Yellow coloured mats from lava tubes of La Palma (Canary Islands, Spain) are dominated by metabolically active Actinobacteria

Abstract

Microbial diversity in lava tubes from Canary Islands (Spain) has never been explored thus far offering a unique opportunity to study subsurface microbiology. Abundant yellow coloured mats developing on coralloid speleothems in a lava tube from La Palma Islands were studied by next-generation sequencing and DNA/RNA clone library analyses for investigating both total and metabolically active bacteria. In addition, morphological and mineralogical characterization was performed by field emission scanning electron microscopy (FESEM), micro-computed tomography, X-ray diffraction and infrared spectroscopy to contextualize sequence data. This approach showed that the coralloid speleothems consist of banded siliceous stalactites composed of opal-A and hydrated halloysite. Analytical pyrolysis was also conducted to infer the possible origin of cave wall pigmentation, revealing that lignin degradation compounds can contribute to speleothem colour. Our RNA-based study showed for the first time that members of the phylum Actinobacteria, with 55% of the clones belonging to Euzebyales order, were metabolically active components of yellow mats. In contrast, the DNA clone library revealed that around 45% of clones were affiliated to Proteobacteria. Composition of microbial phyla obtained by NGS reinforced the DNA clone library data at the phylum level, in which Proteobacteria was the most abundant phylum followed by Actinobacteria.

Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain)

“…Here we demonstrate that, although NGS 16S rRNA sequencing offers a more complete view of the microbial community inhabiting the saline ponds of the Odiel Marshlands, providing more information about the less abundant genera, both NGS and 16S rRNA clone library approaches are comparable regarding the estimation of the major genera found in the sample. This is in agreement with the results obtained by other authors, such as González-Pimentel [ 42 ], who compared both approaches to study the microbial diversity in lava tubes from Canary Islands.…”

Microbial Community Characterizing Vermiculations from Karst Caves and Its Role in Their Formation

“…In this context, our study provides, for the first time, an overview Table 3 Pearson correlation matrices between microbial phyla and geochemical characteristics of the studied vermiculations Table 3 (continued) on the microbial life associated with vermiculations from nonsulfidic karst systems. The NGS approach revealed a biodiversity comparable to those observed in several matrices from different caves [10,19,20,[33][34][35]. Proteobacteria (41.3-54.8%), represented (in decreasing order) by Gamma-, Beta-, Alpha-, and Deltaproteobacteria classes, was the dominant phylum, likely in relation to the wide ranges in metabolism and phenotype, offering the capability to degrade a broad spectrum of organic substrates and to adapt to and thrive in the hostile cave environment [2].…”

Microbial Communities in Vermiculation Deposits from an Alpine Cave

“…We used primers PolF (5′-TGC GAY CCS AAR GCB GAC TC-3′) and PolR (5′-ATS GCC ATC ATY TCR CCG GA -3′) for detecting nifH gene (Poly et al, 2001); Arch-amoAF (5′-STA ATG GTC TGG CTT AGA CG-3′) and Arch-amoAR (5′-GCG GCC ATC CAT CTG TAT CT-3′) for archaeal amoA gene (Francis et al, 2005); and amoA-1F (5′-GGG GTT TCT ACT GGT GGT-3′) and amoA-2R (5′-CCC CTC KGS AAA GCC TTC TTC-3′) for bacterial amoA gene (Rotthauwe et al, 1997). Clone libraries protocol was detailed by Gonzalez-Pimentel et al (2018). Plasmids were sequenced by Secugen Sequencing Services (CSIC, Madrid, Spain).…”