Survey of Genomes - Entomopathogenic Xenorhabdus strains

Brad jumps in with 2 pathogens of insect larvae that do their dirty work in collaboration with tiny soil roundworms that carry the bacteria in their gut. Together, the roundworm and bacteria use insect larvae as food sources and can be used as biocontrol agents for certain plant-eating grubs.

Welcome to Genomics Revolution. This is Brad Goodner from the 2019 Hiram College Genetics course hosting this episode on the genomes of two strains of the genus Xenorhabdus - Xenorhabdus nematophila ATCC 19061 & Xenorhabdus bovienii SS-2004.  I will call them X. nematophila and X. bovienii from here on out.  These strains are in the Bacteria division gamma-Proteobacteria and within the family Enterobacteriaceae, meaning they are closely related to well known human gut symbionts and pathogens such as Escherichia coli and Salmonella enterica.  However, Xenorhabdus strains are not found in the guts of humans, rather they are gut symbionts of particular soil nematodes of the genus Steinernema.  The bacteria are needed for the maturation of the nematodes.  Not only that, the bacteria and nematode host work together to kill certain insect larvae and use them as nutrient sources.  Wow, that is a complex interaction and that is why a group of labs from the U.S. and Europe, including my lab at Hiram College came together to sequence these two genomes.

One of the biggest problems we had with these genomes is that they have lots of repetitive sequences in them, including transposable elements.  This makes it very hard to assemble sequencing reads into the full genome.  Think about it – if the same 400 bp sequence is present 10 times in the genome then how do know which fragments go together?  This is rarely an issue for a genome in Bacteria or Archaea, but it gave us a lot of headaches for the two Xenorhabdus genomes.  To get around this problem, we worked with a company in Madison, WI, called OpGen Technologies to use a genome-wide restriction mapping technique called optical mapping (1).  You very very gently lyse bacterial cells on an electron microscopy grid, cut the DNA as it lays on the grid with a particular restriction enzyme and figure out the length and order of the fragments.  This strategy was critical to getting these genomes done.

The 2 Xenorhabdus genomes each have a single circular chromosome, ranging in size from 4.26-4.43 Mbp.  X. nematophila has an additional plasmid of 155 kbp.  The two genomes encode between 4250 and 4350 proteins.  The Xenorhabdus genomes were compared to two previously sequenced genomes from a closely related genus, Photorhabdus, that lives in the guts of nematodes of the genus Heterorhabditis (2).  The two Bacterial genera inhabit different parts of the nematode gut and the two nematode-bacteria symbioses attack different insect larval hosts.  Comparison of the genomes across the two genera showed that there were many orthologous genes in common, some of which probably deal with basic metabolism but also some that deal with living inside a nematode.  That said, these shared orthologs only account for about half of any one genome.  On the other side of the coin, the two Xenorhabdus strains had many genes in common not found in the  Photorhabdus strains and vice versa.  This means that these two closely related genera of Bacteria do some really different things.  For example, each genus appears to make some unique insect-killing peptides and antimicrobial molecules.  Moreover, we also found that the two genera solved the same ecological problems, such as dealing with oxidative stress, using different strategies.  These two genera diverged from a common ancestor that might have lived inside nematodes but they have converged on solving certain ecological problems from different angles.

Since the publication of these genomes, several labs have tested hypotheses using wildtype and mutant strains in both in vitro and in vivid experiments.  For example, Singh et al. (3) used mutants of X. nematophila unable to make different antimicrobial compounds to figure out how this bacterium kills off competitor Bacterial genera inside a dead insect larva.  Murfin et al. (4) figured out that X. boveinii helps its host nematode outcompete related nonhost nematodes.

Bacteria helping a roundworm kill an caterpillar so that both can benefit even in the presence of competing bacteria or other nematodes.  Who would have guessed that.  Thanks for listening.


References:
(1) Latreille et al., 2007.  BMC Genomics 8:321.  Optical mapping as a routine tool for bacterial genome sequence finishing.
(2) Chasten et al., 2011.  PloS One 6:e27909.  The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes.
(3) Singh et al., 2014.  Applied & Environmental Microbiology 81:754-64.  Role of secondary metabolites in establishment of the mutualistic partnership between Xenorhabdus nematophila and the entomopathogenic nematode Steinernema carpocapsae.
(4) Murfin et al., 2018.  Environmental Microbiology doi: 10.1111/1462-2920.14278 [Epub].  Symbiont-mediated competition: Xenorhabdus bovienii confer an advantage to their nematode host Steinernema affine by killing competitor Steinernema feltiae.