Large-scale biogeography of marine pelagic bacteria and archaea
The dark ocean contains about 70% of the ocean’s microbial cells and 60% of its heterotrophic activity, which is mainly fueled by the flux of organic particles produced in the surface ocean and exported to the bathypelagic ocean (1,000 – 4,000 m depth). The bathypelagic ocean represents a nonhomogen...
| Autor: | |
|---|---|
| Tipo de recurso: | tesis doctoral |
| Fecha de publicación: | 2019 |
| País: | España |
| Institución: | Universitat Politècnica de Catalunya (UPC) |
| Repositorio: | UPCommons. Portal del coneixement obert de la UPC |
| Idioma: | inglés |
| OAI Identifier: | oai:upcommons.upc.edu:2117/129593 |
| Acceso en línea: | https://hdl.handle.net/2117/129593 https://dx.doi.org/10.5821/dissertation-2117-129593 |
| Access Level: | acceso abierto |
| Palabra clave: | Ecologia microbiana Mar -- Contaminació |
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Large-scale biogeography of marine pelagic bacteria and archaea |
| title |
Large-scale biogeography of marine pelagic bacteria and archaea |
| spellingShingle |
Large-scale biogeography of marine pelagic bacteria and archaea Salazar Guiral, Guillem Ecologia microbiana Mar -- Contaminació |
| title_short |
Large-scale biogeography of marine pelagic bacteria and archaea |
| title_full |
Large-scale biogeography of marine pelagic bacteria and archaea |
| title_fullStr |
Large-scale biogeography of marine pelagic bacteria and archaea |
| title_full_unstemmed |
Large-scale biogeography of marine pelagic bacteria and archaea |
| title_sort |
Large-scale biogeography of marine pelagic bacteria and archaea |
| dc.creator.none.fl_str_mv |
Salazar Guiral, Guillem |
| author |
Salazar Guiral, Guillem |
| author_facet |
Salazar Guiral, Guillem |
| author_role |
author |
| dc.contributor.none.fl_str_mv |
Gasol Piqué, Josep Maria González Acinas, Silvia |
| dc.subject.none.fl_str_mv |
Ecologia microbiana Mar -- Contaminació |
| topic |
Ecologia microbiana Mar -- Contaminació |
| description |
The dark ocean contains about 70% of the ocean’s microbial cells and 60% of its heterotrophic activity, which is mainly fueled by the flux of organic particles produced in the surface ocean and exported to the bathypelagic ocean (1,000 – 4,000 m depth). The bathypelagic ocean represents a nonhomogeneous environment and contains a variety of particles that are considered as the main supply of organic carbon to this environment. The microorganisms inhabiting this realm play a pivotal regulatory role in the biogeochemical cycles at a planetary scale. Accordingly, the study of these microorganisms is an essential step to decipher the ecological functioning of the deep ocean. Chapters 1 to 3 in this Thesis are dedicated to the description of the prokaryotic community composition in the bathypelagic ocean at a global scale through the sequencing of ribosomal DNA and RNA fragments using data collected during the Malaspina 2010 expedition. Chapter 1 identifies the dominant prokaryotes in the deep ocean and reveals a high proportion (~50%) of previously undescribed prokaryotes. The water masses and the structure of the deep ocean’s floor, organized into basins, are identified as the main drivers of their biogeography. Chapter 2 addresses the differences between free-living and particle-attached bathypelagic prokaryotic communities. This is shown to be a phylogenetically conserved trait, indicating that the bathypelagic particles and the water surrounding them constitute two distinct niches and that transitions from one to the other have been rare at an evolutionary timescale. Finally, in Chapter 3 we identify a linear relationship between the 16S RNA/DNA ratio and particle attachment preference, suggesting a global relationship between the prokaryote’s preference for a particle-attached lifestyle and their growth rate. While the deep ocean is a highly unexplored environment, a more complete knowledge exists for the epipelagic ocean (0 – 200 m depth). Steep gradients of light intensity and quality, temperature and nutrient availability characterize the oceans and impact on the distribution of species. However, different processes, such as the sinking of particles and the vertical movement of water masses, have been described as mechanisms capable of connecting the surface and deep layers of the ocean. These same processes could transport entire prokaryotic communities, a process theoretically proposed but never tested. In Chapter 4 we develop a tool (mtagger) for the extraction of short 16S ribosomal reads from metagenomes to describe the taxonomical composition of microbial communities. We propose and evaluate technical improvements compared to previous versions as a benchmark for its use in the last chapter. Chapter 5 is dedicated to the development of a modeling tool (disperflux) for the analysis of prokaryotic communities’ connectivity using data collected during the Tara Oceans expedition. We observe and describe a fast-decay relationship between community similarity and depth, which is consistently fitted by a power-law across the whole dataset, with the exception of 5 stations that are compatible with events of whole community export from the photic ocean to the mesopelagic. In summary, this Thesis significantly contributes to the knowledge on the ecological functioning of marine prokaryotes by describing the structure of prokaryotic communities along the bathypelagic realm and the vertical gradient of the ocean and by the development of original methodological tools that may be applied to a variety of environments. |
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2019 |
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2019 2019-02-15 2019 2019-02-25 |
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doctoral thesis http://purl.org/coar/resource_type/c_db06 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
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info:eu-repo/semantics/doctoralThesis |
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doctoralThesis |
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https://hdl.handle.net/2117/129593 https://dx.doi.org/10.5821/dissertation-2117-129593 |
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https://hdl.handle.net/2117/129593 https://dx.doi.org/10.5821/dissertation-2117-129593 |
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Inglés eng |
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Inglés |
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eng |
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open access http://purl.org/coar/access_right/c_abf2 http://creativecommons.org/licenses/by-nc-nd/4.0/ |
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info:eu-repo/semantics/openAccess |
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open access http://purl.org/coar/access_right/c_abf2 http://creativecommons.org/licenses/by-nc-nd/4.0/ |
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openAccess |
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application/pdf |
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Universitat Politècnica de Catalunya |
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Universitat Politècnica de Catalunya |
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Large-scale biogeography of marine pelagic bacteria and archaeaSalazar Guiral, GuillemEcologia microbianaMar -- ContaminacióThe dark ocean contains about 70% of the ocean’s microbial cells and 60% of its heterotrophic activity, which is mainly fueled by the flux of organic particles produced in the surface ocean and exported to the bathypelagic ocean (1,000 – 4,000 m depth). The bathypelagic ocean represents a nonhomogeneous environment and contains a variety of particles that are considered as the main supply of organic carbon to this environment. The microorganisms inhabiting this realm play a pivotal regulatory role in the biogeochemical cycles at a planetary scale. Accordingly, the study of these microorganisms is an essential step to decipher the ecological functioning of the deep ocean. Chapters 1 to 3 in this Thesis are dedicated to the description of the prokaryotic community composition in the bathypelagic ocean at a global scale through the sequencing of ribosomal DNA and RNA fragments using data collected during the Malaspina 2010 expedition. Chapter 1 identifies the dominant prokaryotes in the deep ocean and reveals a high proportion (~50%) of previously undescribed prokaryotes. The water masses and the structure of the deep ocean’s floor, organized into basins, are identified as the main drivers of their biogeography. Chapter 2 addresses the differences between free-living and particle-attached bathypelagic prokaryotic communities. This is shown to be a phylogenetically conserved trait, indicating that the bathypelagic particles and the water surrounding them constitute two distinct niches and that transitions from one to the other have been rare at an evolutionary timescale. Finally, in Chapter 3 we identify a linear relationship between the 16S RNA/DNA ratio and particle attachment preference, suggesting a global relationship between the prokaryote’s preference for a particle-attached lifestyle and their growth rate. While the deep ocean is a highly unexplored environment, a more complete knowledge exists for the epipelagic ocean (0 – 200 m depth). Steep gradients of light intensity and quality, temperature and nutrient availability characterize the oceans and impact on the distribution of species. However, different processes, such as the sinking of particles and the vertical movement of water masses, have been described as mechanisms capable of connecting the surface and deep layers of the ocean. These same processes could transport entire prokaryotic communities, a process theoretically proposed but never tested. In Chapter 4 we develop a tool (mtagger) for the extraction of short 16S ribosomal reads from metagenomes to describe the taxonomical composition of microbial communities. We propose and evaluate technical improvements compared to previous versions as a benchmark for its use in the last chapter. Chapter 5 is dedicated to the development of a modeling tool (disperflux) for the analysis of prokaryotic communities’ connectivity using data collected during the Tara Oceans expedition. We observe and describe a fast-decay relationship between community similarity and depth, which is consistently fitted by a power-law across the whole dataset, with the exception of 5 stations that are compatible with events of whole community export from the photic ocean to the mesopelagic. In summary, this Thesis significantly contributes to the knowledge on the ecological functioning of marine prokaryotes by describing the structure of prokaryotic communities along the bathypelagic realm and the vertical gradient of the ocean and by the development of original methodological tools that may be applied to a variety of environments.El océano profundo contiene el 70% de las células microbianas del océano las cuales suponen el 60% de la actividad heterotrófica. Dicha actividad biológica está mantenida por un flujo de partículas orgánicas producidas en el océano superficial y exportadas al océano batipelágico (1,000 - 4,000 m de profundidad). Éste no es, por tanto, un ambiente homogéneo, sino que contiene una variedad de partículas consideradas el aporte dominante de carbono orgánico. Los microorganismos de este ambiente tienen, por tanto, un papel regulatorio central en los ciclos biogeoquímicos planetarios. Consecuentemente, el estudio de estos microorganismos supone un paso esencial para descifrar el funcionamiento ecológico del océano profundo. Los Capítulos 1 a 3 de esta Tesis están dedicados a la descripción a nivel global de la composición de las comunidades de procariotas en el océano batipelágico mediante la secuenciación de fragmentos del ADN y ARN ribosomal. En el Capítulo 1 se identifican los procariotas dominantes en el océano profundo y se revela la existencia de una alta proporción (~50%) de procariotas previamente no descritos. Se reconocen además las masas de agua y la orografía del fondo oceánico, organizado en cuencas, como factores claves en su biogeografía. En el Capítulo 2 se estudian las diferencias entre las comunidades de procariotas de vida libre y aquellos adheridos a partículas. Este rasgo se demuestra estar conservado filogenéticamente, indicando que las partículas del batipelágico y el agua que las rodea constituyen dos nichos claramente diferenciados y que las transiciones entre uno y otro por parte de los procariotas han sido eventos poco frecuentes a escalas evolutivas. Finalmente se identifica en el Capítulo 3 una relación lineal entre el cociente de 16S ARN/ADN ribosomal y la preferencia a un modo de vida adherido a partículas, lo que sugiere una relación a nivel global entre la adherencia a partículas y su tasa de crecimiento. Mientras el océano profundo es un ambiente ampliamente inexplorado, existe un mayor conocimiento del océano superficial o epipelágico (0 - 200 m de profundidad). Gradientes intensos en la cantidad y calidad de la luz, temperatura y concentración de nutrientes caracterizan a los océanos e influyen en la distribución vertical de las especies. Sin embargo, diferentes procesos, tales como la deposición de partículas o los movimientos verticales de masas de agua, se han descrito como mecanismos capaces de conectar las capas superficiales y profundas del océano. Estos mismos procesos podrían teóricamente exportar comunidades enteras de microorganismos, un proceso teóricamente propuesto pero no evaluado hasta la fecha. En el Capítulo 4 se desarrolla una herramienta informática (mtagger) para la utilización de fragmentos del gen 16S ribosomal extraídos de metagenomas y su utilización para la descripción taxonómica de comunidades de procariotas. En este capítulo se proponen y evalúan mejoras respecto a versiones anteriormente utilizadas, como paso previo a su uso en el último capítulo. El Capítulo 5 está dedicado al desarrollo de un modelo matemático (disperflux) para la descripción de la conectividad vertical entre comunidades de procariotas. Se observa y describe una disminución abrupta de la similitud de las comunidades de procariotas con la profundidad. Esta relación se ajusta a una ecuación potencial que resulta consistente a lo largo de todo el océano, a excepción de 5 localizaciones, que se demuestran compatibles con eventos de exportación masiva de comunidades desde la superficie al océano profundo. En resumen, esta tesis ha contribuido significativamente al conocimiento del funcionamiento ecológico de los procariotas marinos mediante la descripción a nivel global de estas comunidades en el océano profundo y en el gradiente vertical así como mediante el desarrollo de herramientas metodológicas novedosas aplicables a una amplia variedad de entornosUniversitat Politècnica de CatalunyaGasol Piqué, Josep MariaGonzález Acinas, Silvia20192019-02-1520192019-02-25doctoral thesishttp://purl.org/coar/resource_type/c_db06VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/doctoralThesisapplication/pdfhttps://hdl.handle.net/2117/129593https://dx.doi.org/10.5821/dissertation-2117-129593reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2http://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/1295932026-05-27T15:37:01Z |
| score |
15,300719 |