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Hook SE, Smith RA, Waltham N, Warne MSJ. Pesticides in the Great Barrier Reef catchment area: Plausible risks to fish populations. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2024; 20:1256-1279. [PMID: 37994614 DOI: 10.1002/ieam.4864] [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: 08/11/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2023]
Abstract
Waterways that drain the Great Barrier Reef catchment area (GBRCA) transport pollutants to marine habitats, provide a critical corridor between freshwater and marine habitats for migratory fish species, and are of high socioecological value. Some of these waterways contain concentrations of pesticide active ingredients (PAIs) that exceed Australian ecotoxicity threshold values (ETVs) for ecosystem protection. In this article, we use a "pathway to harm" model with five key criteria to assess whether the available information supports the hypothesis that PAIs are or could have harmful effects on fish and arthropod populations. Strong evidence of the first three criteria and circumstantial weaker evidence of the fourth and fifth criteria are presented. Specifically, we demonstrate that exceedances of Australian and New Zealand ETVs for ecosystem protection are widespread in the GBRCA, that the PAI contaminated water occurs (spatially and temporally) in important habitats for fisheries, and that there are clear direct and indirect mechanisms by which PAIs could cause harmful effects. The evidence of individuals and populations of fish and arthropods being adversely affected species is more circumstantial but consistent with PAIs causing harmful effects in the freshwater ecosystems of Great Barrier Reef waterways. We advocate strengthening the links between PAI concentrations and fish health because of the cultural values placed on the freshwater ecosystems by relevant stakeholders and Traditional Owners, with the aim that stronger links between elevated PAI concentrations and changes in recreationally and culturally important fish species will inspire improvements in water quality. Integr Environ Assess Manag 2024;20:1256-1279. © 2023 Commonwealth of Australia and The Commonwealth Scientific and Industrial Research Organisation. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).
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Affiliation(s)
| | - Rachael A Smith
- Office of the Great Barrier Reef, Queensland, Department of Environment and Science, Brisbane, Queensland, Australia
| | - Nathan Waltham
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Michael St J Warne
- Reef Catchments Science Partnership, School of Earth and Environmental Sciences, University of Queensland, St. Lucia, Brisbane, Queensland, Australia
- Water Quality and Investigations, Department of Environment and Science, Brisbane, Queensland, Australia
- Centre for Agroecology, Water and Resilience, Coventry University, West Midlands, UK
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Cao F, Shu W, Liu Q, Wan J, Jiang Z, Liu M, Jiang Y. Distinct structure, assembly, and gene expression of microplankton in two Arctic estuaries with varied terrestrial inputs. ENVIRONMENTAL RESEARCH 2024; 256:119207. [PMID: 38782345 DOI: 10.1016/j.envres.2024.119207] [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: 03/08/2024] [Revised: 05/05/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
The Laptev Sea is a major Marginal Sea in the Western Arctic Ocean. The Arctic amplification brought by global warming influences the hydrological properties of rivers passing through the permafrost zone, which would alter the biological community structure at continental margin. In this study, the structure, assembly, and gene expression of planktonic microbial communities in two estuaries (Protoka Ularovskaya River Estuary, PURE; Lena River Estuary, LRE) of Laptev Sea were examined to investigate the environmental effects of polar rivers. PURE and LRE exhibited distinct environmental characteristics: low temperature and high salinity for PURE, and high temperature and low salinity for LRE, influenced by runoff size. Salinity more closely influenced microbial communities in LRE, with freshwater species playing a significant role in community composition. The findings revealed differences between two estuaries in community composition and diversity. Prokaryotes and microeukaryotes had shown different assembly patterns in response to habitat changes caused by terrestrial freshwater input. Furthermore, compared with the PURE, the co-occurrence and inter-domain network of the LRE, which was more affected by terrestrial input, was more complex and stable. Functional gene prediction revealed a higher gene expression of methane metabolism in LRE than in PURE, particularly those related to methane oxidation, and this conclusion could help better explore the impact of global warming on the methane cycle in the Arctic Marginal Seas. This study explored the increased freshwater runoffs under the background of global warming dramatically affect Arctic microplankton communities from community structure, assembly and gene expression aspects.
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Affiliation(s)
- Furong Cao
- MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Wangxinze Shu
- MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Qian Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266003, China
| | - Jiyuan Wan
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Zhiyang Jiang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Mingjian Liu
- MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
| | - Yong Jiang
- MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China.
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Perneel M, Lagaisse R, Mortelmans J, Maere S, Hablützel PI. Seasonal metabolic dynamics of microeukaryotic plankton: a year-long metatranscriptomic study in a temperate sea. mBio 2024; 15:e0038324. [PMID: 38980008 PMCID: PMC11323732 DOI: 10.1128/mbio.00383-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/11/2024] [Indexed: 07/10/2024] Open
Abstract
Seasonal fluctuations profoundly affect marine microeukaryotic plankton composition and metabolism, but accurately tracking these changes has been a long-standing challenge. In this study, we present a year-long metatranscriptomic data set from the Southern Bight of the North Sea, shedding light on the seasonal dynamics in temperate plankton ecosystems. We observe distinct shifts in active plankton species and their metabolic processes in response to seasonal changes. We characterized the metabolic signatures of different seasonal phases in detail, thereby revealing the metabolic versatility of dinoflagellates, the heterotrophic dietary strategy of Phaeocystis during its late-stage blooms, and stark variations in summer and fall diatom abundance and metabolic activity across nearby sampling stations. Our data illuminate the varied contributions of microeukaryotic taxa to biomass production and nutrient cycling at different times of the year and allow delineation of their ecological niches. IMPORTANCE Ecosystem composition and metabolic functions of temperate marine microeukaryote plankton are strongly influenced by seasonal dynamics. Although monitoring of species composition of microeukaryotes has expanded recently, few methods also contain seasonally resolved information on ecosystem functioning. We generated a year-long spatially resolved metatranscriptomic data set to assess seasonal dynamics of microeukaryote species and their associated metabolic functions in the Southern Bight of the North Sea. Our study underscores the potential of metatranscriptomics as a powerful tool for advancing our understanding of marine ecosystem functionality and resilience in response to environmental changes, emphasizing its potential in continuous marine ecosystem monitoring to enhance our ecological understanding of the ocean's eukaryotic microbiome.
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Affiliation(s)
- Michiel Perneel
- Flanders Marine Institute (VLIZ), Ostend, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | | | | | - Steven Maere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Pascal I. Hablützel
- Flanders Marine Institute (VLIZ), Ostend, Belgium
- Biology Department, Vrije Universiteit Brussel, Brussels, Belgium
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Krinos AI, Bowers RM, Rohwer RR, McMahon KD, Woyke T, Schulz F. Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake. MICROBIOME 2024; 12:133. [PMID: 39030632 PMCID: PMC11265017 DOI: 10.1186/s40168-024-01831-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 05/06/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND Protists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world's best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last 20 years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community and to hypothesize about their interactions with bacteria. RESULTS Based on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukaryotic phytoplankton community over time, which we predict to be a consequence of reduced zooplankton grazing pressures after the invasion of a invasive predator (the spiny water flea) to the lake. The metagenomic data also reveal the presence of the spiny water flea and the zebra mussel, a second invasive species to Lake Mendota, prior to their visual identification during routine monitoring. Furthermore, we use species co-occurrence and co-abundance analysis to connect the protistan community with bacterial taxa. Correlation analysis suggests that protists and bacteria may interact or respond similarly to environmental conditions. Cryptophytes declined in the second decade of the timeseries, while many alveolate groups (e.g., ciliates and dinoflagellates) and diatoms increased in abundance, changes that have implications for food web efficiency in Lake Mendota. CONCLUSIONS We demonstrate that metagenomic sequence-based community analysis can complement existing efforts to monitor protists in Lake Mendota based on microscopy-based count surveys. We observed patterns of seasonal abundance in microeukaryotes in Lake Mendota that corroborated expectations from other systems, including high abundance of cryptophytes in winter and diatoms in fall and spring, but with much higher resolution than previous surveys. Our study identified long-term changes in the abundance of eukaryotic microbes and provided context for the known establishment of an invasive species that catalyzes a trophic cascade involving protists. Our findings are important for decoding potential long-term consequences of human interventions, including invasive species introduction. Video Abstract.
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Affiliation(s)
- Arianna I Krinos
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
- Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge, Woods Hole, MA, USA.
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Robert M Bowers
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robin R Rohwer
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin at Madison, Madison, WI, USA
| | - Tanja Woyke
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Frederik Schulz
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Yu Y, Li YP, Ren K, Hao X, Fru EC, Rønn R, Rivera WL, Becker K, Feng R, Yang J, Rensing C. A brief history of metal recruitment in protozoan predation. Trends Microbiol 2024; 32:465-476. [PMID: 38103995 DOI: 10.1016/j.tim.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023]
Abstract
Metals and metalloids are used as weapons for predatory feeding by unicellular eukaryotes on prokaryotes. This review emphasizes the role of metal(loid) bioavailability over the course of Earth's history, coupled with eukaryogenesis and the evolution of the mitochondrion to trace the emergence and use of the metal(loid) prey-killing phagosome as a feeding strategy. Members of the genera Acanthamoeba and Dictyostelium use metals such as zinc (Zn) and copper (Cu), and possibly metalloids, to kill their bacterial prey after phagocytosis. We provide a potential timeline on when these capacities first evolved and how they correlate with perceived changes in metal(loid) bioavailability through Earth's history. The origin of phagotrophic eukaryotes must have postdated the Great Oxidation Event (GOE) in agreement with redox-dependent modification of metal(loid) bioavailability for phagotrophic poisoning. However, this predatory mechanism is predicted to have evolved much later - closer to the origin of the multicellular metazoans and the evolutionary development of the immune systems.
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Affiliation(s)
- Yanshuang Yu
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuan-Ping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Kexin Ren
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiuli Hao
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Ernest Chi Fru
- Centre for Geobiology and Geochemistry, School of Earth and Ocean Sciences, Cardiff University, CF10 3AT Cardiff, UK
| | - Regin Rønn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Windell L Rivera
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Karsten Becker
- Friedrich Loeffler-Institute for Medical Microbiology, University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Renwei Feng
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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Fu Y, Qu Z, Wang Y, Sun P, Jiao N, Xu D. Biogeographical and biodiversity patterns of planktonic microeukaryotes along the tropical western to eastern Pacific Ocean transect revealed by metabarcoding. Microbiol Spectr 2024; 12:e0242423. [PMID: 38488393 PMCID: PMC10986530 DOI: 10.1128/spectrum.02424-23] [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: 06/12/2023] [Accepted: 03/02/2024] [Indexed: 04/06/2024] Open
Abstract
Microeukaryotic plankton (0.2-200 µm), which are morphologically and genetically highly diverse, play a crucial role in ocean productivity and carbon consumption. The Pacific Ocean (PO), one of the world's largest oligotrophic regions, remains largely unexplored in terms of the biogeography and biodiversity of microeukaryotes based on large-scale sampling. We investigated the horizontal distribution of microeukaryotes along a 16,000 km transect from the west to the east of the PO. The alpha diversity indices showed a distinct decreasing trend from west to east, which was highly correlated with water temperature. The microeukaryotic community, which was clustered into the western, central, and eastern PO groups, displayed a significant distance-decay relationship. Syndiniales, a lineage of parasitic dinoflagellates, was ubiquitously distributed along the transect and dominated the community in terms of both sequence and zero-radius operational taxonomic unit (ZOTU) proportions. The prevailing dominance of Syndiniales-affiliated ZOTUs and their close associations with dinoflagellates, diatoms, and radiolarians, as revealed by SparCC correlation analysis, suggested that parasitism may be an important trophic strategy in the surface waters of the PO. Geographical distance and temperature were the most important environmental factors that significantly correlated with community structure. Overall, our study sheds more light on the distribution pattern of both alpha and beta diversities of microeukaryotic communities and highlighted the importance of parasitisms by Syndiniales across the tropical PO.IMPORTANCEUnderstanding the biogeographical and biodiversity patterns of microeukaryotic communities is essential to comprehending their roles in biogeochemical cycling. In this study, planktonic microeukaryotes were collected along a west-to-east Pacific Ocean transect (ca. 16,000 km). Our study revealed that the alpha diversity indices were highly correlated with water temperature, and the microeukaryotic communities displayed a distinct geographical distance-driven pattern. The predominance of the parasitic dinoflagellate lineage Syndiniales and their close relationship with other microeukaryotic groups suggest that parasitism may be a crucial survival strategy for microeukaryotes in the surface waters of the Pacific Ocean. Our findings expand our understanding of the biodiversity and biogeographical pattern of microeukaryotes and highlight the significance of parasitic Syndiniales in the surface ocean.
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Affiliation(s)
- Yingjun Fu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Zhishuai Qu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Ying Wang
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ping Sun
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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Yuan H, Li L, Wang Y, Lin S. Succession of diversity, assembly mechanisms, and activities of the microeukaryotic community throughout Scrippsiella acuminata (Dinophyceae) bloom phases. HARMFUL ALGAE 2024; 134:102626. [PMID: 38705614 DOI: 10.1016/j.hal.2024.102626] [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: 09/08/2023] [Revised: 04/02/2024] [Accepted: 04/06/2024] [Indexed: 05/07/2024]
Abstract
Harmful algal bloom (HAB) is a rapidly expanding marine ecological hazard. Although numerous studies have been carried out about the ecological impact and the ecological mechanism of HAB outbreaks, few studies have comprehensively addressed the shifts of species composition, metabolic activity level, driving factors and community assembly mechanisms of microeukaryotic plankton in the course of the bloom event. To fill the gap of research, we conducted 18S ribosomal DNA and RNA sequencing during the initiation, development, sustenance and decline stages of a Scrippsiella acuminata (S. acuminata) bloom at the coastal sea of Fujian Province, China. We found that the bloom event caused a decrease in microeukaryotic plankton species diversity and increase in community homogeneity. Our results revealed that the RNA- and DNA-inferred communities were similar, but α-diversity was more dynamic in RNA- than in DNA-inferred communities. The main taxa with high projected metabolic activity (with RNA:DNA ratio as the proxy) during the bloom included dinoflagellates, Cercozoa, Chlorophyta, Protalveolata, and diatoms. The role of deterministic processes in microeukaryotic plankton community assembly increased during the bloom, but stochastic processes were always the dominant assembly mechanism throughout the bloom process. Our findings improve the understanding of temporal patterns, driving factors and assembly mechanisms underlying the microeukarytic plankton community in a dinoflagellate bloom.
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Affiliation(s)
- Huatao Yuan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, and Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361102, China; College of Fisheries, Observation and Research Station on Water Ecosystem in Danjiangkou Reservoir of Henan Province, Henan Normal University, Xinxiang 453007, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, and Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361102, China
| | - Yujie Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, and Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361102, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, and Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen 361102, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao 266000, Shandong, China; Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
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8
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Kajan K, Fuchs BM, Orlić S. Insight into planktonic protistan and fungal communities across the nutrient-depleted environment of the South Pacific Subtropical Gyre. Microbiol Spectr 2024; 12:e0301623. [PMID: 38334383 PMCID: PMC10913754 DOI: 10.1128/spectrum.03016-23] [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: 08/04/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
Ocean microorganisms constitute ~70% of the marine biomass, contribute to ~50% of the Earth's primary production, and play a vital role in global biogeochemical cycles. The marine heterotrophic and mixotrophic protistan and fungal communities have often been overlooked mainly due to limitations in morphological species identification. Despite the accumulation of studies on biogeographic patterns observed in microbial communities, our understanding of the abundance and distribution patterns within the microbial community of the largest subtropical gyre, the South Pacific Gyre (SPG), remains incomplete. Here, we investigated the diversity and vertical composition of protistan and fungal communities in the water column of the ultra-oligotrophic SPG. Our results showed apparent differences in protistan community diversity in the photic and aphotic regions. The entire protistan community diversity was significantly affected by temperature, salinity, oxygen, and nutrient concentrations, while the parasitic community diversity was also affected by chlorophyll a concentration. The parasitic protists were assigned to the class Syndiniales accounting for over 98% of the total parasitic protists, exhibiting higher relative sequence abundance along the water depth and displaying consistent patterns among different sampling stations. In contrast to the protistan community, the fungal community along the SPG primarily clustered based on the sampling station and pelagic zones. In particular, our study reveals a significant presence of parasitic protists and functionally diverse fungi in SPG and their potential impact on carbon cycling in the gyre.IMPORTANCEOur findings carry important implications for understanding the distribution patterns of the previously unrecognized occurrence of parasitic protists and functionally diverse fungi in the nutrient-limited South Pacific Gyre. In particular, our study reveals a significant presence of parasitic Syndiniales, predominantly abundant in the upper 300 m of the aphotic zone in the gyre, and a distinct presence of fungal communities in the aphotic zone at the central part of the gyre. These findings strongly suggest that these communities play a substantial role in yet insufficiently described microbial food web. Moreover, our research enhances our understanding of their contribution to the dynamics of the food webs in oligotrophic gyres and is valuable for projecting the ecological consequences of future climate warming.
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Affiliation(s)
- Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
| | - Bernhard M. Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
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9
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Thweatt JL, Harman CE, Araújo MN, Marlow JJ, Oliver GC, Sabuda MC, Sevgen S, Wilpiszeki RL. Chapter 6: The Breadth and Limits of Life on Earth. ASTROBIOLOGY 2024; 24:S124-S142. [PMID: 38498824 DOI: 10.1089/ast.2021.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Scientific ideas about the potential existence of life elsewhere in the universe are predominantly informed by knowledge about life on Earth. Over the past ∼4 billion years, life on Earth has evolved into millions of unique species. Life now inhabits nearly every environmental niche on Earth that has been explored. Despite the wide variety of species and diverse biochemistry of modern life, many features, such as energy production mechanisms and nutrient requirements, are conserved across the Tree of Life. Such conserved features help define the operational parameters required by life and therefore help direct the exploration and evaluation of habitability in extraterrestrial environments. As new diversity in the Tree of Life continues to expand, so do the known limits of life on Earth and the range of environments considered habitable elsewhere. The metabolic processes used by organisms living on the edge of habitability provide insights into the types of environments that would be most suitable to hosting extraterrestrial life, crucial for planning and developing future astrobiology missions. This chapter will introduce readers to the breadth and limits of life on Earth and show how the study of life at the extremes can inform the broader field of astrobiology.
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Affiliation(s)
- Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA. (Former)
| | - C E Harman
- Planetary Systems Branch, NASA Ames Research Center, Moffett Field, California, USA
| | - M N Araújo
- Biochemistry Department, University of São Paulo, São Carlos, Brazil
| | - Jeffrey J Marlow
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Gina C Oliver
- Department of Geology, San Bernardino Valley College, San Bernardino, California, USA
| | - Mary C Sabuda
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Serhat Sevgen
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Mersin, Turkey
- Blue Marble Space Institute of Science, Seattle, Washington, USA
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10
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Schaible MJ, Szeinbaum N, Bozdag GO, Chou L, Grefenstette N, Colón-Santos S, Rodriguez LE, Styczinski MJ, Thweatt JL, Todd ZR, Vázquez-Salazar A, Adams A, Araújo MN, Altair T, Borges S, Burton D, Campillo-Balderas JA, Cangi EM, Caro T, Catalano E, Chen K, Conlin PL, Cooper ZS, Fisher TM, Fos SM, Garcia A, Glaser DM, Harman CE, Hermis NY, Hooks M, Johnson-Finn K, Lehmer O, Hernández-Morales R, Hughson KHG, Jácome R, Jia TZ, Marlow JJ, McKaig J, Mierzejewski V, Muñoz-Velasco I, Nural C, Oliver GC, Penev PI, Raj CG, Roche TP, Sabuda MC, Schaible GA, Sevgen S, Sinhadc P, Steller LH, Stelmach K, Tarnas J, Tavares F, Trubl G, Vidaurri M, Vincent L, Weber JM, Weng MM, Wilpiszeki RL, Young A. Chapter 1: The Astrobiology Primer 3.0. ASTROBIOLOGY 2024; 24:S4-S39. [PMID: 38498816 DOI: 10.1089/ast.2021.0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The Astrobiology Primer 3.0 (ABP3.0) is a concise introduction to the field of astrobiology for students and others who are new to the field of astrobiology. It provides an entry into the broader materials in this supplementary issue of Astrobiology and an overview of the investigations and driving hypotheses that make up this interdisciplinary field. The content of this chapter was adapted from the other 10 articles in this supplementary issue and thus represents the contribution of all the authors who worked on these introductory articles. The content of this chapter is not exhaustive and represents the topics that the authors found to be the most important and compelling in a dynamic and changing field.
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Affiliation(s)
- Micah J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - G Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Luoth Chou
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
- Georgetown University, Washington DC, USA
| | - Natalie Grefenstette
- Santa Fe Institute, Santa Fe, New Mexico, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Stephanie Colón-Santos
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | - Laura E Rodriguez
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - M J Styczinski
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- University of Washington, Seattle, Washington, USA
| | - Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Zoe R Todd
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Alberto Vázquez-Salazar
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, California, USA
| | - Alyssa Adams
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
| | - M N Araújo
- Biochemistry Department, University of São Paulo, São Carlos, Brazil
| | - Thiago Altair
- Institute of Chemistry of São Carlos, Universidade de São Paulo, São Carlos, Brazil
- Department of Chemistry, College of the Atlantic, Bar Harbor, Maine, USA
| | | | - Dana Burton
- Department of Anthropology, George Washington University, Washington DC, USA
| | | | - Eryn M Cangi
- Laboratory for Atmospheric and Space Physics, University of Colorado Boulder, Boulder, Colorado, USA
| | - Tristan Caro
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado, USA
| | - Enrico Catalano
- Sant'Anna School of Advanced Studies, The BioRobotics Institute, Pisa, Italy
| | - Kimberly Chen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter L Conlin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Z S Cooper
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Theresa M Fisher
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Santiago Mestre Fos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amanda Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin, USA
| | - D M Glaser
- Arizona State University, Tempe, Arizona, USA
| | - Chester E Harman
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ninos Y Hermis
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Physics and Space Sciences, University of Granada, Granada, Spain
| | - M Hooks
- NASA Johnson Space Center, Houston, Texas, USA
| | - K Johnson-Finn
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
- Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Owen Lehmer
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Ricardo Hernández-Morales
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Kynan H G Hughson
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rodrigo Jácome
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Tony Z Jia
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
| | - Jeffrey J Marlow
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Jordan McKaig
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Veronica Mierzejewski
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Israel Muñoz-Velasco
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ceren Nural
- Istanbul Technical University, Istanbul, Turkey
| | - Gina C Oliver
- Department of Geology, San Bernardino Valley College, San Bernardino, California, USA
| | - Petar I Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Chinmayee Govinda Raj
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Mary C Sabuda
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - George A Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Serhat Sevgen
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Mersin, Turkey
| | - Pritvik Sinhadc
- BEYOND: Center For Fundamental Concepts in Science, Arizona State University, Arizona, USA
- Dubai College, Dubai, United Arab Emirates
| | - Luke H Steller
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Australia
| | - Kamil Stelmach
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - J Tarnas
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Frank Tavares
- Space Enabled Research Group, MIT Media Lab, Cambridge, Massachusetts, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Monica Vidaurri
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
- Department of Physics and Astronomy, Howard University, Washington DC, USA
| | - Lena Vincent
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | | | - Amber Young
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Northern Arizona University, Flagstaff, Arizona, USA
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11
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Han B, Shi R, Zhang S, Lian A, Kuang Z, Wu F, Huang L, Huang H. Responses of microeukaryotic community structure to a Phaeocystis globosa bloom in a semi-enclosed subtropical bay. MARINE ENVIRONMENTAL RESEARCH 2024; 195:106374. [PMID: 38277816 DOI: 10.1016/j.marenvres.2024.106374] [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: 10/13/2023] [Revised: 01/10/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024]
Abstract
The occurrence of Phaeocystis globosa, a harmful algal bloom species in Chinese coastal waters, has significant impacts on marine organisms and poses a threat to the safety of coastal nuclear power plants. Although previous studies have established a close association between P. globosa blooms and the bacterial community, the relationship between the microeukaryotic community and P. globosa blooms remains poorly understood. In this study, the variations in the microeukaryotic community resulting from a P. globosa bloom were analyzed using 18S rRNA gene amplicon sequencing. The results indicated that the diversity of the microeukaryotic community during the bloom phase was significantly higher than that during the dissipation phase. The microeukaryotic community compositions varied significantly between the two phases of the P. globosa bloom. During the bloom phase, the dominant microeukaryotic was Viridiplantae, which was then replaced by Dinoflagellata during the dissipation phase. Co-occurrence network analysis showed that the relationship among the microeukaryotic community during the bloom phase was more complex than that during the dissipation phase, and the keystone taxa varied as the bloom progressed. Additionally, microeukaryotic community assembly was primarily driven by stochastic processes during the bloom phase based on the β-nearest taxon distance, whereas it was driven by both deterministic processes and stochastic processes during the dissipation phase. Overall, our findings provide novel insight into the mechanisms and interactions involved in microeukaryotic community dynamics in environments disturbed by P. globosa blooms.
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Affiliation(s)
- Beibei Han
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China; Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Rongjun Shi
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Shufei Zhang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Anji Lian
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Zexing Kuang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Fengxia Wu
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Lingfeng Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China.
| | - Honghui Huang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.
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12
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He J, Huang Y, Li L, Lin S, Ma M, Wang Y, Lin S. Novel Plastid Genome Characteristics in Fugacium kawagutii and the Trend of Accelerated Evolution of Plastid Proteins in Dinoflagellates. Genome Biol Evol 2024; 16:evad237. [PMID: 38155596 PMCID: PMC10781511 DOI: 10.1093/gbe/evad237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023] Open
Abstract
Typical (peridinin-containing) dinoflagellates possess plastid genomes composed of small plasmids named "minicircles". Despite the ecological importance of dinoflagellate photosynthesis in corals and marine ecosystems, the structural characteristics, replication dynamics, and evolutionary forcing of dinoflagellate plastid genomes remain poorly understood. Here, we sequenced the plastid genome of the symbiodiniacean species Fugacium kawagutii and conducted comparative analyses. We identified psbT-coding minicircles, features previously not found in Symbiodiniaceae. The copy number of F. kawagutii minicircles showed a strong diel dynamics, changing between 3.89 and 34.3 copies/cell and peaking in mid-light period. We found that F. kawagutii minicircles are the shortest among all dinoflagellates examined to date. Besides, the core regions of the minicircles are highly conserved within genus in Symbiodiniaceae. Furthermore, the codon usage bias of the plastid genomes in Heterocapsaceae, Amphidiniaceae, and Prorocentraceae species are greatly influenced by selection pressure, and in Pyrocystaceae, Symbiodiniaceae, Peridiniaceae, and Ceratiaceae species are influenced by both natural selection pressure and mutation pressure, indicating a family-level distinction in codon usage evolution in dinoflagellates. Phylogenetic analysis using 12 plastid-encoded proteins and five nucleus-encoded plastid proteins revealed accelerated evolution trend of both plastid- and nucleus-encoded plastid proteins in peridinin- and fucoxanthin-dinoflagellate plastids compared to plastid proteins of nondinoflagellate algae. These findings shed new light on the structure and evolution of plastid genomes in dinoflagellates, which will facilitate further studies on the evolutionary forcing and function of the diverse dinoflagellate plastids. The accelerated evolution documented here suggests plastid-encoded sequences are potentially useful for resolving closely related dinoflagellates.
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Affiliation(s)
- Jiamin He
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yulin Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Sitong Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Minglei Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yujie Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
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13
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Ren K, Mo Y, Xiao P, Rønn R, Xu Z, Xue Y, Chen H, Rivera WL, Rensing C, Yang J. Microeukaryotic plankton evolutionary constraints in a subtropical river explained by environment and bacteria along differing taxonomic resolutions. ISME COMMUNICATIONS 2024; 4:ycae026. [PMID: 38559570 PMCID: PMC10980835 DOI: 10.1093/ismeco/ycae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024]
Abstract
Microeukaryotic plankton communities are keystone components for keeping aquatic primary productivity. Currently, variations in microeukaryotic plankton diversity have often been explained by local ecological factors but not by evolutionary constraints. We used amplicon sequencing of 100 water samples across five years to investigate the ecological preferences of the microeukaryotic plankton community in a subtropical riverine ecosystem. We found that microeukaryotic plankton diversity was less associated with bacterial abundance (16S rRNA gene copy number) than bacterial diversity. Further, environmental effects exhibited a larger influence on microeukaryotic plankton community composition than bacterial community composition, especially at fine taxonomic levels. The evolutionary constraints of microeukaryotic plankton community increased with decreasing taxonomic resolution (from 97% to 91% similarity levels), but not significant change from 85% to 70% similarity levels. However, compared with the bacterial community, the evolutionary constraints were shown to be more affected by environmental variables. This study illustrated possible controlling environmental and bacterial drivers of microeukaryotic diversity and community assembly in a subtropical river, thereby indirectly reflecting on the quality status of the water environment by providing new clues on the microeukaryotic community assembly.
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Affiliation(s)
- Kexin Ren
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yuanyuan Mo
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Peng Xiao
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- National and Local Joint Engineering Research Center for Ecological Treatment Technology of Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Regin Rønn
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Department of Biology, University of Copenhagen, Copenhagen DK2100, Denmark
| | - Zijie Xu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Xue
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Huihuang Chen
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Windell L Rivera
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Christopher Rensing
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Institute of Environmental Microbiology, College of Resources and the Environment, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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14
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Groussman RD, Blaskowski S, Coesel SN, Armbrust EV. MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes. Sci Data 2023; 10:926. [PMID: 38129449 PMCID: PMC10739892 DOI: 10.1038/s41597-023-02842-4] [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: 06/07/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data, resulting in taxonomic annotation of about half of eukaryotic environmental transcripts. Here, we introduce Marine Functional EukaRyotic Reference Taxa (MarFERReT), a marine microbial eukaryotic sequence library designed for use with taxonomic annotation of eukaryotic metatranscriptomes. We gathered 902 publicly accessible marine eukaryote genomes and transcriptomes and assessed their sequence quality and cross-contamination issues, selecting 800 validated entries for inclusion in MarFERReT. Version 1.1 of MarFERReT contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. The MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.
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Affiliation(s)
- R D Groussman
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA.
| | - S Blaskowski
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Molecular Engineering & Sciences Building 3946 W Stevens Way NE, Seattle, WA, 98195, USA
| | - S N Coesel
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA
| | - E V Armbrust
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA.
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15
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Alexander H, Hu SK, Krinos AI, Pachiadaki M, Tully BJ, Neely CJ, Reiter T. Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton. mBio 2023; 14:e0167623. [PMID: 37947402 PMCID: PMC10746220 DOI: 10.1128/mbio.01676-23] [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: 06/30/2023] [Accepted: 09/27/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers' efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.
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Affiliation(s)
- Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Sarah K. Hu
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Arianna I. Krinos
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge and Woods Hole, Massachusetts, USA
| | - Maria Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Benjamin J. Tully
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Christopher J. Neely
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Taylor Reiter
- Population Health and Reproduction, University of California, Davis, Davis, California, USA
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16
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Rozo-Montoya N, Bedoya-Urrego K, Alzate JF. Monitoring potentially pathogenic protists in sewage sludge using Metataxonomics. Food Waterborne Parasitol 2023; 33:e00210. [PMID: 37808003 PMCID: PMC10558727 DOI: 10.1016/j.fawpar.2023.e00210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/10/2023] Open
Abstract
Intestinal parasites continue to pose a significant threat to human health worldwide, particularly among children. Contaminated water and soil serve as major transmission vehicles for these parasites and intestinal protists are among the most prevalent parasites in both developed and developing nations. Traditionally, parasites have been studied using human or animal fecal samples, while studying them in environmental samples has been challenging due to technical limitations. However, advancements in Next-Generation Sequencing (NGS) and bioinformatic approaches now enable the detection of parasite DNA in environmental samples. In this study, we applied a metataxonomic and phylogenetic strategy to detect and classify DNA of protists present in sewage sludge from two major cities in Colombia: Medellin and Cali. We successfully detected several human pathogenic parasites including Giardia intestinalis, Entamoeba histolytica, and Blastocystis sp., among other protists, in all sludge samples examined. We also investigated the entry and exit of parasite DNA from the San Fernando wastewater treatment plant (WWTP). We observed a higher number of parasite DNA sequences in the plant's influent wastewater, but we also detected the discharge of DNA from pathogenic parasites in both effluent waters and biosolids.
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Affiliation(s)
- Nicolas Rozo-Montoya
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
| | - Katherine Bedoya-Urrego
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- Grupo Pediaciencias, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
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17
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Zhang Z, Li D, Xie R, Guo R, Nair S, Han H, Zhang G, Zhao Q, Zhang L, Jiao N, Zhang Y. Plastoquinone synthesis inhibition by tetrabromo biphenyldiol as a widespread algicidal mechanism of marine bacteria. THE ISME JOURNAL 2023; 17:1979-1992. [PMID: 37679430 PMCID: PMC10579414 DOI: 10.1038/s41396-023-01510-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/09/2023]
Abstract
Algae and bacteria have complex and intimate interactions in the ocean. Besides mutualism, bacteria have evolved a variety of molecular-based anti-algal strategies. However, limited by the unknown mechanism of synthesis and action of these molecules, these strategies and their global prevalence remain unknown. Here we identify a novel strategy through which a marine representative of the Gammaproteobacteria produced 3,3',5,5'-tetrabromo-2,2'-biphenyldiol (4-BP), that kills or inhibits diverse phytoplankton by inhibiting plastoquinone synthesis and its effect cascades to many other key metabolic processes of the algae. Through comparative genomic analysis between the 4-BP-producing bacterium and its algicidally inactive mutant, combined with gene function verification, we identified the gene cluster responsible for 4-BP synthesis, which contains genes encoding chorismate lyase, flavin-dependent halogenase and cytochrome P450. We demonstrated that in near in situ simulated algal blooming seawater, even low concentrations of 4-BP can cause changes in overall phytoplankton community structure with a decline in dinoflagellates and diatoms. Further analyses of the gene sequences from the Tara Oceans expeditions and 2750 whole genome sequences confirmed the ubiquitous presence of 4-BP synthetic genes in diverse bacterial members in the global ocean, suggesting that it is a bacterial tool potentially widely used in global oceans to mediate bacteria-algae antagonistic relationships.
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Affiliation(s)
- 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
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dehai Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Ruize Xie
- 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
| | - Ruoyu Guo
- 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
| | - 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
| | - Huan Han
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Guojian Zhang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. &A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. &A. Center, 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
| | - 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.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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18
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Renzi S, Nenciarini S, Bacci G, Cavalieri D. Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome. MICROBIOME RESEARCH REPORTS 2023; 3:2. [PMID: 38455081 PMCID: PMC10917621 DOI: 10.20517/mrr.2023.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 03/09/2024]
Abstract
Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association with their hosts. They are involved in the food industry and pharmaceutical production, but they can also cause diseases in other organisms, making the understanding of their biology mandatory. The ongoing loss of biodiversity due to overexploitation of environmental resources is a growing concern in many countries. Therefore, it becomes crucial to understand the ecology and evolutionary history of these organisms to systematically classify them. To achieve this, it is essential that our knowledge of the mycobiota reaches a level similar to that of the bacterial communities. To overcome the existing challenges in the study of fungal communities, the first step should be the establishment of standardized techniques for the correct identification of species, even from complex matrices, both in wet lab practices and in bioinformatic tools.
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Affiliation(s)
| | | | | | - Duccio Cavalieri
- Correspondence to: Prof. Duccio Cavalieri, Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino 50019, Italy. E-mail:
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19
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Ma M, Yang W, Chen H, Ke W, Gong Y, Hu Q. Transcriptional profile reveals the physiological responses to prey availability in the mixotrophic chrysophyte Poterioochromonas malhamensis. Front Microbiol 2023; 14:1173541. [PMID: 37860135 PMCID: PMC10582637 DOI: 10.3389/fmicb.2023.1173541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
Mixotrophic flagellates, which have diverse nutritional modes and play important roles in connecting the microbial loop with the classical food chain, are ideal models to study the mechanisms of adaptation between different nutritional modes in protists. In their natural ecosystems, mixotrophic flagellates may encounter microalgal prey of different digestibility, which may affect the carbon flow. To date, a molecular biological view of the metabolic processes in the mixotrophic flagellate Poterioochromonas malhamensis during nutritional adaptation and feeding on microalgal prey of different digestibility is still lacking. Accordingly, this study focused on the gene expression differences in P. malhamensis under autotrophy, being fed by the digestible microalga Chlorella sorokiniana GT-1, and being fed by the indigestible microalga C. sorokiniana CMBB-146. Results showed that the growth rate of P. malhamensis under autotrophy was much lower than that when fed by digestible microalgae. Addition of C. sorokiniana CMBB-146 could only increase the growth rate of P. malhamensis in the first 3 days, but the cell concentration of P. malhamensis started to decrease gradually after 4 days. Compared to autotrophic P. malhamensis, total 6,583 and 3,510 genes were significantly and differentially expressed in P. malhamensis fed by digestible microalgae and indigestible microalgae, respectively. Compared to autotrophic cells, genes related to the ribosome, lysosome, glycolysis, gluconeogenesis, TCA cycle, β-oxidation, duplication, and β-1,3-glucan in P. malhamensis grazing on digestible prey were up-regulated, while genes related to light harvesting and key enzymes referring to chlorophyll were down-regulated. Genes related to apoptosis and necrosis in P. malhamensis were up-regulated after grazing on indigestible microalgae compared to the autotrophic group, which we suggest is associated with the up-regulation of genes related to lysosome enzymes. This study provides abundant information on the potential intracellular physiological responses of P. malhamensis during the process of nutritional adaptation.
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Affiliation(s)
- Mingyang Ma
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Wentao Yang
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Hong Chen
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Wanwan Ke
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yingchun Gong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Qiang Hu
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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20
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Wutkowska M, Vader A, Logares R, Pelletier E, Gabrielsen TM. Linking extreme seasonality and gene expression in Arctic marine protists. Sci Rep 2023; 13:14627. [PMID: 37669980 PMCID: PMC10480425 DOI: 10.1038/s41598-023-41204-3] [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: 02/27/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023] Open
Abstract
At high latitudes, strong seasonal differences in light availability affect marine organisms and regulate the timing of ecosystem processes. Marine protists are key players in Arctic aquatic ecosystems, yet little is known about their ecological roles over yearly cycles. This is especially true for the dark polar night period, which up until recently was assumed to be devoid of biological activity. A 12 million transcripts catalogue was built from 0.45 to 10 μm protist assemblages sampled over 13 months in a time series station in an Arctic fjord in Svalbard. Community gene expression was correlated with seasonality, with light as the main driving factor. Transcript diversity and evenness were higher during polar night compared to polar day. Light-dependent functions had higher relative expression during polar day, except phototransduction. 64% of the most expressed genes could not be functionally annotated, yet up to 78% were identified in Arctic samples from Tara Oceans, suggesting that Arctic marine assemblages are distinct from those from other oceans. Our study increases understanding of the links between extreme seasonality and biological processes in pico- and nanoplanktonic protists. Our results set the ground for future monitoring studies investigating the seasonal impact of climate change on the communities of microbial eukaryotes in the High Arctic.
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Affiliation(s)
- Magdalena Wutkowska
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway.
- Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway.
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia.
| | - Anna Vader
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Catalonia, Spain
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Tove M Gabrielsen
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway
- Department of Natural Sciences, University of Agder, Kristiansand, Norway
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21
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Weisse T, Scheffel U, Stadler P. Functional ecology of planktonic ciliates: Measuring mortality rates in response to starvation. J Eukaryot Microbiol 2023; 70:e12969. [PMID: 36825816 PMCID: PMC10952899 DOI: 10.1111/jeu.12969] [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: 11/11/2022] [Revised: 01/24/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023]
Abstract
Population dynamics of aquatic ciliates are controlled "bottom-up" via food supply and "top-down" by grazing and parasitism. While intrinsic growth rates of ciliates under saturating food conditions have been studied in some detail, mortality rates induced by starvation have received little attention thus far. To this end, we examined the response of three algivorous freshwater ciliate species to starvation using three different optical methods. Two of these methods, i.e. ciliate mortality rates (δ) estimated from (i) numerical response experiments and (ii) the rate of decline (ROD) in cell numbers, investigated the response of the ciliate population using conventional light microscopy. The third method, imaging cytometry using a FlowCAM instrument, monitored single cells during the starvation experiment. Like light microscopy, the FlowCAM approach estimated δ based on ROD in the experimental containers. However, imaging cytometry also measured the relative cellular chlorophyll a content in the ciliates' food vacuoles as a proxy for the nutritional status of the cells. The linear decline of the cellular chl. a yielded an independent estimate of δ that was similar to δ calculated from ROD. Additionally, the FlowCAM measurements revealed a high degree of phenotypic plasticity of the ciliates when exposed to starvation.
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Affiliation(s)
- Thomas Weisse
- Research Department for LimnologyUniversity of InnsbruckMondseeAustria
| | - Ulrike Scheffel
- Research Department for LimnologyUniversity of InnsbruckMondseeAustria
| | - Peter Stadler
- Research Department for LimnologyUniversity of InnsbruckMondseeAustria
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22
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Obiol A, López-Escardó D, Salomaki ED, Wiśniewska MM, Forn I, Sà E, Vaqué D, Kolísko M, Massana R. Gene expression dynamics of natural assemblages of heterotrophic flagellates during bacterivory. MICROBIOME 2023; 11:134. [PMID: 37322519 PMCID: PMC10268365 DOI: 10.1186/s40168-023-01571-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Marine heterotrophic flagellates (HF) are dominant bacterivores in the ocean, where they represent the trophic link between bacteria and higher trophic levels and participate in the recycling of inorganic nutrients for regenerated primary production. Studying their activity and function in the ecosystem is challenging since most of the HFs in the ocean are still uncultured. In the present work, we investigated gene expression of natural HF communities during bacterivory in four unamended seawater incubations. RESULTS The most abundant species growing in our incubations belonged to the taxonomic groups MAST-4, MAST-7, Chrysophyceae, and Telonemia. Gene expression dynamics were similar between incubations and could be divided into three states based on microbial counts, each state displaying distinct expression patterns. The analysis of samples where HF growth was highest revealed some highly expressed genes that could be related to bacterivory. Using available genomic and transcriptomic references, we identified 25 species growing in our incubations and used those to compare the expression levels of these specific genes. Video Abstract CONCLUSIONS: Our results indicate that several peptidases, together with some glycoside hydrolases and glycosyltransferases, are more expressed in phagotrophic than in phototrophic species, and thus could be used to infer the process of bacterivory in natural assemblages.
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Affiliation(s)
- Aleix Obiol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain.
| | - David López-Escardó
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Eric D Salomaki
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Monika M Wiśniewska
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Irene Forn
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Elisabet Sà
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain.
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23
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Kong H, Yang EJ, Jiao N, Lee Y, Jung J, Cho KH, Moon JK, Kim JH, Xu D. RNA outperforms DNA-based metabarcoding in assessing the diversity and response of microeukaryotes to environmental variables in the Arctic Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162608. [PMID: 36871742 DOI: 10.1016/j.scitotenv.2023.162608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The Arctic Ocean (AO) has a harsh environment characterized by low temperatures, extensive ice coverage, and periodic freezing and melting of sea ice, which has provided diverse habitats for microorganisms. Prior studies primarily focused on microeukaryote communities in the upper water or sea ice based on environmental DNA, leaving the composition of active microeukaryotes in the diverse AO environments largely unknown. This study provided a vertical assessment of microeukaryote communities in the AO from snow and ice to sea water at a depth of 1670 m using high-throughput sequencing of co-extracted DNA and RNA. RNA extracts depicted microeukaryote community structure and intergroup correlations more accurately and responded more sensitively to environmental conditions than those derived from DNA. Using RNA:DNA ratios as a proxy for relative activity of major taxonomic groups, the metabolic activities of major microeukaryote groups were determined along depth. Analysis of co-occurrence networks showed that parasitism between Syndiniales and dinoflagellates/ciliates in the deep ocean may be significant. This study increased our knowledge of the diversity of active microeukaryote communities and highlighted the importance of using RNA-based sequencing over DNA-based sequencing to examine the relationship between microeukaryote assemblages and the responses of microeukaryotes to environmental variables in the AO.
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Affiliation(s)
- Hejun Kong
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Eun-Jin Yang
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Youngju Lee
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jinyoung Jung
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Kyoung-Ho Cho
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jong-Kuk Moon
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jee-Hoon Kim
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.
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24
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Krinos AI, Cohen NR, Follows MJ, Alexander H. Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly. BMC Bioinformatics 2023; 24:74. [PMID: 36869298 PMCID: PMC9983209 DOI: 10.1186/s12859-022-05121-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/21/2022] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. RESULTS Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach. CONCLUSION We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.
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Affiliation(s)
- Arianna I Krinos
- MIT-WHOI Joint Program in Oceanography and Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA. .,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA. .,Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Natalie R Cohen
- Skidaway Institute of Oceanography, University of Georgia, Savannah, GA, USA
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Harriet Alexander
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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25
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Full-Length Transcriptome Analysis of the Ichthyotoxic Harmful Alga Heterosigma akashiwo (Raphidophyceae) Using Single-Molecule Real-Time Sequencing. Microorganisms 2023; 11:microorganisms11020389. [PMID: 36838354 PMCID: PMC9959365 DOI: 10.3390/microorganisms11020389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
The raphidophyte Heterosigma akashiwo is a harmful algal species. The bloom of this organism has been associated with the massive mortality of fish in many coastal waters. To investigate the molecular mechanism of H. akashiwo blooms, having a reliable reference transcriptome of this species is essential. Therefore, in this study, a full-length transcriptome of H. akashiwo was obtained by single-molecule real-time sequencing. In total, 45.44 Gb subread bases were generated, and 16,668 unigenes were obtained after the sequencing data processing. A total of 8666 (52.00%) unigenes were successfully annotated using seven public databases. Among them, mostly phosphorus and nitrogen metabolism genes were detected. Moreover, there were 300 putative transcription factors, 4392 putative long non-coding RNAs, and 7851 simple sequence repeats predicted. This study provides a valuable reference transcriptome for understanding how H. akashiwo blooms at a molecular level.
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Guo Y, Zhang A, Qin C, Yu G, Ma H. Community assembly patterns and processes of microbiome responses to habitats and Mytilopsis sallei invasion in the tidal zones of the Pearl River Estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159675. [PMID: 36280051 DOI: 10.1016/j.scitotenv.2022.159675] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/10/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
The sustainability of estuarine ecosystem functions depends on the stabilization of microbial ecological processes. However, due to the unique and variable habitat characteristics of estuarine areas, in-depth studies on ecological processes such as the spatial distribution and assembly patterns of microbial community structure are lacking. As methods to elucidate this structure, we used 16S rDNA, 18S rDNA and ITS sequencing technologies to study the composition, diversity, spatial pattern and aggregation mechanism of the bacterial, protist and fungal communities in the tidal zones of the Pearl River Estuary (PRETZ). The abundance of bacterial communities was much higher than that of protists and fungi, and the spatial pattern was obvious in PRETZ. The application of neutral and null models revealed the assembly process of three microbial communities dominated by stochastic processes. Among the stochastic processes, undominated processes (64.03 %, 62.45 %, and 59.29 %) were the most critical processes in the assembly of bacterial, fungal and protist communities. Meanwhile, environmental variables, geographic locations, and biological factors were associated with the composition and assembly of bacterial, protist, and fungal communities. Among the environmental variables, dissolved oxygen and salinity were the main predictors that jointly affected the differences in the community structure of the three microorganisms, and geographic location was the second predictor affecting the community structure of the three microorganisms and had a more pronounced effect on the diversity and network structure of the bacterial and fungal communities. However, biological factors exerted a weaker effect on the microbial community structure than spatial factors and only affected bacteria and protists; the invasive species Mytilopsis sallei only affected the process of protist community assembly. In addition, environmental variables affected the relative importance of stochastic processes. In summary, the formation of microbial communities in the PRETZ was affected by random processes, environmental variables, geographic location, and invasive species.
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Affiliation(s)
- Yu Guo
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China; Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China; Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, China
| | - Ankai Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chuanxin Qin
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China; Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China; Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, China.
| | - Gang Yu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Hongmei Ma
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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27
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Li LJ, Lin C, Huang XR, An XL, Li WJ, Su JQ, Zhu YG. Characterizing potential pathogens from intracellular bacterial community of protists in wastewater treatment plants. ENVIRONMENT INTERNATIONAL 2023; 171:107723. [PMID: 36584423 DOI: 10.1016/j.envint.2022.107723] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/25/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Protists are a trophically diverse and biogeochemically significant component of water environments and are widely reported as hosts of bacteria. However, the potential role of protists in wastewater treatment plants (WWTPs) as reservoirs for human pathogens does not appear to have received adequate attention. Here, a combination of fluorescence-activated cell sorting and Illumina sequencing was applied to characterize the dynamics of the internalized bacterial community of the enriched protists from the influents and effluents of five WWTPs. The results showed that Proteobacteria (mainly Betaproteobacteria) dominate the intracellular bacterial communities of protists in both influents and effluents of WWTPs, accounting for 72.6% of the total intracellular bacterial communities. The most frequently detected genus was Sulfuricurvum in the influent samples, Chryseobacterium and Pseudomonas were most prevalent in the effluent samples. Compared with the influents, a more diverse and abundant intracellular bacterial community was observed in the effluents. Moreover, the potential intracellular bacterial pathogens were 26 times higher in effluents than in influents, with Pseudomonas fluorescens and Pseudomonas putida significantly enriched in effluents. This work provides insights into the dynamics of bacterial communities and potential pathogens harbored by protists in the influents and effluents from WWTPs, contributing to the improved evaluation of biosafety in WWTPs.
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Affiliation(s)
- Li-Juan Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Chenshuo Lin
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xin-Rong Huang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Wen-Jing Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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28
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Li T, Liu G, Yuan H, Chen J, Lin X, Li H, Yu L, Wang C, Li L, Zhuang Y, Senjie L. Eukaryotic plankton community assembly and influencing factors between continental shelf and slope sites in the northern South China Sea. ENVIRONMENTAL RESEARCH 2023; 216:114584. [PMID: 36270532 DOI: 10.1016/j.envres.2022.114584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/11/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Eukaryotic plankton are pivotal members of marine ecosystems playing crucial roles in marine food webs and biogeochemical cycles. However, understanding the patterns and drivers of their community assembly remains a grand challenge. A study was conducted in the northern South China Sea (SCS) to address this issue. Here, 49 samples were collected and size-fractionated from discrete depths at continental shelf and continental slope in the northern SCS over a diel cycle. From high throughput sequencing of the 18S rDNA gene V4 region, 2463 operational taxonomic units (OTUs) were retrieved. Alveolata and Opisthokonta overwhelmingly dominated the assemblages in the abundance (44.76%, 31.08%) and species richness (59%, 12%). Biodiversity was higher in the slope than the shelf and increased with depth. Temperature and salinity appeared to be the most important deterministic drivers of taxon composition. Community structure was influenced by multiple factors in the importance order of: environmental factors (temperature + salinity) > spatial factor > water depth > sampling time. Furthermore, the neutral model explained more variations in the smaller-sized (0.22-3 μm) community (24%) than larger-sized (3-200 μm) community (16%) but generally explained less variations than did deterministic processes. Additionally, our data indicated that the larger plankton might be more environmentally filtered and less plastic whereas the smaller plankton had stronger dispersal ability. This study sheds light on the differential contributions of the deterministic process and stochastic process and complexities of assembly mechanisms in shaping the community assembly of micro-nano and pico-eukaryotic biospheres in a subtropical ocean.
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Affiliation(s)
- Tangcheng Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, 515063, China
| | - Guilin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, 266555, China
| | - Huatao Yuan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Jianwei Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, 266555, China; Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Hongfei Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Cong Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yunyun Zhuang
- Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Lin Senjie
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Department of Marine Sciences, University of Connecticut, Groton, CT, USA.
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Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes. mSystems 2022; 7:e0059522. [PMID: 36448813 PMCID: PMC9765425 DOI: 10.1128/msystems.00595-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Long-read sequencing offers the potential to improve metagenome assemblies and provide more robust assessments of microbial community composition and function than short-read sequencing. We applied Pacific Biosciences (PacBio) CCS (circular consensus sequencing) HiFi shotgun sequencing to 14 marine water column samples and compared the results with those for short-read metagenomes from the corresponding environmental DNA samples. We found that long-read metagenomes varied widely in quality and biological information. The community compositions of the corresponding long- and short-read metagenomes were frequently dissimilar, suggesting higher stochasticity and/or bias associated with PacBio sequencing. Long reads provided few improvements to the assembly qualities, gene annotations, and prokaryotic metagenome-assembled genome (MAG) binning results. However, only long reads produced high-quality eukaryotic MAGs and contigs containing complete zooplankton marker gene sequences. These results suggest that high-quality long-read metagenomes can improve marine community composition analyses and provide important insight into eukaryotic phyto- and zooplankton genetics, but the benefits may be outweighed by the inconsistent data quality. IMPORTANCE Ocean microbes provide critical ecosystem services, but most remain uncultivated. Their communities can be studied through shotgun metagenomic sequencing and bioinformatic analyses, including binning draft microbial genomes. However, most sequencing to date has been done using short-read technology, which rarely yields genome sequences of key microbes like SAR11. Long-read sequencing can improve metagenome assemblies but is hampered by technological shortcomings and high costs. In this study, we compared long- and short-read sequencing of marine metagenomes. We found a wide range of long-read metagenome qualities and minimal improvements to microbiome analyses. However, long reads generated draft genomes of eukaryotic algal species and provided full-length marker gene sequences of zooplankton species, including krill and copepods. These results suggest that long-read sequencing can provide greater genetic insight into the wide diversity of eukaryotic phyto- and zooplankton that interact as part of and with the marine microbiome.
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Da Silva O, Ayata SD, Ser-Giacomi E, Leconte J, Pelletier E, Fauvelot C, Madoui MA, Guidi L, Lombard F, Bittner L. Genomic differentiation of three pico-phytoplankton species in the Mediterranean Sea. Environ Microbiol 2022; 24:6086-6099. [PMID: 36053818 PMCID: PMC10087736 DOI: 10.1111/1462-2920.16171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 08/09/2022] [Indexed: 01/12/2023]
Abstract
For more than a decade, high-throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species-scale as well as their major speciation mechanisms. An increasing number of data obtained from global scale sampling campaigns is becoming publicly available, and we postulate that metagenomic data could contribute to deciphering the processes shaping protist genomic differentiation in the marine realm. As a proof of concept, we developed a findable, accessible, interoperable and reusable (FAIR) pipeline and focused on the Mediterranean Sea to study three a priori abundant protist species: Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata. We compared the genomic differentiation of each species in light of geographic, environmental and oceanographic distances. We highlighted that isolation-by-environment shapes the genomic differentiation of B. prasinos, whereas P. cordata is impacted by geographic distance (i.e. isolation-by-distance). At present time, the use of metagenomics to accurately estimate the genomic differentiation of protists remains challenging since coverages are lower compared to traditional population surveys. However, our approach sheds light on ecological and evolutionary processes occurring within natural marine populations and paves the way for future protist population metagenomic studies.
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Affiliation(s)
- Ophélie Da Silva
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Sakina-Dorothée Ayata
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Sorbonne Université, UMR 7159 CNRS-IRD-MNHN, LOCEAN-IPSL, Paris, France
| | - Enrico Ser-Giacomi
- Sorbonne Université, UMR 7159 CNRS-IRD-MNHN, LOCEAN-IPSL, Paris, France.,Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jade Leconte
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Cécile Fauvelot
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Institut de Recherche pour le Développement (IRD), UMR ENTROPIE, Nouméa, New Caledonia
| | - Mohammed-Amin Madoui
- Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
| | - Lionel Guidi
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Fabien Lombard
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Institut Universitaire de France (IUF), Paris, France
| | - Lucie Bittner
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Institut Universitaire de France (IUF), Paris, France
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31
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Ismail KA, Al Shehhi MR. Upwelling and nutrient dynamics in the Arabian Gulf and sea of Oman. PLoS One 2022; 17:e0276260. [PMID: 36269773 PMCID: PMC9586346 DOI: 10.1371/journal.pone.0276260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 10/03/2022] [Indexed: 11/18/2022] Open
Abstract
This study demonstrates the vertical and horizontal distribution of nutrients and the seasonal response of nutrients to upwelling in the Arabian Gulf and the Sea of Oman. Thus, monthly data on nitrate, phosphate, and silicate are obtained from the World Ocean Atlas 2018 (WOA), as well as estimates of coastal and curl driven upwelling in both regions. The results of the study indicate that the Sea of Oman's surface and deep waters contained higher concentrations of nutrients than the Arabian Gulf by 80%. In addition, both regions have exhibited a general increase in the vertical distribution of nutrients as the depth increases. Among the aforementioned nutrients, nitrate is found to be a more limiting nutrient for phytoplankton growth than phosphate as the nitrate-to-phosphate ratios (N:P) in surface waters are lower (≤ 4.6:1) than the Redfield ratio (16:1). As for the upwelling, curl-driven upwelling accounts for more than half of the total upwelling in both regions, and both play an important role in nutrient transport. Thus, nutrients are upwelled from the subsurface to the mixed layer at a rate of 50% in the Oman Sea from 140 m to 20 m during the summer and to 40 m during the winter. Similarly, the Arabian Gulf shows 50% transport for nitrates, but 32% for phosphates, from 20 m to 5-10 m. However, due to the abundance of diatoms at the surface of the Arabian Gulf, the surface silicate content is 30% higher than that of the deeper waters.
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Affiliation(s)
- Kaltham Abbas Ismail
- Civil Infrastructure and Environmental Engineering, Khalifa University, Abu Dhabi, UAE
| | - Maryam R. Al Shehhi
- Civil Infrastructure and Environmental Engineering, Khalifa University, Abu Dhabi, UAE
- * E-mail:
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32
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Zha Y, Chong H, Yang P, Ning K. Microbial Dark Matter: from Discovery to Applications. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:867-881. [PMID: 35477055 PMCID: PMC10025686 DOI: 10.1016/j.gpb.2022.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/28/2021] [Accepted: 03/22/2022] [Indexed: 01/12/2023]
Abstract
With the rapid increase of the microbiome samples and sequencing data, more and more knowledge about microbial communities has been gained. However, there is still much more to learn about microbial communities, including billions of novel species and genes, as well as countless spatiotemporal dynamic patterns within the microbial communities, which together form the microbial dark matter. In this work, we summarized the dark matter in microbiome research and reviewed current data mining methods, especially artificial intelligence (AI) methods, for different types of knowledge discovery from microbial dark matter. We also provided case studies on using AI methods for microbiome data mining and knowledge discovery. In summary, we view microbial dark matter not as a problem to be solved but as an opportunity for AI methods to explore, with the goal of advancing our understanding of microbial communities, as well as developing better solutions to global concerns about human health and the environment.
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Affiliation(s)
- Yuguo Zha
- MOE Key Laboratory of Molecular Biophysics, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hui Chong
- MOE Key Laboratory of Molecular Biophysics, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Pengshuo Yang
- MOE Key Laboratory of Molecular Biophysics, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Kang Ning
- MOE Key Laboratory of Molecular Biophysics, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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33
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Hu R, Liu S, Saleem M, Xiong Z, Zhou Z, Luo Z, Shu L, He Z, Wang C. Environmentally‐induced reconstruction of microbial communities alters particulate carbon flux of deep chlorophyll maxima in the South China sea. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ruiwen Hu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Songfeng Liu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Muhammad Saleem
- Department of Biological Sciences Alabama State University Montgomery AL USA
| | - Zhiyao Xiong
- School of Marine Sciences Sun Yat‐sen University Zhuhai
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Zhiwen Luo
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Longfei Shu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Zhili He
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
- College of Agronomy Hunan Agricultural University Changsha China
| | - Cheng Wang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
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34
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Protist Diversity and Metabolic Strategy in Freshwater Lakes Are Shaped by Trophic State and Watershed Land Use on a Continental Scale. mSystems 2022; 7:e0031622. [PMID: 35730947 PMCID: PMC9426515 DOI: 10.1128/msystems.00316-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Protists play key roles in aquatic food webs as primary producers, predators, nutrient recyclers, and symbionts. However, a comprehensive view of protist diversity in freshwaters has been challenged by the immense environmental heterogeneity among lakes worldwide. We assessed protist diversity in the surface waters of 366 freshwater lakes across a north temperate to subarctic range covering nearly 8.4 million km2 of Canada. Sampled lakes represented broad gradients in size, trophic state, and watershed land use. Hypereutrophic lakes contained the least diverse and most distinct protist communities relative to nutrient-poor lakes. Greater taxonomic variation among eutrophic lakes was mainly a product of heterotroph and mixotroph diversity, whereas phototroph assemblages were more similar under high-nutrient conditions. Overall, local physicochemical factors, particularly ion and nutrient concentrations, elicited the strongest responses in community structure, far outweighing the effects of geographic gradients. Despite their contrasting distribution patterns, obligate phototroph and heterotroph turnover was predicted by an overlapping set of environmental factors, while the metabolic plasticity of mixotrophs may have made them less predictable. Notably, protist diversity was associated with variation in watershed soil pH and agricultural crop coverage, pointing to human impact on the land-water interface that has not been previously identified in studies on smaller scales. Our study exposes the importance of both within-lake and external watershed characteristics in explaining protist diversity and biogeography, critical information for further developing an understanding of how freshwater lakes and their watersheds are impacted by anthropogenic stressors. IMPORTANCE Freshwater lakes are experiencing rapid changes under accelerated anthropogenic stress and a warming climate. Microorganisms underpin aquatic food webs, yet little is known about how freshwater microbial communities are responding to human impact. Here, we assessed the diversity of protists and their myriad ecological roles in lakes varying in size across watersheds experiencing a range of land use pressures by leveraging data from a continental-scale survey of Canadian lakes. We found evidence of human impact on protist assemblages through an association with lake trophic state and extending to agricultural activity and soil characteristics in the surrounding watershed. Furthermore, trophic state appeared to explain the distributions of phototrophic and heterotrophic protists in contrasting ways. Our findings highlight the vulnerability of lake ecosystems to increased land use and the importance of assessing terrestrial interfaces to elucidate freshwater ecosystem dynamics.
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35
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Kong WL, Machida RJ. Development of transcriptomics-based growth rate indices in two model eukaryotes and relevance to metatranscriptomic datasets. Mol Ecol Resour 2022; 22:2627-2639. [PMID: 35620942 PMCID: PMC9545445 DOI: 10.1111/1755-0998.13652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 05/17/2022] [Indexed: 11/29/2022]
Abstract
Growth rate estimation is important to understand the flow of energy and nutrient elements in an ecosystem, but it has remained challenging, especially on microscopic organisms. In this study, we propose four growth rate indices that use mRNA abundance ratios between nuclear and mitochondrial genes: (1) total nuclear and mitochondrial mRNA ratio (Nuc:Mito‐TmRNA); (2) nuclear and mitochondrial ribosomal protein mRNA ratio (Nuc:Mito‐RPmRNA); (3) gene ontology (GO) terms and total mitochondrial mRNA ratios; and (4) nuclear and mitochondrial specific gene mRNA ratio. We examine these proposed ratios using RNA‐Seq datasets of Daphnia magna, and Saccharomyces cerevisiae retrieved from the NCBI Short Read Archive. The results showed that both Nuc:Mito‐TmRNA and Nuc:Mito‐RPmRNA ratio indices showed significant correlations with the growth rate for both species. A large number of GO terms mRNA ratios showed significant correlations with the growth rate of S. cerevisiae. Lastly, we identified mRNA ratios of several specific nuclear and mitochondrial gene pairs that showed significant correlations. We foresee future implications for the proposed mRNA ratios used in metatranscriptome analyses to estimate the growth rate of communities and species.
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Affiliation(s)
- Wye-Lup Kong
- Biodiversity Program, International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ryuji J Machida
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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36
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Evolution of Phytoplankton as Estimated from Genetic Diversity. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10040456] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Phytoplankton are photosynthetic, single-celled organisms producing almost half of all oxygen on Earth and play a central role as prey for higher organisms, making them irreplaceable in the marine food web. As Global Change proceeds, imposing rapidly intensifying selection pressures, phytoplankton are forced to undergo evolution, local extinction, or redistribution, with potentially cascading effects throughout the marine ecosystem. Recent results from the field of population genetics display high levels of standing genetic diversity in natural phytoplankton populations, providing ample ‘evolutionary options’ and implying high adaptive potential to changing conditions. This potential for adaptive evolution is realized in several studies of experimental evolution, even though most of these studies investigate the evolution of only single strains. This, however, shows that phytoplankton not only evolve from standing genetic diversity, but also rely on de novo mutations. Recent global sampling campaigns show that the immense intraspecific diversity of phytoplankton in the marine ecosystem has been significantly underestimated, meaning we are only studying a minor portion of the relevant variability in the context of Global Change and evolution. An increased understanding of genomic diversity is primarily hampered by the low number of ecologically representative reference genomes of eukaryotic phytoplankton and the functional annotation of these. However, emerging technologies relying on metagenome and transcriptome data may offer a more realistic understanding of phytoplankton diversity.
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37
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Zhang X, Hu Y, Eme L, Maruyama S, Eveleigh RJ, Curtis BA, Sibbald SJ, Hopkins JF, Filloramo GV, van Wijk KJ, Archibald JM. TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets. STAR Protoc 2022; 3:101175. [PMID: 35243369 PMCID: PMC8857567 DOI: 10.1016/j.xpro.2022.101175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Various bioinformatics protocols have been developed for trimming the number of operational taxonomic units (OTUs) in phylogenetic datasets, but they typically require significant manual intervention. Here we present TreeTuner, a semiautomated pipeline that allows both coarse and fine-scale tuning of large protein sequence phylogenetic datasets via the minimization of OTU redundancy. TreeTuner facilitates preliminary investigation of such datasets as well as more rigorous downstream analysis of specific subsets of OTUs. For complete details on the use and execution of this protocol, please refer to Maruyama et al. (2013) and Sibbald et al. (2019).
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Affiliation(s)
- Xi Zhang
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Yining Hu
- Department of Computer Science, Western University, London, ON N6A 5B7, Canada
| | - Laura Eme
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Shinichiro Maruyama
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Robert J.M. Eveleigh
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Bruce A. Curtis
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Shannon J. Sibbald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Julia F. Hopkins
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Gina V. Filloramo
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Klaas J. van Wijk
- Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - John M. Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada
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38
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Wang W, Gao X, Ndayishimiye JC, Lara E, Lahr DJG, Qian H, Ren K, Chen H, Yang J. Population and molecular responses to warming in Netzelia tuberspinifera - An endemic and sensitive protist from East Asia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150897. [PMID: 34653464 DOI: 10.1016/j.scitotenv.2021.150897] [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: 08/01/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
With the effects of global warming becoming ever more obvious, biodiversity conservation is facing severe challenges. Currently, a deeper understanding the mechanisms of the effects of warming on sensitive species has become an important topic in aquatic biodiversity and ecological management. Our study first overcame the "challenge" for a sensitive indicator species (Netzelia tuberspinifera, an endemic testate amoeba species in East Asia) of culturing under laboratory conditions, and then explored its molecular response mechanisms to warming using transcriptomic analysis. Our data indicate that temperature mainly drove the geographical and seasonal variation of N. tuberspinifera populations. Transcriptomic results indicate that when the temperature is <25 °C, rising temperature triggers the biosynthesis of ribosomes; while the temperature is >25 °C, it triggers molecular processes related with cell division, test formation and general biomass increase. However, once the temperature exceeds 40 °C, N. tuberspinifera is unable to survive. Following from these results, the distribution of N. tuberspinifera might expand towards higher altitude or latitude regions under global warming. For the first time, our study showed direct evidence for sensitive protozoa species that presents a very narrow adaptation mechanism to local climate. Our work provides fundamental data for regional biodiversity conservation and scientific reference in subtropical and tropical waterbodies.
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Affiliation(s)
- Wenping Wang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaofei Gao
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Jean Claude Ndayishimiye
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Enrique Lara
- Real Jardın Botanico, CSIC, Plaza de Murillo 2, Madrid 28014, Spain
| | - Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Kexin Ren
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Huihuang Chen
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Weisse T, Montagnes DJS. Ecology of planktonic ciliates in a changing world: Concepts, methods, and challenges. J Eukaryot Microbiol 2021; 69:e12879. [PMID: 34877743 PMCID: PMC9542165 DOI: 10.1111/jeu.12879] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Plankton ecologists ultimately focus on forecasting, both applied and environmental outcomes. We review how appreciating planktonic ciliates has become central to these predictions. We explore the 350‐year‐old canon on planktonic ciliates and examine its steady progression, which has been punctuated by conceptual insights and technological breakthroughs. By reflecting on this process, we offer suggestions as to where future leaps are needed, with an emphasis on predicting outcomes of global warming. We conclude that in terms of climate change research: (i) climatic hotspots (e.g. polar oceans) require attention; (ii) simply adding ciliate measurements to zooplankton/phytoplankton‐based sampling programs is inappropriate; (iii) elucidating the rare biosphere's functional ecology requires culture‐independent genetic methods; (iv) evaluating genetic adaptation (microevolution) and population composition shifts is required; (v) contrasting marine and freshwaters needs attention; (vi) mixotrophy needs attention; (vii) laboratory and field studies must couple automated measurements and molecular assessment of functional gene expression; (viii) ciliate trophic diversity requires appreciation; and (ix) marrying gene expression and function, coupled with climate change scenarios is needed. In short, continued academic efforts and financial support are essential to achieve the above; these will lead to understanding how ciliates will respond to climate change, providing tools for forecasting.
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Affiliation(s)
- Thomas Weisse
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - David J S Montagnes
- Department of Evolution, Ecology, and Behaviour, University of Liverpool, Liverpool, UK
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Behera BK, Dehury B, Rout AK, Patra B, Mantri N, Chakraborty HJ, Sarkar DJ, Kaushik NK, Bansal V, Singh I, Das BK, Rao AR, Rai A. Metagenomics study in aquatic resource management: Recent trends, applied methodologies and future needs. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Resolving the microalgal gene landscape at the strain level: A novel hybrid transcriptome of Emiliania huxleyi CCMP3266. Appl Environ Microbiol 2021; 88:e0141821. [PMID: 34757817 DOI: 10.1128/aem.01418-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microalgae are key ecological players with a complex evolutionary history. Genomic diversity, in addition to limited availability of high-quality genomes, challenge studies that aim to elucidate molecular mechanisms underlying microalgal ecophysiology. Here, we present a novel and comprehensive transcriptomic hybrid approach to generate a reference for genetic analyses, and resolve the microalgal gene landscape at the strain level. The approach is demonstrated for a strain of the coccolithophore microalga Emiliania huxleyi, which is a species complex with considerable genome variability. The investigated strain is commonly studied as a model for algal-bacterial interactions, and was therefore sequenced in the presence of bacteria to elicit the expression of interaction-relevant genes. We applied complementary PacBio Iso-Seq full-length cDNA, and poly(A)-independent Illumina total RNA sequencing, which resulted in a de novo assembled, near complete hybrid transcriptome. In particular, hybrid sequencing improved the reconstruction of long transcripts and increased the recovery of full-length transcript isoforms. To use the resulting hybrid transcriptome as a reference for genetic analyses, we demonstrate a method that collapses the transcriptome into a genome-like dataset, termed "synthetic genome" (sGenome). We used the sGenome as a reference to visually confirm the robustness of the CCMP3266 gene assembly, to conduct differential gene expression analysis, and to characterize novel E. huxleyi genes. The newly-identified genes contribute to our understanding of E. huxleyi genome diversification, and are predicted to play a role in microbial interactions. Our transcriptomic toolkit can be implemented in various microalgae to facilitate mechanistic studies on microalgal diversity and ecology. Importance Microalgae are key players in the ecology and biogeochemistry of our oceans. Efforts to implement genomic and transcriptomic tools in laboratory studies involving microalgae suffer from the lack of published genomes. In the case of coccolithophore microalgae, the problem has long been recognized; the model species Emiliania huxleyi is a species complex with genomes composed of a core, and a large variable portion. To study the role of the variable portion in niche adaptation, and specifically in microbial interactions, strain-specific genetic information is required. Here we present a novel transcriptomic hybrid approach, and generated strain-specific genome-like information. We demonstrate our approach on an E. huxleyi strain that is co-cultivated with bacteria. By constructing a "synthetic genome", we generated comprehensive gene annotations that enabled accurate analyses of gene expression patterns. Importantly, we unveiled novel genes in the variable portion of E. huxleyi that play putative roles in microbial interactions.
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42
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Alacid E, Richards TA. A cell-cell atlas approach for understanding symbiotic interactions between microbes. Curr Opin Microbiol 2021; 64:47-59. [PMID: 34655935 DOI: 10.1016/j.mib.2021.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/23/2021] [Accepted: 09/01/2021] [Indexed: 01/04/2023]
Abstract
Natural environments are composed of a huge diversity of microorganisms interacting with each other to form complex functional networks. Our understanding of the operative nature of host-symbiont associations is limited because propagating such associations in a laboratory is challenging. The advent of single-cell technologies applied to, for example, animal cells and apicomplexan parasites has revolutionized our understanding of development and disease. Such cell atlas approaches generate maps of cell-specific processes and variations within cellular populations. These methods can now be combined with cellular-imaging so that interaction stage versus transcriptome state can be quantized for microbe-microbe interactions. We predict that the combination of these methods applied to the study of symbioses will transform our understanding of many ecological interactions, including those sampled directly from natural environments.
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Affiliation(s)
- Elisabet Alacid
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK.
| | - Thomas A Richards
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK.
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Burki F, Sandin MM, Jamy M. Diversity and ecology of protists revealed by metabarcoding. Curr Biol 2021; 31:R1267-R1280. [PMID: 34637739 DOI: 10.1016/j.cub.2021.07.066] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protists are the dominant eukaryotes in the biosphere where they play key functional roles. While protists have been studied for over a century, it is the high-throughput sequencing of molecular markers from environmental samples - the approach of metabarcoding - that has revealed just how diverse, and abundant, these small organisms are. Metabarcoding is now routine to survey environmental diversity, so data have rapidly accumulated from a multitude of environments and at different sampling scales. This mass of data has provided unprecedented opportunities to study the taxonomic and functional diversity of protists, and how this diversity is organised in space and time. Here, we use metabarcoding as a common thread to discuss the state of knowledge in protist diversity research, from technical considerations of the approach to important insights gained on diversity patterns and the processes that might have structured this diversity. In addition to these insights, we conclude that metabarcoding is on the verge of an exciting added dimension thanks to the maturation of high-throughput long-read sequencing, so that a robust eco-evolutionary framework of protist diversity is within reach.
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Affiliation(s)
- Fabien Burki
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden; Science For Life Laboratory, Uppsala University, 75236 Uppsala, Sweden.
| | - Miguel M Sandin
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden
| | - Mahwash Jamy
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden
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Zou K, Wang R, Xu S, Li Z, Liu L, Li M, Zhou L. Changes in protist communities in drainages across the Pearl River Delta under anthropogenic influence. WATER RESEARCH 2021; 200:117294. [PMID: 34102388 DOI: 10.1016/j.watres.2021.117294] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Drainages in the Pearl River Delta urban agglomeration (PRDUA) host vital aquatic ecosystems and face enormous pressures from human activities in one of the largest urban agglomerations in the world. Despite being crucial components of aquatic ecosystems, the interactions and assembly processes of the protistan community are rarely explored in areas with serious anthropogenic disturbance. To elucidate the mechanisms of these processes, we used environmental DNA sequencing of 18S rDNA to investigate the influence of environmental factors and species interactions on the protistan community and its assembly in drainages of the PRDUA during summer. The protistan community showed a high level of diversity and a marked spatial pattern in this region. Community assembly was driven primarily by stochastic processes based on the Sloan neutral community model, explaining 74.28%, 75.82%, 73.67%, 74.40% and 51.24% of community variations in the BJ (Beijiang), XJ (Xijiang), PRD (Pearl River Delta), PRE (Pearl River Estuary) areas and in total, respectively. Meanwhile, environmental variables including temperature, pH, dissolved oxygen, transparency, nutrients and land use were strongly correlated with the composition and assembly of the protistan community, explaining 40.40% of variation in the protistan community. Furthermore, the bacterial community was simultaneously analysed by the 16S rDNA sequencing. Co-occurrence network analysis revealed that species interactions within bacteria (81.41% positive) or protists (82.80% positive), and those between bacteria and protists (50% positive and 50% negative) impacted the protistan community assembly. In summary, stochastic processes dominated, whereas species interactions and environmental factors also played important roles in shaping the protistan communities in drainages across the PRDUA. This study provides insights into the ecological patterns, assembly processes and species interactions underlying protistan dynamics in urban aquatic ecosystems experiencing serious anthropogenic disturbance.
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Affiliation(s)
- Keshu Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Ruili Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Shannan Xu
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, China
| | - Zhuoying Li
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Li Liu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Min Li
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, China.
| | - Lei Zhou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China.
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45
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Bucchini F, Del Cortona A, Kreft Ł, Botzki A, Van Bel M, Vandepoele K. TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes. Nucleic Acids Res 2021; 49:e101. [PMID: 34197621 PMCID: PMC8464036 DOI: 10.1093/nar/gkab565] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 06/07/2021] [Accepted: 06/16/2021] [Indexed: 12/24/2022] Open
Abstract
Advances in high-throughput sequencing have resulted in a massive increase of RNA-Seq transcriptome data. However, the promise of rapid gene expression profiling in a specific tissue, condition, unicellular organism or microbial community comes with new computational challenges. Owing to the limited availability of well-resolved reference genomes, de novo assembled (meta)transcriptomes have emerged as popular tools for investigating the gene repertoire of previously uncharacterized organisms. Yet, despite their potential, these datasets often contain fragmented or contaminant sequences, and their analysis remains difficult. To alleviate some of these challenges, we developed TRAPID 2.0, a web application for the fast and efficient processing of assembled transcriptome data. The initial processing phase performs a global characterization of the input data, providing each transcript with several layers of annotation, comprising structural, functional, and taxonomic information. The exploratory phase enables downstream analyses from the web application. Available analyses include the assessment of gene space completeness, the functional analysis and comparison of transcript subsets, and the study of transcripts in an evolutionary context. A comparison with similar tools highlights TRAPID’s unique features. Finally, analyses performed within TRAPID 2.0 are complemented by interactive data visualizations, facilitating the extraction of new biological insights, as demonstrated with diatom community metatranscriptomes.
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Affiliation(s)
- François Bucchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Andrea Del Cortona
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Łukasz Kreft
- VIB Bioinformatics Core, VIB, 9052 Ghent, Belgium
| | | | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
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Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. Proc Natl Acad Sci U S A 2021; 118:2011038118. [PMID: 33547239 PMCID: PMC8017926 DOI: 10.1073/pnas.2011038118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Most organisms coordinate key biological events to coincide with the day/night cycle. These diel oscillations are entrained through the activity of light-sensitive photoreceptors that allow organisms to respond rapidly to changes in light exposure. In the ocean, the plankton community must additionally contend with dramatic changes in the quantity and quality of light over depth. Here, we show that the predominantly blue-light field in the open-ocean environment may have driven expansion of blue light-sensitive regulatory elements in open-ocean eukaryotic plankton derived from secondary and tertiary endosymbiosis. The diel transcription of genes encoding light-sensitive elements indicate that photosynthetic and heterotrophic marine protists respond to and anticipate fluctuating light conditions in the dynamic marine environment. The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment.
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47
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Schomaker RA, Dudycha JL. De novo transcriptome assembly of the green alga Ankistrodesmus falcatus. PLoS One 2021; 16:e0251668. [PMID: 33989339 PMCID: PMC8121315 DOI: 10.1371/journal.pone.0251668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/30/2021] [Indexed: 01/11/2023] Open
Abstract
Ankistrodesmus falcatus is a globally distributed freshwater chlorophyte that is a candidate for biofuel production, is used to study the effects of toxins on aquatic communities, and is used as food in zooplankton research. Each of these research fields is transitioning to genomic tools. We created a reference transcriptome for of A. falcatus using NextGen sequencing and de novo assembly methods including Trinity, Velvet-Oases, and EvidentialGene. The assembled transcriptome has a total of 17,997 contigs, an N50 value of 2,462, and a GC content of 64.8%. BUSCO analysis recovered 83.3% of total chlorophyte BUSCOs and 82.5% of the eukaryotic BUSCOs. A portion (7.9%) of these supposedly single-copy genes were found to have transcriptionally active, distinct duplicates. We annotated the assembly using the dammit annotation pipeline, resulting in putative functional annotation for 68.89% of the assembly. Using available rbcL sequences from 16 strains (10 species) of Ankistrodesmus, we constructed a neighbor-joining phylogeny to illustrate genetic distances of our A. falcatus strain to other members of the genus. This assembly will be valuable for researchers seeking to identify Ankistrodesmus sequences in metatranscriptomic and metagenomic field studies and in experiments where separating expression responses of zooplankton and their algal food sources through bioinformatics is important.
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Affiliation(s)
- Rachel A Schomaker
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States of America
| | - Jeffry L Dudycha
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States of America
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48
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Schoenle A, Hohlfeld M, Hermanns K, Mahé F, de Vargas C, Nitsche F, Arndt H. High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans. Commun Biol 2021; 4:501. [PMID: 33893386 PMCID: PMC8065057 DOI: 10.1038/s42003-021-02012-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/08/2021] [Indexed: 02/02/2023] Open
Abstract
Heterotrophic protists (unicellular eukaryotes) form a major link from bacteria and algae to higher trophic levels in the sunlit ocean. Their role on the deep seafloor, however, is only fragmentarily understood, despite their potential key function for global carbon cycling. Using the approach of combined DNA metabarcoding and cultivation-based surveys of 11 deep-sea regions, we show that protist communities, mostly overlooked in current deep-sea foodweb models, are highly specific, locally diverse and have little overlap to pelagic communities. Besides traditionally considered foraminiferans, tiny protists including diplonemids, kinetoplastids and ciliates were genetically highly diverse considerably exceeding the diversity of metazoans. Deep-sea protists, including many parasitic species, represent thus one of the most diverse biodiversity compartments of the Earth system, forming an essential link to metazoans.
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Affiliation(s)
- Alexandra Schoenle
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany.
| | - Manon Hohlfeld
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany
| | - Karoline Hermanns
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany
| | - Frédéric Mahé
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, Univ Montpellier, CIRAD, IRD, Montpellier SupAgro, Montpellier, France
| | - Colomban de Vargas
- CNRS, Sorbonne Université, Station Biologique de Roscoff, UMR7144, ECOMAP-Ecology of Marine Plankton, Roscoff, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara GOSEE, Paris, France
| | - Frank Nitsche
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany
| | - Hartmut Arndt
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany.
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49
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Meisner A, Snoek BL, Nesme J, Dent E, Jacquiod S, Classen AT, Priemé A. Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles. THE ISME JOURNAL 2021; 15:1207-1221. [PMID: 33408369 PMCID: PMC8115648 DOI: 10.1038/s41396-020-00844-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO2 pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO2 emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO2 production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.
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Affiliation(s)
- Annelein Meisner
- grid.4514.40000 0001 0930 2361Microbial Ecology, Department of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden ,grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark ,grid.418375.c0000 0001 1013 0288Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Present Address: Wageningen University & Research, Droevendaalsesteeg 4, Wageningen, The Netherlands
| | - Basten L. Snoek
- grid.5477.10000000120346234Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Joseph Nesme
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Elizabeth Dent
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Samuel Jacquiod
- grid.5613.10000 0001 2298 9313Agroécologie, AgroSup Dijon, INRAE Centre Dijon, Université de Bourgogne Franche-Comté, Dijon, France
| | - Aimée T. Classen
- grid.214458.e0000000086837370Ecology and Evolutionary Biology Department, University of Michigan, Ann Arbor, MI 48109 USA ,grid.59062.380000 0004 1936 7689The Gund Institute for Environment, University of Vermont, Burlington, VT USA ,grid.5254.60000 0001 0674 042XThe Center for Macroecology, Evolution and Climate, The University of Copenhagen, Copenhagen Ø, Denmark
| | - Anders Priemé
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XDepartment of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Øster Voldgade 10, 1350 Copenhagen, Denmark
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50
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Bhattacharjya R, Tiwari A, Marella TK, Bansal H, Srivastava S. New paradigm in diatom omics and genetic manipulation. BIORESOURCE TECHNOLOGY 2021; 325:124708. [PMID: 33487514 DOI: 10.1016/j.biortech.2021.124708] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Diatoms are one of the most heterogeneous eukaryotic plankton known for regulating earth's biogeochemical cycles and maintaining the marine ecosystems ever since the late Eocene epoch. The advent of multidisciplinary omics approach has both epitomized and revolutionized the nature of their chimeric genetic toolkit, ecophysiology, and metabolic adaptability as well as their interaction with other communities. In addition, advanced functional annotation of transcriptomic and proteomic data using cutting edge bioinformatics tools together with high-resolution genome-scale mathematical modeling has effectively proven as the catapult in solving genetic bottlenecks in microbial as well as diatom exploration. In this review, a corroborative summation of the robust work done in manipulating, engineering, and sequencing of the diatom genomes besides underpinning the holistic application of omics in transcription and translation has been discussed in order to shrewd their multifarious novel potential in the field of biotechnology and provide an insight into their dynamic evolutionary relevance.
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Affiliation(s)
- Raya Bhattacharjya
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
| | - Archana Tiwari
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India.
| | - Thomas Kiran Marella
- Algae Biomass Energy System Development Research Center (ABES), Tennodai, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Hina Bansal
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
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