ESTABLISHMENT OF MINIMAL AND MAXIMAL TRANSCRIPT LEVELS FOR NITRATE TRANSPORTER GENES FOR DETECTING NITROGEN DEFICIENCY IN THE MARINE PHYTOPLANKTON ISOCHRYSIS GALBANA (PRYMNESIOPHYCEAE) AND THALASSIOSIRA PSEUDONANA (BACILLARIOPHYCEAE)1

Kang, Lee-Kuo; Hwang, Sheng-Ping L.; Lin, Hsing‐Juh; Chen, Pei-Chung; Chang, Jeng Kuei

doi:10.1111/j.1529-8817.2009.00698.x

Cited by 26 publications

(44 citation statements)

References 36 publications

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“…This technique is similar in concept to targeted assays using qRT-PCR to compare expression patterns between species in culture (66). Briefly, the SGNC of a gene in the field was bounded by the SGNC from each of the nutrient treatments to yield the STD score for both N (STD N ) and P (STD P ) (Fig.…”

Section: Species-specific Resource Utilization Underpins Physiologicamentioning

confidence: 99%

Metatranscriptome analyses indicate resource partitioning between diatoms in the field

Alexander

Jenkins

Rynearson

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

156

160

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Diverse communities of marine phytoplankton carry out half of global primary production. The vast diversity of the phytoplankton has long perplexed ecologists because these organisms coexist in an isotropic environment while competing for the same basic resources (e.g., inorganic nutrients). Differential niche partitioning of resources is one hypothesis to explain this "paradox of the plankton," but it is difficult to quantify and track variation in phytoplankton metabolism in situ. Here, we use quantitative metatranscriptome analyses to examine pathways of nitrogen (N) and phosphorus (P) metabolism in diatoms that cooccur regularly in an estuary on the east coast of the United States (Narragansett Bay). Expression of known N and P metabolic pathways varied between diatoms, indicating apparent differences in resource utilization capacity that may prevent direct competition. Nutrient amendment incubations skewed N/P ratios, elucidating nutrient-responsive patterns of expression and facilitating a quantitative comparison between diatoms. The resource-responsive (RR) gene sets deviated in composition from the metabolic profile of the organism, being enriched in genes associated with N and P metabolism. Expression of the RR gene set varied over time and differed significantly between diatoms, resulting in opposite transcriptional responses to the same environment. Apparent differences in metabolic capacity and the expression of that capacity in the environment suggest that diatom-specific resource partitioning was occurring in Narragansett Bay. This high-resolution approach highlights the molecular underpinnings of diatom resource utilization and how cooccurring diatoms adjust their cellular physiology to partition their niche space.phytoplankton | diatom | nutrient physiology | niche partitioning | metatranscriptomics T he stability and primary productivity of ecosystems have long been linked to the diversity of primary producers (1, 2). This linkage is well documented in terrestrial systems (3-7) and is increasingly being established for marine systems (8-11). Marine phytoplankton generate roughly half of global primary production (12-14) and play a critical role in oceanic ecosystem structure and function. Within the phytoplankton, the diatoms generate an estimated 40% of primary production (15). Thus, diatoms alone exert a profound influence over marine primary production and global carbon (C) cycling, particularly in coastal margins and estuaries.Phytoplankton are extremely diverse, with estimates of over 200,000 extant species (16,17). This dramatic level of taxonomic diversity in the plankton is difficult to resolve with the apparently limited number of niches in the pelagic habitat because these organisms compete for the same two basic resources: light and nutrients. As was highlighted by Hutchinson (18), the phytoplankton violate Gause's law of competitive exclusion, which posits that two organisms competing for the same resources cannot coexist. Much thought has gone toward identifying the cause of the "pa...

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Section: Species-specific Resource Utilization Underpins Physiologicamentioning

confidence: 99%

Metatranscriptome analyses indicate resource partitioning between diatoms in the field

Alexander

Jenkins

Rynearson

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

156

160

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“…Surprisingly, no clear N-starvation response was discernable on the gene expression level, because none of the genes putatively involved in N acquisition, transportation and storage were upregulated under N-starvation. In contrast to P. parvum, the non-toxic and presumably non-mixotroph haptophyte I. galbana, reacts to N-starvation by up-regulation of nitrate and ammonium transporters (Kang et al, 2007(Kang et al, , 2009. In this case, an increase of mRNA level of both transporter genes was observed in N-depleted, to nitrate conditioned cells of I. galbana, but when ammonium and nitrate was provided, the expression of both transporter genes decreased.…”

Section: Nitrogen Starvationmentioning

confidence: 84%

Transcriptomic response of the toxic prymnesiophyte Prymnesium parvum (N. Carter) to phosphorus and nitrogen starvation

et al. 2012

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“…This technique is similar in concept to targeted assays using qRT-PCR to compare expression patterns between species in culture (Kang et al, 2009). Briefly, the of a N or (Figure 3-4C).…”

Section: Identification and Modulation Of Resource Responsive Genes Imentioning

confidence: 99%

Defining the ecological and physiological traits of phytoplankton across marine ecosystems

Alexander¹

2016

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Marine phytoplankton are central players in the global carbon cycle, responsible for nearly half of global primary production. The identification of the factors controlling phytoplankton ecology, physiology, and, ultimately, bloom dynamics has been a central problem in the field of biological oceanography for the past century. Molecular approaches enable the direct examination of species-specific metabolic profiles in mixed, natural communities, a task which was previously intractable. In this thesis, I developed and applied novel analytical tools and bioinformatic pipelines to characterize the physiological response of phytoplankton to their environment at various levels of taxonomic grouping. An in silico Bayesian statistical approach was designed to identify stable reference genes from high-throughput sequence data for use in RT-qPCR assays or metatranscriptome studies. Using a metatranscriptomic approach, the role of resource partitioning in the coexistence of two closely related diatom species in an estuarine system was examined. This study demonstrated that co-occurring diatoms in a dynamic coastal system have apparent differences in their capacity to use nitrogen and phosphorus, and that these differences may facilitate the diversity of the phytoplankton. The second field study focused on the diatom, haptophyte, and dinoflagellate functional groups, using simulated blooms to characterize the traits that govern the magnitude and timing of phytoplankton blooms in the oligotrophic ocean. The results indicated that blooms form when phytoplankton are released from limitation by resources and that the mechanistic basis for the success of one functional group over another may be driven by how efficiently the transcriptome is modulated following a nutrient pulse. The final study looked at the sub-species level, examining the balance of phenotypic plasticity and strain diversity in the success of the coccolithophore Emiliania huxleyi. Results indicated strong control of nitrogen on the species complex and showed that nutrient resupply shifted the strain composition as well as transcript abundance of key biogeochemical genes involved in nutrient acquisition and the life stage of the population. Together, these studies demonstrate the breadth of information that can be garnered through the integration of molecular approaches with traditional biological oceanographic surveys, with each illuminating fundamental questions around phytoplankton ecology and bloom formation. D.), and is a contribution of the Simons Collaboration on Ocean Processes and Ecology (SCOPE).The last five years has been the most interesting, challenging, and rewarding period of my life. I have been given the opportunity not only to freely pursue my academic passions, but to travel the world, interact with amazing people, and grow. Without the support and guidance of my mentors, colleagues, friends, and family, this journey would not have been possible.First and foremost, I wish to thank my advisor Sonya Dyhrman, whose confidence in my sci...

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ESTABLISHMENT OF MINIMAL AND MAXIMAL TRANSCRIPT LEVELS FOR NITRATE TRANSPORTER GENES FOR DETECTING NITROGEN DEFICIENCY IN THE MARINE PHYTOPLANKTON ISOCHRYSIS GALBANA (PRYMNESIOPHYCEAE) AND THALASSIOSIRA PSEUDONANA (BACILLARIOPHYCEAE)¹

Cited by 26 publications

References 36 publications

Metatranscriptome analyses indicate resource partitioning between diatoms in the field

Metatranscriptome analyses indicate resource partitioning between diatoms in the field

Transcriptomic response of the toxic prymnesiophyte Prymnesium parvum (N. Carter) to phosphorus and nitrogen starvation

Defining the ecological and physiological traits of phytoplankton across marine ecosystems

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