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Zhang Y, Huang N, Wang M, Liu H, Jing H. Microbial Eukaryotes Associated With Sediments in Deep-Sea Cold Seeps. Front Microbiol 2021; 12:782004. [PMID: 35003010 PMCID: PMC8740301 DOI: 10.3389/fmicb.2021.782004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/19/2021] [Indexed: 11/30/2022] Open
Abstract
Microbial eukaryotes are key components of the marine food web, but their distribution in deep-sea chemosynthetic ecosystems has not been well studied. Here, high-throughput sequencing of the 18S rRNA gene and network analysis were applied to investigate the diversity, distribution and potential relationships between microbial eukaryotes in samples collected from two cold seeps and one trough in the northern South China Sea. SAR (i.e., Stramenopiles, Alveolata, and Rhizaria) was the predominant group in all the samples, and it was highly affiliated to genotypes with potential symbiotic and parasitic strategies identified from other deep-sea extreme environments (e.g., oxygen deficient zones, bathypelagic waters, and hydrothermal vents). Our findings indicated that specialized lineages of deep-sea microbial eukaryotes exist in chemosynthetic cold seeps, where microbial eukaryotes affiliated with parasitic/symbiotic taxa were prevalent in the community. The biogeographic pattern of the total community was best represented by the intermediate operational taxonomic unit (OTU) category, whose relative abundance ranged 0.01–1% within a sample, and the communities of the two cold seeps were distinct from the trough, which suggests that geographical proximity has no critical impact on the distribution of deep-sea microbial eukaryotes. Overall, this study has laid the foundations for future investigations regarding the ecological function and in situ trophic relationships of microbial eukaryotes in deep-sea ecosystems.
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Affiliation(s)
- Yue Zhang
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ning Huang
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Minxiao Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, Hong Kong SAR, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
- *Correspondence: Hongmei Jing,
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Endolithic Microbial Habitats Hosted in Carbonate Nodules Currently Forming within Sediment at a High Methane Flux Site in the Sea of Japan. GEOSCIENCES 2019. [DOI: 10.3390/geosciences9110463] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Concretionary carbonates in deep-sea methane seep fields are formed as a result of microbial methane degradation, called anaerobic oxidation of methane (AOM). Recently, active microorganisms, including anaerobic methanotrophic archaea, were discovered from methane seep-associated carbonate outcroppings on the seafloor. However sedimentary buried carbonate nodules are a hitherto unknown microbial habitat. In this study, we investigated the microbial community structures in two carbonate nodules collected from a high methane flux site in a gas hydrate field off the Oki islands in the Sea of Japan. The nodules were formed around sulfate-methane interfaces (SMI) corresponding to 0.7 and 2.2 m below the seafloor. Based on a geochemical analysis, light carbon isotopic values ranging from −54.91‰ to −37.32‰ were found from the nodules collected at the shallow SMI depth, which were attributed to the high contributions of AOM-induced carbonate precipitation. Signatures of methanotrophic archaeal populations within the sedimentary buried nodule were detected based on microbial community composition analyses and quantitative real-time PCR targeted 16S rRNA, and functional genes for AOM. These results suggest that the buried carbonate nodule currently develops AOM-related microbial communities, and grows depending on the continued AOM under high methane flux conditions.
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Kisand V, Talas L, Kisand A, Stivrins N, Reitalu T, Alliksaar T, Vassiljev J, Liiv M, Heinsalu A, Seppä H, Veski S. From microbial eukaryotes to metazoan vertebrates: Wide spectrum paleo-diversity in sedimentary ancient DNA over the last ~14,500 years. GEOBIOLOGY 2018; 16:628-639. [PMID: 30035382 DOI: 10.1111/gbi.12307] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/09/2018] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
Most studies that utilize ancient DNA have focused on specific groups of organisms or even single species. Instead, the whole biodiversity of eukaryotes can be described using universal phylogenetic marker genes found within well-preserved sediment cores that cover the post-glacial period. Sedimentary ancient DNA samples from Lake Lielais Svētiņu, eastern Latvia, at a core depth of 1,050 cm in ~150 year intervals were used to determine phylotaxonomy in domain Eukaryota. Phylotaxonomic affiliation of >1,200 eukaryotic phylotypes revealed high richness in all major eukaryotic groups-Alveolata, Stramenopiles, Cercozoa, Chlorophyta, Charophyta, Nucletmycea, and Holozoa. The share of organisms that originate from terrestrial ecosystems was about one third, of which the most abundant molecular operational taxonomic units were Fungi and tracheal/vascular plants, which demonstrates the usefulness of using lake sediments to reconstruct the terrestrial paleoecosystems that surround them. Phylotypes that originate from the lake ecosystem belonged to various planktonic organisms; phyto-, proto,- and macrozooplankton, and vascular aquatic plants. We observed greater richness of several planktonic organisms that can be associated with higher trophic status during the warm climate period between 4,000 and 8,000 years ago and an increase in eukaryotic richness possibly associated with moderate human impact over the last 2,000 years.
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Affiliation(s)
- Veljo Kisand
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Liisi Talas
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Anu Kisand
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Normunds Stivrins
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
- Department of Geography, Faculty of Geography and Earth Sciences, University of Latvia, Riga, Latvia
| | - Triin Reitalu
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Tiiu Alliksaar
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Jüri Vassiljev
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Merlin Liiv
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Atko Heinsalu
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Heikki Seppä
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Siim Veski
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
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