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Archaeal Communities in Deep Terrestrial Subsurface Underneath the Deccan Traps, India

Archaeal community structure and potential functions within the deep, aphotic, oligotrophic, hot, igneous provinces of ∼65 Myr old basalt and its Archean granitic basement was explored through archaeal 16S rRNA gene amplicon sequencing from extracted environmental DNA of rocks. Rock core samples fro...

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Autores principales: Dutta, Avishek, Sar, Pinaki, Sarkar, Jayeeta, Dutta Gupta, Srimanti, Gupta, Abhishek, Bose, Himadri, Mukherjee, Abhijit, Roy, Sukanta
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6646420/
https://www.ncbi.nlm.nih.gov/pubmed/31379755
http://dx.doi.org/10.3389/fmicb.2019.01362
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author Dutta, Avishek
Sar, Pinaki
Sarkar, Jayeeta
Dutta Gupta, Srimanti
Gupta, Abhishek
Bose, Himadri
Mukherjee, Abhijit
Roy, Sukanta
author_facet Dutta, Avishek
Sar, Pinaki
Sarkar, Jayeeta
Dutta Gupta, Srimanti
Gupta, Abhishek
Bose, Himadri
Mukherjee, Abhijit
Roy, Sukanta
author_sort Dutta, Avishek
collection PubMed
description Archaeal community structure and potential functions within the deep, aphotic, oligotrophic, hot, igneous provinces of ∼65 Myr old basalt and its Archean granitic basement was explored through archaeal 16S rRNA gene amplicon sequencing from extracted environmental DNA of rocks. Rock core samples from three distinct horizons, basaltic (BS), transition (weathered granites) (TZ) and granitic (GR) showed limited organic carbon (4–48 mg/kg) and varied concentrations (<1.0–5000 mg/kg) of sulfate, nitrate, nitrite, iron and metal oxides. Quantitative PCR estimated the presence of nearly 10(3)–10(4) archaeal cells per gram of rock. Archaeal communities within BS and GR horizons were distinct. The absence of any common OTU across the samples indicated restricted dispersal of archaeal cells. Younger, relatively organic carbon- and Fe(2)O(3)-rich BS rocks harbor Euryarchaeota, along with varied proportions of Thaumarchaeota and Crenarchaeota. Extreme acid loving, thermotolerant sulfur respiring Thermoplasmataceae, heterotrophic, ferrous-/H-sulfide oxidizing Ferroplasmaceae and Halobacteriaceae were more abundant and closely interrelated within BS rocks. Samples from the GR horizon represent a unique composition with higher proportions of Thaumarchaeota and uneven distribution of Euryarchaeota and Bathyarchaeota affiliated to Methanomicrobia, SAGMCG-1, FHMa11 terrestrial group, AK59 and unclassified taxa. Acetoclastic methanogenic Methanomicrobia, autotrophic SAGMCG-1 and MCG of Thaumarcheaota could be identified as the signature groups within the organic carbon lean GR horizon. Sulfur-oxidizing Sulfolobaceae was relatively more abundant in sulfate-rich amygdaloidal basalt and migmatitic gneiss samples. Methane-oxidizing ANME-3 populations were found to be ubiquitous, but their abundance varied greatly between the analyzed samples. Changes in diversity pattern among the BS and GR horizons highlighted the significance of local rock geochemistry, particularly the availability of organic carbon, Fe(2)O(3) and other nutrients as well as physical constraints (temperature and pressure) in a niche-specific colonization of extremophilic archaeal communities. The study provided the first deep sequencing-based illustration of an intricate association between diverse extremophilic groups (acidophile-halophile-methanogenic), capable of sulfur/iron/methane metabolism and thus shed new light on their potential role in biogeochemical cycles and energy flow in deep biosphere hosted by hot, oligotrophic igneous crust.
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spelling pubmed-66464202019-08-02 Archaeal Communities in Deep Terrestrial Subsurface Underneath the Deccan Traps, India Dutta, Avishek Sar, Pinaki Sarkar, Jayeeta Dutta Gupta, Srimanti Gupta, Abhishek Bose, Himadri Mukherjee, Abhijit Roy, Sukanta Front Microbiol Microbiology Archaeal community structure and potential functions within the deep, aphotic, oligotrophic, hot, igneous provinces of ∼65 Myr old basalt and its Archean granitic basement was explored through archaeal 16S rRNA gene amplicon sequencing from extracted environmental DNA of rocks. Rock core samples from three distinct horizons, basaltic (BS), transition (weathered granites) (TZ) and granitic (GR) showed limited organic carbon (4–48 mg/kg) and varied concentrations (<1.0–5000 mg/kg) of sulfate, nitrate, nitrite, iron and metal oxides. Quantitative PCR estimated the presence of nearly 10(3)–10(4) archaeal cells per gram of rock. Archaeal communities within BS and GR horizons were distinct. The absence of any common OTU across the samples indicated restricted dispersal of archaeal cells. Younger, relatively organic carbon- and Fe(2)O(3)-rich BS rocks harbor Euryarchaeota, along with varied proportions of Thaumarchaeota and Crenarchaeota. Extreme acid loving, thermotolerant sulfur respiring Thermoplasmataceae, heterotrophic, ferrous-/H-sulfide oxidizing Ferroplasmaceae and Halobacteriaceae were more abundant and closely interrelated within BS rocks. Samples from the GR horizon represent a unique composition with higher proportions of Thaumarchaeota and uneven distribution of Euryarchaeota and Bathyarchaeota affiliated to Methanomicrobia, SAGMCG-1, FHMa11 terrestrial group, AK59 and unclassified taxa. Acetoclastic methanogenic Methanomicrobia, autotrophic SAGMCG-1 and MCG of Thaumarcheaota could be identified as the signature groups within the organic carbon lean GR horizon. Sulfur-oxidizing Sulfolobaceae was relatively more abundant in sulfate-rich amygdaloidal basalt and migmatitic gneiss samples. Methane-oxidizing ANME-3 populations were found to be ubiquitous, but their abundance varied greatly between the analyzed samples. Changes in diversity pattern among the BS and GR horizons highlighted the significance of local rock geochemistry, particularly the availability of organic carbon, Fe(2)O(3) and other nutrients as well as physical constraints (temperature and pressure) in a niche-specific colonization of extremophilic archaeal communities. The study provided the first deep sequencing-based illustration of an intricate association between diverse extremophilic groups (acidophile-halophile-methanogenic), capable of sulfur/iron/methane metabolism and thus shed new light on their potential role in biogeochemical cycles and energy flow in deep biosphere hosted by hot, oligotrophic igneous crust. Frontiers Media S.A. 2019-07-16 /pmc/articles/PMC6646420/ /pubmed/31379755 http://dx.doi.org/10.3389/fmicb.2019.01362 Text en Copyright © 2019 Dutta, Sar, Sarkar, Dutta Gupta, Gupta, Bose, Mukherjee and Roy. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Dutta, Avishek
Sar, Pinaki
Sarkar, Jayeeta
Dutta Gupta, Srimanti
Gupta, Abhishek
Bose, Himadri
Mukherjee, Abhijit
Roy, Sukanta
Archaeal Communities in Deep Terrestrial Subsurface Underneath the Deccan Traps, India
title Archaeal Communities in Deep Terrestrial Subsurface Underneath the Deccan Traps, India
title_full Archaeal Communities in Deep Terrestrial Subsurface Underneath the Deccan Traps, India
title_fullStr Archaeal Communities in Deep Terrestrial Subsurface Underneath the Deccan Traps, India
title_full_unstemmed Archaeal Communities in Deep Terrestrial Subsurface Underneath the Deccan Traps, India
title_short Archaeal Communities in Deep Terrestrial Subsurface Underneath the Deccan Traps, India
title_sort archaeal communities in deep terrestrial subsurface underneath the deccan traps, india
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6646420/
https://www.ncbi.nlm.nih.gov/pubmed/31379755
http://dx.doi.org/10.3389/fmicb.2019.01362
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