Joshua Cooper

Northern Kentucky University, Biological Sciences, Faculty Member

University of Oklahoma, Botany & Microbiology, Graduate Student

Followers

Following

Co-authors

Public Views

I'm an aquatic ecologist with a strong interesting in diatom taxonomy and biogeography. I worked on a Master's Degree with Liz Bergey from OU studying the diatom flora of transitional/ephemeral freshwater rock pools in southern Oklahoma, USA. My thesis was: "The diatom biodiversity and biogeography of ephemeral granitic rock pools."

I'm now pursuing my Ph.D in Microbiology at the University of Oklahoma with Dr. Wawrik, studying the transcriptomics of Dinoflagellates, and ultimately Diatoms.
Supervisors: Boris Wawrik and Phil Gibson

less

Julian D Reynolds

Trinity College Dublin

Maria Huete-Ortega

The University of Sheffield

Jayjit Majumdar

University of Kalyani

Kristen J Gremillion

Ohio State University

David Seamon

Kansas State University

Remo Caponi

University of Cologne

Jana Javornik

University of East London

Estella Weiss-Krejci

Austrian Academy of Sciences

Armando Marques-Guedes

UNL - New University of Lisbon

Jon R Sayers

The University of Sheffield

InterestsView All (20)

Uploads

Papers by Joshua Cooper

Transcriptome Analysis of Scrippsiella trochoidea CCMP 3099 Reveals Physiological Changes Related to Nitrate Depletion

Frontiers in microbiology, 2016

Dinoflagellates are a major component of marine phytoplankton and many species are recognized for... more Dinoflagellates are a major component of marine phytoplankton and many species are recognized for their ability to produce harmful algal blooms (HABs). Scrippsiella trochoidea is a non-toxic, marine dinoflagellate that can be found in both cold and tropic waters where it is known to produce "red tide" events. Little is known about the genomic makeup of S. trochoidea and a transcriptome study was conducted to shed light on the biochemical and physiological adaptations related to nutrient depletion. Cultures were grown under N and P limiting conditions and transcriptomes were generated via RNAseq technology. De novo assembly reconstructed 107,415 putative transcripts of which only 41% could be annotated. No significant transcriptomic response was observed in response to initial P depletion, however, a strong transcriptional response to N depletion was detected. Among the down-regulated pathways were those for glutamine/glutamate metabolism as well as urea and nitrate/nitrite...

Occurrence of the Invasive Diatom Didymosphenia Geminata in Southeast Oklahoma

Download

Bacillariophyta: The Diatoms

Aggregated Filter-Feeding Consumers Alter Nutrient Limitation - Consequences for Ecosystem and Community Dynamics

by Joshua Cooper and Kenneth Forshay

Ecology, 2013

Nutrient cycling is a key process linking organisms in ecosystems. This is especially apparent in... more Nutrient cycling is a key process linking organisms in ecosystems. This is especially apparent in 26 stream environments in which nutrients are taken up readily and cycled through the system in a 27 downstream trajectory. Ecological stoichiometry predicts that biogeochemical cycles of different 28 elements are interdependent because the organisms that drive these cycles require fixed ratios of 29 nutrients. There is growing recognition that animals play an important role in biogeochemical 30 cycling across ecosystems. In particular, dense aggregations of consumers can create 31 biogeochemical hotspots in aquatic ecosystems via nutrient translocation. We predicted that 32 filter-feeding freshwater mussels, which occur as speciose, high biomass aggregates, would 33 create biogeochemical hotspots in streams by altering nutrient limitation and algal dynamics. In a 34 field study, we manipulated nitrogen and phosphorus using nutrient-diffusing substrates in areas 35 with high and low mussel abundance, recorded algal growth and community composition, and 36 determined in situ mussel excretion stoichiometry at 18 sites in 3 rivers (Kiamichi, Little, and 37 Mt. Fork rivers, south-central U.S.). Our results indicate that mussels greatly influence 38 ecosystem processes by modifying the nutrients that limit primary productivity. Sites without 39 mussels were N-limited with ~26% higher relative abundances of N-fixing blue-green algae, 40 while sites with high mussel densities were co-limited (N and P) and dominated by diatoms.

Download

Substrate characteristics affect colonization by the bloom-forming diatom Didymosphenia geminata

Aquatic Ecology, 2010

The long-stalked Didymosphenia is capable of forming large blooms and is expanding its range. To ... more The long-stalked Didymosphenia is capable of forming large blooms and is expanding its range. To better understand the colonization dynamics of this species, we investigated the role of substrate characteristics-rock roughness and biofilm condition-on Didymosphenia colonization in a montane Colorado stream. Rocks differing in roughness (shale and sandstone) were treated to manipulate the diatomdominated biofilm by scrubbing or submersion in 30% hydrogen peroxide. Initial chlorophyll concentration differed among rock types (sandstone [ shale) and biofilm treatments (untreated [ scrubbed [ hydrogen peroxide-treated). Rocks were placed in a Didymosphenia bloom area for 8 days. More Didymosphenia colonized the rougher sandstone than the smoother shale, and more colonized stones with intact biofilms than stones with reduced biofilms (intact [ scrubbed [ hydrogen peroxide). These results suggest that rougher stones may be targeted for surveillance for new populations and that the colonization of intact biofilms is consistent with Didymosphenia's habitat in regulated rivers, where biofilm-scouring spates may be suppressed.

Download

Digital imagery of diatoms from the Upper Ohio River Basin and selected tributaries, a work in progress

by Joshua Cooper and Miriam Kannan

As a cosmopolitan group of organisms, algae are important water quality indicators. Diatom taxono... more As a cosmopolitan group of organisms, algae are important water quality indicators. Diatom taxonomy has been recorded from many aquatic systems all over the world. Distinguishing between diatom species involves observations of detailed physical characteristics and specific measurements. We are compiling a taxonomic database of diatom images from the Ohio River Basin as a baseline for identifying common species. The Ohio River was sampled every 5 miles from Pittsburgh, Pennsylvania, to Rising Sun, Indiana, including selected tributaries. The samples were collected using a 10 µm mesh plankton net during the first week of August 2001 and 2002. Samples were boiled in concentrated nitric acid to remove all organic material to ensure an unobstructed view of diatom physical characteristics. The diatoms were mounted in Naphrax® mounting medium and counted under oil immersion (1000x) using a compound light microscope. The images were captured using an Olympus D-12 digital camera. Common taxa consisting of mostly centric forms include five species of Aulacoseira and five species of Cyclotella, which are found throughout the length of the river. These species or varieties can be difficult to identify. This database will be useful to help researchers distinguish among similar species found in the Ohio River Basin so that indicator species can be identified more easily.

Download

Urea uptake and carbon fixation by marine pelagic bacteria and archaea during the Arctic summer and winter seasons

Applied and environmental microbiology, 2014

How Arctic climate change might translate into alterations of biogeochemical cycles of carbon (C)... more How Arctic climate change might translate into alterations of biogeochemical cycles of carbon (C) and nitrogen (N) with respect to inorganic and organic N utilization is not well understood. This study combined 15N uptake rate measurements for ammonium, nitrate, and urea with 15N- and 13C-based DNA stable-isotope probing (SIP). The objective was to identify active bacterial and archeal plankton and their role in N and C uptake during the Arctic summer and winter seasons. We hypothesized that bacteria and archaea would successfully compete for nitrate and urea during the Arctic winter but not during the summer, when phytoplankton dominate the uptake of these nitrogen sources. Samples were collected at a coastal station near Barrow, AK, during August and January. During both seasons, ammonium uptake rates were greater than those for nitrate or urea, and nitrate uptake rates remained lower than those for ammonium or urea. SIP experiments indicated a strong seasonal shift of bacterial a...

Download

Bottom-up biodiversity effects increase resource subsidy flux between ecosystems

Transcriptome Analysis of Scrippsiella trochoidea CCMP 3099 Reveals Physiological Changes Related to Nitrate Depletion

Frontiers in microbiology, 2016