Carbon metabolism snapshot by ddPCR during the early step of Candida albicans phagocytosis by macrophages.

During Candida macrophage interactions, phagocytosed yeast cells feed in order to grow, develop hyphae and escape. Through numerous proteomic and transcriptomic studies, two metabolic phases have been described. A shift to a starvation mode is generally identified as early as one-hour post phagocytosis, followed by a glycolytic growth mode after C. albicans escaped from the macrophage. Healthy macrophages contain low amounts of glucose. To determine if this carbon source was sensed and metabolized by the pathogen, we explored the transcription level of a delimited set of key genes expressed in C. albicans cells during phagocytosis by macrophages, at an early stage of the interaction. This analysis was performed using a technical digital droplet PCR approach to quantify reliably the expression of carbon metabolic genes after 30 min of phagocytosis. Our data confirm the technique of digital droplet PCR for the detection of C. albicans transcripts using cells recovered after a short period of phagocytosis. At this stage, carbon metabolism is clearly oriented towards the use of alternative sources. However, the activation of high-affinity glucose transport system suggests that the low amount of glucose initially present in the macrophages is detected by the pathogen.

Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus.

With 149 currently recognized species, Hypostomus is one of the most species-rich catfish genera in the world, widely distributed over most of the Neotropical region. To clarify the evolutionary history of this genus, we reconstructed a comprehensive phylogeny of Hypostomus based on four nuclear and two mitochondrial markers. A total of 206 specimens collected from the main Neotropical rivers were included in the present study. Combining morphology and a Bayesian multispecies coalescent (MSC) approach, we recovered 85 previously recognized species plus 23 putative new species, organized into 118 'clusters'. We presented the Cluster Credibility (CC) index that provides numerical support for every hypothesis of cluster delimitation, facilitating delimitation decisions. We then examined the correspondence between the morphologically identified species and their inter-specific COI barcode pairwise divergence. The mean COI barcode divergence between morphological sisters species was 1.3 ± 1.2%, and only in 11% of the comparisons the divergence was ≥2%. This indicates that the COI barcode threshold of 2% classically used to delimit fish species would seriously underestimate the number of species in Hypostomus, advocating for a taxon-specific COI-based inter-specific divergence threshold to be used only when approximations of species richness are needed. The phylogeny of the 108 Hypostomus species, together with 35 additional outgroup species, confirms the monophyly of the genus. Four well-supported main lineages were retrieved, hereinafter called super-groups: Hypostomus cochliodon, H. hemiurus, H. auroguttatus, and H. plecostomus super-groups. We present a compilation of diagnostic characters for each super-group. Our phylogeny lays the foundation for future studies on biogeography and on macroevolution to better understand the successful radiation of this Neotropical fish genus.

Genomic characterization of a pectinolytic isolate of Serratia oryzae isolated from lake water.

Only one isolate of Serratia oryzae, the type strain J11-6T has been characterized up to now. This strain was found in the endophytic bacterial flora of rice. As part of an ongoing investigation into pectinolytic bacteria present in lake water in France, a few Serratia strains were isolated, including S32 and J9 identified as new strains of S. oryzae. The genome of strain S32 consists of a circular chromosome of 4,810,389 bp that contains 4,584 protein-coding genes. The genome of S32, as well as those of the type strain J11-6T, contains several genes involved in pectin degradation and in the intracellular assimilation of pectin oligomers. The specific detection of enzyme activities confirmed that strain S32 secretes functional pectinases and that it also produces extracellular cellulase and protease activities. The ability to produce plant cell wall degrading enzymes shows that S. oryzae shares characteristics of plant associated bacteria, including phytopathogens.

Dickeya lacustris sp. nov., a water-living pectinolytic bacterium isolated from lakes in France.

The genus Dickeya is an important group of plant pathogens that currently comprises eight recognized species. Although most Dickeya isolates originated from infected cultivated plants, they have also been repeatedly isolated from water. To better understand the natural diversity of Dickeya, a survey was performed in small lakes surrounded by wetlands in the French region of La Dombes. Several Dickeya isolates were obtained from water or plants from lakes protected from direct agricultural inputs. Sequencing of the gapA gene revealed that five isolates, S12, S15, S24, S29T and S39, belong to a phylogenetic group separated from other Dickeya species. The genomic sequence of strain S29T clearly established its separation from the other known Dickeya species. The in silico DNA-DNA hybridization (isDDH) and average nucleotide identity (ANI) values (<33 and <88 %, respectively) obtained by comparing strain S29T with strains of characterized Dickeya species supported the delineation of a novel species. The closest species to strain S29T is Dickeya aquatica, previously isolated from rivers, suggesting that these strains have a common ancestor adapted to a water environment. Genomic and phenotypic comparisons enabled the identification of traits distinguishing isolates S12, S15, S24, S29T and S39 from D. aquatica and from other Dickeya species. The name Dickeya lacustris sp. nov. is proposed for this taxon with S29T (=CFBP 8647T=LMG 30899T) as the type strain.