[{"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. \r\n\r\nFrom this genetic information, we identified a new cyanobacterium, named Aurora vandensis, that is sister to all other Cyanobacteria, providing evolutionary insights. In addition, we assessed the metabolic capabilities of the Melainabacteria with good genomic coverage to identify their potential ecological roles. None contain photosynthetic genes, and we are evaluating the evolutionary relationships among the Cyanobacteria and Melainabacteria, particularly with respect to metabolic genes that will allow an advancement in understanding of the evolutionary path that lead to oxygenic photosynthesis on Earth.\r\n\r\nThe 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, provide insights into the path and processes involved in the evolution of oxygenic photosynthesis. The research identified a novel cyanobacterial genus that is sister to all other Cyanobacteria, is most closely related to Gloeobacter, and shares evolutionary differences with that genus. Results also show that characterized Melainabacteria lack photosynthesis genes, but their respiration genes provide insight into evolutionary relationships among Melainabacteria and Cyanobacteria. Results provide unexpected constraints. The project focuses on 12 metagenomes, from which Melainabacteria and novel Cyanobacteria bins are annotated and preliminary metabolic pathways will be constructed. The project utilizes 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 are added to the tree using the Evolutionary Placement Algorithm. The researchers built 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, we document a novel and basal cyanobacterium, 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 is constraining key evolutionary processes in the origin of oxygenic photosynthesis. It provides the foundation for future studies by indicating where a genomic record of the evolution of oxygenic photosynthesis may be preserved. Results will are being shared with middle school children through the development of scientific lesson plans in collaboration with teachers.\r\n\r\nThis 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": "0230276 Ward, Bess", "bounds_geometry": "POLYGON((162 -77.2,162.16 -77.2,162.32 -77.2,162.48 -77.2,162.64 -77.2,162.8 -77.2,162.96 -77.2,163.12 -77.2,163.28 -77.2,163.44 -77.2,163.6 -77.2,163.6 -77.26,163.6 -77.32,163.6 -77.38,163.6 -77.44,163.6 -77.5,163.6 -77.56,163.6 -77.62,163.6 -77.68,163.6 -77.74,163.6 -77.8,163.44 -77.8,163.28 -77.8,163.12 -77.8,162.96 -77.8,162.8 -77.8,162.64 -77.8,162.48 -77.8,162.32 -77.8,162.16 -77.8,162 -77.8,162 -77.74,162 -77.68,162 -77.62,162 -77.56,162 -77.5,162 -77.44,162 -77.38,162 -77.32,162 -77.26,162 -77.2))", "dataset_titles": "What Limits Denitrification and Bacterial Growth in Lake Bonney, Taylor Valley, Antarctica?", "datasets": [{"dataset_uid": "600033", "doi": "10.15784/600033", "keywords": "Antarctica; Biota; CTD Data; Dry Valleys; Lake Bonney; Lake Vanda; Microbiology; Taylor Valley", "people": "Ward, Bess", "repository": "USAP-DC", "science_program": null, "title": "What Limits Denitrification and Bacterial Growth in Lake Bonney, Taylor Valley, Antarctica?", "url": "https://www.usap-dc.org/view/dataset/600033"}], "date_created": "Sun, 18 Jan 2009 00:00:00 GMT", "description": "Denitrification is the main process by which fixed nitrogen is lost from ecosystems and the regulation of this process may directly affect primary production and carbon cycling over short and long time scales. Previous investigations of the role of bioactive metals in regulating denitrification in bacteria from permanently ice-covered Lake Bonney in the Taylor Valley of East Antarctica indicated that denitrifying bacteria can be negatively affected by metals such as copper, iron, cadmium, lead, chromium, nickel, silver and zinc; and that there is a distinct difference in denitrifying activity between the east and west lobes of the lake. Low iron concentrations were found to exacerbate the potential toxicity of the other metals, while silver has the potential to specifically inhibit denitrification because of its ability to interfere with copper binding in redox proteins, such as nitrite reductase and nitrous oxide reductase. High silver concentrations might prevent the functioning of nitrous oxide reductase in the same way that simple copper limitation does, thereby causing the buildup of nitrous oxide and resulting in a nonfunctional nitrogen cycle. Other factors, such as oxygen concentration, are likely also to affect bacterial activity in Lake Bonney. This project will investigate silver toxicity, general metal toxicity and oxygen concentration to determine their effect on denitrification in the lake by using a suite of \"sentinel\" strains of denitrifying bacteria (isolated from the lake) incubated in Lake Bonney water and subjected to various treatments. The physiological responses of these strains to changes in metal and oxygen concentration will be quantified by flow cytometric detection of single cell molecular probes whose sensitivity and interpretation have been optimized for the sentinel strains. Understanding the relationships between metals and denitrification is expected to enhance our understanding of not only Lake Bonney\u0027s unusual nitrogen cycle, but more generally, of the potential role of metals in the regulation of microbial nitrogen transformations.\u003cbr/\u003e\u003cbr/\u003eThe broader impacts of this work include not only a better understanding of regional biogeochemistry and global perspectives on these processes; but also the training of graduate students and a substantial outreach effort for school children.", "east": 163.6, "geometry": "POINT(162.8 -77.5)", "instruments": "IN SITU/LABORATORY INSTRUMENTS \u003e PROFILERS/SOUNDERS \u003e CTD", "is_usap_dc": true, "keywords": "FIELD SURVEYS", "locations": null, "north": -77.2, "nsf_funding_programs": "Antarctic Organisms and Ecosystems", "paleo_time": null, "persons": "Ward, Bess", "platforms": "LAND-BASED PLATFORMS \u003e FIELD SITES \u003e FIELD SURVEYS", "repo": "USAP-DC", "repositories": "USAP-DC", "science_programs": null, "south": -77.8, "title": "Collaborative Research: What Limits Denitrification and Bacterial Growth in Lake Bonney, Taylor Valley, Antarctica?", "uid": "p0000223", "west": 162.0}]

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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, we identified a new cyanobacterium, named Aurora vandensis, that is sister to all other Cyanobacteria, providing evolutionary insights. In addition, we assessed the metabolic capabilities of the Melainabacteria with good genomic coverage to identify their potential ecological roles. None contain photosynthetic genes, and we are evaluating the evolutionary relationships among the Cyanobacteria and Melainabacteria, particularly with respect to metabolic genes 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, provide insights into the path and processes involved in the evolution of oxygenic photosynthesis. The research identified a novel cyanobacterial genus that is sister to all other Cyanobacteria, is most closely related to Gloeobacter, and shares evolutionary differences with that genus. Results also show that characterized Melainabacteria lack photosynthesis genes, but their respiration genes provide insight into evolutionary relationships among Melainabacteria and Cyanobacteria. Results provide unexpected constraints. The project focuses on 12 metagenomes, from which Melainabacteria and novel Cyanobacteria bins are annotated and preliminary metabolic pathways will be constructed. The project utilizes 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 are added to the tree using the Evolutionary Placement Algorithm. The researchers built 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, we document a novel and basal cyanobacterium, 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 is constraining key evolutionary processes in the origin of oxygenic photosynthesis. It provides the foundation for future studies by indicating where a genomic record of the evolution of oxygenic photosynthesis may be preserved. Results will are being 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: What Limits Denitrification and Bacterial Growth in Lake Bonney, Taylor Valley, Antarctica?

0230276

2009-01-18

Ward, Bess

What Limits Denitrification and Bacterial Growth in Lake Bonney, Taylor Valley, Antarctica?

USAP-DC

Denitrification is the main process by which fixed nitrogen is lost from ecosystems and the regulation of this process may directly affect primary production and carbon cycling over short and long time scales. Previous investigations of the role of bioactive metals in regulating denitrification in bacteria from permanently ice-covered Lake Bonney in the Taylor Valley of East Antarctica indicated that denitrifying bacteria can be negatively affected by metals such as copper, iron, cadmium, lead, chromium, nickel, silver and zinc; and that there is a distinct difference in denitrifying activity between the east and west lobes of the lake. Low iron concentrations were found to exacerbate the potential toxicity of the other metals, while silver has the potential to specifically inhibit denitrification because of its ability to interfere with copper binding in redox proteins, such as nitrite reductase and nitrous oxide reductase. High silver concentrations might prevent the functioning of nitrous oxide reductase in the same way that simple copper limitation does, thereby causing the buildup of nitrous oxide and resulting in a nonfunctional nitrogen cycle. Other factors, such as oxygen concentration, are likely also to affect bacterial activity in Lake Bonney. This project will investigate silver toxicity, general metal toxicity and oxygen concentration to determine their effect on denitrification in the lake by using a suite of "sentinel" strains of denitrifying bacteria (isolated from the lake) incubated in Lake Bonney water and subjected to various treatments. The physiological responses of these strains to changes in metal and oxygen concentration will be quantified by flow cytometric detection of single cell molecular probes whose sensitivity and interpretation have been optimized for the sentinel strains. Understanding the relationships between metals and denitrification is expected to enhance our understanding of not only Lake Bonney's unusual nitrogen cycle, but more generally, of the potential role of metals in the regulation of microbial nitrogen transformations.<br/><br/>The broader impacts of this work include not only a better understanding of regional biogeochemistry and global perspectives on these processes; but also the training of graduate students and a substantial outreach effort for school children.