Influence of bioturbation by the polychaete Nereis diversicolor on the structure of bacterial communities in oil contaminated coastal sediments

Patterns of change in the structure of bacterial communities monitored by ribosomal intergenic spacer analysis (RISA) in oil contaminated sediments inhabited or not by the marine polychaete Nereis diversicolor were studied during 45 days under laboratory conditions. Results supported by principal component analysis showed a marked response of the bacterial communities to the oil contamination and to the presence of N. diversicolor. Phylogenetic affiliation of specific RISA bands showed that, in the contaminated sediments, the presence of the marine polychaetes favoured the development of bacteria which may play an active role in natural bioremediation processes of oil polluted environments

Response of an archaeal community from anoxic coastal marine sediments to experimental petroleum contamination

To achieve a better understanding of the ecological significance of Archaea in relation to petroleum contamination, we examined the composition of archaeal communities in anoxic coastal marine infralittoral sediments and their response to simulated petroleum contamination. Sediments were collected at an experimental site, and half were mixed with oil. Control and oiled sediments were then reworked into PVC cores that were inserted into the sediment at their sampling site at 20 m water depth. After 503 d of in situ incubation, molecular and statistical analyses clearly showed that petroleum contamination induced significant shifts in the composition of archaeal communities inhabiting these anoxic sediments. Overall, contamination led to a significant decrease in diversity. Control sediments were dominated by Crenarchaeota, whereas in oiled sediments,Euryarchaeota became dominant, as attested by the particular contribution of Methanococcoides, Methanosarcina, and Methanolobus sequences. Methanogens could be indirectly related to the degradation of the added hydrocarbons by participating in syntrophic consortia with hydrocarbon-degrading acetogenic bacteria. In addition, the abundance of anaerobic methane-oxidizing Archaea sequences in oiled sediments could indicate that anaerobic oxidation of methane (AOM) occurs at the depth selected for the analyses. Further studies undertaken to quantify vertical distribution of AOM, methanogenic activity, and their potential causative Archaea would help to enhance understanding of this complex petroleum-contaminated sedimentary system

Isolation of hydrocarbon-degrading extremely halophilic archaea from an uncontaminated hypersaline pond (Camargue, France)

International audienceLittle information exists about the ability of halophilic archaea present in hypersaline environments to degrade hydrocarbons. In order to identify the potential actors of hydrocarbon degradation in these environments, enrichment cultures were prepared using samples collected from a shallow crystallizer pond with no known contamination history in Camargue, France, with n-alkanes provided as source of carbon and energy. Five alkane-degrading halophilic archaeal strains were isolated: one (strain MSNC 2) was closely related to Haloarcula and three (strains MSNC 4, MSNC 14, and MSNC 16) to Haloferax. Biodegradation assays showed that depending on the strain, 32 to 95% (0.5 g/l) of heptadecane was degraded after 30 days of incubation at 40A degrees C in 225 g/l NaCl artificial medium. One of the strains (MSNC 14) was also able to degrade phenanthrene. This work clearly shows for the first time the potential role of halophilic archaea belonging to the genera Haloarcula and Haloferax in the degradation of hydrocarbons in both pristine and hydrocarbon-contaminated hypersaline environmen

Alkane biodegradation and dynamics of phylogenetic subgroups of sulfate-reducing bacteria in an anoxic coastal marine sediment artificially contaminated with oil

International audienceFor 503 days, unoiled control and artificially oiled sediments were incubated in situ at 20 m water depth in a Mediterranean coastal area. Degradation of the aliphatic fraction of the oil added was followed by GC–MS. At the same time, terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA encoding genes was used to detect dynamics in the sulfate-reducing bacteria (SRB) community in response to the oil contamination. Specific polymerase chain reaction (PCR) primer sets for five generic or suprageneric groups of SRB were used for PCR amplification of DNA extracted from sediments. During the experiment, hydrocarbons from C17 to C30 were significantly degraded even in strictly anoxic sediment layers. Of the five SRB groups, only two groups were detected in the sediments (control and oiled), namely the Desulfococcus–Desulfonema–Desulfosarcina-like group and the Desulfovibrio–Desulfomicrobium-like group. Statistical analysis of community patterns revealed dynamic changes over time within these two groups following the contamination. Significant differences in community patterns were recorded in artificially oiled compared with control sediments. Cloning and sequencing of 16S rRNA encoding genes performed after 503 days showed that many of the most abundant sequences were closely related to hydrocarbonoclastic SRB which could have played an active role in the observed biodegradation of aliphatic hydrocarbons. Results from the present study provide useful information on the dynamics of dominant SRB in heavily oil-contaminated sediments and their potential for anaerobic biodegradation for the treatment of spilled oil in anoxic marine environments

Fluxomic assay-assisted diagnosis orientation in a cohort of 11 patients with myopathic form of CPT2 deficiency

International audienceCarnitine palmitoyltransferase type 2 (CPT2) deficiency, a mitochondrial fatty acid oxidation disorder (MFAOD), is a cause of myopathy in its late clinical presentation. As for other MFAODs, its diagnosis may be evocated when blood acylcarnitine profile is abnormal. However, a lack of abnormalities or specificity in this profile is not exclusive of CPT2 deficiency. Our retrospective study reports clinical and biological data in a cohort of 11 patients with circulating acylcamitine profile unconclusive enough for a specific diagnosis orientation. In these patients, CPT2 gene studies was prompted by prior fluxomic explorations of mitochondrial beta-oxidation on intact whole blood cells incubated with pentadeuterated ([16-H-2(3), 15-H-2(2)])-palmitate. Clinical indication for fluxomic explorations was at least one acute rhabdomyolysis episode complicated, in 5 of 11 patients, by acute renal failure. Major trigger of rhabdomyolysis was febrile infection. In all patients, fluxomic data indicated deficient CPT2 function showing normal deuterated palmitoylcarnitine (C16-Cn) formation rates associated with increased ratios between generated C16-Cn and downstream deuterated metabolites (Sigma deuterated C2-Cn to C14-Cn). Subsequent gene studies showed in all patients pathogenic gene variants in either homozygous or compound heterozygous forms. Consistent with literature data, allelic frequency of the c.338C \textgreater T[p.Ser113Leu] mutation amounted to 68.2% in our cohort. Other missense mutations included c.149C \textgreater A[p.Pro50His] (9%), c.200C \textgreater G[p.A1a200Gly] (4.5%) and previously unreported c.1171A \textgreater G[p.ser391Gly] (4.5%) and c.1420G \textgreater C[p.Ala474Pro] (4.5%) mutations. Frameshift c.1666-1667delTT[p.Leu556val*16] mutation (9%) was observed in two patients unknown to be related

Mitochondrial acetoacetyl-CoA thiolase deficiency: basal ganglia impairment may occur independently of ketoacidosis.

Mitochondrial acetoacetyl-CoA thiolase (T2) deficiency affects ketone body and isoleucine catabolism. Neurological impairment may occur secondary to ketoacidotic episodes. However, we observed neuromotor abnormalities without ketoacidotic events in two T2-deficient families. We hypothesized that the neurological signs were related to the genetic defect and may occur independently of ketoacidotic episodes. We therefore conducted a retrospective review on a French T2-deficient patient series searching for neuromotor impairment

Antenatal manifestations of inborn errors of metabolism: biological diagnosis

International audienceInborn errors of metabolism (IEMs) that present with abnormal imaging findings in the second half of pregnancy are mainly lysosomal storage disorders (LSDs), cholesterol synthesis disorders (CSDs), glycogen storage disorder type IV (GSD IV), peroxisomal disorders, mitochondrial fatty acid oxidation defects (FAODs), organic acidurias, aminoacidopathies, congenital disorders of glycosylation (CDGs), and transaldolase deficiency. Their biological investigation requires fetal material. The supernatant of amniotic fluid (AF) is useful for the analysis of mucopolysaccharides, oligosaccharides, sialic acid, lysosphingolipids and some enzyme activities for LSDs, 7- and 8-dehydrocholesterol, desmosterol and lathosterol for CSDs, acylcarnitines for FAODs, organic acids for organic acidurias, and polyols for transaldolase deficiency. Cultured AF or fetal cells allow the measurement of enzyme activities for most IEMs, whole-cell assays, or metabolite measurements. The cultured cells or tissue samples taken after fetal death can be used for metabolic profiling, enzyme activities, and DNA extraction. Fetal blood can also be helpful. The identification of vacuolated cells orients toward an LSD, and plasma is useful for diagnosing peroxisomal disorders, FAODs, CSDs, some LSDs, and possibly CDGs and aminoacidopathies. We investigated AF of 1700 pregnancies after exclusion of frequent etiologies of nonimmune hydrops fetalis and identified 108 fetuses affected with LSDs (6.3 %), 29 of them with mucopolysaccharidosis type VII (MPS VII), and six with GSD IV (0.3 %). In the AF of 873 pregnancies, investigated because of intrauterine growth restriction and/or abnormal genitalia, we diagnosed 32 fetuses affected with Smith-Lemli-Opitz syndrome (3.7 %)