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Wang S, Zhang Z, Yang K, Zhao J, Zhang W, Wang Z, Liang Z, Zhang Y, Zhang Y, Liu J, Zhang L. SMMP: A Deep-Coverage Marine Metaproteome Method for Microbial Community Analysis throughout the Water Column Using 1 L of Seawater. Anal Chem 2024. [PMID: 39001809 DOI: 10.1021/acs.analchem.4c02079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
Marine microbes drive pivotal transformations in planetary-scale elemental cycles and have crucial impacts on global biogeochemical processes. Metaproteomics is a powerful tool for assessing the metabolic diversity and function of marine microbes. However, hundreds of liters of seawater are required for normal metaproteomic analysis due to the sparsity of microbial populations in seawater, which poses a substantial challenge to the widespread application of marine metaproteomics, particularly for deep seawater. Herein, a sensitive marine metaproteomics workflow, named sensitive marine metaproteome analysis (SMMP), was developed by integrating polycarbonate filter-assisted microbial enrichment, solid-phase alkylation-based anti-interference sample preparation, and narrow-bore nanoLC column for trace peptide separation and characterization. The method provided more than 8500 proteins from 1 L of bathypelagic seawater samples, which covered diverse microorganisms and crucial functions, e.g., the detection of key enzymes associated with the Wood-Ljungdahl pathway. Then, we applied SMMP to investigate vertical variations in the metabolic expression patterns of marine microorganisms from the euphotic zone to the bathypelagic zone. Methane oxidation and carbon monoxide (CO) oxidation were active processes, especially in the bathypelagic zone, which provided a remarkable energy supply for the growth and proliferation of heterotrophic microorganisms. In addition, marker protein profiles detected related to ammonia transport, ammonia oxidation, and carbon fixation highlighted that Thaumarchaeota played a critical role in primary production based on the coupled carbon-nitrogen process, contributing to the storage of carbon and nitrogen in the bathypelagic regions. SMMP has low microbial input requirements and yields in-depth metaproteome analysis, making it a prospective approach for comprehensive marine metaproteomic investigations.
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Affiliation(s)
- Songduo Wang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zenghu Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qingdao New Energy Shandong Laboratory, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Kaiguang Yang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiulong Zhao
- Qingdao New Energy Shandong Laboratory, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Weijie Zhang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiting Wang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Liang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongyu Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qingdao New Energy Shandong Laboratory, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Yukui Zhang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhui Liu
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lihua Zhang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Li Y, Kan J, Liu F, Lian K, Liang Y, Shao H, McMinn A, Wang H, Wang M. Depth shapes microbiome assembly and network stability in the Mariana Trench. Microbiol Spectr 2024; 12:e0211023. [PMID: 38084983 PMCID: PMC10783068 DOI: 10.1128/spectrum.02110-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/08/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Exploring microbial interactions and their stability/resilience from the surface to the hadal ocean is critical for further understanding of the microbiome structure and ecosystem function in the Mariana Trench. Vertical gradients did not destabilize microbial communities after long-term evolution and adaption. The uniform niche breadth, diversity, community complexity, and stability of microbiomes in both upper bathypelagic and hadal waters suggest the consistent roles of microbiomes in elemental cycling and adaptive strategies to overcome extreme environmental conditions. Compared with microeukaryotes, bacteria and archaea play a pivotal role in shaping the stability of the hadal microbiome. The consistent co-occurrence stability of microbiomes across vertical gradients was observed in the Mariana Trench. These results illuminate a key principle of microbiomes inhabiting the deepest trench: although distinct microbial communities occupy specific habitats, the interactions within microbial communities remain consistently stable from the upper bathypelagic to the hadal waters.
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Affiliation(s)
- Yi Li
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Jinjun Kan
- Microbiology Division, Stroud Water Research Center, Avondale, Pennsylvania, USA
| | - Feilong Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Kaiyue Lian
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Andrew McMinn
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Hualong Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
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Gorrasi S, Franzetti A, Brandt A, Minzlaff U, Pasqualetti M, Fenice M. Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench. ENVIRONMENTAL MICROBIOME 2023; 18:67. [PMID: 37533108 PMCID: PMC10398949 DOI: 10.1186/s40793-023-00522-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/14/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND The Kuril-Kamchatka Trench (maximum depth 9604 m), located in the NW Pacific Ocean, is among the top seven deepest hadal trenches. The work aimed to investigate the unexplored abyssal-hadal prokaryotic communities of this fascinating, but underrated environment. RESULTS As for the bacterial communities, we found that Proteobacteria (56.1-74.5%), Bacteroidetes (6.5-19.1%), and Actinobacteria (0.9-16.1%) were the most represented bacterial phyla over all samples. Thaumarchaeota (52.9-91.1%) was the most abundant phylum in the archaeal communities. The archaeal diversity was highly represented by the ammonia-oxidizing Nitrosopumilus, and the potential hydrocarbon-degrading bacteria Acinetobacter, Zhongshania, and Colwellia were the main bacterial genera. The α-diversity analysis evidenced that both prokaryotic communities were characterized by low evenness, as indicated by the high Gini index values (> 0.9). The β-diversity analysis (Redundancy Analysis) indicated that, as expected, the depth significantly affected the structure of the prokaryotic communities. The co-occurrence network revealed seven prokaryotic groups that covaried across the abyssal-hadal zone of the Kuril-Kamchatka Trench. Among them, the main group included the most abundant archaeal and bacterial OTUs (Nitrosopumilus OTU A2 and OTU A1; Acinetobacter OTU B1), which were ubiquitous across the trench. CONCLUSIONS This manuscript represents the first attempt to characterize the prokaryotic communities of the KKT abyssal-hadal zone. Our results reveal that the most abundant prokaryotes harbored by the abyssal-hadal zone of Kuril-Kamchatka Trench were chemolithotrophic archaea and heterotrophic bacteria, which did not show a distinctive pattern distribution according to depth. In particular, Acinetobacter, Zhongshania, and Colwellia (potential hydrocarbon degraders) were the main bacterial genera, and Nitrosopumilus (ammonia oxidizer) was the dominant representative of the archaeal diversity.
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Affiliation(s)
- Susanna Gorrasi
- Laboratory of Microbiology, Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.
| | - Andrea Franzetti
- Laboratory of Microbiology, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milano, 20126, Italy
| | - Angelika Brandt
- Senckenberg Research Institute and Natural History Museum, 60325, Frankfurt am Main, Germany
- Institute of Ecology, Diversity and Evolution, Goethe University, 60438, Frankfurt am Main, Germany
| | - Ulrike Minzlaff
- Institute of Ecology, Diversity and Evolution, Goethe University, 60438, Frankfurt am Main, Germany
| | - Marcella Pasqualetti
- Laboratory of Ecology of Marine Fungi - CoNISMa, Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Massimiliano Fenice
- Laboratory of Microbiology, Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.
- Laboratory of Applied Marine Microbiology - CoNISMa, Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.
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Kampouris ID, Gründger GF, Christensen JH, Greer CW, Kjeldsen KU, Boone W, Meire L, Rysgaard S, Vergeynst L. Long-term patterns of hydrocarbon biodegradation and bacterial community composition in epipelagic and mesopelagic zones of an Arctic fjord. JOURNAL OF HAZARDOUS MATERIALS 2023; 446:130656. [PMID: 36603421 DOI: 10.1016/j.jhazmat.2022.130656] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/14/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Oil spill attenuation in Arctic marine environments depends on oil-degrading bacteria. However, the seasonally harsh conditions in the Arctic such as nutrient limitations and sub-zero temperatures limit the activity even for bacteria capable of hydrocarbon metabolism at low temperatures. Here, we investigated whether the variance between epipelagic (seasonal temperature and inorganic nutrient variations) and mesopelagic zone (stable environmental conditions) could limit the growth of oil-degrading bacteria and lead to lower oil biodegradation rates in the epipelagic than in the mesopelagic zone. Therefore, we deployed absorbents coated with three oil types in a SW-Greenland fjord system at 10-20 m (epipelagic) and 615-650 m (mesopelagic) water depth for one year. During this period we monitored the development and succession of the bacterial biofilms colonizing the oil films by 16S rRNA gene amplicon quantification and sequencing, and the progression of oil biodegradation by gas chromatography - mass spectrometry oil fingerprinting analysis. The removal of hydrocarbons was significantly different, with several polycyclic aromatic hydrocarbons showing longer half-life times in the epipelagic than in the mesopelagic zone. Bacterial community composition and density (16S rRNA genes/ cm2) significantly differed between the two zones, with total bacteria reaching to log-fold higher densities (16S rRNA genes/cm2) in the mesopelagic than epipelagic oil-coated absorbents. Consequently, the environmental conditions in the epipelagic zone limited oil biodegradation performance by limiting bacterial growth.
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Affiliation(s)
- Ioannis D Kampouris
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark; Section for Aquatic Biology, Department of Biology, Aarhus University, Aarhus, Denmark.
| | - Grundger Friederike Gründger
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark; Section for Aquatic Biology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Jan H Christensen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montreal, Canada
| | - Kasper Urup Kjeldsen
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Wieter Boone
- Flanders Marine Institute, 8400 Oostende, Belgium
| | - Lorenz Meire
- Department of Estuarine and Delta Systems, Royal Netherlands Institute of Sea Research, Yerseke 4401 NT, the Netherlands; Greenland Climate Research Centre, Greenland Institute of Natural Resources, Nuuk 3900, Greenland
| | - Søren Rysgaard
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark; Section for Aquatic Biology, Department of Biology, Aarhus University, Aarhus, Denmark; Centre for Earth Observation Science, University of Manitoba, Winnipeg, MB, Canada
| | - Leendert Vergeynst
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark; Centre for Water Technology (WATEC), Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark.
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Gao C, Liang Y, Jiang Y, Paez-Espino D, Han M, Gu C, Wang M, Yang Y, Liu F, Yang Q, Gong Z, Zhang X, Luo Z, He H, Guo C, Shao H, Zhou C, Shi Y, Xin Y, Xing J, Tang X, Qin Q, Zhang YZ, He J, Jiao N, McMinn A, Tian J, Suttle CA, Wang M. Virioplankton assemblages from challenger deep, the deepest place in the oceans. iScience 2022; 25:104680. [PMID: 35942087 PMCID: PMC9356048 DOI: 10.1016/j.isci.2022.104680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/25/2022] [Accepted: 06/23/2022] [Indexed: 11/26/2022] Open
Abstract
Hadal ocean biosphere, that is, the deepest part of the world’s oceans, harbors a unique microbial community, suggesting a potential uncovered co-occurring virioplankton assemblage. Herein, we reveal the unique virioplankton assemblages of the Challenger Deep, comprising 95,813 non-redundant viral contigs from the surface to the hadal zone. Almost all of the dominant viral contigs in the hadal zone were unclassified, potentially related to Alteromonadales and Oceanospirillales. 2,586 viral auxiliary metabolic genes from 132 different KEGG orthologous groups were mainly related to the carbon, nitrogen, sulfur, and arsenic metabolism. Lysogenic viral production and integrase genes were augmented in the hadal zone, suggesting the prevalence of viral lysogenic life strategy. Abundant rve genes in the hadal zone, which function as transposase in the caudoviruses, further suggest the prevalence of viral-mediated horizontal gene transfer. This study provides fundamental insights into the virioplankton assemblages of the hadal zone, reinforcing the necessity of incorporating virioplankton into the hadal biogeochemical cycles. The unique virioplankton assemblages of the Challenger Deep were revealed Virus encoded auxiliary metabolic genes relating to the biogeochemical cycling Viruses in deep and hadal zone tend to be lysogenic, and potentially mediate the horizontal gene transfer
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Rampen SW, Friedl T, Rybalka N, Thiel V. The Long chain Diol Index: A marine palaeotemperature proxy based on eustigmatophyte lipids that records the warmest seasons. Proc Natl Acad Sci U S A 2022; 119:e2116812119. [PMID: 35412908 PMCID: PMC9169758 DOI: 10.1073/pnas.2116812119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/11/2022] [Indexed: 12/23/2022] Open
Abstract
Long chain 1,13- and 1,15-diols are lipids which are omnipresent in marine environments, and the Long chain Diol Index (LDI), based on their distributions, has previously been introduced as a proxy for sea surface temperature. The main biological sources for long chain 1,13- and 1,15-diols have remained unknown, but our combined lipid and 23S ribosomal RNA (23S rRNA) analyses on suspended particulate matter from the Mediterranean Sea demonstrate that these lipids are produced by a marine eustigmatophyte group that originated before the currently known eustigmatophytes diversified. The 18S rRNA data confirm the existence of early-branching marine eustigmatophytes, which occur at a global scale. Differences between LDI records and other paleotemperature proxies are generally attributed to differences between the seasons in which the proxy-related organisms occur. Our results, combined with available LDI data from surface sediments, indicate that the LDI primarily registers temperatures from the warmest month when mixed-layer depths, salinity, and nutrient concentrations are low. The LDI may not be applicable in areas where Proboscia diatoms contribute 1,13-diols, but this can be recognized by enhanced contributions of C28 1,12 diol. Freshwater input may also affect the correlation between temperature and the LDI, but relative C32 1,15-diol abundances help to identify and correct for these effects. When taking those factors into account, the calibration error of the LDI is 2.4 °C. As a well-defined proxy for temperatures of the warmest seasons, the LDI can unlock important and previously inaccessible paleoclimate information and will thereby substantially improve our understanding of past climate conditions.
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Affiliation(s)
- Sebastiaan W. Rampen
- Geobiology, Geoscience Centre, University of Göttingen, 37077 Göttingen, Germany
| | - Thomas Friedl
- Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, Göttingen, 37073 Germany
| | - Nataliya Rybalka
- Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, Göttingen, 37073 Germany
| | - Volker Thiel
- Geobiology, Geoscience Centre, University of Göttingen, 37077 Göttingen, Germany
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Mou S, Zhang Z, Zhao H, Nair S, Li Y, Xu K, Tian J, Zhang Y. A dark-tolerant diatom (Chaetoceros) cultured from the deep sea. JOURNAL OF PHYCOLOGY 2022; 58:208-218. [PMID: 35092014 DOI: 10.1111/jpy.13240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Although the extreme conditions of the deep sea are typically not suitable for the growth of photosynthetic algae, accumulating evidence indicates that there are diverse healthy phytoplankton living in this environment. However, living phytoplankton from the deep sea have rarely been isolated and cultivated, and so our understanding of where they come from and how they adapt to (or tolerate) the extreme deep-sea environment is limited. Here, under long-term dark stress and subsequent light treatment, we successfully isolated a diatom from a depth of 1,000 m in the Western Pacific Ocean. Morphological observations and molecular phylogenetic analysis revealed that it is affiliated to the genus Chaetoceros, and thus, we tentatively named it Chaetoceros sp. DS1. We observed that the chloroplast genome of this species, is most closely related to that of Chaetoceros simplex. It was shown to have a strong tolerance to darkness in that it maintained its morphological integrity and vitality for up to 3 months in complete darkness at room temperature. We also demonstrated that Chaetoceros sp. DS1 presented a facultative heterotrophic function. Its growth was promoted by many organic carbon sources (e.g., glycerine, ethanol, and sodium acetate) under low light conditions. However, under dark and high light conditions, the growth promotion effect of organic carbon was not obvious. Indeed, Chaetoceros sp. DS1 grew best under low light conditions, indicating that it likely came from the deeper layer of the euphotic zone. The facultative heterotrophic function of this diatom and tolerance to darkness may help it survive in these conditions or enter a dormant period in the deep sea.
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Affiliation(s)
- Shanli Mou
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zenghu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hanshuang Zhao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shailesh Nair
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuhang Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jiwei Tian
- Physical Oceanography Laboratory/Qingdao Collaborative Innovation Center of Marine Science and Technology, Key Laboratory of Marine Chemistry Theory & Engineering, Ocean University of China, Qingdao, 266101, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Zhao J, Jing H, Wang Z, Wang L, Jian H, Zhang R, Xiao X, Chen F, Jiao N, Zhang Y. Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench. mSystems 2022; 7:e0135821. [PMID: 35089086 PMCID: PMC8725595 DOI: 10.1128/msystems.01358-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/08/2021] [Indexed: 01/12/2023] Open
Abstract
Viruses are ubiquitous in the oceans. Even in the deep sediments of the Mariana Trench, viruses have high productivity. However, little is known about their species composition and survival strategies in that environment. Here, we uncovered novel viral communities (3,206 viral scaffolds) in the upper slope sediments of the Mariana Trench via metagenomic analysis of 15 sediment samples. Most (99%) of the viral scaffolds lack known viral homologs, and ca. 59% of the high-quality viral genomes (total of 111 with completeness of >90%) represent novel genera, including some Phycodnaviridae and jumbo phages. These viruses contain various auxiliary metabolic genes (AMGs) potentially involved in organic carbon degradation, inorganic carbon fixation, denitrification, and assimilatory sulfate reduction, etc. This study provides novel insight into the almost unknown benthic viral communities in the Mariana Trench. IMPORTANCE The Mariana Trench harbors a substantial number of infective viral particles. However, very little is known about the identity, survival strategy, and potential functions of viruses in the trench sediments. Here, through metagenomic analysis, unusual benthic viral communities with high diversity and novelty were discovered. Among them, 59% of the viruses with a genome completeness of >90% represent novel genera. Various auxiliary metabolic genes carried by these viruses reflect the potential adaptive characteristics of viruses in this extreme environment and the biogeochemical cycles that they may participate in. This study gives us a deeper understanding of the peculiarities of viral communities in deep-sea/hadal sediments.
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Affiliation(s)
- Jiulong Zhao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, 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
- University of Chinese Academy of Sciences, Beijing, China
| | - Zengmeng Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Long Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- State Key Laboratory for Marine Environmental Science, Xiamen University, Xiamen, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Zhang
- State Key Laboratory for Marine Environmental Science, Xiamen University, Xiamen, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Chen
- University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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Han Y, Guo C, Guan X, McMinn A, Liu L, Zheng G, Jiang Y, Liang Y, Shao H, Tian J, Wang M. Comparison of Deep-Sea Picoeukaryotic Composition Estimated from the V4 and V9 Regions of 18S rRNA Gene with a Focus on the Hadal Zone of the Mariana Trench. MICROBIAL ECOLOGY 2022; 83:34-47. [PMID: 33811505 DOI: 10.1007/s00248-021-01747-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Diversity of microbial eukaryotes is estimated largely based on sequencing analysis of the hypervariable regions of 18S rRNA genes. But the use of different regions of 18S rRNA genes as molecular markers may generate bias in diversity estimation. Here, we compared the differences between the two most widely used markers, V4 and V9 regions of the 18S rRNA gene, in describing the diversity of epipelagic, bathypelagic, and hadal picoeukaryotes in the Challenger Deep of the Mariana Trench, which is a unique and little explored environment. Generally, the V9 region identified more OTUs in deeper waters than V4, while the V4 region provided greater Shannon diversity than V9. In the epipelagic zone, where Alveolata was the dominant group, picoeukaryotic community compositions identified by V4 and V9 markers are similar at different taxonomic levels. However, in the deep waters, the results of the two datasets show clear differences. These differences were mainly contributed by Retaria, Fungi, and Bicosoecida. The primer targeting the V9 region has an advantage in amplifying Bicosoecids in the bathypelagic and hadal zone of the Mariana Trench, and its high abundance in V9 dataset pointed out the possibility of Bicosoecids as a dominant group in this environment. Chrysophyceae, Fungi, MALV-I, and Retaria were identified as the dominant picoeukaryotes in the bathypelagic and hadal zone and potentially play important roles in deep-sea microbial food webs and biogeochemical cycling by their phagotrophic, saprotrophic, and parasitic life styles. Overall, the use of different markers of 18S rRNA gene allows a better assessment and understanding of the picoeukaryotic diversity in deep-sea environments.
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Affiliation(s)
- Yuye Han
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Cui Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
| | - Xuran Guan
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Lu Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Guiliang Zheng
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yong Jiang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, China
- Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
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Shuwang X, Sun J, Wei Y, Guo C. Size-Fractionated Filtration Combined with Molecular Methods Reveals the Size and Diversity of Picophytoplankton. BIOLOGY 2021; 10:biology10121280. [PMID: 34943195 PMCID: PMC8698306 DOI: 10.3390/biology10121280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/14/2021] [Accepted: 11/27/2021] [Indexed: 06/14/2023]
Abstract
In this study, flow cytometry (FCM) and size-fractionated filtration, together with high-throughput molecular sequencing methods (SM), were used to investigate picophytoplankton. A particle separation filter and a higher-throughput sequencing method were used to evaluate the composition of a euphotic zone of picophytoplankton-especially picoeukaryotic phytoplankton-in the Western Pacific, and the results of flow cytometry, which is a classic way to detect picophytoplankton, were used as a standard to evaluate the reliability of the results of the SMs. Within a water column of 200 m, six water depths (5, 25, 50, 113 (DCM), 150, and 200 m) were established. In order to further study the particle size spectra of the picophytoplankton, size-fractionated filtration was used to separate water samples from each water depth into three particle size ranges: 0.2-0.6, 0.6-1.2, and 1.2-2 μm. A total of 36 (6 × 3 × 2) samples were obtained through PCR amplification of the 18S rRNA V4 hypervariable region and 16S rRNA, which were biased toward phytoplankton plastids, and then high-throughput sequencing was performed. The estimation of the picophytoplankton diameter relied on forward scattering (FSC) through FCM. The estimation of the vertical distribution and diameter of the picophytoplankton using the SM was consistent with the results with FCM; thus, we believe that the estimation of picophytoplankton composition with the SM has value as a reference, although the size-fractionated filtration seemed to cause some deviations. In addition to Prochlorococcus and Synechococcus, the SM was used to evaluate the composition of picoeukaryotic phytoplankton, which mainly included Prymnesiophycea (Haptophyta) (38.15%), Cryptophyceae (Cryptophyta) (22.36%), Dictyochophyceae (Chrysophyta) (12.22%), and Mamiellophyceae (Chlorophyta) (3.31%). In addition, the SM also detected Dinophyceae (Dinoflagellata) (11.69%) sequences and a small number of Bacillariophyceae (Diatom) (1.64%) sequences, which are generally considered to have large particle sizes. The results of the SM also showed that the picoeukaryotic phytoplankton were not evenly distributed in the euphotic layer, and the vertical distributions of the different picoeukaryotic phytoplankton were different. An analysis of correlations with environmental factors showed that temperature was the main environmental factor controlling the vertical distribution of picophytoplankton.
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Affiliation(s)
- Xinze Shuwang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (X.S.); (C.G.)
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan 430074, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Yuqiu Wei
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China;
| | - Congcong Guo
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (X.S.); (C.G.)
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11
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Chen M, Song Y, Feng X, Tang K, Jiao N, Tian J, Zhang Y. Genomic Characteristics and Potential Metabolic Adaptations of Hadal Trench Roseobacter and Alteromonas Bacteria Based on Single-Cell Genomics Analyses. Front Microbiol 2020; 11:1739. [PMID: 32793171 PMCID: PMC7393951 DOI: 10.3389/fmicb.2020.01739] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 07/03/2020] [Indexed: 11/30/2022] Open
Abstract
Heterotrophic bacteria such as those from the Roseobacter group and genus Alteromonas dominate the hadal zones of oceans; however, we know little about the genomic characteristics and potential metabolic adaptations of hadal trench-dwelling bacteria. Here, we report multiple single amplified genomes (SAGs) belonging to Roseobacter and Alteromonas, recovered from the hadal zone of the Mariana Trench. While phylogenetic analyses show that these hadal SAGs cluster with their surface relatives, an analysis of genomic recruitment indicates that they have higher relative abundances in the hadal zone of the Mariana Trench. Comparative genomic analyses between the hadal SAGs and reference genomes of closely related shallow-water relatives indicate that genes involved in the mobilome (prophages and transposons) are overrepresented among the unique genes of the hadal Roseobacter and Alteromonas SAGs; the functional proteins encoded by this category of genes also shows higher amino acid sequence variation than those encoded by other gene sets within the Roseobacter SAGs. We also found that genes involved in cell wall/membrane/envelope biogenesis, transcriptional regulation, and metal transport may be important for the adaptation of hadal Roseobacter and Alteromonas lineages. These results imply that the modification of cell surface-related proteins and transporters is the major direction of genomic evolution in Roseobacter and Alteromonas bacteria adapting to the hadal environment, and that prophages and transposons may be the key factors driving this process.
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Affiliation(s)
- Mingming Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Yu Song
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Xiaoyuan Feng
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Jiwei Tian
- Physical Oceanography Laboratory, Ocean University of China, Qingdao, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
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12
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Fu L, Li D, Mi T, Zhao J, Liu C, Sun C, Zhen Y. Characteristics of the archaeal and bacterial communities in core sediments from Southern Yap Trench via in situ sampling by the manned submersible Jiaolong. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 703:134884. [PMID: 31767325 DOI: 10.1016/j.scitotenv.2019.134884] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/03/2019] [Accepted: 10/06/2019] [Indexed: 06/10/2023]
Abstract
The hadal environment is the deepest part of the ocean and harbors a significant number of unique microbial communities. Here, we collected core sediment samples of Southern Yap Trench with the deep-sea manned submersible Jiaolong and analyzed the microbial community structure and abundance in the samples through high-throughput sequencing and real-time fluorescence quantitative PCR (qPCR), taking physicochemical parameters into account to explore potential environmental drivers and metabolic pathways therein. Considering the typical "V-shape" topography and frequent sediment collapses on trench walls, the core sediments of Southern Yap Trench harbored distinct microbial populations with fluctuating distributions and metabolic processes dominated by Proteobacteria and Thaumarchaeota. To discover the main potential metabolic processes of microbes, functional genes were detected by qPCR. The abundance of bacteria was greater than that of archaea in Southern Yap Trench sediments. The abundance of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), sulfate-reducing bacteria (SRB) and denitrifying bacteria (denitrifier) decreased with increasing depth and decreasing total organic carbon (TOC%) and total nitrogen (TN%) and showed a positive and significant correlation with TOC% (P < 0.01), TN% (P < 0.01), TOC/TN molar ratio (C/N ratio) (P < 0.01) and median grain size (P < 0.01). From the perspective of function based on the 16S rRNA gene, aerobic ammonium oxidization, carbon assimilation, and chemoheterotrophic function may be the dominant processes in Southern Yap Trench sediments. Moreover, considering the isolated geomorphological and hydrological characteristics of Southern Yap Trench, we hypothesized that the distinct hadal microbial ecosystem was driven by the endogenous recycling of organic matter in the hadal sediments associated with the trench geomorphology.
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Affiliation(s)
- Lulu Fu
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Dong Li
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Tiezhu Mi
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Jun Zhao
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Chenggang Liu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Chengjun Sun
- Marine Ecology Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266237, China
| | - Yu Zhen
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
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13
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Yang L, Li H, Zhang Y, Jiao N. Environmental risk assessment of triazine herbicides in the Bohai Sea and the Yellow Sea and their toxicity to phytoplankton at environmental concentrations. ENVIRONMENT INTERNATIONAL 2019; 133:105175. [PMID: 31629173 DOI: 10.1016/j.envint.2019.105175] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/04/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
Herbicides have been increasingly used worldwide and a large amount of herbicide residue eventually enters the ocean via groundwater or surface run-off every year. However, the global coastal pollution status of herbicides and their negative impact on marine life (especially phytoplankton) in natural environmental concentrations are poorly understood except for few special environments (e.g. the Great Barrier Reef, Australia). Our field investigation of the distribution of ten triazine herbicides in the Bohai Sea and the Yellow Sea of China revealed that the concentrations of triazine herbicides exceeded the "No Observed Effect Concentrations" for phytoplankton. Their total concentrations could be as high as 6.61 nmol L-1. Based on the concentration addition model, the toxicity of herbicide homologues is usually cumulative, and the combined toxicity of these ten triazine herbicides could cause 13.2% inhibition on the chlorophyll a fluorescence intensity of a representative diatom species Phaeodactylum tricornutum Pt-1, which corresponds roughly to the toxicity of atrazine in an equivalent concentration of 14.08 nmol L-1. Atrazine in this equivalent-effect concentration could greatly inhibit the growth of cells, the maximum quantum efficiency of photosystem II (Fv/Fm), and nutrient absorption of Phaeodactylum tricornutum Pt-1. Transcriptome analysis revealed that multiple metabolic pathways (Calvin cycle, tricarboxylic acid (TCA) cycle, glycolysis/gluconeogenesis, etc.) related with photosynthesis and carbon metabolism were greatly disturbed, which might ultimately influence the primary productivity of coastal waters. Moreover, with the values of its bioaccumulation factor ranging from 69.6 to 118.9, atrazine was found to be accumulated in algal cells, which indicates that herbicide pollution might eventually affect the marine food web and even threaten the seafood safety of human beings.
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Affiliation(s)
- Liqiang Yang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Hongmei Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
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14
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Liang Y, Wang L, Wang Z, Zhao J, Yang Q, Wang M, Yang K, Zhang L, Jiao N, Zhang Y. Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea. Front Microbiol 2019; 10:1951. [PMID: 31507563 PMCID: PMC6716333 DOI: 10.3389/fmicb.2019.01951] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/08/2019] [Indexed: 11/13/2022] Open
Abstract
A metagenomic analysis of the viral community from five surface and five deep sea water (>2000 m below the surface, mbs) samples collected from the central basin of the South China Sea and adjacent Northwest Pacific Ocean during July-August 2017 was conducted herein. We builded up a South China Sea DNA virome (SCSV) dataset of 29,967 viral Operational Taxonomic Units (vOTUs), which is comparable to the viral populations from the original Tara Ocean and Malaspina expeditions. The most abundant and widespread viral populations were from the uncultivated viruses annotated from the viral metagenomics. Only 74 and 37 vOTUs have similarity with the reported genomes from the cultivated viruses and the single-virus genomics, respectively. The community structures of deep sea viromes in the SCSV were generally different from the surface viromes. The carbon flux and nutrients (PO4 and NOx) were related to the surface and deep sea viromes in the SCSV, respectively. In the SCSV, the annotated vOTUs could be affiliated to the cultivated viruses mainly including Pelagibacter (SAR11) phage HTVC010P, Prochlorococcus phages (P-GSP1, P-SSM4, and P-TIM68), Cyanophages (MED4-184 and MED4-117) and Mycobacterium phages (Sparky and Squirty). It indicated that phage infection to the SAR11 cluster may occur ubiquitously and has significant impacts on bathypelagic SAR11 communities in the deep sea. Meanwhile, as Prochlorococcus is prominently distributed in the euphotic ocean, the existence of their potential phages in the deep sea suggested the sedimentation mechanism might contribute to the formation of the deep sea viromes. Intriguingly, the presence of Mycobacterium phages only in the deep sea viromes, suggests inhabitance of endemic viral populations in the deep sea viromes in the SCSV. This study provided an insight of the viral community in the South China Sea and for the first time uncovered the deep sea viral diversity in the central basin of the South China Sea.
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Affiliation(s)
- Yantao Liang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Long Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Zengmeng Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Jiulong Zhao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Qingwei Yang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Kaiguang Yang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Lihua Zhang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
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15
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Cruz BN, Neuer S. Heterotrophic Bacteria Enhance the Aggregation of the Marine Picocyanobacteria Prochlorococcus and Synechococcus. Front Microbiol 2019; 10:1864. [PMID: 31456778 PMCID: PMC6700329 DOI: 10.3389/fmicb.2019.01864] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/29/2019] [Indexed: 11/13/2022] Open
Abstract
Marine picocyanobacteria are ubiquitous primary producers across the world’s oceans, and play a key role in the global carbon cycle. Recent evidence stemming from in situ investigations have shown that picocyanobacteria are able to sink out of the euphotic zone to depth, which has traditionally been associated with larger, mineral ballasted cells. The mechanisms behind the sinking of picocyanobacteria remain a point of contention, given that they are too small to sink on their own. To gain a mechanistic understanding of the potential role of picocyanobacteria in carbon export, we tested their ability to form “suspended” (5–60 μm) and “visible” (ca. > 0.1 mm) aggregates, as well as their production of transparent exopolymer particles (TEP)—which are a key component in the formation of marine aggregates. Additionally, we investigated if interactions with heterotrophic bacteria play a role in TEP production and aggregation in Prochlorococcus and Synechococcus by comparing xenic and axenic cultures. We observed TEP production and aggregation in batch cultures of axenic Synechococcus, but not in axenic Prochlorococcus. Heterotrophic bacteria enhanced TEP production as well as suspended and visible aggregate formation in Prochlorococcus, while in Synechococcus, aggregation was enhanced with no changes in TEP. Aggregation experiments using a natural plankton community dominated by picocyanobacteria resulted in aggregation only in the presence of the ballasting mineral kaolinite, and only when Synechococcus were in their highest seasonal abundance. Our results point to a different export potential between the two picocyanobacteria, which may be mediated by interactions with heterotrophic bacteria and presence of ballasting minerals. Further studies are needed to clarify the mechanistic role of bacteria in TEP production and aggregation of these picocyanobacteria.
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Affiliation(s)
- Bianca N Cruz
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Susanne Neuer
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, United States
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16
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Cui G, Li J, Gao Z, Wang Y. Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep. PeerJ 2019; 7:e6961. [PMID: 31149407 PMCID: PMC6526897 DOI: 10.7717/peerj.6961] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 04/16/2019] [Indexed: 12/28/2022] Open
Abstract
Microbial communities in hadal sediments are least explored in hadal zone (>6,000 m), especially in the Challenger Deep with high pressure (∼110 M pa at the bottom). In this study, we investigated the microbial communities in the sediments of the slope and trench-axis bottom of the Challenger Deep in the Mariana Trench. Classification of the reads of the 16S rRNA gene amplicons showed vertical distribution of prokaryotic microbial inhabitants from the surface to up to 60 centimeter below surface floor (cmbsf). The most dominant phyla were Proteobacteria, Chloroflexi, Actinobacteria, Planctomycetes and candidate phyla Patescibacteria and Marinimicrobia. Distinct dominant groups in the microbial communities were observed in trench-axis sediment (water depth >8,600 m), compared to the slopes of the Challenger Deep. A sampling site at the northern slope was enriched with archaea from mesophilic Euryarchaeota Marine Group II (MGII) as a biomarker of specific geochemical setting. Among archaeal community, Thaumarchaeota represented by Nitrosopumilus were dominant in the upper layers and diminished drastically in the deeper layers. “Ca. Woesearchaeota”, however, became the dominant group in the deeper layers. Overall, our study provides a better understanding on the pattern of the microbial communities in the deepest hadal sediments on Earth, and highlights the extraordinary diversity still waiting to be discovered.
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Affiliation(s)
- Guojie Cui
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Zhaoming Gao
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
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