Hot Spring Metagenomics

Abstract

Hot springs have been investigated since the XIX century, but isolation and examination of their thermophilic microbial inhabitants did not start until the 1950s. Many thermophilic microorganisms and their viruses have since been discovered, although the real complexity of thermal communities was envisaged when research based on PCR amplification of the 16S rRNA genes arose. Thereafter, the possibility of cloning and sequencing the total environmental DNA, defined as metagenome, and the study of the genes rescued in the metagenomic libraries and assemblies made it possible to gain a more comprehensive understanding of microbial communities—their diversity, structure, the interactions existing between their components, and the factors shaping the nature of these communities. In the last decade, hot springs have been a source of thermophilic enzymes of industrial interest, encouraging further study of the poorly understood diversity of microbial life in these habitats.

Metagenomics of microbial and viral life in terrestrial geothermal environments

“…This holds true also in geothermal environments, although their density is lower (typically 10-100-fold less viruses than host cells) if compared to mesophilic aquatic systems (López-López et al 2013). Despite their importance, the knowledge about the diversity and biology of phages on the microbial communities in these ecosystems is still limited .…”

“…At present, one order and 10 families (Fuselloviridae, Bicaudaviridae, Ampullaviridae, Clavaviridae, Guttaviridae, Lipothrixviridae, Rudiviridae, Globuloviridae, Myoviridae, Siphoviridae) of archaeal viruses have been documented (Fusco et al 2015a, b;Prangishvili 2013;Snyder et al 2015;Wang et al 2015b). Until relatively recent times, the only methodology available to study these viruses was through the cultivation of their hosts (López-López et al 2013). By systematically applying this approach, our knowledge on viruses populating (hyper)thermal environments over the last 30 years has considerably expanded thanks to the pioneer work of Wolfram Zillig and, subsequently, of several groups in Europe and USA (Bize et al 2008;Dellas et al 2013Dellas et al , 2014Diemer and Stedman 2012;Haring et al 2005;Peng et al 2012;Prangishvili et al 2001Prangishvili et al , 2006Prangishvili and Rice et al 2001Rice et al , 2004Snyder et al 2011;Snyder and Young 2013;Zillig et al 1996).…”

“…The first viral metagenomics study lead to the identification of double-stranded DNA viruses in the Octopus (93°C) and Bear Paw (74°C) hot springs (Inskeep et al 2013b). Operons and potentially complete genomes were assembled, thus providing insight to the possibly dominant viral populations within each hot-spring (López-López et al 2013;Schoenfeld et al 2008). Viral metagenomes indicated the predominance of a lytic lifestyle as suggested by the significant proportion of lys-like genes encoding for proteins involved in host cell lysis (López-López et al 2013;Schoenfeld et al 2008).…”

“…Hot springs populated by extreme thermophiles (T opt : 65-79°C) and hyperthermophiles (T opt [ 80°C) (DeCastro et al 2016) are very diverse and some of them show combinations of extreme chemo-physical conditions, such as temperature, acidic or alkaline pHs, high pressure, and high concentrations of salts and heavy metals (López-López et al 2013). As with all studies of environmental microbiology, our understanding of the composition, functional and physiological dynamics, and evolution of extreme-and hyper-thermophilic microbial consortia has lagged substantially behind.…”

Contemporary molecular tools in microbial ecology and their application to advancing biotechnology

“…The application of metagenomics has resulted in a lot of novel enzymes or secondary metabolites for potential industrial use (Iqbal, Feng et al 2012, Lee and Lee 2013, Lewin, Wentzel et al 2013, Lopez-Lopez, Cerdan et al 2013. The practical amalgamation of other "omics" technologies like metatranscriptomics and metaproteomics with metagenomics is emerging as a powerful tool set to study complex microbial communities to help to identify biological molecules for biotechnological purposes (de Castro, Sartori da Silva et al 2013).…”