Consumption and release of dissolved organic %%CONV_ERR%%carbon by marine bacteria in a pulsed-substrate environment: from experiments to modelling

Abstract

To investigate the effects of episodic occurrence of dissolved organic carbon (DOC) in the natural environment, bacterial degradation of labile DOC was studied under laboratory-controlled conditions followed by modelling. A single labile DOC compound was periodically added to the experimental culture and its degradation by a monospecific marine bacterial strain was followed. The measured variables were DOC and bacterial biomass determined from the particulate organic carbon values. Experimental dynamics showed a repetition of 2 successive patterns after each DOC pulse: (1) substrate consumption and bacterial growth in the first few hours after substrate addition, followed by (2) bacterial reduction (organic carbon-related) and associated non-labile DOC release within the next few hours. Based on these experimental results, the Dynamic Energy Budget theory was applied for the first time to such conditions to develop a mechanistic model that comprised 7 parameters and 4 state variables in which bacterial biomass was fractionated into reserve and structure compartments. The model was constructed by accounting for a constant specific maintenance rate and comprised 2 different cell maintenance fluxes, one fuelled from cell reserves when substrate was abundant and one from reserves and cell structures when starvation occurred. This new model of bacterial degradation adequately matched experimental measurements and accurately reproduced the accumulation of non-labile DOC in the culture during the experiment. This model can easily be implemented in an aquatic biogeochemical model and could provide better understanding of the role of bacteria in carbon cycling in fluctuating environments.

Increased bacterial growth efficiency with environmental variability: results from DOC degradation by bacteria in pure culture experiments

“…For the sake of simplicity, we changed the model notation in this study to use symbols that fit more with biogeochemical studies. The differences from those used in Eichinger et al (2009) and in this study are provided in Table 1. Briefly, the DEB theory assumes that bacterial biomass is composed of a reserve (E) and structure (V ).…”

“…The DEB model originates from the dynamic energy budget theory (Kooijman, 2000). It has been specifically developed for the conditions in experiment P and its construction has been extensively described in Eichinger et al (2009). For the sake of simplicity, we changed the model notation in this study to use symbols that fit more with biogeochemical studies.…”

“…Pyruvate was selected as the carbon substrate and Alteromonas infernus as the bacterial strain (refer to Eichinger et al, 2009 for the explanations of these choices). Each medium was autoclaved for 20 min at 110 • C prior to inoculation.…”

“…Most biogeochemical models use simplistic and empirical formulae to represent DOC consumption and bacterial growth, which are respectively described with MichaelisMenten kinetics and Monod formulation. Thus they do not take into account cell maintenance, the importance of which has been highlighted in several studies (del Giorgio and Cole, 1998;Eichinger et al, 2009). The second aim of this paper is to highlight the cell maintenance process using biodegradation assays and varying DOC supplies, in order to study how this affects BGE estimates.…”

Towards a simplification of models using regression trees

“…(iii) The a-conditioned domain is classified through a multivariate regression tree until the b-conditioned part of it is efficiently isolated. organisms [5,[30][31][32]. We here work at the scale of a bacterial cell, where only three trophic compartments can be identified: the particulate matter itself, the dissolved matter and the bacteria compartment.…”