173
the prokaryotic organisms has developed at a
genetic level, based on sequence analyses of
small-subunit ribosomal RNA (16S rRNA), which
now allows a phylogenetic identification of
microorganisms, even of those that have not yet
been isolated and studied in laboratory cultures.
This has revealed much greater species diversity
than had been anticipated just a decade ago and
the number of “species” according to this genetic
diversity has reached ca 10.000, or ten-fold more
than the isolated species, and it is rapidly
growing. The RNA and DNA based methods have
for the first time enabled a true quantification of
defined bacterial groups in nature. By the use of
molecular probes that bind specifically to
ribosomal RNA of selected target organisms both
cultured and uncultured bacteria can now be
identified phylogenetically. When such probes are
fluorescently labelled, a sediment sample may be
stained by the probes and individual cells of the
target bacteria can then be observed and counted
directly under a fluorescense microscope. This
technique is called Fluorescence in situ Hybridization (FISH) and has become an indispensable
tool in biogeochemistry.
As an example of the quantification of bacteria,
Llobet-Brossa et al. (1998) found that the total cell
density of microorganisms in sediment from the
German Wadden Sea was up to 4·10
9
cells cm
-3
.
Such a population density of several billion microorganisms in a teaspoon of mud is typical of
coastal marine sediments. Of all these cells, up to
73% could be identified by FISH as eubacteria and
up to 45% were categorized to known groups of
eubacteria. The sulfate reducing bacteria comprised some 10-15% of the identified microorganisms,
while other members of the group proteobacteria
comprised 25-30%. Surprisingly, members of the
Cytophaga-Flavobacterium group were the most
abundant in all sediment layers. These bacteria are
specialized in the degradation of complex macromolecules and their presence in high numbers
indicates their role in the initial hydrolytic degradation of organic matter.
Such studies of the spatial distribution of
bacteria provide information on where they may
be actively transforming organic or inorganic
compounds, and thereby indicate which processes are likely to take place. This is particularly
important when chemical species are rapidly
recycled so that the dynamics of their production
or consumption is not easily revealed by geochemical analyses. The introduction of high
resolution tools such as microsensors and
molecular probes has helped to overcome one of
the classical problems in biogeochemistry, namely
to identify the relationship between the processes
that biogeochemists analyze, and the microorganisms who carry them out. The magnitude of this
problem may be appreciated when comparing the
scale of bacteria with that of humans. The bacteria
are generally 1-2 µm large, while we are 1-2 m. As
careful biogeochemists we may use a sediment
sample of only 1 cm
3
to study the metabolism of,
e.g. methane producing bacteria. For the study of
the metabolism of humans, this sample size would
by isometric analogy correspond to a soil volume
of 1000 km
3
. Thus, it is not surprising that very
sensitive methods, such as the use of radiotracers, are often necessary when bacterial
processes are to be demonstrated over short
periods of time (hours-days). It is also obvious,
that a 1 cm
3
sample will include a great diversity of
prokaryotic organisms and metabolic reactions
and that a much higher resolution is required to
sort out the activities of individual cells or
clusters of organisms.
5.2
Life and Environments at
Small Scale
The size spectrum of living organisms and of their
environments is so vast that it is difficult to comprehend (Fig. 5.3). The smallest marine bacteria
with a size of <0.4 µm are at the limit of resolution
of the light microscope, whereas the largest
whales may grow to 30 m in length, eight orders of
magnitude larger. The span in biomass is nearly
the third power of this difference, less than (10
8
)
3
or about 10
22
(since whales are not spherical),
which is comparable to the mass ratio between
humans and the entire Earth. It is therefore not
surprising that the world as it appears in the
microscale of bacteria is also vastly different from
the world we humans can perceive and from which
we have learned to appreciate the physical laws of
nature. These are the classical laws of Newton,
relating mass, force and time with mass movement
and flow and with properties such as acceleration,
inertia and gravitation. As we go down in scale
and into the microenvironment of marine bacteria,
these properties lose their significance. Instead,
viscosity becomes the strongest force and molecular diffusion the fastest transport.
5.2
Life and Environments at Small Scale
the prokaryotic organisms has developed at a
genetic level, based on sequence analyses of
small-subunit ribosomal RNA (16S rRNA), which
now allows a phylogenetic identification of
microorganisms, even of those that have not yet
been isolated and studied in laboratory cultures.
This has revealed much greater species diversity
than had been anticipated just a decade ago and
the number of “species” according to this genetic
diversity has reached ca 10.000, or ten-fold more
than the isolated species, and it is rapidly
growing. The RNA and DNA based methods have
for the first time enabled a true quantification of
defined bacterial groups in nature. By the use of
molecular probes that bind specifically to
ribosomal RNA of selected target organisms both
cultured and uncultured bacteria can now be
identified phylogenetically. When such probes are
fluorescently labelled, a sediment sample may be
stained by the probes and individual cells of the
target bacteria can then be observed and counted
directly under a fluorescense microscope. This
technique is called Fluorescence in situ Hybridization (FISH) and has become an indispensable
tool in biogeochemistry.
As an example of the quantification of bacteria,
Llobet-Brossa et al. (1998) found that the total cell
density of microorganisms in sediment from the
German Wadden Sea was up to 4·10
9
cells cm
-3
.
Such a population density of several billion microorganisms in a teaspoon of mud is typical of
coastal marine sediments. Of all these cells, up to
73% could be identified by FISH as eubacteria and
up to 45% were categorized to known groups of
eubacteria. The sulfate reducing bacteria comprised some 10-15% of the identified microorganisms,
while other members of the group proteobacteria
comprised 25-30%. Surprisingly, members of the
Cytophaga-Flavobacterium group were the most
abundant in all sediment layers. These bacteria are
specialized in the degradation of complex macromolecules and their presence in high numbers
indicates their role in the initial hydrolytic degradation of organic matter.
Such studies of the spatial distribution of
bacteria provide information on where they may
be actively transforming organic or inorganic
compounds, and thereby indicate which processes are likely to take place. This is particularly
important when chemical species are rapidly
recycled so that the dynamics of their production
or consumption is not easily revealed by geochemical analyses. The introduction of high
resolution tools such as microsensors and
molecular probes has helped to overcome one of
the classical problems in biogeochemistry, namely
to identify the relationship between the processes
that biogeochemists analyze, and the microorganisms who carry them out. The magnitude of this
problem may be appreciated when comparing the
scale of bacteria with that of humans. The bacteria
are generally 1-2 µm large, while we are 1-2 m. As
careful biogeochemists we may use a sediment
sample of only 1 cm
3
to study the metabolism of,
e.g. methane producing bacteria. For the study of
the metabolism of humans, this sample size would
by isometric analogy correspond to a soil volume
of 1000 km
3
. Thus, it is not surprising that very
sensitive methods, such as the use of radiotracers, are often necessary when bacterial
processes are to be demonstrated over short
periods of time (hours-days). It is also obvious,
that a 1 cm
3
sample will include a great diversity of
prokaryotic organisms and metabolic reactions
and that a much higher resolution is required to
sort out the activities of individual cells or
clusters of organisms.
5.2
Life and Environments at
Small Scale
The size spectrum of living organisms and of their
environments is so vast that it is difficult to comprehend (Fig. 5.3). The smallest marine bacteria
with a size of <0.4 µm are at the limit of resolution
of the light microscope, whereas the largest
whales may grow to 30 m in length, eight orders of
magnitude larger. The span in biomass is nearly
the third power of this difference, less than (10
8
)
3
or about 10
22
(since whales are not spherical),
which is comparable to the mass ratio between
humans and the entire Earth. It is therefore not
surprising that the world as it appears in the
microscale of bacteria is also vastly different from
the world we humans can perceive and from which
we have learned to appreciate the physical laws of
nature. These are the classical laws of Newton,
relating mass, force and time with mass movement
and flow and with properties such as acceleration,
inertia and gravitation. As we go down in scale
and into the microenvironment of marine bacteria,
these properties lose their significance. Instead,
viscosity becomes the strongest force and molecular diffusion the fastest transport.
5.2
Life and Environments at Small Scale