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Li Z, Luk HC, Arromrak BS, Gaitan-Espitia JD. Nitrogen source and availability regulate plastic population dynamics in the marine diatom Thalassiosira weissflogii. MARINE ENVIRONMENTAL RESEARCH 2024; 202:106733. [PMID: 39255628 DOI: 10.1016/j.marenvres.2024.106733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 08/30/2024] [Accepted: 09/02/2024] [Indexed: 09/12/2024]
Abstract
Variation in nitrogen (N) availability significantly influences population dynamics and the productivity of marine phytoplankton. As N availability in the ocean is conditioned by the N source, it is important to understand the capacity of phytoplankton organisms to adjust their physiology and dynamics under different N conditions. We investigated the growth dynamics of Thalassiosira weissflogii, a coastal diatom, in response to different N sources (Nitrate, NO3-; Ammonium, NH4+; urea, CH4N2O) and availabilities (45 and 5 μM). Our findings demonstrate that T. weissflogii can display plastic adjustments in population dynamics to different N sources. These responses evidenced a greater preference for NH4+ and urea than NO3-, particularly under high N availability. The relative growth rate (μ) is higher (1.18 ± 0.01) under NH4+-high treatment compared to NO3--high (1.01 ± 0.01). The carrying capacity (K) varied only among concentrations, indicating equal N utilization efficiency for biomass production. No effects of N source were detected under the low concentration, suggesting that the preference for NH₄⁺ and urea was diminished by limited nitrogen supply due to potential interactions. These results provide valuable insights into the physiological flexibility of T. weissflogii to varying N conditions, shedding light on the ecological success and resilience of this species in highly variable coastal environments.
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Affiliation(s)
- Zhenzhen Li
- Jiangsu Key Laboratory of Marine Bioresources and Environment and Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China; The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
| | - Hau Ching Luk
- The Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
| | - Bovern Suchart Arromrak
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
| | - Juan Diego Gaitan-Espitia
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China; Institute for Climate and Carbon Neutrality, The University of Hong Kong, Hong Kong SAR, China.
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2
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Zhu Y, Mulholland MR, Bernhardt PW, Neeley AR, Widner B, Tapia AM, Echevarria MA. Nitrogen uptake rates and phytoplankton composition across contrasting North Atlantic Ocean coastal regimes north and south of Cape Hatteras. Front Microbiol 2024; 15:1380179. [PMID: 38784802 PMCID: PMC11113559 DOI: 10.3389/fmicb.2024.1380179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
Understanding nitrogen (N) uptake rates respect to nutrient availability and the biogeography of phytoplankton communities is crucial for untangling the complexities of marine ecosystems and the physical, biological, and chemical forces shaping them. In the summer of 2016, we conducted measurements of bulk microbial uptake rates for six 15N-labeled substrates: nitrate, nitrite, ammonium, urea, cyanate, and dissolve free amino acids across distinct marine provinces, including the continental shelf of the Mid-and South Atlantic Bights (MAB and SAB), the Slope Sea, and the Gulf Stream, marking the first instance of simultaneously measuring six different N uptake rates in this dynamic region. Total measured N uptake rates were lowest in the Gulf Stream followed by the SAB. Notably, the MAB exhibited significantly higher N uptake rates compared to the SAB, likely due to the excess levels of pre-existing phosphorus present in the MAB. Together, urea and nitrate uptake contributed approximately 50% of the total N uptake across the study region. Although cyanate uptake rates were consistently low, they accounted for up to 11% of the total measured N uptake at some Gulf Stream stations. Phytoplankton groups were identified based on specific pigment markers, revealing a dominance of diatoms in the shelf community, while Synechococcus, Prochlorococcus, and pico-eukaryotes dominated in oligotrophic Gulf Stream waters. The reported uptake rates in this study were mostly in agreement with previous studies conducted in coastal waters of the North Atlantic Ocean. This study suggests there are distinct regional patterns of N uptake in this physically dynamic region, correlating with nutrient availability and phytoplankton community composition. These findings contribute valuable insights into the intricate interplay of biological and chemical factors shaping N dynamics in disparate marine ecosystems.
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Affiliation(s)
- Yifan Zhu
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
| | - Margaret R. Mulholland
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
| | - Peter W. Bernhardt
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
| | | | - Brittany Widner
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
| | - Alfonso Macías Tapia
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
- Office of Education, National Oceanic and Atmospheric Administration, Silver Spring, MD, United States
| | - Michael A. Echevarria
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
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3
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Anderson SI, Fronda C, Barton AD, Clayton S, Rynearson TA, Dutkiewicz S. Phytoplankton thermal trait parameterization alters community structure and biogeochemical processes in a modeled ocean. GLOBAL CHANGE BIOLOGY 2024; 30:e17093. [PMID: 38273480 DOI: 10.1111/gcb.17093] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/19/2023] [Accepted: 11/20/2023] [Indexed: 01/27/2024]
Abstract
Phytoplankton exhibit diverse physiological responses to temperature which influence their fitness in the environment and consequently alter their community structure. Here, we explored the sensitivity of phytoplankton community structure to thermal response parameterization in a modelled marine phytoplankton community. Using published empirical data, we evaluated the maximum thermal growth rates (μmax ) and temperature coefficients (Q10 ; the rate at which growth scales with temperature) of six key Phytoplankton Functional Types (PFTs): coccolithophores, cyanobacteria, diatoms, diazotrophs, dinoflagellates, and green algae. Following three well-documented methods, PFTs were either assumed to have (1) the same μmax and the same Q10 (as in to Eppley, 1972), (2) a unique μmax but the same Q10 (similar to Kremer et al., 2017), or (3) a unique μmax and a unique Q10 (following Anderson et al., 2021). These trait values were then implemented within the Massachusetts Institute of Technology biogeochemistry and ecosystem model (called Darwin) for each PFT under a control and climate change scenario. Our results suggest that applying a μmax and Q10 universally across PFTs (as in Eppley, 1972) leads to unrealistic phytoplankton communities, which lack diatoms globally. Additionally, we find that accounting for differences in the Q10 between PFTs can significantly impact each PFT's competitive ability, especially at high latitudes, leading to altered modeled phytoplankton community structures in our control and climate change simulations. This then impacts estimates of biogeochemical processes, with, for example, estimates of export production varying by ~10% in the Southern Ocean depending on the parameterization. Our results indicate that the diversity of thermal response traits in phytoplankton not only shape community composition in the historical and future, warmer ocean, but that these traits have significant feedbacks on global biogeochemical cycles.
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Affiliation(s)
- Stephanie I Anderson
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Clara Fronda
- Laboratoire de Physique, Ecole Normale Supérieure, Paris, France
| | - Andrew D Barton
- Scripps Institution of Oceanography and Department of Ecology, Behavior and Evolution, San Diego, California, USA
| | - Sophie Clayton
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, Virginia, USA
| | - Tatiana A Rynearson
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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4
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Alexander H, Hu SK, Krinos AI, Pachiadaki M, Tully BJ, Neely CJ, Reiter T. Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton. mBio 2023; 14:e0167623. [PMID: 37947402 PMCID: PMC10746220 DOI: 10.1128/mbio.01676-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/27/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers' efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.
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Affiliation(s)
- Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Sarah K. Hu
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Arianna I. Krinos
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge and Woods Hole, Massachusetts, USA
| | - Maria Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Benjamin J. Tully
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Christopher J. Neely
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Taylor Reiter
- Population Health and Reproduction, University of California, Davis, Davis, California, USA
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5
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Wutkowska M, Vader A, Logares R, Pelletier E, Gabrielsen TM. Linking extreme seasonality and gene expression in Arctic marine protists. Sci Rep 2023; 13:14627. [PMID: 37669980 PMCID: PMC10480425 DOI: 10.1038/s41598-023-41204-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023] Open
Abstract
At high latitudes, strong seasonal differences in light availability affect marine organisms and regulate the timing of ecosystem processes. Marine protists are key players in Arctic aquatic ecosystems, yet little is known about their ecological roles over yearly cycles. This is especially true for the dark polar night period, which up until recently was assumed to be devoid of biological activity. A 12 million transcripts catalogue was built from 0.45 to 10 μm protist assemblages sampled over 13 months in a time series station in an Arctic fjord in Svalbard. Community gene expression was correlated with seasonality, with light as the main driving factor. Transcript diversity and evenness were higher during polar night compared to polar day. Light-dependent functions had higher relative expression during polar day, except phototransduction. 64% of the most expressed genes could not be functionally annotated, yet up to 78% were identified in Arctic samples from Tara Oceans, suggesting that Arctic marine assemblages are distinct from those from other oceans. Our study increases understanding of the links between extreme seasonality and biological processes in pico- and nanoplanktonic protists. Our results set the ground for future monitoring studies investigating the seasonal impact of climate change on the communities of microbial eukaryotes in the High Arctic.
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Affiliation(s)
- Magdalena Wutkowska
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway.
- Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway.
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia.
| | - Anna Vader
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Catalonia, Spain
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Tove M Gabrielsen
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway
- Department of Natural Sciences, University of Agder, Kristiansand, Norway
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Inomura K, Pierella Karlusich JJ, Dutkiewicz S, Deutsch C, Harrison PJ, Bowler C. High Growth Rate of Diatoms Explained by Reduced Carbon Requirement and Low Energy Cost of Silica Deposition. Microbiol Spectr 2023; 11:e0331122. [PMID: 37010412 PMCID: PMC10269801 DOI: 10.1128/spectrum.03311-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 03/02/2023] [Indexed: 04/04/2023] Open
Abstract
The rapid growth of diatoms makes them one of the most pervasive and productive types of plankton in the world's ocean, but the physiological basis for their high growth rates remains poorly understood. Here, we evaluate the factors that elevate diatom growth rates, relative to other plankton, using a steady-state metabolic flux model that computes the photosynthetic C source from intracellular light attenuation and the carbon cost of growth from empirical cell C quotas, across a wide range of cell sizes. For both diatoms and other phytoplankton, growth rates decline with increased cell volume, consistent with observations, because the C cost of division increases with size faster than photosynthesis. However, the model predicts overall higher growth rates for diatoms due to reduced C requirements and the low energetic cost of Si deposition. The C savings from the silica frustule are supported by metatranscriptomic data from Tara Oceans, which show that the abundance of transcripts for cytoskeleton components in diatoms is lower than in other phytoplankton. Our results highlight the importance of understanding the origins of phylogenetic differences in cellular C quotas, and suggest that the evolution of silica frustules may play a critical role in the global dominance of marine diatoms. IMPORTANCE This study addresses a longstanding issue regarding diatoms, namely, their fast growth. Diatoms, which broadly are phytoplankton with silica frustules, are the world's most productive microorganisms and dominate in polar and upwelling regions. Their dominance is largely supported by their high growth rate, but the physiological reasoning behind that characteristic has been obscure. In this study, we combine a quantitative model and metatranscriptomic approaches and show that diatoms' low carbon requirements and low energy costs for silica frustule production are the key factors supporting their fast growth. Our study suggests that the effective use of energy-efficient silica as a cellular structure, instead of carbon, enables diatoms to be the most productive organisms in the global ocean.
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Affiliation(s)
- Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Juan José Pierella Karlusich
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, INSERM, Université Paris Sciences et Lettres, Paris, France
- Faculty of Arts and Sciences, Division of Science, Harvard University, Cambridge, Massachusetts, USA
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Curtis Deutsch
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
| | - Paul J. Harrison
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, INSERM, Université Paris Sciences et Lettres, Paris, France
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7
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Paul P, Patil JS, Anil AC. Variability in phytoplankton shape dominance in marine pelagic systems: prevalence of different adaptive strategies in the eastern Arabian Sea during the winter monsoon. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:528. [PMID: 37000347 DOI: 10.1007/s10661-023-11062-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Phytoplankton communities from pelagic systems were assessed to explore the potential of using commonly used traits (such as cell geometry and taxa) as ecological function indicators from the data generated during the winter monsoon in the eastern Arabian Sea (AS). Altogether, data from two oceanic, i.e., convective mixing influenced non-oligotrophic northeastern-AS (NEAS-O) and Rossby wave-influenced oligotrophic southeastern-AS (SEAS-O) and one coastal (NEAS-C) cruises were utilized to decipher the ecological inferences. Overall phytoplankton shapes showed a high level of redundancy by selecting only a few dominant shapes (5 of 22 shapes), though taxonomic diversity was rich (164 species). The taxonomic and morphological approach adopted revealed high species and shape diversity in NEAS-O than in high-abundance NEAS-C and low-abundance SEAS-O. Also, the shape diversity and dominant shapes (cylinder, elliptic-prism, and prism-on-parallelogram) remained the same in oceans than NEAS-C where combined (cylinder + 2 half-sphere) and simple (elliptic-prism) shapes dominated. Additionally, the Rossby-wave front and its reminiscence in SEAS-O and sea-surface-temperature fronts in NEAS-C favored simple and combine shaped phytoplankton, respectively. The morphological properties assessment revealed that the dominant shapes adapted the strategy to conserve the optimal surface-to-volume ratio (S:V) irrespective of changes in greatest-axial-linear-dimension (GALD) in NEAS-O and SEAS-O but not in NEAS-C. However, the dominant shapes in the NEAS-O and SEAS-O opted for high S:V with low GALD and low S:V with high GALD, respectively, while high S:V with no relation with GALD in NEAS-C suggests the prevalence of different adaptive strategies to cope with the respective hydrographic conditions, particularly nutrient availability.
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Affiliation(s)
- Pranoy Paul
- CSIR-National Institute of Oceanography, Dona Paula 403004, Goa, India
- School of Earth, Ocean, and Atmospheric Sciences, Goa University, Taleigao Plateau, Taleigao, 403 206, Goa, India
| | - Jagadish S Patil
- CSIR-National Institute of Oceanography, Dona Paula 403004, Goa, India.
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Marshall AJ, Phillips L, Longmore A, Hayden HL, Tang C, Heidelberg KB, Mele P. Using metatranscriptomics to better understand the role of microbial nitrogen cycling in coastal sediment benthic flux denitrification efficiency. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 36992633 DOI: 10.1111/1758-2229.13148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/27/2023] [Indexed: 06/19/2023]
Abstract
Spatial and temporal variability in benthic flux denitrification efficiency occurs across Port Phillip Bay, Australia. Here, we assess the capacity for untargeted metatranscriptomics to resolve spatiotemporal differences in the microbial contribution to benthic nitrogen cycling. The most abundant sediment transcripts assembled were associated with the archaeal nitrifier Nitrosopumilus. In sediments close to external inputs of organic nitrogen, the dominant transcripts were associated with Nitrosopumilus nitric oxide nitrite reduction (nirK). The environmental conditions close to organic nitrogen inputs that select for increased transcription in Nitrosopumilus (amoCAB, nirK, nirS, nmo, hcp) additionally selected for increased transcription of bacterial nitrite reduction (nxrB) and transcripts associated with anammox (hzo) but not denitrification (bacterial nirS/nirk). In sediments that are more isolated from external inputs of organic nitrogen dominant transcripts were associated with nitrous oxide reduction (nosZ) and changes in nosZ transcript abundance were uncoupled from transcriptional profiles associated with archaeal nitrification. Coordinated transcription of coupled community-level nitrification-denitrification was not well supported by metatranscriptomics. In comparison, the abundance of archaeal nirK transcripts were site- and season-specific. This study indicates that the transcription of archaeal nirK in response to changing environmental conditions may be an important and overlooked feature of coastal sediment nitrogen cycling.
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Affiliation(s)
- Alexis J Marshall
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
| | - Lori Phillips
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
| | - Andrew Longmore
- Centre for Aquatic Pollution Identification and Management, Melbourne University, Parkville, Australia
| | - Helen L Hayden
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Caixian Tang
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
| | - Karla B Heidelberg
- Department of Biology, The University of Southern California, Los Angeles, California, USA
| | - Pauline Mele
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
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9
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Zhou J, Song W, Tu Q. To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities. Brief Bioinform 2023; 24:6961613. [PMID: 36575570 DOI: 10.1093/bib/bbac594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/22/2022] [Accepted: 12/04/2022] [Indexed: 12/29/2022] Open
Abstract
High-throughput profiling of microbial functional traits involved in various biogeochemical cycling pathways using shotgun metagenomic sequencing has been routinely applied in microbial ecology and environmental science. Multiple bioinformatics data processing approaches are available, including assembly-based (single-sample assembly and multi-sample assembly) and read-based (merged reads and raw data). However, it remains not clear how these different approaches may differ in data analyses and affect result interpretation. In this study, using two typical shotgun metagenome datasets recovered from geographically distant coastal sediments, the performance of different data processing approaches was comparatively investigated from both technical and biological/ecological perspectives. Microbially mediated biogeochemical cycling pathways, including nitrogen cycling, sulfur cycling and B12 biosynthesis, were analyzed. As a result, multi-sample assembly provided the most amount of usable information for targeted functional traits, at a high cost of computational resources and running time. Single-sample assembly and read-based analysis were comparable in obtaining usable information, but the former was much more time- and resource-consuming. Critically, different approaches introduced much stronger variations in microbial profiles than biological differences. However, community-level differences between the two sampling sites could be consistently observed despite the approaches being used. In choosing an appropriate approach, researchers shall balance the trade-offs between multiple factors, including the scientific question, the amount of usable information, computational resources and time cost. This study is expected to provide valuable technical insights and guidelines for the various approaches used for metagenomic data analysis.
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Affiliation(s)
- Jiayin Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China.,Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, China
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10
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Endo H, Umezawa Y, Takeda S, Suzuki K. Haptophyte communities along the Kuroshio current reveal their geographical sources and ecological traits. Mol Ecol 2023; 32:110-123. [PMID: 36221794 DOI: 10.1111/mec.16734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 12/29/2022]
Abstract
Haptophytes are one of the most ecologically successful phytoplankton groups in the modern ocean and tend to maintain balanced and stable communities across various environments. However, little is known about the mechanisms that enable community stability and ecological success. To reveal the community characteristics and interactions among haptophytes, we conducted comprehensive observations from the upstream to downstream regions of the Kuroshio Current. Haptophyte abundance and taxonomy were assessed using quantitative polymerase chain reaction and metabarcoding of 18S rRNA sequences, respectively. The haptophyte community structure changed abruptly at sites on the shelf-slope of the East China Sea, indicating the strong influence of shelf waters with high phytoplankton biomass on downstream communities. Correlation network analysis combined with the phylogeny suggested that haptophytes can coexist with their close relatives, possibly owing to their nutritional flexibility, thereby escaping from resource competition. Consistently, some noncalcifying haptophyte genera with high mixotrophic capacities such as Chrysochromulina constituted a major component of the co-occurrence network, whereas coccolithophores such as Emiliania/Gephyrocapsa were rarely observed. Our study findings suggest that noncalcifying haptophytes play crucial roles in community diversity and stability, and in sustaining the food web structure in the Kuroshio ecosystems.
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Affiliation(s)
- Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Yu Umezawa
- Department of Environmental Science on Biosphere, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Shigenobu Takeda
- Faculty of Environmental Earth Science, Hokkaido University, Hokkaido, Sapporo, Japan
| | - Koji Suzuki
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
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11
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Le Gac M, Mary L, Metegnier G, Quéré J, Siano R, Rodríguez F, Destombe C, Sourisseau M. Strong population genomic structure of the toxic dinoflagellate Alexandrium minutum inferred from meta-transcriptome samples. Environ Microbiol 2022; 24:5966-5983. [PMID: 36302091 DOI: 10.1111/1462-2920.16257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/20/2022] [Indexed: 01/12/2023]
Abstract
Despite theoretical expectations, marine microeukaryote population are often highly structured and the mechanisms behind such patterns remain to be elucidated. These organisms display huge census population sizes, yet genotyping usually requires clonal strains originating from single cells, hindering proper population sampling. Estimating allelic frequency directly from population wide samples, without any isolation step, offers an interesting alternative. Here, we validate the use of meta-transcriptome environmental samples to determine the population genetic structure of the dinoflagellate Alexandrium minutum. Strain and meta-transcriptome based results both indicated a strong genetic structure for A. minutum in Western Europe, to the level expected between cryptic species. The presence of numerous private alleles, and even fixed polymorphism, would indicate ancient divergence and absence of gene flow between populations. Single nucleotide polymorphisms (SNPs) displaying strong allele frequency differences were distributed throughout the genome, which might indicate pervasive selection from standing genetic variation (soft selective sweeps). However, a few genomic regions displayed extremely low diversity that could result from the fixation of adaptive de novo mutations (hard selective sweeps) within the populations.
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Affiliation(s)
| | - Lou Mary
- Ifremer, Dyneco, Plouzané, France
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12
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Ollison GA, Hu SK, Hopper JV, Stewart BP, Smith J, Beatty JL, Rink LK, Caron DA. Daily dynamics of contrasting spring algal blooms in Santa Monica Bay (central Southern California Bight). Environ Microbiol 2022; 24:6033-6051. [PMID: 35880671 PMCID: PMC10087728 DOI: 10.1111/1462-2920.16137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 01/12/2023]
Abstract
Protistan algae (phytoplankton) dominate coastal upwelling ecosystems where they form massive blooms that support the world's most important fisheries and constitute an important sink for atmospheric CO2 . Bloom initiation is well understood, but the biotic and abiotic forces that shape short-term dynamics in community composition are still poorly characterized. Here, high-frequency (daily) changes in relative abundance dynamics of the metabolically active protistan community were followed via expressed 18S V4 rRNA genes (RNA) throughout two algal blooms during the spring of 2018 and 2019 in Santa Monica Bay (central Southern California Bight). A diatom bloom formed after wind-driven, nutrient upwelling events in both years, but different taxa dominated each year. Whereas diatoms bloomed following elevated nutrients and declined after depletion each year, a massive dinoflagellate bloom manifested under relatively low inorganic nitrogen conditions following diatom bloom senescence in 2019 but not 2018. Network analysis revealed associations between diatoms and cercozoan putative parasitic taxa and syndinean parasites during 2019 that may have influenced the demise of the diatoms, and the transition to a dinoflagellate-dominated bloom.
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Affiliation(s)
- Gerid A Ollison
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Sarah K Hu
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, Massachusetts, USA
| | - Julie V Hopper
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Brittany P Stewart
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Jayme Smith
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Jennifer L Beatty
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Laura K Rink
- Heal the Bay Aquarium, Santa Monica, California, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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13
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Fourquez M, Strzepek RF, Ellwood MJ, Hassler C, Cabanes D, Eggins S, Pearce I, Deppeler S, Trull TW, Boyd PW, Bressac M. Phytoplankton Responses to Bacterially Regenerated Iron in a Southern Ocean Eddy. Microorganisms 2022; 10:microorganisms10081655. [PMID: 36014073 PMCID: PMC9413495 DOI: 10.3390/microorganisms10081655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
In the Subantarctic sector of the Southern Ocean, vertical entrainment of iron (Fe) triggers the seasonal productivity cycle but diminishing physical supply during the spring to summer transition forces microbial assemblages to rapidly acclimate. Here, we tested how phytoplankton and bacteria within an isolated eddy respond to different dissolved Fe (DFe)/ligand inputs. We used three treatments: one that mimicked the entrainment of new DFe (Fe-NEW), another in which DFe was supplied from bacterial regeneration of particles (Fe-REG), and a control with no addition of DFe (Fe-NO). After 6 days, 3.5 (Fe-NO, Fe-NEW) to 5-fold (Fe-REG) increases in Chlorophyll a were observed. These responses of the phytoplankton community were best explained by the differences between the treatments in the amount of DFe recycled during the incubation (Fe-REG, 15% recycled c.f. 40% Fe-NEW, 60% Fe-NO). This additional recycling was more likely mediated by bacteria. By day 6, bacterial production was comparable between Fe-NO and Fe-NEW but was approximately two-fold higher in Fe-REG. A preferential response of phytoplankton (haptophyte-dominated) relative to high nucleic acid (HNA) bacteria was also found in the Fe-REG treatment while the relative proportion of diatoms increased faster in the Fe-NEW and Fe-NO treatments. Comparisons between light and dark incubations further confirmed the competition between picophytoplankton and HNA for DFe. Overall, our results demonstrate great versatility by microorganisms to use different Fe sources that results in highly efficient Fe recycling within surface waters. This study also encourages future research to further investigate the interactions between functional groups of microbes (e.g. HNA and cyanobacteria) to better constraint modeling in Fe and carbon biogeochemical cycles.
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Affiliation(s)
- Marion Fourquez
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart 7004, Australia
- Antarctic Climate and Ecosystems CRC, University of Tasmania, Hobart 7004, Australia
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UMR 110, 13288 Marseille, France
- Correspondence:
| | - Robert F. Strzepek
- Australian Antarctic Program Partnership (AAPP), Institute for Marine and Antarctic Studies, University of Tasmania, Hobart 7004, Australia
| | - Michael J. Ellwood
- Research School of Earth Sciences, Australian National University, Canberra 2601, Australia
| | - Christel Hassler
- Marine and Lake Biogeochemistry, Department F.-A. Forel, University of Geneva, 1205 Geneva, Switzerland
- Institute of Earth Sciences, University of Lausanne, 1015 Lausanne, Switzerland
| | - Damien Cabanes
- Marine and Lake Biogeochemistry, Department F.-A. Forel, University of Geneva, 1205 Geneva, Switzerland
| | - Sam Eggins
- Research School of Earth Sciences, Australian National University, Canberra 2601, Australia
| | - Imojen Pearce
- Australian Antarctic Division (AAD), Kingston 7050, Australia
| | - Stacy Deppeler
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart 7004, Australia
- National Institute of Water and Atmospheric Research, Wellington 6021, New Zealand
| | - Thomas W. Trull
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart 7004, Australia
- Antarctic Climate and Ecosystems CRC, University of Tasmania, Hobart 7004, Australia
- Climate Science Centre, Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart 7004, Australia
| | - Philip W. Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart 7004, Australia
- Antarctic Climate and Ecosystems CRC, University of Tasmania, Hobart 7004, Australia
| | - Matthieu Bressac
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart 7004, Australia
- Laboratoire d’Océanographie de Villefranche, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
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14
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Mailli AA, Jakt LM, Reiss H, Kopp ME, Moum TB. Exploring the potential of mRNA for taxonomic delineation of marine benthic eukaryotes. Mar Genomics 2022; 62:100934. [DOI: 10.1016/j.margen.2022.100934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 10/19/2022]
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15
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Kang Y, Kang CK. Reduced forms of nitrogen control the spatial distribution of phytoplankton communities: The functional winner, dinoflagellates in an anthropogenically polluted estuary. MARINE POLLUTION BULLETIN 2022; 177:113528. [PMID: 35305373 DOI: 10.1016/j.marpolbul.2022.113528] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
The effects of reduced forms of nitrogen (NH4+ and dissolved organic nitrogen (DON)) on the spatial distribution of diatoms and dinoflagellates in an estuarine-coastal water continuum were investigated from 2015 to 2019. The proportion of non-DIN in total nitrogen was utilized as an indicator of DON along with direct measurements of DON. While NO3- originated from Seomjin River, the abundant NH4+ and DON occurred from Gwangyang Bay through Namhae. Diatoms were mostly confined to the upper estuarine system and dinoflagellates dominated in the regions with high levels of NH4+ and DON. Generalized additive models also presented the different responses of diatoms and dinoflagellates to increases in NH4+ and DON. Thus, our results highlight that diatoms dominate in NO3--replete water with full access to the source and dinoflagellates take over the ecologically open niche in an anthropogenically polluted estuary with full access to reduced forms of nitrogen.
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Affiliation(s)
- Yoonja Kang
- Department of Ocean Integrated Science, Chonnam National University, Yeosu, Republic of Korea.
| | - Chang-Keun Kang
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
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16
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Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom. THE ISME JOURNAL 2022; 16:569-579. [PMID: 34482372 PMCID: PMC8776772 DOI: 10.1038/s41396-021-01084-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/13/2021] [Accepted: 08/02/2021] [Indexed: 02/07/2023]
Abstract
Production and use of proteins is under strong selection in microbes, but it is unclear how proteome-level traits relate to ecological strategies. We identified and quantified proteomic traits of eukaryotic microbes and bacteria through an Antarctic phytoplankton bloom using in situ metaproteomics. Different taxa, rather than different environmental conditions, formed distinct clusters based on their ribosomal and photosynthetic proteomic proportions, and we propose that these characteristics relate to ecological differences. We defined and used a proteomic proxy for regulatory cost, which showed that SAR11 had the lowest regulatory cost of any taxa we observed at our summertime Southern Ocean study site. Haptophytes had lower regulatory cost than diatoms, which may underpin haptophyte-to-diatom bloom progression in the Ross Sea. We were able to make these proteomic trait inferences by assessing various sources of bias in metaproteomics, providing practical recommendations for researchers in the field. We have quantified several proteomic traits (ribosomal and photosynthetic proteomic proportions, regulatory cost) in eukaryotic and bacterial taxa, which can then be incorporated into trait-based models of microbial communities that reflect resource allocation strategies.
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17
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Sun P, Liao Y, Wang Y, Yang EJ, Jiao N, Lee Y, Jung J, Cho KH, Moon JK, Xu D. Contrasting Community Composition and Co-Occurrence Relationships of the Active Pico-Sized Haptophytes in the Surface and Subsurface Chlorophyll Maximum Layers of the Arctic Ocean in Summer. Microorganisms 2022; 10:248. [PMID: 35208705 PMCID: PMC8877492 DOI: 10.3390/microorganisms10020248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/10/2022] Open
Abstract
Haptophytes (Hacrobia: Haptophyta), which can perform phototrophic, phagotrophic, or mixotrophic nutritional modes, are critical for element cycling in a variety of aquatic ecosystems. However, their diversity, particularly in the changing Arctic Ocean (AO), remains largely unknown. In the present study, the biodiversity, community composition, and co-occurrence networks of pico-sized haptophytes in the surface water and subsurface chlorophyll maximum (SCM) layer of the AO were explored. Our results found higher alpha diversity estimates in the surface water compared with in the SCM based on high-throughput sequencing of haptophyte specific 18S rRNA. The community composition of the surface water was significantly different from that of the SCM, and water temperature was identified as the primary factor shaping the community compositions. Prymnesiales (mostly Chrysochromulina), uncultured Prymnesiophyceae, and Phaeocystis dominated the surface water communities, whereas Phaeocystis dominated the SCM communities, followed by Chrysochromulina, uncultured Prymnesiophyceae, and the remaining taxa. The communities of the surface water and SCM layer developed relatively independent modules in the metacommunity network. Nodes in the surface water were more closely connected to one another than those in the SCM. Network stability analysis revealed that surface water networks were more stable than SCM networks. These findings suggest that SCM communities are more susceptible to environmental fluctuations than those in surface water and that future global changes (e.g., global warming) may profoundly influence the development, persistence, and service of SCM in the AO.
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Affiliation(s)
- Ping Sun
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
| | - Yuyu Liao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ying Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Eun-Jin Yang
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Youngju Lee
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Jinyoung Jung
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Kyoung-Ho Cho
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Jong-Kuk Moon
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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18
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Complex marine microbial communities partition metabolism of scarce resources over the diel cycle. Nat Ecol Evol 2022; 6:218-229. [DOI: 10.1038/s41559-021-01606-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/01/2021] [Indexed: 12/20/2022]
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19
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Disentangling the Ecological Processes Shaping the Latitudinal Pattern of Phytoplankton Communities in the Pacific Ocean. mSystems 2022; 7:e0120321. [PMID: 35089068 PMCID: PMC8725599 DOI: 10.1128/msystems.01203-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Phytoplankton diversity and community compositions vary across spaces and are fundamentally affected by several deterministic (e.g., environmental selection) and stochastic (e.g., ecological drift) processes. How this suite of different processes regulates the biogeography of phytoplankton remains to be comprehensively explored. Using high-throughput sequencing data and null model analysis, we revealed the ecological processes shaping the latitudinal community structure of three major phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) across the Pacific Ocean (70°N, 170°W to 35°S, 170°W). At the basin scale, heterogeneous selection (selection under heterogeneous environmental conditions) dominated the assembly processes of all phytoplankton groups; however, its relative importance varied greatly at the climatic zonal scale, explaining the distinct latitudinal α- and β-diversity among phytoplankton groups. Assembly processes in Synechococcus and haptophyte communities were mainly controlled by physical and nutrient factors, respectively. High temperature drove Synechococcus communities to be more deterministic with higher diversity, while haptophyte communities were less environmentally selected at low latitudes due to their wide niche breadth and mixotrophic lifestyle. Diatom communities were overwhelmingly dominated by the selection process but with low correlation of measured environmental factors to their community compositions. This could be attributed to the high growth rate of diatoms, as indicated by their lower site occupation frequency than predicted in the neutral community model. Our study showed that heterogeneous selection is the main force that shaped the biogeography of three key phytoplankton groups in the Pacific Ocean, with a latitudinal variation of relative importance due to the distinct traits among phytoplankton. IMPORTANCE Phytoplankton are diverse and abundant as primary producers in the ocean, with diversity and community compositions varying spatially. How fundamental processes (e.g., selection, dispersal, and drift) regulate their global biogeography remains to be comprehensively explored. In this study, we disentangled the ecological processes of three key phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) along the same latitudinal gradients in the Pacific Ocean. Heterogeneous selection, by promoting species richness and reducing similarity between communities, was the dominant process shaping the communities of each phytoplankton group at the basin scale. However, its relative importance varied greatly among different phytoplankton groups in different climate zones, explaining the uneven latitudinal α- and β-diversity. We also highlight the importance of identifying key factors mediating the relative importance of assembly processes in phytoplankton communities, which will enhance our understanding of their biogeography in the ocean and future patterns under climate changes.
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20
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Marine phytoplankton functional types exhibit diverse responses to thermal change. Nat Commun 2021; 12:6413. [PMID: 34741038 PMCID: PMC8571312 DOI: 10.1038/s41467-021-26651-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/01/2021] [Indexed: 11/25/2022] Open
Abstract
Marine phytoplankton generate half of global primary production, making them essential to ecosystem functioning and biogeochemical cycling. Though phytoplankton are phylogenetically diverse, studies rarely designate unique thermal traits to different taxa, resulting in coarse representations of phytoplankton thermal responses. Here we assessed phytoplankton functional responses to temperature using empirically derived thermal growth rates from four principal contributors to marine productivity: diatoms, dinoflagellates, cyanobacteria, and coccolithophores. Using modeled sea surface temperatures for 1950-1970 and 2080-2100, we explored potential alterations to each group's growth rates and geographical distribution under a future climate change scenario. Contrary to the commonly applied Eppley formulation, our data suggest phytoplankton functional types may be characterized by different temperature coefficients (Q10), growth maxima thermal dependencies, and thermal ranges which would drive dissimilar responses to each degree of temperature change. These differences, when applied in response to global simulations of future temperature, result in taxon-specific projections of growth and geographic distribution, with low-latitude coccolithophores facing considerable decreases and cyanobacteria substantial increases in growth rates. These results suggest that the singular effect of changing temperature may alter phytoplankton global community structure, owing to the significant variability in thermal response between phytoplankton functional types.
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21
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Avila-Magaña V, Kamel B, DeSalvo M, Gómez-Campo K, Enríquez S, Kitano H, Rohlfs RV, Iglesias-Prieto R, Medina M. Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress. Nat Commun 2021; 12:5731. [PMID: 34593802 PMCID: PMC8484447 DOI: 10.1038/s41467-021-25950-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 09/01/2021] [Indexed: 02/08/2023] Open
Abstract
As coral reefs struggle to survive under climate change, it is crucial to know whether they have the capacity to withstand changing conditions, particularly increasing seawater temperatures. Thermal tolerance requires the integrative response of the different components of the coral holobiont (coral host, algal photosymbiont, and associated microbiome). Here, using a controlled thermal stress experiment across three divergent Caribbean coral species, we attempt to dissect holobiont member metatranscriptome responses from coral taxa with different sensitivities to heat stress and use phylogenetic ANOVA to study the evolution of gene expression adaptation. We show that coral response to heat stress is a complex trait derived from multiple interactions among holobiont members. We identify host and photosymbiont genes that exhibit lineage-specific expression level adaptation and uncover potential roles for bacterial associates in supplementing the metabolic needs of the coral-photosymbiont duo during heat stress. Our results stress the importance of integrative and comparative approaches across a wide range of species to better understand coral survival under the predicted rise in sea surface temperatures.
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Affiliation(s)
- Viridiana Avila-Magaña
- grid.29857.310000 0001 2097 4281Biology Department, The Pennsylvania State University, University Park, PA USA ,grid.266190.a0000000096214564Ecology and Evolutionary Biology Department, University of Colorado Boulder, Boulder, CO USA
| | - Bishoy Kamel
- grid.266832.b0000 0001 2188 8502Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM USA ,grid.184769.50000 0001 2231 4551Present Address: US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Michael DeSalvo
- grid.266096.d0000 0001 0049 1282School of Natural Sciences, University of California, Merced, CA USA ,grid.418190.50000 0001 2187 0556Thermo Fisher Scientific, Carlsbad, CA USA
| | - Kelly Gómez-Campo
- grid.29857.310000 0001 2097 4281Biology Department, The Pennsylvania State University, University Park, PA USA
| | - Susana Enríquez
- grid.9486.30000 0001 2159 0001Unidad Académica de Sistemas Arrecifales Puerto Morelos, ICMyL, Universidad Nacional Autónoma de México, Cancún, Mexico
| | - Hiroaki Kitano
- grid.452864.9The Systems Biology Institute, Tokyo, Japan ,grid.250464.10000 0000 9805 2626Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Rori V. Rohlfs
- grid.263091.f0000000106792318Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Roberto Iglesias-Prieto
- grid.29857.310000 0001 2097 4281Biology Department, The Pennsylvania State University, University Park, PA USA
| | - Mónica Medina
- grid.29857.310000 0001 2097 4281Biology Department, The Pennsylvania State University, University Park, PA USA
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22
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Groussman RD, Coesel SN, Durham BP, Armbrust EV. Diel-Regulated Transcriptional Cascades of Microbial Eukaryotes in the North Pacific Subtropical Gyre. Front Microbiol 2021; 12:682651. [PMID: 34659137 PMCID: PMC8511712 DOI: 10.3389/fmicb.2021.682651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
Open-ocean surface waters host a diverse community of single-celled eukaryotic plankton (protists) consisting of phototrophs, heterotrophs, and mixotrophs. The productivity and biomass of these organisms oscillate over diel cycles, and yet the underlying transcriptional processes are known for few members of the community. Here, we examined a 4-day diel time series of transcriptional abundance profiles for the protist community (0.2-100 μm in cell size) in the North Pacific Subtropical Gyre near Station ALOHA. De novo assembly of poly-A+ selected metatranscriptomes yielded over 30 million contigs with taxonomic and functional annotations assigned to 54 and 25% of translated contigs, respectively. The completeness of the resulting environmental eukaryotic taxonomic bins was assessed, and 48 genera were further evaluated for diel patterns in transcript abundances. These environmental transcriptome bins maintained reproducible temporal partitioning of total gene family abundances, with haptophyte and ochrophyte genera generally showing the greatest diel partitioning of their transcriptomes. The haptophyte Phaeocystis demonstrated the highest proportion of transcript diel periodicity, while most other protists had intermediate levels of periodicity regardless of their trophic status. Dinoflagellates, except for the parasitoid genus Amoebophrya, exhibit the fewest diel oscillations of transcript abundances. Diel-regulated gene families were enriched in key metabolic pathways; photosynthesis, carbon fixation, and fatty acid biosynthesis gene families had peak times concentrated around dawn, while gene families involved in protein turnover (proteasome and protein processing) are most active during the high intensity daylight hours. TCA cycle, oxidative phosphorylation and fatty acid degradation predominantly peaked near dusk. We identified temporal pathway enrichments unique to certain taxa, including assimilatory sulfate reduction at dawn in dictyophytes and signaling pathways at early evening in haptophytes, pointing to possible taxon-specific channels of carbon and nutrients through the microbial community. These results illustrate the synchrony of transcriptional regulation to the diel cycle and how the protist community of the North Pacific Subtropical Gyre structures their transcriptomes to guide the daily flux of matter and energy through the gyre ecosystem.
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Affiliation(s)
- Ryan D. Groussman
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Sacha N. Coesel
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Bryndan P. Durham
- School of Oceanography, University of Washington, Seattle, WA, United States
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, United States
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23
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Harke MJ, Frischkorn KR, Hennon GMM, Haley ST, Barone B, Karl DM, Dyhrman ST. Microbial community transcriptional patterns vary in response to mesoscale forcing in the North Pacific Subtropical Gyre. Environ Microbiol 2021; 23:4807-4822. [PMID: 34309154 DOI: 10.1111/1462-2920.15677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 07/18/2021] [Indexed: 11/30/2022]
Abstract
The physical and biological dynamics that influence phytoplankton communities in the oligotrophic ocean are complex, changing across broad temporal and spatial scales. Eukaryotic phytoplankton (e.g., diatoms), despite their relatively low abundance in oligotrophic waters, are responsible for a large component of the organic matter flux to the ocean interior. Mesoscale eddies can impact both microbial community structure and function, enhancing primary production and carbon export, but the mechanisms that underpin these dynamics are still poorly understood. Here, mesoscale eddy influences on the taxonomic diversity and expressed functional profiles of surface communities of microeukaryotes and particle-associated heterotrophic bacteria from the North Pacific Subtropical Gyre were assessed over 2 years (spring 2016 and summer 2017). The taxonomic diversity of the microeukaryotes significantly differed by eddy polarity (cyclonic versus anticyclonic) and between sampling seasons/years and was significantly correlated with the taxonomic diversity of particle-associated heterotrophic bacteria. The expressed functional profile of these taxonomically distinct microeukaryotes varied consistently as a function of eddy polarity, with cyclones having a different expression pattern than anticyclones, and between sampling seasons/years. These data suggest that mesoscale forcing, and associated changes in biogeochemistry, could drive specific physiological responses in the resident microeukaryote community, independent of species composition.
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Affiliation(s)
- Matthew J Harke
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA.,Gloucester Marine Genomics Institute, Gloucester, MA, USA
| | - Kyle R Frischkorn
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA
| | - Gwenn M M Hennon
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA.,College of Fisheries and Ocean Sciences, University of Alaska, Fairbanks, AK, USA
| | - Sheean T Haley
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA
| | - Benedetto Barone
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii at Manoa, Honolulu, HI, USA.,Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, USA
| | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii at Manoa, Honolulu, HI, USA.,Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA.,Department of Earth and Environmental Sciences, Columbia University, New York, NY, USA
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24
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Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. Proc Natl Acad Sci U S A 2021; 118:2011038118. [PMID: 33547239 PMCID: PMC8017926 DOI: 10.1073/pnas.2011038118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Most organisms coordinate key biological events to coincide with the day/night cycle. These diel oscillations are entrained through the activity of light-sensitive photoreceptors that allow organisms to respond rapidly to changes in light exposure. In the ocean, the plankton community must additionally contend with dramatic changes in the quantity and quality of light over depth. Here, we show that the predominantly blue-light field in the open-ocean environment may have driven expansion of blue light-sensitive regulatory elements in open-ocean eukaryotic plankton derived from secondary and tertiary endosymbiosis. The diel transcription of genes encoding light-sensitive elements indicate that photosynthetic and heterotrophic marine protists respond to and anticipate fluctuating light conditions in the dynamic marine environment. The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment.
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25
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Bhattacharjya R, Tiwari A, Marella TK, Bansal H, Srivastava S. New paradigm in diatom omics and genetic manipulation. BIORESOURCE TECHNOLOGY 2021; 325:124708. [PMID: 33487514 DOI: 10.1016/j.biortech.2021.124708] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Diatoms are one of the most heterogeneous eukaryotic plankton known for regulating earth's biogeochemical cycles and maintaining the marine ecosystems ever since the late Eocene epoch. The advent of multidisciplinary omics approach has both epitomized and revolutionized the nature of their chimeric genetic toolkit, ecophysiology, and metabolic adaptability as well as their interaction with other communities. In addition, advanced functional annotation of transcriptomic and proteomic data using cutting edge bioinformatics tools together with high-resolution genome-scale mathematical modeling has effectively proven as the catapult in solving genetic bottlenecks in microbial as well as diatom exploration. In this review, a corroborative summation of the robust work done in manipulating, engineering, and sequencing of the diatom genomes besides underpinning the holistic application of omics in transcription and translation has been discussed in order to shrewd their multifarious novel potential in the field of biotechnology and provide an insight into their dynamic evolutionary relevance.
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Affiliation(s)
- Raya Bhattacharjya
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
| | - Archana Tiwari
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India.
| | - Thomas Kiran Marella
- Algae Biomass Energy System Development Research Center (ABES), Tennodai, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Hina Bansal
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
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26
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Bistability in oxidative stress response determines the migration behavior of phytoplankton in turbulence. Proc Natl Acad Sci U S A 2021; 118:2005944118. [PMID: 33495340 PMCID: PMC7865155 DOI: 10.1073/pnas.2005944118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Turbulence has long been known to drive phytoplankton fitness and species succession: motile species dominate in calmer environments and non-motile species in turbulent conditions. Yet a mechanistic understanding of the effect of turbulence on phytoplankton migratory behavior and physiology is lacking. By combining a method to generate turbulent cues, quantification of stress accumulation and physiology, and a mathematical model of stress dynamics, we show that motile phytoplankton use their mechanical stability to sense the intensity of turbulent cues and integrate these cues in time via stress signaling to trigger switches in migratory behavior. The stress-mediated warning strategy we discovered provides a paradigm for how phytoplankton cope with turbulence, thereby potentially governing which species will be successful in a changing ocean. Turbulence is an important determinant of phytoplankton physiology, often leading to cell stress and damage. Turbulence affects phytoplankton migration both by transporting cells and by triggering switches in migratory behavior, whereby vertically migrating cells can actively invert their direction of migration upon exposure to turbulent cues. However, a mechanistic link between single-cell physiology and vertical migration of phytoplankton in turbulence is currently missing. Here, by combining physiological and behavioral experiments with a mathematical model of stress accumulation and dissipation, we show that the mechanism responsible for the switch in the direction of migration in the marine raphidophyte Heterosigma akashiwo is the integration of reactive oxygen species (ROS) signaling generated by turbulent cues. Within timescales as short as tens of seconds, the emergent downward-migrating subpopulation exhibited a twofold increase in ROS, an indicator of stress, 15% lower photosynthetic efficiency, and 35% lower growth rate over multiple generations compared to the upward-migrating subpopulation. The origin of the behavioral split as a result of a bistable oxidative stress response is corroborated by the observation that exposure of cells to exogenous stressors (H2O2, UV-A radiation, or high irradiance), in lieu of turbulence, caused comparable ROS accumulation and an equivalent split into the two subpopulations. By providing a mechanistic link between the single-cell mechanics of swimming and physiology on the one side and the emergent population-scale migratory response and impact on fitness on the other, the ROS-mediated early warning response we discovered contributes to our understanding of phytoplankton community composition in future ocean conditions.
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27
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Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean. ISME JOURNAL 2020; 15:520-533. [PMID: 33033374 DOI: 10.1038/s41396-020-00793-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 01/01/2023]
Abstract
Sunlight is the most important environmental control on diel fluctuations in phytoplankton activity, and understanding diel microbial processes is essential to the study of oceanic biogeochemical cycles. Yet, little is known about the in situ temporal dynamics of phytoplankton metabolic activities and their coordination across different populations. We investigated diel orchestration of phytoplankton activity in photosynthesis, photoacclimation, and photoprotection by analyzing pigment and quinone distributions in combination with metatranscriptomes in surface waters of the North Pacific Subtropical Gyre (NPSG). We found diel cycles in pigment abundances resulting from the balance of their synthesis and consumption. These dynamics suggest that night represents a metabolic recovery phase, refilling cellular pigment stores, while photosystems are remodeled towards photoprotection during daytime. Transcript levels of genes involved in photosynthesis and pigment metabolism had synchronized diel expression patterns among all taxa, reflecting the driving force light imparts upon photosynthetic organisms in the ocean, while other environmental factors drive niche differentiation. For instance, observed decoupling of diel oscillations in transcripts and related pigments indicates that pigment abundances are modulated by environmental factors extending beyond gene expression/regulation reinforcing the need to combine metatranscriptomics with proteomics and metabolomics to fully understand the timing of these critical processes in situ.
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28
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Cieslak MC, Castelfranco AM, Roncalli V, Lenz PH, Hartline DK. t-Distributed Stochastic Neighbor Embedding (t-SNE): A tool for eco-physiological transcriptomic analysis. Mar Genomics 2020; 51:100723. [DOI: 10.1016/j.margen.2019.100723] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/20/2019] [Accepted: 11/01/2019] [Indexed: 01/19/2023]
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29
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Garcia CA, Hagstrom GI, Larkin AA, Ustick LJ, Levin SA, Lomas MW, Martiny AC. Linking regional shifts in microbial genome adaptation with surface ocean biogeochemistry. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190254. [PMID: 32200740 PMCID: PMC7133529 DOI: 10.1098/rstb.2019.0254] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2020] [Indexed: 01/09/2023] Open
Abstract
Linking 'omics measurements with biogeochemical cycles is a widespread challenge in microbial community ecology. Here, we propose applying genomic adaptation as 'biosensors' for microbial investments to overcome nutrient stress. We then integrate this genomic information with a trait-based model to predict regional shifts in the elemental composition of marine plankton communities. We evaluated this approach using metagenomic and particulate organic matter samples from the Atlantic, Indian and Pacific Oceans. We find that our genome-based trait model significantly improves our prediction of particulate C : P (carbon : phosphorus) across ocean regions. Furthermore, we detect previously unrecognized ocean areas of iron, nitrogen and phosphorus stress. In many ecosystems, it can be very challenging to quantify microbial stress. Thus, a carefully calibrated genomic approach could become a widespread tool for understanding microbial responses to environmental changes and the biogeochemical outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- Catherine A. Garcia
- Department of Earth System Science, University of California, Irvine, CA 92697, USA
| | - George I. Hagstrom
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alyse A. Larkin
- Department of Earth System Science, University of California, Irvine, CA 92697, USA
| | - Lucas J. Ustick
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - Simon A. Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Michael W. Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA
| | - Adam C. Martiny
- Department of Earth System Science, University of California, Irvine, CA 92697, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
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30
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Functional Genomics Differentiate Inherent and Environmentally Influenced Traits in Dinoflagellate and Diatom Communities. Microorganisms 2020; 8:microorganisms8040567. [PMID: 32326461 PMCID: PMC7232425 DOI: 10.3390/microorganisms8040567] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
Dinoflagellates and diatoms are among the most prominent microeukaryotic plankton groups, and they have evolved different functional traits reflecting their roles within ecosystems. However, links between their metabolic processes and functional traits within different environmental contexts warrant further study. The functional biodiversity of dinoflagellates and diatoms was accessed with metatranscriptomics using Pfam protein domains as proxies for functional processes. Despite the overall geographic similarity of functional responses, abiotic (i.e., temperature and salinity; ~800 Pfam domains) and biotic (i.e., taxonomic group; ~1500 Pfam domains) factors influencing particular functional responses were identified. Salinity and temperature were identified as the main drivers of community composition. Higher temperatures were associated with an increase of Pfam domains involved in energy metabolism and a decrease of processes associated with translation and the sulfur cycle. Salinity changes were correlated with the biosynthesis of secondary metabolites (e.g., terpenoids and polyketides) and signal transduction processes, indicating an overall strong effect on the biota. The abundance of dinoflagellates was positively correlated with nitrogen metabolism, vesicular transport and signal transduction, highlighting their link to biotic interactions (more so than diatoms) and suggesting the central role of species interactions in the evolution of dinoflagellates. Diatoms were associated with metabolites (e.g., isoprenoids and carotenoids), as well as lysine degradation, which highlights their ecological role as important primary producers and indicates the physiological importance of these metabolic pathways for diatoms in their natural environment. These approaches and gathered information will support ecological questions concerning the marine ecosystem state and metabolic interactions in the marine environment.
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31
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Metegnier G, Paulino S, Ramond P, Siano R, Sourisseau M, Destombe C, Le Gac M. Species specific gene expression dynamics during harmful algal blooms. Sci Rep 2020; 10:6182. [PMID: 32277155 PMCID: PMC7148311 DOI: 10.1038/s41598-020-63326-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/20/2020] [Indexed: 01/10/2023] Open
Abstract
Harmful algal blooms are caused by specific members of microbial communities. Understanding the dynamics of these events requires comparing the strategies developed by the problematic species to cope with environmental fluctuations to the ones developed by the other members of the community. During three consecutive years, the meta-transcriptome of micro-eukaryote communities was sequenced during blooms of the toxic dinoflagellate Alexandrium minutum. The dataset was analyzed to investigate species specific gene expression dynamics. Major shifts in gene expression were explained by the succession of different species within the community. Although expression patterns were strongly correlated with fluctuation of the abiotic environment, and more specifically with nutrient concentration, transcripts specifically involved in nutrient uptake and metabolism did not display extensive changes in gene expression. Compared to the other members of the community, A. minutum displayed a very specific expression pattern, with lower expression of photosynthesis transcripts and central metabolism genes (TCA cycle, glucose metabolism, glycolysis…) and contrasting expression pattern of ion transporters across environmental conditions. These results suggest the importance of mixotrophy, cell motility and cell-to-cell interactions during A. minutum blooms.
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Affiliation(s)
- Gabriel Metegnier
- French Research Institute for Exploitation of the Sea, Ifremer DYNECO PELAGOS, 29280, Plouzané, France.,CNRS, Sorbonne Université, UC, UaCh, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France
| | - Sauvann Paulino
- French Research Institute for Exploitation of the Sea, Ifremer DYNECO PELAGOS, 29280, Plouzané, France
| | - Pierre Ramond
- French Research Institute for Exploitation of the Sea, Ifremer DYNECO PELAGOS, 29280, Plouzané, France.,CNRS, Sorbonne Université, UMR 7144, Station Biologique de Roscoff, CS90074, 29688, Roscoff Cedex, France
| | - Raffaele Siano
- French Research Institute for Exploitation of the Sea, Ifremer DYNECO PELAGOS, 29280, Plouzané, France
| | - Marc Sourisseau
- French Research Institute for Exploitation of the Sea, Ifremer DYNECO PELAGOS, 29280, Plouzané, France
| | - Christophe Destombe
- CNRS, Sorbonne Université, UC, UaCh, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France
| | - Mickael Le Gac
- French Research Institute for Exploitation of the Sea, Ifremer DYNECO PELAGOS, 29280, Plouzané, France.
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32
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Alexander H, Rouco M, Haley ST, Dyhrman ST. Transcriptional response of
Emiliania huxleyi
under changing nutrient environments in the North Pacific Subtropical Gyre. Environ Microbiol 2020; 22:1847-1860. [DOI: 10.1111/1462-2920.14942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Harriet Alexander
- Biology Department Woods Hole Oceanographic Institution Woods Hole MA 02543 USA
| | - Mónica Rouco
- Biology and Paleo Environment Division, Lamont‐Doherty Earth Observatory Columbia University Palisades NY 10964 USA
- Department of Earth and Environmental Sciences Columbia University Palisades NY 10964 USA
| | - Sheean T. Haley
- Biology and Paleo Environment Division, Lamont‐Doherty Earth Observatory Columbia University Palisades NY 10964 USA
| | - Sonya T. Dyhrman
- Biology and Paleo Environment Division, Lamont‐Doherty Earth Observatory Columbia University Palisades NY 10964 USA
- Department of Earth and Environmental Sciences Columbia University Palisades NY 10964 USA
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33
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Abstract
Diatoms are key phytoplankton in the modern ocean that are involved in numerous biotic interactions, ranging from symbiosis to predation and viral infection, which have considerable effects on global biogeochemical cycles. However, despite recent large-scale studies of plankton, we are still lacking a comprehensive picture of the diversity of diatom biotic interactions in the marine microbial community. Through the ecological interpretation of both inferred microbial association networks and available knowledge on diatom interactions compiled in an open-access database, we propose an ecosystems approach for exploring diatom interactions in the ocean. Diatoms are a major component of phytoplankton, believed to be responsible for around 20% of the annual primary production on Earth. As abundant and ubiquitous organisms, they are known to establish biotic interactions with many other members of plankton. Through analyses of cooccurrence networks derived from the Tara Oceans expedition that take into account both biotic and abiotic factors in shaping the spatial distributions of species, we show that only 13% of diatom pairwise associations are driven by environmental conditions; the vast majority are independent of abiotic factors. In contrast to most other plankton groups, on a global scale, diatoms display a much higher proportion of negative correlations with other organisms, particularly toward potential predators and parasites, suggesting that their biogeography is constrained by top-down pressure. Genus-level analyses indicate that abundant diatoms are not necessarily the most connected and that species-specific abundance distribution patterns lead to negative associations with other organisms. In order to move forward in the biological interpretation of cooccurrence networks, an open-access extensive literature survey of diatom biotic interactions was compiled, of which 18.5% were recovered in the computed network. This result reveals the extent of what likely remains to be discovered in the field of planktonic biotic interactions, even for one of the best-known organismal groups. IMPORTANCE Diatoms are key phytoplankton in the modern ocean that are involved in numerous biotic interactions, ranging from symbiosis to predation and viral infection, which have considerable effects on global biogeochemical cycles. However, despite recent large-scale studies of plankton, we are still lacking a comprehensive picture of the diversity of diatom biotic interactions in the marine microbial community. Through the ecological interpretation of both inferred microbial association networks and available knowledge on diatom interactions compiled in an open-access database, we propose an ecosystems approach for exploring diatom interactions in the ocean.
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34
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Yu L, Zhang Y, Li M, Wang C, Lin X, Li L, Shi X, Guo C, Lin S. Comparative metatranscriptomic profiling and microRNA sequencing to reveal active metabolic pathways associated with a dinoflagellate bloom. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 699:134323. [PMID: 31522044 DOI: 10.1016/j.scitotenv.2019.134323] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/05/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
Harmful algal blooms (HABs) have increased as a result of global climate and environmental changes, exerting increasing impacts on the aquatic ecosystem, coastal economy, and human health. Despite great research efforts, our understanding on the drivers of HABs is still limited in part because HAB species' physiology is difficult to probe in situ. Here, we used molecular ecological analyses to characterize a dinoflagellate bloom at Xiamen Harbor, China. Prorocentrum donghaiense was identified as the culprit, which nutrient bioassays showed were not nutrient-limited. Metatranscriptome profiling revealed that P. donghaiense highly expressed genes related to N- and P-nutrient uptake, phagotrophy, energy metabolism (photosynthesis, oxidative phophorylation, and rhodopsin) and carbohydrate metabolism (glycolysis/gluconeogenesis, TCA cycle and pentose phosphate) during the bloom. Many genes in P. donghaiense were up-regulated at night, including phagotrophy and environmental communication genes, and showed active expression in mitosis. Eight microbial defense genes were up-regulated in the bloom compared with previously analyzed laboratory cultures. Furthermore, 76 P. donghaiense microRNA were identified from the bloom, and their target genes exhibited marked differences in amino acid metabolism between the bloom and cultures and the potential of up-regulated antibiotic and cell communication capabilities. These findings, consistent with and complementary to recent reports, reveal major metabolic processes in P. donghaiense potentially important for bloom formation and provide a gene repertoire for developing bloom markers in future research.
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Affiliation(s)
- Liying Yu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yaqun Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Meizhen Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Cong Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xinguo Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; College of Biological Science and Engineering, Fuzhou University, Fujian 350116, China
| | - Chentao Guo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
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35
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Hennon GMM, Dyhrman ST. Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms. HARMFUL ALGAE 2020; 91:101587. [PMID: 32057337 DOI: 10.1016/j.hal.2019.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 06/10/2023]
Abstract
Climate change is predicted to increase the severity and prevalence of harmful algal blooms (HABs). In the past twenty years, omics techniques such as genomics, transcriptomics, proteomics and metabolomics have transformed that data landscape of many fields including the study of HABs. Advances in technology have facilitated the creation of many publicly available omics datasets that are complementary and shed new light on the mechanisms of HAB formation and toxin production. Genomics have been used to reveal differences in toxicity and nutritional requirements, while transcriptomics and proteomics have been used to explore HAB species responses to environmental stressors, and metabolomics can reveal mechanisms of allelopathy and toxicity. In this review, we explore how omics data may be leveraged to improve predictions of how climate change will impact HAB dynamics. We also highlight important gaps in our knowledge of HAB prediction, which include swimming behaviors, microbial interactions and evolution that can be addressed by future studies with omics tools. Lastly, we discuss approaches to incorporate current omics datasets into predictive numerical models that may enhance HAB prediction in a changing world. With the ever-increasing omics databases, leveraging these data for understanding climate-driven HAB dynamics will be increasingly powerful.
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Affiliation(s)
- Gwenn M M Hennon
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States; College of Fisheries and Ocean Sciences University of Alaska Fairbanks Fairbanks, AK, United States
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States; Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States.
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36
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Sordino P, D'Aniello S, Pelletier E, Wincker P, Nittoli V, Stemmann L, Mazzocchi MG, Lombard F, Iudicone D, Caputi L. Into the bloom: Molecular response of pelagic tunicates to fluctuating food availability. Mol Ecol 2019; 29:292-307. [PMID: 31793138 DOI: 10.1111/mec.15321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 01/07/2023]
Abstract
The planktonic tunicates appendicularians and thaliaceans are highly efficient filter feeders on a wide range of prey size including bacteria and have shorter generation times than any other marine grazers. These traits allow some tunicate species to reach high population densities and ensure their success in a favourable environment. However, there are still few studies focusing on which genes and gene pathways are associated with responses of pelagic tunicates to environmental variability. Herein, we present the effect of food availability increase on tunicate community and gene expression at the Marquesas Islands (South-East Pacific Ocean). By using data from the Tara Oceans expedition, we show that changes in phytoplankton density and composition trigger the success of a dominant larvacean species (an undescribed appendicularian). Transcriptional signature to the autotroph bloom suggests key functions in specific physiological processes, i.e., energy metabolism, muscle contraction, membrane trafficking, and proteostasis. The relative abundance of reverse transcription-related Pfams was lower at bloom conditions, suggesting a link with adaptive genetic diversity in tunicates in natural ecosystems. Downstream of the bloom, pelagic tunicates were outcompeted by copepods. Our work represents the first metaomics study of the biological effects of phytoplankton bloom on a key zooplankton taxon.
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Affiliation(s)
| | | | - Eric Pelletier
- CEA - Institut Francois Jacob, Genoscope, Evry, France.,CNRS, UMR, Evry, France.,Université d'Evry Val d'Essonne, Université Paris-Saclay, Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France
| | - Patrick Wincker
- CEA - Institut Francois Jacob, Genoscope, Evry, France.,CNRS, UMR, Evry, France.,Université d'Evry Val d'Essonne, Université Paris-Saclay, Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France
| | | | - Lars Stemmann
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France.,CNRS, UMR 7093, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, Villefranche-sur-Mer, France
| | | | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France.,CNRS, UMR 7093, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, Villefranche-sur-Mer, France
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37
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Hernández Limón MD, Hennon GMM, Harke MJ, Frischkorn KR, Haley ST, Dyhrman ST. Transcriptional patterns of
Emiliania huxleyi
in the North Pacific Subtropical Gyre reveal the daily rhythms of its metabolic potential. Environ Microbiol 2019; 22:381-396. [DOI: 10.1111/1462-2920.14855] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 02/04/2023]
Affiliation(s)
- María D. Hernández Limón
- Lamont Doherty Earth Observatory, Division of Biology and Paleo Environment Columbia University Palisades NY USA
| | - Gwenn M. M. Hennon
- University of Alaska Fairbanks College of Fisheries and Ocean Sciences Fairbanks AK USA
| | - Matthew J. Harke
- Lamont Doherty Earth Observatory, Division of Biology and Paleo Environment Columbia University Palisades NY USA
| | - Kyle R. Frischkorn
- Department of Earth and Environmental Science Columbia University New York NY USA
| | - Sheean T. Haley
- Lamont Doherty Earth Observatory, Division of Biology and Paleo Environment Columbia University Palisades NY USA
| | - Sonya T. Dyhrman
- Department of Earth and Environmental Science Columbia University New York NY USA
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Dumack K, Fiore‐Donno AM, Bass D, Bonkowski M. Making sense of environmental sequencing data: Ecologically important functional traits of the protistan groups Cercozoa and Endomyxa (Rhizaria). Mol Ecol Resour 2019; 20:398-403. [DOI: 10.1111/1755-0998.13112] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Kenneth Dumack
- Institute of Zoology Terrestrial Ecology Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne Cologne Germany
| | - Anna Maria Fiore‐Donno
- Institute of Zoology Terrestrial Ecology Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne Cologne Germany
| | - David Bass
- Centre for Environment Fisheries and Aquaculture Science (Cefas) Weymouth UK
- Department of Life Sciences The Natural History Museum London UK
| | - Michael Bonkowski
- Institute of Zoology Terrestrial Ecology Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne Cologne Germany
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39
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Ku C, Sebé-Pedrós A. Using single-cell transcriptomics to understand functional states and interactions in microbial eukaryotes. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190098. [PMID: 31587645 PMCID: PMC6792447 DOI: 10.1098/rstb.2019.0098] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2019] [Indexed: 12/13/2022] Open
Abstract
Understanding the diversity and evolution of eukaryotic microorganisms remains one of the major challenges of modern biology. In recent years, we have advanced in the discovery and phylogenetic placement of new eukaryotic species and lineages, which in turn completely transformed our view on the eukaryotic tree of life. But we remain ignorant of the life cycles, physiology and cellular states of most of these microbial eukaryotes, as well as of their interactions with other organisms. Here, we discuss how high-throughput genome-wide gene expression analysis of eukaryotic single cells can shed light on protist biology. First, we review different single-cell transcriptomics methodologies with particular focus on microbial eukaryote applications. Then, we discuss single-cell gene expression analysis of protists in culture and what can be learnt from these approaches. Finally, we envision the application of single-cell transcriptomics to protist communities to interrogate not only community components, but also the gene expression signatures of distinct cellular and physiological states, as well as the transcriptional dynamics of interspecific interactions. Overall, we argue that single-cell transcriptomics can significantly contribute to our understanding of the biology of microbial eukaryotes. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- Chuan Ku
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
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40
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Zhang H, He YB, Wu PF, Zhang SF, Xie ZX, Li DX, Lin L, Chen F, Wang DZ. Functional Differences in the Blooming Phytoplankton Heterosigma akashiwo and Prorocentrum donghaiense Revealed by Comparative Metaproteomics. Appl Environ Microbiol 2019; 85:e01425-19. [PMID: 31375486 PMCID: PMC6752027 DOI: 10.1128/aem.01425-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 07/07/2019] [Indexed: 12/21/2022] Open
Abstract
Phytoplankton blooms are natural phenomena in the ocean, which are the results of rapid cell growth of some phytoplankton species in a unique environment. However, little is known about the molecular events occurring during the bloom. Here, we compared metaproteomes of two phytoplankton Heterosigma akashiwo and Prorocentrum donghaiense in the coastal East China Sea. H. akashiwo and P. donghaiense accounted for 7.82% and 4.74% of the phytoplankton community protein abundances in the nonbloom sample, whereas they contributed to 60.13% and 78.09%, respectively, in their individual blooming samples. Compared with P. donghaiense, H. akashiwo possessed a significantly higher abundance of light-harvesting complex proteins, carbonic anhydrasem and RuBisCO. The blooming H. akashiwo cells expressed more proteins related to external nutrient acquisition, such as bicarbonate transporter SLC4, ammonium transporter, nitrite transporter, and alkaline phosphatase, while the blooming P. donghaiense cells highly expressed proteins related to extra- and intracellular organic nutrient utilization, such as amino acid transporter, 5'-nucleotidase, acid phosphatase, and tripeptidyl-peptidase. The strong capabilities of light harvesting, as well as acquisition and assimilation of inorganic carbon, nitrogen, and phosphorus, facilitated the formation of the H. akashiwo bloom under the high turbidity and inorganic nutrient-sufficient condition, whereas the competitive advantages in organic nutrient acquisition and reallocation guaranteed the occurrence of the P. donghaiense bloom under the inorganic nutrient-insufficient condition. This study highlights the power of metaproteomics for revealing the underlying molecular behaviors of different coexisting phytoplankton species and advances our knowledge on the formation of phytoplankton blooms.IMPORTANCE A deep understanding of the mechanisms driving bloom formation is a prerequisite for effective bloom management. Metaproteomics was applied in this study to reveal the adaptive and responsive strategies of two coexisting phytoplankton species, H. akashiwo and P. donghaiense, during their bloom periods. Metabolic features and niche divergence in light harvesting, as well as carbon, nitrogen, and phosphorus acquisition and assimilation likely promoted the bloom occurrence under different environments. The molecular behaviors of coexisting bloom-causing species will give clues for bloom monitoring and management in the oceans.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yan-Bin He
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Peng-Fei Wu
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Shu-Feng Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Dong-Xu Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
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Wilson ST, Hawco NJ, Armbrust EV, Barone B, Björkman KM, Boysen AK, Burgos M, Burrell TJ, Casey JR, DeLong EF, Dugenne M, Dutkiewicz S, Dyhrman ST, Ferrón S, Follows MJ, Foreman RK, Funkey CP, Harke MJ, Henke BA, Hill CN, Hynes AM, Ingalls AE, Jahn O, Kelly RL, Knapp AN, Letelier RM, Ribalet F, Shimabukuro EM, Tabata RKS, Turk-Kubo KA, White AE, Zehr JP, John S, Karl DM. Kīlauea lava fuels phytoplankton bloom in the North Pacific Ocean. Science 2019; 365:1040-1044. [DOI: 10.1126/science.aax4767] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/17/2019] [Indexed: 11/02/2022]
Affiliation(s)
- Samuel T. Wilson
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Nicholas J. Hawco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Benedetto Barone
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Karin M. Björkman
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Angela K. Boysen
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Macarena Burgos
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Timothy J. Burrell
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - John R. Casey
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward F. DeLong
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Mathilde Dugenne
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sonya T. Dyhrman
- Department of Earth and Environmental Sciences, Columbia University, Palisades, NY 10964, USA
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY 10964, USA
| | - Sara Ferrón
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Michael J. Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rhea K. Foreman
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Carolina P. Funkey
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Matthew J. Harke
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY 10964, USA
| | - Britt A. Henke
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Christopher N. Hill
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Annette M. Hynes
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Anitra E. Ingalls
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Oliver Jahn
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rachel L. Kelly
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Angela N. Knapp
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL 32306, USA
| | - Ricardo M. Letelier
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Francois Ribalet
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Eric M. Shimabukuro
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Ryan K. S. Tabata
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Kendra A. Turk-Kubo
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Angelicque E. White
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
| | - Jonathan P. Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Seth John
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - David M. Karl
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai‘i at Manoa, Honolulu, HI 96822, USA
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Wang X, Niu X, Chen Y, Sun Z, Han A, Lou X, Ge J, Li X, Yang Y, Jian J, Gonçalves RJ, Guan W. Transcriptome sequencing of a toxic dinoflagellate, Karenia mikimotoi subjected to stress from solar ultraviolet radiation. HARMFUL ALGAE 2019; 88:101640. [PMID: 31582153 DOI: 10.1016/j.hal.2019.101640] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
Solar ultraviolet radiation (UVR) is a stress factor in aquatic environments and may act directly or indirectly on orgnisms in the upper layers of the water column. However, UVR effects are usually species-specific and difficult to extrapolate. Here we use the HAB-forming, toxic dinoflagellate Karenia mikimotoi (which was found to be relatively resistant in previous studies) to investigate its transcriptional responses to a one-week UVR exposure. For this, batch cultures of K. mikimotoi were grown with and without UVR, and their transcriptomes (generated via RNAseq technology) were compared. RNA-seq generated 45.31 million reads, which were further assembled to 202600 unigenes (>300bp). Among these, ca. 61% were annotated with NCBI, NR, GO, KOG, PFAM, Swiss-Prot, and KEGG database. Transcriptomic analysis revealed 722 differentially expressed unigenes (DEGs, defined as being within a |log2 fold change| ≥ 2 and padj < 0.05) responding to solar UVR, which were only 0.36% of all unigenes. 716 unigenes were down-regulated, and only 6 unigenes were up-regulated in the UVR compared to non-UVR treatment. KEGG pathway further analysis revealed DEGs were involved in the different pathway; genes involved in the ribosome, endocytosis and steroid biosynthesis pathways were highly down-regulated, but this was not the case for those involved in the energy metabolisms (including photosynthesis, oxidative phosphorylation) which may contribute to the sustainable growth observed in UVR treatment. The up-regulated expression of both zinc-finger proteins (ZFPs) and ribosomal protein L11 (RPL11) may be one of the acclimated mechanisms against UVR. In addition, this work identified down-regulated genes involved in fatty acid degradation and the hydrophobic branched chain amino acids (e.g., Valine, leucine, and isoleucine), which act as structural components of cell membranes modulating lipid homeostasis or turnover. In conclusion, the present study suggests that the toxic dinoflagellate K. mikimotoi has limited transcriptomic regulation but confirms that it appears as a tolerant species in response to solar UVR. These findings expand current knowledge of gene expression in HAB-forming species in response to natural environment factors such as solar radiation.
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Affiliation(s)
- Xinjie Wang
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China; Marine Biology Institute, Shantou University, Shantou, Guangdong 515063 China
| | - Xiaoqin Niu
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Yiji Chen
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Zhewei Sun
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Axiang Han
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Xiayuan Lou
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Jingke Ge
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Xuanwen Li
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Yuqian Yang
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Jianbo Jian
- Marine Biology Institute, Shantou University, Shantou, Guangdong 515063 China
| | - Rodrigo J Gonçalves
- Laboratorio de Oceanografía Biológica (LOBio), Centro para el Estudio de Sistemas Marinos (CESIMAR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). U9120ACD, Puerto Madryn, Argentina
| | - Wanchun Guan
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China.
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Strategies among phytoplankton in response to alleviation of nutrient stress in a subtropical gyre. ISME JOURNAL 2019; 13:2984-2997. [PMID: 31439897 DOI: 10.1038/s41396-019-0489-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 07/07/2019] [Accepted: 08/02/2019] [Indexed: 11/08/2022]
Abstract
Despite generally low primary productivity and diatom abundances in oligotrophic subtropical gyres, the North Atlantic Subtropical Gyre (NASG) exhibits significant diatom-driven carbon export on an annual basis. Subsurface pulses of nutrients likely fuel brief episodes of diatom growth, but the exact mechanisms utilized by diatoms in response to these nutrient injections remain understudied within near-natural settings. Here we simulated delivery of subsurface nutrients and compare the response among eukaryotic phytoplankton using a combination of physiological techniques and metatranscriptomics. We show that eukaryotic phytoplankton groups exhibit differing levels of transcriptional responsiveness and expression of orthologous genes in response to release from nutrient limitation. In particular, strategies for use of newly delivered nutrients are distinct among phytoplankton groups. Diatoms channel new nitrate to growth-related strategies while physiological measurements and gene expression patterns of other groups suggest alternative strategies. The gene expression patterns displayed here provide insights into the cellular mechanisms that underlie diatom subsistence during chronic nitrogen-depleted conditions and growth upon nutrient delivery that can enhance carbon export from the surface ocean.
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A kleptoplastidic dinoflagellate and the tipping point between transient and fully integrated plastid endosymbiosis. Proc Natl Acad Sci U S A 2019; 116:17934-17942. [PMID: 31427512 DOI: 10.1073/pnas.1910121116] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plastid endosymbiosis has been a major force in the evolution of eukaryotic cellular complexity, but how endosymbionts are integrated is still poorly understood at a mechanistic level. Dinoflagellates, an ecologically important protist lineage, represent a unique model to study this process because dinoflagellate plastids have repeatedly been reduced, lost, and replaced by new plastids, leading to a spectrum of ages and integration levels. Here we describe deep-transcriptomic analyses of the Antarctic Ross Sea dinoflagellate (RSD), which harbors long-term but temporary kleptoplasts stolen from haptophyte prey, and is closely related to dinoflagellates with fully integrated plastids derived from different haptophytes. In some members of this lineage, called the Kareniaceae, their tertiary haptophyte plastids have crossed a tipping point to stable integration, but RSD has not, and may therefore reveal the order of events leading up to endosymbiotic integration. We show that RSD has retained its ancestral secondary plastid and has partitioned functions between this plastid and the kleptoplast. It has also obtained genes for kleptoplast-targeted proteins via horizontal gene transfer (HGT) that are not derived from the kleptoplast lineage. Importantly, many of these HGTs are also found in the related species with fully integrated plastids, which provides direct evidence that genetic integration preceded organelle fixation. Finally, we find that expression of kleptoplast-targeted genes is unaffected by environmental parameters, unlike prey-encoded homologs, suggesting that kleptoplast-targeted HGTs have adapted to posttranscriptional regulation mechanisms of the host.
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Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. ISME JOURNAL 2019; 13:2817-2833. [PMID: 31320727 PMCID: PMC6794264 DOI: 10.1038/s41396-019-0472-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 06/11/2019] [Accepted: 06/15/2019] [Indexed: 01/06/2023]
Abstract
Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report on the community structure and transcriptional dynamics of microbes in an operationally large size class (>5 μm) predominantly populated by dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria (chiefly Synechococcus), prasinophytes (chiefly Ostreococcus), fungi, archaea, and proteobacteria. Apart from fungi and archaea, all groups exhibited 24-h periodicity in some transcripts, but larger portions of the transcriptome oscillated in phototrophs. Periodic photosynthesis-related transcripts exhibited a temporal cascade across the morning hours, conserved across diverse phototrophic lineages. Pronounced silica:nitrate drawdown, a high flavodoxin to ferredoxin transcript ratio, and elevated expression of other Fe-stress markers indicated Fe-limitation. Fe-stress markers peaked during a photoperiodically adaptive time window that could modulate phytoplankton response to seasonal Fe-limitation. Remarkably, we observed viruses that infect the majority of abundant taxa, often with total transcriptional activity synchronized with putative hosts. Taken together, these data reveal a microbial plankton community that is shaped by recycled production and tightly controlled by Fe-limitation and viral activity.
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Zhang Y, Lin X, Shi X, Lin L, Luo H, Li L, Lin S. Metatranscriptomic Signatures Associated With Phytoplankton Regime Shift From Diatom Dominance to a Dinoflagellate Bloom. Front Microbiol 2019; 10:590. [PMID: 30967855 PMCID: PMC6439486 DOI: 10.3389/fmicb.2019.00590] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/07/2019] [Indexed: 12/19/2022] Open
Abstract
Diatoms and dinoflagellates dominate coastal marine phytoplankton communities as major players of marine biogeochemical cycles and their seasonal succession often leads to harmful algal blooms (HABs). What regulates their respective dominances and the development of the HABs remains elusive. Here we conducted time-sequential metatranscriptomic profiling on a natural assemblage that evolved from diatom dominance to a dinoflagellate bloom to interrogate the underlying major metabolic and ecological drivers. Data reveals similarity between diatoms and dinoflagellates in exhibiting high capacities of energy production, nutrient acquisition, and stress protection in their respective dominance stages. The diatom-to-dinoflagellate succession coincided with an increase in turbidity and sharp declines in silicate and phosphate availability, concomitant with the transcriptomic shift from expression of silicate uptake and urea utilization genes in diatoms to that of genes for light harvesting, diversified phosphorus acquisition and autophagy-based internal nutrient recycling in dinoflagellates. Furthermore, the diatom-dominant community featured strong potential to carbohydrate metabolism and a strikingly high expression of trypsin potentially promoting frustule building. In contrast, the dinoflagellate bloom featured elevated expression of xanthorhodopsin, and antimicrobial defensin genes, indicating potential importance of energy harnessing and microbial defense in bloom development. This study sheds light on mechanisms potentially governing diatom- and dinoflagellate-dominance and regulating bloom development in the natural environment and raises new questions to be addressed in future studies.
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Affiliation(s)
- Yaqun Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xinguo Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Lingxiao Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Hao Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Department of Marine Sciences, University of Connecticut, Groton, CT, United States
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Modelling the complexity of plankton communities exploiting omics potential: From present challenges to an integrative pipeline. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2018.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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48
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Varkey D, Mazard S, Jeffries TC, Hughes DJ, Seymour J, Paulsen IT, Ostrowski M. Stormwater influences phytoplankton assemblages within the diverse, but impacted Sydney Harbour estuary. PLoS One 2018; 13:e0209857. [PMID: 30586428 PMCID: PMC6306231 DOI: 10.1371/journal.pone.0209857] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/12/2018] [Indexed: 01/14/2023] Open
Abstract
Sydney Harbour is subjected to persistent stress associated with anthropogenic activity and global climate change, but is particularly subjected to pulse stress events associated with stormwater input during episodic periods of high rainfall. Photosynthetic microbes underpin metazoan diversity within estuarine systems and are therefore important bioindicators of ecosystem health; yet how stormwater input affects their occurrence and distribution in Sydney Harbour remains poorly understood. We utilised molecular tools (16S/18S rRNA and petB genes) to examine how the phytoplankton community structure (both prokaryotes and eukaryotes) within Sydney Harbour varies between high and low rainfall periods. The relative proportion of phytoplankton sequences was more abundant during the high rainfall period, comprising mainly of diatoms, an important functional group supporting increased productivity within estuarine systems, together with cyanobacteria. Increased spatial variability in the phytoplankton community composition was observed, potentially driven by the steepened physico-chemical gradients associated with stormwater inflow. Conversely, during a low rainfall period, the proportion of planktonic photosynthetic microbes was significantly lower and the persistent phytoplankton were predominantly represented by chlorophyte and dinoflagellate sequences, with lower overall diversity. Differences in phytoplankton composition between the high and low rainfall periods were correlated with temperature, salinity, total nitrogen and silicate. These results suggest that increased frequency of high-rainfall events may change the composition, productivity and health of the estuary. Our study begins to populate the knowledge gap in the phytoplankton community structure and substantial changes associated with transient environmental perturbations, an essential step towards unravelling the dynamics of primary production in a highly urbanised estuarine ecosystem in response to climate change and other anthropogenic stressors.
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Affiliation(s)
- Deepa Varkey
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- * E-mail: (IP); (DV)
| | - Sophie Mazard
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Thomas C. Jeffries
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - David J. Hughes
- University of Technology Sydney, Climate Change Cluster, Ultimo, NSW, Australia
| | - Justin Seymour
- University of Technology Sydney, Climate Change Cluster, Ultimo, NSW, Australia
| | - Ian T. Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- * E-mail: (IP); (DV)
| | - Martin Ostrowski
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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49
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Becker KW, Collins JR, Durham BP, Groussman RD, White AE, Fredricks HF, Ossolinski JE, Repeta DJ, Carini P, Armbrust EV, Van Mooy BAS. Daily changes in phytoplankton lipidomes reveal mechanisms of energy storage in the open ocean. Nat Commun 2018; 9:5179. [PMID: 30518752 PMCID: PMC6281602 DOI: 10.1038/s41467-018-07346-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 10/25/2018] [Indexed: 12/31/2022] Open
Abstract
Sunlight is the dominant control on phytoplankton biosynthetic activity, and darkness deprives them of their primary external energy source. Changes in the biochemical composition of phytoplankton communities over diel light cycles and attendant consequences for carbon and energy flux in environments remain poorly elucidated. Here we use lipidomic data from the North Pacific subtropical gyre to show that biosynthesis of energy-rich triacylglycerols (TAGs) by eukaryotic nanophytoplankton during the day and their subsequent consumption at night drives a large and previously uncharacterized daily carbon cycle. Diel oscillations in TAG concentration comprise 23 ± 11% of primary production by eukaryotic nanophytoplankton representing a global flux of about 2.4 Pg C yr−1. Metatranscriptomic analyses of genes required for TAG biosynthesis indicate that haptophytes and dinoflagellates are active members in TAG production. Estimates suggest that these organisms could contain as much as 40% more calories at sunset than at sunrise due to TAG production. Day-night cycles in the biochemical composition of phytoplankton remain poorly understood. Here, Becker et al. use lipidomic and transcriptomic data from the North Pacific subtropical gyre to describe a daily cycle of production and consumption of energy-rich lipids by eukaryotic phytoplankton.
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Affiliation(s)
- Kevin W Becker
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - James R Collins
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Massachusetts Institute of Technology/Woods Hole Oceanographic Institution Joint Program in Oceanography, Woods Hole, MA, 02543, USA.,School of Oceanography and eScience Institute, University of Washington, Seattle, WA, 98195, USA
| | - Bryndan P Durham
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Ryan D Groussman
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Angelicque E White
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, 97331, USA
| | - Helen F Fredricks
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Justin E Ossolinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Daniel J Repeta
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Paul Carini
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA.,Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, 85721, USA
| | | | - Benjamin A S Van Mooy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.
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50
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Robidart JC, Magasin JD, Shilova IN, Turk-Kubo KA, Wilson ST, Karl DM, Scholin CA, Zehr JP. Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre. ISME JOURNAL 2018; 13:374-387. [PMID: 30254320 DOI: 10.1038/s41396-018-0280-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/26/2018] [Accepted: 08/26/2018] [Indexed: 11/09/2022]
Abstract
Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity in the surface ocean is constrained by nutrients which are supplied, in part, by mixing with deeper water. Little is known about the time scales, frequency, or impact of mixing on microbial communities. We combined in situ sampling using the Environmental Sample Processor and a small-scale mixing experiment with lower euphotic zone water to determine how individual populations respond to mixing. Transcriptional responses were measured using the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) microarray, which targets all three domains of life and viruses. The experiment showed that mixing substantially affects photosynthetic taxa as expected, but surprisingly also showed that populations respond differently to unfiltered deep water which contains particles (organisms and detritus) compared to filtered deep water that only contains nutrients and viruses, pointing to the impact of biological interactions associated with these events. Comparison between experimental and in situ population transcription patterns indicated that manipulated populations can serve as analogs for natural populations, and that natural populations may be frequently or continuously responding to nutrients from deeper waters. Finally, this study also shows that the microarray approach, which is complementary to metatranscriptomic sequencing, is useful for determining the physiological status of in situ microbial communities.
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Affiliation(s)
- J C Robidart
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.,National Oceanography Centre, Southampton, UK
| | - J D Magasin
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - I N Shilova
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.,Second Genome, South San Francisco, CA, USA
| | - K A Turk-Kubo
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - S T Wilson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - D M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - C A Scholin
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - J P Zehr
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.
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