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Qiu GW, Zheng WC, Yang HM, Wang YY, Qi X, Huang D, Dai GZ, Shi H, Price NM, Qiu BS. Phosphorus deficiency alleviates iron limitation in Synechocystis cyanobacteria through direct PhoB-mediated gene regulation. Nat Commun 2024; 15:4426. [PMID: 38789507 PMCID: PMC11126600 DOI: 10.1038/s41467-024-48847-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Iron and phosphorus are essential nutrients that exist at low concentrations in surface waters and may be co-limiting resources for phytoplankton growth. Here, we show that phosphorus deficiency increases the growth of iron-limited cyanobacteria (Synechocystis sp. PCC 6803) through a PhoB-mediated regulatory network. We find that PhoB, in addition to its well-recognized role in controlling phosphate homeostasis, also regulates key metabolic processes crucial for iron-limited cyanobacteria, including ROS detoxification and iron uptake. Transcript abundances of PhoB-targeted genes are enriched in samples from phosphorus-depleted seawater, and a conserved PhoB-binding site is widely present in the promoters of the target genes, suggesting that the PhoB-mediated regulation may be highly conserved. Our findings provide molecular insights into the responses of cyanobacteria to simultaneous iron/phosphorus nutrient limitation.
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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, Hubei, 430079, China
| | - Wen-Can Zheng
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Hao-Ming Yang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Yu-Ying Wang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Xing Qi
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Da Huang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Guo-Zheng Dai
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Neil M Price
- Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, Québec, H3A 1B1, Canada
| | - Bao-Sheng Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China.
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2
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Qin J, Yang J, Zhang J, Liu X, Yu J, Wang Z, Li Y, Guan B, Wang X, Zhao W. Effects of tidal hydrology on soil phosphorus forms in the Yellow River estuary wetland: A field study of soil core translocation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171360. [PMID: 38428613 DOI: 10.1016/j.scitotenv.2024.171360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/03/2024] [Accepted: 02/27/2024] [Indexed: 03/03/2024]
Abstract
Phosphorus (P) forms in soil are related to the P cycle and play an important role in maintaining the productivity and function of wetlands. Tidal hydrology is a key factor controlling soil P forms in estuary wetlands; however, the response of soil P forms to tidal hydrological changes remains unclear. A translocation experiment in the Yellow River Estuary wetland was conducted to study the effect of hydrological changes on P forms in the soil, in which freshwater marsh soils in the supratidal zone were translocated to salt marshes in different intertidal zones (up-high-tidal zone, high-tidal zone, and middle-tidal zone). Over a 23-month experiment, soil properties showed varying changes under different tidal hydrology conditions, with an increase in pH, salinity, Ca2+ and salt ions and a decrease in iron oxide and nutrients. Compared with the control, the content of different forms of phosphorus (total phosphorus, inorganic phosphorus, organic phosphorus, and calcium-bound phosphorus) in the cultured soil cores decreased from 3.3 % to 67.0 % in the intertidal zones, whereas the content of ferrum‑aluminum-bound phosphorus increased from 58.9 % to 65.1 % at the end of the experiment. According to the partial least squares structural equation model, P forms are influenced by tidal hydrology mainly through the mediation of salt ions and nutrient levels. These results suggest that seawater intrusion promotes the release of P in the supratidal zone soil of estuary wetlands.
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Affiliation(s)
- Jifa Qin
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Jisong Yang
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China; Dongying Academy of Agricultural Sciences, Dongying, China.
| | - Jiapeng Zhang
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Xue Liu
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Junbao Yu
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Zhikang Wang
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Yunzhao Li
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Bo Guan
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Xuehong Wang
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Wei Zhao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Nanjing, China.
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3
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Shu H, Shen Y, Wang H, Sun X, Ma J, Lin X. Biogenic Phosphonate Utilization by Globally Distributed Diatom Thalassiosira pseudonana. Microorganisms 2024; 12:761. [PMID: 38674705 PMCID: PMC11051927 DOI: 10.3390/microorganisms12040761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Phosphonates are a class of organic phosphorus (P) compounds that contribute ~25% of dissolved organic P. Recent studies reveal the important role of phosphonates mediated by prokaryotes in the marine P redox cycle. However, its bioavailability by eukaryotic phytoplankton is under debate. 2-Aminoethylphosphonic acid (2-AEP) and 2-amino-3-phosphonopropionic acid (2-AP3) are two biogenic phosphonates in the marine environment. Here, Thalassiosira pseudonana, a common diatom species in the ocean, is able to recover growth from P starvation when provided with 2-AEP and 2-AP3. Moreover, 2-AEP cultures exhibited a more similar growth rate at 12 °C than at 25 °C when compared with inorganic P cultures. The cellular stoichiometry of 2-AEP groups was further determined, the values of which are in-between the P-depleted and DIP-replete cultures. This study provides evidence that biogenic phosphonates could be adopted as alternative P sources to support diatom growth and may provide physiological adaptation.
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Affiliation(s)
- Huilin Shu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; (H.S.); (Y.S.); (H.W.); (X.S.); (J.M.)
- College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Yuan Shen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; (H.S.); (Y.S.); (H.W.); (X.S.); (J.M.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Hongwei Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; (H.S.); (Y.S.); (H.W.); (X.S.); (J.M.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Xueqiong Sun
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; (H.S.); (Y.S.); (H.W.); (X.S.); (J.M.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Jian Ma
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; (H.S.); (Y.S.); (H.W.); (X.S.); (J.M.)
- College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; (H.S.); (Y.S.); (H.W.); (X.S.); (J.M.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
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Zhang XY, Li ZF, Gu HF, Han AQ, Han FX, Ou LJ. Significance of phosphate adsorbed on the cellular surface as a storage pool and its regulation in marine microalgae. MARINE ENVIRONMENTAL RESEARCH 2024; 195:106378. [PMID: 38266549 DOI: 10.1016/j.marenvres.2024.106378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 01/07/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
The increasing prevalence of phosphorus limitation in coastal waters has drawn attention to the bioavailability of cellular surface-adsorbed phosphorus (SP) as a reservoir of phosphorus in phytoplankton. This study examined the storage, utilization, and regulation of SP in the coastal waters of the East China Sea, as well as three cultivated algal bloom species (Skeletonema marinoi, Prorocentrum shikokuense, and Karenia mikimotoi) prevalent in the area. SP accounted for 14.3%-45.5% of particulate phosphorus in the field and laboratory species. After the depletion of external phosphate, the studied species can rapidly transport SP within 3-24 h. The storage of SP is regulated by both external phosphate conditions and the internal growth stage of cells, but it is not influenced by the various cellular surface structures of the studied species. This study highlights the significance of SP as a crucial phosphorus reservoir and the potential use of the SP level as an indicator of phosphorus deficiency in phytoplankton.
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Affiliation(s)
- Xian-Yang Zhang
- Research Center of Harmful Algae and Marine Biology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Jinan University, Guangzhou, China
| | - Zhuo-Fan Li
- Research Center of Harmful Algae and Marine Biology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Jinan University, Guangzhou, China
| | - Hai-Feng Gu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Ai-Qin Han
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Feng-Xian Han
- Analytical and Testing Center, Jinan University, Guangzhou, China.
| | - Lin-Jian Ou
- Research Center of Harmful Algae and Marine Biology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Jinan University, Guangzhou, China.
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5
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Li J, Wang Z, Yang H, Wang Z, Liu F, Chen X, Huang X. Phosphorus forms and zinc concentrations affect the physiological ecology and sinking rate of Thalassiosira weissflogii. MARINE POLLUTION BULLETIN 2024; 200:116124. [PMID: 38325204 DOI: 10.1016/j.marpolbul.2024.116124] [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: 01/04/2024] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024]
Abstract
The combined effects of phosphorus (P) forms and zinc (Zn) concentrations on diatom silicification remain unclear. In this study, we investigate the effects of different Zn concentrations on the growth, cellular silicon content and sinking rate of Thalassiosira weissflogii under different P forms. The results showed that under the dissolved inorganic phosphorus (DIP) treatments, the specific growth rate of T. weissflogii in Zn limitation culture was significantly lower than that in Zn-replete culture. However, T. weissflogii cellular silicon content and sinking rate increased. Moreover, the reduced specific growth rate (7 %, p < 0.05), enhanced ALP activity (63 %, p < 0.05), and sinking rate (20 %, p < 0.05) for Zn-deplete T. weissflogii implied that the bioavailability of dissolved organic phosphorus (DOP) was depressed under Zn deplete medium. This study demonstrates that the physiological ecology and sinking rate of the diatom T. weissflogii were affected by both individual and combined changes in P forms and Zn concentrations.
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Affiliation(s)
- Jiandi Li
- College of Chemistry, Chemical Engineering & Environmental Science, Minnan Normal University, Zhangzhou 363000, China
| | - Zhaofei Wang
- College of Chemistry, Chemical Engineering & Environmental Science, Minnan Normal University, Zhangzhou 363000, China
| | - Hang Yang
- College of Chemistry, Chemical Engineering & Environmental Science, Minnan Normal University, Zhangzhou 363000, China
| | - Zhenfeng Wang
- College of Chemistry, Chemical Engineering & Environmental Science, Minnan Normal University, Zhangzhou 363000, China
| | - Fengjiao Liu
- College of Chemistry, Chemical Engineering & Environmental Science, Minnan Normal University, Zhangzhou 363000, China; Fujian Province Key Laboratory of Modern Analytical Science and Separation Technology, Fujian Province University Key Laboratory of Pollution Monitoring and Control, Minnan Normal University, Zhangzhou 363000, China
| | - Xiaohuang Chen
- College of Chemistry, Chemical Engineering & Environmental Science, Minnan Normal University, Zhangzhou 363000, China; Fujian Province Key Laboratory of Modern Analytical Science and Separation Technology, Fujian Province University Key Laboratory of Pollution Monitoring and Control, Minnan Normal University, Zhangzhou 363000, China
| | - Xuguang Huang
- College of Chemistry, Chemical Engineering & Environmental Science, Minnan Normal University, Zhangzhou 363000, China; Fujian Province Key Laboratory of Modern Analytical Science and Separation Technology, Fujian Province University Key Laboratory of Pollution Monitoring and Control, Minnan Normal University, Zhangzhou 363000, China.
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Wang C, Zhang H, Wang J, Sprecher B, Lin S. Glyphosate (Roundup) as phosphorus nutrient enhances carbon and nitrogen accumulation and up-regulates phosphorus metabolisms in the haptophyte Isochrysis galbana. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169715. [PMID: 38160825 DOI: 10.1016/j.scitotenv.2023.169715] [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: 11/04/2023] [Revised: 12/24/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
Inorganic phosphate limitation for phytoplankton may be intensified with water stratification by global warming, and with the increasing nitrogen: phosphorus (N:P) ratio in coastal zones resulting from continuous anthropogenic N overloading. Under these circumstances, phytoplankton's ability to use dissolved organic phosphorus (DOP) will give species a competitive advantage. In our previous study, we have shown that the haptophyte Isochrysis galbana can use glyphosate (Roundup) as a P nutrient source to support growth, but the mechanism of how remains unexplored. Here, we show that three genes encoding PhnC (IgPhnCs), which exhibit up-regulated expression in glyphosate-grown cultures, are probably responsible for glyphosate uptake, while homologs of PhnK and PhnL (IgPhnK and IgPhnL) probably provide auxiliary support for the intracellular degradation of glyphosate. Meanwhile, we found the use efficiency of glyphosate was low compared with phosphate, probably because glyphosate uptake and hydrolysis cost energy and because glyphosate induces oxidative stress in I. galbana. Meanwhile, genes encoding 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, the target of the herbicide, were up-regulated in glyphosate cultures. Furthermore, our data showed the up-regulation of P metabolisms (transcription) in glyphosate-grown cultures, which further induced the up-regulation of nitrate/nitrite transport and biosynthesis of some amino acids. Meanwhile, glyphosate-grown cells accumulated more C and N, resulting in remarkably high C:N:P ratio, and this, along with the up-regulated P metabolisms, was under transcriptional and epigenetic regulation. This study sheds lights on the mechanism of glyphosate utilization as a source of P nutrient by I. galbana, and these findings have biogeochemical implications.
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Affiliation(s)
- Cong Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361102, China; College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States of America
| | - Jingtian Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361102, China; College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Brittany Sprecher
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States of America
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361102, China; College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361102, China; Department of Marine Sciences, University of Connecticut, Groton, CT, United States of America.
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7
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Liu J, Ding X, Xia X, Zhou L, Liu W, Lai Y, Ke Z, Tan Y. Dissolved organic phosphorus promotes Cyclotella growth and adaptability in eutrophic tropical estuaries. Appl Environ Microbiol 2024; 90:e0163723. [PMID: 38112726 PMCID: PMC10807451 DOI: 10.1128/aem.01637-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 10/31/2023] [Indexed: 12/21/2023] Open
Abstract
Dissolved organic phosphorus (DOP) is an important nutrient for phytoplankton growth in oligotrophic oceans. However, little is known about the impact of DOP on phytoplankton growth in eutrophic waters. In the present study, we conducted field monitoring as well as in situ and laboratory experiments in the Pearl River estuary (PRE). Field observations showed an increase in the nitrogen-to-phosphorus ratio and DOP in recent years in the PRE. The phytoplankton community was dominated by nanophytoplankton Cyclotella in the upper and middle estuary, with high concentrations of DOP and light limitation during the ebb stage of the spring to neap tide in summer. The relative abundance of Cyclotella in natural waters was higher after enrichment with estuarine water with a background of 0.40-0.46 µM DOP, even when dissolved inorganic phosphorus was sufficient (0.55-0.76 µM). In addition, the relative abundance of Cyclotella in natural waters was higher after enrichment with phosphoesters. Laboratory culture results also confirmed that phosphoesters can enhance the growth rate of Cyclotella cryptica. Our study highlights that Cyclotella can become the dominant species in estuaries with increased levels of phosphoesters and low and fluctuating light adaptability and under the joint effect of dynamic processes such as upwelling and tides. Our results provide new insights into the role of Cyclotella in biogeochemical cycles affected by DOP utilization and potential applications in relieving the hypoxia of tropical eutrophic estuaries.IMPORTANCEThis study provides evidence that Cyclotella can become the dominant species in estuaries with increased levels of phosphoesters and low and fluctuating light adaptability and under the joint effect of dynamic processes such as upwelling and tides. Our study provides new insights into the role of Cyclotella in biogeochemical cycles affected by dissolved organic phosphorus utilization, especially affected by anthropogenic inputs and climate change. Potential applications include relieving the hypoxia of tropical eutrophic estuaries.
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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, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xiang Ding
- 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, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomin Xia
- 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, 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, China
| | - Weiwei 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, China
| | - Yanjiao Lai
- 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, China
- University of Chinese Academy of Sciences, Beijing, 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, 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, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
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Mao Y, Lin T, Li H, He R, Ye K, Yu W, He Q. Aerobic methane production by phytoplankton as an important methane source of aquatic ecosystems: Reconsidering the global methane budget. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167864. [PMID: 37866611 DOI: 10.1016/j.scitotenv.2023.167864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/24/2023]
Abstract
Biological methane, a major source of global methane budget, is traditionally thought to be produced in anaerobic environments. However, the recent reports about methane supersaturation occurring in oxygenated water layer, termed as "methane paradox", have challenged this prevailing paradigm. Significantly, growing evidence has indicated that phytoplankton including prokaryotic cyanobacteria and eukaryotic algae are capable of generating methane under aerobic conditions. In this regard, a systematic review of aerobic methane production by phytoplankton is expected to arouse the public attention, contributing to the understanding of methane paradox. Here, we comprehensively summarize the widespread phenomena of methane supersaturation in oxic layers. The remarkable correlation relationships between methane concentration and several key indicators (depth, chlorophyll a level and organic sulfide concentration) indicate the significance of phytoplankton in in-situ methane accumulation. Subsequently, four mechanisms of aerobic methane production by phytoplankton are illustrated in detail, including photosynthesis-driven metabolism, reactive oxygen species (ROS)-driven demethylation of methyl donors, methanogenesis catalyzed by nitrogenase and demethylation of phosphonates catalyzed by CP lyase. The first two pathways occur in various phytoplankton, while the latter two have been specially discovered in cyanobacteria. Additionally, the effects of four crucial factors on aerobic methane production by phytoplankton are also discussed, including phytoplankton species, light, temperature and crucial nutrients. Finally, the measures to control global methane emissions from phytoplankton, the precise intracellular mechanisms of methane production and a more complete global methane budget model are definitely required in the future research on methane production by phytoplankton. This review would provide guidance for future studies of aerobic methane production by phytoplankton and emphasize the potential contribution of aquatic ecosystems to global methane budget.
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Affiliation(s)
- Yufeng Mao
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing 400044, China; Key Laboratory of Hydraulic and Waterway Engineering, Ministry of Education, Chongqing Jiaotong University, Chongqing 400074, China; Lingzhi Environmental Protection Co., Ltd, Wuxi 214200, China
| | - Tong Lin
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Hong Li
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing 400044, China
| | - Ruixu He
- Key Laboratory of Hydraulic and Waterway Engineering, Ministry of Education, Chongqing Jiaotong University, Chongqing 400074, China
| | - Kailai Ye
- Key Laboratory of Hydraulic and Waterway Engineering, Ministry of Education, Chongqing Jiaotong University, Chongqing 400074, China
| | - Weiwei Yu
- Key Laboratory of Hydraulic and Waterway Engineering, Ministry of Education, Chongqing Jiaotong University, Chongqing 400074, China
| | - Qiang He
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing 400044, China.
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Hehenberger E, Guo J, Wilken S, Hoadley K, Sudek L, Poirier C, Dannebaum R, Susko E, Worden AZ. Phosphate Limitation Responses in Marine Green Algae Are Linked to Reprogramming of the tRNA Epitranscriptome and Codon Usage Bias. Mol Biol Evol 2023; 40:msad251. [PMID: 37987557 PMCID: PMC10735309 DOI: 10.1093/molbev/msad251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023] Open
Abstract
Marine algae are central to global carbon fixation, and their productivity is dictated largely by resource availability. Reduced nutrient availability is predicted for vast oceanic regions as an outcome of climate change; however, there is much to learn regarding response mechanisms of the tiny picoplankton that thrive in these environments, especially eukaryotic phytoplankton. Here, we investigate responses of the picoeukaryote Micromonas commoda, a green alga found throughout subtropical and tropical oceans. Under shifting phosphate availability scenarios, transcriptomic analyses revealed altered expression of transfer RNA modification enzymes and biased codon usage of transcripts more abundant during phosphate-limiting versus phosphate-replete conditions, consistent with the role of transfer RNA modifications in regulating codon recognition. To associate the observed shift in the expression of the transfer RNA modification enzyme complement with the transfer RNAs encoded by M. commoda, we also determined the transfer RNA repertoire of this alga revealing potential targets of the modification enzymes. Codon usage bias was particularly pronounced in transcripts encoding proteins with direct roles in managing phosphate limitation and photosystem-associated proteins that have ill-characterized putative functions in "light stress." The observed codon usage bias corresponds to a proposed stress response mechanism in which the interplay between stress-induced changes in transfer RNA modifications and skewed codon usage in certain essential response genes drives preferential translation of the encoded proteins. Collectively, we expose a potential underlying mechanism for achieving growth under enhanced nutrient limitation that extends beyond the catalog of up- or downregulated protein-encoding genes to the cell biological controls that underpin acclimation to changing environmental conditions.
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Affiliation(s)
- Elisabeth Hehenberger
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, CZ
| | - Jian Guo
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Susanne Wilken
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kenneth Hoadley
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
| | - Lisa Sudek
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Camille Poirier
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
| | - Richard Dannebaum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Edward Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, CA
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- Max Planck Institute for Evolutionary Biology, 24306 Plön, DE
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10
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Setta SP, Lerch S, Jenkins BD, Dyhrman ST, Rynearson TA. Oligotrophic waters of the Northwest Atlantic support taxonomically diverse diatom communities that are distinct from coastal waters. JOURNAL OF PHYCOLOGY 2023; 59:1202-1216. [PMID: 37737069 DOI: 10.1111/jpy.13388] [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: 03/06/2023] [Revised: 07/23/2023] [Accepted: 08/09/2023] [Indexed: 09/23/2023]
Abstract
Diatoms are important components of the marine food web and one of the most species-rich groups of phytoplankton. The diversity and composition of diatoms in eutrophic nearshore habitats have been well documented due to the outsized influence of diatoms on coastal ecosystem functioning. In contrast, patterns of both diatom diversity and community composition in offshore oligotrophic regions where diatom biomass is low have been poorly resolved. To compare the diatom diversity and community composition in oligotrophic and eutrophic waters, diatom communities were sampled along a 1,250 km transect from the oligotrophic Sargasso Sea to the coastal waters of the northeast US shelf. Diatom community composition was determined by amplifying and sequencing the 18S rDNA V4 region. Of the 301 amplicon sequence variants (ASVs) identified along the transect, the majority (70%) were sampled exclusively from oligotrophic waters of the Gulf Stream and Sargasso Sea and included the genera Bacteriastrum, Haslea, Hemiaulus, Pseudo-nitzschia, and Nitzschia. Diatom ASV richness did not vary along the transect, indicating that the oligotrophic Sargasso Sea and Gulf Stream are occupied by a diverse diatom community. Although ASV richness was similar between oligotrophic and coastal waters, diatom community composition in these regions differed significantly and was correlated with temperature and phosphate, two environmental variables known to influence diatom metabolism and geographic distribution. In sum, oligotrophic waters of the western North Atlantic harbor diverse diatom assemblages that are distinct from coastal regions, and these open ocean diatoms warrant additional study, as they may play critical roles in oligotrophic ecosystems.
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Affiliation(s)
- Samantha P Setta
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Sarah Lerch
- College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Bethany D Jenkins
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
- College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Sonya T Dyhrman
- Department of Earth and Environmental Sciences, Columbia University, Palisades, New York, USA
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, USA
| | - Tatiana A Rynearson
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
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11
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von Arx JN, Kidane AT, Philippi M, Mohr W, Lavik G, Schorn S, Kuypers MMM, Milucka J. Methylphosphonate-driven methane formation and its link to primary production in the oligotrophic North Atlantic. Nat Commun 2023; 14:6529. [PMID: 37845220 PMCID: PMC10579326 DOI: 10.1038/s41467-023-42304-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023] Open
Abstract
Methylphosphonate is an organic phosphorus compound used by microorganisms when phosphate, a key nutrient limiting growth in most marine surface waters, becomes unavailable. Microbial methylphosphonate use can result in the formation of methane, a potent greenhouse gas, in oxic waters where methane production is traditionally unexpected. The extent and controlling factors of such aerobic methane formation remain underexplored. Here, we show high potential net rates of methylphosphonate-driven methane formation (median 0.4 nmol methane L-1 d-1) in the upper water column of the western tropical North Atlantic. The rates are repressed but still quantifiable in the presence of in-situ or added phosphate, suggesting that some methylphosphonate-driven methane formation persists in phosphate-replete waters. The genetic potential for methylphosphonate utilisation is present in and transcribed by key photo- and heterotrophic microbial taxa, such as Pelagibacterales, SAR116, and Trichodesmium. While the large cyanobacterial nitrogen-fixers dominate in the surface layer, phosphonate utilisation by Alphaproteobacteria appears to become more important in deeper depths. We estimate that at our study site, a substantial part (median 11%) of the measured surface carbon fixation can be sustained by phosphorus liberated from phosphonate utilisation, highlighting the ecological importance of phosphonates in the carbon cycle of the oligotrophic ocean.
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Affiliation(s)
- Jan N von Arx
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Abiel T Kidane
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Miriam Philippi
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Wiebke Mohr
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jana Milucka
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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12
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Masuda T, Inomura K, Mareš J, Kodama T, Shiozaki T, Matsui T, Suzuki K, Takeda S, Deutsch C, Prášil O, Furuya K. Coexistence of Dominant Marine Phytoplankton Sustained by Nutrient Specialization. Microbiol Spectr 2023; 11:e0400022. [PMID: 37458590 PMCID: PMC10441275 DOI: 10.1128/spectrum.04000-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 06/07/2023] [Indexed: 08/19/2023] Open
Abstract
Prochlorococcus and Synechococcus are the two dominant picocyanobacteria in the low-nutrient surface waters of the subtropical ocean, but the basis for their coexistence has not been quantitatively demonstrated. Here, we combine in situ microcosm experiments and an ecological model to show that this coexistence can be sustained by specialization in the uptake of distinct nitrogen (N) substrates at low-level concentrations that prevail in subtropical environments. In field incubations, the response of both Prochlorococcus and Synechococcus to nanomolar N amendments demonstrates N limitation of growth in both populations. However, Prochlorococcus showed a higher affinity to ammonium, whereas Synechococcus was more adapted to nitrate uptake. A simple ecological model demonstrates that the differential nutrient preference inferred from field experiments with these genera may sustain their coexistence. It also predicts that as the supply of NO3- decreases, as expected under climate warming, the dominant genera should undergo a nonlinear shift from Synechococcus to Prochlorococcus, a pattern that is supported by subtropical field observations. Our study suggests that the evolution of differential nutrient affinities is an important mechanism for sustaining the coexistence of genera and that climate change is likely to shift the relative abundance of the dominant plankton genera in the largest biomes in the ocean. IMPORTANCE Our manuscript addresses the following fundamental question in microbial ecology: how do different plankton using the same essential nutrients coexist? Prochlorococcus and Synechococcus are the two dominant picocyanobacteria in the low-nutrient surface waters of the subtropical ocean, which support a significant amount of marine primary production. The geographical distributions of these two organisms are largely overlapping, but the basis for their coexistence in these biomes remains unclear. In this study, we combined in situ microcosm experiments and an ecosystem model to show that the coexistence of these two organisms can arise from specialization in the uptake of distinct nitrogen substrates; Prochlorococcus prefers ammonium, whereas Synechococcus prefers nitrate when these nutrients exist at low concentrations. Our framework can be used for simulating and predicting the coexistence in the future ocean and may provide hints toward understanding other similar types of coexistence.
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Affiliation(s)
- Takako Masuda
- Department of Aquatic Bioscience, The University of Tokyo, Bunkyo, Tokyo, Japan
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czechia
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Jan Mareš
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czechia
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budejovice, Czechia
- Department of Botany, University of South Bohemia, Faculty of Science, České Budejovice, Czechia
| | - Taketoshi Kodama
- Department of Aquatic Bioscience, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Takuhei Shiozaki
- Department of Aquatic Bioscience, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - 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, Bunkyo, Tokyo, Japan
| | - Curtis Deutsch
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
| | - Ondřej Prášil
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czechia
| | - Ken Furuya
- Department of Aquatic Bioscience, The University of Tokyo, Bunkyo, Tokyo, Japan
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13
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Browning TJ, Moore CM. Global analysis of ocean phytoplankton nutrient limitation reveals high prevalence of co-limitation. Nat Commun 2023; 14:5014. [PMID: 37591895 PMCID: PMC10435517 DOI: 10.1038/s41467-023-40774-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 08/09/2023] [Indexed: 08/19/2023] Open
Abstract
Nutrient availability limits phytoplankton growth throughout much of the global ocean. Here we synthesize available experimental data to identify three dominant nutrient limitation regimes: nitrogen is limiting in the stratified subtropical gyres and in the summertime Arctic Ocean, iron is most commonly limiting in upwelling regions, and both nutrients are frequently co-limiting in regions in between the nitrogen and iron limited systems. Manganese can be co-limiting with iron in parts of the Southern Ocean, whilst phosphate and cobalt can be co-/serially limiting in some settings. Overall, an analysis of experimental responses showed that phytoplankton net growth can be significantly enhanced through increasing the number of different nutrients supplied, regardless of latitude, temperature, or trophic status, implying surface seawaters are often approaching nutrient co-limitation. Assessments of nutrient deficiency based on seawater nutrient concentrations and nutrient stress diagnosed via molecular biomarkers showed good agreement with experimentally-assessed nutrient limitation, validating conceptual and theoretical links between nutrient stoichiometry and microbial ecophysiology.
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Affiliation(s)
- Thomas J Browning
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24148, Germany.
| | - C Mark Moore
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, SO14 3ZH, UK.
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14
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Wang Y, Ferrinho S, Connaris H, Goss RJM. The Impact of Viral Infection on the Chemistries of the Earth's Most Abundant Photosynthesizes: Metabolically Talented Aquatic Cyanobacteria. Biomolecules 2023; 13:1218. [PMID: 37627283 PMCID: PMC10452541 DOI: 10.3390/biom13081218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Cyanobacteria are the most abundant photosynthesizers on earth, and as such, they play a central role in marine metabolite generation, ocean nutrient cycling, and the control of planetary oxygen generation. Cyanobacteriophage infection exerts control on all of these critical processes of the planet, with the phage-ported homologs of genes linked to photosynthesis, catabolism, and secondary metabolism (marine metabolite generation). Here, we analyze the 153 fully sequenced cyanophages from the National Center for Biotechnology Information (NCBI) database and the 45 auxiliary metabolic genes (AMGs) that they deliver into their hosts. Most of these AMGs are homologs of those found within cyanobacteria and play a key role in cyanobacterial metabolism-encoding proteins involved in photosynthesis, central carbon metabolism, phosphate metabolism, methylation, and cellular regulation. A greater understanding of cyanobacteriophage infection will pave the way to a better understanding of carbon fixation and nutrient cycling, as well as provide new tools for synthetic biology and alternative approaches for the use of cyanobacteria in biotechnology and sustainable manufacturing.
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Affiliation(s)
- Yunpeng Wang
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Scarlet Ferrinho
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Helen Connaris
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Rebecca J. M. Goss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
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15
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Xiao K, Pan F, Li Y, Li Z, Li H, Guo Z, Wang X, Zheng C. Coastal aquaculture regulates phosphorus cycling in estuarine wetlands: Mobilization, kinetic resupply, and source-sink process. WATER RESEARCH 2023; 234:119832. [PMID: 36889088 DOI: 10.1016/j.watres.2023.119832] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/14/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Estuarine mangrove wetlands have gradually declined owing to the growing construction of aquaculture ponds. How the speciation, transition, and migration of phosphorus (P) adaptively change in the sediments of this pond-wetland ecosystem remains unclear. In this study, we used high-resolution devices to explore the contrasting P behaviors associated with the redox cycles of Fe-Mn-S-As in estuarine and pond sediments. The results showed that the construction of aquaculture ponds increased the content or percentage of the silt, organic carbon, and P fractions in sediments. Dissolved organic P (DOP) concentrations in pore water were fluctuant with depths, accounting for only 18±15% and 20±11% of total dissolved P (TDP) in estuarine and pond sediment, respectively. Furthermore, DOP was less strongly correlated with other P species, including Fe, Mn, and sulfide. The coupling of dissolved reactive P (DRP) and TDP with Fe and sulfide confirmed that P mobility is regulated by Fe redox cycling in estuarine sediments, whereas Fe(III) reduction and sulfate reduction co-regulate P remobilization in pond sediments. The apparent diffusion flux revealed all sediments acting as sources for TDP (0.04-0.1 mg m-2 d-1) to the overlying water, while mangrove sediments were sources of DOP, and pond sediments were major sources of DRP. The DIFS model overestimated the P kinetic resupply ability, which was evaluated using DRP rather than TDP. This study improves our understanding of P cycling and budget in aquaculture pond-mangrove ecosystems and has important implications for understanding water eutrophication more effectively.
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Affiliation(s)
- Kai Xiao
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Feng Pan
- State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China.
| | - Yurui Li
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Zhenyang Li
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hailong Li
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhanrong Guo
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xinhong Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Chunmiao Zheng
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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16
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Fluctuation of growth and photosynthetic characteristics in Prorocentrum shikokuense under phosphorus limitation: Evidence from field and laboratory. Ecol Modell 2023. [DOI: 10.1016/j.ecolmodel.2023.110310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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17
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Chandwadkar P, Acharya C. Inorganic polyphosphate accumulation protects a marine, filamentous cyanobacterium, Anabaena torulosa against uranium toxicity. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2023; 263:107185. [PMID: 37094505 DOI: 10.1016/j.jenvrad.2023.107185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/28/2023] [Accepted: 04/14/2023] [Indexed: 05/03/2023]
Abstract
The intricate dynamics of inorganic polyphosphate (polyP) in response to phosphorus (P) limitation and metal exposure typical of contaminated aquatic environments is poorly understood. Cyanobacteria are important primary producers in aquatic environments that are exposed to P stringency as well as metal contamination. There is a growing concern regarding migration of uranium, generated as a result of anthropogenic activities, into the aquatic environments owing to high mobility and solubility of stable aqueous complexes of uranyl ions. The polyP metabolism in cyanobacteria in context of uranium (U) exposure under P limitation has hardly been explored. In this study, we analyzed the polyP dynamics in a marine, filamentous cyanobacterium Anabaena torulosa under combination of variable phosphate concentrations (overplus and deficient) and uranyl exposure conditions typical of marine environments. Polyphosphate accumulation (polyP+) or deficient (polyP-) conditions were physiologically synthesized in the A. torulosa cultures and were ascertained by (a) toulidine blue staining followed by their visualization using bright field microscopy and (b) scanning electron microscopy in combination with energy dispersive X-ray spectroscopy (SEM/EDX). On exposure to 100 μM of uranyl carbonate at pH 7.8, it was observed that the growth of polyP+ cells under phosphate limitation was hardly affected and these cells exhibited larger amounts of uranium binding as compared to polyP- cells of A. torulosa. In contrast, the polyP- cells displayed extensive lysis when exposed to similar U exposure. Our findings suggest that polyP accumulation played an important role in conferring uranium tolerance in the marine cyanobacterium, A. torulosa. The polyP-mediated uranium tolerance and binding could serve as a suitable strategy for remediation of uranium contamination in aquatic environments.
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Affiliation(s)
- Pallavi Chandwadkar
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - Celin Acharya
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India.
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18
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Roda-Garcia JJ, Haro-Moreno JM, Rodriguez-Valera F, Almagro-Moreno S, López-Pérez M. Single-amplified genomes reveal most streamlined free-living marine bacteria. Environ Microbiol 2023. [PMID: 36755376 DOI: 10.1111/1462-2920.16348] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/04/2023] [Indexed: 02/10/2023]
Abstract
Evolutionary adaptations of prokaryotes to the environment sometimes result in genome reduction. Our knowledge of this phenomenon among free-living bacteria remains scarce. We address the dynamics and limits of genome reduction by examining one of the most abundant bacteria in the ocean, the SAR86 clade. Despite its abundance, comparative genomics has been limited by the absence of pure cultures and the poor representation in metagenome-assembled genomes. We co-assembled multiple previously available single-amplified genomes to obtain the first complete genomes from members of the four families. All families showed a convergent evolutionary trajectory with characteristic features of streamlined genomes, most pronounced in the TMED112 family. This family has a genome size of ca. 1 Mb and only 1 bp as median intergenic distance, exceeding values found in other abundant microbes such as SAR11, OM43 and Prochlorococcus. This genomic simplification led to a reduction in the biosynthesis of essential molecules, DNA repair-related genes, and the ability to sense and respond to environmental factors, which could suggest an evolutionary dependence on other co-occurring microbes for survival (Black Queen hypothesis). Therefore, these reconstructed genomes within the SAR86 clade provide new insights into the limits of genome reduction in free-living marine bacteria.
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Affiliation(s)
- Juan J Roda-Garcia
- Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Jose M Haro-Moreno
- Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA.,National Center for Integrated Coastal Research, University of Central Florida, Orlando, Florida, USA
| | - Mario López-Pérez
- Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
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19
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Fuchsman CA, Garcia Prieto D, Hays MD, Cram JA. Associations between picocyanobacterial ecotypes and cyanophage host genes across ocean basins and depth. PeerJ 2023; 11:e14924. [PMID: 36874978 PMCID: PMC9983427 DOI: 10.7717/peerj.14924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/30/2023] [Indexed: 03/06/2023] Open
Abstract
Background Cyanophages, viruses that infect cyanobacteria, are globally abundant in the ocean's euphotic zone and are a potentially important cause of mortality for marine picocyanobacteria. Viral host genes are thought to increase viral fitness by either increasing numbers of genes for synthesizing nucleotides for virus replication, or by mitigating direct stresses imposed by the environment. The encoding of host genes in viral genomes through horizontal gene transfer is a form of evolution that links viruses, hosts, and the environment. We previously examined depth profiles of the proportion of cyanophage containing various host genes in the Eastern Tropical North Pacific Oxygen Deficient Zone (ODZ) and at the subtropical North Atlantic (BATS). However, cyanophage host genes have not been previously examined in environmental depth profiles across the oceans. Methodology We examined geographical and depth distributions of picocyanobacterial ecotypes, cyanophage, and their viral-host genes across ocean basins including the North Atlantic, Mediterranean Sea, North Pacific, South Pacific, and Eastern Tropical North and South Pacific ODZs using phylogenetic metagenomic read placement. We determined the proportion of myo and podo-cyanophage containing a range of host genes by comparing to cyanophage single copy core gene terminase (terL). With this large dataset (22 stations), network analysis identified statistical links between 12 of the 14 cyanophage host genes examined here with their picocyanobacteria host ecotypes. Results Picyanobacterial ecotypes, and the composition and proportion of cyanophage host genes, shifted dramatically and predictably with depth. For most of the cyanophage host genes examined here, we found that the composition of host ecotypes predicted the proportion of viral host genes harbored by the cyanophage community. Terminase is too conserved to illuminate the myo-cyanophage community structure. Cyanophage cobS was present in almost all myo-cyanophage and did not vary in proportion with depth. We used the composition of cobS phylotypes to track changes in myo-cyanophage composition. Conclusions Picocyanobacteria ecotypes shift with changes in light, temperature, and oxygen and many common cyanophage host genes shift concomitantly. However, cyanophage phosphate transporter gene pstS appeared to instead vary with ocean basin and was most abundant in low phosphate regions. Abundances of cyanophage host genes related to nutrient acquisition may diverge from host ecotype constraints as the same host can live in varying nutrient concentrations. Myo-cyanophage community in the anoxic ODZ had reduced diversity. By comparison to the oxic ocean, we can see which cyanophage host genes are especially abundant (nirA, nirC, and purS) or not abundant (myo psbA) in ODZs, highlighting both the stability of conditions in the ODZ and the importance of nitrite as an N source to ODZ endemic LLV Prochlorococcus.
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Affiliation(s)
- Clara A Fuchsman
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, United States of America
| | - David Garcia Prieto
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, United States of America
| | - Matthew D Hays
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, United States of America
| | - Jacob A Cram
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, United States of America
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20
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Blumberg K, Miller M, Ponsero A, Hurwitz B. Ontology-driven analysis of marine metagenomics: what more can we learn from our data? Gigascience 2022; 12:giad088. [PMID: 37941395 PMCID: PMC10632069 DOI: 10.1093/gigascience/giad088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/30/2023] [Accepted: 09/28/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND The proliferation of metagenomic sequencing technologies has enabled novel insights into the functional genomic potentials and taxonomic structure of microbial communities. However, cyberinfrastructure efforts to manage and enable the reproducible analysis of sequence data have not kept pace. Thus, there is increasing recognition of the need to make metagenomic data discoverable within machine-searchable frameworks compliant with the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for data stewardship. Although a variety of metagenomic web services exist, none currently leverage the hierarchically structured terminology encoded within common life science ontologies to programmatically discover data. RESULTS Here, we integrate large-scale marine metagenomic datasets with community-driven life science ontologies into a novel FAIR web service. This approach enables the retrieval of data discovered by intersecting the knowledge represented within ontologies against the functional genomic potential and taxonomic structure computed from marine sequencing data. Our findings highlight various microbial functional and taxonomic patterns relevant to the ecology of prokaryotes in various aquatic environments. CONCLUSIONS In this work, we present and evaluate a novel Semantic Web architecture that can be used to ask novel biological questions of existing marine metagenomic datasets. Finally, the FAIR ontology searchable data products provided by our API can be leveraged by future research efforts.
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Affiliation(s)
- Kai Blumberg
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Matthew Miller
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Alise Ponsero
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Bonnie Hurwitz
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
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Transcriptomic-Guided Phosphonate Utilization Analysis Unveils Evidence of Clathrin-Mediated Endocytosis and Phospholipid Synthesis in the Model Diatom, Phaeodactylum tricornutum. mSystems 2022; 7:e0056322. [PMID: 36317887 PMCID: PMC9765203 DOI: 10.1128/msystems.00563-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Phosphonates are important components of marine organic phosphorus, but their bioavailability and catabolism by eukaryotic phytoplankton remain enigmatic. Here, diatom Phaeodactylum tricornutum was used to investigate the bioavailability of phosphonates and describe the underlying molecular mechanism. The results showed that 2-aminoethylphosphonic acid (2-AEP) can be utilized as an alternative phosphorus source. Comparative transcriptomics revealed that the utilization of 2-AEP comprised 2 steps, including molecular uptake through clathrin-mediated endocytosis and incorporation into the membrane phospholipids in the form of diacylglyceryl-2-AEP (DAG-2-AEP). In the global ocean, we found the prevalence and dynamic expression pattern of key genes that are responsible for vesicle formation (CLTC, AP-2) and DAG-AEP synthesis (PCYT2, EPT1) in diatom assemblages. This study elucidates a distinctive mechanism of phosphonate utilization by diatoms, and discusses the ecological implications. IMPORTANCE Phosphonates contribute ~25% of total dissolved organic phosphorus in the ocean, and are found to be important for marine phosphorus biogeochemical cycle. As a type of biogenic phosphonate produced by microorganisms, 2-aminoethylphosphonic acid (2-AEP) widely exists in the ocean. It is well known that 2-AEP can be cleaved and utilized by prokaryotes, but its ability to support the growth of eukaryotic phytoplankton remains unclear. Our research identified the bioavailability of 2-AEP for the diatom Phaeodactylum tricornutum, and proposed a distinctive metabolic pathway of 2-AEP utilization. Different from the enzymatic hydrolysis of phosphonates, the results suggested that P. tricornutum utilizes 2-AEP by incorporating it into phospholipid instead of cleaving the C-P bond. Moreover, the ubiquitous distribution of associated representative gene transcripts in the environmental assemblages and the higher gene transcript abundance in the cold regions were observed, which suggests the possible environmental adaption of 2-AEP utilization by diatoms.
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22
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Gobert T, Gautier A, Connan S, Rouget ML, Thibaut T, Stiger-Pouvreau V, Waeles M. Trace metal content from holopelagic Sargassum spp. sampled in the tropical North Atlantic Ocean: Emphasis on spatial variation of arsenic and phosphorus. CHEMOSPHERE 2022; 308:136186. [PMID: 36041518 DOI: 10.1016/j.chemosphere.2022.136186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/04/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
We document for the first time, the spatial distribution at basin scale (North tropical Atlantic Ocean) of As, P and trace metal (TM) concentrations in the three morphotypes belonging to the two holopelagic species Sargassum natans and S. fluitans and three morphotypes: S. natans VIII, S. natans I and S. fluitans III. These samples collected in the North equatorial current (NEC) and in the subtropical Sargasso Sea (sSS) (∼25°N, 60°W) were also compared to coastal samples collected downwind Guadeloupe Island and on the strand of Martinique (mangrove and beach). Along the studied zonal oceanic transect, the highest values of As (range 120-240 μg g-1, dry weight, dw) were found in the sSS area where primary production is highly limited by phosphorus. At these stations, the P content of Sargassum spp. was minimal (range 500-1000 μg g-1, dw) as well as the content in Cd and Zn known for their nutrient-like oceanic behaviors and distributions very similar to P. This illustrates for the first time in the natural environment, the higher bioaccumulation of arsenic in Sargassum spp. in P-limiting conditions which is due to the competition in the phosphate transporter between arsenate and phosphate. As compared to samples collected at sea, the Sargassum spp. collected in the strand of Martinique had (1) lower As concentrations (typical range 30-45 μg g-1, dw) and (2) much higher Al, Fe, Mn, Cr and Co concentrations, showing a certain ability of Sargassum spp. to be depurated of its As content in the coastal zone following competitive exchange with terrigenous metals.
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Affiliation(s)
- Tristan Gobert
- University of Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzane, France
| | - Ambre Gautier
- University of Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzane, France
| | - Solène Connan
- University of Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzane, France
| | | | - Thierry Thibaut
- Aix Marseille University and Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
| | | | - Matthieu Waeles
- University of Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzane, France.
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23
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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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24
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Differentiated Evolutionary Strategies of Genetic Diversification in Atlantic and Pacific Thaumarchaeal Populations. mSystems 2022; 7:e0147721. [PMID: 35695431 PMCID: PMC9239043 DOI: 10.1128/msystems.01477-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Some marine microbes are seemingly “ubiquitous,” thriving across a wide range of environmental conditions. While the increased depth in metagenomic sequencing has led to a growing body of research on within-population heterogeneity in environmental microbial populations, there have been fewer systematic comparisons and characterizations of population-level genetic diversity over broader expanses of time and space. Here, we investigated the factors that govern the diversification of ubiquitous microbial taxa found within and between ocean basins. Specifically, we use mapped metagenomic paired reads to examine the genetic diversity of ammonia-oxidizing archaeal (“Candidatus Nitrosopelagicus brevis”) populations in the Pacific (Hawaii Ocean Time-series [HOT]) and Atlantic (Bermuda Atlantic Time Series [BATS]) Oceans sampled over 2 years. We observed higher nucleotide diversity in “Ca. N. brevis” at HOT, driven by a higher rate of homologous recombination. In contrast, “Ca. N. brevis” at BATS featured a more open pangenome with a larger set of genes that were specific to BATS, suggesting a history of dynamic gene gain and loss events. Furthermore, we identified highly differentiated genes that were regulatory in function, some of which exhibited evidence of recent selective sweeps. These findings indicate that different modes of genetic diversification likely incur specific adaptive advantages depending on the selective pressures that they are under. Within-population diversity generated by the environment-specific strategies of genetic diversification is likely key to the ecological success of “Ca. N. brevis.” IMPORTANCE Ammonia-oxidizing archaea (AOA) are one of the most abundant chemolithoautotrophic microbes in the marine water column and are major contributors to global carbon and nitrogen cycling. Despite their ecological importance and geographical pervasiveness, there have been limited systematic comparisons and characterizations of their population-level genetic diversity over time and space. Here, we use metagenomic time series from two ocean observatories to address the fundamental questions of how abiotic and biotic factors shape the population-level genetic diversity and how natural microbial populations adapt across diverse habitats. We show that the marine AOA “Candidatus Nitrosopelagicus brevis” in different ocean basins exhibits distinct modes of genetic diversification in response to their selective regimes shaped by nutrient availability and patterns of environmental fluctuations. Our findings specific to “Ca. N. brevis” have broader implications, particularly in understanding the population-level responses to the changing climate and predicting its impact on biogeochemical cycles.
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25
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Zhao F, Lin X, Cai K, Jiang Y, Ni T, Chen Y, Feng J, Dang S, Zhou CZ, Zeng Q. Biochemical and structural characterization of the cyanophage-encoded phosphate binding protein: implications for enhanced phosphate uptake of infected cyanobacteria. Environ Microbiol 2022; 24:3037-3050. [PMID: 35590460 DOI: 10.1111/1462-2920.16043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 12/01/2022]
Abstract
To acquire phosphorus, cyanobacteria use the typical bacterial ABC-type phosphate transporter, which is composed of a periplasmic high-affinity phosphate-binding protein PstS and a channel formed by two transmembrane proteins PstC and PstA. A putative pstS gene was identified in the genomes of cyanophages that infect the unicellular marine cyanobacteria Prochlorococcus and Synechococcus. However, it has not been determined whether the cyanophage PstS protein is functional during infection to enhance the phosphate uptake rate of host cells. Here we showed that the cyanophage P-SSM2 PstS protein was abundant in the infected Prochlorococcus NATL2A cells and the host phosphate uptake rate was enhanced after infection. This is consistent with our biochemical and structural analyses showing that the phage PstS protein is indeed a high-affinity phosphate-binding protein. We further modeled the complex structure of phage PstS with host PstCA and revealed three putative interfaces that may facilitate the formation of a chimeric ABC transporter. Our results provide insights into the molecular mechanism by which cyanophages enhance the phosphate uptake rate of cyanobacteria. Phosphate acquisition by infected bacteria can increase the phosphorus contents of released cellular debris and virus particles, which together constitute a significant proportion of the marine dissolved organic phosphorus pool. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Fangxin Zhao
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xingqin Lin
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Kun Cai
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - YongLiang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Tianchi Ni
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yue Chen
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Jianrong Feng
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shangyu Dang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, China
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26
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Zhang K, Li J, Wang J, Lin X, Li L, You Y, Wu X, Zhou Z, Lin S. Functional differentiation and complementation of alkaline phosphatases and choreography of DOP scavenging in a marine diatom. Mol Ecol 2022; 31:3389-3399. [PMID: 35445467 DOI: 10.1111/mec.16475] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/29/2022]
Abstract
Facing phosphate deficiency, phytoplankton use alkaline phosphatase (AP) to scavenge dissolved organophosphate (DOP). AP is a multi-type (e.g. PhoA, PhoD) family of hydrolases and is known as a promiscuous enzyme with broad DOP substrate compatibility. Yet whether the multiple types differentiate on substrates and collaborate to provide physiological flexibility remain elusive. Here we identify PhoA and PhoDs and document the functional differentiation between PhoA and a PhoD (PhoD_45757) in Phaeodactylum tricornutum. CRISPR/Cas9-based mutations and physiological analyses reveal that 1) PhoA is a secreted enzyme and contributes the majority of total AP activity whereas PhoD_45757 is intracellular and contributes a minor fraction of the total AP activity; 2) AP gene expression compensates for each other after one is disrupted; 3) the DOP→PhoA→phosphate_uptake and the DOP_uptake→PhoD→phosphate pathways function interchangeably for some DOP substrates. These findings shed light on the underpinning of AP's multiformity and have important implications in phytoplankton phosphorus-nutrient niche differentiation, physiological plasticity, and competitive strategy.
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Affiliation(s)
- Kaidian Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China.,Department of Marine Sciences, University of Connecticut, Groton, CT, USA.,State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
| | - Jiashun Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jierui Wang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yanchun You
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiaomei Wu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Zhi Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China.,Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong, China.,Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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27
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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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28
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Zhu Y, Feng Y, Browning TJ, Wen Z, Hughes DJ, Hao Q, Zhang R, Meng Q, Wells ML, Jiang Z, Dissanayake PAKN, Priyadarshani WNC, Shou L, Zeng J, Chai F. Exploring Variability of Trichodesmium Photophysiology Using Multi-Excitation Wavelength Fast Repetition Rate Fluorometry. Front Microbiol 2022; 13:813573. [PMID: 35464918 PMCID: PMC9026164 DOI: 10.3389/fmicb.2022.813573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/11/2022] [Indexed: 11/20/2022] Open
Abstract
Fast repetition rate fluorometry (FRRf) allows for rapid non-destructive assessment of phytoplankton photophysiology in situ yet has rarely been applied to Trichodesmium. This gap reflects long-standing concerns that Trichodesmium (and other cyanobacteria) contain pigments that are less effective at absorbing blue light which is often used as the sole excitation source in FRR fluorometers-potentially leading to underestimation of key fluorescence parameters. In this study, we use a multi-excitation FRR fluorometer (equipped with blue, green, and orange LEDs) to investigate photophysiological variability in Trichodesmium assemblages from two sites. Using a multi-LED measurement protocol (447+519+634 nm combined), we assessed maximum photochemical efficiency (F v /F m ), functional absorption cross section of PSII (σ PSII ), and electron transport rates (ETRs) for Trichodesmium assemblages in both the Northwest Pacific (NWP) and North Indian Ocean in the vicinity of Sri Lanka (NIO-SL). Evaluating fluorometer performance, we showed that use of a multi-LED measuring protocol yields a significant increase of F v /F m for Trichodesmium compared to blue-only excitation. We found distinct photophysiological differences for Trichodesmium at both locations with higher average F v /F m as well as lower σ PSII and non-photochemical quenching (NPQ NSV ) observed in the NWP compared to the NIO-SL (Kruskal-Wallis t-test df = 1, p < 0.05). Fluorescence light response curves (FLCs) further revealed differences in ETR response with a lower initial slope (α ETR ) and higher maximum electron turnover rate ( E T R P S I I m a x ) observed for Trichodesmium in the NWP compared to the NIO-SL, translating to a higher averaged light saturation E K (= E T R P S I I m a x /α ETR ) for cells at this location. Spatial variations in physiological parameters were both observed between and within regions, likely linked to nutrient supply and physiological stress. Finally, we applied an algorithm to estimate primary productivity of Trichodesmium using FRRf-derived fluorescence parameters, yielding an estimated carbon-fixation rate ranging from 7.8 to 21.1 mgC mg Chl-a-1 h-1 across this dataset. Overall, our findings demonstrate that capacity of multi-excitation FRRf to advance the application of Chl-a fluorescence techniques in phytoplankton assemblages dominated by cyanobacteria and reveals novel insight into environmental regulation of photoacclimation in natural Trichodesmium populations.
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Affiliation(s)
- Yuanli Zhu
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Yuanyuan Feng
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Thomas J. Browning
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Zuozhu Wen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - David J. Hughes
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Qiang Hao
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Ruifeng Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Qicheng Meng
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Mark L. Wells
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Darling Marine Center, University of Maine, Walpole, ME, United States
| | - Zhibing Jiang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - P. A. K. N. Dissanayake
- Department of Oceanography and Marine Geology, Faculty of Fisheries and Marine Sciences and Technology, University of Ruhuna, Matara, Sri Lanka
| | - W. N. C. Priyadarshani
- National Institute of Oceanography and Marine Sciences, National Aquatic Resources Research and Development Agency, Colombo, Sri Lanka
| | - Lu Shou
- Key Laboratory of Marine Ecosystem 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
| | - Fei Chai
- State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
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29
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Zheng H, Liu B, Xu Y, Zhang Z, Man H, Liu J, Chen F. An Inducible Microbacterium Prophage vB_MoxS-R1 Represents a Novel Lineage of Siphovirus. Viruses 2022; 14:v14040731. [PMID: 35458461 PMCID: PMC9030533 DOI: 10.3390/v14040731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 12/02/2022] Open
Abstract
Lytic and lysogenic infections are the main strategies used by viruses to interact with microbial hosts. The genetic information of prophages provides insights into the nature of phages and their potential influences on hosts. Here, the siphovirus vB_MoxS-R1 was induced from a Microbacterium strain isolated from an estuarine Synechococcus culture. vB_MoxS-R1 has a high replication capability, with an estimated burst size of 2000 virions per cell. vB_MoxS-R1 represents a novel phage genus-based genomic analysis. Six transcriptional regulator (TR) genes were predicted in the vB_MoxS-R1 genome. Four of these TR genes are involved in stress responses, virulence and amino acid transportation in bacteria, suggesting that they may play roles in regulating the host cell metabolism in response to external environmental changes. A glycerophosphodiester phosphodiesterase gene related to phosphorus acquisition was also identified in the vB_MoxS-R1 genome. The presence of six TR genes and the phosphorus-acquisition gene suggests that prophage vB_MoxS-R1 has the potential to influence survival and adaptation of its host during lysogeny. Possession of four endonuclease genes in the prophage genome suggests that vB_MoxS-R1 is likely involved in DNA recombination or gene conversion and further influences host evolution.
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Affiliation(s)
- Hongrui Zheng
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
| | - Binbin Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361000, China
- Correspondence: (Y.X.); (J.L.)
| | - Zefeng Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
| | - Hongcong Man
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, China; (H.Z.); (B.L.); (Z.Z.); (H.M.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Joint Laboratory for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao 266237, China
- Correspondence: (Y.X.); (J.L.)
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA;
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30
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Ajili W, Tovani CB, Fouassier J, de Frutos M, Laurent GP, Bertani P, Djediat C, Marin F, Auzoux-Bordenave S, Azaïs T, Nassif N. Inorganic phosphate in growing calcium carbonate abalone shell suggests a shared mineral ancestral precursor. Nat Commun 2022; 13:1496. [PMID: 35314701 PMCID: PMC8938516 DOI: 10.1038/s41467-022-29169-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/17/2022] [Indexed: 01/30/2023] Open
Abstract
The presence of phosphate from different origins (inorganic, bioorganic) is found more and more in calcium carbonate-based biominerals. Phosphate is often described as being responsible for the stabilization of the transient amorphous calcium carbonate phase. In order to specify the composition of the mineral phase deposited at the onset of carbonated shell formation, the present study investigates, down to the nanoscale, the growing shell from the European abalone Haliotis tuberculata, using a combination of solid state nuclear magnetic resonance, scanning transmission electron microscope and spatially-resolved electron energy loss spectroscopy techniques. We show the co-occurrence of inorganic phosphate with calcium and carbonate throughout the early stages of abalone shell formation. One possible hypothesis is that this first-formed mixed mineral phase represents the vestige of a shared ancestral mineral precursor that appeared early during Evolution. In addition, our findings strengthen the idea that the final crystalline phase (calcium carbonate or phosphate) depends strongly on the nature of the mineral-associated proteins in vivo. Phosphate involvement in calcium carbonate biominerals raises questions on biomineralisation pathways. Here, the authors explore the presence of phosphate in the growing shell of the European abalone and suggest a shared mixed mineral ancestral precursor with final crystal phase being selected by mineral-associated proteins.
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31
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Lomas MW, Bates NR, Johnson RJ, Steinberg DK, Tanioka T. Adaptive carbon export response to warming in the Sargasso Sea. Nat Commun 2022; 13:1211. [PMID: 35260567 PMCID: PMC8904855 DOI: 10.1038/s41467-022-28842-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 02/07/2022] [Indexed: 11/30/2022] Open
Abstract
Ocean ecosystem models predict that warming and increased surface ocean stratification will trigger a series of ecosystem events, reducing the biological export of particulate carbon to the ocean interior. We present a nearly three-decade time series from the open ocean that documents a biological response to ocean warming and nutrient reductions wherein particulate carbon export is maintained, counter to expectations. Carbon export is maintained through a combination of phytoplankton community change to favor cyanobacteria with high cellular carbon-to-phosphorus ratios and enhanced shallow phosphorus recycling leading to increased nutrient use efficiency. These results suggest that surface ocean ecosystems may be more responsive and adapt more rapidly to changes in the hydrographic system than is currently envisioned in earth ecosystem models, with positive consequences for ocean carbon uptake. The ability of the ocean’s biota to sequester carbon is thought to be negatively affected by climate change. Here the authors use time-series data in the Sargasso Sea to show that biotic processes can buffer against these negative impacts.
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Affiliation(s)
- Michael W Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
| | - Nicholas R Bates
- Bermuda Institute for Ocean Sciences, St. Georges, Bermuda.,Department of Ocean and Earth Science, University of Southampton, Southampton, UK
| | | | - Deborah K Steinberg
- Virginia Institute of Marine Science, William & Mary, Gloucester Pt., Virginia, VA, USA
| | - Tatsuro Tanioka
- Department of Earth System Science, University of California, Irvine, CA, USA
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32
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Wen Z, Browning TJ, Cai Y, Dai R, Zhang R, Du C, Jiang R, Lin W, Liu X, Cao Z, Hong H, Dai M, Shi D. Nutrient regulation of biological nitrogen fixation across the tropical western North Pacific. SCIENCE ADVANCES 2022; 8:eabl7564. [PMID: 35119922 PMCID: PMC8816331 DOI: 10.1126/sciadv.abl7564] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Nitrogen fixation is critical for the biological productivity of the ocean, but clear mechanistic controls on this process remain elusive. Here, we investigate the abundance, activity, and drivers of nitrogen-fixing diazotrophs across the tropical western North Pacific. We find a basin-scale coherence of diazotroph abundances and N2 fixation rates with the supply ratio of iron:nitrogen to the upper ocean. Across a threshold of increasing supply ratios, the abundance of nifH genes and N2 fixation rates increased, phosphate concentrations decreased, and bioassay experiments demonstrated evidence for N2 fixation switching from iron to phosphate limitation. In the northern South China Sea, supply ratios were hypothesized to fall around this critical threshold and bioassay experiments suggested colimitation by both iron and phosphate. Our results provide evidence for iron:nitrogen supply ratios being the most important factor in regulating the distribution of N2 fixation across the tropical ocean.
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Affiliation(s)
- Zuozhu Wen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Thomas J. Browning
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Yihua Cai
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Rongbo Dai
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Ruifeng Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Chuanjun Du
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Ruotong Jiang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Wenfang Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Xin Liu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Zhimian Cao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Haizheng Hong
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Minhan Dai
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
| | - Dalin Shi
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
- Corresponding author.
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33
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Wang S, Koedooder C, Zhang F, Kessler N, Eichner M, Shi D, Shaked Y. Colonies of the marine cyanobacterium Trichodesmium optimize dust utilization by selective collection and retention of nutrient-rich particles. iScience 2022; 25:103587. [PMID: 35005537 PMCID: PMC8718973 DOI: 10.1016/j.isci.2021.103587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/01/2021] [Accepted: 12/06/2021] [Indexed: 12/11/2022] Open
Abstract
Trichodesmium, a globally important, N2-fixing, and colony-forming cyanobacterium, employs multiple pathways for acquiring nutrients from air-borne dust, including active dust collection. Once concentrated within the colony core, dust can supply Trichodesmium with nutrients. Recently, we reported a selectivity in particle collection enabling Trichodesmium to center iron-rich minerals and optimize its nutrient utilization. In this follow-up study we examined if colonies select Phosphorus (P) minerals. We incubated 1,200 Trichodesmium colonies from the Red Sea with P-free CaCO3, P-coated CaCO3, and dust, over an entire bloom season. These colonies preferably interacted, centered, and retained P-coated CaCO3 compared with P-free CaCO3. In both studies, Trichodesmium clearly favored dust over all other particles tested, whereas nutrient-free particles were barely collected or retained, indicating that the colonies sense the particle composition and preferably collect nutrient-rich particles. This unique ability contributes to Trichodesmium's current ecological success and may assist it to flourish in future warmer oceans. Natural Trichodesmium colonies collect and maintain dust within their colony core Using synthetic particles we tested if colonies select the particles they collect Colonies selectively collect and retain nutrient-rich over nutrient-free particles Selective collection of particles optimizes their nutrient acquisition from dust
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Affiliation(s)
- Siyuan Wang
- The Freddy and Nadine Herrmann Institute of Earth Sciences, Edmond J. Safra Campus, Givat Ram, Hebrew University of Jerusalem, Jerusalem, Israel.,The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Coco Koedooder
- The Freddy and Nadine Herrmann Institute of Earth Sciences, Edmond J. Safra Campus, Givat Ram, Hebrew University of Jerusalem, Jerusalem, Israel.,The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel.,Israel Limnology and Oceanography Research, Haifa, Israel
| | - Futing Zhang
- The Freddy and Nadine Herrmann Institute of Earth Sciences, Edmond J. Safra Campus, Givat Ram, Hebrew University of Jerusalem, Jerusalem, Israel.,The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Nivi Kessler
- The Freddy and Nadine Herrmann Institute of Earth Sciences, Edmond J. Safra Campus, Givat Ram, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Meri Eichner
- Laboratory of Photosynthesis, Center Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
| | - Dalin Shi
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Yeala Shaked
- The Freddy and Nadine Herrmann Institute of Earth Sciences, Edmond J. Safra Campus, Givat Ram, Hebrew University of Jerusalem, Jerusalem, Israel.,The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
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34
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Zhang K, Zhou Z, Li J, Wang J, Yu L, Lin S. SPX-related genes regulate phosphorus homeostasis in the marine phytoplankton, Phaeodactylum tricornutum. Commun Biol 2021; 4:797. [PMID: 34172821 PMCID: PMC8233357 DOI: 10.1038/s42003-021-02284-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 06/01/2021] [Indexed: 11/18/2022] Open
Abstract
Phosphorus (P) is an essential nutrient for marine phytoplankton. Maintaining intracellular P homeostasis against environmental P variability is critical for phytoplankton, but how they achieve this is poorly understood. Here we identify a SPX gene and investigate its role in Phaeodactylum tricornutum. SPX knockout led to significant increases in the expression of phosphate transporters, alkaline phosphatases (the P acquisition machinery) and phospholipid hydrolases (a mechanism to reduce P demand). These demonstrate that SPX is a negative regulator of both P uptake and P-stress responses. Furthermore, we show that SPX regulation of P uptake and metabolism involves a phosphate starvation response regulator (PHR) as an intermediate. Additionally, we find the SPX related genes exist and operate across the phytoplankton phylogenetic spectrum and in the global oceans, indicating its universal importance in marine phytoplankton. This study lays a foundation for better understanding phytoplankton adaptation to P variability in the future changing oceans.
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Affiliation(s)
- Kaidian Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Zhi Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
| | - Jiashun Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jingtian Wang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China.
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA.
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, China.
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35
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Wu X, Liu H, Ru Z, Tu G, Xing L, Ding Y. Meta-analysis of the response of marine phytoplankton to nutrient addition and seawater warming. MARINE ENVIRONMENTAL RESEARCH 2021; 168:105294. [PMID: 33770674 DOI: 10.1016/j.marenvres.2021.105294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/24/2021] [Accepted: 02/27/2021] [Indexed: 06/12/2023]
Abstract
As an indispensable part of the marine ecosystem, phytoplankton are important prey for zooplankton and various marine animals with important commercial value. The influence of seawater warming and eutrophication on phytoplankton communities is well known, but few studies have explained the effects of the interaction between temperature and nutrients on marine phytoplankton. Through meta-analysis and meta-regression, the phytoplankton responses to the effects of nutrient addition and seawater warming were evaluated in this study. Nitrogen (N) addition led to an increase in phytoplankton biomass, while phosphorus (P) had no significant effect on phytoplankton biomass. However, this result may be biased by the uneven distribution of the research area. N limitation is widespread in the areas where these collected studies were conducted, including many parts of North and South Atlantic and West Pacific Oceans. The key limiting nutrient in other areas lacking corresponding experiments, however, remain unclear. The effect of seawater warming was not significant, which indicates the uncertainty about the effect of temperature on phytoplankton. The results of ANOVA show that nutrient addition and seawater warming had similar effects in various marine habitats (coastal regions, estuaries and open seas), while salinity could have caused the difference in the N effects among the three habitats. Furthermore, our results showed that the impact of temperature depends on nutrient conditions, especially N status, which has rarely been considered before. This result demonstrated the importance of evaluating nutrient limitation patterns when studying climate warming. The impact of rising temperatures may need to be reevaluated because N limitation is common.
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Affiliation(s)
- Xuerong Wu
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Haifei Liu
- School of Environment, Beijing Normal University, Beijing, 100875, China.
| | - Zhiming Ru
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Gangqin Tu
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Liming Xing
- School of Environment, Beijing Normal University, Beijing, 100875, China; Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Yu Ding
- School of Environment, Beijing Normal University, Beijing, 100875, China
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36
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Xu K, Li Y, Li M. Potentiometric Phosphate Ion Sensor Based on Electrochemical Modified Tungsten Electrode. ACS OMEGA 2021; 6:13795-13801. [PMID: 34095671 PMCID: PMC8173557 DOI: 10.1021/acsomega.1c00195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
Determination of phosphate ions in aqueous solutions attracts a great deal of interest in the areas of environment, medicine, and agriculture. As phosphoric acid is a poly basic acid, the different forms of existence at different pH result in direct determination facing a big challenge. Herein, we reported a potentiometric phosphate ion sensor based on a surface-modified tungsten electrode. Pure tungsten was electrodeposited at a constant potential of 0.2 V versus Ag|AgCl in Na2HPO4. WO3 and H3O40PW12·xH2O were electrodeposited on the surface of the tungsten electrode. The modified tungsten electrode was used as a working electrode in a two-electrode system to detect the concentration of phosphate ions in aqueous solutions. The detection limit of the modified tungsten electrode for phosphate ions is 10-6 M from pH 7 to pH 8 and 10-5 M from pH 9 to pH 10. It has good selectivity to other common anions. The long-term monitoring experiment showed that the potential fluctuation was less than ±3 mV in 24 h. Compared to conventional determination methods, the current phosphate ion sensor showed a close value in a real sample. The mechanism of phosphate ion response was investigated in detail. This sensor possesses advantages of simple manufacture, low cost, a wide pH range for detecting, and good selectivity.
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Affiliation(s)
- Kebin Xu
- School
of Metallurgy, Northeastern University, Shenyang 110819, People’s Republic of China
- Liaoning
Key Laboratory for Metallurgical Sensor Material and Technology, Shenyang 110819, People’s Republic of China
| | - Ying Li
- School
of Metallurgy, Northeastern University, Shenyang 110819, People’s Republic of China
- Liaoning
Key Laboratory for Metallurgical Sensor Material and Technology, Shenyang 110819, People’s Republic of China
| | - Min Li
- School
of Metallurgy, Northeastern University, Shenyang 110819, People’s Republic of China
- Liaoning
Key Laboratory for Metallurgical Sensor Material and Technology, Shenyang 110819, People’s Republic of China
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37
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Fernández-Martínez M, Preece C, Corbera J, Cano O, Garcia-Porta J, Sardans J, Janssens IA, Sabater F, Peñuelas J. Bryophyte C:N:P stoichiometry, biogeochemical niches and elementome plasticity driven by environment and coexistence. Ecol Lett 2021; 24:1375-1386. [PMID: 33894025 DOI: 10.1111/ele.13752] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/22/2021] [Accepted: 03/20/2021] [Indexed: 01/13/2023]
Abstract
Ecological stoichiometry and studies of biogeochemical niches have mainly focused on plankton and vascular plants, but the phenotypically closest modern relatives of early plants, bryophytes, have been largely neglected. We analysed C:N:P stoichiometries and elemental compositions (K, Na, Mg, Ca, S, Fe) of 35 widely distributed bryophyte species inhabiting springs. We estimated bryophyte C:N:P ratios and their biogeochemical niches, investigated how elementomes respond to the environment and determined whether they tend to diverge more for coexisting than non-coexisting individuals and species. The median C:N:P was 145:8:1, intermediate between Redfield's ratio for marine plankton and those for vascular plants. Biogeochemical niches were differentiated amongst species and were phylogenetically conserved. Differences in individual and species-specific elementomes increased with coexistence between species. Our results provide an evolutionary bridge between the ecological stoichiometries of algae and vascular plants and suggest that differences in elementomes could be used to understand community assemblages and functional diversity.
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Affiliation(s)
- Marcos Fernández-Martínez
- Research group PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, Wilrijk, Belgium.,Delegació de la Serralada Litoral Central, ICHN, Mataró, Catalonia, Spain
| | - Catherine Preece
- Research group PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, Wilrijk, Belgium.,CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain.,CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, Barcelona, Catalonia, Spain
| | - Jordi Corbera
- Delegació de la Serralada Litoral Central, ICHN, Mataró, Catalonia, Spain
| | - Oriol Cano
- Department of Ecology, University of Barcelona, Barcelona, Catalonia, Spain
| | - Joan Garcia-Porta
- Department of Biology, Washington University in Saint Louis, St. Louis, MO, USA
| | - Jordi Sardans
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain.,CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, Barcelona, Catalonia, Spain
| | - Ivan A Janssens
- Research group PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Francesc Sabater
- Delegació de la Serralada Litoral Central, ICHN, Mataró, Catalonia, Spain.,Department of Ecology, University of Barcelona, Barcelona, Catalonia, Spain
| | - Josep Peñuelas
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain.,CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, Barcelona, Catalonia, Spain
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38
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Ustick LJ, Larkin AA, Garcia CA, Garcia NS, Brock ML, Lee JA, Wiseman NA, Moore JK, Martiny AC. Metagenomic analysis reveals global-scale patterns of ocean nutrient limitation. Science 2021; 372:287-291. [DOI: 10.1126/science.abe6301] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/01/2021] [Indexed: 12/23/2022]
Abstract
Nutrient supply regulates the activity of phytoplankton, but the global biogeography of nutrient limitation and co-limitation is poorly understood. Prochlorococcus adapt to local environments by gene gains and losses, and we used genomic changes as an indicator of adaptation to nutrient stress. We collected metagenomes from all major ocean regions as part of the Global Ocean Ship-based Hydrographic Investigations Program (Bio-GO-SHIP) and quantified shifts in genes involved in nitrogen, phosphorus, and iron assimilation. We found regional transitions in stress type and severity as well as widespread co-stress. Prochlorococcus stress genes, bottle experiments, and Earth system model predictions were correlated. We propose that the biogeography of multinutrient stress is stoichiometrically linked by controls on nitrogen fixation. Our omics-based description of phytoplankton resource use provides a nuanced and highly resolved description of nutrient stress in the global ocean.
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Affiliation(s)
- Lucas J. Ustick
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA
| | - Alyse A. Larkin
- Department of Earth System Science, University of California Irvine, Irvine, CA 92697, USA
| | - Catherine A. Garcia
- Department of Earth System Science, University of California Irvine, Irvine, CA 92697, USA
| | - Nathan S. Garcia
- Department of Earth System Science, University of California Irvine, Irvine, CA 92697, USA
| | - Melissa L. Brock
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA
| | - Jenna A. Lee
- Department of Earth System Science, University of California Irvine, Irvine, CA 92697, USA
| | - Nicola A. Wiseman
- Department of Earth System Science, University of California Irvine, Irvine, CA 92697, USA
| | - J. Keith Moore
- Department of Earth System Science, University of California Irvine, Irvine, CA 92697, USA
| | - Adam C. Martiny
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA
- Department of Earth System Science, University of California Irvine, Irvine, CA 92697, USA
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39
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Mine AH, Coleman ML, Colman AS. Phosphorus Release and Regeneration Following Laboratory Lysis of Bacterial Cells. Front Microbiol 2021; 12:641700. [PMID: 33897649 PMCID: PMC8060472 DOI: 10.3389/fmicb.2021.641700] [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: 12/14/2020] [Accepted: 02/10/2021] [Indexed: 11/30/2022] Open
Abstract
The availability of phosphorus limits primary production in large regions of the oceans, and marine microbes use a variety of strategies to overcome this limitation. One strategy is the production of alkaline phosphatase (APase), which allows hydrolysis of larger dissolved organic phosphorus (DOP) compounds in the periplasm or at the cell surface for transport of orthophosphate into the cell. Cell lysis, driven by grazing and viral infection, releases phosphorus-containing cell components, along with active enzymes that could persist after lysis. The importance of this continued enzymatic activity for orthophosphate regeneration is unknown. We used three model bacteria – Escherichia coli K-12 MG1655, Synechococcus sp. WH7803, and Prochlorococcus sp. MED4 – to assess the impact of continued APase activity after cell lysis, via lysozyme treatment, on orthophosphate regeneration. Direct release of orthophosphate scaled with cell size and was reduced under phosphate-starved conditions where APase activity continued for days after lysis. All lysate incubations showed post-lysis orthophosphate generation suggesting phosphatases other than APase maintain activity. Rates of DOP hydrolysis and orthophosphate remineralization varied post-lysis among strains. Escherichia coli K-12 MG1655 rates of remineralization were 0.6 and 1.2 amol cell–1hr–1 under deplete and replete conditions; Synechococcus WH7803 lysates ranged from 0.04 up to 0.3 amol cell–1hr–1 during phosphorus deplete and replete conditions, respectively, while in Prochlorococcus MED4 lysates, rates were stable at 0.001 amol cell–1hr–1 in both conditions. The range of rates of hydrolysis and regeneration underscores the taxonomic and biochemical variability in the process of nutrient regeneration and further highlights the complexity of quantitatively resolving the major fluxes within the microbial loop.
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Affiliation(s)
- Aric H Mine
- Department of Earth and Environmental Sciences, California State University, Fresno, CA, United States.,Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Albert S Colman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States.,Department of Earth, Environmental and Planetary Sciences, Rice University, Houston, TX, United States
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40
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Qiao H, Zang S, Yan F, Xu Z, Wang L, Wu H. Physiological responses of the diatoms Thalassiosira weissflogii and Thalassiosira pseudonana to nitrogen starvation and high light. MARINE ENVIRONMENTAL RESEARCH 2021; 166:105276. [PMID: 33578138 DOI: 10.1016/j.marenvres.2021.105276] [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: 11/05/2020] [Revised: 01/24/2021] [Accepted: 01/30/2021] [Indexed: 06/12/2023]
Abstract
As oceans warm, the depth of the upper mixed layer is predicted to decrease, resulting in insufficient nutrient supply and higher solar radiation for phytoplankton. In order to understand the photophysiological responses of the key eukaryotic phytoplankton diatoms to high light and nutrient limitation, we grew two diatoms, Thalassiosira weissflogii and Thalassiosira pseudonana under N starvation conditions and exposed them to high visible light. It showed that the large-sized diatom T. weissflogii can maintain photosynthetic activity for a longer period of time under nitrogen starvation as compared with the small-sized diatom T. pseudonana. The electron transfer reaction was inhibited in both diatoms and the fast closing of reaction centers promoted the development of QB non-reducing PSII centers, thus facilitated the rapid induction of NPQ, however, the induction of NPQ depended on the degree of N starvation. N starvation exacerbated the photoinhibition caused by high light. The smaller-sized T. pseudonana had a higher σi value and was more sensitive to high-light, but its PSII repair rate was also higher. In contrast, T. weissflogii was more tolerant to high light with a lower σi value, but the tolerance was severely reduced under N-starvation. This study provides helpful insight into how climate change variables impact diatom's photosynthetic physiology.
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Affiliation(s)
- Hongjin Qiao
- School of Life Science, Ludong University, Yantai, 264025, China; Key Laboratory of Marine Biotechnology in Universities of Shandong, Ludong University,Yantai, 264025, China
| | - Shasha Zang
- School of Life Science, Ludong University, Yantai, 264025, China; Key Laboratory of Marine Biotechnology in Universities of Shandong, Ludong University,Yantai, 264025, China
| | - Fang Yan
- School of Life Science, Ludong University, Yantai, 264025, China; Key Laboratory of Marine Biotechnology in Universities of Shandong, Ludong University,Yantai, 264025, China
| | - Zhiguang Xu
- School of Life Science, Ludong University, Yantai, 264025, China; Key Laboratory of Marine Biotechnology in Universities of Shandong, Ludong University,Yantai, 264025, China
| | - Lei Wang
- School of Life Science, Ludong University, Yantai, 264025, China; Key Laboratory of Marine Biotechnology in Universities of Shandong, Ludong University,Yantai, 264025, China
| | - Hongyan Wu
- School of Life Science, Ludong University, Yantai, 264025, China; Key Laboratory of Marine Biotechnology in Universities of Shandong, Ludong University,Yantai, 264025, China.
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41
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Yamaguchi T, Sato M, Hashihama F, Kato H, Sugiyama T, Ogawa H, Takahashi K, Furuya K. Longitudinal and Vertical Variations of Dissolved Labile Phosphoric Monoesters and Diesters in the Subtropical North Pacific. Front Microbiol 2021; 11:570081. [PMID: 33552003 PMCID: PMC7854537 DOI: 10.3389/fmicb.2020.570081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 10/30/2020] [Indexed: 11/30/2022] Open
Abstract
The labile fraction of dissolved organic phosphorus (DOP) – predominantly consisting of phosphoric esters – is an important microbial P source in the subtropical oligotrophic ocean. However, unlike phosphate, knowledge for labile DOP is still limited due to the scarcity of broad and intensive observations. In this study, we examined the concentrations and size-fractionated hydrolysis rates of labile phosphoric monoesters and diesters along a >10,000 km longitudinal transect in the North Pacific (23°N; upper 200-m layer). Depth-integrated monoesters decreased westward with a maximum difference of fivefold. Vertical profiles of monoesters in the eastern and western basins showed decreasing and increasing trends with depth, respectively. The monoester-depleted shallow layer of the western basin was associated with phosphate depletion and monoesterase activity was predominant in the large size fraction (>0.8 μm), suggesting that monoesters are significant P sources particularly for large microbes. In contrast, diester concentrations were generally lower than monoester concentrations and showed no obvious horizontal or vertical variation in the study area. Despite the unclear distribution pattern of diesters, diesterase activity in the particulate fraction (>0.2 μm) increased in the phosphate-depleted shallow layer of the western basin, suggesting that the targeted diesters in the assay were also important microbial P sources. Diesterase activities in the dissolved fraction (<0.2 μm) were not correlated with ambient phosphate concentrations; however, cell-free diesterase likely played a key role in P cycling, as dissolved diesterase activities were substantially higher than those in the particulate fraction. The horizontal and vertical variability of labile monoesters in the subtropical North Pacific were therefore predominantly regulated by P stress in particularly large microbes, whereas the distributions of labile diesters and diesterase activities were generally independent of microbial P stress, indicating a more complex regulation of diesters to that of monoesters.
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Affiliation(s)
- Tamaha Yamaguchi
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Yokohama, Japan.,Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Mitsuhide Sato
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Fuminori Hashihama
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Haruka Kato
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Takanori Sugiyama
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hiroshi Ogawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Kazutaka Takahashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ken Furuya
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Graduate School of Science and Engineering, Soka University, Tokyo, Japan
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42
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Helliwell KE, Harrison EL, Christie-Oleza JA, Rees AP, Kleiner FH, Gaikwad T, Downe J, Aguilo-Ferretjans MM, Al-Moosawi L, Brownlee C, Wheeler GL. A Novel Ca 2+ Signaling Pathway Coordinates Environmental Phosphorus Sensing and Nitrogen Metabolism in Marine Diatoms. Curr Biol 2020; 31:978-989.e4. [PMID: 33373640 DOI: 10.1016/j.cub.2020.11.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/26/2020] [Accepted: 11/30/2020] [Indexed: 10/22/2022]
Abstract
Diatoms are a diverse and globally important phytoplankton group, responsible for an estimated 20% of carbon fixation on Earth. They frequently form spatially extensive phytoplankton blooms, responding rapidly to increased availability of nutrients, including phosphorus (P) and nitrogen (N). Although it is well established that diatoms are common first responders to nutrient influxes in aquatic ecosystems, little is known of the sensory mechanisms that they employ for nutrient perception. Here, we show that P-limited diatoms use a Ca2+-dependent signaling pathway, not previously described in eukaryotes, to sense and respond to the critical macronutrient P. We demonstrate that P-Ca2+ signaling is conserved between a representative pennate (Phaeodactylum tricornutum) and centric (Thalassiosira pseudonana) diatom. Moreover, this pathway is ecologically relevant, being sensitive to sub-micromolar concentrations of inorganic phosphate and a range of environmentally abundant P forms. Notably, we show that diatom recovery from P limitation requires rapid and substantial increases in N assimilation and demonstrate that this process is dependent on P-Ca2+ signaling. P-Ca2+ signaling thus governs the capacity of diatoms to rapidly sense and respond to P resupply, mediating fundamental cross-talk between the vital nutrients P and N and maximizing diatom resource competition in regions of pulsed nutrient supply.
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Affiliation(s)
- Katherine E Helliwell
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
| | - Ellen L Harrison
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | | | - Andrew P Rees
- Plymouth Marine Laboratory, Plymouth, Devon PL1 3DH, UK
| | - Friedrich H Kleiner
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Trupti Gaikwad
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Joshua Downe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | | | | | - Colin Brownlee
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; School of Ocean and Earth Science, University of Southampton, Southampton SO14 3ZH, UK
| | - Glen L Wheeler
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
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43
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Cheng L, Cai Z, Zhao J, Wang F, Lu M, Deng L, Cui W. Black phosphorus-based 2D materials for bone therapy. Bioact Mater 2020; 5:1026-1043. [PMID: 32695934 PMCID: PMC7355388 DOI: 10.1016/j.bioactmat.2020.06.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/22/2020] [Accepted: 06/08/2020] [Indexed: 02/08/2023] Open
Abstract
Since their discovery, Black Phosphorus (BP)-based nanomaterials have received extensive attentions in the fields of electromechanics, optics and biomedicine, due to their remarkable properties and excellent biocompatibility. The most essential feature of BP is that it is composed of a single phosphorus element, which has a high degree of homology with the inorganic components of natural bone, therefore it has a full advantage in the treatment of bone defects. This review will first introduce the source, physicochemical properties, and degradation products of BP, then introduce the remodeling process of bone, and comprehensively summarize the progress of BP-based materials for bone therapy in the form of hydrogels, polymer membranes, microspheres, and three-dimensional (3D) printed scaffolds. Finally, we discuss the challenges and prospects of BP-based implant materials in bone immune regulation and outlook the future clinical application.
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Affiliation(s)
- Liang Cheng
- Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, PR China
| | - Zhengwei Cai
- Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, PR China
- Jiaxing Key Laboratory of Basic Research and Clinical Translation on Orthopedic Biomaterials, Department of Orthopaedics, The Second Affiliated Hospital of Jiaxing University, 1518 North Huancheng Road, Jiaxing 314000, PR China
| | - Jingwen Zhao
- Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, PR China
| | - Fei Wang
- Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, PR China
| | - Min Lu
- Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, PR China
| | - Lianfu Deng
- Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, PR China
| | - Wenguo Cui
- Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, PR China
- Jiaxing Key Laboratory of Basic Research and Clinical Translation on Orthopedic Biomaterials, Department of Orthopaedics, The Second Affiliated Hospital of Jiaxing University, 1518 North Huancheng Road, Jiaxing 314000, PR China
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44
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Tuttle MJ, Buchan A. Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence. Environ Microbiol 2020; 22:4919-4933. [PMID: 32935433 DOI: 10.1111/1462-2920.15233] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/19/2020] [Accepted: 08/23/2020] [Indexed: 12/12/2022]
Abstract
In the oceans, viruses that infect bacteria (phages) influence a variety of microbially mediated processes that drive global biogeochemical cycles. The nature of their influence is dependent upon infection mode, be it lytic or lysogenic. Temperate phages are predicted to be prevalent in marine systems where they are expected to execute both types of infection modes. Understanding the range and outcomes of temperate phage-host interactions is fundamental for evaluating their ecological impact. Here, we (i) review phage-mediated rewiring of host metabolism, with a focus on marine systems, (ii) consider the range and nature of temperate phage-host interactions, and (iii) draw on studies of cultivated model systems to examine the consequences of lysogeny among several dominant marine bacterial lineages. We also readdress the prevalence of lysogeny among marine bacteria by probing a collection of 1239 publicly available bacterial genomes, representing cultured and uncultivated strains, for evidence of complete prophages. Our conservative analysis, anticipated to underestimate true prevalence, predicts 18% of the genomes examined contain at least one prophage, the majority (97%) were found within genomes of cultured isolates. These results highlight the need for cultivation of additional model systems to better capture the diversity of temperate phage-host interactions in the oceans.
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Affiliation(s)
- Matthew J Tuttle
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
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45
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Zhang T, Qin M, Wei C, Li D, Lu X, Zhang L. Suspended particles phoD alkaline phosphatase gene diversity in large shallow eutrophic Lake Taihu. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 728:138615. [PMID: 32348945 DOI: 10.1016/j.scitotenv.2020.138615] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/08/2020] [Accepted: 04/08/2020] [Indexed: 06/11/2023]
Abstract
The bacterial phoD gene encodes alkaline phosphatase plays an important role in the release of bioavailable inorganic phosphorus (P) from organic P in environmental systems. However, phoD gene diversity in suspended particles in shallow freshwater lakes is poorly understood. In this study, we explored the potential relationship between environmental factors and phoD phosphatase gene in suspended particles in different ecosystem types (lake zones) in Lake Taihu, a large shallow eutrophic lake in China. Quantitative PCR and high-throughput sequencing were used to analyze phoD gene abundance and the phoD-harboring bacterial community composition. Our results indicate that the distribution of phoD gene abundance in suspended particles had a high spatiotemporal heterogeneity. The phoD gene abundance in each lake zone decreased significantly from June to September. The dominant phoD-harboring phylum in all samples was Actinobacteria, followed by Proteobacteria, Cyanobacteria and Gemmatimonadetes. The first predominant phoD-harboring genera varied among samples, but most of them belonged to phylum Actinobacteria. Driven by different environmental factors, the phoD-harboring bacterial community structure varied with sampling month and ecosystem type. Nitrate and ammonia nitrogen were the main environmental drivers of phoD-harboring bacterial community in suspended particles in the river mouth zone, while water pH and dissolved oxygen were important factors for the algae-dominated, macrophyte-dominated and central lake zones.
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Affiliation(s)
- Tingxi Zhang
- Nanjing Normal University, School of Environment, Wenyuan Road 1, Nanjing 210023, China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing 210023, China; Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing 210023, China.
| | - Mengyao Qin
- Nanjing Normal University, School of Environment, Wenyuan Road 1, Nanjing 210023, China
| | - Chao Wei
- Nanjing Normal University, School of Environment, Wenyuan Road 1, Nanjing 210023, China
| | - Defang Li
- Nanjing Normal University, School of Environment, Wenyuan Road 1, Nanjing 210023, China
| | - Xiaoran Lu
- Nanjing Normal University, School of Environment, Wenyuan Road 1, Nanjing 210023, China
| | - Limin Zhang
- Nanjing Normal University, School of Environment, Wenyuan Road 1, Nanjing 210023, China
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46
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Surviving Starvation: Proteomic and Lipidomic Profiling of Nutrient Deprivation in the Smallest Known Free-Living Eukaryote. Metabolites 2020; 10:metabo10070273. [PMID: 32635273 PMCID: PMC7407893 DOI: 10.3390/metabo10070273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/17/2020] [Accepted: 06/27/2020] [Indexed: 11/16/2022] Open
Abstract
Marine phytoplankton, comprising cyanobacteria, micro- and pico-algae are key to photosynthesis, oxygen production and carbon assimilation on Earth. The unicellular green picoalga Ostreococcus tauri holds a key position at the base of the green lineage of plants, which makes it an interesting model organism. O. tauri has adapted to survive in low levels of nitrogen and phosphorus in the open ocean and also during rapid changes in the levels of these nutrients in coastal waters. In this study, we have employed untargeted proteomic and lipidomic strategies to investigate the molecular responses of O. tauri to low-nitrogen and low-phosphorus environments. In the absence of external nitrogen, there was an elevation in the expression of ammonia and urea transporter proteins together with an accumulation of triglycerides. In phosphate-limiting conditions, the expression levels of phosphokinases and phosphate transporters were increased, indicating an attempt to maximise scavenging opportunities as opposed to energy conservation conditions. The production of betaine lipids was also elevated, highlighting a shift away from phospholipid metabolism. This finding was supported by the putative identification of betaine synthase in O. tauri. This work offers additional perspectives on the complex strategies that underpin the adaptive processes of the smallest known free-living eukaryote to alterations in environmental conditions.
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47
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Tang W, Cerdán-García E, Berthelot H, Polyviou D, Wang S, Baylay A, Whitby H, Planquette H, Mowlem M, Robidart J, Cassar N. New insights into the distributions of nitrogen fixation and diazotrophs revealed by high-resolution sensing and sampling methods. ISME JOURNAL 2020; 14:2514-2526. [PMID: 32581316 DOI: 10.1038/s41396-020-0703-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 01/26/2023]
Abstract
Nitrogen availability limits marine productivity across large ocean regions. Diazotrophs can supply new nitrogen to the marine environment via nitrogen (N2) fixation, relieving nitrogen limitation. The distributions of diazotrophs and N2 fixation have been hypothesized to be generally controlled by temperature, phosphorus, and iron availability in the global ocean. However, even in the North Atlantic where most research on diazotrophs and N2 fixation has taken place, environmental controls remain contentious. Here we measure diazotroph composition, abundance, and activity at high resolution using newly developed underway sampling and sensing techniques. We capture a diazotrophic community shift from Trichodesmium to UCYN-A between the oligotrophic, warm (25-29 °C) Sargasso Sea and relatively nutrient-enriched, cold (13-24 °C) subpolar and eastern American coastal waters. Meanwhile, N2 fixation rates measured in this study are among the highest ever recorded globally and show significant increase with phosphorus availability across the transition from the Gulf Stream into subpolar and coastal waters despite colder temperatures and higher nitrate concentrations. Transcriptional patterns in both Trichodesmium and UCYN-A indicate phosphorus stress in the subtropical gyre. Over this iron-replete transect spanning the western North Atlantic, our results suggest that temperature is the major factor controlling the diazotrophic community structure while phosphorous drives N2 fixation rates. Overall, the occurrence of record-high UCYN-A abundance and peak N2 fixation rates in the cold coastal region where nitrate concentrations are highest (~200 nM) challenges current paradigms on what drives the distribution of diazotrophs and N2 fixation.
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Affiliation(s)
- Weiyi Tang
- Division of Earth and Ocean Sciences, Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA.,Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - Elena Cerdán-García
- Department of Ocean and Earth Sciences, National Oceanography Centre, University of Southampton, European Way, SO14 3ZH, Southampton, UK
| | - Hugo Berthelot
- CNRS, Univ Brest, IRD, Ifremer, LEMAR, F-29280 Plouzané, France
| | - Despo Polyviou
- Department of Ocean and Earth Sciences, National Oceanography Centre, University of Southampton, European Way, SO14 3ZH, Southampton, UK
| | - Seaver Wang
- Division of Earth and Ocean Sciences, Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | - Alison Baylay
- Department of Ocean and Earth Sciences, National Oceanography Centre, University of Southampton, European Way, SO14 3ZH, Southampton, UK
| | - Hannah Whitby
- CNRS, Univ Brest, IRD, Ifremer, LEMAR, F-29280 Plouzané, France.,Department of Earth, Ocean and Ecological Sciences, School of Environmental Sciences, University of Liverpool, Liverpool, L69 3GP, UK
| | | | - Matthew Mowlem
- Ocean Technology and Engineering Group, National Oceanography Centre, European Way, SO14 3ZH, Southampton, UK
| | - Julie Robidart
- Ocean Technology and Engineering Group, National Oceanography Centre, European Way, SO14 3ZH, Southampton, UK.
| | - Nicolas Cassar
- Division of Earth and Ocean Sciences, Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA. .,CNRS, Univ Brest, IRD, Ifremer, LEMAR, F-29280 Plouzané, France.
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48
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Zhang X, Ward BB, Sigman DM. Global Nitrogen Cycle: Critical Enzymes, Organisms, and Processes for Nitrogen Budgets and Dynamics. Chem Rev 2020; 120:5308-5351. [DOI: 10.1021/acs.chemrev.9b00613] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Bess B. Ward
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Daniel M. Sigman
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
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49
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Xiao M, Hamilton DP, Chuang A, Burford MA. Intra-population strain variation in phosphorus storage strategies of the freshwater cyanobacterium Raphidiopsis raciborskii. FEMS Microbiol Ecol 2020; 96:5837077. [DOI: 10.1093/femsec/fiaa092] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/12/2020] [Indexed: 01/10/2023] Open
Abstract
ABSTRACT
Several cyanobacteria, including diazotrophic Raphidiopsis raciborskii, can form harmful blooms when dissolved inorganic phosphorus concentrations are very low. We hypothesized that R. raciborskii strains would vary in phosphorus (P) allocations to cell growth and storage, providing resilience of populations to continuously low or variable P supplies. We tested this hypothesis using six toxic strains (producing cylindrospermopsins) isolated from a field population using batch monocultures with and without P and dissolved inorganic nitrogen (DIN). Treatments replete with DIN, irrespective of P addition, had similar exponential growth rates for individual strains. P storage capacity varied 4-fold among strains and was significantly higher in DIN-free treatments than in replete treatments. P was stored by all R. raciborskii strains, in preference to allocation to increase growth rates. P stores decreased with increased growth rate across strains, but weeere not related to the time to P starvation in P-free treatments. The storage capacity of R. raciborskii, combined with strategies to efficiently uptake P, means that P controls may not control R. raciborskii populations in the short term. Intra-population strain variation in P storage capacity will need to be reflected in process-based models to predict blooms of R. raciborskii and other cyanobacteria adapted to low-P conditions.
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Affiliation(s)
- Man Xiao
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - David P Hamilton
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - Ann Chuang
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - Michele A Burford
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
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50
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Moulana A, Anderson RE, Fortunato CS, Huber JA. Selection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus Sulfurovum in Geographically Distinct Deep-Sea Hydrothermal Vents. mSystems 2020; 5:e00673-19. [PMID: 32291353 PMCID: PMC7159903 DOI: 10.1128/msystems.00673-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/30/2020] [Indexed: 12/20/2022] Open
Abstract
Microbial genomes have highly variable gene content, and the evolutionary history of microbial populations is shaped by gene gain and loss mediated by horizontal gene transfer and selection. To evaluate the influence of selection on gene content variation in hydrothermal vent microbial populations, we examined 22 metagenome-assembled genomes (MAGs) (70 to 97% complete) from the ubiquitous vent Epsilonbacteraeota genus Sulfurovum that were recovered from two deep-sea hydrothermal vent regions, Axial Seamount in the northeastern Pacific Ocean (13 MAGs) and the Mid-Cayman Rise in the Caribbean Sea (9 MAGs). Genes involved in housekeeping functions were highly conserved across Sulfurovum lineages. However, genes involved in environment-specific functions, and in particular phosphate regulation, were found mostly in Sulfurovum genomes from the Mid-Cayman Rise in the low-phosphate Atlantic Ocean environment, suggesting that nutrient limitation is an important selective pressure for these bacteria. Furthermore, genes that were rare within the pangenome were more likely to undergo positive selection than genes that were highly conserved in the pangenome, and they also appeared to have experienced gene-specific sweeps. Our results suggest that selection is a significant driver of gene gain and loss for dominant microbial lineages in hydrothermal vents and highlight the importance of factors like nutrient limitation in driving microbial adaptation and evolution.IMPORTANCE Microbes can alter their gene content through the gain and loss of genes. However, there is some debate as to whether natural selection or neutral processes play a stronger role in molding the gene content of microbial genomes. In this study, we examined variation in gene content for the Epsilonbacteraeota genus Sulfurovum from deep-sea hydrothermal vents, which are dynamic habitats known for extensive horizontal gene transfer within microbial populations. Our results show that natural selection is a strong driver of Sulfurovum gene content and that nutrient limitation in particular has shaped the Sulfurovum genome, leading to differences in gene content between ocean basins. Our results also suggest that recently acquired genes undergo stronger selection than genes that were acquired in the more distant past. Overall, our results highlight the importance of natural selection in driving the evolution of microbial populations in these dynamic habitats.
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Affiliation(s)
- Alief Moulana
- Biology Department, Carleton College, Northfield, Minnesota, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Rika E Anderson
- Biology Department, Carleton College, Northfield, Minnesota, USA
| | | | - Julie A Huber
- Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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