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Karen Casciotti. Rogers, Daniel Richard Woods Hole Oceanographic Institution. Joint Program in Oceanography/Applied Ocean Science and Engineering Woods Hole Oceanographic Institution Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences 2010-10-29T18:29:33Z 2010-10-29T18:29:33Z 2010 2010 http://hdl.handle.net/1721.1/59746 670430741 Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2010. Cataloged from PDF version of thesis. Includes bibliographical references. Excess nitrogen input is deleterious to coastal waters, resulting in deterioration of the water quality, increases in harmful algal blooms and disease in commercial fish stocks. A significant portion of this nitrogen enters coastal waters through groundwater systems. Here we use isotopic and molecular biological methods to identify the populations of nitrifiers and denitrifiers, where they occur, and what levels of activity are present through the upper four meters of a coastal groundwater system. This work shows two different populations of putative ammonia-oxidizing archaea (AOA) based on the ammonia mono-oxygenase gene (amoA), one shallow population most closely related to open ocean water column-like sequences and a deeper population that is more closely related to estuarine-like AOA. Interestingly, while the surface population has a potential nitrification rates (456 pmol g-1 sediment day-) similar to marine sediments, the deeper population does not show detectable evidence of nitrification. Between these two archaeal populations resides an active population of ammonia-oxidizing bacteria with similar nitrification rates as the surface AOA population. The upper meter of the aquifer is also an active area of denitrification as evidenced by the coincident drop in nitrate concentration and increase in both 15N (up to + 20. 1%o) and 5180 (up to + 11. 7%o), characteristic of groundwater affected by denitrification. 16S rRNA gene surveys of the organisms present in the upper meter also are similar to soil/sediment type environments including many potential denitrifiers. However, nitrite reductase, nirS and nirK, genes were also recovered from the sediments with nirK dominating in the surface sediments. This contrasts with the deep salt wedge, where the microbial community 16S rRNA genes appear more closely related to marine or reducing sediment/wastewater type organisms, and nirS genes become the dominant denitrification gene. by Daniel Richard Rogers. Ph.D. 164 p. eng Massachusetts Institute of Technology M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 Joint Program in Oceanography/Applied Ocean Science and Engineering. Earth, Atmospheric, and Planetary Sciences. Woods Hole Oceanographic Institution. Groundwater Research Water Nitrogen content Geomicrobiology of nitrogen in a coastal aquifer : isotopic and molecular methods to examine nitrification and denitrification in groundwater Isotopic and molecular methods to examine nitrification and denitrification in groundwater Thesis application/pdf false Publication unknown unknown <Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="bc89b237-a9f2-49c6-83ae-e3c49bef8edc"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Language>eng</Language> <Title>Geomicrobiology of nitrogen in a coastal aquifer : isotopic and molecular methods to examine nitrification and denitrification in groundwater</Title> <Subtitle>Isotopic and molecular methods to examine nitrification and denitrification in groundwater</Subtitle> <PublishedIn> <Publication> </Publication> </PublishedIn> <PublicationDate>2010</PublicationDate> <Authors> <Author> <DisplayName>Rogers, Daniel Richard</DisplayName> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>Massachusetts Institute of Technology</DisplayName> <OrgUnit /> </Publisher> </Publishers> <License>http://dspace.mit.edu/handle/1721.1/7582</License> <Keyword>Joint Program in Oceanography/Applied Ocean Science and Engineering.</Keyword> <Keyword>Earth, Atmospheric, and Planetary Sciences.</Keyword> <Keyword>Woods Hole Oceanographic Institution.</Keyword> <Abstract>Excess nitrogen input is deleterious to coastal waters, resulting in deterioration of the water quality, increases in harmful algal blooms and disease in commercial fish stocks. A significant portion of this nitrogen enters coastal waters through groundwater systems. Here we use isotopic and molecular biological methods to identify the populations of nitrifiers and denitrifiers, where they occur, and what levels of activity are present through the upper four meters of a coastal groundwater system. This work shows two different populations of putative ammonia-oxidizing archaea (AOA) based on the ammonia mono-oxygenase gene (amoA), one shallow population most closely related to open ocean water column-like sequences and a deeper population that is more closely related to estuarine-like AOA. Interestingly, while the surface population has a potential nitrification rates (456 pmol g-1 sediment day-) similar to marine sediments, the deeper population does not show detectable evidence of nitrification. Between these two archaeal populations resides an active population of ammonia-oxidizing bacteria with similar nitrification rates as the surface AOA population. The upper meter of the aquifer is also an active area of denitrification as evidenced by the coincident drop in nitrate concentration and increase in both 15N (up to + 20. 1%o) and 5180 (up to + 11. 7%o), characteristic of groundwater affected by denitrification. 16S rRNA gene surveys of the organisms present in the upper meter also are similar to soil/sediment type environments including many potential denitrifiers. However, nitrite reductase, nirS and nirK, genes were also recovered from the sediments with nirK dominating in the surface sediments. This contrasts with the deep salt wedge, where the microbial community 16S rRNA genes appear more closely related to marine or reducing sediment/wastewater type organisms, and nirS genes become the dominant denitrification gene.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication>