Spillover of bacteria from agriculture into the surrounding soilscape

Lead Research Organisation: Imperial College London
Department Name: Life Sciences

Abstract

Humans now farm almost 40 percent of the Earth's ice-free land. This extreme change in land cover over such a short time is unprecedented in the planet's history, and it is well known to drive extinctions and alter the evolutionary trajectories of species. Yet nearly all of our knowledge of these environmental effects comes from research on plants or animals above ground. In contrast, the effects on soil micro-organisms are poorly understood, despite the key role of these species in decomposition, nutrient cycling, carbon sequestration, and the maintenance of soil fertility on which agriculture depends. In fact, while we know that microbes have the potential to disperse over long distances, we lack even a general understanding of microbial dispersal, or how the arrangement of natural and agricultural systems in modern landscapes affects soil biodiversity. The influence of landscape structure on plants, vertebrates and invertebrates has been studied for decades, but only in recent years has the technology for studying soil microbes been adequate and affordable enough to conduct comparable research belowground.

In addition to driving extinctions of species and altering their interactions, agriculture acts like an environmental filter, only allowing certain species to survive. Furthermore, the high availability of nutrients when fertilizer is added to already fertile soils provides a valuable reward to those species that can rapidly take them up and tolerate the harsh agricultural conditions and chemicals such as pesticides. Such heavily constrained ecosystems, with potential high rewards, are fertile ground for natural selection. Therefore, we have seen the evolution of pesticide resistance in weeds and insect pests of agriculture, and the evolution of antibiotic resistance in microbes. Such examples are likely to be the tip of the iceberg, yet the extent to which microbes evolve in agriculture, and how this affects the functioning of soil ecosystems, remain largely unknown. More importantly, just as weeds can spread out of crops and antibiotic resistance has spread to human diseases, organisms that evolve in agriculture have the potential to spread across the landscape including into natural areas.

We have recently demonstrated that highly-productive agricultural habitats generate an abundance of insects, which then 'spill over' into nearby natural habitats and alter the functioning of ecosystems. This project will test whether similar processes occur in soil microbes and, more importantly, whether the intensification of agriculture drives the evolution of soil microbes and the spread of agriculturally-selected genes across the landscape. We will then test the consequences of this spillover and spread for the ways in which ecosystems function.

Planned Impact

The research will impact the following:

1. Academic ecologists and related disciplines (see Academic Beneficiaries). The research lies at the heart of several fundamental questions in ecology that will have a broad impact on ecology.

2. Staff trained through the research and their future employers. Staff on the project will be trained in transferable skills that are in high-demand among employers in academics, government, and industry. These include skills for molecular biology, bioinformatics, analysis of complex datasets, and field ecology.

3. Agricultural scientists, farmers, and land managers. Spillover of bacteria from agriculture could have significant implications for how agricultural land and adjacent areas are managed.

4. Industry and government. There is enormous interest in developing products that minimise the impact of agriculture on the surrounding landscape. The research will indicate new avenues for industry products and government regulation that mitigate the impacts of microbial spillover.

5. General public. The invisible world of microbes is ignored by the public except for a few special cases (e.g. 'germs'). The research will increase awareness of how microbes impact everyday life, including how they impact cherished natural environments.

Publications

10 25 50
 
Description New or improved research methods developed: Much of the project is devoted to deploying new methods for studying dispersal of bacteria in soil. We have spent considerable time testing these methods, particularly for how to "mark" and "recapture" soil bacteria so that we know how far they have travelled. Details of the methods developed will be published at the conclusion of the project.
Exploitation Route The research approach developed in this project has allowed us to expand the research to understanding dispersal of fungal pathogens, resulting in a funded PhD studentship.
Sectors Agriculture, Food and Drink

 
Description Studentship - Nilita Mukjang
Amount ฿1 (THB)
Organisation Government of Thailand 
Sector Public
Country Thailand
Start 10/2017 
End 10/2020
 
Description BES workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Invited talk at British Ecological Society Microbial Ecology Group.
Year(s) Of Engagement Activity 2017
URL https://www.britishecologicalsociety.org/membership-community/special-interest-groups/microbial-ecol...
 
Description Gordon Research Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Session organiser and invited speaker for the Gordon Research Conference on Microbial Population Biology.
Year(s) Of Engagement Activity 2017
URL https://www.grc.org/microbial-population-biology-conference/2017/
 
Description Mombrikotb BES talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Presentation at British Ecological Society, Liverpool, Dec. 2016, Multiple stressors thematic session.
Year(s) Of Engagement Activity 2017
 
Description Royal Society Committee 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Invited to address the Royal Society Global Environment Research Committee.
Year(s) Of Engagement Activity 2017
URL https://royalsociety.org/about-us/committees/global-environmental-research-committee/
 
Description SOFIIA 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Capacity building workshop in three countries in West Africa, Nigeria, Burkina Faso and Ghana, under the SOFIIA project. In each country, post graduate students and professionals in academia and industry attended a soil microbial ecology session that included introductory and methodological lectures, data analysis in R and a wet lab practical on soil DNA extraction, PCR and gel electrophoresis. Open sessions were held where individuals could bring their own data/experiment to discuss and seeks advice as well as ask more detailed question on the topic. We have receive multiple emails from those who have attend the course with follow up questions and assistance requests and many asking if addition course in the subject area would be held.
Year(s) Of Engagement Activity 2017