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Robicheau BM, Tolman J, Desai D, LaRoche J. Microevolutionary patterns in ecotypes of the symbiotic cyanobacterium UCYN-A revealed from a Northwest Atlantic coastal time series. SCIENCE ADVANCES 2023; 9:eadh9768. [PMID: 37774025 PMCID: PMC10541017 DOI: 10.1126/sciadv.adh9768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/28/2023] [Indexed: 10/01/2023]
Abstract
UCYN-A is a globally important nitrogen-fixing symbiotic microbe often found in colder regions and coastal areas where nitrogen fixation has been overlooked. We present a 3-year coastal Northwest Atlantic time series of UCYN-A by integrating oceanographic data with weekly nifH and16S rRNA gene sequencing and quantitative PCR assays for UCYN-A ecotypes. High UCYN-A relative abundances dominated by A1 to A4 ecotypes reoccurred annually in the coastal Northwest Atlantic. Although UCYN-A was detected every summer/fall, the ability to observe separate ecotypes may be highly dependent on sampling time given intense interannual and weekly variability of ecotype-specific occurrences. Additionally, much of UCYN-A's rarer diversity was populated by short-lived neutral mutational variants, therefore providing insight into UCYN-A's microevolutionary patterns. For instance, rare ASVs exhibited community composition restructuring annually, while also sharing a common connection to a dominant ASV within each ecotype. Our study provides additional perspectives for interpreting UCYN-A intraspecific diversity and underscores the need for high-resolution datasets when deciphering spatiotemporal ecologies within UCYN-A.
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Affiliation(s)
- Brent M. Robicheau
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jennifer Tolman
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Dhwani Desai
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Integrated Microbiome Resource, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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2
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Zehr JP, Capone DG. Unsolved mysteries in marine nitrogen fixation. Trends Microbiol 2023:S0966-842X(23)00235-4. [PMID: 37658011 DOI: 10.1016/j.tim.2023.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 09/03/2023]
Abstract
Biological nitrogen (N2) fixation is critical in global biogeochemical cycles and in sustaining the productivity of the oceans. There remain many unanswered questions, unresolved hypotheses, and unchallenged paradigms. The fundamental balance of N input and losses has not been fully resolved. One of the major N2-fixers, Trichodesmium, remains an enigma with intriguing biological and ecological secrets. Cyanobacterial N2 fixation, once thought to be primarily due to free-living cyanobacteria, now also appears to be dependent on microbial interactions, from microbiomes to unicellular symbioses, which remain poorly characterized. Nitrogenase genes associated with diverse non-cyanobacterial diazotrophs (NCDs) are prevalent, but their significance remains a huge knowledge gap. Answering questions, new and old, such as those discussed here, is needed to understand the ocean's N and C cycles and their responses to environmental change.
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Affiliation(s)
- Jonathan P Zehr
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA.
| | - Douglas G Capone
- Marine and Environmental Biology Section of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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3
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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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4
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Jiang Z, Zhu Y, Sun Z, Zhai H, Zhou F, Yan X, Chen Q, Chen J, Zeng J. Size-fractionated N 2 fixation off the Changjiang Estuary during summer. Front Microbiol 2023; 14:1189410. [PMID: 37228373 PMCID: PMC10203160 DOI: 10.3389/fmicb.2023.1189410] [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: 03/19/2023] [Accepted: 04/18/2023] [Indexed: 05/27/2023] Open
Abstract
Recent evidence has shown active N2 fixation in coastal eutrophic waters, yet the rate and controlling factors remain poorly understood, particularly in large estuaries. The Changjiang Estuary (CE) and adjacent shelf are characterized by fresh, nitrogen-replete Changjiang Diluted Water (CDW) and saline, nitrogen-depletion intruded Kuroshio water (Taiwan Warm Current and nearshore Kuroshio Branch Current), where N2 fixation may be contributed by different groups (i.e., Trichodesmium and heterotrophic diazotrophs). Here, for the first time, we provide direct measurement of size-fractionated N2 fixation rates (NFRs) off the CE during summer 2014 using the 15N2 bubble tracer method. The results demonstrated considerable spatial variations (southern > northern; offshore > inshore) in surface and depth-integrated NFRs, averaging 0.83 nmol N L-1 d-1 and 24.3 μmol N m-2 d-1, respectively. The highest bulk NFR (99.9 μmol N m-2 d-1; mostly contributed by >10 μm fraction) occurred in the southeastern East China Sea, where suffered from strong intrusion of the Kuroshio water characterized by low N/P ratio (<10) and abundant Trichodesmium (up to 10.23 × 106 trichomes m-2). However, low NFR (mostly contributed by <10 μm fraction) was detected in the CE controlled by the CDW, where NOx concentration (up to 80 μmol L-1) and N/P ratio (>100) were high and Trichodesmium abundance was low. The >10 μm fraction accounted for 60% of depth-integrated bulk NFR over the CE and adjacent shelf. We speculated that the present NFR of >10 μm fraction was mostly supported by Trichodesmium. Spearman rank correlation indicated that the NFR was significantly positively correlated with Trichodesmium abundance, salinity, temperature and Secchi depth, but was negatively with turbidity, N/P ratio, NOx, and chlorophyll a concentration. Our study suggests that distribution and size structure of N2 fixation off the CE are largely regulated by water mass (intruded Kuroshio water and CDW) movement and associated diazotrophs (particularly Trichodesmium) and nutrient conditions.
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Affiliation(s)
- Zhibing Jiang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Key Laboratory of Ocean Space Resource Management Technology, Ministry of Natural Resource, Hangzhou, China
- Key Laboratory of Nearshore Engineering Environment and Ecological Security of Zhejiang Province, Hangzhou, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Observation and Research Station of Marine Ecosystem in the Yangtze River Delta, Ministry of Natural Resources, Hangzhou, China
| | - Yuanli Zhu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Key Laboratory of Ocean Space Resource Management Technology, Ministry of Natural Resource, Hangzhou, China
- Observation and Research Station of Marine Ecosystem in the Yangtze River Delta, Ministry of Natural Resources, Hangzhou, China
| | - Zhenhao Sun
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Hongchang Zhai
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Feng Zhou
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Observation and Research Station of Marine Ecosystem in the Yangtze River Delta, Ministry of Natural Resources, Hangzhou, China
| | - Xiaojun Yan
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Quanzhen Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Jiangning Zeng
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Key Laboratory of Ocean Space Resource Management Technology, Ministry of Natural Resource, Hangzhou, China
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5
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Yang N, Lin YA, Merkel CA, DeMers MA, Qu PP, Webb EA, Fu FX, Hutchins DA. Molecular mechanisms underlying iron and phosphorus co-limitation responses in the nitrogen-fixing cyanobacterium Crocosphaera. THE ISME JOURNAL 2022; 16:2702-2711. [PMID: 36008474 PMCID: PMC9666452 DOI: 10.1038/s41396-022-01307-7] [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: 02/27/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
In the nitrogen-limited subtropical gyres, diazotrophic cyanobacteria, including Crocosphaera, provide an essential ecosystem service by converting dinitrogen (N2) gas into ammonia to support primary production in these oligotrophic regimes. Natural gradients of phosphorus (P) and iron (Fe) availability in the low-latitude oceans constrain the biogeography and activity of diazotrophs with important implications for marine biogeochemical cycling. Much remains unknown regarding Crocosphaera's physiological and molecular responses to multiple nutrient limitations. We cultured C. watsonii under Fe, P, and Fe/P (co)-limiting scenarios to link cellular physiology with diel gene expression and observed unique physiological and transcriptional profiles for each treatment. Counterintuitively, reduced growth and N2 fixation resource use efficiencies (RUEs) for Fe or P under P limitation were alleviated under Fe/P co-limitation. Differential gene expression analyses show that Fe/P co-limited cells employ the same responses as single-nutrient limited cells that reduce cellular nutrient requirements and increase responsiveness to environmental change including smaller cell size, protein turnover (Fe-limited), and upregulation of environmental sense-and-respond systems (P-limited). Combined, these mechanisms enhance growth and RUEs in Fe/P co-limited cells. These findings are important to our understanding of nutrient controls on N2 fixation and the implications for primary productivity and microbial dynamics in a changing ocean.
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Affiliation(s)
- Nina Yang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yu-An Lin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Carlin A Merkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Michelle A DeMers
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ping-Ping Qu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric A Webb
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Fei-Xue Fu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - David A Hutchins
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
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6
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Masuda T, Inomura K, Gao M, Armin G, Kotabová E, Bernát G, Lawrenz-Kendrick E, Lukeš M, Bečková M, Steinbach G, Komenda J, Prášil O. The balance between photosynthesis and respiration explains the niche differentiation between Crocosphaera and Cyanothece. Comput Struct Biotechnol J 2022; 21:58-65. [PMID: 36514336 PMCID: PMC9732122 DOI: 10.1016/j.csbj.2022.11.029] [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: 10/14/2022] [Revised: 11/12/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
Crocosphaera and Cyanothece are both unicellular, nitrogen-fixing cyanobacteria that prefer different environments. Whereas Crocosphaera mainly lives in nutrient-deplete, open oceans, Cyanothece is more common in coastal, nutrient-rich regions. Despite their physiological similarities, the factors separating their niches remain elusive. Here we performed physiological experiments on clone cultures and expand upon a simple ecological model to show that their different niches can be sufficiently explained by the observed differences in their photosynthetic capacities and rates of carbon (C) consumption. Our experiments revealed that Cyanothece has overall higher photosynthesis and respiration rates than Crocosphaera. A simple growth model of these microorganisms suggests that C storage and consumption are previously under-appreciated factors when evaluating the occupation of niches by different marine nitrogen fixers.
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Affiliation(s)
- Takako Masuda
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic,Corresponding authors.
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Meng Gao
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Gabrielle Armin
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Eva Kotabová
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Gábor Bernát
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic,Balaton Limnological Research Institute, Eötvös Loránd Research Network (ELKH), Tihany, Hungary
| | - Evelyn Lawrenz-Kendrick
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Martin Lukeš
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Martina Bečková
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Gábor Steinbach
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic,Cellular Imaging Laboratory, Biological Research Center, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Josef Komenda
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Ondřej Prášil
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 37901 Třeboň, Czech Republic,Corresponding authors.
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7
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Camacho A, Rochera C, Picazo A. Effect of experimentally increased nutrient availability on the structure, metabolic activities, and potential microbial functions of a maritime Antarctic microbial mat. Front Microbiol 2022; 13:900158. [PMID: 36212846 PMCID: PMC9539743 DOI: 10.3389/fmicb.2022.900158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
The role of competitive interactions based on resource utilisation was explored in a phototrophic microbial mat from Byers Peninsula (Maritime Antarctica). Shotgun metagenomic profiling of the mat showed a taxonomic and functionally diverse microbial community. The heterotrophic bacterial community was dominated by Proteobacteria, where genera typically found in polar habitats, such as Janthinobacterium, Pseudomonas, and Polaromonas, were highly prevalent. Cyanobacteria played the main role as primary producers, accompanied by diatoms and chlorophytes. To test the potential effects of the inorganic nutrient (N and P) availability on this community, a fully factorial nitrate and phosphorus addition experiment was conducted in situ. The mat exhibited a functional and structural response to the nutrient amendments. Compared to the undisturbed mat, phosphorus fertilisation favoured the growth of (non-heterocystous) cyanobacteria relative to that of diatoms, as indicated by changes in the carotenoid pigment biomarkers. Although no mat accretion was visible, fertilisation improved the phototrophic activity, and, mainly, when P was amended, the production of exopolymeric substances was favoured, whereas further changes in the vertical distribution of primary production activity were observed as well. Illumina amplicon sequencing of the 16S rRNA gene also demonstrated changes in the relative abundance of heterotrophic prokaryotes, which were detectable from the phylum to the genus level and mainly related to the amendment of nitrogen. Predictions made on the functional skills of these shifted prokaryotic communities indicated changes in abundance selecting taxa with a metabolic adaptation to the new nutrient scenarios. They mainly consisted of the enhancement of ecological strategies and metabolic regulatory mechanisms related to the uptake and metabolising of either nitrogen or phosphorus, regulated by its availability whether in a balanced way or not. This study is a pioneer in demonstrating how shifts in the regional dynamic of nutrients might alter the metabolic equilibrium of these initially considered homeostatic benthic communities. They can be accordingly considered as taxonomically diverse microbiomes with a functional repertoire still inclined to respond to the biogeochemical alteration of nutrient cycles, although occurring in a cold extreme environment where biological activity is partially restricted by environmental harshness.
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8
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Masuda T, Inomura K, Kodama T, Shiozaki T, Kitajima S, Armin G, Matsui T, Suzuki K, Takeda S, Sato M, Prášil O, Furuya K. Crocosphaera as a Major Consumer of Fixed Nitrogen. Microbiol Spectr 2022; 10:e0217721. [PMID: 35770981 PMCID: PMC9431459 DOI: 10.1128/spectrum.02177-21] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/05/2022] [Indexed: 11/23/2022] Open
Abstract
Crocosphaera watsonii (hereafter referred to as Crocosphaera) is a key nitrogen (N) fixer in the ocean, but its ability to consume combined-N sources is still unclear. Using in situ microcosm incubations with an ecological model, we show that Crocosphaera has high competitive capability both under low and moderately high combined-N concentrations. In field incubations, Crocosphaera accounted for the highest consumption of ammonium and nitrate, followed by picoeukaryotes. The model analysis shows that cells have a high ammonium uptake rate (~7 mol N [mol N]-1 d-1 at the maximum), which allows them to compete against picoeukaryotes and nondiazotrophic cyanobacteria when combined N is sufficiently available. Even when combined N is depleted, their capability of nitrogen fixation allows higher growth rates compared to potential competitors. These results suggest the high fitness of Crocosphaera in combined-N limiting, oligotrophic oceans heightening its potential significance in its ecosystem and in biogeochemical cycling. IMPORTANCE Crocosphaera watsonii is as a key nitrogen (N) supplier in marine ecosystems, and it has been estimated to contribute up to half of oceanic N2 fixation. Conversely, a recent study reported that Crocosphaera can assimilate combined N and proposed that unicellular diazotrophs can be competitors with non-N2 fixing phytoplankton for combined N. Despite its importance in nitrogen cycling, the methods by which Crocosphaera compete are not currently fully understood. Here, we present a new role of Crocosphaera as a combined-N consumer: a competitor against nondiazotrophic phytoplankton for combined N. In this study, we combined in situ microcosm experiments and an ecosystem model to quantitatively evaluate the combined-N consumption by Crocosphaera and other non-N2 fixing phytoplankton. Our results suggest the high fitness of Crocosphaera in combined-N limiting, oligotrophic oceans and, thus, heightens its potential significance in its ecosystem and in biogeochemical cycling.
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Affiliation(s)
- Takako Masuda
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czech Republic
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Taketoshi Kodama
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| | - Takuhei Shiozaki
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| | - Satoshi Kitajima
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| | - Gabrielle Armin
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Takato Matsui
- Graduate School of Environmental Science/Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - Koji Suzuki
- Graduate School of Environmental Science/Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - Shigenobu Takeda
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| | - Mitsuhide Sato
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| | - Ondřej Prášil
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czech Republic
| | - Ken Furuya
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
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9
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Díaz-Torres O, Lugo-Melchor OY, de Anda J, Pacheco A, Yebra-Montes C, Gradilla-Hernández MS, Senés-Guerrero C. Bacterial Dynamics and Their Influence on the Biogeochemical Cycles in a Subtropical Hypereutrophic Lake During the Rainy Season. Front Microbiol 2022; 13:832477. [PMID: 35479621 PMCID: PMC9037096 DOI: 10.3389/fmicb.2022.832477] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/28/2022] [Indexed: 01/01/2023] Open
Abstract
Lakes in subtropical regions are highly susceptible to eutrophication due to the heavy rainfall, which causes significant runoff of pollutants (e.g., nutrients) to reach surface waters, altering the water quality and influencing the microbial communities that regulate the biogeochemical cycles within these ecosystems. Lake Cajititlán is a shallow, subtropical, and endorheic lake in western Mexico. Nutrient pollution from agricultural activity and wastewater discharge have affected the lake’s water quality, leading the reservoir to a hypereutrophic state, resulting in episodes of fish mortality during the rainy season. This study investigated the temporal dynamics of bacterial communities within Lake Cajititlán and their genes associated with the nitrogen, phosphorus, sulfur, and carbon biogeochemical cycles during the rainy season, as well as the influences of physicochemical and environmental variables on such dynamics. Significant temporal variations were observed in the composition of bacterial communities, of which Flavobacterium and Pseudomonas were the dominant genera. The climatological parameters that were most correlated with the bacterial communities and their functional profiles were pH, DO, ORP, turbidity, TN, EC, NH4+, and NO3–. The bacterial communities displayed variations in their functional composition for nitrogen, phosphorus, and sulfur metabolisms during the sampling months. The bacterial communities within the lake are highly susceptible to nutrient loads and low DO levels during the rainy season. Bacterial communities had a higher relative abundance of genes associated with denitrification, nitrogen fixation, assimilatory sulfate reduction, cysteine, SOX system, and all phosphorus metabolic pathways. The results obtained here enrich our understanding of the bidirectional interactions between bacterial communities and major biogeochemical processes in eutrophic subtropical lakes.
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Affiliation(s)
- Osiris Díaz-Torres
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Unidad de Servicios Analiticos y Metrologicos, Guadalajara, Mexico
| | - Ofelia Yadira Lugo-Melchor
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Unidad de Servicios Analiticos y Metrologicos, Guadalajara, Mexico
| | - José de Anda
- Departamento de Tecnologia Ambiental, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Zapopan, Mexico
| | - Adriana Pacheco
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Monterrey, Mexico
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10
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Rabouille S, Tournier L, Duhamel S, Claquin P, Crispi O, Talec A, Landolfi A, Oschlies A. Organic Phosphorus Scavenging Supports Efficient Growth of Diazotrophic Cyanobacteria Under Phosphate Depletion. Front Microbiol 2022; 13:848647. [PMID: 35401448 PMCID: PMC8990761 DOI: 10.3389/fmicb.2022.848647] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/03/2022] [Indexed: 11/29/2022] Open
Abstract
Considering the reported significant diazotrophic activities in open-ocean regions where primary production is strongly limited by phosphate, we explored the ability of diazotrophs to use other sources of phosphorus to alleviate the phosphate depletion. We tested the actual efficiency of the open-ocean, N2-fixer Crocosphaera watsonii to grow on organic phosphorus as the sole P source, and observed how the P source affects the cellular C, N, and P composition. We obtained equivalent growth efficiencies on AMP and DL-α-glycerophosphate as compared with identical cultures grown on phosphate, and survival of the population on phytic acid. Our results show that Crocosphaera cannot use all phosphomonoesters with the same efficiency, but it can grow without phosphate, provided that usable DOP and sufficient light energy are available. Also, results point out that organic phosphorus uptake is not proportional to alkaline phosphatase activity, demonstrating that the latter is not a suitable proxy to estimate DOP-based growth yields of organisms, whether in culture experiments or in the natural environment. The growth parameters obtained, as a function of the P source, will be critical to improve and calibrate mathematical models of diazotrophic growth and the distribution of nitrogen fixation in the global ocean.
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Affiliation(s)
- Sophie Rabouille
- Laboratoire d'Océanographie de Villefranche (LOV), CNRS, Sorbonne Université, Villefranche-sur-Mer, France.,Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls-sur-Mer, France
| | - Lauralie Tournier
- Laboratoire d'Océanographie de Villefranche (LOV), CNRS, Sorbonne Université, Villefranche-sur-Mer, France
| | - Solange Duhamel
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, United States
| | - Pascal Claquin
- UMR BOREA (CNRS 8067), MNHN, IRD (207), Normandie Université, Université de Caen Normandie, CREC, Luc-sur-Mer, France
| | - Olivier Crispi
- Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls-sur-Mer, France
| | - Amélie Talec
- Laboratoire d'Océanographie de Villefranche (LOV), CNRS, Sorbonne Université, Villefranche-sur-Mer, France
| | - Angela Landolfi
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,CNR ISMAR, Rome, Italy
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11
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Masuda T, Inomura K, Mareš J, Prášil O. Crocosphaera watsonii. Trends Microbiol 2022; 30:805-806. [PMID: 35331632 DOI: 10.1016/j.tim.2022.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Takako Masuda
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 379 01 Třeboň, Czech Republic.
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Jan Mareš
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 379 01 Třeboň, Czech Republic; Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 702/7, 370 05 České Budějovice, Czech Republic
| | - Ondřej Prášil
- Institute of Microbiology, The Czech Academy of Sciences, Opatovický mlýn, 379 01 Třeboň, Czech Republic
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12
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Tian L, Jiang H, Song N, He S, Ali F. Comparing the effects of algae and macrophyte residues' degradation on biological nitrogen fixation in freshwater lake sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:151129. [PMID: 34688766 DOI: 10.1016/j.scitotenv.2021.151129] [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: 05/04/2021] [Revised: 10/15/2021] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
The degradation and mineralization of organic residues are important factors that drive biochemical processes in lake ecosystems. However, the effect of organic matter's degradation on biological nitrogen fixation (BNF) in freshwater lake sediments remains poorly understood. This study investigated the response of sediment nitrogen fixation to the degradations of algae and macrophyte residues through continuous flow mesocosms combined with nifH sequencing analysis and isotope tracing. The results suggested that the active nitrogen fixation of sediments only occurred in the first two weeks of the rapid degradation of organic residues. Degradation of algae and macrophytes residues quickly increased the nifH abundance and the nitrogenase activity (NA) in sediments; however, the maximum NA triggered by algae's degradation (658.2 ± 16.8 ng g-1 day-1) was six times higher than that induced by the degradation of macrophytes residues. There was no significant difference in NA of sediments with the degradation of Potamogeton and Phragmites. Redundancy analysis (RDA) showed that the variation of diazotrophic community in sediment was significantly (p < 0.01) correlated with the concentrations of SO42- and NH4+ in overlying water and the Fe(II) content and Eh in sediment. Overall, the BNF of sediments can quickly respond to the degradation of organic residues, and the degradation of algae has a stronger promoting effect on the nitrogen fixation in sediments than that of macrophyte residues.
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Affiliation(s)
- Linqi Tian
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Na Song
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shangwei He
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Farasat Ali
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
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13
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Overlooked and widespread pennate diatom-diazotroph symbioses in the sea. Nat Commun 2022; 13:799. [PMID: 35145076 PMCID: PMC8831587 DOI: 10.1038/s41467-022-28065-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 01/06/2022] [Indexed: 01/21/2023] Open
Abstract
Persistent nitrogen depletion in sunlit open ocean waters provides a favorable ecological niche for nitrogen-fixing (diazotrophic) cyanobacteria, some of which associate symbiotically with eukaryotic algae. All known marine examples of these symbioses have involved either centric diatom or haptophyte hosts. We report here the discovery and characterization of two distinct marine pennate diatom-diazotroph symbioses, which until now had only been observed in freshwater environments. Rhopalodiaceae diatoms Epithemia pelagica sp. nov. and Epithemia catenata sp. nov. were isolated repeatedly from the subtropical North Pacific Ocean, and analysis of sequence libraries reveals a global distribution. These symbioses likely escaped attention because the endosymbionts lack fluorescent photopigments, have nifH gene sequences similar to those of free-living unicellular cyanobacteria, and are lost in nitrogen-replete medium. Marine Rhopalodiaceae-diazotroph symbioses are a previously overlooked but widespread source of bioavailable nitrogen in marine habitats and provide new, easily cultured model organisms for the study of organelle evolution.
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14
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The marine nitrogen cycle: new developments and global change. Nat Rev Microbiol 2022; 20:401-414. [PMID: 35132241 DOI: 10.1038/s41579-022-00687-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2022] [Indexed: 12/25/2022]
Abstract
The ocean is home to a diverse and metabolically versatile microbial community that performs the complex biochemical transformations that drive the nitrogen cycle, including nitrogen fixation, assimilation, nitrification and nitrogen loss processes. In this Review, we discuss the wealth of new ocean nitrogen cycle research in disciplines from metaproteomics to global biogeochemical modelling and in environments from productive estuaries to the abyssal deep sea. Influential recent discoveries include new microbial functional groups, novel metabolic pathways, original conceptual perspectives and ground-breaking analytical capabilities. These emerging research directions are already contributing to urgent efforts to address the primary challenge facing marine microbiologists today: the unprecedented onslaught of anthropogenic environmental change on marine ecosystems. Ocean warming, acidification, nutrient enrichment and seawater stratification have major effects on the microbial nitrogen cycle, but widespread ocean deoxygenation is perhaps the most consequential for the microorganisms involved in both aerobic and anaerobic nitrogen transformation pathways. In turn, these changes feed back to the global cycles of greenhouse gases such as carbon dioxide and nitrous oxide. At a time when our species casts a lengthening shadow across all marine ecosystems, timely new advances offer us unique opportunities to understand and better predict human impacts on nitrogen biogeochemistry in the changing ocean of the Anthropocene.
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15
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Inomura K, Masuda T, Eichner M, Rabouille S, Zavřel T, Červený J, Vancová M, Bernát G, Armin G, Claquin P, Kotabová E, Stephan S, Suggett DJ, Deutsch C, Prášil O. Quantifying Cyanothece growth under DIC limitation. Comput Struct Biotechnol J 2021; 19:6456-6464. [PMID: 34938417 PMCID: PMC8665340 DOI: 10.1016/j.csbj.2021.11.036] [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: 06/28/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 11/26/2022] Open
Abstract
The photoautotrophic, unicellular N2-fixer, Cyanothece, is a model organism that has been widely used to study photosynthesis regulation, the structure of photosystems, and the temporal segregation of carbon (C) and nitrogen (N) fixation in light and dark phases of the diel cycle. Here, we present a simple quantitative model and experimental data that together, suggest external dissolved inorganic carbon (DIC) concentration as a major limiting factor for Cyanothece growth, due to its high C-storage requirement. Using experimental data from a parallel laboratory study as a basis, we show that after the onset of the light period, DIC was rapidly consumed by photosynthesis, leading to a sharp drop in the rate of photosynthesis and C accumulation. In N2-fixing cultures, high rates of photosynthesis in the morning enabled rapid conversion of DIC to intracellular C storage, hastening DIC consumption to levels that limited further uptake. The N2-fixing condition allows only a small fraction of fixed C for cellular growth since a large fraction was reserved in storage to fuel night-time N2 fixation. Our model provides a framework for resolving DIC limitation in aquatic ecosystem simulations, where DIC as a growth-limiting factor has rarely been considered, and importantly emphasizes the effect of intracellular C allocation on growth rate that varies depending on the growth environment.
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Affiliation(s)
- Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Takako Masuda
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czech Republic
| | - Meri Eichner
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czech Republic
| | - Sophie Rabouille
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, F-66650 Banyuls-sur-mer, France
| | - Tomáš Zavřel
- Department of Adaptive Biotechnologies, Global Change Research Institute, Czech Academy of Sciences, Brno, Czech Republic
| | - Jan Červený
- Department of Adaptive Biotechnologies, Global Change Research Institute, Czech Academy of Sciences, Brno, Czech Republic
| | - Marie Vancová
- Laboratory of Electron Microscopy, Institute of Parasitology, Biology Centre of the Czech Academy of Sciences and Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Gábor Bernát
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czech Republic.,Balaton Limnological Research Institute, Eötvös Loránd Research Network (ELKH), Tihany, Hungary
| | - Gabrielle Armin
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Pascal Claquin
- Laboratoire de Biologie des ORganismes et Ecosystèmes Aquatiques (BOREA), UMR 8067, Muséum National d'Histoire Naturelle, CNRS, IRD Sorbonne Université, Université de Caen Normandie, Normandie Université, Esplanade de la Paix, F-14032 Caen, France
| | - Eva Kotabová
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czech Republic
| | - Susanne Stephan
- Department Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - David J Suggett
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW 2007, Australia
| | - Curtis Deutsch
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Ondřej Prášil
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czech Republic
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16
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Suzuki S, Kawachi M, Tsukakoshi C, Nakamura A, Hagino K, Inouye I, Ishida KI. Unstable Relationship Between Braarudosphaera bigelowii (= Chrysochromulina parkeae) and Its Nitrogen-Fixing Endosymbiont. FRONTIERS IN PLANT SCIENCE 2021; 12:749895. [PMID: 34925404 PMCID: PMC8679911 DOI: 10.3389/fpls.2021.749895] [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: 07/30/2021] [Accepted: 11/10/2021] [Indexed: 06/14/2023]
Abstract
Marine phytoplankton are major primary producers, and their growth is primarily limited by nitrogen in the oligotrophic ocean environment. The haptophyte Braarudosphaera bigelowii possesses a cyanobacterial endosymbiont (UCYN-A), which plays a major role in nitrogen fixation in the ocean. However, host-symbiont interactions are poorly understood because B. bigelowii was unculturable. In this study, we sequenced the complete genome of the B. bigelowii endosymbiont and showed that it was highly reductive and closely related to UCYN-A2 (an ecotype of UCYN-A). We succeeded in establishing B. bigelowii strains and performed microscopic observations. The detailed observations showed that the cyanobacterial endosymbiont was surrounded by a single host derived membrane and divided synchronously with the host cell division. The transcriptome of B. bigelowii revealed that B. bigelowii lacked the expression of many essential genes associated with the uptake of most nitrogen compounds, except ammonia. During cultivation, some of the strains completely lost the endosymbiont. Moreover, we did not find any evidence of endosymbiotic gene transfer from the endosymbiont to the host. These findings illustrate an unstable morphological, metabolic, and genetic relationship between B. bigelowii and its endosymbiont.
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Affiliation(s)
- Shigekatsu Suzuki
- Biodiversity Division, National Institute for Environmental Studies, Ibaraki, Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, Ibaraki, Japan
| | - Chinatsu Tsukakoshi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Atsushi Nakamura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Kyoko Hagino
- Center for Advanced Marine Core Research, Kochi University, Kochi, Japan
| | - Isao Inouye
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Ken-ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
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17
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Liao A, Han D, Song X, Yang S. Impacts of storm events on chlorophyll-a variations and controlling factors for algal bloom in a river receiving reclaimed water. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 297:113376. [PMID: 34325374 DOI: 10.1016/j.jenvman.2021.113376] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Harmful algal bloom is prevalent in the reclaimed-water-source (RWS) river caused by the excessive nutrient's inputs. Rainfall water may be the sole nutrient-diluted water source for the RWS river. However, the effects of storm events on the algal bloom in the RWS river are poorly understood. This study presents chlorophyll-a (Chl-a) variations before, during, and after the initial storm events (Pre-storm, In-storm, and Post-storm) at four representative sites with distinct hydraulic conditions in a dam-regulated RWS river system, Beijing. The response of Chl-a to the initial storm events mostly depends on the ecosystem status that caused by the river hydraulic properties. The upstream is more river-like and downstream is more lake-like. In the river-like system, elevated water temperature (WT, increased by 2 %) could support the dominating algae (diatom) growth (Chl-a increased by 130 %) from Pre-storm to In-storm period. In the lake-like system, the dominant algae (blue algae) declined (Chl-a sharply decreased by 96%-99 %) due to the lower WT (decreased by 3%-7%) and increased flow velocities from Pre-storm to In-storm period. During the Post-storm period, the dominant algae break out (Chl-a surged by 20%-319 %) in the lake-like system caused by the recovered WT (increased by 3%-6%) and flow velocity. The occurrence of algal bloom can be predicted by the Random Forest (RF) model based on water quality parameters such as total nitrogen (TN). The thresholds of algal bloom for the Pre-storm, In-storm, and Post-storm periods were identified as 30 μg/L, 10 μg/L, and 10 μg/L, respectively. The two driven factors were WT and nitrate (NO3-N) for the Pre-storm period and were WT and TN for the In- & Post-storm periods. A higher risk of algal bloom is highlighted during the initial storm events in the RWS river. We propose recommendations for improving water quality in the RWS river systems under the climatic change.
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Affiliation(s)
- Anran Liao
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dongmei Han
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Danish College (SDC), University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China.
| | - Xianfang Song
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Danish College (SDC), University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
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18
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Delmont TO, Pierella Karlusich JJ, Veseli I, Fuessel J, Eren AM, Foster RA, Bowler C, Wincker P, Pelletier E. Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean. ISME JOURNAL 2021; 16:927-936. [PMID: 34697433 DOI: 10.1038/s41396-021-01135-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 12/30/2022]
Abstract
Biological nitrogen fixation contributes significantly to marine primary productivity. The current view depicts few cyanobacterial diazotrophs as the main marine nitrogen fixers. Here, we used 891 Tara Oceans metagenomes derived from surface waters of five oceans and two seas to generate a manually curated genomic database corresponding to free-living, filamentous, colony-forming, particle-attached, and symbiotic bacterial and archaeal populations. The database provides the genomic content of eight cyanobacterial diazotrophs including a newly discovered population related to known heterocystous symbionts of diatoms, as well as 40 heterotrophic bacterial diazotrophs that considerably expand the known diversity of abundant marine nitrogen fixers. These 48 populations encapsulate 92% of metagenomic signal for known nifH genes in the sunlit ocean, suggesting that the genomic characterization of the most abundant marine diazotrophs may be nearing completion. Newly identified heterotrophic bacterial diazotrophs are widespread, express their nifH genes in situ, and also occur in large planktonic size fractions where they might form aggregates that provide the low-oxygen microenvironments required for nitrogen fixation. Critically, we found heterotrophic bacterial diazotrophs to be more abundant than cyanobacterial diazotrophs in most metagenomes from the open oceans and seas, emphasizing the importance of a wide range of heterotrophic populations in the marine nitrogen balance.
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Affiliation(s)
- Tom O Delmont
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France. .,Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France.
| | - Juan José Pierella Karlusich
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France.,Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Iva Veseli
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Jessika Fuessel
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.,Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University Stockholm, Stockholm, 106 91, Sweden
| | - Chris Bowler
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France.,Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara GOsee, Paris, France
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19
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Rabouille S, Randall B, Talec A, Raimbault P, Blasco T, Latifi A, Oschlies A. Independence of a Marine Unicellular Diazotroph to the Presence of NO 3. Microorganisms 2021; 9:microorganisms9102073. [PMID: 34683393 PMCID: PMC8540418 DOI: 10.3390/microorganisms9102073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 11/23/2022] Open
Abstract
Marine nitrogen (N2) fixation was historically considered to be absent or reduced in nitrate (NO3−) rich environments. This is commonly attributed to the lower energetic cost of NO3− uptake compared to diazotrophy in oxic environments. This paradigm often contributes to making inferences about diazotroph distribution and activity in the ocean, and is also often used in biogeochemical ocean models. To assess the general validity of this paradigm beyond the traditionally used model organism Trichodesmium spp., we grew cultures of the unicellular cyanobacterium Crocosphaera watsonii WH8501 long term in medium containing replete concentrations of NO3−. NO3− uptake was measured in comparison to N2 fixation to assess the cultures’ nitrogen source preferences. We further measured culture growth rate, cell stoichiometry, and carbon fixation rate to determine if the presence of NO3− had any effect on cell metabolism. We found that uptake of NO3− by this strain of Crocosphaera was minimal in comparison to other N sources (~2–4% of total uptake). Furthermore, availability of NO3− did not statistically alter N2 fixation rate nor any aspect of cell physiology or metabolism measured (cellular growth rate, cell stoichiometry, cell size, nitrogen fixation rate, nitrogenase activity) in comparison to a NO3− free control culture. These results demonstrate the capability of a marine diazotroph to fix nitrogen and grow independently of NO3−. This lack of sensitivity of diazotrophy to NO3− suggests that assumptions often made about, and model formulations of, N2 fixation should be reconsidered.
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Affiliation(s)
- Sophie Rabouille
- Laboratoire d’Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, F-66650 Banyuls-sur-Mer, France
- Laboratoire d’Océanographie de Villefranche (LOV), CNRS, Sorbonne Université, F-06230 Villefranche-sur-Mer, France; (B.R.); (A.T.); (T.B.)
- Correspondence:
| | - Benjamin Randall
- Laboratoire d’Océanographie de Villefranche (LOV), CNRS, Sorbonne Université, F-06230 Villefranche-sur-Mer, France; (B.R.); (A.T.); (T.B.)
| | - Amélie Talec
- Laboratoire d’Océanographie de Villefranche (LOV), CNRS, Sorbonne Université, F-06230 Villefranche-sur-Mer, France; (B.R.); (A.T.); (T.B.)
| | - Patrick Raimbault
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288 Marseille, France;
| | - Thierry Blasco
- Laboratoire d’Océanographie de Villefranche (LOV), CNRS, Sorbonne Université, F-06230 Villefranche-sur-Mer, France; (B.R.); (A.T.); (T.B.)
| | - Amel Latifi
- Laboratoire de Chimie Bactérienne (LCB), Aix Marseille Université, CNRS, 13284 Marseille, France;
| | - Andreas Oschlies
- GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany;
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20
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Stalder C, ElKateb A, Spangenberg JE, Terhzaz L, Vertino A, Spezzaferri S. Living benthic foraminifera from cold-water coral ecosystems in the eastern Alboran Sea, Western Mediterranean. Heliyon 2021; 7:e07880. [PMID: 34504972 PMCID: PMC8417336 DOI: 10.1016/j.heliyon.2021.e07880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 03/19/2020] [Accepted: 08/24/2021] [Indexed: 11/26/2022] Open
Abstract
Benthic foraminifera (protists with biomineralized tests) coupled with geochemical proxies are used for the first time to characterize present oceanographic conditions occurring in cold-water coral ecosystems (CWC) in the eastern Alboran Sea (Brittlestar Ridge and Cablier Mound), western Mediterranean Sea. Quantitative data on living (stained) benthic foraminifera from 5 box cores retrieved during the MD194 cruise on the RV Marion Dufresne reveal that these organisms are more diverse in presence of corals, where more numerous ecological niches occur than they are in pelagic adjacent sediments. These data confirm that CWC can be considered as “diversity hotspots” also for benthic foraminifera. Geochemical characterization shows that these sediments contain relatively fresh (labile) organic matter but also a reworked refractory component. In particular, the total organic carbon and the δ13Corg values suggest that some of the organic matter may be a mixture of marine and reworked particulate organic matter, compared to typical values from temperate phytoplankton. The δ15N of the organic fraction suggests that important atmospheric N2-fixation and degradation processes occur in the region. Finally, our results show that a more effective advection of freshly exported particulate organic matter from the surface waters occur at the mound top rather than at the mound base or off-mound allowing some coral colonies to survive on the top of mounds in this region. The mud layer covering the coral rubble debris may suggest that the Brittlestar Ridge is today exposed to siltation preventing the growth of corals at the mound base or off-mound.
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Affiliation(s)
- Claudio Stalder
- Department of Geosciences, University of Fribourg, Chemin du Musée 6, CH–1700 Fribourg, Switzerland
| | - Akram ElKateb
- Department of Geosciences, University of Fribourg, Chemin du Musée 6, CH–1700 Fribourg, Switzerland
| | - Jorge E. Spangenberg
- Institute of Earth Surface Dynamics, University of Lausanne, Building Géopolis, CH–1015 Lausanne, Switzerland
| | - Loubna Terhzaz
- ODYSSEE Research Group, Geosciences, Water and Environment Laboratory, Faculty of Sciences in Rabat, Mohammed V University in Rabat, BP 1014 Rabat, Morocco
| | - Agostina Vertino
- Department of Geology, Ghent University, B-9000, Gent, Belgium
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, I-20126, Milan, Italy
| | - Silvia Spezzaferri
- Department of Geosciences, University of Fribourg, Chemin du Musée 6, CH–1700 Fribourg, Switzerland
- Corresponding author.
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21
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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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22
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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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23
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Rabouille S, Campbell DA, Masuda T, Zavřel T, Bernát G, Polerecky L, Halsey K, Eichner M, Kotabová E, Stephan S, Lukeš M, Claquin P, Bonomi-Barufi J, Lombardi AT, Červený J, Suggett DJ, Giordano M, Kromkamp JC, Prášil O. Electron & Biomass Dynamics of Cyanothece Under Interacting Nitrogen & Carbon Limitations. Front Microbiol 2021; 12:617802. [PMID: 33897635 PMCID: PMC8063122 DOI: 10.3389/fmicb.2021.617802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/01/2021] [Indexed: 11/25/2022] Open
Abstract
Marine diazotrophs are a diverse group with key roles in biogeochemical fluxes linked to primary productivity. The unicellular, diazotrophic cyanobacterium Cyanothece is widely found in coastal, subtropical oceans. We analyze the consequences of diazotrophy on growth efficiency, compared to NO3–-supported growth in Cyanothece, to understand how cells cope with N2-fixation when they also have to face carbon limitation, which may transiently affect populations in coastal environments or during blooms of phytoplankton communities. When grown in obligate diazotrophy, cells face the double burden of a more ATP-demanding N-acquisition mode and additional metabolic losses imposed by the transient storage of reducing potential as carbohydrate, compared to a hypothetical N2 assimilation directly driven by photosynthetic electron transport. Further, this energetic burden imposed by N2-fixation could not be alleviated, despite the high irradiance level within the cultures, because photosynthesis was limited by the availability of dissolved inorganic carbon (DIC), and possibly by a constrained capacity for carbon storage. DIC limitation exacerbates the costs on growth imposed by nitrogen fixation. Therefore, the competitive efficiency of diazotrophs could be hindered in areas with insufficient renewal of dissolved gases and/or with intense phytoplankton biomass that both decrease available light energy and draw the DIC level down.
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Affiliation(s)
- Sophie Rabouille
- Sorbonne Université, CNRS, LOV, Villefranche-sur-Mer, France.,Sorbonne Université, CNRS, LOMIC, Banyuls-sur-Mer, France
| | - Douglas A Campbell
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia.,Mount Allison University, Sackville, NB, Canada
| | - Takako Masuda
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Tomáš Zavřel
- Department of Adaptive Biotechnologies, Global Change Research Institute CAS, Brno, Czechia
| | - Gábor Bernát
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia.,Centre for Ecological Research, Balaton Limnological Institute, Klebelsberg Kuno u. 3. 8237 Tihany, Hungary
| | - Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Kimberly Halsey
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Meri Eichner
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Eva Kotabová
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Susanne Stephan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Zur alten Fischerhütte 2, Stechlin, Germany.,Department of Ecology, Berlin Institute of Technology (TU Berlin), Ernst-Reuter-Platz 1, Berlin, Germany
| | - Martin Lukeš
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Pascal Claquin
- UMR BOREA (CNRS 8067), MNHN, IRD (207), Université de Caen Basse-Normandie, Caen, France
| | - José Bonomi-Barufi
- Departamento de Botânica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | | | - Jan Červený
- Department of Adaptive Biotechnologies, Global Change Research Institute CAS, Brno, Czechia
| | - David J Suggett
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Mario Giordano
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia.,Dipartimento di Scienze della Vita e dell'Ambiente, UniversitaÌ Politecnica delle Marche, Ancona, Italy
| | - Jacco C Kromkamp
- NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Utrecht, Netherlands
| | - Ondřej Prášil
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
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24
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Liu LM, Li DL, Deng B, Wang XW, Jiang HB. Special roles for efflux systems in iron homeostasis of non-siderophore-producing cyanobacteria. Environ Microbiol 2021; 24:551-565. [PMID: 33817959 DOI: 10.1111/1462-2920.15506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/03/2021] [Indexed: 11/28/2022]
Abstract
In oligotrophic oceans, low bioavailability of Fe is a key factor limiting primary productivity. However, excessive Fe in cells leads to the Fenton reaction, which is toxic to cells. Cyanobacteria must strictly maintain intracellular Fe homeostasis. Here, we knocked out a series of genes encoding efflux systems in Synechocystis sp. PCC 6803, and found eight genes that are required for high Fe detoxification. Unexpectedly, the HlyBD-TolC efflux system plays an important role in the adaptation of Synechocystis under Fe-deficient conditions. Mutants of HlyD and TolC grew worse than the wild-type strain under low-Fe conditions and showed significantly lower intracellular Fe contents than the wild-type strain. We excluded the possibility that the low Fe sensitivity of the HlyBD-TolC mutants was caused by a loss of the S-layer, the main extracellular protein secreted via this efflux system. Inactivation of the HlyD protein influenced type IV pili formation and direct inactivation of type IV pili related genes affected the adaptation to low-Fe conditions. HlyBD-TolC system is likely involved in the formation of type IV pili and indirectly influenced Fe acquisition. Our findings suggest that efflux system in non-siderophore-producing cyanobacteria can facilitate Fe uptake and help cells adapt to Fe-deficient conditions via novel pathways.
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Affiliation(s)
- Ling-Mei Liu
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, 519080, China
| | - Ding-Lan Li
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Bin Deng
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Xin-Wei Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, 519080, China.,School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Hai-Bo Jiang
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, 519080, China.,School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
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25
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Li L, Wu L, Yang L, Liu C, Li J, Li N. Combined impact of organic matter, phosphorus, nitrate, and ammonia nitrogen on the process of blackwater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:10.1007/s11356-021-13050-1. [PMID: 33630265 DOI: 10.1007/s11356-021-13050-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
Blackwater events are frequently reported over the world and become a serious environmental problem. However, the mechanisms of blackwater occurrence are not fully understood yet. This study simulated the process of blackwater with the combined pollution in an orthogonal experiment, which had 4 factors (TOC, TP, NH4+-N, and NO3--N) and 4 levels (None, Low, Middle, and High). Results showed that the process of water condition changes was divided into two parts, which were "exogenous" and "algae-derived" blackwater, and the influence of four different pollutants on the occurrence of the blackwater was ranked as follows: TOC > TP > NO3--N > NH4+-N. With the increase of organic matter addition, the anaerobic condition in water was prolonged and the concentration of Fe2+ had a significant increase. In addition, under the None phosphorus condition, the descent rates of DO and COD in the water were reduced, and the algae bloom was obviously deferred. Moreover, the addition of organic matter or phosphorus changed the microbial community structure and led to different water processes. Particularly, only on the condition of the high content of TOC and phosphorus, the diversity of sulfate-reducing bacteria (e.g., Pseudomonas, Paludibacter, and Bacteroides) increased significantly, which accounted for 51.4%, causing the significant production of S2- in the water. Water's lack of phosphorus showed a low rate of decomposition of organic matter, which might be the result of a considerable increase in the abundance of aerobic Trichococcus and Malikia. This study shows that organic matter and phosphorus have synergistic effect on blackwater occurrence. In the treatment of blackwater, the exogenous pollutant control should reduce the discharge of organic pollutants, and endogenous control should focus on phosphorus abatement and reduce nitrogen control.
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Affiliation(s)
- Lanmiao Li
- School of Water Resources and Hydropower, Sichuan University, Chengdu, 610065, China
| | - Linjun Wu
- School of Water Resources and Hydropower, Sichuan University, Chengdu, 610065, China
| | - Lingxiao Yang
- School of Water Resources and Hydropower, Sichuan University, Chengdu, 610065, China
| | - Chao Liu
- School of Water Resources and Hydropower, Sichuan University, Chengdu, 610065, China
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Jun Li
- School of Water Resources and Hydropower, Sichuan University, Chengdu, 610065, China
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Naiwen Li
- School of Water Resources and Hydropower, Sichuan University, Chengdu, 610065, China.
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource & Hydropower, Sichuan University, Chengdu, 610065, Sichuan, China.
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26
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Polerecky L, Masuda T, Eichner M, Rabouille S, Vancová M, Kienhuis MVM, Bernát G, Bonomi-Barufi J, Campbell DA, Claquin P, Červený J, Giordano M, Kotabová E, Kromkamp J, Lombardi AT, Lukeš M, Prášil O, Stephan S, Suggett D, Zavřel T, Halsey KH. Temporal Patterns and Intra- and Inter-Cellular Variability in Carbon and Nitrogen Assimilation by the Unicellular Cyanobacterium Cyanothece sp. ATCC 51142. Front Microbiol 2021; 12:620915. [PMID: 33613489 PMCID: PMC7890256 DOI: 10.3389/fmicb.2021.620915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 01/11/2021] [Indexed: 12/05/2022] Open
Abstract
Unicellular nitrogen fixing cyanobacteria (UCYN) are abundant members of phytoplankton communities in a wide range of marine environments, including those with rapidly changing nitrogen (N) concentrations. We hypothesized that differences in N availability (N2 vs. combined N) would cause UCYN to shift strategies of intracellular N and C allocation. We used transmission electron microscopy and nanoscale secondary ion mass spectrometry imaging to track assimilation and intracellular allocation of 13C-labeled CO2 and 15N-labeled N2 or NO3 at different periods across a diel cycle in Cyanothece sp. ATCC 51142. We present new ideas on interpreting these imaging data, including the influences of pre-incubation cellular C and N contents and turnover rates of inclusion bodies. Within cultures growing diazotrophically, distinct subpopulations were detected that fixed N2 at night or in the morning. Additional significant within-population heterogeneity was likely caused by differences in the relative amounts of N assimilated into cyanophycin from sources external and internal to the cells. Whether growing on N2 or NO3, cells prioritized cyanophycin synthesis when N assimilation rates were highest. N assimilation in cells growing on NO3 switched from cyanophycin synthesis to protein synthesis, suggesting that once a cyanophycin quota is met, it is bypassed in favor of protein synthesis. Growth on NO3 also revealed that at night, there is a very low level of CO2 assimilation into polysaccharides simultaneous with their catabolism for protein synthesis. This study revealed multiple, detailed mechanisms underlying C and N management in Cyanothece that facilitate its success in dynamic aquatic environments.
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Affiliation(s)
- Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Takako Masuda
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Meri Eichner
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sophie Rabouille
- Sorbonne Université, CNRS, Laboratoire d’Océanographie de Villefranche, Villefranche-sur-mer, France
- Sorbonne Université, CNRS, Laboratoire d’Océanographie Microbienne, Banyuls-sur-mer, France
| | - Marie Vancová
- Institute of Parasitology, Czech Academy of Sciences, Biology Centre, České Budějovice, Czechia
| | | | - Gabor Bernát
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
- Centre for Ecological Research, Balaton Limnological Institute, Tihany, Hungary
| | - Jose Bonomi-Barufi
- Botany Department, Federal University of Santa Catarina, Campus de Trindade, Florianópolis, Brazil
| | | | - Pascal Claquin
- Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques, FRE 2030, Muséum National d’Histoire Naturelle, CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Normandie Université, Esplanade de la Paix, France
| | - Jan Červený
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czechia
| | - Mario Giordano
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
- STU-UNIVPM Joint Algal Research Center, Marine Biology Institute, College of Sciences, Shantou University, Shantou, China
| | - Eva Kotabová
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Jacco Kromkamp
- NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, Netherlands
| | | | - Martin Lukeš
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Ondrej Prášil
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Susanne Stephan
- Department Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- Department of Ecology, Berlin Institute of Technology, Berlin, Germany
| | - David Suggett
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Tomas Zavřel
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czechia
| | - Kimberly H. Halsey
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
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27
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Cabello AM, Turk‐Kubo KA, Hayashi K, Jacobs L, Kudela RM, Zehr JP. Unexpected presence of the nitrogen-fixing symbiotic cyanobacterium UCYN-A in Monterey Bay, California. JOURNAL OF PHYCOLOGY 2020; 56:1521-1533. [PMID: 32609873 PMCID: PMC7754506 DOI: 10.1111/jpy.13045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/10/2020] [Indexed: 05/20/2023]
Abstract
In the last decade, the known biogeography of nitrogen fixation in the ocean has been expanded to colder and nitrogen-rich coastal environments. The symbiotic nitrogen-fixing cyanobacteria group A (UCYN-A) has been revealed as one of the most abundant and widespread nitrogen-fixers, and includes several sublineages that live associated with genetically distinct but closely related prymnesiophyte hosts. The UCYN-A1 sublineage is associated with an open ocean picoplanktonic prymnesiophyte, whereas UCYN-A2 is associated with the coastal nanoplanktonic coccolithophore Braarudosphaera bigelowii, suggesting that different sublineages may be adapted to different environments. Here, we study the diversity of nifH genes present at the Santa Cruz Municipal Wharf in the Monterey Bay (MB), California, and report for the first time the presence of multiple UCYN-A sublineages, unexpectedly dominated by the UCYN-A2 sublineage. Sequence and quantitative PCR data over an 8-year time-series (2011-2018) showed a shift toward increasing UCYN-A2 abundances after 2013, and a marked seasonality for this sublineage which was present during summer-fall months, coinciding with the upwelling-relaxation period in the MB. Increased abundances corresponded to positive temperature anomalies in MB, and we discuss the possibility of a benthic life stage of the associated coccolithophore host to explain the seasonal pattern. The dominance of UCYN-A2 in coastal waters of the MB underscores the need to further explore the habitat preference of the different sublineages in order to provide additional support for the hypothesis that UCYN-A1 and UCYN-A2 sublineages are different ecotypes.
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Affiliation(s)
- Ana M. Cabello
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
- Centro Oceanográfico de MálagaInstituto Español de OceanografíaFuengirolaMálaga29001Spain
| | - Kendra A. Turk‐Kubo
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
| | - Kendra Hayashi
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
| | - Lucien Jacobs
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
| | - Raphael M. Kudela
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
| | - Jonathan P. Zehr
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
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28
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Qiu GW, Jiang HB, Lis H, Li ZK, Deng B, Shang JL, Sun CY, Keren N, Qiu BS. A unique porin meditates iron-selective transport through cyanobacterial outer membranes. Environ Microbiol 2020; 23:376-390. [PMID: 33196124 DOI: 10.1111/1462-2920.15324] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/02/2020] [Accepted: 11/12/2020] [Indexed: 10/23/2022]
Abstract
Cyanobacteria are globally important primary producers and nitrogen fixers with high iron demands. Low ambient dissolved iron concentrations in many aquatic environments mean that these organisms must maintain sufficient and selective transport of iron into the cell. However, the nature of iron transport pathways through the cyanobacterial outer membrane remains obscure. Here we present multiple lines of experimental evidence that collectively support the existence of a novel class of substrate-selective iron porin, Slr1908, in the outer membrane of the cyanobacterium Synechocystis sp. PCC 6803. Elemental composition analysis and short-term iron uptake assays with mutants in Slr1908 reveal that this protein is primarily involved in inorganic iron uptake and contributes less to the accumulation of other metals. Homologues of Slr1908 are widely distributed in both freshwater and marine cyanobacteria, most notably in unicellular marine diazotrophs. Complementary experiments with a homologue of Slr1908 in Synechococcus sp. PCC 7002 restored the phenotype of Synechocystis knockdown mutants, showing that this siderophore producing species also possesses a porin with a similar function in Fe transport. The involvement of a substrate-selective porins in iron uptake may allow cyanobacteria to tightly control iron flux into the cell, particularly in environments where iron concentrations fluctuate.
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Affiliation(s)
- Guo-Wei Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Hai-Bo Jiang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Hagar Lis
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Zheng-Ke Li
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Bin Deng
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Jin-Long Shang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Chuan-Yu Sun
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Nir Keren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Bao-Sheng Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
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Jiang T, Guo C, Wang M, Wang M, Zhang X, Liu Y, Liang Y, Jiang Y, He H, Shao H, McMinn A. Genome Analysis of Two Novel Synechococcus Phages That Lack Common Auxiliary Metabolic Genes: Possible Reasons and Ecological Insights by Comparative Analysis of Cyanomyoviruses. Viruses 2020; 12:v12080800. [PMID: 32722486 PMCID: PMC7472177 DOI: 10.3390/v12080800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 02/01/2023] Open
Abstract
The abundant and widespread unicellular cyanobacteria Synechococcus plays an important role in contributing to global phytoplankton primary production. In the present study, two novel cyanomyoviruses, S-N03 and S-H34 that infected Synechococcus MW02, were isolated from the coastal waters of the Yellow Sea. S-N03 contained a 167,069-bp genome comprising double-stranded DNA with a G + C content of 50.1%, 247 potential open reading frames and 1 tRNA; S-H34 contained a 167,040-bp genome with a G + C content of 50.1%, 246 potential open reading frames and 5 tRNAs. These two cyanophages contain fewer auxiliary metabolic genes (AMGs) than other previously isolated cyanophages. S-H34 in particular, is currently the only known cyanomyovirus that does not contain any AMGs related to photosynthesis. The absence of such common AMGs in S-N03 and S-H34, their distinct evolutionary history and ecological features imply that the energy for phage production might be obtained from other sources rather than being strictly dependent on the maintenance of photochemical ATP under high light. Phylogenetic analysis showed that the two isolated cyanophages clustered together and had a close relationship with two other cyanophages of low AMG content. Comparative genomic analysis, habitats and hosts across 81 representative cyanomyovirus showed that cyanomyovirus with less AMGs content all belonged to Synechococcus phages isolated from eutrophic waters. The relatively small genome size and high G + C content may also relate to the lower AMG content, as suggested by the significant correlation between the number of AMGs and G + C%. Therefore, the lower content of AMG in S-N03 and S-H34 might be a result of viral evolution that was likely shaped by habitat, host, and their genomic context. The genomic content of AMGs in cyanophages may have adaptive significance and provide clues to their evolution.
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Affiliation(s)
- Tong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
| | - Cui Guo
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- Correspondence:
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
| | - Meiwen Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
| | - Xinran Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
| | - Yundan Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
| | - Yantao Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
| | - Hui He
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
| | - Andrew McMinn
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (T.J.); (M.W.); (M.W.); (X.Z.); (Y.L.); (Y.L.); (Y.J.); (H.H.); (H.S.); (A.M.)
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia
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Abstract
Nitrogen fixation, the reduction of atmospheric dinitrogen gas (N2) to ammonia, is critical for biological productivity but is difficult to study in the vast expanse of the global ocean. Decades of field studies and the infusion of molecular biological, genomic, isotopic, and geochemical modeling approaches have led to new paradigms and questions. The discovery of previously unknown N2-fixing (diazotrophic) microorganisms and unusual physiological adaptations, combined with diagnostic distributions of nutrients and their isotopes as well as measured and modeled biogeographic patterns, have revolutionized our understanding of marine N2 fixation and its role in the global nitrogen cycle. Anthropogenic upper-ocean warming, increased dissolved carbon dioxide, and acidification will affect the distribution and relative importance of specific subgroups of N2 fixers in the sea; these changes have implications for foodwebs and biogeochemical cycles.
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Affiliation(s)
- Jonathan P. Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95003, USA
| | - Douglas G. Capone
- Marine and Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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Liu J, Zhou L, Ke Z, Li G, Tan Y. Phosphorus deficiency induced by aluminum in a marine nitrogen-fixing cyanobacterium Crocosphaera watsonii WH0003. CHEMOSPHERE 2020; 246:125641. [PMID: 31901529 DOI: 10.1016/j.chemosphere.2019.125641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 11/19/2019] [Accepted: 12/11/2019] [Indexed: 06/10/2023]
Abstract
Large amounts of aluminum (Al) enter the ocean through atmospheric dust deposition and river runoffs. However, few studies have reported the effects of Al on marine phytoplankton, especially nitrogen-fixing cyanobacteria. By using the isotope tracer method and quantitative reverse transcription PCR (RT-qPCR), we examined the physiological effect of Al (0.2, 2 and 20 μM) on the unicellular marine nitrogen-fixing cyanobacterium Crocosphaera watsonii in Aquil* medium. We show that Al has an inhibitory physiological effect on C. watsonii, including changes in growth rate, nitrogen fixation rate, carbon fixation rate, cell size, fast rise chlorophyll fluorescence kinetics, cellular photosynthetic pigment and C/N/P content, the same as that of the phosphorus deficient treatment. The ratio of cellular elements C:N:P showed that phosphorus was deficient in the cell of C. watsonii after Al treatment (2 and 20 μM). In addition, Al stimulated the expression of phosphorus-related genes pstS, phoH, phoU, ppK and ppX in C. watsonii. All these results suggest that Al-treated C. watsonii is phosphorus-limited, and that the phosphorus deficiency induced by Al may be one mechanism behind aluminum's toxicity.
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Affiliation(s)
- Jiaxing Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Linbin Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Zhixin Ke
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Heterogeneous nitrogen fixation rates confer energetic advantage and expanded ecological niche of unicellular diazotroph populations. Commun Biol 2020; 3:172. [PMID: 32286494 PMCID: PMC7156374 DOI: 10.1038/s42003-020-0894-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/13/2020] [Indexed: 11/23/2022] Open
Abstract
Nitrogen fixing plankton provide nitrogen to fuel marine ecosystems and biogeochemical cycles but the factors that constrain their growth and habitat remain poorly understood. Here we investigate the importance of metabolic specialization in unicellular diazotroph populations, using laboratory experiments and model simulations. In clonal cultures of Crocosphaera watsonii and Cyanothece sp. spiked with 15N2, cellular 15N enrichment developed a bimodal distribution within colonies, indicating that N2 fixation was confined to a subpopulation. In a model of population metabolism, heterogeneous nitrogen (N2) fixation rates substantially reduce the respiration rate required to protect nitrogenase from O2. The energy savings from metabolic specialization is highest at slow growth rates, allowing populations to survive in deeper waters where light is low but nutrients are high. Our results suggest that heterogeneous N2 fixation in colonies of unicellular diazotrophs confers an energetic advantage that expands the ecological niche and may have facilitated the evolution of multicellular diazotrophs. Takako Masuda et al. show that individual cells in clonal populations of Crocosphaera watsonii and Cyanothece sp exhibit varied nitrogen fixation rates. This heterogeneity within the population decreases the energetic cost of respiration and expands the viable habitats for these unicellular diazotrophs.
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Tromas N, Taranu ZE, Castelli M, Pimentel JSM, Pereira DA, Marcoz R, Shapiro BJ, Giani A. The evolution of realized niches within freshwater
Synechococcus. Environ Microbiol 2020; 22:1238-1250. [DOI: 10.1111/1462-2920.14930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Nicolas Tromas
- Département de sciences biologiquesUniversité de Montréal Montréal QC H2V 2S9 Canada
| | - Zofia E. Taranu
- Environnement et Changement Climatique Canada 105 Rue McGill, Montréal QC H2Y 2E7 Canada
| | | | | | - Daniel A. Pereira
- Federal University of Minas Gerais Belo Horizonte Minas Gerais Brazil
| | - Romane Marcoz
- Département de sciences biologiquesUniversité de Montréal Montréal QC H2V 2S9 Canada
| | - B. Jesse Shapiro
- Département de sciences biologiquesUniversité de Montréal Montréal QC H2V 2S9 Canada
| | - Alessandra Giani
- Federal University of Minas Gerais Belo Horizonte Minas Gerais Brazil
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34
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Abstract
Photosynthesis evolved in the ocean more than 2 billion years ago and is now performed by a wide range of evolutionarily distinct organisms, including both prokaryotes and eukaryotes. Our appreciation of their abundance, distributions, and contributions to primary production in the ocean has been increasing since they were first discovered in the seventeenth century and has now been enhanced by data emerging from the Tara Oceans project, which performed a comprehensive worldwide sampling of plankton in the upper layers of the ocean between 2009 and 2013. Largely using recent data from Tara Oceans, here we review the geographic distributions of phytoplankton in the global ocean and their diversity, abundance, and standing stock biomass. We also discuss how omics-based information can be incorporated into studies of photosynthesis in the ocean and show the likely importance of mixotrophs and photosymbionts.
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Affiliation(s)
- Juan José Pierella Karlusich
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université de Recherche Paris Sciences et Lettres (Université PSL), 75005 Paris, France;
| | - Federico M Ibarbalz
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université de Recherche Paris Sciences et Lettres (Université PSL), 75005 Paris, France;
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université de Recherche Paris Sciences et Lettres (Université PSL), 75005 Paris, France;
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35
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Active nitrogen fixation by Crocosphaera expands their niche despite the presence of ammonium - A case study. Sci Rep 2019; 9:15064. [PMID: 31636357 PMCID: PMC6803696 DOI: 10.1038/s41598-019-51378-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 09/30/2019] [Indexed: 11/09/2022] Open
Abstract
Unicellular nitrogen fixer Crocosphaera contributes substantially to nitrogen fixation in oligotrophic subtropical gyres. They fix nitrogen even when significant amounts of ammonium are available. This has been puzzling since fixing nitrogen is energetically inefficient compared with using available ammonium. Here we show that by fixing nitrogen, Crocosphaera can increase their population and expand their niche despite the presence of ammonium. We have developed a simple but mechanistic model of Crocosphaera based on their growth in steady state culture. The model shows that the growth of Crocosphaera can become nitrogen limited despite their capability to fix nitrogen. When they fix nitrogen, the population increases by up to 78% relative to the case without nitrogen fixation. When we simulate a simple ecological situation where Crocosphaera exists with non-nitrogen-fixing phytoplankton, the relative abundance of Crocosphaera increases with nitrogen fixation, while the population of non-nitrogen-fixing phytoplankton decreases since a larger fraction of fixed nitrogen is consumed by Crocosphaera. Our study quantitatively supports the benefit of nitrogen fixation despite the high electron/energy costs, even when an energetically efficient alternative is available. It demonstrates a competitive aspect of Crocosphaera, permitting them to be regionally significant nitrogen fixers.
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36
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Klähn S, Bolay P, Wright PR, Atilho RM, Brewer KI, Hagemann M, Breaker RR, Hess WR. A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria. Nucleic Acids Res 2019; 46:10082-10094. [PMID: 30085248 PMCID: PMC6212724 DOI: 10.1093/nar/gky709] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/25/2018] [Indexed: 12/19/2022] Open
Abstract
As the key enzyme of bacterial nitrogen assimilation, glutamine synthetase (GS) is tightly regulated. In cyanobacteria, GS activity is controlled by the interaction with inactivating protein factors IF7 and IF17 encoded by the genes gifA and gifB, respectively. We show that a glutamine-binding aptamer within the gifB 5′ UTR of Synechocystis sp. PCC 6803 is critical for the expression of IF17. Binding of glutamine induced structural re-arrangements in this RNA element leading to enhanced protein synthesis in vivo and characterizing it as a riboswitch. Mutagenesis showed the riboswitch mechanism to contribute at least as much to the control of gene expression as the promoter-mediated transcriptional regulation. We suggest this and a structurally related but distinct element, to be designated type 1 and type 2 glutamine riboswitches. Extended biocomputational searches revealed that glutamine riboswitches are exclusively but frequently found in cyanobacterial genomes, where they are primarily associated with gifB homologs. Hence, this RNA-based sensing mechanism is common in cyanobacteria and establishes a regulatory feedback loop that couples the IF17-mediated GS inactivation to the intracellular glutamine levels. Together with the previously described sRNA NsiR4, these results show that non-coding RNA is an indispensable component in the control of nitrogen assimilation in cyanobacteria.
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Affiliation(s)
- Stephan Klähn
- Genetics & Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Department of Solar Materials, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Paul Bolay
- Genetics & Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Patrick R Wright
- Bioinformatics, Technical Faculty, University of Freiburg, Freiburg, Germany
| | - Ruben M Atilho
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Kenneth I Brewer
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Martin Hagemann
- Department of Plant Physiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Ronald R Breaker
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Freiburg Institute for Advanced Studies, University of Freiburg, Germany
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Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host. Proc Natl Acad Sci U S A 2019; 116:15973-15978. [PMID: 31235587 DOI: 10.1073/pnas.1902538116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyanobacteria are one of the most important contributors to oceanic primary production and survive in a wide range of marine habitats. Much effort has been made to understand their ecological features, diversity, and evolution, based mainly on data from free-living cyanobacterial species. In addition, symbiosis has emerged as an important lifestyle of oceanic microbes and increasing knowledge of cyanobacteria in symbiotic relationships with unicellular eukaryotes suggests their significance in understanding the global oceanic ecosystem. However, detailed characteristics of these cyanobacteria remain poorly described. To gain better insight into marine cyanobacteria in symbiosis, we sequenced the genome of cyanobacteria collected from a cell of a pelagic dinoflagellate that is known to host cyanobacterial symbionts within a specialized chamber. Phylogenetic analyses using the genome sequence revealed that the cyanobacterium represents an underdescribed lineage within an extensively studied, ecologically important group of marine cyanobacteria. Metagenomic analyses demonstrated that this cyanobacterial lineage is globally distributed and strictly coexists with its host dinoflagellates, suggesting that the intimate symbiotic association allowed the cyanobacteria to escape from previous metagenomic studies. Furthermore, a comparative analysis of the protein repertoire with related species indicated that the lineage has independently undergone reductive genome evolution to a similar extent as Prochlorococcus, which has the most reduced genomes among free-living cyanobacteria. Discovery of this cyanobacterial lineage, hidden by its symbiotic lifestyle, provides crucial insights into the diversity, ecology, and evolution of marine cyanobacteria and suggests the existence of other undiscovered cryptic cyanobacterial lineages.
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38
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Mareš J, Johansen JR, Hauer T, Zima J, Ventura S, Cuzman O, Tiribilli B, Kaštovský J. Taxonomic resolution of the genus Cyanothece (Chroococcales, Cyanobacteria), with a treatment on Gloeothece and three new genera, Crocosphaera, Rippkaea, and Zehria. JOURNAL OF PHYCOLOGY 2019; 55:578-610. [PMID: 30830691 DOI: 10.1111/jpy.12853] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/06/2018] [Indexed: 06/09/2023]
Abstract
The systematics of single-celled cyanobacteria represents a major challenge due to morphological convergence and application of various taxonomic concepts. The genus Cyanothece is one of the most problematic cases, as the name has been applied to oval-shaped coccoid cyanobacteria lacking sheaths with little regard to their phylogenetic position and details of morphology and ultrastructure. Hereby we analyze an extensive set of complementary genetic and phenotypic evidence to disentangle the relationships among these cyanobacteria. We provide diagnostic characters to separate the known genera Cyanothece, Gloeothece, and Aphanothece, and provide a valid description for Crocosphaera gen. nov. We describe two new genera, Rippkaea and Zehria, to characterize two distinct phylogenetic lineages outside the previously known genera. We further describe 13 new species in total including Cyanothece svehlovae, Gloeothece aequatorialis, G. aurea, G. bryophila, G. citriformis, G. reniformis, Gloeothece tonkinensis, G. verrucosa, Crocosphaera watsonii, C. subtropica, C. chwakensis, Rippkaea orientalis, and Zehria floridana to recognize the intrageneric diversity as rendered by polyphasic analysis. We discuss the close relationship of free-living cyanobacteria from the Crocosphaera lineage to nitrogen-fixing endosymbionts of marine algae. The current study includes several experimental strains (Crocosphaera and "Cyanothece") important for the study of diazotrophy and the global oceanic nitrogen cycle, and provides evidence suggesting ancestral N2 -fixing capability in the chroococcalean lineage.
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Affiliation(s)
- Jan Mareš
- Institute of Hydrobiology, Biology Centre, The Czech Academy of Sciences, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
| | - Jeffrey R Johansen
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
- John Carroll University, Department of Biology, University Heights, Ohio, 44118, USA
| | - Tomáš Hauer
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, CZ-37982, Třeboň, Czech Republic
| | - Jan Zima
- Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, CZ-37982, Třeboň, Czech Republic
- Department of Parasitology, Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice
| | - Stefano Ventura
- Firenze Unit, Institute of Ecosystem Study, National Research Council of Italy, via Madonna del Piano 10, I-500 19, Sesto Fiorentino, Italy
| | - Oana Cuzman
- Institute for the Conservation and Valorization of Cultural Heritage, National Research Council of Italy, via Madonna del Piano 10, I-500 19, Sesto Fiorentino, Italy
| | - Bruno Tiribilli
- Firenze Unit, Institute for Complex Systems, National Research Council of Italy, via Madonna del Piano 10, I-500 19, Sesto Fiorentino, Italy
| | - Jan Kaštovský
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
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Bednarz VN, van de Water JAJM, Rabouille S, Maguer JF, Grover R, Ferrier-Pagès C. Diazotrophic community and associated dinitrogen fixation within the temperate coral Oculina patagonica. Environ Microbiol 2018; 21:480-495. [PMID: 30452101 DOI: 10.1111/1462-2920.14480] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 10/25/2018] [Indexed: 01/08/2023]
Abstract
Dinitrogen (N2 ) fixing bacteria (diazotrophs) are an important source of new nitrogen in oligotrophic environments and represent stable members of the microbiome in tropical corals, while information on corals from temperate oligotrophic regions is lacking. Therefore, this study provides new insights into the diversity and activity of diazotrophs associated with the temperate coral Oculina patagonica from the Mediterranean Sea by combining metabarcoding sequencing of amplicons of both the 16S rRNA and nifH genes and 15 N2 stable isotope tracer analysis to assess diazotroph-derived nitrogen (DDN) assimilation by the coral. Results show that the diazotrophic community of O. patagonica is dominated by autotrophic bacteria (i.e. Cyanobacteria and Chlorobia). The majority of DDN was assimilated into the tissue and skeletal matrix, and DDN assimilation significantly increased in bleached corals. Thus, diazotrophs may constitute an additional nitrogen source for the coral host, when nutrient exchange with Symbiodinium is disrupted (e.g. bleaching) and external food supply is limited (e.g. oligotrophic summer season). Furthermore, we hypothesize that DDN can facilitate the fast proliferation of endolithic algae, which provide an alternative carbon source for bleached O. patagonica. Overall, O. patagonica could serve as a good model for investigating the importance of diazotrophs in coral recovery from bleaching.
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Affiliation(s)
- Vanessa N Bednarz
- Marine Department, Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Monaco, Principality of Monaco
| | - Jeroen A J M van de Water
- Marine Department, Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Monaco, Principality of Monaco
| | - Sophie Rabouille
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7093, LOV, Observatoire océanologique, F-06230, Villefranche/mer, France.,CNRS, UMR 7093, LOV, Observatoire océanologique, F-06230, Villefranche/mer, France
| | - Jean-François Maguer
- LEMAR - UMR 6539 UBO/CNRS/IRD, Institut Universitaire Européen de la Mer, Place Nicolas Copernic, Plouzané 29280, France
| | - Renaud Grover
- Marine Department, Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Monaco, Principality of Monaco
| | - Christine Ferrier-Pagès
- Marine Department, Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Monaco, Principality of Monaco
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Aryal UK, Ding Z, Hedrick V, Sobreira TJP, Kihara D, Sherman LA. Analysis of Protein Complexes in the Unicellular Cyanobacterium Cyanothece ATCC 51142. J Proteome Res 2018; 17:3628-3643. [PMID: 30216071 DOI: 10.1021/acs.jproteome.8b00170] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The unicellular cyanobacterium Cyanothece ATCC 51142 is capable of oxygenic photosynthesis and biological N2 fixation (BNF), a process highly sensitive to oxygen. Previous work has focused on determining protein expression levels under different growth conditions. A major gap of our knowledge is an understanding on how these expressed proteins are assembled into complexes and organized into metabolic pathways, an area that has not been thoroughly investigated. Here, we combined size-exclusion chromatography (SEC) with label-free quantitative mass spectrometry (MS) and bioinformatics to characterize many protein complexes from Cyanothece 51142 cells grown under a 12 h light-dark cycle. We identified 1386 proteins in duplicate biological replicates, and 64% of those proteins were identified as putative complexes. Pairwise computational prediction of protein-protein interaction (PPI) identified 74 822 putative interactions, of which 2337 interactions were highly correlated with published protein coexpressions. Many sequential glycolytic and TCA cycle enzymes were identified as putative complexes. We also identified many membrane complexes that contain cytoplasmic domains. Subunits of NDH-1 complex eluted in a fraction with an approximate mass of ∼669 kDa, and subunits composition revealed coexistence of distinct forms of NDH-1 complex subunits responsible for respiration, electron flow, and CO2 uptake. The complex form of the phycocyanin beta subunit was nonphosphorylated, and the monomer form was phosphorylated at Ser20, suggesting phosphorylation-dependent deoligomerization of the phycocyanin beta subunit. This study provides an analytical platform for future studies to reveal how these complexes assemble and disassemble as a function of diurnal and circadian rhythms.
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Zhou Y, Hu B, Zhao W, Cui D, Tan L, Wang J. Effects of increasing nutrient disturbances on phytoplankton community structure and biodiversity in two tropical seas. MARINE POLLUTION BULLETIN 2018; 135:239-248. [PMID: 30301035 DOI: 10.1016/j.marpolbul.2018.07.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/06/2018] [Accepted: 07/11/2018] [Indexed: 06/08/2023]
Abstract
Statistical analysis of rainfall data from 2005 to 2015 showed that atmospheric deposition supplied large amount of dissolved inorganic nitrogen (38-155 mg·m-2·month-1) in N-deficient South China Sea and Eastern Indian Ocean. To understand marine ecosystem responses to increasing nutrient disturbances, we implemented field mesocosm experiments to study phytoplankton community structure and biodiversity responses to nutrient treatments with nitrate, phosphate and iron across tropical seas. Our results showed that DIN supply would change phytoplankton community structure and stimulated the regime shift from cyanobacteria to diatoms (relative dominance R > 0). Phytoplankton communities were dominated by diatoms (relative abundance >50%) accompanied by high chlorophyll a content with 1.58-39.27 μg·L-1 in DIN-added cultures, whereas cyanobacteria dominated communities (relative abundance >60%) with low biomass of 0.12-0.18 μg·L-1 in undisturbed cultures. Simultaneously increased DIN loading from atmospheric deposition would decrease ecological diversity of tropical seas owing to species competition and succession (Shannon diversity H' decreased to <1).
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Affiliation(s)
- Yuping Zhou
- Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, 266100, PR China; College of Chemistry and Chemical Engineering, Ocean University of China, 266100, PR China
| | - Bo Hu
- College of Chemistry and Chemical Engineering, Ocean University of China, 266100, PR China
| | - Weihong Zhao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, PR China.
| | - Dongyang Cui
- College of Chemistry and Chemical Engineering, Ocean University of China, 266100, PR China
| | - Liju Tan
- College of Chemistry and Chemical Engineering, Ocean University of China, 266100, PR China
| | - Jiangtao Wang
- Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, 266100, PR China; College of Chemistry and Chemical Engineering, Ocean University of China, 266100, PR China.
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Anderson EE, Wilson C, Knap AH, Villareal TA. Summer diatom blooms in the eastern North Pacific gyre investigated with a long-endurance autonomous surface vehicle. PeerJ 2018; 6:e5387. [PMID: 30128189 PMCID: PMC6098680 DOI: 10.7717/peerj.5387] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/17/2018] [Indexed: 11/20/2022] Open
Abstract
Satellite chlorophyll a (chl a) observations have repeatedly noted summertime phytoplankton blooms in the North Pacific subtropical gyre (NPSG), a region of open ocean that is far removed from any land-derived or Ekman upwelling nutrient sources. These blooms are dominated by N2-fixing diatom-cyanobacteria associations of the diatom genera Rhizosolenia Brightwell and Hemiaulus Ehrenberg. Their nitrogen fixing endosymbiont, Richelia intracellularis J.A. Schmidt, is hypothesized to be critical to the development of blooms in this nitrogen limited region. However, due to the remote location and unpredictable duration of the summer blooms, prolonged in situ observations are rare outside of the Station ALOHA time-series off of Hawai'i. In summer, 2015, a proof-of-concept mission using the autonomous vehicle, Honey Badger (Wave Glider SV2; Liquid Robotics, a Boeing company, Sunnyvale, CA, USA), collected near-surface (<20 m) observations in the NPSG using hydrographic, meteorological, optical, and imaging sensors designed to focus on phytoplankton abundance, distribution, and physiology of this bloom-forming region. Hemiaulus and Rhizosolenia cell abundance was determined using digital holography for the entire June-November mission. Honey Badger was not able to reach the 30°N subtropical front region where most of the satellite chl a blooms have been observed, but near-real time navigational control allowed it to transect two blooms near 25°N. The two taxa did not co-occur in large numbers, rather the blooms were dominated by either Hemiaulus or Rhizosolenia. The August 2-4, 2015 bloom was comprised of 96% Hemiaulus and the second bloom, August 15-17, 2015, was dominated by Rhizosolenia (75%). The holograms also imaged undisturbed, fragile Hemiaulus aggregates throughout the sampled area at ∼10 L-1. Aggregated Hemiaulus represented the entire observed population at times and had a widespread distribution independent of the summer export pulse, a dominant annual event suggested to be mediated by aggregate fluxes. Aggregate occurrence was not consistent with a density dependent formation mechanism and may represent a natural growth form in undisturbed conditions. The photosynthetic potential index (Fv:Fm) increased from ∼0.4 to ∼0.6 during both blooms indicating a robust, active phytoplankton community in the blooms. The diel pattern of Fv:Fm (nocturnal maximum; diurnal minimum) was consistent with macronutrient limitation throughout the mission with no evidence of Fe-limitation despite the presence of nitrogen fixing diatom-diazotroph assemblages. During the 5-month mission, Honey Badger covered ∼5,690 km (3,070 nautical miles), acquired 9,336 holograms, and reliably transmitted data onshore in near real-time. Software issues developed with the active fluorescence sensor that terminated measurements in early September. Although images were still useful at the end of the mission, fouling of the LISST-Holo optics was considerable, and appeared to be the most significant issue facing deployments of this duration.
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Affiliation(s)
- Emily E. Anderson
- Department of Marine Science and Marine Science Institute, The University of Texas at Austin, Port Aransas, TX, USA
| | - Cara Wilson
- National Marine Fisheries, National Oceanic and Atmospheric Administration, Monterey, CA, USA
| | - Anthony H. Knap
- Geochemical and Environmental Research Group, Texas A&M University, College Station, TX, USA
| | - Tracy A. Villareal
- Department of Marine Science and Marine Science Institute, The University of Texas at Austin, Port Aransas, TX, USA
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Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol 2018; 3:804-813. [PMID: 29891866 PMCID: PMC6792437 DOI: 10.1038/s41564-018-0176-9] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 05/15/2018] [Indexed: 01/28/2023]
Abstract
Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and thus microbial primary productivity. Until now, cyanobacterial populations have been viewed as the main suppliers of bioavailable nitrogen in this habitat. Although PCR amplicon surveys targeting the nitrogenase reductase gene have revealed the existence of diverse non-cyanobacterial diazotrophic populations, subsequent quantitative PCR surveys suggest that they generally occur in low abundance. Here, we use state-of-the-art metagenomic assembly and binning strategies to recover nearly one thousand non-redundant microbial population genomes from the TARA Oceans metagenomes. Among these, we provide the first genomic evidence for non-cyanobacterial diazotrophs inhabiting surface waters of the open ocean, which correspond to lineages within the Proteobacteria and, most strikingly, the Planctomycetes. Members of the latter phylum are prevalent in aquatic systems, but have never been linked to nitrogen fixation previously. Moreover, using genome-wide quantitative read recruitment, we demonstrate that the discovered diazotrophs were not only widespread but also remarkably abundant (up to 0.3% of metagenomic reads for a single population) in both the Pacific Ocean and the Atlantic Ocean northwest. Our results extend decades of PCR-based gene surveys, and substantiate the importance of heterotrophic bacteria in the fixation of nitrogen in the surface ocean.
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Affiliation(s)
- Tom O Delmont
- Department of Medicine, University of Chicago, Chicago, IL, USA.
| | | | - Alon Shaiber
- Graduate Program in the Biophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Özcan C Esen
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sonny Tm Lee
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Michael S Rappé
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Sebastian Lücker
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA. .,Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA. .,Committee on Microbiology, University of Chicago, Chicago, IL, USA.
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Li YY, Chen XH, Xie ZX, Li DX, Wu PF, Kong LF, Lin L, Kao SJ, Wang DZ. Bacterial Diversity and Nitrogen Utilization Strategies in the Upper Layer of the Northwestern Pacific Ocean. Front Microbiol 2018; 9:797. [PMID: 29922238 PMCID: PMC5996900 DOI: 10.3389/fmicb.2018.00797] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 04/10/2018] [Indexed: 11/13/2022] Open
Abstract
Nitrogen (N) is a primary limiting nutrient for bacterial growth and productivity in the ocean. To better understand bacterial community and their N utilization strategy in different N regimes of the ocean, we examined bacterial diversity, diazotrophic diversity, and N utilization gene expressions in the northwestern Pacific Ocean (NWPO) using a combination of high-throughput sequencing and real-time qPCR methods. 521 and 204 different operational taxonomic units (OTUs) were identified in the 16s rRNA and nifH libraries from nine surface samples. Of the 16s rRNA gene OTUs, 11.9% were observed in all samples while 3.5 and 15.9% were detected only in N-sufficient and N-deficient samples. Proteobacteria, Cyanobacteria and Bacteroidetes dominated the bacterial community. Prochlorococcus and Pseudoalteromonas were the most abundant at the genus level in N-deficient regimes, while SAR86, Synechococcus and SAR92 were predominant in the Kuroshio-Oyashio confluence region. The distribution of the nifH gene presented great divergence among sampling stations: Cyanobacterium_UCYN-A dominated the N-deficient stations, while clusters related to the Alpha-, Beta-, and Gamma-Proteobacteria were abundant in other stations. Temperature was the main factor that determined bacterial community structure and diversity while concentration of NOX-N was significantly correlated with structure and distribution of N2-fixing microorganisms. Expression of the ammonium transporter was much higher than that of urea transporter subunit A (urtA) and ferredoxin-nitrate reductase, while urtA had an increased expression in N-deficient surface water. The predicted ammonium transporter and ammonium assimilation enzymes were most abundant in surface samples while urease and nitrogenase were more abundant in the N-deficient regions. These findings underscore the fact that marine bacteria have evolved diverse N utilization strategies to adapt to different N habitats, and that urea metabolism is of vital ecological importance in N-deficient regimes.
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Affiliation(s)
- Yuan-Yuan Li
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xiao-Huang Chen
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Dong-Xu Li
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Peng-Fei Wu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ling-Fen Kong
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
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45
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Di Cesare A, Cabello-Yeves PJ, Chrismas NAM, Sánchez-Baracaldo P, Salcher MM, Callieri C. Genome analysis of the freshwater planktonic Vulcanococcus limneticus sp. nov. reveals horizontal transfer of nitrogenase operon and alternative pathways of nitrogen utilization. BMC Genomics 2018; 19:259. [PMID: 29661139 PMCID: PMC5902973 DOI: 10.1186/s12864-018-4648-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/05/2018] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Many cyanobacteria are capable of fixing atmospheric nitrogen, playing a crucial role in biogeochemical cycling. Little is known about freshwater unicellular cyanobacteria Synechococcus spp. at the genomic level, despite being recognised of considerable ecological importance in aquatic ecosystems. So far, it has not been shown whether these unicellular picocyanobacteria have the potential for nitrogen fixation. Here, we present the draft-genome of the new pink-pigmented Synechococcus-like strain Vulcanococcus limneticus. sp. nov., isolated from the volcanic Lake Albano (Central Italy). RESULTS The novel species Vulcanococcus limneticus sp. nov. falls inside the sub-cluster 5.2, close to the estuarine/marine strains in a maximum-likelihood phylogenetic tree generated with 259 marker genes with representatives from marine, brackish, euryhaline and freshwater habitats. V.limneticus sp. nov. possesses a complete nitrogenase and nif operon. In an experimental setup under nitrogen limiting and non-limiting conditions, growth was observed in both cases. However, the nitrogenase genes (nifHDK) were not transcribed, i.e., V.limneticus sp. nov. did not fix nitrogen, but instead degraded the phycobilisomes to produce sufficient amounts of ammonia. Moreover, the strain encoded many other pathways to incorporate ammonia, nitrate and sulphate, which are energetically less expensive for the cell than fixing nitrogen. The association of the nif operon to a genomic island, the relatively high amount of mobile genetic elements (52 transposases) and the lower observed GC content of V.limneticus sp. nov. nif operon (60.54%) compared to the average of the strain (68.35%) support the theory that this planktonic strain may have obtained, at some point of its evolution, the nif operon by horizontal gene transfer (HGT) from a filamentous or heterocystous cyanobacterium. CONCLUSIONS In this study, we describe the novel species Vulcanococcus limneticus sp. nov., which possesses a complete nif operon for nitrogen fixation. The finding that in our experimental conditions V.limneticus sp. nov. did not express the nifHDK genes led us to reconsider the actual ecological meaning of these accessory genes located in genomic island that have possibly been acquired via HGT.
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Affiliation(s)
- Andrea Di Cesare
- National Research Council CNR-ISE, Largo Tonolli 50, 28922, Verbania, Italy.,Department of Earth, Environmental, and Life Sciences, University of Genoa, 16132, Genoa, Italy
| | - Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Nathan A M Chrismas
- School of Geographical Sciences, University of Bristol, Bristol, BS8 1SS, UK.,Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK
| | | | - Michaela M Salcher
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Cristiana Callieri
- National Research Council CNR-ISE, Largo Tonolli 50, 28922, Verbania, Italy.
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Boatman TG, Davey PA, Lawson T, Geider RJ. The physiological cost of diazotrophy for Trichodesmium erythraeum IMS101. PLoS One 2018; 13:e0195638. [PMID: 29641568 PMCID: PMC5895029 DOI: 10.1371/journal.pone.0195638] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/26/2018] [Indexed: 11/24/2022] Open
Abstract
Trichodesmium plays a significant role in the oligotrophic oceans, fixing nitrogen in an area corresponding to half of the Earth's surface, representing up to 50% of new production in some oligotrophic tropical and subtropical oceans. Whilst Trichodesmium blooms at the surface exhibit a strong dependence on diazotrophy, colonies at depth or at the surface after a mixing event could be utilising additional N-sources. We conducted experiments to establish how acclimation to varying N-sources affects the growth, elemental composition, light absorption coefficient, N2 fixation, PSII electron transport rate and the relationship between net and gross photosynthetic O2 exchange in T. erythraeum IMS101. To do this, cultures were acclimated to growth medium containing NH4+ and NO3- (replete concentrations) or N2 only (diazotrophic control). The light dependencies of O2 evolution and O2 uptake were measured using membrane inlet mass spectrometry (MIMS), while PSII electron transport rates were measured from fluorescence light curves (FLCs). We found that at a saturating light intensity, Trichodesmium growth was ~ 10% and 13% lower when grown on N2 than with NH4+ and NO3-, respectively. Oxygen uptake increased linearly with net photosynthesis across all light intensities ranging from darkness to 1100 μmol photons m-2 s-1. The maximum rates and initial slopes of light response curves for C-specific gross and net photosynthesis and the slope of the relationship between gross and net photosynthesis increased significantly under non-diazotrophic conditions. We attribute these observations to a reduced expenditure of reductant and ATP for nitrogenase activity under non-diazotrophic conditions which allows NADPH and ATP to be re-directed to CO2 fixation and/or biosynthesis. The energy and reductant conserved through utilising additional N-sources could enhance Trichodesmium's productivity and growth and have major implications for its role in ocean C and N cycles.
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Affiliation(s)
- Tobias G. Boatman
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Phillip A. Davey
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Tracy Lawson
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Richard J. Geider
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
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47
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Henke BA, Turk-Kubo KA, Bonnet S, Zehr JP. Distributions and Abundances of Sublineages of the N 2-Fixing Cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) in the New Caledonian Coral Lagoon. Front Microbiol 2018; 9:554. [PMID: 29674998 PMCID: PMC5895702 DOI: 10.3389/fmicb.2018.00554] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 03/12/2018] [Indexed: 11/21/2022] Open
Abstract
Nitrogen (N2) fixation is a major source of nitrogen that supports primary production in the vast oligotrophic areas of the world’s oceans. The Western Tropical South Pacific has recently been identified as a hotspot for N2 fixation. In the Noumea lagoon (New Caledonia), high abundances of the unicellular N2-fixing cyanobacteria group A (UCYN-A), coupled with daytime N2 fixation rates associated with the <10 μm size fraction, suggest UCYN-A may be an important diazotroph (N2-fixer) in this region. However, little is known about the seasonal variability and diversity of UCYN-A there. To assess this, surface waters from a 12 km transect from the mouth of the Dumbea River to the Dumbea Pass were sampled monthly between July 2012 and March 2014. UCYN-A abundances for two of the defined sublineages, UCYN-A1 and UCYN-A2, were quantified using qPCR targeting the nifH gene, and the nifH-based diversity of UCYN-A was characterized by identifying oligotypes, alternative taxonomic units defined by nucleotide positions with high variability. UCYN-A abundances were dominated by the UCYN-A1 sublineage, peaked in September and October and could be predicted by a suite of nine environmental parameters. At the sublineage level, UCYN-A1 abundances could be predicted based on lower temperatures (<23°C), nitrate concentrations, precipitation, wind speed, while UCYN-A2 abundances could be predicted based on silica, and chlorophyll a concentrations, wind direction, precipitation, and wind speed. Using UCYN-A nifH oligotyping, similar environmental variables explained the relative abundances of sublineages and their associated oligotypes, with the notable exception of the UCYN-A2 oligotype (oligo43) which had relative abundance patterns distinct from the dominant UCYN-A2 oligotype (oligo3). The results support an emerging pattern that UCYN-A is comprised of a diverse group of strains, with sublineages that may have different ecological niches. By identifying environmental factors that influence the composition and abundance of UCYN-A sublineages, this study helps to explain global UCYN-A abundance patterns, and is important for understanding the significance of N2 fixation at local and global scales.
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Affiliation(s)
- Britt A Henke
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Kendra A Turk-Kubo
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Sophie Bonnet
- IRD, MIO, UM 110 - IRD Centre of Noumea, Aix-Marseille University, University of South Toulon Var, CNRS/INSU, Noumea, France
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
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Gimenez Papiol G. Climate conditions, and changes, affect microalgae communities… should we worry? INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2018; 14:181-184. [PMID: 29193695 DOI: 10.1002/ieam.2009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 06/07/2023]
Abstract
Microalgae play a pivotal role in the regulation of Earth's climate and its cycles, but are also affected by climate change, mainly by changes in temperature, light, ocean acidification, water stratification, and precipitation-induced nutrient inputs. The changes and impacts on microalgae communities are difficult to study, predict, and manage, but there is no doubt that there will be changes. These changes will have impacts beyond microalgae communities, and many of them will be negative. Some actions are currently ongoing for the mitigation of some of the negative impacts, such as harmful algal blooms and water quality, but global efforts for reducing CO2 emissions, temperature rises, and ocean acidification are paramount for reducing the impact of climate change on microalgae communities, and eventually, on human well-being. Integr Environ Assess Manag 2018;14:181-184. © 2018 SETAC.
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Affiliation(s)
- Gemma Gimenez Papiol
- Environmental Engineering Laboratory, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
- Present address: Fondazione IMC - Centro Marino Internazionale ONLUS, Località Sa Mardini - Torregrande, Oristano, Sardegna, Italia
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49
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Follett CL, Dutkiewicz S, Karl DM, Inomura K, Follows MJ. Seasonal resource conditions favor a summertime increase in North Pacific diatom-diazotroph associations. ISME JOURNAL 2018; 12:1543-1557. [PMID: 29449611 PMCID: PMC5955908 DOI: 10.1038/s41396-017-0012-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 10/07/2017] [Accepted: 10/24/2017] [Indexed: 12/04/2022]
Abstract
In the North Pacific Subtropical Gyre (NPSG), an annual pulse of sinking organic carbon is observed at 4000 m between July and August, driven by large diatoms found in association with nitrogen fixing, heterocystous, cyanobacteria: Diatom–Diazotroph Associations (DDAs). Here we ask what drives the bloom of DDAs and present a simplified trait-based model of subtropical phototroph populations driven by observed, monthly averaged, environmental characteristics. The ratio of resource supply rates favors nitrogen fixation year round. The relative fitness of DDA traits is most competitive in early summer when the mixed layer is shallow, solar irradiance is high, and phosphorus and iron are relatively abundant. Later in the season, as light intensity drops and phosphorus is depleted, the traits of small unicellular diazotrophs become more competitive. The competitive transition happens in August, at the time when the DDA export event occurs. This seasonal dynamic is maintained when embedded in a more complex, global-scale, ecological model, and provides predictions for the extent of the North Pacific DDA bloom. The model provides a parsimonious and testable hypothesis for the stimulation of DDA blooms.
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Affiliation(s)
- Christopher L Follett
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David M Karl
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Keisuke Inomura
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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Cassar N, Tang W, Gabathuler H, Huang K. Method for High Frequency Underway N 2 Fixation Measurements: Flow-Through Incubation Acetylene Reduction Assays by Cavity Ring Down Laser Absorption Spectroscopy (FARACAS). Anal Chem 2018; 90:2839-2851. [PMID: 29338196 DOI: 10.1021/acs.analchem.7b04977] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Because of the difficulty in resolving the large variability of N2 fixation with current methods which rely on discrete sampling, the development of new methods for high-resolution measurements is highly desirable. We present a new method for high-frequency measurements of aquatic N2 fixation by continuous flow-through incubations and spectral monitoring of the acetylene (C2H2, a substrate analog for N2) reduction to ethylene (C2H4). In this method, named Flow-through Incubation Acetylene Reduction Assays by Cavity Ring-Down Laser Absorption Spectroscopy (FARACAS), dissolved C2H2 is continuously admixed with seawater upstream of a continuous-flow stirred-tank reactor (CFSR) in which C2H2 reduction takes place. Downstream of the flow-through incubator, the C2H4 gas is stripped using a bubble column contactor and circulated with a diaphragm pump into a wavelength-scanned cavity ring down laser absorption spectrometer (CRDS). Our method provides high-resolution and precise mapping of aquatic N2 fixation, its diel cycle, and its response to environmental gradients, and can be adapted to measure other biological processes. The short-duration of the flow-through incubations without preconcentration of cells minimizes potential artifacts such as bottle containment effects while providing near real-time estimates for adaptive sampling. We expect that our new method will improve the characterization of the biogeography and kinetics of aquatic N2 fixation rates.
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Affiliation(s)
- Nicolas Cassar
- Division of Earth and Ocean Sciences, Nicholas School of the Environment, Duke University , Durham, North Carolina 27708, United States.,Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR 6539 UBO/CNRS/IRD/IFREMER, Institut Universitaire Européen de la Mer (IUEM) , Brest, France
| | - Weiyi Tang
- Division of Earth and Ocean Sciences, Nicholas School of the Environment, Duke University , Durham, North Carolina 27708, United States
| | | | - Kuan Huang
- Division of Earth and Ocean Sciences, Nicholas School of the Environment, Duke University , Durham, North Carolina 27708, United States
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