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Characterizing low molecular weight (LMW) dissolved organic matter (DOM) in soils and evaluating the availability of this labile pool is critical to understanding the underlying mechanisms that control carbon storage or release across terrestrial systems. However, due to wide-ranging physicochemical diversity, characterizing this complex mixture of small molecules and how it varies across space remains an analytical challenge. Here, we evaluate an untargeted approach to detect qualitative and relative-quantitative variations in LMW DOM with depth using water extracts from a soil core from the Alaskan Arctic, a unique system that contains nearly half the Earth's terrestrial carbon and is rapidly warming due to climate change. We combined reversed-phase and hydrophilic interaction liquid chromatography, and nano-electrospray ionization coupled with high-resolution tandem mass spectrometry in positive- and negative-ionization mode. The optimized conditions were sensitive, robust, highly complementary, and enabled detection and putative annotations of a wide range of compounds (e.g. amino acids, plant/microbial metabolites, sugars, lipids, peptides). Furthermore, multivariate statistical analyses revealed subtle but consistent and significant variations with depth. Thus, this platform is useful not only for characterizing LMW DOM, but also for quantifying relative variations in LMW DOM availability across space, revealing hotspots of biogeochemical activity for further evaluation.

This corrects the article DOI: 10.1038/srep43355.

Clostridium (Ruminiclostridium) thermocellum is a model organism for its ability to deconstruct plant biomass and convert the cellulose into ethanol. The bacterium forms biofilms adherent to lignocellulosic feedstocks in a continuous cell-monolayer in order to efficiently break down and uptake cellulose hydrolysates. We developed a novel bioreactor design to generate separate sessile and planktonic cell populations for omics studies. Sessile cells had significantly greater expression of genes involved in catabolism of carbohydrates by glycolysis and pyruvate fermentation, ATP generation by proton gradient, the anabolism of proteins and lipids and cellular functions critical for cell division consistent with substrate replete conditions. Planktonic cells had notably higher gene expression for flagellar motility and chemotaxis, cellulosomal cellulases and anchoring scaffoldins, and a range of stress induced homeostasis mechanisms such as oxidative stress protection by antioxidants and flavoprotein co-factors, methionine repair, Fe-S cluster assembly and repair in redox proteins, cell growth control through tRNA thiolation, recovery of damaged DNA by nucleotide excision repair and removal of terminal proteins by proteases. This study demonstrates that microbial attachment to cellulose substrate produces widespread gene expression changes for critical functions of this organism and provides physiological insights for two cells populations relevant for engineering of industrially-ready phenotypes.

Clostridium thermocellum could potentially be used as a microbial biocatalyst to produce renewable fuels directly from lignocellulosic biomass due to its ability to rapidly solubilize plant cell walls. While the organism readily ferments sugars derived from cellulose, pentose sugars from xylan are not metabolized. Here, we show that non-fermentable pentoses inhibit growth and end-product formation during fermentation of cellulose-derived sugars. Metabolomic experiments confirmed that xylose is transported intracellularly and reduced to the dead-end metabolite xylitol. Comparative RNA-seq analysis of xylose-inhibited cultures revealed several up-regulated genes potentially involved in pentose transport and metabolism, which were targeted for disruption. Deletion of the ATP-dependent transporter, CbpD partially alleviated xylose inhibition. A putative xylitol dehydrogenase, encoded by Clo1313_0076, was also deleted resulting in decreased total xylitol production and yield by 41% and 46%, respectively. Finally, xylose-induced inhibition corresponds with the up-regulation and biogenesis of a cyclical AgrD-type, pentapeptide. Medium supplementation with the mature cyclical pentapeptide also inhibits bacterial growth. Together, these findings provide new foundational insights needed for engineering improved pentose utilizing strains of C. thermocellum and reveal the first functional Agr-type cyclic peptide to be produced by a thermophilic member of the Firmicutes.