Human dissemination of genes and microorganisms in Earth's Critical Zone

Abstract

Earth's Critical Zone sustains terrestrial life and consists of the thin planetary surface layer between unaltered rock and the atmospheric boundary. Within this zone, flows of energy and materials are mediated by physical processes and by the actions of diverse organisms. Human activities significantly influence these physical and biological processes, affecting the atmosphere, shallow lithosphere, hydrosphere, and biosphere. The role of organisms includes an additional class of biogeochemical cycling, this being the flow and transformation of genetic information. This is particularly the case for the microorganisms that govern carbon and nitrogen cycling. These biological processes are mediated by the expression of functional genes and their translation into enzymes that catalyze geochemical reactions. Understanding human effects on microbial activity, fitness and distribution is an important component of Critical Zone science, but is highly challenging to investigate across the enormous physical scales of impact ranging from individual organisms to the planet. One arena where this might be tractable is by studying the dynamics and dissemination of genes for antibiotic resistance and the organisms that carry such genes. Here we explore the transport and transformation of microbial genes and cells through Earth's Critical Zone. We do so by examining the origins and rise of antibiotic resistance genes, their subsequent dissemination, and the ongoing colonization of diverse ecosystems by resistant organisms.

Ideas and perspectives: Strengthening the biogeosciences in environmental research networks

“…In China and other locations, there is major uncertainty about the significance of ARGs in agricultural soils and waters receiving N and P recycled directly from animal and urban human wastewater (Zhu et al, 2018).…”

Evidence for co-selection of antibiotic resistance genes and mobile genetic elements in metal polluted urban soils

“…Due to rapid urbanization and intensive anthropogenic activity, a massive volume of potential selective agents (such as heavy metals) and microbes carrying ARGs swarm into urban soils and successfully persist, increasing the level of ARG pollution in urban environments (Wang et al, 2014). These ARGs spread amongst humans and in the environment by horizontal gene transfer (HGT), developing into pathogenic antibiotic-resistant bacteria (pARB) and thereby raising the risk of failure of antibiotic treatments (Zhu et al, 2018). The linkage between soil metals and ARGs from urban and industrially polluted soils has been observed in previous studies (Knapp et al, 2017, Berg et al 2010.…”

Loss of soil microbial diversity exacerbates spread of antibiotic resistance

“…Only a fraction of bacteria in natural environments can be cultivated, so we focused on the relationship between invasibility and microbial diversity at the gene level using the antibiotic resistome as a proxy for invasion (Wright, 2007). The emergence and spread of antibiotic resistance has become a global health threat (Bush et al, 2011;Pruden et al, 2013;Zhu et al, 2013;Su et al, 2017;Zhu et al, 2018), but the factors regulating the environmental dynamics of antibiotic resistance, especially biotic factors, have not been directly addressed. This neglect has hampered our ability to assess the risks of antibiotic resistance due to anthropogenic activities and global environmental change.…”