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Bruhn CS, Lundholm N, Hansen PJ, Wohlrab S, John U. Transition from a mixotrophic/heterotrophic protist community during the dark winter to a photoautotrophic spring community in surface waters of Disko Bay, Greenland. Front Microbiol 2024; 15:1407888. [PMID: 38887716 PMCID: PMC11180815 DOI: 10.3389/fmicb.2024.1407888] [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: 04/08/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
Unicellular eukaryotic plankton communities (protists) are the major basis of the marine food web. The spring bloom is especially important, because of its high biomass. However, it is poorly described how the protist community composition in Arctic surface waters develops from winter to spring. We show that mixotrophic and parasitic organisms are prominent in the dark winter period. The transition period toward the spring bloom event was characterized by a high relative abundance of mixotrophic dinoflagellates, while centric diatoms and the haptophyte Phaeocystis pouchetii dominated the successive phototrophic spring bloom event during the study. The data shows a continuous community shift from winter to spring, and not just a dormant spring community waiting for the right environmental conditions. The spring bloom initiation commenced while sea ice was still scattering and absorbing the sunlight, inhibiting its penetration into the water column. The initial increase in fluorescence was detected relatively deep in the water column at ~55 m depth at the halocline, at which the photosynthetic cells accumulated, while a thick layer of snow and sea ice was still obstructing sunlight penetration of the surface water. This suggests that water column stratification and a complex interplay of abiotic factors eventually promote the spring bloom initiation.
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Affiliation(s)
- Claudia Sabine Bruhn
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz-Centre Potsdam, German Research Centre for Geosciences GFZ, Potsdam, Germany
| | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Per Juel Hansen
- Department of Biology, Marine Biological Station, University of Copenhagen, Helsingør, Denmark
| | - Sylke Wohlrab
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany
| | - Uwe John
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany
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Mora D, Schlüsener M, Fischer H, Kleinteich J, Schulz M, Ternes T, Thiel J, Wick A, Krenek S. From genes to toxins: Profiling Prymnesium parvum during a riverine harmful algal bloom. HARMFUL ALGAE 2024; 136:102644. [PMID: 38876525 DOI: 10.1016/j.hal.2024.102644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/19/2024] [Accepted: 05/12/2024] [Indexed: 06/16/2024]
Abstract
Blooms of Prymnesium parvum, a unicellular alga globally distributed in marine and brackish environments, frequently result in massive fish kills due to the production of toxins called prymnesins by this haptophyte. In August 2022, a harmful algal bloom (HAB) of this species occurred in the lower Oder River (Poland and Germany), which caused mass mortalities of fish and other organisms. This HAB was linked to low discharge of the Oder and mining activities that caused a significant increase in salinity. In this context, we report on the molecular detection and screening of this haptophyte and its toxins in environmental samples and clonal cultures derived thereof. Both conventional PCR and droplet digital PCR assays reliably detected P. parvum in environmental samples. eDNA metabarcoding using the V4 region of the 18S rRNA gene revealed a single Prymnesium sequence variant, but failed to identify it to species level. Four clonal cultures established from environmental samples were unambiguously identified as P. parvum by molecular phylogenetics (near full-length 18S rRNA gene) and light microscopy. Phylogenetic analysis (ITS1-5.8S-ITS2 marker region) placed the cultured phylotype within a clade containing other P. parvum strains known to produce B-type prymnesins. Toxin-screening of the cultures using liquid chromatography-electrospray ionization - time of flight mass spectrometry identified B-type prymnesins, which were also detected in extracts of filter residues from water samples of the Oder collected during the HAB. Overall, our investigation provides a detailed characterization of P. parvum, including their prymnesins, during this HAB in the Oder River, contributing valuable insights into this ecological disaster. In addition, the droplet digital PCR assay established here will be useful for future monitoring of low levels of P. parvum on the Oder River or any other salt-impacted and brackish water bodies.
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Affiliation(s)
- Demetrio Mora
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany; Current address: Observatory for Climate, Environment and Biodiversity (OCEB), Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Michael Schlüsener
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Helmut Fischer
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Julia Kleinteich
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Manoj Schulz
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Thomas Ternes
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Joana Thiel
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Arne Wick
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Sascha Krenek
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany.
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Banchi E, Manna V, Muggia L, Celussi M. Marine Fungal Diversity and Dynamics in the Gulf of Trieste (Northern Adriatic Sea). MICROBIAL ECOLOGY 2024; 87:78. [PMID: 38806848 PMCID: PMC11133070 DOI: 10.1007/s00248-024-02394-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024]
Abstract
Fungi contribute to different important ecological processes, including decomposition of organic matter and nutrient cycling, but in the marine environment the main factors influencing their diversity and dynamics at the spatial and temporal levels are still largely unclear. In this study, we performed DNA metabarcoding on seawater sampled monthly over a year and a half in the Gulf of Trieste (northern Adriatic Sea), targeting the internal transcribed spacer (ITS) and the 18S rRNA gene regions. The fungal communities were diverse, very dynamic, and belonged predominantly to marine taxa. Samples could be clustered in two groups, mainly based on the high (> 30%) or low relative proportion of the ascomycetes Parengyodontium album, which emerged as a key taxon in this area. Dissolved and particulate organic C:N ratio played important roles in shaping the mycoplankton assemblages, suggesting that differently bioavailable organic matter pools may be utilized by different consortia. The proportion of fungal over total reads was 31% for ITS and 0.7% for 18S. ITS had the highest taxonomic resolution but low power to detect early divergent fungal lineages. Our results on composition, distribution, and environmental drivers extended our knowledge of the structure and function of the mycobiome of coastal waters.
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Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics (OGS), Trieste, Italy.
- NBFC, National Biodiversity Future Center, Palermo, Italy.
| | - Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics (OGS), Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics (OGS), Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
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4
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Gaonkar CC, Campbell L. A full-length 18S ribosomal DNA metabarcoding approach for determining protist community diversity using Nanopore sequencing. Ecol Evol 2024; 14:e11232. [PMID: 38606340 PMCID: PMC11007259 DOI: 10.1002/ece3.11232] [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: 03/16/2024] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
Protist diversity studies are frequently conducted using DNA metabarcoding methods. Currently, most studies have utilized short read sequences to assess protist diversity. One limitation of using short read sequences is the low resolution of the markers. For better taxonomic resolution longer sequences of the 18S rDNA are required because the full-length has both conserved and hypervariable regions. In this study, a new primer pair combination was used to amplify the full-length 18S rDNA and its efficacy was validated with a test community and then validated with field samples. Full-length sequences obtained with the Nanopore MinION for protist diversity from field samples were compared with Illumina MiSeq V4 and V8-V9 short reads. Sequences generated from the high-throughput sequencers are Amplicon Sequence Variants (ASVs). Metabarcoding results show high congruency among the long reads and short reads in taxonomic annotation at the major taxonomic group level; however, not all taxa could be successfully detected from sequences. Based on the criteria of ≥95% similarity and ≥1000 bp query length, 298 genera were identified by all markers in the field samples, 250 (84%) were detected by 18S, while only 226 (76%) by V4 and 213 (71%) by V8-V9. Of the total 85 dinoflagellate genera observed, 19 genera were not defined by 18S dinoflagellate ASVs compared to only three among the total 52 diatom genera. The discrepancy in this resolution is due to the lack of taxonomically available 18S reference sequences in particular for dinoflagellates. Overall, this preliminary investigation demonstrates that application of the full-length 18S rDNA approach can be successful in field studies.
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Affiliation(s)
- Chetan C. Gaonkar
- Department of OceanographyTexas A&M UniversityCollege StationTexasUSA
| | - Lisa Campbell
- Department of OceanographyTexas A&M UniversityCollege StationTexasUSA
- Department of BiologyTexas A&M UniversityCollege StationTexasUSA
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5
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Seo HJ, Kim YH, Yang HJ, Park MG, Lee MJ, Kim DJ, Jang SH. Spring protistan communities in response to warming in the northeastern East China Sea. MARINE ENVIRONMENTAL RESEARCH 2024; 196:106376. [PMID: 38316569 DOI: 10.1016/j.marenvres.2024.106376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/05/2024] [Accepted: 01/19/2024] [Indexed: 02/07/2024]
Abstract
The northeastern East China Sea is a highly dynamic marine ecosystem influenced by seasonally varying water mass properties. However, despite being among the world's fastest-warming ocean, there has been limited investigation into the impacts of warming on protistan communities. We collected seawater from two stations (E42 and E46) with different natural protist communities and environmental attributes to investigate the acclimation of the two communities to artificially elevated temperatures (ambient T, +2, and +4 °C). Nutrient and Chl-a conditions reflected oceanographic differences, providing insights into protistan community dynamics. Notably, small-sized autotrophic protists prevailed in the phosphate-deficient E42 community, with mid-incubation heterotrophic conversions. Higher temperatures exacerbated the effects of the P deficiency on the E42 community. While the proportions of Bacillariophyta increased only in the nutrient-balanced E46 communities, those of mixotrophic dinoflagellates increased with elevated temperature, regardless of P deficiency, suggesting that mixotrophy likely aids adaptation in changing marine environments. In summary, the findings of this microcosm study illuminate the potential modulation of spring protistan communities in the northeastern East China Sea under anticipated future warming.
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Affiliation(s)
- Hye Jin Seo
- Department of Oceanography, Chonnam National University, Gwangju 61186, South Korea
| | - Yun Hee Kim
- Department of Oceanography, Chonnam National University, Gwangju 61186, South Korea
| | - Hyun Jun Yang
- Department of Oceanography, Chonnam National University, Gwangju 61186, South Korea
| | - Myung Gil Park
- Department of Oceanography, Chonnam National University, Gwangju 61186, South Korea
| | - Moo Joon Lee
- Department of Marine Biotechnology, Anyang University, Incheon 23038, South Korea
| | - Dae Jin Kim
- Training Ship Administrative Center, Chonnam National University, Yeosu 59626, South Korea
| | - Se Hyeon Jang
- Department of Oceanography, Chonnam National University, Gwangju 61186, South Korea.
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Dobbertin da Costa M, Gast RJ, Millette NC. Temporal and spatial variability of constitutive mixotroph abundance and proportion. FEMS Microbiol Ecol 2024; 100:fiae015. [PMID: 38308512 PMCID: PMC10939395 DOI: 10.1093/femsec/fiae015] [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: 11/01/2023] [Revised: 12/19/2023] [Accepted: 02/01/2024] [Indexed: 02/04/2024] Open
Abstract
Mixotrophic plankton can comprise a substantial portion of the plankton community compared to phytoplankton and zooplankton. However, there is a gap in the understanding of conditions that influence mixotroph prevalence and activity in situ because current methods often over- or underestimate mixotroph abundance. A labeled prey-tracer method was utilized to identify active mixotrophs present at two locations in a temperate estuary over a year. The tracer method was combined with light microscopy data to estimate active mixotroph abundance and proportion. This study estimated that actively grazing mixotrophic taxa were more abundant in the spring and autumn compared to summer. Dinoflagellates typically dominated the mixotrophic taxa except during autumn at the low salinity location when cryptophytes dominated. Further analysis suggested that active mixotroph abundances might not be only regulated by environmental conditions favorable to mixotrophy but, instead, environmental conditions favorable to different mixotrophs utilization of phagotrophy. By focusing on mixotrophic taxa that were identified to be actively grazing at time of sampling, this study provided a more nuanced estimation of mixotroph abundance, increasing the understanding of how mixotrophic abundance and proportion in situ are influenced by the planktonic community composition and environmental factors.
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Affiliation(s)
- Marcella Dobbertin da Costa
- Virginia Institute of Marine Science, William & Mary, 1370 Greate Rd., Gloucester Point, VA 23062, United States
| | - Rebecca J Gast
- Woods Hole Oceanographic Institution, 266 Woods Hole Rd, MS #32, Woods Hole, MA 02543, United States
| | - Nicole C Millette
- Virginia Institute of Marine Science, William & Mary, 1370 Greate Rd., Gloucester Point, VA 23062, United States
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7
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Brown MV, Ostrowski M, Messer LF, Bramucci A, van de Kamp J, Smith MC, Bissett A, Seymour J, Hobday AJ, Bodrossy L. A marine heatwave drives significant shifts in pelagic microbiology. Commun Biol 2024; 7:125. [PMID: 38267685 PMCID: PMC10808424 DOI: 10.1038/s42003-023-05702-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024] Open
Abstract
Marine heatwaves (MHWs) cause disruption to marine ecosystems, deleteriously impacting macroflora and fauna. However, effects on microorganisms are relatively unknown despite ocean temperature being a major determinant of assemblage structure. Using data from thousands of Southern Hemisphere samples, we reveal that during an "unprecedented" 2015/16 Tasman Sea MHW, temperatures approached or surpassed the upper thermal boundary of many endemic taxa. Temperate microbial assemblages underwent a profound transition to niche states aligned with sites over 1000 km equatorward, adapting to higher temperatures and lower nutrient conditions bought on by the MHW. MHW conditions also modulate seasonal patterns of microbial diversity and support novel assemblage compositions. The most significant affects of MHWs on microbial assemblages occurred during warmer months, when temperatures exceeded the upper climatological bounds. Trends in microbial response across several MHWs in different locations suggest these are emergent properties of temperate ocean warming, which may facilitate monitoring, prediction and adaptation efforts.
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Affiliation(s)
- Mark V Brown
- CSIRO Environment, Hobart, Australia.
- Climate Change Cluster, University of Technology Sydney, Ultimo, Australia.
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, Ultimo, Australia
| | - Lauren F Messer
- Division of Biological and Environmental Sciences, University of Stirling, Stirling, Scotland
| | - Anna Bramucci
- Climate Change Cluster, University of Technology Sydney, Ultimo, Australia
| | | | | | | | - Justin Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, Australia
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Mills DB, Simister RL, Sehein TR, Hallam SJ, Sperling EA, Crowe SA. Constraining the oxygen requirements for modern microbial eukaryote diversity. Proc Natl Acad Sci U S A 2024; 121:e2303754120. [PMID: 38165897 PMCID: PMC10786294 DOI: 10.1073/pnas.2303754120] [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: 03/06/2023] [Accepted: 11/07/2023] [Indexed: 01/04/2024] Open
Abstract
Eukaryotes originated prior to the establishment of modern marine oxygen (O2) levels. According to the body fossil and lipid biomarker records, modern (crown) microbial eukaryote lineages began diversifying in the ocean no later than ~800 Ma. While it has long been predicted that increasing atmospheric O2 levels facilitated the early diversification of microbial eukaryotes, the O2 levels needed to permit this diversification remain unconstrained. Using time-resolved geochemical parameter and gene sequence information from a model marine oxygen minimum zone spanning a range of dissolved O2 levels and redox states, we show that microbial eukaryote taxonomic richness and phylogenetic diversity remain the same until O2 declines to around 2 to 3% of present atmospheric levels, below which these diversity metrics become significantly reduced. Our observations suggest that increasing O2 would have only directly promoted early crown-eukaryote diversity if atmospheric O2 was below 2 to 3% of modern levels when crown-eukaryotes originated and then later met or surpassed this range as crown-eukaryotes diversified. If atmospheric O2 was already consistently at or above 2 to 3% of modern levels by the time that crown-eukaryotes originated, then the subsequent diversification of modern microbial eukaryotes was not directly driven by atmospheric oxygenation.
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Affiliation(s)
- Daniel B. Mills
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333Munich, Germany
- Department of Earth and Planetary Sciences, Stanford University, Stanford, CA94305
- The Penn State Extraterrestrial Intelligence Center, The Pennsylvania State University, University Park, PA16802
| | - Rachel L. Simister
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Taylor R. Sehein
- Department of Biological Sciences, Smith College, Northampton, MA01063
| | - Steven J. Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
- Bradshaw Research Initiative for Minerals and Mining, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Ecosystem Services, Commercialization Platforms and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Erik A. Sperling
- Department of Earth and Planetary Sciences, Stanford University, Stanford, CA94305
| | - Sean A. Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
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Atteia A, Bec B, Gianaroli C, Serais O, Quétel I, Lagarde F, Gobet A. Evaluation of sequential filtration and centrifugation to capture environmental DNA and survey microbial eukaryotic communities in aquatic environments. Mol Ecol Resour 2024; 24:e13887. [PMID: 37899641 DOI: 10.1111/1755-0998.13887] [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: 08/03/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023]
Abstract
Sequential membrane filtration of water samples is commonly used to monitor the diversity of aquatic microbial eukaryotes. This capture method is efficient to focus on specific taxonomic groups within a size fraction, but it is time-consuming. Centrifugation, often used to collect microorganisms from pure culture, could be seen as an alternative to capture microbial eukaryotic communities from environmental samples. Here, we compared the two capture methods to assess diversity and ecological patterns of eukaryotic communities in the Thau lagoon, France. Water samples were taken twice a month over a full year and sequential filtration targeting the picoplankton (0.2-3 μm) and larger organisms (>3 μm) was used in parallel to centrifugation. The microbial eukaryotic community in the samples was described using an environmental DNA approach targeting the V4 region of the 18S rRNA gene. The most abundant divisions in the filtration fractions and the centrifugation pellet were Dinoflagellata, Metazoa, Ochrophyta, Cryptophyta. Chlorophyta were dominant in the centrifugation pellet and the picoplankton fraction but not in the larger fraction. Diversity indices and structuring patterns of the community in the two size fractions and the centrifugation pellet were comparable. Twenty amplicon sequence variants were significantly differentially abundant between the two size fractions and the centrifugation pellet, and their temporal patterns of abundance in the two fractions combined were similar to those obtained with centrifugation. Overall, centrifugation led to similar ecological conclusions as the two filtrated fractions combined, thus making it an attractive time-efficient alternative to sequential filtration.
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Affiliation(s)
- Ariane Atteia
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Béatrice Bec
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | | | - Ophélie Serais
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Isaure Quétel
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Franck Lagarde
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
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Clerissi C, Huot C, Portet A, Gourbal B, Toulza E. Covariation between microeukaryotes and bacteria associated with Planorbidae snails. PeerJ 2023; 11:e16639. [PMID: 38144201 PMCID: PMC10740603 DOI: 10.7717/peerj.16639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/19/2023] [Indexed: 12/26/2023] Open
Abstract
Background Microbial communities associated with macroorganisms might affect host physiology and homeostasis. Bacteria are well studied in this context, but the diversity of microeukaryotes, as well as covariations with bacterial communities, remains almost unknown. Methods To study microeukaryotic communities associated with Planorbidae snails, we developed a blocking primer to reduce amplification of host DNA during metabarcoding analyses. Analyses of alpha and beta diversities were computed to describe microeukaryotes and bacteria using metabarcoding of 18S and 16S rRNA genes, respectively. Results Only three phyla (Amoebozoa, Opisthokonta and Alveolata) were dominant for microeukaryotes. Bacteria were more diverse with five dominant phyla (Proteobacteria, Bacteroidetes, Tenericutes, Planctomycetes and Actinobacteria). The composition of microeukaryotes and bacteria were correlated for the Biomphalaria glabrata species, but not for Planorbarius metidjensis. Network analysis highlighted clusters of covarying taxa. Among them, several links might reflect top-down control of bacterial populations by microeukaryotes, but also possible competition between microeukaryotes having opposite distributions (Lobosa and Ichthyosporea). The role of these taxa remains unknown, but we believe that the blocking primer developed herein offers new possibilities to study the hidden diversity of microeukaryotes within snail microbiota, and to shed light on their underestimated interactions with bacteria and hosts.
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Affiliation(s)
- Camille Clerissi
- Current Affiliation: PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Camille Huot
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - Anaïs Portet
- Current Affiliation: MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Benjamin Gourbal
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - Eve Toulza
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
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11
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Abdul Manaff AHN, Hii KS, Luo Z, Liu M, Law IK, Teng ST, Akhir MF, Gu H, Leaw CP, Lim PT. Mapping harmful microalgal species by eDNA monitoring: A large-scale survey across the southwestern South China Sea. HARMFUL ALGAE 2023; 129:102515. [PMID: 37951609 DOI: 10.1016/j.hal.2023.102515] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/02/2023] [Accepted: 09/23/2023] [Indexed: 11/14/2023]
Abstract
A large-scale sampling was undertaken during a research cruise across the South China Sea in August 2016, covering an area of about 100,000 km2 to investigate the molecular diversity and distributions of micro-eukaryotic protists, with a focus on the potentially harmful microalgal (HAB) species along the east coast of Peninsular Malaysia. Environmental DNAs from 30 stations were extracted and DNA metabarcoding targeting the V4 and V9 markers in the 18S rDNA was performed. Many protistan molecular units, including previously unreported HAB taxa, were discovered for the first time in the water. Our findings also revealed interesting spatial distribution patterns, with a marked signal of compositional turnover between latitudinal regimes of water masses, where dinophytes and diatom compositions were among the most strongly enhanced at the fronts, leading to distinct niches. Our results further confirmed the widespread distribution of HAB species, such as the toxigenic Alexandrium tamiyavaichii and Pseudo-nitzschia species, and the fish-killing Margalefidinium polykrikoides and Karlodinium veneficum. The molecular information obtained from this study provides an updated HAB species inventory and a toolset that could facilitate existing HAB monitoring schemes in the region to better inform management decisions.
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Affiliation(s)
| | - Kieng Soon Hii
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, Bachok, Kelantan, Malaysia
| | - Zhaohe Luo
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Minlu Liu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Ing Kuo Law
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, Bachok, Kelantan, Malaysia
| | - Sing Tung Teng
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Mohd Fadzil Akhir
- Institute of Oceanography and Environment, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia
| | - Haifeng Gu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, Bachok, Kelantan, Malaysia.
| | - Po Teen Lim
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, Bachok, Kelantan, Malaysia.
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Al-khlifeh E, Khadem S, Hausmann B, Berry D. Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley. Front Microbiol 2023; 14:1258775. [PMID: 37954239 PMCID: PMC10637782 DOI: 10.3389/fmicb.2023.1258775] [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: 07/14/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023] Open
Abstract
Host phylogeny and the environment play vital roles in shaping animal microbiomes. However, the effects of these variables on the diversity and richness of the gut microbiome in different bioclimatic zones remain underexplored. In this study, we investigated the effects of host phylogeny and bioclimatic zone on the diversity and composition of the gut microbiota of two heterospecific rodent species, the spiny mouse Acomys cahirinus and the house mouse Mus musculus, in three bioclimatic zones of the African Great Rift Valley (GRV). We confirmed host phylogeny using the D-loop sequencing method and analyzed the influence of host phylogeny and bioclimatic zone parameters on the rodent gut microbiome using high-throughput amplicon sequencing of 16S rRNA gene fragments. Phylogenetic analysis supported the morphological identification of the rodents and revealed a marked genetic difference between the two heterospecific species. We found that bioclimatic zone had a significant effect on the gut microbiota composition while host phylogeny did not. Microbial alpha diversity of heterospecific hosts was highest in the Mediterranean forest bioclimatic zone, followed by the Irano-Turanian shrubland, and was lowest in the Sudanian savanna tropical zone. The beta diversity of the two rodent species showed significant differences across the Mediterranean, Irano-Turanian, and Sudanian regions. The phyla Firmicutes and Bacteroidetes were highly abundant, and Deferribacterota, Cyanobacteria and Proteobacteria were also prominent. Amplicon sequence variants (ASVs) were identified that were unique to the Sudanian bioclimatic zone. The core microbiota families recovered in this study were consistent among heterospecific hosts. However, diversity decreased in conspecific host populations found at lower altitudes in Sudanian bioclimatic zone. The composition of the gut microbiota is linked to the adaptation of the host to its environment, and this study underscores the importance of incorporating climatic factors such as elevation and ambient temperature, in empirical microbiome research and is the first to describe the rodent gut microbiome from the GRV.
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Affiliation(s)
- Enas Al-khlifeh
- Laboratory of Immunology, Department of Medical Laboratory Science, Al-Balqa Applied University, Al-Salt, Jordan
| | - Sanaz Khadem
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
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13
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Grižančić L, Baričević A, Smodlaka Tanković M, Vlašiček I, Knjaz M, Podolšak I, Kogovšek T, Pfannkuchen MA, Marić Pfannkuchen D. A metabarcode based (species) inventory of the northern Adriatic phytoplankton. Biodivers Data J 2023; 11:e106947. [PMID: 38318520 PMCID: PMC10840511 DOI: 10.3897/bdj.11.e106947] [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: 05/29/2023] [Accepted: 08/29/2023] [Indexed: 02/07/2024] Open
Abstract
Background The northern Adriatic is characterised as the coldest and most productive marine area of the Mediterranean, which is due to high nutrient levels introduced by river discharges, the largest of which is the Italian Po River (at the same time also the largest freshwater input into the Mediterranean). The northern Adriatic is a very shallow marine ecosystem with ocean current patterns that result in long retention times of plankton in the area. The northern Adriatic phytoplankton biodiversity and abundance are well-studied, through many scientific and long-term monitoring reports. These datasets were based on phytoplankton morphological traits traditionally obtained with light microscopy. The most recent comprehensive eastern Adriatic phytoplankton checklist was published more than 20 years ago and is still valuable today. Since phytoplankton taxonomy and systematics are constantly being reviewed (partly also due to new molecular methods of species identification that complement classical methodologies), checklists need to be updated and complemented. Today, metabarcoding of molecular markers gains more and more importance in biodiversity research and monitoring. Here, we report the use of high throughput sequencing methods to re-examine taxonomic richness and provide updated knowledge of phytoplankton diversity in the eastern northern Adriatic to complement the standardised light microscopy method. New information This study aimed to report an up-to-date list of the phytoplankton taxonomic richness and phylogenetic relationships in the eastern northern Adriatic, based on sequence variability of barcoding genes resolved with advanced molecular tools, namely metabarcoding. Here, metabarcoding is used to complement standardised light microscopy to advance conventional monitoring and research of phytoplankton communities for the purpose of assessing biodiversity and the status of the marine environments. Monthly two-year net sampling targeted six phytoplankton groups including Bacillariophyceae (diatoms) and Chrysophyceae (golden algae) belonging to Ochrophyta, Dinophyceae (dinoflagellates), Cryptophyceae (cryptophytes), Haptophyta (mostly coccolithophorids) and Chlorophyta with Prasinophyceae (prasinophytes) and Chlorophyceae (protist green algae). Generated sequence data were taxonomically assigned and redistributed in two kingdoms, five classes, 32 orders, 49 families and 67 genera. The most diverse group were dinoflagellates, comprising of 34 found genera (48.3%), following by diatoms with 23 (35.4%) and coccolithophorids with three genera (4.0%). In terms of genetic diversity, results were a bit different: a great majority of sequences with one nucleotide tolerance (ASVs, Amplicon sequence variants) assigned to species or genus level were dinoflagellates (83.8%), 13.7% diatoms and 1.6% Chlorophyta, respectively. Although many taxa have not been detected that have been considered as common in this area, metabarcoding revealed five diatoms and 20 dinoflagellate genera that were not reported in previous checklists, along with a few species from other targeted groups that have been reported previously. We here describe the first comprehensive 18S metabarcode inventory for the northern Adriatic Sea.
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Affiliation(s)
- Lana Grižančić
- Ruder Boskovic Institute, Centre for Marine Research, Rovinj-Rovigno, CroatiaRuder Boskovic Institute, Centre for Marine ResearchRovinj-RovignoCroatia
| | - Ana Baričević
- Ruder Boskovic Institute, Centre for Marine Research, Rovinj-Rovigno, CroatiaRuder Boskovic Institute, Centre for Marine ResearchRovinj-RovignoCroatia
| | - Mirta Smodlaka Tanković
- Ruder Boskovic Institute, Centre for Marine Research, Rovinj-Rovigno, CroatiaRuder Boskovic Institute, Centre for Marine ResearchRovinj-RovignoCroatia
| | - Ivan Vlašiček
- Ruder Boskovic Institute, Centre for Marine Research, Rovinj-Rovigno, CroatiaRuder Boskovic Institute, Centre for Marine ResearchRovinj-RovignoCroatia
| | - Mia Knjaz
- Ruder Boskovic Institute, Centre for Marine Research, Rovinj-Rovigno, CroatiaRuder Boskovic Institute, Centre for Marine ResearchRovinj-RovignoCroatia
| | - Ivan Podolšak
- Ruder Boskovic Institute, Centre for Marine Research, Rovinj-Rovigno, CroatiaRuder Boskovic Institute, Centre for Marine ResearchRovinj-RovignoCroatia
| | - Tjaša Kogovšek
- Ruder Boskovic Institute, Centre for Marine Research, Rovinj-Rovigno, CroatiaRuder Boskovic Institute, Centre for Marine ResearchRovinj-RovignoCroatia
| | - Martin Andreas Pfannkuchen
- Ruder Boskovic Institute, Centre for Marine Research, Rovinj-Rovigno, CroatiaRuder Boskovic Institute, Centre for Marine ResearchRovinj-RovignoCroatia
| | - Daniela Marić Pfannkuchen
- Ruder Boskovic Institute, Centre for Marine Research, Rovinj-Rovigno, CroatiaRuder Boskovic Institute, Centre for Marine ResearchRovinj-RovignoCroatia
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14
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Flegontova O, Lukeš J, Horák A. Intragenomic diversity of the V9 hypervariable domain in eukaryotes has little effect on metabarcoding. iScience 2023; 26:107291. [PMID: 37554448 PMCID: PMC10404988 DOI: 10.1016/j.isci.2023.107291] [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: 08/04/2022] [Revised: 05/05/2023] [Accepted: 07/03/2023] [Indexed: 08/10/2023] Open
Abstract
Metabarcoding revolutionized our understanding of diversity and ecology of microorganisms in different habitats. However, it is also associated with several inherent biases, one of which is associated with intragenomic diversity of a molecular barcode. Here, we compare intragenomic variability of the V9 region of the 18S rRNA gene in 19 eukaryotic phyla abundant in marine plankton. The level of intragenomic variability is comparable across all the phyla, and in most genomes and transcriptomes one V9 sequence and one OTU is predominant. However, most of the variability observed at the barcode level is probably caused by sequencing errors and is mitigated by using a denoising tool, DADA2. The SWARM algorithm commonly used in metabarcoding studies is not optimal for collapsing genuine and erroneous sequences into a single OTU, leading to an overestimation of diversity in metabarcoding data. For an unknown reason, SWARM inflates diversity of eupelagonemids more than that of other eukaryotes.
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Affiliation(s)
- Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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15
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Baricevic A, Maric Pfannkuchen D, Smodlaka Tankovic M, Knjaz M, Vlasicek I, Grizancic L, Kogovsek T, Pfannkuchen M. Identification of the heterotrophic nanoflagellate Bilabrum latius in the southern Adriatic (Mediterranean Sea). Eur J Protistol 2023; 90:125999. [PMID: 37352685 DOI: 10.1016/j.ejop.2023.125999] [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: 03/27/2023] [Revised: 05/23/2023] [Accepted: 06/06/2023] [Indexed: 06/25/2023]
Abstract
Heterotrophic flagellates (HF) represent an important protist group in marine ecosystem functioning. Characterised by high taxonomic diversity, identification and classification of HF is often difficult using classical methods of light microscopy (LM). Complementing LM with molecular methods, such as barcoding, enables reliable taxonomic identification of even small size nanoflagellates that share similar or unnoticeable morphological features. The order Bicosoecida is a group of heterotrophic nanoflagellates that are important part of protist plankton and benthic communities of the world oceans. Recently, on the basis of high-resolution light microscopy and barcoding, a new bicosoecid genus, Bilabrum, was described with B. latius sp. as a type species. Our study reports on identification of B. latius from co-culture with the diatom species Chaetoceros affinis isolated from fresh plankton samples collected in the southern Adriatic. This detection of the Adriatic B.latius represents first record of this species outside itś up to now known and described habitat (deep-sea sediment of the South - East Atlantic Ocean) and in diatom co-culture.
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Affiliation(s)
- Ana Baricevic
- Ruđer Bošković Institute, Center for Marine Research, G. Paliaga 5, Rovinj, Croatia.
| | | | | | - Mia Knjaz
- Ruđer Bošković Institute, Center for Marine Research, G. Paliaga 5, Rovinj, Croatia
| | - Ivan Vlasicek
- Ruđer Bošković Institute, Center for Marine Research, G. Paliaga 5, Rovinj, Croatia
| | - Lana Grizancic
- Ruđer Bošković Institute, Center for Marine Research, G. Paliaga 5, Rovinj, Croatia
| | - Tjasa Kogovsek
- Ruđer Bošković Institute, Center for Marine Research, G. Paliaga 5, Rovinj, Croatia
| | - Martin Pfannkuchen
- Ruđer Bošković Institute, Center for Marine Research, G. Paliaga 5, Rovinj, Croatia
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16
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Kezlya E, Tseplik N, Kulikovskiy M. Genetic Markers for Metabarcoding of Freshwater Microalgae: Review. BIOLOGY 2023; 12:1038. [PMID: 37508467 PMCID: PMC10376359 DOI: 10.3390/biology12071038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
The metabarcoding methods for studying the diversity of freshwater microalgae and routine biomonitoring are actively used in modern research. A lot of experience has been accumulated already, and many methodological questions have been solved (such as the influence of the methods and time of sample conservation, DNA extraction and bioinformatical processing). The reproducibility of the method has been tested and confirmed. However, one of the main problems-choosing a genetic marker for the study-still lacks a clear answer. We analyzed 70 publications and found out that studies on eukaryotic freshwater microalgae use 12 markers (different nuclear regions 18S and ITS and plastids rbcL, 23S and 16S). Each marker has its peculiarities; they amplify differently and have various levels of efficiency (variability) in different groups of algae. The V4 and V9 18S and rbcL regions are used most often. We concentrated especially on the studies that compare the results of using different markers and microscopy. We summarize the data on the primers for each region and on how the choice of a marker affects the taxonomic composition of a community.
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Affiliation(s)
- Elena Kezlya
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 127276 Moscow, Russia
| | - Natalia Tseplik
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 127276 Moscow, Russia
| | - Maxim Kulikovskiy
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 127276 Moscow, Russia
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17
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Romano F, Pitta P, John U. Community dynamics and co-occurrence relationships of pelagic ciliates and their potential prey at a coastal and an offshore station in the ultra-oligotrophic Eastern Mediterranean Sea. Front Genet 2023; 14:1219085. [PMID: 37547468 PMCID: PMC10400710 DOI: 10.3389/fgene.2023.1219085] [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: 05/08/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023] Open
Abstract
Ciliates have been recognized as one of the major components of the microbial food web, especially in ultra-oligotrophic waters, such as the Eastern Mediterranean Sea, where nutrients are scarce and the microbial community is dominated by pico- and nano-sized organisms. For this reason, ciliates play an important role in these ecosystems since they are the main planktonic grazers. Regardless the importance of these organisms, little is known about the community structure of heterotrophic and mixotrophic ciliates and how they are associated to their potential prey. In this study, we used 18S V4 rRNA gene metabarcoding to analyze ciliate community dynamics and how the relationship with potential prey changes according to different seasons and depths. Samples were collected seasonally at two stations of the Eastern Mediterranean Sea (HCB: coastal, M3A: offshore) from the surface and deep chlorophyll maximum (DCM) layers. The ciliate community structure varied across depths in HCB and across seasons in M3A, and the network analysis showed that in both stations, mixotrophic oligotrichs were positively associated with diatoms and showed few negative associations with ASVs annotated as marine Stramenopiles (MAST). On the other hand, heterotrophic tintinnids showed negative relationships in both HCB and M3A stations, mostly with Ochrophyta and Chlorophyta. These results showed, in first place that, although the two stations are close to each other, the ciliate dynamics differed between them. Moreover, mixotrophic and heterotrophic ciliates may have different ecological niches since mixotrophic ciliates may be more selective compared to heterotrophic species regarding their prey. These findings are the first glimpse into an understanding of the dynamics between heterotrophic and mixotrophic ciliates and their role in microbial assemblages and dynamics of ultra-oligotrophic environments.
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Affiliation(s)
- Filomena Romano
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
- Hellenic Centre for Marine Research, Institute of Oceanography, Heraklion, Greece
| | - Paraskevi Pitta
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Uwe John
- Ecological Chemistry, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
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18
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Wei J, Fontaine L, Valiente N, Dörsch P, Hessen DO, Eiler A. Trajectories of freshwater microbial genomics and greenhouse gas saturation upon glacial retreat. Nat Commun 2023; 14:3234. [PMID: 37270637 DOI: 10.1038/s41467-023-38806-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 05/15/2023] [Indexed: 06/05/2023] Open
Abstract
Due to climate warming, ice sheets around the world are losing mass, contributing to changes across terrestrial landscapes on decadal time spans. However, landscape repercussions on climate are poorly constrained mostly due to limited knowledge on microbial responses to deglaciation. Here, we reveal the genomic succession from chemolithotrophy to photo- and heterotrophy and increases in methane supersaturation in freshwater lakes upon glacial retreat. Arctic lakes at Svalbard also revealed strong microbial signatures form nutrient fertilization by birds. Although methanotrophs were present and increased along lake chronosequences, methane consumption rates were low even in supersaturated systems. Nitrous oxide oversaturation and genomic information suggest active nitrogen cycling across the entire deglaciated landscape, and in the high Arctic, increasing bird populations serve as major modulators at many sites. Our findings show diverse microbial succession patterns, and trajectories in carbon and nitrogen cycle processes representing a positive feedback loop of deglaciation on climate warming.
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Affiliation(s)
- Jing Wei
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
| | - Laurent Fontaine
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
| | - Nicolas Valiente
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
- Division of Terrestrial Ecosystem Research, Center of Microbiology and Environmental Systems Science, University of Vienna, 1030, Vienna, Austria
| | - Peter Dörsch
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Dag O Hessen
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
| | - Alexander Eiler
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway.
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19
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Cerfonteyn M, Groben R, Vaulot D, Guðmundsson K, Vannier P, Pérez-Hernández MD, Marteinsson VÞ. The distribution and diversity of eukaryotic phytoplankton in the Icelandic marine environment. Sci Rep 2023; 13:8519. [PMID: 37231140 DOI: 10.1038/s41598-023-35537-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/19/2023] [Indexed: 05/27/2023] Open
Abstract
Phytoplankton play a crucial role in the marine food web and are sensitive indicators of environmental change. Iceland is at the center of a contrasting hydrography, with cold Arctic water coming in from the north and warmer Atlantic water from the south, making this geographical location very sensitive to climate change. We used DNA metabarcoding to determine the biogeography of phytoplankton in this area of accelerating change. Seawater samples were collected in spring (2012-2018), summer (2017) and winter (2018) together with corresponding physico-chemical metadata around Iceland. Amplicon sequencing of the V4 region of the 18S rRNA gene indicates that eukaryotic phytoplankton community composition is different between the northern and southern water masses, with some genera completely absent from Polar Water masses. Emiliania was more dominant in the Atlantic-influenced waters and in summer, and Phaeocystis was more dominant in the colder, northern waters and in winter. The Chlorophyta picophytoplankton genus, Micromonas, was similarly dominant to the dominant diatom genus, Chaetoceros. This study presents an extensive dataset which can be linked with other 18s rRNA datasets for further investigation into the diversity and biogeography of marine protists in the North Atlantic.
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Affiliation(s)
- Mia Cerfonteyn
- Matís, Vinlandsleið 12, 113, Reykjavík, Iceland.
- Faculty of Food Science and Nutrition, University of Iceland, Læknagarður, Vatnsmyrarvegur 16, 101, Reykjavík, Iceland.
- Marine and Freshwater Research Institute, Fornubúðir 5, 220, Hafnarfjörður, Iceland.
| | - René Groben
- Matís, Vinlandsleið 12, 113, Reykjavík, Iceland
| | - Daniel Vaulot
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Kristinn Guðmundsson
- Marine and Freshwater Research Institute, Fornubúðir 5, 220, Hafnarfjörður, Iceland
| | | | - María Dolores Pérez-Hernández
- Unidad Océano y Clima, Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Unidad Asociada ULPGC-CSIC, Las Palmas de Gran Canaria, Spain
| | - Viggó Þór Marteinsson
- Matís, Vinlandsleið 12, 113, Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Læknagarður, Vatnsmyrarvegur 16, 101, Reykjavík, Iceland
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20
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Li S, Ren K, Yan X, Tsyganov AN, Mazei Y, Smirnov A, Mazei N, Zhang Y, Rensing C, Yang J. Linking biodiversity and ecological function through extensive microeukaryotic movement across different habitats in six urban parks. IMETA 2023; 2:e103. [PMID: 38868434 PMCID: PMC10989963 DOI: 10.1002/imt2.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/08/2023] [Accepted: 03/22/2023] [Indexed: 06/14/2024]
Abstract
Highly diverse but divergent microeukaryotes dwell in all types of habitats in urban park ecosystems. Extensive microbial migration occurs between both terrestrial and aquatic habitats. Microbial movement is beneficial to the maintenance of biodiversity and the exchange of functional guilds.
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Affiliation(s)
- Shuzhen Li
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed EcologyInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
| | - Kexin Ren
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed EcologyInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
| | - Xue Yan
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed EcologyInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
| | | | - Yuri Mazei
- Lomonosov Moscow State UniversityMoscowRussia
- Faculty of BiologyShenzhen MSU‐BIT UniversityShenzhenChina
- A. N. Severtsov Institute of Ecology and EvolutionRussian Academy of SciencesMoscowRussia
| | - Alexey Smirnov
- Department of Invertebrate Zoology, Faculty of BiologySt. Petersburg UniversitySt. PetersburgRussia
| | | | - Yiyue Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Christopher Rensing
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed EcologyInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
- Institute of Environmental Microbiology, College of Resources and the EnvironmentFujian Agriculture & Forestry UniversityFuzhouChina
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed EcologyInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
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21
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Clagnan E, Dell'Orto M, Štěrbová K, Grivalský T, Artur Câmara Manoel J, Masojídek J, D'Imporzano G, Gabriel Acién-Fernández F, Adani F. Impact of photobioreactor design on microalgae-bacteria communities grown on wastewater: Differences between thin-layer cascade and thin-layer raceway ponds. BIORESOURCE TECHNOLOGY 2023; 374:128781. [PMID: 36828223 DOI: 10.1016/j.biortech.2023.128781] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Thin-layer (TL) photobioreactors (PBRs) are characterised by high productivity. However, their use is limited to lab/pilot-scale, and a deeper level of characterisation is needed to reach industrial scale and test the resistance of multiple microalgae. Here, the performance and composition of eight microalgal communities cultivated in the two main TLs design (thin-layer cascade (TLC) and thin-layer raceway pond (RW)) were investigated through Illumina sequencing. Chlorella vulgaris showed robustness in both designs and often acted as an "invasive" species. Inoculum and reactor type brought variability. Eukaryotic microalgae inocula led to a more robust and stable community (higher similarity), however, RWs were characterised by a higher variability and did not favour the eukaryotic microalgae. The only cyanobacterial inoculum, Nostoc piscinale, was maintained, however the community was variable between designs. The reactor design had an effect on the N cycle with the TLC and RW configurations, enhancing nitrification and denitrification respectively.
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Affiliation(s)
- Elisa Clagnan
- Gruppo Ricicla Labs., Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli studi di Milano, Via Celoria 2, 20133, Italy.
| | - Marta Dell'Orto
- Gruppo Ricicla Labs., Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli studi di Milano, Via Celoria 2, 20133, Italy
| | - Karolína Štěrbová
- Centre Algatech, Laboratory of Algal Biotechnology, Institute of Microbiology CAS, Novohradská 237, 37901 Třeboň, Czech Republic
| | - Tomáš Grivalský
- Centre Algatech, Laboratory of Algal Biotechnology, Institute of Microbiology CAS, Novohradská 237, 37901 Třeboň, Czech Republic
| | - João Artur Câmara Manoel
- Centre Algatech, Laboratory of Algal Biotechnology, Institute of Microbiology CAS, Novohradská 237, 37901 Třeboň, Czech Republic
| | - Jiří Masojídek
- Centre Algatech, Laboratory of Algal Biotechnology, Institute of Microbiology CAS, Novohradská 237, 37901 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
| | - Giuliana D'Imporzano
- Gruppo Ricicla Labs., Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli studi di Milano, Via Celoria 2, 20133, Italy
| | - Francisco Gabriel Acién-Fernández
- Department of Chemical Engineering, CIESOL Solar Energy Research Centre, University of Almeria, Cañada San Urbano, s/n, 04120 Almeria, Spain
| | - Fabrizio Adani
- Gruppo Ricicla Labs., Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli studi di Milano, Via Celoria 2, 20133, Italy
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22
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Turk Dermastia T, Vascotto I, Francé J, Stanković D, Mozetič P. Evaluation of the rbcL marker for metabarcoding of marine diatoms and inference of population structure of selected genera. Front Microbiol 2023; 14:1071379. [PMID: 36950161 PMCID: PMC10026700 DOI: 10.3389/fmicb.2023.1071379] [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: 10/16/2022] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
Diatoms are one of the most important phytoplankton groups in the world's oceans. There are responsible for up to 40% of the photosynthetic activity in the Ocean, and they play an important role in the silicon and carbon cycles by decoupling carbon from atmospheric interactions through sinking and export. These processes are strongly influenced by the taxonomic composition of diatom assemblages. Traditionally, these have been assessed using microscopy, which in some cases is not reliable or reproducible. Next-generation sequencing enabled us to study diversity in a high-throughput manner and uncover new distribution patterns and diversity. However, phylogenetic markers used for this purpose, such as various 18S rDNA regions, are often insufficient because they cannot distinguish between some taxa. In this work, we demonstrate the performance of the chloroplast-encoded rbcL marker for metabarcoding marine diatoms compared to microscopy and 18S-V9 metabarcoding using a series of monthly samples from the Gulf of Trieste (GoT), northern Adriatic Sea. We demonstrate that rbcL is able to detect more taxa compared to 18S-V9 metabarcoding or microscopy, while the overall structure of the diatom assemblage was comparable to the other two methods with some variations, that were taxon dependent. In total, 6 new genera and 22 new diatom species for the study region were identified. We were able to spot misidentification of genera obtained with microscopy such as Pseudo-nitzschia galaxiae, which was mistaken for Cylindrotheca closterium, as well as genera that were completely overlooked, such as Minidiscus and several genera from the Cymatosiraceae family. Furthermore, on the example of two well-studied genera in the region, namely Chaetoceros and particularly Pseudo-nitzschia, we show how the rbcL method can be used to infer even deeper phylogenetic and ecologically significant differences at the species population level. Despite a very thorough community analysis obtained by rbcL the incompleteness of reference databases was still evident, and we shed light on possible improvements. Our work has further implications for studies dealing with taxa distribution and population structure, as well as carbon and silica flux models and networks.
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Affiliation(s)
- Timotej Turk Dermastia
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Ivano Vascotto
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Janja Francé
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - David Stanković
- Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
| | - Patricija Mozetič
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
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23
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Décima M, Stukel MR, Nodder SD, Gutiérrez-Rodríguez A, Selph KE, Dos Santos AL, Safi K, Kelly TB, Deans F, Morales SE, Baltar F, Latasa M, Gorbunov MY, Pinkerton M. Salp blooms drive strong increases in passive carbon export in the Southern Ocean. Nat Commun 2023; 14:425. [PMID: 36732522 PMCID: PMC9894854 DOI: 10.1038/s41467-022-35204-6] [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: 04/09/2021] [Accepted: 11/23/2022] [Indexed: 02/04/2023] Open
Abstract
The Southern Ocean contributes substantially to the global biological carbon pump (BCP). Salps in the Southern Ocean, in particular Salpa thompsoni, are important grazers that produce large, fast-sinking fecal pellets. Here, we quantify the salp bloom impacts on microbial dynamics and the BCP, by contrasting locations differing in salp bloom presence/absence. Salp blooms coincide with phytoplankton dominated by diatoms or prymnesiophytes, depending on water mass characteristics. Their grazing is comparable to microzooplankton during their early bloom, resulting in a decrease of ~1/3 of primary production, and negative phytoplankton rates of change are associated with all salp locations. Particle export in salp waters is always higher, ranging 2- to 8- fold (average 5-fold), compared to non-salp locations, exporting up to 46% of primary production out of the euphotic zone. BCP efficiency increases from 5 to 28% in salp areas, which is among the highest recorded in the global ocean.
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Affiliation(s)
- Moira Décima
- National Institute of Water and Atmospheric Research (NIWA), Hataitai, Wellington, 6021, New Zealand. .,Scripps Institution of Oceanography, University of California at San Diego, San Diego, CA, 92093, USA.
| | - Michael R Stukel
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, 32304, USA.,Center for Ocean-Atmospheric Prediction Studies, Florida State University, Tallahassee, FL, 32310, USA
| | - Scott D Nodder
- National Institute of Water and Atmospheric Research (NIWA), Hataitai, Wellington, 6021, New Zealand
| | - Andrés Gutiérrez-Rodríguez
- National Institute of Water and Atmospheric Research (NIWA), Hataitai, Wellington, 6021, New Zealand.,Instituto Español de Oceanografía, Centro Oceanográfico de Gijón, Avenida Príncipe de Asturias, 70 bis, 33212, Gijón, Spain
| | - Karen E Selph
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Adriana Lopes Dos Santos
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Karl Safi
- National Institute of Water and Atmospheric Research, P.O. Box 11-115, Hamilton, New Zealand
| | - Thomas B Kelly
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, 32304, USA.,College of Fisheries and Ocean Sciences, University of Alaska, Fairbanks, AK, 99775, USA
| | - Fenella Deans
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Federico Baltar
- Department of Functional & Evolutionary Ecology, University of Vienna, Vienna, 1090, Austria
| | - Mikel Latasa
- Instituto Español de Oceanografía, Centro Oceanográfico de Gijón, Avenida Príncipe de Asturias, 70 bis, 33212, Gijón, Spain
| | - Maxim Y Gorbunov
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Matt Pinkerton
- National Institute of Water and Atmospheric Research (NIWA), Hataitai, Wellington, 6021, New Zealand
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24
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Vincent F, Gralka M, Schleyer G, Schatz D, Cabrera-Brufau M, Kuhlisch C, Sichert A, Vidal-Melgosa S, Mayers K, Barak-Gavish N, Flores JM, Masdeu-Navarro M, Egge JK, Larsen A, Hehemann JH, Marrasé C, Simó R, Cordero OX, Vardi A. Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms. Nat Commun 2023; 14:510. [PMID: 36720878 PMCID: PMC9889395 DOI: 10.1038/s41467-023-36049-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 01/13/2023] [Indexed: 02/01/2023] Open
Abstract
Algal blooms are hotspots of marine primary production and play central roles in microbial ecology and global elemental cycling. Upon demise of the bloom, organic carbon is partly respired and partly transferred to either higher trophic levels, bacterial biomass production or sinking. Viral infection can lead to bloom termination, but its impact on the fate of carbon remains largely unquantified. Here, we characterize the interplay between viral infection and the composition of a bloom-associated microbiome and consequently the evolving biogeochemical landscape, by conducting a large-scale mesocosm experiment where we monitor seven induced coccolithophore blooms. The blooms show different degrees of viral infection and reveal that only high levels of viral infection are followed by significant shifts in the composition of free-living bacterial and eukaryotic assemblages. Intriguingly, upon viral infection the biomass of eukaryotic heterotrophs (thraustochytrids) rivals that of bacteria as potential recyclers of organic matter. By combining modeling and quantification of active viral infection at a single-cell resolution, we estimate that viral infection causes a 2-4 fold increase in per-cell rates of extracellular carbon release in the form of acidic polysaccharides and particulate inorganic carbon, two major contributors to carbon sinking into the deep ocean. These results reveal the impact of viral infection on the fate of carbon through microbial recyclers of organic matter in large-scale coccolithophore blooms.
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Affiliation(s)
- Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Developmental Biology Unit, European Molecular Biological Laboratory, 69117, Heidelberg, Germany
| | - Matti Gralka
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02145, MA, USA.,Systems Biology Lab, Amsterdam Institute for Life and Environment (A-Life)/Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081, Amsterdam, The Netherlands
| | - Guy Schleyer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | | | - Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Andreas Sichert
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02145, MA, USA.,Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Kyle Mayers
- NORCE Norwegian Research Centre, 5008, Bergen, Norway
| | - Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - J Michel Flores
- Department of Earth and Planetary Science, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | | | - Jorun Karin Egge
- Department of Biological Sciences (BIO), University of Bergen, 5020, Bergen, Norway
| | - Aud Larsen
- NORCE Norwegian Research Centre, 5008, Bergen, Norway.,Department of Biological Sciences (BIO), University of Bergen, 5020, Bergen, Norway
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Celia Marrasé
- Institut de Ciències del Mar, CSIC, 08003, Barcelona, Spain
| | - Rafel Simó
- Institut de Ciències del Mar, CSIC, 08003, Barcelona, Spain
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02145, MA, USA
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel.
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25
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Gaonkar CC, Campbell L. Metabarcoding reveals high genetic diversity of harmful algae in the coastal waters of Texas, Gulf of Mexico. HARMFUL ALGAE 2023; 121:102368. [PMID: 36639185 DOI: 10.1016/j.hal.2022.102368] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/10/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Environmental-DNA (eDNA) for metabarcoding is a rapid and effective means to investigate microplankton community composition and species diversity. The objective of this study was to examine the genetic diversity of the phytoplankton community in the Gulf of Mexico, with particular emphasis on harmful algal bloom species. Samples were collected at stations along the coast of Texas in September-October 2017 that were inundated by low salinity waters in the aftermath of Hurricane Harvey. Metabarcodes were generated from the eDNA targeting both the V4 and V8-V9 regions of the 18S rDNA gene. Evaluation of the metabarcodes revealed an unexpectedly high number of harmful algal species during this short period, including five that had not been documented in this region previously. A total of 36 harmful algal species could be differentiated based on V4 and V8-V9 metabarcode markers. Using a phylogenetic approach, the taxonomic resolution of each marker differed and not all species could be differentiated using solely one marker. The V4 region resolved species within some genera (e.g., Heterocapsa), while the V8-V9 marker was necessary to resolve species within other genera (e.g., Chattonella). In other cases, species differentiation within a genus required a combination of both markers (e.g., Prorocentrum, Karenia), or another marker will be needed to resolve all species (e.g., Alexandrium, Dinophysis). We conclude that no single marker can delineate all species, so it is recommended HAB monitoring programs use more than one marker. Overall, the observed diversity of HAB species along the Texas coast using metabarcoding exceeded reports from other parts of the world.
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Affiliation(s)
- Chetan C Gaonkar
- Department of Oceanography, Texas A&M University, College Station, TX 77843, USA
| | - Lisa Campbell
- Department of Oceanography, Texas A&M University, College Station, TX 77843, USA.
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26
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Greco M, Morard R, Darling K, Kucera M. Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera. PeerJ 2023; 11:e15255. [PMID: 37123000 PMCID: PMC10143585 DOI: 10.7717/peerj.15255] [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: 10/24/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Ribosomal intragenomic variability in prokaryotes and eukaryotes is a genomic feature commonly studied for its inflationary impact on molecular diversity assessments. However, the evolutionary mechanisms and distribution of this phenomenon within a microbial group are rarely explored. Here, we investigate the intragenomic variability in 33 species of planktonic foraminifera, calcifying marine protists, by inspecting 2,403 partial SSU sequences obtained from single-cell clone libraries. Our analyses show that polymorphisms are common among planktonic foraminifera species, but the number of polymorphic sites significantly differs among clades. With our molecular simulations, we could assess that most of these mutations are located in paired regions that do not affect the secondary structure of the SSU fragment. Finally, by mapping the number of polymorphic sites on the phylogeny of the clades, we were able to discuss the evolution and potential sources of intragenomic variability in planktonic foraminifera, linking this trait to the distinctive nuclear and genomic dynamics of this microbial group.
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Affiliation(s)
- Mattia Greco
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Institut de Ciències del Mar (ICM), Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Raphaël Morard
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kate Darling
- School of Geosciences, University of Edinburgh, Edinburgh, United Kingdom
- Biological and Environmental Sciences, University of Stirling, Stirling, United Kingdom
| | - Michal Kucera
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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27
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Clagnan E, D'Imporzano G, Dell'Orto M, Bani A, Dumbrell AJ, Parati K, Acién-Fernández FG, Portillo-Hahnefeld A, Martel-Quintana A, Gómez-Pinchetti JL, Adani F. Centrate as a sustainable growth medium: Impact on microalgal inocula and bacterial communities in tubular photobioreactor cultivation systems. BIORESOURCE TECHNOLOGY 2022; 363:127979. [PMID: 36126844 DOI: 10.1016/j.biortech.2022.127979] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/11/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Centrate is a low-cost alternative to synthetic fertilizers for microalgal cultivation, reducing environmental burdens and remediation costs. Adapted microalgae need to be selected and characterised to maximise biomass production and depuration efficiency. Here, the performance and composition of six microalgal communities cultivated both on synthetic media and centrate within semi-open tubular photobioreactors were investigated through Illumina sequencing. Biomass grown on centrate, exposed to a high concentration of ammonium, showed a higher quantity of nitrogen (5.6% dry weight) than the biomass grown on the synthetic media nitrate (3.9% dry weight). Eukaryotic inocula were replaced by other microalgae while cyanobacterial inocula were maintained. Communities were generally similar for the same inoculum between media, however, inoculation with cyanobacteria led to variability within the eukaryotic community. Where communities differed, centrate resulted in a higher richness and diversity. The higher nitrogen of centrate possibly led to higher abundance of genes coding for N metabolism enzymes.
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Affiliation(s)
- Elisa Clagnan
- Gruppo Ricicla labs., Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli studi di Milano, Via Celoria 2, 20133, Italy
| | - Giuliana D'Imporzano
- Gruppo Ricicla labs., Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli studi di Milano, Via Celoria 2, 20133, Italy.
| | - Marta Dell'Orto
- Gruppo Ricicla labs., Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli studi di Milano, Via Celoria 2, 20133, Italy
| | - Alessia Bani
- Gruppo Ricicla labs., Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli studi di Milano, Via Celoria 2, 20133, Italy; School of Life Science, University of Essex, Wivenhoe Park, Colchester, Essex CO3 4SQ, UK; Istituto Sperimentale Lazzaro Spallanzani, loc La Quercia, 2602 Rivolta d'Adda, CR, Italy
| | - Alex J Dumbrell
- School of Life Science, University of Essex, Wivenhoe Park, Colchester, Essex CO3 4SQ, UK
| | - Katia Parati
- Istituto Sperimentale Lazzaro Spallanzani, loc La Quercia, 2602 Rivolta d'Adda, CR, Italy
| | - Francisco Gabriel Acién-Fernández
- Department of Chemical Engineering, CIESOL Solar Energy Research Centre, University of Almeria, Cañada San Urbano, s/n, 04120 Almeria, Spain
| | - Agustín Portillo-Hahnefeld
- Spanish Bank of Algae (BEA), Institute of Oceanography and Global Change (IOCAG), University of Las Palmas de Gran Canaria, Muelle de Taliarte s/n, 35214 Telde, Canary Islands, Spain
| | - Antera Martel-Quintana
- Spanish Bank of Algae (BEA), Institute of Oceanography and Global Change (IOCAG), University of Las Palmas de Gran Canaria, Muelle de Taliarte s/n, 35214 Telde, Canary Islands, Spain
| | - Juan Luis Gómez-Pinchetti
- Spanish Bank of Algae (BEA), Institute of Oceanography and Global Change (IOCAG), University of Las Palmas de Gran Canaria, Muelle de Taliarte s/n, 35214 Telde, Canary Islands, Spain
| | - Fabrizio Adani
- Gruppo Ricicla labs., Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli studi di Milano, Via Celoria 2, 20133, Italy
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28
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Vaulot D, Sim CWH, Ong D, Teo B, Biwer C, Jamy M, Lopes dos Santos A. metaPR 2 : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists. Mol Ecol Resour 2022; 22:3188-3201. [PMID: 35762265 PMCID: PMC9796713 DOI: 10.1111/1755-0998.13674] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/26/2022] [Accepted: 06/20/2022] [Indexed: 01/07/2023]
Abstract
In recent years, metabarcoding has become the method of choice for investigating the composition and assembly of microbial eukaryotic communities. The number of environmental data sets published has increased very rapidly. Although unprocessed sequence files are often publicly available, processed data, in particular clustered sequences, are rarely available in a usable format. Clustered sequences are reported as operational taxonomic units (OTUs) with different similarity levels or more recently as amplicon sequence variants (ASVs). This hampers comparative studies between different environments and data sets, for example examining the biogeographical patterns of specific groups/species, as well analysing the genetic microdiversity within these groups. Here, we present a newly-assembled database of processed 18S rRNA metabarcodes that are annotated with the PR2 reference sequence database. This database, called metaPR2 , contains 41 data sets corresponding to more than 4000 samples and 90,000 ASVs. The database, which is accessible through both a web-based interface (https://shiny.metapr2.org) and an R package, should prove very useful to all researchers working on protist diversity in a variety of systems.
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Affiliation(s)
- Daniel Vaulot
- UMR 7144, ECOMAP, CNRSSorbonne Université, Station Biologique de RoscoffRoscoffFrance
| | | | - Denise Ong
- Asian School of the EnvironmentNanyang Technological UniversitySingapore
| | - Bryan Teo
- Asian School of the EnvironmentNanyang Technological UniversitySingapore
| | - Charlie Biwer
- Department of Organismal Biology (Systematic Biology)Uppsala UniversityUppsalaSweden
| | - Mahwash Jamy
- Department of Organismal Biology (Systematic Biology)Uppsala UniversityUppsalaSweden
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29
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Lee HB, Jeong DH, Cho BC, Park JS. The Diversity Patterns of Rare to Abundant Microbial Eukaryotes Across a Broad Range of Salinities in a Solar Saltern. MICROBIAL ECOLOGY 2022; 84:1103-1121. [PMID: 34779881 PMCID: PMC9747883 DOI: 10.1007/s00248-021-01918-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Solar salterns are excellent artificial systems for examining species diversity and succession along salinity gradients. Here, the eukaryotic community in surface water of a Korean solar saltern (30 to 380 practical salinity units) was investigated from April 2019 to October 2020 using Illumina sequencing targeting the V4 and V9 regions of 18S rDNA. A total of 926 operational taxonomic units (OTUs) and 1,999 OTUs were obtained with the V4 and V9 regions, respectively. Notably, most of the OTUs were microbial eukaryotes, and the high-abundance groups (> 5% relative abundance (RA), Alveolata, Stramenopila, Archaeplastida, and Opisthokonta) usually accounted for > 90% of the total cumulative read counts and > 80% of all OTUs. Moreover, the high-abundance Alveolata (larger forms) and Stramenopila (smaller forms) groups displayed a significant inverse relationship, probably due to predator-prey interactions. Most of the low-abundance (0.1-5% RA) and rare (< 0.1% RA) groups remained small portion during the field surveys. Taxonomic novelty (at < 90% sequence identity) was high in the Amoebozoa, Cryptista, Haptista, Rhizaria, and Stramenopila groups (69.8% of all novel OTUs), suggesting the presence of a large number of hidden species in hypersaline environments. Remarkably, the high-abundance groups had little overlap with the other groups, implying the weakness of rare-to-prevalent community dynamics. The low-abundance Discoba group alone temporarily became the high-abundance group, suggesting that it is an opportunistic group. Overall, the composition and diversity of the eukaryotic community in hypersaline environments may be persistently stabilized, despite diverse disturbance events.
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Affiliation(s)
- Hyeon Been Lee
- Department of Oceanography, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Dong Hyuk Jeong
- Department of Oceanography, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Byung Cheol Cho
- School of Earth and Environmental Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Saemangeum Environmental Research Center, Kunsan National University, Kunsan, 54150, Republic of Korea
| | - Jong Soo Park
- Department of Oceanography, Kyungpook National University, Daegu, 41566, Republic of Korea.
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30
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John U, Šupraha L, Gran-Stadniczeñko S, Bunse C, Cembella A, Eikrem W, Janouškovec J, Klemm K, Kühne N, Naustvoll L, Voss D, Wohlrab S, Edvardsen B. Spatial and biological oceanographic insights into the massive fish-killing bloom of the haptophyte Chrysochromulina leadbeateri in northern Norway. HARMFUL ALGAE 2022; 118:102287. [PMID: 36195411 DOI: 10.1016/j.hal.2022.102287] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 05/04/2022] [Accepted: 07/03/2022] [Indexed: 06/16/2023]
Abstract
A bloom of the fish-killing haptophyte Chrysochromulina leadbeateri in northern Norway during May and June 2019 was the most harmful algal event ever recorded in the region, causing massive mortalities of farmed salmon. Accordingly, oceanographic and biodiversity aspects of the bloom were studied in unprecedented detail, based on metabarcoding and physico-chemical and biotic factors related with the dynamics and distribution of the bloom. Light- and electron-microscopical observations of nanoplankton samples from diverse locations confirmed that C. leadbeateri was dominant in the bloom and the primary cause of associated fish mortalities. Cell counts by light microscopy and flow cytometry were obtained throughout the regional bloom within and adjacent to five fjord systems. Metabarcoding sequences of the V4 region of the 18S rRNA gene from field material collected during the bloom and a cultured isolate from offshore of Tromsøy island confirmed the species identification. Sequences from three genetic markers (18S, 28S rRNA gene and ITS region) verified the close if not identical genetic similarity to C. leadbeateri from a previous massive fish-killing bloom in 1991 in northern Norway. The distribution and cell abundance of C. leadbeateri and related Chrysochromulina species in the recent incident were tracked by integrating observations from metabarcoding sequences of the V4 region of the 18S rRNA gene. Metabarcoding revealed at least 14 distinct Chrysochromulina variants, including putative cryptic species. C. leadbeateri was by far the most abundant of these species, but with high intraspecific genetic variability. Highest cell abundance of up to 2.7 × 107 cells L - 1 of C. leadbeateri was found in Balsfjorden; the high cell densities were associated with stratification near the pycnocline (at ca. 12 m depth) within the fjord. The cell abundance of C. leadbeateri showed positive correlations with temperature, negative correlation with salinity, and a slightly positive correlation with ambient phosphate and nitrate concentrations. The spatio-temporal succession of the C. leadbeateri bloom suggests independent initiation from existing pre-bloom populations in local zones, perhaps sustained and supplemented over time by northeastward advection of the bloom from the fjords.
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Affiliation(s)
- Uwe John
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany; Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heersstraße 231, 26129 Oldenburg, Germany.
| | - Luka Šupraha
- Section for Aquatic Biology and Toxicology, Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway
| | - Sandra Gran-Stadniczeñko
- Section for Aquatic Biology and Toxicology, Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway
| | - Carina Bunse
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heersstraße 231, 26129 Oldenburg, Germany; ICBM: Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Allan Cembella
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Wenche Eikrem
- Section for Aquatic Biology and Toxicology, Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway
| | - Jan Janouškovec
- Section for Aquatic Biology and Toxicology, Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway
| | - Kerstin Klemm
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Nancy Kühne
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Lars Naustvoll
- Institute of Marine Research, P.O box 1871 Nordnes, NO-5817 Bergen, Norway
| | - Daniela Voss
- ICBM: Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Sylke Wohlrab
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany; Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heersstraße 231, 26129 Oldenburg, Germany
| | - Bente Edvardsen
- Section for Aquatic Biology and Toxicology, Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway
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Russo L, Casella V, Marabotti A, Jordán F, Congestri R, D'Alelio D. Trophic hierarchy in a marine community revealed by network analysis on co-occurrence data. FOOD WEBS 2022. [DOI: 10.1016/j.fooweb.2022.e00246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Salmaso N, Vasselon V, Rimet F, Vautier M, Elersek T, Boscaini A, Donati C, Moretto M, Pindo M, Riccioni G, Stefani E, Capelli C, Lepori F, Kurmayer R, Mischke U, Klemenčič AK, Novak K, Greco C, Franzini G, Fusato G, Giacomazzi F, Lea A, Menegon S, Zampieri C, Macor A, Virgilio D, Zanut E, Zorza R, Buzzi F, Domaizon I. DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155175. [PMID: 35421505 DOI: 10.1016/j.scitotenv.2022.155175] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
The taxonomic identification of organisms based on the amplification of specific genetic markers (metabarcoding) implicitly requires adequate discriminatory information and taxonomic coverage of environmental DNA sequences in taxonomic databases. These requirements were quantitatively examined by comparing the determination of cyanobacteria and microalgae obtained by metabarcoding and light microscopy. We used planktic and biofilm samples collected in 37 lakes and 22 rivers across the Alpine region. We focused on two of the most used and best represented genetic markers in the reference databases, namely the 16S rRNA and 18S rRNA genes. A sequence gap analysis using blastn showed that, in the identity range of 99-100%, approximately 30% (plankton) and 60% (biofilm) of the sequences did not find any close counterpart in the reference databases (NCBI GenBank). Similarly, a taxonomic gap analysis showed that approximately 50% of the cyanobacterial and eukaryotic microalgal species identified by light microscopy were not represented in the reference databases. In both cases, the magnitude of the gaps differed between the major taxonomic groups. Even considering the species determined under the microscope and represented in the reference databases, 22% and 26% were still not included in the results obtained by the blastn at percentage levels of identity ≥95% and ≥97%, respectively. The main causes were the absence of matching sequences due to amplification and/or sequencing failure and potential misidentification in the microscopy step. Our results quantitatively demonstrated that in metabarcoding the main obstacles in the classification of 16S rRNA and 18S rRNA sequences and interpretation of high-throughput sequencing biomonitoring data were due to the existence of important gaps in the taxonomic completeness of the reference databases and the short length of reads. The study focused on the Alpine region, but the extent of the gaps could be much greater in other less investigated geographic areas.
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Affiliation(s)
- Nico Salmaso
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Valentin Vasselon
- OFB, Pôle R&D ECLA, Site INRAE CARRTEL, 75bis av. de Corzent - CS 50511, FR-74203 Thonon les Bains cedex, France.
| | - Frédéric Rimet
- INRAE, UMR Carrtel, Université Savoie Mont Blanc, Pole R&D ECLA, 75bis av. de Corzent - CS 50511, FR-74203 Thonon les Bains cedex, France.
| | - Marine Vautier
- INRAE, UMR Carrtel, Université Savoie Mont Blanc, Pole R&D ECLA, 75bis av. de Corzent - CS 50511, FR-74203 Thonon les Bains cedex, France.
| | - Tina Elersek
- National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia.
| | - Adriano Boscaini
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Marco Moretto
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Giulia Riccioni
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Erika Stefani
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
| | - Camilla Capelli
- Institute of Earth Sciences, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Flora Ruchat-Roncati 15, 6850 Mendrisio, Switzerland.
| | - Fabio Lepori
- Institute of Earth Sciences, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Flora Ruchat-Roncati 15, 6850 Mendrisio, Switzerland.
| | - Rainer Kurmayer
- Research Department for Limnology, University of Innsbruck, Mondseestraße 9, 5310 Mondsee, Austria.
| | - Ute Mischke
- Bavarian Environment Agency, Ref. 83, Wielenbach, Germany.
| | | | - Katarina Novak
- Slovenian Environment Agency, Vojkova 1b, 1000 Ljubljana, Slovenia.
| | - Claudia Greco
- Italian National Institute for Environmental Protection and Research (ISPRA), Ozzano, Italy.
| | - Giorgio Franzini
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via A. Dominutti 8, 37135 Verona, Italy.
| | - Giampaolo Fusato
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via A. Dominutti 8, 37135 Verona, Italy.
| | - Federica Giacomazzi
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via A. Dominutti 8, 37135 Verona, Italy.
| | - Alessia Lea
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via Ospedale Civile 24, 35121 Padova, Italy.
| | - Silvia Menegon
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via Santa Barbara 5/a, 31100 Treviso, Italy.
| | - Chiara Zampieri
- ARPAV, Regional Agency for Environmental Protection and Prevention of Veneto, Via A. Dominutti 8, 37135 Verona, Italy.
| | - Arianna Macor
- ARPA FVG, Regional Environmental Protection Agency of Friuli Venezia Giulia, Via Cairoli 14, 33057 Palmanova, UD, Italy.
| | - Damiano Virgilio
- ARPA FVG, Regional Environmental Protection Agency of Friuli Venezia Giulia, Via Cairoli 14, 33057 Palmanova, UD, Italy.
| | - Elisa Zanut
- ARPA FVG, Regional Environmental Protection Agency of Friuli Venezia Giulia, Via Cairoli 14, 33057 Palmanova, UD, Italy.
| | - Raffaella Zorza
- ARPA FVG, Regional Environmental Protection Agency of Friuli Venezia Giulia, Via Cairoli 14, 33057 Palmanova, UD, Italy.
| | - Fabio Buzzi
- ARPA Lombardia, Sede di Lecco, U.O. Laghi e Monitoraggio Biologico Fiumi, Italy.
| | - Isabelle Domaizon
- INRAE, UMR Carrtel, Université Savoie Mont Blanc, Pole R&D ECLA, 75bis av. de Corzent - CS 50511, FR-74203 Thonon les Bains cedex, France.
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Martin JL, Santi I, Pitta P, John U, Gypens N. Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.85794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Plankton metabarcoding is increasingly implemented in marine ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on microscopy (morphological). 18S rRNA gene is the most widely used marker for groups’ and species’ detection and classification within marine eukaryotic microorganisms. These datasets have commonly relied on the acquisition of organismal abundances directly from the number of DNA sequences (i.e. reads). Besides the inherent technical biases in metabarcoding, the largely varying 18S rRNA gene copy numbers (GCN) among marine protists (ranging from tens to thousands) is one of the most important biological biases for species quantification. In this work, we present a gene copy number correction factor (CF) for four marine planktonic groups: Bacillariophyta, Dinoflagellata, Ciliophora miscellaneous and flagellated cells. On the basis of the theoretical assumption that ‘1 read’ is equivalent to ‘1 GCN’, we used the GCN median values per plankton group to calculate the corrected cell number and biomass relative abundances. The species-specific absolute GCN per cell were obtained from various studies published in the literature. We contributed to the development of a species-specific 18S rRNA GCN database proposed by previous authors. To assess the efficiency of the correction factor we compared the metabarcoding, morphological and corrected relative abundances (in cell number and biomass) of 15 surface water samples collected in the Belgian Coastal Zone. Results showed that the application of the correction factor over metabarcoding results enables us to significantly improve the estimates of cell abundances for Dinoflagellata, Ciliophora and flagellated cells, but not for Bacillariophyta. This is likely to due to large biovolume plasticity in diatoms not corresponding to genome size and gene copy numbers. C-biomass relative abundance estimations directly from amplicon reads were only improved for Dinoflagellata and Ciliophora. The method is still facing biases related to the low number of species GCN assessed. Nevertheless, the increase of species in the GCN database may lead to the refinement of the proposed correction factor.
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34
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Kanjer L, Filek K, Mucko M, Majewska R, Gračan R, Trotta A, Panagopoulou A, Corrente M, Di Bello A, Bosak S. Surface microbiota of Mediterranean loggerhead sea turtles unraveled by 16S and 18S amplicon sequencing. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.907368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The loggerhead sea turtle is considered a keystone species with a major ecological role in Mediterranean marine environment. As is the case with other wild reptiles, their outer microbiome is rarely studied. Although there are several studies on sea turtle’s macro-epibionts and endo-microbiota, there has been little research on epibiotic microbiota associated with turtle skin and carapace. Therefore we aimed to provide the identification of combined epibiotic eukaryotic, bacterial and archaeal microbiota on Mediterranean loggerhead sea turtles. In this study, we sampled skins and carapaces of 26 loggerheads from the Mediterranean Sea during 2018 and 2019. To investigate the overall microbial diversity and composition, amplicon sequencing of 16S and 18S rRNA genes was performed. We found that the Mediterranean loggerhead sea turtle epibiotic microbiota is a reservoir of a vast variety of microbial species. Microbial communities mostly varied by different locations and seas, while within bacterial communities’ significant difference was observed between sampled body sites (carapace vs. skin). In terms of relative abundance, Proteobacteria and Bacteroidota were the most represented phyla within prokaryotes, while Alveolata and Stramenopiles thrived among eukaryotes. This study, besides providing a first survey of microbial eukaryotes on loggerheads via metabarcoding, identifies fine differences within both bacterial and eukaryotic microbial communities that seem to reflect the host anatomy and habitat. Multi-domain epi-microbiome surveys provide additional layers of information that are complementary with previous morphological studies and enable better understanding of the biology and ecology of these vulnerable marine reptiles.
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Liu S, Cui Z, Zhao Y, Chen N. Composition and spatial-temporal dynamics of phytoplankton community shaped by environmental selection and interactions in the Jiaozhou Bay. WATER RESEARCH 2022; 218:118488. [PMID: 35489150 DOI: 10.1016/j.watres.2022.118488] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
The Jiaozhou Bay as a model marine ecosystem in China has been intensively investigated over the last 90 years. However, detailed phytoplankton community composition, spatial-temporal dynamics, and its assembly mechanism were still unclear. To address these, we systematically examined the composition and spatial-temporal dynamics of phytoplankton in the Jiaozhou Bay through high-throughput sequencing of 18S rDNA V4. Analysis of 468 samples from 12 sampling sites over one full year revealed much higher phytoplankton diversity than previous reports, and strong seasonal succession patterns. Some phytoplankton also showed spatial variations, although the phytoplankton community didn't show significant distance-decay pattern. Environmental factors (especially temperature), species-species interrelationships and unique resting stages were uncovered to be the main contributors instead of stochastic process in shaping the phytoplankton community assembly. The overwhelming positive correlations between phytoplankton and other protists suggested that coevolution might be critical in this marine ecosystem. Complementary distributions of different amplicon sequence variants (ASVs) of same genera, such as Skeletonema marinoi (ASV_2) and Skeletonema tropicum (ASV_263) of the genus Skeletonema, suggested that phytoplankton have evolved differentially to exploit a wide range of ecological niches. This study laid a solid foundation for asertaining phytoplankton composition and spatial-temporal dynamics in temperate seawaters and mechanisms underlying phytoplankton community assembly, allowing in-depth studies of marine ecology.
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Affiliation(s)
- 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 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zongmei Cui
- 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 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 10039, 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 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, 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 266200, 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, British Columbia, V5A 1S6, Canada.
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36
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O’Brien J, McParland EL, Bramucci AR, Ostrowski M, Siboni N, Ingleton T, Brown MV, Levine NM, Laverock B, Petrou K, Seymour J. The Microbiological Drivers of Temporally Dynamic Dimethylsulfoniopropionate Cycling Processes in Australian Coastal Shelf Waters. Front Microbiol 2022; 13:894026. [PMID: 35783424 PMCID: PMC9240709 DOI: 10.3389/fmicb.2022.894026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/20/2022] [Indexed: 01/04/2023] Open
Abstract
The organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact marine DMS (O) (P) concentrations, but the dynamic nature of these microbial interactions is still poorly resolved. Here, we examined the relationships between microbial community dynamics with DMS (O) (P) concentrations during a 2-year oceanographic time series conducted on the east Australian coast. Heterogenous temporal patterns were apparent in chlorophyll a (chl a) and DMSP concentrations, but the relationship between these parameters varied over time, suggesting the phytoplankton and bacterial community composition were affecting the net DMSP concentrations through differential DMSP production and degradation. Significant increases in DMSP were regularly measured in spring blooms dominated by predicted high DMSP-producing lineages of phytoplankton (Heterocapsa, Prorocentrum, Alexandrium, and Micromonas), while spring blooms that were dominated by predicted low DMSP-producing phytoplankton (Thalassiosira) demonstrated negligible increases in DMSP concentrations. During elevated DMSP concentrations, a significant increase in the relative abundance of the key copiotrophic bacterial lineage Rhodobacterales was accompanied by a three-fold increase in the gene, encoding the first step of DMSP demethylation (dmdA). Significant temporal shifts in DMS concentrations were measured and were significantly correlated with both fractions (0.2-2 μm and >2 μm) of microbial DMSP lyase activity. Seasonal increases of the bacterial DMSP biosynthesis gene (dsyB) and the bacterial DMS oxidation gene (tmm) occurred during the spring-summer and coincided with peaks in DMSP and DMSO concentration, respectively. These findings, along with significant positive relationships between dsyB gene abundance and DMSP, and tmm gene abundance with DMSO, reinforce the significant role planktonic bacteria play in producing DMSP and DMSO in ocean surface waters. Our results highlight the highly dynamic nature and myriad of microbial interactions that govern sulfur cycling in coastal shelf waters and further underpin the importance of microbial ecology in mediating important marine biogeochemical processes.
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Affiliation(s)
- James O’Brien
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Erin L. McParland
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Anna R. Bramucci
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Timothy Ingleton
- Water, Wetlands and Coastal Science, NSW Department of Planning, Industry and Environment, Lidcombe, NSW, Australia
| | - Mark V. Brown
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Naomi M. Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Bonnie Laverock
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Katherina Petrou
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Justin Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
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37
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Caracciolo M, Rigaut-Jalabert F, Romac S, Mahé F, Forsans S, Gac JP, Arsenieff L, Manno M, Chaffron S, Cariou T, Hoebeke M, Bozec Y, Goberville E, Le Gall F, Guilloux L, Baudoux AC, de Vargas C, Not F, Thiébaut E, Henry N, Simon N. Seasonal dynamics of marine protist communities in tidally mixed coastal waters. Mol Ecol 2022; 31:3761-3783. [PMID: 35593305 PMCID: PMC9543310 DOI: 10.1111/mec.16539] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 12/29/2021] [Accepted: 04/19/2022] [Indexed: 12/01/2022]
Abstract
Major seasonal community reorganizations and associated biomass variations are landmarks of plankton ecology. However, the processes of plankton community turnover rates have not been fully elucidated so far. Here, we analyse patterns of planktonic protist community succession in temperate latitudes, based on quantitative taxonomic data from both microscopy counts (cells >10 μm) and ribosomal DNA metabarcoding (size fraction >3 μm, 18S rRNA gene) from plankton samples collected bimonthly over 8 years (2009–2016) at the SOMLIT‐Astan station (Roscoff, Western English Channel). Based on morphology, diatoms were clearly the dominating group all year round and over the study period. Metabarcoding uncovered a wider diversity spectrum and revealed the prevalence of Dinophyceae and diatoms but also of Cryptophyta, Chlorophyta, Cercozoa, Syndiniales and Ciliophora in terms of read counts and or richness. The use of morphological and molecular analyses in combination allowed improving the taxonomic resolution and to identify the sequence of the dominant species and OTUs (18S V4 rDNA‐derived taxa) that drive annual plankton successions. We detected that some of these dominant OTUs were benthic as a result of the intense tidal mixing typical of the French coasts in the English Channel. Our analysis of the temporal structure of community changes point to a strong seasonality and resilience. The temporal structure of environmental variables (especially Photosynthetic Active Radiation, temperature and macronutrients) and temporal structures generated by species life cycles and or species interactions, are key drivers of the observed cyclic annual plankton turnover.
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Affiliation(s)
| | | | | | | | | | | | - Laure Arsenieff
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | | | - Samuel Chaffron
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Laboratoire des Sciences du Numérique de Nantes (LS2N), CNRS, UMR6004, Université de Nantes, Ecole Centrale de Nantes, 44322, Nantes, France
| | - Thierry Cariou
- Institut de recherche pour le développement (IRD), Délégation Régionale Ouest, IMAGO, Plouzané, France
| | - Mark Hoebeke
- CNRS, Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff, 29680, Roscoff, France
| | | | - Eric Goberville
- Unité biologie des organismes et écosystèmes aquatiques (BOREA), Muséum National D'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS, IRD, CP53, 61 rue Buffon 75005, Paris, France
| | | | - Loïc Guilloux
- Sorbonne Université, Roscoff, France.,Mediterranean Institute of Oceanography (MIO), Campus de Luminy case 901, 163 Av. de Luminy, 13288 Marseille cedex 9, France
| | | | - Colomban de Vargas
- Sorbonne Université, Roscoff, France.,Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | | | - Eric Thiébaut
- Sorbonne Université, Roscoff, France.,Sorbonne Université, CNRS, OSU STAMAR, UMS2017, 4 Place Jussieu, 75252 Paris cedex 05, France
| | - Nicolas Henry
- Sorbonne Université, Roscoff, France.,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, FR 2424, ABiMS Platform, Station Biologique de Roscoff, 29680, Roscoff, France
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38
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Grattepanche JD, Jeffrey WH, Gast RJ, Sanders RW. Diversity of Microbial Eukaryotes Along the West Antarctic Peninsula in Austral Spring. Front Microbiol 2022; 13:844856. [PMID: 35651490 PMCID: PMC9149413 DOI: 10.3389/fmicb.2022.844856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
During a cruise from October to November 2019, along the West Antarctic Peninsula, between 64.32 and 68.37°S, we assessed the diversity and composition of the active microbial eukaryotic community within three size fractions: micro- (> 20 μm), nano- (20-5 μm), and pico-size fractions (5-0.2 μm). The communities and the environmental parameters displayed latitudinal gradients, and we observed a strong similarity in the microbial eukaryotic communities as well as the environmental parameters between the sub-surface and the deep chlorophyll maximum (DCM) depths. Chlorophyll concentrations were low, and the mixed layer was shallow for most of the 17 stations sampled. The richness of the microplankton was higher in Marguerite Bay (our southernmost stations), compared to more northern stations, while the diversity for the nano- and pico-plankton was relatively stable across latitude. The microplankton communities were dominated by autotrophs, mostly diatoms, while mixotrophs (phototrophs-consuming bacteria and kleptoplastidic ciliates, mostly alveolates, and cryptophytes) were the most abundant and active members of the nano- and picoplankton communities. While phototrophy was the dominant trophic mode, heterotrophy (mixotrophy, phagotrophy, and parasitism) tended to increase southward. The samples from Marguerite Bay showed a distinct community with a high diversity of nanoplankton predators, including spirotrich ciliates, and dinoflagellates, while cryptophytes were observed elsewhere. Some lineages were significantly related-either positively or negatively-to ice coverage (e.g., positive for Pelagophyceae, negative for Spirotrichea) and temperature (e.g., positive for Cryptophyceae, negative for Spirotrichea). This suggests that climate changes will have a strong impact on the microbial eukaryotic community.
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Affiliation(s)
| | - Wade H. Jeffrey
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, FL, United States
| | - Rebecca J. Gast
- Department of Biology, Woods Hole Oceanographic Institution, Pensacola, MA, United States
| | - Robert W. Sanders
- Department of Biology, Temple University, Philadelphia, PA, United States
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39
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Latz MAC, Grujcic V, Brugel S, Lycken J, John U, Karlson B, Andersson A, Andersson AF. Short- and long-read metabarcoding of the eukaryotic rRNA operon: evaluation of primers and comparison to shotgun metagenomics sequencing. Mol Ecol Resour 2022; 22:2304-2318. [PMID: 35437888 DOI: 10.1111/1755-0998.13623] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/17/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
High-throughput sequencing for analysis of microbial diversity has evolved vastly over the last decade. Currently the go-to method for studying microbial eukaryotes is short-read metabarcoding of variable regions of the 18S rRNA gene with <500 bp amplicons. However, there is a growing interest in applying long-read sequencing of amplicons covering the rRNA operon for improving taxonomic resolution. For both methods, the choice of primers is crucial. It determines if community members are covered, if they can be identified at a satisfactory taxonomic level, and if the obtained community profile is representative. Here, we designed new primers targeting 18S and 28S rRNA based on 177,934 and 21,072 database sequences, respectively. The primers were evaluated in silico along with published primers on reference sequence databases and marine metagenomics datasets. We further evaluated a subset of the primers for short- and long-read sequencing on environmental samples in vitro and compared the obtained community profile with primer-unbiased metagenomic sequencing. Of the short-read pairs, a new V6-V8 pair and the V4_Balzano pair used with a simplified PCR protocol provided good results in silico and in vitro. Fewer differences were observed between the long-read primer pairs. The long-read amplicons and ITS1 alone provided higher taxonomic resolution than V4. Together, our results represent a reference and guide for selection of robust primers for research on and environmental monitoring of microbial eukaryotes.
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Affiliation(s)
- Meike A C Latz
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden.,University of Copenhagen, Department of Plant and Environmental Sciences, Frederiksberg C, Denmark
| | - Vesna Grujcic
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Sonia Brugel
- Umeå University, Department of Ecology and Environmental Sciences, Umeå, Sweden
| | - Jenny Lycken
- Swedish Meteorological and Hydrological Institute, Oceanographic Research, Gothenburg, Sweden
| | - Uwe John
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Bengt Karlson
- Swedish Meteorological and Hydrological Institute, Oceanographic Research, Gothenburg, Sweden
| | - Agneta Andersson
- Umeå University, Department of Ecology and Environmental Sciences, Umeå, Sweden
| | - Anders F Andersson
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden
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40
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Longobardi L, Dubroca L, Margiotta F, Sarno D, Zingone A. Photoperiod-driven rhythms reveal multi-decadal stability of phytoplankton communities in a highly fluctuating coastal environment. Sci Rep 2022; 12:3908. [PMID: 35273208 PMCID: PMC8913669 DOI: 10.1038/s41598-022-07009-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/09/2022] [Indexed: 11/09/2022] Open
Abstract
Phytoplankton play a pivotal role in global biogeochemical and trophic processes and provide essential ecosystem services. However, there is still no broad consensus on how and to what extent their community composition responds to environmental variability. Here, high-frequency oceanographic and biological data collected over more than 25 years in a coastal Mediterranean site are used to shed light on the temporal patterns of phytoplankton species and assemblages in their environmental context. Because of the proximity to the coast and due to large-scale variations, environmental conditions showed variability on the short and long-term scales. Nonetheless, an impressive regularity characterised the annual occurrence of phytoplankton species and their assemblages, which translated into their remarkable stability over decades. Photoperiod was the dominant factor related to community turnover and replacement, which points at a possible endogenous regulation of biological processes associated with species-specific phenological patterns, in analogy with terrestrial plants. These results highlight the considerable stability and resistance of phytoplankton communities in response to different environmental pressures, which contrast the view of these organisms as passively undergoing changes that occur at different temporal scales in their habitat, and show how, under certain conditions, biological processes may prevail over environmental forcing.
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Affiliation(s)
- Lorenzo Longobardi
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Laurent Dubroca
- Institut Français de Recherche Pour l'Exploitation de la Mer, IFREMER, Laboratoire Ressources Halieutiques de Port-en-Bessin, 14520, Port-en-Bessin-Huppain, France
| | - Francesca Margiotta
- Research Infrastructures for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Diana Sarno
- Research Infrastructures for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Adriana Zingone
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy. .,Research Infrastructures for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
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41
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Diao C, Jia H, Guo S, Hou G, Xian W, Zhang H. Biodiversity exploration in autumn using environmental DNA in the South China sea. ENVIRONMENTAL RESEARCH 2022; 204:112357. [PMID: 34774836 DOI: 10.1016/j.envres.2021.112357] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/30/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
The South China Sea (SCS) is an important part of the Indo-Pacific convergence zone, with high biodiversity and abundant marine resources. Traditional methods are primarily used to monitor biodiversity. However, a few studies have used environmental DNA (eDNA) metabarcoding to research the assemblage structure of the SCS. This study used eDNA metabarcoding to survey the SCS assemblage and its relationship with environmental factors over a month-long time-series (August 30th to September 30th, 2020) of seawater samples from the central part of the SCS (9°-20°86' N, 113°-118°47' E). 32 stations were divided into six groups (A, B, C, D, E, F) according to longitude. We collected water samples, extracted eDNA, and amplified 18S rRNA gene V4 region (18S V4), 18S rRNA gene V9 region (18S V9), and 12S rRNA gene (12S). Krona diagrams were used to show species composition. We identified 192 phytoplankton, 104 invertebrate, and 61 fish species from 18S V4, 18S V9, and 12S, respectively. Generally, the three assemblage structures exhibited an increase in species diversity with increasing longitude. Group E had the highest fish diversity. Groups F and C had the highest phytoplankton and invertebrate diversity, respectively. Canonical correspondence analysis showed that four factors (chlorophyll a, depth, salinity, and temperature) were correlated with assemblage structure. Chlorophyll a was the main environmental factor that affected fish, phytoplankton, and invertebrate assemblage structures; salinity was strongly correlated with fish and invertebrate assemblage structures; temperature was a key factor that impacted fish and invertebrate assemblage structures; and depth was strongly correlated with invertebrate assemblage structure. Our results revealed that eDNA metabarcoding is a powerful tool for improving detection rate and using multiple markers is an effective approach for monitoring biodiversity. This study provided information that can be used to enhance biodiversity protection efforts in the SCS.
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Affiliation(s)
- Caoyun Diao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Jia
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; China School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shujin Guo
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Gang Hou
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524000, China
| | - Weiwei Xian
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Hui Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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O'Brien J, McParland EL, Bramucci AR, Siboni N, Ostrowski M, Kahlke T, Levine NM, Brown MV, van de Kamp J, Bodrossy L, Messer LF, Petrou K, Seymour JR. Biogeographical and seasonal dynamics of the marine Roseobacter community and ecological links to DMSP-producing phytoplankton. ISME COMMUNICATIONS 2022; 2:16. [PMID: 37938744 PMCID: PMC9723663 DOI: 10.1038/s43705-022-00099-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 11/09/2023]
Abstract
Ecological interactions between marine bacteria and phytoplankton play a pivotal role in governing the ocean's major biogeochemical cycles. Among these, members of the marine Roseobacter Group (MRG) can establish mutualistic relationships with phytoplankton that are, in part, maintained by exchanges of the organosulfur compound, dimethylsulfoniopropionate (DMSP). Yet most of what is known about these interactions has been derived from culture-based laboratory studies. To investigate temporal and spatial co-occurrence patterns between members of the MRG and DMSP-producing phytoplankton we analysed 16S and 18S rRNA gene amplicon sequence variants (ASVs) derived from 5 years of monthly samples from seven environmentally distinct Australian oceanographic time-series. The MRG and DMSP-producer communities often displayed contemporaneous seasonality, which was greater in subtropical and temperate environments compared to tropical environments. The relative abundance of both groups varied latitudinally, displaying a poleward increase, peaking (MRG at 33% of total bacteria, DMSP producers at 42% of eukaryotic phototrophs) during recurrent spring-summer phytoplankton blooms in the most temperate site (Maria Island, Tasmania). Network analysis identified 20,140 significant positive correlations between MRG ASVs and DMSP producers and revealed that MRGs exhibit significantly stronger correlations to high DMSP producers relative to other DMSP-degrading bacteria (Pelagibacter, SAR86 and Actinobacteria). By utilising the power of a continental network of oceanographic time-series, this study provides in situ confirmation of interactions found in laboratory studies and demonstrates that the ecological dynamics of an important group of marine bacteria are shaped by the production of an abundant and biogeochemically significant organosulfur compound.
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Affiliation(s)
- James O'Brien
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia.
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, Australia.
| | - Erin L McParland
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Anna R Bramucci
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - Tim Kahlke
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - Naomi M Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Mark V Brown
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | | | | | - Lauren F Messer
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Katherina Petrou
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia.
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Lin Y, Vidjak O, Ezgeta-Balić D, Bojanić Varezić D, Šegvić-Bubić T, Stagličić N, Zhan A, Briski E. Plankton diversity in Anthropocene: Shipping vs. aquaculture along the eastern Adriatic coast assessed through DNA metabarcoding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:151043. [PMID: 34673064 DOI: 10.1016/j.scitotenv.2021.151043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Coastal ecosystems globally are exposed to the most pervasive anthropogenic activities, caused by a suite of human infrastructure and enterprises such as shipping ports, aquaculture facilities, fishing, and tourism. These anthropogenic activities may lead to changes in ecosystem biodiversity, followed by loss of ecosystem functioning and services. Shipping industry and aquaculture have also been recognized as the main vectors for introduction of marine non-indigenous species (NIS) worldwide. In this study, we used DNA metabarcoding-based methods to investigate plankton biodiversity under varying anthropogenic pressures (shipping and bivalve aquaculture) along the eastern Adriatic coast (the northernmost part of the Mediterranean Sea). Our comparative assessment revealed similar community structures among investigated coastal locations (Northern, Central and Southern Adriatic). When the whole plankton communities were considered, they did not differ significantly between port and aquaculture sites. However, the proportion of the unique zOTUs in the port samples was remarkably higher than that in aquaculture sites (40.5% vs 8.2%), indicating that port areas may receive higher abundance and species richness of NIS than aquaculture sites. Further important difference between the two types of anthropogenically impacted habitats was a high abundance of three notorious invaders - M. leidyi, M. gigas, and H. elegans in late summer at the aquaculture site in Northern Adriatic. Therefore, the plankton community of the area is under pressure not only from aquaculture activities, but also establishment of NIS. Port areas are probably under greater introduction pressure from NIS, but aquaculture sites may experience greater community changes due to their establishment.
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Affiliation(s)
- Yaping Lin
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China.
| | - Olja Vidjak
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, 21000 Split, Croatia
| | - Daria Ezgeta-Balić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, 21000 Split, Croatia
| | | | - Tanja Šegvić-Bubić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, 21000 Split, Croatia
| | - Nika Stagličić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, 21000 Split, Croatia
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Elizabeta Briski
- GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
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44
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Moynihan MA, Goodkin NF, Morgan KM, Kho PYY, Lopes Dos Santos A, Lauro FM, Baker DM, Martin P. Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef. THE ISME JOURNAL 2022; 16:233-246. [PMID: 34294880 PMCID: PMC8692400 DOI: 10.1038/s41396-021-01054-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 06/23/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
The role of diazotrophs in coral physiology and reef biogeochemistry remains poorly understood, in part because N2 fixation rates and diazotrophic community composition have only been jointly analyzed in the tissue of one tropical coral species. We performed field-based 15N2 tracer incubations during nutrient-replete conditions to measure diazotroph-derived nitrogen (DDN) assimilation into three species of scleractinian coral (Pocillopora acuta, Goniopora columna, Platygyra sinensis). Using multi-marker metabarcoding (16S rRNA, nifH, 18S rRNA), we analyzed DNA- and RNA-based communities in coral tissue and skeleton. Despite low N2 fixation rates, DDN assimilation supplied up to 6% of the holobiont's N demand. Active coral-associated diazotrophs were chiefly Cluster I (aerobes or facultative anaerobes), suggesting that oxygen may control coral-associated diazotrophy. Highest N2 fixation rates were observed in the endolithic community (0.20 µg N cm-2 per day). While the diazotrophic community was similar between the tissue and skeleton, RNA:DNA ratios indicate potential differences in relative diazotrophic activity between these compartments. In Pocillopora, DDN was found in endolithic, host, and symbiont compartments, while diazotrophic nifH sequences were only observed in the endolithic layer, suggesting a possible DDN exchange between the endolithic community and the overlying coral tissue. Our findings demonstrate that coral-associated diazotrophy is significant, even in nutrient-rich waters, and suggest that endolithic microbes are major contributors to coral nitrogen cycling on reefs.
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Affiliation(s)
- Molly A Moynihan
- Earth Observatory of Singapore, Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore.
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore.
| | - Nathalie F Goodkin
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
- Earth Observatory of Singapore, Nanyang Technological University, Singapore, Singapore
- American Museum of Natural History, New York, NY, USA
| | - Kyle M Morgan
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Phyllis Y Y Kho
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | | | - Federico M Lauro
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - David M Baker
- Division for Ecology and Biodiversity, School of Biological Sciences, University of Hong Kong, Hong Kong, PR China
- The Swire Institute of Marine Science, University of Hong Kong, Hong Kong, PR China
| | - Patrick Martin
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
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45
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Han Y, Guo C, Guan X, McMinn A, Liu L, Zheng G, Jiang Y, Liang Y, Shao H, Tian J, Wang M. Comparison of Deep-Sea Picoeukaryotic Composition Estimated from the V4 and V9 Regions of 18S rRNA Gene with a Focus on the Hadal Zone of the Mariana Trench. MICROBIAL ECOLOGY 2022; 83:34-47. [PMID: 33811505 DOI: 10.1007/s00248-021-01747-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Diversity of microbial eukaryotes is estimated largely based on sequencing analysis of the hypervariable regions of 18S rRNA genes. But the use of different regions of 18S rRNA genes as molecular markers may generate bias in diversity estimation. Here, we compared the differences between the two most widely used markers, V4 and V9 regions of the 18S rRNA gene, in describing the diversity of epipelagic, bathypelagic, and hadal picoeukaryotes in the Challenger Deep of the Mariana Trench, which is a unique and little explored environment. Generally, the V9 region identified more OTUs in deeper waters than V4, while the V4 region provided greater Shannon diversity than V9. In the epipelagic zone, where Alveolata was the dominant group, picoeukaryotic community compositions identified by V4 and V9 markers are similar at different taxonomic levels. However, in the deep waters, the results of the two datasets show clear differences. These differences were mainly contributed by Retaria, Fungi, and Bicosoecida. The primer targeting the V9 region has an advantage in amplifying Bicosoecids in the bathypelagic and hadal zone of the Mariana Trench, and its high abundance in V9 dataset pointed out the possibility of Bicosoecids as a dominant group in this environment. Chrysophyceae, Fungi, MALV-I, and Retaria were identified as the dominant picoeukaryotes in the bathypelagic and hadal zone and potentially play important roles in deep-sea microbial food webs and biogeochemical cycling by their phagotrophic, saprotrophic, and parasitic life styles. Overall, the use of different markers of 18S rRNA gene allows a better assessment and understanding of the picoeukaryotic diversity in deep-sea environments.
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Affiliation(s)
- Yuye Han
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Cui Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
| | - Xuran Guan
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Lu Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Guiliang Zheng
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yong Jiang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, China
- Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
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46
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Weig AR, Löder MGJ, Ramsperger AFRM, Laforsch C. In situ Prokaryotic and Eukaryotic Communities on Microplastic Particles in a Small Headwater Stream in Germany. Front Microbiol 2021; 12:660024. [PMID: 34912303 PMCID: PMC8667586 DOI: 10.3389/fmicb.2021.660024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 11/04/2021] [Indexed: 01/04/2023] Open
Abstract
The ubiquitous use of plastic products in our daily life is often accompanied by improper disposal. The first interactions of plastics with organisms in the environment occur by overgrowth or biofilm formation on the particle surface, which can facilitate the ingestion by animals. In order to elucidate the colonization of plastic particles by prokaryotic and eukaryotic microorganisms in situ, we investigated microbial communities in biofilms on four different polymer types and on mineral particles in a small headwater stream 500 m downstream of a wastewater treatment plant in Germany. Microplastic and mineral particles were exposed to the free-flowing water for 4 weeks in spring and in summer. The microbial composition of the developing biofilm was analyzed by 16S and 18S amplicon sequencing. Despite the expected seasonal differences in the microbial composition of pro- and eukaryotic communities, we repeatedly observed polymer type-specific differentiation in both seasons. The order of polymer type-specific prokaryotic and eukaryotic community distances calculated by Robust Aitchison principal component analysis (PCA) was the same in spring and summer samples. However, the magnitude of the distance differed considerably between polymer types. Prokaryotic communities on polyethylene particles exhibited the most considerable difference to other particles in summer, while eukaryotic communities on polypropylene particles showed the most considerable difference to other spring samples. The most contributing bacterial taxa to the polyethylene-specific differentiation belong to the Planctomycetales, Saccharimonadales, Bryobacterales, uncultured Acidiomicrobia, and Gemmatimonadales. The most remarkable differences in eukaryotic microorganism abundances could be observed in several distinct groups of Ciliophora (ciliates) and Chlorophytes (green algae). Prediction of community functions from taxonomic abundances revealed differences between spring and summer, and – to a lesser extent – also between polymer types and mineral surfaces. Our results show that different microplastic particles were colonized by different biofilm communities. These findings may be used for advanced experimental designs to investigate the role of microorganisms on the fate of microplastic particles in freshwater ecosystems.
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Affiliation(s)
- Alfons R Weig
- Genomics and Bioinformatics, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
| | - Martin G J Löder
- Animal Ecology, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
| | - Anja F R M Ramsperger
- Animal Ecology, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany.,Biological Physics, University of Bayreuth, Bayreuth, Germany
| | - Christian Laforsch
- Animal Ecology, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
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Morillas-España A, Sánchez-Zurano A, Gómez-Serrano C, Ciardi M, Acién G, Clagnan E, Adani F, Lafarga T. Potential of the cyanobacteria Anabaena sp. and Dolichospermum sp. for being produced using wastewater or pig slurry: Validation using pilot-scale raceway reactors. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102517] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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48
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Clarke LJ, Suter L, Deagle BE, Polanowski AM, Terauds A, Johnstone GJ, Stark JS. Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems. PeerJ 2021; 9:e12458. [PMID: 34820189 PMCID: PMC8601059 DOI: 10.7717/peerj.12458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/18/2021] [Indexed: 01/18/2023] Open
Abstract
Antarctic benthic ecosystems support high biodiversity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and sampling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. However, significantly different communities were detected in the two sample types at sites where both were collected (i.e., where paired samples were available). For example, nematodes and echinoderms were more likely to be detected exclusively in sediment and water eDNA samples, respectively. eDNA from water and sediment core samples are complementary sample types, with epifauna more likely to be detected in water column samples and infauna in sediment. More reference DNA sequences are needed for infauna/meiofauna to increase the proportion of sequences and number of taxa that can be identified. Developing a better understanding of the temporal and spatial dynamics of eDNA at low temperatures would also aid interpretation of eDNA signals from polar environments. Our results provide a preliminary scan of benthic metazoan communities in the Vestfold Hills, with additional markers required to provide a comprehensive biodiversity survey. However, our study demonstrates the choice of sample type for eDNA studies of benthic ecosystems (sediment, water or both) needs to be carefully considered in light of the research or monitoring question of interest.
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Affiliation(s)
- Laurence J Clarke
- Australian Antarctic Division, Kingston, Tasmania, Australia.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Leonie Suter
- Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Bruce E Deagle
- Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, Australia
| | | | - Aleks Terauds
- Australian Antarctic Division, Kingston, Tasmania, Australia
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49
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Metz S, Huber P, Accattatis V, Lopes Dos Santos A, Bigeard E, Unrein F, Chambouvet A, Not F, Lara E, Devercelli M. Freshwater protists: unveiling the unexplored in a large floodplain system. Environ Microbiol 2021; 24:1731-1745. [PMID: 34783136 DOI: 10.1111/1462-2920.15838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/23/2021] [Accepted: 10/31/2021] [Indexed: 12/25/2022]
Abstract
Protists play a fundamental role in all ecosystems, but we are still far from estimating the total diversity of many lineages, in particular in highly diverse environments, such as freshwater. Here, we survey the protist diversity of the Paraná River using metabarcoding, and we applied an approach that includes sequence similarity and phylogeny to evaluate the degree of genetic novelty of the protists' communities against the sequences described in the reference database PR2 . We observed that ~28% of the amplicon sequence variants were classified as novel according to their similarity with sequences from the reference database; most of them were related to heterotrophic groups traditionally overlooked in freshwater systems. This lack of knowledge extended to those groups within the green algae (Archaeplastida) that are well documented such as Mamiellophyceae, and also to the less studied Pedinophyceae, for which we found sequences representing novel deep-branching clusters. Among the groups with potential novel protists, Bicosoecida (Stramenopiles) were the best represented, followed by Codosiga (Opisthokonta), and the Perkinsea (Alveolata). This illustrates the lack of knowledge on freshwater planktonic protists and also the need for isolation and/or cultivation of new organisms to better understand their role in ecosystem functioning.
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Affiliation(s)
- Sebastian Metz
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, Plouzané, F-29280, France.,Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Buenos Aires, Argentina
| | - Paula Huber
- Departamento de Hidrobiologia, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, São Paulo, 13565-905, Brazil.,Instituto Nacional de Limnología (INALI), Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Ciudad Universitaria, Santa Fe, Argentina
| | - Victoria Accattatis
- Departamento de Hidrobiologia, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, São Paulo, 13565-905, Brazil
| | | | - Estelle Bigeard
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin UMR7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Fernando Unrein
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Buenos Aires, Argentina
| | | | - Fabrice Not
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin UMR7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Enrique Lara
- Real Jardín Botánico de Madrid, CSIC, Madrid, 28014, Spain
| | - Melina Devercelli
- Departamento de Hidrobiologia, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, São Paulo, 13565-905, Brazil
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50
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Shemi A, Alcolombri U, Schatz D, Farstey V, Vincent F, Rotkopf R, Ben-Dor S, Frada MJ, Tawfik DS, Vardi A. Dimethyl sulfide mediates microbial predator-prey interactions between zooplankton and algae in the ocean. Nat Microbiol 2021; 6:1357-1366. [PMID: 34697459 DOI: 10.1038/s41564-021-00971-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 09/01/2021] [Indexed: 12/11/2022]
Abstract
Phytoplankton are key components of the oceanic carbon and sulfur cycles1. During bloom events, some species can emit large amounts of the organosulfur volatile dimethyl sulfide (DMS) into the ocean and consequently the atmosphere, where it can modulate aerosol formation and affect climate2,3. In aquatic environments, DMS plays an important role as a chemical signal mediating diverse trophic interactions. Yet, its role in microbial predator-prey interactions remains elusive with contradicting evidence for its role in either algal chemical defence or in the chemo-attraction of grazers to prey cells4,5. Here we investigated the signalling role of DMS during zooplankton-algae interactions by genetic and biochemical manipulation of the algal DMS-generating enzyme dimethylsulfoniopropionate lyase (DL) in the bloom-forming alga Emiliania huxleyi6. We inhibited DL activity in E. huxleyi cells in vivo using the selective DL-inhibitor 2-bromo-3-(dimethylsulfonio)-propionate7 and overexpressed the DL-encoding gene in the model diatom Thalassiosira pseudonana. We showed that algal DL activity did not serve as an anti-grazing chemical defence but paradoxically enhanced predation by the grazer Oxyrrhis marina and other microzooplankton and mesozooplankton, including ciliates and copepods. Consumption of algal prey with induced DL activity also promoted O. marina growth. Overall, our results demonstrate that DMS-mediated grazing may be ecologically important and prevalent during prey-predator dynamics in aquatic ecosystems. The role of algal DMS revealed here, acting as an eat-me signal for grazers, raises fundamental questions regarding the retention of its biosynthetic enzyme through the evolution of dominant bloom-forming phytoplankton in the ocean.
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Affiliation(s)
- Adva Shemi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Uria Alcolombri
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.,Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Viviana Farstey
- The Inter-University Institute for Marine Sciences, Eilat, Israel
| | - Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Rotkopf
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Miguel J Frada
- The Inter-University Institute for Marine Sciences, Eilat, Israel.,Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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