Contributions of the bacterial communities to the microcystin degradation and nutrient transformations during aerobic composting of algal sludge.

Aerobic composting is a useful method for managing and disposing of salvaged algal sludge. To optimize the composting process and improve compost quality, it is necessary to understand the functions and responses of microbial communities therein. This work studied the degradation process of organic matter and the assemblage of bacterial communities in algal sludge composting via 16S rRNA amplicon sequencing. The results showed that 77.08% of the microcystin was degraded during the thermophilic stage of composting, which was the main period for microcystin degradation. Bacterial community composition and diversity changed significantly during the composting, and gradually stabilized as the compost matured. Different composting stages may be dominated by different module groups separately, as shown in the co-occurrence networks of composting bacterial communities. In the networks, all bacteria associated with microcystin degradation were identified as connectors between different module groups. The algal sludge composting process was driven primarily by deterministic processes, and the main driving forces for bacterial community assembly were temperature, dissolved organic carbon, ammonium, and microcystin. At last, by applying the structural equation modeling method, the bacterial communities under influences of physiochemical properties were proved as the main mediators for the microcystin degradation. This study provides valuable insights into the optimization of bacterial communities in composting to improve the efficiency of microcystin degradation and the quality of the compost product.

Season-specific impacts of climate change on canopy-forming seaweed communities.

Understory assemblages associated with canopy-forming species such as trees, kelps, and rockweeds should respond strongly to climate stressors due to strong canopy-understory interactions. Climate change can directly and indirectly modify these assemblages, particularly during more stressful seasons and climate scenarios. However, fully understanding the seasonal impacts of different climate conditions on canopy-reliant assemblages is difficult due to a continued emphasis on studying single-species responses to a single future climate scenario during a single season. To examine these emergent effects, we used mesocosm experiments to expose seaweed assemblages associated with the canopy-forming golden rockweed, Silvetia compressa, to elevated temperature and pCO2 conditions reflecting two projected greenhouse emission scenarios (RCP 2.6 [low] & RCP 4.5 [moderate]). Assemblages were grown in the presence and absence of Silvetia, and in two seasons. Relative to ambient conditions, predicted climate scenarios generally suppressed Silvetia biomass and photosynthetic efficiency. However, these effects varied seasonally-both future scenarios reduced Silvetia biomass in summer, but only the moderate scenario did so in winter. These reductions shifted the assemblage, with more extreme shifts occurring in summer. Contrarily, future scenarios did not shift assemblages within Silvetia Absent treatments, suggesting that climate primarily affected assemblages indirectly through changes in Silvetia. Mesocosm experiments were coupled with a field Silvetia removal experiment to simulate the effects of climate-mediated Silvetia loss on natural assemblages. Consistent with the mesocosm experiment, Silvetia loss resulted in season-specific assemblage shifts, with weaker effects observed in winter. Together, our study supports the hypotheses that climate-mediated changes to canopy-forming species can indirectly affect the associated assemblage, and that these effects vary seasonally. Such seasonality is important to consider as it may provide periods of recovery when conditions are less stressful, especially if we can reduce the severity of future climate scenarios.

Competition Increases Risk of Species Extinction during Extreme Warming.

AbstractTemperature and interspecific competition are fundamental drivers of community structure in natural systems and can interact to affect many measures of species performance. However, surprisingly little is known about the extent to which competition affects extinction temperatures during extreme warming. This information is important for evaluating future threats to species from extreme high-temperature events and heat waves, which are rising in frequency and severity around the world. Using experimental freshwater communities of rotifers and ciliates, this study shows that interspecific competition can lower the threshold temperature at which local extinction occurs, reducing time to extinction during periods of sustained warming by as much as 2 weeks. Competitors may lower extinction temperatures by altering biochemical characteristics of the natural environment that affect temperature tolerance (e.g., levels of dissolved oxygen, nutrients, and metabolic wastes) or by accelerating population decline through traditional effects of resource depletion on life history parameters that affect population growth rates. The results suggest that changes in community structure in space and time could drive variability in upper thermal limits.

Dissecting Gut-Microbial Community Interactions using a Gut Microbiome-on-a-Chip.

While the human gut microbiota has a significant impact on gut health and disease, understanding of the roles of gut microbes, interactions, and collective impact of gut microbes on various aspects of human gut health is limited by the lack of suitable in vitro model system that can accurately replicate gut-like environment and enable the close visualization on causal and mechanistic relationships between microbial constitutents and the gut. , In this study, we present a scalable Gut Microbiome-on-a-Chip (GMoC) with great imaging capability and scalability, providing a physiologically relevant dynamic gut-microbes interfaces. This chip features a reproducible 3D stratified gut epithelium derived from Caco-2 cells (µGut), mimicking key intestinal architecture, functions, and cellular complexity, providing a physiolocially relevant gut environment for microbes residing in the gut. Incorporating tumorigenic bacteria, enterotoxigenic Bacteroides fragilis (ETBF), into the GMoC enable the observation of pathogenic behaviors of ETBF, leading to µGut disruption and pro-tumorigenic signaling activations. Pre-treating the µGut with a beneficial gut microbe Lactobacillus spp., effectively prevent ETBF-mediated gut pathogenesis, preserving the healthy state of the µGut through competition-mediated colonization resistance. The GMoC holds potential as a valuable tool for exploring unknown roles of gut microbes in microbe-induced pathogenesis and microbe-based therapeutic development.

Increasing ambient temperatures trigger shifts in activity patterns and temporal partitioning in a large carnivore guild.

Shifts in species' interactions are implicated as an important proximate cause underpinning climate-change-related extinction. However, there is little empirical evidence on the pathways through which climate conditions, such as ambient temperature, impact community dynamics. The timing of activities is a widespread behavioural adaptation to environmental variability, and temporal partitioning is a key mechanism that facilitates coexistence, especially within large carnivore communities. We investigated temperature impacts on community dynamics through its influence on the diel activity of, and temporal partitioning amongst, four sympatric species of African large carnivores: lions (Panthera leo), leopards (Panthera pardus), cheetahs (Acinonyx jubatus) and African wild dogs (Lycaon pictus). Activity of all species was shaped by a combination of light availability and temperature, with most species becoming more nocturnal and decreasing activity levels with increasing temperatures. A nocturnal shift was most pronounced in cheetahs, the most diurnal species during median temperatures. This shift increased temporal overlap between cheetahs and other carnivore species by up to 15.92%, highlighting the importance of considering the responses of interacting sympatric species when inferring climate impacts on ecosystems. Our study provides evidence that temperature can significantly affect temporal partitioning within a carnivore guild by generating asymmetrical behavioural responses amongst functionally similar species.

Therapeutic compounds from medicinal plant endophytes: molecular and metabolic adaptations.

During the last few decades, endophytes have attracted increased attention due to their ability to produce a plethora of bioactive secondary metabolites. These compounds not only help the endophytes to outcompete other plant-associated microbes or pathogens through quorum sensing, but also enable them to surmount the plant immune system. However, only a very few studies have described the interlink between various biochemical and molecular factors of host-microbe interactions involved in the production of these pharmacological metabolites. The peculiar mechanisms by which endophytes modulate plant physiology and metabolism through elicitors, as well as how they use transitional compounds of primary and secondary metabolism as nutrients and precursors for the synthesis of new compounds or enhancing existing metabolites, are still less understood. This study thus attempts to address the aspects of synthesis of such metabolites used in therapeutics by the endophytes in the light of their ecological significance, adaptation, and intercommunity interactions. Our study explores how endophytes adapt to the specific host environment, especially in medicinal plants that produce metabolites with pharmacological potential and simultaneously modulate host gene expression for the biosynthesis of these metabolites. We also discuss the differential interactions of fungal and bacterial endophytes with their hosts.

Microbiome composition modulates secondary metabolism in a multispecies bacterial community.

Bacterial secondary metabolites are a major source of antibiotics and other bioactive compounds. In microbial communities, these molecules can mediate interspecies interactions and responses to environmental change. Despite the importance of secondary metabolites in human health and microbial ecology, little is known about their roles and regulation in the context of multispecies communities. In a simplified model of the rhizosphere composed of Bacillus cereus, Flavobacterium johnsoniae, and Pseudomonas koreensis, we show that the dynamics of secondary metabolism depend on community species composition and interspecies interactions. Comparative metatranscriptomics and metametabolomics reveal that the abundance of transcripts of biosynthetic gene clusters (BGCs) and metabolomic molecular features differ between monocultures or dual cultures and a tripartite community. In both two- and three-member cocultures, P. koreensis modified expression of BGCs for zwittermicin, petrobactin, and other secondary metabolites in B. cereus and F. johnsoniae, whereas the BGC transcriptional response to the community in P. koreensis itself was minimal. Pairwise and tripartite cocultures with P. koreensis displayed unique molecular features that appear to be derivatives of lokisin, suggesting metabolic handoffs between species. Deleting the BGC for koreenceine, another P. koreensis metabolite, altered transcript and metabolite profiles across the community, including substantial up-regulation of the petrobactin and bacillibactin BGCs in B. cereus, suggesting that koreenceine represses siderophore production. Results from this model community show that bacterial BGC expression and chemical output depend on the identity and biosynthetic capacity of coculture partners, suggesting community composition and microbiome interactions may shape the regulation of secondary metabolism in nature.

Community Interaction Co-limitation: Nutrient Limitation in a Marine Microbial Community Context.

The simultaneous limitation of productivity by two or more nutrients, commonly referred to as nutrient co-limitation, affects microbial communities throughout the marine environment and is of profound importance because of its impacts on various biogeochemical cycles. Multiple types of co-limitation have been described, enabling distinctions based on the hypothesized mechanisms of co-limitation at a biochemical level. These definitions usually pertain to individuals and do not explicitly, or even implicitly, consider complex ecological dynamics found within a microbial community. However, limiting and co-limiting nutrients can be produced in situ by a subset of microbial community members, suggesting that interactions within communities can underpin co-limitation. To address this, we propose a new category of nutrient co-limitation, community interaction co-limitation (CIC). During CIC, one part of the community is limited by one nutrient, which results in the insufficient production or transformation of a biologically produced nutrient that is required by another part of the community, often primary producers. Using cobalamin (vitamin B12) and nitrogen fixation as our models, we outline three different ways CIC can arise based on current literature and discuss CIC's role in biogeochemical cycles. Accounting for the inherent and complex roles microbial community interactions play in generating this type of co-limitation requires an expanded toolset - beyond the traditional approaches used to identify and study other types of co-limitation. We propose incorporating processes and theories well-known in microbial ecology and evolution to provide meaningful insight into the controls of community-based feedback loops and mechanisms that give rise to CIC in the environment. Finally, we highlight the data gaps that limit our understanding of CIC mechanisms and suggest methods to overcome these and further identify causes and consequences of CIC. By providing this framework for understanding and identifying CIC, we enable systematic examination of the impacts this co-limitation can have on current and future marine biogeochemical processes.

The Effect of Perceived Value on Consumers' Repurchase Intention of Commercial Ice Stadium: The Mediating Role of Community Interactions.

The 2022 Beijing Winter Olympics has created unprecedented opportunities for China's commercial ice rinks, where improving consumers' repurchase intention is essential for their high-quality development. This paper explores the mediation effect of community interactions between perceived value and commercial ice rink consumers' repurchase intention based on the theory of perceived value. Through a questionnaire survey, we collected 347 valid questionnaire from consumers of commercial ice rinks. Based on a structural equation model, the results show that consumers' perceived risk value significantly impacts community interactions and consumers' repurchase intention. Perceived functional, social, and emotional values positively affect community interactions but have an insignificant impact on the consumers' repurchase intention. Community interactions play a full mediation role between perceived emotional and social values and consumers' repurchase intention; they play partially mediating role between consumers' perceived risk value and repurchase intention and do not have mediating role between perceived functional value and consumers' repurchase intention. Therefore, we provide some practical suggestions: extending commercial ice rink product lines, creating unique intellectual property systems, improving consumer sports career planning, and enhancing risk management.

Community response of arbuscular mycorrhizal fungi to extreme drought in a cold-temperate grassland.

Climate extremes pose enormous threats to natural ecosystems. Arbuscular mycorrhizal (AM) fungi are key plant symbionts that can affect plant community dynamics and ecosystem stability. However, knowledge about how AM fungal communities respond to climate extremes in natural ecosystems remains elusive. Based on a grassland extreme drought experiment in Inner Mongolia, we investigated the response of AM fungal communities to extreme drought in association with plant communities. The experiment simulated two types of extreme drought (chronic/intense) of once-in-20-year occurrence. AM fungal richness and community composition exhibited high sensitivity to extreme drought and were more sensitive to intense drought than chronic drought. This community sensitivity (i.e. decline in richness and shifts in community composition) of AM fungi can be jointly explained by soil moisture, plant richness, and aboveground productivity. Notably, the robustness of the plant-AM fungal community co-response increased with drought intensity. Our results indicate that AM fungal communities are sensitive to climate extremes, and we propose that the plant community mediates AM fungal community responses. Given the ubiquitous nature of AM associations, their climate sensitivity may have profound consequences on plant communities and ecosystem stability under climate change.

Appendectomy Is Associated With Alteration of Human Gut Bacterial and Fungal Communities.

Recent research has revealed the importance of the appendix in regulating the intestinal microbiota and mucosal immunity. However, the changes that occur in human gut microbial communities after appendectomy have never been analyzed. We assessed the alterations in gut bacterial and fungal populations associated with a history of appendectomy. In this cross-sectional study, we investigated the association between appendectomy and the gut microbiome using 16S and ITS2 sequencing on fecal samples from 30 healthy individuals with prior appendectomy (HwA) and 30 healthy individuals without appendectomy (HwoA). Analysis showed that the gut bacterial composition of samples from HwA was less diverse than that of samples from HwoA and had a lower abundance of Roseburia, Barnesiella, Butyricicoccus, Odoribacter, and Butyricimonas species, most of which were short-chain fatty acids-producing microbes. The HwA subgroup analysis indicated a trend toward restoration of the HwoA bacterial microbiome over time after appendectomy. HwA had higher gut fungi composition and diversity than HwoA, even 5 years after appendectomy. Compared with those in samples from HwoA, the abundance correlation networks in samples from HwA displayed more complex fungal-fungal and fungal-bacterial community interactions. This study revealed a marked impact of appendectomy on gut bacteria and fungi, which was particularly durable for fungi.

Corrigendum: Characterization of the Interactive Effects of Labile and Recalcitrant Organic Matter on Microbial Growth and Metabolism.

[This corrects the article DOI: 10.3389/fmicb.2019.00493.].

Microbial Community Interactions Are Sensitive to Small Changes in Temperature.

Microbial communities are essential for human and environmental health, often forming complex interaction networks responsible for driving ecosystem processes affecting their local environment and their hosts. Disturbances of these communities can lead to loss of interactions and thereby important ecosystem functionality. The research on what drives interactions in microbial communities is still in its infancy, and much information has been gained from the study of model communities. One purpose of using these model microbial communities is that they can be cultured under controlled conditions. Yet, it is not well known how fluctuations of abiotic factors such as temperature affect their interaction networks. In this work, we have studied the effect of temperature on interactions between the members of the model community THOR, which consists of three bacterial species: Pseudomonas koreensis, Flavobacterium johnsoniae, and Bacillus cereus. Our results show that the community-intrinsic properties resulting from their interspecies interactions are highly dependent on incubation temperature. We also found that THOR biofilms had remarkably different abundances of their members when grown at 11, 18, and 25°C. The results suggest that the sensitivity of community interactions to changes in temperature is influenced, but not completely dictated, by different growth rates of the individual members at different temperatures. Our findings likely extend to other microbial communities and environmental parameters. Thus, temperature could affect community stability and may influence diverse processes including soil productivity, bioprocessing, and disease suppression. Moreover, to establish reproducibility between laboratories working with microbial model communities, it is crucial to ensure experimental stability, including carefully managed temperature conditions.

Microbial community composition interacts with local abiotic conditions to drive colonization resistance in human gut microbiome samples.

Biological invasions can alter ecosystem stability and function, and predicting what happens when a new species or strain arrives remains a major challenge in ecology. In the mammalian gastrointestinal tract, susceptibility of the resident microbial community to invasion by pathogens has important implications for host health. However, at the community level, it is unclear whether susceptibility to invasion depends mostly on resident community composition (which microbes are present), or also on local abiotic conditions (such as nutrient status). Here, we used a gut microcosm system to disentangle some of the drivers of susceptibility to invasion in microbial communities sampled from humans. We found resident microbial communities inhibited an invading Escherichia coli strain, compared to community-free control treatments, sometimes excluding the invader completely (colonization resistance). These effects were stronger at later time points, when we also detected altered community composition and nutrient availability. By separating these two components (microbial community and abiotic environment), we found taxonomic composition played a crucial role in suppressing invasion, but this depended critically on local abiotic conditions (adapted communities were more suppressive in nutrient-depleted conditions). This helps predict when resident communities will be most susceptible to invasion, with implications for optimizing treatments based on microbiota management.

Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities.

Quantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and carbon acquisition potential (CAP) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrate's degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.

Bacterial Membrane Vesicles as Mediators of Microbe - Microbe and Microbe - Host Community Interactions.

Bacterial membrane vesicles are proteoliposomal nanoparticles produced by both Gram-negative and Gram-positive bacteria. As they originate from the outer surface of the bacteria, their composition and content is generally similar to the parent bacterium's membrane and cytoplasm. However, there is ample evidence that preferential packaging of proteins, metabolites, and toxins into vesicles does occur. Incorporation into vesicles imparts a number of benefits to the cargo, including protection from degradation by other bacteria, the host organism, or environmental factors, maintenance of a favorable microenvironment for enzymatic activity, and increased potential for long-distance movement. This enables vesicles to serve specialized functions tailored to changing or challenging environments, particularly in regard to microbial community interactions including quorum sensing, biofilm formation, antibiotic resistance, antimicrobial peptide expression and deployment, and nutrient acquisition. Additionally, based on their contents, vesicles play crucial roles in host-microbe interactions as carriers of virulence factors and other modulators of host cell function. Here, we discuss recent advances in our understanding of how vesicles function as signals both within microbial communities and between pathogenic or commensal microbes and their mammalian hosts. We also highlight a few areas that are currently ripe for additional research, including the mechanisms of selective cargo packaging into membrane vesicles and of cargo processing once it enters mammalian host cells, the function of vesicles in transfer of nucleic acids among bacteria, and the possibility of engineering commensal bacteria to deliver cargo of interest to mammalian hosts in a controlled manner.

Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations.

BACKGROUND: Network inference is an important aim of systems biology. It enables the transformation of OMICs datasets into biological knowledge. It consists of reverse engineering gene regulatory networks from OMICs data, such as RNAseq or mass spectrometry-based proteomics data, through computational methods. This approach allows to identify signalling pathways involved in specific biological functions. The ability to infer causality in gene regulatory networks, in addition to correlation, is crucial for several modelling approaches and allows targeted control in biotechnology applications. METHODS: We performed simulations according to the approximate Bayesian computation method, where the core model consisted of a steady-state simulation algorithm used to study gene regulatory networks in systems for which a limited level of details is available. The simulations outcome was compared to experimentally measured transcriptomics and proteomics data through approximate Bayesian computation. RESULTS: The structure of small gene regulatory networks responsible for the regulation of biological functions involved in biomining were inferred from multi OMICs data of mixed bacterial cultures. Several causal inter- and intraspecies interactions were inferred between genes coding for proteins involved in the biomining process, such as heavy metal transport, DNA damage, replication and repair, and membrane biogenesis. The method also provided indications for the role of several uncharacterized proteins by the inferred connection in their network context. CONCLUSIONS: The combination of fast algorithms with high-performance computing allowed the simulation of a multitude of gene regulatory networks and their comparison to experimentally measured OMICs data through approximate Bayesian computation, enabling the probabilistic inference of causality in gene regulatory networks of a multispecies bacterial system involved in biomining without need of single-cell or multiple perturbation experiments. This information can be used to influence biological functions and control specific processes in biotechnology applications.

The relative contributions of climate, soil, diversity and interactions to leaf trait variation and spectrum of invasive Solidago canadensis.

BACKGROUND: Invasive plants commonly occupy diverse habitats and thus must adapt to changing environmental pressures through altering their traits and economics spectra, and addressing these patterns and their drivers has an importantly ecological and/or evolutionary significance. However, few studies have considered the role of multiple biotic and abiotic factors in shaping trait variation and spectra. In this study, we determined seven leaf traits of 66 Solidago canadensis populations, and quantified the relative contributions of climate, soil properties, native plant diversity, and S. canadensis-community interactions (in total 16 factors) to leaf trait variation and spectrum with multimodel inference. RESULTS: Overall, the seven leaf traits had high phenotypic variation, and this variation was highest for leaf dry matter content and lowest for leaf carbon concentration. The per capita contribution of climate to the mean leaf trait variation was highest (7.5%), followed by soil properties (6.2%), S. canadensis-community interactions (6.1%), and native plant diversity (5.4%); the dominant factors underlying trait variation varied with leaf traits. Leaf production potential was negatively associated with leaf stress-tolerance potential, and the relative contributions to this trade-off followed in order: native plant diversity (7.7%), climate (6.9%), S. canadensis-community interactions (6.2%), and soil properties (5.6%). Climate, diversity, soil, and interactions had positive, neutral or negative effects. CONCLUSIONS: Climate, soil, diversity, and interactions contribute differentially to the leaf trait variation and economics spectrum of S. canadensis, and their relative importance and directions depend on plant functional traits.

Characterization of the Interactive Effects of Labile and Recalcitrant Organic Matter on Microbial Growth and Metabolism.

Geochemical models typically represent organic matter (OM) as consisting of multiple, independent pools of compounds, each accessed by microorganisms at different rates. However, recent findings indicate that organic compounds can interact within microbial metabolisms. The relevance of interactive effects within marine systems is debated and a mechanistic understanding of its complexities, including microbe-substrate relationships, is lacking. As a first step toward uncovering mediating processes, the interactive effects of distinct pools of OM on the growth and respiration of marine bacteria, individual strains and a simple, constructed community of Roseobacter lineage members were tested. Isolates were provided with natural organic matter (NOM) and different concentrations (1, 4, 40, 400 µM-C) and forms of labile OM (acetate, casamino acids, tryptone, coumarate). The microbial response to the mixed substrate regimes was assessed using viable counts and respiration in two separate experiments. Two marine bacteria and a six-member constructed community were assayed with these experiments. Both synergistic and antagonistic growth responses were evident for all strains, but all were transient. The specific substrate conditions promoting a response, and the direction of that response, varied amongst species. These findings indicate that the substrate conditions that result in OM interactive effects are both transient and species-specific and thus influenced by both the composition and metabolic potential of a microbial community.

How Microbial Aggregates Protect against Nanoparticle Toxicity.

The increasing use and discharge of nanoparticles (NPs) pose risks to microorganisms that maintain the health of aquatic ecosystems. Although NPs are toxic to microorganisms, they tend to form microbial aggregates to protect themselves. Two main mechanisms account for the reduced toxicity: the dense physical structure acts as a barrier to NP exposure in the interior of the aggregate, and aggregation stabilizes a complex microbial ecosystem that enhances the ability of the community to adapt to prolonged NP exposure. We highlight the opportunities and challenges for managing microbial aggregates in wastewater treatment to remove or control NPs. For example, understanding the resistance mechanisms can help to design smart NPs that are less toxic to useful microorganisms or more toxic towards pathogenic microorganisms.