Rogers DR, Casciotti KL. Abundance and Diversity of Archaeal Ammonia Oxidizers in a Coastal Groundwater System. Applied and Environmental Microbiology [Internet]. 2010;76 :7938-7948. Publisher's VersionAbstract

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 in Cape Cod, MA. 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 saltwater wedge. Both of these AOA populations are coincident with increases in the abundance of group I crenarchaeota 16S rRNA gene copies.

Edwards KJ, Bach W, McCollom TM, Rogers DR. Neutrophilic Iron-Oxidizing Bacteria in the Ocean: Their Habitats, Diversity, and Roles in Mineral Deposition, Rock Alteration, and Biomass Production in the Deep-Sea. Geomicrobiology Journal. 2004;21 :393-404.Abstract

The importance of metals to life has long been appreciated. Iron (Fe) is the fourth most abundant element overall, and the second most abundant element that is redox-active in near-surface aqueous habitats, rendering it the most important environmental metal. While it has long been recognized that microorganisms participate in the global iron cycle, appreciation for the pivotal role that redox cycling of iron plays in energy conservation among diverse prokaryotes has grown substantially in the past decade. In addition, redox reactions involving Fe are linked to several other biogeochemical cycles (e.g., carbon), with significant ecological ramifications. The increasing appreciation for the role of microbes in redox transformations of Fe is reflected in a recent surge in biological and environmental studies of microorganisms that conserve energy for growth from redox cycling of Fe compounds, particularly in the deep ocean. Here we highlight some of the key habitats where microbial Fe-oxidation plays significant ecological and biogeochemical roles in the oceanic regime, and provide a synthesis of recent studies concerning this important physiological group. We also provide the first evidence that microbial Fe-oxidizing bacteria are a critical factor in the kinetics of mineral dissolution at the seafloor, by accelerating dissolution by 6-8 times over abiotic rates. We assert that these recent studies, which indicate that microbial Fe-oxidation is widespread in the deep-sea, combined with the apparent role that this group play in promoting rock and mineral weathering, indicate that a great deal more attention to these microorganisms is warranted in order to elucidate the full physiological and phylogenetic diversity and activity of the neutrophilic Fe-oxidizing bacteria in the oceans.

Rogers DR, Santelli CM, Edwards KJ. Geomicrobiology of deep-sea deposits: estimating community diversity from low-temperature seafloor rocks and minerals. Geobiology [Internet]. 2003;1 :109. Publisher's VersionAbstract
Edwards KJ, Rogers DR, Wirsen CO, McCollom TM. Isolation and Characterization of Novel Psychrophilic, Neutrophilic, Fe-Oxidizing, Chemolithoautotrophic {alpha}- and {gamma}-Proteobacteria from the Deep Sea. Appl. Environ. Microbiol. [Internet]. 2003;69 :2906-2913. Publisher's VersionAbstract

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{degrees}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 {gamma}-Proteobacteria most closely related to the heterotrophic bacterium Marinobacter aquaeolei (87 to 94% sequence similarity). A second group of isolates are {alpha}-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.

Visscher PT, Baumgartner LK, Buckley DH, Rogers DR, Hogan ME, Raleigh CD, Turk KA, Marais DDJ. Dimethyl sulphide and methanethiol formation in microbial mats: potential pathways for biogenic signatures. Environ Microbiol [Internet]. 2003;5 :296-308. Publisher's VersionAbstract
Edwards KJ, Bach W, Rogers DR. Geomicrobiology of the Ocean Crust: A Role for Chemoautotrophic Fe-Bacteria. Biol Bull [Internet]. 2003;204 :180-185. Publisher's VersionAbstract

The delicate balance of the major global biogeochemical cycles greatly depends on the transformation of Earth materials at or near its surface. The formation and degradation of rocks, minerals, and organic matter are pivotal for the balance, maintenance, and future of many of these cycles. Microorganisms also play a crucial role, determining the transformation rates, pathways, and end products of these processes. While most of Earth's crust is oceanic rather than terrestrial, few studies have been conducted on ocean crust transformations, particularly those mediated by endolithic (rock-hosted) microbial communities. The biology and geochemistry of deep-sea and sub-seafloor environments are generally more complicated to study than in terrestrial or near-coastal regimes. As a result, fewer, and more targeted, studies usually homing in on specific sites, are most common. We are studying the role of endolithic microorganisms in weathering seafloor crustal materials, including basaltic glass and sulfide minerals, both in the vicinity of seafloor hydrothermal vents and off-axis at unsedimented (young) ridge flanks. We are using molecular phylogenetic surveys and laboratory culture studies to define the size, diversity, physiology, and distribution of microorganisms in the shallow ocean crust. Our data show that an unexpected diversity of microorganisms directly participate in rock weathering at the seafloor, and imply that endolithic microbial communities contribute to rock, mineral, and carbon transformations.

Visscher PT, Hoeft SE, Surgeon TML, Rogers DR, Bebout BM, Thompson, J S J, Reid RP. Microelectrode measurements in stromatolites: Unraveling the Earth's past?. In: Taillefert M, Rozan TF Environmental Electrochemistry: Analyses of Trace Element Biogeochemistry. 811th ed. Washington, DC: Oxford University Press ; 2002.Abstract
Visscher PT, Rogers DR, Hoeft SE. Methyl bromide degradation by marine bacteria isolated from Long Island Sound. Van Patten M. The Fifth Biennial Long Island Sound Research Conference. 2000 :17-22.Abstract
Tang KW, Rogers DR, Dam HG, Visscher PT. Seasonal distribution of DMSP among seston, dissolved matter and zooplankton along a transect in the Long Island Sound estuary. Marine Ecology Progress Series. 2000;206 :1-11.Abstract
Hoeft SE, Rogers DR, Visscher PT. Metabolism of methyl bromide and dimethyl sulfide by marine bacteria isolated from coastal and open waters. Aquatic Microbial Ecology. 2000;21 :221-230.Abstract