Ana-Belen Martin-Cuadrado

Ana-Belen Martin-Cuadrado
University of Alicante | UA · Phisiology, Genetics and Microbiology

About

82
Publications
12,735
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
4,082
Citations

Publications

Publications (82)
Article
Full-text available
Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea that forms large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as “banquettes.” These banquettes accumulate on the shore, where they can prevent erosion, although they also cause social concer...
Article
Full-text available
Vibrio coralliilyticus and Vibrio mediterranei are important coral pathogens capable of inducing serious coral damage, which increases severely when they infect the host simultaneously. This has consequences related to the dispersion of these pathogens among different locations that could enhance deleterious effects on coral reefs. However, the mec...
Article
Full-text available
Host recognition by phage-encoded receptor binding proteins (RBPs) constitutes the first step in all phage infections and the most critical determinant of host specificity. By characterizing new types of RBPs and identifying their essential chaperones, we hope to expand the repertoire of known phage-host recognition machineries. Due to their geneti...
Article
Full-text available
The bacterium Myxococcus xanthus exhibits a complex multicellular life cycle. In the presence of nutrients, cells prey cooperatively. Upon starvation, they enter a developmental cycle wherein cells aggregate to produce macroscopic fruiting bodies filled with resistant myxospores. We used RNA-Seq technology to examine the transcriptome of the 96 hr...
Article
Peñahueca is an athalassohaline hypersaline inland ephemeral lake originated under semiarid conditions in the central Iberian Peninsula (Spain). Its chemical composition makes it extreme for microbial life as well as a terrestrial analogue of other planetary environments. To investigate the persistence of microbial life associated with sulfate‐rich...
Preprint
Full-text available
The bacteria Myxococcus xanthus exhibit a complex multicellular life cycle. In the presence of nutrients, cells prey cooperatively. Upon starvation, they enter a developmental cycle wherein cells aggregate to produce macroscopic fruiting bodies filled with resistant myxospores. We used RNA-Seq technology to examine the global transcriptome of the 9...
Article
Current metagenomic tools allow the recovery of microbial genomes directly from the environment. This can be accomplished by binning metagenomic contigs according to their coverage and tetranucleotide frequency, followed by an estimation of the bin quality. The public availability of bioinformatics tools, together with the decreasing cost of next g...
Article
Full-text available
Background Haloquadratum walsbyi dominates saturated thalassic lakes worldwide where they can constitute up to 80-90% of the total prokaryotic community. Despite the abundance of the enigmatic square-flattened cells, only 7 isolates are currently known with 2 genomes fully sequenced and annotated due to difficulties to grow them under laboratory co...
Article
Full-text available
Freshwater picocyanobacteria including Synechococcus remain poorly studied at the genomic level, compared to their marine representatives. Here, using a metagenomic assembly approach we discovered two novel Synechococcus sp. genomes from two freshwater reservoirs Tous and Lake Lanier, both sharing 96% average nucleotide identity and displaying high...
Article
Marine Euryarchaeota remain among the least understood major components of marine microbial communities. Marine group II Euryarchaeota (MG-II) are more abundant in surface waters (4–20% of the total prokaryotic community), whereas marine group III Euryarchaeota (MG-III) are generally considered low-abundance members of deep mesopelagic and bathypel...
Chapter
Ha.lo.qua.dra'tum. Gr. masc. n. hals, halos salt, L. neut. n. quadratum square, N.L. neut. n. Haloquadratum salt square. Euryarchaeota / Halobacteria / Halobacteriales / Halobacteriaceae The haloarchaeal species Haloquadratum walsbyi, the only member described of the genus Haloquadratum, dominates NaCl saturated thalassic lakes worldwide. These mic...
Chapter
Archaea constitute one of the three recognized phylogenetic groups of organisms living on the planet, and the latest to be discovered. Most Archaea resist cultivation and are studied using molecular methods. High-throughput amplicon sequencing and metagenomic approaches have been key in uncovering hitherto unknown archaeal diversity, their metaboli...
Article
Full-text available
Haloquadratum walsbyi represents up to 80 % of cells in NaCl-saturated brines worldwide, but is notoriously difficult to maintain under laboratory conditions. In order to establish the extent of genetic diversity in a natural population of this microbe, we screened a H. walsbyi enriched metagenomic fosmid library and recovered seven novel version o...
Article
Full-text available
Marine Group (MG) I (currently known as Thaumarchaeota) and MG II Archaea were first reported over two decades ago. While significant progress has been made on MG I microbiology and ecology, the progress on MG II has been noticeably slower. The common understanding is that while MG I mainly function as chemolithoautotrophs and occur predominantly i...
Article
Full-text available
Alteromonas spp. are heterotrophic gammaproteobacteria commonly found in marine environments. We present here the draft genome sequence of Alteromonas macleodii MIT1002, which was isolated from an enrichment culture of the marine cyanobacterium Prochlorococcus NATL2A. This genome contains a mixture of features previously seen only within either the...
Article
Full-text available
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 esse...
Article
Full-text available
Different strains of the same prokaryotic species, even very similar ones, vary in large regions of their genomes. This flexible genome represents a huge reservoir of diversity that allows prokaryotes to exploit their environment efficiently. Most of the flexible genome is concentrated in genomic islands, some of which are present in all the strain...
Article
Full-text available
Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the carbon and nitrogen cycles in the ocean. In this study, we assembled AOA draft genomes from two deep marine sediments from Donghae, South Korea, and Svalbard, Arctic region, by sequencing the enriched metagenomes. Three major microorganism clusters belon...
Article
Full-text available
A metagenome was obtained by pyrosequencing the total prokaryotic DNA from the water of a pond with intermediate salinity (13% salts) from a saltern located in Santa Pola, Spain. We analysed and compared the phylogenic and metabolic diversity of this saltern pond with respect to other two metagenomes obtained previously from the same saltern (ponds...
Article
Full-text available
Marine salterns are composed of several shallow ponds with a salinity gradient, from seawater to salt saturation, with gradually changing microbial populations. Here, we report the metagenome sequencing of the prokaryotic microbiota of two ponds with 13% and 33% salinity from a saltern in Santa Pola, Spain.
Article
Full-text available
Four novel, closely related podoviruses, which displayed lytic activity against the gamma-proteobacterium Alteromonas macleodii, have been isolated and sequenced. Alterophages AltAD45-P1 to P4 were obtained from water recovered near a fish farm in the Mediterranean Sea. Their morphology indicates that they belong to the Podoviridae. Their linear an...
Article
Full-text available
Biodiversity estimates based on ribosomal operon sequence diversity rely on the premise that a sequence is characteristic of a single specific taxon or operational taxonomic unit (OTU). Here, we have studied the sequence diversity of 14 ribosomal RNA operons (rrn) contained in the genomes of two isolates (five operons in each genome) and four metag...
Article
Full-text available
We have analyzed a natural population of the marine bacterium, Alteromonas macleodii, from a single sample of seawater to evaluate the genomic diversity present. We performed full genome sequencing of four isolates and 161 metagenomic fosmid clones, all of which were assigned to A. macleodii by sequence similarity. Out of the four strain genomes, A...
Article
Full-text available
Ammonia-oxidizing archaea (AOA) typically predominate over ammonia-oxidizing bacteria in marine sediments. We herein present the draft genome sequence of an ammonia-oxidizing archaeon, “Candidatus Nitrosopumilus sediminis” AR2, which was enriched in culture from a marine sediment obtained off Svalbard, within the Arctic Circle. The typical genes in...
Article
Full-text available
The genome of Alteromonas macleodii strain ATCC 27126T has been resequenced and closed into a single contig. We describe here the genome of this important and globally distributed marine bacterium.
Article
Full-text available
Cellular metagenomes are primarily used for investigating microbial community structure and function. However, cloned fosmids from such metagenomes capture phage genome fragments that can be used as a source of phage genomes. We show that fosmid cloning from cellular metagenomes and sequencing at a high coverage is a credible alternative to constru...
Article
Full-text available
Alteromonas macleodii is a marine gammaproteobacterium with widespread distribution in temperate or tropical waters. We describe three genomes of isolates from surface waters around Europe (Atlantic, Mediterranean and Black Sea) and compare them with a previously described deep Mediterranean isolate (AltDE) that belongs to a widely divergent clade....
Article
Full-text available
Sulfur-oxidizing bacteria are common microorganisms in a variety of sulfide-rich environments. They play important roles in the global sulfur cycle on earth. Here, we present a high-quality draft genome sequence of a sulfur-oxidizing bacterium, “Candidatus Sulfurovum sediminum” strain AR, which belongs to the class Epsilonproteobacteria and dominat...
Article
Full-text available
The abundance of quorum quenching (QQ) activity was evaluated in cultivable bacteria obtained from oceanic and estuarine seawater and compared with the frequency of QQ enzyme sequences in the available marine metagenomic collections. The possible role of the high QQ activity found among marine bacteria is discussed.
Article
Full-text available
Metaviriomes, the viral genomes present in an environment, have been studied by direct sequencing of the viral DNA or by cloning in small insert libraries. The short reads generated by both approaches make it very difficult to assemble and annotate such flexible genomic entities. Many environmental viruses belong to unknown groups or prey on uncult...
Data
Dendogram showing the distribution of viral sequences according to their tetranucleotide frequency. Oligonucleotide analysis of the fosmids was done using the on-line tools in http://insilico.ehu.es and a dendrogram was constructed applying the UPGMA clustering of the Euclidean distance of the frequencies. In red, the prokaryote genomes and in bold...
Data
Identification of proto-spacer adjacent motifs (PAMs) of the two CRISPR/Cas systems of H. walsbyi. Regions containing proto-spacers (positions −33 to 0) with over 90% identity to subtype I-D (6 entries) or I-B (9 entries) spacers of strains HBSQ001 and C23T, were obtained from the nr database (http://www.ncbi.nlm.nih.gov/BLAST/). Proto-spacer seque...
Data
Alignment of the CRISPR sequence of eHP-16 fosmid and the most similar CRISPRs found in the nr/nt collection of GenBank database. When CRISPRs are located in a chromosome, only the name of the harboring strain is indicated and when in a plasmid, the name of the replicon is also shown between brackets. Mismatches with respect to the CRISPR in the fo...
Data
Genomic organization of the non classified fosmids. Colour code as in Figure 1. (TIF)
Article
Full-text available
We describe the microbiota of two hypersaline saltern ponds, one of intermediate salinity (19%) and a NaCl saturated crystallizer pond (37%) using pyrosequencing. The analyses of these metagenomes (nearly 784 Mb) reaffirmed the vast dominance of Haloquadratum walsbyi but also revealed novel, abundant and previously unsuspected microbial groups. We...
Article
Acylhomoserine lactone (AHLs)-mediated quorum-sensing (QS) processes seem to be common in the marine environment and among marine pathogenic bacteria, but no data are available on the prevalence of bacteria capable of interfering with QS in the sea, a process that has been generally termed 'quorum quenching' (QQ). One hundred and sixty-six strains...
Article
Full-text available
In yeast, enzymes with β-glucanase activity are thought to be necessary in morphogenetic events that require controlled hydrolysis of the cell wall. Comparison of the sequence of the Saccharomyces cerevisiae exo-β(1,3)-glucanase Exg1 with the Schizosaccharomyces pombe genome allowed the identification of three genes that were named exg1+ (locus SPB...
Article
Full-text available
SUMMARY: Bacterial strains belonging to the same species vary considerably in gene content. Thus, the genetic repertoire of a given species (its "pan-genome") is much larger than the gene content of individual strains. These variations in DNA material, together with differences in genomic structure and nucleotide polymorphisms among strains, confer...
Article
Full-text available
The deep chlorophyll maximum (DCM) is a zone of maximal photosynthetic activity, generally located toward the base of the photic zone in lakes and oceans. In the tropical waters, this is a permanent feature, but in the Mediterranean and other temperate waters, the DCM is a seasonal phenomenon. The metagenome from a single sample of a mature Mediter...
Article
Full-text available
The species composition and metabolic potential of microbial and viral communities are predictable and stable for most ecosystems. This apparent stability contradicts theoretical models as well as the viral-microbial dynamics observed in simple ecosystems, both of which show Kill-the-Winner behavior causing cycling of the dominant taxa. Microbial a...
Data
The Hairdresser software. Executable file, source code and example files of The Hairdresser software.
Data
Haloquadratum walsbyi DSM 16790 genome and metagenomic islands. (a) GC-content of Haloquadratum walsbyi genome plotted with a sliding window of 1000 nucleotides. Location of integrases and IS transposases along the genome are indicated. (b) Coverage of Santa Pola saltern crystallizer metagenomic reads. (c) Coverage of San Diego saltern crystallizer...
Data
Salinibacter ruber DSM 13855 genome and metagenomic islands. (a) Coverage of San Diego saltern crystallizer metagenomic reads as revealed by MUMmer analysis. Y axis reflects its nucleotide percent identity to syntenic region. (b) Coverage of Santa Pola saltern crystallizer metagenomic reads as revealed by BLAST analysis. Y axis reflects number of h...