Artisanal and small-scale gold mining (ASGM) in Madre de Dios, Peru, continues to expand rapidly, raising concerns about increases in loading of mercury (Hg) to the environment. We measured physicochemical parameters in water and sampled and analyzed sediments and fish from multiple sites along one ASGM-impacted river and two unimpacted rivers in the region to examine whether Hg concentrations were elevated and possibly related to ASGM activity. We also analyzed the 308 fish samples, representing 36 species, for stable isotopes (δ¹⁵N and δ¹³C) to estimate their trophic position. Trophic position was positively correlated with the log-transformed Hg concentrations in fish among all sites. There was a lack of relationship between Hg concentrations in fish and either Hg concentrations in sediments or ASGM activity among sites, suggesting that fish Hg concentrations alone is not an ideal bioindicator of site-specific Hg contamination in the region. Fish Hg concentrations were not elevated in the ASGM-impacted river relative to the other two rivers; however, sediment Hg concentrations were highest in the ASGM-impacted river. Degraded habitat conditions and commensurate shifts in fish species and ecological processes may influence Hg bioaccumulation in the ASGM-impacted river. More research is needed on food web dynamics in the region to elucidate any effects caused by ASGM, especially through feeding relationships and food sources.

Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts (“host selection”) and the fitness of microbes (“trait-mediated microbial selection”). Additionally, the fitness effects of traits on microbes can be modified by their hosts (“host-mediated microbial selection”). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong parental contribution, when host-mediated selection acts on microbes concomitantly. We present a computational framework that integrates different selective processes acting on the evolution of microbiomes. Our framework demonstrates that selection acting on microbes can have a strong effect on microbial diversities and fitnesses, whereas selection on hosts can have weaker outcomes.