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Lin T, Feng Y, Miao W, Wang S, Bao Z, Shao Z, Zhang D, Wang X, Jiang H, Zhang H. Elevated temperature alters bacterial community from mutualism to antagonism with Skeletonema costatum: insights into the role of a novel species, Tamlana sp. MS1. mSphere 2024:e0019824. [PMID: 38940599 DOI: 10.1128/msphere.00198-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/15/2024] [Indexed: 06/29/2024] Open
Abstract
Skeletonema costatum, a cosmopolitan diatom primarily inhabiting coastal ecosystems, exhibits a typically close yet variable relationship with heterotrophic bacteria. The increasing temperature of surface seawater is expected to substantially affect the viability and ecological dynamics of S. costatum, potentially altering its relationship with bacteria. However, it remains unclear to what extent the elevated temperature could change these relationships. Here, the relationship between axenic S. costatum and natural seawater bacteria underwent a dramatic shift from mutualism to antagonism as the co-culture temperature increased from 20°C to 25°C. The co-occurrence network indicated significantly increased complexity of interaction between S. costatum and bacteria community after temperature elevation, especially with Flavobacteriaceae, implying their potential role in eliminating S. costatum under higher temperatures. Additionally, a Flavobacteriaceae isolate, namely MS1 identified as Tamlana genus, was isolated from the co-culture system at 25°C. MS1 had a remarkable ability to eliminate S. costatum, with the mortality rate at 25°C steadily rising from 30.2% at 48 h to 92.4% at 120 h. However, it promoted algal growth to some extent at 20°C. These results demonstrated that increased temperature promotes MS1 shifts from mutualism to antagonism with S. costatum. According to the comparative genomics analysis, changes in the lifestyle of MS1 were attributed to the increased gliding motility and attachment of MS1 under elevated temperature, enabling it to exert an algicidal effect through direct contact with alga. This investigation provided an advanced understanding of interactions between phytoplankton and bacteria in future warming oceanic ecosystems. IMPORTANCE Ocean warming profoundly influences the growth and metabolism of phytoplankton and bacteria, thereby significantly reshaping their interactions. Previous studies have shown that warming can change bacterial lifestyle from mutualism to antagonism with phytoplankton, but the underlying mechanism remains unclear. In this study, we found that high temperature promotes Tamlana sp. MS1 adhesion to Skeletonema costatum, leading to algal lysis through direct contact, demonstrating a transition in lifestyle from mutualism to antagonism with increasing temperature. Furthermore, the gliding motility of MS1 appears to be pivotal in mediating the transition of its lifestyle. These findings not only advance our understanding of the phytoplankton-bacteria relationship under ocean warming but also offer valuable insights for predicting the impact of warming on phytoplankton carbon sequestration.
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Affiliation(s)
- Tenghui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yumeng Feng
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Wenfei Miao
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Shuqi Wang
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhen Bao
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zeyuan Shao
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Xinwei Wang
- School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Haibo Jiang
- School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
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Xu X, He M, Xue Q, Li X, Liu A. Genome-based taxonomic classification of the genus Sulfitobacter along with the proposal of a new genus Parasulfitobacter gen. nov. and exploring the gene clusters associated with sulfur oxidation. BMC Genomics 2024; 25:389. [PMID: 38649849 PMCID: PMC11034169 DOI: 10.1186/s12864-024-10269-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/29/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The genus Sulfitobacter, a member of the family Roseobacteraceae, is widely distributed in the ocean and is believed to play crucial roles in the global sulfur cycle. However, gene clusters associated with sulfur oxidation in genomes of the type strains of this genus have been poorly studied. Furthermore, taxonomic errors have been identified in this genus, potentially leading to significant confusion in ecological and evolutionary interpretations in subsequent studies of the genus Sulfitobacter. This study aims to investigate the taxonomic status of this genus and explore the metabolism associated with sulfur oxidation. RESULTS This study suggests that Sulfitobacter algicola does not belong to Sulfitobacter and should be reclassified into a novel genus, for which we propose the name Parasulfitobacter gen. nov., with Parasulfitobacter algicola comb. nov. as the type species. Additionally, enzymes involved in the sulfur oxidation process, such as the sulfur oxidization (Sox) system, the disulfide reductase protein family, and the sulfite dehydrogenase (SoeABC), were identified in almost all Sulfitobacter species. This finding implies that the majority of Sulfitobacter species can oxidize reduced sulfur compounds. Differences in the modular organization of sox gene clusters among Sulfitobacter species were identified, along with the presence of five genes with unknown function located in some of the sox gene clusters. Lastly, this study revealed the presence of the demethylation pathway and the cleavage pathway used by many Sulfitobacter species to degrade dimethylsulfoniopropionate (DMSP). These pathways enable these bacteria to utilize DMSP as important source of sulfur and carbon or as a defence strategy. CONCLUSIONS Our findings contribute to interpreting the mechanism by which Sulfitobacter species participate in the global sulfur cycle. The taxonomic rearrangement of S. algicola into the novel genus Parasulfitobacter will prevent confusion in ecological and evolutionary interpretations in future studies of the genus Sulfitobacter.
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Affiliation(s)
- Xiaokun Xu
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China
| | - Mengdan He
- School of Basic Medical Sciences, Shandong Second Medical University, 261042, Weifang, Shandong, P. R. China
| | - Qingjie Xue
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China
| | - Xiuzhen Li
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China
| | - Ang Liu
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China.
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3
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Han D, Park KT, Kim H, Kim TH, Jeong MK, Nam SI. Interaction between phytoplankton and heterotrophic bacteria in Arctic fjords during the glacial melting season as revealed by eDNA metabarcoding. FEMS Microbiol Ecol 2024; 100:fiae059. [PMID: 38621717 PMCID: PMC11067963 DOI: 10.1093/femsec/fiae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/07/2024] [Accepted: 04/13/2024] [Indexed: 04/17/2024] Open
Abstract
The hydrographic variability in the fjords of Svalbard significantly influences water mass properties, causing distinct patterns of microbial diversity and community composition between surface and subsurface layers. However, surveys on the phytoplankton-associated bacterial communities, pivotal to ecosystem functioning in Arctic fjords, are limited. This study investigated the interactions between phytoplankton and heterotrophic bacterial communities in Svalbard fjord waters through comprehensive eDNA metabarcoding with 16S and 18S rRNA genes. The 16S rRNA sequencing results revealed a homogenous community composition including a few dominant heterotrophic bacteria across fjord waters, whereas 18S rRNA results suggested a spatially diverse eukaryotic plankton distribution. The relative abundances of heterotrophic bacteria showed a depth-wise distribution. By contrast, the dominant phytoplankton populations exhibited variable distributions in surface waters. In the network model, the linkage of phytoplankton (Prasinophytae and Dinophyceae) to heterotrophic bacteria, particularly Actinobacteria, suggested the direct or indirect influence of bacterial contributions on the fate of phytoplankton-derived organic matter. Our prediction of the metabolic pathways for bacterial activity related to phytoplankton-derived organic matter suggested competitive advantages and symbiotic relationships between phytoplankton and heterotrophic bacteria. Our findings provide valuable insights into the response of phytoplankton-bacterial interactions to environmental changes in Arctic fjords.
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Affiliation(s)
- Dukki Han
- Department of Marine Molecular Bioscience, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
| | - Ki-Tae Park
- Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Environmental Sciences and Biotechnology, Hallym University, Chuncheon 24252, Republic of Korea
| | - Haryun Kim
- East Sea Research Institute, Korea Institute of Ocean Science & Technology, Uljin 36315, Republic of Korea
| | - Tae-Hoon Kim
- Department of Oceanography, Faculty of Earth Systems and Environmental Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Man-Ki Jeong
- Department of Smart Fisheries Resources Management, Chonnam National University, Yeosu 59626, Republic of Korea
| | - Seung-Il Nam
- Korea Polar Research Institute, Incheon 21990, Republic of Korea
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4
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Celussi M, Manna V, Banchi E, Fonti V, Bazzaro M, Flander-Putrle V, Klun K, Kralj M, Orel N, Tinta T. Annual recurrence of prokaryotic climax communities in shallow waters of the North Mediterranean. Environ Microbiol 2024; 26:e16595. [PMID: 38418391 DOI: 10.1111/1462-2920.16595] [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: 09/11/2023] [Accepted: 02/02/2024] [Indexed: 03/01/2024]
Abstract
In temperate coastal environments, wide fluctuations of biotic and abiotic factors drive microbiome dynamics. To link recurrent ecological patterns with planktonic microbial communities, we analysed a monthly-sampled 3-year time series of 16S rRNA amplicon sequencing data, alongside environmental variables, collected at two stations in the northern Adriatic Sea. Time series multivariate analyses allowed us to identify three stable, mature communities (climaxes), whose recurrence was mainly driven by changes in photoperiod and temperature. Mixotrophs (e.g., Ca. Nitrosopumilus, SUP05 clade, and Marine Group II) thrived under oligotrophic, low-light conditions, whereas copiotrophs (e.g., NS4 and NS5 clades) bloomed at higher temperatures and substrate availability. The early spring climax was characterised by a more diverse set of amplicon sequence variants, including copiotrophs associated with phytoplankton-derived organic matter degradation, and photo-auto/heterotrophic organisms (e.g., Synechococcus sp., Roseobacter clade), whose rhythmicity was linked to photoperiod lengthening. Through the identification of recurrent climax assemblages, we begin to delineate a typology of ecosystem based on microbiome composition and functionality, allowing for the intercomparison of microbial assemblages among different biomes, a still underachieved goal in the omics era.
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Affiliation(s)
- Mauro Celussi
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Elisa Banchi
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Viviana Fonti
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
| | - Matteo Bazzaro
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
| | | | - Katja Klun
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Martina Kralj
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
| | - Neža Orel
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Tinkara Tinta
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
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5
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Kuhlisch C, Shemi A, Barak-Gavish N, Schatz D, Vardi A. Algal blooms in the ocean: hot spots for chemically mediated microbial interactions. Nat Rev Microbiol 2024; 22:138-154. [PMID: 37833328 DOI: 10.1038/s41579-023-00975-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2023] [Indexed: 10/15/2023]
Abstract
The cycling of major nutrients in the ocean is affected by large-scale phytoplankton blooms, which are hot spots of microbial life. Diverse microbial interactions regulate bloom dynamics. At the single-cell level, interactions between microorganisms are mediated by small molecules in the chemical crosstalk that determines the type of interaction, ranging from mutualism to pathogenicity. Algae interact with viruses, bacteria, parasites, grazers and other algae to modulate algal cell fate, and these interactions are dependent on the environmental context. Recent advances in mass spectrometry and single-cell technologies have led to the discovery of a growing number of infochemicals - metabolites that convey information - revealing the ability of algal cells to govern biotic interactions in the ocean. The diversity of infochemicals seems to account for the specificity in cellular response during microbial communication. Given the immense impact of algal blooms on biogeochemical cycles and climate regulation, a major challenge is to elucidate how microscale interactions control the fate of carbon and the recycling of major elements in the ocean. In this Review, we discuss microbial interactions and the role of infochemicals in algal blooms. We further explore factors that can impact microbial interactions and the available tools to decipher them in the natural environment.
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Affiliation(s)
- Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Adva Shemi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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6
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Branscombe L, Harrison EL, Choong ZYD, Swink C, Keys M, Widdicombe C, Wilson WH, Cunliffe M, Helliwell K. Cryptic bacterial pathogens of diatoms peak during senescence of a winter diatom bloom. THE NEW PHYTOLOGIST 2024; 241:1292-1307. [PMID: 38037269 DOI: 10.1111/nph.19441] [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: 07/12/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023]
Abstract
Diatoms are globally abundant microalgae that form extensive blooms in aquatic ecosystems. Certain bacteria behave antagonistically towards diatoms, killing or inhibiting their growth. Despite their crucial implications to diatom blooms and population health, knowledge of diatom antagonists in the environment is fundamentally lacking. We report systematic characterisation of the diversity and seasonal dynamics of bacterial antagonists of diatoms via plaque assay sampling in the Western English Channel (WEC), where diatoms frequently bloom. Unexpectedly, peaks in detection did not occur during characteristic spring diatom blooms, but coincided with a winter bloom of Coscinodiscus, suggesting that these bacteria likely influence distinct diatom host populations. We isolated multiple bacterial antagonists, spanning 4 classes and 10 bacterial orders. Notably, a diatom attaching Roseobacter Ponticoccus alexandrii was isolated multiple times, indicative of a persistent environmental presence. Moreover, many isolates had no prior reports of antagonistic activity towards diatoms. We verified diatom growth inhibitory effects of eight isolates. In all cases tested, these effects were activated by pre-exposure to diatom organic matter. Discovery of widespread 'cryptic' antagonistic activity indicates that bacterial pathogenicity towards diatoms is more prevalent than previously recognised. Finally, examination of the global biogeography of WEC antagonists revealed co-occurrence patterns with diatom host populations in marine waters globally.
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Affiliation(s)
- Laura Branscombe
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Ellen L Harrison
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Zhi Yi Daniel Choong
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Courtney Swink
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Matthew Keys
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
| | | | - William H Wilson
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Michael Cunliffe
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Katherine Helliwell
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
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7
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Kim KE, Joo HM, Kim YJ, Kang D, Lee TK, Jung SW, Ha SY. Ecological Interaction between Bacteriophages and Bacteria in Sub-Arctic Kongsfjorden Bay, Svalbard, Norway. Microorganisms 2024; 12:276. [PMID: 38399681 PMCID: PMC10893223 DOI: 10.3390/microorganisms12020276] [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: 12/30/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Marine virus diversity and their relationships with their hosts in the marine environment remain unclear. This study investigated the co-occurrence of marine DNA bacteriophages (phages) and bacteria in the sub-Arctic area of Kongsfjorden Bay in Svalbard (Norway) in April and June 2018 using metagenomics tools. Of the marine viruses identified, 48-81% were bacteriophages of the families Myoviridae, Siphoviridae, and Podoviridae. Puniceispirillum phage HMO-2011 was dominant (7.61%) in April, and Puniceispirillum phage HMO-2011 (3.32%) and Pelagibacter phage HTVC008M (3.28%) were dominant in June. Gammaproteobacteria (58%), including Eionea flava (14.3%) and Pseudomonas sabulinigri (12.2%), were dominant in April, whereas Alphaproteobacteria (87%), including Sulfitobacter profundi (51.5%) and Loktanella acticola (32.4%), were dominant in June. The alpha diversity of the bacteriophages and bacterial communities exhibited opposite patterns. The diversity of the bacterial community was higher in April and lower in June. Changes in water temperature and light can influence the relationship between bacteria and bacteriophages.
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Affiliation(s)
- Kang Eun Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (K.E.K.); (Y.J.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea;
| | - Hyoung Min Joo
- Unit of Next Generation IBRV Building Program, Korea Polar Research Institute, Incheon 21990, Republic of Korea;
| | - Yu Jin Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (K.E.K.); (Y.J.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea;
| | - Donhyug Kang
- Marine Domain & Security Research Department, Korea Institute of Ocean Science & Technology, Busan 49111, Republic of Korea;
| | - Taek-Kyun Lee
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea;
- Risk Assessment Research Center, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
| | - Seung Won Jung
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (K.E.K.); (Y.J.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea;
| | - Sun-Yong Ha
- Division of Polar Ocean Science Research, Korea Polar Research Institute, Incheon 21990, Republic of Korea
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8
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Sun X, Wai OWH, Xie J, Li X. Biomineralization To Prevent Microbially Induced Corrosion on Concrete for Sustainable Marine Infrastructure. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:522-533. [PMID: 38052449 PMCID: PMC10785763 DOI: 10.1021/acs.est.3c04680] [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: 06/16/2023] [Revised: 11/05/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023]
Abstract
Microbially induced corrosion (MIC) on concrete represents a serious issue impairing the lifespan of coastal/marine infrastructure. However, currently developed concrete corrosion protection strategies have limitations in wide applications. Here, a biomineralization method was proposed to form a biomineralized film on concrete surfaces for corrosion inhibition. Laboratory seawater corrosion experiments were conducted under different conditions [e.g., chemical corrosion (CC), MIC, and biomineralization for corrosion inhibition]. A combination of chemical and mechanical property measurements of concrete (e.g., sulfate concentrations, permeability, mass, and strength) and a genotypic-based investigation of formed concrete biofilms was conducted to evaluate the effectiveness of the biomineralization approach on corrosion inhibition. The results show that MIC resulted in much higher corrosion rates than CC. However, the biomineralization treatment effectively inhibited corrosion because the biomineralized film decreased the total and relative abundance of sulfate-reducing bacteria (SRB) and acted as a protective layer to control the diffusion of sulfate and isolate the concrete from the corrosive SRB communities, which helps extend the lifespan of concrete structures. Moreover, this technique had no negative impact on the native marine microbial communities. Our study contributes to the potential application of biomineralization for corrosion inhibition to achieve long-term sustainability for major marine concrete structures.
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Affiliation(s)
- Xiaohao Sun
- Department
of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Onyx W. H. Wai
- Department
of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
- Research
Institute for Sustainable Urban Development, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, China
| | - Jiawen Xie
- Department
of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Xiangdong Li
- Department
of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
- Research
Institute for Sustainable Urban Development, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, China
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9
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Lang-Yona N, Flores JM, Nir-Zadock TS, Nussbaum I, Koren I, Vardi A. Impact of airborne algicidal bacteria on marine phytoplankton blooms. THE ISME JOURNAL 2024; 18:wrae016. [PMID: 38442732 PMCID: PMC10944695 DOI: 10.1093/ismejo/wrae016] [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: 01/09/2024] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 03/07/2024]
Abstract
Ocean microbes are involved in global processes such as nutrient and carbon cycling. Recent studies indicated diverse modes of algal-bacterial interactions, including mutualism and pathogenicity, which have a substantial impact on ecology and oceanic carbon sequestration, and hence, on climate. However, the airborne dispersal and pathogenicity of bacteria in the marine ecosystem remained elusive. Here, we isolated an airborne algicidal bacterium, Roseovarius nubinhibens, emitted to the atmosphere as primary marine aerosol (referred also as sea spray aerosols) and collected above a coccolithophore bloom in the North Atlantic Ocean. The aerosolized bacteria retained infective properties and induced lysis of Gephyrocapsa huxleyi cultures.This suggests that the transport of marine bacteria through the atmosphere can effectively spread infection agents over vast oceanic regions, highlighting its significance in regulating the cell fate in algal blooms.
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Affiliation(s)
- Naama Lang-Yona
- Department of Plant and Environmental Science, Weizmann Institute of Science, Rehovot 7610001, Israel
- Technion - Israel Institute of Technology, Environmental, Water and Agricultural Engineering, Haifa 3200003, Israel
| | - J Michel Flores
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tal Sharon Nir-Zadock
- Department of Plant and Environmental Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Inbal Nussbaum
- Department of Plant and Environmental Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ilan Koren
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Science, Weizmann Institute of Science, Rehovot 7610001, Israel
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10
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Câmara Dos Reis M, Romac S, Le Gall F, Marie D, Frada MJ, Koplovitz G, Cariou T, Henry N, de Vargas C, Jeanthon C. Exploring the phycosphere of Emiliania huxleyi: From bloom dynamics to microbiome assembly experiments. Mol Ecol 2023; 32:6507-6522. [PMID: 36541038 DOI: 10.1111/mec.16829] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 10/11/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Coccolithophores have global ecological and biogeochemical significance as the most important calcifying marine phytoplankton group. The structure and selection of prokaryotic communities associated with the most abundant coccolithophore and bloom-forming species, Emiliania huxleyi, are still poorly known. In this study, we assessed the diversity of bacterial communities associated with an E. huxleyi bloom in the Celtic Sea (Eastern North Atlantic), exposed axenic E. huxleyi cultures to prokaryotic communities derived from bloom and non-bloom conditions, and followed the dynamics of their microbiome composition over one year. Bloom-associated prokaryotic communities were dominated by SAR11, Marine group II Euryarchaeota and Rhodobacterales and contained substantial proportions of known indicators of phytoplankton bloom demises such as Flavobacteriaceae and Pseudoalteromonadaceae. The taxonomic richness of bacteria derived from natural communities associated with axenic E. huxleyi rapidly shifted and then stabilized over time. The succession of microorganisms recruited from the environment was consistently dependent on the composition of the initial bacterioplankton community. Phycosphere-associated communities derived from the E. huxleyi bloom were highly similar to one another, suggesting deterministic processes, whereas cultures from non-bloom conditions show an effect of stochasticity. Overall, this work sheds new light on the importance of the initial inoculum composition in microbiome recruitment and elucidates the temporal dynamics of its composition and long-term stability.
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Affiliation(s)
- Mariana Câmara Dos Reis
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Sarah Romac
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Florence Le Gall
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Dominique Marie
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Miguel J Frada
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
- Department of Ecology, Evolution and Behavior, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gil Koplovitz
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Thierry Cariou
- Sorbonne Université, Centre National de la Recherche Scientifique, FR2424, Station Biologique de Roscoff, Roscoff, France
| | - Nicolas Henry
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Christian Jeanthon
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
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11
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Cai G, Yu X, Wang H, Zheng T, Azam F. Nutrient-dependent interactions between a marine copiotroph Alteromonas and a diatom Thalassiosira pseudonana. mBio 2023; 14:e0094023. [PMID: 37772817 PMCID: PMC10653928 DOI: 10.1128/mbio.00940-23] [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: 04/18/2023] [Accepted: 08/11/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE As the major producers and consumers, phytoplankton and bacteria play central roles in marine ecosystems and their interactions show great ecological significance. Whether mutualistic or antagonistic, the interaction between certain phytoplankton and bacterial species is usually seen as a derivative of intrinsic physiological properties and rarely changes. This study demonstrated that the interactions between the ubiquitously co-occurring bacteria and diatom, Alteromonas and Thalassiosira pseudonana, varied with nutrient conditions. They overcame hardship together in oligotrophic seawater but showed antagonistic effects against each other under nutrient amendment. The contact-dependent algicidal behavior of Alteromonas based on protease activity solved the paradox among bacterial proliferation, nutrient viability, and algal demise haunting other known non-contact-dependent algicidal processes and might actually trigger the collapse of algal blooms in situ. The chemotactic and swarming movement of Alteromonas might also contribute greatly to the breakdown of "marine snow," which could redirect the carbon sequestration pathway in the ocean.
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Affiliation(s)
- Guanjing Cai
- Biology Department and Institute of Marine Sciences, College of Science, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaoqi Yu
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, China
| | - Hui Wang
- Biology Department and Institute of Marine Sciences, College of Science, and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Tianling Zheng
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, China
| | - Farooq Azam
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
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12
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Hevroni G, Vincent F, Ku C, Sheyn U, Vardi A. Daily turnover of active giant virus infection during algal blooms revealed by single-cell transcriptomics. SCIENCE ADVANCES 2023; 9:eadf7971. [PMID: 37824628 PMCID: PMC10569711 DOI: 10.1126/sciadv.adf7971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
Abstract
Giant viruses infect many unicellular eukaryotes, including algae that form massive oceanic blooms. Despite the major impact of viruses on the marine ecosystem, the ability to quantify and assess active viral infection in nature remains a major challenge. We applied single-cell RNA sequencing, to profile virus and host transcriptomes of 12,000 single algal cells from a coccolithophore bloom. Viral infection was detected already at early exponential bloom phase, negatively correlating with the bloom intensity. A consistent percent of infected coccolithophores displayed the early phase of viral replication for several consecutive days, indicating a daily turnover and continuous virocell-associated metabolite production, potentially affecting the surrounding microbiome. Linking single-cell infection state to host physiology revealed that infected cells remained calcified even in the late infection stage. These findings stress the importance of studying host-virus dynamics in natural populations, at single-cell resolution, to better understand virus life cycle and its impact on microbial food webs.
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13
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Li CY, Cao HY, Curson ARJ, Wang P, Todd JD, Zhang YZ. Dimethylsulfoniopropionate and its catabolites are important chemical signals mediating marine microbial interactions. Trends Microbiol 2023; 31:992-994. [PMID: 37481345 DOI: 10.1016/j.tim.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/24/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur compound with key ecological roles in marine environments. This paper offers a brief insight into the mechanisms, environmental diversity, and importance of DMSP-mediated marine microbial interactions, including algae-microzooplankton interactions, bacteria-microzooplankton interactions, and algae-bacteria interactions. We also highlight current challenges that warrant further investigation.
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Affiliation(s)
- Chun-Yang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hai-Yan Cao
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Peng Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Yu-Zhong Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
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14
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Beiralas R, Ozer N, Segev E. Abundant Sulfitobacter marine bacteria protect Emiliania huxleyi algae from pathogenic bacteria. ISME COMMUNICATIONS 2023; 3:100. [PMID: 37740057 PMCID: PMC10517135 DOI: 10.1038/s43705-023-00311-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 09/24/2023]
Abstract
Emiliania huxleyi is a unicellular micro-alga that forms massive oceanic blooms and plays key roles in global biogeochemical cycles. Mounting studies demonstrate various stimulatory and inhibitory influences that bacteria have on the E. huxleyi physiology. To investigate these algal-bacterial interactions, laboratory co-cultures have been established by us and by others. Owing to these co-cultures, various mechanisms of algal-bacterial interactions have been revealed, many involving bacterial pathogenicity towards algae. However, co-cultures represent a significantly simplified system, lacking the complexity of bacterial communities. In order to investigate bacterial pathogenicity within an ecologically relevant context, it becomes imperative to enhance the microbial complexity of co-culture setups. Phaeobacter inhibens bacteria are known pathogens that cause the death of E. huxleyi algae in laboratory co-culture systems. The bacteria depend on algal exudates for growth, but when algae senesce, bacteria switch to a pathogenic state and induce algal death. Here we investigate whether P. inhibens bacteria can induce algal death in the presence of a complex bacterial community. We show that an E. huxleyi-associated bacterial community protects the alga from the pathogen, although the pathogen occurs within the community. To study how the bacterial community regulates pathogenicity, we reduced the complex bacterial community to a five-member synthetic community (syncom). The syncom is comprised of a single algal host and five isolated bacterial species, which represent major bacterial groups that are naturally associated with E. huxleyi. We discovered that a single bacterial species in the reduced community, Sulfitobacter pontiacus, protects the alga from the pathogen. We further found that algal protection from P. inhibens pathogenicity is a shared trait among several Sulfitobacter species. Algal protection by bacteria might be a common phenomenon with ecological significance, which is overlooked in reduced co-culture systems.
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Affiliation(s)
- Roni Beiralas
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Noy Ozer
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Einat Segev
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel.
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15
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Rontani JF, Bonin P. Cellular Damage of Bacteria Attached to Senescent Phytoplankton Cells as a Result of the Transfer of Photochemically Produced Singlet Oxygen: A Review. Microorganisms 2023; 11:1565. [PMID: 37375067 DOI: 10.3390/microorganisms11061565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Several studies set out to explain the presence of high proportions of photooxidation products of cis-vaccenic acid (generally considered to be of bacterial origin) in marine environments. These studies show that these oxidation products result from the transfer of singlet oxygen from senescent phytoplankton cells to the bacteria attached to them in response to irradiation by sunlight. This paper summarizes and reviews the key findings of these studies, i.e., the demonstration of the process at work and the effect of different parameters (intensity of solar irradiance, presence of bacterial carotenoids, and presence of polar matrices such as silica, carbonate, and exopolymeric substances around phytoplankton cells) on this transfer. A large part of this review looks at how this type of alteration of bacteria can affect the preservation of algal material in the marine environment, especially in polar regions where conditions drive increased transfer of singlet oxygen from sympagic algae to bacteria.
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Affiliation(s)
- Jean-François Rontani
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Patricia Bonin
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
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16
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Abada A, Beiralas R, Narvaez D, Sperfeld M, Duchin-Rapp Y, Lipsman V, Yuda L, Cohen B, Carmieli R, Ben-Dor S, Rocha J, Huang Zhang I, Babbin AR, Segev E. Aerobic bacteria produce nitric oxide via denitrification and promote algal population collapse. THE ISME JOURNAL 2023:10.1038/s41396-023-01427-8. [PMID: 37173383 DOI: 10.1038/s41396-023-01427-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023]
Abstract
Microbial interactions govern marine biogeochemistry. These interactions are generally considered to rely on exchange of organic molecules. Here we report on a novel inorganic route of microbial communication, showing that algal-bacterial interactions between Phaeobacter inhibens bacteria and Gephyrocapsa huxleyi algae are mediated through inorganic nitrogen exchange. Under oxygen-rich conditions, aerobic bacteria reduce algal-secreted nitrite to nitric oxide (NO) through denitrification, a well-studied anaerobic respiratory mechanism. The bacterial NO is involved in triggering a cascade in algae akin to programmed cell death. During death, algae further generate NO, thereby propagating the signal in the algal population. Eventually, the algal population collapses, similar to the sudden demise of oceanic algal blooms. Our study suggests that the exchange of inorganic nitrogen species in oxygenated environments is a potentially significant route of microbial communication within and across kingdoms.
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Affiliation(s)
- Adi Abada
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Roni Beiralas
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Delia Narvaez
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Martin Sperfeld
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Yemima Duchin-Rapp
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Valeria Lipsman
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Lilach Yuda
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Bar Cohen
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Raanan Carmieli
- Depertment of Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Department of Life Science Core Facilities, The Weizmann Institute of Science, Rehovot, Israel
| | - Jorge Rocha
- CIDEA Consortium Conacyt-Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Mexico
| | - Irene Huang Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew R Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Einat Segev
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel.
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17
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Transcriptome response of Antarctic Phaeodactylum tricornutum ICE-H producing dimethylsulphoniopropionate to hypersaline stress. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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18
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Vincent F, Gralka M, Schleyer G, Schatz D, Cabrera-Brufau M, Kuhlisch C, Sichert A, Vidal-Melgosa S, Mayers K, Barak-Gavish N, Flores JM, Masdeu-Navarro M, Egge JK, Larsen A, Hehemann JH, Marrasé C, Simó R, Cordero OX, Vardi A. Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms. Nat Commun 2023; 14:510. [PMID: 36720878 PMCID: PMC9889395 DOI: 10.1038/s41467-023-36049-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 01/13/2023] [Indexed: 02/01/2023] Open
Abstract
Algal blooms are hotspots of marine primary production and play central roles in microbial ecology and global elemental cycling. Upon demise of the bloom, organic carbon is partly respired and partly transferred to either higher trophic levels, bacterial biomass production or sinking. Viral infection can lead to bloom termination, but its impact on the fate of carbon remains largely unquantified. Here, we characterize the interplay between viral infection and the composition of a bloom-associated microbiome and consequently the evolving biogeochemical landscape, by conducting a large-scale mesocosm experiment where we monitor seven induced coccolithophore blooms. The blooms show different degrees of viral infection and reveal that only high levels of viral infection are followed by significant shifts in the composition of free-living bacterial and eukaryotic assemblages. Intriguingly, upon viral infection the biomass of eukaryotic heterotrophs (thraustochytrids) rivals that of bacteria as potential recyclers of organic matter. By combining modeling and quantification of active viral infection at a single-cell resolution, we estimate that viral infection causes a 2-4 fold increase in per-cell rates of extracellular carbon release in the form of acidic polysaccharides and particulate inorganic carbon, two major contributors to carbon sinking into the deep ocean. These results reveal the impact of viral infection on the fate of carbon through microbial recyclers of organic matter in large-scale coccolithophore blooms.
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Affiliation(s)
- Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Developmental Biology Unit, European Molecular Biological Laboratory, 69117, Heidelberg, Germany
| | - Matti Gralka
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02145, MA, USA.,Systems Biology Lab, Amsterdam Institute for Life and Environment (A-Life)/Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081, Amsterdam, The Netherlands
| | - Guy Schleyer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | | | - Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Andreas Sichert
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02145, MA, USA.,Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Kyle Mayers
- NORCE Norwegian Research Centre, 5008, Bergen, Norway
| | - Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - J Michel Flores
- Department of Earth and Planetary Science, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | | | - Jorun Karin Egge
- Department of Biological Sciences (BIO), University of Bergen, 5020, Bergen, Norway
| | - Aud Larsen
- NORCE Norwegian Research Centre, 5008, Bergen, Norway.,Department of Biological Sciences (BIO), University of Bergen, 5020, Bergen, Norway
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Celia Marrasé
- Institut de Ciències del Mar, CSIC, 08003, Barcelona, Spain
| | - Rafel Simó
- Institut de Ciències del Mar, CSIC, 08003, Barcelona, Spain
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02145, MA, USA
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel.
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19
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Complete Genome Sequence of Phaeobacter sp. Strain G2, Isolated from a Lab Culture of the Calcifying Alga Emiliania huxleyi. Microbiol Resour Announc 2023; 12:e0106722. [PMID: 36448822 PMCID: PMC9872643 DOI: 10.1128/mra.01067-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
We report the complete genome sequence of Phaeobacter sp. strain G2, which was isolated from a lab culture of the coccolithophore alga Emiliania huxleyi strain RCC 1216. The 4,963,472-bp sequence has a G+C content of 58.85% and was assembled using Illumina short reads and Oxford Nanopore Technologies long reads.
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20
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Barak-Gavish N, Dassa B, Kuhlisch C, Nussbaum I, Brandis A, Rosenberg G, Avraham R, Vardi A. Bacterial lifestyle switch in response to algal metabolites. eLife 2023; 12:e84400. [PMID: 36691727 PMCID: PMC9873259 DOI: 10.7554/elife.84400] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023] Open
Abstract
Unicellular algae, termed phytoplankton, greatly impact the marine environment by serving as the basis of marine food webs and by playing central roles in the biogeochemical cycling of elements. The interactions between phytoplankton and heterotrophic bacteria affect the fitness of both partners. It is becoming increasingly recognized that metabolic exchange determines the nature of such interactions, but the underlying molecular mechanisms remain underexplored. Here, we investigated the molecular and metabolic basis for the bacterial lifestyle switch, from coexistence to pathogenicity, in Sulfitobacter D7 during its interaction with Emiliania huxleyi, a cosmopolitan bloom-forming phytoplankter. To unravel the bacterial lifestyle switch, we analyzed bacterial transcriptomes in response to exudates derived from algae in exponential growth and stationary phase, which supported the Sulfitobacter D7 coexistence and pathogenicity lifestyles, respectively. In pathogenic mode, Sulfitobacter D7 upregulated flagellar motility and diverse transport systems, presumably to maximize assimilation of E. huxleyi-derived metabolites released by algal cells upon cell death. Algal dimethylsulfoniopropionate (DMSP) was a pivotal signaling molecule that mediated the transition between the lifestyles, supporting our previous findings. However, the coexisting and pathogenic lifestyles were evident only in the presence of additional algal metabolites. Specifically, we discovered that algae-produced benzoate promoted the growth of Sulfitobacter D7 and hindered the DMSP-induced lifestyle switch to pathogenicity, demonstrating that benzoate is important for maintaining the coexistence of algae and bacteria. We propose that bacteria can sense the physiological state of the algal host through changes in the metabolic composition, which will determine the bacterial lifestyle during interaction.
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Affiliation(s)
- Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Bareket Dassa
- Life Sciences Core Facilities, Weizmann Institute of ScienceRehovotIsrael
| | - Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Inbal Nussbaum
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of ScienceRehovotIsrael
| | - Gili Rosenberg
- Department of Biological Regulation, Weizmann Institute of ScienceRehovotIsrael
| | - Roi Avraham
- Department of Biological Regulation, Weizmann Institute of ScienceRehovotIsrael
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
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21
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Dynamic Diatom-Bacteria Consortia in Synthetic Plankton Communities. Appl Environ Microbiol 2022; 88:e0161922. [PMID: 36300970 PMCID: PMC9680611 DOI: 10.1128/aem.01619-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The marine food web is fueled by phototrophic phytoplankton. These algae are central primary producers responsible for the fixation of ca. 40% of the global CO
2
.
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22
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Sanchez-Garcia S, Wang H, Wagner-Döbler I. The microbiome of the dinoflagellate Prorocentrum cordatum in laboratory culture and its changes at higher temperatures. Front Microbiol 2022; 13:952238. [PMID: 36246277 PMCID: PMC9555710 DOI: 10.3389/fmicb.2022.952238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
In the ocean, phytoplankton are dependent on communities of bacteria living in the phycosphere, a hot spot of metabolic and genetic exchange. Many types of interactions between phytoplankton and phycosphere bacteria have been shown, but it is unclear if the microbial communities associated with microalgae strains in culture collections are beneficial or harmful to the host strain. Here, we studied the microbial communities associated with four strains of the dinoflagellate Prorocentrum cordatum that had been isolated from distant geographical locations and maintained in culture collection for hundreds of generations. Community composition was determined by 16S rRNA gene amplicon sequencing. The dinoflagellate host strain was the strongest parameter separating communities, while growth phase, lifestyle (particle-attached versus free-living) and temperature had only a modulating effect. Although the strains had been isolated from distant locations in the Atlantic and Pacific Ocean, 14 ASVs were shared among all strains, the most abundant ones being Gilvibacter, Marivita, uncultivated Rhodobacteraceae, Marinobacter, Hyphomonadaceae, Cupriavidus, Variovorax, and Paucibacter. Adaptation to higher temperatures resulted in specific changes in each phycosphere microbiome, including increased abundance of rare community members. We then compared the growth of the four xenic cultures to that of the axenic P. cordatum CCMP1329. At 20°C, growth of the xenic cultures was similar or slower than that of CCMP1329. At 26°C, all four xenic cultures experienced a death phase, while the axenic culture stably remained in the stationary phase. At 30°C, only two of the xenic cultures were able to grow. A shift of dinoflagellate metabolism from autotrophy to mixotrophy and competition between dinoflagellate and bacteria for limiting nutrients, including essential vitamins, may contribute to these differences in growth patterns.
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23
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Nef C, Dittami S, Kaas R, Briand E, Noël C, Mairet F, Garnier M. Sharing Vitamin B12 between Bacteria and Microalgae Does Not Systematically Occur: Case Study of the Haptophyte Tisochrysis lutea. Microorganisms 2022; 10:microorganisms10071337. [PMID: 35889056 PMCID: PMC9323062 DOI: 10.3390/microorganisms10071337] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 02/01/2023] Open
Abstract
Haptophyte microalgae are key contributors to microbial communities in many environments. It has been proposed recently that members of this group would be virtually all dependent on vitamin B12 (cobalamin), an enzymatic cofactor produced only by some bacteria and archaea. Here, we examined the processes of vitamin B12 acquisition by haptophytes. We tested whether co-cultivating the model species Tisochrysis lutea with B12-producing bacteria in vitamin-deprived conditions would allow the microalga to overcome B12 deprivation. While T. lutea can grow by scavenging vitamin B12 from bacterial extracts, co-culture experiments showed that the algae did not receive B12 from its associated bacteria, despite bacteria/algae ratios supposedly being sufficient to allow enough vitamin production. Since other studies reported mutualistic algae–bacteria interactions for cobalamin, these results question the specificity of such associations. Finally, cultivating T. lutea with a complex bacterial consortium in the absence of the vitamin partially rescued its growth, highlighting the importance of microbial interactions and diversity. This work suggests that direct sharing of vitamin B12 is specific to each species pair and that algae in complex natural communities can acquire it indirectly by other mechanisms (e.g., after bacterial lysis).
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Affiliation(s)
- Charlotte Nef
- Physiologie et Biotechnologie des Algues, IFREMER, Rue de l’Ile d’Yeu, F-44311 Nantes, France;
- Correspondence:
| | - Simon Dittami
- Station Biologique de Roscoff, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne University, F-29680 Roscoff, France;
| | - Raymond Kaas
- Physiologie et Biotechnologie des Algues, IFREMER, Rue de l’Ile d’Yeu, F-44311 Nantes, France;
| | - Enora Briand
- GENALG, PHYTOX, IFREMER, F-44000 Nantes, France; (E.B.); (M.G.)
| | - Cyril Noël
- SEBIMER, IRSI, IFREMER, F-29280 Brest, France;
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24
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Transcriptome analysis of Antarctic Rhodococcus sp. NJ-530 in the response to dimethylsulfoniopropionate. Polar Biol 2022. [DOI: 10.1007/s00300-022-03049-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Eliason O, Segev E. Coccolith Sr/Ca is a robust temperature and growth rate indicator that withstands dynamic microbial interactions. GEOBIOLOGY 2022; 20:435-443. [PMID: 35048494 PMCID: PMC9305965 DOI: 10.1111/gbi.12487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 12/06/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Coccolithophores are a diverse group of calcifying microalgae that have left a prominent fossil record on Earth. Various coccolithophore relics, both organic and inorganic, serve as proxies for reconstruction of past oceanic conditions. Emiliania huxleyi is the most widely distributed representative of the coccolithophores in modern oceans and is known to engage in dynamic interactions with bacteria. Algal-bacterial interactions influence various aspects of algal physiology and alter algal alkenone unsaturation (UK'37 ), a frequently used organic coccolithophore-derived paleo-temperature proxy. Whether algal-bacterial interactions influence inorganic coccolithophore-derived paleo-proxies is yet unknown. A commonly used inorganic proxy for past productivity and sea surface temperature is the Sr/Ca ratio of the coccolith calcite. Interestingly, during interactions between bacteria and a population of calcifying algae, bacteria were shown to physically attach only to non-calcified algal cells, suggesting an influence on algal calcification. In this study, we explore the effects of algal-bacterial interactions on calcification and coccolith Sr/Ca ratios. We find that while bacteria attach only to non-calcified algal cells, coccolith cell coverage and overall calcite production in algal populations with and without bacteria is similar. Furthermore, we find that Sr/Ca values are impacted only by water temperature and algal growth rate, regardless of bacterial influences on algal physiology. Our observations reinforce the robustness of coccolith Sr/Ca ratios as a paleo-proxy independent of microbial interactions and highlight a fundamental difference between organic and inorganic paleo-proxies.
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Affiliation(s)
- Or Eliason
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Einat Segev
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
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26
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Kalaitzidou MP, Alvanou MV, Papageorgiou KV, Lattos A, Sofia M, Kritas SK, Petridou E, Giantsis IA. Pollution Indicators and HAB-Associated Halophilic Bacteria Alongside Harmful Cyanobacteria in the Largest Mussel Cultivation Area in Greece. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095285. [PMID: 35564680 PMCID: PMC9104808 DOI: 10.3390/ijerph19095285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/16/2022]
Abstract
Taking into consideration the essential contribution of Mytilus galloprovincialis farming, it is of rising importance to add knowledge regarding bacterial species occurrence in water samples from aquaculture zones from the point of view of both the organism and public health. In the present study, we investigated the bacterial community existing in water samples from six Mytilus galloprovincialis aquaculture areas in the Thermaikos gulf, northern Greece, that may provoke toxicity in aquatic organisms and humans and may indicate environmental pollution in mussel production as well as algal blooms. Bacterial species were identified molecularly by sequencing of a partial 16s rRNA segment and were analyzed phylogenetically for the confirmation of the bacterial taxonomy. The results obtained revealed the presence of four bacterial genera (Halomonas sp., Planococcus sp., Sulfitobacter sp., and Synechocystis sp.). Members of the Halomonas and Sulfitobacter genera have been isolated from highly polluted sites, Planococcus bacteria have been identified in samples derived directly from plastic debris, and Synechocystis bacteria are in line with microcystin detection. In this context, the monitoring of the bacteria community in mussel aquaculture water samples from the Thermaikos gulf, the largest mussel cultivation area in Greece, represents an indicator of water pollution, microplastics presence, algal blooms, and toxin presence.
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Affiliation(s)
- Maria P. Kalaitzidou
- National Reference Laboratory for Marine Biotoxins, Department of Food Microbiology, Biochemical Control, Residues, Marine Biotoxins and Other Water Toxins, Directorate of Veterinary Center of Thessaloniki, Ministry of Rural Development and Food, 54627 Thessaloniki, Greece;
| | - Maria V. Alvanou
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece; (M.V.A.); (A.L.)
| | - Konstantinos V. Papageorgiou
- 3rd Military Veterinary Hospital, General Staff, Hellenic Ministry of Defense, 15th Km Thessaloniki-Vasilika, 57001 Thessaloniki, Greece;
| | - Athanasios Lattos
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece; (M.V.A.); (A.L.)
| | - Marina Sofia
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece;
| | - Spyridon K. Kritas
- Laboratory of Microbiology and Infectious Diseases, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.K.K.); (E.P.)
| | - Evanthia Petridou
- Laboratory of Microbiology and Infectious Diseases, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.K.K.); (E.P.)
| | - Ioannis A. Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece; (M.V.A.); (A.L.)
- Correspondence:
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27
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Coyne KJ, Wang Y, Johnson G. Algicidal Bacteria: A Review of Current Knowledge and Applications to Control Harmful Algal Blooms. Front Microbiol 2022; 13:871177. [PMID: 35464927 PMCID: PMC9022068 DOI: 10.3389/fmicb.2022.871177] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/01/2022] [Indexed: 12/19/2022] Open
Abstract
Interactions between bacteria and phytoplankton in aqueous ecosystems are both complex and dynamic, with associations that range from mutualism to parasitism. This review focuses on algicidal interactions, in which bacteria are capable of controlling algal growth through physical association or the production of algicidal compounds. While there is some evidence for bacterial control of algal growth in the field, our understanding of these interactions is largely based on laboratory culture experiments. Here, the range of these algicidal interactions is discussed, including specificity of bacterial control, mechanisms for activity, and insights into the chemical and biochemical analysis of these interactions. The development of algicidal bacteria or compounds derived from bacteria for control of harmful algal blooms is reviewed with a focus on environmentally friendly or sustainable methods of application. Potential avenues for future research and further development and application of bacterial algicides for the control of algal blooms are presented.
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Affiliation(s)
- Kathryn J. Coyne
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States
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28
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Moran MA, Kujawinski EB, Schroer WF, Amin SA, Bates NR, Bertrand EM, Braakman R, Brown CT, Covert MW, Doney SC, Dyhrman ST, Edison AS, Eren AM, Levine NM, Li L, Ross AC, Saito MA, Santoro AE, Segrè D, Shade A, Sullivan MB, Vardi A. Microbial metabolites in the marine carbon cycle. Nat Microbiol 2022; 7:508-523. [PMID: 35365785 DOI: 10.1038/s41564-022-01090-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/23/2022] [Indexed: 01/08/2023]
Abstract
One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.
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Affiliation(s)
- Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA.
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - William F Schroer
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Shady A Amin
- Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Nicholas R Bates
- Bermuda Institute of Ocean Sciences, St George's, Bermuda.,School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Erin M Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Rogier Braakman
- Departments of Earth, Atmospheric and Planetary Sciences, and Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - C Titus Brown
- Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Scott C Doney
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA, USA
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, USA.,Department of Earth and Environmental Science, Columbia University, Palisades, NY, USA
| | - Arthur S Edison
- Departments of Biochemistry and Genetics, Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA.,Helmholtz-Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, Oldenburg, Germany
| | - Naomi M Levine
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada
| | - Mak A Saito
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Daniel Segrè
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, and Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
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29
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Resolving the microalgal gene landscape at the strain level: A novel hybrid transcriptome of Emiliania huxleyi CCMP3266. Appl Environ Microbiol 2021; 88:e0141821. [PMID: 34757817 DOI: 10.1128/aem.01418-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microalgae are key ecological players with a complex evolutionary history. Genomic diversity, in addition to limited availability of high-quality genomes, challenge studies that aim to elucidate molecular mechanisms underlying microalgal ecophysiology. Here, we present a novel and comprehensive transcriptomic hybrid approach to generate a reference for genetic analyses, and resolve the microalgal gene landscape at the strain level. The approach is demonstrated for a strain of the coccolithophore microalga Emiliania huxleyi, which is a species complex with considerable genome variability. The investigated strain is commonly studied as a model for algal-bacterial interactions, and was therefore sequenced in the presence of bacteria to elicit the expression of interaction-relevant genes. We applied complementary PacBio Iso-Seq full-length cDNA, and poly(A)-independent Illumina total RNA sequencing, which resulted in a de novo assembled, near complete hybrid transcriptome. In particular, hybrid sequencing improved the reconstruction of long transcripts and increased the recovery of full-length transcript isoforms. To use the resulting hybrid transcriptome as a reference for genetic analyses, we demonstrate a method that collapses the transcriptome into a genome-like dataset, termed "synthetic genome" (sGenome). We used the sGenome as a reference to visually confirm the robustness of the CCMP3266 gene assembly, to conduct differential gene expression analysis, and to characterize novel E. huxleyi genes. The newly-identified genes contribute to our understanding of E. huxleyi genome diversification, and are predicted to play a role in microbial interactions. Our transcriptomic toolkit can be implemented in various microalgae to facilitate mechanistic studies on microalgal diversity and ecology. Importance Microalgae are key players in the ecology and biogeochemistry of our oceans. Efforts to implement genomic and transcriptomic tools in laboratory studies involving microalgae suffer from the lack of published genomes. In the case of coccolithophore microalgae, the problem has long been recognized; the model species Emiliania huxleyi is a species complex with genomes composed of a core, and a large variable portion. To study the role of the variable portion in niche adaptation, and specifically in microbial interactions, strain-specific genetic information is required. Here we present a novel transcriptomic hybrid approach, and generated strain-specific genome-like information. We demonstrate our approach on an E. huxleyi strain that is co-cultivated with bacteria. By constructing a "synthetic genome", we generated comprehensive gene annotations that enabled accurate analyses of gene expression patterns. Importantly, we unveiled novel genes in the variable portion of E. huxleyi that play putative roles in microbial interactions.
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30
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Shemi A, Alcolombri U, Schatz D, Farstey V, Vincent F, Rotkopf R, Ben-Dor S, Frada MJ, Tawfik DS, Vardi A. Dimethyl sulfide mediates microbial predator-prey interactions between zooplankton and algae in the ocean. Nat Microbiol 2021; 6:1357-1366. [PMID: 34697459 DOI: 10.1038/s41564-021-00971-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 09/01/2021] [Indexed: 12/11/2022]
Abstract
Phytoplankton are key components of the oceanic carbon and sulfur cycles1. During bloom events, some species can emit large amounts of the organosulfur volatile dimethyl sulfide (DMS) into the ocean and consequently the atmosphere, where it can modulate aerosol formation and affect climate2,3. In aquatic environments, DMS plays an important role as a chemical signal mediating diverse trophic interactions. Yet, its role in microbial predator-prey interactions remains elusive with contradicting evidence for its role in either algal chemical defence or in the chemo-attraction of grazers to prey cells4,5. Here we investigated the signalling role of DMS during zooplankton-algae interactions by genetic and biochemical manipulation of the algal DMS-generating enzyme dimethylsulfoniopropionate lyase (DL) in the bloom-forming alga Emiliania huxleyi6. We inhibited DL activity in E. huxleyi cells in vivo using the selective DL-inhibitor 2-bromo-3-(dimethylsulfonio)-propionate7 and overexpressed the DL-encoding gene in the model diatom Thalassiosira pseudonana. We showed that algal DL activity did not serve as an anti-grazing chemical defence but paradoxically enhanced predation by the grazer Oxyrrhis marina and other microzooplankton and mesozooplankton, including ciliates and copepods. Consumption of algal prey with induced DL activity also promoted O. marina growth. Overall, our results demonstrate that DMS-mediated grazing may be ecologically important and prevalent during prey-predator dynamics in aquatic ecosystems. The role of algal DMS revealed here, acting as an eat-me signal for grazers, raises fundamental questions regarding the retention of its biosynthetic enzyme through the evolution of dominant bloom-forming phytoplankton in the ocean.
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Affiliation(s)
- Adva Shemi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Uria Alcolombri
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.,Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Viviana Farstey
- The Inter-University Institute for Marine Sciences, Eilat, Israel
| | - Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Rotkopf
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Miguel J Frada
- The Inter-University Institute for Marine Sciences, Eilat, Israel.,Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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31
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Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise. Proc Natl Acad Sci U S A 2021; 118:2021586118. [PMID: 33707211 PMCID: PMC7980383 DOI: 10.1073/pnas.2021586118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Marine viruses are the most abundant biological entity in the ocean and are considered as major evolutionary drivers of microbial life [C. A. Suttle, Nat. Rev. Microbiol. 5, 801-812 (2007)]. Yet, we lack quantitative approaches to assess their impact on the marine ecosystem. Here, we provide quantification of active viral infection in the bloom forming single-celled phytoplankton Emiliania huxleyi infected by the large virus EhV, using high-throughput single-molecule messenger RNA in situ hybridization (smFISH) of both virus and host transcripts. In natural samples, viral infection reached only 25% of the population despite synchronized bloom demise exposing the coexistence of infected and noninfected subpopulations. We prove that photosynthetically active cells chronically release viral particles through nonlytic infection and that viral-induced cell lysis can occur without viral release, thus challenging major assumptions regarding the life cycle of giant viruses. We could also assess active infection in cell aggregates linking viral infection and carbon export to the deep ocean [C. P. Laber et al., Nat. Microbiol. 3, 537-547 (2018)] and suggest a potential host defense strategy by enrichment of infected cells in sinking aggregates. Our approach can be applied to diverse marine microbial systems, opening a mechanistic dimension to the study of biotic interactions in the ocean.
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32
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Roth Rosenberg D, Haber M, Goldford J, Lalzar M, Aharonovich D, Al-Ashhab A, Lehahn Y, Segrè D, Steindler L, Sher D. Particle-associated and free-living bacterial communities in an oligotrophic sea are affected by different environmental factors. Environ Microbiol 2021; 23:4295-4308. [PMID: 34036706 DOI: 10.1111/1462-2920.15611] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/23/2021] [Indexed: 12/20/2022]
Abstract
In the oceans and seas, environmental conditions change over multiple temporal and spatial scales. Here, we ask what factors affect the bacterial community structure across time, depth and size fraction during six seasonal cruises (2 years) in the ultra-oligotrophic Eastern Mediterranean Sea. The bacterial community varied most between size fractions (free-living (FL) vs. particle-associated), followed by depth and finally season. The FL community was taxonomically richer and more stable than the particle-associated (PA) one, which was characterized by recurrent 'blooms' of heterotrophic bacteria such as Alteromonas and Ralstonia. The heterotrophic FL and PA communities were also correlated with different environmental parameters: the FL population correlated with depth and phytoplankton, whereas PA bacteria were correlated primarily with the time of sampling. A significant part of the variability in community structure could, however, not be explained by the measured parameters. The metabolic potential of the PA community, predicted from 16S rRNA amplicon data using PICRUSt, was enriched in pathways associated with the degradation and utilization of biological macromolecules, as well as plastics, other petroleum products and herbicides. The FL community was enriched in predicted pathways for the metabolism of inositol phosphate, a potential phosphorus source, and of polycyclic aromatic hydrocarbons.
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Affiliation(s)
- Dalit Roth Rosenberg
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Markus Haber
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | | | - Maya Lalzar
- Bioinformatics Support Unit, University of Haifa, Haifa, Israel
| | - Dikla Aharonovich
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Ashraf Al-Ashhab
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.,Microbial Metagenomics Division, Dead Sea and Arava Science Center, Masada, Israel
| | - Yoav Lehahn
- Department of Maritime Geosciences, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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33
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Schatz D, Schleyer G, Saltvedt MR, Sandaa RA, Feldmesser E, Vardi A. Ecological significance of extracellular vesicles in modulating host-virus interactions during algal blooms. ISME JOURNAL 2021; 15:3714-3721. [PMID: 34083751 PMCID: PMC8630046 DOI: 10.1038/s41396-021-01018-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 12/01/2022]
Abstract
Extracellular vesicles are produced by organisms from all kingdoms and serve a myriad of functions, many of which involve cell-cell signaling, especially during stress conditions and host-pathogen interactions. In the marine environment, communication between microorganisms can shape trophic level interactions and population succession, yet we know very little about the involvement of vesicles in these processes. In a previous study, we showed that vesicles produced during viral infection by the ecologically important model alga Emiliania huxleyi, could act as a pro-viral signal, by expediting infection and enhancing the half-life of the virus in the extracellular milieu. Here, we expand our laboratory findings and show the effect of vesicles on natural populations of E. huxleyi in a mesocosm setting. We profile the small-RNA (sRNA) cargo of vesicles that were produced by E. huxleyi during bloom succession, and show that vesicles applied to natural assemblages expedite viral infection and prolong the half-life of this major mortality agent of E. huxleyi. We subsequently reveal that exposure of the natural assemblage to E. huxleyi-derived vesicles modulates not only host-virus dynamics, but also other components of the microbial food webs, thus emphasizing the importance of extracellular vesicles to microbial interactions in the marine environment.
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Affiliation(s)
- Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Guy Schleyer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Marius R Saltvedt
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ester Feldmesser
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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34
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Kuhlisch C, Schleyer G, Shahaf N, Vincent F, Schatz D, Vardi A. Viral infection of algal blooms leaves a unique metabolic footprint on the dissolved organic matter in the ocean. SCIENCE ADVANCES 2021; 7:7/25/eabf4680. [PMID: 34144983 PMCID: PMC8213229 DOI: 10.1126/sciadv.abf4680] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/06/2021] [Indexed: 05/23/2023]
Abstract
Algal blooms are hotspots of primary production in the ocean, forming the basis of the marine food web and fueling the dissolved organic matter (DOM) pool. Viruses are key players in controlling algal demise, thereby diverting biomass from higher trophic levels to the DOM pool, a process termed the "viral shunt." To decode the metabolic footprint of the viral shunt in the environment, we induced a bloom of Emiliania huxleyi and followed its succession using untargeted exometabolomics. We show that bloom succession induces dynamic changes in the exometabolic landscape. We found a set of chlorine-iodine-containing metabolites that were induced by viral infection and released during bloom demise. These metabolites were further detected in virus-infected oceanic E. huxleyi blooms. Therefore, we propose that halogenation with both chlorine and iodine is a distinct hallmark of the virus-induced DOM of E. huxleyi, providing insights into the metabolic consequences of the viral shunt.
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Affiliation(s)
- Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Guy Schleyer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Shahaf
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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35
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Bacterial Quorum-Sensing Signal Arrests Phytoplankton Cell Division and Impacts Virus-Induced Mortality. mSphere 2021; 6:6/3/e00009-21. [PMID: 33980670 PMCID: PMC8125044 DOI: 10.1128/msphere.00009-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Bacteria and phytoplankton form close associations in the ocean that are driven by the exchange of chemical compounds. The bacterial signal 2-heptyl-4-quinolone (HHQ) slows phytoplankton growth; however, the mechanism responsible remains unknown. Interactions between phytoplankton and heterotrophic bacteria fundamentally shape marine ecosystems by controlling primary production, structuring marine food webs, mediating carbon export, and influencing global climate. Phytoplankton-bacterium interactions are facilitated by secreted compounds; however, linking these chemical signals, their mechanisms of action, and their resultant ecological consequences remains a fundamental challenge. The bacterial quorum-sensing signal 2-heptyl-4-quinolone (HHQ) induces immediate, yet reversible, cellular stasis (no cell division or mortality) in the coccolithophore Emiliania huxleyi; however, the mechanism responsible remains unknown. Using transcriptomic and proteomic approaches in combination with diagnostic biochemical and fluorescent cell-based assays, we show that HHQ exposure leads to prolonged S-phase arrest in phytoplankton coincident with the accumulation of DNA damage and a lack of repair despite the induction of the DNA damage response (DDR). While this effect is reversible, HHQ-exposed phytoplankton were also protected from viral mortality, ascribing a new role of quorum-sensing signals in regulating multitrophic interactions. Furthermore, our data demonstrate that in situ measurements of HHQ coincide with areas of enhanced micro- and nanoplankton biomass. Our results suggest bacterial communication signals as emerging players that may be one of the contributing factors that help structure complex microbial communities throughout the ocean. IMPORTANCE Bacteria and phytoplankton form close associations in the ocean that are driven by the exchange of chemical compounds. The bacterial signal 2-heptyl-4-quinolone (HHQ) slows phytoplankton growth; however, the mechanism responsible remains unknown. Here, we show that HHQ exposure leads to the accumulation of DNA damage in phytoplankton and prevents its repair. While this effect is reversible, HHQ-exposed phytoplankton are also relieved of viral mortality, elevating the ecological consequences of this complex interaction. Further results indicate that HHQ may target phytoplankton proteins involved in nucleotide biosynthesis and DNA repair, both of which are crucial targets for viral success. Our results support microbial cues as emerging players in marine ecosystems, providing a new mechanistic framework for how bacterial communication signals mediate interspecies and interkingdom behaviors.
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Bucciarelli E, Stiger-Pouvreau V, Connan S. A New Protocol Using Acidification for Preserving DMSP in Macroalgae and Comparison with Existing Protocols. JOURNAL OF PHYCOLOGY 2021; 57:689-693. [PMID: 33295639 DOI: 10.1111/jpy.13113] [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: 06/25/2020] [Revised: 11/04/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) plays many important physiological and ecological roles in macroalgae. The most common method to measure DMSP is by gas chromatography analysis of the dimethylsulfide (DMS) produced after NaOH hydrolysis (pH > 12). Storage of DMS, however, is not recommended for more than a week. We investigated if acidification can be a suitable method to preserve DMSP in macroalgal samples over three months of storage, compared to widely used protocols such as drying and freezing at -20°C. The DMSP content of green (Ulva sp. and Ulva compressa), red (Chondrus crispus), and brown (Bifurcaria bifurcata) macroalgae were analyzed: 24 h after NaOH addition (control values); and after acidification (0.2 mol · L HCl-1 ) for 24 h of fresh material, followed by NaOH addition for 24 h. These values were compared to measurements after 3-month storage of samples that had been either dried in a heater (60°C for a night, and storage at room temperature), or frozen at -20°C, or kept in 0.2 mol · L HCl-1 . There was no significant difference between DMSP measurements on freshly collected material and after acidification of the samples, whether 24 h later or after 3 months of storage. This was in contrast to 3-month storage protocols involving overnight drying at 60°C (75-98% DMSP loss), and to a lesser degree freezing at -20°C (37-80% DMSP loss). We thus advise to acidify macroalgal samples for preservation over long periods of time rather than drying or freezing, when assaying DMSP content.
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Affiliation(s)
- Eva Bucciarelli
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280 Plouzane, France
| | | | - Solène Connan
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280 Plouzane, France
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Chhalodia AK, Dickschat JS. Breakdown of 3-(allylsulfonio)propanoates in bacteria from the Roseobacter group yields garlic oil constituents. Beilstein J Org Chem 2021; 17:569-580. [PMID: 33727980 PMCID: PMC7934745 DOI: 10.3762/bjoc.17.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/19/2021] [Indexed: 11/24/2022] Open
Abstract
Two analogues of 3-(dimethylsulfonio)propanoate (DMSP), 3-(diallylsulfonio)propanoate (DAllSP), and 3-(allylmethylsulfonio)propanoate (AllMSP), were synthesized and fed to marine bacteria from the Roseobacter clade. These bacteria are able to degrade DMSP into dimethyl sulfide and methanethiol. The DMSP analogues were also degraded, resulting in the release of allylated sulfur volatiles known from garlic. For unknown compounds, structural suggestions were made based on their mass spectrometric fragmentation pattern and confirmed by the synthesis of reference compounds. The results of the feeding experiments allowed to conclude on the substrate tolerance of DMSP degrading enzymes in marine bacteria.
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Affiliation(s)
- Anuj Kumar Chhalodia
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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Caruana AMN, Le Gac M, Hervé F, Rovillon GA, Geffroy S, Malo F, Abadie E, Amzil Z. Alexandrium pacificum and Alexandrium minutum: Harmful or environmentally friendly? MARINE ENVIRONMENTAL RESEARCH 2020; 160:105014. [PMID: 32907732 DOI: 10.1016/j.marenvres.2020.105014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/29/2020] [Accepted: 05/10/2020] [Indexed: 06/11/2023]
Abstract
Alexandrium minutum and Alexandrium pacificum are representatives of the dinoflagellate genus that regularly proliferate on the French coasts and other global coastlines. These harmful species may threaten shellfish harvest and human health due to their ability to synthesize neurotoxic alkaloids of the saxitoxin group. However, some dinoflagellates such as A. minutum, and as reported here A. pacificum as well, may also have a beneficial impact on the environment by producing dimethylsulfoniopropionate-DMSP, the precursor of dimethylsulfur-DMS and sulfate aerosols involved in climate balance. However, environmental conditions might influence Alexandrium physiology towards the production of harmful or environmentally friendly compounds. After assessing the influence of two salinity regimes (33 and 38) relative to each species origin (Atlantic French coast and Mediterranean Lagoon respectively), it appears that DMSP and toxin content was variable between the three experimented strains and that higher salinity disadvantages toxin production and tends to favor the production of the osmolytes DMSP and glycine betaine. Hence, this key metabolite production is strain and species-dependent and is influenced by environmental conditions of salinity which in turn, can diversely affect the environment. Widespread coastal blooms of A. minutum and A. pacificum, although being a risk for seafood contamination with toxins, are also a DMSP and DMS source that potentially contribute to the ecosystem structuration and climate. Regarding recent advances in DMSP biosynthesis pathway, 3 dsyB homologs were found in A. minutum but no homolog of the diatom sequence TpMMT.
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Affiliation(s)
| | | | - Fabienne Hervé
- IFREMER-Phycotoxins Laboratory, F - 44311, Nantes, France
| | | | - Solène Geffroy
- IFREMER-Phycotoxins Laboratory, F - 44311, Nantes, France
| | - Florent Malo
- IFREMER-Phycotoxins Laboratory, F - 44311, Nantes, France
| | - Eric Abadie
- MARBEC, Université de Montpellier, CNRS, IFREMER, IRD, Sète, France
| | - Zouher Amzil
- IFREMER-Phycotoxins Laboratory, F - 44311, Nantes, France
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Cryptic speciation of a pelagic Roseobacter population varying at a few thousand nucleotide sites. ISME JOURNAL 2020; 14:3106-3119. [PMID: 32814868 DOI: 10.1038/s41396-020-00743-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/28/2020] [Accepted: 08/07/2020] [Indexed: 01/14/2023]
Abstract
A drop of seawater contains numerous microspatial niches at the scale relevant to microbial activities. Examples are abiotic niches such as detrital particles that show different sizes and organic contents, and biotic niches resulting from bacteria-phage and bacteria-phytoplankton interactions. A common practice to investigate the impact of microenvironments on bacterial evolution is to separate the microenvironments physically and compare the bacterial inhabitants from each. It remains poorly understood, however, which microenvironment primarily drives bacterioplankton evolution in the pelagic ocean. By applying a dilution cultivation approach to an undisturbed coastal water sample, we isolate a bacterial population affiliated with the globally dominant Roseobacter group. Although varying at just a few thousand nucleotide sites across the whole genomes, members of this clonal population are diverging into two genetically separated subspecies. Genes underlying speciation are not unique to subspecies but instead clustered at the shared regions that represent ~6% of the genomic DNA. They are primarily involved in vitamin synthesis, motility, oxidative defense, carbohydrate, and amino acid utilization, consistent with the known strategies that roseobacters take to interact with phytoplankton and particles. Physiological assays corroborate that one subspecies outcompetes the other in these traits. Our results indicate that the microenvironments in the pelagic ocean represented by phytoplankton and organic particles are likely important niches that drive the cryptic speciation of the Roseobacter population, though microhabitats contributed by other less abundant pelagic hosts cannot be ruled out.
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Zhang F, Fan Y, Zhang D, Chen S, Bai X, Ma X, Xie Z, Xu H. Effect and mechanism of the algicidal bacterium Sulfitobacter porphyrae ZFX1 on the mitigation of harmful algal blooms caused by Prorocentrum donghaiense. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114475. [PMID: 33618477 DOI: 10.1016/j.envpol.2020.114475] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/12/2020] [Accepted: 03/25/2020] [Indexed: 06/12/2023]
Abstract
Sulfitobacter porphyrae ZFX1, isolated from surface seawater of the East China Sea during a Prorocentrum donghaiense bloom recession, exhibits high algicidal activity against P. donghaiense. To evaluate the algicidal effect of ZFX1, the algicidal mode and stability were investigated. The results showed that ZFX1 indirectly attacked algae by secreting algicidal compounds, and the algicidal activity of the ZFX1 supernatant was insensitive to different temperatures, light intensities and pH values (pH 3-12). To explore the algicidal mechanism of the ZFX1 supernatant, its effects on the morphological and ultrastructural alterations, photosynthetic capacity, reactive oxygen species (ROS) and antioxidative system of P. donghaiense were investigated. Scanning and transmission electron microscopy revealed that the ZFX1 supernatant destroyed the algal cell membrane structure and caused intracellular leakage. The decrease in the chlorophyll a content and the marked declines in both the photosynthetic efficiency (Fv/Fm) and the electron transport rate (rETR) indicated that the ZFX1 supernatant could damage the photosynthetic system of P. donghaiense. The excessive production of ROS in algal cells demonstrated the oxidative damage triggered by the ZFX1 supernatant. Although the antioxidant defense system of P. donghaiense was activated to scavenge excessive ROS, lipid oxidation occurred. The fatty acid composition profile indicated that the ZFX1 supernatant markedly increased the contents of two saturated fatty acids and a monounsaturated fatty acid and decreased the proportion of two polyunsaturated fatty acids, which resulted in lipids with a lower degree of unsaturation (DU). The decline in the DU decreased the lipid fluidity and rigidified the membrane system, and these effects destroyed the function of the membrane system and ultimately resulted in algal cell death. Therefore, ZFX1 probably plays a key role in mitigating P. donghaiense bloom by inducing lipid oxidation, decreasing the DU of lipids and ultimately destroying the membrane systems of algal cells.
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Affiliation(s)
- Fuxing Zhang
- State Key Laboratory of Cellular Stress Biology, and School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Yongxiang Fan
- State Key Laboratory of Cellular Stress Biology, and School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Danyang Zhang
- State Key Laboratory of Cellular Stress Biology, and School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Shuangshuang Chen
- State Key Laboratory of Cellular Stress Biology, and School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Xue Bai
- State Key Laboratory of Cellular Stress Biology, and School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Xiaohong Ma
- State Key Laboratory of Cellular Stress Biology, and School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Zhong Xie
- State Key Laboratory of Cellular Stress Biology, and School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Hong Xu
- State Key Laboratory of Cellular Stress Biology, and School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, Fujian, 361102, PR China.
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Lin Z, Chen B, Zhao L. Fluorescence-based bioassays with dose-response curve and relative potency in measuring algicidal virulence of Bacillus sp. B1 exudates against Heterosigma akashiwo. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 724:137691. [PMID: 32247969 DOI: 10.1016/j.scitotenv.2020.137691] [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: 12/13/2019] [Revised: 02/14/2020] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
This study demonstrated a Bacillus strain, B1, which was isolated from Pearl river estuary, China, and extracted extracellular algicidal compounds (EACs), exhibited algicidal effects against H. akashiwo upon fertilization experiments (>90% growth inhibition when exposed to 10% volume concentration of EACs within 96 h). Here we evaluated the feasibility of fluorescence-based bioassays (auto or stained fluorescence detected from on PAM fluorometry and flow cytometry) in quantifying algicidal potency of EACs released from Bacillus sp. B1 on H. akashiwo. Esterase activity and maximum photosystem II quantum yield (Fv/Fm) inhibition were used as sensitive endpoints in the bioassays. Logarithmic dose-response curve (DRC) based on three-parameters log-logistic model was applied to derived effective EACs concentrations (ECy, y being typically 10%, 50% or 90% of maximal effect) and relative potency (RP) was used to compare esterase activity and Fv/Fm inhibition sensitivities in dose-dependent manner. Esterase activity inhibition was more sensitive when exposed to low-dose EACs (RP10, fv/fm = 0.57 ± 0.01 < 1), conversely, Fv/Fm inhibition was accepted as a sensitive parameter when H. akashiwo exposed to higher-EACs doses. The fluorescence-based bioassays with dose-response curve and relative potency will help to assess bacterial virulence against H. akashiwo and its physiological mechanistic studies, and may be applicable for further insights into the role and influence of bacteria producing bioactive compounds in harmful algae blooms and shaping marine ecosystems.
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Affiliation(s)
- Zehong Lin
- School of Environment, Jinan University, Panyu Campus, Guangzhou, Guangdong 511443, China
| | - Binbin Chen
- School of Environment, Jinan University, Panyu Campus, Guangzhou, Guangdong 511443, China
| | - Ling Zhao
- School of Environment, Jinan University, Panyu Campus, Guangzhou, Guangdong 511443, China.
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Stock W, Blommaert L, De Troch M, Mangelinckx S, Willems A, Vyverman W, Sabbe K. Host specificity in diatom-bacteria interactions alleviates antagonistic effects. FEMS Microbiol Ecol 2020; 95:5606784. [PMID: 31647551 DOI: 10.1093/femsec/fiz171] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/23/2019] [Indexed: 11/13/2022] Open
Abstract
While different microalgae tend to be associated with different bacteria, it remains unclear whether such specific associations are beneficial for the microalgae. We assessed the impact of bacterial isolates, derived from various marine benthic diatoms, on the growth of several strains belonging to the Cylindrotheca closterium diatom species complex. We first tested the effect of 35 different bacterial isolates on the growth of a single C. closterium strain, and then evaluated the impact of 8 of these isolates on the growth of 6 C. closterium strains and 1 Cylindrotheca fusiformis strain. Surprisingly, most interactions were neutral to antagonistic. The interactions were highly specific, with diatom growth in the presence of specific bacteria differing between Cylindrotheca strains and species, and closely related bacteria eliciting contrasting diatom growth responses. These differences could be related to the origin of the bacterial isolates, as only isolates from foreign diatom hosts significantly reduced diatom growth, implying coadaptation between different Cylindrotheca strains and their associated bacteria. Interestingly, the antagonistic effect of a Marinobacter strain was alleviated by the presence of a microbial inoculum that was native to the diatom host, suggesting that coadapted bacteria might also benefit their host indirectly by preventing the establishment of harmful bacteria.
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Affiliation(s)
- Willem Stock
- Laboratory of Protistology and Aquatic Ecology, Biology Department, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium
| | - Lander Blommaert
- Laboratory of Protistology and Aquatic Ecology, Biology Department, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium
| | - Marleen De Troch
- Marine Biology, Biology Department, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium
| | - Sven Mangelinckx
- SynBioC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Biology Department, Ghent University, Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Biology Department, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology, Biology Department, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium
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Wang W, Qu C, Wang X, Gao X, Zhang H, Miao J. Identification of a functional dddD-Rh for dimethyl sulfide production in the Antarctic Rhodococcus sp. NJ-530. J Basic Microbiol 2020; 60:639-648. [PMID: 32378236 DOI: 10.1002/jobm.202000032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/11/2020] [Accepted: 04/20/2020] [Indexed: 11/11/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) is widespread in the oceans, and its biological metabolite, dimethyl sulfide (DMS), plays an important role in the atmosphere. The Antarctic region has become a hotspot in DMS studies due to the high spatial and temporal variability in DMS(P) concentration, but the level of bacterial DMS production remains unclear. In this study, a bacterium isolated from Antarctic floating ice, Rhodococcus sp. NJ-530, was found to metabolize DMSP into DMS, and the rate of DMS production was measured as 3.96 pmol·mg protein-1 ·h-1 . Rhodococcus sp. NJ-530 had a DddD-Rh enzyme containing two CaiB domains, which belonged to the CoA-transferase III superfamily. However, the DddD-Rh had a molecular weight of 73.21 kDa, which was very different from previously characterized DddD enzymes in sequence and evolution. In vitro assays showed that DddD-Rh was functional in the presence of acetyl-CoA. This was the first functional DddD from Gram-positive Actinobacteria. Moreover, a quantitative real-time polymerase chain reaction revealed that high temperature facilitated the expression of dddD-Rh, and changes of salinity had little effect on it. This study adds new evidence to the bacterial DMS production in the Southern Ocean and provides a basis for investigating the metabolic mechanism of DMSP in extreme environments.
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Affiliation(s)
- Wenyu Wang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Changfeng Qu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xixi Wang
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Xuxu Gao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Honghai Zhang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Jinlai Miao
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, National Laboratory for Marine Science and Technology, Qingdao, China
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Ku C, Sheyn U, Sebé-Pedrós A, Ben-Dor S, Schatz D, Tanay A, Rosenwasser S, Vardi A. A single-cell view on alga-virus interactions reveals sequential transcriptional programs and infection states. SCIENCE ADVANCES 2020; 6:eaba4137. [PMID: 32490206 PMCID: PMC7239649 DOI: 10.1126/sciadv.aba4137] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/10/2020] [Indexed: 05/12/2023]
Abstract
The discovery of giant viruses infecting eukaryotes from diverse ecosystems has revolutionized our understanding of the evolution of viruses and their impact on protist biology, yet knowledge on their replication strategies and transcriptome regulation remains limited. Here, we profile single-cell transcriptomes of the globally distributed microalga Emiliania huxleyi and its specific giant virus during infection. We detected profound heterogeneity in viral transcript levels among individual cells. Clustering single cells based on viral expression profiles enabled reconstruction of the viral transcriptional trajectory. Reordering cells along this path unfolded highly resolved viral genetic programs composed of genes with distinct promoter elements that orchestrate sequential expression. Exploring host transcriptome dynamics across the viral infection states revealed rapid and selective shutdown of protein-encoding nuclear transcripts, while the plastid and mitochondrial transcriptomes persisted into later stages. Single-cell RNA-seq opens a new avenue to unravel the life cycle of giant viruses and their unique hijacking strategies.
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Affiliation(s)
- Chuan Ku
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Uri Sheyn
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Arnau Sebé-Pedrós
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Shilo Rosenwasser
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
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Zeng YX, Zhang YH, Li HR, Luo W. Complete genome of Sulfitobacter sp. BSw21498 isolated from seawater of Arctic Kongsfjorden. Mar Genomics 2020; 53:100769. [PMID: 32229098 DOI: 10.1016/j.margen.2020.100769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/20/2020] [Accepted: 03/20/2020] [Indexed: 10/24/2022]
Abstract
The genus Sulfitobacter has been mostly found in marine and hypersaline environments. Members of this genus were observed to be associated with marine microalgae by inducing cell death of algae and degrading of algae-derived dimethylsulfoniopropionate (DMSP). Here we reported the complete genome sequence of strain Sulfitobacter sp. BSw21498 isolated from seawater of Kongsfjorden, an Arctic fjord in Svalbard. The strain contained a circular chromosome of 3,097,372 bp with G+C content of 58.55 mol% and a plasmid of 147,547 bp with G+C content of 56.53 mol%. In particular, a gene for DMSP lyase DddL was found in the genome, rendering Sulfitobacter sp. strain BSw21498 one of the Rhodobacterales bacteria equipped with the potential for DMSP degradation.
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Affiliation(s)
- Yin-Xin Zeng
- Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, People's Republic of China.
| | - Yi-He Zhang
- Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, People's Republic of China; College of Life Sciences, Yantai University, Yantai 264005, People's Republic of China
| | - Hui-Rong Li
- Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, People's Republic of China
| | - Wei Luo
- Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, People's Republic of China
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Fu H, Uchimiya M, Gore J, Moran MA. Ecological drivers of bacterial community assembly in synthetic phycospheres. Proc Natl Acad Sci U S A 2020; 117:3656-3662. [PMID: 32015111 PMCID: PMC7035482 DOI: 10.1073/pnas.1917265117] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In the nutrient-rich region surrounding marine phytoplankton cells, heterotrophic bacterioplankton transform a major fraction of recently fixed carbon through the uptake and catabolism of phytoplankton metabolites. We sought to understand the rules by which marine bacterial communities assemble in these nutrient-enhanced phycospheres, specifically addressing the role of host resources in driving community coalescence. Synthetic systems with varying combinations of known exometabolites of marine phytoplankton were inoculated with seawater bacterial assemblages, and communities were transferred daily to mimic the average duration of natural phycospheres. We found that bacterial community assembly was predictable from linear combinations of the taxa maintained on each individual metabolite in the mixture, weighted for the growth each supported. Deviations from this simple additive resource model were observed but also attributed to resource-based factors via enhanced bacterial growth when host metabolites were available concurrently. The ability of photosynthetic hosts to shape bacterial associates through excreted metabolites represents a mechanism by which microbiomes with beneficial effects on host growth could be recruited. In the surface ocean, resource-based assembly of host-associated communities may underpin the evolution and maintenance of microbial interactions and determine the fate of a substantial portion of Earth's primary production.
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Affiliation(s)
- He Fu
- Department of Marine Sciences, University of Georgia, Athens, GA 30602
| | - Mario Uchimiya
- Department of Marine Sciences, University of Georgia, Athens, GA 30602
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602
| | - Jeff Gore
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA 30602;
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Alejandre-Colomo C, Harder J, Fuchs BM, Rosselló-Móra R, Amann R. High-throughput cultivation of heterotrophic bacteria during a spring phytoplankton bloom in the North Sea. Syst Appl Microbiol 2020; 43:126066. [PMID: 32019686 DOI: 10.1016/j.syapm.2020.126066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/11/2019] [Accepted: 01/09/2020] [Indexed: 01/22/2023]
Abstract
On-going studies of phytoplankton-bacterioplankton interactions at the long-term ecological research site Helgoland Roads have indicated that many of the heterotrophic bacterial taxa have not yet been cultivated. A high-throughput approach combining whole cell matrix-assisted laser desorption ionization - time of flight mass spectroscopy with 16S rRNA gene sequencing was applied to the spring bloom of 2016. Aiming at an assessment of cultivability during a spring bloom, cultivation on solid marine media had to be used since dilution to extinction would not have been feasible for a high-throughput approach, as performed in this study. A total of 5023 isolates were obtained from nine weekly samples on eight different solid media between the early-bloom and post-bloom periods. Most of the 4136 strains identified affiliated with Bacteroidetes (13.3%), Gammaproteobacteria (26.9%), Alphaproteobacteria (40.6%) and Actinobacteria (6.7%). Of the 271 operational phylogenetic units (OPUs) identified, 13 are likely to represent novel genera and 143 novel species. A comparison with 16S rRNA gene tag data indicated that most of the isolates were rather rare in surface waters, with the exception of five OPUs affiliating with Rhodobacteraceae, Polaribacter, Psychromonas and Pseudoalteromonas. The effort yielded many novel isolates, yet most of the abundant heterotrophic bacteria still remained elusive. The large strain collection obtained will not only provide insights into the succession of the cultivable fraction of the bacterioplankton, but also enable fine-tuned taxonomic and physiological follow-up studies for improving our knowledge on heterotrophic bacteria in North Sea waters.
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Affiliation(s)
- Carlota Alejandre-Colomo
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain; Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Bernhard M Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain.
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
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48
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Zhang XH, Liu J, Liu J, Yang G, Xue CX, Curson ARJ, Todd JD. Biogenic production of DMSP and its degradation to DMS-their roles in the global sulfur cycle. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1296-1319. [PMID: 31231779 DOI: 10.1007/s11427-018-9524-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/16/2019] [Indexed: 01/08/2023]
Abstract
Dimethyl sulfide (DMS) is the most abundant form of volatile sulfur in Earth's oceans, and is mainly produced by the enzymatic clevage of dimethylsulfoniopropionate (DMSP). DMS and DMSP play important roles in driving the global sulfur cycle and may affect climate. DMSP is proposed to serve as an osmolyte, a grazing deterrent, a signaling molecule, an antioxidant, a cryoprotectant and/or as a sink for excess sulfur. It was long believed that only marine eukaryotes such as phytoplankton produce DMSP. However, we recently discovered that marine heterotrophic bacteria can also produce DMSP, making them a potentially important source of DMSP. At present, one prokaryotic and two eukaryotic DMSP synthesis enzymes have been identified. Marine heterotrophic bacteria are likely the major degraders of DMSP, using two known pathways: demethylation and cleavage. Many phytoplankton and some fungi can also cleave DMSP. So far seven different prokaryotic and one eukaryotic DMSP lyases have been identified. This review describes the global distribution pattern of DMSP and DMS, the known genes for biosynthesis and cleavage of DMSP, and the physiological and ecological functions of these important organosulfur molecules, which will improve understanding of the mechanisms of DMSP and DMS production and their roles in the environment.
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Affiliation(s)
- Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Ji Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jingli Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Guipeng Yang
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266071, China
| | - Chun-Xu Xue
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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Unmasking cellular response of a bloom-forming alga to viral infection by resolving expression profiles at a single-cell level. PLoS Pathog 2019; 15:e1007708. [PMID: 31017983 PMCID: PMC6502432 DOI: 10.1371/journal.ppat.1007708] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/06/2019] [Accepted: 03/15/2019] [Indexed: 12/31/2022] Open
Abstract
Infection by large dsDNA viruses can lead to a profound alteration of host transcriptome and metabolome in order to provide essential building blocks to support the high metabolic demand for viral assembly and egress. Host response to viral infection can typically lead to diverse phenotypic outcome that include shift in host life cycle and activation of anti-viral defense response. Nevertheless, there is a major bottleneck to discern between viral hijacking strategies and host defense responses when averaging bulk population response. Here we study the interaction between Emiliania huxleyi, a bloom-forming alga, and its specific virus (EhV), an ecologically important host-virus model system in the ocean. We quantified host and virus gene expression on a single-cell resolution during the course of infection, using automatic microfluidic setup that captures individual algal cells and multiplex quantitate PCR. We revealed high heterogeneity in viral gene expression among individual cells. Simultaneous measurements of expression profiles of host and virus genes at a single-cell level allowed mapping of infected cells into newly defined infection states and allowed detection specific host response in a subpopulation of infected cell which otherwise masked by the majority of the infected population. Intriguingly, resistant cells emerged during viral infection, showed unique expression profiles of metabolic genes which can provide the basis for discerning between viral resistant and susceptible cells within heterogeneous populations in the marine environment. We propose that resolving host-virus arms race at a single-cell level will provide important mechanistic insights into viral life cycles and will uncover host defense strategies. Almost all of our current understanding of the molecular mechanisms that govern host-pathogen interactions in the ocean is derived from experiments carried out at the population level, neglecting any heterogeneity. Here we used a single cell approach to unmask the phenotypic heterogeneity produced within infected populations of the cosmopolitan bloom-forming alga Emiliania huxleyi by its specific lytic virus. We found high variability in expression of viral genes among individual cells. This heterogeneity was used to map cells into their infection state and allowed to uncover a yet unrecognized host response. We also provide evidence that variability in host metabolic states provided a sensitive tool to decipher between susceptible and resistant cells.
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In plaque-mass spectrometry imaging of a bloom-forming alga during viral infection reveals a metabolic shift towards odd-chain fatty acid lipids. Nat Microbiol 2019; 4:527-538. [PMID: 30718847 PMCID: PMC6420086 DOI: 10.1038/s41564-018-0336-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 12/04/2018] [Indexed: 01/02/2023]
Abstract
Tapping into the metabolic cross-talk between a host and its virus can reveal unique strategies employed during infection. Viral infection is a dynamic process that generates an evolving metabolic landscape. Gaining a continuous view into the infection process is highly challenging and is limited by current metabolomics approaches, which typically measure the average of the entire population at various stages of infection. Here, we took an innovative approach to study the metabolic basis of host-virus interactions between the bloom-forming alga Emiliania huxleyi and its specific virus. We combined a classical method in virology, the plaque assay, with advanced mass spectrometry imaging (MSI), an approach we termed ‘in plaque-MSI’. Taking advantage of the spatial characteristics of the plaque, we mapped the metabolic landscape induced during infection in a high spatiotemporal resolution, unfolding the infection process in a continuous manner. Further unsupervised spatially-aware clustering, combined with known lipid biomarkers, revealed a systematic metabolic shift during infection towards lipids containing the odd-chain fatty acid pentadecanoic acid (C15:0). Applying ‘in plaque-MSI’ might facilitate the discovery of bioactive compounds that mediate the chemical arms race of host-virus interactions in diverse model systems.
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