Using 13C enriched acetate in isotope labelling incubation experiments: a note of caution.

Vapour-phase fumigation with HCl is routinely used to remove inorganic carbon in preparation for the measurement of the concentration and δ13C value of organic carbon in a sample using elemental analysis coupled to an isotope ratio mass spectrometer. Acidification of the sample to be analyzed can lead to the loss of low molecular weight conjugate bases as volatile organic acids during the acidification and/or the drying steps following fumigation, through protonation of the conjugate base and volatilization. Such loss could lead to a severe bias in incubation experiments where 13C-enriched compounds such as acetate are used to trace reaction pathways or metabolites in a cultivation medium or a mesocosm for example. In this work, we enriched a carbonate-free freshwater sediment with 1-13C sodium acetate by 5, 10 and 20 ‰ relative to the δ13C value of the natural organic carbon of the sediment, and then tested the effects of HCl fumigation, drying at 50 °C and drying at room temperature, alone or in combination, on the measured δ13C values. We found that fumigation and drying at 50 °C, alone or in combination, both lead to the loss of the majority of the 13C-enriched acetate spike.

The Ubiquitous Soil Terpene Geosmin Acts as a Warning Chemical.

Known as the smell of earth after rain, geosmin is an odorous terpene detectable by humans at picomolar concentrations. Geosmin production is heavily conserved in actinobacteria, myxobacteria, cyanobacteria, and some fungi, but its biological activity is poorly understood. We theorized that geosmin was an aposematic signal used to indicate the unpalatability of toxin-producing microbes, discouraging predation by eukaryotes. Consistent with this hypothesis, we found that geosmin altered the behavior of the bacteriophagous nematode Caenorhabditis elegans on agar plates in the absence of bacteria. Normal movement was restored in mutant worms lacking differentiated ASE (amphid neurons, single ciliated endings) neurons, suggesting that geosmin is a taste detected by the nematodal gustatory system. In a predation assay, geosmin and the related terpene 2-methylisoborneol reduced grazing on the bacterium Streptomyces coelicolor. Predation was restored by the removal of both terpene biosynthetic pathways or the introduction of C. elegans that lacked differentiated ASE taste neurons, leading to the apparent death of both bacteria and worms. While geosmin and 2-methylisoborneol appeared to be nontoxic, grazing triggered bacterial sporulation and the production of actinorhodin, a pigment coproduced with a number of toxic metabolites. In this system, geosmin thus appears to act as a warning signal indicating the unpalatability of its producers and reducing predation in a manner that benefits predator and prey. This suggests that molecular signaling may affect microbial predator-prey interactions in a manner similar to that of the well-studied visual markers of poisonous animal prey. IMPORTANCE One of the key chemicals that give soil its earthy aroma, geosmin is a frequent water contaminant produced by a range of unrelated microbes. Many animals, including humans, are able to detect geosmin at minute concentrations, but the benefit that this compound provides to its producing organisms is poorly understood. We found that geosmin repelled the bacterial predator Caenorhabditis elegans in the absence of bacteria and reduced contact between the worms and the geosmin-producing bacterium Streptomyces coelicolor in a predation assay. While geosmin itself appears to be nontoxic to C. elegans, these bacteria make a wide range of toxic metabolites, and grazing on them harmed the worms. In this system, geosmin thus appears to indicate unpalatable bacteria, reducing predation and benefiting both predator and prey. Aposematic signals are well known in animals, and this work suggests that metabolites may play a similar role in the microbial world.

Influence of dose-death interval on colchicine and metabolite distribution in decomposed skeletal tissues.

The semi-quantitative analysis of decomposed bone of rats exposed to colchicine and euthanized following different time intervals postexposure (i.e., dose-death interval, DDI) is described. Rats received colchicine (50 mg/kg, i.p.) and were euthanized 30 min (DDI1; n = 4), 60 min (DDI2; n = 4), or 180 min (DDI3; n = 4) postdose. Drug-free animals (n = 3) served as negative controls. Perimortem heart plasma was collected. Remains were decomposed to skeleton outdoors and then collected and sorted (skull, vertebrae, rib, pelvis, femur, tibia). Bones were dried, pulverized, and prepared by microwave-assisted extraction and microplate solid-phase extraction (MAE-MPSPE), followed by analysis for colchicine, 3-demethylcolchicine (3DMC), and 2-demethylcolchicine (2DMC) by ultra-high-performance liquid chromatography with photodiode array detection (UHPLC-PDA) at 350 nm. Bone type was a main effect (Kruskall-Wallis, p < 0.05) with respect to drug level (expressed as mass-normalized response ratio, RR/m) for each analyte, at each DDI. For all samples, DDI was a main effect (Kruskall-Wallis, p < 0.05) with respect to analyte level, and the ratio of analyte levels (RR3DMC/RRCOLCH, RR2DMC/RRCOLCH, and RR2DMC/RR3DMC). Bone COLCH levels varied by 19-fold, 12-fold, and 60-fold across all bone types in the DDI1, DDI2, and DDI3 groups, respectively. Bone 3DMC levels varied by 12-fold, 11-fold and 17-fold across all bone types in the DDI1, DDI2, and DDI3 groups, respectively. Bone 2DMC levels varied by 20-fold, 14-fold, and 14-fold across all bone types in the DDI1, DDI2, and DDI3 groups, respectively. Values of RR3DMC/RRCOLCH varied by 16-fold, 5-fold, and 5-fold across all bone types in the DDI1, DDI2, and DDI3 groups, respectively. Values of RR2DMC/RRCOLCH varied by 10-fold, 6-fold, and 12-fold across all bone types in the DDI1, DDI2, and DDI3 groups, respectively. Values of RR2DMC/RR3DMC varied by 3-fold, 5-fold, and 2-fold across all bone types in the DDI1, DDI2, and DDI3 groups, respectively. Measured analyte levels in bone correlated poorly with corresponding levels in blood (r = -0.65-+0.31). Measured values of RR2DMC/RRCOLCH and RR2DMC/RR3DMC in bone also correlated poorly with corresponding values in blood. Measured values of RR3DMC/RRCOLCH were well correlated with corresponding blood levels for all bone types except skull (r = 0.91-0.97).