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Masuda T, Mareš J, Shiozaki T, Inomura K, Fujiwara A, Prášil O. Crocosphaera watsonii - A widespread nitrogen-fixing unicellular marine cyanobacterium. JOURNAL OF PHYCOLOGY 2024; 60:604-620. [PMID: 38551849 DOI: 10.1111/jpy.13450] [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: 05/05/2023] [Revised: 12/14/2023] [Accepted: 02/08/2024] [Indexed: 06/12/2024]
Abstract
Crocosphaera watsonii is a unicellular N2-fixing (diazotrophic) cyanobacterium observed in tropical and subtropical oligotrophic oceans. As a diazotroph, it can be a source of bioavailable nitrogen (N) to the microbial community in N-limited environments, and this may fuel primary production in the regions where it occurs. Crocosphaera watsonii has been the subject of intense study, both in culture and in field populations. Here, we summarize the current understanding of the phylogenetic and physiological diversity of C. watsonii, its distribution, and its ecological niche. Analysis of the relationships among the individual Crocosphaera species and related free-living and symbiotic lineages of diazotrophs based on the nifH gene have shown that the C. watsonii group holds a basal position and that its sequence is more similar to Rippkaea and Zehria than to other Crocosphaera species. This finding warrants further scrutiny to determine if the placement is related to a horizontal gene transfer event. Here, the nifH UCYN-B gene copy number from a recent synthesis effort was used as a proxy for relative C. watsonii abundance to examine patterns of C. watsonii distribution as a function of environmental factors, like iron and phosphorus concentration, and complimented with a synthesis of C. watsonii physiology. Furthermore, we have summarized the current knowledge of C. watsonii with regards to N2 fixation, photosynthesis, and quantitative modeling of physiology. Because N availability can limit primary production, C. watsonii is widely recognized for its importance to carbon and N cycling in ocean ecosystems, and we conclude this review by highlighting important topics for further research on this important species.
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Affiliation(s)
- Takako Masuda
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czech Republic
- Japan Fisheries Research and Education Agency, Shiogama, Miyagi, Japan
| | - Jan Mareš
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czech Republic
- Institute of Hydrobiology, Biology Centre, The Czech Academy of Sciences, České Budejovice, Czech Republic
| | - Takuhei Shiozaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Amane Fujiwara
- Research Institute for Global Change, JAMSTEC, Yokosuka, Japan
| | - Ondřej Prášil
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czech Republic
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2
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Sun X, Xiao Y, Yong C, Sun H, Li S, Huang H, Jiang H. Interactions between the nitrogen-fixing cyanobacterium Trichodesmium and siderophore-producing cyanobacterium Synechococcus under iron limitation. ISME COMMUNICATIONS 2024; 4:ycae072. [PMID: 38873030 PMCID: PMC11171426 DOI: 10.1093/ismeco/ycae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/07/2024] [Indexed: 06/15/2024]
Abstract
As diazotrophic cyanobacteria of tremendous biomass, Trichodesmium continuously provide a nitrogen source for carbon-fixing cyanobacteria and drive the generation of primary productivity in marine environments. However, ocean iron deficiencies limit growth and metabolism of Trichodesmium. Recent studies have shown the co-occurrence of Trichodesmium and siderophore-producing Synechococcus in iron-deficient oceans, but whether siderophores secreted by Synechococcus can be used by Trichodesmium to adapt to iron deficiency is not clear. We constructed a mutant Synechococcus strain unable to produce siderophores to explore this issue. Synechococcus filtrates with or without siderophores were added into a Trichodesmium microbial consortium consisting of Trichodesmium erythraeum IMS 101 as the dominant microbe with chronic iron deficiency. By analyzing the physiological phenotype, metagenome, and metatranscriptome, we investigated the interactions between the nitrogen-fixing cyanobacterium Tricodesmium and siderophore-producing cyanobacterium Synechococcus under conditions of iron deficiency. The results indicated that siderophores secreted by Synechococcus are likely to chelate with free iron in the culture medium of the Trichodesmium consortium, reducing the concentration of bioavailable iron and posing greater challenges to the absorption of iron by Trichodesmium. These findings revealed the characteristics of iron-competitive utilization between diazotrophic cyanobacteria and siderophore-producing cyanobacteria, as well as potential interactions, and provide a scientific basis for understanding the regulatory effects of nutrient limitation on marine primary productivity.
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Affiliation(s)
- Xumei Sun
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People’s Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 1 Jintang Road, Zhuhai, Guangdong, 519000, People’s Republic of China
| | - Yan Xiao
- School of Life Sciences, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei, 430079, People’s Republic of China
| | - Chengwen Yong
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People’s Republic of China
| | - Hansheng Sun
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People’s Republic of China
| | - Shuangqing Li
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People’s Republic of China
| | - Hailong Huang
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People’s Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 1 Jintang Road, Zhuhai, Guangdong, 519000, People’s Republic of China
| | - Haibo Jiang
- School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang, 315211, People’s Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 1 Jintang Road, Zhuhai, Guangdong, 519000, People’s Republic of China
- School of Life Sciences, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei, 430079, People’s Republic of China
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3
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Koedooder C, Zhang F, Wang S, Basu S, Haley ST, Tolic N, Nicora CD, Glavina del Rio T, Dyhrman ST, Gledhill M, Boiteau RM, Rubin-Blum M, Shaked Y. Taxonomic distribution of metabolic functions in bacteria associated with Trichodesmium consortia. mSystems 2023; 8:e0074223. [PMID: 37916816 PMCID: PMC10734445 DOI: 10.1128/msystems.00742-23] [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: 07/26/2023] [Accepted: 09/21/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Colonies of the cyanobacteria Trichodesmium act as a biological hotspot for the usage and recycling of key resources such as C, N, P, and Fe within an otherwise oligotrophic environment. While Trichodesmium colonies are known to interact and support a unique community of algae and particle-associated microbes, our understanding of the taxa that populate these colonies and the gene functions they encode is still limited. Characterizing the taxa and adaptive strategies that influence consortium physiology and its concomitant biogeochemistry is critical in a future ocean predicted to have increasingly resource-depleted regions.
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Affiliation(s)
- Coco Koedooder
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
- Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Futing Zhang
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Siyuan Wang
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Subhajit Basu
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
- Microsensor Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sheean T. Haley
- Lamont-Doherty Earth Observatory, Columbia University, New York, USA
| | - Nikola Tolic
- Earth and Biological Sciences, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie D. Nicora
- Earth and Biological Sciences, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tijana Glavina del Rio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sonya T. Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, New York, USA
- Department of Earth and Environmental Sciences, Columbia University, New York, USA
| | | | - Rene M. Boiteau
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, USA
| | | | - Yeala Shaked
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
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4
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Naseema Rasheed R, Pourbakhtiar A, Mehdizadeh Allaf M, Baharlooeian M, Rafiei N, Alishah Aratboni H, Morones-Ramirez JR, Winck FV. Microalgal co-cultivation -recent methods, trends in omic-studies, applications, and future challenges. Front Bioeng Biotechnol 2023; 11:1193424. [PMID: 37799812 PMCID: PMC10548143 DOI: 10.3389/fbioe.2023.1193424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023] Open
Abstract
The burgeoning human population has resulted in an augmented demand for raw materials and energy sources, which in turn has led to a deleterious environmental impact marked by elevated greenhouse gas (GHG) emissions, acidification of water bodies, and escalating global temperatures. Therefore, it is imperative that modern society develop sustainable technologies to avert future environmental degradation and generate alternative bioproduct-producing technologies. A promising approach to tackling this challenge involves utilizing natural microbial consortia or designing synthetic communities of microorganisms as a foundation to develop diverse and sustainable applications for bioproduct production, wastewater treatment, GHG emission reduction, energy crisis alleviation, and soil fertility enhancement. Microalgae, which are photosynthetic microorganisms that inhabit aquatic environments and exhibit a high capacity for CO2 fixation, are particularly appealing in this context. They can convert light energy and atmospheric CO2 or industrial flue gases into valuable biomass and organic chemicals, thereby contributing to GHG emission reduction. To date, most microalgae cultivation studies have focused on monoculture systems. However, maintaining a microalgae monoculture system can be challenging due to contamination by other microorganisms (e.g., yeasts, fungi, bacteria, and other microalgae species), which can lead to low productivity, culture collapse, and low-quality biomass. Co-culture systems, which produce robust microorganism consortia or communities, present a compelling strategy for addressing contamination problems. In recent years, research and development of innovative co-cultivation techniques have substantially increased. Nevertheless, many microalgae co-culturing technologies remain in the developmental phase and have yet to be scaled and commercialized. Accordingly, this review presents a thorough literature review of research conducted in the last few decades, exploring the advantages and disadvantages of microalgae co-cultivation systems that involve microalgae-bacteria, microalgae-fungi, and microalgae-microalgae/algae systems. The manuscript also addresses diverse uses of co-culture systems, and growing methods, and includes one of the most exciting research areas in co-culturing systems, which are omic studies that elucidate different interaction mechanisms among microbial communities. Finally, the manuscript discusses the economic viability, future challenges, and prospects of microalgal co-cultivation methods.
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Affiliation(s)
| | - Asma Pourbakhtiar
- School of Chemical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | | | - Maedeh Baharlooeian
- Department of Marine Biology, Faculty of Marine Science and Oceanography, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
| | - Nahid Rafiei
- Regulatory Systems Biology Lab, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, Nuevo León, Mexico
| | - Hossein Alishah Aratboni
- Regulatory Systems Biology Lab, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, Nuevo León, Mexico
| | - Jose Ruben Morones-Ramirez
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, Nuevo León, Mexico
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Universidad Autonoma de Nuevo Leon (UANL), Av Universidad s/n, CD. Universitaria, San Nicolás de los Garza, Nuevo León, Mexico
| | - Flavia Vischi Winck
- Regulatory Systems Biology Lab, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
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5
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El-Seedi HR, El-Mallah MF, Yosri N, Alajlani M, Zhao C, Mehmood MA, Du M, Ullah H, Daglia M, Guo Z, Khalifa SAM, Shou Q. Review of Marine Cyanobacteria and the Aspects Related to Their Roles: Chemical, Biological Properties, Nitrogen Fixation and Climate Change. Mar Drugs 2023; 21:439. [PMID: 37623720 PMCID: PMC10456358 DOI: 10.3390/md21080439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
Marine cyanobacteria are an ancient group of photosynthetic microbes dating back to 3.5 million years ago. They are prolific producers of bioactive secondary metabolites. Over millions of years, natural selection has optimized their metabolites to possess activities impacting various biological targets. This paper discusses the historical and existential records of cyanobacteria, and their role in understanding the evolution of marine cyanobacteria through the ages. Recent advancements have focused on isolating and screening bioactive compounds and their respective medicinal properties, and we also discuss chemical property space and clinical trials, where compounds with potential pharmacological effects, such as cytotoxicity, anticancer, and antiparasitic properties, are highlighted. The data have shown that about 43% of the compounds investigated have cytotoxic effects, and around 8% have anti-trypanosome activity. We discussed the role of different marine cyanobacteria groups in fixing nitrogen percentages on Earth and their outcomes in fish productivity by entering food webs and enhancing productivity in different agricultural and ecological fields. The role of marine cyanobacteria in the carbon cycle and their outcomes in improving the efficiency of photosynthetic CO2 fixation in the chloroplasts of crop plants, thus enhancing the crop plant's yield, was highlighted. Ultimately, climate changes have a significant impact on marine cyanobacteria where the temperature rises, and CO2 improves the cyanobacterial nitrogen fixation.
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Affiliation(s)
- Hesham R. El-Seedi
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- International Joint Research Laboratory of Intelligent Agriculture and Agri-Products Processing, Jiangsu University, Jiangsu Education Department, Nanjing 210024, China
- Department of Chemistry, Faculty of Science, Islamic University of Madinah, Madinah 42351, Saudi Arabia
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt;
| | - Mohamed F. El-Mallah
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt;
| | - Nermeen Yosri
- Chemistry Department of Medicinal and Aromatic Plants, Research Institute of Medicinal and Aromatic Plants (RIMAP), Beni-Suef University, Beni-Suef 62514, Egypt;
- China Light Industry Key Laboratory of Food Intelligent Detection & Processing, School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China;
| | - Muaaz Alajlani
- Faculty of Pharmacy, Al-Sham Private University, Damascus 0100, Syria;
| | - Chao Zhao
- College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Muhammad A. Mehmood
- Bioenergy Research Center, Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Ming Du
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China;
| | - Hammad Ullah
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Maria Daglia
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Zhiming Guo
- China Light Industry Key Laboratory of Food Intelligent Detection & Processing, School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China;
| | - Shaden A. M. Khalifa
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- Psychiatry and Psychology Department, Capio Saint Göran’s Hospital, Sankt Göransplan 1, 112 19 Stockholm, Sweden
| | - Qiyang Shou
- Second Clinical Medical College, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou 310053, China
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6
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Johnson C, Dubbs LL, Piehler M. Reframing the contribution of pelagic Sargassum epiphytic N2 fixation. PLoS One 2023; 18:e0289485. [PMID: 37527268 PMCID: PMC10393174 DOI: 10.1371/journal.pone.0289485] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 07/19/2023] [Indexed: 08/03/2023] Open
Abstract
Though nitrogen fixation by epiphytic diazotrophs on pelagic Sargassum has been recognized for decades, it has been assumed to contribute insignificantly to the overall marine nitrogen budget. This six-year study reframes this concept through long-term measurements of Sargassum community nitrogen fixation rates, and by extrapolating mass-specific rates to a theoretical square meter portion of Sargassum mat allowing for comparison of these rates to those of other marine and coastal diazotrophs. On 24 occasions from 2015 to 2021, rates of nitrogen fixation were measured using whole fronds of Sargassum collected from the western edge of the Gulf Stream off Cape Hatteras, North Carolina. Across all dates, mass-specific rates ranged from 0 to 37.77 μmol N g-1 h-1 with a mean of 4.156 μmol N g-1 h-1. Extrapolating using a mat-specific density of Sargassum, these rates scale to a range of 0 to 30,916 μmol N m-2 d-1 and a mean of 3,697 μmol N m-2 d-1. Quantifying this community's rates of nitrogen fixation over several years captured the sometimes-extreme variability in rates, characteristic of marine diazotrophs, which has not been reported in the literature to date. When these measurements are considered alongside estimates of the density of pelagic Sargassum, rates of nitrogen fixation by Sargassum's epiphytic diazotrophs rival that of their coastal macrophyte and planktonic counterparts. Given Sargassum's wide and expanding geographic range, the results of this study suggest this community may contribute reactive nitrogen on a meaningful, basin-wide scale, which merits further study.
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Affiliation(s)
- Claire Johnson
- Environment, Ecology and Energy Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lindsay L. Dubbs
- Environment, Ecology and Energy Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Institute for the Environment, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Coastal Studies Institute, East Carolina University, Wanchese, North Carolina, United States of America
| | - Michael Piehler
- Institute for the Environment, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Earth, Marine and Environmental Sciences Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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7
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Muñoz-Marín MDC, Magasin JD, Zehr JP. Open ocean and coastal strains of the N2-fixing cyanobacterium UCYN-A have distinct transcriptomes. PLoS One 2023; 18:e0272674. [PMID: 37130101 PMCID: PMC10153697 DOI: 10.1371/journal.pone.0272674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 02/18/2023] [Indexed: 05/03/2023] Open
Abstract
Decades of research on marine N2 fixation focused on Trichodesmium, which are generally free-living cyanobacteria, but in recent years the endosymbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) has received increasing attention. However, few studies have shed light on the influence of the host versus the habitat on UCYN-A N2 fixation and overall metabolism. Here we compared transcriptomes from natural populations of UCYN-A from oligotrophic open-ocean versus nutrient-rich coastal waters, using a microarray that targets the full genomes of UCYN-A1 and UCYN-A2 and known genes for UCYN-A3. We found that UCYN-A2, usually regarded as adapted to coastal environments, was transcriptionally very active in the open ocean and appeared to be less impacted by habitat change than UCYN-A1. Moreover, for genes with 24 h periodic expression we observed strong but inverse correlations among UCYN-A1, A2, and A3 to oxygen and chlorophyll, which suggests distinct host-symbiont relationships. Across habitats and sublineages, genes for N2 fixation and energy production had high transcript levels, and, intriguingly, were among the minority of genes that kept the same schedule of diel expression. This might indicate different regulatory mechanisms for genes that are critical to the symbiosis for the exchange of nitrogen for carbon from the host. Our results underscore the importance of N2 fixation in UCYN-A symbioses across habitats, with consequences for community interactions and global biogeochemical cycles.
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Affiliation(s)
- María Del Carmen Muñoz-Marín
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - Jonathan D Magasin
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
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8
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Landa M, Turk-Kubo KA, Cornejo-Castillo FM, Henke BA, Zehr JP. Critical Role of Light in the Growth and Activity of the Marine N 2-Fixing UCYN-A Symbiosis. Front Microbiol 2021; 12:666739. [PMID: 34025621 PMCID: PMC8139342 DOI: 10.3389/fmicb.2021.666739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/08/2021] [Indexed: 11/27/2022] Open
Abstract
The unicellular N2-fixing cyanobacteria UCYN-A live in symbiosis with haptophytes in the Braarudosphaera bigelowii lineage. Maintaining N2-fixing symbioses between two unicellular partners requires tight coordination of multiple biological processes including cell growth and division and, in the case of the UCYN-A symbiosis, N2 fixation of the symbiont and photosynthesis of the host. In this system, it is thought that the host photosynthesis supports the high energetic cost of N2 fixation, and both processes occur during the light period. However, information on this coordination is very limited and difficult to obtain because the UCYN-A symbiosis has yet to be available in culture. Natural populations containing the UCYN-A2 symbiosis were manipulated to explore the effects of alterations of regular light and dark periods and inhibition of host photosynthesis on N2 fixation (single cell N2 fixation rates), nifH gene transcription, and UCYN-A2 cell division (fluorescent in situ hybridization and nifH gene abundances). The results showed that the light period is critical for maintenance of regular patterns of gene expression, N2 fixation and symbiont replication and cell division. This study suggests a crucial role for the host as a producer of fixed carbon, rather than light itself, in the regulation and implementation of these cellular processes in UCYN-A.
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Affiliation(s)
- Marine Landa
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
| | | | - Britt A Henke
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
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9
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Mutalipassi M, Riccio G, Mazzella V, Galasso C, Somma E, Chiarore A, de Pascale D, Zupo V. Symbioses of Cyanobacteria in Marine Environments: Ecological Insights and Biotechnological Perspectives. Mar Drugs 2021; 19:227. [PMID: 33923826 PMCID: PMC8074062 DOI: 10.3390/md19040227] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 01/07/2023] Open
Abstract
Cyanobacteria are a diversified phylum of nitrogen-fixing, photo-oxygenic bacteria able to colonize a wide array of environments. In addition to their fundamental role as diazotrophs, they produce a plethora of bioactive molecules, often as secondary metabolites, exhibiting various biological and ecological functions to be further investigated. Among all the identified species, cyanobacteria are capable to embrace symbiotic relationships in marine environments with organisms such as protozoans, macroalgae, seagrasses, and sponges, up to ascidians and other invertebrates. These symbioses have been demonstrated to dramatically change the cyanobacteria physiology, inducing the production of usually unexpressed bioactive molecules. Indeed, metabolic changes in cyanobacteria engaged in a symbiotic relationship are triggered by an exchange of infochemicals and activate silenced pathways. Drug discovery studies demonstrated that those molecules have interesting biotechnological perspectives. In this review, we explore the cyanobacterial symbioses in marine environments, considering them not only as diazotrophs but taking into consideration exchanges of infochemicals as well and emphasizing both the chemical ecology of relationship and the candidate biotechnological value for pharmaceutical and nutraceutical applications.
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Affiliation(s)
- Mirko Mutalipassi
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Gennaro Riccio
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Valerio Mazzella
- Department of Integrated Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
| | - Christian Galasso
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Emanuele Somma
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri, 34127 Trieste, Italy;
- Department of Marine Biotechnology, Ischia Marine Centre, Stazione Zoologica Anton Dohrn, Punta San Pietro, 80077 Naples, Italy;
| | - Antonia Chiarore
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy;
| | - Donatella de Pascale
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Valerio Zupo
- Department of Marine Biotechnology, Ischia Marine Centre, Stazione Zoologica Anton Dohrn, Punta San Pietro, 80077 Naples, Italy;
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10
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Farnelid H, Turk-Kubo K, Zehr JP. Cell sorting reveals few novel prokaryote and photosynthetic picoeukaryote associations in the oligotrophic ocean. Environ Microbiol 2020; 23:1469-1480. [PMID: 33295132 PMCID: PMC8048811 DOI: 10.1111/1462-2920.15351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 12/04/2020] [Indexed: 11/28/2022]
Abstract
Close associations between single‐celled marine organisms can have a central role in biogeochemical processes and are of great interest for understanding the evolution of organisms. The global significance of such associations raises the question of whether unidentified associations are yet to be discovered. In this study, fluorescence‐activated cell sorted photosynthetic picoeukayote (PPE) populations and single cells were analysed by sequencing of 16S rRNA genes in the oligotrophic North Pacific Subtropical Gyre. Samples were collected during two cruises, spanning depths near the deep chlorophyll maximum, where the abundance of PPEs was highest. The association between the widespread and significant nitrogen (N2)‐fixing cyanobacterium, UCYN‐A and its prymnesiophyte host was prevalent in both population and single‐cell sorts. Several bacterial sequences, affiliating with previously described symbiotic taxa were detected but their detection was rare and not well replicated, precluding identification of novel tightly linked species‐specific associations. Similarly, no enrichment of dominant seawater taxa such as Prochlorococcus, SAR11 or Synechococcus was observed suggesting that these were not systematically ingested by the PPE in this study. The results indicate that apart from the UCYN‐A symbiosis, similar tight species‐specific associations with PPEs are unusual in the oligotrophic ocean.
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Affiliation(s)
- Hanna Farnelid
- Ocean Sciences Department, University of California, Santa Cruz, CA, USA.,Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Kendra Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, CA, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, CA, USA
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11
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Quantifying Oxygen Management and Temperature and Light Dependencies of Nitrogen Fixation by Crocosphaera watsonii. mSphere 2019; 4:4/6/e00531-19. [PMID: 31826967 PMCID: PMC6908418 DOI: 10.1128/msphere.00531-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Crocosphaera is a major dinitrogen (N2)-fixing microorganism, providing bioavailable nitrogen (N) to marine ecosystems. The N2-fixing enzyme nitrogenase is deactivated by oxygen (O2), which is abundant in marine environments. Using a cellular scale model of Crocosphaera sp. and laboratory data, we quantify the role of three O2 management strategies by Crocosphaera sp.: size adjustment, reduced O2 diffusivity, and respiratory protection. Our model predicts that Crocosphaera cells increase their size under high O2 Using transmission electron microscopy, we show that starch granules and thylakoid membranes are located near the cytoplasmic membranes, forming a barrier for O2 The model indicates a critical role for respiration in protecting the rate of N2 fixation. Moreover, the rise in respiration rates and the decline in ambient O2 with temperature strengthen this mechanism in warmer water, providing a physiological rationale for the observed niche of Crocosphaera at temperatures exceeding 20°C. Our new measurements of the sensitivity to light intensity show that the rate of N2 fixation reaches saturation at a lower light intensity (∼100 μmol m-2 s-1) than photosynthesis and that both are similarly inhibited by light intensities of >500 μmol m-2 s-1 This suggests an explanation for the maximum population of Crocosphaera occurring slightly below the ocean surface.IMPORTANCE Crocosphaera is one of the major N2-fixing microorganisms in the open ocean. On a global scale, the process of N2 fixation is important in balancing the N budget, but the factors governing the rate of N2 fixation remain poorly resolved. Here, we combine a mechanistic model and both previous and present laboratory studies of Crocosphaera to quantify how chemical factors such as C, N, Fe, and O2 and physical factors such as temperature and light affect N2 fixation. Our study shows that Crocosphaera combines multiple mechanisms to reduce intracellular O2 to protect the O2-sensitive N2-fixing enzyme. Our model, however, indicates that these protections are insufficient at low temperature due to reduced respiration and the rate of N2 fixation becomes severely limited. This provides a physiological explanation for why the geographic distribution of Crocosphaera is confined to the warm low-latitude ocean.
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12
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Gavelis GS, Gile GH. How did cyanobacteria first embark on the path to becoming plastids?: lessons from protist symbioses. FEMS Microbiol Lett 2019; 365:5079637. [PMID: 30165400 DOI: 10.1093/femsle/fny209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/23/2018] [Indexed: 12/13/2022] Open
Abstract
Symbioses between phototrophs and heterotrophs (a.k.a 'photosymbioses') are extremely common, and range from loose and temporary associations to obligate and highly specialized forms. In the history of life, the most transformative was the 'primary endosymbiosis,' wherein a cyanobacterium was engulfed by a eukaryote and became genetically integrated as a heritable photosynthetic organelle, or plastid. By allowing the rise of algae and plants, this event dramatically altered the biosphere, but its remote origin over one billion years ago has obscured the sequence of events leading to its establishment. Here, we review the genetic, physiological and developmental hurdles involved in early primary endosymbiosis. Since we cannot travel back in time to witness these evolutionary junctures, we will draw on examples of unicellular eukaryotes (protists) spanning diverse modes of photosymbiosis. We also review experimental approaches that could be used to recreate aspects of early primary endosymbiosis on a human timescale.
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Affiliation(s)
- Gregory S Gavelis
- School of Life Sciences, Arizona State University, Room 611, Life Science Tower E, 427 E, Tyler Mall, Tempe, AZ 85287, USA
| | - Gillian H Gile
- School of Life Sciences, Arizona State University, Room 611, Life Science Tower E, 427 E, Tyler Mall, Tempe, AZ 85287, USA
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13
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Cornejo-Castillo FM, Muñoz-Marín MDC, Turk-Kubo KA, Royo-Llonch M, Farnelid H, Acinas SG, Zehr JP. UCYN-A3, a newly characterized open ocean sublineage of the symbiotic N 2 -fixing cyanobacterium Candidatus Atelocyanobacterium thalassa. Environ Microbiol 2018; 21:111-124. [PMID: 30255541 DOI: 10.1111/1462-2920.14429] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 09/06/2018] [Accepted: 09/22/2018] [Indexed: 12/01/2022]
Abstract
The symbiotic unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is one of the most abundant and widespread nitrogen (N2 )-fixing cyanobacteria in the ocean. Although it remains uncultivated, multiple sublineages have been detected based on partial nitrogenase (nifH) gene sequences, including the four most commonly detected sublineages UCYN-A1, UCYN-A2, UCYN-A3 and UCYN-A4. However, very little is known about UCYN-A3 beyond the nifH sequences from nifH gene diversity surveys. In this study, single cell sorting, DNA sequencing, qPCR and CARD-FISH assays revealed discrepancies involving the identification of sublineages, which led to new information on the diversity of the UCYN-A symbiosis. 16S rRNA and nifH gene sequencing on single sorted cells allowed us to identify the 16S rRNA gene of the uncharacterized UCYN-A3 sublineage. We designed new CARD-FISH probes that allowed us to distinguish and observe UCYN-A2 in a coastal location (SIO Pier; San Diego) and UCYN-A3 in an open ocean location (Station ALOHA; Hawaii). Moreover, we reconstructed about 13% of the UCYN-A3 genome from Tara Oceans metagenomic data. Finally, our findings unveil the UCYN-A3 symbiosis in open ocean waters suggesting that the different UCYN-A sublineages are distributed along different size fractions of the plankton defined by the cell-size ranges of their prymnesiophyte hosts.
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Affiliation(s)
- Francisco M Cornejo-Castillo
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.,Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Maria Del Carmen Muñoz-Marín
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.,Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - Kendra A Turk-Kubo
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Hanna Farnelid
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.,Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
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14
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Yao S, Lyu S, An Y, Lu J, Gjermansen C, Schramm A. Microalgae-bacteria symbiosis in microalgal growth and biofuel production: a review. J Appl Microbiol 2018; 126:359-368. [PMID: 30168644 DOI: 10.1111/jam.14095] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 06/24/2018] [Accepted: 08/22/2018] [Indexed: 01/19/2023]
Abstract
Photosynthetic microalgae can capture solar energy and convert it to bioenergy and biochemical products. In nature or industrial processes, microalgae live together with bacterial communities and may maintain symbiotic relationships. In general interactions, microalgae exude dissolved organic carbon that becomes available to bacteria. In return, the bacteria remineralize sulphur, nitrogen and phosphorous to support the further growth of microalgae. In specific interactions, heterotrophic bacteria supply B vitamins as organic cofactors or produce siderophores to bind iron, which could be utilized by microalgae, while the algae supply fixed carbon to the bacteria in return. In this review, we focus on mutualistic relationship between microalgae and bacteria, summarizing recent studies on the mechanisms involved in microalgae-bacteria symbiosis. Symbiotic bacteria on promoting microalgal growth are described and the relevance of microalgae-bacteria interactions for biofuel production processes is discussed. Symbiotic microalgae-bacteria consortia could be utilized to improve microalgal biomass production and to enrich the biomass with valuable chemical and energy compounds. The suitable control of such biological interactions between microalgae and bacteria will help to improve the microalgae-based biomass and biofuel production in the future.
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Affiliation(s)
- S Yao
- Microbiology Group, College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China.,Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus C, Denmark
| | - S Lyu
- Microbiology Group, College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Y An
- Microbiology Group, College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - J Lu
- Microbial Engineering Group, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Roskilde, Denmark
| | - C Gjermansen
- Microbial Engineering Group, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Roskilde, Denmark
| | - A Schramm
- Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus C, Denmark
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15
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Robidart JC, Magasin JD, Shilova IN, Turk-Kubo KA, Wilson ST, Karl DM, Scholin CA, Zehr JP. Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre. ISME JOURNAL 2018; 13:374-387. [PMID: 30254320 DOI: 10.1038/s41396-018-0280-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/26/2018] [Accepted: 08/26/2018] [Indexed: 11/09/2022]
Abstract
Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity in the surface ocean is constrained by nutrients which are supplied, in part, by mixing with deeper water. Little is known about the time scales, frequency, or impact of mixing on microbial communities. We combined in situ sampling using the Environmental Sample Processor and a small-scale mixing experiment with lower euphotic zone water to determine how individual populations respond to mixing. Transcriptional responses were measured using the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) microarray, which targets all three domains of life and viruses. The experiment showed that mixing substantially affects photosynthetic taxa as expected, but surprisingly also showed that populations respond differently to unfiltered deep water which contains particles (organisms and detritus) compared to filtered deep water that only contains nutrients and viruses, pointing to the impact of biological interactions associated with these events. Comparison between experimental and in situ population transcription patterns indicated that manipulated populations can serve as analogs for natural populations, and that natural populations may be frequently or continuously responding to nutrients from deeper waters. Finally, this study also shows that the microarray approach, which is complementary to metatranscriptomic sequencing, is useful for determining the physiological status of in situ microbial communities.
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Affiliation(s)
- J C Robidart
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.,National Oceanography Centre, Southampton, UK
| | - J D Magasin
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - I N Shilova
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.,Second Genome, South San Francisco, CA, USA
| | - K A Turk-Kubo
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - S T Wilson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - D M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - C A Scholin
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - J P Zehr
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.
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16
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Farnelid H, Turk-Kubo K, Ploug H, Ossolinski JE, Collins JR, Van Mooy BAS, Zehr JP. Diverse diazotrophs are present on sinking particles in the North Pacific Subtropical Gyre. ISME JOURNAL 2018; 13:170-182. [PMID: 30116043 PMCID: PMC6299005 DOI: 10.1038/s41396-018-0259-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/03/2018] [Accepted: 07/26/2018] [Indexed: 11/09/2022]
Abstract
Sinking particles transport carbon and nutrients from the surface ocean into the deep sea and are considered hot spots for bacterial diversity and activity. In the oligotrophic oceans, nitrogen (N2)-fixing organisms (diazotrophs) are an important source of new N but the extent to which these organisms are present and exported on sinking particles is not well known. Sinking particles were collected every 6 h over a 2-day period using net traps deployed at 150 m in the North Pacific Subtropical Gyre. The bacterial community and composition of diazotrophs associated with individual and bulk sinking particles was assessed using 16S rRNA and nifH gene amplicon sequencing. The bacterial community composition in bulk particles remained remarkably consistent throughout time and space while large variations of individually picked particles were observed. This difference suggests that unique biogeochemical conditions within individual particles may offer distinct ecological niches for specialized bacterial taxa. Compared to surrounding seawater, particle samples were enriched in different size classes of globally significant N2-fixing cyanobacteria including Trichodesmium, symbionts of diatoms, and the unicellular cyanobacteria Crocosphaera and UCYN-A. The particles also contained nifH gene sequences of diverse non-cyanobacterial diazotrophs suggesting that particles could be loci for N2 fixation by heterotrophic bacteria. The results demonstrate that diverse diazotrophs were present on particles and that new N may thereby be directly exported from surface waters on sinking particles.
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Affiliation(s)
- Hanna Farnelid
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA. .,Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
| | - Kendra Turk-Kubo
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Helle Ploug
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Justin E Ossolinski
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - James R Collins
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.,MIT/WHOI Joint Program in Oceanography, University of Washington, Seattle, WA, USA.,School of Oceanography and eScience Institute, University of Washington, Seattle, WA, USA
| | - Benjamin A S Van Mooy
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA
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17
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Cheung S, Suzuki K, Saito H, Umezawa Y, Xia X, Liu H. Highly heterogeneous diazotroph communities in the Kuroshio Current and the Tokara Strait, Japan. PLoS One 2017; 12:e0186875. [PMID: 29059241 PMCID: PMC5653367 DOI: 10.1371/journal.pone.0186875] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 10/09/2017] [Indexed: 11/18/2022] Open
Abstract
In this study, we used 454-pyrosequencing to report the highly diverse diazotroph communities in the Kuroshio and its adjacent waters along a transect across the Tokara Strait, Japan. Terrestrial input from the islands resulted in a highly heterogeneous diazotroph community within a relatively small geographic region, which was presumably caused by the remarkably different responses of UCYN-A2, UCYN-C and Trichodesmium to the steep environmental gradient. On the other hand, most major cyanobacterial OTUs found in this study were also detected in an unpublished dataset from the upstream Kuroshio, which suggests transportation of diazotrophs by the Kuroshio in large geographic scale. A significant amount of UCYN-C was found in the Kuroshio and offshore stations, suggesting the importance of this potentially overlooked group in the western North Pacific Ocean (WNPO). Moreover, a novel sublineage of UCYN-B was defined, which was predominant in an oligotrophic water sample; and it was also found to be widely distributed in oceanic waters. In addition, the apparent increase in relative abundance of UCYN-A2 from offshore to near-shore water provides evidence for the earlier and under-debating view that UCYN-A2 prefers coastal conditions. Our report provides new knowledge for understanding the phylogeny and ecology of unicellular cyanobacterial diazotrophs in WNPO.
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Affiliation(s)
- Shunyan Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Koji Suzuki
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - Hiroaki Saito
- Atmosphere and Ocean Research Institute, The University of Tokyo, Tokyo, Japan
| | - Yu Umezawa
- Faculty of Fisheries, Nagasaki University, Nagasaki, Japan
| | - Xiaomin Xia
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
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18
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Conroy BJ, Steinberg DK, Song B, Kalmbach A, Carpenter EJ, Foster RA. Mesozooplankton Graze on Cyanobacteria in the Amazon River Plume and Western Tropical North Atlantic. Front Microbiol 2017; 8:1436. [PMID: 28824569 PMCID: PMC5540951 DOI: 10.3389/fmicb.2017.01436] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 07/14/2017] [Indexed: 11/18/2022] Open
Abstract
Diazotrophic cyanobacteria, those capable of fixing di-nitrogen (N2), are considered one of the major sources of new nitrogen (N) in the oligotrophic tropical ocean, but direct incorporation of diazotrophic N into food webs has not been fully examined. In the Amazon River-influenced western tropical North Atlantic (WTNA), diatom diazotroph associations (DDAs) and the filamentous colonial diazotrophs Trichodesmium have seasonally high abundances. We sampled epipelagic mesozooplankton in the Amazon River plume and WTNA in May-June 2010 to investigate direct grazing by mesozooplankton on two DDA populations: Richelia associated with Rhizosolenia diatoms (het-1) and Hemiaulus diatoms (het-2), and on Trichodesmium using highly specific qPCR assays targeting nitrogenase genes (nifH). Both DDAs and Trichodesmium occurred in zooplankton gut contents, with higher detection of het-2 predominantly in calanoid copepods (2.33-16.76 nifH copies organism-1). Abundance of Trichodesmium was low (2.21-4.03 nifH copies organism-1), but they were consistently detected at high salinity stations (>35) in calanoid copepods. This suggests direct grazing on DDAs, Trichodesmium filaments and colonies, or consumption as part of sinking aggregates, is common. In parallel with the qPCR approach, a next generation sequencing analysis of 16S rRNA genes identified that cyanobacterial assemblage associated with zooplankton guts was dominated by the non-diazotrophic unicellular phylotypes Synechococcus (56%) and Prochlorococcus (26%). However, in two separate calanoid copepod samples, two unicellular diazotrophs Candidatus Atelocyanobacterium thalassa (UCYN-A) and Crocosphaera watsonii (UCYN-B) were present, respectively, as a small component of cyanobacterial assemblages (<2%). This study represents the first evidence of consumption of DDAs, Trichodesmium, and unicellular cyanobacteria by calanoid copepods in an area of the WTNA known for high carbon export. These diazotroph populations are quantitatively important in the global N budget, widespread and hence, the next step is to accurately quantify grazing. Nonetheless, these results highlight a direct pathway of diazotrophic N into the food web and have important implications for biogeochemical cycles, particularly oligotrophic regions where N2 fixation is the main source of new nitrogen.
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Affiliation(s)
- Brandon J. Conroy
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, WilliamsburgVA, United States
| | - Deborah K. Steinberg
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, WilliamsburgVA, United States
| | - Bongkuen Song
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, WilliamsburgVA, United States
| | - Andrew Kalmbach
- Department of Biology, Romberg Tiburon Center for Environmental Studies, San Francisco State University, TiburonCA, United States
| | - Edward J. Carpenter
- Department of Biology, Romberg Tiburon Center for Environmental Studies, San Francisco State University, TiburonCA, United States
| | - Rachel A. Foster
- Ocean Sciences, University of California, Santa Cruz, Santa CruzCA, United States
- Department of Ecology, Environment and Plant Sciences, Stockholm UniversityStockholm, Sweden
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19
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Sargent EC, Hitchcock A, Johansson SA, Langlois R, Moore CM, LaRoche J, Poulton AJ, Bibby TS. Evidence for polyploidy in the globally important diazotroph Trichodesmium. FEMS Microbiol Lett 2016; 363:fnw244. [PMID: 27797867 DOI: 10.1093/femsle/fnw244] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/31/2016] [Accepted: 10/19/2016] [Indexed: 12/13/2022] Open
Abstract
Polyploidy is a well-described trait in some prokaryotic organisms; however, it is unusual in marine microbes from oligotrophic environments, which typically display a tendency towards genome streamlining. The biogeochemically significant diazotrophic cyanobacterium Trichodesmium is a potential exception. With a relatively large genome and a comparatively high proportion of non-protein-coding DNA, Trichodesmium appears to allocate relatively more resources to genetic material than closely related organisms and microbes within the same environment. Through simultaneous analysis of gene abundance and direct cell counts, we show for the first time that Trichodesmium spp. can also be highly polyploid, containing as many as 100 genome copies per cell in field-collected samples and >600 copies per cell in laboratory cultures. These findings have implications for the widespread use of the abundance of the nifH gene (encoding a subunit of the N2-fixing enzyme nitrogenase) as an approach for quantifying the abundance and distribution of marine diazotrophs. Moreover, polyploidy may combine with the unusual genomic characteristics of this genus both in reflecting evolutionary dynamics and influencing phenotypic plasticity and ecological resilience.
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Affiliation(s)
- Elizabeth C Sargent
- Ocean and Earth Science, University of Southampton, National Oceanography Centre Southampton, Southampton SO14 3ZH, UK
| | - Andrew Hitchcock
- Ocean and Earth Science, University of Southampton, National Oceanography Centre Southampton, Southampton SO14 3ZH, UK
| | - S Andreas Johansson
- Ocean and Earth Science, University of Southampton, National Oceanography Centre Southampton, Southampton SO14 3ZH, UK
| | - Rebecca Langlois
- Department of Biology, Life Science Centre, Dalhousie University, 1355 Oxford Street, Halifax, NS B3H 4R2, Canada
| | - C Mark Moore
- Ocean and Earth Science, University of Southampton, National Oceanography Centre Southampton, Southampton SO14 3ZH, UK
| | - Julie LaRoche
- Department of Biology, Life Science Centre, Dalhousie University, 1355 Oxford Street, Halifax, NS B3H 4R2, Canada
| | - Alex J Poulton
- Ocean Biogeochemistry and Ecosystems, National Oceanography Centre Southampton, Southampton SO14 3ZH, UK
| | - Thomas S Bibby
- Ocean and Earth Science, University of Southampton, National Oceanography Centre Southampton, Southampton SO14 3ZH, UK
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20
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Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre. mSystems 2016; 1:mSystems00024-16. [PMID: 27822538 PMCID: PMC5069773 DOI: 10.1128/msystems.00024-16] [Citation(s) in RCA: 238] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/12/2016] [Indexed: 01/08/2023] Open
Abstract
Marine plastic debris has become a significant concern in ocean ecosystems worldwide. Little is known, however, about its influence on microbial community structure and function. In 2008, we surveyed microbial communities and metabolic activities in seawater and on plastic on an oceanographic expedition through the "great Pacific garbage patch." The concentration of plastic particles in surface seawater within different size classes (2 to 5 mm and >5 mm) ranged from 0.35 to 3.7 particles m-3 across sampling stations. These densities and the particle size distribution were consistent with previous values reported in the North Pacific Ocean. Net community oxygen production (NCP = gross primary production - community respiration) on plastic debris was positive and so net autotrophic, whereas NCP in bulk seawater was close to zero. Scanning electron microscopy and metagenomic sequencing of plastic-attached communities revealed the dominance of a few metazoan taxa and a diverse assemblage of photoautotrophic and heterotrophic protists and bacteria. Bryozoa, Cyanobacteria, Alphaproteobacteria, and Bacteroidetes dominated all plastic particles, regardless of particle size. Bacteria inhabiting plastic were taxonomically distinct from the surrounding picoplankton and appeared well adapted to a surface-associated lifestyle. Genes with significantly higher abundances among plastic-attached bacteria included che genes, secretion system genes, and nifH genes, suggesting enrichment for chemotaxis, frequent cell-to-cell interactions, and nitrogen fixation. In aggregate, our findings suggest that plastic debris forms a habitat for complex microbial assemblages that have lifestyles, metabolic pathways, and biogeochemical activities that are distinct from those of free-living planktonic microbial communities. IMPORTANCE Marine plastic debris is a growing concern that has captured the general public's attention. While the negative impacts of plastic debris on oceanic macrobiota, including mammals and birds, are well documented, little is known about its influence on smaller marine residents, including microbes that have key roles in ocean biogeochemistry. Our work provides a new perspective on microbial communities inhabiting microplastics that includes its effect on microbial biogeochemical activities and a description of the cross-domain communities inhabiting plastic particles. This study is among the first molecular ecology, plastic debris biota surveys in the North Pacific Subtropical Gyre. It has identified fundamental differences in the functional potential and taxonomic composition of plastic-associated microbes versus planktonic microbes found in the surrounding open-ocean habitat. Author Video: An author video summary of this article is available.
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Blank CE, Hinman NW. Cyanobacterial and algal growth on chitin as a source of nitrogen; ecological, evolutionary, and biotechnological implications. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.02.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Riou V, Fonseca-Batista D, Roukaerts A, Biegala IC, Prakya SR, Magalhães Loureiro C, Santos M, Muniz-Piniella AE, Schmiing M, Elskens M, Brion N, Martins MA, Dehairs F. Importance of N2-Fixation on the Productivity at the North-Western Azores Current/Front System, and the Abundance of Diazotrophic Unicellular Cyanobacteria. PLoS One 2016; 11:e0150827. [PMID: 26958844 PMCID: PMC4784884 DOI: 10.1371/journal.pone.0150827] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 02/19/2016] [Indexed: 11/21/2022] Open
Abstract
To understand the impact of the northwestern Azores Current Front (NW-AzC/AzF) system on HCO3−-and N2-fixation activities and unicellular diazotrophic cyanobacteria (UCYN) distribution, we combined geochemical and biological approaches from the oligotrophic surface to upper mesopelagic waters. N2-fixation was observed to sustain 45–85% of the HCO3−-fixation in the picoplanktonic fraction performing 47% of the total C-fixation at the deep chlorophyll maximum north and south of the AzF. N2-fixation rates as high as 10.9 μmol N m-3 d-1 and surface nitrate δ15N as low as 2.7‰ were found in the warm (18–24°C), most saline (36.5–37.0) and least productive waters south of the AzF, where UCYN were the least abundant. However, picoplanktonic UCYN abundances up to 55 cells mL-1 were found at 45–200m depths in the coolest nutrient-rich waters north of the AzF. In this area, N2-fixation rates up to 4.5 μmol N m-3 d-1 were detected, associated with depth-integrated H13CO3−-fixation rates at least 50% higher than observed south of the AzF. The numerous eddies generated at the NW-AzC/AzF seem to enhance exchanges of plankton between water masses, as well as vertical and horizontal diapycnal diffusion of nutrients, whose increase probably enhances the growth of diazotrophs and the productivity of C-fixers.
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Affiliation(s)
- Virginie Riou
- Aix-Marseille Université, Mediterranean Institute of Oceanography (MIO), UM 110 CNRS/INSU, IRD, 13288 Marseille, Université du Sud Toulon-Var, 83957, La Garde, France
- IMAR—Institute of Marine Research, Centre of IMAR at the University of the Azores, Horta, Portugal
- * E-mail:
| | - Debany Fonseca-Batista
- Aix-Marseille Université, Mediterranean Institute of Oceanography (MIO), UM 110 CNRS/INSU, IRD, 13288 Marseille, Université du Sud Toulon-Var, 83957, La Garde, France
- Analytical, Environmental and Geo-Chemistry & Earth System Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Arnout Roukaerts
- Analytical, Environmental and Geo-Chemistry & Earth System Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Isabelle C. Biegala
- Aix-Marseille Université, Mediterranean Institute of Oceanography (MIO), UM 110 CNRS/INSU, IRD, 13288 Marseille, Université du Sud Toulon-Var, 83957, La Garde, France
| | - Shree Ram Prakya
- IMAR—Institute of Marine Research, Centre of IMAR at the University of the Azores, Horta, Portugal
| | - Clara Magalhães Loureiro
- CIBIO, Research Center in Biodiversity and Genetic Resources, InBIO Associated Laboratory, Department of Oceanography and Fisheries, Horta, Portugal
- DOP/UAz – Department of Oceanography and Fisheries, University of the Azores, Azores, Portugal
| | - Mariana Santos
- IPMA, I.P.—Portuguese Institute of Ocean and Atmosphere, Lisbon, Portugal
- MARE—Marine and Environmental Sciences Centre, Lisbon, Portugal
| | - Angel E. Muniz-Piniella
- Analytical, Environmental and Geo-Chemistry & Earth System Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mara Schmiing
- IMAR—Institute of Marine Research, Centre of IMAR at the University of the Azores, Horta, Portugal
- MARE—Marine and Environmental Sciences Centre, Lisbon, Portugal
- DOP/UAz – Department of Oceanography and Fisheries, University of the Azores, Azores, Portugal
| | - Marc Elskens
- Analytical, Environmental and Geo-Chemistry & Earth System Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Natacha Brion
- Analytical, Environmental and Geo-Chemistry & Earth System Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - M. Ana Martins
- CIBIO, Research Center in Biodiversity and Genetic Resources, InBIO Associated Laboratory, Department of Oceanography and Fisheries, Horta, Portugal
- DOP/UAz – Department of Oceanography and Fisheries, University of the Azores, Azores, Portugal
| | - Frank Dehairs
- Analytical, Environmental and Geo-Chemistry & Earth System Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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Nitric Oxide Mediates Biofilm Formation and Symbiosis in Silicibacter sp. Strain TrichCH4B. mBio 2015; 6:e00206-15. [PMID: 25944856 PMCID: PMC4436077 DOI: 10.1128/mbio.00206-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
UNLABELLED Nitric oxide (NO) plays an important signaling role in all domains of life. Many bacteria contain a heme-nitric oxide/oxygen binding (H-NOX) protein that selectively binds NO. These H-NOX proteins often act as sensors that regulate histidine kinase (HK) activity, forming part of a bacterial two-component signaling system that also involves one or more response regulators. In several organisms, NO binding to the H-NOX protein governs bacterial biofilm formation; however, the source of NO exposure for these bacteria is unknown. In mammals, NO is generated by the enzyme nitric oxide synthase (NOS) and signals through binding the H-NOX domain of soluble guanylate cyclase. Recently, several bacterial NOS proteins have also been reported, but the corresponding bacteria do not also encode an H-NOX protein. Here, we report the first characterization of a bacterium that encodes both a NOS and H-NOX, thus resembling the mammalian system capable of both synthesizing and sensing NO. We characterized the NO signaling pathway of the marine alphaproteobacterium Silicibacter sp. strain TrichCH4B, determining that the NOS is activated by an algal symbiont, Trichodesmium erythraeum. NO signaling through a histidine kinase-response regulator two-component signaling pathway results in increased concentrations of cyclic diguanosine monophosphate, a key bacterial second messenger molecule that controls cellular adhesion and biofilm formation. Silicibacter sp. TrichCH4B biofilm formation, activated by T. erythraeum, may be an important mechanism for symbiosis between the two organisms, revealing that NO plays a previously unknown key role in bacterial communication and symbiosis. IMPORTANCE Bacterial nitric oxide (NO) signaling via heme-nitric oxide/oxygen binding (H-NOX) proteins regulates biofilm formation, playing an important role in protecting bacteria from oxidative stress and other environmental stresses. Biofilms are also an important part of symbiosis, allowing the organism to remain in a nutrient-rich environment. In this study, we show that in Silicibacter sp. strain TrichCH4B, NO mediates symbiosis with the alga Trichodesmium erythraeum, a major marine diazotroph. In addition, Silicibacter sp. TrichCH4B is the first characterized bacteria to harbor both the NOS and H-NOX proteins, making it uniquely capable of both synthesizing and sensing NO, analogous to mammalian NO signaling. Our study expands current understanding of the role of NO in bacterial signaling, providing a novel role for NO in bacterial communication and symbiosis.
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Abby SS, Touchon M, De Jode A, Grimsley N, Piganeau G. Bacteria in Ostreococcus tauri cultures - friends, foes or hitchhikers? Front Microbiol 2014; 5:505. [PMID: 25426102 PMCID: PMC4224133 DOI: 10.3389/fmicb.2014.00505] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/08/2014] [Indexed: 11/13/2022] Open
Abstract
Marine phytoplankton produce half of the oxygen we breathe and their astounding diversity is just starting to be unraveled. Many microbial phytoplankton are thought to be phototrophic, depending solely on inorganic sources of carbon and minerals for growth rather than preying on other planktonic cells. However, there is increasing evidence that symbiotic associations, to a large extent with bacteria, are required for vitamin or nutrient uptake for many eukaryotic microalgae. Here, we use in silico approaches to look for putative symbiotic interactions by analysing the gene content of microbial communities associated with 13 different Ostreococcus tauri (Chlorophyta, Mamilleophyceae) cultures sampled from the Mediterranean Sea. While we find evidence for bacteria in all cultures, there is no ubiquitous bacterial group, and the most prevalent group, Flavobacteria, is present in 10 out of 13 cultures. Among seven of the microbiomes, we detected genes predicted to encode type 3 secretion systems (T3SS, in 6/7 microbiomes) and/or putative type 6 secretion systems (T6SS, in 4/7 microbiomes). Phylogenetic analyses show that the corresponding genes are closely related to genes of systems identified in bacterial-plant interactions, suggesting that these T3SS might be involved in cell-to-cell interactions with O. tauri.
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Affiliation(s)
- Sophie S Abby
- Institut Pasteur, Microbial Evolutionary Genomics Paris, France ; CNRS, UMR 3525 Paris, France
| | - Marie Touchon
- Institut Pasteur, Microbial Evolutionary Genomics Paris, France ; CNRS, UMR 3525 Paris, France
| | - Aurelien De Jode
- CNRS, UMR 7232, Biologie Intégrative des Organismes Marins, Observatoire Océanologique Banyuls-sur-Mer, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7232, BIOM, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Nigel Grimsley
- CNRS, UMR 7232, Biologie Intégrative des Organismes Marins, Observatoire Océanologique Banyuls-sur-Mer, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7232, BIOM, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Gwenael Piganeau
- CNRS, UMR 7232, Biologie Intégrative des Organismes Marins, Observatoire Océanologique Banyuls-sur-Mer, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7232, BIOM, Observatoire Océanologique, Banyuls-sur-Mer, France
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Nuester J, Newville M, Twining BS. Distributions of iron, phosphorus and sulfur along trichomes of the cyanobacteria Trichodesmium. Metallomics 2014; 6:1141-9. [DOI: 10.1039/c4mt00042k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Changes in the elemental composition within trichomes of the nonheterocystous cyanobacteriaTrichodesmiumare potentially related to N2-fixation.
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Affiliation(s)
| | - Matthew Newville
- Center for Advanced Radiation Sources
- The University of Chicago
- Argonne, USA
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