Evolution of host-bacterial associations

Microbes associated with eukaryotic hosts are fantastic examples of symbiotic relationships between species, with nutritional and other benefits to both partners. However, since most microbes remain uncultured and unexplored, we are only just beginning to understand the breadth and depth of such interactions using metagenomic approaches. Co-evolutionary dynamics with gut microbes are particularly interesting in host groups such as insects, which encompass a wide range of dietary, ecological, and life history variation. We are trying to understand the ecological and evolutionary processes governing insect-gut microbial interactions. These projects are funded by NCBS core funds and a research grant from ICGEB. We have also recently started exploring plant-associated microbes; this work is funded by a North East Region Collaborative grant from DBT.

Host-specific, temporal, and spatial variation in insect gut microbiomes

Dragonflies are top insect predators in aquatic ecosystems, and are thought to be generalists in both larval and adult stages. Ashwin analysed culturable bacteria isolated from the guts of dragonflies  from different geographic locations in south India (Nair and Agashe 2016, Curr Sci). His initial work showed surprisingly strong impacts of host species, sampling time and sampling location on the gut community composition. These findings are supported by a more exhaustive analysis of dragonfly gut bacterial diversity using 16S rRNA amplicon sequencing (Deb, Nair and Agashe, in prep). Rittik is now testing whether the host-specificity of microbiomes arises from dietary specialization across dragonflies, or due to host-specific selective pressures imposed within the gut.

Insects diet may vary not only across space, but also across development: many insects undergo dramatic dietary shifts across their life cycle. For instance, butterfly larvae typically feed on leaves, whereas adults usually feed on nectar or other liquids. What is the impact of these diet shifts on their microbiomes, and are the microbes important for host fitness? To answer these questions, Kruttika is using 16S rRNA sequencing and manipulative experiments with wild-caught butterflies. Her preliminary analyses indicate substantial variability in microbiomes across host species, diet, and developmental stage. Kruttika’s ongoing experiments will tell us whether preventing microbial colonization affects host fitness. This work is conducted in collaboration with Krushnamegh Kunte at NCBS.

The microbiome of a generalist

There are many wonderful examples of specialist insects that associate with microbial symbionts that improve host fitness. The  host-symbiont relationship can perhaps evolve more readily in specialists, where vertical transmission of the symbiont may be easier. How do such relationships evolve in generalists? To understand this better, Aparna is analysing host-bacterial associations in the red flour beetle, a generalist pest of stored grains. Her preliminary results suggest that multiple fitness components of the flour beetle indeed depend on the microbiome: preventing bacterial colonization reduces fitness dramatically. Aparna is now trying to determine which bacteria are responsible, and what is the basis of the association.

The evolution of rice-associated Methylobacteria

We are testing for mutualistic associations between Methylobacterium species and traditionally cultivated rice landraces from North-Eastern India. Previously published work suggests that M. oryzae and M. phyllospherae use methanol emitted by rice leaves as a primary carbon source, and may produce growth hormones that enhance host growth. Pratibha is testing whether genetically distinct, isolated rice varieties in northeastern India have co-evolved specific associations with their local Methylobacterium partners. If she finds specific associations between local rice and associated Methylobacterium species, we aim to characterize the chemical and genetic basis of the association. This work is conducted in collaboration with P. V. Shivaprasad and Radhika Venkatesan at NCBS.