Metagenomics of microbial and viral life in terrestrial geothermal environments

Abstract

Geothermally heated regions of Earth, such as terrestrial volcanic areas (fumaroles, hot springs, and geysers) and deep-sea hydrothermal vents, represent a variety of different environments populated by extremophilic archaeal and bacterial microorganisms. Since most of these microbes thriving in such harsh biotopes, they are often recalcitrant to cultivation; therefore, ecological, physiological and phylogenetic studies of these microbial populations have been hampered for a long time. More recently, culture-independent methodologies coupled with the fast development of next generation sequencing technologies as well as with the continuous advances in computational biology, have allowed the production of large amounts of metagenomic data. Specifically, these approaches have assessed the phylogenetic composition and functional potential of microbial consortia thriving within these habitats, shedding light on how extreme physico-chemical conditions and biological interactions have shaped such microbial communities. Metagenomics allowed to better understand that the exposure to an extreme range of selective pressures in such severe environments, accounts for genomic flexibility and metabolic versatility of microbial and viral communities, and makes extreme-and hyper-thermophiles suitable for bioprospecting purposes, representing an interesting source for novel thermostable proteins that can be potentially used in several industrial processes.Keywords Hyperthermophiles Á Geothermal environments Á Microbial and viral metagenomics Á CRISPR Á Enzyme discovery BackgroundHot 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 A. Strazzulli Á M. Moracci Á P. Contursi

Diversity of dsDNA Viruses in a South African Hot Spring Assessed by Metagenomics and Microscopy

“…Due to constant high temperatures, often associated with high acidity, hot springs have been shown to harbor unique consortia of thermophilic bacteria and archaea [ 2 ]. Hot spring virus communities, while having received attention in recent years, have been limited to only a few thermal springs, mainly sampled from Yellowstone National Park in the United States [ 3 , 4 , 5 , 6 , 7 ]. The majority of these reported virus community analyses were conducted in boiling, acidic springs (between ca.…”

Spatial Metagenomics of Three Geothermal Sites in Pisciarelli Hot Spring Focusing on the Biochemical Resources of the Microbial Consortia

“…Thus, extremozymes are ideal tools for industrial applications where harsh chemical and physical conditions are encountered. However, the difficulties in cultivating extremophiles severely limit access to this class of biocatalysts, thereby metagenomic approaches are now largely used for extremozyme discovery [ 14 , 15 , 16 , 17 ].…”

“…The increasing amounts of metagenomic data and fully sequenced genomes now allow us to systematically explore these microbial communities [ 14 , 18 ], enabling us to investigate the uncultured microbial population, the mechanisms of possible adaptation to biogeochemical cycles, and the lifestyles of extreme organisms, and to discover new extremozymes [ 19 ].…”

Discovery of hyperstable carbohydrate‐active enzymes through metagenomics of extreme environments

“…The interest in extremophiles has boosted metagenomics studies of extreme environments [12][13][14][15][16], and, more recently, remarkable examples of the discovery of novel extremozymes for industrial applications from sequence-based screenings have been reported [17][18][19].…”