Genomic Diversity of “Deep Ecotype” Alteromonas macleodii Isolates: Evidence for Pan-Mediterranean Clonal Frames

López‐Pérez, Mario; Gonzaga, Aitor; Rodrı́guez-Valera, Francisco

doi:10.1093/gbe/evt089

Cited by 57 publications

(126 citation statements)

References 67 publications

(107 reference statements)

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“…3C). All the aforementioned characteristics suggest assignment of the respective GIs into the additive type, according to the definition by López-Pérez et al (29), which applies to 54% of the 24 GI positions.…”

Section: Figmentioning

confidence: 99%

“…3B). For replacement GIs, as defined by López-Pérez et al (29), homologous recombination is the most likely transfer mechanism (30). Another characteristic for replacement GIs is the presence of genes with similar assigned function but completely different genes in the GIs of different genomes.…”

Section: Figmentioning

confidence: 99%

“…GIs were initially associated with virulence in pathogenic bacteria, termed pathogenicity islands (23,24), but are also frequently found in nonpathogenic bacteria (25)(26)(27)(28). Corresponding to the mechanisms of gene acquisition and loss, two types of GIs can be distinguished (29). Additive GIs stem from the legacy of mobile genetic elements and can harbor a varied number of gene cassettes.…”

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confidence: 99%

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Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool

Hoetzinger

Schmidt

Jezberová

et al. 2017

Appl Environ Microbiol

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Microdiversification of a planktonic freshwater bacterium was studied by comparing 37 Polynucleobacter asymbioticus strains obtained from three geographically separated sites in the Austrian Alps. Genome comparison of nine strains revealed a core genome of 1.8 Mb, representing 81% of the average genome size. Seventy-five percent of the remaining flexible genome is clustered in genomic islands (GIs). Twenty-four genomic positions could be identified where GIs are potentially located. These positions are occupied strain specifically from a set of 28 GI variants, classified according to similarities in their gene content. One variant, present in 62% of the isolates, encodes a pathway for the degradation of aromatic compounds, and another, found in 78% of the strains, contains an operon for nitrate assimilation. Both variants were shown in ecophysiological tests to be functional, thus providing the potential for microniche partitioning. In addition, detected interspecific horizontal exchange of GIs indicates a large gene pool accessible to Polynucleobacter species. In contrast to core genes, GIs are spread more successfully across spatially separated freshwater habitats. The mobility and functional diversity of GIs allow for rapid evolution, which may be a key aspect for the ubiquitous occurrence of Polynucleobacter bacteria.IMPORTANCE Assessing the ecological relevance of bacterial diversity is a key challenge for current microbial ecology. The polyphasic approach which was applied in this study, including targeted isolation of strains, genome analysis, and ecophysiological tests, is crucial for the linkage of genetic and ecological knowledge. Particularly great importance is attached to the high number of closely related strains which were investigated, represented by genome-wide average nucleotide identities (ANI) larger than 97%. The extent of functional diversification found on this narrow phylogenetic scale is compelling. Moreover, the transfer of metabolically relevant genomic islands between more distant members of the Polynucleobacter community provides important insights toward a better understanding of the evolution of these globally abundant freshwater bacteria.

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Section: Figmentioning

confidence: 99%

Section: Figmentioning

confidence: 99%

mentioning

confidence: 99%

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Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool

Hoetzinger

Schmidt

Jezberová

et al. 2017

Appl Environ Microbiol

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“…First of all, there is the problem of the concurrent diversity. There are always several clones coexisting at any given time that although similar are by no means identical (Rodriguez-Valera et al, 2009;Gonzaga et al, 2012;Lopez-Perez et al, 2013;Kashtan et al, 2014). Secondly, some regions of these genomes are hypervariable, i.e.…”

Section: Genomic Reconstruction Of Mgiib Representativesmentioning

confidence: 99%

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

et al. 2014

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We have analyzed metagenomic fosmid clones from the deep chlorophyll maximum (DCM), which, by genomic parameters, correspond to the 16S ribosomal RNA (rRNA)-defined marine Euryarchaeota group IIB (MGIIB). The fosmid collections associated with this group add up to 4 Mb and correspond to at least two species within this group. From the proposed essential genes contained in the collections, we infer that large sections of the conserved regions of the genomes of these microbes have been recovered. The genomes indicate a photoheterotrophic lifestyle, similar to that of the available genome of MGIIA (assembled from an estuarine metagenome in Puget Sound, Washington Pacific coast), with a proton-pumping rhodopsin of the same kind. Several genomic features support an aerobic metabolism with diversified substrate degradation capabilities that include xenobiotics and agar. On the other hand, these MGIIB representatives are non-motile and possess similar genome size to the MGIIA-assembled genome, but with a lower GC content. The large phylogenomic gap with other known archaea indicates that this is a new class of marine Euryarchaeota for which we suggest the name Thalassoarchaea. The analysis of recruitment from available metagenomes indicates that the representatives of group IIB described here are largely found at the DCM (ca. 50 m deep), in which they are abundant (up to 0.5% of the reads), and at the surface mostly during the winter mixing, which explains formerly described 16S rRNA distribution patterns. Their uneven representation in environmental samples that are close in space and time might indicate sporadic blooms.

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“…SXT integrates itself into the chromosome of V. cholerae in a site-specific manner at the 5= end of prfC, a gene coding for the peptide release factor RF3 (6). Since the discovery of SXT, SXT or related ICEs have been found to be prevalent in the seventh pandemic isolates of V. cholerae and sporadically present in other Vibrio species (7)(8)(9) and other Gammaproteobacteria of clinical origin or isolated from the aquatic environment, such as Photobacterium (10), Proteus (11), Alteromonas (12), Marinomonas (13), and Shewanella (9,14) species. SXT is closely related to R391, an ICE conferring resistance to kanamycin and mercury, originally detected in a 1967 South African isolate of Providencia rettgeri (15,16).…”

mentioning

confidence: 99%

A λ Cro-Like Repressor Is Essential for the Induction of Conjugative Transfer of SXT/R391 Elements in Response to DNA Damage

Poulin-Laprade

Burrus

2015

J Bacteriol

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Integrative and conjugative elements (ICEs) of the SXT/R391 family are the main contributors to acquired multidrug resistance in the seventh pandemic lineage of Vibrio cholerae, the etiological agent of the diarrheal disease cholera. Conjugative transfer of SXT/R391 ICEs is triggered by antibiotics and agents promoting DNA damage through RecA-dependent autoproteolysis of SetR, an ICE-encoded CI-like repressor. Here, we describe the role of CroS, a distant Cro homolog, as a key component contributing to the regulation of expression of the activator SetCD that orchestrates the expression of the conjugative transfer genes. We show that deletion of croS abolishes the SOS response-dependent induction of SXT despite the presence of a functional setR gene. Using quantitative reverse transcription-PCR and lacZ reporter assays, we also show that CroS represses setR and setCD expression by binding to operator sites shared with SetR. Furthermore, we provide evidence of an additional operator site bound by SetR and CroS. Finally, we show that SetCD expression generates a positive feedback loop due to SXT excision and replication in a fraction of the cell population. Together, these results refine our understanding of the genetic regulation governing the propagation of major vectors of multidrug resistance. IMPORTANCEHealthcare systems worldwide are challenged by an alarming drug resistance crisis caused by the massive and rapid propagation of antibiotic resistance genes and the associated emergence of multidrug-resistant pathogenic bacteria. SXT/R391 ICEs contribute to this phenomenon not only in clinical and environmental vibrios but also in several members of the family Enterobacteriaceae. We have identified and characterized here the regulator CroS as a key factor in the stimulation of conjugative transfer of these ICEs in response to DNA-damaging agents. We have also untangled conflicting evidence regarding autoactivation of transfer by the master activator of SXT/R391 ICEs, SetCD. Discovery of CroS provides a clearer and more complete understanding of the regulatory network that governs the dissemination of SXT/R391 ICEs in bacterial populations. Cholera is a severe infectious disease caused by the ingestion of food or water contaminated by Vibrio cholerae. This disease remains widespread in regions with limited access to clean water and where poor sanitation allows easy dissemination of the bacterium in drinking water sources. Cholera is characterized by a profuse watery diarrhea that rapidly induces massive fluid loss, causing severe dehydration of the patient, which may lead to death within 24 h of symptom onset. Although epidemic cholera is usually caused by V. cholerae O1, the unusual serogroup O139 emerged in the early 1990s as the cause of a cholera outbreak in India (1). O139 clinical isolates were found to be resistant to sulfamethoxazole and trimethoprim, two antibiotics commonly used for the treatment of severe cases of cholera (2). This resistance was found to be transmissible and linked to an integ...

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Genomic Diversity of “Deep Ecotype” Alteromonas macleodii Isolates: Evidence for Pan-Mediterranean Clonal Frames

Cited by 57 publications

References 67 publications

Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool

Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

A λ Cro-Like Repressor Is Essential for the Induction of Conjugative Transfer of SXT/R391 Elements in Response to DNA Damage

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