(^) In the bathypelagic zone (below 1000 m) where ammonia is essentially
undetectable, archaea most likely utilize organic matter and live heterotrophically.
Bathypelagic archaea have a larger genome size than those in shallower waters
(suggesting an opportunistic lifestyle), and they also have a gene repertoire indicative
of a surface-attached life, e.g. genes for pili (hair-like appendages for attaching to
surfaces) and genes for exoenzymes. Baltar et al. (2009) found a strong correlation
between the distribution of suspended particulate material and electron-transport
activity in waters below 1000 m, further suggesting that deep-water prokaryotic
activity is predominantly located on suspended particles. The relative contributions of
bacteria and archaea to carbon and nitrogen metabolism in the bathypelagic zone
remain to be shown.
Bacterial Abundance and Production in the
Euphotic Zone
(^) Given that the most abundant marine bacteria are not readily cultured, it is
understandable that microbiologists have turned to bulk measures of activity to
evaluate what the typically 10^6 bacteria per milliliter are doing metabolically and in
generating new bacterial biomass. Most of the techniques involve uptake or
metabolism of radio-labeled substrates, but oxygen consumption is also determined as
a measure of microbial respiration. The most widely applied measurements of
bacterial production are based on DNA (Fuhrman & Azam 1982) and protein
(Kirchman et al. 1985) synthesis, with protein now generally preferred (Box 5.1).
Box 5.1 Determination of bacterial growth rates
(^) Thymidine, a constituent needed for replication of DNA, is added to seawater samples as tritiated
thymidine (abbreviated TdR, Thymine deoxyRibose). The choice of [H^3 ]-thymidine (TdR) is dictated
by the fact that it is not utilized in RNA production as are the other three DNA nucleotide bases.
There is also evidence that thymidine is not taken up by eukaryotes or cyanobacteria using nM
concentrations in short incubations. Thus, it is strictly indicative of heterotrophic, bacterial activity.
Thus, samples need not be filtered with a large pore filter to remove non-bacterial organisms before
the measurement, avoiding disruptive effects of filtration. It is assumed that tritium in thymidine
taken up and not metabolized is returned to the medium. After a short incubation under simulated
natural conditions (temperature, light), the bacteria are filtered out (using very small pores), then
radioassayed for their tritium activity. Incorporated TdR is taken to be a measure of cell reproduction
by the bacteria. The results are compared to calibrations done as follows. A culture is established by
removing grazers from a seawater sample by relatively coarse filtration (∼1.0 μm) and then by
diluting the filtrate with bacteria-free, filtered (∼0.2 μm) seawater, typically at a ratio of 9 : 1. Next,
the increase of bacterial numbers is traced by direct counts under natural habitat conditions of
temperature and light over a period of several days to a week. Uptake of TdR is measured repeatedly
in small samples of the culture throughout this incubation. Assuming exponential growth, the
bacterial increase, which can be determined by direct counts, provides a measure of growth rate,
dN/dt = μN. It is expected that the change over time in TdR-uptake, v(t) mol h−1, will be proportional