[{"awards": "1620976 Johnson, Sarah", "bounds_geometry": "POLYGON((160 -77,160.3 -77,160.6 -77,160.9 -77,161.2 -77,161.5 -77,161.8 -77,162.1 -77,162.4 -77,162.7 -77,163 -77,163 -77.1,163 -77.2,163 -77.3,163 -77.4,163 -77.5,163 -77.6,163 -77.7,163 -77.8,163 -77.9,163 -78,162.7 -78,162.4 -78,162.1 -78,161.8 -78,161.5 -78,161.2 -78,160.9 -78,160.6 -78,160.3 -78,160 -78,160 -77.9,160 -77.8,160 -77.7,160 -77.6,160 -77.5,160 -77.4,160 -77.3,160 -77.2,160 -77.1,160 -77))", "dataset_titles": "GenBank Sequence Read Archive with accession numbers SRR8217969 - SRR8217976 and project accession PRJNA506221", "datasets": [{"dataset_uid": "200164", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "GenBank Sequence Read Archive with accession numbers SRR8217969 - SRR8217976 and project accession PRJNA506221", "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA506221/"}], "date_created": "Tue, 01 Sep 2020 00:00:00 GMT", "description": "Despite recent advances, we still know little about how life and its traces persist in extremely harsh conditions. What survival strategies do cells employ when pushed to their limit? Using a new technique, this project will investigate whether Antarctic paleolakes harbor \"microbial seed banks,\" or caches of viable microbes adapted to past paleoenvironments that could help transform our understanding of how cells survive over ancient timescales. Findings from this investigation could also illuminate novel DNA repair pathways with possible biomedical and biotechnology applications and help to refine life detection strategies for Mars. The project will bring Antarctic research to Georgetown University\u0027s campus for the first time, providing training opportunities in cutting edge analytical techniques for multiple students and a postdoctoral fellow. The field site will be the McMurdo Dry Valleys, which provide an unrivaled opportunity to investigate fundamental questions about the persistence of microbial life. Multiple lines of evidence, from interbedded and overlying ashfall deposits to parameterized models, suggest that the large-scale landforms there have remained essentially fixed as far back as the middle of the Miocene Epoch (i.e., ~8 million years ago). This geologic stability, coupled with geographic isolation and a steady polar climate, mean that biological activity has probably undergone few qualitative changes over the last one to two million years. The team will sample paleolake facies using sterile techniques from multiple Dry Valleys sites and extract DNA from entombed organic material. Genetic material will then be sequenced using Pacific Biosciences\u0027 Single Molecule, Real-Time DNA sequencing technology, which sequences native DNA as opposed to amplified DNA, thereby eliminating PCR primer bias, and enables read lengths that have never before been possible. The data will be analyzed with a range of bioinformatic techniques, with results that stand to impact our understanding of cell biology, Antarctic paleobiology, microbiology and biogeography, biotechnology, and planetary science.", "east": 163.0, "geometry": "POINT(161.5 -77.5)", "instruments": null, "is_usap_dc": true, "keywords": "ECOSYSTEM FUNCTIONS; COMMUNITY DYNAMICS; BACTERIA/ARCHAEA; CYANOBACTERIA (BLUE-GREEN ALGAE); LABORATORY; Dry Valleys", "locations": "Dry Valleys", "north": -77.0, "nsf_funding_programs": "Antarctic Organisms and Ecosystems; Antarctic Earth Sciences", "paleo_time": null, "persons": "Johnson, Sarah", "platforms": "OTHER \u003e PHYSICAL MODELS \u003e LABORATORY", "repo": "NCBI GenBank", "repositories": "NCBI GenBank", "science_programs": null, "south": -78.0, "title": "EAGER: Single-Molecule DNA Sequencing of Antarctic Paleolakes", "uid": "p0010125", "west": 160.0}, {"awards": "1745341 Sumner, Dawn", "bounds_geometry": "POLYGON((161.595 -77.527,161.5953 -77.527,161.5956 -77.527,161.5959 -77.527,161.5962 -77.527,161.5965 -77.527,161.5968 -77.527,161.5971 -77.527,161.5974 -77.527,161.5977 -77.527,161.598 -77.527,161.598 -77.5271,161.598 -77.5272,161.598 -77.5273,161.598 -77.5274,161.598 -77.5275,161.598 -77.5276,161.598 -77.5277,161.598 -77.5278,161.598 -77.5279,161.598 -77.528,161.5977 -77.528,161.5974 -77.528,161.5971 -77.528,161.5968 -77.528,161.5965 -77.528,161.5962 -77.528,161.5959 -77.528,161.5956 -77.528,161.5953 -77.528,161.595 -77.528,161.595 -77.5279,161.595 -77.5278,161.595 -77.5277,161.595 -77.5276,161.595 -77.5275,161.595 -77.5274,161.595 -77.5273,161.595 -77.5272,161.595 -77.5271,161.595 -77.527))", "dataset_titles": "GP0191362, Gp0191371; JAAXLU000000000, JAAXLT000000000", "datasets": [{"dataset_uid": "200152", "doi": "", "keywords": null, "people": null, "repository": "IMG Gold", "science_program": null, "title": "GP0191362, Gp0191371", "url": "https://gold.jgi.doe.gov/study?id=Gs0127369"}, {"dataset_uid": "200151", "doi": "", "keywords": null, "people": null, "repository": "NCBI GenBank", "science_program": null, "title": "JAAXLU000000000, JAAXLT000000000", "url": "https://www.ncbi.nlm.nih.gov/nuccore/JAAXLU000000000"}], "date_created": "Mon, 22 Jun 2020 00:00:00 GMT", "description": "Atmospheric oxygen rose suddenly approximately 2.4 billion years ago after Cyanobacteria evolved the ability to produce oxygen through photosynthesis (oxygenic photosynthesis). This change permanently altered the future of life on Earth, yet little is known about the evolutionary processes leading to it. The Melainabacteria were first discovered in 2013 and are closely related non-photosynthetic relatives of the first group of organisms capable of oxygenic photosynthesis. This project will utilize existing data on metagenomes from microbial mats in Lake Vanda, an ice-covered lake in Antarctica where many sequences of Melainabacteria have been previously identified. From this genetic information, the project aims to assess the metabolic capabilities of these Melainabacteria and identify their potential ecological roles. The project will additionally evaluate the evolutionary relationships among the Cyanobacteria and Melainabacteria and closely related organisms that will allow an advancement in understanding of the evolutionary path that lead to oxygenic photosynthesis on Earth. The project will focus on extracting evolutionary information from the genomic data of Melainabacteria and Sericytochromatia, recently-described groups closely related to but basal to the Cyanobacteria. The characterization of novel members of these groups in samples from Lake Vanda, Antarctica, will provide insights into the path and processes involved in the evolution of oxygenic photosynthesis. The research will focus on assessing the metabolic capabilities of Melainabacteri, deriving the evolutionary relationships among Melainabacteria and Cyanobacteria and reconstructing potential evolutionary pathways leading to oxygenic photosynthesis. The project will focus on 12 metagenomes where the researchers expect to obtain genomes for at least the eight most abundant Melainabacteria in the dataset. Melainabacteria bins will be annotated and preliminary metabolic pathways will be constructed. The project will utilize full-length sequences of marker genes from across the bacterial domain with a particular focus on taxa that are oxygenic or anoxygenic phototrophs and use the marker genes, to build a rooted \"backbone\" tree. Incomplete or short sequences from the metagenomes will be added to the tree using the Evolutionary Placement Algorithm. The researchers will also build a corresponding phylogenetic tree using a Bayesian framework and compare their topologies. By doing so, the project aims to improve the understanding of the evolution of oxygenic photosynthesis, which caused the most significant change in Earth\u0027s surface chemistry. Specifically, they will document a significantly broader metabolic diversity within the Melainabacteria than has been previously identified, gain significant insights into their metabolic evolution, their evolutionary relationships with the Cyanobacteria, and the evolutionary steps leading to the origin of oxygenic photosynthesis. This research will have the overall effect of constraining key evolutionary processes in the origin of oxygenic photosynthesis. It will provide the foundation for future studies by indicating where a genomic record of the evolution of oxygenic photosynthesis may be preserved. Results will also be shared with middle school children through the development of scientific lesson plans in collaboration with teachers. This award reflects NSF\u0027s statutory mission and has been deemed worthy of support through evaluation using the Foundation\u0027s intellectual merit and broader impacts review criteria.", "east": 161.598, "geometry": "POINT(161.5965 -77.5275)", "instruments": null, "is_usap_dc": true, "keywords": "USAP-DC; FIELD INVESTIGATION; CYANOBACTERIA (BLUE-GREEN ALGAE); Lake Vanda; LABORATORY; LAKE/POND; Genetic Analysis", "locations": "Lake Vanda", "north": -77.527, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Sumner, Dawn; Eisen, Jonathan; Tazi, Loubna", "platforms": "LAND-BASED PLATFORMS \u003e FIELD SITES \u003e FIELD INVESTIGATION; OTHER \u003e PHYSICAL MODELS \u003e LABORATORY", "repo": "IMG Gold", "repositories": "IMG Gold; NCBI GenBank", "science_programs": null, "south": -77.528, "title": "Evolution of Oxygenic Photosynthesis as Preserved in Melainabacterial Genomes from Lake Vanda, Antarctica", "uid": "p0010112", "west": 161.595}, {"awards": "1745053 Salvatore, Mark; 1744849 Sokol, Eric; 1744785 Barrett, John", "bounds_geometry": "POLYGON((162.92 -77.56,162.971 -77.56,163.022 -77.56,163.073 -77.56,163.124 -77.56,163.175 -77.56,163.226 -77.56,163.277 -77.56,163.328 -77.56,163.379 -77.56,163.43 -77.56,163.43 -77.571,163.43 -77.582,163.43 -77.593,163.43 -77.604,163.43 -77.615,163.43 -77.626,163.43 -77.637,163.43 -77.648,163.43 -77.659,163.43 -77.67,163.379 -77.67,163.328 -77.67,163.277 -77.67,163.226 -77.67,163.175 -77.67,163.124 -77.67,163.073 -77.67,163.022 -77.67,162.971 -77.67,162.92 -77.67,162.92 -77.659,162.92 -77.648,162.92 -77.637,162.92 -77.626,162.92 -77.615,162.92 -77.604,162.92 -77.593,162.92 -77.582,162.92 -77.571,162.92 -77.56))", "dataset_titles": "McMurdo Dry Valleys LTER: Microbial mat biomass and Normalized Difference Vegetation Index (NDVI) values from Lake Fryxell Basin, Antarctica, January 2018", "datasets": [{"dataset_uid": "200344", "doi": "10.6073/pasta/9acbbde9abc1e013f8c9fd9c383327f4", "keywords": null, "people": null, "repository": "EDI", "science_program": null, "title": "McMurdo Dry Valleys LTER: Microbial mat biomass and Normalized Difference Vegetation Index (NDVI) values from Lake Fryxell Basin, Antarctica, January 2018", "url": "https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-mcm.263.1"}], "date_created": "Wed, 03 Jul 2019 00:00:00 GMT", "description": "Microbial mats are found throughout the McMurdo Dry Valleys where summer snowmelt provides liquid water that allows these mats to flourish. Researchers have long studied the environmental conditions microbial mats need to grow. Despite these efforts, it has been difficult to develop a broad picture of these unique ecosystems. Recent advances in satellite technology now provide researchers an exciting new tool to study these special Antarctic ecosystems from space using the unique spectral signatures associated with microbial mats. This new technology not only offers the promise that microbial mats can be mapped and studied from space, this research will also help protect these delicate environments from potentially harmful human impacts that can occur when studying them from the ground. This project will use satellite imagery and spectroscopic techniques to identify and map microbial mat communities and relate their properties and distributions to both field and lab-based measurements. This research provides an exciting new tool to help document and understand the distribution of a major component of the Antarctic ecosystem in the McMurdo Dry Valleys. The goal of this project is to establish quantitative relationships between spectral signatures derived from orbit and the physiological status and biogeochemical properties of microbial mat communities in Taylor Valley, Antarctica, as measured by field and laboratory analyses on collected samples. The goal wioll be met by (1) refining atmospheric correction techniques using in situ radiometric rectification to derive accurate surface spectra; (2) collecting multispectral orbital images concurrent with in situ sampling and spectral measurements in the field to ensure temporal comparability; (3) measuring sediment, water, and microbial mat samples for organic and inorganic carbon content, essential biogeochemical nutrients, and chlorophyll-a to determine relevant mat characteristics; and (4) quantitatively associating these laboratory-derived characteristics with field-derived and orbital spectral signatures and parameters. The result of this work will be a more robust quantitative link between the distribution of microbial mat communities and their biogeochemical properties to landscape-scale spectral signatures. This award reflects NSF\u0027s statutory mission and has been deemed worthy of support through evaluation using the Foundation\u0027s intellectual merit and broader impacts review criteria.", "east": 163.43, "geometry": "POINT(163.175 -77.615)", "instruments": null, "is_usap_dc": true, "keywords": "RIVERS/STREAM; CYANOBACTERIA (BLUE-GREEN ALGAE); USAP-DC; Taylor Valley; INFRARED IMAGERY; WORLDVIEW-2; WORLDVIEW-3; Antarctica; FIELD INVESTIGATION; Amd/Us; ACTIVE LAYER", "locations": "Antarctica; Taylor Valley", "north": -77.56, "nsf_funding_programs": "Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems; Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Salvatore, Mark; Barrett, John; Sokol, Eric", "platforms": "LAND-BASED PLATFORMS \u003e FIELD SITES \u003e FIELD INVESTIGATION; SPACE-BASED PLATFORMS \u003e EARTH OBSERVATION SATELLITES \u003e WORLDVIEW \u003e WORLDVIEW-2; SPACE-BASED PLATFORMS \u003e EARTH OBSERVATION SATELLITES \u003e WORLDVIEW \u003e WORLDVIEW-3", "repo": "EDI", "repositories": "EDI", "science_programs": null, "south": -77.67, "title": "COLLABORATIVE RESEARCH: Remote Characterization of Microbial Mats in Taylor Valley, Antarctica, through In Situ Sampling and Spectral Validation", "uid": "p0010036", "west": 162.92}]

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EAGER: Single-Molecule DNA Sequencing of Antarctic Paleolakes

1620976

2020-09-01

Johnson, Sarah

GenBank Sequence Read Archive with accession numbers SRR8217969 - SRR8217976 and project accession PRJNA506221

NCBI GenBank

Despite recent advances, we still know little about how life and its traces persist in extremely harsh conditions. What survival strategies do cells employ when pushed to their limit? Using a new technique, this project will investigate whether Antarctic paleolakes harbor "microbial seed banks," or caches of viable microbes adapted to past paleoenvironments that could help transform our understanding of how cells survive over ancient timescales. Findings from this investigation could also illuminate novel DNA repair pathways with possible biomedical and biotechnology applications and help to refine life detection strategies for Mars. The project will bring Antarctic research to Georgetown University's campus for the first time, providing training opportunities in cutting edge analytical techniques for multiple students and a postdoctoral fellow. The field site will be the McMurdo Dry Valleys, which provide an unrivaled opportunity to investigate fundamental questions about the persistence of microbial life. Multiple lines of evidence, from interbedded and overlying ashfall deposits to parameterized models, suggest that the large-scale landforms there have remained essentially fixed as far back as the middle of the Miocene Epoch (i.e., ~8 million years ago). This geologic stability, coupled with geographic isolation and a steady polar climate, mean that biological activity has probably undergone few qualitative changes over the last one to two million years. The team will sample paleolake facies using sterile techniques from multiple Dry Valleys sites and extract DNA from entombed organic material. Genetic material will then be sequenced using Pacific Biosciences' Single Molecule, Real-Time DNA sequencing technology, which sequences native DNA as opposed to amplified DNA, thereby eliminating PCR primer bias, and enables read lengths that have never before been possible. The data will be analyzed with a range of bioinformatic techniques, with results that stand to impact our understanding of cell biology, Antarctic paleobiology, microbiology and biogeography, biotechnology, and planetary science.

Evolution of Oxygenic Photosynthesis as Preserved in Melainabacterial Genomes from Lake Vanda, Antarctica

1745341

2020-06-22

Sumner, Dawn; Eisen, Jonathan; Tazi, Loubna

GP0191362, Gp0191371	IMG Gold
JAAXLU000000000, JAAXLT000000000	NCBI GenBank

Atmospheric oxygen rose suddenly approximately 2.4 billion years ago after Cyanobacteria evolved the ability to produce oxygen through photosynthesis (oxygenic photosynthesis). This change permanently altered the future of life on Earth, yet little is known about the evolutionary processes leading to it. The Melainabacteria were first discovered in 2013 and are closely related non-photosynthetic relatives of the first group of organisms capable of oxygenic photosynthesis. This project will utilize existing data on metagenomes from microbial mats in Lake Vanda, an ice-covered lake in Antarctica where many sequences of Melainabacteria have been previously identified. From this genetic information, the project aims to assess the metabolic capabilities of these Melainabacteria and identify their potential ecological roles. The project will additionally evaluate the evolutionary relationships among the Cyanobacteria and Melainabacteria and closely related organisms that will allow an advancement in understanding of the evolutionary path that lead to oxygenic photosynthesis on Earth. The project will focus on extracting evolutionary information from the genomic data of Melainabacteria and Sericytochromatia, recently-described groups closely related to but basal to the Cyanobacteria. The characterization of novel members of these groups in samples from Lake Vanda, Antarctica, will provide insights into the path and processes involved in the evolution of oxygenic photosynthesis. The research will focus on assessing the metabolic capabilities of Melainabacteri, deriving the evolutionary relationships among Melainabacteria and Cyanobacteria and reconstructing potential evolutionary pathways leading to oxygenic photosynthesis. The project will focus on 12 metagenomes where the researchers expect to obtain genomes for at least the eight most abundant Melainabacteria in the dataset. Melainabacteria bins will be annotated and preliminary metabolic pathways will be constructed. The project will utilize full-length sequences of marker genes from across the bacterial domain with a particular focus on taxa that are oxygenic or anoxygenic phototrophs and use the marker genes, to build a rooted "backbone" tree. Incomplete or short sequences from the metagenomes will be added to the tree using the Evolutionary Placement Algorithm. The researchers will also build a corresponding phylogenetic tree using a Bayesian framework and compare their topologies. By doing so, the project aims to improve the understanding of the evolution of oxygenic photosynthesis, which caused the most significant change in Earth's surface chemistry. Specifically, they will document a significantly broader metabolic diversity within the Melainabacteria than has been previously identified, gain significant insights into their metabolic evolution, their evolutionary relationships with the Cyanobacteria, and the evolutionary steps leading to the origin of oxygenic photosynthesis. This research will have the overall effect of constraining key evolutionary processes in the origin of oxygenic photosynthesis. It will provide the foundation for future studies by indicating where a genomic record of the evolution of oxygenic photosynthesis may be preserved. Results will also be shared with middle school children through the development of scientific lesson plans in collaboration with teachers. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

COLLABORATIVE RESEARCH: Remote Characterization of Microbial Mats in Taylor Valley, Antarctica, through In Situ Sampling and Spectral Validation

1745053
1744849
1744785

2019-07-03

Salvatore, Mark; Barrett, John; Sokol, Eric

McMurdo Dry Valleys LTER: Microbial mat biomass and Normalized Difference Vegetation Index (NDVI) values from Lake Fryxell Basin, Antarctica, January 2018

EDI

Microbial mats are found throughout the McMurdo Dry Valleys where summer snowmelt provides liquid water that allows these mats to flourish. Researchers have long studied the environmental conditions microbial mats need to grow. Despite these efforts, it has been difficult to develop a broad picture of these unique ecosystems. Recent advances in satellite technology now provide researchers an exciting new tool to study these special Antarctic ecosystems from space using the unique spectral signatures associated with microbial mats. This new technology not only offers the promise that microbial mats can be mapped and studied from space, this research will also help protect these delicate environments from potentially harmful human impacts that can occur when studying them from the ground. This project will use satellite imagery and spectroscopic techniques to identify and map microbial mat communities and relate their properties and distributions to both field and lab-based measurements. This research provides an exciting new tool to help document and understand the distribution of a major component of the Antarctic ecosystem in the McMurdo Dry Valleys. The goal of this project is to establish quantitative relationships between spectral signatures derived from orbit and the physiological status and biogeochemical properties of microbial mat communities in Taylor Valley, Antarctica, as measured by field and laboratory analyses on collected samples. The goal wioll be met by (1) refining atmospheric correction techniques using in situ radiometric rectification to derive accurate surface spectra; (2) collecting multispectral orbital images concurrent with in situ sampling and spectral measurements in the field to ensure temporal comparability; (3) measuring sediment, water, and microbial mat samples for organic and inorganic carbon content, essential biogeochemical nutrients, and chlorophyll-a to determine relevant mat characteristics; and (4) quantitatively associating these laboratory-derived characteristics with field-derived and orbital spectral signatures and parameters. The result of this work will be a more robust quantitative link between the distribution of microbial mat communities and their biogeochemical properties to landscape-scale spectral signatures. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

USAP-DC