Browsing by Author "Alcorta Loyola, Jaime Andrés"

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    Compensatory Transcriptional Response of Fischerella thermalis to Thermal Damage of the Photosynthetic Electron Transfer Chain
    (2022) Vergara-Barros, Pablo; Alcorta Loyola, Jaime Andrés; Casanova-Katny, Angélica; Nürnberg, Dennis J.; Díez, Beatriz
    Key organisms in the environment, such as oxygenic photosynthetic primary producers (photosynthetic eukaryotes and cyanobacteria), are responsible for fixing most of the carbon globally. However, they are affected by environmental conditions, such as temperature, which in turn affect their distribution. Globally, the cyanobacterium Fischerella thermalis is one of the main primary producers in terrestrial hot springs with thermal gradients up to 60 °C, but the mechanisms by which F. thermalis maintains its photosynthetic activity at these high temperatures are not known. In this study, we used molecular approaches and bioinformatics, in addition to photophysiological analyses, to determine the genetic activity associated with the energy metabolism of F. thermalis both in situ and in high-temperature (40 °C to 65 °C) cultures. Our results show that photosynthesis of F. thermalis decays with temperature, while increased transcriptional activity of genes encoding photosystem II reaction center proteins, such as PsbA (D1), could help overcome thermal damage at up to 60 °C. We observed that F. thermalis tends to lose copies of the standard G4 D1 isoform while maintaining the recently described D1INT isoform, suggesting a preference for photoresistant isoforms in response to the thermal gradient. The transcriptional activity and metabolic characteristics of F. thermalis, as measured by metatranscriptomics, further suggest that carbon metabolism occurs in parallel with photosynthesis, thereby assisting in energy acquisition under high temperatures at which other photosynthetic organisms cannot survive. This study reveals that, to cope with the harsh conditions of hot springs, F. thermalis has several compensatory adaptations, and provides emerging evidence for mixotrophic metabolism as being potentially relevant to the thermotolerance of this species. Ultimately, this work increases our knowledge about thermal adaptation strategies of cyanobacteria.
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    Distribution and Activity of Sulfur-Metabolizing Bacteria along the Temperature Gradient in Phototrophic Mats of the Chilean Hot Spring Porcelana
    (2023) Konrad, Ricardo; Vergara Barros, Pablo; Alcorta Loyola, Jaime Andrés; Alcamán Arias, María E.; Levicán, Gloria; Ridley, Christina; Diez Moreno, Beatriz
    In terrestrial hot springs, some members of the microbial mat community utilize sulfur chemical species for reduction and oxidization metabolism. In this study, the diversity and activity of sulfur-metabolizing bacteria were evaluated along a temperature gradient (48–69 °C) in non-acidic phototrophic mats of the Porcelana hot spring (Northern Patagonia, Chile) using complementary meta-omic methodologies and specific amplification of the aprA (APS reductase) and soxB (thiosulfohydrolase) genes. Overall, the key players in sulfur metabolism varied mostly in abundance along the temperature gradient, which is relevant for evaluating the possible implications of microorganisms associated with sulfur cycling under the current global climate change scenario. Our results strongly suggest that sulfate reduction occurs throughout the whole temperature gradient, being supported by different taxa depending on temperature. Assimilative sulfate reduction is the most relevant pathway in terms of taxonomic abundance and activity, whereas the sulfur-oxidizing system (Sox) is likely to be more diverse at low rather than at high temperatures. Members of the phylum Chloroflexota showed higher sulfur cycle-related transcriptional activity at 66 °C, with a potential contribution to sulfate reduction and oxidation to thiosulfate. In contrast, at the lowest temperature (48 °C), Burkholderiales and Acetobacterales (both Pseudomonadota, also known as Proteobacteria) showed a higher contribution to dissimilative sulfate reduction/oxidation as well as to thiosulfate metabolism. Cyanobacteriota and Planctomycetota were especially active in assimilatory sulfate reduction. Analysis of the aprA and soxB genes pointed to members of the order Burkholderiales (Gammaproteobacteria) as the most dominant and active along the temperature gradient for these genes. Changes in the diversity and activity of different sulfur-metabolizing bacteria in photoautotrophic microbial mats along a temperature gradient revealed their important role in hot spring environments, especially the main primary producers (Chloroflexota/Cyanobacteriota) and diazotrophs (Cyanobacteriota), showing that carbon, nitrogen, and sulfur cycles are highly linked in these extreme systems.
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    Effects of hydrogeochemistry on the microbial ecology of terrestrial hot springs
    (2023) Barbosa, Carla; Tamayo Leiva, Javier Alejandro; Alcorta Loyola, Jaime Andrés; Salgado Salgado, Oscar Alexis; Daniele, Linda; Morata, Diego; Diez Moreno, Beatriz
    Temperature, pH, and hydrochemistry of terrestrial hot springs play a critical role in shaping thermal microbial communities. However, the interactions of biotic and abiotic factors at this terrestrial-aquatic interface are still not well understood on a global scale, and the question of how underground events influence microbial communities remains open. To answer this, 11 new samples obtained from the El Tatio geothermal field were analyzed by 16S rRNA amplicon sequencing (V4 region), along with 191 samples from previous publications obtained from the Taupo Volcanic Zone, the Yellowstone Plateau Volcanic Field, and the Eastern Tibetan Plateau, with their temperature, pH, and major ion concentration. Microbial alpha diversity was lower in acid-sulfate waters, and no significant correlations were found with temperature. However, moderate correlations were observed between chemical parameters such as pH (mostly constrained to temperatures below 70°C), SO4 2− and abundances of members of the phyla Armatimonadota, Deinococcota, Chloroflexota, Campilobacterota, and Thermoplasmatota. pH and SO4 2− gradients were explained by phase separation of sulfur-rich hydrothermal fluids and oxidation of reduced sulfur in the steam phase, which were identified as key processes shaping these communities. Ordination and permutational analysis of variance showed that temperature, pH, and major element hydrochemistry explain only 24% of the microbial community structure. Therefore, most of the variance remained unexplained, suggesting that other environmental or biotic factors are also involved and highlighting the environmental complexity of the ecosystem and its great potential to test niche theory ecological associated questions.
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    Fischerella thermalis: a model organism to study thermophilic diazotrophy, photosynthesis and multicellularity in cyanobacteria
    (2019) Alcorta Loyola, Jaime Andrés; Vergara-Barros, Pablo; Antonaru, Laura A.; Alcamán-Arias, María E.; Nürnberg, Dennis J.; Díez, Beatriz
    The true-branching cyanobacterium Fischerella thermalis (also known as Mastigocladus laminosus) is widely distributed in hot springs around the world. Morphologically, it has been described as early as 1837. However, its taxonomic placement remains controversial. F. thermalis belongs to the same genus as mesophilic Fischerella species but forms a monophyletic clade of thermophilic Fischerella strains and sequences from hot springs. Their recent divergence from freshwater or soil true-branching species and the ongoing process of specialization inside the thermal gradient make them an interesting evolutionary model to study. F. thermalis is one of the most complex prokaryotes. It forms a cellular network in which the main trichome and branches exchange metabolites and regulators via septal junctions. This species can adapt to a variety of environmental conditions, with its photosynthetic apparatus remaining active in a temperature range from 15 to 58 °C. Together with its nitrogen-fixing ability, this allows it to dominate in hot spring microbial mats and contribute significantly to the de novo carbon and nitrogen input. Here, we review the current knowledge on the taxonomy and distribution of F. thermalis, its morphological complexity, and its physiological adaptations to an extreme environment.
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    Genomic changes related with the adaptation to thermal environments on the origins of Fischerella thermalis species and other hot spring cyanobacteria
    (2023) Alcorta Loyola, Jaime Andrés; Diez Moreno, Beatriz; Pontificia Universidad Católica de Chile. Facultad de Ciencias Biológicas
    Los organismos termófilos están ampliamente distribuidos en el árbol de la vida y habitan ambientes extremos como lo son las fuentes termales terrestres. Sin embargo, su polifilia exalta la pregunta sobre qué propiedades genómicas les han permitido adaptarse muchas veces independientemente a este nicho. Uno de los miembros más importantes en un tipo de comunidades microbianas de fuentes termales son las cianobacterias, quienes son capaces de realizar fotosíntesis oxigénica e incluso fijación de nitrógeno. Estas bacterias pueden vivir hasta los 73 °C, y hay tres grupos que han sido largamente estudiados tanto a través de microscopía, aislados en cultivo, secuenciación de genomas, y metagenómica: las unicelulares (por ejemplo, Synechococcus y Thermosynechococcus termófilos), las filamentosas no formadoras de heterocistos (por ejemplo, Thermoleptolyngbya) y las filamentosas ramificadas formadoras de heterocistos (por ejemplo, Fischerella). Aún así, hay una gran falta de información genómica de otros miembros que han sido cultivados o identificados sólo a través de perfiles de 16S rRNA en muestras ambientales. En esta tesis, nuestro objetivo fue descifrar la diversidad de cianobacterias de fuentes termales a través de la recuperación de genomas ensamblados desde metagenomas y también estudiar las características distintivas cuando son comparadas con genomas de cianobacterias no termales, para descubrir sus adaptaciones genómicas y los mecanismos evolutivos potencialmente involucrados en la divergencia hacia ambientes con altas temperaturas. Por lo tanto, hemos recuperado 57 genomas ensamblados desde metagenomas (MAGs por sus siglas en inglés) cianobacterianos de media y alta calidad, provenientes de 21 metagenomas globales de tapetes microbianos fototróficos termales (32 – 75 °C). Estos MAGs se distribuyeron a lo largo de 10 ordenes de un total de 15 en el phylum, y representaron una alta novedad desde el nivel de orden al de especies, donde incluso un 74 % no se pudo asociar a ninguna especie conocida. Junto a los genomas de cianobacterias de fuentes termales y ambientes no termales cercanos a estos MAGs, se realizaron comparaciones en las que observamos claras diferencias como un tamaño de genoma más pequeño, mayor contenido de GC; proteínas más pequeñas, hidrofóbicas y básicas, y una mayor dependencia en los sistemas de defensa tipo CRISPR-cas además de un enriquecimiento en funciones metabólicas como transporte de iones inorgánicos y metabolismo de aminoácidos en los genomas termales. Estas diferencias muestran que las cianobacterias de fuentes termales tienen características genómicas comunes para adaptarse a su ambiente. Además, el mecanismo que les permitió divergir y adaptarse fue estudiado con mayor profundidad en el género Fischerella. Para esto, secuenciamos 4 cepas aisladas y recuperamos 19 MAGs, los que nos permitieron comparar junto a 48 genomas de la NCBI (National Center for Biotechnology Information, USA) un total de 64 genomas termales versus 7 genomas de otros ambientes de este género. Todas las secuencias codificantes fueron clasificadas en cerca de 14.300 ortogrupos (grupos de secuencias ortólogas) de los cuales 2.805 estuvieron presentes en casi todos los genomas (el genoma esencial o core en inglés) y 21 estuvieron presentes en casi todos los genomas termales y ausentes en los no termales (genoma accesorio de Fischerella y esencial termal). Para inferir una posible historia de la adquisición de la termofilia, exploramos principalmente tres mecanismos que son: transferencia horizontal de genes (HGT por sus siglas en inglés), duplicación génica y fijación de mutaciones. Junto con eso, quisimos ver si es que los genes seleccionados podrían tener una correlación con la temperatura a través del reclutamiento de secuencias en 21 muestras de metatranscriptomas ambientales (45 – 66 °C). Nuestros resultados apuntaron al mecanismo de HGT, más que a los otros dos; identificando un gen accessorio de Fischerella y esencial termal potencialmente adquirido por HGT independientemente en dos ramas termales y con una correlación positiva con la temperatura, sugiriendo un posible rol de esta metiltransferasa dependiente de S-adenosil-L-metionina en la adaptación a este ambiente extremo. Por lo tanto, sugerimos una secuencia de eventos en la historia del género Fischerella, el cual a través de la especiación alopátrica de los clados termales, estos divergieron y siguieron distintos mecanismos para lidiar con sus ambientes diferentes a los no termales. Las especies termales de Fischerella parecieron seguir una vía de reducción genómica (genome streamlining en inglés), que ha sido seguida por muchos extremófilos, y tendieron a mantener más estables sus genomas, mientras que el grupo de Fischerella no termal pareció seguir un camino de expansión genómica, siendo susceptibles a la transferencia de plásmidos, HGT y a la actividad de transposasas. Sobretodo, nuestros resultados resaltan el rol de la transferencia lateral de genes (HGT) en las cianobacterias de comunidades microbianas termales como un jugador principal en su adaptación que les condujo a ser parte de los miembros dominantes en los tapetes microbianos de fuentes terrestres termales no ácidas de todo el mundo.
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    Genomic Features for Desiccation Tolerance and Sugar Biosynthesis in the Extremophile Gloeocapsopsis sp. UTEX B3054
    (2019) Urrejola, Catalina; Alcorta Loyola, Jaime Andrés; Salas, Loreto; Vásquez, Mónica; Polz, Martin; Vicuña, Rafael; Díez, Beatriz
    For tolerating extreme desiccation, cyanobacteria are known to produce both compatible solutes at intracellular level and a copious amount of exopolysaccharides as a protective coat. However, these molecules make cyanobacterial cells refractory to a broad spectrum of cell disruption methods, hindering genome sequencing, and molecular studies. In fact, few genomes are already available from cyanobacteria from extremely desiccated environments such as deserts. In this work, we report the 5.4 Mbp draft genome (with 100% of completeness in 105 contigs) of Gloeocapsopsis sp. UTEX B3054 (subsection I; Order Chroococcales), a cultivable sugar-rich and hardly breakable hypolithic cyanobacterium from the Atacama Desert. Our in silico analyses focused on genomic features related to sugar-biosynthesis and adaptation to dryness. Among other findings, screening of Gloeocapsopsis genome revealed a unique genetic potential related to the biosynthesis and regulation of compatible solutes and polysaccharides. For instance, our findings showed for the first time a novel genomic arrangement exclusive of Chroococcaceae cyanobacteria associated with the recycling of trehalose, a compatible solute involved in desiccation tolerance. Additionally, we performed a comparative genome survey and analyses to entirely predict the highly diverse pool of glycosyltransferases enzymes, key players in polysaccharide biosynthesis and the formation of a protective coat to dryness. We expect that this work will set the fundamental genomic framework for further research on microbial tolerance to desiccation and to a wide range of other extreme environmental conditions. The study of microorganisms like Gloeocapsopsis sp. UTEX B3054 will contribute to expand our limited understanding regarding water optimization and molecular mechanisms allowing extremophiles to thrive in xeric environments such as the Atacama Desert.
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    High-Quality Draft Genome Sequence of Fischerella thermalis JSC-11, a Siderophilic Cyanobacterium with Bioremediation Potential
    (2022) Brown, Igor; Woyke, Tanja; Ivanova, Natalia; Shapiro, Nicole; Alcorta Loyola, Jaime Andrés; Chistoserdov, Andrei; Pan, Donald; Sarkisova, Svetlana; Tringe, Susannah G.; Maresca, Julia A.
    Here, we report the draft genome sequence of the siderophilic cyanobacterium Fischerella thermalis JSC-11, which was isolated from an iron-depositing hot spring. JSC-11 has bioremediation potential because it is capable of both extracellular absorption and intracellular mineralization of colloidal iron. This genomic information will facilitate the exploration of JSC-11 for bioremediation.
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    Physiological and gene expression responses to nitrogen regimes and temperatures in Mastigocladus sp strain CHP1, a predominant thermotolerant cyanobacterium of hot springs.
    (2017) Alcamán, M. Estrella; Alcorta Loyola, Jaime Andrés; Bergman, Birgitta; Vásquez Pérez, Luz Mónica; Polz, Martin; Diez Moreno, Beatriz
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    Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803
    (2023) Nies, Fabián; Wein, Tanita; Hanke, Dustin M.; Springstein, Benjamin L.; Alcorta Loyola, Jaime Andrés; Taubenheim, Claudia; Dagan, Tal
    Small cryptic plasmids have no clear effect on the host fitness and theirfunctional repertoire remains obscure. The naturally competent cyanobacte-riumSynechocystissp. PCC 6803 harbours several small cryptic plasmids;whether their evolution with this species is supported by horizontal transferremains understudied. Here, we show that the small cryptic plasmid DNA istransferred in the population exclusively by natural transformation, wherethe transfer frequency of plasmid-encoded genes is similar to that ofchromosome-encoded genes. Establishing a system to follow gene transfer,we compared the transfer frequency of genes encoded in cryptic plasmidspCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations oftwoSynechocystissp. PCC 6803 labtypes (termed Kiel and Sevilla). Ourresults reveal that plasmid gene transfer frequency depends on the recipientlabtype. Furthermore, gene transfer via whole plasmid uptake in the Sevillalabtype ranged among the lowest detected transfer rates in our experi-ments. Our study indicates that horizontal DNA transfer via natural transfor-mation is frequent in the evolution of small cryptic plasmids that reside innaturally competent organisms. Furthermore, we suggest that the contribu-tion of natural transformation to cryptic plasmid persistence inSynechocys-tisis limited.
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    Structure and dispersion of the conjugative mobilome in surface ocean bacterioplankton
    (2024) Tamayo Leiva, Javier Alejandro Ignacio; Alcorta Loyola, Jaime Andrés; Sepúlveda, Felipe; Fuentes-Alburquenque, Sebastián; Arroyo González, José Ignacio; González-Pastor, José Eduardo; Diez Moreno, Beatriz Eugenia
    Mobile genetic elements (MGEs), collectively referred to as the “mobilome”, can have a significant impact on the fitness of microbial communities and therefore on ecological processes. Marine MGEs have mainly been associated with wide geographical and phylogenetic dispersal of adaptative traits. However, whether the structure of this mobilome exhibits deterministic patterns in the natural community is still an open question. The aim of this study was to characterize the structure of the conjugative mobilome in the ocean surface bacterioplankton by searching the publicly available marine metagenomes from the TARA Oceans survey, together with molecular markers, such as relaxases and type IV coupling proteins of the type IV secretion system (T4SS). The T4SS machinery was retrieved in more abundance than relaxases in the surface marine bacterioplankton. Moreover, among the identified MGEs, mobilizable elements were the most abundant, outnumbering self-conjugative sequences. Detection of a high number of incomplete T4SSs provides insight into possible strategies related to trans-acting activity between MGEs, and accessory functions of the T4SS (e.g., protein secretion), allowing the host to maintain a lower metabolic burden in the highly dynamic marine system. Additionally, the results demonstrate a wide geographical dispersion of MGEs throughout oceanic regions, while the Southern Ocean appears segregated from other regions. The marine mobilome also showed a high similarity of functions present in known plasmid databases. Moreover, cargo genes were mostly related to DNA processing, but scarcely associated with antibiotic resistance. Finally, within the MGEs, integrative and conjugative elements showed wider marine geographic dispersion than plasmids.
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    Taxonomic Novelty and Distinctive Genomic Features of Hot Spring Cyanobacteria
    (2020) Alcorta Loyola, Jaime Andrés; Alarcon Schumacher, T.; Salgado Salgado, Oscar Alexis; Diez Moreno, Beatriz
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    Temperature modulates Fischerella thermalis ecotypes in Porcelana Hot Spring
    (2018) Alcorta Loyola, Jaime Andrés; Espinoza Lara, Sebastián Andrés; Tomeu, Viver; Alcaman Arias, María E.; Trefault Carrillo, Nicole Natalie; Rosselló-Móra, Ramon; Díez, Beatriz
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    The order of trait emergence in the evolution of cyanobacterial multicellularity
    (2019) Hammerschmidt, Katrin; Landan, Giddy; Domingues Kümmel Tria, Fernando; Alcorta Loyola, Jaime Andrés; Dagan, Tal
    The transition from unicellular to multicellular organisms is one of the most significant events in the history of life. Key to this process is the emergence of Darwinian individuality at the higher level: groups must become single entities capable of reproduction for selection to shape their evolution. Evolutionary transitions in individuality are characterized by cooperation between the lower level entities and by division of labor. Theory suggests that division of labor may drive the transition to multicellularity by eliminating the trade-off between two incompatible processes that cannot be performed simultaneously in one cell. Here we examine the evolution of the most ancient multicellular transition known today, that of cyanobacteria, where we reconstruct the sequence of ecological and phenotypic trait evolution. Our results show that the prime driver of multicellularity in cyanobacteria was the expansion in metabolic capacity offered by nitrogen fixation, which was accompanied by the emergence of the filamentous morphology and succeeded by a reproductive life cycle. This was followed by the progression of multicellularity into higher complexity in the form of differentiated cells and patterned multicellularity.