1
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Cadena LR, Edgcomb V, Lukeš J. Gazing into the abyss: A glimpse into the diversity, distribution, and behaviour of heterotrophic protists from the deep-sea floor. Environ Microbiol 2024; 26:e16598. [PMID: 38444221 DOI: 10.1111/1462-2920.16598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/08/2024] [Indexed: 03/07/2024]
Abstract
The benthic biome of the deep-sea floor, one of the largest biomes on Earth, is dominated by diverse and highly productive heterotrophic protists, second only to prokaryotes in terms of biomass. Recent evidence suggests that these protists play a significant role in ocean biogeochemistry, representing an untapped source of knowledge. DNA metabarcoding and environmental sample sequencing have revealed that deep-sea abyssal protists exhibit high levels of specificity and diversity across local regions. This review aims to provide a comprehensive summary of the known heterotrophic protists from the deep-sea floor, their geographic distribution, and their interactions in terms of parasitism and predation. We offer an overview of the most abundant groups and discuss their potential ecological roles. We argue that the exploration of the biodiversity and species-specific features of these protists should be integrated into broader deep-sea research and assessments of how benthic biomes may respond to future environmental changes.
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Affiliation(s)
- Lawrence Rudy Cadena
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Virginia Edgcomb
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
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2
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Hu SK, Anderson RE, Pachiadaki MG, Edgcomb VP, Serres MH, Sylva SP, German CR, Seewald JS, Lang SQ, Huber JA. Microbial eukaryotic predation pressure and biomass at deep-sea hydrothermal vents. THE ISME JOURNAL 2024; 18:wrae004. [PMID: 38366040 PMCID: PMC10939315 DOI: 10.1093/ismejo/wrae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/22/2023] [Accepted: 01/12/2024] [Indexed: 02/18/2024]
Abstract
Deep-sea hydrothermal vent geochemistry shapes the foundation of the microbial food web by fueling chemolithoautotrophic microbial activity. Microbial eukaryotes (or protists) play a critical role in hydrothermal vent food webs as consumers and hosts of symbiotic bacteria, and as a nutritional source to higher trophic levels. We measured microbial eukaryotic cell abundance and predation pressure in low-temperature diffuse hydrothermal fluids at the Von Damm and Piccard vent fields along the Mid-Cayman Rise in the Western Caribbean Sea. We present findings from experiments performed under in situ pressure that show cell abundances and grazing rates higher than those done at 1 atmosphere (shipboard ambient pressure); this trend was attributed to the impact of depressurization on cell integrity. A relationship between the protistan grazing rate, prey cell abundance, and temperature of end-member hydrothermal vent fluid was observed at both vent fields, regardless of experimental approach. Our results show substantial protistan biomass at hydrothermally fueled microbial food webs, and when coupled with improved grazing estimates, suggest an important contribution of grazers to the local carbon export and supply of nutrient resources to the deep ocean.
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Affiliation(s)
- Sarah K Hu
- Department of Oceanography, Texas A&M University, College Station, TX 77843, United States
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Rika E Anderson
- Biology Department, Carleton College, Northfield, MN 55057, United States
| | - Maria G Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Virginia P Edgcomb
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Margrethe H Serres
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Sean P Sylva
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Christopher R German
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Jeffrey S Seewald
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Susan Q Lang
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Julie A Huber
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
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3
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Flegontova O, Flegontov P, Jachníková N, Lukeš J, Horák A. Water masses shape pico-nano eukaryotic communities of the Weddell Sea. Commun Biol 2023; 6:64. [PMID: 36653511 PMCID: PMC9849203 DOI: 10.1038/s42003-023-04452-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
Polar oceans belong to the most productive and rapidly changing environments, yet our understanding of this fragile ecosystem remains limited. Here we present an analysis of a unique set of DNA metabarcoding samples from the western Weddell Sea sampled throughout the whole water column and across five water masses with different characteristics and different origin. We focus on factors affecting the distribution of planktonic pico-nano eukaryotes and observe an ecological succession of eukaryotic communities as the water masses move away from the surface and as oxygen becomes depleted with time. At the beginning of this succession, in the photic zone, algae, bacteriovores, and predators of small eukaryotes dominate the community, while another community develops as the water sinks deeper, mostly composed of parasitoids (syndinians), mesoplankton predators (radiolarians), and diplonemids. The strongly correlated distribution of syndinians and diplonemids along the depth and oxygen gradients suggests their close ecological link and moves us closer to understanding the biological role of the latter group in the ocean ecosystem.
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Affiliation(s)
- Olga Flegontova
- grid.418338.50000 0001 2255 8513Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic ,grid.412684.d0000 0001 2155 4545Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Pavel Flegontov
- grid.418338.50000 0001 2255 8513Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic ,grid.412684.d0000 0001 2155 4545Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Nikola Jachníková
- grid.14509.390000 0001 2166 4904Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Julius Lukeš
- grid.418338.50000 0001 2255 8513Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic ,grid.14509.390000 0001 2166 4904Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Aleš Horák
- grid.418338.50000 0001 2255 8513Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic ,grid.14509.390000 0001 2166 4904Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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4
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Prokopchuk G, Korytář T, Juricová V, Majstorović J, Horák A, Šimek K, Lukeš J. Trophic flexibility of marine diplonemids - switching from osmotrophy to bacterivory. THE ISME JOURNAL 2022; 16:1409-1419. [PMID: 35042972 PMCID: PMC9039065 DOI: 10.1038/s41396-022-01192-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/23/2021] [Accepted: 01/06/2022] [Indexed: 05/03/2023]
Abstract
Diplonemids are one of the most abundant groups of heterotrophic planktonic microeukaryotes in the world ocean and, thus, are likely to play an essential role in marine ecosystems. So far, only few species have been introduced into a culture, allowing basic studies of diplonemid genetics, morphology, ultrastructure, metabolism, as well as endosymbionts. However, it remains unclear whether these heterotrophic flagellates are parasitic or free-living and what are their predominant dietary patterns and preferred food items. Here we show that cultured diplonemids, maintained in an organic-rich medium as osmotrophs, can gradually switch to bacterivory as a sole food resource, supporting positive growth of their population, even when fed with a low biovolume of bacteria. We further observed remarkable differences in species-specific feeding patterns, size-selective grazing preferences, and distinct feeding strategies. Diplonemids can discriminate between low-quality food items and inedible particles, such as latex beads, even after their ingestion, by discharging them in the form of large waste vacuoles. We also detected digestion-related endogenous autofluorescence emitted by lysosomes and the activity of a melanin-like material. We present the first evidence that these omnipresent protists possess an opportunistic lifestyle that provides a considerable advantage in the generally food resource-limited marine environments.
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Affiliation(s)
- Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
| | - Tomáš Korytář
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Fisheries and Protection of Waters, University of South Bohemia, České Budějovice, Czech Republic
| | - Valéria Juricová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jovana Majstorović
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Karel Šimek
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Hydrobiology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
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5
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Protistan grazing impacts microbial communities and carbon cycling at deep-sea hydrothermal vents. Proc Natl Acad Sci U S A 2021; 118:2102674118. [PMID: 34266956 DOI: 10.1073/pnas.2102674118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Microbial eukaryotes (or protists) in marine ecosystems are a link between primary producers and all higher trophic levels, and the rate at which heterotrophic protistan grazers consume microbial prey is a key mechanism for carbon transport and recycling in microbial food webs. At deep-sea hydrothermal vents, chemosynthetic bacteria and archaea form the base of a food web that functions in the absence of sunlight, but the role of protistan grazers in these highly productive ecosystems is largely unexplored. Here, we pair grazing experiments with a molecular survey to quantify protistan grazing and to characterize the composition of vent-associated protists in low-temperature diffuse venting fluids from Gorda Ridge in the northeast Pacific Ocean. Results reveal protists exert higher predation pressure at vents compared to the surrounding deep seawater environment and may account for consuming 28 to 62% of the daily stock of prokaryotic biomass within discharging hydrothermal vent fluids. The vent-associated protistan community was more species rich relative to the background deep sea, and patterns in the distribution and co-occurrence of vent microbes provide additional insights into potential predator-prey interactions. Ciliates, followed by dinoflagellates, Syndiniales, rhizaria, and stramenopiles, dominated the vent protistan community and included bacterivorous species, species known to host symbionts, and parasites. Our findings provide an estimate of protistan grazing pressure within hydrothermal vent food webs, highlighting the important role that diverse protistan communities play in deep-sea carbon cycling.
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6
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Schauberger C, Middelboe M, Larsen M, Peoples LM, Bartlett DH, Kirpekar F, Rowden AA, Wenzhöfer F, Thamdrup B, Glud RN. Spatial variability of prokaryotic and viral abundances in the Kermadec and Atacama Trench regions. LIMNOLOGY AND OCEANOGRAPHY 2021; 66:2095-2109. [PMID: 34239169 PMCID: PMC8248377 DOI: 10.1002/lno.11711] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 12/01/2020] [Accepted: 01/04/2021] [Indexed: 05/31/2023]
Abstract
Hadal trenches represent the deepest part of the ocean and are dynamic depocenters with intensified prokaryotic activity. Here, we explored the distribution and drivers of prokaryotic and viral abundance from the ocean surface and 40 cm into sediments in two hadal trench regions with contrasting surface productivity. In the water column, prokaryotic and viral abundance decreased with water depth before reaching a rather stable level at ~ 4000 m depth at both trench systems, while virus to prokaryote ratios were increasing with depth, presumably reflecting the declining availability of organic material. Prokaryotic and viral abundances in sediments were lower at the adjacent abyssal sites than at the hadal sites and declined exponentially with sediment depth, closely tracking the attenuation of total organic carbon (TOC) content. In contrast, hadal sediment exhibited erratic depth profiles of prokaryotes and viruses with many subsurface peaks. The prokaryotic abundance correlated well to extensive fluctuations in TOC content at centimeter scale, which were likely caused by recurring mass wasting events. Yet while prokaryotic and viral abundances cross correlated well in the abyssal sediments, there was no clear correlation in the hadal sites. The results suggested that dynamic depositional conditions and higher substrate availability result in a high spatial heterogeneity in viral and prokaryotic abundances in hadal sediments in comparison to more stable abyssal settings. We argue that these conditions enhance the relatively importance of viruses for prokaryotic mortality and carbon recycling in hadal settings.
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Affiliation(s)
- Clemens Schauberger
- Department of Biology, Nordcee and HADALUniversity of Southern DenmarkOdenseDenmark
| | - Mathias Middelboe
- Department of Biology, Nordcee and HADALUniversity of Southern DenmarkOdenseDenmark
- Marine Biological Section, Department of BiologyUniversity of CopenhagenHelsingørDenmark
| | - Morten Larsen
- Department of Biology, Nordcee and HADALUniversity of Southern DenmarkOdenseDenmark
| | - Logan M. Peoples
- Marine Biology Research Division, Scripps Institution of OceanographyUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Douglas H. Bartlett
- Marine Biology Research Division, Scripps Institution of OceanographyUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Finn Kirpekar
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Ashley A. Rowden
- National Institute of Water and Atmospheric ResearchWellingtonNew Zealand
- School of Biological Sciences, Victoria University of WellingtonWellingtonNew Zealand
| | - Frank Wenzhöfer
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine ResearchBremerhavenGermany
- Max Planck Institute for Marine Microbiology and EcologyBremenGermany
| | - Bo Thamdrup
- Department of Biology, Nordcee and HADALUniversity of Southern DenmarkOdenseDenmark
| | - Ronnie N. Glud
- Department of Biology, Nordcee and HADALUniversity of Southern DenmarkOdenseDenmark
- Department of Ocean and Environmental SciencesTokyo University of Marine Science and TechnologyTokyoJapan
- Danish Institute for Advanced Study – DIAS, University of Southern DenmarkOdenseDenmark
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7
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Flegontova O, Flegontov P, Londoño PAC, Walczowski W, Šantić D, Edgcomb VP, Lukeš J, Horák A. Environmental determinants of the distribution of planktonic diplonemids and kinetoplastids in the oceans. Environ Microbiol 2020; 22:4014-4031. [PMID: 32779301 DOI: 10.1111/1462-2920.15190] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/07/2020] [Indexed: 12/26/2022]
Abstract
We analysed a widely used barcode, the V9 region of the 18S rRNA gene, to study the effect of environmental conditions on the distribution of two related heterotrophic protistan lineages in marine plankton, kinetoplastids and diplonemids. We relied on a major published dataset (Tara Oceans) where samples from the mesopelagic zone were available from just 32 of 123 locations, and both groups are most abundant in this zone. To close sampling gaps and obtain more information from the deeper ocean, we collected 57 new samples targeting especially the mesopelagic zone. We sampled in three geographic regions: the Arctic, two depth transects in the Adriatic Sea, and the anoxic Cariaco Basin. In agreement with previous studies, both protist groups are most abundant and diverse in the mesopelagic zone. In addition to that, we found that their abundance, richness, and community structure also depend on geography, oxygen concentration, salinity, temperature, and other environmental variables reflecting the abundance of algae and nutrients. Both groups studied here demonstrated similar patterns, although some differences were also observed. Kinetoplastids and diplonemids prefer tropical regions and nutrient-rich conditions and avoid high oxygen concentration, high salinity, and high density of algae.
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Affiliation(s)
- Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Paula Andrea Castañeda Londoño
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Biocenter, University of Würzburg, Würzburg, Germany
| | | | | | - Virginia P Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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8
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Xie Y, Floehr T, Zhang X, Xiao H, Yang J, Xia P, Burton GA, Hollert H. In situ microbiota distinguished primary anthropogenic stressor in freshwater sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 239:189-197. [PMID: 29655065 DOI: 10.1016/j.envpol.2018.03.099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 03/17/2018] [Accepted: 03/27/2018] [Indexed: 05/10/2023]
Abstract
Conventional assessment and evaluation of sediment quality are based on laboratory-based ecotoxicological and chemical measurements with lack of concern for ecological relevance. Microbiotas in sediment are responsive to pollutants and can be used as alternative ecological indicators of sediment pollutants; however, the linkage between the microbial ecology and ecotoxicological endpoints in response to sediment contamination has been poorly evaluated. Here, in situ microbiotas from the Three Gorges Reservoir (TGR) area of the Yangtze River were characterized by DNA metabarcoding approaches, and then, changes of in situ microbiotas were compared with the ecotoxicological endpoint, aryl hydrocarbon receptor (AhR) mediated activity, and level of polycyclic aromatic hydrocarbons (PAHs) in sediments. PAHs and organic pollutant mixtures mediating AhR activity had different effects on the structures of microbiotas. Specifically, Shannon indices of protistan communities were negatively correlated with the levels of AhR mediated activity and PAHs. The sediment AhR activity was positively correlated with the relative abundance of prokaryotic Acetobacteraceae, but had a negative correlation with protistan Oxytrichidae. Furthermore, a quantitative classification model was built to predict the level of AhR activity based on the relative abundances of Acetobacteraceae and Oxytrichidae. These results suggested that in situ Protista communities could provide a useful tool for monitoring and assessing ecological stressors. The observed responses of microbial community provided supplementary evidence to support that the AhR-active pollutants, such as PAHs, were the primary stressors of the aquatic community in TGR area.
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Affiliation(s)
- Yuwei Xie
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Tilman Floehr
- Institute for Environmental Research, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, China.
| | - Hongxia Xiao
- Institute for Environmental Research, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - G Allen Burton
- School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, USA
| | - Henner Hollert
- Institute for Environmental Research, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
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9
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Xie Y, Zhang X, Yang J, Kim S, Hong S, Giesy JP, Yim UH, Shim WJ, Yu H, Khim JS. eDNA-based bioassessment of coastal sediments impacted by an oil spill. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 238:739-748. [PMID: 29625298 DOI: 10.1016/j.envpol.2018.02.081] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 02/25/2018] [Accepted: 02/26/2018] [Indexed: 06/08/2023]
Abstract
Oil spills offshore can cause long-term ecological effects on coastal marine ecosystems. Despite their important ecological roles in the cycling of energy and nutrients in food webs, effects on bacteria, protists or arthropods are often neglected. Environmental DNA (eDNA) metabarcoding was applied to characterize changes in the structure of micro- and macro-biota communities of surface sediments over a 7-year period since the occurrence of Hebei Spirit oil spill on December 7, 2007. Alterations in diversities and structures of micro- and macro-biota were observed in the contaminated area where concentrations of polycyclic aromatic hydrocarbons were greater. Successions of bacterial, protists and metazoan communities revealed long-term ecological effects of residual oil. Residual oil dominated the largest cluster of the community-environment association network. Presence of bacterial families (Aerococcaceae and Carnobacteriaceae) and the protozoan family (Platyophryidae) might have conferred sensitivity of communities to oil pollution. Hydrocarbon-degrading bacterial families (Anaerolinaceae, Desulfobacteraceae, Helicobacteraceae and Piscirickettsiaceae) and algal family (Araphid pennate) were resistant to adverse effects of spilt oil. The protistan family (Subulatomonas) and arthropod families (Folsomia, Sarcophagidae Opomyzoidea, and Anomura) appeared to be positively associated with residual oil pollution. eDNA metabarcoding can provide a powerful tool for assessing effects of anthropogenic pollution, such as oil spills on sediment communities and its long-term trends in coastal marine environments.
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Affiliation(s)
- Yuwei Xie
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China.
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Seonjin Kim
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seongjin Hong
- Department of Ocean Environmental Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - John P Giesy
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China; Department of Veterinary Biomedical Sciences and Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Biological Sciences, University of Hong Kong, Hong Kong, SAR, China; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Un Hyuk Yim
- Oil and POPs Research Group, Korea Institute of Ocean Science and Technology (KIOST), Geoje, Republic of Korea
| | - Won Joon Shim
- Oil and POPs Research Group, Korea Institute of Ocean Science and Technology (KIOST), Geoje, Republic of Korea
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Jong Seong Khim
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul, 08826, Republic of Korea.
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10
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Johnke J, Boenigk J, Harms H, Chatzinotas A. Killing the killer: predation between protists and predatory bacteria. FEMS Microbiol Lett 2017; 364:3746136. [PMID: 28444379 DOI: 10.1093/femsle/fnx089] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/20/2017] [Indexed: 02/05/2023] Open
Abstract
Predation by microbes is one of the main drivers of bacterial mortality in the environment. In most ecosystems multiple micropredators compete at least partially for the same bacterial resource. Predatory interactions between these micropredators might lead to shifts within microbial communities. Integrating these interactions is therefore crucial for the understanding of ecosystem functioning. In this study, we investigated the predation between two groups of micropredators, i.e. phagotrophic protists and Bdellovibrio and like organisms (BALOs). BALOs are obligate predators of Gram-negative bacteria. We hypothesised that protists can prey upon BALOs despite the small size and high swimming speed of the latter, which makes them potentially hard to capture. Predation experiments including three protists, i.e. one filter feeder and two interception feeder, showed that BALOs are a relevant prey for these protists. The growth rate on BALOs differed for the respective protists. The filter feeding ciliate was growing equally well on the BALOs and on Escherichia coli, whereas the two flagellate species grew less well on the BALOs compared to E. coli. However, BALOs might not be a favourable food source in resource-rich environments as they are not enabling all protists to grow as much as on bacteria of bigger volume.
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Affiliation(s)
- Julia Johnke
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
| | - Jens Boenigk
- Biodiversity Department and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, 45117 Essen, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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11
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Lara E, Vaqué D, Sà EL, Boras JA, Gomes A, Borrull E, Díez-Vives C, Teira E, Pernice MC, Garcia FC, Forn I, Castillo YM, Peiró A, Salazar G, Morán XAG, Massana R, Catalá TS, Luna GM, Agustí S, Estrada M, Gasol JM, Duarte CM. Unveiling the role and life strategies of viruses from the surface to the dark ocean. SCIENCE ADVANCES 2017; 3:e1602565. [PMID: 28913418 PMCID: PMC5587022 DOI: 10.1126/sciadv.1602565] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 08/09/2017] [Indexed: 05/31/2023]
Abstract
Viruses are a key component of marine ecosystems, but the assessment of their global role in regulating microbial communities and the flux of carbon is precluded by a paucity of data, particularly in the deep ocean. We assessed patterns in viral abundance and production and the role of viral lysis as a driver of prokaryote mortality, from surface to bathypelagic layers, across the tropical and subtropical oceans. Viral abundance showed significant differences between oceans in the epipelagic and mesopelagic, but not in the bathypelagic, and decreased with depth, with an average power-law scaling exponent of -1.03 km-1 from an average of 7.76 × 106 viruses ml-1 in the epipelagic to 0.62 × 106 viruses ml-1 in the bathypelagic layer with an average integrated (0 to 4000 m) viral stock of about 0.004 to 0.044 g C m-2, half of which is found below 775 m. Lysogenic viral production was higher than lytic viral production in surface waters, whereas the opposite was found in the bathypelagic, where prokaryotic mortality due to viruses was estimated to be 60 times higher than grazing. Free viruses had turnover times of 0.1 days in the bathypelagic, revealing that viruses in the bathypelagic are highly dynamic. On the basis of the rates of lysed prokaryotic cells, we estimated that viruses release 145 Gt C year-1 in the global tropical and subtropical oceans. The active viral processes reported here demonstrate the importance of viruses in the production of dissolved organic carbon in the dark ocean, a major pathway in carbon cycling.
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Affiliation(s)
- Elena Lara
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
- Institute of Marine Sciences, National Research Council (CNR-ISMAR), Castello 2737/F Arsenale-Tesa 104, 30122 Venezia, Italy
| | - Dolors Vaqué
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Elisabet Laia Sà
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Julia A. Boras
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Ana Gomes
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Encarna Borrull
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Cristina Díez-Vives
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Eva Teira
- Departamento de Ecología y Biología Animal, Universidad de Vigo, University of Vigo, 36310 Vigo, Spain
| | - Massimo C. Pernice
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Francisca C. Garcia
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Avenida Príncipe de Asturias, 70, 33212 Gijón/Xixón, Spain
| | - Irene Forn
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Yaiza M. Castillo
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Aida Peiró
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Guillem Salazar
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Xosé Anxelu G. Morán
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ramon Massana
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Teresa S. Catalá
- Instituto de Investigaciones Marinas, CSIC, Eduardo Cabello, 6, 36208 Vigo, Spain
- Departamento de Ecología and Instituto del Agua, Universidad de Granada, Avenida del Hospicio, S/N, 18010 Granada, Spain
| | | | - Susana Agustí
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Marta Estrada
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Josep M. Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Carlos M. Duarte
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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Xie Y, Wang J, Yang J, Giesy JP, Yu H, Zhang X. Environmental DNA metabarcoding reveals primary chemical contaminants in freshwater sediments from different land-use types. CHEMOSPHERE 2017; 172:201-209. [PMID: 28068572 DOI: 10.1016/j.chemosphere.2016.12.117] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/13/2016] [Accepted: 12/23/2016] [Indexed: 06/06/2023]
Abstract
Land-use intensification threatens freshwater biodiversity. Freshwater eukaryotic communities are affected by multiple chemical contaminants with a land-use specific manner. However, biodiversities of eukaryotes and their associations with multiple chemical contaminants are largely unknown. This study characterized in situ eukaryotic communities in sediments exposed to mixtures of chemical contaminants and assessed relationships between various environmental variables and eukaryotic communities in sediments from the Nanfei River. Eukaryotic communities in the sediment samples were dominated by Annelida, Arthropoda, Rotifera, Ochrophyta, Chlorophyta and Ciliophora. Alpha-diversities (Shannon entropy) and structures of eukaryotic communities were significantly different between land-use types. According to the results of multiple statistical tests (PCoA, distLM, Mantel and network analysis), dissimilarity of eukaryotic community structures revealed the key effects of pyrethroid insecticides, manganese, zinc, lead, chromium and polycyclic aromatic hydrocarbons (PAHs) on eukaryotic communities in the sediment samples from the Nanfei River. Furthermore, taxa associated with land-use types were identified and several sensitive eukaryotic taxa to some of the primary contaminants were identified as potential indicators to monitor effects of the primary chemical contaminants. Overall, environmental DNA metabarcoding on in situ eukaryotic communities provided a powerful tool for biomonitoring and identifying primary contaminants and their complex effects on benthic eukaryotic communities in freshwater sediments.
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Affiliation(s)
- Yuwei Xie
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Jizhong Wang
- Laboratory for Nanomineralogy and Environmental Material, School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - John P Giesy
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China; Department of Veterinary Biomedical Sciences and Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; School of Biological Sciences, University of Hong Kong, Hong Kong Special Administrative Region; Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong Special Administrative Region
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China.
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Cobián Güemes AG, Youle M, Cantú VA, Felts B, Nulton J, Rohwer F. Viruses as Winners in the Game of Life. Annu Rev Virol 2016; 3:197-214. [DOI: 10.1146/annurev-virology-100114-054952] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Vito Adrian Cantú
- Computational Sciences Research Center, San Diego State University, San Diego, California 92182
| | - Ben Felts
- Department of Mathematics and Statistics, San Diego State University, San Diego, California 92182
| | - James Nulton
- Department of Mathematics and Statistics, San Diego State University, San Diego, California 92182
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, California 92182;
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Edgcomb VP. Marine protist associations and environmental impacts across trophic levels in the twilight zone and below. Curr Opin Microbiol 2016; 31:169-175. [PMID: 27092409 DOI: 10.1016/j.mib.2016.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 11/28/2022]
Abstract
Marine protists are integral to marine food webs and exhibit complex relationships with other microbial taxa. Phagotrophic protists contribute significantly to carbon turnover in the sunlit ocean and evidence suggests grazing in the dark ocean can be significant as well. New in situ sampling technologies hold great promise for more accurately accessing these impacts. The molecular signatures of parasitic protists comprise significant fractions of many high-throughput sequencing datasets, suggesting a major role in controlling populations of their host(s). The prokaryotic symbionts of free-living protists can be numerous, and, particularly in low-oxygen to anoxic marine habitats, their collective metabolisms may contribute significantly to biogeochemical cycling. This short review addresses principally planktonic communities in the mesopelagic and bathypelagic dark ocean.
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Affiliation(s)
- V P Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, USA.
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