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Astorga-Elo, M., Ramirez-Flandes, S., DeLong, E. F., & Ulloa, O. (2015). Genomic potential for nitrogen assimilation in uncultivated members of Prochlorococcus from an anoxic marine zone. Isme J., 9(5), 1264–1267.
Abstract: 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 information from several isolates. Currently, all available Prochlorococcus genomes show their incapacity for nitrate utilization. However, environmental sequence data suggest that some uncultivated lineages may have acquired this capacity. Here we report that uncultivated low-light-adapted Prochlorococcus from the nutrient-rich, low-light, anoxic marine zone (AMZ) of the eastern tropical South Pacific have the genetic potential for nitrate uptake and assimilation. All genes involved in this trait were found syntenic with those present in marine Synechococcus. Genomic and phylogenetic analyses also suggest that these genes have not been aquired recently, but perhaps were retained from a common ancestor, highlighting the basal characteristics of the AMZ lineages within Prochlorococcus.
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Goles, E., Montalva-Medel, M., Mortveit, H., & Ramirez-Flandes, S. (2015). Block Invariance in Elementary Cellular Automata. J. Cell. Autom., 10(1-2), 119–135.
Abstract: 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 is said block-invariant if the set of periodic configurations is independent of the choice of the block updating. When the sets of the partition are singletons we have the sequential updating: vertices are updated one by one following a permutation pi. In [5] the authors analyzed the pi-invariance of the 2(8) = 256 possible ECA rules (or the 88 non-redundant rules subset). Their main result was that for all n > 3, exactly 41 of these non-redundant rules are pi-invariant. In this paper we determine the subset of these 41 rules that are block invariant. More precisely, for all n > 3, exactly 15 of these rules are block invariant. Moreover, we deduce that block invariance also implies that the attractor structure itself is independent of the choice of the block update.
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Plominsky, A. M., Henriquez-Castillo, C., Delherbe, N., Podell, S., Ramirez-Flandes, S., Ugalde, J. A., et al. (2018). Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation. Front. Microbiol., 9, 13 pp.
Abstract: 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 diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cahuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cahuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cahuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (>30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them.
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Ramirez-Flandes, S., Gonzalez, B., & Ulloa, O. (2019). Redox traits characterize the organization of global microbial communities. Proc. Natl. Acad. Sci. U. S. A., 116(9), 3630–3635.
Abstract: The structure of biological communities is conventionally described as profiles of taxonomic units, whose ecological functions are assumed to be known or, at least, predictable. In environmental microbiology, however, the functions of a majority of microorganisms are unknown and expected to be highly dynamic and collectively redundant, obscuring the link between taxonomic structure and ecosystem functioning. Although genetic trait-based approaches at the community level might overcome this problem, no obvious choice of gene categories can be identified as appropriate descriptive units in a general ecological context. We used 247 microbial metagenomes from 18 biomes to determine which set of genes better characterizes the differences among biomes on the global scale. We show that profiles of oxidoreductase genes support the highest biome differentiation compared with profiles of other categories of enzymes, general protein-coding genes, transporter genes, and taxonomic gene markers. Based on oxidoreductases' description of microbial communities, the role of energetics in differentiation and particular ecosystem function of different biomes become readily apparent. We also show that taxonomic diversity is decoupled from functional diversity, e. g., grasslands and rhizospheres were the most diverse biomes in oxidoreductases but not in taxonomy. Considering that microbes underpin biogeochemical processes and nutrient recycling through oxidoreductases, this functional diversity should be relevant for a better understanding of the stability and conservation of biomes. Consequently, this approach might help to quantify the impact of environmental stressors on microbial ecosystems in the context of the global-scale biome crisis that our planet currently faces.
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