Rogers
Daniel R.
Rogers
Daniel R.
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PreprintAbundance and diversity of archaeal ammonia oxidizers in a coastal groundwater system( 2010-10-12) Rogers, Daniel R. ; Casciotti, Karen L.Nitrification, the microbially-catalyzed oxidation of ammonia to nitrate, is a key process in the nitrogen cycle. Archaea have been implicated in the first part of the nitrification pathway (oxidation of ammonia to nitrite), but the ecology and physiology of these organisms remain largely unknown. This work describes two different populations of sediment-associated ammonia-oxidizing archaea (AOA) in a coastal groundwater system on Cape Cod, Massachusetts. Sequence analysis of the ammonia monooxygenase subunit A gene (amoA) shows that one population of putative AOA inhabits the upper meter of the sediment where they may experience frequent ventilation with tidally-driven overtopping and infiltration of bay water supplying dissolved oxygen, ammonium and perhaps organic carbon. A genetically distinct population occurs deeper in the sediment, in a mixing zone between a nitrate- and oxygen-rich freshwater zone and a reduced, ammonium-bearing salt water wedge. Both of these AOA populations are coincident with increases in the abundance of Group I crenarchaeota 16S rRNA gene copies.
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ArticleIsolation and characterization of novel psychrophilic, neutrophilic, Fe-oxidizing, chemolithoautotrophic α- and γ-proteobacteria from the deep sea(American Society for Microbiology, 2003-05) Edwards, Katrina J. ; Rogers, Daniel R. ; Wirsen, Carl O. ; McCollom, Thomas M.We report the isolation and physiological characterization of novel, psychrophilic, iron-oxidizing bacteria (FeOB) from low-temperature weathering habitats in the vicinity of the Juan de Fuca deep-sea hydrothermal area. The FeOB were cultured from the surfaces of weathered rock and metalliferous sediments. They are capable of growth on a variety of natural and synthetic solid rock and mineral substrates, such as pyrite (FeS2), basalt glass (~10 wt% FeO), and siderite (FeCO3), as their sole energy source, as well as numerous aqueous Fe substrates. Growth temperature characteristics correspond to the in situ environmental conditions of sample origin; the FeOB grow optimally at 3 to 10°C and at generation times ranging from 57 to 74 h. They are obligate chemolithoautotrophs and grow optimally under microaerobic conditions in the presence of an oxygen gradient or anaerobically in the presence of nitrate. None of the strains are capable of using any organic or alternate inorganic substrates tested. The bacteria are phylogenetically diverse and have no close Fe-oxidizing or autotrophic relatives represented in pure culture. One group of isolates are γ-Proteobacteria most closely related to the heterotrophic bacterium Marinobacter aquaeolei (87 to 94% sequence similarity). A second group of isolates are α-Proteobacteria most closely related to the deep-sea heterotrophic bacterium Hyphomonas jannaschiana (81 to 89% sequence similarity). This study provides further evidence for the evolutionarily widespread capacity for Fe oxidation among bacteria and suggests that FeOB may play an unrecognized geomicrobiological role in rock weathering in the deep sea.
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ArticleComparison of oyster aquaculture methods and their potential to from coastal ecosystems(Frontiers Media, 2021-03-24) Mara, Paraskevi ; Edgcomb, Virginia P. ; Sehein, Taylor R. ; Beaudoin, David J. ; Martinsen, Chuck ; Lovely, Christina ; Belcher, Bridget ; Cox, Rebecca ; Curran, Meghan ; Farnan, Claire ; Giannini, Peter ; Lott, Sarah ; Paquette, Kyle ; Pinckney, Anna ; Schafer, Natalie ; Surgeon-Rogers, Tonna-Marie ; Rogers, Daniel R.Coastal ecosystems are impacted by excessive nutrient inputs that cause degradation of water quality and impairments of ecosystem functioning. Regulatory and management efforts to enhance nutrient export from coastal ecosystems include sustainable oyster aquaculture that removes nitrogen in the form of oyster biomass and increases particulate export to underlying sediments where increased organic material may enhance microbial denitrification. To better understand the impacts of oyster aquaculture on nitrogen removal, we examined bacterial processes in sediments underlying three of the most common aquaculture methods that vary in the proximity of oysters to the sediments. Sediment samples underlying sites managed with these different aquaculture methods were examined using the 16S rRNA gene to assess microbial community structure, gene expression analyses to examine nitrogen and sulfur cycling genes, and nitrogen gas flux measurements. All sites were located in the same hydrodynamic setting within Waquoit Bay, MA during 2018 and 2019. Although sediments under the different oyster farming practices showed similar communities, ordination analysis revealed discrete community groups formed along the sampling season. Measured N2 fluxes and expression of key genes involved in denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) increased during mid-summer and into fall in both years primarily under bottom cages. While all three oyster growing methods enhanced nitrogen removal relative to the control site, gene expression data indicate that the nitrogen retaining process of DNRA is particularly enhanced after end of July under bottom cages, and to a lesser extent, under suspended and floating bags. The choice of gear can also potentially increase processes that induce nitrogen retention in the form of ammonia in the underlying sediments over time, thus causing deviations from predicted nitrogen removal. If nitrogen removal is a primary objective, monitoring for these shifts is essential for making decisions about siting and size of aquaculture sites from year to year.
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ThesisGeomicrobiology of nitrogen in a coastal aquifer : isotopic and molecular methods to examine nitrification and denitrification in groundwater(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2010-06) Rogers, Daniel R.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 monooxygenase 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-1) 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 δ15N (up to + 20.1‰) and δ18O (up to + 11.7‰), 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.