The alpha diversity of ecologic communities is affected by many biotic and abiotic drivers and, in turn, affects ecosystem functioning. Yet, patterns of alpha diversity in host-associated microbial communities (microbiomes) are poorly studied and the appropriateness of general theory is untested.

Resource limitation is a fundamental factor governing the composition and function of ecological communities. However, the role of resource supply in structuring the intestinal microbiome has not been established and represents a challenge for mammals that rely on microbial symbionts for digestion: too little supply might starve the microbiome while too much supply might starve the host. Here, we present evidence that microbiota occupy a habitat limited in total nitrogen supply within the large intestines of 30 mammal species. Furthermore, lowering dietary protein levels in mice reduced bacterial fecal concentrations. A gradient of stoichiometry along the length of the gut was consistent with the hypothesis that intestinal nitrogen limitation results from host absorption of dietary nutrients. Nitrogen availability though is also likely shaped by host-microbe interactions: levels of host-secreted nitrogen were altered in germfree mice and when bacterial loads were reduced via experimental antibiotic treatment. Single-cell spectrometry revealed that members of the phylum Bacteroidetes consumed nitrogen in the large intestine more readily than other commensal taxa. Collectively, our findings support a model where nitrogen limitation arises from preferential host utilization of dietary nutrients, and we speculate that this resource limitation could enable hosts to regulate microbial communities in the large intestine. Furthermore, commensal microbiota may have adapted to nitrogen-limited settings, suggesting why excess dietary protein has been associated with degraded gut microbial ecosystems.

How host and microbial factors combine to structure gut microbial communities remains incompletely understood. Redox potential is an important environmental feature affected by both host and microbial actions. We assessed how antibiotics, which can impact host and microbial function, change redox state and how this contributes to post-antibiotic succession. We showed gut redox potential increased within hours of an antibiotic dose in mice. Host and microbial functioning changed under treatment, but shifts in redox potentials could be attributed specifically to bacterial suppression in a host-free ex vivo human gut microbiota model. Redox dynamics were linked to blooms of the bacterial family Enterobacteriaceae. Ecological succession to pre-treatment composition was associated with recovery of gut redox, but also required dispersal from unaffected gut communities. As bacterial competition for electron acceptors can be a key ecological factor structuring gut communities, these results support the potential for manipulating gut microbiota through managing bacterial respiration.

These findings support the hypothesis that abnormal gut microbial communities are a host factor related to V. cholerae susceptibility.

Trophic cascades-the indirect effects of carnivores on plants mediated by herbivores-are common across ecosystems, but their influence on biogeochemical cycles, particularly the terrestrial carbon cycle, are largely unexplored. Here, using a 13 C pulse-chase experiment, we demonstrate how trophic structure influences ecosystem carbon dynamics in a meadow system. By manipulating the presence of herbivores and predators, we show that even without an initial change in total plant or herbivore biomass, the cascading effects of predators in this system begin to affect carbon cycling through enhanced carbon fixation by plants. Prolonged cascading effects on plant biomass lead to slowing of carbon loss via ecosystem respiration and reallocation of carbon among plant aboveground and belowground tissues. Consequently, up to 1.4-fold more carbon is retained in plant biomass when carnivores are present compared with when they are absent, owing primarily to greater carbon storage in grass and belowground plant biomass driven largely by predator nonconsumptive (fear) effects on herbivores. Our data highlight the influence that the mere presence of predators, as opposed to direct consumption of herbivores, can have on carbon uptake, allocation, and retention in terrestrial ecosystems.experimental ecosystem ecology | animal-mediated carbon cycling | carbon tracer experiment | carbon retention T rophic downgrading-the disproportionate loss of species occupying top trophic levels of ecosystems-is a symptom of global biodiversity decline (1). Cutting short trophic chains in ecosystems causes significant changes in plant community biomass, composition, and diversity (2). These changes come about because loss of carnivores leads to increased impacts of herbivores on plant biomass through changes in herbivore density and foraging strategies (3).It is becoming increasingly recognized that the cascading effects of carnivores may affect ecosystem carbon dynamics as well. By altering the impact of herbivores on plants, carnivores may indirectly regulate the amount and type of plant biomass available for photosynthetic carbon fixation and storage (3-5). Moreover, herbivory can trigger physiological adjustments in the remaining damaged plants, including reduction in photosynthetic rates and increased respiration (6-8). Accordingly, we hypothesized that carnivores should increase plant community carbon fixation and reduce respiration, thereby increasing carbon retention, by causing herbivores to reduce their foraging impacts on plants. We tested this hypothesis with a 13 CO 2 pulse-chase field experiment in a grassland ecosystem in northeastern Connecticut.Using established methods to discern indirect effects of carnivores on plants in ecosystems (9), we applied three experimental treatments in replicated 0.25-m 2 fine-mesh enclosures (Fig. S1): (i) plants only (control), (ii) plants and herbivores (+ herbivore), and (iii) plants, herbivores, and carnivores (+ carnivore). The first treatment served as a control for animal effects, the + he...