Joshua T. Cooper

Aggregated filter-feeding consumers alter nutrient limitation: consequences for ecosystem and community dynamics.

Nutrient cycling is a key process linking organisms in ecosystems. This is especially apparent in stream environments in which nutrients are taken up readily and cycled through the system in a downstream trajectory. Ecological stoichiometry predicts that biogeochemical cycles of different elements are interdependent because the organisms that drive these cycles require fixed ratios of nutrients. There is growing recognition that animals play an important role in biogeochemical cycling across ecosystems. In particular, dense aggregations of consumers can create biogeochemical hotspots in aquatic ecosystems via nutrient translocation. We predicted that filter-feeding freshwater mussels, which occur as speciose, high-biomass aggregates, would create biogeochemical hotspots in streams by altering nutrient limitation and algal dynamics. In a field study, we manipulated nitrogen and phosphorus using nutrient-diffusing substrates in areas with high and low mussel abundance, recorded algal growth and community composition, and determined in situ mussel excretion stoichiometry at 18 sites in three rivers (Kiamichi, Little, and Mountain Fork Rivers, south-central United States). Our results indicate that mussels greatly influence ecosystem processes by modifying the nutrients that limit primary productivity. Sites without mussels were N-limited with -26% higher relative abundances of N-fixing blue-green algae, while sites with high mussel densities were co-limited (N and P) and dominated by diatoms. These results corroborated the results of our excretion experiments; our path analysis indicated that mussel excretion has a strong influence on stream water column N:P. Due to the high N:P of mussel excretion, strict N-limitation was alleviated, and the system switched to being co-limited by both N and P. This shows that translocation of nutrients by mussel aggregations is important to nutrient dynamics and algal species composition in these rivers. Our study highlights the importance of consumers and this imperiled faunal group on nutrient cycling and community dynamics in aquatic ecosystems.

Bottom‐up biodiversity effects increase resource subsidy flux between ecosystems

Although biodiversity can increase ecosystem productivity and adjacent ecosystems are often linked by resource flows between them, the relationship between biodiversity and resource subsidies is not well understood. Here we test the influence of biodiversity on resource subsidy flux by manipulating freshwater mussel species richness and documenting the effects on a trophic cascade from aquatic to terrestrial ecosystems. In a mesocosm experiment, mussel effects on algae were linked through stable isotope analyses to mussel-derived nitrogen subsidies, but mussel biodiversity effects on algal accumulation were not significant. In contrast, mussel biodiversity significantly increased aquatic insect emergence rates, because aquatic insects were responding to mussel-induced changes in algal community structure instead of algal accumulation. In turn, mussel biodiversity also significantly increased terrestrial spider abundance as spiders tracked increases in aquatic insect prey after a reproduction event. In a comparative field study, we found that sites with greater mussel species richness had higher aquatic insect emergence rates. These results show that, because food webs in adjacent ecosystems are often linked, biodiversity effects in one ecosystem can influence adjacent ecosystems as well.

Urea Uptake and Carbon Fixation by Marine Pelagic Bacteria and Archaea during the Arctic Summer and Winter Seasons

ABSTRACT 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 and archaeal N utilization from ammonium during the summer to urea during the winter but did not support a similar seasonal pattern of nitrate utilization. Analysis of 16S rRNA gene sequences obtained from each SIP fraction implicated marine group I Crenarchaeota (MGIC) as well as Betaproteobacteria, Firmicutes, SAR11, and SAR324 in N uptake from urea during the winter. Similarly, 13C SIP data suggested dark carbon fixation for MGIC, as well as for several proteobacterial lineages and the Firmicutes. These data are consistent with urea-fueled nitrification by polar archaea and bacteria, which may be advantageous under dark conditions.

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

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 transporters. Transcripts for ammonia transporters displayed both up- and down-regulation, perhaps related to a shift to higher affinity transporters. Genes for the utilization of DON compounds were up-regulated. These included transcripts for amino acids transporters, polyamine oxidase, and extracellular proteinase and peptidases. N depletion also triggered down regulation of transcripts related to the production of Photosystems I & II and related proteins. These data are consistent with a metabolic strategy that conserves N while maximizing sustained metabolism by emphasizing the relative contribution of organic N sources. Surprisingly, the transcriptome also contained transcripts potentially related to secondary metabolite production, including a homolog to the Short Isoform Saxitoxin gene (sxtA) from Alexandrium fundyense, which was significantly up-regulated under N-depletion. A total of 113 unique hits to Sxt genes, covering 17 of the 34 genes found in C. raciborskii were detected, indicating that S. trochoidea has previously unrecognized potential for the production of secondary metabolites with potential toxicity.

Benthic algal community composition across a watershed: coupling processes between land and water

One of the main goals of ecology is to understand how the abiotic environment influences the biotic characteristics of the ecosystem. Various processes at multiple scales interact to affect the physical and chemical environments that are experienced by organisms, which ultimately influence community composition. We aimed to understand the processes that control benthic algae community composition within a watershed. We investigated the impact of both land cover and physiochemical variables on benthic algal community composition. We sampled benthic algae along with multiple habitat and water chemistry parameters within three microhabitats across eight sites along the mainstem of the Kiamichi River in southeastern Oklahoma. We used the benthic light availability model to assess the amount of light reaching the bottom of the stream. Additionally, we conducted a GIS analysis of the watershed to determine the land cover affecting each of these sites. Several of the in-stream site-scale variables that were measured (e.g., conductivity, pH and canopy cover) were strongly correlated with both position within the watershed and percent agriculture within the watershed. The physiochemical parameters that were correlated with watershed position and land cover were then used to understand the linkage with algae community composition. Algae genera composition was strongly correlated with both light reaching the bottom of the stream and conductivity. Our results suggest a hierarchy of factors that determine species composition and show the dependence of community composition on differing light regimes.

Shifting effects of rock roughness across a benthic food web

Habitat heterogeneity affects the spatial pattern of stream organisms, but it is unclear how broadly heterogeneity affects the distribution of organisms within a food web. Specifically, rougher rocks have greater algal biomass than smoother rocks, and we hypothesized bottom-up food web control of food web structure, in which rougher rocks would also have higher grazer and predator abundance. We surveyed algal biomass and macroinvertebrates on rocks of differing roughness. We also conducted a field experiment to separately examine rock roughness and algal biomass effects by manipulating algal biomass by raking or scrubbing rocks within created rock clusters. Neither the survey nor the experiment strongly supported a bottom-up scenario. Algal biomass increased with rock roughness. Grazing mayfly abundance was distributed evenly among geologic rock types, except for a higher abundance of baetids on rocks with large cavities, where predatory stoneflies were also abundant. In the rock cluster experiment, the moderate raking disturbance produced higher grazer abundance and reduced algal biomass relative to unmanipulated controls. We concluded that fine-scale roughness directly promoted algal biomass, whereas larger-grain roughness (crevices) affected the distribution of the food web components by forming clumped distributions of grazing baetid mayflies and predatory stoneflies.

Characterization of the diatom flora in the Lower Mountain Fork (Oklahoma, USA), a novel regulated river with a disjunct population of the diatom Didymosphenia geminata (Bacillariophyta)

ABSTRACT Regulated rivers are novel ecosystems with altered temperature and flow regimes that can be used to test distribution patterns of microscopic organisms, such as diatoms. Our objective was to describe the spatial and seasonal patterns of diatoms in a cold-water, oligotrophic river within a region of warm-water, mesotrophic rivers. The Lower Mountain Fork, in south-east Oklahoma (USA), is maintained as a year-around, stocked fishery by the release of cold, hypolimnetic water from Broken Bow Lake and is the southern-most known site of Didymosphenia geminata in North America. Epilithic diatoms were sampled six times at nine sites over a distance of 15.5 km and, within this area, 27 times at the site of the main Didymosphenia bloom. Percentage composition data were analysed for assemblage composition using multivariate analysis, nutrient specificity using a diatom-based metric, and species associations using similarity profiles. Eighty-eight taxa were found, of which 10 were unidentifiable and included local undescribed species and species clusters. Three species [Gomphonema (parvulum morph), Achnanthidium rivulare and Achnanthidium minutissimum] comprised over 60% of the diatom abundance at all sites, and downstream and seasonal patterns were evident for both these and less abundant taxa. Notably, diatom assemblages in the three sites below the dam were similar to that at the lowermost site, below a much smaller dam. The oligotraphentic diatom assemblage reflected the water chemistry of the river. The Didymosphenia bloom had been scoured by a large spate prior to the study and the species was present at two of the nine sites in low numbers but failed to bloom during the study, possibly because of a trend towards increasing phosphorus concentrations in the reservoir (Didymosphenia blooms under low P concentrations). No other species shared Didymosphenia’s distribution pattern over the study reach, highlighting the novelty of Didymosphenia’s presence in the river.

Botanical Phylo-Cards: A Tree-Thinking Game to Teach Plant Evolution

Abstract Students often have limited understanding of the major innovations in plant evolution. We developed a card sorting activity based on tree thinking that is suitable for students with a wide range of abilities and experience. Through this activity, students learn how scientists organize taxa into biologically meaningful, natural groups that illustrate important events in terrestrial plant evolution. The activity corresponds to several NGSS standards and is suitable for use in classroom or laboratory settings and as a public educational outreach activity. The Botanical Phylo-Card Game addresses several components of Next Generation Science Standards (NGSS Lead States, 2013) such as Inheritance/Variation in Traits (3-LS3-1, HS-LS3-1, HS-LS4-2) and Natural Selection/Evolution (MS-LS4-2, HS-LS4-1). The game involves disciplinary core ideas about biodiversity, evolution, and common ancestry; crosscutting concepts regarding identification and interpretation of patterns; and scientific practices of constructing explanations and engaging in arguments from evidence that can guide individualized implementation and assessment of the activity by different instructors.