To provide context for the diversification of archosaurs—the group that includes crocodilians, dinosaurs, and birds—we generated draft genomes of three crocodilians:Alligator mississippiensis(the American alligator),Crocodylus porosus(the saltwater crocodile), andGavialis gangeticus(the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.

The large legume genusMimosais known to be associated with both alphaproteobacterial and betaproteobacterial symbionts, depending on environment and plant taxonomy, e.g., Brazilian species are preferentially nodulated byBurkholderia, whereas those in Mexico are associated with alphaproteobacterial symbionts. Little is known, however, about the symbiotic preferences ofMimosaspp. at the southern subtropical limits of the genus. In the present study, rhizobia were isolated from field-collected nodules fromMimosaspecies that are native to a region in southern Uruguay. Phylogenetic analyses of sequences of the 16S rRNA,recA, andgyrBcore genome and thenifHandnodAsymbiosis-essential loci confirmed that all the isolates belonged to the genusCupriavidus. However, none were in the well-described symbiotic speciesC. taiwanensis, but instead they were closely related to other species, such asC. necator, and to species not previously known to be symbiotic (or diazotrophic), such asC. basilensisandC. pinatubonensis. Selection of these novelCupriavidussymbionts by UruguayanMimosaspp. is most likely due to their geographical separation from their Brazilian cousins and to the characteristics of the soils in which they were found.IMPORTANCEWith the aim of exploring the diversity of rhizobia associated with nativeMimosaspecies, symbionts were isolated from root nodules on fiveMimosaspecies that are native to a region in southern Uruguay, Sierra del Abra de Zabaleta. In contrast to data obtained in the major centers of diversification of the genusMimosa, Brazil and Mexico, where it is mainly associated withBurkholderiaandRhizobium/Ensifer, respectively, the present study has shown that all the isolated symbiotic bacteria belonged to the genusCupriavidus. Interestingly, none of nodules contained bacteria belonging to the well-described symbiotic speciesC. taiwanensis, but instead they were related to otherCupriavidusspecies such asC. necatorandC. pinatubonensis. These data suggest the existence of a higher diversity within beta-rhizobialCupriavidusthan was previously suspected, and thatMimosaspp. from Sierra del Abra de Zabaleta, may be natural reservoirs for novel rhizobia.

In the past few decades Acinetobacter baumannii has emerged as a notorious nosocomial pathogen because of its ability to acquire genetic material and persist in extreme environments. Recently, human serum albumin (HSA) was shown to significantly increase natural transformation frequency in A. baumannii. This observation led us to perform transcriptomic analysis of strain A118 under HSA induction to identify genes that are altered by HSA. Our results revealed the statistically significant differential expression of 296 protein-coding genes, including those associated with motility, biofilm formation, metabolism, efflux pumps, capsule synthesis, and transcriptional regulation. Phenotypic analysis of these traits showed an increase in surface-associated motility, a decrease in biofilm formation, reduced activity of a citric acid cycle associated enzyme, and increased survival associated with zinc availability. Furthermore, the expression of genes known to play a role in pathogenicity and antibiotic resistance were altered. These genes included those associated with RND-type efflux pumps, the type VI secretion system, iron acquisition/metabolism, and ß-lactam resistance. Together, these results illustrate how human products, in particular HSA, may play a significant role in both survival and persistence of A. baumannii.

Acinetobacter johnsonii rarely causes human infections. While most A. johnsonii isolates are susceptible to virtually all antibiotics, strains harboring a variety of β-lactamases have recently been described. An A. johnsonii Aj2199 clinical strain recovered from a hospital in Buenos Aires produces PER-2 and OXA-58. We decided to delve into its genome by obtaining the whole genome sequence of the Aj2199 strain. Genome comparison studies on Aj2199 revealed 240 unique genes and a close relation to strain WJ10621, isolated from the urine of a patient in China. Genomic analysis showed evidence of horizontal genetic transfer (HGT) events. Forty-five insertion sequences and two intact prophages were found in addition to several resistance determinants such as bla_PER-2, bla_OXA-58, bla_TEM-1, strA, strB, ereA, sul1, aacC2 and a new variant of bla_OXA-211, called bla_OXA-498. In particular, bla_PER-2 and bla_TEM-1 are present within the typical contexts previously described in the Enterobacteriaceae family. These results suggest that A. johnsonii actively acquires exogenous DNA from other bacterial species and concomitantly becomes a reservoir of resistance genes.