Publications

4482

Abstract With the aim of describing the human microbiota by the means of culture methods, culturomics was developed in order to target previously un‐isolated bacterial species and describe it via the taxono‐genomics approach. While performing a descriptive study of the human gut microbiota of the pygmy people, strain Marseille‐P4678 T has been isolated from a stool sample of a healthy 39‐year‐old pygmy male. Cells of this strain were Gram‐positive cocci, spore‐forming, non‐motile, catalase‐positive and oxidase‐negative, and grow optimally at 37°C under anaerobic conditions. Its 16S rRNA gene sequence exhibited 89.69% of sequence similarity with Parvimonas micra strain 3119 B T ( NR 036934.1), its phylogenetically closest species with standing in nomenclature. The genome of strain Marseille‐P4678 T is 2,083,161 long with 28.26 mol% of G+C content. Based on its phenotypic, biochemical, genotypic and proteomic profile, this bacterium was classified as a new bacterial genus and species Miniphocibacter massiliensis gen. nov., sp. nov. with the type strain Marseille‐P4678 T .

“ Ca. Nitrotoga” is a NOB of high environmental relevance, but physiological data exist for only a few representatives. Initially, it was detected in specialized niches of low temperature and low nitrite concentrations, but later on, its ubiquitous distribution revealed its critical role for N removal in engineered systems like WWTPs. In this study, we analyzed the competition between Nitrotoga and Nitrospira in bioreactors and identified conditions where the K strategist Ns. defluvii was almost replaced by Nitrotoga sp. BS. We show that the pH value is an important factor that regulates the composition of the nitrite-oxidizing enrichment with a dominance of Nitrotoga sp. BS versus Ns. defluvii at a neutral pH of 7.4 in combination with a temperature of 17°C. The physiological diversity of novel Nitrotoga cultures improves our knowledge about niche differentiation of NOB with regard to functional nitrification under suboptimal conditions.

AbstractThe relationship between Bactrocera oleae (Rossi 1790) and its endosymbiont Candidatus Erwinia dacicola is important to achieving effective control of the olive fly population in the field. This bacterium plays a crucial role in the life of B. oleae and is necessary for its fitness. Thus, in the absence of the endosymbiont, B. oleae wild populations in the field might decrease considerably. Copper is one of the most used antimicrobials for horticultural crops worldwide, and its efficacy against Ca. E. dacicola has been demonstrated in field trials. Propolis is another natural antimicrobial compound largely used for its activity in several fields. If propolis and copper prove to be efficient against wild populations of the endosymbiont B. oleae in the field, such a biological restraint might improve sustainable agriculture. We evaluated, under laboratory conditions, the effect of two different copper products (at two different concentrations, 5% and 20%) and propolis on the content of Ca. E. dacicola in the eggs and in the adult oesophageal bulbs of B. oleae. Bulbs were extracted twice, after 2 and 5 weeks of exposure. Real‐time PCR on the bulbs showed a reduction in Ca. E. dacicola content in flies treated with copper (at both 5% and 20%), and from the first to the second extraction, while flies treated with propolis showed an increment of the relative abundance of Ca. E. dacicola. Both copper products (5% and 20%) reduced the egg production after 2 and 5 weeks in comparison with the control and propolis treatments. Moreover, adult mortality was significantly higher with propolis compared with the other treatments. Thus, our results encourage further research in order to develop new tools for the control of the olive fly in the framework of an integrated pest management strategy.

As one group of the most important functional phosphorus removal organisms, “ Candidatus Accumulibacter,” affiliated with the Rhodocyclus group of the Betaproteobacteria , is a widely recognized and studied PAO in the field of biological wastewater treatment. The morphotypes and population structure of clade-level “ Candidatus Accumulibacter” were studied through novel FISH-staining-flow cytometry, which involved denitrifying phosphorus removal (DPR) achieving carbon and energy savings and simultaneous removal of N and P, thus inferring the different denitrifying phosphorus removal abilities of these clades. Additionally, based on this method, in situ quantification for specific polyphosphate-accumulating organisms (PAOs) enables a more efficient process and more accurate result. The establishment of FISH-staining-flow cytometry makes cell sorting of clade-level noncultivated organisms available.

‘ Candidatus Liberibacter asiaticus’ ( CL as) is associated with the most destructive disease of citrus, huanglongbing ( HLB ). The most widely used methods for detection of CL as are PCR ‐based and require purification of DNA from plant samples. Elution of DNA from tissue prints made on nitrocellulose membranes followed by qPCR ( TPE ‐ qPCR ) was compared to DNA extraction of plant tissue followed by PCR (X‐ PCR ) by testing the same tissue samples. The former estimated a higher CL as population in tissue prints than the latter ( t ‐test; P  =   0.009). All extracts prepared for TPE ‐ qPCR throughout the experiment were also tested by conventional PCR and 80.8% were identified as positive. A similar set of stem and petiole tissue samples was tested by TPE ‐ qPCR and immunoassay. Although the detection rate by TPE ‐ qPCR was higher than by immunoassay, about 6% of tissue prints were positive by immunoassay but not by TPE ‐ qPCR . Thus, a higher detection rate would be achieved by combining TPE ‐ qPCR with immunoassay. Significant differences were observed in the performance of nitrocellulose membranes from different manufacturers in these assays. Immunotissue prints showed that the spatial distribution pattern of CL as infection varied widely from one sample to another, but the patterns were highly correlated among serial sections from the same sample, suggesting that CL as preferentially colonizes adjacent phloem cells in a vertical rather than horizontal direction.

Abstract‘Candidatus Liberibacter solanacearum’ (Lso) has emerged as a serious threat on solanaceous and apiaceous crops worldwide. Five Lso haplotypes (LsoA, LsoB, LsoC, LsoD and LsoE) have been identified so far. To decipher genetic relationships between Lso strains, a MLSA study of seven housekeeping genes (acnA, atpD, ftsZ, glnA, glyA, gnd and groEL) was performed on a representative bacterial collection of 49 Lso strains. In all, 5415 bp spanning the seven loci were obtained from each of the 49 strains of our bacterial collection. Analysis of sequence data was consistent with a clonal population structure with no evidence of recombination. Phylogenies reconstructed from individual genes, and with concatenated data, were globally congruent with each other. In addition to the five highly supported and distinct genetic clusters, which correspond to the five established haplotypes, our phylogenetic data revealed the presence of a sixth haplotype, designated ‘LsoG’. This new haplotype is currently represented by two strains from France which had distinct sequences in four out of the seven tested housekeeping genes. Altogether, the data presented here provide new information regarding the genetic structure of Lso and the evolutionary history of the haplotypes defined within this bacterial species.

Here, we report the draft genome sequence of a phytoplasma discovered in grapevine. The genome size is 600,116 nucleotides (nt), with 597 predicted open reading frames.

Abstract Large reservoirs of natural gas in the oceanic subsurface sustain complex communities of anaerobic microbes, including archaeal lineages with potential to mediate oxidation of hydrocarbons such as methane and butane. Here we describe a previously unknown archaeal phylum, Helarchaeota, belonging to the Asgard superphylum and with the potential for hydrocarbon oxidation. We reconstruct Helarchaeota genomes from metagenomic data derived from hydrothermal deep-sea sediments in the hydrocarbon-rich Guaymas Basin. The genomes encode methyl-CoM reductase-like enzymes that are similar to those found in butane-oxidizing archaea, as well as several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. We suggest that members of the Helarchaeota have the potential to activate and subsequently anaerobically oxidize hydrothermally generated short-chain hydrocarbons.