The Evolutionary Success of the Marine Bacterium SAR11 Analyzed through a Metagenomic Perspective

The SAR11 clade of Alphaproteobacteria is the most abundant group of planktonic cells in the near-surface epipelagic waters of the ocean, but the mechanisms underlying its exceptional success have not been fully elucidated. Here, we applied a metagenomic approach to explore microdiversity patterns by measuring the accumulation of synonymous and nonsynonymous mutations as well as homologous recombination in populations of SAR11 from different aquatic habitats (marine epipelagic, bathypelagic, and surface freshwater). The patterns of mutation accumulation and recombination were compared to those of other groups of representative marine microbes with multiple ecological strategies that share the same marine habitat, namely, Cyanobacteria (Prochlorococcus and Synechococcus), Archaea (“Candidatus Nitrosopelagicus” and Marine Group II Thalassoarchaea), and some heterotrophic marine bacteria (Alteromonas and Erythrobacter). SAR11 populations showed widespread recombination among distantly related members, preventing divergence leading to a genetically stable population. Moreover, their high intrapopulation sequence diversity with an enrichment in synonymous replacements supports the idea of a very ancient divergence and the coexistence of multiple different clones. However, other microbes analyzed seem to follow different evolutionary dynamics where processes of diversification driven by geographic and ecological instability produce a higher number of nonsynonymous replacements and lower intrapopulation sequence diversity. Together, these data shed light on some of the evolutionary and ecological processes that lead to the large genomic diversity in SAR11. Furthermore, this approach can be applied to other similar microbes that are difficult to culture in the laboratory, but abundant in nature, to investigate the underlying dynamics of their genomic evolution.This work was supported by grants VIREVO CGL2016-76273-P (AEI/FEDER, EU) (cofunded with FEDER funds) from the Spanish Ministerio de Economía, Industria, y Competitividad and HIDRAS3 PROMETEU/2019/009 from the Generalitat Valenciana to F.R.-V. and by grants CGL2013-40564-R and SAF2013-49267-EXP from the Spanish Ministerio de Economía, Industria, y Competitividad; grant ACIF/2015/332 from the Generalitat Valenciana; and grant 5334 from the Betty Moore Foundation to M.M.-G. F.R.-V. was also a beneficiary of the 5top100-program of the Ministry for Science and Education of Russia. J.M.H.-M. was supported by a Ph.D. fellowship from the Spanish Ministerio de Economía y Competitividad (BES-2014-067828). F.H.C. was supported by a postdoctoral fellowship from the Generalitat Valenciana (APOSTD/2018/186). M.L.-P. was supported by a postdoctoral fellowship from the Spanish Ministerio de Economía, Industria, y Competitividad (IJCI-2017-34002)

Diversity and Ecology of Aquatic Viruses

Jornada Nous avenços en ecologia microbiana, 4 de febrer de 2022 en BarcelonaPeer reviewe

Machine Learning Applied to Marine Ecology

The need to understand the dynamics of biological communities has never been more pressing. Ecosystems and the biological diversity therein are currently threatened b y anthropogenic impacts. Developing strategies to reduce these impacts is of fundamental importance for the conservation of Earth ́s ecosystems. Doing so depends on the comprehensive and mechanistic understanding of how these ecosystems function, which has been a central goal of ecology. Although undeniable advances have been made, our understanding of the processes driving ecosystem functioning are still limited. This is specially true for the case of mechanistic models that can shed light on these process and also provide reliable predictions for future scenarios. Obtaining such models would allow us to anticipate the extension of anthropogenic impacts at the global scale and also help to develop strategies to mitigate them. [...]Peer reviewe

Are viruses the key to understanding the impact of climate change on the marine microbiome? No, but I still like them anyway

Seminar TREC - Plankton, 23 February 2024, BarcelonaPeer reviewe

Metagenomics in polluted aquatic environments

16 p. : il.Metagenomics is defined as the culture-independent genomic analysis of biological assemblages providing access to the whole set of genes and genomes from a sample. It encompasses a variety of techniques that are based on (i) total DNA extraction from samples followed by PCR amplification of specific genes, (ii) library construction or amplification and sequencing of the whole genetic material. These methodologies have successfully been applied in studies of composition, dynamics, and functions of microbial communities in a variety of ecosystems including those subjected to anthropogenic modifications (Gilbert & Dupont, 2011). Culture independent methods allow the analysis of a set of metabolic genes from microbial communities, which can be used to determine how environmental conditions such as pollution can shape community composition and the diversity of genes associated with biogeochemical cycles such as those of carbon, nitrogen, and phosphorus (Singh et al., 2009). This approach is also useful for the discovery of novel environmental microorganisms and genes, with important applications for biotechnology, medicine, and bioremediation (Cardoso et al., 2011). This applicability has resulted in a recent sharp increase in studies focusing in the metagenomic analysis of polluted sites. Their aim is to characterize microbial communities from a diverse set of environments such as freshwater, marine sediments, open ocean, pelagic ecosystems, soil, and host-associated communities. An example of these initiatives is the Global Ocean Sampling Expedition (GOS), which assessed the genetic diversity of marine microbial communities around the Earth. Since 2003, an enormous amount of data has been generated by GOS helping scientists to reveal the microbial diversity and also allowing them to better understand microbial phylogeny and ecology (Gilbert & Dupont, 2011)

Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake

18 pages, 5 figures, 2 tables, supplementary material https://www.frontiersin.org/articles/10.3389/fmicb.2021.701414/full#supplementary-material.-- Data Availability Statement: All DNA sequence FASTQ files are deposited in the NCBI Nucleotide Archive under SRR14023866 (CB2 Bacterial and Archaeal), SRR 14023937 (GSL 3510 Bacterial and Archaeal), SRR14023877 (GB14 Bacterial and Archaeal), SRR14023878 (CB2 Viral), SRR14023865 (GSL3510 Viral), and SRR14023938 (GB14 Viral). The Bioproject id is PRJNA714934. The NCBI genome accession numbers for the MAGs and viral assemblies are shown in Supplementary Table S10Viruses play vital biogeochemical and ecological roles by (a) expressing auxiliary metabolic genes during infection, (b) enhancing the lateral transfer of host genes, and (c) inducing host mortality. Even in harsh and extreme environments, viruses are major players in carbon and nutrient recycling from organic matter. However, there is much that we do not yet understand about viruses and the processes mediated by them in the extreme environments such as hypersaline habitats. The Great Salt Lake (GSL) in Utah, United States is a hypersaline ecosystem where the biogeochemical role of viruses is poorly understood. This study elucidates the diversity of viruses and describes virus–host interactions in GSL sediments along a salinity gradient. The GSL sediment virosphere consisted of Haloviruses (32.07 ± 19.33%) and members of families Siphoviridae (39.12 ± 19.8%), Myoviridae (13.7 ± 6.6%), and Podoviridae (5.43 ± 0.64%). Our results demonstrate that salinity alongside the concentration of organic carbon and inorganic nutrients (nitrogen and phosphorus) governs the viral, bacteria, and archaeal diversity in this habitat. Computational host predictions for the GSL viruses revealed a wide host range with a dominance of viruses that infect Proteobacteria, Actinobacteria, and Firmicutes. Identification of auxiliary metabolic genes for photosynthesis (psbA), carbon fixation (rbcL, cbbL), formaldehyde assimilation (SHMT), and nitric oxide reduction (NorQ) shed light on the roles played by GSL viruses in biogeochemical cycles of global relevanceThe funding for this project was provided by the United States National Science Foundation with project number 1510255With the institutional support of the ‘Severo OchoaCentre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

Investigating the viral ecology and contribution to the microbial ecology in full-scale mesophilic anaerobic digesters

11 pages, 5 figures, supplementary data https://doi.org/10.1016/j.chemosphere.2023.140743.-- Availability of data and materials: The raw sequences and metadata were submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). The project number is PRJNA872498In an attempt to assess the diversity of viruses and their potential to modulate the metabolism of functional microorganisms in anaerobic digesters, we collected digestate from three mesophilic anaerobic digesters in full-scale wastewater treatment plants treating real municipal wastewater. The reads were analyzed using bioinformatics algorithms to elucidate viral diversity, identify their potential role in modulating the metabolism of functional microorganisms, and provide essential genomic information for the potential use of virus-mediated treatment in controlling the anaerobic digester microbiome. We found that Siphoviridae was the dominant family in mesophilic anaerobic digesters, followed by Myoviridae and Podoviridae. Lysogeny was prevalent in mesophilic anaerobic digesters as the majority of metagenome-assembled genomes contained at least one viral genome within them. One virus within the genome of an acetoclastic methanogen (Methanothrix soehngenii) was observed with a gene (fwdE) acquired via lateral transfer from hydrogenotrophic methanogens. The virus-mediated acquisition of fwdE gene enables possibility of mixotrophic methanogenesis in Methanothrix soehngenii. This evidence highlighted that lysogeny provides fitness advantage to methanogens in anaerobic digesters by adding flexibility to changing substrates. Similarly, we found auxiliary metabolic genes, such as cellulase and alpha glucosidase, of bacterial origin responsible for sludge hydrolysis in viruses. Additionally, we discovered novel viral genomes and provided genomic information on viruses infecting acidogenic, acetogenic, and pathogenic bacteria that can potentially be used for virus-mediated treatment to deal with the souring problem in anaerobic digesters and remove pathogens from biosolids before land application. Collectively, our study provides a genome-level understanding of virome in conjunction with the microbiome in anaerobic digesters that can be used to optimize the anaerobic digestion process for efficient biogas generationThe funding from this project was provided by the United States National Science Foundation with grant number 1804158. However, the views and data discussion expressed are those of the authors and do not necessarily reflect any role of the funding agency. FHC was supported by a Juan de la Cierva - Incoporación fellowship (Grant IJC2019-039859-I).With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

La ciència tampoc no es deslliura del racisme

[EN] Racial aggressions have historically existed in the scientific field and eradicating them is the responsibility of each and every one of the people who are part of it[ES] Las agresiones raciales han existido históricamente en el ámbito científico y erradicarlas es responsabilidad de todas y cada una de las personas que forman parte de este[CAT] Les agressions racials han existit històricament en l'àmbit científic i eradicar-les és responsabilitat de totes i cadascuna de les persones que en formen partPeer reviewe