to 2 × 10^6 cells ml−1 – huge values compared to plate counts. This method continues
in use with very little change, except that other stains, including DAPI, YoPro and
SYBR, are often substituted for acridine orange (Plate 5.1).
(^) Within a very short time, microbiologists were making direct counts at every depth
in every part of the world ocean. They were also faced with an array of new questions
for which some answers are in, but many are still under study. What is the biological
character and activity of these numerous bacteria that don’t grow readily on seawater
agar? Why do they not respond to the stimulus of food enrichment and form plate
colonies? Are they “oligotrophs”, essentially poisoned by concentrated molecular
food? Are all of the cells alive, or, if alive, are they metabolically active? If they are
metabolically active, how fast are they growing and respiring? What different kinds of
bacteria are present in the mixture? What controls their abundance? What is their role
in the elemental cycles of the sea and the biosphere generally? All of these questions
were immediately obvious when AODCs first became available. Some of them were
also evident in basic respirometry studies of coastal waters. There was more
respiration in filtrates than could be accounted for by plate-count bacteria. Pomeroy
(1974) listed the questions in a paper considered a founding manifesto of modern
marine microbiology. So, after some biological preliminaries, we will review the
status of those questions.
Prokaryotes
(^) These are the cellular organisms having no nuclear membrane surrounding a
specialized cell organelle (nucleus or “karyon”) housing DNA and processing its
information. Rather, the strands of genetic material in prokaryotes are suspended
within the general cytoplasm of the cell, although there may be differentiation of a
subregion of the cell, a nucleoid, specialized for genetic processes. Based on
biochemical and genetic sequence differences, two strongly distinct prokaryote
groups, often now termed “Domains”, are recognized, the Archaea and the Bacteria.
Controversy exists over whether the term “prokaryote” is still valid. Pace (2006)
argues that since Archaea and Bacteria are not monophyletic, the term “prokaryote” is
obsolete. However, others find the term useful for grouping organisms without nuclei
(Whitman 2009). We choose to continue using the prokaryote/eukaryote distinction
here, but remind the reader that this distinction does not involve an evolutionary
relationship.
Archaea
(^) Microbiologists have only recognized this group as strongly distinct since the mid-
1970s, initially from the sequence difference of their ribosomal RNA (see below)