Herbicides are one of the most widely used chemicals in agriculture. While they are known to be harmful to nontarget organisms, the effects of herbicides on the composition and functioning of soil microbial communities remain unclear. Here we show that application of three widely used herbicides-glyphosate, glufosinate, and dicamba-increase the prevalence of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in soil microbiomes without clear changes in the abundance, diversity and composition of bacterial communities. Mechanistically, these results could be explained by a positive selection for more tolerant genotypes that acquired several mutations in previously well-characterized herbicide and ARGs. Moreover, herbicide exposure increased cell membrane permeability and conjugation frequency of multidrug resistance plasmids, promoting ARG movement between bacteria. A similar pattern was found in agricultural soils across 11 provinces in China, where herbicide application, and the levels of glyphosate residues in soils, were associated with increased ARG and MGE abundances relative to herbicide-free control sites. Together, our results show that herbicide application can enrich ARGs and MGEs by changing the genetic composition of soil microbiomes, potentially contributing to the global antimicrobial resistance problem in agricultural environments.

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Herbicide Selection Promotes Antibiotic Resistance in Soil Microbiomes.

Microbiome research has gained considerable interest due to the emerging evidence of its impact on human and animal health. As in other animals, the gut-associated microbiota of mosquitoes affect host fitness and other phenotypes. It is now well established that microbes can alter pathogen transmission in mosquitoes, either positively or negatively, and avenues are being explored to exploit microbes for vector control. However, less attention has been paid to how microbiota affect phenotypes that impact vectorial capacity. Several mosquito and pathogen components, such as vector density, biting rate, survival, vector competence, and the pathogen extrinsic incubation period all influence pathogen transmission. Recent studies also indicate that mosquito gut-associated microbes can impact each of these components, and therefore ultimately modulate vectorial capacity. Promisingly, this expands the options available to exploit microbes for vector control by also targeting parameters that affect vectorial capacity. However, there are still many knowledge gaps regarding  mosquito–microbe interactions  that need to be addressed in order to exploit them efficiently. Here, we review current evidence of impacts of the microbiome on aspects of vectorial capacity, and we highlight likely opportunities for novel vector control strategies and areas where further studies are required.

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The microbiome and mosquito vectorial capacity: rich potential for discovery and translation.

Because it is only possible to test chemical for effects on a restricted range of species and exposure scenarios, ecotoxicologists are faced with a significant challenge of how to translate the measurement in model species into predictions of impacts for the wider range of species in ecosystems. Because of this challenge, within ecotoxicology there is no more fundamental aspect than understanding than the nature of the traits that determine sensitivity. To account for the uncertainties of species extrapolations in risk assessment, ‘safety factors’ or species sensitivity distributions are commonly used. While valuable as pragmatic tools, these approaches have no mechanistic grounding. Here we highlight how mechanistic information that is increasing available for a range of traits can be used to be understand and potentially predict species sensitivity to chemicals. We review current knowledge on how toxicokinetic, toxicodynamic, physiological and ecological traits contribute to difference in sensitivity. We go on to discuss how this information is being used to make predictions of sensitivity using correlative and trait-based approaches, including comparisons of target receptor orthologues. Finally, we discuss how the emerging knowledge and associated tools can be used to enhance theoretical and applied ecotoxicological research through improvements in mechanistic modelling, predictive ecotoxicology, SSD development, mixture toxicity assessment, chemical design, biotechnology application and mechanistically informed monitoring.

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Species Sensitivity to Toxic Substances: Evolution, Ecology and Applications

Insects are the most diverse group of animals and colonize almost all environments on our planet. This diversity is reflected in the structure and function of the microbial communities inhabiting the insect digestive system. As in mammals, the gut microbiota of insects can have important symbiotic functions, complementing host nutrition, facilitating dietary breakdown or providing protection against pathogens. There is an increasing number of insect models that are experimentally tractable, facilitating mechanistic studies of gut microbiota-host interactions. In this Review, we will summarize recent findings that have advanced our understanding of the molecular mechanisms underlying the symbiosis between insects and their gut microbiota. We will open the article with a general introduction to the insect gut microbiota and then turn towards the discussion of particular mechanisms and molecular processes governing the colonization of the insect gut environment as well as the diverse beneficial roles mediated by the gut microbiota. The Review highlights that, although the gut microbiota of insects is an active field of research with implications for fundamental and applied science, we are still in an early stage of understanding molecular mechanisms. However, the expanding capability to culture microbiomes and to manipulate microbe-host interactions in insects promises new molecular insights from diverse symbioses.

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Mechanisms underlying gut microbiota-host interactions in insects.

Insects' intestinal microbes have profound effects on the host's physiological traits, which can impact their physiology at both the local (gut) and systemic (body) levels. Nevertheless, the molecular mechanisms underlying host-microbiota interactions, especially in non-model insects, remain elusive. Recently, tissue-specific transcriptomic analysis has been highlighted as a robust tool in studying host-microbe interactions. Plagiodera versicolora is a worldwide leaf-eating pest that primarily feeds on willows and poplar. The interplay between gut microflora and this host beetle has yet to be studied. Herein, we investigate the effects of the gut microbiota on the body mass of P. versicolora larvae, compare the nutrition status of larvae in absence and presence of gut microbiota, and profile gut bacterial loads throughout its developmental larval stages. We then perform comparative transcriptomic analysis of gut and body tissues in axenic and non-axenic larvae. Finally, we confirm the expression patterns of representative genes in nutritional metabolism and immunity. Results show that weight growth is retarded in conventional larvae, with a concomitant increase of total bacterial load by the 5th development day, and germ-free larvae have a higher glucose content than conventional-reared larvae. Both nutritional and immunological analyses indicate that gut bacteria are a burden in the beetle's larval development. These findings elucidate the impacts of gut microbiota on P. versicolora, and provide insight into tissue-specific responses to gut microflora in this pest at the genetic level, boosting our understanding of the molecular mechanisms underlying host-microbe interactions in leaf beetles and beyond.

Metabolic and immunological effects of gut microbiota in leaf beetles at the local and systemic levels.

https://www.cell.com/cell-host-microbe/pdfExtended/S1931-3128(20)30048-2

Olivia Velasquez

Papers

Changes in Microbiome Confer Multigenerational Host Resistance after Sub-toxic Pesticide Exposure.