Salvador Ramirez-Flandes

Sulfur-oxidizing γ-proteobacteria are abundant in marine oxygen-deficient waters, and appear to play a key role in a previously unrecognized cryptic sulfur cycle. Metagenomic analyses of members of the uncultured SUP05 lineage in the Canadian seasonally anoxic fjord Saanich Inlet (SI), hydrothermal plumes in the Guaymas Basin (GB) and single cell g...

Significance Biological communities are conventionally described as assemblages of species, whose ecological roles are known or predictable from their observable morphology. In microbial ecology, such a taxonomic approach is hindered by limited capacity to discriminate among different microbes, which bear highly dynamic genomes and establish comple...

Significance The marine unicellular cyanobacterium Prochlorococcus is the most abundant photosynthetic organism on Earth. Members of this genus are classically thought to be adapted to high-oxygen and nutrient-poor ocean conditions, with a principle divergence between high-light and low-light ecotypes. We show that the most basal Prochlorococcus li...

A current paradigm in marine biodiversity states that faunal richness decreases with depth. However, the deep-ocean ecosystem has been significantly under-sampled, hindering a complete view of its biodiversity. This situation is accentuated in ultra-deep waters, where the remote and extreme conditions unfit the traditional sampling methods. Using e...

Gammaproteobacteria of the genus Alteromonas are prominent members of pelagic marine microbial communities, playing critical roles in the aerobic degradation of particulate organic matter. Comparative genomic studies of these microorganisms have mainly focused on the metabolic and genomic plasticity of strains isolated primarily from oxygenated env...

The strong seasonal variability in physical-chemical conditions of the Eastern South Pacific Ocean creates an ideal setting to study spatiotemporal distribution of key marine microbial communities. We herein report a nearly 4-year-long time series of the variability in amoA gene counts of ammonia oxidizing archaea (AOA) and bacteria (betaproteobact...

Anoxic marine zones (AMZs), also known as ‘oxygen‐deficient zones’, contribute to the loss of fixed nitrogen from the ocean by anaerobic microbial processes. While these microbial processes associated with the nitrogen cycle have been extensively studied, those linked to the carbon cycle in AMZs have received much less attention, particularly the a...

Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic di...

Phytoplankton cells are excellent biosensors for environmental monitoring and toxicity assessments in different natural systems. Green algae, in particular, appear to be more responsive to copper (Cu) disturbances. This is interesting considering that Cu pollution in coastal environments has increased over the last century, with enormous repercussi...

Seasonal wind-driven upwelling, high primary production in surface waters, and oxygen deficiency in subsurface waters characterize the coastal ecosystem of the subtropical eastern South Pacific (ESP), and shape the nature and dynamics of the microbial community structure and function. We investigated the diversity, abundance, and transcriptional le...

Cyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic marine organisms and key factors in the global carbon cycle. The understanding of their distribution and ecological importance in oligotrophic tropical and subtropical waters, and their differentiation into distinct ecotypes, is based on genetic and physiological inform...

Consider an elementary cellular automaton (ECA) under periodic boundary conditions. Given an arbitrary partition of the set of vertices we consider the block updating, i.e. the automaton’s local function is applied from the first to the last set of the partition such that vertices belonging to the same set are updated synchronously. The automaton i...

Unlabelled: Phylogenetic analyses today involve dealing with computer files in different formats and often several computer programs. Although some widely used applications have integrated important functionalities for such analyses, they still work with local resources only: input/output files (users have to manage them) and local computing (user...

The composition of ammonia-oxidizing bacteria from the β-Proteobacteria subclass (βAOB) was studied in the surface and upper-oxycline oxic waters (2- to 50-m depth, ∼200 to 44 μM O2) and within the oxygen minimum zone (OMZ) suboxic waters (50- to 400-m depth, ≤10 μM O2) of the eastern South Pacific off northern Chile. This study was carried out thr...

In recent years, our group has been studying the microbial communities of the water column associated with the oxygen minimum zone (OMZ) off northern Chile and Peru, trying to understand who the main players are in the OMZ biogeochemical cycles and which metabolic strategies they are using. For that, we are combining flow cytometry, molecular techn...