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  • 1
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    The marine phosphorus cycle (2014)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 4 (2013): 105, doi:10.3389/fmicb.2013.00105.
    Description: Phosphorus, the 13th element to be discovered on our planet, has a rich and varied history spanning match-making, bombs, fertilizer, and pesticides. Entire islands economies (Nauru) have collapsed in the mad hunt for phosphorus rock (Gowdy and McDaniel, 1999). Mineral reserves of this critical and valuable element are now being so rapidly mined from our Earth's crust that we are approaching a point where demand exceeds supply (Cordell et al., 2009). Why such a storied element? The answer rests in the fact that phosphorus is an essential ingredient in every known recipe for life: it is integral for energy storage, cell structure, and the very genetic material that encodes all life on the planet. Phosphorus is in fact, the staff of life (Karl, 2000), the scaffolding on which all biomass is built. Just as phosphorus fertilizer supports the growth of agricultural crops, phosphorus supply supports the growth of photosynthetic organisms, or phytoplankton, at the base of the marine food web.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
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    Transcriptional shifts highlight the role of nutrients in harmful brown tide dynamics (2019)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wurch, L. L., Alexander, H., Frischkorn, K. R., Haley, S. T., Gobler, C. J., & Dyhrman, S. T. Transcriptional shifts highlight the role of nutrients in harmful brown tide dynamics. Frontiers in Microbiology, 10, (2019):136, doi:10.3389/fmicb.2019.00136.
    Description: Harmful algal blooms (HABs) threaten ecosystems and human health worldwide. Controlling nitrogen inputs to coastal waters is a common HAB management strategy, as nutrient concentrations often suggest coastal blooms are nitrogen-limited. However, defining best nutrient management practices is a long-standing challenge: in part, because of difficulties in directly tracking the nutritional physiology of harmful species in mixed communities. Using metatranscriptome sequencing and incubation experiments, we addressed this challenge by assaying the in situ physiological ecology of the ecosystem destructive alga, Aureococcus anophagefferens. Here we show that gene markers of phosphorus deficiency were expressed in situ, and modulated by the enrichment of phosphorus, which was consistent with the observed growth rate responses. These data demonstrate the importance of phosphorus in controlling brown-tide dynamics, suggesting that phosphorus, in addition to nitrogen, should be evaluated in the management and mitigation of these blooms. Given that nutrient concentrations alone were suggestive of a nitrogen-limited ecosystem, this study underscores the value of directly assaying harmful algae in situ for the development of management strategies.
    Description: This research was funded by NOAA Grant NA15NOS4780199 (SD), NA09NOA4780206 (SD and CG), and NA15NOS4780183 (CG) through the ECOHAB Program, publication number ECO929. Partial support was also provided by the World Surf League through the Columbia Center for Climate and Life, the Woods Hole Oceanographic Institution Coastal Ocean Institute, and the Link Foundation. Kyle Frischkorn was funded under a National Science Foundation Graduate Research Fellowship.
    Keywords: harmful algal bloom ; Aureococcus anophagefferens ; brown tide ; nutrient physiology ; metatranscriptomics
    Repository Name: Woods Hole Open Access Server
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  • 3
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    Identifying reference genes with stable expression from high throughput sequence data (2014)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 3 (2012): 385, doi:10.3389/fmicb.2012.00385.
    Description: Genes that are constitutively expressed across multiple environmental stimuli are crucial to quantifying differentially expressed genes, particularly when employing quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays. However, the identification of these potential reference genes in non-model organisms is challenging and is often guided by expression patterns in distantly related organisms. Here, transcriptome datasets from the diatom Thalassiosira pseudonana grown under replete, phosphorus-limited, iron-limited, and phosphorus and iron co-limited nutrient regimes were analyzed through literature-based searches for homologous reference genes, k-means clustering, and analysis of sequence counts (ASC) to identify putative reference genes. A total of 9759 genes were identified and screened for stable expression. Literature-based searches surveyed 18 generally accepted reference genes, revealing 101 homologs in T. pseudonana with variable expression and a wide range of mean tags per million. k-means analysis parsed the whole transcriptome into 15 clusters. The two most stable clusters contained 709 genes, but still had distinct patterns in expression. ASC analyses identified 179 genes that were stably expressed (posterior probability 〈 0.1 for 1.25 fold change). Genes known to have a stable expression pattern across the test treatments, like actin, were identified in this pool of 179 candidate genes. ASC can be employed on data without biological replicates and was more robust than the k-means approach in isolating genes with stable expression. The intersection of the genes identified through ASC with commonly used reference genes from the literature suggests that actin and ubiquitin ligase may be useful reference genes for T. pseudonana and potentially other diatoms. With the wealth of transcriptome sequence data becoming available, ASC can be easily applied to transcriptome datasets from other phytoplankton to identify reference genes.
    Description: This research was funded by the National Science Foundation grant #OCE-0723667 (to Sonya T. Dyhrman, Mak A. Saito, Bethany D. Jenkins, and Tatiana A. Rynearson). Harriet Alexander is funded under a National Defense Science and Engineering Graduate (NDSEG) Fellowship.
    Keywords: Thalassiosira pseudonana ; Diatom ; Phytoplankton ; Housekeeping genes ; RT-qPCR ; Transcriptome ; Relative gene expression ; Reference gene
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
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    Arsenate resistance in the unicellular marine diazotroph Crocosphaera watsonii (2014)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2011. This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited. The definitive version was published in Frontiers in Microbiology 2 (2011): 214, doi:10.3389/fmicb.2011.00214.
    Description: The toxic arsenate ion can behave as a phosphate analog, and this can result in arsenate toxicity especially in areas with elevated arsenate to phosphate ratios like the surface waters of the ocean gyres. In these systems, cellular arsenate resistance strategies would allow phytoplankton to ameliorate the effects of arsenate transport into the cell. Despite the potential coupling between arsenate and phosphate cycling in oligotrophic marine waters, relatively little is known about arsenate resistance in the nitrogen-fixing marine cyanobacteria that are key components of the microbial community in low nutrient systems. The unicellular diazotroph, Crocosphaera watsonii WH8501, was able to grow at reduced rates with arsenate additions up to 30 nM, and estimated arsenate to phosphate ratios of 6:1. The genome of strain WH8501 contains homologs for arsA, arsH, arsB, and arsC, allowing for the reduction of arsenate to arsenite and the pumping of arsenite out of the cell. The short-term addition of arsenate to the growth medium had no effect on nitrogen fixation. However, arsenate addition did result in the up-regulation of the arsB gene with increasing arsenate concentrations, indicating the induction of the arsenate detoxification response. The arsB gene was also up-regulated by phosphorus stress in concert with a gene encoding the high-affinity phosphate binding protein pstS. Both genes were down-regulated when phosphate was re-fed to phosphorus-stressed cells. A field survey of surface water from the low phosphate western North Atlantic detected expression of C. watsonii arsB, suggestive of the potential importance of arsenate resistance strategies in this and perhaps other systems.
    Description: This research was funded in part by the National Science Foundation #OCE-0451419, and the Center for Microbial Oceanography: Research and Education.
    Keywords: Cyanobacteria ; Phosphorus ; Marine ; Arsenate ; Diazotroph ; Crocosphaera
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
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    The genetic diversity of Mesodinium and associated cryptophytes (2017)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 2017, doi:10.3389/fmicb.2016.02017.
    Description: Ciliates from the genus Mesodinium are globally distributed in marine and freshwater ecosystems and may possess either heterotrophic or mixotrophic nutritional modes. Members of the Mesodinium major/rubrum species complex photosynthesize by sequestering and maintaining organelles from cryptophyte prey, and under certain conditions form periodic or recurrent blooms (= red tides). Here, we present an analysis of the genetic diversity of Mesodinium and cryptophyte populations from 10 environmental samples (eight globally dispersed habitats including five Mesodinium blooms), using group-specific primers for Mesodinium partial 18S, ITS, and partial 28S rRNA genes as well as cryptophyte large subunit RuBisCO genes (rbcL). In addition, 22 new cryptophyte and four new M. rubrum cultures were used to extract DNA and sequence rbcL and 18S-ITS-28S genes, respectively, in order to provide a stronger phylogenetic context for our environmental sequences. Bloom samples were analyzed from coastal Brazil, Chile, two Northeastern locations in the United States, and the Pribilof Islands within the Bering Sea. Additionally, samples were also analyzed from the Baltic and Barents Seas and coastal California under non-bloom conditions. Most blooms were dominated by a single Mesodinium genotype, with coastal Brazil and Chile blooms composed of M. major and the Eastern USA blooms dominated by M. rubrum variant B. Sequences from all four blooms were dominated by Teleaulax amphioxeia-like cryptophytes. Non-bloom communities revealed more diverse assemblages of Mesodinium spp., including heterotrophic species and the mixotrophic Mesodinium chamaeleon. Similarly, cryptophyte diversity was also higher in non-bloom samples. Our results confirm that Mesodinium blooms may be caused by M. major, as well as multiple variants of M. rubrum, and further implicate T. amphioxeia as the key cryptophyte species linked to these phenomena in temperate and subtropical regions.
    Description: MJ thanks the funding support of the National Science Foundations Grants NSF-OCE 1031718 and NSF-IOS 1326228.
    Repository Name: Woods Hole Open Access Server
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