Chapter One: Geomicrobiology and Metagenomics of Terrestrisl Deep Subsurface Microbiomes

Merja Itävaara (Corresponding author), Heikki Salavirta, Kaisa Marjamaa, T. Ruskeeniemi

Research output: Chapter in Book/Report/Conference proceedingChapter or book articleProfessional

7 Citations (Scopus)

Abstract

Fractures in the deep subsurface of Earth's crust are inhabited by diverse microbial communities that participate in biogeochemical cycles of the Earth. Life on Earth, which arose c. 3.5e4.0 billion years ago, reaches down at least 5 km in the crust. Deep mines, caves, and boreholes have provided scientists with opportunities to sample deep subsurface microbiomes and to obtain information on the species diversity and functions. A wide variety of bacteria, archaea, eukaryotes, and viruses are now known to reside in the crust, but their functions are still largely unknown. The crust at different depths has varying geological composition and hosts endemic microbiomes accordingly. The diversity is driven by geological formations and gases evolving from deeper depths. Cooperation among different species is still mostly unexplored, but viruses are known to restrict density of bacterial and archaeal populations. Due to the complex growth requirements of the deep subsurface microbiomes, the new knowledge about their diversity and functions is mostly obtained by molecular methods, eg, meta'omics'. Geomicrobiology is a multidisciplinary research area combining disciplines from geology, mineralogy, geochemistry, and microbiology. Geomicrobiology is concerned with the interaction of microorganisms and geological processes. At the surface of mineralogical or rock surfaces, geomicrobial processes occur mainly under aerobic conditions. In the deep subsurface, however, the environmental conditions are reducing and anaerobic. The present chapter describes the world of microbiomes in deep terrestrial geological environments as well as metagenomic and metatranscriptomic methods suitable for studies of these enigmatic communities.
Original languageEnglish
Title of host publicationAdvances in Applied Microbiology
EditorsSima Sariaslani, Michael Gadd
PublisherElsevier
Pages1-77
ISBN (Print)978-0-12-804803-0
DOIs
Publication statusPublished - 2016
MoE publication typeD2 Article in professional manuals or guides or professional information systems or text book material

Publication series

NameAdvances in Applied Microbiology
PublisherElsevier
Volume94
ISSN (Print)0065-2164

Fingerprint

geomicrobiology
crust
virus
biogeochemical cycle
microbiology
eukaryote
oxic conditions
cave
microbial community
species diversity
mineralogy
borehole
microorganism
geochemistry
environmental conditions
geology
bacterium
gas
rock
method

Keywords

  • deep biosphere
  • biogeochemistry
  • terrestrial
  • deep life
  • metagenomics

Cite this

Itävaara, M., Salavirta, H., Marjamaa, K., & Ruskeeniemi, T. (2016). Chapter One: Geomicrobiology and Metagenomics of Terrestrisl Deep Subsurface Microbiomes. In S. Sariaslani, & M. Gadd (Eds.), Advances in Applied Microbiology (pp. 1-77). Elsevier. Advances in Applied Microbiology, Vol.. 94 https://doi.org/10.1016/bs.aambs.2015.12.001
Itävaara, Merja ; Salavirta, Heikki ; Marjamaa, Kaisa ; Ruskeeniemi, T. / Chapter One: Geomicrobiology and Metagenomics of Terrestrisl Deep Subsurface Microbiomes. Advances in Applied Microbiology. editor / Sima Sariaslani ; Michael Gadd. Elsevier, 2016. pp. 1-77 (Advances in Applied Microbiology, Vol. 94).
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Itävaara, M, Salavirta, H, Marjamaa, K & Ruskeeniemi, T 2016, Chapter One: Geomicrobiology and Metagenomics of Terrestrisl Deep Subsurface Microbiomes. in S Sariaslani & M Gadd (eds), Advances in Applied Microbiology. Elsevier, Advances in Applied Microbiology, vol. 94, pp. 1-77. https://doi.org/10.1016/bs.aambs.2015.12.001

Chapter One: Geomicrobiology and Metagenomics of Terrestrisl Deep Subsurface Microbiomes. / Itävaara, Merja (Corresponding author); Salavirta, Heikki; Marjamaa, Kaisa; Ruskeeniemi, T.

Advances in Applied Microbiology. ed. / Sima Sariaslani; Michael Gadd. Elsevier, 2016. p. 1-77 (Advances in Applied Microbiology, Vol. 94).

Research output: Chapter in Book/Report/Conference proceedingChapter or book articleProfessional

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T1 - Chapter One: Geomicrobiology and Metagenomics of Terrestrisl Deep Subsurface Microbiomes

AU - Itävaara, Merja

AU - Salavirta, Heikki

AU - Marjamaa, Kaisa

AU - Ruskeeniemi, T.

PY - 2016

Y1 - 2016

N2 - Fractures in the deep subsurface of Earth's crust are inhabited by diverse microbial communities that participate in biogeochemical cycles of the Earth. Life on Earth, which arose c. 3.5e4.0 billion years ago, reaches down at least 5 km in the crust. Deep mines, caves, and boreholes have provided scientists with opportunities to sample deep subsurface microbiomes and to obtain information on the species diversity and functions. A wide variety of bacteria, archaea, eukaryotes, and viruses are now known to reside in the crust, but their functions are still largely unknown. The crust at different depths has varying geological composition and hosts endemic microbiomes accordingly. The diversity is driven by geological formations and gases evolving from deeper depths. Cooperation among different species is still mostly unexplored, but viruses are known to restrict density of bacterial and archaeal populations. Due to the complex growth requirements of the deep subsurface microbiomes, the new knowledge about their diversity and functions is mostly obtained by molecular methods, eg, meta'omics'. Geomicrobiology is a multidisciplinary research area combining disciplines from geology, mineralogy, geochemistry, and microbiology. Geomicrobiology is concerned with the interaction of microorganisms and geological processes. At the surface of mineralogical or rock surfaces, geomicrobial processes occur mainly under aerobic conditions. In the deep subsurface, however, the environmental conditions are reducing and anaerobic. The present chapter describes the world of microbiomes in deep terrestrial geological environments as well as metagenomic and metatranscriptomic methods suitable for studies of these enigmatic communities.

AB - Fractures in the deep subsurface of Earth's crust are inhabited by diverse microbial communities that participate in biogeochemical cycles of the Earth. Life on Earth, which arose c. 3.5e4.0 billion years ago, reaches down at least 5 km in the crust. Deep mines, caves, and boreholes have provided scientists with opportunities to sample deep subsurface microbiomes and to obtain information on the species diversity and functions. A wide variety of bacteria, archaea, eukaryotes, and viruses are now known to reside in the crust, but their functions are still largely unknown. The crust at different depths has varying geological composition and hosts endemic microbiomes accordingly. The diversity is driven by geological formations and gases evolving from deeper depths. Cooperation among different species is still mostly unexplored, but viruses are known to restrict density of bacterial and archaeal populations. Due to the complex growth requirements of the deep subsurface microbiomes, the new knowledge about their diversity and functions is mostly obtained by molecular methods, eg, meta'omics'. Geomicrobiology is a multidisciplinary research area combining disciplines from geology, mineralogy, geochemistry, and microbiology. Geomicrobiology is concerned with the interaction of microorganisms and geological processes. At the surface of mineralogical or rock surfaces, geomicrobial processes occur mainly under aerobic conditions. In the deep subsurface, however, the environmental conditions are reducing and anaerobic. The present chapter describes the world of microbiomes in deep terrestrial geological environments as well as metagenomic and metatranscriptomic methods suitable for studies of these enigmatic communities.

KW - deep biosphere

KW - biogeochemistry

KW - terrestrial

KW - deep life

KW - metagenomics

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DO - 10.1016/bs.aambs.2015.12.001

M3 - Chapter or book article

SN - 978-0-12-804803-0

T3 - Advances in Applied Microbiology

SP - 1

EP - 77

BT - Advances in Applied Microbiology

A2 - Sariaslani, Sima

A2 - Gadd, Michael

PB - Elsevier

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Itävaara M, Salavirta H, Marjamaa K, Ruskeeniemi T. Chapter One: Geomicrobiology and Metagenomics of Terrestrisl Deep Subsurface Microbiomes. In Sariaslani S, Gadd M, editors, Advances in Applied Microbiology. Elsevier. 2016. p. 1-77. (Advances in Applied Microbiology, Vol. 94). https://doi.org/10.1016/bs.aambs.2015.12.001