abundance data for varied crustal lithologies to estimate the total abundance of
continental microbes. Their estimate is 2 to 6 x 10
29 cells, or 22–31 gigatons of C.
That’s a big chunk of Earth’s total inventory of ~10
30 prokaryotic cells (Whitman
et al. 1998; Kallmeyer et al. 2012) and ~ 550 gigatons of biomass C (Bar-On et al.
2018). Since a large proportion of these subsurface microbes are
chemolithoautotrophs, the primary producer base or foundation of the deep biomass
pyramid is indeed vast.
So, the deep biosphere has been in place for a very long time, possibly the entire
3.5 to 4 billion-year span of life on Earth; it’s widespread and deeply penetrating;
and it contains myriad individual organisms. Given these characteristics and also the
physical as well as chemical diversity of its potential microhabitats, it is perhaps not
surprising that subsurface microbes have evolved into many different forms. Molecular sequencing analyses have revealed a diversity of bacteria and archaea, with
many taxa being first discovered in the subsurface. Examples of these are the
archaeal phyla first discovered by Ken Takai and others that have now been
proposed as novel phyla such as the Bathyarchaeota, Hadesarchaea, and
Aigarchaeota (Colman et al. 2017). Some of these subsurface microbes may be
indigenous, i.e., unique to their subsurface habits, such as D. audaxviator, which has
been detected exclusively deep underground; others appear to inhabit the surface
world, as well. All told, the diversity is huge. How huge? Magnabosco et al. (2018)
borrowed a scaling model from Locey and Lennon (2016), applying it to a sequence
dataset compiled from a large number of subsurface studies, and from that model
estimated that the total bacterial and archaeal species richness for the Earth’s
continental subsurface could be as high as one trillion OTUs (operational taxonomic
units, the molecular microbial ecologists’ stand-in for the concept of species, which
strictly speaking doesn’t apply to prokaryotes). Considering that this is approximately the same as Locey’s and Lennon’s own estimate for worldwide species
richness, we see again that life underground deserves vastly more study (and
funding, of course!).
The deep subsurface habitats beneath the oceans, i.e., deep-sea sediments and
rock, harbor microbes, too, but there are some fundamental differences between the
marine and continental habitats. Many, if not most, microbes in ocean sediment
could be considered essentially accidental tourists that settled out from the water
column above, along with dissolved and particulate organics, and now they’re
slowly metabolizing that organic matter and also slowly depleting their own cellular
reserves. H 2 -utilizing chemolithotrophs occur in the marine subsurface, too, but
these marine SLiMEs are less prevalent than in continental systems. The continental
SLiMEs are not only actively metabolizing geochemically generated inorganic substrates; they’re interacting in complex communities of chemoautotrophs, with the
products of one group forming essential metabolites for another. Maggie Lau et al.
(2016) used a full suite of “-omics” (metagenomics (DNA), transcriptomics (RNA),
and proteomics (protein)) analyses to characterize complex trophic interactions
among chemolithoautotrophs in fluid-filled fractures 1.3 km deep in South Africa.
There, methanogens form the base of the trophic pyramid, although somewhat
oddly, it’s an inverted pyramid wherein the methanogens are the primary producers,
7 Lithotrophic (“Stone-Eating”) Microbes Provide the Foundation for Deep. . .
135
continental microbes. Their estimate is 2 to 6 x 10
29 cells, or 22–31 gigatons of C.
That’s a big chunk of Earth’s total inventory of ~10
30 prokaryotic cells (Whitman
et al. 1998; Kallmeyer et al. 2012) and ~ 550 gigatons of biomass C (Bar-On et al.
2018). Since a large proportion of these subsurface microbes are
chemolithoautotrophs, the primary producer base or foundation of the deep biomass
pyramid is indeed vast.
So, the deep biosphere has been in place for a very long time, possibly the entire
3.5 to 4 billion-year span of life on Earth; it’s widespread and deeply penetrating;
and it contains myriad individual organisms. Given these characteristics and also the
physical as well as chemical diversity of its potential microhabitats, it is perhaps not
surprising that subsurface microbes have evolved into many different forms. Molecular sequencing analyses have revealed a diversity of bacteria and archaea, with
many taxa being first discovered in the subsurface. Examples of these are the
archaeal phyla first discovered by Ken Takai and others that have now been
proposed as novel phyla such as the Bathyarchaeota, Hadesarchaea, and
Aigarchaeota (Colman et al. 2017). Some of these subsurface microbes may be
indigenous, i.e., unique to their subsurface habits, such as D. audaxviator, which has
been detected exclusively deep underground; others appear to inhabit the surface
world, as well. All told, the diversity is huge. How huge? Magnabosco et al. (2018)
borrowed a scaling model from Locey and Lennon (2016), applying it to a sequence
dataset compiled from a large number of subsurface studies, and from that model
estimated that the total bacterial and archaeal species richness for the Earth’s
continental subsurface could be as high as one trillion OTUs (operational taxonomic
units, the molecular microbial ecologists’ stand-in for the concept of species, which
strictly speaking doesn’t apply to prokaryotes). Considering that this is approximately the same as Locey’s and Lennon’s own estimate for worldwide species
richness, we see again that life underground deserves vastly more study (and
funding, of course!).
The deep subsurface habitats beneath the oceans, i.e., deep-sea sediments and
rock, harbor microbes, too, but there are some fundamental differences between the
marine and continental habitats. Many, if not most, microbes in ocean sediment
could be considered essentially accidental tourists that settled out from the water
column above, along with dissolved and particulate organics, and now they’re
slowly metabolizing that organic matter and also slowly depleting their own cellular
reserves. H 2 -utilizing chemolithotrophs occur in the marine subsurface, too, but
these marine SLiMEs are less prevalent than in continental systems. The continental
SLiMEs are not only actively metabolizing geochemically generated inorganic substrates; they’re interacting in complex communities of chemoautotrophs, with the
products of one group forming essential metabolites for another. Maggie Lau et al.
(2016) used a full suite of “-omics” (metagenomics (DNA), transcriptomics (RNA),
and proteomics (protein)) analyses to characterize complex trophic interactions
among chemolithoautotrophs in fluid-filled fractures 1.3 km deep in South Africa.
There, methanogens form the base of the trophic pyramid, although somewhat
oddly, it’s an inverted pyramid wherein the methanogens are the primary producers,
7 Lithotrophic (“Stone-Eating”) Microbes Provide the Foundation for Deep. . .
135