Widespread bacterial use of lanthanides for methylotrophy across ecosystems
Author(s)
Warters, Leilani
Advisor(s)
Editor(s)
Collections
Supplementary to:
Permanent Link
Abstract
Methylotrophs are aerobic bacteria that consume one-carbon compounds as carbon and energy sources. Methylotrophs use the enzyme methanol dehydrogenase (MDH) to oxidize methanol to formaldehyde. MDH requires either calcium or lanthanides as a
cofactor. Despite being classified as light rare earth elements, lanthanides are relatively common in the Earth’s crust but poorly soluble in most environments. Accumulating evidence suggests that lanthanide-dependent MDHs encoded by the gene xoxF, are more widespread than calcium-dependent MDHs encoded by the gene mxaF. In this thesis, I first
studied the prevalence of lanthanide utilization in laboratory experiments using a model methylotroph alphaproteobacterium, Methylorubrum extorquens AM1. At 1 μM, lanthanides (La, Ce, or Nd) supported fastest growth and highest cell density of M. extorquens. At 100 μM, M. extorquens grew optimally with Ca, while Ce, Nd, and Eu
suppressed growth. Second, I studied the environmental abundance and relevance of lanthanide-dependent MDH using environmental metatranscriptomes in the Joint Genome Institute’s (JGI) Integrated Microbial Genome (IMG) database. XoxF amino acid sequences can be distinguished from MxaF sequences by an extra aspartate in XoxF
sequences. I found that xoxF genes were transcribed in all ecosystems (soils, freshwaters, sediments, salt marshes, seawater, and hot springs), whereas mxaF was only transcribed in
one freshwater ecosystem and one soil ecosystem. The majority of transcribed xoxF genes in marine environments belonged to the classes Alphaproteobacteria and
Gammaproteobacteria (including Burkholderiales). Transcribed xoxF genes in terrestrial environments showed more taxonomic diversity, with many belonging to the phyla Nitrososphaerota, Actinomycetota, Chloroflexota, Myxococcota, and Gemmatimonadota.
This thesis highlights the importance of lanthanide-dependent methylotrophy in global biogeochemical cycles and suggests that previously unidentified methylotrophs are active
in global environments.
Sponsor
Date
2024-11-20
Extent
Resource Type
Text
Resource Subtype
Thesis