Key to living in the extreme desert soils of eastern Antarctica: a chemolithotrophic lifestyle
Mitchell Peninsula is located at the south of the Windmill Islands, Eastern Antarctica. It is described as a nutrient poor, extreme polar desert and limited knowledge on the microbial diversity of the soils in this area exists. We examined the microbial taxonomic composition and metabolic potential of Mitchell Peninsula soils using 16S metagenomics and shotgun metagenomics. We found the site to be a potential biodiversity hotspot, containing a high abundance of Candidate Phyla WPS2 and AD3. Subsequently, differential binning was used to recover 23 draft genomes, including 3 genomes from WPS-2 and two from AD3. Further analysis of the metagenome revealed a novel Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) gene to be abundant in the bacterial community, despite a lack of evidence for photosynthesis related genes. We believe that unlike many other Antarctic regions, chemolithautrophic carbon fixation via CBB cycle is the dominant carbon fixation pathway, hence this pathway is providing the key to survival is this very dry, hostile environment.
Identification of a new catalytic function of class I fumarases
Fumarases catalyze the reversible hydration of fumarate to (S)-malate as part of the citric acid cycle. Interestingly, some prokaryotes like Escherichia coli or Burkholderiaspp. possess more than one enzyme that catalyzes the fumarase reaction. The E. coligenome for instance encodes three fumarase genes designated as fumA, fumB and fumC, where fumarases A and B belong to class I and fumarase C to class II fumarases. Questions have been raised as to why the same reaction in the same cell is catalyzed by mechanistically different enzymes. Here we identified an additional enzymatic function of class I fumarases and two examples where enzyme promiscuity allows bacteria to access novel substrates that otherwise would remain untouched.
Heterogeneity in diazotroph diversity and activity within a putative hotspot for marine nitrogen fixation
Australia’s tropical waters represent predicted “hotspots” for nitrogen (N2) fixation based on empirical and modelled data. However, the identity, activity and ecology of N2 fixing bacteria (diazotrophs) within this region are virtually unknown. By coupling DNA and cDNA sequencing of nitrogenase genes (nifH) with size fractionated N2 fixation rate measurements, we elucidated diazotroph dynamics across the shelf region of the Arafura and Timor Seas (ATS) and oceanic Coral Sea during Austral spring and winter. During spring, Trichodesmium dominated ATS assemblages, comprising 60% of nifH DNA sequences, while Candidatus Atelocyanobacterium thalassa (UCYN-A) comprised 42% in the Coral Sea. In contrast, during winter the relative abundance of heterotrophic unicellular diazotrophs (∂-proteobacteria and gamma-24774A11) increased in both regions, concomitant with a marked decline in UCYN-A sequences, whereby this clade effectively disappeared in the Coral Sea. Conservative estimates of N2 fixation rates ranged from < 1 to 91 nmol L-1 d-1, and size fractionation indicated that unicellular organisms dominated N2 fixation during both spring and winter, but average unicellular rates were up to 10-fold higher in winter than spring. Relative abundances of UCYN-A1 and gamma-24774A11 nifH transcripts negatively correlated to silicate and phosphate, suggesting an affinity for oligotrophy. Our results indicate that Australia’s tropical waters are indeed hotspots for N2 fixation, and that regional physicochemical characteristics drive differential contributions of cyanobacterial and heterotrophic phylotypes to N2 fixation.
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The Centre for Systems Genomics is holding a 1-day symposium on metagenomics and microbiome research, Tuesday November 17 at Bio21.
Interested in presenting? Register now! and complete the abstract section.
This free event will feature talks on a range of microbiome-related topics including new computational and lab methods, covering a range of application areas including the human microbiome in health and disease, environmental metagenomics, ecology, agriculture and ancient DNA.