Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs

Menzel, Peter; Gudbergsdottir, Soley; Rike, Anne Gunn; Lü, Lin; Zhang, Qi; Contursi, Patrizia; Moracci, Marco; Kristjánsson, Jakob K.; Bolduc, Benjamin; Гаврилов, С. Н.; Ravin, Nikolai V.; Mardanov, Andrey V.; Bonch-Osmolovskaya, E. A.; Young, Mark; Krogh, Anders; Peng, Xu

doi:10.1007/s00248-015-0576-9

Cited by 103 publications

(94 citation statements)

References 46 publications

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“…Crenarchaeota (Sulfolobales) (Inskeep et al 2013a) (Inskeep et al 2013b) (Menzel et al 2015) (Bolduc et al 2012) 15 MG N.R.…”

Section: Low Concentration Of Dissolved Oxygen and Sulfidementioning

confidence: 99%

“…The authors were able to obtain nine novel partial or nearly complete genomes of novel genogroups or genotypes of the putative RNA viruses previously identified by Bolduc et al (2012). Viral sequences were also retrieved from the metagenomic dataset obtained in a recent study on the NL10 (Menzel et al 2015). Among the viral families, Lipothrixiviridae, is the most abundant and Rudiviridae and Ampullaviridae members were also identified together with viral sequences assigned to Pyrobaculum spherical virus (PSV) and Thermoproteus tenax virus 1 (TTV1) (Haring et al 2004;Neumann et al 1989).…”

Section: Yellowstone National Park Usamentioning

confidence: 99%

“…Faster analysis can be obtained with the Illumina MiSeq instrument. However, despite there is evidence that the MiSeq offers valuable information for shotgun sequencing and can Rev Environ Sci Biotechnol (2017) 16:425-454 431 Table 1 State-of-the-art of the microbial metagenomics in geothermal environments worldwide Crenarchaeota (Sulfolobales) (Inskeep et al 2010) (Inskeep et al 2013a) (Inskeep et al 2013b) (Menzel et al 2015) 14 NL 58…”

Section: Next Generation Sequencing Technologymentioning

confidence: 99%

“…1) usually produce millions of short sequence reads up to 800 bp. To date, the most used sequencing techniques are Roche 454 and Illumina that have now been extensively applied to metagenomic from geothermal environments (Inskeep et al 2013b;Menzel et al 2015) (Table 1).…”

Section: Next Generation Sequencing Technologymentioning

confidence: 99%

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Metagenomics of microbial and viral life in terrestrial geothermal environments

Strazzulli

Fusco

Cobucci‐Ponzano

et al. 2017

Rev Environ Sci Biotechnol

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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

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“…Crenarchaeota (Sulfolobales) (Inskeep et al 2013a) (Inskeep et al 2013b) (Menzel et al 2015) (Bolduc et al 2012) 15 MG N.R.…”

Section: Low Concentration Of Dissolved Oxygen and Sulfidementioning

confidence: 99%

Section: Yellowstone National Park Usamentioning

confidence: 99%

Section: Next Generation Sequencing Technologymentioning

confidence: 99%

Section: Next Generation Sequencing Technologymentioning

confidence: 99%

See 2 more Smart Citations

Metagenomics of microbial and viral life in terrestrial geothermal environments

Strazzulli

Fusco

Cobucci‐Ponzano

et al. 2017

Rev Environ Sci Biotechnol

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“…Molecular studies have documented the presence of a significant number of cultured and uncultured Crenarchaeota in Uzon Caldera thermal pools. It was reported that Crenarchaeota inhabited not only high-temperature springs (Wemheuer et al, 2013;Chernyh et al, 2015), but also springs with moderate temperatures (Perevalova et al, 2008;Burgess et al, 2012;Menzel et al, 2015). At the time of writing, many thermophilic and hyperthermophilic crenarchaeotes have been isolated from hot springs of Uzon Caldera, including members of genera Desulfurococcus (Bonch- Osmolovskaya et al, 1988;Perevalova et al, 2005;Kublanov et al, 2009), Thermoproteus (Bonch- Osmolovskaya et al, 1990), Acidilobus (Prokofeva et al, 2000;2009), Vulcanisaeta (Prokofeva et al, 2005), Fervidicoccus (Perevalova et al, 2010) and Pyrobaculum (Slobodkina et al, 2015).…”

mentioning

confidence: 99%

Thermogladius calderae gen. nov., sp. nov., an anaerobic, hyperthermophilic crenarchaeote from a Kamchatka hot spring

Kochetkova¹,

Kublanov²,

Toshchakov

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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An obligately anaerobic, hyperthermophilic, organoheterotrophic archaeon, strain 1633 T , was isolated from a terrestrial hot spring of the Uzon Caldera (Kamchatka Peninsula, Russia). Cells were regular cocci, 0.5-0.9 mm in diameter, with one flagellum. The temperature range for growth was 80-95 8C, with an optimum at 84 8C. Strain 1633 T grew on yeast extract, beef extract, peptone, cellulose and cellobiose. No growth was detected on other sugars or carbohydrates, organic acids, or under autotrophic conditions. The only detected growth products were CO 2 , acetate, and H 2 . The growth rate was stimulated by elemental sulfur, which was reduced to hydrogen sulfide. The in silico-calculated G+C content of the genomic DNA of strain 1633 T was 55.64 mol%. 16S rRNA gene sequence analysis placed strain 1633 T together with the non-validly published 'Thermogladius shockii' strain WB1 in a separate genus-level cluster within the family Desulfurococcaceae. Average nucleotide identity (ANI) results revealed 75.72 % identity between strain 1633 T and 'Thermogladius shockii' WB1. Based on these results we propose a novel genus and species with the name Thermogladius calderae gen. nov., sp. nov. The type strain of the type species is 1633 T (5DSM 22663 T 5VKM B-2946 T ).The vast majority of cultured Crenarchaeota have been isolated from terrestrial geothermal environments (Huber & Stetter, 2006). Located in Far East of Russia, Kamchatka Peninsula is a volcanically active area with hundreds of associated volcanoes and areas with geothermal activity, among which Uzon Caldera is the largest. Molecular studies have documented the presence of a significant number of cultured and uncultured Crenarchaeota in Uzon Caldera thermal pools. It was reported that Crenarchaeota inhabited not only high-temperature springs (Wemheuer et al., 2013;Chernyh et al., 2015), but also springs with moderate temperatures (Perevalova et al., 2008;Burgess et al., 2012;Menzel et al., 2015). At the time of writing, many thermophilic and hyperthermophilic crenarchaeotes have been isolated from hot springs of Uzon Caldera, including members of genera Desulfurococcus Slobodkina et al., 2015). Here we report the isolation of strain 1633 T obtained from a hot spring of the Uzon Caldera, and found to be closely related to 'Thermogladius shockii', a species with a name that was effectively, but never validly, published (Osburn & Amend, 2011).Strain 1633 T was isolated from a sample of mixed water and black mud from a freshwater hot spring (548 30.0479 N 1598 56.8519 E) located in the West Thermal Field of Uzon Caldera. The in situ water temperature and Abbreviations: ANI, average nucleotide identity; GDGT, glycerol dibiphytanyl glycerol tetraether.The GenBank/EMBL/DDBJ accession number for the complete genome sequence of Thermogladius calderae 1633 T is CP003531. The genome sequencing project of 'Thermogladius shockii' WB1 is available in the GenBank/EMBL/DDBJ databases under accession number PRJEB12686.

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Insights into the Substrate Promiscuity of Novel Hydroxysteroid Dehydrogenases

Bertuletti

Ferrandi²,

Marzorati³

et al. 2020

Adv Synth Catal

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Hydroxysteroid dehydrogenases (HSDHs) are valuable biocatalysts for the regio‐ and stereoselective modification of steroids, bile acids and other steroid derivatives. In this work, we investigated the substrate promiscuity of this highly selective class of enzymes. In order to reach this goal, a preliminary search of HSDH homologues in in‐house or public available (meta)genomes was carried out. Eight novel NAD(H)‐dependent HSDHs, showing either 7α‐, 7β‐, or 12α‐HSDH activity, and including, for the first time, enzymes from extremophilic microorganisms, were identified, recombinantly produced, and characterized. Among the novel HSDHs, four highly active (up to 92 U mg−1) NAD(H)‐dependent 7β‐HSDHs showing negligible similarity towards previously described 7β‐HSDHs, were discovered. These enzymes, along with previously characterized HSDHs, were tested as biocatalysts for the stereoselective reduction of a panel of substrates including two α‐ketoesters of pharmaceutical interest and selected ketones that partially resemble the structural features of steroids. All the reactions were coupled with a suitable cofactor regeneration system. Regarding the α‐ketoesters, nearly all of the tested HSDHs showed a good activity toward the selected substrates, yielding the reduced α‐hydroxyester with up to 99% conversions and enantiomeric excesses. On the other hand, only the 7β‐HSDHs from Collinsella aerofaciens and Clostridium absonum showed appreciable activity toward more complex ketones, i. e., (±)‐trans‐1‐decalone, but with interesting as well as different selectivity.

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Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs

Cited by 103 publications

References 46 publications

Metagenomics of microbial and viral life in terrestrial geothermal environments

Metagenomics of microbial and viral life in terrestrial geothermal environments

Thermogladius calderae gen. nov., sp. nov., an anaerobic, hyperthermophilic crenarchaeote from a Kamchatka hot spring

Insights into the Substrate Promiscuity of Novel Hydroxysteroid Dehydrogenases

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