Biology subjects

Martinez-Hernandez, F.

Publications and source records attributed to Martinez-Hernandez, F..

3 recordsLinked to original sources

bioRxiv2025

Illuminating the active virosphere with BONCAT and single virus genomic sequencing technologies

Marine viruses impact biogeochemical cycles through cell lysis, releasing organic matter and nutrients that fuel ocean productivity. Identifying and quantifying the specific viruses active in these processes remains a priority in the field. Here, we introduce a click-chemistry method to fluorescently label, sort, and sequence the genomes of newly produced viral particles released from transcriptionally active host microbial cells, alongside the analysis of co-occurring inactive cells and viruses in environmental samples. This approach, called viral BONCAT-FACS, combines biorthogonal non-canonical amino acid tagging (BONCAT) with environmental sample incubation, followed by single-virus and single-cell sorting by flow cytometry (FACS). Genomic analysis of translationally-active cells and new viral progeny in coastal seawater incubations confirmed BONCAT labeling and successful sorting of diverse marine bacteria, microeukaryotic cells, and virioplankton, with stark differences in the predicted turnover of specific groups of infecting viruses, including Pelagiphages, Methylophages, a Flavobacteriales-associated novel "Far-T4" clade, algae-infecting giant NCLDV viruses, and parasitic virophages. Sequenced BONCAT-active cells showed a strong enrichment in viral contigs relative to the inactive cell fraction, suggestive of a large proportion of translationally-active virocells. This study illustrates the effectiveness of viral BONCAT-FACS for uncovering genome-resolved viral-host dynamics. By providing a direct approach for tracking active viral infections in natural environments, this method enhances our ability to investigate behavior and interactions of these nanoscale predators, expanding our understanding of their role in ecosystem dynamics.

microbiology↗

bioRxiv2023

New avenues for potentially seeking microbial responses to climate change beneath Antarctic ice shelves

The signs of climate change are undeniable, and the impact of these changes on ecosystem function heavily depends on the response of microbes that underpin the food web. Antarctic ice shelf is a massive mass of floating ice that extends from the continent into the ocean, exerting a profound influence on global carbon cycles. Beneath Antarctic ice shelves, marine ice stores valuable genetic information, where marine microbial communities before the industrial revolution are archived. Here, in this proof-of-concept, by employing a combination of single-cell genomics and metagenomics, we have been able to sequence frozen microbial DNA ({asymp}300 years old) stored in the marine ice core B15 collected from the Filchnner-Ronne Ice Shelf. Metagenomic data indicated that Proteobacteria and Thaumarchaeota (e.g. Nitrosopumilus spp.) followed by Actinobacteria (e.g. Actinomarinales) were abundant. Remarkably, our data allow us to travel to the past and calibrate genomic and genetic evolutionary changes for ecologically relevant microbes and functions, such as Nitrosopumilus spp., preserved in the marine ice ({asymp}300 years old) with those collected recently in seawater under an ice shelf (year 2017). The evolutionary divergence for the ammonia monooxygenase gene amoA involved in chemolithoautotrophy was about 0.88 amino acid and 2.8 nucleotide substitution rate per 100 sites in a century, while the accumulated rate of genomic SNPs was 2,467 per 1 Mb of genome and 100 years. Whether these evolutionary changes remained constant over the last 300 years or accelerated during post-industrial periods remains an open question that will be further elucidated. ImportanceSeveral efforts have been undertaken to predict the response of microbes under climate change, mainly based on short-term microcosm experiments under forced conditions. A common concern is that manipulative experiments cannot properly simulate the response of microbes to climate change, which is a long-term evolutionary process. In this proof-of-concept study with a limited sample size, we demonstrate a novel approach yet to be fully explored in science for accessing genetic information from putative past marine microbes preserved under Antarctic Ice shelves before Industrial revolution. This potentially allow us estimating evolutionary changes as exemplified in our study. We advocate for gathering a more comprehensive Antarctic marine ice core datasets across various periods and sites. Such a dataset would enable the establishment of a robust baseline, facilitating a better assessment of the potential effects of climate change on key genetic signatures of microbes.

microbiology↗

bioRxiv2020

The relic ecosystem of Gymnosporia senegalensis (Lam.) Loes. in an agricultural plastic sea: past, present and future scenarios

Gymnosporia senegalensis is a shrub belonging to the Celastraceae family, which is native to tropical savannahs. Its only European populations are distributed discontinuously along the south-eastern coast of the Iberian Peninsula, forming plant communities with great ecological value, unique in Europe. As it is an endangered species that makes up plant communities with great palaeoecological significance, the development of species distribution models is of major interest under different climatic scenarios, past, present and future, based on the fact that the climate could play a relevant role in the distribution of this species as well as in the conformation of the communities in which it is integrated. Palaeoecological models were generated for the Maximum Interglacial, Last Maximum Glacial and Middle Holocene periods. The results obtained showed that the widest distribution of this species, and the maximum suitability of its habitat, occurred during the Last Glacial Maximum, when the temperatures of the peninsular southeast were not as contrasting as those of the rest of the European continent and were favored by higher rainfall. Under these conditions, large territories could act as shelters during the glacial period, a hypothesis reflected in the models results for this period, which exhibit a further expansion of G. senegalensis ecological niche. The future projection of models in around 2070, for four Representative Concentration Pathway (RCP) according to the fifth report of the Intergovernmental Panel on Climate Change IPCC, showed that the most favorable areas for this species would be Campo de Dalias (southern portion of Almeria province) as it presents the bioclimatic characteristics of greater adjustment to G. senegalensis ecological niche model. Currently, these areas are almost totally destroyed and heavily altered by intensive agriculture under plastic, also causing a severe fragmentation of the habitat, which implies a prospective extinction scenario in the near future.

ecology↗