(along with trees and other plants on land). Photosynthesis, and for this essay I use
that term in reference to oxygenic photosynthesis, is the proces by which organisms
fix their own organic carbon from carbon dioxide using water and produce oxygen as
a by-product. It is important to note that the appearance of oxygen-producing
organisms on its own was not enough to oxygenate the atmosphere. In order for
the atmosphere (and the ocean, in fact) to become oxygenated, there had to be a net
burial of photosynthetically produced organic carbon. If there was no net burial, that
organic carbon would all be remineralized to CO 2 by bacterial respiration, and it
would be a zero-sum game: all the O 2 produced by photosynthesis would be respired
back to CO 2 , and the seas and atmosphere would remain devoid of O 2 . Today, this
process is still occurring and is called the biological carbon pump by oceanographers: microscopic algae in the surface waters fix CO 2 into organic carbon via
photosynthesis, and before all this organic carbon is respired away by bacterial
respiration, some of it gets buried in the deep ocean and we get a net production
of O 2 , both in the upper ocean, and in turn in the atmosphere. Unfortunately, we as
humans have been reversing this process over the last couple of hundred years by
drilling into the ocean floor, collecting old buried algae (we call this oil), and burning
it to produce energy and sending CO 2 into the atmosphere. A majority of this CO 2
goes back into the ocean, but the biological carbon pump is not fast enough to catch
up. This has led to, among other things, increased temperatures and ocean
acidification.
Before the 1970s, bacteria in the oceans were believed to be insignificant to
global biogeochemical cycles. It was thought that algae and cyanobacteria (collectively referred to as phytoplankton) fixed CO 2 and then this material was eaten by
organisms in higher trophic levels or sank down to the bottom, but bacteria played
little role in any of these processes. At that time, bacteria were believed to be simply
decomposers of dead material, and their only interactions with phytoplankton was to
provide remineralized nutrients for photosynthesis. This view radically changed,
starting with the work of Lawrence Pomeroy in the 1970s who first measured that the
highest metabolic activity in a volume of seawater seemed to be in the smallest-sized
organisms (under 2 micrometers in diameter; Pomeroy 1974). Subsequent work
discovered that bacteria in lakes and oceans were three orders of magnitude
(1000X) more abundant than previously thought (Hobbie et al. 1977). In the early
1980s, the term “microbial loop” was coined in a seminal paper (Azam et al. 1983)
that provided a framework to explain the role of bacteria in the biogeochemistry of
the oceans, lakes, and seas: bacteria are constantly metabolizing organic carbon
produced by phytoplankton and this feeds an entire, previously unknown ecosystem.
Subsequent work in the 1990s discovered that aquatic viruses are major contributors
to the biogeochemistry of the microbial loop (Fuhrman 1999).
Fast forward to today: aquatic microbiology is a dominant discipline, but microbial processes still lag behind in large-scale modeling efforts. Often, microbes are
not even explicitly represented in such models, but in terms of biology, they are
central to studies of aquatic carbon cycling. In particular, due to the fact that most
aquatic microbes cannot be cultivated on their own, they are generally studied with
genomic techniques, which enable the identification of their function through the
206
X. Mayali
that term in reference to oxygenic photosynthesis, is the proces by which organisms
fix their own organic carbon from carbon dioxide using water and produce oxygen as
a by-product. It is important to note that the appearance of oxygen-producing
organisms on its own was not enough to oxygenate the atmosphere. In order for
the atmosphere (and the ocean, in fact) to become oxygenated, there had to be a net
burial of photosynthetically produced organic carbon. If there was no net burial, that
organic carbon would all be remineralized to CO 2 by bacterial respiration, and it
would be a zero-sum game: all the O 2 produced by photosynthesis would be respired
back to CO 2 , and the seas and atmosphere would remain devoid of O 2 . Today, this
process is still occurring and is called the biological carbon pump by oceanographers: microscopic algae in the surface waters fix CO 2 into organic carbon via
photosynthesis, and before all this organic carbon is respired away by bacterial
respiration, some of it gets buried in the deep ocean and we get a net production
of O 2 , both in the upper ocean, and in turn in the atmosphere. Unfortunately, we as
humans have been reversing this process over the last couple of hundred years by
drilling into the ocean floor, collecting old buried algae (we call this oil), and burning
it to produce energy and sending CO 2 into the atmosphere. A majority of this CO 2
goes back into the ocean, but the biological carbon pump is not fast enough to catch
up. This has led to, among other things, increased temperatures and ocean
acidification.
Before the 1970s, bacteria in the oceans were believed to be insignificant to
global biogeochemical cycles. It was thought that algae and cyanobacteria (collectively referred to as phytoplankton) fixed CO 2 and then this material was eaten by
organisms in higher trophic levels or sank down to the bottom, but bacteria played
little role in any of these processes. At that time, bacteria were believed to be simply
decomposers of dead material, and their only interactions with phytoplankton was to
provide remineralized nutrients for photosynthesis. This view radically changed,
starting with the work of Lawrence Pomeroy in the 1970s who first measured that the
highest metabolic activity in a volume of seawater seemed to be in the smallest-sized
organisms (under 2 micrometers in diameter; Pomeroy 1974). Subsequent work
discovered that bacteria in lakes and oceans were three orders of magnitude
(1000X) more abundant than previously thought (Hobbie et al. 1977). In the early
1980s, the term “microbial loop” was coined in a seminal paper (Azam et al. 1983)
that provided a framework to explain the role of bacteria in the biogeochemistry of
the oceans, lakes, and seas: bacteria are constantly metabolizing organic carbon
produced by phytoplankton and this feeds an entire, previously unknown ecosystem.
Subsequent work in the 1990s discovered that aquatic viruses are major contributors
to the biogeochemistry of the microbial loop (Fuhrman 1999).
Fast forward to today: aquatic microbiology is a dominant discipline, but microbial processes still lag behind in large-scale modeling efforts. Often, microbes are
not even explicitly represented in such models, but in terms of biology, they are
central to studies of aquatic carbon cycling. In particular, due to the fact that most
aquatic microbes cannot be cultivated on their own, they are generally studied with
genomic techniques, which enable the identification of their function through the
206
X. Mayali