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2008 Annual Science Report

Pennsylvania State University Reporting  |  JUL 2007 – JUN 2008

Genomics of Sulfidic Cave Extremophiles (Supplement to NNA04CC06A)

Project Summary

We investigated the ecology and evolutionary relationships among extremely acid-loving bacteria and archaea living in biofilms called “snottites” in sulfidic caves in Italy and Mexico. The acid-loving microbes form the base of food chains cut off from the surface, and present rare examples of microbially dominated ecosystems (like ecosystems present for much of earth history and those potentially elsewhere in the universe). The snottites are also important because they help us learn how life adapts to environmental conditions much different from the ones that can be tolerated by our own species (pH 0-1). Future work based on the foundation presented here will reveal how subsurface microorganisms in geographically isolated “geochemical islands” are related to each other and to microorganisms living at the earth’s surface.

4 Institutions
3 Teams
0 Publications
0 Field Sites
Field Sites

Project Progress

PSARC funds fully or partially supported the publication of 4 manuscripts and 6 abstracts last year. Field expeditions allowed us to make geochemical measurements and sample subsurface microbial communities in sulfidic caves hosting extreme acidophiles (snottites), including the Frasassi cave system (13°C) and Grotta Nuova del Rio Garaffo (45°C) in Italy.

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We used a combination of metagenomic, phylogenetic, lipid, and culture-based analyses to investigate the ecology, biogeochemistry, and biosignatures of the extreme acidophile (pH 0-2) communities. 16S rDNA clone libraries contained at most two archaeal and six bacterial species. Fluorescence in situ hybridization (FISH) of snottites from over 12 cave locations confirmed that snottites are among the simplest microbial communities known, and that they are dominated by Acidithiobacillus and Ferroplasma species, with smaller populations of Acidimicrobium species and other bacteria, filamentous fungi, and protists. As described previously, nearly complete genomic coverage of an Acidithiobacillus strain was obtained using a metagenomics approach (work of Ph. D. student Dan Jones, postdoc Dattagupta, technician Schaperdoth).

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Acidithiobacillus strains isolated from cave samples on autotrophic media confirm that they are primary producers and that they excrete abundant extracellular polymers similar to those in snottite matrices. Lipid analyses (work of Ph.D. students Heidi Albrecht and Kat Dawson) revealed that snottite Acidithiobacillus isolates are capable of synthesizing up to 10 or more membrane hopanoids, an unusually high number compared to the 0-2 hopanoid structures produced by most other bacteria. We hypothesize that the membrane stiffening hopanoid compounds are one of the important mechanisms of acid adaptation in this bacterium. We were also able to enrich extremely acidophilic organoheterotrophs from the snottites (work of undergraduate Jignasha Patel and astrobiology REU student Stephanie Spielman). The cave acidophile project was highlighted in an interview for MicrobeWorld Radio (American Society for Microbiology).

A newly discovered (non-acidophile) microbial community was obtained from deep within the Frasassi cave system in the anoxic water of a stratified lake. This community is of strong interest due to the potentially extreme energy limitation of the environment, and because of the unusual form of the biofilms (thick vertical “ropes” several meters long). 14-carbon dating of the biofilm suggests that it is extremely slow growing and may be thousands of years old. Archaea retrieved in 16S rDNA clone libraries are not related to cultivated organisms and have unknown metabolic capabilities. The presence of mcrA-related genes amplified from the biofilm suggests that methane cycling may be a source of usable energy, but neither mcrA nor 16S rDNA sequences show close relationships with known methanogens or anaerobic methane oxidizers.