Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms

Area of Science:

• Paleoclimatology
• Microbiology
• Environmental Science

Background:

• Glacier ice archives microorganisms, providing a record of past climate and microbial evolution over tens to hundreds of thousands of years.
• Analyzing ancient ice microorganisms is challenging due to low biomass, limited sample availability, and potential contamination.
• Existing methods for surface decontamination are insufficient; novel in silico decontamination protocols are needed for accurate microbial analysis of glacial ice.

Purpose of the Study:

• To apply advanced 'clean' sampling techniques combined with in silico decontamination to investigate microorganisms archived in Tibetan Plateau glacier ice.
• To assess the effectiveness of in silico decontamination by comparing microbial profiles from glacial ice and various control samples.
• To understand microbial community structure and its relationship to climate change as recorded in ancient ice.

Main Methods:

• Collected ice core samples (GS3) from the Guliya ice cap at depths of ∼41 m (D41, ∼20,000 years) and ∼49 m (D49, ∼30,000 years).
• Established four types of 'background' controls: sterile water artificial ice core, air samples from processing labs, and a blank sterile water sample.
• Utilized amplicon sequencing and quantitative PCR (qPCR) for microbial analysis, applying in silico proportional removal of contaminant taxa identified in controls.

Main Results:

• Identified 29 microbial genera in control samples, which contained 50-100 times less 16S DNA than glacial ice samples, confirming their contaminant status.
• In silico decontamination successfully removed low-abundance contaminant taxa, revealing distinct microbial communities between the D41 and D49 ice samples.
• Prokaryotic 16S DNA amplicon sequencing profiles were repeatable and nearly identical between standard and pre-amplified methods, validating the approach.

Conclusions:

• The study successfully established 'clean' procedures and in silico decontamination methods for studying low-biomass microbial communities in ancient glacier ice.
• Contaminant-controlled microbial profiles showed significant differences between ice depths, correlating with past climate changes.
• Commonly found genera like Methylobacterium and Sphingomonas suggest widespread distribution of certain microbes across glacier environments.