the impact of viruses on shaping microbial composition and influencing metabolic functions in Daqu. These results improve our comprehension of viruses and microbes in Daqu microbial communities and provide valuable insights for enhancing quality control in Daqu production.

Initial abiotic factors as key drivers in core microbe assembly: Regulatory effects on flavor profiles in light-flavor Baijiu

Instability in initial abiotic factors of open solid-state fermentation systems can significantly alter Baijiu's flavor profile, but the mechanisms governing microbial interactions and flavor formation remain unclear. This study comprehensively monitored changes in abiotic factors, microbial communities, and flavor profiles across two distinct fermentation processes in a Baijiu distillery, which differed significantly in their management of initial abiotic factors. Our results revealed significant differences in abiotic factors between the two groups, including moisture, ethanol, acidity, glucose, and organic acid levels. The assembly of microbial communities in fermented grains was primarily driven by deterministic processes. The moisture content in the fermented grains positively affected the growth and metabolism of core microbiota. The rapid proliferation and metabolism of core microbes led to a rapid increase in the acidity of the fermented grains, alongside a significant accumulation of ethyl lactate. This study provides technical support and theoretical guidance for Baijiu production.

DyMMM-LEAPS: An ML-based framework for modulating evenness and stability in synthetic microbial communities

There have been a growing number of computational strategies to aid in the design of synthetic microbial consortia. A framework to identify regions in parametric space to maximize two essential properties, evenness and stability, is critical. In this study, we introduce DyMMM-LEAPS (dynamic multispecies metabolic modeling-locating evenness and stability in large parametric space), an extension of the DyMMM framework. Our method explores the large parametric space of genetic circuits in synthetic microbial communities to identify regions of evenness and stability. Due to the high computational costs of exhaustive sampling, we utilize adaptive sampling and surrogate modeling to reduce the number of simulations required to map the vast space. Our framework predicts engineering targets and computes their operating ranges to maximize the probability of the engineered community to have high evenness and stability. We demonstrate our approach by simulating five cocultures and one three-strain culture with different social interactions (cooperation, competition, and predation) employing quorum-sensing-based genetic circuits. In addition to guiding circuit tuning, our pipeline gives an opportunity for a detailed analysis of pockets of evenness and stability for the circuit under investigation, which can further help dissect the relationship between the two properties. DyMMM-LEAPS is easily customizable and can be expanded to a larger community with more complex interactions.

Activating Biocake Communities Retards Jumps of Transmembrane Pressure in Membrane Bioreactors

Sudden jump of transmembrane pressure (TMP) in membrane bioreactors (MBRs), associated with abrupt aggravation of membrane fouling, limits practical applications of MBRs and calls for effective mitigation strategies. While the TMP jump is generally related to the bacterial activity of biocakes, the mechanisms underlying the TMP jump remain unclear. Herein, we conducted various backwash protocols with different nutrient (e.g., nitrate and sodium acetate) loadings on fouled membranes in MBRs to reveal the critical role of bacterial activity of biocakes for the TMP jump. The filtration tests showed a lower TMP jump rate for the membrane backwashed with a nutrient solution (a mixture of 180 mg/L NaNO3 and 200 mg/L NaAc, averaged at 1.40 kPa/d) than that backwashed with tap water (averaged at 3.56 kPa/d), implying that TMP jump could be efficiently mitigated by providing sufficient nutrients to biocake bacteria. The characterization of biocakes showed that high-nutrient solution backwash considerably increased bacterial viability and activity, while considerably reducing biomolecule accumulation on membranes. The keystone taxa (e.g., g_Aeromonas and o_Chitinophagaceae) in the network of nutrient-enriched biocake communities were involved in nitrate reduction and biomolecule degradation. Ecological null model analyses revealed that the deterministic manner mainly shaped biocake communities with high-nutrient availability. Overall, this study highlights the significance of the bacterial activity of biocakes for TMP development and provides potential alternatives for controlling membrane fouling.

Deciphering the core microbes and their interactions in spontaneous Baijiu fermentation: A comprehensive review

The spontaneous Baijiu fermentation system harbors a complex microbiome that is highly dynamic in time and space and varies depending on the Jiuqu starters and environmental factors. The intricate microbiota presents in the fermentation environment is responsible for carrying out various reactions. These reactions necessitate the interaction among the core microbes to influence the community function, ultimately shaping the distinct Baijiu styles through the process of spontaneous fermentation. Numerous studies have been conducted to enhance our understanding of the diversity, succession, and function of microbial communities with the aim of improving fermentation manipulation. However, a comprehensive and critical assessment of the core microbes and their interaction remains one of the significant challenges in the Baijiu fermentation industry. This paper focuses on the fermentation properties of core microbes. We discuss the state of the art of microbial traceability, highlighting the crucial role of environmental and starter microbiota in the Baijiu brewing microbiome. Also, we discuss the various interactions between microbes in the Baijiu production system and propose a potential conceptual framework that involves constructing predictive network models to simplify and quantify microbial interactions using co-culture models. This approach offers effective strategies for understanding the core microbes and their interactions, thus beneficial for the management of microbiota and the regulation of interactions in Baijiu fermentation processes.

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.

Saccharomyces boulardii enhances anti-inflammatory effectors and AhR activation via metabolic interactions in probiotic communities

Metabolic exchanges between strains in gut microbial communities shape their composition and interactions with the host. This study investigates the metabolic synergy between potential probiotic bacteria and Saccharomyces boulardii, aiming to enhance anti-inflammatory effects within a multi-species probiotic community. By screening a collection of 85 potential probiotic bacterial strains, we identified two strains that demonstrated a synergistic relationship with S. boulardii in pairwise co-cultivation. Furthermore, we computationally predicted cooperative communities with symbiotic relationships between S. boulardii and these bacteria. Experimental validation of 28 communities highlighted the role of S. boulardii as a key player in microbial communities, significantly boosting the community's cell number and production of anti-inflammatory effectors, thereby affirming its essential role in improving symbiotic dynamics. Based on our observation, one defined community significantly activated the aryl hydrocarbon receptor-a key regulator of immune response-280-fold more effectively than the community without S. boulardii. This study underscores the potential of microbial communities for the design of more effective probiotic formulations.

Nitrogen transfer and cross-feeding between Azotobacter chroococcum and Paracoccus aminovorans promotes pyrene degradation

Nitrogen is a limiting nutrient for degraders function in hydrocarbon-contaminated environments. Biological nitrogen fixation by diazotrophs is a natural solution for supplying bioavailable nitrogen. Here, we determined whether the diazotroph Azotobacter chroococcum HN can provide nitrogen to the polycyclic aromatic hydrocarbon-degrading bacterium Paracoccus aminovorans HPD-2 and further explored the synergistic interactions that facilitate pyrene degradation in nitrogen-deprived environments. We found that A. chroococcum HN and P. aminovorans HPD-2 grew and degraded pyrene more quickly in co-culture than in monoculture. Surface-enhanced Raman spectroscopy combined with 15N stable isotope probing (SERS - 15N SIP) demonstrated that A. chroococcum HN provided nitrogen to P. aminovorans HPD-2. Metabolite analysis and feeding experiments confirmed that cross-feeding occurred between A. chroococcum HN and P. aminovorans HPD-2 during pyrene degradation. Transcriptomic and metabolomic analyses further revealed that co-culture significantly upregulated key pathways such as nitrogen fixation, aromatic compound degradation, protein export, and the TCA cycle in A. chroococcum HN and quorum sensing, aromatic compound degradation and ABC transporters in P. aminovorans HPD-2. Phenotypic and fluorescence in situ hybridization (FISH) assays demonstrated that A. chroococcum HN produced large amounts of biofilm and was located at the bottom of the biofilm in co-culture, whereas P. aminovorans HPD-2 attached to the surface layer and formed a bridge-like structure with A. chroococcum HN. This study demonstrates that distinct syntrophic interactions occur between A. chroococcum HN and P. aminovorans HPD-2 and provides support for their combined use in organic pollutant degradation in nitrogen-deprived environments.

Microbial Biofilms for Environmental Bioremediation of Heavy Metals: a Review

Heavy metal pollution caused due to various industrial and mining activities poses a serious threat to all forms of life in the environment because of the persistence and toxicity of metal ions. Microbial-mediated bioremediation including microbial biofilms has received significant attention as a sustainable tool for heavy metal removal as it is considered safe, effective, and feasible. The biofilm matrix is dynamic, having microbial cells as major components with constantly changing and evolving microenvironments. This review summarizes the bioremediation potential of bacterial biofilms for different metal ions. The composition and mechanism of biofilm formation along with interspecies communication among biofilm-forming bacteria have been discussed. The interaction of biofilm-associated microbes with heavy metals takes place through a variety of mechanisms. These include biosorption and bioaccumulation in which the microbes interact with the metal ions leading to their conversion from a highly toxic form to a less toxic form. Such interactions are facilitated via the negative charge of the extracellular polymeric substances on the surface of the biofilm with the positive charge of the metal ions and the high cell densities and high concentrations of cell-cell signaling molecules within the biofilm matrix. Furthermore, the impact of the anodic and cathodic redox potentials in a bioelectrochemical system (BES) for the reduction, removal, and recovery of numerous heavy metal species provides an interesting insight into the bacterial biofilm-mediated bioelectroremediation process. The review concludes that biofilm-linked bioremediation is a viable option for the mitigation of heavy metal pollution in water and ecosystem recovery.

Linking plant functional genes to rhizosphere microbes: a review

The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.

Assembly strategies for polyethylene-degrading microbial consortia based on the combination of omics tools and the "Plastisphere"

Numerous microorganisms and other invertebrates that are able to degrade polyethylene (PE) have been reported. However, studies on PE biodegradation are still limited due to its extreme stability and the lack of explicit insights into the mechanisms and efficient enzymes involved in its metabolism by microorganisms. In this review, current studies of PE biodegradation, including the fundamental stages, important microorganisms and enzymes, and functional microbial consortia, were examined. Considering the bottlenecks in the construction of PE-degrading consortia, a combination of top-down and bottom-up approaches is proposed to identify the mechanisms and metabolites of PE degradation, related enzymes, and efficient synthetic microbial consortia. In addition, the exploration of the plastisphere based on omics tools is proposed as a future principal research direction for the construction of synthetic microbial consortia for PE degradation. Combining chemical and biological upcycling processes for PE waste could be widely applied in various fields to promote a sustainable environment.

SynMADE: synthetic microbiota across diverse ecosystems

The past two decades have witnessed rapid advances in engineering individual microbial strains to produce biochemicals and biomaterials. However, engineering microbial consortia has been relatively slow. Using systems and synthetic biology approaches, researchers have been developing tools for engineering complex microbiota. In this opinion article, I discuss future directions and visions regarding developing microbiota as a biomanufacturing host. Specifically, I propose that we can develop the soil microbial community itself as a huge bioreactor. Ultimately, researchers will provide a generalizable system that enables us to understand a microbial consortium's interaction and metabolism on diverse temporal and spatial scales to address global problems, including the climate crisis, food inequality, the issue of waste, and sustainable bioproduction.

Agent-Based Modeling of Microbial Communities

Microbial communities are complex living systems that populate the planet with diverse functions and are increasingly harnessed for practical human needs. To deepen the fundamental understanding of their organization and functioning as well as to facilitate their engineering for applications, mathematical modeling has played an increasingly important role. Agent-based models represent a class of powerful quantitative frameworks for investigating microbial communities because of their individualistic nature in describing cells, mechanistic characterization of molecular and cellular processes, and intrinsic ability to produce emergent system properties. This review presents a comprehensive overview of recent advances in agent-based modeling of microbial communities. It surveys the state-of-the-art algorithms employed to simulate intracellular biomolecular events, single-cell behaviors, intercellular interactions, and interactions between cells and their environments that collectively serve as the driving forces of community behaviors. It also highlights three lines of applications of agent-based modeling, namely, the elucidation of microbial range expansion and colony ecology, the design of synthetic gene circuits and microbial populations for desired behaviors, and the characterization of biofilm formation and dispersal. The review concludes with a discussion of existing challenges, including the computational cost of the modeling, and potential mitigation strategies.

Individual-Based Modeling of Spatial Dynamics of Chemotactic Microbial Populations

One important direction of synthetic biology is to establish desired spatial structures from microbial populations. Underlying this structural development process are different driving factors, among which bacterial motility and chemotaxis serve as a major force. Here, we present an individual-based, biophysical computational framework for mechanistic and multiscale simulation of the spatiotemporal dynamics of motile and chemotactic microbial populations. The framework integrates cellular movement with spatial population growth, mechanical and chemical cellular interactions, and intracellular molecular kinetics. It is validated by a statistical comparison of single-cell chemotaxis simulations with reported experiments. The framework successfully captures colony range expansion of growing isogenic populations and also reveals chemotaxis-modulated, spatial patterns of a two-species amensal community. Partial differential equation-based models subsequently validate these simulation findings. This study provides a versatile computational tool to uncover the fundamentals of microbial spatial ecology as well as to facilitate the design of synthetic consortia for desired spatial patterns.

Reconstruction of a Soil Microbial Network Induced by Stress Temperature

The microbial community is viewed as a network of diverse microorganisms connected by various interspecific interactions. While the stress gradient hypothesis (SGH) predicts that positive interactions are favored in more stressful environments, the prediction has been less explored in complex microbial communities due to the challenges of identifying interactions. Here, by applying a nonlinear time series analysis to the amplicon-based diversity time series data of the soil microbiota cultured under less stressful (30°C) or more stressful (37°C) temperature conditions, we show how the microbial network responds to temperature stress. While the genera that persisted only under the less stressful condition showed fewer positive effects, the genera that appeared only under the more stressful condition received more positive effects, in agreement with SGH. However, temperature difference also induced reconstruction of the community network, leading to an increased proportion of negative interactions at the whole-community level. The anti-SGH pattern can be explained by the stronger competition caused by increased metabolic rate and population densities. IMPORTANCE By combining amplicon-based diversity survey with recently developed nonlinear analytical tools, we successfully determined the interaction networks of more than 150 natural soil microbial genera under less or more temperature stress and explored the applicability of the stress gradient hypothesis to soil microbiota, shedding new light on the well-known hypothesis.

State-Space-Based Framework for Predicting Microbial Interaction Variability in Wastewater Treatment Plants

Substantial attempts have been made to control microbial communities for environmental integrity, biosystem performance, and human health. However, it is difficult to manipulate microbial communities in practice due to the varying and nonlinear nature of interspecific interaction networks. Here, we develop a manifold-based framework to investigate the patterns of microbial interaction variability in wastewater treatment plants using manifold geometric properties and design a simple control strategy to manipulate the microbes in nonlinear communities. We validate our framework using the readily available and nonsequential microbiome profiles of wastewater treatment plants. Our results show that some microbes in the activated sludge and anammox communities display deterministic rival or cooperative relationships and constitute a stable subnetwork within the whole nonlinear community network. We further use a simulation to demonstrate that these microbes can be used to drive a microbe in a target direction regardless of the community dynamics. Overall, our framework can provide a time-efficient solution to select effective control inputs for reliable manipulation in varying microbial networks, opening up new possibilities across a range of biological fields, including wastewater treatment plants.

A systematic, complexity-reduction approach to dissect the kombucha tea microbiome

One defining goal of microbiome research is to uncover mechanistic causation that dictates the emergence of structural and functional traits of microbiomes. However, the extraordinary degree of ecosystem complexity has hampered the realization of the goal. Here, we developed a systematic, complexity-reducing strategy to mechanistically elucidate the compositional and metabolic characteristics of microbiome by using the kombucha tea microbiome as an example. The strategy centered around a two-species core that was abstracted from but recapitulated the native counterpart. The core was convergent in its composition, coordinated on temporal metabolic patterns, and capable for pellicle formation. Controlled fermentations uncovered the drivers of these characteristics, which were also demonstrated translatable to provide insights into the properties of communities with increased complexity and altered conditions. This work unravels the pattern and process underlying the kombucha tea microbiome, providing a potential conceptual framework for mechanistic investigation of microbiome behaviors.

Construction of Synthetic Microbial Ecosystems and the Regulation of Population Proportion

With the development of synthetic biology, the design and application of microbial consortia have received increasing attention. However, the construction of synthetic ecosystems is still hampered by our limited ability to rapidly develop microbial consortia with the required dynamics and functions. By using modular design, we constructed synthetic competitive and symbiotic ecosystems with Escherichia coli. Two ecological relationships were realized by reconfiguring the layout between the communication and effect modules. Furthermore, we designed inducible synthetic ecosystems to regulate subpopulation ratios. With the addition of different inducers, a wide range of strain ratios between subpopulations was achieved. These inducible synthetic ecosystems enabled a larger volume of population regulation and simplified culture conditions. The synthetic ecosystems we constructed combined both basic and applied functionalities and expanded the toolkit of synthetic biology research.

A call to arms for cell-cell interactions between bacteria in the plant microbiome

Next-generation sequencing and computational biology has unravelled the different bacterial groups populating plant microbiomes. In addition, microbiologists have discovered many different mechanisms of cell-cell interactions that take place between bacteria. Bacteria use four prevalent mechanisms for intercellular interactions; however, their pertinent role in the formation and maintenance of plant microbiomes is currently unknown. We argue that it is overdue to speed up research on the biotic cell-cell interactions that take place between bacteria in plant microbiomes. This research will have a major impact on both fundamental sciences and translational agriculture via the development of bacterial prebiotic compounds as well probiotics competence, resulting in a more sustainable agriculture of economically important crops.

A light tunable differentiation system for the creation and control of consortia in yeast

Artificial microbial consortia seek to leverage division-of-labour to optimize function and possess immense potential for bioproduction. Co-culturing approaches, the preferred mode of generating a consortium, remain limited in their ability to give rise to stable consortia having finely tuned compositions. Here, we present an artificial differentiation system in budding yeast capable of generating stable microbial consortia with custom functionalities from a single strain at user-defined composition in space and in time based on optogenetically-driven genetic rewiring. Owing to fast, reproducible, and light-tunable dynamics, our system enables dynamic control of consortia composition in continuous cultures for extended periods. We further demonstrate that our system can be extended in a straightforward manner to give rise to consortia with multiple subpopulations. Our artificial differentiation strategy establishes a novel paradigm for the creation of complex microbial consortia that are simple to implement, precisely controllable, and versatile to use.

Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions

Microorganisms are a fundamental part of virtually every ecosystem on earth. Understanding how collectively they interact, assemble, and function as communities has become a prevalent topic both in fundamental and applied research. Owing to multiple advances in technology, answering questions at the microbial system or network level is now within our grasp. To map and characterize microbial interaction networks, numerous computational approaches have been developed; however, experimentally validating microbial interactions is no trivial task. Microbial interactions are context-dependent, and their complex nature can result in an array of outcomes, not only in terms of fitness or growth, but also in other relevant functions and phenotypes. Thus, approaches to experimentally capture microbial interactions involve a combination of culture methods and phenotypic or functional characterization methods. Here, through our perspective of food microbiologists, we highlight the breadth of innovative and promising experimental strategies for their potential to capture the different dimensions of microbial interactions and their high-throughput application to answer the question; are microbial interaction patterns or network architecture similar along different contextual scales? We further discuss the experimental approaches used to build various types of networks and study their architecture in the context of cell biology and how they translate at the level of microbial ecosystem.

Ecological Linkages between a Biofilm Ecosystem and Reactor Performance: The Specificity of Biofilm Development Phases

In biofilm-based engineered ecosystems, the reactor performance was closely linked to interspecies interactions within a biofilm ecosystem, whereas the ecological processes underpinning such linkage were still unenlightened. Herein, the principles of community succession and assembly were integrated to capture the ecological laws of biofilm development by molecular ecological networks and assembly model analysis based on the 16S rRNA sequencing analysis and metagenomics in a well-controlled moving bed biofilm reactor. At the initial colonization phase (days 0-2, driven by initial colonizers), interspecific cooperation (74.18%) facilitated initial biofilm formation, whereas some pioneers, and keystone species disappeared at later phases. At the accumulation phase (days 3-30, rapid biofilm development), interspecific cooperation (81.41 ± 5.07%) contributed to rapid biofilm development and keystone species were mainly involved in quorum sensing or positively correlated with extracellular polymeric substance production. At the maturation phase (days 31-106, a well-adapted quasi-equilibrium state), increased interspecific competition (32.74 ± 4.77%) and higher small-world property facilitated the rapid information transportation and pollutant treatment, and keystone species were positively correlated with the removal of COD and NH₄⁺-N. Homogenizing dispersal diminished the contemporary community dissimilarities, while turnover but rather nestedness governed the temporal variations in the biofilm succession period. This study highlighted the specificity of ecological processes at distinct biofilm development phases, which would advance our understanding on the development-to-function linkages in biofilm-based treatment processes.

The spatial organization of microbial communities during range expansion

Microbes in nature often live in dense and diverse communities exhibiting a variety of spatial structures. Microbial range expansion is a universal ecological process that enables populations to form spatial patterns. It can be driven by both passive and active processes, for example, mechanical forces from cell growth and bacterial motility. In this review, we provide a taste of recent creative and sophisticated efforts being made to address basic questions in spatial ecology and pattern formation during range expansion. We especially highlight the role of motility to shape community structures, and discuss the research challenges and future directions.

Vertical and horizontal quorum-sensing-based multicellular communications

Quorum sensing (QS) plays an important role in both natural and synthetic microbial systems. The complexity of QS entails multilayer controls, biomolecular crosstalk, and population-based interactions. In this review, we divide complex QS-based interactions into vertical and horizontal interactions. With respect to the former, we discuss QS-based interactions among phages, bacteria, and hosts in natural microbial systems, which are based on various QS signals and hormones. With regard to the latter, we highlight manipulations of QS-based interactions for multicomponent synthetic microbial consortia. We further present the recent and emerging applications of manipulating these interactions (collectively referred to as 'QS communication networks') in natural and synthetic microbiota. Finally, we identify key challenges in engineering diverse QS communication networks for various future applications.

Formation, characterization and modeling of emergent synthetic microbial communities

Microbial communities colonize plant tissues and contribute to host function. How these communities form and how individual members contribute to shaping the microbial community are not well understood. Synthetic microbial communities, where defined individual isolates are combined, can serve as valuable model systems for uncovering the organizational principles of communities. Using genome-defined organisms, systematic analysis by computationally-based network reconstruction can lead to mechanistic insights and the metabolic interactions between species. In this study, 10 bacterial strains isolated from the Populus deltoides rhizosphere were combined and passaged in two different media environments to form stable microbial communities. The membership and relative abundances of the strains stabilized after around 5 growth cycles and resulted in just a few dominant strains that depended on the medium. To unravel the underlying metabolic interactions, flux balance analysis was used to model microbial growth and identify potential metabolic exchanges involved in shaping the microbial communities. These analyses were complemented by growth curves of the individual isolates, pairwise interaction screens, and metaproteomics of the community. A fast growth rate is identified as one factor that can provide an advantage for maintaining presence in the community. Final community selection can also depend on selective antagonistic relationships and metabolic exchanges. Revealing the mechanisms of interaction among plant-associated microorganisms provides insights into strategies for engineering microbial communities that can potentially increase plant growth and disease resistance. Further, deciphering the membership and metabolic potentials of a bacterial community will enable the design of synthetic communities with desired biological functions.

Synthetic co-cultures: novel avenues for bio-based processes

In nature, microorganisms live in multi-species communities allowing microbial interactions. These interactions are lost upon establishing a pure culture, increasing the metabolic burden and limiting the metabolic potential of the isolated microbe. In the past years, synthetic microbial co-cultivation, using well-defined consortia of two or more microbes, was increasingly explored for innovative applications in biotechnology. As such, interspecies interactions take place without the complexity of an open mixed culture, minimizing undesired side reactions. Ultimately, synthetic co-cultivation allows to take well-characterized microbes 'off-the-shelf' to create ecosystems with improved process capabilities. This review highlights some of the recent developments on co-cultivation, focusing on waste-to-chemicals conversions. It also addresses fundamental knowledge on microbial interactions deriving from these studies, which is important to further develop our ability to engineer functional co-cultures for bioproduction.

Cryopreservation and Resuscitation of Natural Aquatic Prokaryotic Communities

Experimental reproducibility in aquatic microbial ecology is critical to predict the dynamics of microbial communities. However, controlling the initial composition of naturally occurring microbial communities that will be used as the inoculum in experimental setups is challenging, because a proper method for the preservation of those communities is lacking. To provide a feasible method for preservation and resuscitation of natural aquatic prokaryote assemblages, we developed a cryopreservation procedure applied to natural aquatic prokaryotic communities. We studied the impact of inoculum size, processing time, and storage time on the success of resuscitation. We further assessed the effect of different growth media supplemented with dissolved organic matter (DOM) prepared from naturally occurring microorganisms on the recovery of the initially cryopreserved communities obtained from two sites that have contrasting trophic status and environmental heterogeneity. Our results demonstrated that the variability of the resuscitation process among replicates decreased with increasing inoculum size. The degree of similarity between initial and resuscitated communities was influenced by both the growth medium and origin of the community. We further demonstrated that depending on the inoculum source, 45-72% of the abundant species in the initially natural microbial communities could be detected as viable cells after cryopreservation. Processing time and long-term storage up to 12 months did not significantly influence the community composition after resuscitation. However, based on our results, we recommend keeping handling time to a minimum and ensure identical incubation conditions for repeated resuscitations from cryo-preserved aliquots at different time points. Given our results, we recommend cryopreservation as a promising tool to advance experimental research in the field of microbial ecology.

Structured environments foster competitor coexistence by manipulating interspecies interfaces

Natural environments, like soils or the mammalian gut, frequently contain microbial consortia competing within a niche, wherein many species contain genetically encoded mechanisms of interspecies competition. Recent computational work suggests that physical structures in the environment can stabilize local competition between species that would otherwise be subject to competitive exclusion under isotropic conditions. Here we employ Lotka-Volterra models to show that interfacial competition localizes to physical structures, stabilizing competitive ecological networks of many species, even with significant differences in the strength of competitive interactions between species. Within a limited range of parameter space, we show that for stable communities the length-scale of physical structure inversely correlates with the width of the distribution of competitive fitness, such that physical environments with finer structure can sustain a broader spectrum of interspecific competition. These results highlight the potentially stabilizing effects of physical structure on microbial communities and lay groundwork for engineering structures that stabilize and/or select for diverse communities of ecological, medical, or industrial utility.

Deciphering the succession dynamics of dominant and rare genera in biofilm development process

Deciphering the succession dynamics of dominant and rare taxa is crucial to understand the stability and ecosystem functions of biofilm communities. However, the essential laws of the succession dynamics based on dominant and rare taxa were still unenlightened. Herein, we investigated the succession dynamics of dominant and rare genera in multi-species biofilms developed in flow cells fed with 10 and 40 mg-TOC/L LB broth. The relative abundance of dominant genera (Enterobacteria and Acinetobacter) decreased remarkably (from 94.63% to 73.22%) in 10 mg-TOC/L LB broth, whereas they kept relatively steady (93.75 ± 4.23%) along with the cultivation time in 40 mg-TOC/L LB broth. Fluorescence in situ hybridization showed that rare genera tended to form clusters at both concentrations, while weaker dispersal of dominant genera caused patchier biofilm structures in 10 mg-TOC/L LB broth compared to that in 40 mg-TOC/L LB broth. Null model analyses further demonstrated that the stochastic ecological drift was more pronounced in the community assembly of biofilms in 10 mg-TOC/L LB broth (73.33%) than those in 40 mg-TOC/L LB broth (60.95%), weakening the competitive superiority of dominant taxa in the patchier biofilms. In addition, the co-occurrence network reflected that the positive interactions among rare genera contributed to exclude dominant genera in 10 mg-TOC/L LB broth, whereas negative interactions only occurred between the dominant Enterobacter and Acinetobacter or rare Comamonas in 40 mg-TOC/L LB broth. This study highlighted the distinctive succession dynamics of dominant and rare genera in biofilms at different substrate concentrations, which would advance our understanding of the biofilm communities in biofilm-related process.

Regularized S-Map Reveals Varying Bacterial Interactions

There is a growing awareness that bacterial interactions follow a highly nonlinear pattern in reality. However, it is challenging to track the varying bacterial interactions using pairwise correlation analysis, which fails to explore their potential effects on the behavior of microbes. Here, we utilized a regularized sequential locally weighted global linear map (S-map) to capture the varying interspecific interactions from the time series data of a bacterial community under exposure to nitrite. Our results show that bacterial interactions are highly variable and that asymmetric interactions dominate the interaction pattern in a community. Furthermore, we propose a Jacobian coefficient-based statistical method to predict the harmony level of a bacterial community at each successive ecosystem state. The results show that the bacterial community exhibits a higher harmony level in nitrite-treated samples than in the control group. We show that the community harmony level is positively associated with the specific endogenous respiration rates and biofilm formation of the culture. In addition, the community tends to process lower diversity and structural stability under zero- and high-nitrite stresses. We demonstrate that the harmony level, rather than structural stability, is a useful index for unveiling the underlying mechanism of bacterial performance. Overall, the regularized S-map can help us to understand bacterial interactions in ecosystems more accurately than previous approaches.IMPORTANCE It has long been acknowledged that bacterial interactions play important roles in community structure and function. Revealing the interaction variability can allow an understanding of how bacteria respond to perturbation and why bacterial community performance changes. Such information should improve our skills in engineering bacterial communities (e.g., in a wastewater treatment plant) and achieve better removal performance and lower energy consumption.

Integrative Circuit-Host Modeling of a Genetic Switch in Varying Environments

Synthetic biology is advancing into a new phase where real-world applications are emphasized. There is hence an urgent need for mathematical modeling that can quantitatively describe the behaviors of genetic devices in natural, fluctuating environments. We utilize an integrative circuit-host modeling framework to examine the dynamics of a genetic switch and its host cell in varying environments. For both steady-state and transient cases, we find increasing nutrient reduces the bistability region of the phase space and eventually drives the switch from bistability to monostability. In response, cellular growth and proteome partitioning experience the same transition. Antibiotic perturbations cause the similar circuit and host responses as nutrient variations. However, one difference is the trend of growth rate, which augments with nutrient but declines with antibiotic levels. The framework provides a mechanistic scheme to account for both the dynamic and static characteristics of the circuit-host system upon environmental perturbations, underscoring the intimacy of gene circuits and their hosts and elucidating the complexity of circuit behaviors arising from environmental variations.