The Evolution of Bacterial Mutualism with Eukaryotic Hosts

Lead Research Organisation: Queen Mary University of London
Department Name: Sch of Biological & Behavioural Sciences

Abstract

Bacteria: friend or foe?

All plants and animals share some form of intimate relationship with bacteria. Although we often focus on harmful bacteria that cause diseases, recent research has shown that many bacteria that live within animals are actually beneficial. Whether this is the light-producing bacteria that live within fireflies that help them attract mates to the 100 trillion bacterial cells that live within our guts that aid in digestion, beneficial microbes are both ever-present and important to all organisms on the planet.

My research explores how animals form beneficial relationships with symbiotic microbes by asking: What are the factors that produce stable mutually beneficial unions between animals and microbes, and what cause these relationships to break down? To answer these questions I focus on a single group of organisms that have evolved fascinating relationships with microbes, insects. Insects are host to a diverse community of symbiotic microbes that have profound effects on their biology. These effects include, protecting insects from natural enemies, such as parasitic wasp and pathogenic fungus, providing insects with protection against heat stress and assist insects in gaining nutrients.

A peculiar feature of these helpful microbes is that only certain populations of insects have them, whereas others do not. In addition, only certain bacterial strains provide benefits to their insect hosts whereas others do not. This natural variation presents a perfect opportunity to ask questions such as: why do certain populations of insect hosts contain beneficial microbes whereas others do not? And, why do only some of the symbiotic microbes provide benefits to insects, and how does the loss of beneficial function impact their relationship with their host?

To answer these questions I use modern DNA technology that allow me to identity factors that influence beneficial microbial functions at a molecular level, as well as explore the evolution of host-microbe relationships over millions of years. The application of these modern techniques to the intriguing variation in the bacterial symbionts of insects provides a general understanding of the factors that maintain and degrade beneficial relationships with bacteria in all plants and animals.

Host-microbe relationships are everywhere in nature, and understanding the factors that maintain and degrade these relationships has important implications in both agriculture and health. My research will not only provide novel insight into the gain and loss of beneficial traits in bacteria, but also has great potential in understanding the gain and loss of harmful traits in bacterial pathogens. Of more immediate application, my research can lead to practical solutions for managing insect pests in agriculture and those that vector major human diseases. Pesticides were common solutions to deal with pests, however there is strong pressure to reduce pesticide use to moderate our reliance on environmental harmful chemicals. Many insect pests have evolved mutualistic relationships with symbiotic bacteria such as, Triatoma bugs that vector Chagas disease, tsetse fly that vector sleeping sickness, cereal weevils that devastates crops around the world, and all sap sucking insects. Research to exploit the relationship between bacteria and insect hosts for the biological control of pests, termed Symbiont-Based Control Strategies, is a preferred strategy to chemical control due to the reduced environmental impact. My research is a critical first step in advancing our understanding of insect-bacteria relationships in many pest species, by revealing both the molecular mechanisms by which bacteria and hosts interact, as well as the conditions that promote stable relationships between bacteria and host. The knowledge from this research can be used to help develop practical solutions for managing pests in agriculture, forestry and those that vector major human diseases.

Planned Impact

The proposed research is academic in nature and the primary beneficiaries will be the scientific community. However, aphids are one of the most damaging pests in agriculture in the European Union, and this research can translate to economic benefits if used by applied scientists to improve pest management. As such, potential beneficiaries include: 1) the pest control sector stands to benefit through the control of pests in agriculture, forestry and those that vector diseases in humans, and 2) the general public, through the use of this research as a tool to teach non-specialist audiences about insect biology and symbiosis.

Pest Control

Who will benefit? This research stands to benefit biocontrol companies, medical entomologists and practitioners that work in forestry and agriculture.

ow will they benefit? Pesticides are the chief method by which farmers deal with aphids, however there is strong pressure to reduce the use of environmentally damaging chemical pesticides. Knowledge from this research has potential to aid in managing pest through manipulating the relationship between symbiont and insect host. Many insect pests have evolved mutualistic relationships with symbiotic bacteria such as, Triatoma bugs that vector Chagas disease, tsetse fly that vector sleeping sickness and the cereal weevil that devastates cereal crops. Research to exploit symbiosis for the biological control of insect pests, termed Symbiont-Based Control Strategies (SCS), has great potential to move us away from chemical control. Over 150 SCS projects have been funded at a national level in Europe (COST Action 850). My research specifically addresses the EU mandate on applied SCS research by identifying both fitness gains in symbiotic partnerships (through bacterial mutualism) and the characterization of new molecular mechanisms. The results of this research directly contributes to the COST Action 850 initiative, which can be used to direct applied science in the management of pests in agriculture and those that vector important human diseases.

The public

Who will benefit? Gardeners, horticulturalists, farmers and the general public.

How will they benefit? During the fellowship I will use a number of outreach activities to engage the general public with my research as well as promote my findings to media. Results from the proposed research will be distributed through the Oxford Martin School Programme on the Future of Food. This initiative, directed by collaborator Prof Godfray, aims to link research at Oxford University on the food system, including, of relevance here, pest management.
Public outreach. In addition, I will work with Alison Foster (Senior Curator at the Botanic Garden) in developing lectures to be presented to the general public, which will include results from this research. Lectures will target non-specialist audience and teach insect biology, diversity and the importance of beneficial bacteria in the lives of insect and all animals and plants.
Media. Apart from the above outreach activities I will design a new webpage to present this research to a wide audience. I will also collaborate with Oxford University Press office to write press releases for all of my publications and be available for interviews and questions from journalists.

Publications

10 25 50
 
Description These key findings are based on the award being active for 1 year: Using multi-locus sequence typing (MLST) we have preliminary phylogenies for four different facultative symbiont species that infect different species of host aphids. This has revealed dozens of previously uncharacterized symbiont isolates infecting aphids. We are currently analysing the data to try and understand what factors are responsible for the phylogenetic distribution of each symbiont species.

Key findings from year 2: The evolution of host-symbiont dependency is governed by transmission mode and symbiont function, published in Nature Communications. Host symbiont genotype interactions influence whether a symbiosis successfully establishes, and how virulent the host is, in press at BMC Evolutionary Biology. We have also develop a large database looking into the evolution of dependency and its links to nutrition deficiencies in insects. We have done additional field collections to target specific hypotheses on the horizontal transfer of different facultative symbionts, specifically to address the symbiont Horizontal Gene Pool hypothesis, using the MLST scheme mentioned in year 1.

Key finding of year 3. We have identified multiple cases where normally facultative symbionts have formed permanent relationships with different aphids species. These cases represent independent transitions into obligate symbioses, highlighting key evolutionary events when the symbiont horizontal gene pool has stabilised.

Key finding from year 4. Extending from the year 3 findings where we investigated the transitions to obligate symbioses. We identify four independent transitions to the same co-obligate symbiosis in different aphids. Comparing recent and ancient associations allows us to investigate intermediate stages of metabolic and anatomical integration of Serratia. We find that these uniquely replicated evolutionary events support the idea that co-obligate associations initiate in a predictable manner, through parallel evolutionary processes. These findings were recently accepted for publication in Current Biology.

Key findings from year 5. We have three on-going projects related to Sections 1 and 2 of my fellowship. Preliminary findings are as follows. Project 1 - We are currently assessing what factors are responsible for the phylogenetic distribution the symbiont Hamiltonella. Using experimental manipulations where we microinject different Hamiltonella strains into different aphid species suggests there are incompatibilities between certain symbionts strains and aphid species. This suggests co-adaption between symbionts and host that may limit horizontal transfer of symbionts - and their adaptive traits - between aphid species. We are now conducting qPCR and in situ experiments to confirm results. A second comparative project working off of findings from Project 1.3 is investigating what aspects of insects diets lead to obligate symbioses and the consequences of this for insect diversification. Key findings are diets limited in B-vitamins, in particular B5 and B6, tend to lead to reliance on symbionts, and these lead to the extremes of diversification, from very high diversification in herbivores to very low in blood-feeding insects. Finally, from Project 2, we have now collected and MLST sequenced strains of the symbiont Regiella insecticola from >20 aphids species. We are currently growing the symbionts in insect cell medium using a novel technology developed by collaborator Kerry Oliver. We expect genome sequencing to commence soon.

Key findings Year 6: In Project 1, we recently demonstrated that the distributions of the symbiont Hamiltonella defensa is governed by local adaptation to host and parasitoids, which was published in Proc. R. Soc B this year (Wu et al 2022). Our project on the evolution of obligate symbiosis and its consequences for insect diversification was recently accepted in Nature Ecology and Evolution (Cornwallis et al in press). From Project 2, we sequenced the genomes of 20 lineages Regiella insecticola. Initially genome analysis has shown massive genome rearrangments in the symbionts and we are currently running experiments to determine whether these explain the different Regiella phenotypes it bestowes on hosts, which include; protection against parasitoids, protections from fungal pathogens, and increasing host fecundity on certain plants. We have also sequenced the genomes of six Hamiltonella lineages from the major pea aphid biotypes. This has revealed gains and losses of toxin cassettes that underlie lineages specific differences in protection against different species of parasitoid wasps. Through the NERC fellowship I have also developed several collaborations that are now bearing fruit. First, we have revealed several new symbioses found in ants. We published out first paper on it this year in ISME (Jackson et al 2022) which demonstrated different ant lineages have convergently evolved symbioses with Sodalis-like symbionts, that are housed in specialised host derived organs, that we hypothesis provision their hosts with the amino acid tyrosine, which is important for cuticle thickening when proteins are scarce. Finally, I have also developed a project investigating the symbioses found in marine annelid worms that is set to dissect how evolving to occupy different extreme deep sea niches has shaped host-symbiont genome evolution. Two papers from this collaboration are currently in review.
Exploitation Route We will be taking the finding forward as described above and in laboratory experiments to test whether the presence of symbiont isolates in particular aphid species has an adaptive basis. We will be investigating the genomic basis involved in transitions to permanent symbiosis from the findings in year 3. Parallel evolution of obligate symbioses will lead to further studies on a more mechanistic understanding of how these relationships evolve. Symbiont driven niche expansion of insects will broadly inform how obligate symbioses evolve and their impacts on animal diversification. Our ant research is developing a novel system for studying how and why nutritional symbioses evolve in omnivorous animals, this includes, but is not exclusive to, providing a new system to study organ evolution (e.g. bacteriomes).
Sectors Agriculture

Food and Drink

Education

Environment

 
Description The fellowship is primarily academic in nature, and therefore we expect the major beneficiaries to be the academic community. However, aphids contain some of the most globally important pest species and therefore our findings have potential to help understanding their impact in agriculture and in forestry. The facultative symbionts we are studying provide aphids with key traits that can lead to adaptive evolution, which have been shown to severely impacting their pest status. I am currently in the early stages of fostering collaboration with Dr. Glen Powell from NIAB EMR to better understand how symbionts impact major insect pests of fruit horticulture, to help with biological control efficacy to reduce dependency on pesticides and other harmful chemicals. This is in the early stages of development, but we hope impacts can be recognised in a couple years.
Sector Agriculture, Food and Drink,Environment
Impact Types Economic

Policy & public services

 
Description BBSRC-NSF/BIO - Host immune suppression as a key adaptation enabling bacterial symbioses
Amount £432,267 (GBP)
Funding ID BB/W001632/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2022 
End 08/2025
 
Title Comparative database for - Symbioses shape feeding niches and diversification across insects 
Description Large comparative data set of insect family diets, symbiosis status, and diversification 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact Broadening our understanding of insect diversification of environmental, ecological and societal importance. Generating massive new comparative resources for future studies. 
URL https://www.nature.com/articles/s41559-023-02058-0
 
Title Data sets, genetic data, and code from study on aphid symbiont population dynamics - Local adaptation to hosts and parasitoids shape Hamiltonella defensa genotypes across aphid species 
Description Data and scripts are available online: https://doi.org/10.5281/zenodo.7097415 [60]. The GenBank accession numbers for Sanger sequences determined in this study are ON928985 to ON929011 (Aphid COI), ON931787 to ON932056 (Hamiltonella MLST), ON993437 - ON993619 (Parasitoid COI). The GenBank accession number for the raw data of Illumina sequencing used in this study is PRJNA863469. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact Broadening our understanding of insect symbioses of economic, environmental and societal importance. Generating new genetic resources for future studies. 
URL https://zenodo.org/records/7097415
 
Title Genomic data from a study on aphid symbiosis - Parallel evolution in the integration of a co-obligate aphid symbiosis 
Description Genome sequencing and assembly 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Broadening our understanding of insect symbioses of environmental, economic and societal importance. Generating new genomics and genetic resources for future studies. 
URL https://www.ncbi.nlm.nih.gov/bioproject/PRJNA605335/
 
Title Genomic data from a study on deep sea annelids - Distinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms 
Description Comparative genomics of Osedax and Vestimentifera 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact Broadening our understanding of annelid symbioses of environmental and societal importance. Generating new genomics resources for future studies. 
URL https://www.ebi.ac.uk/ena/browser/view/PRJEB55047
 
Title Genomic data from publication - A dynamic epibiont community associated with the bone-eating polychaete genus Osedax 
Description whale fall metagenome Genome sequencing and assembly 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact Broadening our understanding of deep sea microbial communities. Generating new genomics and genetic resources for future studies. 
URL https://www.ncbi.nlm.nih.gov/bioproject/PRJNA813420
 
Title Genomic/genetic data from publication - Convergent evolution of a nutritional symbiosis in ants 
Description Generation of new genomic and genetic data to further research. BioProject accession PRJNA639935. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact Broadening our understanding of insect symbioses of environmental and societal importance. Generating new genomics and genetic resources for future studies. 
URL https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA639935
 
Title Supplementary table S1-8 from Local adaptation to hosts and parasitoids shape Hamiltonella defensa genotypes across aphid species 
Description Supplementary tables S1 to S8 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
URL https://rs.figshare.com/articles/dataset/Supplementary_table_S1-8_from_Local_adaptation_to_hosts_and...
 
Title Supplementary table S1-8 from Local adaptation to hosts and parasitoids shape Hamiltonella defensa genotypes across aphid species 
Description Supplementary tables S1 to S8 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
URL https://rs.figshare.com/articles/dataset/Supplementary_table_S1-8_from_Local_adaptation_to_hosts_and...
 
Description Annelid symbiosis genome hub with Dr Chema Martin 
Organisation Queen Mary University of London
Country United Kingdom 
Sector Academic/University 
PI Contribution Analysis of bacteria genomic data, writing of two papers, and two grants - Wellcome Trust Seed Award and Wellcome Sanger Genome Hub - both of which were successful. Two papers emerged from the collaboration, in Nature Communications and mBio.
Collaborator Contribution Analysis of eukaryotic genomic data and providing of annelid samples, writing papers and grant together
Impact Two publications, Nature Communications (https://www.nature.com/articles/s41467-023-38521-6) and mBio (https://journals.asm.org/doi/10.1128/mbio.03140-22). Two successful grants, one Wellcome Trust Seed Award and Wellcome Sanger Genome Hub involving a consortium of 11 groups, "Bacterial symbiosis as an adaptation to extreme environments in annelid worms" led by Dr Martin, I am a Co-I.
Start Year 2018
 
Description Ant symbiosis ecological genomics with Jan Oettler and Jurgen Heinz 
Organisation Regensburg University of Applied Science
Country Germany 
Sector Academic/University 
PI Contribution Intellectual contribution, data analysis and collection, paper writing
Collaborator Contribution Providing insect samples for analyses, intellectual contribution, paper writing
Impact Two publications on ant symbioses in ISME (https://www.nature.com/articles/s41396-022-01256-1) and Frontiers in Microbiology (https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1044286/full)
Start Year 2018
 
Description Formica ant symbiosis project with Heikki Helanterä 
Organisation University of Oulu
Country Finland 
Sector Academic/University 
PI Contribution Intellectual contribution, data analysis and writing papers
Collaborator Contribution Providing samples, help with field collections, writing papers
Impact Two papers in ISME (https://www.nature.com/articles/s41396-022-01256-1) and Frontiers in Microbiology (https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1044286/full) and one grant applications which was unsuccessful.
Start Year 2018
 
Description Invited departmental seminars and international conferences 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I have presented research from this fellowship at the following:

Conferences
2023 Gordon Research Conference - Microbial Population Biology, Andover, USA
2022 EMBL Cellular mechanisms of symbiosis, Heidelburg, DE
2022 Gordon Research Conference - Animal Microbe Symbiosis, Lucca, IT
2018 Reef Microbiome Workshop, Barbados
2018 International Society for Microbial Ecology, Leipzig, DE

Invited departmental or institutional seminars
2024 Zoology departmental seminar, University of Oxford, UK
2024 Ecology and Evolutionary Biology departmental seminar - Helsinki, FIN
2023 University of Helsinki, Faculty of Biological and Environmental Sciences, Helsinki, FI.
2023 University of Western Ontario, Department of Biology, London, CA.
2019 University of Regensburg, Department of Biology, Regensburg, DE.
2018 Concordia University, Department of Biology, Montreal, CA.
Year(s) Of Engagement Activity 2018,2019,2022,2023,2024