Biology subjects

Rivas-Santisteban, J.

Publications and source records attributed to Rivas-Santisteban, J..

4 recordsLinked to original sources

bioRxiv2026

Of Brobdingnag and Lilliput, or how the area of an island may determine the size of the bodies and genomes that inhabit it, along with their mutation rates

Insular gigantism and dwarfism are commonly framed by the island rule, whereby small species become larger and large species smaller. Yet why large species diminish, and why some taxa depart from this rule, remain unclear. Here I propose a neutral null model linking island area to body and genome evolution. Island Biogeography Theory predicts that smaller islands support lower census populations, while Damuths law predicts an inverse relationship between body mass and population density. If effective population size, Ne, declines at a different rate from island area, effective density, De = Ne/area, will also change. Under the drift-barrier hypothesis, variation in Ne may further influence genome size and mutation rate, {micro}. Island area may therefore jointly predict body mass, genome size and {micro}. Analyses of global and datasets and particular species are broadly consistent with this expectation, although the observed associations are generally modest.

evolutionary biology↗

bioRxiv2025

Temperature and pH universally govern protein diversity in hydrothermal spring communities, but they do so differently

A general understanding of how extreme temperature and pH might universally shape the evolution of protein variants is lacking. Importantly, while pH is differentially regulated in microbial compartments, temperature is not. We hypothesise that these variables may partly explain the within-genome variability in protein rates of single-celled organisms, since genes encode proteins allocated to different compartments. To test this hypothesis, we examine the number of unique sequence contributors assigned to a KEGG across species as a coarse proxy for accumulated evolutionary divergence. Under a naive null expectation, orthologs of equal abundance should be represented by a similar number of variants. We examine sequence diversity in 17 metagenomes from El Tatio geothermal field (Chile), spanning temperatures of 45-62 {degrees}C, and pH values of 7.2-9.3. At equal abundance, warmer temperature is weakly associated to more ortholog variants, while alkaline pH is associated to fewer (in the ranges examined). The inclusion of these variables in the model robustly improved the prediction of the community-level within-KO unique sequence contributors from metagenomic abundance. KO variant diversity in the periplasm was only significantly affected by pH increases, providing partial support to the compartment hypothesis.

evolutionary biology↗

bioRxiv2024

Microbial nitrogen guilds in the oceans: from the bathypelagic to the ocean surface

Ecological guilds quantify the incidence and extent of resource transformation functions, irrespective of the species involved. Therefore, tackling the microbial nitrogen guilds is key to our understanding of the oceanic nitrogen cycle, but quantitative estimates of guild contribution across varying depths and under specific environmental conditions have yet to be accomplished. In this study, we examine the main picoplankton guilds participating in nitrogen cycling within the low and mid-latitude ocean ecosystems, from the surface down to 4000 m, using data obtained from 75 samples belonging to 11 stations in the Malaspina (MP) dataset. In particular, we used a quantitative approach to investigate the stability of nitrogen acquisition and nitrogen-redox guilds separately. Our results showed that nitrogen acquisition guilds are more stable and redundant than nitrogen-redox guilds across depths and site specific conditions. For example, differential conditions such as nitrogen depletion and oxygen availability affected the two groups of guilds in different ways. These findings have implications for the understanding of global nitrogen fluxes and the biospheres functional diversification.

microbiology↗

bioRxiv2023

Quantifying microbial guilds

The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we identify and distinguish functional implementations, which are sequence spaces that have different ways of carrying out the function. We demonstrate the value of our approach with two case studies: the ammonia oxidation and polyamine uptake guilds from the Malaspina circumnavigation cruise, revealing novel ecological dynamics of the latter in marine ecosystems. Thus, the quantification of guilds helps to assess the functional role of different taxonomic groups with profound implications on the study of microbial communities.

ecology↗