9
Microbial Carbon Cycling in Pelagic
Ecosystems: Microbial Methods
for Ecosystem Scientists
Jonathan J. Cole
Introduction
In almost any ecosystem, microorganisms are responsible for most of the respiration and a large
portion of the nutrient cycling. It is understandable, then, that ecologists working at the ecosystem scale would be naturally drawn to the study
of microorganisms. The factors that regulate the
abundance, distribution, growth rate, and respiration of these microorganisms are in large measure
the factors that regulate some of the functioning
of the ecosystem.
For a microbiologist interested in ecosystem
processes, planktonic systems have some distinct
advantages over most other environments as a focus for study. Planktonic bacteria are reasonably
well dispersed, at least at the scale of milliliters to
liters (see Duarte and Vaque 1992; Vaque and Pace
1992). The dilute nature of planktonic systems implies that bacteria will usually be found surrounded by water rather than attached to particles.
And, although water chemistry does vary substantially among different types of aquatic ecosystems,
most are dilute enough that techniques developed
in one type are generally transferable to another
without a great deal of modification. For these reasons process-level microbiology has progressed
more rapidly in planktonic systems than in some
others.
In this chapter, I discuss some of the techniques
in use by microbiologists interested in carbon cycling in planktonic systems. While this restriction
reduces the topic to the tractable, it also leaves out
a great deal of new and exciting work on microbial
diversity and genetics, microbial processes in other
138
types of aquatic habitats (sediments, wetlands,
groundwater) and microbial cycling of other elements. I focus on several aspects of microbial
communities and processes: abundance and biomass, secondary production, respiration, growth
efficiency, and use of specific substrates. I try to
highlight new methodological developments that
would be of use to ecosystem scientists.
To guide the discussion, I show two examples
of the importance of bacteria to carbon (C) cycling
in pelagic ecosystems in Figure 9.1. Bacteria draw
on organic substrates from the pool of dissolved
organic C (DOC). This DOC can originate from
primary production within the system (autochthonous source) and from the input of organic C from
outside of the system (allochthonous sources).
When bacteria process this organic matter, they
produce new bacterial biomass (bacterial secondary production) and they respire organic C to dissolved inorganic C (DIC). Figure 9.1A represents
the pelagic region of the open ocean; Figure 9.1B
represents an oligotrophic clearwater lake. Broadly
similar patterns are seen in humic lakes (Hessen
et al. 1990; Vezina and Pace 1994) and coastal
waters as well (Vezina and Platt 1988). Planktonic
bacterial respiration accounts for more than 30%
of the total respiration of all heterotrophs and is
of similar magnitude to the respiration of all zooplankton. Bacterial secondary production is coequal with that of zooplankton, and averages,
among systems, about 20 to 30% of planktonic
primary production (Cole et al. 1988; Simon et al.
1992) (Figure 9.2). This bacterial secondary production is an important food source to grazers, and
can support the demands of protozoans and a sub-
Microbial Carbon Cycling in Pelagic
Ecosystems: Microbial Methods
for Ecosystem Scientists
Jonathan J. Cole
Introduction
In almost any ecosystem, microorganisms are responsible for most of the respiration and a large
portion of the nutrient cycling. It is understandable, then, that ecologists working at the ecosystem scale would be naturally drawn to the study
of microorganisms. The factors that regulate the
abundance, distribution, growth rate, and respiration of these microorganisms are in large measure
the factors that regulate some of the functioning
of the ecosystem.
For a microbiologist interested in ecosystem
processes, planktonic systems have some distinct
advantages over most other environments as a focus for study. Planktonic bacteria are reasonably
well dispersed, at least at the scale of milliliters to
liters (see Duarte and Vaque 1992; Vaque and Pace
1992). The dilute nature of planktonic systems implies that bacteria will usually be found surrounded by water rather than attached to particles.
And, although water chemistry does vary substantially among different types of aquatic ecosystems,
most are dilute enough that techniques developed
in one type are generally transferable to another
without a great deal of modification. For these reasons process-level microbiology has progressed
more rapidly in planktonic systems than in some
others.
In this chapter, I discuss some of the techniques
in use by microbiologists interested in carbon cycling in planktonic systems. While this restriction
reduces the topic to the tractable, it also leaves out
a great deal of new and exciting work on microbial
diversity and genetics, microbial processes in other
138
types of aquatic habitats (sediments, wetlands,
groundwater) and microbial cycling of other elements. I focus on several aspects of microbial
communities and processes: abundance and biomass, secondary production, respiration, growth
efficiency, and use of specific substrates. I try to
highlight new methodological developments that
would be of use to ecosystem scientists.
To guide the discussion, I show two examples
of the importance of bacteria to carbon (C) cycling
in pelagic ecosystems in Figure 9.1. Bacteria draw
on organic substrates from the pool of dissolved
organic C (DOC). This DOC can originate from
primary production within the system (autochthonous source) and from the input of organic C from
outside of the system (allochthonous sources).
When bacteria process this organic matter, they
produce new bacterial biomass (bacterial secondary production) and they respire organic C to dissolved inorganic C (DIC). Figure 9.1A represents
the pelagic region of the open ocean; Figure 9.1B
represents an oligotrophic clearwater lake. Broadly
similar patterns are seen in humic lakes (Hessen
et al. 1990; Vezina and Pace 1994) and coastal
waters as well (Vezina and Platt 1988). Planktonic
bacterial respiration accounts for more than 30%
of the total respiration of all heterotrophs and is
of similar magnitude to the respiration of all zooplankton. Bacterial secondary production is coequal with that of zooplankton, and averages,
among systems, about 20 to 30% of planktonic
primary production (Cole et al. 1988; Simon et al.
1992) (Figure 9.2). This bacterial secondary production is an important food source to grazers, and
can support the demands of protozoans and a sub-