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MacVittie S, Doroodian S, Alberto A, Sogin M. Microbiome depletion and recovery in the sea anemone, Exaiptasia diaphana, following antibiotic exposure. mSystems 2024; 9:e0134223. [PMID: 38757963 DOI: 10.1128/msystems.01342-23] [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: 12/11/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
Microbial species that comprise host-associated microbiomes play an essential role in maintaining and mediating the health of plants and animals. While defining the role of individual or even complex communities is important toward quantifying the effect of the microbiome on host health, it is often challenging to develop causal studies that link microbial populations to changes in host fitness. Here, we investigated the impacts of reduced microbial load following antibiotic exposure on the fitness of the anemone, Exaiptasia diaphana and subsequent recovery of the host's microbiome. Anemones were exposed to two different types of antibiotic solutions for 3 weeks and subsequently held in sterilized seawater for a 3-week recovery period. Our results revealed that both antibiotic treatments reduced the overall microbial load during and up to 1 week post-treatment. The observed reduction in microbial load was coupled with reduced anemone biomass, halted asexual reproduction rates, and for one of the antibiotic treatments, the partial removal of the anemone's algal symbiont. Finally, our amplicon sequencing results of the 16S rRNA gene revealed that anemone bacterial composition only shifted in treated individuals during the recovery phase of the experiment, where we also observed a significant reduction in the overall diversity of the microbial community. Our work implies that the E. diaphana's microbiome contributes to host fitness and that the recovery of the host's microbiome following disturbance with antibiotics leads to a reduced, but stable microbial state.IMPORTANCEExaiptasia diaphana is an emerging model used to define the cellular and molecular mechanisms of coral-algal symbioses. E. diaphana also houses a diverse microbiome, consisting of hundreds of microbial partners with undefined function. Here, we applied antibiotics to quantify the impact of microbiome removal on host fitness as well as define trajectories in microbiome recovery following disturbance. We showed that reduction of the microbiome leads to negative impacts on host fitness, and that the microbiome does not recover to its original composition while held under aseptic conditions. Rather the microbiome becomes less diverse, but more consistent across individuals. Our work is important because it suggests that anemone microbiomes play a role in maintaining host fitness, that they are susceptible to disturbance events, and that it is possible to generate gnotobiotic individuals that can be leveraged in microbiome manipulation studies to investigate the role of individual species on host health.
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Affiliation(s)
- Sophie MacVittie
- Department of Molecular Cell Biology, University of California, Merced, California, USA
| | - Saam Doroodian
- Department of Molecular Cell Biology, University of California, Merced, California, USA
| | - Aaron Alberto
- Department of Molecular Cell Biology, University of California, Merced, California, USA
| | - Maggie Sogin
- Department of Molecular Cell Biology, University of California, Merced, California, USA
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2
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Hu H, Kristensen JM, Herbold CW, Pjevac P, Kitzinger K, Hausmann B, Dueholm MKD, Nielsen PH, Wagner M. Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants. MICROBIOME 2024; 12:55. [PMID: 38493180 PMCID: PMC10943839 DOI: 10.1186/s40168-024-01769-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/23/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), and their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance and diversity of Patescibacteria due to the low coverage of commonly used PCR primers for this highly divergent bacterial phylum. Therefore, our current understanding of the global diversity, distribution, and ecological role of Patescibacteria in WWTPs is very incomplete. This is particularly relevant as Patescibacteria are considered to be associated with microbial host cells and can therefore influence the abundance and temporal variability of other microbial groups that are important for WWTP functioning. RESULTS Here, we evaluated the in silico coverage of widely used 16S rRNA gene-targeted primer pairs and redesigned a primer pair targeting the V4 region of bacterial and archaeal 16S rRNA genes to expand its coverage for Patescibacteria. We then experimentally evaluated and compared the performance of the original and modified V4-targeted primers on 565 WWTP samples from the MiDAS global sample collection. Using the modified primer pair, the percentage of ASVs classified as Patescibacteria increased from 5.9 to 23.8%, and the number of detected patescibacterial genera increased from 560 to 1576, while the detected diversity of the remaining microbial community remained similar. Due to this significantly improved coverage of Patescibacteria, we identified 23 core genera of Patescibacteria in WWTPs and described the global distribution pattern of these unusual microbes in these systems. Finally, correlation network analysis revealed potential host organisms that might be associated with Patescibacteria in WWTPs. Interestingly, strong indications were found for an association between Patescibacteria of the Saccharimonadia and globally abundant polyphosphate-accumulating organisms of the genus Ca. Phosphoribacter. CONCLUSIONS Our study (i) provides an improved 16S rRNA gene V4 region-targeted amplicon primer pair inclusive of Patescibacteria with little impact on the detection of other taxa, (ii) reveals the diversity and distribution patterns of Patescibacteria in WWTPs on a global scale, and (iii) provides new insights into the ecological role and potential hosts of Patescibacteria in WWTPs. Video Abstract.
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Affiliation(s)
- Huifeng Hu
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Universitätsring 1, 1010, Vienna, Austria
| | - Jannie Munk Kristensen
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Craig William Herbold
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Te Kura Putaiao Koiora, School of Biological Sciences, Te Whare Wananga o Waitaha, University of Canterbury, Otautahi, Christchurch, Aotearoa, New Zealand
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna , University of Vienna, Vienna, Austria
| | - Katharina Kitzinger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna , University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjaer Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
- Joint Microbiome Facility of the Medical University of Vienna , University of Vienna, Vienna, Austria.
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3
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Fu S, Li H, He F, Wang R, Zhang Y, Zhang Z, Li H. Targeted amplicon sequencing facilitated a novel risk assessment framework for assessing the prevalence of broad spectrum bacterial and coronavirus diseases. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168797. [PMID: 38007133 DOI: 10.1016/j.scitotenv.2023.168797] [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: 09/04/2023] [Revised: 10/27/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
How to effectively leverage wastewater data to estimate the risk of various infectious diseases remains a great challenge. To address this issue, we conducted continuous wastewater surveillance in Dalian city during the summer-autumn seasons of 2022, targeting coronavirus and bacterial diseases. The surveillance included daily sampling at a wastewater treatment plant (WWTP) and weekly sampling in three sewersheds. Targeting the bacteria's 16S rRNA gene and the coronavirus's RNA-dependent RNA polymerase (RdRp) gene, we first employed RT-PCR and amplicon sequencing techniques to analyze the presence and phylogenetic relationship of detected coronavirus and bacterial pathogens. Next, qPCR was used to quantify the abundances of detected coronavirus and bacterial species. Based on the daily shedding dynamics of SARS-CoV-2, a novel model was developed to predict daily new cases. Based on the medium shedding density of 12 pathogens, two thresholds of sewage pathogen load (indicating 0.1 % and 1 % infection rates) were proposed. Our PanCoV RT-PCR detected coronavirus on 12th August and from 26th August to 12th September 2022. Targeted amplicon sequencing further identified human coronavirus OC43 (hCoV-OC43) on 12th August and the SARS-CoV-2 Omicron variant since 26th August in samples from WWTPs and sewersheds. Phylogenetic analysis revealed that hCoV-OC43 from this study belonged to genotype K and suggested a close relationship between the amplified coronavirus sequences from wastewater and clinical samples in a local COVID-19 outbreak on 26th August. Amplicon sequencing targeting the bacterial 16S rRNA gene also revealed the presence of several bacterial pathogens. Finally, we assessed the microbial risk of specific pathogens in sewersheds and identified a number of pathogens that reached high (>1 % prevalence) and medium risk levels (>0.1 % prevalence) at sewershed B. Our findings underline wastewater surveillance as a valuable early warning system for coronavirus and other waterborne bacterial diseases, complementing public health response measures.
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Affiliation(s)
- Songzhe Fu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China.
| | - Haifeng Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China
| | - Fenglan He
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, China
| | - Rui Wang
- College of Marine Science and Environment, Dalian Ocean University, Dalian 116023, China
| | - Yixiang Zhang
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Shanghai, China
| | - Ziqiang Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China
| | - Hui Li
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, China.
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Xu S, Huang H, Chen S, Muhammad ZUA, Wei W, Xie W, Jiang H, Hou S. Recovery of 1887 metagenome-assembled genomes from the South China Sea. Sci Data 2024; 11:197. [PMID: 38351104 PMCID: PMC10864278 DOI: 10.1038/s41597-024-03050-4] [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: 11/22/2023] [Accepted: 02/05/2024] [Indexed: 02/16/2024] Open
Abstract
The South China Sea (SCS) is a marginal sea characterized by strong land-sea biogeochemical interactions. SCS has a distinctive landscape with a multitude of seamounts in its basin. Seamounts create "seamount effects" that influence the diversity and distribution of planktonic microorganisms in the surrounding oligotrophic waters. Although the vertical distribution and community structure of marine microorganisms have been explored in certain regions of the global ocean, there is a lack of comprehensive microbial genomic surveys for uncultured microorganisms in SCS, particularly in the seamount regions. Here, we employed a metagenomic approach to study the uncultured microbial communities sampled from the Xianbei seamount region to the North Coast waters of SCS. A total of 1887 non-redundant prokaryotic metagenome-assembled genomes (MAGs) were reconstructed, of which, 153 MAGs were classified as high-quality MAGs based on the MIMAG standards. The community structure and genomic information provided by this dataset could be used to analyze microbial distribution and metabolism in the SCS.
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Affiliation(s)
- Shuaishuai Xu
- Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Hailong Huang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Songze Chen
- Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Ecological and Environmental Monitoring Center of Guangdong Province, Shenzhen, 518049, China
| | - Zain Ul Arifeen Muhammad
- Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wenya Wei
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510632, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510632, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Haibo Jiang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Shengwei Hou
- Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
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5
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Cram JA, Hollins A, McCarty AJ, Martinez G, Cui M, Gomes ML, Fuchsman CA. Microbial diversity and abundance vary along salinity, oxygen, and particle size gradients in the Chesapeake Bay. Environ Microbiol 2024; 26:e16557. [PMID: 38173306 DOI: 10.1111/1462-2920.16557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Marine snow and other particles are abundant in estuaries, where they drive biogeochemical transformations and elemental transport. Particles range in size, thereby providing a corresponding gradient of habitats for marine microorganisms. We used standard normalized amplicon sequencing, verified with microscopy, to characterize taxon-specific microbial abundances, (cells per litre of water and per milligrams of particles), across six particle size classes, ranging from 0.2 to 500 μm, along the main stem of the Chesapeake Bay estuary. Microbial communities varied in salinity, oxygen concentrations, and particle size. Many taxonomic groups were most densely packed on large particles (in cells/mg particles), yet were primarily associated with the smallest particle size class, because small particles made up a substantially larger portion of total particle mass. However, organisms potentially involved in methanotrophy, nitrite oxidation, and sulphate reduction were found primarily on intermediately sized (5-180 μm) particles, where species richness was also highest. All abundant ostensibly free-living organisms, including SAR11 and Synecococcus, appeared on particles, albeit at lower abundance than in the free-living fraction, suggesting that aggregation processes may incorporate them into particles. Our approach opens the door to a more quantitative understanding of the microscale and macroscale biogeography of marine microorganisms.
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Affiliation(s)
- Jacob A Cram
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Ashley Hollins
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Alexandra J McCarty
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
- Marine Advisory Program, Virginia Institute of Marine Science, Gloucester, Virginia, USA
| | | | - Minming Cui
- Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maya L Gomes
- Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Clara A Fuchsman
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
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6
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Hobart KK, Greensky Z, Hernandez K, Feinberg JM, Bailey JV, Jones DS. Microbial communities from weathered outcrops of a sulfide-rich ultramafic intrusion, and implications for mine waste management. Environ Microbiol 2023; 25:3512-3526. [PMID: 37667903 DOI: 10.1111/1462-2920.16489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 07/20/2023] [Indexed: 09/06/2023]
Abstract
The Duluth Complex (DC) contains sulfide-rich magmatic intrusions that represent one of the largest known economic deposits of copper, nickel, and platinum group elements. Previous work showed that microbial communities associated with experimentally-weathered DC waste rock and tailings were dominated by uncultivated taxa and organisms not typically associated with mine waste. However, those experiments were designed for kinetic testing and do not necessarily represent the conditions expected for long-term environmental weathering. We used 16S rRNA gene methods to characterize the microbial communities present on the surfaces of naturally-weathered and historically disturbed outcrops of DC material. Rock surfaces were dominated by diverse uncultured Ktedonobacteria, Acetobacteria, and Actinobacteria, with abundant algae and other phototrophs. These communities were distinct from microbial assemblages from experimentally-weathered DC rocks, suggesting different energy and nutrient resources in environmental samples. Sulfide mineral incubations performed with and without algae showed that photosynthetic microorganisms could have an inhibitory effect on autotrophic populations, resulting in slightly lower sulfate release and differences in dominant microorganisms. The microbial assemblages from these weathered outcrops show how communities develop during weathering of sulfide-rich DC rocks and represent baseline data that could evaluate the effectiveness of future reclamation of waste produced by large-scale mining operations.
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Affiliation(s)
- Kathryn K Hobart
- Department of Earth & Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Rock Magnetism, University of Minnesota, Minneapolis, Minnesota, USA
| | - ZhaaZhaawaanong Greensky
- Department of Earth & Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kimberly Hernandez
- Department of Earth & Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Joshua M Feinberg
- Department of Earth & Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Rock Magnetism, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jake V Bailey
- Department of Earth & Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Daniel S Jones
- Department of Earth & Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Earth and Environmental Science, New Mexico Institute of Mining and Technology, Socorro, New Mexico, USA
- National Cave and Karst Research Institute, Carlsbad, New Mexico, USA
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7
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Barbosa C, Tamayo-Leiva J, Alcorta J, Salgado O, Daniele L, Morata D, Díez B. Effects of hydrogeochemistry on the microbial ecology of terrestrial hot springs. Microbiol Spectr 2023; 11:e0024923. [PMID: 37754764 PMCID: PMC10581198 DOI: 10.1128/spectrum.00249-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/13/2023] [Indexed: 09/28/2023] Open
Abstract
Temperature, pH, and hydrochemistry of terrestrial hot springs play a critical role in shaping thermal microbial communities. However, the interactions of biotic and abiotic factors at this terrestrial-aquatic interface are still not well understood on a global scale, and the question of how underground events influence microbial communities remains open. To answer this, 11 new samples obtained from the El Tatio geothermal field were analyzed by 16S rRNA amplicon sequencing (V4 region), along with 191 samples from previous publications obtained from the Taupo Volcanic Zone, the Yellowstone Plateau Volcanic Field, and the Eastern Tibetan Plateau, with their temperature, pH, and major ion concentration. Microbial alpha diversity was lower in acid-sulfate waters, and no significant correlations were found with temperature. However, moderate correlations were observed between chemical parameters such as pH (mostly constrained to temperatures below 70°C), SO4 2- and abundances of members of the phyla Armatimonadota, Deinococcota, Chloroflexota, Campilobacterota, and Thermoplasmatota. pH and SO4 2- gradients were explained by phase separation of sulfur-rich hydrothermal fluids and oxidation of reduced sulfur in the steam phase, which were identified as key processes shaping these communities. Ordination and permutational analysis of variance showed that temperature, pH, and major element hydrochemistry explain only 24% of the microbial community structure. Therefore, most of the variance remained unexplained, suggesting that other environmental or biotic factors are also involved and highlighting the environmental complexity of the ecosystem and its great potential to test niche theory ecological associated questions. IMPORTANCE This is the first approach to investigate whether geothermal processes could have an influence on the ecology of thermal microbial communities on a global scale. In addition to temperature and pH, microbial communities are structured by sulfate concentrations, which depends on the tectono-magmatic settings (such as the depth of magmatic chambers) and the local settings (such as the availability of a confining layer separating NaCl waters from steam after phase separation) and the possibility of mixing with more diluted fluids. Comparison of microbial communities from different geothermal areas by homogeneous sequence processing showed that no significant geographic distance decay was detected on the microbial communities according to Bray-Curtis, Jaccard, unweighted, and weighted Unifrac similarity/dissimilarity indices. Instead, an ancient potential divergence in the same taxonomic groups is suggested between globally distant thermal zones.
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Affiliation(s)
- Carla Barbosa
- Department of Geology, University of Chile, Santiago, Chile
- Andean Geothermal Center of Excellence (CEGA-Fondap), University of Chile, Santiago, Chile
| | - Javier Tamayo-Leiva
- Department of Molecular Genetics and Microbiology, Pontifical Catholic University of Chile, Santiago, Chile
- Center for Climate and Resilience Research (CR)2, University of Chile, Santiago, Chile
- Millennium Institute Center of Genome Regulation (CGR), Santiago, Chile
| | - Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Pontifical Catholic University of Chile, Santiago, Chile
- Millennium Institute Center of Genome Regulation (CGR), Santiago, Chile
| | - Oscar Salgado
- Department of Molecular Genetics and Microbiology, Pontifical Catholic University of Chile, Santiago, Chile
- Laboratorio de Bioinformática, Facultad de Educación, Universidad Adventista de Chile, Chillán, Chile
| | - Linda Daniele
- Department of Geology, University of Chile, Santiago, Chile
- Andean Geothermal Center of Excellence (CEGA-Fondap), University of Chile, Santiago, Chile
| | - Diego Morata
- Department of Geology, University of Chile, Santiago, Chile
- Andean Geothermal Center of Excellence (CEGA-Fondap), University of Chile, Santiago, Chile
| | - Beatríz Díez
- Department of Molecular Genetics and Microbiology, Pontifical Catholic University of Chile, Santiago, Chile
- Center for Climate and Resilience Research (CR)2, University of Chile, Santiago, Chile
- Millennium Institute Center of Genome Regulation (CGR), Santiago, Chile
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Xu S, Li G, He C, Huang Y, Yu D, Deng H, Tong Z, Wang Y, Dupuy C, Huang B, Shen Z, Xu J, Gong J. Diversity, community structure, and quantity of eukaryotic phytoplankton revealed using 18S rRNA and plastid 16S rRNA genes and pigment markers: a case study of the Pearl River Estuary. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:415-430. [PMID: 37637251 PMCID: PMC10449762 DOI: 10.1007/s42995-023-00186-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/11/2023] [Indexed: 08/29/2023]
Abstract
Understanding consistencies and discrepancies in characterizing diversity and quantity of phytoplankton is essential for better modeling ecosystem change. In this study, eukaryotic phytoplankton in the Pearl River Estuary, South China Sea were investigated using nuclear 18S rRNA and plastid 16S or 23S rRNA genes and pigment analysis. It was found that 18S abundance poorly explained the variations in total chlorophyll a (Chl-a). However, the ratios of log-transformed 18S abundance to Chl-a in the major phytoplankton groups were generally environment dependent, suggesting that the ratio has potential as an indicator of the physiological state of phytoplankton. The richness of 18S-based operational taxonomic units was positively correlated with the richness of 16S-based amplicon sequence variants of the whole phytoplankton community, but insignificant or weak for individual phytoplankton groups. Overall, the 18S based, rather than the 16S based, community structure had a greater similarity to pigment-based estimations. Relative to the pigment data, the proportion of haptophytes in the 18S dataset, and diatoms and cryptophytes in the 16S dataset, were underestimated. This study highlights that 18S metabarcoding tends to reflect biomass-based community organization of eukaryotic phytoplankton. Because there were lower copy numbers of plastid 16S than 18S per genome, metabarcoding of 16S probably approximates cell abundance-based community organization. Changes in biomass organization of the pigment-based community were sensitive to environmental changes. Taken together, multiple methodologies are recommended to be applied to more accurately profile the diversity and community composition of phytoplankton in natural ecosystems. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00186-x.
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Affiliation(s)
- Shumin Xu
- School of Marine Sciences, Sun Yat-Sen University (Zhuhai Campus), and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000 China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510006 China
| | - Guihao Li
- School of Marine Sciences, Sun Yat-Sen University (Zhuhai Campus), and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000 China
| | - Cui He
- School of Marine Sciences, Sun Yat-Sen University (Zhuhai Campus), and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000 China
| | - Yi Huang
- School of Marine Sciences, Sun Yat-Sen University (Zhuhai Campus), and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000 China
| | - Dan Yu
- School of Marine Sciences, Sun Yat-Sen University (Zhuhai Campus), and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000 China
| | - Huiwen Deng
- School of Marine Sciences, Sun Yat-Sen University (Zhuhai Campus), and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000 China
| | - Zhuyin Tong
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102 China
| | - Yichong Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102 China
| | - Christine Dupuy
- BIOFEEL, UMRi LIENSs, La Rochelle Université/CNRS, La Rochelle, France
| | - Bangqin Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102 China
| | - Zhuo Shen
- School of Marine Sciences, Sun Yat-Sen University (Zhuhai Campus), and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000 China
| | - Jie Xu
- Centre for Regional Oceans, Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Jun Gong
- School of Marine Sciences, Sun Yat-Sen University (Zhuhai Campus), and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000 China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510006 China
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Ruvindy R, Barua A, Bolch CJS, Sarowar C, Savela H, Murray SA. Genomic copy number variability at the genus, species and population levels impacts in situ ecological analyses of dinoflagellates and harmful algal blooms. ISME COMMUNICATIONS 2023; 3:70. [PMID: 37422553 PMCID: PMC10329664 DOI: 10.1038/s43705-023-00274-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/10/2023]
Abstract
The application of meta-barcoding, qPCR, and metagenomics to aquatic eukaryotic microbial communities requires knowledge of genomic copy number variability (CNV). CNV may be particularly relevant to functional genes, impacting dosage and expression, yet little is known of the scale and role of CNV in microbial eukaryotes. Here, we quantify CNV of rRNA and a gene involved in Paralytic Shellfish Toxin (PST) synthesis (sxtA4), in 51 strains of 4 Alexandrium (Dinophyceae) species. Genomes varied up to threefold within species and ~7-fold amongst species, with the largest (A. pacificum, 130 ± 1.3 pg cell-1 /~127 Gbp) in the largest size category of any eukaryote. Genomic copy numbers (GCN) of rRNA varied by 6 orders of magnitude amongst Alexandrium (102- 108 copies cell-1) and were significantly related to genome size. Within the population CNV of rRNA was 2 orders of magnitude (105 - 107 cell-1) in 15 isolates from one population, demonstrating that quantitative data based on rRNA genes needs considerable caution in interpretation, even if validated against locally isolated strains. Despite up to 30 years in laboratory culture, rRNA CNV and genome size variability were not correlated with time in culture. Cell volume was only weakly associated with rRNA GCN (20-22% variance explained across dinoflagellates, 4% in Gonyaulacales). GCN of sxtA4 varied from 0-102 copies cell-1, was significantly related to PSTs (ng cell-1), displaying a gene dosage effect modulating PST production. Our data indicate that in dinoflagellates, a major marine eukaryotic group, low-copy functional genes are more reliable and informative targets for quantification of ecological processes than unstable rRNA genes.
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Affiliation(s)
- Rendy Ruvindy
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Abanti Barua
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Christopher J S Bolch
- Institute for Marine & Antarctic Studies, University of Tasmania, Launceston, 7248, TAS, Australia
| | - Chowdhury Sarowar
- Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, NSW, Australia
| | - Henna Savela
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW, 2007, Australia
- Finnish Environment Institute, Marine Research Centre, Helsinki, Finland
| | - Shauna A Murray
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW, 2007, Australia.
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10
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Fletcher-Hoppe C, Yeh YC, Raut Y, Weissman JL, Fuhrman JA. Symbiotic UCYN-A strains co-occurred with El Niño, relaxed upwelling, and varied eukaryotes over 10 years off Southern California. ISME COMMUNICATIONS 2023; 3:63. [PMID: 37355737 PMCID: PMC10290647 DOI: 10.1038/s43705-023-00268-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/05/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
Biological nitrogen fixation, the conversion of N2 gas into a bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a focal point due to its streamlined metabolism, intimate partnership with a haptophyte host, and broad distribution. Here, we explore the environmental parameters that govern UCYN-A's presence at the San Pedro Ocean Time-series (SPOT), its host specificity, and statistically significant interactions with non-host eukaryotes from 2008-2018. 16S and 18S rRNA gene sequences were amplified by "universal primers" from monthly samples and resolved into Amplicon Sequence Variants, allowing us to observe multiple UCYN-A symbioses. UCYN-A1 relative abundances increased following the 2015-2016 El Niño event. This "open ocean ecotype" was present when coastal upwelling declined, and Ekman transport brought tropical waters into the region. Network analyses reveal all strains of UCYN-A co-occur with dinoflagellates including Lepidodinium, a potential predator, and parasitic Syndiniales. UCYN-A2 appeared to pair with multiple hosts and was not tightly coupled to its predominant host, while UCYN-A1 maintained a strong host-symbiont relationship. These biological relationships are particularly important to study in the context of climate change, which will alter UCYN-A distribution at regional and global scales.
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Affiliation(s)
- Colette Fletcher-Hoppe
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
| | - Yi-Chun Yeh
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
- Department of Global Ecology, Carnegie Institution for Science, Stanford University, Stanford, CA, USA
| | - Yubin Raut
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
| | - J L Weissman
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
- Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Jed A Fuhrman
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA.
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11
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Wijaya W, Suhaimi Z, Chua CX, Sunil RS, Kolundžija S, Rohaizat AMB, Azmi NBM, Hazrin-Chong NH, Lauro FM. Frequent pulse disturbances shape resistance and resilience in tropical marine microbial communities. ISME COMMUNICATIONS 2023; 3:55. [PMID: 37280348 PMCID: PMC10244338 DOI: 10.1038/s43705-023-00260-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 05/02/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023]
Abstract
The Johor Strait separates the island of Singapore from Peninsular Malaysia. A 1-kilometer causeway built in the early 1920s in the middle of the strait effectively blocks water flowing to/from either side, resulting in low water turnover rates and build-up of nutrients in the inner Strait. We have previously shown that short-term rather than seasonal environmental changes influence microbial community composition in the Johor Strait. Here, we present a temporally-intensive study that uncovers the factors keeping the microbial populations in check. We sampled the surface water at four sites in the inner Eastern Johor Strait every other day for two months, while measuring various water quality parameters, and analysed 16S amplicon sequences and flow-cytometric counts. We discovered that microbial community succession revolves around a common stable state resulting from frequent pulse disturbances. Among these, sporadic riverine freshwater input and regular tidal currents influence bottom-up controls including the availability of the limiting nutrient nitrogen and its biological release in readily available forms. From the top-down, marine viruses and predatory bacteria limit the proliferation of microbes in the water. Harmful algal blooms, which have been observed historically in these waters, may occur only when there are simultaneous gaps in the top-down and bottom-up controls. This study gains insight into complex interactions between multiple factors contributing to a low-resistance but high-resilience microbial community and speculate about rare events that could lead to the occurrence of an algal bloom.
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Affiliation(s)
- Winona Wijaya
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Zahirah Suhaimi
- Department of Anthropology, University of California Santa Cruz, Santa Cruz, CA, USA
- Center for Southeast Asian Coastal Interactions, Santa Cruz, CA, USA
| | - Cherlyn Xin'Er Chua
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Rohan Shawn Sunil
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Sandra Kolundžija
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | | | - Norzarifah Binti Md Azmi
- Department of Biological Sciences and Biotechnology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Nur Hazlin Hazrin-Chong
- Department of Biological Sciences and Biotechnology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Federico M Lauro
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore.
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore.
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12
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Nam NN, Do HDK, Loan Trinh KT, Lee NY. Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods 2023; 12:foods12112140. [PMID: 37297385 DOI: 10.3390/foods12112140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
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Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 72820, Vietnam
| | - Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
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13
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Cha T, Kim HH, Keum J, Kwak MJ, Park JY, Hoh JK, Kim CR, Jeon BH, Park HK. Gut microbiome profiling of neonates using Nanopore MinION and Illumina MiSeq sequencing. Front Microbiol 2023; 14:1148466. [PMID: 37256051 PMCID: PMC10225602 DOI: 10.3389/fmicb.2023.1148466] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/17/2023] [Indexed: 06/01/2023] Open
Abstract
This study aimed to evaluate the difference in gut microbiomes between preterm and term infants using third-generation long-read sequencing (Oxford Nanopore Technologies, ONT) compared with an established gold standard, Illumina (second-generation short-read sequencing). A total of 69 fecal samples from 51 term (T) and preterm (P) infants were collected at 7 and 28 days of life. Gut colonization profiling was performed by 16S rRNA gene sequencing using ONT. We used Illumina to validate and compare the patterns in 13 neonates. Using bioinformatic analysis, we identified features that differed between P and T. Both T1 and P1 microbiomes were dominated by Firmicutes (Staphylococcus and Enterococcus), whereas sequentially showed dominant transitions to Lactobacillus (p < 0.001) and Streptococcus in T2 (p = 0.001), and pathogenic bacteria (Klebsiella) in P2 (p = 0.001). The abundance of beneficial bacteria (Bifidobacterium and Lactobacillus) increased in T2 (p = 0.026 and p < 0.001, respectively). These assignments were correlated with the abundance at the species-level. Bacterial α-diversity increased in T (p = 0.005) but not in P (p = 0.156), and P2 showed distinct β-diversity clustering than T2 (p = 0.001). The ONT reliably identified pathogenic bacteria at the genus level, and taxonomic profiles were comparable to those identified by Illumina at the genus level. This study shows that ONT and Illumina are highly correlated. P and T had different microbiome profiles, and the α- and β-diversity varied. ONT sequencing has potential for pathogen detection in neonates in clinical settings.
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Affiliation(s)
- Teahyen Cha
- Department of Pediatrics, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Hoo Hugo Kim
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, Republic of Korea
| | - Jihyun Keum
- Department of Obstetrics and Gynecology, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Min-Jin Kwak
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jae Yong Park
- Division of Microbiome, Int-Gen Company, Seoul, Republic of Korea
| | - Jeong Kyu Hoh
- Department of Obstetrics and Gynecology, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Chang-Ryul Kim
- Department of Pediatrics, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, Republic of Korea
| | - Hyun-Kyung Park
- Department of Pediatrics, Hanyang University College of Medicine, Seoul, Republic of Korea
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14
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Deutschmann IM, Krabberød AK, Latorre F, Delage E, Marrasé C, Balagué V, Gasol JM, Massana R, Eveillard D, Chaffron S, Logares R. Disentangling temporal associations in marine microbial networks. MICROBIOME 2023; 11:83. [PMID: 37081491 PMCID: PMC10120119 DOI: 10.1186/s40168-023-01523-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 03/19/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Microbial interactions are fundamental for Earth's ecosystem functioning and biogeochemical cycling. Nevertheless, they are challenging to identify and remain barely known. Omics-based censuses are helpful in predicting microbial interactions through the statistical inference of single (static) association networks. Yet, microbial interactions are dynamic and we have limited knowledge of how they change over time. Here, we investigate the dynamics of microbial associations in a 10-year marine time series in the Mediterranean Sea using an approach inferring a time-resolved (temporal) network from a single static network. RESULTS A single static network including microbial eukaryotes and bacteria was built using metabarcoding data derived from 120 monthly samples. For the decade, we aimed to identify persistent, seasonal, and temporary microbial associations by determining a temporal network that captures the interactome of each individual sample. We found that the temporal network appears to follow an annual cycle, collapsing, and reassembling when transiting between colder and warmer waters. We observed higher association repeatability in colder than in warmer months. Only 16 associations could be validated using observations reported in literature, underlining our knowledge gap in marine microbial ecological interactions. CONCLUSIONS Our results indicate that marine microbial associations follow recurrent temporal dynamics in temperate zones, which need to be accounted for to better understand the functioning of the ocean microbiome. The constructed marine temporal network may serve as a resource for testing season-specific microbial interaction hypotheses. The applied approach can be transferred to microbiome studies in other ecosystems. Video Abstract.
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Affiliation(s)
- Ina Maria Deutschmann
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain.
| | - Anders K Krabberød
- Department of Biosciences/Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, p.b. 1066 Blindern, N-0316, Oslo, Norway
| | - Francisco Latorre
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Erwan Delage
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, F-75016, Paris, France
| | - Cèlia Marrasé
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Vanessa Balagué
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Josep M Gasol
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Ramon Massana
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Damien Eveillard
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, F-75016, Paris, France
| | - Samuel Chaffron
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, F-75016, Paris, France
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de La Barceloneta, 37-49, 08003, Barcelona, Spain.
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15
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Barak N, Fadeev E, Brekhman V, Aharonovich D, Lotan T, Sher D. Selecting 16S rRNA Primers for Microbiome Analysis in a Host-Microbe System: The Case of the Jellyfish Rhopilema nomadica. Microorganisms 2023; 11:microorganisms11040955. [PMID: 37110378 PMCID: PMC10144005 DOI: 10.3390/microorganisms11040955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
Amplicon sequencing of the 16S rRNA gene is extensively used to characterize bacterial communities, including those living in association with eukaryotic hosts. Deciding which region of the 16S rRNA gene to analyze and selecting the appropriate PCR primers remains a major decision when initiating any new microbiome study. Based on a detailed literature survey of studies focusing on cnidarian microbiomes, we compared three commonly used primers targeting different hypervariable regions of the 16S rRNA gene, V1V2, V3V4, and V4V5, using the jellyfish Rhopilema nomadica as a model. Although all primers exhibit a similar pattern in bacterial community composition, the performance of the V3V4 primer set was superior to V1V2 and V4V5. The V1V2 primers misclassified bacteria from the Bacilli class and exhibited low classification resolution for Rickettsiales, which represent the second most abundant 16S rRNA gene sequence in all the primers. The V4V5 primer set detected almost the same community composition as the V3V4, but the ability of these primers to also amplify the eukaryotic 18S rRNA gene may hinder bacterial community observations. However, after overcoming the challenges possessed by each one of those primers, we found that all three of them show very similar bacterial community dynamics and compositions. Nevertheless, based on our results, we propose that the V3V4 primer set is potentially the most suitable for studying jellyfish-associated bacterial communities. Our results suggest that, at least for jellyfish samples, it may be feasible to directly compare microbial community estimates from different studies, each using different primers but otherwise similar experimental protocols. More generally, we recommend specifically testing different primers for each new organism or system as a prelude to large-scale 16S rRNA gene amplicon analyses, especially of previously unstudied host-microbe associations.
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Affiliation(s)
- Noga Barak
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel
| | - Eduard Fadeev
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
| | - Vera Brekhman
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel
| | - Dikla Aharonovich
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel
| | - Tamar Lotan
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel
| | - Daniel Sher
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel
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16
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Lu J, Shu Y, Zhang H, Zhang S, Zhu C, Ding W, Zhang W. The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms. Int J Mol Sci 2023; 24:ijms24076491. [PMID: 37047466 PMCID: PMC10095273 DOI: 10.3390/ijms24076491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023] Open
Abstract
The development of metagenomics has opened up a new era in the study of marine microbiota, which play important roles in biogeochemical cycles. In recent years, the global ocean sampling expeditions have spurred this research field toward a deeper understanding of the microbial diversities and functions spanning various lifestyles, planktonic (free-living) or sessile (biofilm-associated). In this review, we deliver a comprehensive summary of marine microbiome datasets generated in global ocean expeditions conducted over the last 20 years, including the Sorcerer II GOS Expedition, the Tara Oceans project, the bioGEOTRACES project, the Micro B3 project, the Bio-GO-SHIP project, and the Marine Biofilms. These datasets have revealed unprecedented insights into the microscopic life in our oceans and led to the publication of world-leading research. We also note the progress of metatranscriptomics and metaproteomics, which are confined to local marine microbiota. Furthermore, approaches to transforming the global ocean microbiome datasets are highlighted, and the state-of-the-art techniques that can be combined with data analyses, which can present fresh perspectives on marine molecular ecology and microbiology, are proposed.
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Affiliation(s)
- Jie Lu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
| | - Yi Shu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
| | - Heng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Shangxian Zhang
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Chengrui Zhu
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
- Correspondence: (W.D.); (W.Z.)
| | - Weipeng Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
- Correspondence: (W.D.); (W.Z.)
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17
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Huang H, Xu S, Li S, Wang X, Guo K, Yan R, Xie W, Yin K, Hou S, Jiang H. Diversity and Distribution of Harmful Algal Bloom Species from Seamount to Coastal Waters in the South China Sea. Microbiol Spectr 2023; 11:e0416922. [PMID: 36815795 PMCID: PMC10100961 DOI: 10.1128/spectrum.04169-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/26/2023] [Indexed: 02/24/2023] Open
Abstract
Mount Xianbei is one of the largest shallow seamounts located in the middle of the South China Sea (SCS), which might play a role in shaping the biodiversity of surrounding continental coastal waters, particularly the diversity of phytoplankton species causing frequent harmful algal blooms (HABs) in northern SCS. However, the diversity, composition, and distribution of phytoplankton species in the seamount regions of Xianbei remain largely unexplored. In this study, samples around and outside the seamount regions were collected during a late summer cruise of 2021 to test whether seamounts play a role in HAB species propagation. In total, we identified 19 HAB species across all samples using the ASV-based DNA metabarcoding approach, 6 of which had not been reported previously in the SCS, suggesting a diverse HAB species in the SCS. Specifically, 16 HAB species were found in the seamount region of Xianbei, and 5 of them were also found in the coastal waters, indicating a close connection between seamount and coastal waters. This study was the first attempt to explore HAB species' spatial diversity and vertical distribution in the seamount region of Xianbei at single-nucleotide resolution, which provides a novel explanation for the coastal HAB occurrence in the northern SCS. IMPORTANCE There are a number of seamounts under the water of the South China Sea (SCS). The seamounts might play a role in shaping the biodiversity of surrounding continental coastal waters. However, there is no direct evidence revealing the relationship of the biodiversity of phytoplankton between seamounts and coastal waters in the SCS, especially those species having the potential to form harmful algal blooms (HABs). Some HAB species might proliferate in certain geographic locations, while others may be broadly distributed across oceanic provinces. In this study, we provided a detailed analysis of phytoplankton composition and molecular detection of HAB species from seamount to coastal waters in the SCS, which suggested a strong interaction in the HAB species between the two areas. This finding provides new insights into the diversity and distribution of HABs in seamounts and their role in shaping the composition and the occurrence of HABs in coastal water.
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Affiliation(s)
- Hailong Huang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China
| | - Shuaishuai Xu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Shuangqing Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Xinwei Wang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Kangli Guo
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Rongman Yan
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei Xie
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Kedong Yin
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shengwei Hou
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Haibo Jiang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
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18
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Effects of phytoplankton, viral communities, and warming on free-living and particle-associated marine prokaryotic community structure. Nat Commun 2022; 13:7905. [PMID: 36550140 PMCID: PMC9780322 DOI: 10.1038/s41467-022-35551-4] [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: 04/14/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Free-living and particle-associated marine prokaryotes have physiological, genomic, and phylogenetic differences, yet factors influencing their temporal dynamics remain poorly constrained. In this study, we quantify the entire microbial community composition monthly over several years, including viruses, prokaryotes, phytoplankton, and total protists, from the San-Pedro Ocean Time-series using ribosomal RNA sequencing and viral metagenomics. Canonical analyses show that in addition to physicochemical factors, the double-stranded DNA viral community is the strongest factor predicting free-living prokaryotes, explaining 28% of variability, whereas the phytoplankton (via chloroplast 16S rRNA) community is strongest with particle-associated prokaryotes, explaining 31% of variability. Unexpectedly, protist community explains little variability. Our findings suggest that biotic interactions are significant determinants of the temporal dynamics of prokaryotes, and the relative importance of specific interactions varies depending on lifestyles. Also, warming influenced the prokaryotic community, which largely remained oligotrophic summer-like throughout 2014-15, with cyanobacterial populations shifting from cold-water ecotypes to warm-water ecotypes.
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19
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Duhamel S, Hamilton CW, Pálsson S, Björnsdóttir SH. Microbial Response to Increased Temperatures Within a Lava-Induced Hydrothermal System in Iceland: An Analogue for the Habitability of Volcanic Terrains on Mars. ASTROBIOLOGY 2022; 22:1176-1198. [PMID: 35920884 DOI: 10.1089/ast.2021.0124] [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: 06/15/2023]
Abstract
Fossil hydrothermal systems on Mars are important exploration targets because they may have once been habitable and could still preserve evidence of microbial life. We investigated microbial communities within an active lava-induced hydrothermal system associated with the 2014-2015 eruption of Holuhraun in Iceland as a Mars analogue. In 2016, the microbial composition in the lava-heated water differed substantially from that of the glacial river and spring water sources that fed into the system. Several taxonomic and metabolic groups were confined to the water emerging from the lava and some showed the highest sequence similarities to subsurface ecosystems, including to the predicted thermophilic and deeply branching Candidatus Acetothermum autotrophicum. Measurements show that the communities were affected by temperature and other environmental factors. In particular, comparing glacial river water incubated in situ (5.7°C, control) with glacial water incubated within a lava-heated stream (17.5°C, warm) showed that microbial abundance, richness, and diversity increased in the warm treatment compared with the control, with the predicted major metabolism shifting from lithotrophy toward organotrophy and possibly phototrophy. In addition, thermophilic bacteria isolated from the lava-heated water and a nearby acidic hydrothermal system included the known endospore-formers Geobacillus stearothermophilus and Paenibacillus cisolokensis as well as a potentially novel taxon within the order Hyphomicrobiales. Similar lava-water interactions on Mars could therefore have generated habitable environments for microbial communities.
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Affiliation(s)
- Solange Duhamel
- Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
- Lunar and Planetary Laboratory, University of Arizona, Tucson, Arizona, USA
- Division of Biology and Paleo Environment, Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, USA
| | | | - Snæbjörn Pálsson
- Department of Biology, University of Iceland, Reykjavík, Iceland
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20
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Banavar A, Amirkolaei SK, Duscher L, Khairunisa BH, Mukhopadhyay B, Schwarz M, Urick S, Ovissipour R. Nutritional Evaluation of Black Soldier Fly Frass as an Ingredient in Florida Pompano (Trachinotus carolinus L.) Diets. Animals (Basel) 2022; 12:ani12182407. [PMID: 36139267 PMCID: PMC9495079 DOI: 10.3390/ani12182407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/15/2022] [Accepted: 09/09/2022] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Carnivorous fish species, such as the Florida pompano, currently require expensive and unsustainable feed in order to be raised in an aquaculture setting. A waste product of the black soldier fly, frass has the potential to be an alternative carbohydrate source for these fish. This study aims to assess the potential of frass to mimic the growth, body, composition, and intestinal microbiome of pompano that can be achieved through commercial feed. Three diets with varying frass levels as well as a control diet were developed. The frass was found to increase the visceral somatic index and lower the hepatosomatic index. The frass did not alter the body composition or improve the growth performance, leading to a lower specific growth rate and higher feed conversion rate. The microbiome analysis showed the highest diversity of the gut flora in the control diet, while the frass diets showed signs of community imbalance. This may have been due to the decreased starch in the frass, which is usually metabolized by those microbial communities. Overall, frass diets are not ideal for carnivorous fish diets, but have could have potential for feed replacement in herbivore and detritivore fish species. Abstract The aquaculture industry is in need of sustainable fish feed to reduce the use of expensive and environmentally invasive wild-caught fish currently fed to many carnivorous species. The black soldier fly (BSF) has become a popular sustainable alternative protein source; however, the nutritional waste byproduct of BSF, frass, has not been extensively studied as a feed replacement in carnivorous species. This study evaluates the potential of BSF frass on the growth, body composition, and intestinal microbiome of the Florida pompano, Trachinotus carolinus. Four experimental diets were formulated containing different levels of frass, replacing plant-based carbohydrate sources. As a result of this study, the frass did not improve the growth performance, resulting in a lower specific growth rate and higher feed conversion rate. While the frass diets did not alter the body composition, the visceral somatic index (VSI) significantly increased compared to the control diet and the hepatosomatic index (HIS) was lowered. The microbiome analysis showed high variation among the diets, with the control diet having the most distinct consortia, which may have been driven by the increased levels of starch compared to frass diets. This study indicates that BSF frass may not be a suitable feed replacement for carnivorous pompano; however, frass could still potentially be a replacement feed for herbivore or detritivore fish and should be further studied.
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Affiliation(s)
- Amiti Banavar
- Future Foods Lab and Cellular Agriculture Initiative, Virginia Seafood Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University, Hampton, VA 23699, USA
- Department of Food Science and Technology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Samad Keramat Amirkolaei
- Future Foods Lab and Cellular Agriculture Initiative, Virginia Seafood Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University, Hampton, VA 23699, USA
| | - Lexi Duscher
- Future Foods Lab and Cellular Agriculture Initiative, Virginia Seafood Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University, Hampton, VA 23699, USA
| | - Bela Haifa Khairunisa
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Michael Schwarz
- Virginia Seafood Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University, Hampton, VA 23699, USA
| | - Steve Urick
- Virginia Seafood Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University, Hampton, VA 23699, USA
| | - Reza Ovissipour
- Future Foods Lab and Cellular Agriculture Initiative, Virginia Seafood Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University, Hampton, VA 23699, USA
- Department of Food Science and Technology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
- Correspondence:
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21
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Milke F, Sanchez-Garcia S, Dlugosch L, McNichol J, Fuhrman J, Simon M, Wagner-Döbler I. Composition and Biogeography of Planktonic Pro- and Eukaryotic Communities in the Atlantic Ocean: Primer Choice Matters. Front Microbiol 2022; 13:895875. [PMID: 35836413 PMCID: PMC9273945 DOI: 10.3389/fmicb.2022.895875] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/18/2022] [Indexed: 01/02/2023] Open
Abstract
Basin-scale biogeographic observations of marine pelagic pro- and eukaryotic communities are necessary to understand forces driving community composition and for providing a baseline to monitor global change. Deep sequencing of rRNA genes provides community composition at high resolution; yet, it is unclear how the choice of primers affects biogeographic patterns. Here, we re-amplified 16S rRNA genes from DNA sampled during R/V Polarstern Cruise ANT28-5 over a latitudinal transect across the Atlantic Ocean from 52°S to 47°N using universal V4-V5 primers and compared the results with those obtained previously with V5-V6 bacteria-specific primers. For validation of our results, we inferred community composition based on 16S rRNA genes of metagenomes from the same stations and single amplified genomes (SAGs) from the Global Ocean Reference Genome (GORG) database. We found that the universal V4-V5 primers retrieved SAR11 clades with similar relative proportions as those found in the GORG database while the V5-V6 primers recovered strongly diverging clade abundances. We confirmed an inverse bell-shaped distance-decay relationship and a latitudinal diversity gradient that did not decline linearly with absolute latitude in the Atlantic Ocean. Patterns were modified by sampling depth, sequencing depth, choice of primers, and abundance filtering. Especially richness patterns were not robust to methodological change. This study offers a detailed picture of the Atlantic Ocean microbiome using a universal set of PCR primers that allow for the conjunction of biogeographical patterns among organisms from different domains of life.
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Affiliation(s)
- Felix Milke
- Institute for Chmistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Selene Sanchez-Garcia
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Leon Dlugosch
- Institute for Chmistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jesse McNichol
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jed Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Meinhard Simon
- Institute for Chmistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Irene Wagner-Döbler
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
- *Correspondence: Irene Wagner-Döbler,
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22
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Caracciolo M, Rigaut-Jalabert F, Romac S, Mahé F, Forsans S, Gac JP, Arsenieff L, Manno M, Chaffron S, Cariou T, Hoebeke M, Bozec Y, Goberville E, Le Gall F, Guilloux L, Baudoux AC, de Vargas C, Not F, Thiébaut E, Henry N, Simon N. Seasonal dynamics of marine protist communities in tidally mixed coastal waters. Mol Ecol 2022; 31:3761-3783. [PMID: 35593305 PMCID: PMC9543310 DOI: 10.1111/mec.16539] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 12/29/2021] [Accepted: 04/19/2022] [Indexed: 12/01/2022]
Abstract
Major seasonal community reorganizations and associated biomass variations are landmarks of plankton ecology. However, the processes of plankton community turnover rates have not been fully elucidated so far. Here, we analyse patterns of planktonic protist community succession in temperate latitudes, based on quantitative taxonomic data from both microscopy counts (cells >10 μm) and ribosomal DNA metabarcoding (size fraction >3 μm, 18S rRNA gene) from plankton samples collected bimonthly over 8 years (2009–2016) at the SOMLIT‐Astan station (Roscoff, Western English Channel). Based on morphology, diatoms were clearly the dominating group all year round and over the study period. Metabarcoding uncovered a wider diversity spectrum and revealed the prevalence of Dinophyceae and diatoms but also of Cryptophyta, Chlorophyta, Cercozoa, Syndiniales and Ciliophora in terms of read counts and or richness. The use of morphological and molecular analyses in combination allowed improving the taxonomic resolution and to identify the sequence of the dominant species and OTUs (18S V4 rDNA‐derived taxa) that drive annual plankton successions. We detected that some of these dominant OTUs were benthic as a result of the intense tidal mixing typical of the French coasts in the English Channel. Our analysis of the temporal structure of community changes point to a strong seasonality and resilience. The temporal structure of environmental variables (especially Photosynthetic Active Radiation, temperature and macronutrients) and temporal structures generated by species life cycles and or species interactions, are key drivers of the observed cyclic annual plankton turnover.
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Affiliation(s)
| | | | | | | | | | | | - Laure Arsenieff
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | | | - Samuel Chaffron
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Laboratoire des Sciences du Numérique de Nantes (LS2N), CNRS, UMR6004, Université de Nantes, Ecole Centrale de Nantes, 44322, Nantes, France
| | - Thierry Cariou
- Institut de recherche pour le développement (IRD), Délégation Régionale Ouest, IMAGO, Plouzané, France
| | - Mark Hoebeke
- CNRS, Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff, 29680, Roscoff, France
| | | | - Eric Goberville
- Unité biologie des organismes et écosystèmes aquatiques (BOREA), Muséum National D'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS, IRD, CP53, 61 rue Buffon 75005, Paris, France
| | | | - Loïc Guilloux
- Sorbonne Université, Roscoff, France.,Mediterranean Institute of Oceanography (MIO), Campus de Luminy case 901, 163 Av. de Luminy, 13288 Marseille cedex 9, France
| | | | - Colomban de Vargas
- Sorbonne Université, Roscoff, France.,Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | | | - Eric Thiébaut
- Sorbonne Université, Roscoff, France.,Sorbonne Université, CNRS, OSU STAMAR, UMS2017, 4 Place Jussieu, 75252 Paris cedex 05, France
| | - Nicolas Henry
- Sorbonne Université, Roscoff, France.,Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,CNRS, Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff, 29680, Roscoff, France
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23
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Krabberød AK, Deutschmann IM, Bjorbækmo MFM, Balagué V, Giner CR, Ferrera I, Garcés E, Massana R, Gasol JM, Logares R. Long-term patterns of an interconnected core marine microbiota. ENVIRONMENTAL MICROBIOME 2022; 17:22. [PMID: 35526063 PMCID: PMC9080219 DOI: 10.1186/s40793-022-00417-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/20/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Ocean microbes constitute ~ 70% of the marine biomass, are responsible for ~ 50% of the Earth's primary production and are crucial for global biogeochemical cycles. Marine microbiotas include core taxa that are usually key for ecosystem function. Despite their importance, core marine microbes are relatively unknown, which reflects the lack of consensus on how to identify them. So far, most core microbiotas have been defined based on species occurrence and abundance. Yet, species interactions are also important to identify core microbes, as communities include interacting species. Here, we investigate interconnected bacteria and small protists of the core pelagic microbiota populating a long-term marine-coastal observatory in the Mediterranean Sea over a decade. RESULTS Core microbes were defined as those present in > 30% of the monthly samples over 10 years, with the strongest associations. The core microbiota included 259 Operational Taxonomic Units (OTUs) including 182 bacteria, 77 protists, and 1411 strong and mostly positive (~ 95%) associations. Core bacteria tended to be associated with other bacteria, while core protists tended to be associated with bacteria. The richness and abundance of core OTUs varied annually, decreasing in stratified warmers waters and increasing in colder mixed waters. Most core OTUs had a preference for one season, mostly winter, which featured subnetworks with the highest connectivity. Groups of highly associated taxa tended to include protists and bacteria with predominance in the same season, particularly winter. A group of 13 highly-connected hub-OTUs, with potentially important ecological roles dominated in winter and spring. Similarly, 18 connector OTUs with a low degree but high centrality were mostly associated with summer or autumn and may represent transitions between seasonal communities. CONCLUSIONS We found a relatively small and dynamic interconnected core microbiota in a model temperate marine-coastal site, with potential interactions being more deterministic in winter than in other seasons. These core microbes would be essential for the functioning of this ecosystem over the year. Other non-core taxa may also carry out important functions but would be redundant and non-essential. Our work contributes to the understanding of the dynamics and potential interactions of core microbes possibly sustaining ocean ecosystem function.
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Affiliation(s)
- Anders K Krabberød
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, 0316, Oslo, Norway.
| | - Ina M Deutschmann
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Marit F M Bjorbækmo
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, 0316, Oslo, Norway
| | - Vanessa Balagué
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Caterina R Giner
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Isabel Ferrera
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, 29640, Fuengirola, Málaga, Spain
| | - Esther Garcés
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Ramon Massana
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Josep M Gasol
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
- Centre for Marine Ecosystems Research, School of Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Ramiro Logares
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, 0316, Oslo, Norway.
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain.
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24
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Yeh YC, Fuhrman JA. Contrasting diversity patterns of prokaryotes and protists over time and depth at the San-Pedro Ocean Time series. ISME COMMUNICATIONS 2022; 2:36. [PMID: 37938286 PMCID: PMC9723720 DOI: 10.1038/s43705-022-00121-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 06/18/2023]
Abstract
Community dynamics are central in microbial ecology, yet we lack studies comparing diversity patterns among marine protists and prokaryotes over depth and multiple years. Here, we characterized microbes at the San-Pedro Ocean Time series (2005-2018), using SSU rRNA gene sequencing from two size fractions (0.2-1 and 1-80 μm), with a universal primer set that amplifies from both prokaryotes and eukaryotes, allowing direct comparisons of diversity patterns in a single set of analyses. The 16S + 18S rRNA gene composition in the small size fraction was mostly prokaryotic (>92%) as expected, but the large size fraction unexpectedly contained 46-93% prokaryotic 16S rRNA genes. Prokaryotes and protists showed opposite vertical diversity patterns; prokaryotic diversity peaked at mid-depth, protistan diversity at the surface. Temporal beta-diversity patterns indicated prokaryote communities were much more stable than protists. Although the prokaryotic communities changed monthly, the average community stayed remarkably steady over 14 years, showing high resilience. Additionally, particle-associated prokaryotes were more diverse than smaller free-living ones, especially at deeper depths, contributed unexpectedly by abundant and diverse SAR11 clade II. Eukaryotic diversity was strongly correlated with the diversity of particle-associated prokaryotes but not free-living ones, reflecting that physical associations result in the strongest interactions, including symbioses, parasitism, and decomposer relationships.
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Affiliation(s)
- Yi-Chun Yeh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA.
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25
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Pierella Karlusich JJ, Pelletier E, Zinger L, Lombard F, Zingone A, Colin S, Gasol JM, Dorrell RG, Henry N, Scalco E, Acinas SG, Wincker P, de Vargas C, Bowler C. A robust approach to estimate relative phytoplankton cell abundances from metagenomes. Mol Ecol Resour 2022; 23:16-40. [PMID: 35108459 PMCID: PMC10078663 DOI: 10.1111/1755-0998.13592] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022]
Abstract
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.
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Affiliation(s)
- Juan José Pierella Karlusich
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Eric Pelletier
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Fabien Lombard
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Océanographie de Villefranche (LOV), 06230, Villefranche-sur-Mer, France.,Institut Universitaire de France (IUF), Paris, France
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Sébastien Colin
- European Molecular Biology Laboratory, Heidelberg, Germany.,Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, 29680, Roscoff, France.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Richard G Dorrell
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France
| | - Nicolas Henry
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Patrick Wincker
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Colomban de Vargas
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, 29680, Roscoff, France
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
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26
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Deutschmann IM, Lima-Mendez G, Krabberød AK, Raes J, Vallina SM, Faust K, Logares R. Disentangling environmental effects in microbial association networks. MICROBIOME 2021; 9:232. [PMID: 34823593 PMCID: PMC8620190 DOI: 10.1186/s40168-021-01141-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 07/20/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Ecological interactions among microorganisms are fundamental for ecosystem function, yet they are mostly unknown or poorly understood. High-throughput-omics can indicate microbial interactions through associations across time and space, which can be represented as association networks. Associations could result from either ecological interactions between microorganisms, or from environmental selection, where the association is environmentally driven. Therefore, before downstream analysis and interpretation, we need to distinguish the nature of the association, particularly if it is due to environmental selection or not. RESULTS We present EnDED (environmentally driven edge detection), an implementation of four approaches as well as their combination to predict which links between microorganisms in an association network are environmentally driven. The four approaches are sign pattern, overlap, interaction information, and data processing inequality. We tested EnDED on networks from simulated data of 50 microorganisms. The networks contained on average 50 nodes and 1087 edges, of which 60 were true interactions but 1026 false associations (i.e., environmentally driven or due to chance). Applying each method individually, we detected a moderate to high number of environmentally driven edges-87% sign pattern and overlap, 67% interaction information, and 44% data processing inequality. Combining these methods in an intersection approach resulted in retaining more interactions, both true and false (32% of environmentally driven associations). After validation with the simulated datasets, we applied EnDED on a marine microbial network inferred from 10 years of monthly observations of microbial-plankton abundance. The intersection combination predicted that 8.3% of the associations were environmentally driven, while individual methods predicted 24.8% (data processing inequality), 25.7% (interaction information), and up to 84.6% (sign pattern as well as overlap). The fraction of environmentally driven edges among negative microbial associations in the real network increased rapidly with the number of environmental factors. CONCLUSIONS To reach accurate hypotheses about ecological interactions, it is important to determine, quantify, and remove environmentally driven associations in marine microbial association networks. For that, EnDED offers up to four individual methods as well as their combination. However, especially for the intersection combination, we suggest using EnDED with other strategies to reduce the number of false associations and consequently the number of potential interaction hypotheses. Video abstract.
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Affiliation(s)
- Ina Maria Deutschmann
- Institute of Marine Sciences, CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003 Barcelona, Spain
| | - Gipsi Lima-Mendez
- Research Unit in Biology of Microorganisms (URBM), University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium
| | - Anders K. Krabberød
- Department of Biosciences/Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, p.b. 1066 Blindern, N-0316 Oslo, Norway
| | - Jeroen Raes
- VIB Center for Microbiology, Herestraat 49-1028, 3000 Leuven, Belgium
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Molecular Bacteriology, Herestraat 49, 3000 Leuven, Belgium
| | - Sergio M. Vallina
- Spanish Institute of Oceanography (IEO - CSIC), Ave Principe de Asturias 70 Bis, 33212 Gijon, Spain
| | - Karoline Faust
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Molecular Bacteriology, Herestraat 49, 3000 Leuven, Belgium
| | - Ramiro Logares
- Institute of Marine Sciences, CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003 Barcelona, Spain
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Abstract
Although previous research demonstrates that skin-associated archaea are rarely detected within human skin microbiome data, exist at relatively low abundance, and are primarily affiliated with the Methanobacteriota and Halobacteriota phyla, other studies suggest that archaea are consistently detected and relatively abundant on human skin, with skin “archaeomes” dominated by putative ammonia oxidizers of the Nitrososphaeria class (Thermoproteota phylum, formerly Thaumarchaeota). Here, we evaluated new and existing 16S rRNA gene sequence data sourced from mammalian skin and skin-associated surfaces and generated with two commonly used universal prokaryotic primer sets to assess archaeal prevalence, relative abundance, and taxonomic distribution. Archaeal 16S rRNA gene sequences were detected in only 17.5% of 1,688 samples by high-throughput sequence data, with most of the archaeon-positive samples associated with nonhuman mammalian skin. Only 5.9% of human-associated skin sample data sets contained sequences affiliated with archaeal 16S rRNA genes. When detected, the relative abundance of sequences affiliated with archaeal amplicon sequence variants (ASVs) was less than 1% for most mammalian skin samples and did not exceed 2% for any samples. Although several computer keyboard microbial profiles were dominated by Nitrososphaeria sequences, all other skin microbiome data sets tested were primarily composed of sequences affiliated with Methanobacteriota and Halobacteriota phyla. Our findings revise downward recent estimates of human skin archaeal distributions and relative abundances, especially those affiliated with the Nitrososphaeria, reflecting a limited and infrequent archaeal presence within the mammalian skin microbiome. IMPORTANCE The current state of research on mammalian skin-associated archaea is limited, with the few papers focusing on potential skin archaeal communities often in disagreement with each other. As such, there is no consensus on the prevalence or taxonomic composition of archaea on mammalian skin. Mammalian skin health is in part influenced by its complex microbiota and consortium of bacteria and potential archaea. Without a clear foundational analysis and characterization of the mammalian skin archaeome, it will be difficult for future research to explore the potential impact of skin-associated archaea on skin health and function. The current work provides a much-needed analysis of the mammalian skin archaeome and contributes to building a foundation from which further discussion and exploration of the skin archaeome might continue.
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