Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Major Sources of Organic Matter in a Complex Coral Reef Lagoon: Identification from Isotopic Signatures (δ13C and δ15N)

International audienceA wide investigation was conducted into the main organic matter (OM) sources supporting coral reef trophic networks in the lagoon of New Caledonia. Sampling included different reef locations (fringing, intermediate and barrier reef), different associated ecosystems (mangroves and seagrass beds) and rivers. In total, 30 taxa of macrophytes, plus pools of particulate and sedimentary OM (POM and SOM) were sampled. Isotopic signatures (C and N) of each OM sources was characterized and the composition of OM pools assessed. In addition, spatial and seasonal variations of reef OM sources were examined. Mangroves isotopic signatures were the most C-depleted (-30.17 ± 0.41 ‰) and seagrass signatures were the most C-enriched (-4.36 ± 0.72 ‰). Trichodesmium spp. had the most N-depleted signatures (-0.14 ± 0.03 ‰) whereas mangroves had the most N-enriched signatures (6.47 ± 0.41 ‰). The composition of POM and SOM varied along a coast-to-barrier reef gradient. River POM and marine POM contributed equally to coastal POM, whereas marine POM represented 90% of the POM on barrier reefs, compared to 10% river POM. The relative importance of river POM, marine POM and mangroves to the SOM pool decreased from fringing to barrier reefs. Conversely, the relative importance of seagrass, Trichodesmium spp. and macroalgae increased along this gradient. Overall, spatial fluctuations in POM and SOM were much greater than in primary producers. Seasonal fluctuations were low for all OM sources. Our results demonstrated that a large variety of OM sources sustain coral reefs, varying in their origin, composition and role and suggest that δ13C was a more useful fingerprint than δ15N in this endeavour. This study also suggested substantial OM exchanges and trophic connections between coral reefs and surrounding ecosystems. Finally, the importance of accounting for environmental characteristics at small temporal and spatial scales before drawing general patterns is highlighted

C and N stable isotopes enlighten the trophic behaviour of the dugong (Dugong dugon)

International audienceAbstract The dugong ( Dugong dugon ), a large marine mammal herbivore of the Indo-Pacific, is vulnerable to extinction at a global scale due to a combination of human-related threats including habitat degradation. The species forages on seagrass habitats (marine phanerogams) and plays a key role in the functioning and sensitivity of these declining coastal ecosystems. The trophic behaviour and plasticity of dugong populations in response to extrinsic and intrinsic factors are therefore crucial features to both dugong and seagrass conservation. Yet, this knowledge remains limited to few visual observations and analyses of mouth, stomach or faecal contents of stranded individuals. We take advantage of a long-term monitoring of stranded individuals from the endangered New Caledonian population to depict features of dugongs’ trophic ecology from Carbon and Nitrogen stable isotopes. A total of 59 dugong skin samples were used to portrait the stable isotope niche of dugongs according to their sex and maturity. In light of previous work conducted in New Caledonia, a subset of these samples was used to model the trophic mix of dugong males and females. Our stable isotope mixing models used C and N isotope values of 10 taxa bbelonging to five divisions of metazoans, plants, and chromists. Our results represent the first estimate of the species dietary niche in the isotopic space. They suggest that the diet of dugong calves overlaps more with that of adult females (δ 13 C: − 6.38 ± 1.13 ‰; δ 15 N: 2.49 ± 1.10 ‰) than males (δ 13 C: − 5.92 ± 1.10 ‰; δ 15 N: 3.69 ± 1.28 ‰). Further, we highlight differences in the expected trophic mix of dugong adult males and females. From these, we formulate a sex-specific foraging behaviour hypothesis in dugongs, whereby lactating females could forage over smaller spatial ranges but more diverse food sources thanmales. The study emphasizes the importance of long-term stranding monitoring programs to study the ecology of marine mammals.. Finally, it depicts an ecological feature that may contribute to the sensitivity of vulnerable dugongs to ongoing changes on tropical coastal ecosystems

Spatial variability of metallic and organic contamination of anguilliform fish in New Caledonia

International audienceNew Caledonia is one of the main hot spots of biodiversity on the planet. Large amounts of contaminants are discharged into the lagoon as a result of increasing anthropogenic activities such as intense mining, urbanization and industrialization. Concentrations of 14 trace elements and 26 persistent organic pollutants (POPs: PCBs and pesticides) were measured in the muscles of two anguilliform fish species, over a coast to barrier reef gradient in two lagoon areas differently exposed to anthropic disturbances. This study emphasizes the high trace element contamination status of anguilliform fish and also highlights slight but perceptible organic pollution. The contamination extends throughout the lagoon, from coast to barrier reef, even in areas remote from emission points. High levels of trace elements, especially those linked to mining activities (i.e. Co, Cr, Fe, Mn and Ni), were detected in coastal sites. Furthermore the large dispersion of most POPs throughout the entire lagoon poses the question of their potential toxicity on marine organisms from numerous habitats. Our results underline the need for long term monitoring of various contaminants over large spatial and time scales

Mean δ¹³C and δ¹⁵N isotopic ratios (± sd) of primary producers sampled in the SW lagoon of New Caledonia (data from 2010 and 2011 pooled).

<p>Mean δ¹³C and δ¹⁵N isotopic ratios (± sd) of primary producers sampled in the SW lagoon of New Caledonia (data from 2010 and 2011 pooled).</p

Mean isotopic signatures (± sd) in carbon (δ¹³C) and nitrogen (δ¹⁵N) for the different sources of organic matter sampled along coast-to-ocean gradients, both zones and seasons pooled, in the SW lagoon of New Caledonia in 2011.

<p>POM = particulate organic matter, SOM = sedimentary organic matter, FR = fringing reef, IR = intermediate reef and BR = barrier reef.</p><p>Only sources present on at least two reef types were shown.</p

Relative importance of river POM, marine POM and <i>Trichodesmium</i> spp. (Tricho.) in the isotopic composition of coral reef POM on fringing, intermediate, and barrier reefs.

<p>Shaded boxes represent, from dark to light grey, 50%, 75%, and 95% Bayesian credibility intervals.</p