Biology subjects

Kohl, K. D.

Publications and source records attributed to Kohl, K. D..

6 recordsLinked to original sources

bioRxiv2025

Exploring local and regional drivers of microbial biodiversity across freshwater ponds

AimPonds 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. LocationEastern, USA Time periodSummer, 2022 TaxaBacteria and Fungi MethodsWe 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. ResultsWe 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. ConclusionsPond 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.

ecology↗

bioRxiv2025

Phylosymbiosis in the making: Host-associated microbiota and host gene expression profiles exhibit discordant timing of phylogenetic congruence over early mammalian development

Gut microbial communities often mirror host phylogenetic relationships, an eco-evolutionary pattern known as phylosymbiosis. While phylosymbiosis is well documented in adult mammals, the developmental timing and mechanisms underlying its emergence remain unknown. Here, we use four captive-bred species of Peromyscus mice, a powerful model for studying natural variation in animal biology, to investigate the assembly of the intestinal microbiota and the emergence of phylosymbiotic signatures from birth through weaning. We combine 16S rRNA microbiome profiling with whole-tissue transcriptomics across three developmental stages (newborn, pre-weaning, and weaning) to test when during development the microbiome and host transcriptome exhibit evolutionary signatures. While parental feces and maternal mammary skin harbored phylosymbiotic communities, the intestines of newborn pups did not. Phylosymbiosis only emerged in pups at the pre-weaning stage of development and was sustained through weaning. Gut microbial diversity increased with age across species, and developmental stage was a stronger driver of community composition than host species identity, with a 1.5-2x larger effect size. Strikingly, host gene expression profiles showed the opposite pattern: transcriptome-based dendrograms were congruent with host phylogeny only at birth, not at later stages. Gene co-expression modules that showed correlation with host phylogenetic distance at birth were mainly enriched for metabolic pathways, such as lysosome activity, fat and vitamin digestion and absorption, and glycan metabolism. This work provides the first evidence, to our knowledge, in vertebrates that phylosymbiosis is not a fixed property of host-microbiome systems, but an emergent feature with distinct developmental dynamics in both the microbiome and the host transcriptome. Our results begin to reveal the complex and dynamic nature by which mammalian host-microbiome relationships are established and maintained across both evolutionary and developmental and time scales.

evolutionary biology↗

bioRxiv2024

Artificial Selection and the Skin Microbiome Independently Predict Parasite Resistance

Host responses to parasite infection involve several interacting systems. Host genetics determine much of the response, but it is increasingly clear that the host-associated microbiome also plays a role. Genetically determined systems and the microbiome can also interact; for example, the microbiome can modulate the immune response, and vice versa. However, it remains unclear how such interactions between the host immune system and the microbiome may influence the hosts overall response to parasites. To investigate how host genetics and the microbiome interact to shape responses to parasites, we imposed truncation selection on Trinidadian guppies (Poecilia reticulata) for low and high resistance to the specialist ectoparasite Gyrodactylus turnbulli. After 3-6 generations of breeding without parasites, we sampled the skin-associated microbiome and infected fish from each line. We applied Dirichlet Multinomial Modeling (DMM) machine-learning to identify bacterial community types across lines and evaluated how selection line and community type explained variations in infection severity. Our findings showed that among females, the resistant line had significantly lower infection severity, while the susceptible line had higher infection severity. Among males, only the susceptible line experienced higher infection severity compared to the other lines. Line did not explain skin microbial diversity, structure or composition. Our DMM analysis revealed three distinct bacterial community types, independent of artificial selection lines, which explained just as much variation in infection load as selection line. Overall, we found that the microbiome and host genetics independently predict infection severity, highlighting the microbiomes active role in host-parasite interactions.

ecology↗

bioRxiv2021

Experimental depletion of gut microbiota diversity reduces host thermal tolerance and fitness under heat stress in a vertebrate ectotherm

Predicting the responses of ectotherms to climate change is a global conservation priority which requires identifying factors that influence how animals respond physiologically to changing temperature. Host-associated microbial communities impact animal physiology and have been shown to influence host thermal tolerance in invertebrate systems. However, the role of commensal microbiota in thermal tolerance of ectothermic vertebrates is unknown. Here we show that experimentally depleting the diversity of the tadpole gut microbiome through environmental water sterilization reduces the hosts acute thermal tolerance to both heat and cold, alters the thermal sensitivity of locomotor performance, and reduces animal survival under acute heat stress. We show that these tadpoles have reduced activities of mitochondrial enzymes and altered metabolic rates compared to tadpoles colonized with a diverse microbiota, which could underlie differences in thermal phenotypes. Our results demonstrate, for the first time, a link between the gut microbiome of an ectothermic vertebrate and the hosts thermal tolerance, performance, and fitness, thus highlighting the importance of considering host-associated microbial communities when predicting species responses to climate change.

ecology↗

bioRxiv2020

Microbial control over host diet selection

Diet selection is a fundamental aspect of animal behavior with numerous ecological and evolutionary implications. While the underlying mechanisms are complex, the availability of essential dietary nutrients can strongly influence diet selection behavior. The gut microbiome has been shown to metabolize many of these same nutrients, leading to the untested hypothesis that intestinal microbiota may influence diet selection. Here we show that germ-free mice colonized by gut microbiota from three rodent species with distinct foraging strategies differentially selected diets that varied in macronutrient composition. Specifically, we found that herbivore-conventionalized mice voluntarily selected a higher protein:carbohydrate ratio diet, while omnivore- and carnivore-conventionalized mice selected a lower P:C ratio diet. In support of the long-standing hypothesis that tryptophan - the essential amino acid precursor of serotonin - serves as a peripheral signal regulating diet selection, bacterial genes involved in tryptophan metabolism and plasma tryptophan availability prior to the selection trial were significantly correlated with subsequent voluntary carbohydrate intake. Finally, herbivore-conventionalized mice exhibited larger intestinal compartments associated with microbial fermentation, broadly reflecting the intestinal morphology of their donor species. Together, these results demonstrate that gut microbiome can influence host diet selection behavior, perhaps by mediating the availability of essential amino acids, thereby revealing a novel mechanism by which the gut microbiota can influence host foraging behavior. SIGNIFICANCEThe behavior of diet choice or diet selection can have wide-reaching implications, scaling from individual animals to ecological and evolutionary processes. Previous work in this area has largely ignored the potential for intestinal microbiota to modulate these signals. This notion has been highly speculated for years but has not yet been explicitly tested. Here we show that germ-free mice colonized by differential microbiomes (from wild rodents with varying natural feeding strategies) exhibited significant differences in their voluntary dietary selection. Specifically, differences in voluntary carbohydrate selection were associated with plasma amino acid levels and bacterial genes involved in the metabolism of tryptophan. Together, these results demonstrate a role for the microbiome in host nutritional physiology and behavior.

microbiology↗

bioRxiv2018

Metagenomic sequencing provides insights into the location of microbial detoxification in the gut of a small mammalian herbivore

Microbial detoxification of plant defense compounds influences the use of certain plants as food sources by herbivores. The location of microbial detoxification along the gut could have profound influences on the distribution, metabolism, and tolerance to toxic compounds. Stephens woodrats (Neotoma stephensi) specialize on juniper, which is heavily defended by numerous defensive compounds, such as oxalate, phenolics, and monoterpenes. Woodrats maintain two gut chambers harboring dense microbial communities: a foregut chamber proximal to the major site of toxin absorption, and a cecal chamber in their hindgut. We performed several experiments to investigate the location of microbial detoxification in the woodrat gut. First, we measured levels of toxins across gut chambers. Compared to food material, oxalate concentrations were immediately lower in the foregut chamber, while concentrations of terpenes remain high in the foregut, and are lowest in the cecal chamber. We also conducted metagenomic sequencing of the foregut and cecal chambers to compare microbial functions. We found that the majority of genes associated with detoxification functions were more abundant in the cecal chamber. However, some genes associated with degradation of oxalate and phenolic compounds were more abundant in the foregut. Thus, it seems that microbial detoxification may take place in various chambers depending on the class of chemical compound. We hypothesize that the location of microbial detoxification could impact the tolerance of animals to these compounds, which may have ecological and evolutionary consequences.

microbiology↗