1
|
Liu F, Li J, Jin S, Liu L. Molecular diversity and seasonal dynamics of Ostreococcus (Mamiellophyceae, Chlorophyta) in typical mariculture bays based on metabarcoding analysis. MARINE ENVIRONMENTAL RESEARCH 2024; 202:106764. [PMID: 39332317 DOI: 10.1016/j.marenvres.2024.106764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/30/2024] [Accepted: 09/20/2024] [Indexed: 09/29/2024]
Abstract
Ostreococcus (Mamiellophyceae, Chlorophyta) is a cosmopolitan genus of marine pico-phytoplankton and the smallest free-living photosynthetic eukaryotes with cell size of 1-2 μm. To understand the diversity and spatio-temporal distribution of Ostreococcus in the Rongcheng coastal regions in northern China, metabarcoding analysis based on the 18S rDNA V4 molecular marker was applied to study the molecular diversity and seasonal dynamics of Ostreococcus in three typical mariculture bays (Rongcheng Bay, Lidao Bay and Sanggou Bay). A total of 103 amplicon sequence variants (ASVs) annotated as Ostreococcus were detected in these three typical mariculture bays throughout the year. The top five ASVs in terms of abundance were ASV4, ASV9, ASV14, ASV28 and ASV109, totally occupying 99.1% of Ostreococcus reads. Phylogenetic analysis showed that these five dominant ASVs represented two Ostreococcus ecotypes (OI and OII) and were grouped into four Ostreococcus clades including Ostreococcus lucimarinus (ASV9) and Ostreococcus tauri (ASV28 and ASV109) in OI, and Ostreococcus sp. RC1 (ASV4) and Ostreococcus sp. RC2 (ASV14) in OII, which provided direct evidence to support the co-existence of two ecotypes in the Rongcheng coastal regions. Five dominant ASVs in OI and OII exhibited two distinct seasonal distribution patterns. Three dominant ASVs (ASV9, ASV28 and ASV109) in OI could be detected in all four seasons of the year, exhibiting native distribution properties, while two ASVs (ASV4 and ASV14) in OII decreased sharply in winter and could not be detected in spring, exhibiting characteristics of alien inputs. The composition, succession and association of Ostreococcus community were mainly driven by water temperature in these mariculture bays. This study helps us systematically understand the molecular diversity and distribution patterns of Ostreococcus in typical mariculture bays in northern China, laying the foundation for understanding and revealing the ecological functions of pico-phytoplankton.
Collapse
Affiliation(s)
- Feng Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences (IOCAS), Qingdao, Shandong, 266000, PR China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, PR China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 101408, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, 266000, PR China.
| | - Jiamin Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences (IOCAS), Qingdao, Shandong, 266000, PR China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, 266000, PR China
| | - Shuangle Jin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences (IOCAS), Qingdao, Shandong, 266000, PR China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, PR China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 101408, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, 266000, PR China
| | - Liang Liu
- Rongcheng Ocean and Fishery Monitoring and Disaster Mitigation Center, Rongcheng, Shandong, 264300, PR China
| |
Collapse
|
2
|
de la Iglesia-Vélez B, Díaz-Pérez L, Acuña JL, Morán XAG. Spatial and seasonal variability of picoplankton abundance and growth rates in the southern Bay of Biscay. MARINE ENVIRONMENTAL RESEARCH 2024; 194:106331. [PMID: 38181718 DOI: 10.1016/j.marenvres.2023.106331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/21/2023] [Accepted: 12/27/2023] [Indexed: 01/07/2024]
Abstract
Autotrophic and heterotrophic picoplankton play fundamental roles in marine food webs and biogeochemical cycles. However, their growth responses have seldom been jointly assessed, including many temperate regions such as the Bay of Biscay. There, previous studies have shown their relevance in carbon fluxes. We describe here the spatio-temporal variability of the abundances and growth rates of the picoplanktonic groups routinely distinguished by flow cytometry (Synechococcus and Prochlorococcus cyanobacteria, two groups of differently sized picoeukaryotes and two groups of heterotrophic bacteria distinguished by their relative nucleic acid content) in the central Cantabrian Sea (S Bay of Biscay). To that end, from February to December 2021 we collected surface water on 5 occasions from 6 stations distributed along the S Bay of Biscay (6-3°W) and incubated it after removing protistan grazers in order to determine their dynamics along the seasonal cycle as well as the inshore-offshore and the west-east gradients. Seasonal variations in initial and maximum abundances generally matched previous knowledge of the region but growth rates were more variable, with Prochlorococcus and high nucleic acid (HNA) bacteria showing the maximum values (up to 2 d-1) while negative growth was observed in one third of Synechococcus incubations. Temporal differences generally overrode differences along the inshore-offshore gradient in trophic status while in situ and maximum abundances of most of the groups generally decreased towards the east following the increase in stratification and lower nutrient availability. Responses to stratification suggest Prochlorococcus and low nucleic acid (LNA) cells may prevail among autotrophic and heterotrophic bacteria, respectively, in a warmer ocean.
Collapse
Affiliation(s)
| | - Laura Díaz-Pérez
- Centro Oceanográfico de Gijón/Xixón (IEO-CSIC), 33212, Gijón/Xixón, Spain
| | - José Luis Acuña
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo/Uviéu, 33071, Oviedo/Uviéu, Spain
| | | |
Collapse
|
3
|
Tamm M, Nõges T, Nõges P, Panksep K, Zingel P, Agasild H, Freiberg R, Hunt T, Tõnno I. Factors influencing the pigment composition and dynamics of photoautotrophic picoplankton in shallow eutrophic lakes. PLoS One 2022; 17:e0267133. [PMID: 35617295 PMCID: PMC9135284 DOI: 10.1371/journal.pone.0267133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 04/04/2022] [Indexed: 11/19/2022] Open
Abstract
Photoautotrophic picoplankton (0.2–2 μm) can be a major contributor to primary production and play a significant part in the ecosystem carbon flow. However, the understanding about the dynamics of both eukaryotic and prokaryotic components of picoplankton in shallow eutrophic freshwater environments is still poor. Very few studies in these ecosystems reveal the taxonomic composition of picoeukaryotes. The main objective of this study was to investigate the seasonal dynamics of phototrophic picoplankton with the emphasis on the eukaryote community composition in a large shallow, eutrophic lake of the northern temperate zone (Lake Võrtsjärv). Phytoplankton pigments were employed to determine the taxonomic composition of photoautotrophic picoplankton. We found out that photoautotrophic picoplankton constitutes an important part of the phytoplankton community in Lake Võrtsjärv and its contribution can be highly variable (from ~9.3% to ~39%) in different years. The eukaryotic photoautotrophic picoplankton was dominated by diatoms followed by chrysophytes and other minor groups. Picoeukaryotes were prevailing in low-light conditions and low temperatures as their predominance in the picoplankton community was tightly linked to the presence or absence of ice cover. Ice cover strongly suppressed the growth of picocyanobacteria. Total phosphorus, turbidity and metazooplankton abundance had a clear relationship with photoautotrophic picoplankton chlorophyll a.
Collapse
Affiliation(s)
- Marju Tamm
- Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
- * E-mail:
| | - Tiina Nõges
- Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Peeter Nõges
- Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Kristel Panksep
- Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Priit Zingel
- Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Helen Agasild
- Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Rene Freiberg
- Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Triin Hunt
- Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Ilmar Tõnno
- Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| |
Collapse
|
4
|
Shuwang X, Sun J, Wei Y, Guo C. Size-Fractionated Filtration Combined with Molecular Methods Reveals the Size and Diversity of Picophytoplankton. BIOLOGY 2021; 10:biology10121280. [PMID: 34943195 PMCID: PMC8698306 DOI: 10.3390/biology10121280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/14/2021] [Accepted: 11/27/2021] [Indexed: 06/14/2023]
Abstract
In this study, flow cytometry (FCM) and size-fractionated filtration, together with high-throughput molecular sequencing methods (SM), were used to investigate picophytoplankton. A particle separation filter and a higher-throughput sequencing method were used to evaluate the composition of a euphotic zone of picophytoplankton-especially picoeukaryotic phytoplankton-in the Western Pacific, and the results of flow cytometry, which is a classic way to detect picophytoplankton, were used as a standard to evaluate the reliability of the results of the SMs. Within a water column of 200 m, six water depths (5, 25, 50, 113 (DCM), 150, and 200 m) were established. In order to further study the particle size spectra of the picophytoplankton, size-fractionated filtration was used to separate water samples from each water depth into three particle size ranges: 0.2-0.6, 0.6-1.2, and 1.2-2 μm. A total of 36 (6 × 3 × 2) samples were obtained through PCR amplification of the 18S rRNA V4 hypervariable region and 16S rRNA, which were biased toward phytoplankton plastids, and then high-throughput sequencing was performed. The estimation of the picophytoplankton diameter relied on forward scattering (FSC) through FCM. The estimation of the vertical distribution and diameter of the picophytoplankton using the SM was consistent with the results with FCM; thus, we believe that the estimation of picophytoplankton composition with the SM has value as a reference, although the size-fractionated filtration seemed to cause some deviations. In addition to Prochlorococcus and Synechococcus, the SM was used to evaluate the composition of picoeukaryotic phytoplankton, which mainly included Prymnesiophycea (Haptophyta) (38.15%), Cryptophyceae (Cryptophyta) (22.36%), Dictyochophyceae (Chrysophyta) (12.22%), and Mamiellophyceae (Chlorophyta) (3.31%). In addition, the SM also detected Dinophyceae (Dinoflagellata) (11.69%) sequences and a small number of Bacillariophyceae (Diatom) (1.64%) sequences, which are generally considered to have large particle sizes. The results of the SM also showed that the picoeukaryotic phytoplankton were not evenly distributed in the euphotic layer, and the vertical distributions of the different picoeukaryotic phytoplankton were different. An analysis of correlations with environmental factors showed that temperature was the main environmental factor controlling the vertical distribution of picophytoplankton.
Collapse
Affiliation(s)
- Xinze Shuwang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (X.S.); (C.G.)
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan 430074, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Yuqiu Wei
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China;
| | - Congcong Guo
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (X.S.); (C.G.)
| |
Collapse
|
5
|
Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. Proc Natl Acad Sci U S A 2021; 118:2011038118. [PMID: 33547239 PMCID: PMC8017926 DOI: 10.1073/pnas.2011038118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Most organisms coordinate key biological events to coincide with the day/night cycle. These diel oscillations are entrained through the activity of light-sensitive photoreceptors that allow organisms to respond rapidly to changes in light exposure. In the ocean, the plankton community must additionally contend with dramatic changes in the quantity and quality of light over depth. Here, we show that the predominantly blue-light field in the open-ocean environment may have driven expansion of blue light-sensitive regulatory elements in open-ocean eukaryotic plankton derived from secondary and tertiary endosymbiosis. The diel transcription of genes encoding light-sensitive elements indicate that photosynthetic and heterotrophic marine protists respond to and anticipate fluctuating light conditions in the dynamic marine environment. The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment.
Collapse
|
6
|
Glasner B, Henríquez-Castillo C, Alfaro FD, Trefault N, Andrade S, De la Iglesia R. Decoupling of biotic and abiotic patterns in a coastal area affected by chronic metal micronutrients disturbances. MARINE POLLUTION BULLETIN 2021; 166:111608. [PMID: 33838915 DOI: 10.1016/j.marpolbul.2020.111608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 06/12/2023]
Abstract
Coastal systems are highly productive areas for primary productivity and ecosystem services and host a large number of human activities. Since industrialization, metal micronutrients in these regions have increased. Phytoplankton use metals as micronutrients in metabolic processes, but in excess, had deleterious effects. In coastal systems, picoeukaryotes represent a diverse and abundant group with widespread distribution and fundamental roles in biogeochemical cycling. We combined different approaches to explore picoeukaryotes seasonal variability in a chronically metal polluted coastal area at the south-eastern Pacific Ocean. Through remote and field measurements to monitor environmental conditions and 18S rRNA gene sequencing for taxonomic profiling, we determined metal chronic effect on picoeukaryote community's structure. Our results revealed a stable richness and a variable distribution of the relative abundance, despite the physicochemical seasonal variations. These results suggest that chronic metal contamination influences temporal heterogeneity of picoeukaryote communities, with a decoupling between abiotic and biotic patterns.
Collapse
Affiliation(s)
- B Glasner
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - C Henríquez-Castillo
- Laboratorio de Fisiología y Genética Marina (FIGEMA), Centro de Estudios Avanzados de Zonas Áridas (CEAZA), Coquimbo, Chile; Facultad de Ciencias del Mar, Universidad Catolica del Norte, Coquimbo, Chile
| | - F D Alfaro
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Camino La Piramide 5750, Huechuraba, Santiago, Chile; Instituto de Ecología & Biodiversidad (IEB), Casilla 653, Santiago, Chile
| | - N Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Camino La Piramide 5750, Huechuraba, Santiago, Chile
| | - S Andrade
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Camino La Piramide 5750, Huechuraba, Santiago, Chile
| | - R De la Iglesia
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
| |
Collapse
|
7
|
Piwosz K, Mukherjee I, Salcher MM, Grujčić V, Šimek K. CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology. Front Microbiol 2021; 12:640066. [PMID: 33746931 PMCID: PMC7970053 DOI: 10.3389/fmicb.2021.640066] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
Phagotrophic protists are key players in aquatic food webs. Although sequencing-based studies have revealed their enormous diversity, ecological information on in situ abundance, feeding modes, grazing preferences, and growth rates of specific lineages can be reliably obtained only using microscopy-based molecular methods, such as Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). CARD-FISH is commonly applied to study prokaryotes, but less so to microbial eukaryotes. Application of this technique revealed that Paraphysomonas or Spumella-like chrysophytes, considered to be among the most prominent members of protistan communities in pelagic environments, are omnipresent but actually less abundant than expected, in contrast to little known groups such as heterotrophic cryptophyte lineages (e.g., CRY1), cercozoans, katablepharids, or the MAST lineages. Combination of CARD-FISH with tracer techniques and application of double CARD-FISH allow visualization of food vacuole contents of specific flagellate groups, thus considerably challenging our current, simplistic view that they are predominantly bacterivores. Experimental manipulations with natural communities revealed that larger flagellates are actually omnivores ingesting both prokaryotes and other protists. These new findings justify our proposition of an updated model of microbial food webs in pelagic environments, reflecting more authentically the complex trophic interactions and specific roles of flagellated protists, with inclusion of at least two additional trophic levels in the nanoplankton size fraction. Moreover, we provide a detailed CARD-FISH protocol for protists, exemplified on mixo- and heterotrophic nanoplanktonic flagellates, together with tips on probe design, a troubleshooting guide addressing most frequent obstacles, and an exhaustive list of published probes targeting protists.
Collapse
Affiliation(s)
- Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland
- Centre ALGATECH, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Indranil Mukherjee
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia
| | - Michaela M. Salcher
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia
| | - Vesna Grujčić
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Karel Šimek
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia
| |
Collapse
|
8
|
Li R, Hu C, Wang J, Sun J, Wang Y, Jiao N, Xu D. Biogeographical Distribution and Community Assembly of Active Protistan Assemblages Along an Estuary to a Basin Transect of the Northern South China Sea. Microorganisms 2021; 9:microorganisms9020351. [PMID: 33578968 PMCID: PMC7916720 DOI: 10.3390/microorganisms9020351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 11/21/2022] Open
Abstract
Marine protists are essential for globally critical biological processes, including the biogeochemical cycles of matter and energy. However, compared with their prokaryotic counterpart, it remains largely unclear how environmental factors determine the diversity and distribution of the active protistan communities on the regional scale. In the present study, the biodiversity, community composition, and potential drivers of the total, abundant, and rare protistan groups were studied using high throughput sequencing on the V9 hyper-variable regions of the small subunit ribosomal RNA (SSU rRNA) along an estuary to basin transect in the northern South China Sea. Overall, Bacillariophyta and Cercozoa were abundant in the surface water; heterotrophic protists including Spirotrichea and marine stramenopiles 3 (MAST-3) were more abundant in the subsurface waters near the heavily urbanized Pearl River estuary; Chlorophyta and Pelagophyceae were abundant at the deep chlorophyll maximum depth, while Hacrobia, Radiolaria, and Excavata were the abundant groups in the deep water. Salinity, followed by water depth, temperature, and other biological factors, were the primary factors controlling the distinct vertical and horizontal distribution of the total and abundant protists. Rare taxa were driven by water depth, followed by temperature, salinity, and the concentrations of PO43−. The active protistan communities were mainly driven by dispersal limitation, followed by drift and other ecological processes.
Collapse
Affiliation(s)
- Ran Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.L.); (C.H.); (J.W.); (Y.W.)
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, China
| | - Chen Hu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.L.); (C.H.); (J.W.); (Y.W.)
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, China
| | - Jianning Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.L.); (C.H.); (J.W.); (Y.W.)
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, China
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan 430000, China;
| | - Ying Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.L.); (C.H.); (J.W.); (Y.W.)
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.L.); (C.H.); (J.W.); (Y.W.)
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, China
- Correspondence: (N.J.); (D.X.)
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (R.L.); (C.H.); (J.W.); (Y.W.)
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, China
- Correspondence: (N.J.); (D.X.)
| |
Collapse
|
9
|
Phoma BS, Makhalanyane TP. Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands. MICROBIAL ECOLOGY 2021; 81:396-409. [PMID: 32935183 DOI: 10.1007/s00248-020-01589-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Physicochemical variables limit and control the distribution of microbial communities in all environments. In the oceans, this may significantly influence functional processes such the consumption of dissolved organic material and nutrient sequestration. Yet, the relative contributions of physical factors, such as water mass variability and depth, on functional processes are underexplored. We assessed microbial community structure and functionality in the Prince Edward Islands (PEIs) using 16S rRNA gene amplicon analysis and extracellular enzymatic activity assays, respectively. We found that depth and nutrients substantially drive the structural patterns of bacteria and archaea in this region. Shifts from epipelagic to bathypelagic zones were linked to decreases in the activities of several extracellular enzymes. These extracellular enzymatic activities were positively correlated with several phyla including several Alphaproteobacteria (including members of the SAR 11 clade and order Rhodospirillales) and Cyanobacteria. We show that depth-dependent variables may be essential drivers of community structure and functionality in the PEIs.
Collapse
Affiliation(s)
- Boitumelo Sandra Phoma
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
- Marine Microbiomics Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - Thulani Peter Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria, 0028, South Africa.
- Marine Microbiomics Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa.
| |
Collapse
|
10
|
Ramond P, Siano R, Schmitt S, de Vargas C, Marié L, Memery L, Sourisseau M. Phytoplankton taxonomic and functional diversity patterns across a coastal tidal front. Sci Rep 2021; 11:2682. [PMID: 33514820 PMCID: PMC7846791 DOI: 10.1038/s41598-021-82071-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/26/2020] [Indexed: 01/30/2023] Open
Abstract
Oceanic physics at fine scale; e.g. eddies, fronts, filaments; are notoriously difficult to sample. However, an increasing number of theoretical approaches hypothesize that these processes affect phytoplankton diversity which have cascading effects on regional ecosystems. In 2015, we targeted the Iroise Sea (France) and evidenced the setting up of the Ushant tidal front from the beginning of spring to late summer. Seawater samples were taken during three sampling cruises and DNA-barcoding allowed us to investigate patterns of eukaryotic phytoplankton diversity across this front. First focusing on patterns of taxonomic richness, we evidenced that the front harbored a hotspot of eukaryotic phytoplankton diversity sustained throughout summer. We then detail the ecological processes leading to the formation of this hotspot by studying shifts in community composition across the Iroise Sea. Physical mixing mingled the communities surrounding the front, allowing the formation of a local ecotone, but it was cycles of disturbances and nutrient inputs over the front that allowed a decrease in competitive exclusion, which maintained a higher diversity of rare phytoplankton taxa. These processes did not select a specific ecological strategy as inferred by a trait approach coupled to our taxonomic approach. Instead the front favored higher richness within widespread strategies, resulting in functional redundancy. We detail how fine-scale ocean physics affect phytoplankton diversity and suppose that this interplay is a major control on regional ecosystems.
Collapse
Affiliation(s)
- Pierre Ramond
- grid.464101.60000 0001 2203 0006Sorbonne Université, CNRS-UMR7144-Station Biologique de Roscoff, Place Georges Teissier, 29688 Roscoff, France ,Ifremer-Centre de Brest, DYNECO/Pelagos, Technopôle Brest Iroise, 29280 Plouzané, France ,grid.10914.3d0000 0001 2227 4609Department of Marine Microbiology and Biogeochemistry, NIOZ-Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, The Netherlands
| | - Raffaele Siano
- Ifremer-Centre de Brest, DYNECO/Pelagos, Technopôle Brest Iroise, 29280 Plouzané, France
| | - Sophie Schmitt
- Ifremer-Centre de Brest, DYNECO/Pelagos, Technopôle Brest Iroise, 29280 Plouzané, France
| | - Colomban de Vargas
- grid.464101.60000 0001 2203 0006Sorbonne Université, CNRS-UMR7144-Station Biologique de Roscoff, Place Georges Teissier, 29688 Roscoff, France ,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Louis Marié
- grid.503286.aLaboratoire d’Océanographie Physique et Spatiale (LOPS), UMR 6523 Univ. Brest, CNRS, IFREMER, IRD, Plouzané, France
| | - Laurent Memery
- grid.463763.30000 0004 0638 0577Laboratoire des Sciences de l’Environnement MARin (LEMAR), UMR 6539 Univ. Brest, CNRS, IFREMER, IRD, Plouzané, France
| | - Marc Sourisseau
- Ifremer-Centre de Brest, DYNECO/Pelagos, Technopôle Brest Iroise, 29280 Plouzané, France
| |
Collapse
|
11
|
Castillo YM, Sebastián M, Forn I, Grimsley N, Yau S, Moraru C, Vaqué D. Visualization of Viral Infection Dynamics in a Unicellular Eukaryote and Quantification of Viral Production Using Virus Fluorescence in situ Hybridization. Front Microbiol 2020; 11:1559. [PMID: 32765451 PMCID: PMC7379908 DOI: 10.3389/fmicb.2020.01559] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/16/2020] [Indexed: 11/13/2022] Open
Abstract
One of the major challenges in viral ecology is to assess the impact of viruses in controlling the abundance of specific hosts in the environment. To this end, techniques that enable the detection and quantification of virus-host interactions at the single-cell level are essential. With this goal in mind, we implemented virus fluorescence in situ hybridization (VirusFISH) using as a model the marine picoeukaryote Ostreococcus tauri and its virus Ostreococcus tauri virus 5 (OtV5). VirusFISH allowed the visualization and quantification of the proportion of infected cells during an infection cycle in experimental conditions. We were also able to quantify the abundance of free viruses released during cell lysis, discriminating OtV5 from other mid-level fluorescence phages in our non-axenic infected culture that were not easily distinguishable with flow cytometry. Our results showed that although the major lysis of the culture occurred between 24 and 48 h after OtV5 inoculation, some new viruses were already produced between 8 and 24 h. With this work, we demonstrate that VirusFISH is a promising technique to study specific virus-host interactions in non-axenic cultures and establish a framework for its application in complex natural communities.
Collapse
Affiliation(s)
- Yaiza M Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain
| | - Marta Sebastián
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain.,Institute of Oceanography and Global Change (IOCAG), University of Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria, Spain
| | - Irene Forn
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain
| | - Nigel Grimsley
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanographic Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Sheree Yau
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain.,Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanographic Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Cristina Moraru
- Department of the Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain
| |
Collapse
|
12
|
Mangot JF, Forn I, Obiol A, Massana R. Constant abundances of ubiquitous uncultured protists in the open sea assessed by automated microscopy. Environ Microbiol 2018; 20:3876-3889. [PMID: 30209866 DOI: 10.1111/1462-2920.14408] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/06/2018] [Accepted: 09/08/2018] [Indexed: 11/28/2022]
Abstract
Protists have fundamental ecological roles in marine environments and their diversity is being increasingly explored, yet little is known about the quantitative importance of specific taxa in these ecosystems. Here we optimized a newly developed automated system of image acquisition and image analysis to enumerate minute uncultured cells of different sizes targeted by fluorescence in situ hybridization. The automated counting routine was highly reproducible, well correlated with manual counts, and was then applied on surface and deep chlorophyll maximum samples from the Malaspina 2010 circumnavigation. The three targeted uncultured taxa (MAST-4, MAST-7 and MAST-1C) were found in virtually all samples from several ocean basins (Atlantic, Indian and Pacific) in fairly constant cell abundances, following typical lognormal distributions. Their global abundances averaged 49, 23 and 7 cells ml-1 , respectively, and altogether the three groups accounted for about 10%-20% of heterotrophic picoeukaryotes. Our innovative high-throughput cell counting routine allows for the first time a direct assessment of the biogeographic distribution of small protists (< 5 μm) and shows the ubiquity in sunlit oceans of three bacterivorous taxa, suggesting their key roles in marine ecosystems.
Collapse
Affiliation(s)
- Jean-François Mangot
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), E-08003 Barcelona, Catalonia, Spain
| | - Irene Forn
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), E-08003 Barcelona, Catalonia, Spain
| | - Aleix Obiol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), E-08003 Barcelona, Catalonia, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), E-08003 Barcelona, Catalonia, Spain
| |
Collapse
|
13
|
Mestre M, Ferrera I, Borrull E, Ortega-Retuerta E, Mbedi S, Grossart HP, Gasol JM, Sala MM. Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum. Mol Ecol 2017; 26:6827-6840. [PMID: 29117634 DOI: 10.1111/mec.14421] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 01/26/2023]
Abstract
Biotic and abiotic particles shape the microspatial architecture that defines the microbial aquatic habitat, being particles highly variable in size and quality along oceanic horizontal and vertical gradients. We analysed the prokaryotic (bacterial and archaeal) diversity and community composition present in six distinct particle size classes ranging from the pico- to the microscale (0.2 to 200 μm). Further, we studied their variations along oceanographic horizontal (from the coast to open oceanic waters) and vertical (from the ocean surface into the meso- and bathypelagic ocean) gradients. In general, prokaryotic community composition was more variable with depth than in the transition from the coast to the open ocean. Comparing the six size-fractions, distinct prokaryotic communities were detected in each size-fraction, and whereas bacteria were more diverse in the larger size-fractions, archaea were more diverse in the smaller size-fractions. Comparison of prokaryotic community composition among particle size-fractions showed that most, but not all, taxonomic groups have a preference for a certain size-fraction sustained with depth. Species sorting, or the presence of diverse ecotypes with distinct size-fraction preferences, may explain why this trend is not conserved in all taxa.
Collapse
Affiliation(s)
- Mireia Mestre
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Encarna Borrull
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Eva Ortega-Retuerta
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain.,Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, UMR 7621, Université Pierre and Marie Curie (Paris 06), Sorbonne Universités, Banyuls-sur-Mer, France
| | - Susan Mbedi
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany.,Museum für Naturkunde - Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Hans-Peter Grossart
- Experimental Limnology, IGB-Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany.,Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - M Montserrat Sala
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| |
Collapse
|
14
|
Tucker SJ, McManus GB, Katz LA, Grattepanche JD. Distribution of Abundant and Active Planktonic Ciliates in Coastal and Slope Waters Off New England. Front Microbiol 2017; 8:2178. [PMID: 29250036 PMCID: PMC5715329 DOI: 10.3389/fmicb.2017.02178] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 10/23/2017] [Indexed: 11/18/2022] Open
Abstract
Despite their important role of linking microbial and classic marine food webs, data on biogeographical patterns of microbial eukaryotic grazers are limited, and even fewer studies have used molecular tools to assess active (i.e., those expressing genes) community members. Marine ciliate diversity is believed to be greatest at the chlorophyll maximum, where there is an abundance of autotrophic prey, and is often assumed to decline with depth. Here, we assess the abundant (DNA) and active (RNA) marine ciliate communities throughout the water column at two stations off the New England coast (Northwest Atlantic)—a coastal station 43 km from shore (40 m depth) and a slope station 135 km off shore (1,000 m). We analyze ciliate communities using a DNA fingerprinting technique, Denaturing Gradient Gel Electrophoresis (DGGE), which captures patterns of abundant community members. We compare estimates of ciliate communities from SSU-rDNA (abundant) and SSU-rRNA (active) and find complex patterns throughout the water column, including many active lineages below the photic zone. Our analyses reveal (1) a number of widely-distributed taxa that are both abundant and active; (2) considerable heterogeneity in patterns of presence/absence of taxa in offshore samples taken 50 m apart throughout the water column; and (3) three distinct ciliate assemblages based on position from shore and depth. Analysis of active (RNA) taxa uncovers biodiversity hidden to traditional DNA-based approaches (e.g., clone library, rDNA amplicon studies).
Collapse
Affiliation(s)
- Sarah J Tucker
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, United States.,Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA, United States
| | | |
Collapse
|