Degradation of macroalgal detritus in shallow coastal Antarctic sediments.

Glaciers along the western Antarctic Peninsula are retreating at unprecedented rates, opening up sublittoral rocky substrate for colonization by marine organisms such as macroalgae. When macroalgae are physically detached due to storms or erosion, their fragments can accumulate in seabed hollows, where they can be grazed upon by herbivores or be degraded microbially or be sequestered. To understand the fate of the increasing amount of macroalgal detritus in Antarctic shallow subtidal sediments, a mesocosm experiment was conducted to track 13C- and 15N-labeled macroalgal detritus into the benthic bacterial, meiofaunal, and macrofaunal biomass and respiration of sediments from Potter Cove (King George Island). We compared the degradation pathways of two macroalgae species: one considered palatable for herbivores (the red algae Palmaria decipiens) and other considered nonpalatable for herbivores (the brown algae Desmarestia anceps). The carbon from Palmaria was recycled at a higher rate than that of Desmarestia, with herbivores such as amphipods playing a stronger role in the early degradation process of the Palmaria fragments and the microbial community taking over at a later stage. In contrast, Desmarestia was more buried in the subsurface sediments, stimulating subsurface bacterial degradation. Macrofauna probably relied indirectly on Desmarestia carbon, recycled by bacteria and microphytobenthos. The efficient cycling of the nutrients and carbon from the macroalgae supports a positive feedback loop among bacteria, microphytobenthos, and meiofaunal and macrofaunal grazers, resulting in longer term retention of macroalgal nutrients in the sediment, hence creating a food bank for the benthos.

Critical transitions in suspended sediment dynamics in a temperate meso-tidal estuary.

There is growing consensus that human interventions can fundamentally change fine sediment transport in estuaries. Critical transitions in response to human interventions have been hypothesized based on indirect observational evidence and theoretical understanding. So far direct evidence has been lacking. Based on a 20 year data-set of surface suspended particulate matter (SPM) concentrations, we present empirical evidence of critical transitions in a temperate meso-tidal estuary. In 2008-2009 the SPM dynamics of the Scheldt estuary (Belgium/The Netherlands) changed dramatically. Not only did the total amount of sediment in suspension increase, a new maximum turbidity zone (MTZ) at typical winter discharges appeared. At intermediate and low summer discharges the longitudinal distribution of SPM now flickers between two markedly different states. Our data suggest that a range of human interventions (fairway widening and deepening, dredging and dumping activities) set the scene leading to the observed transitions. Moreover the freshwater MTZ in the Scheldt and in its major tributary exhibit an increasing sensitivity towards freshwater discharge, coinciding with water quality improvements. This suggests large scale impacts of changes in eutrophication status on estuarine sediment dynamics. This has largely been a blind spot in morphodynamic research.

False-positive rifampicin resistance on Xpert® MTB/RIF caused by a silent mutation in the rpoB gene.

The Xpert® MTB/RIF assay detects the presence of Mycobacterium tuberculosis and its resistance to rifampicin (RMP) directly in sputum samples. Discrepant results were observed in a case of smear-positive pulmonary tuberculosis that was Xpert-resistant but phenotypically susceptible to RMP. Complementary investigations (repeat Xpert, Genotype®MTBDRplus assay and sequencing of the rpoB gene) revealed the presence of a silent mutation in the rpoB gene, leading to the conclusion of a false-positive Xpert result. As misinterpretation of Xpert results may lead to inappropriate treatment, the presence of rpoB mutations should be confirmed by sequencing the rpoB gene.

Combining monitoring data and modeling identifies PAHs as emerging contaminants in the arctic.

Protecting Arctic ecosystems against potential adverse effects from anthropogenic activities is recognized as a top priority. In particular, understanding the accumulation and effects of persistent organic pollutants (POPs) in these otherwise pristine ecosystems remains a scientific challenge. Here, we combine more than 20,000 tissue concentrations, a food web bioaccumulation model, and time trend analyses to demonstrate that the concentrations of legacy-POPs in the Barents/Norwegian Sea fauna decreased 10-fold between 1985 and 2010, which reflects regulatory efforts to restrict these substances. In contrast, concentrations of fossil fuel derived PAHs in lower trophic levels (invertebrates and fish) increased 10 to 30 fold over the past 25 years and now dominate the summed POP burden (25 POPs, including 11 PAHs) in these biota. Before 2000, PCBs dominated the summed POP burden in top predators. Our findings indicate that the debate on the environmental impacts of fossil fuel burning should move beyond the expected seawater temperature increase and examine the possible environmental impact of fossil fuel derived PAHs.

Uncertainties in ecological, chemical and physiological parameters of a bioaccumulation model: implications for internal concentrations and tissue based risk quotients.

Bioaccumulation models predict internal contaminant concentrations (c(i)) using ecological, chemical and physiological parameters. Here we analyse the effect of uncertainties on these parameters on bioaccumulation model predictions. Simultaneously considering the uncertainties on all these parameters in a bioaccumulation model resulted in uncertainty ranges of c(i) that increased with the octanol water partition coefficient K(ow) and reached maxima of up to 1.25 log units for mesozooplankton and up to 1.45 log units fish at logK(ow)=8. A global sensitivity analysis (SA) was performed to rank the contribution of different parameters to the observed uncertainty. The SA demonstrated that this interspecies difference resulted predominantly from uncertain production rates of fish. The K(ow), the water concentration and organic carbon-octanol proportionality constant were important drivers of uncertainty on c(i) for both species. A tissue based risk quotient (RQ(tissue)) combining uncertainty on c(i) with realistic tissue based effect thresholds indicated that fish were up to 10 times more probable to have RQ(tissue)>1 than mesozooplankton, depending on the considered threshold value. Conventional exposure based risk quotients were up to 5 times less probable to exceed one than were corresponding RQ(tissue), and this for both species.

Inferring chemical effects on carbon flows in aquatic food webs: methodology and case study.

The majority of ecotoxicological enclosure experiments monitor species abundances at different chemical concentrations. Here, we present a new modelling approach that estimates changes in food web flows from such data and show that population- and food web level effects are revealed that are not apparent from abundance data alone. For the case of cypermethrin in freshwater enclosures, photosynthesis and excretion (d(-1)) of phytoplankton at 3.643 microg L(-1) cypermethrin were 30% lower and 100% higher than in the control, respectively. The ingestion rate of mesozooplankton (d(-1)) was 6 times higher in the treated enclosures than in the control as food concentration increased with insecticide exposure. With increasing cypermethrin concentrations, nanoflagellates progressively relied on phytoplankton as their main food source, which rendered the food web less stable. We conclude that this tool has excellent potential to analyse the wealth of enclosure data as it only needs species abundance and general constraints.

Disruption of adhC reveals a large duplication in the Mycobacterium smegmatis mc(2)155 genome.

Disruption of the adhC gene of Mycobacterium smegmatis mc(2)155, by standard gene replacement methods, revealed that there are two copies of this gene within a large duplication of the M. smegmatis mc(2)155 genome. M. smegmatis AdhC(+/-) and M. smegmatis AdhC(-/-) mutants were obtained when one or two adhC copies, respectively, were disrupted by homologous recombination. Southern blot analysis of DraI restriction digests of the DNA from these mutants and from wild-type M. smegmatis mc(2)155, resolved by PFGE, showed that the duplication size may be at least approximately 250 kb. The single and double knockout mutants were characterized and compared with the M. smegmatis wild-type. A growth disadvantage and a different morphology were associated with the loss of expression of one or both of the adhC copies, but both mutants were still acid-fast. Findings in this study indicate that the process of chromosomal duplication in M. smegmatis is ongoing and remains a potent source of genome dynamics. Hence, the M. smegmatis mc(2)155 genome might be larger than previously thought.

Molecular and biochemical characterisation of Mycobacterium smegmatis alcohol dehydrogenase C.

The gene encoding of an alcohol dehydrogenase C (ADHC) from Mycobacterium smegmatis was cloned and sequenced. The protein encoded by this gene has 78% identity with Mycobacterium tuberculosis and Mycobacterium bovis BCG ADHC. The M. smegmatis ADHC was purified from M. smegmatis and the kinetic parameters of this enzyme showed that using NADPH as electron donor it has a strong preference for aliphatic and aromatic aldehyde substrates. Like the M. bovis BCG ADHC, this enzyme is more likely to act as an aldehyde reductase than as an alcohol dehydrogenase. The discovery of such an ADHC in a fast-growing, and easily engineered mycobacterial species opens the way to the utilisation of this M. smegmatis enzyme as a convenient model for the study of the physiological role of this alcohol dehydrogenase in mycobacteria.

Evidence for specific and non-covalent binding of lipids to natural and recombinant Mycobacterium bovis BCG hsp60 proteins, and to the Escherichia coli homologue GroEL.

Heat-shock proteins (Hsps) from various origins are known to share a conserved structure and are assumed to be key partners in the biogenesis of proteins. Fractionation of the mycobacterial Hsp60, a 65 kDa protein also called Cpn60, from Mycobacterium bovis BCG zinc-deficient culture filtrate on phenyl-Sepharose followed by Western blotting revealed the existence of four Hsp60-1 and Hsp60-2 forms, based on their hydrophobicity behaviour. Hsp60-2 species were further purified by ion-exchange chromatography and partial amino acid sequences of cyanogen bromide (CNBr) peptides of purified Hsp60-2 species showed identity with the amino acid sequence deduced from the hsp60-2 gene, indicating that the various Hsp60-2 forms are encoded by the same gene. In addition, the mycobacterial Hsp60-2 was overexpressed in E. coli using the pRR3Hsp60-2 plasmid and analysed on phenyl-Sepharose. The elution pattern of the recombinant Hsp60-2, as well as that of Escherichia coli GroEL, was similar to that of the native Hsp60-2 from the culture filtrate of M. bovis BCG and entirely different from that of the mycobacterial antigen 85. Extraction of mycobacterial Hsp60-2 forms, recombinant BCG Hsp60-2 and E. coli GroEL with organic solvents releases various amounts of non-covalently bound lipids. The presence of lipids on Hsp60-2 was confirmed by labelling M. bovis BCG with radioactive palmitate. The radioactivity was specifically associated with Hsp60 in the aqueous phase and the 19 and 38 kDa lipoproteins in the Triton X-114 phase. Analysis of the lipids extracted from purified Hsp60-2, recombinant BCG Hsp60-2 and E. coli GroEL by TLC showed the same pattern for all the samples. Acid methanolysis of the lipids followed by GC analysis led to the identification of C(16:0), C(18:0) and C(18:1) as the major fatty acyl constituents, and of methylglycoside in these proteins. Altogether, these data demonstrate that lipids are non-covalently bound to Hsp60-2 and homologous proteins.

Overexpression, purification and characterization of Mycobacterium bovis BCG alcohol dehydrogenase.

A previous study of the effect of zinc deprivation on Mycobacterium bovis BCG pointed out the potential importance of an alcohol dehydrogenase for maintaining the hydrophobic character of the cell envelope. In this report, the effect of the overexpression of the M. bovis BCG alcohol dehydrogenase (ADH) in Mycobacterium smegmatis and M. bovis BCG is described. The purification of the enzyme was performed to apparent homogeneity from overexpressing M. bovis BCG cells and its kinetic parameters were determined. The enzyme showed a strong preference for both aromatic and aliphatic aldehydes while the corresponding alcohols were processed 100-1000-fold less efficiently. The best kcat/Km values were found with benzaldehyde > 3-methoxybenzaldehyde > octanal > coniferaldehyde. A phylogenetic analysis clearly revealed that the M. bovis BCG ADH together with the ADHs from Bacillus subtilis and Helicobacter pylori formed a sister group of the class C medium-chain alcohol dehydrogenases, the plant cinnamyl alcohol dehydrogenases (CADs). Comparison of the kinetic properties of our ADH with some related class C enzymes indicated that the mycobacterial enzyme substrate profile resembled that of the CADs involved in plant defence rather than those implicated in lignification. A possible role for the M. bovis BCG ADH in the biosynthesis of the lipids composing the mycobacterial cell envelope is proposed.