Living on a (Pr)Air; Characterising atmospheric chemosynthesis in bacteria and cold desert microbiomes

• Main Author: Ray, Angelique
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: UNSW, Sydney 2022
• Subjects: Microbial ecology; Primary production; Atmospheric gases; Trace gas oxidation; Atmospheric chemosynthesis; Cold deserts; Metagenomics; Transcriptomics; Bacterial culture; qPCR; anzsrc-for: 31 BIOLOGICAL SCIENCES; anzsrc-for: 41 ENVIRONMENTAL SCIENCES; Adams Flat; Antarctic; Arctic; Calvin; Robinson Ridge; The Antarctic; Antarc*
• Online Access: http://hdl.handle.net/1959.4/100642; https://doi.org/10.26190/unsworks/24349

Cold desert soils are one of the most hostile environments on Earth, notoriously scarce in liquid water and nutrients, and exposed to highly variable levels of sunlight. Whilst higher taxa are frequently out selected by the harsh conditions, microorganisms have adapted a breath of unique strategies to survive and become widely established within this niche. Despite this, photoautotrophs are reported as scarce within a growing number of cold desert environments, and soil oligotrophy frequently limits geochemical nutrient oxidation by chemoautotrophs. The first-order processes that supply carbon and energy to the broader trophic webs remain an elusive gap in our understanding of cold desert soil ecology. In 2017, a primary production strategy reliant upon the RuBisCO form IE driven Calvin-Benson-Bassham (CBB) cycle and the oxidation of atmospheric H2 and CO by high-affinity enzymes, since coined as ‘atmospheric chemosynthesis’, was identified in soil microbiomes from two Eastern Antarctic sites; Robinson Ridge and Adams Flat. This thesis builds on this initial discovery, revealing that atmospheric chemosynthesis is a significant form of bacterial primary production occurring throughout cold deserts globally. Moreover, we investigate atmospheric chemosynthesis in two cultured bacterial isolates, Rhodococcus opacus (DSM 43205) and Mycobacterium agri (DSM 44515). First, we aimed to investigate how widely dispersed the genetic determinates of atmospheric chemosynthesis are and identify their environmental drivers within oligotrophic cold edaphic deserts. We hypothesised that trace gas chemosynthetic marker genes would be widespread throughout polar communities, and that their abundance relative to community size would increase in drier, more nutrient-poor soils. Using qPCR, we quantified the 16S rRNA gene alongside the RuBisCO form IE (rbcL1E) and high-affinity 1h [NiFe]-hydrogenase large subunit (hhyL) genes in 122 soil microbiomes from 14 cold deserts spanning the Antarctic, Arctic and Tibetan Plateau. Both genes ...