Kevin D. Kohl

Sperm cooperation can improve fertilization success in species with intense sperm competition, but the mechanisms that assemble cooperative groups remain unclear. We tested whether extracellular zinc, an abundant component of the epididymal and seminal environment, promotes sperm clustering in the deer mouse, Peromyscus maniculatus. Zinc increased the proportion of sperm in groups, and these groups persisted after washout, suggesting that zinc induces relatively stable sperm-sperm interactions. Chelation reduced clustering, indicating that these interactions remain reversible. Deer mouse sperm also accumulated on zinc-conjugated beads, whereas sperm from the non-clustering house mouse, Mus musculus, did not, consistent with a species-specific, zinc-dependent adhesive property. Together, these findings identify extracellular zinc as a candidate signal that promotes cooperative sperm clustering and suggest that extracellular zinc may provide a physiological cue that enables cooperative sperm behavior in species under strong sperm competition.

Ponds are biodiversity hotspots that harbor diverse macro-organisms and microbial communities, despite being isolated, highly variable environments with island-like features. These factors may give rise to unique biogeographic patterns and drivers of microbial community diversity. Here, we evaluated environmental and regional drivers of pond fungal and bacterial biodiversity to determine whether these communities follow commonly observed biogeographical trends. We collected water and muck from 40 ponds across 8 states in the Eastern USA and sequenced sections of the 16S rRNA and ITS1 genes to survey the bacterial and fungal communities and test (1) whether these communities follow latitudinal diversity gradients and distance decay relationships, and (2) if variation in community composition or richness was related to specific environmental or land-use factors. We found that pond microbial communities exhibit distinct distribution patterns and relationships with environmental drivers depending on the microhabitat and microbial taxa. For example, muck fungal communities followed latitudinal diversity gradients, but bacterial communities did not. Abiotic conditions explained more variation than surrounding land use or the distance between sites, with temperature universally linked to microbial biodiversity. However, all sample types displayed weak distance-decay relationships, likely because of low spatial autocorrelation in environmental conditions and the lack of connectivity across ponds.

To holistically understand the biology of animals, we must unravel the complexities and specificities of host-microbe interactions across animal taxa. Birds represent enigmatic and scientifically compelling hosts in which to understand these interactions. Here, we present a brief summary of a series of conversations among avian microbiome researchers regarding methodological challenges facing the avian microbiome field, where most research to date has focused on bacterial communities of the gut. Collectively, we acknowledged a commonly shared but underreported issue facing the avian microbiome field: that of difficulty in obtaining high-quality and high-yield microbial DNA from avian fecal samples. We discuss some of the potential reasons underlying low DNA yields, such as inhibitory compounds and rapid DNA degradation, and provide recommendations for how researchers in the avian microbiome field might cope with these methodological challenges. Collective and dedicated efforts to address these challenges will be required for a robust understanding of host-microbe interactions in avian systems.

Recent advances in the field of wild avian microbiome research have significantly deepened our understanding of the eco‐evolutionary dynamics of bird–microbe interactions. Consequently, the field is now approaching a pivotal moment in uncovering the ultimate factors shaping avian microbiome structure, especially in relation to birds' ecological, evolutionary, and dietary diversity. Yet, avian microbiome researchers face persistent methodological challenges. Based on discussions from a round table session at the 2023 European Ornithologists' Union Congress in Lund, Sweden, which brought together researchers studying host–microbe interactions across avian systems, here we highlight shared obstacles and potential solutions to strengthen the prospects of the field. This work outlines and discusses key challenges faced, and considerations to be taken into account by avian microbiome researchers throughout the scientific process, while pinpointing areas of research that need attention to advance the field. Disseminating these insights can foster innovation and collaboration, while providing a roadmap for young and new scientists who are interested in the field of avian microbiomes.

Microbiome science has revolutionized our understanding of host–microbe interactions, with mammalian hosts providing a unique and diverse system to study these associations. This Special Feature presents a compelling synthesis of studies that use microbiome science to explore mammals as holobionts (i.e., an individual host and its associated microorganisms), highlighting how these microbial communities play important roles in the ecology and evolution of mammalian hosts. The studies showcase diverse mammalian models—such as bats, chipmunks, groundhogs, and spotted hyenas—and highlight the importance of factors including diet, phylogeny, and gut anatomy in shaping microbial communities. The research presented in this Special Feature also emphasizes the need for more mammalogy researchers to embrace the field of microbiology by developing robust data collection protocols and experimental models to examine these complex systems. Long-term datasets from mammalian hosts will be powerful tools for understanding stochasticity in host–microbe associations, a poorly understood area even in simple model systems. Furthermore, this Special Feature highlights the importance of inclusive knowledge in microbiome sciences. The workshop hosted as part of the symposium, “Using the Mammalian Microbiome as a Framework to Explore Historical Knowledge and Object Interpretation as Methods for Enhancing Understanding,” provided opportunities for structured and free-form reflections. Our efforts were motivated by the increasing recognition that practices of academic science are strengthened when philosophy, Indigenous knowledge systems, and the humanities are incorporated. Overall, the studies presented in this Special Feature demonstrate the power of microbiome science to advance our understanding of mammalian ecology, evolution, physiology, health, and conservation. We hope that this Special Feature inspires more mammalogists to venture into microbiome research, enabling a re-examination of mammalian biology through the lens of the holobiont concept.

Aim: Ponds are isolated, highly variable environments that exhibit low spatial autocorrelation of environmental variables and have island-like features, which may give rise to unique biogeographic patterns compared to terrestrial and lotic environments. Here, we evaluate whether commonly observed biogeographical patterns apply to microbial biodiversity in pond fungal and bacterial communities. Specifically, we tested (1) whether these communities follow latitudinal diversity gradients and distance decay relationships, and (2) if variation in community composition or richness was related to specific environmental or land-use factors. Location: Eastern, USA Time period: Summer, 2022 Taxa: Bacteria and Fungi Methods: We collected water and muck from 39 ponds across 8 states in the Eastern USA. We extracted DNA from these samples and sequenced sections of the 16S rRNA and ITS1 genes to survey the bacterial and fungal communities, before evaluating biogeographical patterns. Results: We found evidence of latitudinal diversity gradients in muck fungal communities, but not bacterial communities. We observed weak distance decay relationships in all sample types. Community richness was related to some environmental filters, where conductivity was positively related to water bacterial richness, but negatively related to muck fungal richness. Environmental drivers explained low to moderate variation in microbial composition, with temperature universally linked to microbial biodiversity. Conclusions: Pond microbiomes exhibit unique biogeographic patterns depending on the microhabitat and microbial taxa in question, with land use and abiotic conditions, especially temperature, explaining some variation in microbial biodiversity across sites. Our findings suggest that the low spatial autocorrelation in environmental conditions and the lack of connectivity across ponds provides a useful framework for investigating localized drivers of microbial diversity.

Phenotypic plasticity is a major mechanism whereby organisms adjust their traits within‐generations to changes in environmental conditions. In the context of range expansions, plasticity is thought to be especially important, as plastic changes in traits can lead to rapid adaptation. One epigenetic process in particular, DNA methylation, enables organisms to adjust gene expression contingent on the environment, which suggests it may play a role in range expansions. At present, we know little about how methylation is regulated in wildlife, especially expression of the enzymes responsible for altering methyl marks on the genome. In this study, we compared expression of three epigenetic regulator genes (DNA methyltransferase 1, DNMT1; DNA methyltransferase 3, DNMT3; and one ten‐eleven translocation methylcytosine dioxygenase, TET2) in three tissues (gut, liver, and spleen) of house sparrows Passer domesticus from nine countries. Some countries are in the native range of the species (Israel, the Netherlands, Norway, Spain, and Vietnam) whereas others are sites the species has colonized in the last 150 years (i.e. Australia, Canada, New Zealand, and Senegal). In this exploratory study, we asked whether non‐native birds and/or birds from sites with comparatively unpredictable climates would express different levels of these genes. We found that all three genes were expressed more in sparrows from the native range and from areas with more stable temperatures. Expression of all three genes was also strongly correlated among‐locations and within‐individuals, but mean expression was quite different among tissues. Many factors (e.g. urbanization of the capture site, sex of the bird) did not significantly affect gene expression, but others surprisingly did (e.g. latitude). Our results suggest that these enzymes could be important in range expansions or geographic distribution generally, but more detailed investigations will be insightful.

Most animal species harbor distinct microbiomes that exhibit eco-evolutionary patterns termed ‘phylosymbiosis’, by which the composition of these communities reflect host evolutionary history. However, most studies documenting these patterns, especially in mammals, have been conducted at single time points in adult animals. Thus, the processes by which phylosymbiotic signals emerge during early mammalian life stages are unclear. Here, we compared gut microbial communities from pups of four species of Peromyscus mice ( P. californicus , P. leucopus , P. polionotus , and P. maniculatus ) bred in captivity, collecting samples from three developmental timepoints (birth, mid-weaning, and weaning). Further, we evaluated host gene expression in large intestine tissue and used a novel application of congruence to compare host gene expression profiles across developmental stages as a means to investigate potential mechanisms by which hosts select their microbiome. We find that Peromyscus pups are not born with phylosymbiotic large intestinal microbial communities, but that these signatures emerge halfway through the weaning period. Strikingly, the host gene expression profiles exhibit different trajectories, such that host transcriptomic profiles closely reflect host phylogeny at birth, but this pattern weakens over development. Finally, Peromyscus spp . exhibit a significant number of differentially expressed genes across all developmental stages, including some clusters of genes implicated in host-microbe interactions. Collectively, these data demonstrate complex community assembly processes in early mammalian development and establish Peromyscus spp . as a powerful model to explore how transcriptomic variation influences host selection and microbiota filtering.

To efficiently digest food resources that may vary spatially and temporally, animals maintain physiological flexibility across levels of organization. For example, in response to dietary shifts, animals may exhibit changes in the expression of digestive enzymes, the size of digestive organs or the structure of their gut microbiome. A ‘Grand Challenge’ in comparative physiology is to understand how components of flexibility across organizational levels may scale to cumulatively determine organismal performance. Here, we conducted feeding trials on three rodent species with disparate feeding strategies: herbivorous montane voles (Microtus montanus), omnivorous white-footed mice (Peromyscus leucopus) and carnivorous grasshopper mice (Onychomys torridus). For each species, four groups of individuals were presented with diets that varied in carbohydrate, fiber and protein content. After 4–5 weeks, we measured organismal performance in the form of nutrient digestibility (dry matter, nitrogen, fiber). We also measured gut anatomy and organ size, and conducted enzyme assays on various tissues to measure activities of carbohydrases and peptidases. We found some shared physiological responses, e.g. fiber generally increased gut size across species. However, the specifics of these responses were distinct across species, suggesting different capacities for flexibility. Thus, in the context of digestion, we still lack an understanding of how flexibility across organizational levels may scale to determine whole-animal performance.

The success of introduced species often relies on flexible traits, including immune system traits. While theories predict non-natives will have weak defences due to decreased parasite pressure, effective parasite surveillance remains crucial, as infection risk is rarely zero and the evolutionary novelty of infection is elevated in non-native areas. This study examines the relationship between parasite surveillance and cytokine responsiveness in native and non-native house sparrows, hypothesizing that non-natives maintain high pathogen surveillance while avoiding costly inflammation. We made this specific prediction, as this pattern could enable invaders to effectively mitigate pathogen risk in a manner commensurate with the life-history priorities of a colonizing organism (i.e. rapid maturation and high reproductive effort). To test this hypothesis, we measured TLR -2 and TLR -4 expression, markers of pathogen surveillance and cytokine responses (changes in IL-1β and IL-10 ), regulators of inflammation, to a simulated bacterial infection. In non-native sparrows, we found that as TLR -4 expression increased, IL-1β and IL-10 responses decreased, a relationship not observed in native sparrows. Additionally, higher body condition predicted larger IL-1β and IL-10 responses in all birds. These findings suggest that high TLR-4 surveillance may mitigate strong inflammatory responses in non-native sparrows, with pathological and resource-based costs driving immune variation among and within populations.