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Knjaz M, Baricevic A, Tankovic MS, Kuzat N, Vlasicek I, Grizancic L, Podolsak I, Pfannkuchen M, Kogovsek T, Pfannkuchen DM. First regional reference database of northern Adriatic diatom transcriptomes. Sci Rep 2024; 14:16209. [PMID: 39003315 PMCID: PMC11246432 DOI: 10.1038/s41598-024-67043-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024] Open
Abstract
Marine microbial communities form the basis for the functioning of marine ecosystems and the conservation of biodiversity. With the application of metagenomics and metatranscriptomics in marine environmental studies, significant progress has been made in analysing the functioning of microbial communities as a whole. These molecular techniques are highly dependent on reliable, well-characterised, comprehensive and taxonomically diverse sequenced reference transcriptomes of microbial organisms. Here we present a set of 12 individual transcriptome assemblies derived from 6 representative diatom species from the northern Adriatic Sea grown under 2 environmentally relevant growth conditions (phosphate replete vs. phosphate deprived). After filtering the reads and assembly, an average number of 64,932 transcripts per assembly was obtained, of which an average of 8856 were assigned to functionally known proteins. Of all assigned transcripts, an average of 6483 proteins were taxonomically assigned to diatoms (Bacillariophyta). On average, a higher number of assigned proteins was detected in the transcriptome assemblies of diatoms grown under replete media condition. On average, 50% of the mapped proteins were shared between the two growth conditions. All recorded proteins in the dataset were classified into 24 COG categories, with approximately 25% belonging to the unknown function and the remaining 75% belonging to all other categories. The resulting diatom reference database for the northern Adriatic, focussing on the response to nutrient limitation as characteristic for the region and predicted for the future world oceans, provides a valuable resource for analysing environmental metatranscriptome and metagenome data. Each northern Adriatic transcriptome can also be used by itself as a reference database for the (meta)transcriptomes and gene expression studies of the associated species that will be generated in the future.
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Affiliation(s)
- Mia Knjaz
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Ana Baricevic
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia.
| | | | - Natasa Kuzat
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Ivan Vlasicek
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Lana Grizancic
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Ivan Podolsak
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | | | - Tjasa Kogovsek
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
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Bayramova E, Petrova D, Marchenkov A, Morozov A, Galachyants Y, Zakharova Y, Bedoshvili Y, Likhoshway Y. Differential Expression of Stress Adaptation Genes in a Diatom Ulnaria acus under Different Culture Conditions. Int J Mol Sci 2024; 25:2314. [PMID: 38396992 PMCID: PMC10888605 DOI: 10.3390/ijms25042314] [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: 01/16/2024] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Diatoms are a group of unicellular eukaryotes that are essential primary producers in aquatic ecosystems. The dynamic nature of their habitat necessitates a quick and specific response to various stresses. However, the molecular mechanisms of their physiological adaptations are still underexplored. In this work, we study the response of the cosmopolitan freshwater diatom Ulnaria acus (Bacillariophyceae, Fragilariophycidae, Licmophorales, Ulnariaceae, Ulnaria) in relation to a range of stress factors, namely silica deficiency, prolonged cultivation, and interaction with an algicidal bacterium. Fluorescent staining and light microscopy were used to determine the physiological state of cells under these stresses. To explore molecular reactions, we studied the genes involved in the stress response-type III metacaspase (MC), metacaspase-like proteases (MCP), death-specific protein (DSP), delta-1-pyrroline-5-carboxylate dehydrogenase (ALDH12), and glutathione synthetase (GSHS). We have described the structure of these genes, analyzed the predicted amino acid sequences, and measured their expression dynamics in vitro using qRT-PCR. We demonstrated that the expression of UaMC1, UaMC3, and UaDSP increased during the first five days of silicon starvation. On the seventh day, it was replaced with the expression of UaMC2, UaGSHS, and UaALDH. After 45 days of culture, cells stopped growing, and the expression of UaMC1, UaMC2, UaGSHS, and UaDSP increased. Exposure to an algicidal bacterial filtrate induced a higher expression of UaMC1 and UaGSHS. Thus, we can conclude that these proteins are involved in diatoms' adaptions to environmental changes. Further, these data show that the molecular adaptation mechanisms in diatoms depend on the nature and exposure duration of a stress factor.
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Affiliation(s)
| | | | | | | | | | | | - Yekaterina Bedoshvili
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia; (E.B.); (D.P.); (A.M.); (A.M.); (Y.G.); (Y.Z.); (Y.L.)
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3
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Walworth NG, Espinoza JL, Argyle PA, Hinners J, Levine NM, Doblin MA, Dupont CL, Collins S. Genus-Wide Transcriptional Landscapes Reveal Correlated Gene Networks Underlying Microevolutionary Divergence in Diatoms. Mol Biol Evol 2023; 40:msad218. [PMID: 37874344 PMCID: PMC10595192 DOI: 10.1093/molbev/msad218] [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: 04/28/2023] [Revised: 08/24/2023] [Accepted: 09/21/2023] [Indexed: 10/25/2023] Open
Abstract
Marine microbes like diatoms make up the base of marine food webs and drive global nutrient cycles. Despite their key roles in ecology, biogeochemistry, and biotechnology, we have limited empirical data on how forces other than adaptation may drive diatom diversification, especially in the absence of environmental change. One key feature of diatom populations is frequent extreme reductions in population size, which can occur both in situ and ex situ as part of bloom-and-bust growth dynamics. This can drive divergence between closely related lineages, even in the absence of environmental differences. Here, we combine experimental evolution and transcriptome landscapes (t-scapes) to reveal repeated evolutionary divergence within several species of diatoms in a constant environment. We show that most of the transcriptional divergence can be captured on a reduced set of axes, and that repeatable evolution can occur along a single major axis of variation defined by core ortholog expression comprising common metabolic pathways. Previous work has associated specific transcriptional changes in gene networks with environmental factors. Here, we find that these same gene networks diverge in the absence of environmental change, suggesting these pathways may be central in generating phenotypic diversity as a result of both selective and random evolutionary forces. If this is the case, these genes and the functions they encode may represent universal axes of variation. Such axes that capture suites of interacting transcriptional changes during diversification improve our understanding of both global patterns in local adaptation and microdiversity, as well as evolutionary forces shaping algal cultivation.
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Affiliation(s)
- Nathan G Walworth
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA
- J.Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Phoebe A Argyle
- Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Jana Hinners
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- Helmholtz-Zentrum Hereon, 21502 Geesthacht, Germany
| | - Naomi M Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA
| | - Martina A Doblin
- Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | | | - Sinéad Collins
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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Wang Y, Zhai WD, Wu C. Algal cell viability assessment: The role of environmental factors in phytoplankton population dynamics. MARINE POLLUTION BULLETIN 2023; 189:114743. [PMID: 36898274 DOI: 10.1016/j.marpolbul.2023.114743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
The viability of algal cells is one of the most fundamental issues in marine ecological research. In this work, a method was designed to identify algal cell viability based on digital holography and deep learning, which divided algal cells into three categories: active, weak, and dead cells. This method was applied to measure algal cells in surface waters of the East China Sea in spring, revealing about 4.34 %-23.29 % weak cells and 3.98 %-19.47 % dead cells. Levels of nitrate and chlorophyll a were the main factors affecting the viability of algal cells. Furthermore, algal viability changes during the heating and cooling were observed in laboratory experiments: high temperatures led to an increase in weak algal cells. This may provide an explanation for why most harmful algal blooms occur in warming months. This study provided a novel insight into how to identify the viability of algal cells and understand their significance in the ocean.
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Affiliation(s)
- Yanyan Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Wei-Dong Zhai
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China.
| | - Chi Wu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Laboratory for Marine Mineral Resources, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China.
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5
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Yang L, Yang Q, Lin L, Luan T, Tam NFY. Characterization of benthic biofilms in mangrove sediments and their variation in response to nutrients and contaminants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159391. [PMID: 36240915 DOI: 10.1016/j.scitotenv.2022.159391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/30/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Diatom-dominated biofilms and associated extracellular polymeric substances (EPS) may adapt to the stress of long-term exposure to nutrients and anthropogenic contaminants. However, such interactions in contaminated mangrove sediments have rarely been reported. Based on the in situ characterization of biofilm components and environmental factors, the present study aimed to explore the key factors involved in shaping sediment biofilms through correlational and multivariate analyses. The pennate diatom Navicula is the core taxon that plays a crucial role in balancing the abundance of Nitzschia and Cyclotella, and is the main producer of bound-polysaccharides. The taxa composition shifts in a high N/P matrix, with the populations of pennate diatoms increasing but that of centric diatoms decreasing. High nutrient concentrations yield more number of diatoms and elevated levels of EPS. Bacteria are the main consumers of EPS and tend to be more symbiotic with Nitzschia than the other two diatom taxa. Some bound-polysaccharides dominated by arabinose and glucose units are transformed into the colloidal fraction, whereas other conservative ones serve as structural materials in concert with the bound-proteins. The planktonic phase of Cyclotella breaks down the structural EPS secreted by pennate diatoms in a process that directly affects the dynamic renewal of benthic biofilms. Most heavy metals as well as bisphenol A inhibit the abundance of bacteria and diatoms but enhance most EPS fractions except bound-polysaccharides. The response of structural EPS to specific contaminants varies, exhibiting increases in Co and Ni levels but decreases in nonylphenol and methylparaben levels. The present study improves our understanding of the microbial carbon loop of benthic biofilms in mangrove ecosystems under stress by nutrients and mixed contaminants.
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Affiliation(s)
- Lihua Yang
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Qian Yang
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China; State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510600, China
| | - Li Lin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Tiangang Luan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
| | - Nora F Y Tam
- School of Science and Technology, Hong Kong Metropolitan University, Hong Kong, China; State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong, China.
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Sehein TR, Gast RJ, Pachiadaki M, Guillou L, Edgcomb VP. Parasitic infections by Group II Syndiniales target selected dinoflagellate host populations within diverse protist assemblages in a model coastal pond. Environ Microbiol 2022; 24:1818-1834. [PMID: 35315564 DOI: 10.1111/1462-2920.15977] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 03/13/2022] [Indexed: 11/29/2022]
Abstract
Protists are integral to marine food webs and biogeochemical cycles; however, there is a paucity of data describing specific ecological niches for some of the most abundant taxa in marker gene libraries. Syndiniales are one such group, often representing the majority of sequence reads recovered from picoplankton samples across the global ocean. However, the prevalence and impacts of syndinian parasitism in marine environments remains unclear. We began to address these critical knowledge gaps by generating a high-resolution time series (March-October 2018) in a productive coastal pond. Seasonal shifts in protist populations, including parasitic Syndiniales, were documented during periods of higher primary productivity and increased summer temperature-driven stratification. Elevated concentrations of infected hosts and free-living parasite spores occurred at nearly monthly intervals in July, August, and September. We suggest intensifying stratification during this period correlated with the increased prevalence of dinoflagellates that were parasitized by Group II Syndiniales. Infections in some protist populations were comparable to previously reported large single-taxon dinoflagellate blooms. Infection dynamics in Salt Pond demonstrated the propagation of syndinian parasites through mixed protist assemblages and highlighted patterns of host/parasite interactions that better reflect many other marine environments where single taxon blooms are uncommon.
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Affiliation(s)
- Taylor R Sehein
- MIT-WHOI Joint Program in Biological Oceanography, Cambridge and Woods Hole, MA, United States
| | - Rebecca J Gast
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Maria Pachiadaki
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Laure Guillou
- Sorbonne Université & Centre National pour la Recherche Scientifique, Station Biologique de Roscoff, UMR7144, Roscoff, France
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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Deng Y, Vallet M, Pohnert G. Temporal and Spatial Signaling Mediating the Balance of the Plankton Microbiome. ANNUAL REVIEW OF MARINE SCIENCE 2022; 14:239-260. [PMID: 34437810 DOI: 10.1146/annurev-marine-042021-012353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The annual patterns of plankton succession in the ocean determine ecological and biogeochemical cycles. The temporally fluctuating interplay between photosynthetic eukaryotes and the associated microbiota balances the composition of aquatic planktonic ecosystems. In addition to nutrients and abiotic factors, chemical signaling determines the outcome of interactions between phytoplankton and their associated microbiomes. Chemical mediators control essential processes, such as the development of key morphological, physiological, behavioral, and life-history traits during algal growth. These molecules thus impact species succession and community composition across time and space in processes that are highlighted in this review. We focus on spatial, seasonal, and physiological dynamics that occur during the early association of algae with bacteria, the exponential growth of a bloom, and its decline and recycling. We also discuss how patterns from field data and global surveys might be linked to the actions of metabolic markers in natural phytoplankton assemblages.
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Affiliation(s)
- Yun Deng
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Marine Vallet
- Research Group Phytoplankton Community Interactions, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany;
- Research Group Phytoplankton Community Interactions, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
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Liu L, Feng Y, Hu S, Li H, Li Y, Ke J, Long X. PDCD4 suppresses autophagy and promotes apoptosis via Akt in chondrocytes of temporomandibular joint osteoarthritis. Oral Dis 2021. [DOI: 10.1111/odi.13559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Li Liu
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) Key Laboratory of Oral Biomedicine Ministry of Education (KLOBM) School and Hospital of Stomatology Wuhan University Wuhan Hubei Province China
| | - Yaping Feng
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) Key Laboratory of Oral Biomedicine Ministry of Education (KLOBM) School and Hospital of Stomatology Wuhan University Wuhan Hubei Province China
| | - Shiyu Hu
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) Key Laboratory of Oral Biomedicine Ministry of Education (KLOBM) School and Hospital of Stomatology Wuhan University Wuhan Hubei Province China
| | - Huimin Li
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) Key Laboratory of Oral Biomedicine Ministry of Education (KLOBM) School and Hospital of Stomatology Wuhan University Wuhan Hubei Province China
| | - Yanyan Li
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) Key Laboratory of Oral Biomedicine Ministry of Education (KLOBM) School and Hospital of Stomatology Wuhan University Wuhan Hubei Province China
| | - Jin Ke
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) Key Laboratory of Oral Biomedicine Ministry of Education (KLOBM) School and Hospital of Stomatology Wuhan University Wuhan Hubei Province China
| | - Xing Long
- Department of Oral and Maxillofacial Surgery School and Hospital of Stomatology Wuhan University Wuhan Hubei Province China
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9
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Zhao Y, Tang X, Lv M, Liu Q, Li J, Zhang B, Li L, Zhang X, Zhao Y. The molecular response mechanisms of a diatom Thalassiosira pseudonana to the toxicity of BDE-47 based on whole transcriptome analysis. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 229:105669. [PMID: 33142158 DOI: 10.1016/j.aquatox.2020.105669] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/16/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
Polybrominated diphenyl ethers (PBDEs) are ubiquitously distributed persistent organic pollutants (POPs) in marine environments. Phytoplankton are the entrance of PBDEs entering to biotic environments from abiotic environments, while the responding mechanisms of phytoplankton to PBDEs have not been full established. Therefore, we chose the model diatom Thalassiosira pseudonana in this study, by integrating whole transcriptome analysis with physiological-biochemical data, to reveal the molecular responding mechanisms of T. pseudonana to the toxicity of BDE-47. Our results indicated the changes of genes expressions correlated to the physiological-biochemical changes, and there were multiple molecular mechanisms of T. pseudonana responding to the toxicity of BDE-47: Gene expressions evidence explained the suppression of light reaction and proved the occurrence of cellular oxidative stress; In the meanwhile, up-regulations of genes in pathways involving carbon metabolisms happened, including the Calvin cycle, glycolysis, TCA cycle, fatty acid synthesis, and triacylglycerol synthesis; Lastly, DNA damage was found and three outcome including DNA repair, cell cycle arrest and programmed cell death (PCD) happened, which could finally inhibit the cell division and population growth of T. pseudonana. This study presented the most complete molecular responding mechanisms of phytoplankton cells to PBDEs, and provided valuable information of various PBDEs-sensitive genes with multiple functions for further research involving organic pollutants and phytoplankton.
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Affiliation(s)
- Yirong Zhao
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China
| | - Xuexi Tang
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
| | - Mengchen Lv
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China
| | - Qian Liu
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China
| | - Jun Li
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China
| | - Bihan Zhang
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China
| | - Luying Li
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China
| | - Xinxin Zhang
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Yan Zhao
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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