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Shi R, Han T, Qi Z, Huang H. Responses of attached bacterial communities to blooms of the swimming shelled pteropod Creseis acicula in Daya Bay, southern China. FEMS Microbiol Ecol 2024; 100:fiae034. [PMID: 38521983 DOI: 10.1093/femsec/fiae034] [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: 10/18/2023] [Revised: 02/29/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024] Open
Abstract
The shelled pteropod Creseis acicula is a marine pelagic shellfish widely distributed from temperate to tropical seas around the world. From June to July 2020, a C. acicula bloom first happened in the Daya Bay, southern China, and its density reached the highest value (5600 ind. m-3) ever recorded around the world. However, few studies have investigated the responses of bacterial communities to the C. acicula bloom. In the present study, we examined the community profiles of three communities of bacteria including the free-living and particle-attached bacteria in the blooming and reference waters, and bacteria attached to the whole body and shell of C. acicula using a high-throughput sequencing method. The results indicated that the C. acicula bloom had a greater impact on particle-attached bacteria than free-living bacteria. Among the bloom-sensitive particle-attached bacteria, the predominant bacterial phyla were Pseudomonadota, Bacteroidota and Verrucomicrobiota in the blooming areas, whereas they were Actinomycetota and Planctomycetota in the reference areas. Specifically, fecal bacteria Haloferula and Halioglobus spp. were significantly enriched in the blooming waters and accumulated on C. acicula shells. Conversely, the significantly lower relative abundance of Nocardioides sp. in the blooming area and accumulated on the whole body of C. acicula indicated their attachment to particles consumed by C. acicula. Overall, our results suggested that the C. acicula bloom influenced marine bacteria, particularly particle-attached bacteria, by increasing (e.g. providing shells and feces) or decreasing (e.g. filter-feeding the suspended particles) the abundance of available substances.
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Affiliation(s)
- Rongjun Shi
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs of China, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China
| | - Tingting Han
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs of China, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China
| | - Zhanhui Qi
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs of China, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China
| | - Honghui Huang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs of China, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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2
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Stevens BLF, Peacock EE, Crockford ET, Shalapyonok A, Neubert MG, Sosik HM. Distinct responses to warming within picoplankton communities across an environmental gradient. GLOBAL CHANGE BIOLOGY 2024; 30:e17316. [PMID: 38767231 DOI: 10.1111/gcb.17316] [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: 12/08/2023] [Revised: 04/01/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024]
Abstract
Picophytoplankton are a ubiquitous component of marine plankton communities and are expected to be favored by global increases in seawater temperature and stratification associated with climate change. Eukaryotic and prokaryotic picophytoplankton have distinct ecology, and global models predict that the two groups will respond differently to future climate scenarios. At a nearshore observatory on the Northeast US Shelf, however, decades of year-round monitoring have shown these two groups to be highly synchronized in their responses to environmental variability. To reconcile the differences between regional and global predictions for picophytoplankton dynamics, we here investigate the picophytoplankton community across the continental shelf gradient from the nearshore observatory to the continental slope. We analyze flow cytometry data from 22 research cruises, comparing the response of picoeukaryote and Synechococcus communities to environmental variability across time and space. We find that the mechanisms controlling picophytoplankton abundance differ across taxa, season, and distance from shore. Like the prokaryote, Synechococcus, picoeukaryote division rates are limited nearshore by low temperatures in winter and spring, and higher temperatures offshore lead to an earlier spring bloom. Unlike Synechococcus, picoeukaryote concentration in summer decreases dramatically in offshore surface waters and exhibits deeper subsurface maxima. The offshore picoeukaryote community appears to be nutrient limited in the summer and subject to much greater loss rates than Synechococcus. This work both produces and demonstrates the necessity of taxon- and site-specific knowledge for accurately predicting the responses of picophytoplankton to ongoing environmental change.
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Affiliation(s)
- Bethany L F Stevens
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Emily E Peacock
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - E Taylor Crockford
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Alexi Shalapyonok
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Michael G Neubert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Heidi M Sosik
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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3
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Chan YF, Chung CC, Gong GC, Lin IJ, Hsu CW. Seasonal Patterns of Picocyanobacterial Community Structure in the Kuroshio Current. BIOLOGY 2023; 12:1424. [PMID: 37998023 PMCID: PMC10669657 DOI: 10.3390/biology12111424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/03/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023]
Abstract
The nutrient-scarce, warm, and high-salinity Kuroshio current has a profound impact on both the marine ecology of the northwestern Pacific Ocean and the global climate. This study aims to reveal the seasonal dynamics of picoplankton in the subtropical Kuroshio current. Our results showed that one of the picocyanobacteria, Synechococcus, mainly distributed in the surface water layer regardless of seasonal changes, and the cell abundance ranged from 104 to 105 cells mL-1. In contrast, the maximum concentration of the other picocyanobacteria, Prochlorococcus, was maintained at more than 105 cells mL-1 throughout the year. In the summer and the autumn, Prochlorococcus were mainly concentrated at the water layer near the bottom of the euphotic zone. They were evenly distributed in the euphotic zone in the spring and winter. The stirring effect caused by the monsoon determined their distribution in the water column. In addition, the results of 16S rRNA gene diversity analysis showed that the seasonal changes in the relative abundance of Synechococcus and Prochlorococcus in the surface water of each station accounted for 20 to 40% of the total reads. The clade II of Synechococcus and the High-light II of Prochlorococcus were the dominant strains in the waters all year round. Regarding other picoplankton, Proteobacteria and Actinobacteria occupied 45% and 10% of the total picoplankton in the four seasons. These data should be helpful for elucidating the impacts of global climate changes on marine ecology and biogeochemical cycles in the Western Boundary Currents in the future.
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Affiliation(s)
- Ya-Fan Chan
- Department of Microbiology, Soochow University, Taipei 11101, Taiwan;
| | - Chih-Ching Chung
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung 20224, Taiwan; (G.-C.G.); (I.-J.L.); (C.-W.H.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung 20224, Taiwan
| | - Gwo-Ching Gong
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung 20224, Taiwan; (G.-C.G.); (I.-J.L.); (C.-W.H.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung 20224, Taiwan
| | - I-Jung Lin
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung 20224, Taiwan; (G.-C.G.); (I.-J.L.); (C.-W.H.)
| | - Ching-Wei Hsu
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung 20224, Taiwan; (G.-C.G.); (I.-J.L.); (C.-W.H.)
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4
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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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5
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Abstract
Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome data set of the Ocean Sampling Day (June 21st, 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus, and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study reveals several important characteristics and specificities of the coastal communities of Synechococcus worldwide. IMPORTANCE Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent years, the use of global metagenomics data sets has greatly improved our knowledge of "who is where" by describing the distribution of Synechococcus clades or ecotypes in the open ocean. However, little is known about the global distribution of Synechococcus ecotypes in coastal areas, where Synechococcus is often the dominant phytoplanktonic organism. Here, we leverage the global Ocean Sampling Day metagenomics data set to describe Synechococcus community composition in coastal areas worldwide, revealing striking community shifts, in particular along the coasts of Europe. As temperature appears as an important driver of the community composition, we also characterize the thermal preferenda of 8 Synechococcus strains, bringing new insights into the adaptation to temperature of the dominant Synechococcus clades.
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Wang F, Wei Y, Zhang G, Zhang L, Sun J. Picophytoplankton in the West Pacific Ocean: A Snapshot. Front Microbiol 2022; 13:811227. [PMID: 35391721 PMCID: PMC8981306 DOI: 10.3389/fmicb.2022.811227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/10/2022] [Indexed: 12/02/2022] Open
Abstract
Marine picophytoplankton have crucial ecological value and make an important contribution to marine primary productivity. While biomass of phytoplankton in general is projected to decline as a result of global warming, picophytoplankton will likely dominate in the future oceans due to their growth advantages in an oligotrophic environment. To better understand the biography of picophytoplankton, we undertook a comprehensive study of the distribution patterns of picophytoplankton, carbon biomass, and Chl a concentrations, etc. based on large-scale sampling in the tropical Western Pacific Ocean. In terms of cellular abundance, Prochlorococcus was the most abundant group (averaging [1.03 ± 0.40] × 104 cells/mL), followed by Synechococcus (averaging [1.31 ± 1.22] × 103 cells/mL) and then picoeucaryote (averaging [4.83 ± 2.84] × 102 cells/mL). The picophytoplankton size-fractionated chlorophyll a (Pico-Chl a) accounted for about 30% of the total Chl a, with Prochlorococcus and picoeukaryotes contributing 41 and 35%, respectively, of the Pico-Chl a-normalized carbon biomass, indicating the ecological importance of picophytoplankton as the primary producers. In terms of biogeographic distribution, the picophytoplankton communities exhibited contrasting patterns. The surface distribution of Prochlorococcus and Synechococcus was concentrated in the low latitude of the 142°E section, while picoeucaryote was more abundant near the 130°E and equator sections. Synechococcus was higher in the shallow layer at 25 m, and it was extremely tolerant of high-light irradiation, while Prochlorococcus and picoeucaryote were distributed in the deep Chlorophyll maximum layer (DCM) (about 100 m). From the carbon-to-Chlorophyll a ratios, which was derived from Prochlorococcus and picoeucaryote population groups, we found that the ratio varied widely, from 0.19 to 75.56, and was highest at the depth of 200 m. Of these, Prochlorococcus had an important contribution. The correlation analysis of environmental factors showed that Prochlorococcus, Synechococcus, and picoeucaryote were negatively correlated with nutrient concentration. We concluded that Prochlorococcus group was dominant in the WPO, both in abundance and biomass, and the various abiotic factors such as temperature, salinity, and nutrient concentrations were closely correlated with the spatial variation in the picophytoplankton community. These findings aid our understanding of how contrasting environmental conditions influence picophytoplankton community and the importance of picophytoplankton in contributing the carbon pool in the oligotrophic ocean.
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Affiliation(s)
- Feng Wang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,Key Laboratory of Ocean Circulation and Waves, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yuqiu Wei
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Guicheng Zhang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Linlin Zhang
- Key Laboratory of Ocean Circulation and Waves, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Jun Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, China.,College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, China.,Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
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7
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Spatiotemporal Variation in Phytoplankton and Physiochemical Factors during Phaeocystis globosa Red-Tide Blooms in the Northern Beibu Gulf of China. WATER 2022. [DOI: 10.3390/w14071099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Phaeocystis globosa blooms frequently in the Beibu Gulf of China. This species has a distinct life cycle that includes colonies and solitary cells. Colonies are formed during a bloom, while solitary cells are produced between blooms. Information about the abundance of solitary cells and other picophytoplankton in the northern Beibu Gulf is limited. To elucidate phytoplankton variation trends during periods of frequent P. globosa blooms and to determine the main physiochemical factors affecting phytoplankton distribution, four cruises were conducted between November 2018 and April 2019. Seawater was collected, and water temperature, salinity, and nutrient concentrations were simultaneously determined. Redundancy analysis was performed to understand the relationship between environmental factors and phytoplankton assemblages. Seven phytoplankton clusters were present during the cruises. Picophytoplankton abundance (including Synechococcus and Picoeukaryote groups I and II) dominated during the four cruises. Synechococcus abundance was restricted by the low temperatures in winter, decreasing from November to February and increasing in April. Picoeukaryote I abundance was almost unaffected by low temperatures and was mainly affected by nutrient concentration. P. globosa solitary cell abundance increased from November to January and decreased in February and April, and phosphorus was the key factor affecting P. globosa blooms. This is the first study to reveal the abundance and distribution of P. globosa solitary cells in this area.
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8
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Shuwang X, Sun J, Wei Y, Guo C. Size-Fractionated Filtration Combined with Molecular Methods Reveals the Size and Diversity of Picophytoplankton. BIOLOGY 2021; 10:biology10121280. [PMID: 34943195 PMCID: PMC8698306 DOI: 10.3390/biology10121280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/14/2021] [Accepted: 11/27/2021] [Indexed: 06/14/2023]
Abstract
In this study, flow cytometry (FCM) and size-fractionated filtration, together with high-throughput molecular sequencing methods (SM), were used to investigate picophytoplankton. A particle separation filter and a higher-throughput sequencing method were used to evaluate the composition of a euphotic zone of picophytoplankton-especially picoeukaryotic phytoplankton-in the Western Pacific, and the results of flow cytometry, which is a classic way to detect picophytoplankton, were used as a standard to evaluate the reliability of the results of the SMs. Within a water column of 200 m, six water depths (5, 25, 50, 113 (DCM), 150, and 200 m) were established. In order to further study the particle size spectra of the picophytoplankton, size-fractionated filtration was used to separate water samples from each water depth into three particle size ranges: 0.2-0.6, 0.6-1.2, and 1.2-2 μm. A total of 36 (6 × 3 × 2) samples were obtained through PCR amplification of the 18S rRNA V4 hypervariable region and 16S rRNA, which were biased toward phytoplankton plastids, and then high-throughput sequencing was performed. The estimation of the picophytoplankton diameter relied on forward scattering (FSC) through FCM. The estimation of the vertical distribution and diameter of the picophytoplankton using the SM was consistent with the results with FCM; thus, we believe that the estimation of picophytoplankton composition with the SM has value as a reference, although the size-fractionated filtration seemed to cause some deviations. In addition to Prochlorococcus and Synechococcus, the SM was used to evaluate the composition of picoeukaryotic phytoplankton, which mainly included Prymnesiophycea (Haptophyta) (38.15%), Cryptophyceae (Cryptophyta) (22.36%), Dictyochophyceae (Chrysophyta) (12.22%), and Mamiellophyceae (Chlorophyta) (3.31%). In addition, the SM also detected Dinophyceae (Dinoflagellata) (11.69%) sequences and a small number of Bacillariophyceae (Diatom) (1.64%) sequences, which are generally considered to have large particle sizes. The results of the SM also showed that the picoeukaryotic phytoplankton were not evenly distributed in the euphotic layer, and the vertical distributions of the different picoeukaryotic phytoplankton were different. An analysis of correlations with environmental factors showed that temperature was the main environmental factor controlling the vertical distribution of picophytoplankton.
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Affiliation(s)
- Xinze Shuwang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (X.S.); (C.G.)
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan 430074, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Yuqiu Wei
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China;
| | - Congcong Guo
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (X.S.); (C.G.)
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9
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Gao P, Du G, Zhao D, Wei Q, Zhang X, Qu L, Gong X. Influences of Seasonal Monsoons on the Taxonomic Composition and Diversity of Bacterial Community in the Eastern Tropical Indian Ocean. Front Microbiol 2021; 11:615221. [PMID: 33574800 PMCID: PMC7870504 DOI: 10.3389/fmicb.2020.615221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/22/2020] [Indexed: 01/03/2023] Open
Abstract
The Indian Ocean is characterized by its complex physical systems and strong seasonal monsoons. To better understand effects of seasonal monsoon-driven circulation on the bacterioplanktonic community structure in surface waters and the bacterial distribution response to vertical stratification, patterns of seasonal, and vertical distribution of bacterial communities in the Eastern Tropical Indian Ocean were investigated using 16S rRNA gene profiling. Water samples were collected during the Southwest monsoon (from June to August), the fall inter-monsoon (from October and November) and the Northeast monsoon (from December to January), respectively, onboard during three cruises from July 2016 to January 2018. Surface bacterioplankton communities in these three seasons and in the upper water (3-300 m with six depths) during the Northeast monsoon contained a diverse group of taxa, mainly Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, and Chloroflexi. Redundancy discriminant analysis (RDA) uncovered that temperature, salinity, and dissolved oxygen (DO) were crucial environmental parameters that affected the structure of bacterial community in overall surface samples. However, significant differences in the composition of the bacterial community are likely due to changes in concentrations of salinity during the fall inter-monsoon, while phosphate for both the Southwest monsoon and the Northeast monsoon. Pearson's analysis revealed that the seasonal variation rather than the vertical variation of environmental factors had a more significant impact on the composition of bacterial community. In addition, a clear seasonal pattern of bacterial co-occurrence showed that inter-taxa associations during the fall inter-monsoon were closer than during the Northeast monsoon and the Southwest monsoon. Overall, our results implied clear differences in the composition of bacterial community, with more pronounced seasonal variation compared to the vertical variation in response to environmental changes.
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Affiliation(s)
- Ping Gao
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), Qingdao, China
| | - Guangxun Du
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Duo Zhao
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qinsheng Wei
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Xuelei Zhang
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Lingyun Qu
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), Qingdao, China
| | - Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
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10
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Laurenceau R, Raho N, Forget M, Arellano AA, Chisholm SW. Frequency of mispackaging of Prochlorococcus DNA by cyanophage. THE ISME JOURNAL 2021; 15:129-140. [PMID: 32929209 PMCID: PMC7852597 DOI: 10.1038/s41396-020-00766-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/27/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023]
Abstract
Prochlorococcus cells are the numerically dominant phototrophs in the open ocean. Cyanophages that infect them are a notable fraction of the total viral population in the euphotic zone, and, as vehicles of horizontal gene transfer, appear to drive their evolution. Here we examine the propensity of three cyanophages-a podovirus, a siphovirus, and a myovirus-to mispackage host DNA in their capsids while infecting Prochlorococcus, the first step in phage-mediated horizontal gene transfer. We find the mispackaging frequencies are distinctly different among the three phages. Myoviruses mispackage host DNA at low and seemingly fixed frequencies, while podo- and siphoviruses vary in their mispackaging frequencies by orders of magnitude depending on growth light intensity. We link this difference to the concentration of intracellular reactive oxygen species and protein synthesis rates, both parameters increasing in response to higher light intensity. Based on our findings, we propose a model of mispackaging frequency determined by the imbalance between the production of capsids and the number of phage genome copies during infection: when protein synthesis rate increase to levels that the phage cannot regulate, they lead to an accumulation of empty capsids, in turn triggering more frequent host DNA mispackaging errors.
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Affiliation(s)
- Raphaël Laurenceau
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Nicolas Raho
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mathieu Forget
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institut de Biologie de l'Ecole Normale Supérieure, Département de Biologie, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Aldo A Arellano
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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11
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Liu S, Baetge N, Comstock J, Opalk K, Parsons R, Halewood E, English CJ, Giovannoni S, Bolaños LM, Nelson CE, Vergin K, Carlson CA. Stable Isotope Probing Identifies Bacterioplankton Lineages Capable of Utilizing Dissolved Organic Matter Across a Range of Bioavailability. Front Microbiol 2020; 11:580397. [PMID: 33117322 PMCID: PMC7575717 DOI: 10.3389/fmicb.2020.580397] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/03/2020] [Indexed: 01/04/2023] Open
Abstract
Bacterioplankton consume about half of the dissolved organic matter (DOM) produced by phytoplankton. DOM released from phytoplankton consists of a myriad of compounds that span a range of biological reactivity from labile to recalcitrant. Linking specific bacterioplankton lineages to the incorporation of DOM compounds into biomass is important to understand microbial niche partitioning. We conducted a series of DNA-stable isotope probing (SIP) experiments using 13C-labeled substrates of varying lability including amino acids, cyanobacteria lysate, and DOM from diatom and cyanobacteria isolates concentrated on solid phase extraction PPL columns (SPE-DOM). Amendments of substrates into Sargasso Sea bacterioplankton communities were conducted to explore microbial response and DNA-SIP was used to determine which lineages of Bacteria and Archaea were responsible for uptake and incorporation. Greater increases in bacterioplankton abundance and DOC removal were observed in incubations amended with cyanobacteria-derived lysate and amino acids compared to the SPE-DOM, suggesting that the latter retained proportionally more recalcitrant DOM compounds. DOM across a range of bioavailability was utilized by diverse prokaryotic taxa with copiotrophs becoming the most abundant 13C-incorporating taxa in the amino acid treatment and oligotrophs becoming the most abundant 13C-incorporating taxa in SPE-DOM treatments. The lineages that responded to SPE-DOM amendments were also prevalent in the mesopelagic of the Sargasso Sea, suggesting that PPL extraction of phytoplankton-derived DOM isolates compounds of ecological relevance to oligotrophic heterotrophic bacterioplankton. Our study indicates that DOM quality is an important factor controlling the diversity of the microbial community response, providing insights into the roles of different bacterioplankton in resource exploitation and efficiency of marine carbon cycling.
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Affiliation(s)
- Shuting Liu
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Nicholas Baetge
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Jacqueline Comstock
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Keri Opalk
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Rachel Parsons
- Bermuda Institute of Ocean Sciences, Saint George, Bermuda
| | - Elisa Halewood
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Chance J English
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Stephen Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Luis M Bolaños
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Hawai'i Sea Grant, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Kevin Vergin
- Microbial DNA Analytics, Phoenix, OR, United States
| | - Craig A Carlson
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
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12
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Hunter‐Cevera KR, Neubert MG, Olson RJ, Shalapyonok A, Solow AR, Sosik HM. Seasons of Syn. LIMNOLOGY AND OCEANOGRAPHY 2020; 65:1085-1102. [PMID: 32612307 PMCID: PMC7319482 DOI: 10.1002/lno.11374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/17/2019] [Accepted: 09/30/2019] [Indexed: 06/11/2023]
Abstract
Synechococcus is a widespread and important marine primary producer. Time series provide critical information for identifying and understanding the factors that determine abundance patterns. Here, we present the results of analysis of a 16-yr hourly time series of Synechococcus at the Martha's Vineyard Coastal Observatory, obtained with an automated, in situ flow cytometer. We focus on understanding seasonal abundance patterns by examining relationships between cell division rate, loss rate, cellular properties (e.g., cell volume, phycoerythrin fluorescence), and environmental variables (e.g., temperature, light). We find that the drivers of cell division vary with season; cells are temperature-limited in winter and spring, but light-limited in the fall. Losses to the population also vary with season. Our results lead to testable hypotheses about Synechococcus ecophysiology and a working framework for understanding the seasonal controls of Synechococcus cell abundance in a temperate coastal system.
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Affiliation(s)
- Kristen R. Hunter‐Cevera
- Josephine Bay Paul CenterMarine Biological LaboratoryWoods HoleMassachusetts
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Michael G. Neubert
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Robert J. Olson
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Alexi Shalapyonok
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Andrew R. Solow
- Marine Policy CenterWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Heidi M. Sosik
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
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13
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Al-Otaibi N, Huete-Stauffer TM, Calleja ML, Irigoien X, Morán XAG. Seasonal variability and vertical distribution of autotrophic and heterotrophic picoplankton in the Central Red Sea. PeerJ 2020; 8:e8612. [PMID: 32140305 PMCID: PMC7045887 DOI: 10.7717/peerj.8612] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/21/2020] [Indexed: 12/21/2022] Open
Abstract
The Red Sea is characterized by higher temperatures and salinities than other oligotrophic tropical regions. Here, we investigated the vertical and seasonal variations in the abundance and biomass of autotrophic and heterotrophic picoplankton. Using flow cytometry, we consistently observed five groups of autotrophs (Prochlorococcus, two populations of Synechococcus separated by their relative phycoerythrin fluorescence, low (LF-Syn) and high (HF-Syn), and two differently-sized groups of picoeukaryotes, small (Speuk) and large (Lpeuk)) and two groups of heterotrophic prokaryotes of low and high nucleic acid content (LNA and HNA, respectively). Samples were collected in 15 surveys conducted from 2015 to 2017 at a 700-m depth station in the central Red Sea. Surface temperature ranged from 24.6 to 32.6 °C with a constant value of 21.7 °C below 200 m. Integrated (0-100 m) chlorophyll a concentrations were low, with maximum values in fall (24.0 ± 2.7 mg m-2) and minima in spring and summer (16.1 ± 1.9 and 1.1 mg m-2, respectively). Picoplankton abundance was generally lower than in other tropical environments. Vertical distributions differed for each group, with Synechococcus and LNA prokaryotes more abundant at the surface while Prochlorococcus, picoeukaryotes and HNA prokaryotes peaked at the deep chlorophyll maximum, located between 40 and 76 m. Surface to 100 m depth-weighted abundances exhibited clear seasonal patterns for Prochlorococcus, with maxima in summer (7.83 × 104 cells mL-1, July 2015) and minima in winter (1.39 × 104 cells mL-1, January 2015). LF-Syn (0.32 - 2.70 × 104 cells mL-1 ), HF-Syn (1.11 - 3.20 × 104 cells mL-1) and Speuk (0.99 - 4.81 × 102 cells mL-1) showed an inverse pattern to Prochlorococcus, while Lpeuk (0.16 - 7.05 × 104 cells mL-1) peaked in fall. Synechococcus unexpectedly outnumbered Prochlorococcus in winter and at the end of fall. The seasonality of heterotrophic prokaryotes (2.29 - 4.21×105 cells mL-1 ) was less noticeable than autotrophic picoplankton. The contribution of HNA cells was generally low in the upper layers, ranging from 36% in late spring and early summer to ca. 50% in winter and fall. Autotrophs dominated integrated picoplankton biomass in the upper 100 m, with 1.4-fold higher values in summer than in winter (mean 387 and 272 mg C m-2, respectively). However, when the whole water column was considered, the biomass of heterotrophic prokaryotes exceeded that of autotrophic picoplankton with an average of 411 mg C m-2. Despite being located in tropical waters, our results show that the picoplankton community seasonal differences in the central Red Sea are not fundamentally different from higher latitude regions.
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Affiliation(s)
- Najwa Al-Otaibi
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Tamara M Huete-Stauffer
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maria Ll Calleja
- Department of Climate Geochemistry, Max Planck Institute for Chemistry (MPIC), Mainz, Germany
| | - Xabier Irigoien
- AZTI - Marine Research, Pasaia, Spain.,Basque Foundation for Science, IKERBASQUE, Bilbao, Spain
| | - Xosé Anxelu G Morán
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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14
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Heterotroph Interactions Alter Prochlorococcus Transcriptome Dynamics during Extended Periods of Darkness. mSystems 2018; 3:mSystems00040-18. [PMID: 29854954 PMCID: PMC5974335 DOI: 10.1128/msystems.00040-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/01/2018] [Indexed: 12/13/2022] Open
Abstract
Microbes evolve within complex ecological communities where biotic interactions impact both individual cells and the environment as a whole. Here we examine how cellular regulation in the marine cyanobacterium Prochlorococcus is influenced by a heterotrophic bacterium, Alteromonas macleodii, under different light conditions. We monitored the transcriptome of Prochlorococcus, grown either alone or in coculture, across a diel light:dark cycle and under the stress of extended darkness-a condition that cells would experience when mixed below the ocean's euphotic zone. More Prochlorococcus transcripts exhibited 24-h periodic oscillations in coculture than in pure culture, both over the normal diel cycle and after the shift to extended darkness. This demonstrates that biotic interactions, and not just light, can affect timing mechanisms in Prochlorococcus, which lacks a self-sustaining circadian oscillator. The transcriptomes of replicate pure cultures of Prochlorococcus lost their synchrony within 5 h of extended darkness and reflected changes in stress responses and metabolic functions consistent with growth cessation. In contrast, when grown with Alteromonas, replicate Prochlorococcus transcriptomes tracked each other for at least 13 h in the dark and showed signs of continued biosynthetic and metabolic activity. The transcriptome patterns suggest that the heterotroph may be providing energy or essential biosynthetic substrates to Prochlorococcus in the form of organic compounds, sustaining this autotroph when it is deprived of solar energy. Our findings reveal conditions where mixotrophic metabolism may benefit marine cyanobacteria and highlight new impacts of community interactions on basic Prochlorococcus cellular processes. IMPORTANCEProchlorococcus is the most abundant photosynthetic organism on the planet. These cells play a central role in the physiology of surrounding heterotrophs by supplying them with fixed organic carbon. It is becoming increasingly clear, however, that interactions with heterotrophs can affect autotrophs as well. Here we show that such interactions have a marked impact on the response of Prochlorococcus to the stress of extended periods of darkness, as reflected in transcriptional dynamics. These data suggest that diel transcriptional rhythms within Prochlorococcus, which are generally considered to be strictly under the control of light quantity, quality, and timing, can also be influenced by biotic interactions. Together, these findings provide new insights into the importance of microbial interactions on Prochlorococcus physiology and reveal conditions where heterotroph-derived compounds may support autotrophs-contrary to the canonical autotroph-to-heterotroph trophic paradigm.
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15
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Delmont TO, Eren AM. Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PeerJ 2018; 6:e4320. [PMID: 29423345 PMCID: PMC5804319 DOI: 10.7717/peerj.4320] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/13/2018] [Indexed: 12/13/2022] Open
Abstract
Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations of the relative distribution of microbial genomes and individual genes across environments through read recruitment analyses. Combining these complementary approaches can yield unique insights into the functional basis of microbial niche partitioning and fitness, however, advanced software solutions are lacking. Here we present an integrated analysis and visualization strategy that provides an interactive and reproducible framework to generate pangenomes and to study them in conjunction with metagenomes. To investigate its utility, we applied this strategy to a Prochlorococcus pangenome in the context of a large-scale marine metagenomic survey. The resulting Prochlorococcus metapangenome revealed remarkable differential abundance patterns between very closely related isolates that belonged to the same phylogenetic cluster and that differed by only a small number of gene clusters in the pangenome. While the relationships between these genomes based on gene clusters correlated with their environmental distribution patterns, phylogenetic analyses using marker genes or concatenated single-copy core genes did not recapitulate these patterns. The metapangenome also revealed a small set of core genes that mostly occurred in hypervariable genomic islands of the Prochlorococcus populations, which systematically lacked read recruitment from surface ocean metagenomes. Notably, these core gene clusters were all linked to sugar metabolism, suggesting potential benefits to Prochlorococcus from a high sequence diversity of sugar metabolism genes. The rapidly growing number of microbial genomes and increasing availability of environmental metagenomes provide new opportunities to investigate the functioning and the ecology of microbial populations, and metapangenomes can provide unique insights for any taxon and biome for which genomic and sufficiently deep metagenomic data are available.
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Affiliation(s)
- Tom O. Delmont
- Department of Medicine, University of Chicago, Chicago, IL, United States of America
| | - A. Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, United States of America
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, United States of America
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16
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Li J, Jiang X, Jing Z, Li G, Chen Z, Zhou L, Zhao C, Liu J, Tan Y. Spatial and seasonal distributions of bacterioplankton in the Pearl River Estuary: The combined effects of riverine inputs, temperature, and phytoplankton. MARINE POLLUTION BULLETIN 2017; 125:199-207. [PMID: 28823423 DOI: 10.1016/j.marpolbul.2017.08.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 08/08/2017] [Accepted: 08/13/2017] [Indexed: 06/07/2023]
Abstract
In this study, we used flow cytometry and 16S rRNA gene pyrosequencing to investigate bacterioplankton (heterotrophic bacteria and picocyanobacteria) abundance and community structure in surface waters along the Pearl River Estuary. The results showed significant differences in bacterioplankton dynamics between fresh- and saltwater sites and between wet and dry season. Synechococcus constituted the majority of picocyanobacteria in both seasons. During the wet season, Synechococcus reached extremely high abundance at the mouth of the estuary, and heterotrophic bacteria were highly abundant (>106cellsml-1) throughout the studied region. At the same time, bacterioplankton decreased dramatically during the dry season. Pyrosequencing data indicated that salinity was a key parameter in shaping microbial community structure during both seasons. Phytoplankton was also an important factor; the proportion of Synechococcus and Rhodobacteriales was elevated at the frontal zone with higher chlorophyll a during the wet season, whereas Synechococcus were markedly reduced during the dry season.
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Affiliation(s)
- Jiajun Li
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Xin Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Zhiyou Jing
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Zuozhi Chen
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Linbin Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Chunyu Zhao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaxing Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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17
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Lambrecht J, Cichocki N, Hübschmann T, Koch C, Harms H, Müller S. Flow cytometric quantification, sorting and sequencing of methanogenic archaea based on F 420 autofluorescence. Microb Cell Fact 2017; 16:180. [PMID: 29084543 PMCID: PMC5663091 DOI: 10.1186/s12934-017-0793-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/24/2017] [Indexed: 02/08/2023] Open
Abstract
Background The widely established production of CH4 from renewable biomass in industrial scale anaerobic reactors may play a major role in the future energy supply. It relies on methanogenic archaea as key organisms which represent the bottleneck in the process. The quantitative analysis of these organisms can help to maximize process performance, uncover disturbances before failure, and may ultimately lead to community-based process control schemes. Existing qPCR and fluorescence microscopy-based methods are very attractive but can be cost-intensive and laborious. Results In this study we present an autofluorescence-based, flow cytometric method for the fast low-cost quantification of methanogenic archaea in complex microbial communities and crude substrates. The method was applied to a methanogenic enrichment culture (MEC) and digester samples (DS). The methanogenic archaea were quantified using the distinct fluorescence of their cofactor F420 in a range from 3.7 × 108 (± 3.3 × 106) cells mL−1 and 1.8 x 109 (± 1.1 × 108) cells mL−1. We evaluated different fixation methods and tested the sample stability. Stable abundance and fluorescence intensity were recorded up to 26 days during aerobic storage in PBS at 6 °C. The discrimination of the whole microbial community from the ubiquitous particle noise was facilitated by SYBR Green I staining and enabled calculation of relative abundances of methanogenic archaea of up to 9.64 ± 0.23% in the MEC and up to 4.43 ± 0.74% in the DS. The metaprofiling of the mcrA gene reinforced the results. Conclusions The presented method allows for fast and reliable quantification of methanogenic archaea in microbial communities under authentic digester conditions and can thus be useful for process monitoring and control in biogas digesters. Electronic supplementary material The online version of this article (10.1186/s12934-017-0793-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johannes Lambrecht
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Nicolas Cichocki
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Thomas Hübschmann
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Christin Koch
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany.
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18
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Li J, Jiang X, Li G, Jing Z, Zhou L, Ke Z, Tan Y. Distribution of picoplankton in the northeastern South China Sea with special reference to the effects of the Kuroshio intrusion and the associated mesoscale eddies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 589:1-10. [PMID: 28273592 DOI: 10.1016/j.scitotenv.2017.02.208] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 02/23/2017] [Accepted: 02/26/2017] [Indexed: 06/06/2023]
Abstract
We investigated picoplankton distribution patterns and environmental variables along an east-to-west transect in the northeastern South China Sea (SCS) during late winter 2016, giving us the opportunity to examine the impacts of the Kuroshio intrusion and the associated eddies. The results indicated that the subsurface (50-75m) phytoplankton biomass chlorophyll (Chl a) maximum (SCM) disappeared and was replaced by higher Chl a in the middle part of the transect due to the impacts of the Kuroshio intrusion and mesoscale eddies. Both flow cytometry and pyrosequencing data revealed that picoplankton abundance and community structure were significantly influenced by perturbations in complex physical processes. Picoeukaryotes represented most of the total phytoplankton biomass, and their maximum abundance (>104cellsmL-1) occurred within cyclonic eddy-affected regions (Stations 11 and 12), whereas the abundance of Prochlorococcus was the lowest in these regions. Prochlorococcus showed a higher abundance in the Kuroshio-affected area, while Synechococcus was mostly distributed at the upper well-lit depths, with its maximum abundance observed in surface waters (0-30m) adjacent to the cyclonic eddy center. Heterotrophic bacteria (HBA) displayed high abundance along the transect, consistent with the total phytoplankton biomass. Phylogenetic analysis revealed 26 bacterial phyla, with major components belonging to Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes, as well as SAR406. Notably, relatively more Rhodobacterales, Flavobacteriales, Alteromonadales, and Vibrionales that were distributed in surface waters of the cyclonic eddy center were specifically associated with the phytoplankton (mainly picoeukaryotes) bloom. Our study highlights the impacts of the Kuroshio intrusion in regulating the microbial ecology of the northeastern SCS and the potential coupling between phytoplankton and bacteria.
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Affiliation(s)
- Jiajun Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, West Xin(')gang Road 164#, Guangzhou 510301, China
| | - Xin Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, West Xin(')gang Road 164#, Guangzhou 510301, China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, West Xin(')gang Road 164#, Guangzhou 510301, China
| | - Zhiyou Jing
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Linbin Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, West Xin(')gang Road 164#, Guangzhou 510301, China
| | - Zhixin Ke
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, West Xin(')gang Road 164#, Guangzhou 510301, China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, West Xin(')gang Road 164#, Guangzhou 510301, China.
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19
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Jiang X, Li J, Ke Z, Xiang C, Tan Y, Huang L. Characteristics of picoplankton abundances during a Thalassiosira diporocyclus bloom in the Taiwan Bank in late winter. MARINE POLLUTION BULLETIN 2017; 117:66-74. [PMID: 28139232 DOI: 10.1016/j.marpolbul.2017.01.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/28/2016] [Accepted: 01/23/2017] [Indexed: 05/25/2023]
Abstract
To understand the variations of picoplankton (Prochlorococcus, Synechococcus, picoeukaryotes, and heterotrophic bacteria) abundances during diatom bloom, the distribution of picoplankton in the Taiwan Bank, South China Sea was investigated using flow cytometry during a Thalassiosira diporocyclus bloom in March 2016. The results indicated an abrupt abundance decrease for Prochlorococcus, Synechococcus, and picoeukaryotes within the bloom area while the abundance of heterotrophic bacteria showed no significant difference between the bloom and non-bloom areas. We found two sub-groups of heterotrophic bacteria: high- and low-nucleic acid content (HNA and LNA) bacteria with HNA dominated in the bloom area whereas LNA dominated in the non-bloom area. Among the picoplankton components, HNA represented the highest (61.1%) carbon biomass in the bloom area while picoeukaryotes represented the highest (37.6%) in the non-bloom area. Our findings implied that heterotrophic bacteria, especially HNA, played an essential role during the diatom bloom.
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Affiliation(s)
- Xin Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiajun Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhixin Ke
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Chenhui Xiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Liangmin Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Ecosystem Structure and Dynamics in the North Pacific Subtropical Gyre: New Views of an Old Ocean. Ecosystems 2017. [DOI: 10.1007/s10021-017-0117-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Kazamia E, Helliwell KE, Purton S, Smith AG. How mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes. Ecol Lett 2017; 19:810-22. [PMID: 27282316 PMCID: PMC5103174 DOI: 10.1111/ele.12615] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/03/2016] [Accepted: 04/07/2016] [Indexed: 01/05/2023]
Abstract
Extensive sampling and metagenomics analyses of plankton communities across all aquatic environments are beginning to provide insights into the ecology of microbial communities. In particular, the importance of metabolic exchanges that provide a foundation for ecological interactions between microorganisms has emerged as a key factor in forging such communities. Here we show how both studies of environmental samples and physiological experimentation in the laboratory with defined microbial co‐cultures are being used to decipher the metabolic and molecular underpinnings of such exchanges. In addition, we explain how metabolic modelling may be used to conduct investigations in reverse, deducing novel molecular exchanges from analysis of large‐scale data sets, which can identify persistently co‐occurring species. Finally, we consider how knowledge of microbial community ecology can be built into evolutionary theories tailored to these species’ unique lifestyles. We propose a novel model for the evolution of metabolic auxotrophy in microorganisms that arises as a result of symbiosis, termed the Foraging‐to‐Farming hypothesis. The model has testable predictions, fits several known examples of mutualism in the aquatic world, and sheds light on how interactions, which cement dependencies within communities of microorganisms, might be initiated.
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Affiliation(s)
- Elena Kazamia
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | | | - Saul Purton
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Alison Gail Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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22
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Liang Y, Bai X, Jiang Y, Wang M, He J, McMinn A. Distribution of marine viruses and their potential hosts in Prydz Bay and adjacent Southern Ocean, Antarctic. Polar Biol 2015. [DOI: 10.1007/s00300-015-1787-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Berube PM, Biller SJ, Kent AG, Berta-Thompson JW, Roggensack SE, Roache-Johnson KH, Ackerman M, Moore LR, Meisel JD, Sher D, Thompson LR, Campbell L, Martiny AC, Chisholm SW. Physiology and evolution of nitrate acquisition in Prochlorococcus. THE ISME JOURNAL 2015; 9:1195-207. [PMID: 25350156 PMCID: PMC4409163 DOI: 10.1038/ismej.2014.211] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/08/2014] [Accepted: 09/23/2014] [Indexed: 01/01/2023]
Abstract
Prochlorococcus is the numerically dominant phototroph in the oligotrophic subtropical ocean and carries out a significant fraction of marine primary productivity. Although field studies have provided evidence for nitrate uptake by Prochlorococcus, little is known about this trait because axenic cultures capable of growth on nitrate have not been available. Additionally, all previously sequenced genomes lacked the genes necessary for nitrate assimilation. Here we introduce three Prochlorococcus strains capable of growth on nitrate and analyze their physiology and genome architecture. We show that the growth of high-light (HL) adapted strains on nitrate is ∼17% slower than their growth on ammonium. By analyzing 41 Prochlorococcus genomes, we find that genes for nitrate assimilation have been gained multiple times during the evolution of this group, and can be found in at least three lineages. In low-light adapted strains, nitrate assimilation genes are located in the same genomic context as in marine Synechococcus. These genes are located elsewhere in HL adapted strains and may often exist as a stable genetic acquisition as suggested by the striking degree of similarity in the order, phylogeny and location of these genes in one HL adapted strain and a consensus assembly of environmental Prochlorococcus metagenome sequences. In another HL adapted strain, nitrate utilization genes may have been independently acquired as indicated by adjacent phage mobility elements; these genes are also duplicated with each copy detected in separate genomic islands. These results provide direct evidence for nitrate utilization by Prochlorococcus and illuminate the complex evolutionary history of this trait.
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Affiliation(s)
- Paul M Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven J Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alyssa G Kent
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | - Jessie W Berta-Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sara E Roggensack
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kathryn H Roache-Johnson
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
- Department of Biological Sciences, University of Southern Maine, Portland, ME, USA
| | - Marcia Ackerman
- Department of Biological Sciences, University of Southern Maine, Portland, ME, USA
| | - Lisa R Moore
- Department of Biological Sciences, University of Southern Maine, Portland, ME, USA
| | - Joshua D Meisel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel Sher
- Department of Marine Biology, University of Haifa, Haifa, Israel
| | - Luke R Thompson
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
| | - Lisa Campbell
- Department of Oceanography, Texas A&M University, College Station, TX, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, Irvine, CA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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25
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Dekel-Bird NP, Sabehi G, Mosevitzky B, Lindell D. Host-dependent differences in abundance, composition and host range of cyanophages from the Red Sea. Environ Microbiol 2014; 17:1286-99. [DOI: 10.1111/1462-2920.12569] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 07/15/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Naama P. Dekel-Bird
- Faculty of Biology; Technion - Israel Institute of Technology; Haifa 32000 Israel
| | - Gazalah Sabehi
- Faculty of Biology; Technion - Israel Institute of Technology; Haifa 32000 Israel
| | - Bar Mosevitzky
- Faculty of Biology; Technion - Israel Institute of Technology; Haifa 32000 Israel
| | - Debbie Lindell
- Faculty of Biology; Technion - Israel Institute of Technology; Haifa 32000 Israel
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26
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Efficient CO2 fixation by surface Prochlorococcus in the Atlantic Ocean. ISME JOURNAL 2014; 8:2280-9. [PMID: 24763372 PMCID: PMC4992072 DOI: 10.1038/ismej.2014.56] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 03/06/2014] [Accepted: 03/11/2014] [Indexed: 11/08/2022]
Abstract
Nearly half of the Earth's surface is covered by the ocean populated by the most abundant photosynthetic organisms on the planet--Prochlorococcus cyanobacteria. However, in the oligotrophic open ocean, the majority of their cells in the top half of the photic layer have levels of photosynthetic pigmentation barely detectable by flow cytometry, suggesting low efficiency of CO2 fixation compared with other phytoplankton living in the same waters. To test the latter assumption, CO2 fixation rates of flow cytometrically sorted (14)C-labelled phytoplankton cells were directly compared in surface waters of the open Atlantic Ocean (30°S to 30°N). CO2 fixation rates of Prochlorococcus are at least 1.5-2.0 times higher than CO2 fixation rates of the smallest plastidic protists and Synechococcus cyanobacteria when normalised to photosynthetic pigmentation assessed using cellular red autofluorescence. Therefore, our data indicate that in oligotrophic oceanic surface waters, pigment minimisation allows Prochlorococcus cells to harvest plentiful sunlight more effectively than other phytoplankton.
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Grimes DJ, Ford TE, Colwell RR, Baker-Austin C, Martinez-Urtaza J, Subramaniam A, Capone DG. Viewing marine bacteria, their activity and response to environmental drivers from orbit: satellite remote sensing of bacteria. MICROBIAL ECOLOGY 2014; 67:489-500. [PMID: 24477922 PMCID: PMC4058845 DOI: 10.1007/s00248-013-0363-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 12/26/2013] [Indexed: 05/24/2023]
Abstract
Satellite-based remote sensing of marine microorganisms has become a useful tool in predicting human health risks associated with these microscopic targets. Early applications were focused on harmful algal blooms, but more recently methods have been developed to interrogate the ocean for bacteria. As satellite-based sensors have become more sophisticated and our ability to interpret information derived from these sensors has advanced, we have progressed from merely making fascinating pictures from space to developing process models with predictive capability. Our understanding of the role of marine microorganisms in primary production and global elemental cycles has been vastly improved as has our ability to use the combination of remote sensing data and models to provide early warning systems for disease outbreaks. This manuscript will discuss current approaches to monitoring cyanobacteria and vibrios, their activity and response to environmental drivers, and will also suggest future directions.
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Affiliation(s)
- D. Jay Grimes
- Gulf Coast Research Laboratory, The University of Southern Mississippi, 703 East Beach Drive, Ocean Springs, MS 39564, USA
| | - Tim E. Ford
- University of New England, 716 Stevens Avenue, Portland, ME 04103, USA,
| | - Rita R. Colwell
- Center for Bioinformatics and Computational Biology, UMIACS, University of Maryland, 3103 Biomolecular Sciences Building #296, College Park, MD 20742, USA,
| | - Craig Baker-Austin
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset, UK,
| | - Jaime Martinez-Urtaza
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK,
| | - Ajit Subramaniam
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY 10964, USA,
| | - Douglas G. Capone
- Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA 90089-0371, USA,
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28
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Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proc Natl Acad Sci U S A 2013; 110:9824-9. [PMID: 23703908 DOI: 10.1073/pnas.1307701110] [Citation(s) in RCA: 622] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Cyanobacteria Prochlorococcus and Synechococcus account for a substantial fraction of marine primary production. Here, we present quantitative niche models for these lineages that assess present and future global abundances and distributions. These niche models are the result of neural network, nonparametric, and parametric analyses, and they rely on >35,000 discrete observations from all major ocean regions. The models assess cell abundance based on temperature and photosynthetically active radiation, but the individual responses to these environmental variables differ for each lineage. The models estimate global biogeographic patterns and seasonal variability of cell abundance, with maxima in the warm oligotrophic gyres of the Indian and the western Pacific Oceans and minima at higher latitudes. The annual mean global abundances of Prochlorococcus and Synechococcus are 2.9 ± 0.1 × 10(27) and 7.0 ± 0.3 × 10(26) cells, respectively. Using projections of sea surface temperature as a result of increased concentration of greenhouse gases at the end of the 21st century, our niche models projected increases in cell numbers of 29% and 14% for Prochlorococcus and Synechococcus, respectively. The changes are geographically uneven but include an increase in area. Thus, our global niche models suggest that oceanic microbial communities will experience complex changes as a result of projected future climate conditions. Because of the high abundances and contributions to primary production of Prochlorococcus and Synechococcus, these changes may have large impacts on ocean ecosystems and biogeochemical cycles.
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29
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López-Lozano A, Diez J, Alaoui S, Moreno-Vivián C, García-Fernández JM. Nitrate is reduced by heterotrophic bacteria but not transferred to Prochlorococcus in non-axenic cultures. FEMS Microbiol Ecol 2012; 41:151-60. [PMID: 19709249 DOI: 10.1111/j.1574-6941.2002.tb00976.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Abstract The ability to assimilate nitrate in non-axenic isolates of Prochlorococcus spp. was addressed in this work, particularly in three low-irradiance adapted strains originating from ocean depths with measurable nitrate concentrations. None of the studied strains was able to use nitrate as the sole nitrogen source. Nitrate reductase (NR; EC 1.6.6.2) activity was, however, detected using the methyl viologen/dithionite assay in crude extracts from all studied Prochlorococcus strains. Characterization of this activity unambiguously demonstrated its enzymatic origin. We observed that NR activity did not decrease in vivo under darkness. Attempts to detect the narB gene (coding for NR in other cyanobacteria) by PCR with primers designed on the basis of the specific codon usage in Prochlorococcus were unsuccessful. However, when primers were designed considering the codon frequencies typical of other bacteria, we could amplify different fragments of nas genes, coding for bacterial assimilatory NRs. Similar amplification products were obtained using colonies of contaminant bacteria from Prochlorococcus cultures as PCR template. Furthermore, NR activity was found in cultures of these contaminants, demonstrating the non-cyanobacterial origin of the enzyme. These results strongly suggest that the studied strains of Prochlorococcus lack NR, in spite of inhabiting environments with nitrate as the main nitrogen source. In addition, they indicate that the nitrite produced by heterotrophic bacteria is not transferred to Prochlorococcus for growth, thus discarding a trophic nitrogen chain between heterotrophic bacteria and Prochlorococcus in the studied cultures.
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Affiliation(s)
- Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, 1 planta, Campus de Rabanales, Universidad de Córdoba, E-14071 Córdoba, Spain
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30
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Malmstrom RR, Rodrigue S, Huang KH, Kelly L, Kern SE, Thompson A, Roggensack S, Berube PM, Henn MR, Chisholm SW. Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. ISME JOURNAL 2012; 7:184-98. [PMID: 22895163 DOI: 10.1038/ismej.2012.89] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Prochlorococcus is the numerically dominant photosynthetic organism throughout much of the world's oceans, yet little is known about the ecology and genetic diversity of populations inhabiting tropical waters. To help close this gap, we examined natural Prochlorococcus communities in the tropical Pacific Ocean using a single-cell whole-genome amplification and sequencing. Analysis of the gene content of just 10 single cells from these waters added 394 new genes to the Prochlorococcus pan-genome--that is, genes never before seen in a Prochlorococcus cell. Analysis of marker genes, including the ribosomal internal transcribed sequence, from dozens of individual cells revealed several representatives from two uncultivated clades of Prochlorococcus previously identified as HNLC1 and HNLC2. While the HNLC clades can dominate Prochlorococcus communities under certain conditions, their overall geographic distribution was highly restricted compared with other clades of Prochlorococcus. In the Atlantic and Pacific oceans, these clades were only found in warm waters with low Fe and high inorganic P levels. Genomic analysis suggests that at least one of these clades thrives in low Fe environments by scavenging organic-bound Fe, a process previously unknown in Prochlorococcus. Furthermore, the capacity to utilize organic-bound Fe appears to have been acquired horizontally and may be exchanged among other clades of Prochlorococcus. Finally, one of the single Prochlorococcus cells sequenced contained a partial genome of what appears to be a prophage integrated into the genome.
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Affiliation(s)
- Rex R Malmstrom
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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31
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Petersen TW, Brent Harrison C, Horner DN, van den Engh G. Flow cytometric characterization of marine microbes. Methods 2012; 57:350-8. [PMID: 22796378 DOI: 10.1016/j.ymeth.2012.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 06/18/2012] [Accepted: 07/02/2012] [Indexed: 11/26/2022] Open
Abstract
The analysis of marine phytoplankton using flow cytometry has enabled the discovery of new taxa and has contributed new understanding to the dynamics and ecological contributions of phytoplankton to the global carbon cycle. Marine phytoplankton are uniquely suited to analysis by flow cytometry because of their size, pigment content, and ability to remain in suspension. Cytometric analysis of marine populations is not without challenges. Phytoplankton communities span a broad range of sizes. The smallest microbes are a few tenths of a micron, while the largest are a few tenths of a millimeter. The improvement of cytometric measurements of scattered laser light allows one to investigate marine microbes whose sizes span several orders of magnitude. To effectively leverage the advantages that marine microbes possess, cytometers have to be carefully engineered for marine use.
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Affiliation(s)
- Timothy W Petersen
- Becton Dickinson Biosciences, Advanced Cytometry Group, 12730 28th Ave NE, Seattle, WA 98125, USA.
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32
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Michotey V, Guasco S, Boeuf D, Morezzi N, Durieux B, Charpy L, Bonin P. Spatio-temporal diversity of free-living and particle-attached prokaryotes in the tropical lagoon of Ahe atoll (Tuamotu Archipelago) and its surrounding oceanic waters. MARINE POLLUTION BULLETIN 2012; 65:525-537. [PMID: 22289391 DOI: 10.1016/j.marpolbul.2012.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 01/04/2012] [Accepted: 01/06/2012] [Indexed: 05/31/2023]
Abstract
Spatio-temporal variability of prokaryotic water column communities inside and outside a Polynesian tropical lagoon subjected to pearl oysters farming was assessed in terms of abundance by quantitative PCR and diversity by DGGE. Communities and operational taxonomic units (OTUs) were analysed according to dry/rainy seasons and free-living/particle-attached state. Bacterial density was higher in the lagoon compared to ocean and a seasonal trend was observed. No influence of the localisation within lagoon or of the planktonic/attached states was noticed on bacterial abundance and diversity. The OTUs belonged to Cyanobacteria, to heterotrophic groups in Proteobacteria and Flavobacteria. Archaeal abundance showed seasonal tendency and particle-prevalence, but no effect of lagoon or oceanic location was observed. Lagoon and oceanic archaeal diversity were different and Euryarchaeota (MG-II, MBG, and Halobacteria) were detected. During the dry season, planktonic and particle-associated community differed, whereas at rainy season, both communities were similar and included members usually associated with coral.
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Affiliation(s)
- V Michotey
- Aix-Marseille Université, Mediterranean Institute of Oceanography (MIO), 13288 Marseille Cedex 09, France.
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Mendonça A, Arístegui J, Vilas JC, Montero MF, Ojeda A, Espino M, Martins A. Is there a seamount effect on microbial community structure and biomass? The case study of Seine and Sedlo seamounts (northeast Atlantic). PLoS One 2012; 7:e29526. [PMID: 22279538 PMCID: PMC3261146 DOI: 10.1371/journal.pone.0029526] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Accepted: 11/30/2011] [Indexed: 11/19/2022] Open
Abstract
Seamounts are considered to be "hotspots" of marine life but, their role in oceans primary productivity is still under discussion. We have studied the microbial community structure and biomass of the epipelagic zone (0-150 m) at two northeast Atlantic seamounts (Seine and Sedlo) and compared those with the surrounding ocean. Results from two cruises to Sedlo and three to Seine are presented. Main results show large temporal and spatial microbial community variability on both seamounts. Both Seine and Sedlo heterotrophic community (abundance and biomass) dominate during winter and summer months, representing 75% (Sedlo, July) to 86% (Seine, November) of the total plankton biomass. In Seine, during springtime the contribution to total plankton biomass is similar (47% autotrophic and 53% heterotrophic). Both seamounts present an autotrophic community structure dominated by small cells (nano and picophytoplankton). It is also during spring that a relatively important contribution (26%) of large cells to total autotrophic biomass is found. In some cases, a "seamount effect" is observed on Seine and Sedlo microbial community structure and biomass. In Seine this is only observed during spring through enhancement of large autotrophic cells at the summit and seamount stations. In Sedlo, and despite the observed low biomasses, some clear peaks of picoplankton at the summit or at stations within the seamount area are also observed during summer. Our results suggest that the dominance of heterotrophs is presumably related to the trapping effect of organic matter by seamounts. Nevertheless, the complex circulation around both seamounts with the presence of different sources of mesoscale variability (e.g. presence of meddies, intrusion of African upwelling water) may have contributed to the different patterns of distribution, abundances and also changes observed in the microbial community.
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Affiliation(s)
- Ana Mendonça
- Department of Oceanography and Fisheries, University of the Azores, Horta, Portugal.
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34
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Mühling M. On the culture-independent assessment of the diversity and distribution of Prochlorococcus. Environ Microbiol 2011; 14:567-79. [DOI: 10.1111/j.1462-2920.2011.02589.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Treusch AH, Demir-Hilton E, Vergin KL, Worden AZ, Carlson CA, Donatz MG, Burton RM, Giovannoni SJ. Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids. ISME JOURNAL 2011; 6:481-92. [PMID: 21955994 DOI: 10.1038/ismej.2011.117] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phytoplankton species vary in their physiological properties, and are expected to respond differently to seasonal changes in water column conditions. To assess these varying distribution patterns, we used 412 samples collected monthly over 12 years (1991-2004) at the Bermuda Atlantic Time-Series Study site, located in the northwestern Sargasso Sea. We measured plastid 16S ribosomal RNA gene abundances with a terminal restriction fragment length polymorphism approach and identified distribution patterns for members of the Prymnesiophyceae, Pelagophyceae, Chrysophyceae, Cryptophyceae, Bacillariophyceae and Prasinophyceae. The analysis revealed dynamic bloom patterns by these phytoplankton taxa that begin early in the year, when the mixed layer is deep. Previously, unreported open-ocean prasinophyte blooms dominated the plastid gene signal during convective mixing events. Quantitative PCR confirmed the blooms and transitions of Bathycoccus, Micromonas and Ostreococcus populations. In contrast, taxa belonging to the pelagophytes and chrysophytes, as well as cryptophytes, reached annual peaks during mixed layer shoaling, while Bacillariophyceae (diatoms) were observed only episodically in the 12-year record. Prymnesiophytes dominated the integrated plastid gene signal. They were abundant throughout the water column before mixing events, but persisted in the deep chlorophyll maximum during stratified conditions. Various models have been used to describe mechanisms that drive vernal phytoplankton blooms in temperate seas. The range of taxon-specific bloom patterns observed here indicates that different 'spring bloom' models can aptly describe the behavior of different phytoplankton taxa at a single geographical location. These findings provide insight into the subdivision of niche space by phytoplankton and may lead to improved predictions of phytoplankton responses to changes in ocean conditions.
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Affiliation(s)
- Alexander H Treusch
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
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36
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Novel lineages of Prochlorococcus and Synechococcus in the global oceans. ISME JOURNAL 2011; 6:285-97. [PMID: 21955990 DOI: 10.1038/ismej.2011.106] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Picocyanobacteria represented by Prochlorococcus and Synechococcus have an important role in oceanic carbon fixation and nutrient cycling. In this study, we compared the community composition of picocyanobacteria from diverse marine ecosystems ranging from estuary to open oceans, tropical to polar oceans and surface to deep water, based on the sequences of 16S-23S rRNA internal transcribed spacer (ITS). A total of 1339 ITS sequences recovered from 20 samples unveiled diverse and several previously unknown clades of Prochlorococcus and Synechococcus. Six high-light (HL)-adapted Prochlorococcus clades were identified, among which clade HLVI had not been described previously. Prochlorococcus clades HLIII, HLIV and HLV, detected in the Equatorial Pacific samples, could be related to the HNLC clades recently found in the high-nutrient, low-chlorophyll (HNLC), iron-depleted tropical oceans. At least four novel Synechococcus clades (out of six clades in total) in subcluster 5.3 were found in subtropical open oceans and the South China Sea. A niche partitioning with depth was observed in the Synechococcus subcluster 5.3. Members of Synechococcus subcluster 5.2 were dominant in the high-latitude waters (northern Bering Sea and Chukchi Sea), suggesting a possible cold-adaptation of some marine Synechococcus in this subcluster. A distinct shift of the picocyanobacterial community was observed from the Bering Sea to the Chukchi Sea, which reflected the change of water temperature. Our study demonstrates that oceanic systems contain a large pool of diverse picocyanobacteria, and further suggest that new genotypes or ecotypes of picocyanobacteria will continue to emerge, as microbial consortia are explored with advanced sequencing technology.
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Barnett JP, Robinson C, Scanlan DJ, Blindauer CA. The Tat protein export pathway and its role in cyanobacterial metalloprotein biosynthesis. FEMS Microbiol Lett 2011; 325:1-9. [PMID: 22092855 DOI: 10.1111/j.1574-6968.2011.02391.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 08/11/2011] [Accepted: 08/16/2011] [Indexed: 11/27/2022] Open
Abstract
The Tat pathway is a common protein translocation system that is found in the bacterial cytoplasmic membrane, as well as in the cyanobacterial and plant thylakoid membranes. It is unusual in that the Tat pathway transports fully folded, often metal cofactor-containing proteins across these membranes. In bacteria, the Tat pathway plays an important role in the biosynthesis of noncytoplasmic metalloproteins. By compartmentalizing protein folding to the cytoplasm, the potentially aberrant binding of non-native metal ions to periplasmic proteins is avoided. To date, most of our understanding of Tat function has been obtained from studies using Escherichia coli as a model organism but cyanobacteria have an extra layer of complexity with proteins targeted to both the cytoplasmic and thylakoid membranes. We examine our current understanding of the Tat pathway in cyanobacteria and its role in metalloprotein biosynthesis.
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Affiliation(s)
- James P Barnett
- Department of Chemistry, University of Warwick, Coventry, UK.
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38
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Thompson AW, Huang K, Saito MA, Chisholm SW. Transcriptome response of high- and low-light-adapted Prochlorococcus strains to changing iron availability. ISME JOURNAL 2011; 5:1580-94. [PMID: 21562599 DOI: 10.1038/ismej.2011.49] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Prochlorococcus contributes significantly to ocean primary productivity. The link between primary productivity and iron in specific ocean regions is well established and iron limitation of Prochlorococcus cell division rates in these regions has been shown. However, the extent of ecotypic variation in iron metabolism among Prochlorococcus and the molecular basis for differences is not understood. Here, we examine the growth and transcriptional response of Prochlorococcus strains, MED4 and MIT9313, to changing iron concentrations. During steady state, MIT9313 sustains growth at an order-of-magnitude lower iron concentration than MED4. To explore this difference, we measured the whole-genome transcriptional response of each strain to abrupt iron starvation and rescue. Only four of the 1159 orthologs of MED4 and MIT9313 were differentially expressed in response to iron in both strains. However, in each strain, the expression of over a hundred additional genes changed, many of which are in labile genomic regions, suggesting a role for lateral gene transfer in establishing diversity of iron metabolism among Prochlorococcus. Furthermore, we found that MED4 lacks three genes near the iron-deficiency-induced gene (idiA) that are present and induced by iron stress in MIT9313. These genes are interesting targets for studying the adaptation of natural Prochlorococcus assemblages to local iron conditions as they show more diversity than other genomic regions in environmental metagenomic databases.
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Affiliation(s)
- Anne W Thompson
- MIT Department of Civil and Environmental Engineering, Cambridge, MA02139, USA
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Rynearson TA, Palenik B. Learning to read the oceans genomics of marine phytoplankton. ADVANCES IN MARINE BIOLOGY 2011; 60:1-39. [PMID: 21962749 DOI: 10.1016/b978-0-12-385529-9.00001-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The phytoplankton are key members of marine ecosystems, generating about half of global primary productivity, supporting valuable fisheries and regulating global biogeochemical cycles. Marine phytoplankton are phylogenetically diverse and are comprised of both prokaryotic and eukaryotic species. In the last decade, new insights have been gained into the ecology and evolution of these important organisms through whole genome sequencing projects and more recently, through both transcriptomics and targeted metagenomics approaches. Sequenced genomes of cyanobacteria are generally small, ranging in size from 1.8 to 9 million base pairs (Mbp). Eukaryotic genomes, in general, have a much larger size range and those that have been sequenced range from 12 to 57 Mbp. Whole genome sequencing projects have revealed key features of the evolutionary history of marine phytoplankton, their varied responses to environmental stress, their ability to scavenge and store nutrients and their unique ability to form elaborate cellular coverings. We have begun to learn how to read the 'language' of marine phytoplankton, as written in their DNA. Here, we review the ecological and evolutionary insights gained from whole genome sequencing projects, illustrate how these genomes are yielding information on marine natural products and informing nanotechnology as well as make suggestions for future directions in the field of marine phytoplankton genomics.
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Affiliation(s)
- Tatiana A Rynearson
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA.
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Lavin P, González B, Santibáñez JF, Scanlan DJ, Ulloa O. Novel lineages of Prochlorococcus thrive within the oxygen minimum zone of the eastern tropical South Pacific. ENVIRONMENTAL MICROBIOLOGY REPORTS 2010; 2:728-38. [PMID: 23766277 DOI: 10.1111/j.1758-2229.2010.00167.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The eastern tropical Pacific Ocean holds two of the main oceanic oxygen minimum zones of the global ocean. The presence of an oxygen-depleted layer at intermediate depths, which also impinges on the seafloor and in some cases the euphotic zone, plays a significant role in structuring both pelagic and benthic communities, and also in the vertical partitioning of microbial assemblages. Here, we assessed the genetic diversity and distribution of natural populations of the cyanobacteria Prochlorococcus and Synechococcus within oxic and suboxic waters of the eastern tropical Pacific using cloning and sequencing, and terminal restriction fragment length polymorphism (T-RFLP) analyses applied to the 16S-23S rRNA internal transcribed spacer region. With the T-RFLP approach we could discriminate 19 cyanobacterial clades, of which 18 were present in the study region. Synechococcus was more abundant in the surface oxic waters of the eastern South Pacific, while Prochlorococcus dominated the subsurface low-oxygen waters. Two of the dominant clades in the oxygen-deficient waters belong to novel and yet uncultivated lineages of low-light adapted Prochlorococcus.
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Affiliation(s)
- Paris Lavin
- Programa de Doctorado, Departamento de Botánica, Universidad de Concepción, Concepción, Chile. Departamento de Oceanografía and Centro de Investigación Oceanográfica en el Pacifico Sudoriental, Universidad de Concepción, Concepción, Chile. Departamento de Genética Molecular y Microbiología, Center for Advanced Studies in Ecology and Biodiversity, and Millennium Nucleus on Microbial Ecology and Environmental Microbiology and Biotechnology, Pontificia Universidad Católica de Chile, Santiago, Chile. Facultad de Ingeniería y Ciencia, Universidad Adolfo Ibáñez, Santiago, Chile. Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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Shalapyonok A, Olson RJ, Shalapyonok LS. Ultradian Growth in Prochlorococcus spp. Appl Environ Microbiol 2010; 64:1066-9. [PMID: 16349513 PMCID: PMC106368 DOI: 10.1128/aem.64.3.1066-1069.1998] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Species of the widespread marine prokaryote Prochlorococcus exhibited ultradian growth (faster than 1 division per day) both in situ and in culture, even though cell division is strictly phased to the light-dark cycle. Under optimal conditions a second DNA replication and cell division closely followed, but did not overlap with, the first division. The timing of cell cycle events was not affected by light intensity or duration, suggesting control by a light-triggered timer or circadian clock rather than by completion of a light-dependent assimilation phase. This mode of ultradian growth has not been observed previously and poses new questions about the regulation of cellular rhythms in prokaryotes. In addition, it implies that conclusions regarding the lack of nutrient limitation of Prochlorococcus in the open ocean, which were based on the appearance that cells were growing at their maximal rate, need to be reconsidered.
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Affiliation(s)
- A Shalapyonok
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543
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Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans. ISME JOURNAL 2010; 4:1252-64. [PMID: 20463762 DOI: 10.1038/ismej.2010.60] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To better understand the temporal and spatial dynamics of Prochlorococcus populations, and how these populations co-vary with the physical environment, we followed monthly changes in the abundance of five ecotypes-two high-light adapted and three low-light adapted-over a 5-year period in coordination with the Bermuda Atlantic Time Series (BATS) and Hawaii Ocean Time-series (HOT) programs. Ecotype abundance displayed weak seasonal fluctuations at HOT and strong seasonal fluctuations at BATS. Furthermore, stable 'layered' depth distributions, where different Prochlorococcus ecotypes reached maximum abundance at different depths, were maintained consistently for 5 years at HOT. Layered distributions were also observed at BATS, although winter deep mixing events disrupted these patterns each year and produced large variations in ecotype abundance. Interestingly, the layered ecotype distributions were regularly reestablished each year after deep mixing subsided at BATS. In addition, Prochlorococcus ecotypes each responded differently to the strong seasonal changes in light, temperature and mixing at BATS, resulting in a reproducible annual succession of ecotype blooms. Patterns of ecotype abundance, in combination with physiological assays of cultured isolates, confirmed that the low-light adapted eNATL could be distinguished from other low-light adapted ecotypes based on its ability to withstand temporary exposure to high-intensity light, a characteristic stress of the surface mixed layer. Finally, total Prochlorococcus and Synechococcus dynamics were compared with similar time series data collected a decade earlier at each location. The two data sets were remarkably similar-testimony to the resilience of these complex dynamic systems on decadal time scales.
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Hewson I, Poretsky RS, Tripp HJ, Montoya JP, Zehr JP. Spatial patterns and light-driven variation of microbial population gene expression in surface waters of the oligotrophic open ocean. Environ Microbiol 2010; 12:1940-56. [PMID: 20406287 DOI: 10.1111/j.1462-2920.2010.02198.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Because bacterioplankton production rates do not vary strongly across vast expanses of the ocean, it is unclear how variability in community structure corresponds with functional variability in the open ocean. We surveyed community transcript functional profiles at eight locations in the open ocean, in both the light and in the dark, using the genomic subsystems approach, to understand variability in gene expression patterns in surface waters. Metatranscriptomes from geographically distinct areas and collected during the day and night shared a large proportion of metabolic functional similarity (74%) at the finest metabolic resolution possible. The variability between metatranscriptomes could be explained by phylogenetic differences between libraries (Mantel test, P < 0.0001). Several key gene expression pathways, including Photosystem I, Photosystem II and ammonium uptake, demonstrated the most variability both geographically and between light and dark. Libraries were dominated by transcripts of the cyanobacterium Prochlorocococcus marinus, where most geographical and diel variability between metatranscriptomes reflected between-station differences in cyanobacterial phototrophic metabolism. Our results demonstrate that active genetic machinery in surface waters of the ocean is dominated by photosynthetic microorganisms and their site-to-site variability, while variability in the remainder of assemblages is dependent on local taxonomic composition.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, Cornell University, Wing Hall 403, Ithaca, NY 14853, USA.
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Seasonality and vertical structure of microbial communities in an ocean gyre. ISME JOURNAL 2009; 3:1148-63. [PMID: 19494846 DOI: 10.1038/ismej.2009.60] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Vertical, seasonal and geographical patterns in ocean microbial communities have been observed in many studies, but the resolution of community dynamics has been limited by the scope of data sets, which are seldom up to the task of illuminating the highly structured and rhythmic patterns of change found in ocean ecosystems. We studied vertical and temporal patterns in the microbial community composition in a set of 412 samples collected from the upper 300 m of the water column in the northwestern Sargasso Sea, on cruises between 1991 and 2004. The region sampled spans the extent of deep winter mixing and the transition between the euphotic and the upper mesopelagic zones, where most carbon fixation and reoxidation occurs. A bioinformatic pipeline was developed to de-noise, normalize and align terminal restriction fragment length polymorphism (T-RFLP) data from three restriction enzymes and link T-RFLP peaks to microbial clades. Non-metric multidimensional scaling statistics resolved three microbial communities with distinctive composition during seasonal stratification: a surface community in the region of lowest nutrients, a deep chlorophyll maximum community and an upper mesopelagic community. A fourth microbial community was associated with annual spring blooms of eukaryotic phytoplankton that occur in the northwestern Sargasso Sea as a consequence of winter convective mixing that entrains nutrients to the surface. Many bacterial clades bloomed in seasonal patterns that shifted with the progression of stratification. These richly detailed patterns of community change suggest that highly specialized adaptations and interactions govern the success of microbial populations in the oligotrophic ocean.
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Scanlan DJ, Ostrowski M, Mazard S, Dufresne A, Garczarek L, Hess WR, Post AF, Hagemann M, Paulsen I, Partensky F. Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev 2009; 73:249-99. [PMID: 19487728 PMCID: PMC2698417 DOI: 10.1128/mmbr.00035-08] [Citation(s) in RCA: 433] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45 degrees N to 40 degrees S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level.
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Affiliation(s)
- D J Scanlan
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
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Immunofluorescence flow cytometry technique for enumeration of the brown-tide alga, Aureococcus anophagefferens. Appl Environ Microbiol 2008; 74:6931-40. [PMID: 18820052 DOI: 10.1128/aem.00996-08] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new immunologically based flow cytometry (IFCM) technique was developed to enumerate Aureococcus anophagefferens, a small pelagophyte alga that is the cause of "brown tides" in bays and estuaries of the mid-Atlantic states along the U.S. coast. The method utilizes a monoclonal antibody conjugated to fluorescein isothiocyanate (FITC-MAb) to label the surface of A. anophagefferens cells which are then detected and enumerated by using a flow cytometer. Optimal conditions for FITC-MAb staining, including solution composition, incubation times, and FITC-MAb concentrations, were determined. The FITC-MAb method was tested for cross-reactivity with nontarget, similarly sized, photoautotrophic protists, and the method was compared to an enzyme-linked immunosorbent assay (ELISA) using the same MAb. Comparisons of the IFCM technique to traditional microscopy enumeration of cultures and spiked environmental samples showed consistent agreement over several orders of magnitude (r(2) > 0.99). Comparisons of the IFCM and ELISA techniques for enumerating cells from a predation experiment showed a substantial overestimation (up to 10 times higher) of the ELISA in the presence of consumers of A. anophagefferens, presumably due to egested cell fragments that retained antigenicity, using the ELISA method, but were not characterized as whole algal cells by the IFCM method. Application of the IFCM method to environmental "brown-tide" samples taken from the coastal bays of Maryland demonstrated its efficacy in resolving A. anophagefferens abundance levels throughout the course of a bloom and over a large range of abundance values. IFCM counts of the brown-tide alga from natural samples were consistently lower than those obtained using the ELISA method and were equivalent to those of the polyclonal immunofluorescence microscopy technique, since both methods discriminate intact cells. Overall, the IFCM approach was an accurate and relatively simple technique for the rapid enumeration of A. anophagefferens in natural samples over a wide range of abundance values (10(3) to 10(6) cells ml(-1)).
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Sandaa RA, Clokie M, Mann NH. Photosynthetic genes in viral populations with a large genomic size range from Norwegian coastal waters. FEMS Microbiol Ecol 2007; 63:2-11. [PMID: 17999684 DOI: 10.1111/j.1574-6941.2007.00400.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
This study reports the diversity of uncultured environmental viruses harbouring photosynthetic genes (psbA and psbD) in samples from cold seawater (latitude above 60 degrees ). The viral community in coastal Norwegian waters was separated according to genome size using pulse field gel electrophoresis. Viral populations within a wide genome size range (31-380 kb) were investigated for the presence of the psbA and psbD genes using PCR, combined with cloning and sequencing. The results show the presence of photosynthetic genes in viral populations from all size ranges. Thus, valuable information could be obtained about the size class to which viral particles that encode photosynthesis genes belong. The wide genomic size range detected implies that a different cyanophage profile has been observed than has been reported previously. Thus, the method of phage gene detection applied here may represent a truer picture of phage diversity in general or that there is a larger range of size profile for viruses with psbA and psbD in higher latitudes than for the better-studied lower latitudes. Alternatively, a picture of diversity based on a different set of biases than that from either isolation-based research or from conventional metagenomic approaches may be observed.
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Rabouille S, Edwards CA, Zehr JP. Modelling the vertical distribution of Prochlorococcus and Synechococcus in the North Pacific Subtropical Ocean. Environ Microbiol 2007; 9:2588-602. [PMID: 17803782 DOI: 10.1111/j.1462-2920.2007.01376.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A simple model was developed to examine the vertical distribution of Prochlorococcus and Synechococcus ecotypes in the water column, based on their adaptation to light intensity. Model simulations were compared with a 14-year time series of Prochlorococcus and Synechococcus cell abundances at Station ALOHA in the North Pacific Subtropical Gyre. Data were analysed to examine spatial and temporal patterns in abundances and their ranges of variability in the euphotic zone, the surface mixed layer and the layer in the euphotic zone but below the base of the mixed layer. Model simulations show that the apparent occupation of the whole euphotic zone by a genus can be the result of a co-occurrence of different ecotypes that segregate vertically. The segregation of ecotypes can result simply from differences in light response. A sensitivity analysis of the model, performed on the parameter alpha (initial slope of the light-response curve) and the DIN concentration in the upper water column, demonstrates that the model successfully reproduces the observed range of vertical distributions. Results support the idea that intermittent mixing events may have important ecological and geochemical impacts on the phytoplankton community at Station ALOHA.
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Affiliation(s)
- Sophie Rabouille
- Ocean Sciences Department, University of California, Santa Cruz, CA 95064, USA.
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Coleman ML, Chisholm SW. Code and context: Prochlorococcus as a model for cross-scale biology. Trends Microbiol 2007; 15:398-407. [PMID: 17693088 DOI: 10.1016/j.tim.2007.07.001] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2007] [Revised: 06/19/2007] [Accepted: 07/27/2007] [Indexed: 11/28/2022]
Abstract
Prochlorococcus is a simple cyanobacterium that is abundant throughout large regions of the oceans, and has become a useful model for studying the nature and regulation of biological diversity across all scales of complexity. Recent work has revealed that environmental factors such as light, nutrients and predation influence diversity in different ways, changing our image of the structure and dynamics of the global Prochlorococcus population. Advances in metagenomics, transcription profiling and global ecosystem modeling promise to deliver an even greater understanding of this system and further demonstrate the power of cross-scale systems biology.
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Affiliation(s)
- Maureen L Coleman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Garczarek L, Dufresne A, Rousvoal S, West NJ, Mazard S, Marie D, Claustre H, Raimbault P, Post AF, Scanlan DJ, Partensky F. High vertical and low horizontal diversity of Prochlorococcus ecotypes in the Mediterranean Sea in summer. FEMS Microbiol Ecol 2007; 60:189-206. [PMID: 17391326 DOI: 10.1111/j.1574-6941.2007.00297.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Natural populations of the marine cyanobacterium Prochlorococcus exist as two main ecotypes, inhabiting different layers of the ocean's photic zone. These so-called high light- (HL-) and low light (LL-) adapted ecotypes are both physiologically and genetically distinct. HL strains can be separated into two major clades (HLI and HLII), whereas LL strains are more diverse. Here, we used several molecular techniques to study the genetic diversity of natural Prochlorococcus populations during the Prosope cruise in the Mediterranean Sea in the summer of 1999. Using a dot blot hybridization technique, we found that HLI was the dominant HL group and was confined to the upper mixed layer. In contrast, LL ecotypes were only found below the thermocline. Secondly, a restriction fragment length polymorphism analysis of PCR-amplified pcb genes (encoding the major light-harvesting proteins of Prochlorococcus) suggested that there were at least four genetically different ecotypes, occupying distinct but overlapping light niches in the photic zone. At comparable depths, similar banding patterns were observed throughout the sampled area, suggesting a horizontal homogenization of ecotypes. Nevertheless, environmental pcb gene sequences retrieved from different depths at two stations proved all different at the nucleotide level, suggesting a large genetic microdiversity within those ecotypes.
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Affiliation(s)
- Laurence Garczarek
- Station Biologique, UMR 7144 CNRS & Université Pierre et Marie Curie, Roscoff, France.
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