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Nguyen A, Ustick LJ, Larkin AA, Martiny AC. Global Phylogeography and Microdiversity of the Marine Diazotrophic Cyanobacteria Trichodesmium and UCYN-A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603225. [PMID: 39026769 PMCID: PMC11257549 DOI: 10.1101/2024.07.12.603225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Cyanobacterial diazotrophs, specifically the genera Trichodesmium and UCYN-A, play a pivotal role in marine nitrogen cycling through their capacity for nitrogen fixation. Despite their global distribution, the microdiversity and environmental drivers of these diazotrophs remain underexplored. This study provides a comprehensive analysis of the global diversity and distribution of Trichodesmium and UCYN-A using the nitrogenase gene ( nifH ) as a genetic marker. We sequenced 954 samples from the Pacific, Atlantic, and Indian Oceans as part of the Bio-GO-SHIP project. Our results reveal significant phylogenetic and biogeographic differences between and within the two genera. Trichodesmium exhibited greater microdiversity compared to UCYN-A, with clades showing region-specific distribution. Trichodesmium clades were primarily influenced by temperature and nutrient availability, and particularly frequent in regions of phosphorus stress. In contrast UCYN-A was found in regions of iron stress. UCYN-A clades demonstrated a more homogeneous distributions, with a single sequencing variant within the UCYN-A1 clade dominating across varied environments. The biogeographic patterns and environmental correlations of Trichodesmium and UCYN-A highlight the role of microdiversity in their ecological adaptation and reflect their different ecological strategies. This study underscores the importance of characterizing the global patterns of fine-scale genetic diversity to better understand the functional roles and distribution of marine nitrogen-fixing cyanobacteria.
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2
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Eichner M, Inomura K, Pierella Karlusich JJ, Shaked Y. Better together? Lessons on sociality from Trichodesmium. Trends Microbiol 2023; 31:1072-1084. [PMID: 37244772 DOI: 10.1016/j.tim.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 04/30/2023] [Accepted: 05/01/2023] [Indexed: 05/29/2023]
Abstract
The N2-fixing cyanobacterium Trichodesmium is an important player in the oceanic nitrogen and carbon cycles. Trichodesmium occurs both as single trichomes and as colonies containing hundreds of trichomes. In this review, we explore the benefits and disadvantages of colony formation, considering physical, chemical, and biological effects from nanometer to kilometer scale. Showing that all major life challenges are affected by colony formation, we claim that Trichodesmium's ecological success is tightly linked to its colonial lifestyle. Microbial interactions in the microbiome, chemical gradients within the colony, interactions with particles, and elevated mobility in the water column shape a highly dynamic microenvironment. We postulate that these dynamics are key to the resilience of Trichodesmium and other colony formers in our changing environment.
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Affiliation(s)
- Meri Eichner
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic.
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | | | - Yeala Shaked
- Freddy and Nadine Herrmann Institute of Earth Sciences, Hebrew University, Jerusalem, Israel; Interuniversity Institute for Marine Sciences, Eilat, Israel
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3
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Yang N, Lin YA, Merkel CA, DeMers MA, Qu PP, Webb EA, Fu FX, Hutchins DA. Molecular mechanisms underlying iron and phosphorus co-limitation responses in the nitrogen-fixing cyanobacterium Crocosphaera. THE ISME JOURNAL 2022; 16:2702-2711. [PMID: 36008474 PMCID: PMC9666452 DOI: 10.1038/s41396-022-01307-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
In the nitrogen-limited subtropical gyres, diazotrophic cyanobacteria, including Crocosphaera, provide an essential ecosystem service by converting dinitrogen (N2) gas into ammonia to support primary production in these oligotrophic regimes. Natural gradients of phosphorus (P) and iron (Fe) availability in the low-latitude oceans constrain the biogeography and activity of diazotrophs with important implications for marine biogeochemical cycling. Much remains unknown regarding Crocosphaera's physiological and molecular responses to multiple nutrient limitations. We cultured C. watsonii under Fe, P, and Fe/P (co)-limiting scenarios to link cellular physiology with diel gene expression and observed unique physiological and transcriptional profiles for each treatment. Counterintuitively, reduced growth and N2 fixation resource use efficiencies (RUEs) for Fe or P under P limitation were alleviated under Fe/P co-limitation. Differential gene expression analyses show that Fe/P co-limited cells employ the same responses as single-nutrient limited cells that reduce cellular nutrient requirements and increase responsiveness to environmental change including smaller cell size, protein turnover (Fe-limited), and upregulation of environmental sense-and-respond systems (P-limited). Combined, these mechanisms enhance growth and RUEs in Fe/P co-limited cells. These findings are important to our understanding of nutrient controls on N2 fixation and the implications for primary productivity and microbial dynamics in a changing ocean.
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Affiliation(s)
- Nina Yang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yu-An Lin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Carlin A Merkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Michelle A DeMers
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ping-Ping Qu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric A Webb
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Fei-Xue Fu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - David A Hutchins
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
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4
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Cerdan-Garcia E, Baylay A, Polyviou D, Woodward EMS, Wrightson L, Mahaffey C, Lohan MC, Moore CM, Bibby TS, Robidart JC. Transcriptional responses of Trichodesmium to natural inverse gradients of Fe and P availability. THE ISME JOURNAL 2022; 16:1055-1064. [PMID: 34819612 PMCID: PMC8941076 DOI: 10.1038/s41396-021-01151-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 12/28/2022]
Abstract
The filamentous diazotrophic cyanobacterium Trichodesmium is responsible for a significant fraction of marine di-nitrogen (N2) fixation. Growth and distribution of Trichodesmium and other diazotrophs in the vast oligotrophic subtropical gyres is influenced by iron (Fe) and phosphorus (P) availability, while reciprocally influencing the biogeochemistry of these nutrients. Here we use observations across natural inverse gradients in Fe and P in the North Atlantic subtropical gyre (NASG) to demonstrate how Trichodesmium acclimates in situ to resource availability. Transcriptomic analysis identified progressive upregulation of known iron-stress biomarker genes with decreasing Fe availability, and progressive upregulation of genes involved in the acquisition of diverse P sources with decreasing P availability, while genes involved in N2 fixation were upregulated at the intersection under moderate Fe and P availability. Enhanced N2 fixation within the Fe and P co-stressed transition region was also associated with a distinct, consistent metabolic profile, including the expression of alternative photosynthetic pathways that potentially facilitate ATP generation required for N2 fixation with reduced net oxygen production. The observed response of Trichodesmium to availability of both Fe and P supports suggestions that these biogeochemically significant organisms employ unique molecular, and thus physiological responses as adaptations to specifically exploit the Fe and P co-limited niche they construct.
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Affiliation(s)
- E Cerdan-Garcia
- Ocean and Earth Science, University of Southampton, Southampton, SO14 3ZH, UK.
| | - A Baylay
- Ocean and Earth Science, University of Southampton, Southampton, SO14 3ZH, UK
| | - D Polyviou
- National Oceanography Centre, Southampton, SO14 3ZH, UK
| | | | - L Wrightson
- Earth, Ocean and Ecological Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - C Mahaffey
- Earth, Ocean and Ecological Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - M C Lohan
- Ocean and Earth Science, University of Southampton, Southampton, SO14 3ZH, UK
| | - C M Moore
- Ocean and Earth Science, University of Southampton, Southampton, SO14 3ZH, UK
| | - T S Bibby
- Ocean and Earth Science, University of Southampton, Southampton, SO14 3ZH, UK
| | - J C Robidart
- National Oceanography Centre, Southampton, SO14 3ZH, UK.
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5
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Wen Z, Browning TJ, Cai Y, Dai R, Zhang R, Du C, Jiang R, Lin W, Liu X, Cao Z, Hong H, Dai M, Shi D. Nutrient regulation of biological nitrogen fixation across the tropical western North Pacific. SCIENCE ADVANCES 2022; 8:eabl7564. [PMID: 35119922 PMCID: PMC8816331 DOI: 10.1126/sciadv.abl7564] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Nitrogen fixation is critical for the biological productivity of the ocean, but clear mechanistic controls on this process remain elusive. Here, we investigate the abundance, activity, and drivers of nitrogen-fixing diazotrophs across the tropical western North Pacific. We find a basin-scale coherence of diazotroph abundances and N2 fixation rates with the supply ratio of iron:nitrogen to the upper ocean. Across a threshold of increasing supply ratios, the abundance of nifH genes and N2 fixation rates increased, phosphate concentrations decreased, and bioassay experiments demonstrated evidence for N2 fixation switching from iron to phosphate limitation. In the northern South China Sea, supply ratios were hypothesized to fall around this critical threshold and bioassay experiments suggested colimitation by both iron and phosphate. Our results provide evidence for iron:nitrogen supply ratios being the most important factor in regulating the distribution of N2 fixation across the tropical ocean.
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Affiliation(s)
- Zuozhu Wen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Thomas J. Browning
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Yihua Cai
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Rongbo Dai
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Ruifeng Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Chuanjun Du
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Ruotong Jiang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Wenfang Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Xin Liu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Zhimian Cao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Haizheng Hong
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Minhan Dai
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Dalin Shi
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
- Corresponding author.
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Yamaguchi T, Sato M, Hashihama F, Kato H, Sugiyama T, Ogawa H, Takahashi K, Furuya K. Longitudinal and Vertical Variations of Dissolved Labile Phosphoric Monoesters and Diesters in the Subtropical North Pacific. Front Microbiol 2021; 11:570081. [PMID: 33552003 PMCID: PMC7854537 DOI: 10.3389/fmicb.2020.570081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 10/30/2020] [Indexed: 11/30/2022] Open
Abstract
The labile fraction of dissolved organic phosphorus (DOP) – predominantly consisting of phosphoric esters – is an important microbial P source in the subtropical oligotrophic ocean. However, unlike phosphate, knowledge for labile DOP is still limited due to the scarcity of broad and intensive observations. In this study, we examined the concentrations and size-fractionated hydrolysis rates of labile phosphoric monoesters and diesters along a >10,000 km longitudinal transect in the North Pacific (23°N; upper 200-m layer). Depth-integrated monoesters decreased westward with a maximum difference of fivefold. Vertical profiles of monoesters in the eastern and western basins showed decreasing and increasing trends with depth, respectively. The monoester-depleted shallow layer of the western basin was associated with phosphate depletion and monoesterase activity was predominant in the large size fraction (>0.8 μm), suggesting that monoesters are significant P sources particularly for large microbes. In contrast, diester concentrations were generally lower than monoester concentrations and showed no obvious horizontal or vertical variation in the study area. Despite the unclear distribution pattern of diesters, diesterase activity in the particulate fraction (>0.2 μm) increased in the phosphate-depleted shallow layer of the western basin, suggesting that the targeted diesters in the assay were also important microbial P sources. Diesterase activities in the dissolved fraction (<0.2 μm) were not correlated with ambient phosphate concentrations; however, cell-free diesterase likely played a key role in P cycling, as dissolved diesterase activities were substantially higher than those in the particulate fraction. The horizontal and vertical variability of labile monoesters in the subtropical North Pacific were therefore predominantly regulated by P stress in particularly large microbes, whereas the distributions of labile diesters and diesterase activities were generally independent of microbial P stress, indicating a more complex regulation of diesters to that of monoesters.
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Affiliation(s)
- Tamaha Yamaguchi
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Yokohama, Japan.,Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Mitsuhide Sato
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Fuminori Hashihama
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Haruka Kato
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Takanori Sugiyama
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hiroshi Ogawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Kazutaka Takahashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ken Furuya
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Graduate School of Science and Engineering, Soka University, Tokyo, Japan
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7
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Tang W, Cerdán-García E, Berthelot H, Polyviou D, Wang S, Baylay A, Whitby H, Planquette H, Mowlem M, Robidart J, Cassar N. New insights into the distributions of nitrogen fixation and diazotrophs revealed by high-resolution sensing and sampling methods. ISME JOURNAL 2020; 14:2514-2526. [PMID: 32581316 DOI: 10.1038/s41396-020-0703-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 01/26/2023]
Abstract
Nitrogen availability limits marine productivity across large ocean regions. Diazotrophs can supply new nitrogen to the marine environment via nitrogen (N2) fixation, relieving nitrogen limitation. The distributions of diazotrophs and N2 fixation have been hypothesized to be generally controlled by temperature, phosphorus, and iron availability in the global ocean. However, even in the North Atlantic where most research on diazotrophs and N2 fixation has taken place, environmental controls remain contentious. Here we measure diazotroph composition, abundance, and activity at high resolution using newly developed underway sampling and sensing techniques. We capture a diazotrophic community shift from Trichodesmium to UCYN-A between the oligotrophic, warm (25-29 °C) Sargasso Sea and relatively nutrient-enriched, cold (13-24 °C) subpolar and eastern American coastal waters. Meanwhile, N2 fixation rates measured in this study are among the highest ever recorded globally and show significant increase with phosphorus availability across the transition from the Gulf Stream into subpolar and coastal waters despite colder temperatures and higher nitrate concentrations. Transcriptional patterns in both Trichodesmium and UCYN-A indicate phosphorus stress in the subtropical gyre. Over this iron-replete transect spanning the western North Atlantic, our results suggest that temperature is the major factor controlling the diazotrophic community structure while phosphorous drives N2 fixation rates. Overall, the occurrence of record-high UCYN-A abundance and peak N2 fixation rates in the cold coastal region where nitrate concentrations are highest (~200 nM) challenges current paradigms on what drives the distribution of diazotrophs and N2 fixation.
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Affiliation(s)
- Weiyi Tang
- Division of Earth and Ocean Sciences, Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA.,Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - Elena Cerdán-García
- Department of Ocean and Earth Sciences, National Oceanography Centre, University of Southampton, European Way, SO14 3ZH, Southampton, UK
| | - Hugo Berthelot
- CNRS, Univ Brest, IRD, Ifremer, LEMAR, F-29280 Plouzané, France
| | - Despo Polyviou
- Department of Ocean and Earth Sciences, National Oceanography Centre, University of Southampton, European Way, SO14 3ZH, Southampton, UK
| | - Seaver Wang
- Division of Earth and Ocean Sciences, Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | - Alison Baylay
- Department of Ocean and Earth Sciences, National Oceanography Centre, University of Southampton, European Way, SO14 3ZH, Southampton, UK
| | - Hannah Whitby
- CNRS, Univ Brest, IRD, Ifremer, LEMAR, F-29280 Plouzané, France.,Department of Earth, Ocean and Ecological Sciences, School of Environmental Sciences, University of Liverpool, Liverpool, L69 3GP, UK
| | | | - Matthew Mowlem
- Ocean Technology and Engineering Group, National Oceanography Centre, European Way, SO14 3ZH, Southampton, UK
| | - Julie Robidart
- Ocean Technology and Engineering Group, National Oceanography Centre, European Way, SO14 3ZH, Southampton, UK.
| | - Nicolas Cassar
- Division of Earth and Ocean Sciences, Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA. .,CNRS, Univ Brest, IRD, Ifremer, LEMAR, F-29280 Plouzané, France.
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8
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Frischkorn KR, Haley ST, Dyhrman ST. Transcriptional and Proteomic Choreography Under Phosphorus Deficiency and Re-supply in the N 2 Fixing Cyanobacterium Trichodesmium erythraeum. Front Microbiol 2019; 10:330. [PMID: 30891009 PMCID: PMC6411698 DOI: 10.3389/fmicb.2019.00330] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 02/08/2019] [Indexed: 01/27/2023] Open
Abstract
The N2 fixing cyanobacterium Trichodesmium is a critically important organism in oligotrophic marine ecosystems, supplying “new” nitrogen (N) to the otherwise N-poor tropical and subtropical regions where it occurs. Low concentrations of phosphorus (P) in these regions can constrain Trichodesmium distribution and N2 fixation rates. Physiological characterization of a single species in a mixed community can be challenging, and ‘omic approaches are increasingly important tools for tracking nutritional physiology in a taxon-specific manner. As such, studies examining the dynamics of gene and protein markers of physiology (e.g., nutrient stress) are critical for the application and interpretation of such ‘omic data in situ. Here we leveraged combined transcriptomics, proteomics, and enzyme activity assays to track the physiological response of Trichodesmium erythraeum IMS101 to P deficiency and subsequent P re-supply over 72 h of sampling. P deficiency resulted in differential gene expression, protein abundance, and enzyme activity that highlighted a synchronous shift in P physiology with increases in the transcripts and corresponding proteins for hydrolyzing organic phosphorus, taking up phosphate with higher affinity, and modulating intracellular P demand. After P deficiency was alleviated, gene expression of these biomarkers was reduced to replete levels within 4 h of P amendment. A number of these gene biomarkers were adjacent to putative pho boxes and their expression patterns were similar to a sphR response regulator. Protein products of the P deficiency biomarkers were slow to decline, with 84% of the original P deficient protein set still significantly differentially expressed after 72 h. Alkaline phosphatase activity tracked with proteins for this enzyme. With the rapid turnover time of transcripts, they appear to be good biomarkers of a P stress phenotype, whereas proteins, with a slower turnover time, may better reflect cellular activities. These results highlight the importance of validating and pairing transcriptome and proteome data that can be applied to physiological studies of key species in situ.
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Affiliation(s)
- Kyle R Frischkorn
- Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States.,Lamont-Doherty Earth Observatory, Palisades, NY, United States
| | - Sheean T Haley
- Lamont-Doherty Earth Observatory, Palisades, NY, United States
| | - Sonya T Dyhrman
- Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States.,Lamont-Doherty Earth Observatory, Palisades, NY, United States
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