Identifying labile DOM components in a coastal ocean through depleted bacterial transcripts and chemical signals

Abstract

Understanding which compounds comprising the complex and dynamic marine dissolved organic matter (DOM) pool are important in supporting heterotrophic bacterial production remains a major challenge. We eliminated sources of labile phytoplankton products, advected terrestrial material and photodegradation products to coastal microbial communities by enclosing water samples in situ for 24 h in the dark. Bacterial genes for which expression decreased between the beginning and end of the incubation and chemical formulae that were depleted over this same time frame were used as indicators of bioavailable compounds, an approach that avoids augmenting or modifying the natural DOM pool. Transport- and metabolism-related genes whose relative expression decreased implicated osmolytes, carboxylic acids, fatty acids, sugars and organic sulfur compounds as candidate bioreactive molecules. FT-ICR MS analysis of depleted molecular formulae implicated functional groups ~ 30-40 Da in size cleaved from semi-polar components of DOM as bioreactive components. Both gene expression and FT-ICR MS analyses indicated higher lability of compounds with sulfur and nitrogen heteroatoms. Untargeted methodologies able to integrate biological and chemical perspectives can be effective strategies for characterizing the labile microbial metabolites participating in carbon flux.

Dissolved Organic Matter Composition in a Marsh‐Dominated Estuary: Response to Seasonal Forcing and to the Passage of a Hurricane

“…This is consistent with biodegradation not explaining the dominant patterns of DOM composition variability observed in the system (Figures 5a, 5b, and 7). We note that a fraction of the decreased DOC measured during the experiments likely encompassed components of the DOM pool that cannot be detected by the techniques used here (Vorobev et al, 2018). For example, saccharides are known to be labile (Kirchman et al, 2001;Rich et al, 1996), but they are not well retained by SPE.…”

Molecular characteristics of microbially mediated transformations of Synechococcus‐derived dissolved organic matter as revealed by incubation experiments

“…However, the chemical complexity of DOM pools and the genetic diversity of microorganisms involved in their cycling has hindered our understanding of their interactions. The development of high throughput DNA sequencing approaches has led to the recognition of diverse marine bacterial communities and metabolic functions via a large number of studies (Zhang et al ., ; Bergauer et al ., ; Vorobev et al ., ). Concomitantly, ultrahigh‐resolution mass spectrometry, Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR MS), has been widely used to analyse complex marine DOM reservoirs (Koch et al ., ; Osterholz et al ., ; Rossel et al ., ; Medeiros et al ., ; Vorobev et al ., ).…”

Highly variable mRNA half‐life time within marine bacterial taxa and functional genes

“…Alc. Vorobev et al, 2018). The high transcript abundance of Enterobacteriaceae and other bacteria detected in this study might be due to the close vicinity of the sampling location to a fish cannery, releasing high amounts of untreated wastewater (Paliaga et al, 2017).…”

“…), but no significant correlations between the relative abundance and T 1/2 were found. The families Vibrionaceae and Rhodospirillaceae are among the most abundant bacterial families in the coastal northern Adriatic Sea (Steiner et al ., unpublished), and frequently are the most active taxa in marine environmental communities (McCarren et al ., ; Bergauer et al ., ; Vorobev et al ., ). The high transcript abundance of Enterobacteriaceae and other bacteria detected in this study might be due to the close vicinity of the sampling location to a fish cannery, releasing high amounts of untreated wastewater (Paliaga et al ., ).…”