E. van Tilburg Bernardes, Veronika Kuchařová Pettersen, M. W. Gutierrez
et al.
The gut microbiome consists of a multi-kingdom microbial community. Whilst the role of bacteria as causal contributors governing host physiological development is well established, the role of fungi remains to be determined. Here, we use germ-free mice colonized with defined species of bacteria, fungi, or both to differentiate the causal role of fungi on microbiome assembly, immune development, susceptibility to colitis, and airway inflammation. Fungal colonization promotes major shifts in bacterial microbiome ecology, and has an independent effect on innate and adaptive immune development in young mice. While exclusive fungal colonization is insufficient to elicit overt dextran sulfate sodium-induced colitis, bacterial and fungal co-colonization increase colonic inflammation. Ovalbumin-induced airway inflammation reveals that bacterial, but not fungal colonization is necessary to decrease airway inflammation, yet fungi selectively promotes macrophage infiltration in the airway. Together, our findings demonstrate a causal role for fungi in microbial ecology and host immune functionality, and therefore prompt the inclusion of fungi in therapeutic approaches aimed at modulating early life microbiomes. The immunomodulatory role of commensal gut fungi and interactions with bacteria remain unclear. Here, using germ-free mice colonized with defined species of bacteria and fungi, the authors find that fungal colonization induces changes in bacterial microbiome ecology while having an independent effect on innate and adaptive immunity in mice.
Many organisms team up with microbes for defense against predators, parasites, parasitoids, or pathogens. Here we review the described protective symbioses between animals (including marine invertebrates, nematodes, insects, and vertebrates) and bacteria, fungi, and dinoflagellates. We focus on associations where the microbial natural products mediating the protective activity have been elucidated or at least strong evidence for the role of symbiotic microbes in defense is available. In addition to providing an overview of the known defensive animal-microbe symbioses, we aim to derive general patterns on the chemistry, ecology, and evolution of such associations.
Understanding functional diversity, the range and variability of species' roles and actions within their communities, is key to predicting and preserving the functions that sustain both nature and human well-being. In this paper, we provide a comprehensive review of the literature on functional diversity measurement. We begin by consolidating essential criteria that effective measures of functional diversity should meet. We then evaluate fifteen widely used functional diversity metrics against these criteria and assess their performance across six synthetic ecosystem scenarios where optimal behavior is known. Surprisingly, our analysis reveals that none of the widely used metrics fully satisfy all the established requirements, and all fail in at least one ecosystem scenario. In particular, we find that almost all metrics flagrantly violate set monotonicity and distance monotonicity, requirements that adding a novel species should increase diversity, and that the magnitude of that increase should grow with trait dissimilarity. We also find that metrics fail to decline when rare, functionally extreme species are lost, and even increase when a perfectly redundant species is added. These critical flaws leave them blind to the very biodiversity loss that functional diversity measures are intended to detect. Our findings underscore the urgent need to develop a new generation of functional diversity metrics that more accurately reflect ecological realities.
Amy A. Gault, Susan A. Welsh, Arapera Paewai
et al.
ABSTRACT In response to intensified agricultural impacts on Aotearoa New Zealand's river systems, our study sought to demonstrate a novel approach for assessing freshwater quality through environmental DNA (eDNA) and promote a holistic understanding of ecological health. Employing 13 eDNA tree‐of‐life metabarcoding assays alongside 11 standard physicochemical attributes, we generated a comprehensive temporal and spatial dataset along a 3.5 km section of an upper river catchment. The study catchment moves from a culturally significant native bush area, through sheep and beef farming, to an organic dairy farm, capturing the transition through varying land uses. Our analysis focused on the detections of key culturally significant taonga (treasured) species, known animal sources of fecal contamination, and the taxon‐independent community index (TICI) as a measure of ecological health. We identified 479 species including whīo/native blue duck, long and short finned tuna/eels, kaharore bully/cockabully, kōkopu/dwarf galaxias, and kōura/freshwater crayfish. Although Escherichia coli (E. coli) levels did not significantly vary across sites, eDNA sequence counts of cattle and deer were significant predictors of a site's E. coli levels, suggesting that eDNA could be a valuable indicator of fecal contamination sources. TICI scores were strongly correlated with changes in water quality attributes (Adj‐R2 = 0.92) and consistently detected subtle declines driven by increased pastoral land use. Community leadership was central to our methodology, enabling local stakeholders, including mana whenua and farmers, to actively participate in water monitoring and data interpretation. This approach not only fulfilled regulatory requirements but also fostered a deep connection with the river, enhancing community‐led conservation efforts. By enhancing the mauri (life force) of the community through active participation and capacity building, this approach exemplifies sustainable, collaborative efforts in environmental management and revitalization.
Abstract The gut microbiome plays a pivotal role in human health, yet its complexity has long eluded detailed study under physiologically relevant conditions. Hydrogel-based models are revolutionizing microbiome research by bridging the gap between traditional in vitro systems and the complexity of in vivo environments. These advanced systems replicate key physical and biochemical features of the gastrointestinal tract, offering unprecedented opportunities to study microbial behavior, adaptation, and interactions within three-dimensional, tunable architectures. Unlike suspension cultures, hydrogels provide porous, mucosa-like environments that enable the cultivation of mucosa-associated microbes, co-culturing with human cells, and mimicking healthy and disease-related states. This review explores the transformative potential of hydrogel matrices in unveiling the spatial organization, nutrient gradients, and community communication that define microbial ecosystems. By integrating the benefits of in vitro and in vivo models, hydrogel-based platforms promise to accelerate discoveries in microbiome science, with far-reaching implications for understanding human health and developing targeted therapeutics. Video Abstract
Esteban Charria-Girón, Rita Toshe, Artit Khonsanit
et al.
Cordyceps species are widespread entomopathogens and promising biocontrol agents that produce diverse secondary metabolites, yet the roles of these molecules during the infection process remain unclear. To interpret how fungal chemistry contributes to host colonization, we compared the metabolomes and virulence traits of two strains of phylogenetically distinct Cordyceps species (C. javanica and C. blackwelliae) and assessed their effects on beet armyworms (fungiSpodoptera exigua). Virulence assays revealed species-dependent pathogenicity, with C. javanica showing the highest virulence. Combining untargeted metabolomics, feature-based molecular networking (FBMN), 3D electron-diffraction crystallography and comprehensive 1D/2D NMR, we gained insights into their metabolomic traits. For instance, C. javanica displayed notable beauveriolide diversity, including three previously undescribed derivatives (1–3), while C. blackwelliae produced mainly diketopiperazines in vitro. The FBMN results revealed putative beauveriolide analogs in the C. blackwelliae extracts, unlike the cadaver analysis, revealing beauvericins in infected corpses. Remarkably, the crude extracts obtained from authentic insect cadavers contained beauveriolides and beauvericins, providing in vivo chemical evidences of their production during infection for the first time. Moreover, bioassays with purified compounds showed that insecticidal activity cannot be attributed across all beauveriolides but depends on amino-acid composition, implying multifunctional roles beyond direct toxicity. Altogether, these results reveal context-dependent metabolic reprogramming and species-specific chemical strategies in entomopathogenic fungi, with implications for microbial ecology, host specificity, and the rational development of fungal biocontrol agents. The results of this study also give rise to the need for more intensified study on the chemical composition of the insect cadavers that are colonized by other entomopathogens.
Abstract Anthocyanins are natural water-soluble polyphenols present in fruits and vegetables. Health-promoting effects attributed to anthocyanins are mainly associated with oxidative stress inhibition and gut microbiota modulation. Dietary anthocyanins undergo a complex metabolism after ingestion and interact with endogenous and microbial enzymes, leading to the production of a large number of circulating and excreted anthocyanin metabolites and catabolic products. To date, the bioavailability and health benefits of anthocyanins have been widely documented. Although there are several papers that illustrated the metabolism of anthocyanins, the effects of dietary anthocyanins on the modulation of the gut microbial ecology and on the growth of certain microbial species are still poorly understood. The present paper summarizes the recent data on the absorption of anthocyanins in the upper gastrointestine and the metabolism of anthocyanins by gut microbiota. The modulatory effects of anthocyanins from different sources on gut microbiota are also discussed.
Social-ecological systems research aims to understand the nature of social-ecological phenomena, to find ways to foster or manage conditions under which desired phenomena occur or to reduce the negative consequences of undesirable phenomena. Such challenges are often addressed using dynamical systems models (DSM) or agent-based models (ABM). Here we develop an iterative procedure for combining DSM and ABM to leverage their strengths and gain insights that surpass insights obtained by each approach separately. The procedure uses results of an ABM as inputs for a DSM development. In the following steps, results of the DSM analyses guide future analysis of the ABM and vice versa. This dialogue, more than having a tight connection between the models, enables pushing the research frontier, expanding the set of research questions and insights. We illustrate our method with the example of poverty traps and innovation in agricultural systems, but our conclusions are general and can be applied to other DSM-ABM combinations.
Francesca De Santa, Georgios Strimpakos, Nicole Marchetti
et al.
Abstract Background Intestinal microbial composition not only affects the health of the gut but also influences centrally mediated systems involved in mood, through the “gut-brain” axis, a bidirectional communication between gut microbiota and the brain. In this context, the modulation of intestinal microbiota and its metabolites through the administration of probiotics seems to represent a very promising approach in the treatment of the central nervous system alterations. Early postnatal life is a critical period during which the brain undergoes profound and essential modulations in terms of maturation and plasticity. Maternal separation (MS), i.e., the disruption of the mother–pup interaction, represents a pivotal paradigm in the study of stress-related mood disorders, by inducing persistent changes in the immune system, inflammatory processes, and emotional behavior in adult mammals. Results We conducted experiments to investigate whether sustained consumption of a multi-strain probiotic formulation by adult male mice could mitigate the effects of maternal separation. Our data demonstrated that the treatment with probiotics was able to totally reverse the anxiety- and depressive-like behavior; normalize the neuro-inflammatory state, by restoring the resting state of microglia; and finally induce a proneurogenic effect. Mice subjected to maternal separation showed changes in microbiota composition compared to the control group that resulted in permissive colonization by the administered multi-strain probiotic product. As a consequence, the probiotic treatment also significantly affected the production of SCFA and in particular the level of butyrate. Conclusion Gut microbiota and its metabolites mediate the therapeutic action of the probiotic mix on MS-induced brain dysfunctions. Our findings extend the knowledge on the use of probiotics as a therapeutic tool in the presence of alterations of the emotional sphere that significantly impact on gut microbiota composition. Video Abstract
AbstractCollectively, we have been reviewers for microbial ecology, genetics and genomics studies that include environmental DNA (eDNA), microbiome studies, and whole bacterial genome biology forMicrobial Ecologyand other journals for about three decades. Here, we wish to point out trends and point to areas of study that readers, especially those moving into the next generation of microbial ecology research, might learn and consider. In this communication, we arenotsaying the work currently being accomplished in microbial ecology and restoration biology is inadequate. What we are saying is that a significant milestone in microbial ecology has been reached, and approaches that may have been overlooked or were unable to be completed before should be reconsidered in moving forward into a new more ecological era where restoration of the ecological trajectory of systems has become critical. It is our hope that this introduction, along with the papers that make up this special issue, will address the sense of immediacy and focus needed to move into the next generation of microbial ecology study.
This work addresses the ecological-adaptive cruise control problem for connected electric vehicles by a computationally efficient robust control strategy. The problem is formulated in the space-domain with a realistic description of the nonlinear electric powertrain model and motion dynamics to yield a convex optimal control problem (OCP). The OCP is approached by a novel robust model predictive control (RMPC) method handling various disturbances due to modelling mismatch and inaccurate leading vehicle information. The RMPC problem is solved by semi-definite programming relaxation and single linear matrix inequality (sLMI) techniques for further enhanced computational efficiency. The performance of the proposed real-time robust ecological-adaptive cruise control (REACC) method is evaluated using an experimentally collected driving cycle. Its robustness is verified by comparison with a nominal MPC which is shown to result in speed-limit constraint violations. The energy economy of the proposed method outperforms a state-of-the-art time-domain RMPC scheme, as a more precisely fitted convex powertrain model can be integrated into the space-domain scheme. The additional comparison with a traditional constant distance following strategy (CDFS) further verifies the effectiveness of the proposed REACC. Finally, it is verified that the REACC can be potentially implemented in real-time owing to the sLMI and resulting convex algorithm.
Claudia Huaylla, Marcelo N Kuperman, Lucas A. Garibaldi
Networks are a convenient way to represent many interactions among different entities as they provide an efficient and clear methodology to evaluate and organize relevant data. While there are many features for characterizing networks there is a quantity that seems rather elusive: Complexity. The quantification of the complexity of networks is nowadays a fundamental problem. Here, we present a novel tool for identifying the complexity of ecological networks. We compare the behavior of two relevant indices of complexity: K-complexity and Single value decomposition (SVD) entropy. For that, we use real data and null models. Both null models consist of randomized networks built by swapping a controlled number of links of the original ones. We analyze 23 plant-pollinator and 19 host-parasite networks as case studies. Our results show interesting features in the behavior for the K-complexity and SVD entropy with clear differences between pollinator-plant and host-parasite networks, especially when the degree distribution is not preserved. Although SVD entropy has been widely used to characterize network complexity, our analyses show that K-complexity is a more reliable tool. Additionally, we show that degree distribution and density are important drivers of network complexity and should be accounted for in future studies.
The connection between active perception and the limits of performance provide a path to understanding naturalistic behavior. We can take a comparative cognitive modeling perspective to understand the limits of this performance and the existence of superperformance. We will discuss two categories that are hypothesized to originate in terms of coevolutionary relationships and evolutionary trade offs: supersamplers and superplanners. Supersamplers take snapshots of their sensory world at a very high sampling rate. Examples include flies (vision) and frogs (audition) with ecological specializations. Superplanners internally store information to evaluate and act upon multiple features of spatiotemporal environments. Slow lorises and turtles provide examples of superplanning capabilities. The Gibsonian Information (GI) paradigm is used to evaluate sensory sampling and planning with respect to direct perception and its role in capturing environmental information content. By contrast, superplanners utilize internal models of the environment to compensate for normal rates of sensory sampling, and this relationship often exists as a sampling/planning tradeoff. Supersamplers and superplanners can exist in adversarial relationships, or longer-term as coevolutionary relationships. Moreover, the tradeoff between sampling and planning capacity can break down, providing relativistic regimes. We can apply the principles of superperformance to human augmentation technologies.
Abstract Background Normally, a salt amount greater than 3.5% (w/v) is defined as hypersaline. Large amounts of hypersaline wastewater containing organic pollutants need to be treated before it can be discharged into the environment. The most critical aspect of the biological treatment of saline wastewater is the inhibitory/toxic effect exerted on bacterial metabolism by high salt concentrations. Although efforts have been dedicated to improving the performance through the use of salt-tolerant or halophilic bacteria, the diversities of the strains and the range of substrate spectrum remain limited, especially in chlorophenol wastewater treatment. Results In this study, a salt-tolerant chlorophenol-degrading strain was generated from Rhodococcus rhodochrous DSM6263, an original aniline degrader, by adaptive laboratory evolution. The evolved strain R. rhodochrous CP-8 could tolerant 8% NaCl with 4-chlorophenol degradation capacity. The synonymous mutation in phosphodiesterase of strain CP-8 may retard the hydrolysis of cyclic adenosine monophosphate (cAMP), which is a key factor reported in the osmoregulation. The experimentally verified up-regulation of intracellular cAMP level in the evolved strain CP-8 contributes to the improvement of growth phenotype under high osmotic condition. Additionally, a point mutant of the catechol 1,2-dioxygenase, CatAN211S, was revealed to show the 1.9-fold increment on activity, which the mechanism was well explained by molecular docking analysis. Conclusions This study developed one chlorophenol-degrading strain with extraordinary capacity of salt tolerance, which showed great application potential in hypersaline chlorophenol wastewater treatment. The synonymous mutation in phosphodiesterase resulted in the change of intracellular cAMP concentration and then increase the osmotic tolerance in the evolved strain. The catechol 1,2-dioxygenase mutant with improved activity also facilitated chlorophenol removal since it is the key enzyme in the degradation pathway.