The pigment that you are describing may be a pyomelanin (also known as
alkaptomelanin). It is produced by the oxidation of homogentisic (HGA) acid
and the polymerization of the oxidation products. We work with several strains
of marine bacteria that produce pyomelanin, the cultures turn dark red
(burgundy) and then dark brown. HGA is produced as a normal intermediate
in the tyrosine catabolic pathway by the enzyme 4-hydroxyphenylpyruvate
dioxigenase (HPPD), when this enzyme is overproduced, there is an excess of
HGA synthesized, which is excreted into the culture medium where it
undergoes oxidation. We have cloned the gene coding for HPPD from several
marine bacteria and observed the same phenomenon in E. coli.
If you don't think that your strain is producing pyomelanin, check out the
book "Pigment Microbiology" (1992) by P.Z. Margalith, which provides an
excellent review on microbial pigments.
Ernesto J. Quintero
Department of Microbiology
University of Maryland, College Park