Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave

Abstract

Microbial diversity in Movile Cave (Romania) was studied using bacterial and archaeal 16S rRNA gene sequence and functional gene analyses, including ribulose-1,5-bisphosphate carboxylase/ oxygenase (RuBisCO), soxB (sulfate thioesterase/thiohydrolase) and amoA (ammonia monooxygenase). Sulfur oxidizers from both Gammaproteobacteria and Betaproteobacteria were detected in 16S rRNA, soxB and RuBisCO gene libraries. DNA-based stable-isotope probing analyses using 13 C-bicarbonate showed that Thiobacillus spp. were most active in assimilating CO 2 and also implied that ammonia and nitrite oxidizers were active during incubations. Nitrosomonas spp. were detected in both 16S rRNA and amoA gene libraries from the 'heavy' DNA and sequences related to nitriteoxidizing bacteria Nitrospira and Candidatus 'Nitrotoga' were also detected in the 'heavy' DNA, which suggests that ammonia/nitrite oxidation may be another major primary production process in this unique ecosystem. A significant number of sequences associated with known methylotrophs from the Betaproteobacteria were obtained, including Methylotenera, Methylophilus and Methylovorus, supporting the view that cycling of one-carbon compounds may be an important process within Movile Cave. Other sequences detected in the bacterial 16S rRNA clone library included Verrucomicrobia, Firmicutes, Bacteroidetes, alphaproteobacterial Rhodobacterales and gammaproteobacterial Xanthomonadales. Archaeal 16S rRNA sequences retrieved were restricted within two groups, namely the Deep-sea Hydrothermal Vent Euryarchaeota group and the Miscellaneous Crenarchaeotic group. No sequences related to known sulfur-oxidizing archaea, ammonia-oxidizing archaea, methanogens or anaerobic methane-oxidizing archaea were detected in this clone library. The results provided molecular biological evidence to support the hypothesis that Movile Cave is driven by chemolithoautotrophy, mainly through sulfur oxidation by sulfur-oxidizing bacteria and reveal that ammonia-and nitrite-oxidizing bacteria may also be major primary producers in Movile Cave.

Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave

“…Avenues for understanding alternate non-photosynthetic primary production strategies are limited to subterranean or deep-sea ecosystems that function in the absence of sunlight. A significant amount of research has been devoted to characterizing primary production in ecosystems such as hydrothermal vents (reviewed by Nakagawa and Takai, 2008) and sulfidic caves (Sarbu et al, 1996;Chen et al, 2009;Engel et al, 2010;Jones et al, 2012), where supplies of reduced sulfur, hydrogen or methane support rich chemolithoautotophic activity; however, the energy dynamics of carbonate caves are less well defined. Carbonate cave communities are presumed to be sustained by allocthonous carbon sourced from photic surface ecosystems and entering the cave with vadose-zone drip water, surface water flow or the behavior of macrofauna (Laiz et al, 1999;Simon et al, 2003;Barton et al, 2004).…”

Organic matter enrichment affects archaea community in limestone cave sediments

“…Among the eight Crenarchaeota OTUs, three were grouped with soil archaea, one was related to the Nitrosocaldus genus, and four were archaea from a marine environ- ment. The Euryarchaeota and Creanarchaeota taxa are dominant in archaea communities in limestone caves (Chelius and Moore, 2004;Chen et al, 2009), including Crenarchaeota from marine environments that have previously been found in caves (Chelius and Moore, 2004).…”

“…These micro-organisms are a monophyletic group of phenotypically diverse prokaryotes. Initially, it was believed that they were found only in extreme environments; however, several articles have demonstrated that archaea probably occur in all environments that support life, including caves (Gonzalez et al, 2006;Chen et al, 2009;Jarrel et al, 2011). This group was found to be important for ecological relationships in several environments, particularly because of their role in biogeochemical cycles (Kudo et al, 1997;Chen et al, 2009;Jarrel et al, 2011).…”

La vida temprana en la Tierra y los primeros ecosistemas terrestres

“…En contraste con los ambientes subaéreos dominados por comunidades fotosintéticas, los microbios subterráneos requieren un metabolismo quimiosintético para la productividad primaria, tal vez confinado a la oxidación de compuestos con azufre y hierro (principales fuentes de energía de tales ambientes) para sustentar su crecimiento y continuidad (Sarbu et al, 1996;Chen et al, 2009;Porter et al, 2009). Debido a que estas vías metabólicas son menos energéticas que la fotosíntesis (i.e.…”