The microbiology of seawater
The world’s oceans cover some 70 per cent of the Earth’s surface and have a fairly constant salt content of 3.5 per cent (w/v). The depth to which light can penetrate varies, but is limited to the first 100 metres or so. A world of permanent darkness exists at greater depths, however in spite of the absence of photosynthesis, oxygen is often still present. This is because the generally low levels of mineral nutrients in seawater limit the amount of primary production, and therefore heterotrophic activity. At extreme depths, however, anoxic conditions prevail.
Compared to freshwater habitats, marine ecosystems show much less variability in both temperature and pH, although there are exceptions to this general rule. A more pertinent issue in marine environments is that of pressure; this increases progressively in deeper waters, and at 1000 metres reaches around 100 times normal atmospheric pressure. Concomitant with this increase in pressure is a decrease in temperature and nutrients. Surprisingly, however, certain members of the Archaea have been isolated even from these extreme conditions.
In contrast to terrestrial ecosystems, where plants are responsible for most of the energy fixation via photo-synthesis, marine primary production is largely micro-bial, in the shape of members of the phytoplankton. As we have seen, such forms are restricted to those zones where light is able to penetrate. Also found here may be protozoans and fungi that feed on the phytoplankton. Because of thehigh salt concentration of seawater, the bacteria that are typically found in such environments differ from those in freshwater. In the last decade or so, the presence of ultramicrobacteria has been detected in marine ecosystems at relatively high densities; these are around one-tenth of the size of ‘normal’ bacteria. Marine bacteria are of necessity halophilic. Anaerobic decomposing bacteria inhabit the benthic zone, carrying out reactions similar to those that occur in freshwater sediments, whilst the profundal zone is largely free of microbial life.
Detection and isolation of microorganisms in the environment
As we emphasised in the last, microorganisms rarely, if ever, exist in nature as pure cultures but rather form mixed populations. Methods are required, therefore, for the detection and isolation of specific microbial types from such mixtures. The traditional method of isolation is the use of an enrichment culture. As examples, aerobic incubation with a supply of nitrite would assist in the isolation of nitrifying bacteria such as Nitrobacterfrom mud or sewage, whilst a minimal medium containing FeSO4 at pH 2 would encourage the isolation of A. ferrooxidans from a water sample.
We now know however that there are many types of microorganism in the environment that have so far resisted all attempts to culture them in the laboratory (often referred to as viable but non-culturable). The use of modern molecular techniques has helped us to identify the existence of a much broader range of bacteria and archaea than had previously been thought to exist. The extreme sensitivity of such methods means that we are able to demonstrate the presence of even a single copy of a particular bacterium in a mixed population. One such technique is called fluorescence in situ hybridisation (FISH). This uses a probe comprising a short sequence of single-stranded DNA or RNA that is unique to a particular microorganism, attached to a fluorescent dye. The microorganisms are fixed to a glass slide and incubated with the probe. The rules of base pairing in nucleic acids mean that the probe will seek out its complementary sequence, and cells carrying this sequence can be visualised under a fluorescence microscope. The most commonly used ‘target’ is ribosomal RNA, since this shows sequence variation from one microbial type to another, and because there are multiple copies within each cell, providing a stronger response. The polymerase chain reaction (PCR) is another valuable tool in the identification of specific nucleic acid sequences. Other methods, not dependent on DNA, include the use of fluorescence-labelled antibodies raised against specific microorganisms.