Heat Shock Response of the Active Microbiome From Perennial Cave Ice

Abstract

Ice caves constitute the newly investigated frozen and secluded model habitats for evaluating the resilience of ice-entrapped microbiomes in response to climate changes. This survey identified the total and active prokaryotic and eukaryotic communities from millennium-old ice accumulated in Scarisoara cave (Romania) using Illumina shotgun sequencing of the ribosomal RNA (rRNA) and messenger RNA (mRNA)-based functional analysis of the metatranscriptome. Also, the response of active microbiome to heat shock treatment mimicking the environmental shift during ice melting was evaluated at both the taxonomic and metabolic levels. The putatively active microbial community was dominated by bacterial taxa belonging to Proteobacteria and Bacteroidetes, which are highly resilient to thermal variations, while the scarcely present archaea belonging to Methanomicrobia was majorly affected by heat shock. Among eukaryotes, the fungal rRNA community was shared between the resilient Chytridiomycota and Blastocladiomycota, and the more sensitive Ascomycota and Basidiomycota taxa. A complex microeukaryotic community highly represented by Tardigrada and Rotifera (Metazoa), Ciliophora and Cercozoa (Protozoa), and Chlorophyta (Plantae) was evidenced for the first time in this habitat. This community showed a quick reaction to heat shock, followed by a partial recovery after prolonged incubation at 4°C due to possible predation processes on the prokaryotic cluster. Analysis of mRNA differential gene expression revealed the presence of an active microbiome in the perennial ice from the Scarisoara cave and associated molecular mechanisms for coping with temperature variations by the upregulation of genes involved in enzyme recovery, energy storage, carbon and nitrogen regulation, and cell motility. This first report on the active microbiome embedded in perennial ice from caves and its response to temperature stress provided a glimpse into the impact of glaciers melting and the resilience mechanisms in this habitat, contributing to the knowledge on the functional role of active microbes in frozen environments and their response to climatic changes.

Concurrent stimulation of diflufenican biodegradation and changes in the active microbiome in gravel revealed by Total RNA

“…The enhanced biotransformation was accompanied by a change in the composition of the active microbial community in the alfalfa amended treatment compared to the control treatment. The TotalRNA approach applied in the present study has the strength of revealing changes in the composition of the active microbial community across all domains of life as demonstrated in previous studies investigating the active microbiome of permafrost soil (Schostag et al ., 2019), wood ash amended agricultural and forest soil (Bang-Andreasen et al ., 2020), and perennial cave ice (Mondini et al ., 2022).…”

Abrupt permafrost thaw triggers microbial bloom and grazer succession

“…Ciliates and Amoebozoa have been observed in Siberian permafrost previously (Shatilovich et al, 2009). Particularly, the ciliates highly abundant in both transition zones, Spirotrichea and Oligohymenophorea, were also formerly found in ice caves, indicating possible cold adaptation (Mondini et al, 2022). One potential explanation for the high abundance of protozoa in freshly thawed permafrost could be that several cyst- and resting-stage-forming protist taxa have previously responded quickly to environmental changes (Rønn et al, 2012).…”

“…Resulting concentrations were normalised for the sample weight and used for extraction ratios of extracted RNA to DNA (RNA:DNA). The RNA was further DNase-treated, cDNA synthesised, and metabarcoded as described by Mondini and colleagues (Mondini et al, 2022). All purification and library preparation steps were executed in a dedicated PCR clean room and for all nucleic acid concentrations evaluated with the TapeStation 4150 (Agilent Technologies, Santa Clara, California, US).…”

The geomicrobiology of limestone, sulfuric acid speleogenetic, and volcanic caves: basic concepts and future perspectives

“…Metatranscriptomics consists of sequencing and quantifying the relative abundance of mRNAs in a sample to determine the functional activities of a given microbiome ( Bashiardes et al, 2016 ). Although crucial for understanding the regulation of gene expression in microbial communities ( Zhang et al, 2021 ), this technique has occasionally been applied to cave microbiome research ( Mondini et al, 2022 ). It could be combined with proteomics and metabolomics ( Idle and Gonzalez, 2007 ; Roldán et al, 2018 ) to systematically quantify protein expression and identify metabolites from cave samples.…”

“…Given the continuous improvement of next-generation sequencing (NGS) and analytical chemistry methods, various culture-independent approaches are being applied to cave microbiomes, e.g., 16S rRNA metataxonomic profiling ( Biagioli et al, 2023 ), metagenomic shotgun sequencing ( Wiseschart et al, 2019 ; Turrini et al, 2020 ), metatranscriptomics ( Mondini et al, 2022 ) and proteomics ( van Spanning et al, 2022 ). In parallel, high-magnification and fluorescence microscopies have contributed to unveiling biofilm-like structures on cave surfaces, identifying and quantifying specific taxa composing these communities, and studying the functional properties of individual microbial components ( Jones et al, 2023 ).…”