Universität zu Köln

Acosta, Eduardo ORCID: 0000-0002-1490-3679 (2024). Exploring the diversity and activity of microeukaryotes from modern and ancient ecosystems from the Atacama Desert. PhD thesis, Universität zu Köln.

PDF Thesis Eduardo.pdf - Published Version Download (27MB)

Abstract

The crescent interest of microbiologists on the ecology of protiststs is revealing new community assemblages in the natural ecosystems, changing the paradigms on the habitability of extreme environments. Consequently, questions on the ecology of microorganisms as the protists have been refined and supported by high-throughput sequencing (HTS). This approach can be used to uncover previously unknown global patterns of microbes, aiming to extend our knowledge on the biogeography of protists, even in challenging environments. The continual refinement of these technologies has enabled the detection of microbial communities relying on the environmental sequencing of hypervariable regions of gene sequences, commonly used as phylogenetic markers (e.g., ribosomal genes). Therefore, monoclonal cultures of the unicellular protists are urgently needed to check such results. The progressive curation of reference databases has helped to increase the confidence on the use of environmental sequencing and techniques involving the amplificaAon of marker genes from the genetic pool found in nature (e.g., metabarcoding). Such approaches must consider parallel cultivation approaches, aiming to back up the detection of protist lineages across areas of unknown diversity as the natural laboratories found across the ancient Atacama Desert. As recently uncovered, the Atacama Desert can be inhabited by the primordial prokaryotes (bacteria and archaea), in unique habitats distributed in this desert, sustaining life even at the dry limit. Biotic factors controlling their populations, as the recent free-living protists, are understudied in the most arid desert on Earth, and the functions and structure of their communities is yet to be studied. In this study, the Atacama Desert was used as a model system for the study of potentially extremophile protists, including understudied areas as arid soils, biofilms and microbial mats. The relative abundance of the protists communities in the arid Atacama could hide a great gap in the fundamental knowledge of the microbial ecology surviving in the vicinity of areas considered to be analogous to the neighbor planet, Mars. We hypothesized that the uncultivable protists detectable by metabarcoding and the structure of their communities, correlate with the environmental gradients and that their active physiological state can be detected in microhabitats of this desert. We focus on protists due to earlier findings describing a novel diversity of species from diverse groups as heterotrophic flagellates and ciliates, as well as to the description of protist communities in hypersaline systems by metabarcoding. As the ancient Atacama covers an extensive area, we focused on microbial habitats which could serve as a good source of protist diversity, as those found at the limits of the arid zones. The coastal hills facing the Pacific Ocean and the sparse areas covered by biological crusts and biofilms could hide the keys to adaptation, enduring scarce water regimes. Interesting microbial structures growing at the benthic sediments of Andean Lagoons represent hotspots of biodiversity and could serve as a reservoir of protist life. We studied the diversity of protists constituting these sediments and studied their stratification at a millimeter-scale to assess the microbial guilds at a small scale (e.g., ciliates, flagellates and amoebae). Additionally, we tested for correlation of protist taxa with the water column properties at five remote basins found across the Atacama and the Andean plateau aiming evaluate their association to abiotic factors. Finally, the occurrence of these groups in datasets obtained by the modern metabarcoding approach was estimated to infer their potential interaction based on correlation patterns across different habitats (e.g., soils and benthic microbial mats). The identification of such significant correlated taxa could shed light on the members of these communities which could help the human to prioritize on potential keystone species in conservation initiatives. The microbial life able to thrive an extreme environment as the Atacama Desert could hide the adaptation mechanisms useful to understand the population dynamics in remote microhabitats threatened by the current climate change scenario.

Item Type:	Thesis (PhD thesis)
Translated abstract:	Abstract Language The crescent interest of microbiologists on the ecology of protiststs is revealing new community assemblages in the natural ecosystems, changing the paradigms on the habitability of extreme environments. Consequently, questions on the ecology of microorganisms as the protists have been refined and supported by high-throughput sequencing (HTS). This approach can be used to uncover previously unknown global patterns of microbes, aiming to extend our knowledge on the biogeography of protists, even in challenging environments. The continual refinement of these technologies has enabled the detection of microbial communities relying on the environmental sequencing of hypervariable regions of gene sequences, commonly used as phylogenetic markers (e.g., ribosomal genes). Therefore, monoclonal cultures of the unicellular protists are urgently needed to check such results. The progressive curation of reference databases has helped to increase the confidence on the use of environmental sequencing and techniques involving the amplificaAon of marker genes from the genetic pool found in nature (e.g., metabarcoding). Such approaches must consider parallel cultivation approaches, aiming to back up the detection of protist lineages across areas of unknown diversity as the natural laboratories found across the ancient Atacama Desert. As recently uncovered, the Atacama Desert can be inhabited by the primordial prokaryotes (bacteria and archaea), in unique habitats distributed in this desert, sustaining life even at the dry limit. Biotic factors controlling their populations, as the recent free-living protists, are understudied in the most arid desert on Earth, and the functions and structure of their communities is yet to be studied. In this study, the Atacama Desert was used as a model system for the study of potentially extremophile protists, including understudied areas as arid soils, biofilms and microbial mats. The relative abundance of the protists communities in the arid Atacama could hide a great gap in the fundamental knowledge of the microbial ecology surviving in the vicinity of areas considered to be analogous to the neighbor planet, Mars. We hypothesized that the uncultivable protists detectable by metabarcoding and the structure of their communities, correlate with the environmental gradients and that their active physiological state can be detected in microhabitats of this desert. We focus on protists due to earlier findings describing a novel diversity of species from diverse groups as heterotrophic flagellates and ciliates, as well as to the description of protist communities in hypersaline systems by metabarcoding. As the ancient Atacama covers an extensive area, we focused on microbial habitats which could serve as a good source of protist diversity, as those found at the limits of the arid zones. The coastal hills facing the Pacific Ocean and the sparse areas covered by biological crusts and biofilms could hide the keys to adaptation, enduring scarce water regimes. Interesting microbial structures growing at the benthic sediments of Andean Lagoons represent hotspots of biodiversity and could serve as a reservoir of protist life. We studied the diversity of protists constituting these sediments and studied their stratification at a millimeter-scale to assess the microbial guilds at a small scale (e.g., ciliates, flagellates and amoebae). Additionally, we tested for correlation of protist taxa with the water column properties at five remote basins found across the Atacama and the Andean plateau aiming evaluate their association to abiotic factors. Finally, the occurrence of these groups in datasets obtained by the modern metabarcoding approach was estimated to infer their potential interaction based on correlation patterns across different habitats (e.g., soils and benthic microbial mats). The identification of such significant correlated taxa could shed light on the members of these communities which could help the human to prioritize on potential keystone species in conservation initiatives. The microbial life able to thrive an extreme environment as the Atacama Desert could hide the adaptation mechanisms useful to understand the population dynamics in remote microhabitats threatened by the current climate change scenario. English
Creators:	Creators Email ORCID ORCID Put Code Acosta, Eduardo acosta.solisdeovando@gmail.com orcid.org/0000-0002-1490-3679 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-735949
Date:	2024
Place of Publication:	Cologne, Germany
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Ehemalige Fakultäten, Institute, Seminare > Faculty of Mathematics and Natural Sciences
Subjects:	Natural sciences and mathematics
Uncontrolled Keywords:	Keywords Language Protists, Next generation sequencing English Metabarcoding, high altitude English Soil, Microbial mats, Biofilms, microbial communities, Atacama Desert, Andean Lagoons English
Date of oral exam:	15 March 2024
Referee:	Name Academic Title Arndt, Hartmut Prof. Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/73594