The European green crab
Carcinus maenas
and its sister species
C. aestuarii
are highly invasive species causing damage to coastal ecosystems and contributing to severe economic losses worldwide.
C. ...maenas
was first detected at the Atlantic Patagonian coast in 2001. In this work, we studied the diet of the green crab in a recently invaded location in Golfo Nuevo, using three complementary techniques: direct stomach observation, metabarcoding of gut content and stable isotope analysis. Direct stomach observation and metabarcoding showed that green crabs have a broad omnivorous diet, ingesting most of the phyla present in the study area. Gut content metabarcoding allowed a detailed description of algal diversity and revealed other taxa that went unnoticed in the visual stomach analysis. Stable isotope analysis showed that the major contribution to the crabs' diet was from the phytoplankton chain (by bivalve consumption) and not directly from algae. This study approach combining three complementary techniques also allowed us to detect some differences in the diet between sexes, which suggests that male and female crabs are not as ecologically equivalent as previously thought. Besides, we detected sequences corresponding to
C. aestuarii
suggesting that the green crab Patagonian population is a hybrid of both sister species. These findings are key to understanding the impacts green crabs can have on the local ecosystem.
Full text
Available for:
EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
is one of the most important nosocomial pathogens able to rapidly develop extensive drug resistance. Here, we study the role of accessory genome in the success of the globally disseminated clone 1 ...(GC1) with functional and genomic approaches. Comparative genomics was performed with available GC1 genomes (
= 106) against other
high-risk and sporadic clones. Genetic traits related to accessory genome were found common and conserved along time as two novel regions of genome plasticity, and a CRISPR-Cas system acquired before clonal diversification located at the same loci as "sedentary" modules. Although identified within hotspot for recombination, other block of accessory genome was also "sedentary" in lineage 1 of GC1 with signs of microevolution as the AbaR0-type genomic island (GI) identified in A144 and in A155 strains which were maintained one month in independent experiments without antimicrobial pressure. The prophage YMC/09/02/B1251_ABA_BP was found to be "mobile" since, although it was shared by all GC1 genomes, it showed high intrinsic microevolution as well as mobility to different insertion sites. Interestingly, a wide variety of Insertion Sequences (IS), probably acquired by the flow of plasmids related to Rep_3 superfamily was found. These IS showed dissimilar genomic location amongst GC1 genomes presumably associated with promptly niche adaptation. On the other hand, a type VI secretion system and three efflux pumps were subjected to deep processes of genomic loss in
but not in GC1. As a whole, these findings suggest that preservation of some genetic modules of accessory genome harbored by strains from different continents in combination with great plasticity of IS and varied flow of plasmids, may be central features of the genomic structure of GC1. Competition of A144 and A155 versus A118 (ST 404/ND) without antimicrobial pressure suggested a higher ability of GC1 to grow over a clone with sporadic behavior which explains, from an ecological perspective, the global achievement of this successful pandemic clone in the hospital habitat. Together, these data suggest an essential role of still unknown properties of "mobile" and "sedentary" accessory genome that is preserved over time under different antibiotic or stress conditions.
Ovenbirds represent a clade of exclusively Neotropical birds that are exceptionally diverse, despite their rather dull, melanin-based plumage. In general, sexes are considered monomorphic in size and ...colour, but several authors have reported females of some species within this family as being slightly paler than their conspecific counterparts. Our aim was to assess levels of sexual dichromatism in a set of ovenbird species representing a diversity of genera and plumage patterns;
Furnarius rufus
,
Phleocryptes melanops
,
Synallaxis spixi
and
Schoeniophylax phryganophilus
. For each species, we quantified sexual differences in brightness and colouration among 8–10 different plumage regions through modelling avian perceptual colour-space distances. To best inform our visual modelling parameters, we successfully sequenced the SWS1 gene fragment (associated with short-wavelength, including ultraviolet, visual sensitivity in birds) for one species,
P. melanops
, and found it possessed an amino acid sequence consistent with the VS-type SWS1 visual system. This provides further evidence supporting the presence of VS-sensitive opsin in ovenbirds. Among all four species, females were consistently brighter than males in at least one plumage patch, but chromatic colour differences between sexes were significant only for the throat patches of
Schoeniophylax phryganophilus
. Overall, we interpret ovenbirds to exhibit very low levels of sexual dichromatism, manifest mainly by achromatic colour differences.
•WGS analysis and comparison of two A. baumannii strains belonging to emergent ST25 and sporadic ST172.•Molecular characterisation revealed differences in the content of antibiotic resistance genes ...and mobile genetic elements.•Differences at the genomic level can in part explain the success of ST25 in comparison with ST172.•Characterisation of a previously uncharacterised ST (ST172) and further characterisation of the widely studied ST25.
Acinetobacter baumannii is an opportunistic nosocomial pathogen that is the main focus of attention in clinical settings owing to its intrinsic ability to persist in the hospital environment and its capacity to acquire determinants of resistance and virulence. Here we present the genomic sequencing, molecular characterisation and genomic comparison of two A. baumannii strains belonging to two different sequence types (STs), one sporadic and one widely distributed in our region.
Whole-genome sequencing (WGS) of Ab42 and Ab376 was performed using Illumina MiSeq-I and the genomes were assembled with SPAdes. ARG-ANNOT, CARD-RGI, ISfinder, PHAST, PlasmidFinder, plasmidSPAdes and IslandViewer were used to analyse both genomes.
Genome analysis revealed that Ab42 belongs to ST172, an uncommon ST, whilst Ab376 belongs to ST25, a widely distributed ST. Molecular characterisation showed the presence of two antibiotic resistance genes in Ab42 and nine in Ab376. No insertion sequences were detected in Ab42, however 22 were detected in Ab376. Moreover, two prophages were found in Ab42 and three in Ab376. In addition, a CRISPR-cas type I-Fb and two plasmids, one of which harboured an AbGRI1-like island, were found in Ab376.
We present WGS analysis of twoA. baumannii strains belonging to two different STs. These findings allowed us to characterise a previously undescribed ST (ST172) and provide new insights to the widely studied ST25.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Short wavelength visual sensitivity in birds is determined mostly by the type of photopigment present in the short-wavelength sensitive cone 1 (SWS1) which varies between clades and takes two main ...forms: the violet sensitive type (VS) and ultraviolet sensitive type (UVS). The common ancestor of passerines is thought to have been UVS, but there were at least 8 transitions between both types of visual sensitivity, even within species of the same family (Maluridae). The type of visual system a species has is a key parameter of avian visual models employed to describe chromatic visual perception and assess if colour differences are discernible by birds. Cardinalidae and Thraupidae together include more than 400 very diverse species that were model organisms in many bird colouration studies. However, visual sensitivity has been characterised for only one species of each of these families so far. Here, we obtained partial genetic sequences of the SWS1 opsin gene that determines the spectral sensitivity of the photopigment for a phylogenetically broad species sample of these families. All cardinals and tanagers studied here have SWS1 sequences corresponding with UVS sensitivity, suggesting that this character is conserved in these bird families despite their highly diverse range of plumage colours and habitat types.
Full text
Available for:
BFBNIB, GIS, IJS, KISLJ, NUK, PNG, UL, UM, UPUK
Abstract
Over the last two centuries, the Red-and-Green Macaw (Ara chloropterus) has become locally extinct in Argentina. In an attempt to restore its key ecosystem functions as both disperser and ...regulator of large-seeded plants, a reintroduction project was initiated at the Iberá National Park in northeastern Argentina. The ability of released individuals to find food is crucial, especially when working with captive-bred animals, as long-term establishment of a self-sustaining population depends on their short-term ability to exploit wild food sources. Monitoring of feeding habits is usually conducted through behavioral observation, but in recent years DNA metabarcoding has emerged as an alternative for obtaining highly resolved data on diet composition. In this study, we use a combination of both techniques to characterize the breadth and composition of the reintroduced macaws' diet. In addition, we compare the efficiency of both observational and molecular techniques to assess diet composition in a frugivorous bird. Individuals fed on a variety of plant species (n = 49) belonging to a broad phylogenetic spectrum (28 families). Dietary richness estimated by direct observation and DNA metabarcoding was similar, though smaller than the combination of the two datasets as both techniques detected at least 15 species not recorded by the other method. While the total number of detected species was higher for observational data, the rate of species-detection per sampling day was higher for DNA metabarcoding. These results suggest that a combination of both methods is required in order to obtain the most accurate account of the total diversity of the diet of a bird species. The ability of reintroduced macaws to successfully exploit local food resources throughout the year indicates a good level of adjustment to the release site, an important step towards the creation of a stable, self-sustaining population of Red-and-Green Macaws in Northern Argentina.
• The STs of 93 isolates from Buenos Aires and Rosario hospitals were achieved by Bartual (B) and Pasteur (P) schemes. • CC113B/CC79P prevailed among Buenos Aires isolates, at least in 1992–2010. • ...CC109B/CC1P prevailed among Rosario isolates, but CC113B/CC79P was also found. • CC110B/ST25P apparently increased over the last years. • Several single locus variants (SLV) of STs from CC79P, previously annoted as a singleton, were described.
As a way to contribute to the assessment of Acinetobacter baumannii clinical population structure, multi-locus sequence typing (MLST) was performed in a collection of 93 isolates from Buenos Aires (1983–2012) and Rosario (2006–2009) hospitals. Sequence types (STs) were achieved by Bartual (B) and Institut Pasteur (P) schemes. PFGE typing, antimicrobial susceptibility assays, and the amplification of the OXA carbapenemase genes most prevalent in our region, were also performed.
e-Burst clustered the 25 STsB (15 novels) into 5 clonal complexes (CC) and 5 singletons, and grouped the 18 STsP (12 novels) into 3 CC and 4 singletons. Bartual scheme divided the CC79P into two groups. CC113B/CC79P prevailed in Buenos Aires at least in 1992–2009, being responsible for epidemic and for endemic infections and acquiring the XDR (extensively drug-resistant) pattern throughout the years. While, CC119B/CC79P was apparently present before the CC113B/CC79Pdomain. CC103B/CC15P was the second most prevalent CC. Interestingly, CC110B/ST25P apparently increased over the last years. Conversely, CC109B/CC1P (international clone I) predominated in Rosario, although the presence of CC113B/CC79P, CC103B/CC15P and CC110B/ST25P was observed. Nineteen novel STs clustered in CC79P, CC15P, CC113B, CC109B and CC103B, suggesting their clonal expansion during persistence. PFGE typing proved transmission of strains intra- and inter-hospitals in each city. Except for one, all the recent isolates (2007–2012) harboured the blaOXA-23-like. All isolates were susceptible to colistin. Tigecycline MIC90 was 1mg/L and the rifampicin MIC>512mg/l was found among isolates in three hospitals.
In conclusion, the international clone II (CC92B/CC2P) was not found among our isolates. CC113B/CC79P, CC103B/CC15P, and ST25P, suggested also as major components in the A. baumannii population together with the international clone I, were present in Buenos Aires and Rosario with different prevalence rate. Their recent isolates showed high distribution of the blaOXA-23-like as well as the XDR pattern.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
PDF
