Biological Oceanography

(^) Bacteria have a moderately stout cell wall constructed of a polymer of alternating
acetyl glucosamine and acetyl muramic acid. The chains are strongly cross-linked into
a three-dimensional web by short chains of amino acids. This wall structure is termed
peptidoglycan or murein, a molecular structure diagnostic of Bacteria (see Mathews et
al. 2000). Bacteria tend to dominate the microbial communities of less-extreme
habitats, although forms capable of metabolizing inorganic substrates –
chemolithotrophs and thermophiles – are found among them as well as in the
Archaea, although Archaea survive to greater extremes. All Bacteria (and Archaea)
are specialized in respect to habitat conditions supporting their growth, the substrates
they can consume, and the products generated by their metabolism. Many support
their growth and division using organic matter with energy derived from glycolysis. A
few are more versatile. Some use energy from “inorganic” reactions to drive synthesis
of organic matter.
(^) In a long period after their discovery in the mid-19th century, the tools available for
classifying bacteria were limited. Light microscopy revealed variation in shape and in
presence of fine flagellae. Thus, the classification began with shape: round (coccoid,
e.g. Pneumococcus), tubular (rods, e.g. Bacillus), bent rods (e.g. Vibrio), and helices
(spirochaetes, e.g. Spirillum). Rods are most likely to have flagellae and modest
motility. Most of the rest of the characteristics of bacteria relate to their infectivity and
the biochemistry of both their constituents and the metabolic reactions in which they
participate. Infectious bacteria produce rather specific syndromes and tend to
specialize in respect to hosts, which is a huge and well-studied subject. Bacteria (and
archaea) mediating chemical transformations in natural habitats to derive sustenance
and energy are classified by those reactions. The tendency to specialization makes this
an effective tool. Hans Christian Gram introduced a broad division related to cell-wall
biochemistry by application of iodine and the stain crystal violet to bacteria stuck to
microscope slides. Cells retaining the stain after an alcohol rinse are Gram-positive;
those rinsing clear of it are Gram-negative. Gram-positive bacteria have relatively
simple cell walls in which the outer layer is murein. Gram-negative cell walls
incorporate large fractions of lipoglycans, molecules of mixed lipid and carbohydrate
character, which coat the murein and prevent dye bonding.
(^) The vast majority of free-living pelagic bacteria are coccoid or slightly elongate and
Gram-negative. Some rods are found as well, often with one flagellum. Rods are more
common among bacteria attached to particulate aggregations such as “marine snow”.
The refined stages of classifying bacteria occasionally depend upon morphology
(flagellae present, flagellae absent) and always depend upon determinations of
metabolic activity (oxidase present, oxidase absent). Sochard et al. (1979) provide a
good protocol for this mode of identification, with examples of a marine application.
More recently, bacterial classification is primarily based on nucleic acid structure.