1
|
Shen Z, Yu B, Gong Y, Shao K, Gao G, Tang X. Unraveling the impact of climatic warming and wetting on eukaryotic microbial diversity and assembly mechanisms: A 10-year case study in Lake Bosten, NW China. Water Res 2024; 256:121559. [PMID: 38579508 DOI: 10.1016/j.watres.2024.121559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 03/29/2024] [Accepted: 03/30/2024] [Indexed: 04/07/2024]
Abstract
Over the last six decades, northwest China has undergone a significant climatic shift from "warm-dry" to "warm-wet", profoundly impacting the structures and functions of lake ecosystem across the region. However, the influences of this climatic transition on the diversity patterns, co-occurrence network, and assembly processes of eukaryotic microbial communities in lake ecosystem, along with the underlying mechanisms, remain largely unexplored. To bridge this knowledge gap, our study focused on Lake Bosten, the largest inland freshwater body in China, conducting a comprehensive analysis. Firstly, we examined the dynamics of key water quality parameters in the lake based on long-term monitoring data (1992-2022). Subsequently, we collected 93 water samples spanning two distinctive periods: low water level (WL) and high total dissolved solids (TDS) (PerWLTDS; 2010-2011; attributed to "warm-dry" climate), and high WL and low TDS (PerTDSWL; 2021-2022; associated with "warm-wet" climate). Eukaryotic microorganisms were further investigated using 18S rRNA gene sequencing and various statistical methods. Our findings revealed that climatic warming and wetting significantly increased eukaryotic microbial α-diversity (all Wilcox. test: P<0.05), while simultaneously reducing β-diversity (all Wilcox. test: P<0.001) and network complexity. Through the two sampling periods, assembly mechanisms of eukaryotic microorganisms were predominantly influenced by dispersal limitation (DL) and drift (DR) within stochastic processes, alongside homogeneous selection (HoS) within deterministic processes. WL played a mediating role in eukaryotic microbial DL and HoS processes in the PerTDSWL, whereas water quality and α-diversity influenced the DL process in the PerWLTDS. Collectively, these results underscore the direct and indirect impacts of "warm-wet" conditions on the eukaryotic microorganisms within Lake Bosten. This study provides valuable insights into the evolutionary dynamics of lake ecosystems under such climatic conditions and aids in predicting the ecological ramifications of global climatic changes.
Collapse
Affiliation(s)
- Zhen Shen
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Bobing Yu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yi Gong
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China.
| |
Collapse
|
2
|
Latz MAC, Andersson A, Brugel S, Hedblom M, Jurdzinski KT, Karlson B, Lindh M, Lycken J, Torstensson A, Andersson AF. A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea. Sci Data 2024; 11:18. [PMID: 38168085 PMCID: PMC10761891 DOI: 10.1038/s41597-023-02825-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
The Baltic Sea is one of the largest brackish water environments on earth and is characterised by pronounced physicochemical gradients and seasonal dynamics. Although the Baltic Sea has a long history of microscopy-based plankton monitoring, DNA-based metabarcoding has so far mainly been limited to individual transect cruises or time-series of single stations. Here we report a dataset covering spatiotemporal variation in prokaryotic and eukaryotic microbial communities and physicochemical parameters. Within 13-months between January 2019 and February 2020, 341 water samples were collected at 22 stations during monthly cruises along the salinity gradient. Both salinity and seasonality are strongly reflected in the data. Since the dataset was generated with both metabarcoding and microscopy-based methods, it provides unique opportunities for both technical and ecological analyses, and is a valuable biodiversity reference for future studies, in the prospect of climate change.
Collapse
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.
| | - Agneta Andersson
- Umeå University, Department of Ecology and Environmental Sciences, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, SE-905 71, Hörnefors, Sweden
| | - Sonia Brugel
- Umeå University, Department of Ecology and Environmental Sciences, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, SE-905 71, Hörnefors, Sweden
| | - Mikael Hedblom
- Swedish Meteorological and Hydrological Institute, Community Planning Services - Oceanography, Västra Frölunda, Sweden
| | - Krzysztof T Jurdzinski
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Bengt Karlson
- Swedish Meteorological and Hydrological Institute, Oceanographic Research, Västra Frölunda, Sweden
| | - Markus Lindh
- Swedish Meteorological and Hydrological Institute, Community Planning Services - Oceanography, Västra Frölunda, Sweden
| | - Jenny Lycken
- Swedish Meteorological and Hydrological Institute, Community Planning Services - Oceanography, Västra Frölunda, Sweden
| | - Anders Torstensson
- Swedish Meteorological and Hydrological Institute, Community Planning Services - Oceanography, Västra Frölunda, Sweden
| | - Anders F Andersson
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden.
| |
Collapse
|
3
|
van der Loos LM, D'hondt S, Engelen AH, Pavia H, Toth GB, Willems A, Weinberger F, De Clerck O, Steinhagen S. Salinity and host drive Ulva-associated bacterial communities across the Atlantic-Baltic Sea gradient. Mol Ecol 2023; 32:6260-6277. [PMID: 35395701 DOI: 10.1111/mec.16462] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/21/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
The green seaweed Ulva is a model system to study seaweed-bacteria interactions, but the impact of environmental drivers on the dynamics of these interactions is little understood. In this study, we investigated the stability and variability of the seaweed-associated bacteria across the Atlantic-Baltic Sea salinity gradient. We characterized the bacterial communities of 15 Ulva sensu lato species along 2,000 km of coastline in a total of 481 samples. Our results demonstrate that the Ulva-associated bacterial composition was strongly structured by both salinity and host species (together explaining between 34% and 91% of the variation in the abundance of the different bacterial genera). The largest shift in the bacterial consortia coincided with the horohalinicum (5-8 PSU, known as the transition zone from freshwater to marine conditions). Low-salinity communities especially contained high relative abundances of Luteolibacter, Cyanobium, Pirellula, Lacihabitans and an uncultured Spirosomaceae, whereas high-salinity communities were predominantly enriched in Litorimonas, Leucothrix, Sulfurovum, Algibacter and Dokdonia. We identified a small taxonomic core community (consisting of Paracoccus, Sulfitobacter and an uncultured Rhodobacteraceae), which together contributed to 14% of the reads per sample, on average. Additional core taxa followed a gradient model, as more core taxa were shared between neighbouring salinity ranges than between ranges at opposite ends of the Atlantic-Baltic Sea gradient. Our results contradict earlier statements that Ulva-associated bacterial communities are taxonomically highly variable across individuals and largely stochastically defined. Characteristic bacterial communities associated with distinct salinity regions may therefore facilitate the host's adaptation across the environmental gradient.
Collapse
Affiliation(s)
- Luna M van der Loos
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Sofie D'hondt
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Aschwin H Engelen
- Marine Microbial Ecology & Biotechnology, CCMAR, University of Algarve, Faro, Portugal
| | - Henrik Pavia
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Gunilla B Toth
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Anne Willems
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Sophie Steinhagen
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| |
Collapse
|
4
|
Meyer R, Appeltans W, Duncan WD, Dimitrova M, Gan YM, Stjernegaard Jeppesen T, Mungall C, Paul DL, Provoost P, Robertson T, Schriml L, Suominen S, Walls R, Sweetlove M, Ung V, Van de Putte A, Wallis E, Wieczorek J, Buttigieg PL. Aligning Standards Communities for Omics Biodiversity Data: Sustainable Darwin Core-MIxS Interoperability. Biodivers Data J 2023; 11:e112420. [PMID: 37829294 PMCID: PMC10565567 DOI: 10.3897/bdj.11.e112420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
The standardization of data, encompassing both primary and contextual information (metadata), plays a pivotal role in facilitating data (re-)use, integration, and knowledge generation. However, the biodiversity and omics communities, converging on omics biodiversity data, have historically developed and adopted their own distinct standards, hindering effective (meta)data integration and collaboration. In response to this challenge, the Task Group (TG) for Sustainable DwC-MIxS Interoperability was established. Convening experts from the Biodiversity Information Standards (TDWG) and the Genomic Standards Consortium (GSC) alongside external stakeholders, the TG aimed to promote sustainable interoperability between the Minimum Information about any (x) Sequence (MIxS) and Darwin Core (DwC) specifications. To achieve this goal, the TG utilized the Simple Standard for Sharing Ontology Mappings (SSSOM) to create a comprehensive mapping of DwC keys to MIxS keys. This mapping, combined with the development of the MIxS-DwC extension, enables the incorporation of MIxS core terms into DwC-compliant metadata records, facilitating seamless data exchange between MIxS and DwC user communities. Through the implementation of this translation layer, data produced in either MIxS- or DwC-compliant formats can now be efficiently brokered, breaking down silos and fostering closer collaboration between the biodiversity and omics communities. To ensure its sustainability and lasting impact, TDWG and GSC have both signed a Memorandum of Understanding (MoU) on creating a continuous model to synchronize their standards. These achievements mark a significant step forward in enhancing data sharing and utilization across domains, thereby unlocking new opportunities for scientific discovery and advancement.
Collapse
Affiliation(s)
- Raïssa Meyer
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Reserach, Bremerhaven, GermanyAlfred Wegener Institute, Helmholtz Centre for Polar and Marine ReserachBremerhavenGermany
- Max Planck Institute for Marine Microbiology, Bremen, GermanyMax Planck Institute for Marine MicrobiologyBremenGermany
- University of Bremen, Faculty of Geosciences, Bremen, GermanyUniversity of Bremen, Faculty of GeosciencesBremenGermany
| | - Ward Appeltans
- Intergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System (OBIS), Oostende, BelgiumIntergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System (OBIS)OostendeBelgium
| | - William D. Duncan
- University of Florida, Gainesville, United States of AmericaUniversity of FloridaGainesvilleUnited States of America
| | - Mariya Dimitrova
- Bulgarian Academy of Sciences, Sofia, BulgariaBulgarian Academy of SciencesSofiaBulgaria
- Pensoft Publishers, Sofia, BulgariaPensoft PublishersSofiaBulgaria
| | - Yi-Ming Gan
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Thomas Stjernegaard Jeppesen
- Global Biodiversity Information Facility (GBIF), Copenhagen, DenmarkGlobal Biodiversity Information Facility (GBIF)CopenhagenDenmark
| | - Christopher Mungall
- Lawrence Berkeley National Laboratory, National Microbiome Data Collaborative (NMDC), Berkeley, United States of AmericaLawrence Berkeley National Laboratory, National Microbiome Data Collaborative (NMDC)BerkeleyUnited States of America
| | - Deborah L Paul
- University of Illinois, Illinois Natural History Survey, Species File Group, Champaign-Urbana, United States of AmericaUniversity of Illinois, Illinois Natural History Survey, Species File GroupChampaign-UrbanaUnited States of America
| | - Pieter Provoost
- Intergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System (OBIS), Oostende, BelgiumIntergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System (OBIS)OostendeBelgium
| | - Tim Robertson
- Global Biodiversity Information Facility (GBIF), Copenhagen, DenmarkGlobal Biodiversity Information Facility (GBIF)CopenhagenDenmark
| | - Lynn Schriml
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA, Baltimore, United States of AmericaDepartment of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USABaltimoreUnited States of America
| | - Saara Suominen
- Intergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System (OBIS), Oostende, BelgiumIntergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System (OBIS)OostendeBelgium
| | - Ramona Walls
- Critical Path Institute, Tucson, United States of AmericaCritical Path InstituteTucsonUnited States of America
| | - Maxime Sweetlove
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Visotheary Ung
- UMR 7205 CNRS-MNHN-SU-EPHE-UA, Paris, FranceUMR 7205 CNRS-MNHN-SU-EPHE-UAParisFrance
| | - Anton Van de Putte
- Royal Belgian Institute of Natural Sciences, Université Libre de Bruxelles, Brussels, BelgiumRoyal Belgian Institute of Natural Sciences, Université Libre de BruxellesBrusselsBelgium
| | - Elycia Wallis
- Atlas of Living Australia, CSIRO, Melbourne, AustraliaAtlas of Living Australia, CSIROMelbourneAustralia
| | - John Wieczorek
- University of California, Berkeley, United States of AmericaUniversity of CaliforniaBerkeleyUnited States of America
| | - Pier Luigi Buttigieg
- Helmholtz Metadata Collaboration, GEOMAR Helmholtz Centre for Ocean Research, Kiel, GermanyHelmholtz Metadata Collaboration, GEOMAR Helmholtz Centre for Ocean ResearchKielGermany
| |
Collapse
|
5
|
Aguilera A, Alegria Zufia J, Bas Conn L, Gurlit L, Śliwińska-Wilczewska S, Budzałek G, Lundin D, Pinhassi J, Legrand C, Farnelid H. Ecophysiological analysis reveals distinct environmental preferences in closely related Baltic Sea picocyanobacteria. Environ Microbiol 2023; 25:1674-1695. [PMID: 37655642 DOI: 10.1111/1462-2920.16384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/31/2023] [Indexed: 09/02/2023]
Abstract
Cluster 5 picocyanobacteria significantly contribute to primary productivity in aquatic ecosystems. Estuarine populations are highly diverse and consist of many co-occurring strains, but their physiology remains largely understudied. In this study, we characterized 17 novel estuarine picocyanobacterial strains. Phylogenetic analysis of the 16S rRNA and pigment genes (cpcB and cpeBA) uncovered multiple estuarine and freshwater-related clusters and pigment types. Assays with five representative strains (three phycocyanin rich and two phycoerythrin rich) under temperature (10-30°C), light (10-190 μmol photons m-2 s-1 ), and salinity (2-14 PSU) gradients revealed distinct growth optima and tolerance, indicating that genetic variability was accompanied by physiological diversity. Adaptability to environmental conditions was associated with differential pigment content and photosynthetic performance. Amplicon sequence variants at a coastal and an offshore station linked population dynamics with phylogenetic clusters, supporting that strains isolated in this study represent key ecotypes within the Baltic Sea picocyanobacterial community. The functional diversity found within strains with the same pigment type suggests that understanding estuarine picocyanobacterial ecology requires analysis beyond the phycocyanin and phycoerythrin divide. This new knowledge of the environmental preferences in estuarine picocyanobacteria is important for understanding and evaluating productivity in current and future ecosystems.
Collapse
Affiliation(s)
- Anabella Aguilera
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Javier Alegria Zufia
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Laura Bas Conn
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Leandra Gurlit
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Sylwia Śliwińska-Wilczewska
- Mount Allison University, Sackville, New Brunswick, Canada
- Laboratory of Marine Plant Ecophysiology, Institute of Oceanography, University of Gdansk, Gdynia, Poland
| | - Gracjana Budzałek
- Laboratory of Marine Plant Ecophysiology, Institute of Oceanography, University of Gdansk, Gdynia, Poland
| | - Daniel Lundin
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Catherine Legrand
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- School of Business, Innovation and Sustainability, Halmstad University, Halmstad, Sweden
| | - Hanna Farnelid
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| |
Collapse
|
6
|
Carvalho da Silva V, Fernandes N. Protist taxonomic and functional diversity in aquatic ecosystems of the Brazilian Atlantic Forest. PeerJ 2023; 11:e15762. [PMID: 37547721 PMCID: PMC10402703 DOI: 10.7717/peerj.15762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023] Open
Abstract
The Brazilian Atlantic Forest and its associated ecosystems are highly biodiverse but still understudied, especially with respect to eukaryotic microbes. Protists represent the largest proportion of eukaryotic diversity and play important roles in nutrient cycling and maintenance of the ecosystems in which they occur. However, much of protist diversity remains unknown, particularly in the Neotropics. Understanding the taxonomic and functional diversity of these organisms is urgently needed, not only to fill this gap in our knowledge, but also to enable the development of public policies for biological conservation. This is the first study to investigate the taxonomic and trophic diversity of the major protist groups in freshwater systems and brackish coastal lagoons located in fragments of the Brazilian Atlantic Forest by DNA metabarcoding, using high-throughput sequencing of the gene coding for the V4 region of the 18S rRNA gene. We compared α and β diversity for all protist communities and assessed the relative abundance of phototrophic, consumer, and parasitic taxa. We found that the protist communities of coastal lagoons are as diverse as the freshwater systems studied in terms of α diversity, although differed significantly in terms of taxonomic composition. Our results still showed a notable functional homogeneity between the trophic groups in freshwater environments. Beta diversity was higher among freshwater samples, suggesting a greater level of heterogeneity within this group of samples concerning the composition and abundance of OTUs.Ciliophora was the most represented group in freshwater, while Diatomea dominated diversity in coastal lagoons.
Collapse
|
7
|
Sachs M, Dünn M, Arndt H. Benthic Heterotrophic Protist Communities of the Southern Baltic Analyzed with the Help of Curated Metabarcoding Studies. Biology (Basel) 2023; 12:1010. [PMID: 37508439 PMCID: PMC10376117 DOI: 10.3390/biology12071010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
Abstract
Heterotrophic protists are key components of marine ecosystems. They act as controllers of bacterial and microphytobenthos production and contribute significantly to the carbon flux to higher trophic levels. Still, metabarcoding studies on benthic protist communities are much less frequent than for planktonic organisms. Especially in the Baltic Sea, representing the largest brackish water environment on earth, so far, no extensive metabarcoding studies have been conducted to assess the diversity of benthic protists in this unique and diverse habitat. This study aims to give first insights into the diversity of benthic protist communities in two different regions of the Baltic Sea, Fehmarnbelt, and Oderbank. Using amplicon sequencing of the 18S rDNA V9 region of over 100 individual sediment samples, we were able to show significant differences in the community composition between the two regions and to give insights into the vertical distribution of protists within the sediment (0-20 cm). The results indicate that the differences in community composition in the different regions might be explained by several abiotic factors such as salinity and water depth, but are also influenced by methodological aspects such as differences between DNA and RNA results.
Collapse
Affiliation(s)
- Maria Sachs
- Institute of Zoology, General Ecology, Biocenter Cologne, University of Cologne, Zuelpicherstr. 47b, 51069 Cologne, Germany
| | - Manon Dünn
- Institute of Zoology, General Ecology, Biocenter Cologne, University of Cologne, Zuelpicherstr. 47b, 51069 Cologne, Germany
| | - Hartmut Arndt
- Institute of Zoology, General Ecology, Biocenter Cologne, University of Cologne, Zuelpicherstr. 47b, 51069 Cologne, Germany
| |
Collapse
|
8
|
Novotny A, Serandour B, Kortsch S, Gauzens B, Jan KMG, Winder M. DNA metabarcoding highlights cyanobacteria as the main source of primary production in a pelagic food web model. Sci Adv 2023; 9:eadg1096. [PMID: 37126549 PMCID: PMC10132751 DOI: 10.1126/sciadv.adg1096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Models that estimate rates of energy flow in complex food webs often fail to account for species-specific prey selectivity of diverse consumer guilds. While DNA metabarcoding is increasingly used for dietary studies, methodological biases have limited its application for food web modeling. Here, we used data from dietary metabarcoding studies of zooplankton to calculate prey selectivity indices and assess energy fluxes in a pelagic resource-consumer network. We show that food web dynamics are influenced by prey selectivity and temporal match-mismatch in growth cycles and that cyanobacteria are the main source of primary production in the investigated coastal pelagic food web. The latter challenges the common assumption that cyanobacteria are not supporting food web productivity, a result that is increasingly relevant as global warming promotes cyanobacteria dominance. While this study provides a method for how DNA metabarcoding can be used to quantify energy fluxes in a marine food web, the approach presented here can easily be extended to other ecosystems.
Collapse
Affiliation(s)
- Andreas Novotny
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Baptiste Serandour
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Susanne Kortsch
- Spatial Foodweb Ecology Group, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Environmental and Marine Biology, Åbo Akademi University, Turku 20500, Finland
| | - Benoit Gauzens
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Kinlan M G Jan
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Monika Winder
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| |
Collapse
|
9
|
Serandour B, Jan KMG, Novotny A, Winder M. Opportunistic vs selective feeding strategies of zooplankton under changing environmental conditions. J Plankton Res 2023; 45:389-403. [PMID: 37012975 PMCID: PMC10066809 DOI: 10.1093/plankt/fbad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/25/2023] [Indexed: 06/19/2023]
Abstract
The plankton community consists of diverse interacting species. The estimation of species interactions in nature is challenging. There is limited knowledge on how plankton interactions are influenced by environmental conditions because of limited understanding of zooplankton feeding strategies and factors affecting trophic interactions. In this study, we used DNA-metabarcoding to investigate trophic interactions in mesozooplankton predators and the influence of prey availability on their feeding behavior. We found that mesozooplankton feeding strategies vary within species across an environmental gradient. Some species, such as Temora longicornis consistently used a selective strategy, while diets of Centropages hamatus and Acartia spp. varied between stations, showing a trophic plasticity with the prey community. We found a dominance of Synechococcales reads in Temora's gut content and a high prey diversity for the cladoceran Evadne nordmanni. Our study shows the wide range of prey species that supports mesozooplankton community and helps to understand the spatial and temporal complexity of plankton species interactions and discriminate the selectivity ability of four zooplankton key species. Due to the central role of plankton in marine waters, a better comprehension of the spatiotemporal variability in species interactions helps to estimate fluxes to benthic and pelagic predators.
Collapse
Affiliation(s)
- Baptiste Serandour
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Universitetsvägen 10A, SE-106 91, Stockholm, Sweden
| | - Kinlan M G Jan
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Universitetsvägen 10A, SE-106 91, Stockholm, Sweden
| | - Andreas Novotny
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Universitetsvägen 10A, SE-106 91, Stockholm, Sweden
| | - Monika Winder
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Universitetsvägen 10A, SE-106 91, Stockholm, Sweden
| |
Collapse
|
10
|
Liu Q, Li Y, Wang H, Yang G, Kan J, Yang M, Yu X, Guo C, Wang M, Wang W, Zhang Q, Zhu J, Zhao X, Jiang Y. Assembly and Network Stability of Planktonic Microorganisms under the Influence of Salinity Gradient: an Arctic Case Study from the Lena River Estuary to the Laptev Sea. Microbiol Spectr 2023; 11:e0211522. [PMID: 36744927 PMCID: PMC10100684 DOI: 10.1128/spectrum.02115-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/18/2023] [Indexed: 02/07/2023] Open
Abstract
The diversity and primary productivity in the Arctic ecosystem are rapidly changing due to global warming. Microorganisms play a vital role in biogeochemical cycling. However, the diversity of planktonic microorganism communities in the Laptev Sea, one of the most important marginal seas of the Western Arctic Ocean, have not been studied sufficiently in depth. The diversity and community structure of the planktonic microorganisms in the surface water were investigated at 20 stations on the Lena River flowing into the Laptev Sea. Multivariate statistical analyses demonstrated clear spatial patterns in the α diversity and community structure for microorganisms under different salinity levels. Co-occurrence networks of microbial communities revealed that spatial variation promoted differentiation of the characteristics and stability of microbial networks in the Laptev Sea. Contrary to expectations, abundant taxa were found to not have a large influence on the stability and resilience of microbial interactions in the region. On the contrary, less-abundant taxa were found to have far greater influence. The stability and resilience of the prokaryotic and microeukaryotic networks in the Lena River estuary and the continental shelf provided valuable insights into the impact of freshwater and land inflow disturbances on microbial assemblage. Overall, these results enhance our understanding of the composition of microbial communities and provide insights into how spatial changes of abundant versus rare species alter the nature and stability of microbial networks from the Lena River estuary to the Laptev Sea. In addition, this study explored microbial interactions and their ability to resist future disturbances. IMPORTANCE The regime of the Laptev Sea depends closely on the runoff of the Lena River. Microorganisms are essential components of aquatic food webs and play a significant role in polar ecosystems. In this study, we provided a basic microbial data set as well as new insights into the microbial networks from the Lena River estuary to the Laptev Sea, while exploring their potential to resist future disturbances. A comprehensive and systematic study of the community structure and function of the planktonic microorganisms in the Laptev Sea would greatly enhance our understanding of how polar microbial communities respond to the salinity gradient under climate warming.
Collapse
Affiliation(s)
- Qian Liu
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Chemistry Theory and Technology, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yan Li
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hualong Wang
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Guipeng Yang
- Key Laboratory of Marine Chemistry Theory and Technology, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ministry of Education, Ocean University of China, Qingdao, China
| | - Jinjun Kan
- Microbiology Division, Stroud Water Research Center, Avondale, Pennsylvania, USA
| | - Mengyao Yang
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiaowen Yu
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Cui Guo
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Min Wang
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
| | - Wei Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Qingli Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Jiancheng Zhu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xianyong Zhao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yong Jiang
- College of Marine Life Science & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
| |
Collapse
|
11
|
Wu J, Zhu Z, Waniek JJ, Niu M, Wang Y, Zhang Z, Zhou M, Zhang R. The biogeography and co-occurrence network patterns of bacteria and microeukaryotes in the estuarine and coastal waters. Mar Environ Res 2023; 184:105873. [PMID: 36628821 DOI: 10.1016/j.marenvres.2023.105873] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/02/2023] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
Community and diversity shifts of bacteria and microeukaryotes with strong environmental and spatial variations have been unveiled in the Pearl River Estuary (PRE) and northern coastal part of South China Sea (SCS). However, it is not clear what the determining factors shape the microbial community and how the biotic interactions respond to the estuarine and oceanic environment. Here, we established the multiple regression models (MRM) and co-occurrence networks on microbial communities in PRE and SCS habitats. The results showed that there were significant differences of the abiotic factors affecting the bacterial and microeukaryotic communities between PRE and SCS habitats. Salinity explained the largest variations to the microbial community dissimilarities in PRE. Whereas spatial and environmental factors determined the microbial community dissimilarities in SCS. Positive relations between parasitic lineages (e.g. Perkinsea and Cercozoa) and algal taxa (Dinophyceae, Cryptophyta, Chlorophyta and Ochrophyta) dominated in the PRE network. While parasites Syndiniales positively correlated with other Syndiniales and protists in SCS. Strong positive associations among autotrophic and heterotrophic groups were revealed in both niches. Therefore, the biotic interactions are also important and may be responsible for the unexplained variations of the abiotic factors from MRM models. Microbial network in the PRE estuarine water had weakened resistance to environmental disturbances, while the SCS network had greater capacity to maintain network stability. This study shed light on the different mechanisms of abiotic and biotic factors in shaping the compositions of bacteria and microeukaryotes between PRE and SCS niches, and highlights the weakening effect of environmental disturbances on the microbial network stability.
Collapse
Affiliation(s)
- Jinnan Wu
- School of Oceanography, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Zhu Zhu
- School of Oceanography, Shanghai Jiao Tong University, 200030, Shanghai, China.
| | - Joanna J Waniek
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestrasse 15, 18119, Rostock, Germany
| | - Mingyang Niu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Yuntao Wang
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, 310000, Hangzhou, Zhejiang, China
| | - Zhaoru Zhang
- School of Oceanography, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Meng Zhou
- School of Oceanography, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Ruifeng Zhang
- School of Oceanography, Shanghai Jiao Tong University, 200030, Shanghai, China.
| |
Collapse
|
12
|
Karlson B, Arneborg L, Johansson J, Linders J, Liu Y, Olofsson M. A suggested climate service for cyanobacteria blooms in the Baltic Sea - Comparing three monitoring methods. Harmful Algae 2022; 118:102291. [PMID: 36195413 PMCID: PMC9559175 DOI: 10.1016/j.hal.2022.102291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 05/06/2023]
Abstract
Dense blooms of filamentous cyanobacteria are recurrent phenomena in the Baltic Sea, with occasional negative effects on the surrounding ecosystem, as well as on tourism, human health, aquaculture, and fisheries. Establishing a climate service is therefore suggested; including multi-method observations of cyanobacteria biomass, biodiversity, and biogeography, in correspondence to biotic and abiotic factors. Three different approaches were compared for determination of spatial and temporal variability and trends of the blooms; 1) microscopy-based long-term data, 2) satellite remote sensing, and 3) phycocyanin fluorescence mounted on a merchant vessel. Firstly, microscopy-based data on cyanobacteria biomass from the period 2000-2020 showed that the toxin producing genus Nodularia and non-toxic Aphanizomenon both had summer means of 15 µg C L-1, while Dolichospermum was less dominant with a mean of 8 µg C L-1. Some years also the Kattegat was affected by cyanobacteria blooms, likely transported here by ocean currents. Secondly, the satellite remote sensing time series for the period 2002-2020 indicated that near surface blooms were most frequent in the Northern Baltic Proper and that near surface blooms have increased in the Bothnian Sea, starting later in the season than in the Baltic Proper. The largest extents (i.e., total area covered) were observed in 2005, 2008, and 2018. Thirdly, phycocyanin fluorescence from a flow through sensor mounted on a merchant vessel was used as a proxy for cyanobacteria biomass and correlated to cyanobacteria biomass estimated by microscopy. However, the satellite remote sensing data on surface accumulations showed little resemblance to the data on cyanobacteria biomass based on water sampling and microscopy, interpreted as an effect of methods. Sensors on satellites mainly detect surface accumulations of cyanobacteria while the microscopy data was based on samples 0-10 m, thereby comprising a larger community. Data from satellite remote sensing of cyanobacteria was correlated to the phycocyanin fluorescence indicating that similar bio-optical properties are observed. Finally, results from a downscaled ocean climate model (NEMONordic) were used to produce future scenarios for temperature and salinity, which directly affects cyanobacteria blooms in the Baltic Sea, supposedly by increasing in abundance and change in species composition. Short-term forecasts can be used together with observations for early warning of cyanobacteria blooms, and we suggest an internationally coordinated cyanobacteria observation and warning system for the Baltic Sea area.
Collapse
Affiliation(s)
- Bengt Karlson
- Research and Development, Oceanography, Swedish Meteorological and Hydrological Institute, Västra Frölunda, Sweden.
| | - Lars Arneborg
- Research and Development, Oceanography, Swedish Meteorological and Hydrological Institute, Västra Frölunda, Sweden
| | - Johannes Johansson
- Oceanographic Services, Swedish Meteorological and Hydrological Institute, Västra Frölunda, Sweden
| | - Johanna Linders
- Oceanographic Services, Swedish Meteorological and Hydrological Institute, Västra Frölunda, Sweden
| | - Ye Liu
- Research and Development, Oceanography, Swedish Meteorological and Hydrological Institute, Västra Frölunda, Sweden
| | - Malin Olofsson
- Research and Development, Oceanography, Swedish Meteorological and Hydrological Institute, Västra Frölunda, Sweden; Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
13
|
Wang Z, Liu L, Tang Y, Li A, Liu C, Xie C, Xiao L, Lu S. Phytoplankton community and HAB species in the South China Sea detected by morphological and metabarcoding approaches. Harmful Algae 2022; 118:102297. [PMID: 36195422 DOI: 10.1016/j.hal.2022.102297] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 07/23/2022] [Accepted: 08/01/2022] [Indexed: 06/16/2023]
Abstract
The southern Chinese coast is one of the most developed regions in China and is an area where harmful algal blooms (HABs) have occurred frequently. In this study, differences in the phytoplankton community between microscopic observations and 18S rDNA metabarcoding were compared in 89 surface water samples collected from the southern Chinese coast and the western South China Sea (SCS). This is the first report investigating the phytoplankton community and HAB species using a combination of morphological and metabarcoding approaches in this sea area. There were substantial differences in phytoplankton community structure detected by the two methods. Microscopic observation revealed diatom predominance in the phytoplankton community, while metabarcoding indicated dinoflagellate dominance. The phytoplankton community structure obtained by microscopic observation better reflects the real situation in the water column. Metabarcoding annotated more species than morphospecies observed by microscopy. Haptophyta and Cryptophyta were the specific phyla detected in metabarcoding but were missed in microscopy due to their small size. Conversely, some taxa were found in microscopic analysis alone, such as species in Dinophysis, Prorocentrum, and Scrippsiella, suggesting some biases during metabarcoding and gaps in sequence databases. Metabarcoding is superior for detecting morphologically cryptic, small-sized and HAB taxa, such as unarmored dinoflagellates, nanosized hatophytes and chlorophytes, as well as multiple species in Alexandrium, Pseudonitzschia, and Chaetoceros in our study. A total of 62 HAB taxa were identified in this study, including blooming and potentially toxic species. Diatom abundances generally decreased southward, while those of dinoflagellates and haptophytes showed the opposite trend. Chlorophytes were mainly distributed in coastal waters, especially in the Pearl River Estuary. Phytoplankton community structures were shaped by nutrients and salinity, and phosphorus was the most limiting factor for phytoplankton growth. The phytoplankton community in the western SCS showed unique characteristics away from those in the coastal sea areas. The results suggest that the combination of morphological and metabarcoding approaches comprehensively reveals the phytoplankton community structure and diversity of HAB species.
Collapse
Affiliation(s)
- Zhaohui Wang
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
| | - Lei Liu
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yali Tang
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Aifeng Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Chao Liu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Changliang Xie
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Lijuan Xiao
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
| | - Songhui Lu
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
| |
Collapse
|
14
|
Ohore OE, Wei Y, Wang Y, Nwankwegu AS, Wang Z. Tracking the influence of antibiotics, antibiotic resistomes, and salinity gradient in modulating microbial community assemblage of surface water and the ecological consequences. Chemosphere 2022; 305:135428. [PMID: 35760129 DOI: 10.1016/j.chemosphere.2022.135428] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 06/15/2023]
Abstract
The ecological impacts of antibiotics and antibiotic resistance genes (ARGs) on water ecology remain elusive in natural environments. We investigated the influence of antibiotics, ARGs and salinity gradient on the surface water ecosystem. Cefquinome (104.2 ± 43.6 ng/L) and cefminox (16.2 ± 7.50 ng/L) cephalosporins were predominant in all sites. Antibiotic contamination was increased in the estuary ecosystems compared to the freshwater ecosystems by 6%. Bacterial diversity could resist changes in salinity, but the relative abundance of some bacterial genera; Pseudoalteromonas, Glaciecola, norank_f__Arcobacteraceae, and Pseudohongiella was increased in the estuary zone (salinity>0.2%). The eukaryotic composition was increased in the subsaline environments (<0.2%), but the higher salinity in the saline zone inhibited the eukaryotic diversity. The relative abundance of ARGs was significantly higher in the estuary than in freshwater ecosystems, and ARGs interactions and mobile elements (aac(6')-Ib(aka_aacA4)-01, tetR-02, aacC, intI1, intI-1(clinic), qacEdelta1-01, and strB) were the predominant factors responsible for the ARGs propagation. Antibiotics associated with corresponding and non-corresponding ARGs and potentially created an adverse environment that increased the predation and pathogenicity of the aquatic food web and inhibited the metabolic functions. Surface water are first-line-ecosystems receiving antibiotics and ARGs hence our findings provided vital insights into understanding their ecological consequences on surface water ecosystems.
Collapse
Affiliation(s)
- Okugbe Ebiotubo Ohore
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, And Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Address: 243 Daxue Road, Shantou, Guangdong, 515063, China
| | - Yunjie Wei
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, And Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Address: 243 Daxue Road, Shantou, Guangdong, 515063, China
| | - Yuwen Wang
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, And Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Address: 243 Daxue Road, Shantou, Guangdong, 515063, China
| | - Amechi S Nwankwegu
- College of Resources and Environment, Southwest University, Chongqing, 400716, China
| | - Zhen Wang
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, And Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Address: 243 Daxue Road, Shantou, Guangdong, 515063, China.
| |
Collapse
|
15
|
Soerensen AL, Feinberg A, Schartup AT. Selenium concentration in herring from the Baltic Sea tracks decadal and spatial trends in external sources. Environ Sci Process Impacts 2022; 24:1319-1329. [PMID: 35212334 PMCID: PMC9491286 DOI: 10.1039/d1em00418b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Selenium (Se) has a narrow range between nutritionally optimal and toxic concentrations for many organisms, including fish and humans. However, the degree to which humans are affecting Se concentrations in coastal food webs with diffuse Se sources is not well described. Here we examine large-scale drivers of spatio-temporal variability in Se concentration in herring from the Baltic Sea (coastal sea) to explore the anthropogenic impact on a species from the pelagic food web. We analyze data from three herring muscle time series covering three decades (1979-2010) and herring liver time series from 20 stations across the Baltic Sea covering a fourth decade (2009-2019). We find a 0.7-2.0% per annum (n = 26-30) Se decline in herring muscle samples from 0.34 ± 0.02 μg g-1 ww in 1979-1981 to 0.18 ± 0.03 μg g-1 ww in 2008-2010. This decrease continues in the liver samples during the fourth decade (6 of 20 stations show significant decrease). We also find increasing North-South and East-West gradients in herring Se concentrations. Using our observations, modelled Se deposition (spatio-temporal information) and estimated Se river discharge (spatial information), we show that the spatial variability in herring Se tracks the variability in external source loads. Further, between 1979 and 2010 we report a ∼5% per annum decline in direct Se deposition and a more gradual, 0.7-2.0% per annum, decline in herring Se concentrations. The slower rate of decrease for herring can be explained by stable or only slowly decreasing riverine inputs of Se to the Baltic Sea as well as recycling of Se within the coastal system. Both processes can reduce the effect of the trend predicted from direct Se deposition. We show that changing atmospheric emissions of Se may influence Se concentrations of a pelagic fish species in a coastal area through direct deposition and riverine inputs from the terrestrial landscape.
Collapse
Affiliation(s)
- Anne L Soerensen
- Department of Environmental Research and Monitoring, Swedish Museum of Natural History, Stockholm, Sweden.
| | - Aryeh Feinberg
- Institute for Data, Systems, and Society, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Amina T Schartup
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| |
Collapse
|
16
|
Zufia JA, Legrand C, Farnelid H. Seasonal dynamics in picocyanobacterial abundance and clade composition at coastal and offshore stations in the Baltic Sea. Sci Rep 2022; 12:14330. [PMID: 35995823 PMCID: PMC9395346 DOI: 10.1038/s41598-022-18454-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/11/2022] [Indexed: 11/11/2022] Open
Abstract
Picocyanobacteria (< 2 µm in diameter) are significant contributors to total phytoplankton biomass. Due to the high diversity within this group, their seasonal dynamics and relationship with environmental parameters, especially in brackish waters, are largely unknown. In this study, the abundance and community composition of phycoerythrin rich picocyanobacteria (PE-SYN) and phycocyanin rich picocyanobacteria (PC-SYN) were monitored at a coastal (K-station) and at an offshore station (LMO; ~ 10 km from land) in the Baltic Sea over three years (2018–2020). Cell abundances of picocyanobacteria correlated positively to temperature and negatively to nitrate (NO3) concentration. While PE-SYN abundance correlated to the presence of nitrogen fixers, PC-SYN abundance was linked to stratification/shallow waters. The picocyanobacterial targeted amplicon sequencing revealed an unprecedented diversity of 2169 picocyanobacterial amplicons sequence variants (ASVs). A unique assemblage of distinct picocyanobacterial clades across seasons was identified. Clade A/B dominated the picocyanobacterial community, except during summer when low NO3, high phosphate (PO4) concentrations and warm temperatures promoted S5.2 dominance. This study, providing multiyear data, links picocyanobacterial populations to environmental parameters. The difference in the response of the two functional groups and clades underscore the need for further high-resolution studies to understand their role in the ecosystem.
Collapse
Affiliation(s)
- Javier Alegria Zufia
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Catherine Legrand
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.,School of Business, Innovation and Sustainability, Halmstad University, Halmstad, Sweden
| | - Hanna Farnelid
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
| |
Collapse
|
17
|
Broman E, Izabel-Shen D, Rodríguez-Gijón A, Bonaglia S, Garcia SL, Nascimento FJA. Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem. Microbiome 2022; 10:126. [PMID: 35965333 PMCID: PMC9377124 DOI: 10.1186/s40168-022-01321-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/05/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities potentially changing the diversity of functional genes and its associated metabolic processes. In this study, we investigated spatial variability and how environmental variables structure the diversity and composition of benthic functional genes and metabolic pathways across various fundamental environmental gradients. We analyzed metagenomic data from sediment samples, measured related abiotic data (e.g., salinity, oxygen and carbon content), covering 59 stations spanning 1,145 km across the Baltic Sea. RESULTS The composition of genes and microbial communities were mainly structured by salinity plus oxygen, and the carbon to nitrogen (C:N) ratio for specific metabolic pathways related to nutrient transport and carbon metabolism. Multivariate analyses indicated that the compositional change in functional genes was more prominent across environmental gradients compared to changes in microbial taxonomy even at genus level, and indicate functional diversity adaptation to local environments. Oxygen deficient areas (i.e., dead zones) were more different in gene composition when compared to oxic sediments. CONCLUSIONS This study highlights how benthic functional genes are structured over spatial distances and by environmental gradients and resource availability, and suggests that changes in, e.g., oxygenation, salinity, and carbon plus nitrogen content will influence functional metabolic pathways in benthic habitats. Video Abstract.
Collapse
Affiliation(s)
- Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Dandan Izabel-Shen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Alejandro Rodríguez-Gijón
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Stefano Bonaglia
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Sarahi L. Garcia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Francisco J. A. Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| |
Collapse
|
18
|
Li K, Guan W, He P, Li K. Comparison of bacterial communities on the surface of concrete breakwater structures and ambient bacterioplankton. Lett Appl Microbiol 2022; 75:1193-1202. [PMID: 35831926 DOI: 10.1111/lam.13787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/03/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Breakwater structures made of concrete are used widely around the world, and the bacteria living on these surfaces can cause the concrete to deteriorate. In this study, we collected bacterial biofilms from concrete breakwater structures located along the coast of an island, a mainland coast, and a freshwater riverbank as well as planktonic water samples from each site, and we analyzed their bacterial community structures using Illumina sequencing. At the phylum level, Proteobacteria and Actinobacteria dominated planktonic samples, whereas Cyanobacteria, Proteobacteria, and Bacteroidetes dominated the biofilm samples. High Cyanobacteria abundance was found in all biofilm samples. Bacterial communities significantly varied between planktonic and biofilm samples and between biofilm samples from seawater and freshwater. Only a small number of bacterial operational taxonomic units were shared by planktonic and biofilm samples from each sampling site. The permanganate index in ambient water had a more significant impact on biofilm bacterial communities than on planktonic samples. Additionally, ammonia nitrogen and total nitrogen contents were positively correlated and salinity was negatively correlated with bacterial beta diversity in biofilm samples.
Collapse
Affiliation(s)
- Kui Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Weibing Guan
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Peimin He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Kejun Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| |
Collapse
|
19
|
Novotny A, Jan KMG, Dierking J, Winder M. Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy. Sci Rep 2022; 12:10952. [PMID: 35768563 DOI: 10.1038/s41598-022-15116-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/17/2022] [Indexed: 11/28/2022] Open
Abstract
Marine communities undergo rapid changes related to human-induced ecosystem pressures. The Baltic Sea pelagic food web has experienced several regime shifts during the past century, resulting in a system where competition between the dominant planktivorous mesopredatory clupeid fish species herring (Clupea harengus) and sprat (Sprattus sprattus) and the rapidly increasing stickleback (Gasterosteus aculeatus) population is assumed to be high. Here, we investigate diet overlap between these three planktivorous fishes in the Baltic Sea, utilizing DNA metabarcoding on the 18S rRNA gene and the COI gene, targeted qPCR, and microscopy. Our results show niche differentiation between clupeids and stickleback, and highlight that rotifers play an important role in this pattern, as a resource that is not being used by the clupeids nor by other zooplankton in spring. We further show that all the diet assessment methods used in this study are consistent, but also that DNA metabarcoding describes the plankton-fish link at the highest taxonomic resolution. This study suggests that rotifers and other understudied soft-bodied prey may have an important function in the pelagic food web and that the growing population of pelagic stickleback may be supported by the open feeding niche offered by the rotifers.
Collapse
|
20
|
Wagner NY, Andersen DT, Hahn AS, McLaughlin R, Johnson SS. Draft Genome Sequence from a Putative New Genus and Species in the Family M1A02 within the Phylum Planctomycetes, Isolated from Benthic Pinnacle Mats in Lake Untersee, Antarctica. Microbiol Resour Announc 2022; 11:e0119221. [PMID: 35442084 DOI: 10.1128/mra.01192-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the draft genome sequence for a new putative genus and species in the family M1A02 within the order Phycisphaerales. Isolated from the metagenome of a benthic pinnacle-shaped mat in the Antarctic Lake Untersee, the members of this family have been found in biofilms and freshwater environments.
Collapse
|
21
|
Wang S, Sen K, He Y, Bai M, Wang G. Riverine Inputs Impact the Diversity and Population Structure of Heterotrophic Fungus-like Protists and Bacterioplankton in the Coastal Waters of the South China Sea. Water 2022; 14:1580. [DOI: 10.3390/w14101580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Labyrinthulomycetes protists (LP) play an important role in ocean carbon cycling with an ubiquitous presence in marine ecosystems. As one of the most important environmental factors, salinity is known to regulate their diverse metabolic activities. However, impacts of salinity gradient on their distribution and ecological functions in natural habitats remain largely unknown. In this study, the dynamics of LP abundance and community structure were examined in the surface water of plume, offshore, and pelagic habitats in the South China Sea (SCS). The highest (5.59 × 105 copies L−1) and lowest (5.28 × 104 copies L−1) abundance of LP were found to occur in the waters of plume and pelagic habitats, respectively. Multiple dimensional scaling (MDS) analysis revealed a strong relationship between salinity and LP community variation (p < 0.05, rho = 0.67). Unexpectedly, relative low LP diversity was detected in the brackish water samples of the plume. Moreover, our results indicated the genus Aplanochytrium dominated LP communities in offshore and pelagic, while Aurantiochytrium and Ulkenia were common in the plume. Physiological and metabolic features of these genera suggested that LP ecological functions were also largely varied along this salinity gradient. Clearly, the salinity gradient likely regulates the diversity and functional partitioning of marine protistan micro-eukaryotes in the world’s oceans.
Collapse
|
22
|
Jiang X, Zhu Z, Wu J, Lian E, Liu D, Yang S, Zhang R. Bacterial and Protistan Community Variation across the Changjiang Estuary to the Ocean with Multiple Environmental Gradients. Microorganisms 2022; 10:991. [PMID: 35630434 PMCID: PMC9144284 DOI: 10.3390/microorganisms10050991] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 02/01/2023] Open
Abstract
Plankton microorganisms play central roles in the marine food web and global biogeochemical cycles, while their distribution and abundance are affected by environmental variables. The determinants of microbial community composition and diversity in estuaries and surrounding waters with multiple environmental gradients at a fine scale remain largely unclear. Here, we investigated bacterial and protistan community assembly in surface waters from 27 stations across the Changjiang Estuary to the ocean, with salinity ranging from 0 to 32.1, using 16S rRNA and 18S rRNA gene amplicon sequencing. Statistical analyses revealed that salinity is the major factor structuring both bacterial and protistan communities. Salinity also acted as a significant environmental determinant influencing alpha-diversity patterns. Alpha diversity indices for bacterial and protistan communities revealed a species minimum in higher-salinity waters (22.1–32.1). Contrary to the protistan community, the highest bacterial diversity was identified in medium-salinity waters (2.8–18.8), contrasting Remane’s Artenminimum concept. The distribution of major planktonic taxa followed the expected pattern, and the salinity boundary for Syndiniales was specifically identified. These findings revealed the significant effects of salinity on the microbial community across an estuary to ocean transect and the distinct response to salinity between bacterial and protistan communities.
Collapse
|
23
|
Laber CP, Pontiller B, Bunse C, Osbeck CMG, Pérez-Martínez C, Di Leo D, Lundin D, Legrand C, Pinhassi J, Farnelid H. Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak. Front Microbiol 2022; 13:828459. [PMID: 35615500 PMCID: PMC9125215 DOI: 10.3389/fmicb.2022.828459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
The picophytoplankton Synechococcus is a globally abundant autotroph that contributes significantly to primary production in the oceans and coastal areas. These cyanobacteria constitute a diverse genus of organisms that have developed independent niche spaces throughout aquatic environments. Here, we use the 16S V3–V4 rRNA gene region and flow cytometry to explore the diversity of Synechococcus within the picophytoplankton community in the Gullmar Fjord, on the west coast of Sweden. We conducted a station-based 1-year time series and two transect studies of the fjord. Our analysis revealed that within the large number of Synechococcus amplicon sequence variants (ASVs; 239 in total), prevalent ASVs phylogenetically clustered with clade representatives in both marine subcluster 5.1 and 5.2. The near-surface composition of ASVs shifted from spring to summer, when a 5.1 subcluster dominated community developed along with elevated Synechococcus abundances up to 9.3 × 104 cells ml–1. This seasonal dominance by subcluster 5.1 was observed over the length of the fjord (25 km), where shifts in community composition were associated with increasing depth. Unexpectedly, the community shift was not associated with changes in salinity. Synechococcus abundance dynamics also differed from that of the photosynthetic picoeukaryote community. These results highlight how seasonal variations in environmental conditions influence the dynamics of Synechococcus clades in a high latitude threshold fjord.
Collapse
Affiliation(s)
- Christien P. Laber
- Centre for Ecology and Evolution in Microbial Model Systems – EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
- *Correspondence: Christien P. Laber,
| | - Benjamin Pontiller
- Centre for Ecology and Evolution in Microbial Model Systems – EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Carina Bunse
- Centre for Ecology and Evolution in Microbial Model Systems – EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Christofer M. G. Osbeck
- Centre for Ecology and Evolution in Microbial Model Systems – EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Clara Pérez-Martínez
- Centre for Ecology and Evolution in Microbial Model Systems – EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Danilo Di Leo
- Centre for Ecology and Evolution in Microbial Model Systems – EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems – EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Catherine Legrand
- Centre for Ecology and Evolution in Microbial Model Systems – EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
- School of Business, Innovation and Sustainability, Halmstad University, Halmstad, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems – EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Hanna Farnelid
- Centre for Ecology and Evolution in Microbial Model Systems – EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| |
Collapse
|
24
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
25
|
Lew S, Glińska-Lewczuk K, Burandt P, Kulesza K, Kobus S, Obolewski K. Salinity as a Determinant Structuring Microbial Communities in Coastal Lakes. Int J Environ Res Public Health 2022; 19:ijerph19084592. [PMID: 35457457 PMCID: PMC9028135 DOI: 10.3390/ijerph19084592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/29/2022] [Accepted: 04/06/2022] [Indexed: 02/06/2023]
Abstract
The response of bacterioplankton structure to salinity level in coastal lakes (n = 9) along the southern Baltic Sea coastline was studied. In terms of mean salinity levels (0.2−5.2 PSU), the lakes represented freshwater, transitional, and brackish types. Results showed that salinity determines the spatial and seasonal distribution patterns of microorganisms in costal lakes. Increased salinity contributed to a significant decline in total bacterial numbers (TBN). The TBN was lowest in brackish lakes in autumn (4 × 106 cells/mL) and highest in freshwater lakes in summer (7.11 × 106 cells/mL). The groups of Proteobacteria are appropriate bioindicators in any classifications of coastal ecosystems, particularly at low-haline stress. Alpha- and Gamma- subclasses of Proteobacteria are identifiers for brackish habitats, while Betaproteobacteria, due to their intolerance to haline stress, prefer freshwater habitats. Counts of euryhaline Actinobacteria, the dominant group of bacterioplankton (31.8%), decreased significantly with increased salinity. Actinobacteria and Deltaproteobacteria were identifiers of transitional lakes. Cytophaga-Flavobacteria showed affinity with freshwater ecosystems, but this relation was not statistically significant (p > 0.05). The bacteria groups correlated with other physico-chemical parameters of water, such as oxygenation (Actinobacteria) or organic carbon (Betaproteobacteria, Deltaproteobacteria). The impact of hydrological connectivity and salt-water interference on the microbiota structure and biogeochemistry of coastal waters should be considered in the assessment of the ecological status of coastal lakes.
Collapse
Affiliation(s)
- Sylwia Lew
- Department of Microbiology and Mycology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Str. 1a, 10-719 Olsztyn, Poland;
- Correspondence:
| | - Katarzyna Glińska-Lewczuk
- Department of Water Management and Climatology, University of Warmia and Mazury in Olsztyn, Łódzki Sq. 2, 10-719 Olsztyn, Poland; (K.G.-L.); (P.B.); (S.K.)
| | - Paweł Burandt
- Department of Water Management and Climatology, University of Warmia and Mazury in Olsztyn, Łódzki Sq. 2, 10-719 Olsztyn, Poland; (K.G.-L.); (P.B.); (S.K.)
| | - Klaudia Kulesza
- Department of Microbiology and Mycology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Str. 1a, 10-719 Olsztyn, Poland;
| | - Szymon Kobus
- Department of Water Management and Climatology, University of Warmia and Mazury in Olsztyn, Łódzki Sq. 2, 10-719 Olsztyn, Poland; (K.G.-L.); (P.B.); (S.K.)
| | - Krystian Obolewski
- Department of Hydrobiology, Kazimierz Wielki University in Bydgoszcz, Powstańców Wielkopolskich Str. 10, 85-090 Bydgoszcz, Poland;
| |
Collapse
|
26
|
Abstract
Phytoplankton are photosynthetic, single-celled organisms producing almost half of all oxygen on Earth and play a central role as prey for higher organisms, making them irreplaceable in the marine food web. As Global Change proceeds, imposing rapidly intensifying selection pressures, phytoplankton are forced to undergo evolution, local extinction, or redistribution, with potentially cascading effects throughout the marine ecosystem. Recent results from the field of population genetics display high levels of standing genetic diversity in natural phytoplankton populations, providing ample ‘evolutionary options’ and implying high adaptive potential to changing conditions. This potential for adaptive evolution is realized in several studies of experimental evolution, even though most of these studies investigate the evolution of only single strains. This, however, shows that phytoplankton not only evolve from standing genetic diversity, but also rely on de novo mutations. Recent global sampling campaigns show that the immense intraspecific diversity of phytoplankton in the marine ecosystem has been significantly underestimated, meaning we are only studying a minor portion of the relevant variability in the context of Global Change and evolution. An increased understanding of genomic diversity is primarily hampered by the low number of ecologically representative reference genomes of eukaryotic phytoplankton and the functional annotation of these. However, emerging technologies relying on metagenome and transcriptome data may offer a more realistic understanding of phytoplankton diversity.
Collapse
|
27
|
Mujakić I, Piwosz K, Koblížek M. Phylum Gemmatimonadota and Its Role in the Environment. Microorganisms 2022; 10:microorganisms10010151. [PMID: 35056600 PMCID: PMC8779627 DOI: 10.3390/microorganisms10010151] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/06/2023] Open
Abstract
Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.
Collapse
Affiliation(s)
- Izabela Mujakić
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237, 379 81 Třeboň, Czech Republic; (I.M.); (K.P.)
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
| | - Kasia Piwosz
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237, 379 81 Třeboň, Czech Republic; (I.M.); (K.P.)
- National Marine Fisheries Research Institute, Kołłątaja 1, 81-332 Gdynia, Poland
| | - Michal Koblížek
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237, 379 81 Třeboň, Czech Republic; (I.M.); (K.P.)
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
- Correspondence:
| |
Collapse
|
28
|
Xu Z, Cheung S, Endo H, Xia X, Wu W, Chen B, Ho NHE, Suzuki K, Li M, Liu H, Bik H, Alvarez E. Disentangling the Ecological Processes Shaping the Latitudinal Pattern of Phytoplankton Communities in the Pacific Ocean. mSystems. [PMID: 35089068 PMCID: PMC8725599 DOI: 10.1128/msystems.01203-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Phytoplankton diversity and community compositions vary across spaces and are fundamentally affected by several deterministic (e.g., environmental selection) and stochastic (e.g., ecological drift) processes. How this suite of different processes regulates the biogeography of phytoplankton remains to be comprehensively explored. Using high-throughput sequencing data and null model analysis, we revealed the ecological processes shaping the latitudinal community structure of three major phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) across the Pacific Ocean (70°N, 170°W to 35°S, 170°W). At the basin scale, heterogeneous selection (selection under heterogeneous environmental conditions) dominated the assembly processes of all phytoplankton groups; however, its relative importance varied greatly at the climatic zonal scale, explaining the distinct latitudinal α- and β-diversity among phytoplankton groups. Assembly processes in Synechococcus and haptophyte communities were mainly controlled by physical and nutrient factors, respectively. High temperature drove Synechococcus communities to be more deterministic with higher diversity, while haptophyte communities were less environmentally selected at low latitudes due to their wide niche breadth and mixotrophic lifestyle. Diatom communities were overwhelmingly dominated by the selection process but with low correlation of measured environmental factors to their community compositions. This could be attributed to the high growth rate of diatoms, as indicated by their lower site occupation frequency than predicted in the neutral community model. Our study showed that heterogeneous selection is the main force that shaped the biogeography of three key phytoplankton groups in the Pacific Ocean, with a latitudinal variation of relative importance due to the distinct traits among phytoplankton. IMPORTANCE Phytoplankton are diverse and abundant as primary producers in the ocean, with diversity and community compositions varying spatially. How fundamental processes (e.g., selection, dispersal, and drift) regulate their global biogeography remains to be comprehensively explored. In this study, we disentangled the ecological processes of three key phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) along the same latitudinal gradients in the Pacific Ocean. Heterogeneous selection, by promoting species richness and reducing similarity between communities, was the dominant process shaping the communities of each phytoplankton group at the basin scale. However, its relative importance varied greatly among different phytoplankton groups in different climate zones, explaining the uneven latitudinal α- and β-diversity. We also highlight the importance of identifying key factors mediating the relative importance of assembly processes in phytoplankton communities, which will enhance our understanding of their biogeography in the ocean and future patterns under climate changes.
Collapse
|
29
|
Alegria Zufia J, Farnelid H, Legrand C. Seasonality of Coastal Picophytoplankton Growth, Nutrient Limitation, and Biomass Contribution. Front Microbiol 2021; 12:786590. [PMID: 34938282 PMCID: PMC8685431 DOI: 10.3389/fmicb.2021.786590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Picophytoplankton in the Baltic Sea includes the simplest unicellular cyanoprokaryotes (Synechococcus/Cyanobium) and photosynthetic picoeukaryotes (PPE). Picophytoplankton are thought to be a key component of the phytoplankton community, but their seasonal dynamics and relationships with nutrients and temperature are largely unknown. We monitored pico- and larger phytoplankton at a coastal site in Kalmar Sound (K-Station) weekly during 2018. Among the cyanoprokaryotes, phycoerythrin-rich picocyanobacteria (PE-rich) dominated in spring and summer while phycocyanin-rich picocyanobacteria (PC-rich) dominated during autumn. PE-rich and PC-rich abundances peaked during summer (1.1 × 105 and 2.0 × 105 cells mL–1) while PPE reached highest abundances in spring (1.1 × 105 cells mL–1). PPE was the main contributor to the total phytoplankton biomass (up to 73%). To assess nutrient limitation, bioassays with combinations of nitrogen (NO3 or NH4) and phosphorus additions were performed. PE-rich and PC-rich growth was mainly limited by nitrogen, with a preference for NH4 at >15°C. The three groups had distinct seasonal dynamics and different temperature ranges: 10°C and 17–19°C for PE-rich, 13–16°C for PC-rich and 11–15°C for PPE. We conclude that picophytoplankton contribute significantly to the carbon cycle in the coastal Baltic Sea and underscore the importance of investigating populations to assess the consequences of the combination of high temperature and NH4 in a future climate.
Collapse
Affiliation(s)
- Javier Alegria Zufia
- Marine Phytoplankton Ecology and Applications Laboratory (MPEA), Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Hanna Farnelid
- Marine Phytoplankton Ecology and Applications Laboratory (MPEA), Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Catherine Legrand
- Marine Phytoplankton Ecology and Applications Laboratory (MPEA), Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.,School of Business, Innovation and Sustainability, Halmstad University, Halmstad, Sweden
| |
Collapse
|
30
|
Sildever S, Laas P, Kolesova N, Lips I, Lips U, Nagai S. Plankton biodiversity and species co-occurrence based on environmental DNA – a multiple marker study. MBMG 2021. [DOI: 10.3897/mbmg.5.72371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Metabarcoding in combination with high-throughput sequencing (HTS) allows simultaneous detection of multiple taxa by targeting single or several taxonomically informative gene regions from environmental DNA samples. In this study, a multiple-marker HTS approach was applied to investigate the plankton diversity and seasonal succession in the Baltic Sea from winter to autumn. Four different markers targeting the 16S, 18S, and 28S ribosomal RNA genes were employed, including a marker for more efficient dinoflagellate detection. Typical seasonal changes were observed in phyto- and bacterioplankton communities. In phytoplankton, the appearance patterns of selected common, dominant, or harmful species followed the patterns also confirmed based on 20 years of phytoplankton monitoring data. In the case of zooplankton, both macro- and microzooplankton species were detected. However, no seasonal patterns were detected in their appearance. In total, 15 and 2 new zoo- and phytoplankton species were detected from the Baltic Sea. HTS approach was especially useful for detecting microzooplankton species as well as for investigating the co-occurrence and potential interactions of different taxa. The results of this study further exemplify the efficiency of metabarcoding for biodiversity monitoring and the advantage of employing multiple markers through the detection of species not identifiable based on a single marker survey and/or by traditional morphology-based methods.
Collapse
|
31
|
Sjöqvist C, Delgado LF, Alneberg J, Andersson AF. Ecologically coherent population structure of uncultivated bacterioplankton. ISME J 2021; 15:3034-3049. [PMID: 33953362 PMCID: PMC8443644 DOI: 10.1038/s41396-021-00985-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/31/2021] [Accepted: 04/09/2021] [Indexed: 02/03/2023]
Abstract
Bacterioplankton are main drivers of biogeochemical cycles and important components of aquatic food webs. While sequencing-based studies have revealed how bacterioplankton communities are structured in time and space, relatively little is known about intraspecies diversity patterns and their ecological relevance. Here, we use the newly developed software POGENOM (POpulation GENomics from Metagenomes) to investigate genomic diversity and differentiation in metagenome-assembled genomes from the Baltic Sea, and investigate their genomic variation using metagenome data spanning a 1700 km transect and covering seasonal variation at one station. The majority of the investigated species, representing several major bacterioplankton clades, displayed population structures correlating significantly with environmental factors such as salinity and temperature. Population differentiation was more pronounced over spatial than temporal scales. We discovered genes that have undergone adaptation to different salinity regimes, potentially responsible for the populations' existence along with the salinity range. This in turn implies the broad existence of ecotypes that may remain undetected by rRNA gene sequencing. Our findings emphasize the importance of physiological barriers, and highlight the role of adaptive divergence as a structuring mechanism of bacterioplankton species.
Collapse
Affiliation(s)
- Conny Sjöqvist
- grid.5037.10000000121581746KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden ,grid.13797.3b0000 0001 2235 8415Åbo Akademi University, Faculty of Science and Engineering, Environmental and Marine Biology, Åbo, Finland
| | - Luis Fernando Delgado
- grid.5037.10000000121581746KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| | - Johannes Alneberg
- grid.5037.10000000121581746KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| | - Anders F. Andersson
- grid.5037.10000000121581746KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| |
Collapse
|
32
|
Charvet S, Kim E, Subramaniam A, Montoya J, Duhamel S. Small pigmented eukaryote assemblages of the western tropical North Atlantic around the Amazon River plume during spring discharge. Sci Rep 2021; 11:16200. [PMID: 34376772 DOI: 10.1038/s41598-021-95676-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Small pigmented eukaryotes (⩽ 5 µm) are an important, but overlooked component of global marine phytoplankton. The Amazon River plume delivers nutrients into the oligotrophic western tropical North Atlantic, shades the deeper waters, and drives the structure of microphytoplankton (> 20 µm) communities. For small pigmented eukaryotes, however, diversity and distribution in the region remain unknown, despite their significant contribution to open ocean primary production and other biogeochemical processes. To investigate how habitats created by the Amazon river plume shape small pigmented eukaryote communities, we used high-throughput sequencing of the 18S ribosomal RNA genes from up to five distinct small pigmented eukaryote cell populations, identified and sorted by flow cytometry. Small pigmented eukaryotes dominated small phytoplankton biomass across all habitat types, but the population abundances varied among stations resulting in a random distribution. Small pigmented eukaryote communities were consistently dominated by Chloropicophyceae (0.8-2 µm) and Bacillariophyceae (0.8-3.5 µm), accompanied by MOCH-5 at the surface or by Dinophyceae at the chlorophyll maximum. Taxonomic composition only displayed differences in the old plume core and at one of the plume margin stations. Such results reflect the dynamic interactions of the plume and offshore oceanic waters and suggest that the resident small pigmented eukaryote diversity was not strongly affected by habitat types at this time of the year.
Collapse
|
33
|
Abstract
Alternative pathways of energy transfer guarantee the functionality and productivity in marine food webs that experience strong seasonality. Nevertheless, the complexity of zooplankton interactions is rarely considered in trophic studies because of the lack of detailed information about feeding interactions in nature. In this study, we used DNA metabarcoding to highlight the diversity of trophic niches in a wide range of micro- and mesozooplankton, including ciliates, rotifers, cladocerans, copepods and their prey, by sequencing 16- and 18S rRNA genes. Our study demonstrates that the zooplankton trophic niche partitioning goes beyond both phylogeny and size and reinforces the importance of diversity in resource use for stabilizing food web efficiency by allowing for several different pathways of energy transfer. We further highlight that small, rarely studied zooplankton (rotifers and ciliates) fill an important role in the Baltic Sea pelagic primary production pathways and the potential of ciliates, rotifers and crustaceans in the utilization of filamentous and picocyanobacteria within the pelagic food web. The approach used in this study is a suitable entry point to ecosystem-wide food web modelling considering species-specific resource use of key consumers.
Collapse
Affiliation(s)
- Andreas Novotny
- Department of Ecology, Environment, and Plant Science, Stockholm University, Svante Arrhenius Väg 20A, 106 91 Stockholm, Sweden
| | - Sara Zamora-Terol
- Department of Ecology, Environment, and Plant Science, Stockholm University, Svante Arrhenius Väg 20A, 106 91 Stockholm, Sweden
| | - Monika Winder
- Department of Ecology, Environment, and Plant Science, Stockholm University, Svante Arrhenius Väg 20A, 106 91 Stockholm, Sweden
| |
Collapse
|
34
|
Mattsson L, Sörenson E, Capo E, Farnelid HM, Hirwa M, Olofsson M, Svensson F, Lindehoff E, Legrand C. Functional Diversity Facilitates Stability Under Environmental Changes in an Outdoor Microalgal Cultivation System. Front Bioeng Biotechnol 2021; 9:651895. [PMID: 33968914 PMCID: PMC8100445 DOI: 10.3389/fbioe.2021.651895] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/23/2021] [Indexed: 01/22/2023] Open
Abstract
Functionally uniform monocultures have remained the paradigm in microalgal cultivation despite the apparent challenges to avoid invasions by other microorganisms. A mixed microbial consortium approach has the potential to optimize and maintain biomass production despite of seasonal changes and to be more resilient toward contaminations. Here we present a 3-year outdoor production of mixed consortia of locally adapted microalgae and bacteria in cold temperate latitude. Microalgal consortia were cultivated in flat panel photobioreactors using brackish Baltic Sea water and CO2 from a cement factory (Degerhamn, Cementa AB, Heidelberg Cement Group) as a sustainable CO2 source. To evaluate the ability of the microbial consortia to maintain stable biomass production while exposed to seasonal changes in both light and temperature, we tracked changes in the microbial community using molecular methods (16S and 18S rDNA amplicon sequencing) and monitored the biomass production and quality (lipid, protein, and carbohydrate content) over 3 years. Despite changes in environmental conditions, the mixed consortia maintained stable biomass production by alternating between two different predominant green microalgae (Monoraphidium and Mychonastes) with complementary tolerance to temperature. The bacterial population was few taxa co-occured over time and the composition did not have any connection to the shifts in microalgal taxa. We propose that a locally adapted and mixed microalgal consortia, with complementary traits, can be useful for optimizing yield of commercial scale microalgal cultivation.
Collapse
Affiliation(s)
- Lina Mattsson
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Eva Sörenson
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Eric Capo
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Hanna Maria Farnelid
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Maurice Hirwa
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden.,Axis Communications, Lund, Sweden
| | | | - Fredrik Svensson
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Elin Lindehoff
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Catherine Legrand
- Department of Biology and Environmental Science, Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| |
Collapse
|
35
|
Garrison CE, Field EK. Introducing a "core steel microbiome" and community functional analysis associated with microbially influenced corrosion. FEMS Microbiol Ecol 2021; 97:5998222. [PMID: 33220682 DOI: 10.1093/femsec/fiaa237] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
Microorganisms attached to aquatic steel structures play key roles in nutrient cycling and structural degradation processes. Corrosion-causing microbes are often the focus of studies involving microbially influenced corrosion, yet the roles of remaining community members remain unclear. This study characterizes the composition and functional potential of a 'core steel microbiome' across stainless steel types (304 and 316) and historic shipwreck steel along salinity gradients in North Carolina estuaries. We found higher phylogenetic evenness and diversity on steel surfaces compared to sediment, and at lower salinities. The core steel microbiome was composed of heterotrophic generalist taxa, and community composition was most strongly influenced by salinity. Substrate type was a secondary factor becoming more influential at higher salinities. The core steel microbiome included members of Sphingobacteriia, Cytophagia, Anaerolineaceae, Verrucomicrobiaceae, Chitinophagaceae, and Rheinheimera. While salinity differences led to phylogenetic separations across microbial community assemblages, functional genes were conserved across salinity and steel type. Generalist taxa on steel surfaces likely provide functional stability and biofilm protection for the community with limited functional trade-offs compared to surrounding environments. Further, characterization of a core steel microbiome increases the understanding of these complex steel surface microbial communities and their similarities to core microbiomes in other environments.
Collapse
Affiliation(s)
- Cody E Garrison
- Department of Biology, East Carolina University, 1000 E 5th St, Greenville, NC 27858, USA
| | - Erin K Field
- Department of Biology, East Carolina University, 1000 E 5th St, Greenville, NC 27858, USA
| |
Collapse
|
36
|
Piwosz K, Mukherjee I, Salcher MM, Grujčić V, Šimek K. CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology. Front Microbiol 2021; 12:640066. [PMID: 33746931 PMCID: PMC7970053 DOI: 10.3389/fmicb.2021.640066] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
Phagotrophic protists are key players in aquatic food webs. Although sequencing-based studies have revealed their enormous diversity, ecological information on in situ abundance, feeding modes, grazing preferences, and growth rates of specific lineages can be reliably obtained only using microscopy-based molecular methods, such as Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). CARD-FISH is commonly applied to study prokaryotes, but less so to microbial eukaryotes. Application of this technique revealed that Paraphysomonas or Spumella-like chrysophytes, considered to be among the most prominent members of protistan communities in pelagic environments, are omnipresent but actually less abundant than expected, in contrast to little known groups such as heterotrophic cryptophyte lineages (e.g., CRY1), cercozoans, katablepharids, or the MAST lineages. Combination of CARD-FISH with tracer techniques and application of double CARD-FISH allow visualization of food vacuole contents of specific flagellate groups, thus considerably challenging our current, simplistic view that they are predominantly bacterivores. Experimental manipulations with natural communities revealed that larger flagellates are actually omnivores ingesting both prokaryotes and other protists. These new findings justify our proposition of an updated model of microbial food webs in pelagic environments, reflecting more authentically the complex trophic interactions and specific roles of flagellated protists, with inclusion of at least two additional trophic levels in the nanoplankton size fraction. Moreover, we provide a detailed CARD-FISH protocol for protists, exemplified on mixo- and heterotrophic nanoplanktonic flagellates, together with tips on probe design, a troubleshooting guide addressing most frequent obstacles, and an exhaustive list of published probes targeting protists.
Collapse
Affiliation(s)
- Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland
- Centre ALGATECH, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Indranil Mukherjee
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia
| | - Michaela M. Salcher
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia
| | - Vesna Grujčić
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Karel Šimek
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia
| |
Collapse
|
37
|
Karlson B, Andersen P, Arneborg L, Cembella A, Eikrem W, John U, West JJ, Klemm K, Kobos J, Lehtinen S, Lundholm N, Mazur-Marzec H, Naustvoll L, Poelman M, Provoost P, De Rijcke M, Suikkanen S. Harmful algal blooms and their effects in coastal seas of Northern Europe. Harmful Algae 2021; 102:101989. [PMID: 33875185 DOI: 10.1016/j.hal.2021.101989] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 06/12/2023]
Abstract
Harmful algal blooms (HAB) are recurrent phenomena in northern Europe along the coasts of the Baltic Sea, Kattegat-Skagerrak, eastern North Sea, Norwegian Sea and the Barents Sea. These HABs have caused occasional massive losses for the aquaculture industry and have chronically affected socioeconomic interests in several ways. This status review gives an overview of historical HAB events and summarises reports to the Harmful Algae Event Database from 1986 to the end of year 2019 and observations made in long term monitoring programmes of potentially harmful phytoplankton and of phycotoxins in bivalve shellfish. Major HAB taxa causing fish mortalities in the region include blooms of the prymnesiophyte Chrysochromulina leadbeateri in northern Norway in 1991 and 2019, resulting in huge economic losses for fish farmers. A bloom of the prymesiophyte Prymnesium polylepis (syn. Chrysochromulina polylepis) in the Kattegat-Skagerrak in 1988 was ecosystem disruptive. Blooms of the prymnesiophyte Phaeocystis spp. have caused accumulations of foam on beaches in the southwestern North Sea and Wadden Sea coasts and shellfish mortality has been linked to their occurrence. Mortality of shellfish linked to HAB events has been observed in estuarine waters associated with influx of water from the southern North Sea. The first bloom of the dictyochophyte genus Pseudochattonella was observed in 1998, and since then such blooms have been observed in high cell densities in spring causing fish mortalities some years. Dinoflagellates, primarily Dinophysis spp., intermittently yield concentrations of Diarrhetic Shellfish Toxins (DST) in blue mussels, Mytilus edulis, above regulatory limits along the coasts of Norway, Denmark and the Swedish west coast. On average, DST levels in shellfish have decreased along the Swedish and Norwegian Skagerrak coasts since approximately 2006, coinciding with a decrease in the cell abundance of D. acuta. Among dinoflagellates, Alexandrium species are the major source of Paralytic Shellfish Toxins (PST) in the region. PST concentrations above regulatory levels were rare in the Skagerrak-Kattegat during the three decadal review period, but frequent and often abundant findings of Alexandrium resting cysts in surface sediments indicate a high potential risk for blooms. PST levels often above regulatory limits along the west coast of Norway are associated with A. catenella (ribotype Group 1) as the main toxin producer. Other Alexandrium species, such as A. ostenfeldii and A. minutum, are capable of producing PST among some populations but are usually not associated with PSP events in the region. The cell abundance of A. pseudogonyaulax, a producer of the ichthyotoxin goniodomin (GD), has increased in the Skagerrak-Kattegat since 2010, and may constitute an emerging threat. The dinoflagellate Azadinium spp. have been unequivocally linked to the presence of azaspiracid toxins (AZT) responsible for Azaspiracid Shellfish Poisoning (AZP) in northern Europe. These toxins were detected in bivalve shellfish at concentrations above regulatory limits for the first time in Norway in blue mussels in 2005 and in Sweden in blue mussels and oysters (Ostrea edulis and Crassostrea gigas) in 2018. Certain members of the diatom genus Pseudo-nitzschia produce the neurotoxin domoic acid and analogs known as Amnesic Shellfish Toxins (AST). Blooms of Pseudo-nitzschia were common in the North Sea and the Skagerrak-Kattegat, but levels of AST in bivalve shellfish were rarely above regulatory limits during the review period. Summer cyanobacteria blooms in the Baltic Sea are a concern mainly for tourism by causing massive fouling of bathing water and beaches. Some of the cyanobacteria produce toxins, e.g. Nodularia spumigena, producer of nodularin, which may be a human health problem and cause occasional dog mortalities. Coastal and shelf sea regions in northern Europe provide a key supply of seafood, socioeconomic well-being and ecosystem services. Increasing anthropogenic influence and climate change create environmental stressors causing shifts in the biogeography and intensity of HABs. Continued monitoring of HAB and phycotoxins and the operation of historical databases such as HAEDAT provide not only an ongoing status report but also provide a way to interpret causes and mechanisms of HABs.
Collapse
Affiliation(s)
- Bengt Karlson
- Swedish Meteorological and Hydrological Institute, Research and Development, Oceanography, Sven Källfelts gata 15, SE-426 71 Västra Frölunda, Sweden.
| | - Per Andersen
- Aarhus University, Marine Ecology, Vejlsøvej 25, 8600 Silkeborg, Denmark
| | - Lars Arneborg
- Swedish Meteorological and Hydrological Institute, Research and Development, Oceanography, Sven Källfelts gata 15, SE-426 71 Västra Frölunda, Sweden
| | - Allan Cembella
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Wenche Eikrem
- University of Oslo, Department of Biosciences, P. O. Box 1066 Blindern, Oslo 0316, Norway; Norwegian Institute for Water Research. Gaustadalleen 21, 0349 Oslo, Norway
| | - Uwe John
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany; Helmholtz Institute for Functional Marine Biodiversity, Ammerländer Heerstraße 231, 26129 Oldenburg, Germany
| | - Jennifer Joy West
- CICERO Center for International Climate Research, P.O. Box 1129, 0318 Blindern, Oslo Norway
| | - Kerstin Klemm
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Justyna Kobos
- University of Gdansk, Institute of Oceanography, Division of Marine Biotechnology, Marszalka Pilsudskiego 46, 81-378 Gdynia; POLAND
| | - Sirpa Lehtinen
- Finnish Environment Institute (SYKE), Marine Research Centre, Agnes Sjöbergin katu 2, 00790 Helsinki, Finland
| | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen K, Denmark
| | - Hanna Mazur-Marzec
- University of Gdansk, Institute of Oceanography, Division of Marine Biotechnology, Marszalka Pilsudskiego 46, 81-378 Gdynia; POLAND
| | - Lars Naustvoll
- Institute of Marine Research, Flødevigen Marine Research Station, N-4817 His, Norway
| | - Marnix Poelman
- Wageningen UR, Wageningen Marine Research, P.O. box 77, 4400 AB, Yerseke, The Netherlands
| | - Pieter Provoost
- Intergovernmental Oceanographic Commission, Project Office for IODE, Wandelaarkaai 7/61 - 8400 Oostende, Belgium
| | - Maarten De Rijcke
- Flanders Marine Institute (VLIZ), Wandelaarkaai 7, B-8400 Oostende, Belgium
| | - Sanna Suikkanen
- Finnish Environment Institute (SYKE), Marine Research Centre, Agnes Sjöbergin katu 2, 00790 Helsinki, Finland
| |
Collapse
|
38
|
Gorokhova E, El-Shehawy R, Lehtiniemi M, Garbaras A. How Copepods Can Eat Toxins Without Getting Sick: Gut Bacteria Help Zooplankton to Feed in Cyanobacteria Blooms. Front Microbiol 2021; 11:589816. [PMID: 33510717 PMCID: PMC7835405 DOI: 10.3389/fmicb.2020.589816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/17/2020] [Indexed: 11/13/2022] Open
Abstract
Toxin-producing cyanobacteria can be harmful to aquatic biota, although some grazers utilize them with often beneficial effects on their growth and reproduction. It is commonly assumed that gut microbiota facilitates host adaptation to the diet; however, the evidence for adaptation mechanisms is scarce. Here, we investigated the abundance of mlrA genes in the gut of the Baltic copepods Acartia bifilosa and Eurytemora affinis during cyanobacteria bloom season (August) and outside it (February). The mlrA genes are unique to microcystin and nodularin degraders, thus indicating the capacity to break down these toxins by the microbiota. The mlrA genes were expressed in the copepod gut year-round, being >10-fold higher in the summer than in the winter populations. Moreover, they were significantly more abundant in Eurytemora than Acartia. To understand the ecological implications of this variability, we conducted feeding experiments using summer- and winter-collected copepods to examine if/how the mlrA abundance in the microbiota affect: (1) uptake of toxic Nodularia spumigena, (2) uptake of a non-toxic algal food offered in mixtures with N. spumigena, and (3) concomitant growth potential in the copepods. The findings provide empirical evidence that the occurrence of mlrA genes in the copepod microbiome facilitates nutrient uptake and growth when feeding on phytoplankton mixtures containing nodularin-producing cyanobacteria; thus, providing an adaptation mechanism to the cyanobacteria blooms.
Collapse
Affiliation(s)
- Elena Gorokhova
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
| | - Rehab El-Shehawy
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
| | - Maiju Lehtiniemi
- Marine Research Centre, Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Andrius Garbaras
- Mass Spectrometry Laboratory, Center for Physical Science and Technology, Vilnius, Lithuania
| |
Collapse
|
39
|
Olofsson M, Hagan JG, Karlson B, Gamfeldt L. Large seasonal and spatial variation in nano- and microphytoplankton diversity along a Baltic Sea-North Sea salinity gradient. Sci Rep 2020; 10:17666. [PMID: 33077730 PMCID: PMC7572517 DOI: 10.1038/s41598-020-74428-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 09/30/2020] [Indexed: 11/09/2022] Open
Abstract
Aquatic phytoplankton experience large fluctuations in environmental conditions during seasonal succession and across salinity gradients, but the impact of this variation on their diversity is poorly understood. We examined spatio-temporal variation in nano- and microphytoplankton (> 2 µm) community structure using almost two decades of light-microscope based monitoring data. The dataset encompasses 19 stations that span a salinity gradient from 2.8 to 35 along the Swedish coastline. Spatially, both regional and local phytoplankton diversity increased with broad-scale salinity variation. Diatoms dominated at high salinity and the proportion of cyanobacteria increased with decreasing salinity. Temporally, cell abundance peaked in winter-spring at high salinity but in summer at low salinity. This was likely due to large filamentous cyanobacteria blooms that occur in summer in low salinity areas, but which are absent in higher salinities. In contrast, phytoplankton local diversity peaked in spring at low salinity but in fall and winter at high salinity. Whilst differences in seasonal variation in cell abundance were reasonably well-explained by variation in salinity and nutrient availability, variation in local-scale phytoplankton diversity was poorly predicted by environmental variables. Overall, we provide insights into the causes of spatio-temporal variation in coastal phytoplankton community structure while also identifying knowledge gaps.
Collapse
Affiliation(s)
- Malin Olofsson
- Research and Development, Oceanography, Swedish Meteorological and Hydrological Institute, Sven Källfelts gata 15, 426 71, Västra Frölunda, Sweden. .,Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Box 7050, 750 07, Uppsala, Sweden.
| | - James G Hagan
- Department of Marine Sciences, University of Gothenburg, Box 100, 405 30 Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden
| | - Bengt Karlson
- Research and Development, Oceanography, Swedish Meteorological and Hydrological Institute, Sven Källfelts gata 15, 426 71, Västra Frölunda, Sweden
| | - Lars Gamfeldt
- Department of Marine Sciences, University of Gothenburg, Box 100, 405 30 Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden.,Centre for Sea and Society, Box 260, 405 30, Gothenburg, Sweden
| |
Collapse
|
40
|
Ferro L, Hu YO, Gentili FG, Andersson AF, Funk C. DNA metabarcoding reveals microbial community dynamics in a microalgae-based municipal wastewater treatment open photobioreactor. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.102043] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
41
|
Zamora-Terol S, Novotny A, Winder M. Reconstructing marine plankton food web interactions using DNA metabarcoding. Mol Ecol 2020; 29:3380-3395. [PMID: 32681684 DOI: 10.1111/mec.15555] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/02/2020] [Accepted: 07/10/2020] [Indexed: 01/03/2023]
Abstract
Knowledge of zooplankton in situ diet is critical for accurate assessment of marine ecosystem function and structure, but due to methodological constraints, there is still a limited understanding of ecological networks in marine ecosystems. Here, we used DNA-metabarcoding to study trophic interactions, with the aim to unveil the natural diet of zooplankton species under temporal variation of food resources. Several target consumers, including copepods and cladocerans, were investigated by sequencing 16S rRNA and 18S rRNA genes to identify prokaryote and eukaryote potential prey present in their guts. During the spring phytoplankton bloom, we found a dominance of diatom and dinoflagellate trophic links to copepods. During the summer period, zooplankton including cladocerans showed a more diverse diet dominated by cyanobacteria and heterotrophic prey. Our study suggests that copepods present trophic plasticity, changing their natural diet over seasons, and adapting their feeding strategies to the available prey spectrum, with some species being more selective. We did not find a large overlap of prey consumed by copepods and cladocerans, based on prey diversity found in their guts, suggesting that they occupy different roles in the trophic web. This study represents the first molecular approach to investigate several zooplankton-prey associations under seasonal variation, and highlights how, unlike other techniques, the diversity coverage is high when using DNA, allowing the possibility to detect a wide range of trophic interactions in plankton communities.
Collapse
Affiliation(s)
- Sara Zamora-Terol
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Andreas Novotny
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Monika Winder
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| |
Collapse
|
42
|
Bonaglia S, Hedberg J, Marzocchi U, Iburg S, Glud RN, Nascimento FJA. Meiofauna improve oxygenation and accelerate sulfide removal in the seasonally hypoxic seabed. Mar Environ Res 2020; 159:104968. [PMID: 32662428 PMCID: PMC7369627 DOI: 10.1016/j.marenvres.2020.104968] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/22/2020] [Accepted: 03/25/2020] [Indexed: 05/03/2023]
Abstract
Oxygen depleted areas are widespread in the marine realm. Unlike macrofauna, meiofauna are abundant in hypoxic sediments. We studied to what extent meiofauna affect oxygen availability, sulfide removal and microbial communities. Meiofauna were extracted alive and added to intact sediments simulating abundance gradients previously reported in the area. A total of 324 porewater microprofiles were recorded over a 3-week incubation period and microbial community structure and cable bacteria densities were determined at the end of the experiment. At high abundances meiofauna activity deepened oxygen penetration by 85%, 59%, and 62% after 5, 14, and 22 days, respectively, compared to control sediment with scarce meiofauna. After 6 days, meiofauna increased the volume of oxidized, sulfide-free sediment by 68% and reduced sulfide fluxes from 8.8 to 0.4 mmol m-2 d-1. After 15 days, the difference with the control attenuated due to the presence of a cable bacteria population, which facilitated sulfides oxidation in all treatments. 16S rRNA gene analysis revealed that meiofauna affected microbial community structure (beta diversity). Thus, meiofauna bioturbation plays an important role in deepening oxygen penetration, counteracting euxinia and in structuring microbial diversity of hypoxic sediments. Co-existence with cable bacteria demonstrates neutralism interaction between these two ecosystem engineers.
Collapse
Affiliation(s)
- Stefano Bonaglia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden; Nordcee, Department of Biology, University of Southern Denmark, Denmark.
| | - Johanna Hedberg
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Ugo Marzocchi
- Department of Biosciences, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Sven Iburg
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Ronnie N Glud
- Nordcee, Department of Biology, University of Southern Denmark, Denmark; Department of Ocean and Environmental Sciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | | |
Collapse
|
43
|
Alneberg J, Bennke C, Beier S, Bunse C, Quince C, Ininbergs K, Riemann L, Ekman M, Jürgens K, Labrenz M, Pinhassi J, Andersson AF. Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes. Commun Biol 2020; 3:119. [PMID: 32170201 PMCID: PMC7070063 DOI: 10.1038/s42003-020-0856-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 02/25/2020] [Indexed: 11/16/2022] Open
Abstract
The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes’ placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data. Alneberg et al. conduct metagenomics binning of water samples collected over major environmental gradients in the Baltic Sea. They use machine-learning to predict the placement of genome clusters along niche gradients based on the content of functional genes.
Collapse
Affiliation(s)
- Johannes Alneberg
- Department of Gene Technology, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Christin Bennke
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | - Sara Beier
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.,CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, Sorbonne Université, Banyuls/mer, France
| | - Carina Bunse
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus, University, Kalmar, Sweden.,Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany.,Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | | | - Karolina Ininbergs
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Lasse Riemann
- Department of Biology, Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Martin Ekman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | | | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus, University, Kalmar, Sweden
| | - Anders F Andersson
- Department of Gene Technology, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
| |
Collapse
|
44
|
Yau S, Lopes Dos Santos A, Eikrem W, Gérikas Ribeiro C, Gourvil P, Balzano S, Escande ML, Moreau H, Vaulot D. Mantoniella beaufortii and Mantoniella baffinensis sp. nov. (Mamiellales, Mamiellophyceae), two new green algal species from the high arctic 1. J Phycol 2020; 56:37-51. [PMID: 31608987 DOI: 10.1111/jpy.12932] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
Members of the class Mamiellophyceae comprise species that can dominate picophytoplankton diversity in polar waters. Yet, polar species are often morphologically indistinguishable from temperate species, although clearly separated by molecular features. Here we examine four Mamiellophyceae strains from the Canadian Arctic. The 18S rRNA and Internal Transcribed Spacer 2 (ITS2) gene phylogeny place these strains within the family Mamiellaceae (Mamiellales, Mamiellophyceae) in two separate clades of the genus Mantoniella. ITS2 synapomorphies support their placement as two new species, Mantoniella beaufortii and Mantoniella baffinensis. Both species have round green cells with diameter between 3 and 5 μm, one long flagellum and a short flagellum (~1 μm) and are covered by spiderweb-like scales, making both species similar to other Mantoniella species. Morphologically, M. beaufortii and M. baffinensis are most similar to the cosmopolitan M. squamata with only minor differences in scale structure distinguishing them. Screening of global marine metabarcoding data sets indicates M. beaufortii has only been recorded in seawater and sea ice samples from the Arctic, while no environmental barcode matches M. baffinensis. Like other Mamiellophyceae genera that have distinct polar and temperate species, the polar distribution of these new species suggests they are cold or ice-adapted Mantoniella species.
Collapse
Affiliation(s)
- Sheree Yau
- Integrative Marine Biology Laboratory (BIOM), CNRS, UMR7232, Sorbonne Université, Banyuls sur Mer, France
| | - Adriana Lopes Dos Santos
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore, Singapore
- Centro de Genómica, Ecología y Medio Ambiente, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Santiago, Chile
| | - Wenche Eikrem
- Norwegian Institute for Water Research, Gaustadallèen 21, 0349, Oslo, Norway
- Department of Biosciences, University of Oslo, P.O. box 1066, Blindern, Oslo, 0316, Norway
- Natural History Museum, University of Oslo, P.O. box 1172 Blindern, 0318, Oslo, Norway
| | | | - Priscillia Gourvil
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, France
| | - Sergio Balzano
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Naples, Italy
| | - Marie-Line Escande
- Integrative Marine Biology Laboratory (BIOM), CNRS, UMR7232, Sorbonne Université, Banyuls sur Mer, France
| | - Hervé Moreau
- Integrative Marine Biology Laboratory (BIOM), CNRS, UMR7232, Sorbonne Université, Banyuls sur Mer, France
| | - Daniel Vaulot
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, France
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore, Singapore
| |
Collapse
|
45
|
Nagai S, Chen H, Kawakami Y, Yamamoto K, Sildever S, Kanno N, Oikawa H, Yasuike M, Nakamura Y, Hongo Y, Fujiwara A, Kobayashi T, Gojobori T. Monitoring of the toxic dinoflagellate Alexandrium catenella in Osaka Bay, Japan using a massively parallel sequencing (MPS)-based technique. Harmful Algae 2019; 89:101660. [PMID: 31672234 DOI: 10.1016/j.hal.2019.101660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/10/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
Since 2002, blooms of Alexandrium catenella sensu Fraga et al. (2015) and paralytic shellfish toxicity events have occurred almost yearly in Osaka Bay, Japan. To better understand the triggers for reoccurring A. catenella blooms in Osaka Bay, phytoplankton community was monitored during the spring seasons of 2012-2015. Monitoring was performed using massively parallel sequencing (MPS)-based technique on amplicon sequences of the 18S rRNA gene. Dense blooms of A. catenella occurred every year except in 2012, however, there was no significant correlation with the environmental parameters investigated. Plankton community diversity decreased before and middle of the A. catenella blooms, suggesting that the decline in diversity could be an indicator for the bloom occurrence. The yearly abundance pattern of A. catenella cells obtained by morphology-based counting coincided with the relative sequence abundances, which supports the effectiveness of MPS-based phytoplankton monitoring.
Collapse
Affiliation(s)
- Satoshi Nagai
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan.
| | - Hungyen Chen
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Yoko Kawakami
- AXIOHELIX Co. Ltd, -12-17 Kandaizumicho, Chiyoda-ku, Tokyo, 101-0024, Japan
| | - Keigo Yamamoto
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, 2926-1 Tanigawa, Misaki, Sen-Nan, Osaka, 599-0311, Japan
| | - Sirje Sildever
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Nanako Kanno
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Hiroshi Oikawa
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Motoshige Yasuike
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Yoji Nakamura
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Yuki Hongo
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Atushi Fujiwara
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Takanori Kobayashi
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia
| |
Collapse
|
46
|
Salonen IS, Chronopoulou PM, Leskinen E, Koho KA. Metabarcoding successfully tracks temporal changes in eukaryotic communities in coastal sediments. FEMS Microbiol Ecol 2019; 95:5188675. [PMID: 30452623 DOI: 10.1093/femsec/fiy226] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/16/2018] [Indexed: 01/19/2023] Open
Abstract
Metabarcoding is a method that combines high-throughput DNA sequencing and DNA-based identification. Previously, this method has been successfully used to target spatial variation of eukaryote communities in marine sediments, however, the temporal changes in these communities remain understudied. Here, we follow the temporal changes of the eukaryote communities in Baltic Sea surface sediments collected from two coastal localities during three seasons of two consecutive years. Our study reveals that the structure of the sediment eukaryotic ecosystem was primarily driven by annual and seasonal changes in prevailing environmental conditions, whereas spatial variation was a less significant factor in explaining the variance in eukaryotic communities over time. Therefore, our data suggests that shifts in regional climate regime or large-scale changes in the environment are the overdriving factors in shaping the coastal eukaryotic sediment ecosystems rather than small-scale changes in local environmental conditions or heterogeneity in ecosystem structure. More studies targeting temporal changes are needed to further understand the long-term trends in ecosystem stability and response to climate change. Furthermore, this work contributes to the recent efforts in developing metabarcoding applications for environmental biomonitoring, proving a comprehensive option for traditional monitoring approaches.
Collapse
Affiliation(s)
- I S Salonen
- Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Program, University of Helsinki, Viikinkaari 1, Helsinki FI-00790, Finland.,Faculty of Biological and Environmental Sciences, Helsinki Institute of Sustainability Science (HELSUS), Ylopistonkatu 3, Helsinki FI-00014, Finland
| | - P-M Chronopoulou
- Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Program, University of Helsinki, Viikinkaari 1, Helsinki FI-00790, Finland.,Faculty of Biological and Environmental Sciences, Helsinki Institute of Sustainability Science (HELSUS), Ylopistonkatu 3, Helsinki FI-00014, Finland
| | - E Leskinen
- Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Program, University of Helsinki, Viikinkaari 1, Helsinki FI-00790, Finland.,Faculty of Biological and Environmental Sciences, Tvärminne Zoological Station, University of Helsinki, J. A. Palménin tie 260, Hanko FI-10900, Finland
| | - K A Koho
- Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Program, University of Helsinki, Viikinkaari 1, Helsinki FI-00790, Finland.,Faculty of Biological and Environmental Sciences, Helsinki Institute of Sustainability Science (HELSUS), Ylopistonkatu 3, Helsinki FI-00014, Finland
| |
Collapse
|
47
|
Rojas-Jimenez K, Rieck A, Wurzbacher C, Jürgens K, Labrenz M, Grossart HP. A Salinity Threshold Separating Fungal Communities in the Baltic Sea. Front Microbiol 2019; 10:680. [PMID: 30984159 PMCID: PMC6449873 DOI: 10.3389/fmicb.2019.00680] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/18/2019] [Indexed: 02/02/2023] Open
Abstract
Salinity is a significant factor for structuring microbial communities, but little is known for aquatic fungi, particularly in the pelagic zone of brackish ecosystems. In this study, we explored the diversity and composition of fungal communities following a progressive salinity decline (from 34 to 3 PSU) along three transects of ca. 2000 km in the Baltic Sea, the world's largest estuary. Based on 18S rRNA gene sequence analysis, we detected clear changes in fungal community composition along the salinity gradient and found significant differences in composition of fungal communities established above and below a critical value of 8 PSU. At salinities below this threshold, fungal communities resembled those from freshwater environments, with a greater abundance of Chytridiomycota, particularly of the orders Rhizophydiales, Lobulomycetales, and Gromochytriales. At salinities above 8 PSU, communities were more similar to those from marine environments and, depending on the season, were dominated by a strain of the LKM11 group (Cryptomycota) or by members of Ascomycota and Basidiomycota. Our results highlight salinity as an important environmental driver also for pelagic fungi, and thus should be taken into account to better understand fungal diversity and ecological function in the aquatic realm.
Collapse
Affiliation(s)
- Keilor Rojas-Jimenez
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | - Angelika Rieck
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Christian Wurzbacher
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- Chair of Urban Water Systems Engineering, Technical University of Munich, Munich, Germany
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | | | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| |
Collapse
|
48
|
Alfatah M, Wong JH, Nge CE, Kong KW, Low KN, Leong CY, Crasta S, Munusamy M, Chang AML, Hoon S, Ng SB, Kanagasundaram Y, Arumugam P. Hypoculoside, a sphingoid base-like compound from Acremonium disrupts the membrane integrity of yeast cells. Sci Rep 2019; 9:710. [PMID: 30679518 PMCID: PMC6345779 DOI: 10.1038/s41598-018-35979-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/09/2018] [Indexed: 11/15/2022] Open
Abstract
We have isolated Hypoculoside, a new glycosidic amino alcohol lipid from the fungus Acremonium sp. F2434 belonging to the order Hypocreales and determined its structure by 2D-NMR (Nuclear Magnetic Resonance) spectroscopy. Hypoculoside has antifungal, antibacterial and cytotoxic activities. Homozygous profiling (HOP) of hypoculoside in Saccharomyces cerevisiae (budding yeast) revealed that several mutants defective in vesicular trafficking and vacuolar protein transport are sensitive to hypoculoside. Staining of budding yeast cells with the styryl dye FM4-64 indicated that hypoculoside damaged the vacuolar structure. Furthermore, the propidium iodide (PI) uptake assay showed that hypoculoside disrupted the plasma membrane integrity of budding yeast cells. Interestingly, the glycosidic moiety of hypoculoside is required for its deleterious effect on growth, vacuoles and plasma membrane of budding yeast cells.
Collapse
Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Jin Huei Wong
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Choy Eng Nge
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Kiat Whye Kong
- Molecular Engineering Laboratory, 61 Biopolis Drive, #03-12, Proteos, 13867, Singapore
| | - Kia Ngee Low
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Chung Yan Leong
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Sharon Crasta
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Madhaiyan Munusamy
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | | | - Shawn Hoon
- Molecular Engineering Laboratory, 61 Biopolis Drive, #03-12, Proteos, 13867, Singapore
| | - Siew Bee Ng
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671, Singapore.
| | | | - Prakash Arumugam
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671, Singapore.
| |
Collapse
|
49
|
Marquina D, Andersson AF, Ronquist F. New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods. Mol Ecol Resour 2018; 19:90-104. [PMID: 30226026 PMCID: PMC7379581 DOI: 10.1111/1755-0998.12942] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/27/2018] [Accepted: 09/07/2018] [Indexed: 11/29/2022]
Abstract
Insect metabarcoding has been mainly based on PCR amplification of short fragments within the “barcoding region” of the gene cytochrome oxidase I (COI). However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make the results less reliable and impede the detection of species that are present in the sample. We identify new primers for insect metabarcoding using computational approaches (ecoprimers and degeprime) applied to the most comprehensive reference databases of mitochondrial genomes of Hexapoda assembled to date. New primers are evaluated in silico against previously published primers in terms of taxonomic coverage and resolution of the corresponding amplicons. For the latter criterion, we propose a new index, exclusive taxonomic resolution, which is a more biologically meaningful measure than the standard index used today. Our results show that the best markers are found in the ribosomal RNA genes (12S and 16S); they resolve about 90% of the genetically distinct species in the reference database. Some markers in protein‐coding genes provide similar performance but only at much higher levels of primer degeneracy. Combining two of the best individual markers improves the effective taxonomic resolution with up to 10%. The resolution is strongly dependent on insect taxon: COI primers detect 40% of Hymenoptera, while 12S primers detect 12% of Collembola. Our results indicate that amplicon‐based metabarcoding of insect samples can be improved by choosing other primers than those commonly used today.
Collapse
Affiliation(s)
- Daniel Marquina
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| |
Collapse
|
50
|
Stefanidou N, Genitsaris S, Lopez-Bautista J, Sommer U, Moustaka-Gouni M. Unicellular Eukaryotic Community Response to Temperature and Salinity Variation in Mesocosm Experiments. Front Microbiol 2018; 9:2444. [PMID: 30356732 PMCID: PMC6189394 DOI: 10.3389/fmicb.2018.02444] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/24/2018] [Indexed: 12/24/2022] Open
Abstract
Climate change has profound impacts on marine biodiversity and biodiversity changes in turn might affect the community sensitivity to impacts of abiotic changes. We used mesocosm experiments and Next Generation Sequencing to study the response of the natural Baltic and Mediterranean unicellular eukaryotic plankton communities (control and +6°C heat shock) to subsequent salinity changes (-5 psu, +5 psu). The impact on Operational Taxonomic Unit (OTU) richness, taxonomic and functional composition and rRNA:rDNA ratios were examined. Our results showed that heat shock leads to lower OTU richness (21% fewer OTUs in the Baltic and 14% fewer in the Mediterranean) and a shift in composition toward pico- and nanophytoplankton and heterotrophic related OTUs. Heat shock also leads to increased rRNA:rDNA ratios for pico- and micrograzers. Less than 18% of shared OTUs were found among the different salinities indicating the crucial role of salinity in shaping communities. The response of rRNA:rDNA ratios varied highly after salinity changes. In both experiments the diversity decrease brought about by heat shock influenced the sensitivity to salinity changes. The heat shock either decreased or increased the sensitivity of the remaining community, depending on whether it removed the more salinity-sensitive or the salinity-tolerant taxa.
Collapse
Affiliation(s)
- Natassa Stefanidou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Savvas Genitsaris
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece.,School of Economics, Business Administration and Legal Studies, International Hellenic University, Thermi, Greece
| | - Juan Lopez-Bautista
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, United States
| | - Ulrich Sommer
- Geomar Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Maria Moustaka-Gouni
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| |
Collapse
|