William D. Orsi
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View article: Urea use drives niche separation between dominant marine ammonia oxidizing archaea
Urea use drives niche separation between dominant marine ammonia oxidizing archaea Open
Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms in the ocean and play a critical role in marine nitrogen cycling. Recently, urea has been shown to serve as an additional substrate for marine AOA, with substantial…
View article: Deoxygenation effects on the interaction between microbial metabolisms and dissolved organic matter cycling in the seasonally anoxic Mariager Fjord (Denmark, North Sea)
Deoxygenation effects on the interaction between microbial metabolisms and dissolved organic matter cycling in the seasonally anoxic Mariager Fjord (Denmark, North Sea) Open
Seawater stores as much carbon in the form of dissolved organic matter (DOM) as there is CO2 in the atmosphere. Over a period of just 50 years (from 1960 to 2010) global oceanic oxygen reserves have been reduced by 2% and the anoxic waters…
View article: The Rise of Algae promoted eukaryote predation in the Neoproterozoic benthos
The Rise of Algae promoted eukaryote predation in the Neoproterozoic benthos Open
The proliferation of marine algae in the Neoproterozoic Era is thought to have stimulated the ecology of predatory microbial eukaryotes. To test this proposal, we introduced algal particulate matter (APM) to marine sediments underlying a m…
View article: Identifying the active microbes driving organosulfur cycling from taurine and methionine in marine sediment
Identifying the active microbes driving organosulfur cycling from taurine and methionine in marine sediment Open
Studies on microbial sulfur cycling in marine sediment have primarily centered on the cycling of inorganic sulfur. The microbial diversity underlying the cycling of organosulfur compounds is largely unexplored. In this study, we present th…
View article: Principal role of fungi in soil carbon stabilization during early pedogenesis in the high Arctic
Principal role of fungi in soil carbon stabilization during early pedogenesis in the high Arctic Open
Climate warming is causing widespread deglaciation and pioneer soil formation over glacial deposits. Melting glaciers expose rocky terrain and glacial till sediment that is relatively low in biomass, oligotrophic, and depleted in nutrients…
View article: Quantifying genome-specific carbon fixation in a 750-meter deep subsurface hydrothermal microbial community
Quantifying genome-specific carbon fixation in a 750-meter deep subsurface hydrothermal microbial community Open
Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isoto…
View article: Alkaline vents recreated in two dimensions to study pH gradients, precipitation morphology, and molecule accumulation
Alkaline vents recreated in two dimensions to study pH gradients, precipitation morphology, and molecule accumulation Open
Alkaline vents (AVs) are hypothesized to have been a setting for the emergence of life, by creating strong gradients across inorganic membranes within chimney structures. In the past, three-dimensional chimney structures were formed under …
View article: White and green rust chimneys accumulate RNA in a ferruginous chemical garden
White and green rust chimneys accumulate RNA in a ferruginous chemical garden Open
Mechanisms of nucleic acid accumulation were likely critical to life's emergence in the ferruginous oceans of the early Earth. How exactly prebiotic geological settings accumulated nucleic acids from dilute aqueous solutions, is poorly und…
View article: Body-Plan Reorganization in a Sponge Correlates with Microbiome Change
Body-Plan Reorganization in a Sponge Correlates with Microbiome Change Open
Mounting evidence suggests that animals and their associated bacteria interact via intricate molecular mechanisms, and it is hypothesized that disturbances to the microbiome influence animal development. Here, we show that the loss of a ke…
View article: Sargasso Sea Vibrio bacteria: Underexplored potential pathovars in a perturbed habitat
Sargasso Sea Vibrio bacteria: Underexplored potential pathovars in a perturbed habitat Open
We fully sequenced the genomes of 16 Vibrio cultivars isolated from eel larvae, plastic marine debris (PMD), the pelagic brown macroalga Sargassum, and seawater samples collected from the Caribbean and Sargasso Seas of the North Atlantic O…
View article: Alkaline vents recreated in two dimensions to study pH gradients, precipitation morphology and molecule accumulation
Alkaline vents recreated in two dimensions to study pH gradients, precipitation morphology and molecule accumulation Open
Alkaline vents (AV) are hypothesized to have been a setting for the emergence of life, by creating strong gradients across inorganic membranes within chimney structures. In the past, 3-dimensional chimney structures were formed under labor…
View article: A rapid method for measuring ATP + ADP + AMP in marine sediment
A rapid method for measuring ATP + ADP + AMP in marine sediment Open
In this report, I describe a method for rapid measurement of total adenylate (ATP + ADP + AMP) in marine sediment samples for estimating microbial biomass. A simple ‘boil and dilute’ method is described here, whereby adding boiled MilliQ w…
View article: Spatial dynamics of marine dissolved organic matter in the Benguela upwelling system
Spatial dynamics of marine dissolved organic matter in the Benguela upwelling system Open
Marine dissolved organic matter (DOM) is one of the largest active carbon pools on Earth, storing one thousand times more carbon than all living organisms in the ocean combined, and similar amounts of carbon than all CO2 in the atmospheric…
View article: Dissolved organic sulfur utilization by marine benthic microbial communities revealed by quantitative DNA stable isotope probing
Dissolved organic sulfur utilization by marine benthic microbial communities revealed by quantitative DNA stable isotope probing Open
Microbial metabolisms are directly responsible for the production, degradation and recycling of dissolved organic matter (DOM) in the ocean. Many compounds within the DOM contain sulfur (dissolved organic sulfur, DOS) and in sum they repre…
View article: Carbon metabolism and biogeography of candidate phylum “Candidatus Bipolaricaulota” in geothermal environments of Biga Peninsula, Turkey
Carbon metabolism and biogeography of candidate phylum “Candidatus Bipolaricaulota” in geothermal environments of Biga Peninsula, Turkey Open
Terrestrial hydrothermal springs and aquifers are excellent sites to study microbial biogeography because of their high physicochemical heterogeneity across relatively limited geographic regions. In this study, we performed 16S rRNA gene s…
View article: Decoding geobiological evolution from microbiomes
Decoding geobiological evolution from microbiomes Open
Genomic records of genetic recombination and mutation rates indicate that freshwater ammonia-oxidizing archaea have evolved through paleoclimate and geohydrological history.
View article: White and green rust chimneys accumulate RNA in a ferruginous chemical garden
White and green rust chimneys accumulate RNA in a ferruginous chemical garden Open
Mechanisms of nucleic acid accumulation were likely critical to the emergence of life in the ferruginous oceans of the early Earth. How exactly prebiotic geological settings accumulated nucleic acids from dilute aqueous solutions, is poorl…
View article: High-resolution vertical biogeochemical profiles in the hyporheic zone reveal insights into microbial methane cycling
High-resolution vertical biogeochemical profiles in the hyporheic zone reveal insights into microbial methane cycling Open
Facing the challenges of climate change, policy making relies on sound greenhouse gas (GHG) budgets. Rivers and streams emit large quantities of the potent GHG methane (CH4), but their global impact on atmospheric CH4 concentrations is hig…
View article: Quantitative microbial ecology: Future challenges and opportunities
Quantitative microbial ecology: Future challenges and opportunities Open
Trying to figure out what a given microbe, or microbial group, is doing in a natural environmental sample is challenging. The overwhelming majority of microbial species have never been cultivated (Kuypers, 2007; Rappe & Giovannoni, 2003; S…
View article: Body-plan reorganization in a sponge correlates with microbiome change
Body-plan reorganization in a sponge correlates with microbiome change Open
Mounting evidence suggests that animals and their associated bacteria interact via intricate molecular mechanisms, and it is hypothesized that disturbances to the microbiome can influence animal development. Sponges diverged from other ani…
View article: High-resolution vertical biogeochemical profiles in the hyporheic zone reveal insights into microbial methane cycling
High-resolution vertical biogeochemical profiles in the hyporheic zone reveal insights into microbial methane cycling Open
Facing the challenges of climate change, policy making relies on sound greenhouse gas (GHG) budgets. Rivers and streams emit large quantities of the potent GHG methane (CH4), but their global impact on atmospheric CH4 concentrations is hig…
View article: Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf
Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf Open
Microbial activities in oxygen minimum zones (OMZs) transform inorganic fixed nitrogen into greenhouse gases, impacting the Earth’s climate and nutrient equilibrium. Coastal OMZs are predicted to expand with global change and increase carb…
View article: Spatial variance in river bed methane cycling – measurement and interpretation of geochemical profiles linked with quantitative PCR and 16S rRNA sequencing
Spatial variance in river bed methane cycling – measurement and interpretation of geochemical profiles linked with quantitative PCR and 16S rRNA sequencing Open
<p>Rivers and streams are often supersaturated in methane (CH<sub>4</sub>) and emit significant amounts of this potent greenhouse gas to the atmosphere. Methane is produced by methanogenic archaea in anaerobic sediments w…
View article: Pangenomics of Candidatus Bipolaricaulota in hydrothermal aquifers of Biga Peninsula, Turkey
Pangenomics of Candidatus Bipolaricaulota in hydrothermal aquifers of Biga Peninsula, Turkey Open
We surveyed the microbial diversity of eleven different deep geothermal aquifers and springs across the tectonically active Biga Peninsula (Turkey), a hydrothermal setting that is historically undersampled for environmental microbial commu…