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Wang L, Lu X, Xing Z, Teng X, Wang S, Liu T, Zheng L, Wang X, Qu J. Macrogenomics Reveals Effects on Marine Microbial Communities during Oplegnathus punctatus Enclosure Farming. BIOLOGY 2024; 13:618. [PMID: 39194557 DOI: 10.3390/biology13080618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 08/29/2024]
Abstract
(1) Background: Laizhou Bay is an important aquaculture area in the north of China. Oplegnathus punctatus is one of the species with high economic benefits. In recent years, the water environment of Laizhou Bay has reached a mild eutrophication level, while microorganisms are an important group between the environment and species. In this study, we evaluated alterations in environmental elements, microbial populations, and antibiotic resistance genes (ARGs) along with their interconnections during Oplegnathus punctatus net culture. (2) Methods: A total of 142 samples from various water layers were gathered for metagenome assembly analysis. Mariculture increases the abundance of microorganisms in this culture area and makes the microbial community structure more complex. The change had more significant effects on sediment than on seawater. (3) Results: Certain populations of cyanobacteria and Candidatus Micrarchaecta in seawater, and Actinobacteria and Thaumarchaeota in sediments showed high abundance in the mariculture area. Antibiotic resistance genes in sediments were more sensitive to various environmental factors, especially oxygen solubility and salinity. (4) Conclusions: These findings highlight the complex and dynamic nature of microorganism-environment-ARG interactions, characterized by regional specificity and providing insights for a more rational use of marine resources.
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Affiliation(s)
- Lijun Wang
- College of Life Science, Yantai University, Yantai 264005, China
| | - Xiaofei Lu
- College of Life Science, Yantai University, Yantai 264005, China
| | - Zhikai Xing
- College of Life Science, Yantai University, Yantai 264005, China
| | - Xindong Teng
- Qingdao International Travel Healthcare Center, Qingdao 266071, China
| | - Shuang Wang
- College of Life Science, Yantai University, Yantai 264005, China
| | - Tianyi Liu
- College of Life Science, Yantai University, Yantai 264005, China
| | - Li Zheng
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China
| | - Xumin Wang
- College of Life Science, Yantai University, Yantai 264005, China
| | - Jiangyong Qu
- College of Life Science, Yantai University, Yantai 264005, China
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2
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Miao W, Wang S, Lin T, Yan Y, Bao Z, Zhang D, Jiang Z, Zhang H. Interaction patterns and assembly mechanisms of dinoflagellates and diatoms in a coastal bay suffering from long-term eutrophication. mSphere 2024; 9:e0036624. [PMID: 38940511 PMCID: PMC11288026 DOI: 10.1128/msphere.00366-24] [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: 04/30/2024] [Accepted: 06/11/2024] [Indexed: 06/29/2024] Open
Abstract
Dinoflagellates and diatoms are highly prevalent and ecologically important phytoplankton in coastal waters, greatly contributing to primary productivity in marine ecosystems. Although their composition and diversity have been extensively elucidated in the open ocean, their interaction patterns and community assembly in long-term eutrophic coastal waters remain poorly understood. This investigation aimed to elucidate the seasonal successional patterns of dinoflagellates and diatoms by 18S rRNA gene amplicon sequencing in a semi-enclosed bay. The results revealed that dinoflagellate and diatom communities have pronounced seasonal succession patterns, which are primarily associated with temperature. Furthermore, the most prevalent species throughout the year were Heterocapsa rotundata and Skeletonema costatum. Moreover, the assembly of dinoflagellate and diatom communities was mainly dominated by stochastic processes, with drift being the major factor. The co-occurrence of dinoflagellates and diatoms showed seasonal patterns, with the highest interactions observed in autumn. In addition, interactions of Syndiniales with dinoflagellates and diatoms highlighted the roles of parasites in eutrophic conditions. Flavobacteriaceae and Rhodobacteraceae are the bacterial taxa that most frequently interacted with dinoflagellates and diatoms, with interactions between dinoflagellates and bacteria being more complex than those between diatoms and bacteria. Overall, this study provides results that deepen our understanding of the phytoplankton dynamics in coastal eutrophic waters.IMPORTANCEDinoflagellates and diatoms are major phytoplankton groups in coastal waters. The composition and diversity of dinoflagellates and diatoms in the open ocean have been well documented; however, it remains uncertain to what extent their adaptation to long-term eutrophic conditions influences their response to environmental disturbances. Here, we investigated the interactions and assembly processes of dinoflagellates and diatoms in a eutrophic bay throughout the whole year. Our findings revealed that interactions between dinoflagellates and diatoms are primarily shaped by seasonal transitions, while prolonged eutrophic conditions tend to amplify stochastic processes in community assembly. These findings provide novel perspectives on the influence of long-term eutrophication on phytoplankton dynamics within eutrophic waters.
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Affiliation(s)
- Wenfei Miao
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Shuqi Wang
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Tenghui Lin
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yi Yan
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhen Bao
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Zhibing Jiang
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Huajun Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
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3
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Hu F, Jiang H, Wan B, Ducea MN, Gao L, Wu FY. Latitude-dependent oxygen fugacity in arc magmas. Nat Commun 2024; 15:6050. [PMID: 39025886 PMCID: PMC11258285 DOI: 10.1038/s41467-024-50337-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024] Open
Abstract
The redox state of arc mantle has been considered to be more oxidized and diverse than that of the mid-ocean ridge, but the cause of the variation is debated. We examine the redox state of the Cenozoic global arc mantle by compiling measured/calculated fO2 of olivine-hosted melt inclusions from arc magma and modeled fO2 based on V/Sc and Cu/Zr ratios of arc basaltic rocks. The results indicate that the redox state of Cenozoic arc mantle is latitude dependent, with less oxidized arc mantle in the low latitudes, contrasting with a near constant across-latitude trend in the mid-ocean ridges. We propose that such a latitude-dependent pattern in the arc mantle may be controlled by the variation in the redox state of subducted sediment, possibly related to a latitudinal variation in the primary production of phytoplankton, which results in more organic carbon and sulfide deposited on the low-latitude ocean floor. Our findings provide evidence for the impact of the surface environment on Earth's upper mantle.
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Affiliation(s)
- Fangyang Hu
- State Key Laboratory of Lithospheric and Environmental Coevolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China.
| | - Hehe Jiang
- State Key Laboratory of Lithospheric and Environmental Coevolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
| | - Bo Wan
- State Key Laboratory of Lithospheric and Environmental Coevolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
| | - Mihai N Ducea
- Faculty of Geology and Geophysics, University of Bucharest, Bucharest, Romania
- Department of Geosciences, University of Arizona, Tucson, AZ, USA
| | - Lei Gao
- State Key Laboratory of Geological Processes and Mineral Resources, School of Earth Sciences and Resources, China University of Geosciences, Beijing, China
| | - Fu-Yuan Wu
- State Key Laboratory of Lithospheric and Environmental Coevolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
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4
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Edwards KF, Rii YM, Li Q, Peoples LM, Church MJ, Steward GF. Trophic strategies of picoeukaryotic phytoplankton vary over time and with depth in the North Pacific Subtropical Gyre. Environ Microbiol 2024; 26:e16689. [PMID: 39168489 DOI: 10.1111/1462-2920.16689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 07/26/2024] [Indexed: 08/23/2024]
Abstract
In oligotrophic oceans, the smallest eukaryotic phytoplankton are both significant primary producers and predators of abundant bacteria such as Prochlorococcus. However, the drivers and consequences of community dynamics among these diverse protists are not well understood. Here, we investigated how trophic strategies along the autotrophy-mixotrophy spectrum vary in importance over time and across depths at Station ALOHA in the North Pacific Subtropical Gyre. We combined picoeukaryote community composition from a 28-month time-series with traits of diverse phytoplankton isolates from the same location, to examine trophic strategies across 13 operational taxonomic units and 8 taxonomic classes. We found that autotrophs and slower-grazing mixotrophs tended to prevail deeper in the photic zone, while the most voracious mixotrophs were relatively abundant near the surface. Within the mixed layer, there was greater phagotrophy when conditions were most stratified and when Chl a concentrations were lowest, although the greatest temporal variation in trophic strategy occurred at intermediate depths (45-100 m). Dynamics at this site are consistent with previously described spatial patterns of trophic strategies. The success of relatively phagotrophic phytoplankton at shallower depths in the most stratified waters suggests that phagotrophy is a competitive strategy for acquiring nutrients when energy from light is plentiful.
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Affiliation(s)
- Kyle F Edwards
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
| | - Yoshimi M Rii
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, USA
| | - Qian Li
- School of Oceanography, Shanghai Jiao Tong University, Shanghai Shi, China
| | - Logan M Peoples
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Matthew J Church
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Grieg F Steward
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, and Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
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5
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Wang C, Gu J, Li W, Wang J, Wang Z, Lin Q. Metabarcoding reveals a high diversity and complex eukaryotic microalgal community in coastal waters of the northern Beibu Gulf, China. Front Microbiol 2024; 15:1403964. [PMID: 38903786 PMCID: PMC11188352 DOI: 10.3389/fmicb.2024.1403964] [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: 03/20/2024] [Accepted: 05/24/2024] [Indexed: 06/22/2024] Open
Abstract
Beibu Gulf is an important semi-enclosed bay located in the northwestern South China Sea, and is famous for its high bio-productivity and rich bio-diversity. The fast development along the Beibu Gulf Economical Rim has brought pressure to the environment, and algal blooms occurred frequently in the gulf. In this study, surface water samples and micro-plankton samples (20-200 μm) were collected in the northern Beibu Gulf coast. Diversity and distribution of eukaryotic planktonic microalgae were analyzed by both metabarcoding and microscopic analyses. Metabarcoding revealed much higher diversity and species richness of microalgae than morphological observation, especially for dinoflagellates. Metabarcoding detected 144 microalgal genera in 8 phyla, while microscopy only detected 40 genera in 2 phyla. The two methods revealed different microalgal community structures. Dinoflagellates dominated in microalgal community based on metabarcoding due to their high copies of 18 s rRNA gene, and diatoms dominated under microscopy. Altogether 48 algal bloom and/or toxic species were detected in this study, 34 species by metabarcoding and 19 species by microscopy. Our result suggested a high potential risk of HABs in the Beibu Gulf. Microalgal community in the surface water samples demonstrated significantly higher OTU/species richness, alpha diversity, and abundance than those in the micro-plankton samples, although more HAB taxa were detected by microscopic observations in the micro-plankton samples. Furthermore, nano-sized taxa, such as those in chlorophytes, haptophytes, and chrysophyceans, occurred more abundantly in the surface water samples. This study provided a comprehensive morphological and molecular description of microalgal community in the northern Beibu Gulf.
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Affiliation(s)
| | | | | | | | - Zhaohui Wang
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qiuqi Lin
- College of Life Science and Technology, Jinan University, Guangzhou, China
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6
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Rammel T, Nagarkar M, Palenik B. Temporal and spatial diversity and abundance of cryptophytes in San Diego coastal waters. JOURNAL OF PHYCOLOGY 2024; 60:668-684. [PMID: 38721968 DOI: 10.1111/jpy.13451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/02/2023] [Accepted: 01/29/2024] [Indexed: 06/12/2024]
Abstract
Cryptophytes (class Cryptophyceae) are bi-flagellated eukaryotic protists with mixed nutritional modes and cosmopolitan distribution in aquatic environments. Despite their ubiquitous presence, their molecular diversity is understudied in coastal waters. Weekly 18S rRNA gene amplicon sequencing at the Scripps Institution of Oceanography pier (La Jolla, California) in 2016 revealed 16 unique cryptophyte amplicon sequence variants (ASVs), with two dominant "clade 4" ASVs. The diversity of cryptophytes was lower than what is often seen in other phytoplankton taxa. One ASV represented a known Synechococcus grazer, while the other one appeared not to have cultured representatives and an unknown potential for mixotrophy. These two dominant ASVs were negatively correlated, suggesting possible niche differentiation. The cryptophyte population in nearby San Diego Bay was surveyed in 2019 and showed the increasing dominance of a different clade 4 ASV toward the back of the bay where conditions are warmer, saltier, and shallower relative to other areas in the bay. An ASV representing a potentially chromatically acclimating cryptophyte species also suggested that San Diego Bay exerts differing ecological selection pressures than nearby coastal waters. Cryptophyte and Synechococcus cell abundance at the SIO Pier from 2011 to 2017 showed that cryptophytes were consistently present and had a significant correlation with Synechococcus abundance, but no detectable seasonality. The demonstrated mixotrophy of some cryptophytes suggests that grazing on these and perhaps other bacteria is important for their ecological success. Using several assumptions, we calculated that cryptophytes could consume up to 44% (average 6%) of the Synechococcus population per day. This implies that cryptophytes could significantly influence Synechococcus abundance.
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Affiliation(s)
- Tristin Rammel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Maitreyi Nagarkar
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Brian Palenik
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
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Madhuri S, Lepetit B, Fürst AH, Kroth PG. A Knockout of the Photoreceptor PtAureo1a Results in Altered Diel Expression of Diatom Clock Components. PLANTS (BASEL, SWITZERLAND) 2024; 13:1465. [PMID: 38891274 PMCID: PMC11174801 DOI: 10.3390/plants13111465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024]
Abstract
Plants and algae use light not only for driving photosynthesis but also to sense environmental cues and to adjust their circadian clocks via photoreceptors. Aureochromes are blue-light-dependent photoreceptors that also function as transcription factors, possessing both a LOV and a bZIP domain. Aureochromes so far have only been detected in Stramenopile algae, which include the diatoms. Four paralogues of aureochromes have been identified in the pennate model diatom Phaeodactylum tricornutum: PtAureo1a, 1b, 1c, and 2. While it was shown recently that diatoms have a diel rhythm, the molecular mechanisms and components regulating it are still largely unknown. Diel gene expression analyses of wild-type P. tricornutum, a PtAureo1a knockout strain, and the respective PtAureo1 complemented line revealed that all four aureochromes have a different diel regulation and that PtAureo1a has a strong co-regulatory influence on its own transcription, as well as on that of other genes encoding different blue-light photoreceptors (CPF1, 2 and 4), proteins involved in photoprotection (Lhcx1), and specific bHLH transcription factors (RITMO1). Some of these genes completely lost their circadian expression in the PtAureo1a KO mutant. Our results suggest a major involvement of aureochromes in the molecular clock of diatoms.
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Affiliation(s)
| | | | | | - Peter G. Kroth
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany; (S.M.); (B.L.); (A.H.F.)
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Bui QTN, Pradhan B, Kim HS, Ki JS. Environmental Factors Modulate Saxitoxins (STXs) Production in Toxic Dinoflagellate Alexandrium: An Updated Review of STXs and Synthesis Gene Aspects. Toxins (Basel) 2024; 16:210. [PMID: 38787062 PMCID: PMC11125744 DOI: 10.3390/toxins16050210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/25/2024] Open
Abstract
The marine dinoflagellate Alexandrium is known to form harmful algal blooms (HABs) and produces saxitoxin (STX) and its derivatives (STXs) that cause paralytic shellfish poisoning (PSP) in humans. Cell growth and cellular metabolism are affected by environmental conditions, including nutrients, temperature, light, and the salinity of aquatic systems. Abiotic factors not only engage in photosynthesis, but also modulate the production of toxic secondary metabolites, such as STXs, in dinoflagellates. STXs production is influenced by a variety of abiotic factors; however, the relationship between the regulation of these abiotic variables and STXs accumulation seems not to be consistent, and sometimes it is controversial. Few studies have suggested that abiotic factors may influence toxicity and STXs-biosynthesis gene (sxt) regulation in toxic Alexandrium, particularly in A. catenella, A. minutum, and A. pacificum. Hence, in this review, we focused on STXs production in toxic Alexandrium with respect to the major abiotic factors, such as temperature, salinity, nutrients, and light intensity. This review informs future research on more sxt genes involved in STXs production in relation to the abiotic factors in toxic dinoflagellates.
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Affiliation(s)
- Quynh Thi Nhu Bui
- Department of Life Science, Sangmyung University, Seoul 03016, Republic of Korea; (Q.T.N.B.); (H.-S.K.)
| | - Biswajita Pradhan
- Department of Biotechnology, Sangmyung University, Seoul 03016, Republic of Korea;
- Department of Botany, Model Degree College, Rayagada 765017, Odisha, India
| | - Han-Sol Kim
- Department of Life Science, Sangmyung University, Seoul 03016, Republic of Korea; (Q.T.N.B.); (H.-S.K.)
| | - Jang-Seu Ki
- Department of Life Science, Sangmyung University, Seoul 03016, Republic of Korea; (Q.T.N.B.); (H.-S.K.)
- Department of Biotechnology, Sangmyung University, Seoul 03016, Republic of Korea;
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Kalvelage J, Wöhlbrand L, Senkler J, Schumacher J, Ditz N, Bischof K, Winklhofer M, Klingl A, Braun HP, Rabus R. Conspicuous chloroplast with light harvesting-photosystem I/II megacomplex in marine Prorocentrum cordatum. PLANT PHYSIOLOGY 2024; 195:306-325. [PMID: 38330164 PMCID: PMC11181951 DOI: 10.1093/plphys/kiae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 02/10/2024]
Abstract
Marine photosynthetic (micro)organisms drive multiple biogeochemical cycles and display a large diversity. Among them, the bloom-forming, free-living dinoflagellate Prorocentrum cordatum CCMP 1329 (formerly P. minimum) stands out with its distinct cell biological features. Here, we obtained insights into the structural properties of the chloroplast and the photosynthetic machinery of P. cordatum using microscopic and proteogenomic approaches. High-resolution FIB/SEM analysis revealed a single large chloroplast (∼40% of total cell volume) with a continuous barrel-like structure, completely lining the inner face of the cell envelope and enclosing a single reticular mitochondrium, the Golgi apparatus, as well as diverse storage inclusions. Enriched thylakoid membrane fractions of P. cordatum were comparatively analyzed with those of the well-studied model-species Arabidopsis (Arabidopsis thaliana) using 2D BN DIGE. Strikingly, P. cordatum possessed a large photosystem-light harvesting megacomplex (>1.5 MDa), which is dominated by photosystems I and II (PSI, PSII), chloroplast complex I, and chlorophyll a-b binding light harvesting complex proteins. This finding parallels the absence of grana in its chloroplast and distinguishes from the predominant separation of PSI and PSII complexes in A. thaliana, indicating a different mode of flux balancing. Except for the core elements of the ATP synthase and the cytb6f-complex, the composition of the other complexes (PSI, PSII, and pigment-binding proteins, PBPs) of P. cordatum differed markedly from those of A. thaliana. Furthermore, a high number of PBPs was detected, accounting for a large share of the total proteomic data (∼65%) and potentially providing P. cordatum with flexible adaptation to changing light regimes.
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Affiliation(s)
- Jana Kalvelage
- School of Mathematics and Science, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg, Germany
| | - Lars Wöhlbrand
- School of Mathematics and Science, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg, Germany
| | - Jennifer Senkler
- Faculty of Natural Sciences, Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Julian Schumacher
- School of Mathematics and Science, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg, Germany
| | - Noah Ditz
- Faculty of Natural Sciences, Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Kai Bischof
- Faculty Biology/Chemistry, University of Bremen & MARUM, 28359 Bremen, Germany
| | - Michael Winklhofer
- School of Mathematics and Science, Institute of Biology and Environmental Sciences (IBU), Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg, Germany
- Research Center Neurosensory Science, School of Mathematics and Science, Carl von Ossietzky University of Oldenburg, 26129 Oldenburg, Germany
| | - Andreas Klingl
- Faculty of Biology, Botany, Ludwig-Maximilians-Universität LMU München, 82152 Planegg-Martinsried, Germany
| | - Hans-Peter Braun
- Faculty of Natural Sciences, Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Ralf Rabus
- School of Mathematics and Science, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg, Germany
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Novák Vanclová AM, Nef C, Füssy Z, Vancl A, Liu F, Bowler C, Dorrell RG. New plastids, old proteins: repeated endosymbiotic acquisitions in kareniacean dinoflagellates. EMBO Rep 2024; 25:1859-1885. [PMID: 38499810 PMCID: PMC11014865 DOI: 10.1038/s44319-024-00103-y] [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: 11/24/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 03/20/2024] Open
Abstract
Dinoflagellates are a diverse group of ecologically significant micro-eukaryotes that can serve as a model system for plastid symbiogenesis due to their susceptibility to plastid loss and replacement via serial endosymbiosis. Kareniaceae harbor fucoxanthin-pigmented plastids instead of the ancestral peridinin-pigmented ones and support them with a diverse range of nucleus-encoded plastid-targeted proteins originating from the haptophyte endosymbiont, dinoflagellate host, and/or lateral gene transfers (LGT). Here, we present predicted plastid proteomes from seven distantly related kareniaceans in three genera (Karenia, Karlodinium, and Takayama) and analyze their evolutionary patterns using automated tree building and sorting. We project a relatively limited ( ~ 10%) haptophyte signal pointing towards a shared origin in the family Chrysochromulinaceae. Our data establish significant variations in the functional distributions of these signals, emphasizing the importance of micro-evolutionary processes in shaping the chimeric proteomes. Analysis of plastid genome sequences recontextualizes these results by a striking finding the extant kareniacean plastids are in fact not all of the same origin, as two of the studied species (Karlodinium armiger, Takayama helix) possess plastids from different haptophyte orders than the rest.
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Affiliation(s)
- Anna Mg Novák Vanclová
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.
- Institute Jacques Monod, Paris, France.
| | - Charlotte Nef
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Zoltán Füssy
- Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Adél Vancl
- Faculty of Mathematics and Physics, Charles University, Prague, Czechia
| | - Fuhai Liu
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Centre de Recherches Interdisciplinaires, Paris, France
- Tsinghua-UC Berkeley Shenzhen Institute, Shenzhen, China
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Richard G Dorrell
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, Sorbonne Université, Paris, France.
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Joli N, Concia L, Mocaer K, Guterman J, Laude J, Guerin S, Sciandra T, Bruyant F, Ait-Mohamed O, Beguin M, Forget MH, Bourbousse C, Lacour T, Bailleul B, Nef C, Savoie M, Tremblay JE, Campbell DA, Lavaud J, Schwab Y, Babin M, Bowler C. Hypometabolism to survive the long polar night and subsequent successful return to light in the diatom Fragilariopsis cylindrus. THE NEW PHYTOLOGIST 2024; 241:2193-2208. [PMID: 38095198 DOI: 10.1111/nph.19387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/17/2023] [Indexed: 02/09/2024]
Abstract
Diatoms, the main eukaryotic phytoplankton of the polar marine regions, are essential for the maintenance of food chains specific to Arctic and Antarctic ecosystems, and are experiencing major disturbances under current climate change. As such, it is fundamental to understand the physiological mechanisms and associated molecular basis of their endurance during the long polar night. Here, using the polar diatom Fragilariopsis cylindrus, we report an integrative analysis combining transcriptomic, microscopic and biochemical approaches to shed light on the strategies used to survive the polar night. We reveal that in prolonged darkness, diatom cells enter a state of quiescence with reduced metabolic and transcriptional activity, during which no cell division occurs. We propose that minimal energy is provided by respiration and degradation of protein, carbohydrate and lipid stores and that homeostasis is maintained by autophagy in prolonged darkness. We also report internal structural changes that manifest the morphological acclimation of cells to darkness, including the appearance of a large vacuole. Our results further show that immediately following a return to light, diatom cells are able to use photoprotective mechanisms and rapidly resume photosynthesis, demonstrating the remarkable robustness of polar diatoms to prolonged darkness at low temperature.
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Affiliation(s)
- Nathalie Joli
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Lorenzo Concia
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Karel Mocaer
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL) & Collaboration for Joint PhD Degree between the European Molecular Biology Laboratory and the Heidelberg University, Faculty of Biosciences, 69117, Heidelberg, Germany
| | - Julie Guterman
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Juliette Laude
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Sebastien Guerin
- Takuvik International Research Laboratory, Université Laval (Canada) & CNRS (France), Département de Biologie and Québec-Océan, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Theo Sciandra
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Takuvik International Research Laboratory, Université Laval (Canada) & CNRS (France), Département de Biologie and Québec-Océan, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Flavienne Bruyant
- Takuvik International Research Laboratory, Université Laval (Canada) & CNRS (France), Département de Biologie and Québec-Océan, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Ouardia Ait-Mohamed
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Marine Beguin
- Takuvik International Research Laboratory, Université Laval (Canada) & CNRS (France), Département de Biologie and Québec-Océan, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Marie-Helene Forget
- Takuvik International Research Laboratory, Université Laval (Canada) & CNRS (France), Département de Biologie and Québec-Océan, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Clara Bourbousse
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Thomas Lacour
- Laboratoire PHYSiologie des micro ALGues (PDG-ODE-PHYTOX-PHYSALG), Centre Atlantique, 44 311, Nantes, France
| | - Benjamin Bailleul
- Laboratory of Chloroplast Biology and Light Sensing in Microalgae, Institut de Biologie Physico Chimique, CNRS, Sorbonne Université, Paris, 75005, France
| | - Charlotte Nef
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Mireille Savoie
- Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada
| | | | | | - Johann Lavaud
- Takuvik International Research Laboratory, Université Laval (Canada) & CNRS (France), Département de Biologie and Québec-Océan, Université Laval, Québec, QC, G1V 0A6, Canada
- UMR 6539 LEMAR-Laboratory of Environmental Marine Sciences, CNRS/Univ Brest/Ifremer/IRD, IUEM-Institut Européen de la Mer, Technopôle Brest-Iroise, rue Dumont d'Urville, 29280, Plouzané, France
| | - Yannick Schwab
- Cell Biology and Biophysics Unit and Electron Microscopy Core Facility, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Marcel Babin
- Takuvik International Research Laboratory, Université Laval (Canada) & CNRS (France), Département de Biologie and Québec-Océan, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
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12
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Truchon AR, Chase EE, Gann ER, Moniruzzaman M, Creasey BA, Aylward FO, Xiao C, Gobler CJ, Wilhelm SW. Kratosvirus quantuckense: the history and novelty of an algal bloom disrupting virus and a model for giant virus research. Front Microbiol 2023; 14:1284617. [PMID: 38098665 PMCID: PMC10720644 DOI: 10.3389/fmicb.2023.1284617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/30/2023] [Indexed: 12/17/2023] Open
Abstract
Since the discovery of the first "giant virus," particular attention has been paid toward isolating and culturing these large DNA viruses through Acanthamoeba spp. bait systems. While this method has allowed for the discovery of plenty novel viruses in the Nucleocytoviricota, environmental -omics-based analyses have shown that there is a wealth of diversity among this phylum, particularly in marine datasets. The prevalence of these viruses in metatranscriptomes points toward their ecological importance in nutrient turnover in our oceans and as such, in depth study into non-amoebal Nucleocytoviricota should be considered a focal point in viral ecology. In this review, we report on Kratosvirus quantuckense (née Aureococcus anophagefferens Virus), an algae-infecting virus of the Imitervirales. Current systems for study in the Nucleocytoviricota differ significantly from this virus and its relatives, and a litany of trade-offs within physiology, coding potential, and ecology compared to these other viruses reveal the importance of K. quantuckense. Herein, we review the research that has been performed on this virus as well as its potential as a model system for algal-virus interactions.
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Affiliation(s)
- Alexander R Truchon
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Emily E Chase
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Eric R Gann
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Surgical Critical Care Initiative (SC2i), Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, University of Miami, Miami, FL, United States
| | - Brooke A Creasey
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Chuan Xiao
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, United States
| | | | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
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Ding X, Liu J, Liu W, Dai S, Ke Z, Guo J, Lai Y, Tan Y. Phytoplankton Communities Miniaturization Driven by Extreme Weather in Subtropical Estuary under Climate Changes. WATER RESEARCH 2023; 245:120588. [PMID: 37716296 DOI: 10.1016/j.watres.2023.120588] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/18/2023]
Abstract
Estuarine ecosystems are subject to extreme weather and climatic events, particularly global climate change. To characterize the effects of extreme weather, such as heavy precipitation and cold waves, on phytoplankton communities, four seasonal cruises were conducted in the subtropical Pearl River Estuary. Among the main phytoplankton taxa, small (pico- and nano-sized) phytoplankton accounted for approximately 50% and 70% in the upstream estuary. In spring, summer, and autumn, small-sized phytoplankton communities were dominated by Chlorophyta (20-45%), Ochrophyta (Bacillariophyceae; 25-40%), and Dinoflagellata (20-25%), associated with high phytoplankton network stability and river discharge. In winter, small phytoplankton communities were dominated by Cryptophyta (50%), Dinoflagellata (25%), and Ochrophyta (Bacillariophyceae; 10%), which were associated with low network stability and temperature. Low light and high nutrient conditions induced by large river discharge favored the growth of the smallest known brackish Chlorophyta, such as Ostreococcus tauri. Low temperatures provided a competitive advantage for the survival of the small-sized cryptophyte genus Teleaulax, especially in the upstream estuary during the 2020/2021 extreme cold wave period. Our findings highlight the impact of extreme weather induced by climatic events on the miniaturization of phytoplankton communities in subtropical estuaries by altering temperature, light availability, and nutrient dynamics.
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Affiliation(s)
- Xiang Ding
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiaxing Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Weiwei Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Sheng Dai
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Zhixin Ke
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Jia Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanjiao Lai
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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14
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Laso-Jadart R, O'Malley M, Sykulski AM, Ambroise C, Madoui MA. Holistic view of the seascape dynamics and environment impact on macro-scale genetic connectivity of marine plankton populations. BMC Ecol Evol 2023; 23:46. [PMID: 37658324 PMCID: PMC10472650 DOI: 10.1186/s12862-023-02160-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Plankton seascape genomics studies have revealed different trends from large-scale weak differentiation to microscale structures. Previous studies have underlined the influence of the environment and seascape on species differentiation and adaptation. However, these studies have generally focused on a few single species, sparse molecular markers, or local scales. Here, we investigated the genomic differentiation of plankton at the macro-scale in a holistic approach using Tara Oceans metagenomic data together with a reference-free computational method. RESULTS We reconstructed the FST-based genomic differentiation of 113 marine planktonic taxa occurring in the North and South Atlantic Oceans, Southern Ocean, and Mediterranean Sea. These taxa belong to various taxonomic clades spanning Metazoa, Chromista, Chlorophyta, Bacteria, and viruses. Globally, population genetic connectivity was significantly higher within oceanic basins and lower in bacteria and unicellular eukaryotes than in zooplankton. Using mixed linear models, we tested six abiotic factors influencing connectivity, including Lagrangian travel time, as proxies of oceanic current effects. We found that oceanic currents were the main population genetic connectivity drivers, together with temperature and salinity. Finally, we classified the 113 taxa into parameter-driven groups and showed that plankton taxa belonging to the same taxonomic rank such as phylum, class or order presented genomic differentiation driven by different environmental factors. CONCLUSION Our results validate the isolation-by-current hypothesis for a non-negligible proportion of taxa and highlight the role of other physicochemical parameters in large-scale plankton genetic connectivity. The reference-free approach used in this study offers a new systematic framework to analyse the population genomics of non-model and undocumented marine organisms from a large-scale and holistic point of view.
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Affiliation(s)
- Romuald Laso-Jadart
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 3 rue Michel-Ange, Paris, France
| | - Michael O'Malley
- STOR-i Centre for Doctoral Training/Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
| | - Adam M Sykulski
- STOR-i Centre for Doctoral Training/Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
| | | | - Mohammed-Amin Madoui
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GO-SEE, 3 rue Michel-Ange, Paris, France.
- Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-Aux-Roses, France.
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, 21000, Dijon, France.
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15
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Kalvelage J, Wöhlbrand L, Schoon RA, Zink FM, Correll C, Senkler J, Eubel H, Hoppenrath M, Rhiel E, Braun HP, Winklhofer M, Klingl A, Rabus R. The enigmatic nucleus of the marine dinoflagellate Prorocentrum cordatum. mSphere 2023; 8:e0003823. [PMID: 37358287 PMCID: PMC10449503 DOI: 10.1128/msphere.00038-23] [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: 01/23/2023] [Accepted: 02/20/2023] [Indexed: 06/27/2023] Open
Abstract
The marine, bloom-forming dinoflagellate Prorocentrum cordatum CCMP 1329 (formerly P. minimum) has a genome atypical of eukaryotes, with a large size of ~4.15 Gbp, organized in plentiful, highly condensed chromosomes and packed in a dinoflagellate-specific nucleus (dinokaryon). Here, we apply microscopic and proteogenomic approaches to obtain new insights into this enigmatic nucleus of axenic P. cordatum. High-resolution focused ion beam/scanning electron microscopy analysis of the flattened nucleus revealed highest density of nuclear pores in the vicinity of the nucleolus, a total of 62 tightly packed chromosomes (~0.4-6.7 µm3), and interaction of several chromosomes with the nucleolus and other nuclear structures. A specific procedure for enriching intact nuclei was developed to enable proteomic analyses of soluble and membrane protein-enriched fractions. These were analyzed with geLC and shotgun approaches employing ion-trap and timsTOF (trapped-ion-mobility-spectrometry time-of-flight) mass spectrometers, respectively. This allowed identification of 4,052 proteins (39% of unknown function), out of which 418 were predicted to serve specific nuclear functions; additional 531 proteins of unknown function could be allocated to the nucleus. Compaction of DNA despite very low histone abundance could be accomplished by highly abundant major basic nuclear proteins (HCc2-like). Several nuclear processes including DNA replication/repair and RNA processing/splicing can be fairly well explained on the proteogenomic level. By contrast, transcription and composition of the nuclear pore complex remain largely elusive. One may speculate that the large group of potential nuclear proteins with currently unknown functions may serve yet to be explored functions in nuclear processes differing from those of typical eukaryotic cells. IMPORTANCE Dinoflagellates form a highly diverse group of unicellular microalgae. They provide keystone species for the marine ecosystem and stand out among others by their very large, unusually organized genomes embedded in the nuclei markedly different from other eukaryotic cells. Functional insights into nuclear and other cell biological structures and processes of dinoflagellates have long been hampered by the paucity of available genomic sequences. The here studied cosmopolitan P. cordatum belongs to the harmful algal bloom-forming, marine dinoflagellates and has a recently de novo assembled genome. We present a detailed 3D reconstruction of the P. cordatum nucleus together with comprehensive proteogenomic insights into the protein equipment mastering the broad spectrum of nuclear processes. This study significantly advances our understanding of mechanisms and evolution of the conspicuous dinoflagellate cell biology.
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Affiliation(s)
- Jana Kalvelage
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Robin-Alexander Schoon
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Fiona-Marine Zink
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Christina Correll
- Plant Development, Botany, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany
| | - Jennifer Senkler
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Holger Eubel
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Mona Hoppenrath
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences (IBU), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Wilhelmshaven, Germany
| | - Erhard Rhiel
- Planktology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Hans-Peter Braun
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Michael Winklhofer
- Sensory Biology of Animals, Institute of Biology and Environmental Sciences (IBU), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Research Center Neurosensory Science, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Andreas Klingl
- Plant Development, Botany, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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16
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Pencik O, Durdakova M, Molnarova K, Kucsera A, Klofac D, Kolackova M, Adam V, Huska D. Microplastics and nanoplastics toxicity assays: A revision towards to environmental-relevance in water environment. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131476. [PMID: 37172431 DOI: 10.1016/j.jhazmat.2023.131476] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/07/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023]
Abstract
Plastic pollution poses a serious risk to the oceans, freshwater ecosystems, and land-based agricultural production. Most plastic waste enters rivers and then reaches the oceans, where its fragmentation process begins and the forming of microplastics (MPs) and nanoplastics (NPs). These particles increase their toxicity by the exposition to external factors and binding environmental pollutants, including toxins, heavy metals, persistent organic pollutants (POPs), halogenated hydrocarbons (HHCs), and other chemicals, which further and cumulatively increase the toxicity of these particles. A major disadvantage of many MNPs in vitro studies is that they do not use environmentally relevant microorganisms, which play a vital role in geobiochemical cycles. In addition, factors such as the polymer type, shapes, and sizes of the MPs and NPs, their exposure times and concentrations must be taken into account in in vitro experiments. Last but not least, it is important to ask whether to use aged particles with bound pollutants. All these factors affect the predicted effects of these particles on living systems, which may not be realistic if they are insufficiently considered. In this article, we summarize the latest findings on MNPs in the environment and propose some recommendations for future in vitro experiments on bacteria, cyanobacteria, and microalgae in water ecosystems.
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Affiliation(s)
- Ondrej Pencik
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1665/1, 613 00 Brno, Czech Republic
| | - Michaela Durdakova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1665/1, 613 00 Brno, Czech Republic
| | - Katarina Molnarova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1665/1, 613 00 Brno, Czech Republic
| | - Attila Kucsera
- Department of Molecular Biology and Radiobiology, Mendel University in Brno, Zemědělská 1665/1, 613 00 Brno, Czech Republic
| | - Daniel Klofac
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Zemědělská 1665/1, 613 00 Brno, Czech Republic
| | - Martina Kolackova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1665/1, 613 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1665/1, 613 00 Brno, Czech Republic
| | - Dalibor Huska
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1665/1, 613 00 Brno, Czech Republic.
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17
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Dobretsov S, Rittschof D. "Omics" Techniques Used in Marine Biofouling Studies. Int J Mol Sci 2023; 24:10518. [PMID: 37445696 DOI: 10.3390/ijms241310518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Biofouling is the growth of organisms on wet surfaces. Biofouling includes micro- (bacteria and unicellular algae) and macrofouling (mussels, barnacles, tube worms, bryozoans, etc.) and is a major problem for industries. However, the settlement and growth of some biofouling species, like oysters and corals, can be desirable. Thus, it is important to understand the process of biofouling in detail. Modern "omic" techniques, such as metabolomics, metagenomics, transcriptomics, and proteomics, provide unique opportunities to study biofouling organisms and communities and investigate their metabolites and environmental interactions. In this review, we analyze the recent publications that employ metagenomic, metabolomic, and proteomic techniques for the investigation of biofouling and biofouling organisms. Specific emphasis is given to metagenomics, proteomics and publications using combinations of different "omics" techniques. Finally, this review presents the future outlook for the use of "omics" techniques in marine biofouling studies. Like all trans-disciplinary research, environmental "omics" is in its infancy and will advance rapidly as researchers develop the necessary expertise, theory, and technology.
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Affiliation(s)
- Sergey Dobretsov
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoud 123, Muscat P.O. Box 34, Oman
| | - Daniel Rittschof
- Nicholas School of the Environment, Duke University, Beaufort, NC 28516, USA
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18
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Chen H, Barton S, Yang M, Rickaby REM, Bouman HA, Compton RG. AI facilitated fluoro-electrochemical phytoplankton classification. Chem Sci 2023; 14:5872-5879. [PMID: 37293636 PMCID: PMC10246652 DOI: 10.1039/d3sc01741a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/02/2023] [Indexed: 06/10/2023] Open
Abstract
Marine phytoplankton is extremely diverse. Counting and characterising phytoplankton is essential for understanding climate change and ocean health not least since phytoplankton extensively biomineralize carbon dioxide whilst generating 50% of the planet's oxygen. We report the use of fluoro-electrochemical microscopy to distinguish different taxonomies of phytoplankton by the quenching of their chlorophyll-a fluorescence using chemical species oxidatively electrogenerated in situ in seawater. The rate of chlorophyll-a quenching of each cell is characteristic of the species-specific structural composition and cellular content. But with increasing diversity and extent of phytoplankton species under study, human interpretation and distinction of the resulting fluorescence transients becomes increasingly and prohibitively difficult. Thus, we further report a neural network to analyse these fluorescence transients, with an accuracy >95% classifying 29 phytoplankton strains to their taxonomic orders. This method transcends the state-of-the-art. The success of the fluoro-electrochemical microscopy combined with AI provides a novel, flexible and highly granular solution to phytoplankton classification and is adaptable for autonomous ocean monitoring.
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Affiliation(s)
- Haotian Chen
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Samuel Barton
- Department of Earth Sciences, University of Oxford South Parks Road Oxford OX1 3AN UK
| | - Minjun Yang
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Rosalind E M Rickaby
- Department of Earth Sciences, University of Oxford South Parks Road Oxford OX1 3AN UK
| | - Heather A Bouman
- Department of Earth Sciences, University of Oxford South Parks Road Oxford OX1 3AN UK
| | - Richard G Compton
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
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Akcaalan R, Ozbayram EG, Kaleli A, Cam AO, Koker L, Albay M. Does environmental DNA reflect the actual phytoplankton diversity in the aquatic environment? Case study of marine mucilage in the Sea of Marmara. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27528-7. [PMID: 37178301 DOI: 10.1007/s11356-023-27528-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
The present study was designed to assess the effectiveness of the eDNA metabarcoding approach to determine the phytoplankton composition in the marine environment with a special focus on mucilage episodes in the Sea of Marmara. For this purpose, the samples were collected from 5 different sites located in the Sea of Marmara and the northern Aegean Sea during the mucilage episode in June 2021. The phytoplankton diversity was analyzed morphologically and by 18S rRNA gene amplicon sequencing, and the dataset of both methods was compared, accordingly. The results showed significant differences between methods in terms of composition and the abundance of the phytoplankton groups. While Miozoa was the most abundant group by metabarcoding, light microscopy (LM) indicated a dominance of Bacillariophyta. Katablepharidophyta was found at lower abundances by the metabarcoding (representing < 1% of the community); the members of this phylum were not observed by a microscope. At the lower taxonomic levels, Chaetoceros was the only genus detected in all samples by both methods. Additionally, while mucilage-forming Gonyaulax fragilis, Cylindrotheca closterium, and Thalassiosira rotula were detected to species-level by LM, metabarcoding was able to determine these organisms at the genus level. On the other hand, the genus Arcocellulus was found in all metabarcoding datasets and not detected by microscopy. The results indicated that metabarcoding can detect a greater number of genera and reveal taxa that were overlooked by light microscopy but to develop a complete picture of phytoplankton diversity in the sample, microscopical observations still are in need.
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Affiliation(s)
- Reyhan Akcaalan
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey.
| | - Emine Gozde Ozbayram
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
| | - Aydın Kaleli
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
| | - Ayca Oguz Cam
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
| | - Latife Koker
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
| | - Meric Albay
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
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20
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Chu M, Zhang X. Alien species invasion of deep-sea bacteria into mouse gut microbiota. J Adv Res 2023; 45:101-115. [PMID: 35690372 PMCID: PMC10006512 DOI: 10.1016/j.jare.2022.05.011] [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: 03/22/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 11/28/2022] Open
Abstract
INTRODUCTION Deep sea has numerous bacteria which dominate in the biomass of deep-sea sediments. Some deep-sea bacteria may possess the capacity to destroy mammal health by the alteration of gut microbiota, acting as potential pathogens. OBJECTIVES Pathogenic bacteria are great threats to human health. However, the ultimate origin of pathogenic bacteria has not been intensively explored. In this study, therefore, the influence of deep-sea bacteria on the gut microbiota was evaluated on a global scale. METHODS The bacteria isolated from each of 106 deep-sea sediment samples were transplanted into mice in our study to assess the infectiousness of deep-sea bacteria. RESULTS The results showed that some bacteria from deep sea, an area that has existed since the earth was formed, could proliferate in mouse gut. Based on the infectious evaluation of the bacteria from each of 106 deep-sea sediments, the bacteria isolated from 13 sediments invaded the gut bacterial communities of mice, leading to the significant alteration of mouse gut microbiota. Among the 13 deep-sea sediments, the bacteria isolated from 9 sediments could destroy mouse health by inducing glucose metabolism deterioration, liver damage and inflammatory symptom. As an example, a bacterium was isolated from deep-sea sediment DP040, which was identified to be Bacillus cereus (termed as Bacillus cereus DP040). Bacillus cereus DP040 could invade the gut microbiota of mice to change the gut microbial structure, leading to inflammatory symptom of mice. The deep-sea sediments containing the bacteria destroying the health of mice were distributed in hydrothermal vent, mid-ocean ridge and hadal trench of the Indian Ocean, the Atlantic Ocean and the Pacific Ocean. CONCLUSION Our findings demonstrate that deep sea is an important origin of potential pathogenic bacteria and provide the first biosecurity insight into the alien species invasion of deep-sea bacteria into mammal gut microbiota.
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Affiliation(s)
- Mengqi Chu
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Xiaobo Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People's Republic of China.
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21
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Zheng X, Xu K, Naoum J, Lian Y, Wu B, He Z, Yan Q. Deciphering microeukaryotic-bacterial co-occurrence networks in coastal aquaculture ponds. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:44-55. [PMID: 37073331 PMCID: PMC10077187 DOI: 10.1007/s42995-022-00159-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 12/06/2022] [Indexed: 05/03/2023]
Abstract
Microeukaryotes and bacteria are key drivers of primary productivity and nutrient cycling in aquaculture ecosystems. Although their diversity and composition have been widely investigated in aquaculture systems, the co-occurrence bipartite network between microeukaryotes and bacteria remains poorly understood. This study used the bipartite network analysis of high-throughput sequencing datasets to detect the co-occurrence relationships between microeukaryotes and bacteria in water and sediment from coastal aquaculture ponds. Chlorophyta and fungi were dominant phyla in the microeukaryotic-bacterial bipartite networks in water and sediment, respectively. Chlorophyta also had overrepresented links with bacteria in water. Most microeukaryotes and bacteria were classified as generalists, and tended to have symmetric positive and negative links with bacteria in both water and sediment. However, some microeukaryotes with high density of links showed asymmetric links with bacteria in water. Modularity detection in the bipartite network indicated that four microeukaryotes and twelve uncultured bacteria might be potential keystone taxa among the module connections. Moreover, the microeukaryotic-bacterial bipartite network in sediment harbored significantly more nestedness than that in water. The loss of microeukaryotes and generalists will more likely lead to the collapse of positive co-occurrence relationships between microeukaryotes and bacteria in both water and sediment. This study unveils the topology, dominant taxa, keystone species, and robustness in the microeukaryotic-bacterial bipartite networks in coastal aquaculture ecosystems. These species herein can be applied for further management of ecological services, and such knowledge may also be very useful for the regulation of other eutrophic ecosystems. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00159-6.
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Affiliation(s)
- Xiafei Zheng
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, 315100 China
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Kui Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization Technology, College of Life Sciences, Hubei Normal University, Huangshi, 435002 China
| | - Jonathan Naoum
- Department of Biological Sciences, Ecotoxicology of Aquatic Microorganisms Laboratory, GRIL-EcotoQ-TOXEN, Université Du Québec À Montréal, Succursale Centre-Ville, Montreal, QC Canada
| | - Yingli Lian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
- Animal Husbandry and Fisheries Research Center of Guangdong Haid Group CO., Ltd. Key Laboratory of Microecological Resources and Utilization in Breeding Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, 510006 China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
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22
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Edwards KF, Li Q, McBeain KA, Schvarcz CR, Steward GF. Trophic strategies explain the ocean niches of small eukaryotic phytoplankton. Proc Biol Sci 2023; 290:20222021. [PMID: 36695036 PMCID: PMC9874276 DOI: 10.1098/rspb.2022.2021] [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] [Indexed: 01/26/2023] Open
Abstract
A large fraction of marine primary production is performed by diverse small protists, and many of these phytoplankton are phagotrophic mixotrophs that vary widely in their capacity to consume bacterial prey. Prior analyses suggest that mixotrophic protists as a group vary in importance across ocean environments, but the mechanisms leading to broad functional diversity among mixotrophs, and the biogeochemical consequences of this, are less clear. Here we use isolates from seven major taxa to demonstrate a tradeoff between phototrophic performance (growth in the absence of prey) and phagotrophic performance (clearance rate when consuming Prochlorococcus). We then show that trophic strategy along the autotrophy-mixotrophy spectrum correlates strongly with global niche differences, across depths and across gradients of stratification and chlorophyll a. A model of competition shows that community shifts can be explained by greater fitness of faster-grazing mixotrophs when nutrients are scarce and light is plentiful. Our results illustrate how basic physiological constraints and principles of resource competition can organize complexity in the surface ocean ecosystem.
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Affiliation(s)
- Kyle F. Edwards
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
| | - Qian Li
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA,Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA,School of Oceanography, Shanghai Jiao Tong University, 1954 Huashan Rd, Shanghai Shi, Xuhui Qu 200240, China
| | - Kelsey A. McBeain
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
| | - Christopher R. Schvarcz
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA,Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
| | - Grieg F. Steward
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA,Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
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23
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Different Geographic Strains of Dinoflagellate Karlodinium veneficum Host Highly Diverse Fungal Community and Potentially Serve as Possible Niche for Colonization of Fungal Endophytes. Int J Mol Sci 2023; 24:ijms24021672. [PMID: 36675187 PMCID: PMC9865425 DOI: 10.3390/ijms24021672] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/03/2023] [Accepted: 01/08/2023] [Indexed: 01/18/2023] Open
Abstract
In numerous studies, researchers have explored the interactions between fungi and their hosting biota in terrestrial systems, while much less attention has been paid to the counterpart interactions in aquatic, and particularly marine, ecosystems. Despite the growing recognition of the potential functions of fungi in structuring phytoplankton communities, the current insights were mostly derived from phytoplankton hosts, such as diatoms, green microalgae, and cyanobacteria. Dinoflagellates are the second most abundant group of phytoplankton in coastal marine ecosystems, and they are notorious for causing harmful algal blooms (HABs). In this study, we used high-throughput amplicon sequencing to capture global snapshots of specific fungal assemblages associated with laboratory-cultured marine dinoflagellate. We investigated a total of 13 clonal cultures of the dinoflagellate Karlodinium veneficum that were previously isolated from 5 geographic origins and have been maintained in our laboratory from several months to more than 14 years. The total recovered fungal microbiome, which consisted of 349 ASVs (amplicon sequencing variants, sequences clustered at a 100% sequence identity), could be assigned to 4 phyla, 18 classes, 37 orders, 65 families, 97 genera, and 131 species. The fungal consortium displayed high diversity and was dominated by filamentous fungi and ascomycetous and basidiomycetous yeasts. A core set of three genera among all the detected fungi was constitutively present in the K. veneficum strains isolated from geographically distant regions, with the top two most abundant genera, Thyridium and Pseudeurotium, capable of using hydrocarbons as the sole or major source of carbon and energy. In addition, fungal taxa previously documented as endophytes in other hosts were also found in all tested strains of K. veneficum. Because host-endophyte interactions are highly variable and strongly case-dependent, these fungal taxa were not necessarily genuine endosymbionts of K. veneficum; instead, it raised the possibility that dinoflagellates could potentially serve as an alternative ecological niche for the colonization of fungal endophytes. Our findings lay the foundation for further investigations into the potential roles or functions of fungi in the regulation of the growth dynamics and HABs of marine dinoflagellates in the field.
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24
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Li W, Wang B, Xiao J, Yang M, Xu S, Liu CQ. Phytoplankton cell size control can be affected by photosynthetic light energy utilization. Front Microbiol 2022; 13:1008606. [PMID: 36406451 PMCID: PMC9667819 DOI: 10.3389/fmicb.2022.1008606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/06/2022] [Indexed: 11/28/2022] Open
Abstract
Phytoplankton cell size is well known as an essential functional trait, but its control factors are still unclear. Considering light provides the necessary energy for phytoplankton survival, we hypothesized that photosynthetic light energy utilization could influence phytoplankton cell size control. Several scenarios were conducted to understand the relationship between Fv /Fm and cell size for phytoplankton interspecies, and metatranscriptome in the field and transcriptome in the laboratory were used to understand relevant molecular mechanisms. The results indicated that there was a universal significant positive relationship between Fv /Fm and cell volume in general. The molecular evidence demonstrated that light utilization by phytoplankton regulates their cell size by harmonizing the generation and allocation of chemical energy and fixed carbon in the cell. Phytoplankton cell size would cease to enlarge once the increased light energy conversion and subsequent fixed carbon could no longer satisfy the increasing demand of size enlargement. This unity of energy and matter in shaping phytoplankton size results in cell size being an important functional trait. This study is the first to discover the above molecular mechanisms and is helpful to deepen the understanding on the cell size control of phytoplankton.
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25
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The Porifera microeukaryome: Addressing the neglected associations between sponges and protists. Microbiol Res 2022; 265:127210. [PMID: 36183422 DOI: 10.1016/j.micres.2022.127210] [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: 05/02/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/22/2022]
Abstract
While bacterial and archaeal communities of sponges are intensively studied, given their importance to the animal's physiology as well as sources of several new bioactive molecules, the potential and roles of associated protists remain poorly known. Historically, culture-dependent approaches dominated the investigations of sponge-protist interactions. With the advances in omics techniques, these associations could be visualized at other equally important scales. Of the few existing studies, there is a strong tendency to focus on interactions with photosynthesizing taxa such as dinoflagellates and diatoms, with fewer works dissecting the interactions with other less common groups. In addition, there are bottlenecks and inherent biases in using primer pairs and bioinformatics approaches in the most commonly used metabarcoding studies. Thus, this review addresses the issues underlying this association, using the term "microeukaryome" to refer exclusively to protists associated with an animal host. We aim to highlight the diversity and community composition of protists associated with sponges and place them on the same level as other microorganisms already well studied in this context. Among other shortcomings, it could be observed that the biotechnological potential of the microeukaryome is still largely unexplored, possibly being a valuable source of new pharmacological compounds, enzymes and metabolic processes.
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26
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Kim J, Armin G, Inomura K. Saturating relationship between phytoplankton growth rate and nutrient concentration explained by macromolecular allocation. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100167. [PMID: 36518172 PMCID: PMC9742995 DOI: 10.1016/j.crmicr.2022.100167] [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: 04/13/2022] [Revised: 08/22/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Phytoplankton account for about a half of photosynthesis in the world, making them a key player in the ecological and biogeochemical systems. One of the key traits of phytoplankton is their growth rate because it indicates their productivity and affects their competitive capability. The saturating relationship between phytoplankton growth rate and environmental nutrient concentration has been widely observed yet the mechanisms behind the relationship remain elusive. Here we use a mechanistic model and metadata of phytoplankton to show that the saturating relationship between growth rate and nitrate concentration can be interpreted by intracellular macromolecular allocation. At low nitrate levels, the diffusive nitrate transport linearly increases with the nitrate concentration, while the internal nitrogen requirement increases with the growth rate, leading to a non-linear increase in the growth rate with nitrate. This increased nitrogen requirement is due to the increased allocation to biosynthetic and photosynthetic molecules. The allocation to these molecules reaches a maximum at high nitrate concentration and the growth rate ceases to increase despite high nitrate availability due to carbon limitation. The produced growth rate and nitrate relationships are consistent with the data of phytoplankton across taxa. Our study provides a macromolecular interpretation of the widely observed growth-nutrient relationship and highlights that the key control of the phytoplankton growth exists within the cell.
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Affiliation(s)
- Jongsun Kim
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Gabrielle Armin
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
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27
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Bai Y, Cao T, Dautermann O, Buschbeck P, Cantrell MB, Chen Y, Lein CD, Shi X, Ware MA, Yang F, Zhang H, Zhang L, Peers G, Li X, Lohr M. Green diatom mutants reveal an intricate biosynthetic pathway of fucoxanthin. Proc Natl Acad Sci U S A 2022; 119:e2203708119. [PMID: 36095219 PMCID: PMC9499517 DOI: 10.1073/pnas.2203708119] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/08/2022] [Indexed: 01/17/2023] Open
Abstract
Fucoxanthin is a major light-harvesting pigment in ecologically important algae such as diatoms, haptophytes, and brown algae (Phaeophyceae). Therefore, it is a major driver of global primary productivity. Species of these algal groups are brown colored because the high amounts of fucoxanthin bound to the proteins of their photosynthetic machineries enable efficient absorption of green light. While the structure of these fucoxanthin-chlorophyll proteins has recently been resolved, the biosynthetic pathway of fucoxanthin is still unknown. Here, we identified two enzymes central to this pathway by generating corresponding knockout mutants of the diatom Phaeodactylum tricornutum that are green due to the lack of fucoxanthin. Complementation of the mutants with the native genes or orthologs from haptophytes restored fucoxanthin biosynthesis. We propose a complete biosynthetic path to fucoxanthin in diatoms and haptophytes based on the carotenoid intermediates identified in the mutants and in vitro biochemical assays. It is substantially more complex than anticipated and reveals diadinoxanthin metabolism as the central regulatory hub connecting the photoprotective xanthophyll cycle and the formation of fucoxanthin. Moreover, our data show that the pathway evolved by repeated duplication and neofunctionalization of genes for the xanthophyll cycle enzymes violaxanthin de-epoxidase and zeaxanthin epoxidase. Brown algae lack diadinoxanthin and the genes described here and instead use an alternative pathway predicted to involve fewer enzymes. Our work represents a major step forward in elucidating the biosynthesis of fucoxanthin and understanding the evolution, biogenesis, and regulation of the photosynthetic machinery in algae.
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Affiliation(s)
- Yu Bai
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878
| | - Tianjun Cao
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Oliver Dautermann
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität, 55099 Mainz, Germany
| | - Paul Buschbeck
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität, 55099 Mainz, Germany
| | - Michael B. Cantrell
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878
| | - Yinjuan Chen
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Instrumentation and Service Center for Molecular Sciences, Westlake University, Hangzhou 310024, China
| | - Christopher D. Lein
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität, 55099 Mainz, Germany
| | - Xiaohuo Shi
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Instrumentation and Service Center for Molecular Sciences, Westlake University, Hangzhou 310024, China
| | - Maxwell A. Ware
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878
| | - Fenghua Yang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Huan Zhang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Lihan Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, Hangzhou 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Graham Peers
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878
| | - Xiaobo Li
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Martin Lohr
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität, 55099 Mainz, Germany
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28
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DNA metabarcoding data reveals harmful algal-bloom species undescribed previously at the northern Antarctic Peninsula region. Polar Biol 2022. [DOI: 10.1007/s00300-022-03084-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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29
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Wang Y, Wang J, Chen Y, Liu S, Zhao Y, Chen N. Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10024. [PMID: 36011659 PMCID: PMC9408514 DOI: 10.3390/ijerph191610024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/07/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
The Bacillariophyceae is a species-rich, ecologically significant class of Bacillariophyta. Despite their critical importance in marine ecosystems as primary producers and in the development of harmful algal blooms (HABs), taxonomic research on Bacillariophyceae species has been hindered because of their limited morphological features, plasticity of morphologies, and the low resolution of common molecular markers. Hence molecular markers with improved resolution are urgently needed. Organelle genomes, which can be constructed efficiently with the recent development of high throughput DNA sequencing technologies and the advancement of bioinformatics tools, have been proposed as super barcodes for their higher resolution for distinguishing different species and intra-species genomic variations. In this study, we tested the value of full-length chloroplast genomes (cpDNAs) as super barcodes for distinguishing diatom species, by constructing cpDNAs of 11 strains of the class Bacillariophyceae, including Nitzschia ovalis, Nitzschia traheaformis, Cylindrotheca spp., Psammodictyon constrictum, Bacillaria paxillifer, two strains of Haslea tsukamotoi, Haslea avium, Navicula arenaria, and Pleurosigma sp. Comparative analysis of cpDNAs revealed that cpDNAs were not only adequate for resolving different species, but also for enabling recognition of high levels of genome rearrangements between cpDNAs of different species, especially for species of the genera Nitzschia, Cylindrotheca, Navicula and Haslea. Additionally, comparative analysis suggested that the positioning of species in the genus Haslea should be transferred to the genus Navicula. Chloroplast genome-based evolutionary analysis suggested that the Bacillariophyceae species first appeared during the Cretaceous period and the diversity of species rose after the mass extinction about 65 Mya. This study highlighted the value of cpDNAs in research on the biodiversity and evolution of Bacillariophyceae species, and, with the construction of more cpDNAs representing additional genera, deeper insight into the biodiversity and evolutionary relationships of Bacillariophyceae species will be gained.
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Affiliation(s)
- Yichao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jing Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shuya Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yongfang Zhao
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
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30
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Zhang Z, Li H, Shen W, Du X, Li S, Wei Z, Zhang Z, Feng K, Deng Y. The large-scale spatial patterns of ecological networks between phytoplankton and zooplankton in coastal marine ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154285. [PMID: 35248637 DOI: 10.1016/j.scitotenv.2022.154285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/22/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Although autotrophic phytoplankton and heterotrophic zooplankton both play important roles in the food web of marine ecosystem, their comprehensive interactions and spatial patterns at continental scale remain poorly studied. Here, we collected 251 seawater samples along 13,000 km of Chinese coastline, and microscopically investigated the latitudinal gradients of planktonic diversities. In total, 307 phytoplanktonic and 311 zooplanktonic species were visually identified. Using the newly developed Inter-Domain Ecological Networks (IDENs) approach, the phytoplankton-zooplankton interaction networks were constructed. We found that the phyto-zooplankton network structure was varied across three regions, more complex and numerous connections along the southern coast than in the north. In addition, some particular associations between zooplanktonic and phytoplanktonic groups were found to be localized in specific regions. Furthermore, the seawater temperature and salinity were the major driving force for shaping planktonic interaction networks. These results provide a deeper understanding of planktonic biogeography and phytoplankton-zooplankton interaction patterns.
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Affiliation(s)
- Zheng Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Wenli Shen
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Xiongfeng Du
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shuzhen Li
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Ziyan Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhaojing Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.
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31
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Broad phylogenetic and functional diversity among mixotrophic consumers of Prochlorococcus. THE ISME JOURNAL 2022; 16:1557-1569. [PMID: 35145244 PMCID: PMC9122939 DOI: 10.1038/s41396-022-01204-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 11/26/2022]
Abstract
Small eukaryotic phytoplankton are major contributors to global primary production and marine biogeochemical cycles. Many taxa are thought to be mixotrophic, but quantitative studies of phagotrophy exist for very few. In addition, little is known about consumers of Prochlorococcus, the abundant cyanobacterium at the base of oligotrophic ocean food webs. Here we describe thirty-nine new phytoplankton isolates from the North Pacific Subtropical Gyre (Station ALOHA), all flagellates ~2–5 µm diameter, and we quantify their ability to graze Prochlorococcus. The mixotrophs are from diverse classes (dictyochophytes, haptophytes, chrysophytes, bolidophytes, a dinoflagellate, and a chlorarachniophyte), many from previously uncultured clades. Grazing ability varied substantially, with specific clearance rate (volume cleared per body volume) varying over ten-fold across isolates and six-fold across genera. Slower grazers tended to create more biovolume per prey biovolume consumed. Using qPCR we found that the haptophyte Chrysochromulina was most abundant among the isolated mixotrophs at Station ALOHA, with 76–250 cells mL−1 across depths in the upper euphotic zone (5–100 m). Our results show that within a single ecosystem the phototrophs that ingest bacteria come from many branches of the eukaryotic tree, and are functionally diverse, indicating a broad range of strategies along the spectrum from phototrophy to phagotrophy.
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32
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Xie ZX, Yan KQ, Kong LF, Gai YB, Jin T, He YB, Wang YY, Chen F, Lin L, Lin ZL, Xu HK, Shao ZZ, Liu SQ, Wang DZ. Metabolic tuning of a stable microbial community in the surface oligotrophic Indian Ocean revealed by integrated meta-omics. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:277-290. [PMID: 37073226 PMCID: PMC10077294 DOI: 10.1007/s42995-021-00119-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/25/2021] [Indexed: 05/03/2023]
Abstract
Understanding the mechanisms, structuring microbial communities in oligotrophic ocean surface waters remains a major ecological endeavor. Functional redundancy and metabolic tuning are two mechanisms that have been proposed to shape microbial response to environmental forcing. However, little is known about their roles in the oligotrophic surface ocean due to less integrative characterization of community taxonomy and function. Here, we applied an integrated meta-omics-based approach, from genes to proteins, to investigate the microbial community of the oligotrophic northern Indian Ocean. Insignificant spatial variabilities of both genomic and proteomic compositions indicated a stable microbial community that was dominated by Prochlorococcus, Synechococcus, and SAR11. However, fine tuning of some metabolic functions that are mainly driven by salinity and temperature was observed. Intriguingly, a tuning divergence occurred between metabolic potential and activity in response to different environmental perturbations. Our results indicate that metabolic tuning is an important mechanism for sustaining the stability of microbial communities in oligotrophic oceans. In addition, integrated meta-omics provides a powerful tool to comprehensively understand microbial behavior and function in the ocean. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-021-00119-6.
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Affiliation(s)
- Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005 China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005 China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Zhuhai, 519082 China
| | - Ke-Qiang Yan
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Shenzhen, 518083 China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083 China
| | - Ling-Fen Kong
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005 China
| | - Ying-Bao Gai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, 361005 China
- State Key Laboratory Breeding Base of Marine Genetic Resources/Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005 China
| | - Tao Jin
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Shenzhen, 518083 China
| | - Yan-Bin He
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Shenzhen, 518083 China
| | - Ya-Yu Wang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Shenzhen, 518083 China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202 USA
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005 China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Zhuhai, 519082 China
| | - Zhi-Long Lin
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Shenzhen, 518083 China
| | - Hong-Kai Xu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Shenzhen, 518083 China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083 China
| | - Zong-Ze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, Xiamen, 361005 China
- State Key Laboratory Breeding Base of Marine Genetic Resources/Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005 China
| | - Si-Qi Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Shenzhen, 518083 China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005 China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Zhuhai, 519082 China
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Wang Y, Liu S, Wang J, Yao Y, Chen Y, Xu Q, Zhao Z, Chen N. Diatom Biodiversity and Speciation Revealed by Comparative Analysis of Mitochondrial Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:749982. [PMID: 35401648 PMCID: PMC8987724 DOI: 10.3389/fpls.2022.749982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically significant groups of phytoplankton, comprising 100,000-200,000 species in three classes Bacillariophyceae, Mediophyceae, and Coscinodiscophyceae. However, due to the limited resolution of common molecular markers including 18S rDNA, 28S rDNA, ITS, rbcL, and cox1, diatom biodiversity has not been adequately ascertained. Organelle genomes including mitochondrial genomes (mtDNAs) have been proposed to be "super barcodes" for distinguishing diatom species because of their rich genomic content, and the rapid progress of DNA sequencing technologies that has made it possible to construct mtDNAs with increasing throughout and decreasing cost. Here, we constructed complete mtDNAs of 15 diatom species including five Coscinodiscophyceae species (Guinardia delicatula, Guinardia striata, Stephanopyxis turris, Paralia sulcata, and Actinocyclus sp.), four Mediophyceae species (Hemiaulus sinensis, Odontella aurita var. minima, Lithodesmioides sp., and Helicotheca tamesis), and six Bacillariophyceae species (Nitzschia ovalis, Nitzschia sp., Nitzschia traheaformis, Cylindrotheca closterium, Haslea tsukamotoi, and Pleurosigma sp.) to test the practicality of using mtDNAs as super barcodes. We found that mtDNAs have much higher resolution compared to common molecular markers as expected. Comparative analysis of mtDNAs also suggested that mtDNAs are valuable in evolutionary studies by revealing extensive genome rearrangement events with gene duplications, gene losses, and gains and losses of introns. Synteny analyses of mtDNAs uncovered high conservation among species within an order, but extensive rearrangements including translocations and/or inversions between species of different orders within a class. Duplication of cox1 was discovered for the first time in diatoms in Nitzschia traheaformis and Haslea tsukamotoi. Molecular dating analysis revealed that the three diatom classes split 100 Mya and many diatom species appeared since 50 Mya. In conclusion, more diatom mtDNAs representing different orders will play great dividends to explore biodiversity and speciation of diatoms in different ecological regions.
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Affiliation(s)
- Yichao Wang
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Planetary and Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Shuya Liu
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jing Wang
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yanxin Yao
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Planetary and Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yang Chen
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Planetary and Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Qing Xu
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zengxia Zhao
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Nansheng Chen
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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34
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Pierella Karlusich JJ, Pelletier E, Zinger L, Lombard F, Zingone A, Colin S, Gasol JM, Dorrell RG, Henry N, Scalco E, Acinas SG, Wincker P, de Vargas C, Bowler C. A robust approach to estimate relative phytoplankton cell abundances from metagenomes. Mol Ecol Resour 2022; 23:16-40. [PMID: 35108459 PMCID: PMC10078663 DOI: 10.1111/1755-0998.13592] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022]
Abstract
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.
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Affiliation(s)
- Juan José Pierella Karlusich
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Eric Pelletier
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Fabien Lombard
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Océanographie de Villefranche (LOV), 06230, Villefranche-sur-Mer, France.,Institut Universitaire de France (IUF), Paris, France
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Sébastien Colin
- European Molecular Biology Laboratory, Heidelberg, Germany.,Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, 29680, Roscoff, France.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Richard G Dorrell
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France
| | - Nicolas Henry
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Patrick Wincker
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Colomban de Vargas
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, 29680, Roscoff, France
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
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35
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Le Reun N, Bramucci A, O’Brien J, Ostrowski M, Brown MV, Van de Kamp J, Bodrossy L, Raina JB, Ajani P, Seymour J. Diatom Biogeography, Temporal Dynamics, and Links to Bacterioplankton across Seven Oceanographic Time-Series Sites Spanning the Australian Continent. Microorganisms 2022; 10:microorganisms10020338. [PMID: 35208793 PMCID: PMC8880096 DOI: 10.3390/microorganisms10020338] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 11/30/2022] Open
Abstract
Diatom communities significantly influence ocean primary productivity and carbon cycling, but their spatial and temporal dynamics are highly heterogeneous and are governed by a complex diverse suite of abiotic and biotic factors. We examined the seasonal and biogeographical dynamics of diatom communities in Australian coastal waters using amplicon sequencing data (18S-16S rRNA gene) derived from a network of oceanographic time-series spanning the Australian continent. We demonstrate that diatom community composition in this region displays significant biogeography, with each site harbouring distinct community structures. Temperature and nutrients were identified as the key environmental contributors to differences in diatom communities at all sites, collectively explaining 21% of the variability observed in diatoms assemblages. However, specific groups of bacteria previously implicated in mutualistic ecological interactions with diatoms (Rhodobacteraceae, Flavobacteriaceae and Alteromonadaceae) also explained a further 4% of the spatial dynamics observed in diatom community structure. We also demonstrate that the two most temperate sites (Port Hacking and Maria Island) exhibited strong seasonality in diatom community and that at these sites, winter diatom communities co-occurred with higher proportion of Alteromonadaceae. In addition, we identified significant co-occurrence between specific diatom and bacterial amplicon sequence variants (ASVs), with members of the Roseobacter and Flavobacteria clades strongly correlated with some of the most abundant diatom genera (Skeletonema, Thalassiosira, and Cylindrotheca). We propose that some of these co-occurrences might be indicative of ecologically important interactions between diatoms and bacteria. Our analyses reveal that in addition to physico-chemical conditions (i.e., temperature, nutrients), the relative abundance of specific groups of bacteria appear to play an important role in shaping the spatial and temporal dynamics of marine diatom communities.
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Affiliation(s)
- Nine Le Reun
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (N.L.R.); (A.B.); (J.O.); (M.O.); (J.-B.R.)
| | - Anna Bramucci
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (N.L.R.); (A.B.); (J.O.); (M.O.); (J.-B.R.)
| | - James O’Brien
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (N.L.R.); (A.B.); (J.O.); (M.O.); (J.-B.R.)
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (N.L.R.); (A.B.); (J.O.); (M.O.); (J.-B.R.)
| | - Mark V. Brown
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia;
| | - Jodie Van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia; (J.V.d.K.); (L.B.)
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia; (J.V.d.K.); (L.B.)
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (N.L.R.); (A.B.); (J.O.); (M.O.); (J.-B.R.)
| | - Penelope Ajani
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia;
| | - Justin Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia; (N.L.R.); (A.B.); (J.O.); (M.O.); (J.-B.R.)
- Correspondence:
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36
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Kumazawa M, Nishide H, Nagao R, Inoue-Kashino N, Shen JR, Nakano T, Uchiyama I, Kashino Y, Ifuku K. Molecular phylogeny of fucoxanthin-chlorophyll a/c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity. PHYSIOLOGIA PLANTARUM 2022; 174:e13598. [PMID: 34792189 DOI: 10.1111/ppl.13598] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/06/2021] [Accepted: 11/16/2021] [Indexed: 05/12/2023]
Abstract
Diatoms adapt to various aquatic light environments and play major roles in the global carbon cycle using their unique light-harvesting system, i.e. fucoxanthin chlorophyll a/c binding proteins (FCPs). Structural analyses of photosystem II (PSII)-FCPII and photosystem I (PSI)-FCPI complexes from the diatom Chaetoceros gracilis have revealed the localization and interactions of many FCPs; however, the entire set of FCPs has not been characterized. Here, we identify 46 FCPs in the newly assembled genome and transcriptome of C. gracilis. Phylogenetic analyses suggest that these FCPs can be classified into five subfamilies: Lhcr, Lhcf, Lhcx, Lhcz, and the novel Lhcq, in addition to a distinct type of Lhcr, CgLhcr9. The FCPs in Lhcr, including CgLhcr9 and some Lhcqs, have orthologous proteins in other diatoms, particularly those found in the PSI-FCPI structure. By contrast, the Lhcf subfamily, some of which were found in the PSII-FCPII complex, seems to be diversified in each diatom species, and the number of Lhcqs differs among species, indicating that their diversification may contribute to species-specific adaptations to light. Further phylogenetic analyses of FCPs/light-harvesting complex (LHC) proteins using genome data and assembled transcriptomes of other diatoms and microalgae in public databases suggest that our proposed classification of FCPs is common among various red-lineage algae derived from secondary endosymbiosis of red algae, including Haptophyta. These results provide insights into the loss and gain of FCP/LHC subfamilies during the evolutionary history of the red algal lineage.
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Affiliation(s)
- Minoru Kumazawa
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Hiroyo Nishide
- National Institute for Basic Biology, National Institutes of Natural Sciences, Aichi, Japan
| | - Ryo Nagao
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | | | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Takeshi Nakano
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Ikuo Uchiyama
- National Institute for Basic Biology, National Institutes of Natural Sciences, Aichi, Japan
| | - Yasuhiro Kashino
- Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Kentaro Ifuku
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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37
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Martin K, Schmidt K, Toseland A, Boulton CA, Barry K, Beszteri B, Brussaard CPD, Clum A, Daum CG, Eloe-Fadrosh E, Fong A, Foster B, Foster B, Ginzburg M, Huntemann M, Ivanova NN, Kyrpides NC, Lindquist E, Mukherjee S, Palaniappan K, Reddy TBK, Rizkallah MR, Roux S, Timmermans K, Tringe SG, van de Poll WH, Varghese N, Valentin KU, Lenton TM, Grigoriev IV, Leggett RM, Moulton V, Mock T. The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole. Nat Commun 2021; 12:5483. [PMID: 34531387 PMCID: PMC8446083 DOI: 10.1038/s41467-021-25646-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change.
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Affiliation(s)
- Kara Martin
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Katrin Schmidt
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew Toseland
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bánk Beszteri
- Department of Biology, University of Duisburg-Essen, Essen, Essen, Germany
| | | | - Alicia Clum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris G Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Emiley Eloe-Fadrosh
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Allison Fong
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Brian Foster
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bryce Foster
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael Ginzburg
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Marcel Huntemann
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia N Ivanova
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikos C Kyrpides
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Erika Lindquist
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Supratim Mukherjee
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Krishnaveni Palaniappan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - T B K Reddy
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mariam R Rizkallah
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Simon Roux
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Klaas Timmermans
- Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Susannah G Tringe
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Willem H van de Poll
- Centre for Isotope Research - Oceans, Energy and Sustainability Research Institute Groningen, Faculty of Science and Engineering, University of Groningen, AG Groningen, The Netherlands
| | - Neha Varghese
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Klaus U Valentin
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | | | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Plant and Microbial Biology Department, University of California, Berkeley, CA, USA
| | | | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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38
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Chaffron S, Delage E, Budinich M, Vintache D, Henry N, Nef C, Ardyna M, Zayed AA, Junger PC, Galand PE, Lovejoy C, Murray AE, Sarmento H, Acinas SG, Babin M, Iudicone D, Jaillon O, Karsenti E, Wincker P, Karp-Boss L, Sullivan MB, Bowler C, de Vargas C, Eveillard D. Environmental vulnerability of the global ocean epipelagic plankton community interactome. SCIENCE ADVANCES 2021; 7:eabg1921. [PMID: 34452910 PMCID: PMC8397264 DOI: 10.1126/sciadv.abg1921] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/09/2021] [Indexed: 05/05/2023]
Abstract
Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles and help regulate climate. Although global surveys are starting to reveal ecological drivers underlying planktonic community structure and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here, we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network-the community interactome-and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar) and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change and forecasted the most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios while identifying plausible plankton bioindicators for ocean monitoring of climate change.
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Affiliation(s)
- Samuel Chaffron
- Université de Nantes, CNRS UMR 6004, LS2N, F-44000 Nantes, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
| | - Erwan Delage
- Université de Nantes, CNRS UMR 6004, LS2N, F-44000 Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
| | - Marko Budinich
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Damien Vintache
- Université de Nantes, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Nicolas Henry
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Charlotte Nef
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Mathieu Ardyna
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, F-06230, Villefranche-sur-Mer, Paris, France
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Pedro C Junger
- Department of Hydrobiology, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, 13565-905 São Carlos, SP, Brazil
| | - Pierre E Galand
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Banyuls-sur-Mer, 66500 Paris, France
| | - Connie Lovejoy
- Département de biologie, Faculté des sciences et Institut de biologie intégrative et des systèmes (IBIS) 1030, ave de la Médecine, Université Laval, Québec, QC, Canada
| | - Alison E Murray
- Division of Earth and Ecosystem Science, Desert Research Institute, Reno, NV 89512, USA
| | - Hugo Sarmento
- Department of Hydrobiology, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, 13565-905 São Carlos, SP, Brazil
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona 08003, Spain
| | - Marcel Babin
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, F-06230, Villefranche-sur-Mer, Paris, France
- Takuvik International Research Laboratory, Université Laval and CNRS, Québec, QC, Canada
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples 80121, Italy
| | - Olivier Jaillon
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, 91057 Paris, France
| | - Eric Karsenti
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Patrick Wincker
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, 91057 Paris, France
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Damien Eveillard
- Université de Nantes, CNRS UMR 6004, LS2N, F-44000 Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
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39
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Sadeghi M, Tomaru Y, Ahola T. RNA Viruses in Aquatic Unicellular Eukaryotes. Viruses 2021; 13:v13030362. [PMID: 33668994 PMCID: PMC7996518 DOI: 10.3390/v13030362] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 12/24/2022] Open
Abstract
Increasing sequence information indicates that RNA viruses constitute a major fraction of marine virus assemblages. However, only 12 RNA virus species have been described, infecting known host species of marine single-celled eukaryotes. Eight of these use diatoms as hosts, while four are resident in dinoflagellate, raphidophyte, thraustochytrid, or prasinophyte species. Most of these belong to the order Picornavirales, while two are divergent and fall into the families Alvernaviridae and Reoviridae. However, a very recent study has suggested that there is extraordinary diversity in aquatic RNA viromes, describing thousands of viruses, many of which likely use protist hosts. Thus, RNA viruses are expected to play a major ecological role for marine unicellular eukaryotic hosts. In this review, we describe in detail what has to date been discovered concerning viruses with RNA genomes that infect aquatic unicellular eukaryotes.
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Affiliation(s)
- Mohammadreza Sadeghi
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (M.S.); (T.A.)
| | - Yuji Tomaru
- Environment and Fisheries Applied Techniques Research Department, Fisheries Technology Institute, Fisheries Research and Education Agency, Hatsukaichi, Hiroshima 739-0452, Japan;
| | - Tero Ahola
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (M.S.); (T.A.)
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40
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Giovagnetti V, Ruban AV. The mechanism of regulation of photosystem I cross-section in the pennate diatom Phaeodactylum tricornutum. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:561-575. [PMID: 33068431 DOI: 10.1093/jxb/eraa478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Photosystems possess distinct fluorescence emissions at low (77K) temperature. PSI emits in the long-wavelength region at ~710-740 nm. In diatoms, a successful clade of marine primary producers, the contribution of PSI-associated emission (710-717 nm) has been shown to be relatively small. However, in the pennate diatom Phaeodactylum tricornutum, the source of the long-wavelength emission at ~710 nm (F710) remains controversial. Here, we addressed the origin and modulation of F710 fluorescence in this alga grown under continuous and intermittent light. The latter condition led to a strong enhancement in F710. Biochemical and spectral properties of the photosynthetic complexes isolated from thylakoid membranes were investigated for both culture conditions. F710 emission appeared to be associated with PSI regardless of light acclimation. To further assess whether PSII could also contribute to this emission, we decreased the concentration of PSII reaction centres and core antenna by growing cells with lincomycin, a chloroplast protein synthesis inhibitor. The treatment did not diminish F710 fluorescence. Our data suggest that F710 emission originates from PSI under the conditions tested and is enhanced in intermittent light-grown cells due to increased energy flow from the FCP antenna to PSI.
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Affiliation(s)
- Vasco Giovagnetti
- Department of Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Alexander V Ruban
- Department of Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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41
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Grigoriev IV, Hayes RD, Calhoun S, Kamel B, Wang A, Ahrendt S, Dusheyko S, Nikitin R, Mondo SJ, Salamov A, Shabalov I, Kuo A. PhycoCosm, a comparative algal genomics resource. Nucleic Acids Res 2021; 49:D1004-D1011. [PMID: 33104790 PMCID: PMC7779022 DOI: 10.1093/nar/gkaa898] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/21/2020] [Accepted: 10/23/2020] [Indexed: 12/22/2022] Open
Abstract
Algae are a diverse, polyphyletic group of photosynthetic eukaryotes spanning nearly all eukaryotic lineages of life and collectively responsible for ∼50% of photosynthesis on Earth. Sequenced algal genomes, critical to understanding their complex biology, are growing in number and require efficient tools for analysis. PhycoCosm (https://phycocosm.jgi.doe.gov) is an algal multi-omics portal, developed by the US Department of Energy Joint Genome Institute to support analysis and distribution of algal genome sequences and other ‘omics’ data. PhycoCosm provides integration of genome sequence and annotation for >100 algal genomes with available multi-omics data and interactive web-based tools to enable algal research in bioenergy and the environment, encouraging community engagement and data exchange, and fostering new sequencing projects that will further these research goals.
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Affiliation(s)
- Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Richard D Hayes
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sara Calhoun
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bishoy Kamel
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alice Wang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Steven Ahrendt
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sergey Dusheyko
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Roman Nikitin
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor Shabalov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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42
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Pierella Karlusich JJ, Bowler C, Biswas H. Carbon Dioxide Concentration Mechanisms in Natural Populations of Marine Diatoms: Insights From Tara Oceans. FRONTIERS IN PLANT SCIENCE 2021; 12:657821. [PMID: 33995455 PMCID: PMC8119650 DOI: 10.3389/fpls.2021.657821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/23/2021] [Indexed: 05/08/2023]
Abstract
Marine diatoms, the most successful photoautotrophs in the ocean, efficiently sequester a significant part of atmospheric CO2 to the ocean interior through their participation in the biological carbon pump. However, it is poorly understood how marine diatoms fix such a considerable amount of CO2, which is vital information toward modeling their response to future CO2 levels. The Tara Oceans expeditions generated molecular data coupled with in situ biogeochemical measurements across the main ocean regions, and thus provides a framework to compare diatom genetic and transcriptional flexibility under natural CO2 variability. The current study investigates the interlink between the environmental variability of CO2 and other physicochemical parameters with the gene and transcript copy numbers of five key enzymes of diatom CO2 concentration mechanisms (CCMs): Rubisco activase and carbonic anhydrase (CA) as part of the physical pathway, together with phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, and malic enzyme as part of the potential C4 biochemical pathway. Toward this aim, we mined >200 metagenomes and >220 metatranscriptomes generated from samples of the surface layer of 66 globally distributed sampling sites and corresponding to the four main size fractions in which diatoms can be found: 0.8-5 μm, 5-20 μm, 20-180 μm, and 180-2,000 μm. Our analyses revealed that the transcripts for the enzymes of the putative C4 biochemical CCM did not in general display co-occurring profiles. The transcripts for CAs were the most abundant, with an order of magnitude higher values than the other enzymes, thus implying the importance of physical CCMs in diatom natural communities. Among the different classes of this enzyme, the most prevalent was the recently characterized iota class. Consequently, very little information is available from natural diatom assemblages about the distribution of this class. Biogeographic distributions for all the enzymes show different abundance hotspots according to the size fraction, pointing to the influence of cell size and aggregation in CCMs. Environmental correlations showed a complex pattern of responses to CO2 levels, total phytoplankton biomass, temperature, and nutrient concentrations. In conclusion, we propose that biophysical CCMs are prevalent in natural diatom communities.
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Affiliation(s)
- Juan José Pierella Karlusich
- Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Chris Bowler
- Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Haimanti Biswas
- CSIR National Institute of Oceanography, Biological Oceanography Division, Dona Paula, India
- *Correspondence: Haimanti Biswas,
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43
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Olofsson M, Hagan JG, Karlson B, Gamfeldt L. Large seasonal and spatial variation in nano- and microphytoplankton diversity along a Baltic Sea-North Sea salinity gradient. Sci Rep 2020; 10:17666. [PMID: 33077730 PMCID: PMC7572517 DOI: 10.1038/s41598-020-74428-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 09/30/2020] [Indexed: 11/09/2022] Open
Abstract
Aquatic phytoplankton experience large fluctuations in environmental conditions during seasonal succession and across salinity gradients, but the impact of this variation on their diversity is poorly understood. We examined spatio-temporal variation in nano- and microphytoplankton (> 2 µm) community structure using almost two decades of light-microscope based monitoring data. The dataset encompasses 19 stations that span a salinity gradient from 2.8 to 35 along the Swedish coastline. Spatially, both regional and local phytoplankton diversity increased with broad-scale salinity variation. Diatoms dominated at high salinity and the proportion of cyanobacteria increased with decreasing salinity. Temporally, cell abundance peaked in winter-spring at high salinity but in summer at low salinity. This was likely due to large filamentous cyanobacteria blooms that occur in summer in low salinity areas, but which are absent in higher salinities. In contrast, phytoplankton local diversity peaked in spring at low salinity but in fall and winter at high salinity. Whilst differences in seasonal variation in cell abundance were reasonably well-explained by variation in salinity and nutrient availability, variation in local-scale phytoplankton diversity was poorly predicted by environmental variables. Overall, we provide insights into the causes of spatio-temporal variation in coastal phytoplankton community structure while also identifying knowledge gaps.
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Affiliation(s)
- Malin Olofsson
- Research and Development, Oceanography, Swedish Meteorological and Hydrological Institute, Sven Källfelts gata 15, 426 71, Västra Frölunda, Sweden.
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Box 7050, 750 07, Uppsala, Sweden.
| | - James G Hagan
- Department of Marine Sciences, University of Gothenburg, Box 100, 405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden
| | - Bengt Karlson
- Research and Development, Oceanography, Swedish Meteorological and Hydrological Institute, Sven Källfelts gata 15, 426 71, Västra Frölunda, Sweden
| | - Lars Gamfeldt
- Department of Marine Sciences, University of Gothenburg, Box 100, 405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden
- Centre for Sea and Society, Box 260, 405 30, Gothenburg, Sweden
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44
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Sunagawa S, Acinas SG, Bork P, Bowler C, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, de Vargas C. Tara Oceans: towards global ocean ecosystems biology. Nat Rev Microbiol 2020; 18:428-445. [PMID: 32398798 DOI: 10.1038/s41579-020-0364-5] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2020] [Indexed: 12/14/2022]
Abstract
A planetary-scale understanding of the ocean ecosystem, particularly in light of climate change, is crucial. Here, we review the work of Tara Oceans, an international, multidisciplinary project to assess the complexity of ocean life across comprehensive taxonomic and spatial scales. Using a modified sailing boat, the team sampled plankton at 210 globally distributed sites at depths down to 1,000 m. We describe publicly available resources of molecular, morphological and environmental data, and discuss how an ecosystems biology approach has expanded our understanding of plankton diversity and ecology in the ocean as a planetary, interconnected ecosystem. These efforts illustrate how global-scale concepts and data can help to integrate biological complexity into models and serve as a baseline for assessing ecosystem changes and the future habitability of our planet in the Anthropocene epoch.
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Affiliation(s)
- Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences-CSIC, Barcelona, Spain
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | | | - Damien Eveillard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Université de Nantes, CNRS, UMR6004, LS2N, Nantes, France
| | - Gabriel Gorsky
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | | | - Eric Karsenti
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Stephane Pesant
- PANGAEA, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Patrick Wincker
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie Francois Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France. .,Sorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, France.
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