Diana Nemergut | bioRxiv Science

bioRxiv2016

Dissolved organic matter and inorganic mercury loadings favor novel methylators and fermentation metabolisms in oligotrophic sediments

Recent advances have allowed for greater investigation into microbial regulation of mercury toxicity in the environment. In wetlands in particular, dissolved organic matter (DOM) may influence methylmercury (MeHg) production both through chemical interactions and through substrate effects on microbiomes. We conducted microcosm experiments in two disparate wetland environments (oligotrophic unvegetated and high-C vegetated sediments) to examine the impacts of plant leachate and inorganic mercury loadings (20 mg/L HgCl2) on microbiomes, DOM cycling, and MeHg production in the St. Louis River Estuary. Our research reveals the greater relative capacity for mercury methylation in vegetated over unvegetated sediments. Further, our work shows how mercury cycling in oligotrophic unvegetated sediments may be susceptible to DOM inputs in the St. Louis River Estuary: microcosms receiving leachate produced substantially more MeHg than unamended microcosms. We also demonstrate (1) changes in microbiome structure towards Clostridia, (2) metagenomic shifts toward fermentation, and (3) degradation of complex DOM; all of which coincide with elevated net MeHg production in unvegetated microcosms receiving leachate. Finally, we examine microbial operational taxonomic units (OTUs) classified as known potential methylators and identify important organisms for future research in the Great Lakes region. Together, our work shows the influence of wetland vegetation in controlling MeHg production in the Great Lakes region and provides evidence that this may be due to both enhanced microbial activity as well as differences in microbiome composition.

Ecology↗

bioRxiv2016

Understanding How Microbiomes Influence the Systems they Inhabit: Insight from Ecosystem Ecology

Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits) from and those properties that are currently unable to be predicted from constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.

Microbiology↗