Horizontal gene transfer and biogeography of isolated thermal acidic bacterial communities

Graduation Date

2015

Document Type

Project

Program

Other

Program

Project (M.S.)--Humboldt State University, Biology, 2015

Committee Chair Name

Mark Wilson

Committee Chair Affiliation

HSU Faculty or Staff

Keywords

Hawai’i Volcanoes National Park, HVNP, Horizontal gene transfer, LVNP, Alicyclobacilus, Lassen Volcanic National Park, Humboldt State University -- Projects -- Biology, Biogeography

Abstract

A number of isolated high temperature, low pH geothermal sites exist in Lassen Volcanic National Park (LVNP) and Hawai'i Volcanoes National Park (HVNP) that allow for the growth of thermoacidophilic microbial communities. Horizontal gene transfer (HGT) may be particularly important in these communities because it allows for ecotype divergence of closely related organisms. Previous work with LVNP isolates suggested that HGT has been occurring within species of Alicyclobacillus and between Alicyclobacillus spp. and other bacterial genera within hydrothermal communities. It was found that bacteria which possessed divergent 16S rRNA gene sequences had nearly identical protein-coding genes. Isolated thermal acidic systems also provide an opportunity to test hypotheses about microbial dispersal and biogeography, as the sites have island-like characteristics (localized regions of specialized habitats surrounded by inhospitable habitat). This thesis project aimed to 1) investigate whether HGT was occurring among a set of Alicyclobacillus tolerans and A. acidocaldarius isolates from HVNP, 2) determine whether there were geographical limits to the spread of alleles among sites within a park and between LVNP and HVNP, and 3) investigate the mechanisms by which HGT might be occurring in Alicyclobacillus. A phylogenetic tree based on cpn60 gene sequences was consistent with HGT of the cpn60 gene. A Bacillus isolate possessed a cpn60 allele that was identical to that of HVNP A. tolerans isolates. One A. tolerans isolate which possesses 16S rRNA, gyrB, keto, and eftu genes that cluster with those of the other HVNP A. tolerans isolates, possesses a cpn60 allele that belongs to distantly related Gram positive bacteria. Numerous examples of incongruent phylogenetic trees likely caused by HGT were also found among LVNP isolates. Evidence for rapid dispersal between HVNP and LVNP was evident in the A. tolerans dataset; identical alleles were found in A. tolerans isolates from sites that are separated by ~4000 km. However, biogeographical clustering of alleles was found in A. acidocaldarius isolates, including in LVNP sites separated by ~3 km. The traC gene, associated with conjugation, was found in A. tolerans and A. acidocaldarius LVNP isolates, and pulsed-field gel electrophoresis detected the presence of a 100-150 kbp plasmid in an A. tolerans isolate. SEM of filter-mated pairs of isolates showed the presence of the pili-like structures, but not in pure cultures of these strains. Analysis of a draft genome of an A. acidocaldarius isolate revealed the presence of numerous genes related to transformation and conjugation. Collectively, the results support a high rate of HGT among the Alicyclobacillus isolates and suggest that conjugation may be an important process of HGT among these Gram positive species in these environments. The A. tolerans data suggest that rapid dispersal between HVNP and LVNP sites is likely, but the A. acidocaldarius data suggest that in some cases this dispersal is not enough to overcome forces favoring local biogeographical specialization. The difference between the A. tolerans and the A. acidocaldarius results is surprising and suggests that even among closely related species the forces of dispersal, HGT and ecotype divergence are operating in strikingly different ways.

https://scholarworks.calstate.edu/concern/theses/pr76f583s

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