Bibliography
Diepenbroek, M., Gobe, H., Reinke, M., Schindler, U., Schlitzer,
R., Sieger, R., and Wefer, G., 2002. PANGAEA-an information
system for environmental sciences. Computers and
Geosciences, 28, 1201–1210.
DEEP BIOSPHERE
Axel Schippers
Federal Institute for Geosciences and Natural Resources,
Hannover, Germany
Synonyms
Deep subseafloor biosphere; Deep subsurface biosphere
Definition
Deep biosphere. Jørgensen and Boetius (2007) define the
seafloor as the top meter layer of the seabed that is bioturbated by animals and porous ocean crust that is penetrated
by seawater, whereas the deep subsurface, which harbors
the deep biosphere, comprises the sediment and rock that
is deeper than 1 m below the seafloor (mbsf).
Introduction
The Earth’s deep biosphere includes a variety of subsurface habitats, such as mines and deep aquifer systems in
the continental realm and sediments and igneous rock in
the marine realm. The terrestrial deep subsurface biosphere has been studied in various geological formations
(e.g., Gold, 1992; Pedersen, 1993, 1997; Stevens and
McKinley, 1995; Amy and Haldeman, 1997; Chapelle
et al., 2002; Moser et al., 2003; Lin et al., 2006; Fry
et al., 2009; Borgonie et al., 2011; Breuker et al., 2011;
Itävaara et al., 2011; Edwards et al., 2012) but is not in
the scope of this entry. Jørgensen and Boetius (2007)
and Edwards et al. (2012) defined the seafloor as the top
meter layer of the seabed that is bioturbated by animals
and porous ocean crust that is penetrated by seawater,
whereas the deep subsurface, which harbors the deep biosphere, comprises the sediment and rock that is deeper
than 1 m below the seafloor. Several review papers have
been published about the marine deep biosphere
(Jørgensen, 2000; Parkes et al., 2000; Parkes and
Wellsbury, 2004; Teske, 2005; Teske, 2006a; Teske,
2006b; Jørgensen et al., 2006; Jørgensen and Boetius,
2007; Fry et al., 2008; Mascarelli, 2009; Schrenk et al.,
2010; Edwards et al., 2012; Hoehler and Jørgensen,
2013; Lever, 2013; Orcutt et al., 2013a; Teske et al.,
2013; Parkes et al., 2014). This entry gives an overview
about the marine deep biosphere in deeply buried sediments and in the ocean crust considering the deep biosphere biomass, the predominant microorganisms and
their diversity and activity, as well as implications for biogeochemistry. The marine deep biosphere has been
explored at various ocean sites mainly within the framework of the Ocean Drilling Program (ODP) and the Integrated Ocean Drilling Program (IODP).
The deep biosphere in marine sediments
Biomass
Organic carbon from marine primary production is usually
the energy source feeding the deep biosphere. Only about
1 % of the total marine primary production of organic carbon is available for deep-sea sediment microorganisms
(Hedges, 1992). For the largest part of the ocean seafloor,
the organic carbon amount available on the ocean seafloor
from sedimentation is on average 1 g of carbon per m
2 per
year (Jahnke and Jackson, 1992). Most of the organic carbon is degraded within the top 1-m sediment, and the
organic carbon content in the deep subsurface comprises
approximately 0.1–1 % of sediment by dry weight
(Jørgensen and Boetius, 2007). In deep sediments with
extremely low organic carbon flux, radiolysis of water
may provide hydrogen and thus an energy source for autotrophic microorganisms independent of photosynthesis
(Jørgensen and D’Hondt, 2006; D’Hondt et al., 2009).
A fundamental question in deep biosphere research is
its size or the biomass of living cells. This topic was first
comprehensively addressed by the research group of
Parkes et al. (1994, 2000). For counting of microbial cells
under a fluorescence microscope, the cells in a sediment
sample were stained with the DNA-intercalating dye acridine orange, and the number of total cells counted is given
as acridine orange direct counts (AODC). Using this
method for building up an AODC database, the first report
about an existence of a deep biosphere in several hundred
meters deeply buried sediments was published (Parkes
et al., 1994). Studies of contamination potential have demonstrated that it is possible to obtain core samples without
outside contamination (Smith et al., 2000), and the enumeration of prokaryotes is now a standard protocol
onboard the IODP drillships JOIDES Resolution (Lever
et al., 2006) and Chikyu (Yanagawa et al., 2013). The total
number of prokaryotes (Bacteria and Archaea) in the subsurface sediments decreases with sediment depth mainly
because it is controlled by the organic carbon content of
the sediment as it is the main microbial substrate (Parkes
et al., 2000; D’Hondt et al., 2004; Roussel et al., 2008).
This data was then further extrapolated to calculate a
global biomass of the deep biosphere, and it was estimated
that marine sediments harbor over half of all prokaryotic
cells on Earth (Whitman et al., 1998). However, these estimates were mainly derived from organic carbon-rich,
meso- to eutrophic sediments from continental margins
and/or upwelling areas. A recent study included organic
carbon-lean, oligotrophic subsurface sediments which
contain much less cells and showed that the total cell
counts varied between ocean sites by ca. five orders of
magnitude (Figure 1; Kallmeyer et al., 2012). They estimated Earth’s total number of microbes and living biomass to be 50–78 % and 10–45 %, respectively, lower
144
DEEP BIOSPHERE
Diepenbroek, M., Gobe, H., Reinke, M., Schindler, U., Schlitzer,
R., Sieger, R., and Wefer, G., 2002. PANGAEA-an information
system for environmental sciences. Computers and
Geosciences, 28, 1201–1210.
DEEP BIOSPHERE
Axel Schippers
Federal Institute for Geosciences and Natural Resources,
Hannover, Germany
Synonyms
Deep subseafloor biosphere; Deep subsurface biosphere
Definition
Deep biosphere. Jørgensen and Boetius (2007) define the
seafloor as the top meter layer of the seabed that is bioturbated by animals and porous ocean crust that is penetrated
by seawater, whereas the deep subsurface, which harbors
the deep biosphere, comprises the sediment and rock that
is deeper than 1 m below the seafloor (mbsf).
Introduction
The Earth’s deep biosphere includes a variety of subsurface habitats, such as mines and deep aquifer systems in
the continental realm and sediments and igneous rock in
the marine realm. The terrestrial deep subsurface biosphere has been studied in various geological formations
(e.g., Gold, 1992; Pedersen, 1993, 1997; Stevens and
McKinley, 1995; Amy and Haldeman, 1997; Chapelle
et al., 2002; Moser et al., 2003; Lin et al., 2006; Fry
et al., 2009; Borgonie et al., 2011; Breuker et al., 2011;
Itävaara et al., 2011; Edwards et al., 2012) but is not in
the scope of this entry. Jørgensen and Boetius (2007)
and Edwards et al. (2012) defined the seafloor as the top
meter layer of the seabed that is bioturbated by animals
and porous ocean crust that is penetrated by seawater,
whereas the deep subsurface, which harbors the deep biosphere, comprises the sediment and rock that is deeper
than 1 m below the seafloor. Several review papers have
been published about the marine deep biosphere
(Jørgensen, 2000; Parkes et al., 2000; Parkes and
Wellsbury, 2004; Teske, 2005; Teske, 2006a; Teske,
2006b; Jørgensen et al., 2006; Jørgensen and Boetius,
2007; Fry et al., 2008; Mascarelli, 2009; Schrenk et al.,
2010; Edwards et al., 2012; Hoehler and Jørgensen,
2013; Lever, 2013; Orcutt et al., 2013a; Teske et al.,
2013; Parkes et al., 2014). This entry gives an overview
about the marine deep biosphere in deeply buried sediments and in the ocean crust considering the deep biosphere biomass, the predominant microorganisms and
their diversity and activity, as well as implications for biogeochemistry. The marine deep biosphere has been
explored at various ocean sites mainly within the framework of the Ocean Drilling Program (ODP) and the Integrated Ocean Drilling Program (IODP).
The deep biosphere in marine sediments
Biomass
Organic carbon from marine primary production is usually
the energy source feeding the deep biosphere. Only about
1 % of the total marine primary production of organic carbon is available for deep-sea sediment microorganisms
(Hedges, 1992). For the largest part of the ocean seafloor,
the organic carbon amount available on the ocean seafloor
from sedimentation is on average 1 g of carbon per m
2 per
year (Jahnke and Jackson, 1992). Most of the organic carbon is degraded within the top 1-m sediment, and the
organic carbon content in the deep subsurface comprises
approximately 0.1–1 % of sediment by dry weight
(Jørgensen and Boetius, 2007). In deep sediments with
extremely low organic carbon flux, radiolysis of water
may provide hydrogen and thus an energy source for autotrophic microorganisms independent of photosynthesis
(Jørgensen and D’Hondt, 2006; D’Hondt et al., 2009).
A fundamental question in deep biosphere research is
its size or the biomass of living cells. This topic was first
comprehensively addressed by the research group of
Parkes et al. (1994, 2000). For counting of microbial cells
under a fluorescence microscope, the cells in a sediment
sample were stained with the DNA-intercalating dye acridine orange, and the number of total cells counted is given
as acridine orange direct counts (AODC). Using this
method for building up an AODC database, the first report
about an existence of a deep biosphere in several hundred
meters deeply buried sediments was published (Parkes
et al., 1994). Studies of contamination potential have demonstrated that it is possible to obtain core samples without
outside contamination (Smith et al., 2000), and the enumeration of prokaryotes is now a standard protocol
onboard the IODP drillships JOIDES Resolution (Lever
et al., 2006) and Chikyu (Yanagawa et al., 2013). The total
number of prokaryotes (Bacteria and Archaea) in the subsurface sediments decreases with sediment depth mainly
because it is controlled by the organic carbon content of
the sediment as it is the main microbial substrate (Parkes
et al., 2000; D’Hondt et al., 2004; Roussel et al., 2008).
This data was then further extrapolated to calculate a
global biomass of the deep biosphere, and it was estimated
that marine sediments harbor over half of all prokaryotic
cells on Earth (Whitman et al., 1998). However, these estimates were mainly derived from organic carbon-rich,
meso- to eutrophic sediments from continental margins
and/or upwelling areas. A recent study included organic
carbon-lean, oligotrophic subsurface sediments which
contain much less cells and showed that the total cell
counts varied between ocean sites by ca. five orders of
magnitude (Figure 1; Kallmeyer et al., 2012). They estimated Earth’s total number of microbes and living biomass to be 50–78 % and 10–45 %, respectively, lower
144
DEEP BIOSPHERE