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Meta-omics analysis of microbially induced carbonate precipitation at a CO2 rich geyser in Utah

ABSTRACT: Microbially induced carbonate precipitation (MICP) refers to the biogeochemical process in which calcium carbonate is precipitated by altering the local geochemical environment (Mortensen et al. 2011). These alterations occur as a by-product of common microbial metabolic activities by increasing the local carbonate content as well as pH thereby saturating the solution in respect to carbonate. To better understand the microbial ecology of MICP on a community level in natural environments, we chose to evaluate microbial communities derived from travertine adjacent to Crystal Geyser (CG), Utah. CG is a cold-driven, CO2 rich geyser which is surrounded by colorful travertine that has been suggested to be generated through microbial processes. We used a cultivation-independent, multi-omics approach combined with geochemical measurements to investigate metabolic pathways and physiologies potentially involved in MICP at CG. We collected samples from the top 20 cm of travertine adjacent to Crystal Geyser, Utah in November 2019 and June 2021 (38.9384° N, 110.1354° W) wearing gloves at all times. We sampled 1 m away from the borehole (CG-1) and 10 m away from the borehole (CG-10). We preserved all collected samples in RNAlater-like solution (Menke et al., 2017, Front. Microbiol. 8) in a 1:10 sediment: RNAlater-like solution ratio as previously validated (Jensen et al. (2021, Micro. Spec. 2021, 9:2)

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Archaea Bacteria Eukaryota (eucaryotes)

SUBMITTER: Marlene Violette

LAB HEAD: Manuel Kleiner

PROVIDER: PXD041379 | Pride | 2024-11-18

REPOSITORIES: Pride

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Source:

			Action	DRS
	CG-10_V3_Clstr95.fasta	Fasta
	CG-1_V3_Clstr95.fasta	Fasta
	MJ030_MJ03101_CG-1-1_900ng_Run1.msfView	Msf
	MJ030_MJ03101_CG-1-1_900ng_Run1.pep.xml	Pepxml
	MJ030_MJ03101_CG-1-1_900ng_Run1.raw	Raw

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Project description:Methylation is a repressive modification of DNA prevalent throughout mammalian genomes yet mostly absent at CG rich stretches referred to as CGI. Here we identify their building principles by parallel genomic targeting of sequence libraries. Iterative insertions generated over 3,000 variants of genome-derived and artificial sequences at the same genomic site. Single molecule profiling of the methylation status of this collection allowed modeling the contribution of CG content and DNA binding factors towards the unmethylated state. It made the surprising prediction that the majority of CGs within endogenous islands are susceptible to methylation changes modulated by the presence of transcription factors, which is indeed confirmed by genome-wide methylation dynamics during multiple cellular differentiations. Our model further predicts blocks of constitutively unmethylated CGs independent from TF binding, which have a median size of ~300bp but are only present in half of all islands. Their constitutively unmethylated state is a hallmark of untransformed cells but their increased methylation is a specific and predictive feature of cancer. This study quantifies the two principal mechanisms governing methylation patterns in mammalian genomes. It provides a framework to interpret methylation data across normal and cancer samples and refines the concept of CpG islands. Methylation is a repressive modification of DNA prevalent throughout mammalian genomes yet mostly absent at CG rich stretches referred to as CGI. Here we identify their building principles by parallel genomic targeting of sequence libraries. Iterative insertions generated over 3,000 variants of genome-derived and artificial sequences at the same genomic site. Single molecule profiling of the methylation status of this collection allowed modeling the contribution of CG content and DNA binding factors towards the unmethylated state. It made the surprising prediction that the majority of CGs within endogenous islands are susceptible to methylation changes modulated by the presence of transcription factors, which is indeed confirmed by genome-wide methylation dynamics during multiple cellular differentiations. Our model further predicts blocks of constitutively unmethylated CGs independent from TF binding, which have a median size of ~300bp but are only present in half of all islands. Their constitutively unmethylated state is a hallmark of untransformed cells but their increased methylation is a specific and predictive feature of cancer. This study quantifies the two principal mechanisms governing methylation patterns in mammalian genomes. It provides a framework to interpret methylation data across normal and cancer samples and refines the concept of CpG islands. Libraries of DNA sequences were constructed either by mouse genome (129S6) or E.coli genome (NC_010473.1) subrepresentation or custom synthesis. DNA fragments were inserted into the genome of mouse embryonic stem cells by recombination mediated casette exchange (RMCE) at the B-globin locus. Methylation status of the inserted DNA sequences was profiled by bisulfite sequencing using a pair of universal primers flanking the fragments.

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Meta-omics analysis of microbially induced carbonate precipitation at a CO2 rich geyser in Utah

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