Geoscience Reference
In-Depth Information
concentrations (e.g., Yamashita and Tanoue,
2003
). Proteins and their degradation products
are thought to comprise a biodegradable fraction of DOM preferred by bacteria. Thus, it is
widely assumed that among a sample set, the relative amount of amino acid-like FDOM is
an indication of the presence and proportion of labile organic carbon and nitrogen present
(Hudson et al.,
2008
and references therein; Fellman et al., 2009 a,b; Hood et al.,
2009
).
However, although amino acid-like FDOM may serve as a proxy measurement for bio-
available DOM, we currently do not understand the relationships among bacterial meta-
bolic activity, bacterial degradation of DOM, and the presence of amino acid-like FDOM
signals (e.g., Cammack et al.,
2004
). For example, laboratory incubation and field meso-
cosm studies have shown that bacterial degradation can be a source and a sink for amino
acid-like FDOM (Moran et al.,
2000
; Yamashita and Tanoue,
2003
; Boyd and Osburn,
2004
; Cammack et al.,
2004
; Stedmon and Markager,
2005b
, Nieto-Cid et al.,
2006
), which
has contributed to the difficulty in unambiguously relating amino acid-like FDOM signals
to DOM bioavailability. In some bacterial incubation studies, this fluorescence has been
shown to increase as a function of incubation time (Moran et al.,
2000
; Cammack et al.,
2004
; Boyd and Osburn,
2004
), whereas in other studies with a different source of DOM,
it decreases as a function of incubation time (Yamashita and Tanoue,
2004
; Stedmon and
Markager,
2005b
; Nieto-Cid et al.,
2006
).
There are several possible mechanisms for the production and removal of amino acid-
like FDOM observed during bacterial degradation of DOM. In one case, this material is
simply a byproduct of DOM degradation by bacteria. For example, it is possible that bac-
terial degradation of protein residues may lead to conformational changes (denaturation)
that increase fluorescence from tryptophan and tyrosine residues (Determann et al.,
1998
;
Lakowicz,
2006
). This scenario would lead to an increase in amino acid-like FDOM sig-
nals, which does not necessarily reflect a direct product of bacterial degradation. Here the
accumulation of amino acid-like FDOM as a function of incubation time indicates either
that this material is not being consumed by bacteria, or that the bacterial uptake rate is less
than the production rate (positive net production).
An alternative explanation for the production of amino acid-like FDOM as a function
of incubation time is that bacteria directly produce the material during biosynthesis and
growth. For example, Cammack et al. (
2004
) hypothesized that amino acid-like FDOM
was a product of bacterial growth, based on strong, positive correlations between bacterial
growth rates and fluorescence. However, the formation pathways and form of fluorescent
moieties produced directly by bacteria during degradation of DOM have not been deter-
mined and remain unclear; for example, would these constituents leak from bacterial cells
and if so under what conditions? In addition, fluorescent amino acids are energetically
costly to produce (Akashi et al.,
2002
), so it is less likely that fluorescent amino acids would
accumulate over time unless bacteria are experiencing little or no limitation to growth.
In either the first or second case, the presence of amino acid-like FDOM is likely an
indication of the presence of bioavailable DOM. In the first case, accumulation of this fluo-
rescence as a function of incubation time indicates that bacteria preferentially consume
other labile DOM fractions, while concurrently (and indirectly) increasing amino acid-like
