101
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Pourtois J, Tarnita CE, Bonachela JA. Impact of Lytic Phages on Phosphorus- vs. Nitrogen-Limited Marine Microbes. Front Microbiol 2020; 11:221. [PMID: 32153528 PMCID: PMC7047511 DOI: 10.3389/fmicb.2020.00221] [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: 09/27/2019] [Accepted: 01/30/2020] [Indexed: 11/13/2022] Open
Abstract
Lytic viruses kill almost 20% of marine bacteria every day, re-routing nutrients away from the higher trophic levels of the marine food web and back in the microbial loop. Importantly, the effect of this inflow of key elements on the ecosystem depends on the nutrient requirements of bacteria as well as on the elemental composition of the viruses that infect them. Therefore, the influence of viruses on the ecosystem could vary depending on which nutrient is limiting. In this paper, we considered an existing multitrophic model (nutrient, bacteria, zooplankton, and viruses) that accounts for nitrogen limitation, and developed a phosphorus-limited version to assess whether the limiting nutrient alters the role of viruses in the ecosystem. For both versions, we evaluated the stationary state of the system with and without viruses. In agreement with existing results, nutrient release increased with viruses for nitrogen–limited systems, while zooplankton abundance and export to higher trophic levels decreased. We found this to be true also for phosphorus-limited systems, although nutrient release increased less than in nitrogen-limited systems. The latter supports a nutrient-specific response of the ecosystem to viruses. Bacterial concentration decreased in the phosphorus-limited system but increased in most nitrogen-limited cases due to a switch from mostly bottom-up to entirely top-down control by viruses. Our results also show that viral concentration is best predicted by a power-law of bacterial concentration with exponent different from 1. Finally, we found a positive correlation between carbon export and viruses regardless of the limiting nutrient, which led us to suggest viral abundance as a predictor of carbon sink.
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Affiliation(s)
- Julie Pourtois
- Department of Biology, Stanford University, Stanford, CA, United States.,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States
| | - Corina E Tarnita
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States
| | - Juan A Bonachela
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, United States
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102
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Howard-Varona C, Lindback MM, Bastien GE, Solonenko N, Zayed AA, Jang H, Andreopoulos B, Brewer HM, Glavina Del Rio T, Adkins JN, Paul S, Sullivan MB, Duhaime MB. Phage-specific metabolic reprogramming of virocells. ISME JOURNAL 2020; 14:881-895. [PMID: 31896786 PMCID: PMC7082346 DOI: 10.1038/s41396-019-0580-z] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/25/2019] [Accepted: 12/17/2019] [Indexed: 12/22/2022]
Abstract
Ocean viruses are abundant and infect 20–40% of surface microbes. Infected cells, termed virocells, are thus a predominant microbial state. Yet, virocells and their ecosystem impacts are understudied, thus precluding their incorporation into ecosystem models. Here we investigated how unrelated bacterial viruses (phages) reprogram one host into contrasting virocells with different potential ecosystem footprints. We independently infected the marine Pseudoalteromonas bacterium with siphovirus PSA-HS2 and podovirus PSA-HP1. Time-resolved multi-omics unveiled drastically different metabolic reprogramming and resource requirements by each virocell, which were related to phage–host genomic complementarity and viral fitness. Namely, HS2 was more complementary to the host in nucleotides and amino acids, and fitter during infection than HP1. Functionally, HS2 virocells hardly differed from uninfected cells, with minimal host metabolism impacts. HS2 virocells repressed energy-consuming metabolisms, including motility and translation. Contrastingly, HP1 virocells substantially differed from uninfected cells. They repressed host transcription, responded to infection continuously, and drastically reprogrammed resource acquisition, central carbon and energy metabolisms. Ecologically, this work suggests that one cell, infected versus uninfected, can have immensely different metabolisms that affect the ecosystem differently. Finally, we relate phage–host genome complementarity, virocell metabolic reprogramming, and viral fitness in a conceptual model to guide incorporating viruses into ecosystem models.
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Affiliation(s)
- Cristina Howard-Varona
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH, 43210, USA
| | - Morgan M Lindback
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI, 48109, USA
| | - G Eric Bastien
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI, 48109, USA
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH, 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH, 43210, USA
| | - HoBin Jang
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH, 43210, USA
| | - Bill Andreopoulos
- US Department of Energy Joint Genome Institute, 1800 Mitchell Dr #100, Walnut Creek, CA, 94598, USA
| | - Heather M Brewer
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), 902 Battelle Blvd, Richland, WA, 99354, USA
| | - Tijana Glavina Del Rio
- US Department of Energy Joint Genome Institute, 1800 Mitchell Dr #100, Walnut Creek, CA, 94598, USA
| | - Joshua N Adkins
- Biological Science Division, PNNL, 902 Battelle Blvd, Richland, WA, 99354, USA
| | - Subhadeep Paul
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH, 43210, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH, 43210, USA. .,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, 2070 Neil Ave, Columbus, OH, 43210, USA. .,Center for RNA Biology, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, USA.
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI, 48109, USA.
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103
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Bar-On YM, Milo R. The Biomass Composition of the Oceans: A Blueprint of Our Blue Planet. Cell 2019; 179:1451-1454. [DOI: 10.1016/j.cell.2019.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/10/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022]
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104
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Zimmerman AE, Howard-Varona C, Needham DM, John SG, Worden AZ, Sullivan MB, Waldbauer JR, Coleman ML. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nat Rev Microbiol 2019; 18:21-34. [PMID: 31690825 DOI: 10.1038/s41579-019-0270-x] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2019] [Indexed: 12/23/2022]
Abstract
Ecosystems are controlled by 'bottom-up' (resources) and 'top-down' (predation) forces. Viral infection is now recognized as a ubiquitous top-down control of microbial growth across ecosystems but, at the same time, cell death by viral predation influences, and is influenced by, resource availability. In this Review, we discuss recent advances in understanding the biogeochemical impact of viruses, focusing on how metabolic reprogramming of host cells during lytic viral infection alters the flow of energy and nutrients in aquatic ecosystems. Our synthesis revealed several emerging themes. First, viral infection transforms host metabolism, in part through virus-encoded metabolic genes; the functions performed by these genes appear to alleviate energetic and biosynthetic bottlenecks to viral production. Second, viral infection depends on the physiological state of the host cell and on environmental conditions, which are challenging to replicate in the laboratory. Last, metabolic reprogramming of infected cells and viral lysis alter nutrient cycling and carbon export in the oceans, although the net impacts remain uncertain. This Review highlights the need for understanding viral infection dynamics in realistic physiological and environmental contexts to better predict their biogeochemical consequences.
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Affiliation(s)
- Amy E Zimmerman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | | | - David M Needham
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Seth G John
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, USA.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA.
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105
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Wei W, Wang N, Cai L, Zhang C, Jiao N, Zhang R. Impacts of Freshwater and Seawater Mixing on the Production and Decay of Virioplankton in a Subtropical Estuary. MICROBIAL ECOLOGY 2019; 78:843-854. [PMID: 30972435 PMCID: PMC6842343 DOI: 10.1007/s00248-019-01362-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
Virioplankton is an important component of the aquatic ecosystem and plays multiple ecological and biogeochemical roles. Although the spatial and temporal distributions and dynamics of virioplankton have been well investigated in riverine and marine environments, little is known about the dynamics and environmental controlling mechanisms of virioplankton in estuaries. In this study, viral abundance, production and decay were examined in the Pearl River Estuary (PRE), one of the largest estuaries in China. The influences of freshwater and seawater mixing on viral ecological dynamics were evaluated with several cross-transplant experiments. In PRE, viral abundance, production and decay rates varied from 2.72 ± 0.09 to 27.5 ± 1.07 × 106 viruses ml-1, 7.98 ± 2.33 to 16.27 ± 2.85% h-1 and 0.80 ± 0.23 to 3.74 ± 0.98% h-1, respectively. When the riverine and marine microbial community were transferred into simulated brackish water, viral production rates were markedly inhibited by 83.8% and 47.3%, respectively. The decay of riverine and marine virioplankton was inhibited by 21.1% and 34.2%, respectively, in simulated brackish water. These results indicate change of estuarine environmental factors significantly alters the dynamics of riverine and marine virioplankton. In addition, the effects of mixing on viral production and decay differed between high- and low-fluorescence viruses. High-fluorescence viruses seemed more resistant to decay than low-fluorescence viruses, whereas the production of marine low-fluorescence viruses seemed more resistant to inhibition than that of marine high-fluorescence viruses. Together, these results provide new insights into the ecological dynamics of virioplankton in estuarine environments.
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Affiliation(s)
- Wei Wei
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Nannan Wang
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Lanlan Cai
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China.
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China.
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.
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106
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Castillo YM, Mangot J, Benites LF, Logares R, Kuronishi M, Ogata H, Jaillon O, Massana R, Sebastián M, Vaqué D. Assessing the viral content of uncultured picoeukaryotes in the global‐ocean by single cell genomics. Mol Ecol 2019; 28:4272-4289. [DOI: 10.1111/mec.15210] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 07/23/2019] [Accepted: 08/01/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Yaiza M. Castillo
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
| | - Jean‐François Mangot
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
| | - Luiz Felipe Benites
- Integrative Biology of Marine Organisms (BIOM) CNRS Oceanological Observatory of Banyuls Sorbonne University Banyuls‐sur‐Mer France
| | - Ramiro Logares
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
| | - Megumi Kuronishi
- Bioinformatic Center Institute for Chemical Research Kyoto University Uji Japan
| | - Hiroyuki Ogata
- Bioinformatic Center Institute for Chemical Research Kyoto University Uji Japan
| | - Olivier Jaillon
- Génomique Métabolique Genoscope Institut de biologie François Jacob CEA CNRS Université d'Evry Université Paris‐Saclay Evry France
| | - Ramon Massana
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
| | - Marta Sebastián
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
- Institute of Oceanography and Global Change (IOCAG) University of Las Palmas de Gran Canaria Telde Spain
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography Institute of Marine Sciences (ICM) CSIC Barcelona Spain
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107
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Abstract
The building blocks of a virus derived from de novo biosynthesis during infection and/or catabolism of preexisting host cell biomass, and the relative contribution of these 2 sources has important consequences for understanding viral biogeochemistry. We determined the uptake of extracellular nitrogen (N) and its biosynthetic incorporation into both virus and host proteins using an isotope-labeling proteomics approach in a model marine cyanobacterium Synechococcus WH8102 infected by a lytic cyanophage S-SM1. By supplying dissolved N as 15N postinfection, we found that proteins in progeny phage particles were composed of up to 41% extracellularly derived N, while proteins of the infected host cell showed almost no isotope incorporation, demonstrating that de novo amino acid synthesis continues during infection and contributes specifically and substantially to phage replication. The source of N for phage protein synthesis shifted over the course of infection from mostly host derived in the early stages to more medium derived later on. We show that the photosystem II reaction center proteins D1 and D2, which are auxiliary metabolic genes (AMGs) in the S-SM1 genome, are made de novo during infection in an apparently light-dependent manner. We also identified a small set of host proteins that continue to be produced during infection; the majority are homologs of AMGs in S-SM1 or other viruses, suggesting selective continuation of host protein production during infection. The continued acquisition of nutrients by the infected cell and their utilization for phage replication are significant for both evolution and biogeochemical impact of viruses.
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108
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Microbial transformation of virus-induced dissolved organic matter from picocyanobacteria: coupling of bacterial diversity and DOM chemodiversity. ISME JOURNAL 2019; 13:2551-2565. [PMID: 31227815 DOI: 10.1038/s41396-019-0449-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/27/2019] [Accepted: 05/03/2019] [Indexed: 02/01/2023]
Abstract
Picocyanobacteria make up half of the ocean's primary production, and they are subjected to frequent viral infection. Viral lysis of picocyanobacteria is a major driving force converting biologically fixed carbon into dissolved organic carbon (DOC). Viral-induced dissolved organic matter (vDOM) released from picocyanobacteria provides complex organic matter to bacterioplankton in the marine ecosystem. In order to understand how picocyanobacterial vDOM are transformed by bacteria and the impact of this process on bacterial community structure, viral lysate of picocyanobacteria was incubated with coastal seawater for 90 days. The transformation of vDOM was analyzed by ultrahigh-resolution mass spectrometry and the shift of bacterial populations analyzed using high-throughput sequencing technology. Addition of picocyanobacterial vDOM introduced abundant nitrogen components into the coastal water, which were largely degraded during the 90 days' incubation period. However, some DOM signatures were accumulated and the total assigned formulae number increased over time. In contrast to the control (no addition of vDOM), bacterial community enriched with vDOM changed markedly with increased biodiversity indices. The network analysis showed that key bacterial species formed complex relationship with vDOM components, suggesting the potential correspondence between bacterial populations and DOM molecules. We demonstrate that coastal bacterioplankton are able to quickly utilize and transform lysis products of picocyanobacteria, meanwhile, bacterial community varies with changing chemodiverisity of DOM. vDOM released from picocyanobacteria generated a complex labile DOM pool, which was converted to a rather stable DOM pool after microbial processing in the time frame of days to weeks.
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109
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Zheng Q, Chen Q, Cai R, He C, Guo W, Wang Y, Shi Q, Chen C, Jiao N. Molecular characteristics of microbially mediated transformations of Synechococcus-derived dissolved organic matter as revealed by incubation experiments. Environ Microbiol 2019; 21:2533-2543. [PMID: 31044472 DOI: 10.1111/1462-2920.14646] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/24/2019] [Accepted: 04/29/2019] [Indexed: 11/28/2022]
Abstract
In this study, we investigated the microbially mediated transformation of labile Synechococcus-derived DOM to RDOM using a 60-day experimental incubation system. Three phases of TOC degradation activity (I, II and III) were observed following the addition of Synechococcus-derived DOM. The phases were characterized by organic carbon consumption rates of 8.77, 1.26 and 0.16 μmol L-1 day-1 , respectively. Excitation emission matrix analysis revealed the presence of three FDOM components including tyrosine-like, fulvic acid-like, and humic-like molecules. The three components also exhibited differing biological availabilities that could be considered as labile DOM (LDOM), semi-labile DOM (SLDOM) and RDOM, respectively. DOM molecular composition was also evaluated using FT-ICR MS. Based on differing biological turnover rates and normalized intensity values, a total of 1704 formulas were identified as candidate LDOM, SLDOM and RDOM molecules. Microbial transformation of LDOM to RDOM tended to proceed from high to low molecular weight, as well as from molecules with high to low double bond equivalent (DBE) values. Relatively higher aromaticity was observed in the formulas of RDOM molecules relative to those of LDOM molecules. FDOM components provide valuable proxy information to investigate variation in the bioavailability of DOM. These results suggest that coordinating fluorescence spectroscopy and FT-ICR MS of DOM, as conducted here, is an effective strategy to identify and characterize LDOM, SLDOM and RDOM molecules in incubation experiments emulating natural systems. The results described here provide greater insight into the metabolism of phytoplankton photosynthate by heterotrophic bacteria in marine environments.
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Affiliation(s)
- Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Collage of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.,Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Qi Chen
- State Key Laboratory for Marine Environmental Science, Collage of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.,Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Ruanhong Cai
- State Key Laboratory for Marine Environmental Science, Collage of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.,Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
| | - Weidong Guo
- State Key Laboratory for Marine Environmental Science, Collage of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.,Key Laboratory of Coastal and Wetland Ecosystems, Ministry of Education, Xiamen University, Xiamen, People's Republic of China
| | - Yu Wang
- State Key Laboratory for Marine Environmental Science, Collage of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.,Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
| | - Chang Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, People's Republic of China.,Xisha Deep Sea Marine Environment Observation and Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sansha, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Collage of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.,Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
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110
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Talmy D, Beckett SJ, Taniguchi DAA, Brussaard CPD, Weitz JS, Follows MJ. An empirical model of carbon flow through marine viruses and microzooplankton grazers. Environ Microbiol 2019; 21:2171-2181. [PMID: 30969467 DOI: 10.1111/1462-2920.14626] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 04/03/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022]
Abstract
Viruses and microzooplankton grazers represent major sources of mortality for marine phytoplankton and bacteria, redirecting the flow of organic material throughout the world's oceans. Here, we investigate the use of nonlinear population models of interactions between phytoplankton, viruses and grazers as a means to quantitatively constrain the flow of carbon through marine microbial ecosystems. We augment population models with a synthesis of laboratory-based estimates of prey, predator and viral life history traits that constrain transfer efficiencies. We then apply the model framework to estimate loss rates in the California Current Ecosystem (CCE). With our empirically parameterized model, we estimate that, of the total losses mediated by viruses and microzooplankton grazing at the focal CCE site, 22 ± 3%, 46 ± 27%, 3 ± 2% and 29 ± 20% were directed to grazers, sloppy feeding (as well as excretion and respiration), viruses and viral lysate respectively. We identify opportunities to leverage ecosystem models and conventional mortality assays to further constrain the quantitative rates of critical ecosystem processes.
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Affiliation(s)
- David Talmy
- Department of Microbiology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Stephen J Beckett
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Darcy A A Taniguchi
- Biology Department, California State University San Marcos, San Marcos, CA, USA
| | - Corina P D Brussaard
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute of Sea Research and University of Utrecht, Utrecht, the Netherlands
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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111
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Pan D, Morono Y, Inagaki F, Takai K. An Improved Method for Extracting Viruses From Sediment: Detection of Far More Viruses in the Subseafloor Than Previously Reported. Front Microbiol 2019; 10:878. [PMID: 31110497 PMCID: PMC6501758 DOI: 10.3389/fmicb.2019.00878] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/05/2019] [Indexed: 01/21/2023] Open
Abstract
Viruses are the most abundant biological entities on Earth and perform essential ecological functions in aquatic environments by mediating biogeochemical cycling and lateral gene transfer. Cellular life as well as viruses have been found in deep subseafloor sediment. However, the study of deep sediment viruses has been hampered by the complexities involved in efficiently extracting viruses from a sediment matrix. Here, we developed a new method for the extraction of viruses from sediment based on density separation using a Nycodenz density step gradient. The density separation method resulted in up to 2 orders of magnitude greater recovery of viruses from diverse subseafloor sediments compared to conventional methods. The density separation method also showed more consistent performance between samples of different sediment lithology, whereas conventional virus extraction methods were highly inconsistent. Using this new method, we show that previously published virus counts have underestimated viral abundances by up to 2 orders of magnitude. These improvements suggest that the carbon contained within viral biomass in the subseafloor environment may potentially be revised upward to 0.8-3.7 Gt from current estimates of 0.2 Gt. The vastly improved recovery of viruses indicate that viruses represent a far larger pool of organic carbon in subseafloor environments than previously estimated.
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Affiliation(s)
- Donald Pan
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Nankoku, Japan
- Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Nankoku, Japan
- Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
- Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science and Technology, Yokohama, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
- Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
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112
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Li Y, Sun H, Yang W, Chen G, Xu H. Dynamics of Bacterial and Viral Communities in Paddy Soil with Irrigation and Urea Application. Viruses 2019; 11:E347. [PMID: 31014039 PMCID: PMC6520780 DOI: 10.3390/v11040347] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 01/21/2023] Open
Abstract
Viruses are ubiquitous in natural systems. By influencing bacterial abundance (BA) and community structure through lysis-lysogenic conversion, viruses are involved in various ecological processes. In agricultural management, nitrogen addition and irrigation should be considered as important factors that can modify soil viral dynamics but have been ignored. In our study, short-term dynamics of autochthonous soil viral and bacterial abundance and diversity after irrigation and urea application were examined in a long-term experimental paddy field. Urea addition delayed the emergence of peak viral abundance for three days, suggesting that viruses are sensitive to N addition. Under short-term eutrophic conditions through urea application, viruses undertake a lysogenic-biased strategy. Moreover, nitrogen-fixing bacteria were most likely specifically lysed in urea-treated soil, which suggests that soil viruses block N accumulation by killing nitrogen-fixing bacteria. To the best of our knowledge, this study is the first to investigate dynamic changes in autochthonous viruses in paddy fields.
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Affiliation(s)
- Yuting Li
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- National Field Observation and Research Station of Shenyang Agro-Ecosystems, Shenyang 110016, China.
| | - Hao Sun
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Weichao Yang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Guanxiong Chen
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Hui Xu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
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113
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Baltar F, De Corte D, Thomson B, Yokokawa T. Teasing apart the different size pools of extracellular enzymatic activity in the ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 660:690-696. [PMID: 30743954 DOI: 10.1016/j.scitotenv.2019.01.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/03/2019] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
Extracellular enzymatic activity (EEA) is performed by cell-associated and cell-free (i.e., "dissolved") enzymes. This cell-free fraction is operationally defined as passing through a 0.22 μm filter. The contribution of cell-free to total EEA is comparable to the cell-associated counterpart, so it is critical to understand what controls the relative importance of cell-free versus cell-associated EEA. However, attempts to tease apart the contribution of EEAs in the so-called dissolved fraction (<0.22 μm) in general, and of the nanoparticle size fraction (0.020-0.20 μm) in particular, to the total EEA pool are lacking. Here we performed experiments with Northern and Southern Hemisphere coastal waters to characterize the potential contribution of that nanoparticle fraction to the total EEA fraction of alkaline phosphatase, beta-glucosidase and leucine aminopeptidase. We found a significant contribution (in both hemispheres) of the nanoparticle fraction to the total EEA pool (up to 53%) that differed depending on the enzyme type and location. Collectively, our results indicate that a significant fraction of the so-called "dissolved EEA" is not really dissolved but associated to nanoparticles, colloidal nanogels and/or viruses. Thus, the total marine EEA pool can actually be divided into a cell-associated, undissolved-cell-free (associated to nano-particle of different origins such as viruses and nanogels) and a dissolved-cell-free pools. Our results also imply that the dissolved EEA pool is more complex than thus far anticipated. Future research will be now needed to further characterize the factors controlling the relative importance of these different pools of EEA, which are key in the recycling of organic matter in the ocean.
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Affiliation(s)
- Federico Baltar
- Department of Limnology and Bio-Oceanography, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria; Department of Marine Science, University of Otago, New Zealand.
| | - Daniele De Corte
- Japanese Agency for Marine-Earth Science and Technology (JAMSTEC), Japan
| | - Blair Thomson
- Department of Limnology and Bio-Oceanography, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria; Department of Marine Science, University of Otago, New Zealand
| | - Taichi Yokokawa
- Japanese Agency for Marine-Earth Science and Technology (JAMSTEC), Japan
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114
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Cheng K, Frenken T, Brussaard CPD, Van de Waal DB. Cyanophage Propagation in the Freshwater Cyanobacterium Phormidium Is Constrained by Phosphorus Limitation and Enhanced by Elevated pCO 2. Front Microbiol 2019; 10:617. [PMID: 30984143 PMCID: PMC6449453 DOI: 10.3389/fmicb.2019.00617] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/11/2019] [Indexed: 11/17/2022] Open
Abstract
Intensification of human activities has led to changes in the availabilities of CO2 and nutrients in freshwater ecosystems, which may greatly alter the physiological status of phytoplankton. Viruses require hosts for their reproduction and shifts in phytoplankton host physiology through global environmental change may thus affect viral infections as well. Various studies have investigated the impacts of single environmental factors on phytoplankton virus propagation, yet little is known about the impacts of multiple factors, particularly in freshwater systems. We therefore tested the combined effects of phosphorus limitation and elevated pCO2 on the propagation of a cyanophage infecting a freshwater cyanobacterium. To this end, we cultured Phormidium in P-limited chemostats under ambient (400 μatm) and elevated (800 μatm) pCO2 at growth rates of 0.6, 0.3, and 0.05 d-1. Host C:P ratios generally increased with strengthened P-limitation and with elevated pCO2. Upon host steady state conditions, virus growth characteristics were obtained in separate infection assays where hosts were infected by the double-stranded DNA cyanophage PP. Severe P-limitation (host growth 0.05 d-1) led to a 85% decrease in cyanophage production rate and a 73% decrease in burst size compared to the 0.6 d-1 grown P-limited cultures. Elevated pCO2 induced a 96% increase in cyanophage production rate and a 57% increase in burst size, as well as an 85% shorter latent period as compared to ambient pCO2 at the different host growth rates. In addition, elevated pCO2 caused a decrease in the plaquing efficiency and an increase in the abortion percentage for the 0.05 d-1 P-limited treatment, while the plaquing efficiency increased for the 0.6 d-1 P-limited cultures. Together, our results demonstrate interactive effects of elevated pCO2 and P-limitation on cyanophage propagation, and show that viral propagation is generally constrained by P-limitation but enhanced with elevated pCO2. Our findings indicate that global change will likely have a severe impact on virus growth characteristics and thereby on the control of cyanobacterial hosts in freshwater ecosystems.
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Affiliation(s)
- Kai Cheng
- Hubei Key Laboratory of Ecological Restoration for River-Lakes and Algal Utilization, College of Resources and Environmental Engineering, Hubei University of Technology, Wuhan, China.,Department of Aquatic Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Thijs Frenken
- Department of Aquatic Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Corina P D Brussaard
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research and University of Utrecht, Texel, Netherlands
| | - Dedmer B Van de Waal
- Department of Aquatic Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
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115
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Larsen ML, Wilhelm SW, Lennon JT. Nutrient stoichiometry shapes microbial coevolution. Ecol Lett 2019; 22:1009-1018. [DOI: 10.1111/ele.13252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/10/2018] [Accepted: 02/18/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Megan L. Larsen
- Department of Biology Indiana University Bloomington IN47405USA
| | - Steven W. Wilhelm
- Department of Microbiology University of Tennessee Knoxville TN37996 USA
| | - Jay T. Lennon
- Department of Biology Indiana University Bloomington IN47405USA
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116
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Kupczok A, Neve H, Huang KD, Hoeppner MP, Heller KJ, Franz CMAP, Dagan T. Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades. Mol Biol Evol 2019; 35:1147-1159. [PMID: 29688542 PMCID: PMC5913663 DOI: 10.1093/molbev/msy027] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The evolution of asexual organisms is driven not only by the inheritance of genetic modification but also by the acquisition of foreign DNA. The contribution of vertical and horizontal processes to genome evolution depends on their rates per year and is quantified by the ratio of recombination to mutation. These rates have been estimated for bacteria; however, no estimates have been reported for phages. Here, we delineate the contribution of mutation and recombination to dsDNA phage genome evolution. We analyzed 34 isolates of the 936 group of Siphoviridae phages using a Lactococcus lactis strain from a single dairy over 29 years. We estimate a constant substitution rate of 1.9 × 10−4 substitutions per site per year due to mutation that is within the range of estimates for eukaryotic RNA and DNA viruses. The reconstruction of recombination events reveals a constant rate of five recombination events per year and 4.5 × 10−3 nucleotide alterations due to recombination per site per year. Thus, the recombination rate exceeds the substitution rate, resulting in a relative effect of recombination to mutation (r/m) of ∼24 that is homogenous over time. Especially in the early transcriptional region, we detect frequent gene loss and regain due to recombination with phages of the 936 group, demonstrating the role of the 936 group pangenome as a reservoir of genetic variation. The observed substitution rate homogeneity conforms to the neutral theory of evolution; hence, the neutral theory can be applied to phage genome evolution and also to genetic variation brought about by recombination.
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Affiliation(s)
- Anne Kupczok
- Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Kiel, Germany
| | - Kun D Huang
- Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Marc P Hoeppner
- Institute of Clinical Molecular Biology (IKMB), Kiel University, Kiel, Germany
| | - Knut J Heller
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food), Kiel, Germany
| | - Tal Dagan
- Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel, Germany
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117
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Calero-Cáceres W, Balcázar JL. Antibiotic resistance genes in bacteriophages from diverse marine habitats. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:452-455. [PMID: 30447583 DOI: 10.1016/j.scitotenv.2018.11.166] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/18/2018] [Accepted: 11/11/2018] [Indexed: 06/09/2023]
Abstract
Although antibiotic resistance represents a significant and growing threat to human and environmental health worldwide, the contribution of bacteriophages (phages) to the acquisition and spread of antibiotic resistance genes (ARGs) in the environment has not been extensively explored. In this study, a comprehensive analysis of several viromes from diverse marine habitats was performed to investigate whether or not phages carry ARGs. The analysis provides strong evidence that phages from marine habitats are potential reservoirs of ARGs. In fact, genes conferring resistance to aminocoumarin, bacitracin and multidrug resistance (particularly the mexB gene) were found in all analyzed marine viromes. Given this, the role of phages as reservoirs of ARGs should not be underestimated considering their global distribution.
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Affiliation(s)
- William Calero-Cáceres
- UTA-RAM-OneHealth Group, Centro de Investigaciones Agropecuarias, Facultad de Ciencias Agropecuarias, Universidad Técnica de Ambato, Tungurahua, Ecuador
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), University of Girona, Girona, Spain.
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118
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Welkie DG, Rubin BE, Diamond S, Hood RD, Savage DF, Golden SS. A Hard Day's Night: Cyanobacteria in Diel Cycles. Trends Microbiol 2019; 27:231-242. [PMID: 30527541 PMCID: PMC6377297 DOI: 10.1016/j.tim.2018.11.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/31/2022]
Abstract
Cyanobacteria are photosynthetic prokaryotes that are influential in global geochemistry and are promising candidates for industrial applications. Because the livelihood of cyanobacteria is directly dependent upon light, a comprehensive understanding of metabolism in these organisms requires taking into account the effects of day-night transitions and circadian regulation. These events synchronize intracellular processes with the solar day. Accordingly, metabolism is controlled and structured differently in cyanobacteria than in heterotrophic bacteria. Thus, the approaches applied to engineering heterotrophic bacteria will need to be revised for the cyanobacterial chassis. Here, we summarize important findings related to diurnal metabolism in cyanobacteria and present open questions in the field.
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Affiliation(s)
- David G Welkie
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Benjamin E Rubin
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Spencer Diamond
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA 94720, USA
| | - Rachel D Hood
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA
| | - David F Savage
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA
| | - Susan S Golden
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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119
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Finke JF, Suttle CA. The Environment and Cyanophage Diversity: Insights From Environmental Sequencing of DNA Polymerase. Front Microbiol 2019; 10:167. [PMID: 30800109 PMCID: PMC6375837 DOI: 10.3389/fmicb.2019.00167] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/22/2019] [Indexed: 11/13/2022] Open
Abstract
Globally distributed and abundant cyanophages in the family Myoviridae have dsDNA genomes with variable gene content, including host-derived auxiliary metabolic genes (AMGs) that potentially can facilitate viral replication. However, it is not well understood how this variation in gene content interacts with environmental variables to shape cyanomyovirus communities. This project correlated the genetic repertoire of cyanomyoviruses with their phyologeny, and investigated cyanomyovirus ecotype distribution as a function of environmental conditions across locations and seasons. Reference cyanomyovirus genomes were compared for their overlap in gene content to infer phyologenetic distances, and these distances were compared to distances calculated based on DNA polymerase (gp43) gene sequences. In turn, gp43 partial gene sequences amplified from natural cyanophage communities were used to describe cyanomyovirus community composition and to assess the relationship between environmental variables. The results showed the following: (1) DNA polymerase gene phylogeny generally correlated with the similarity in gene content among reference cyanomyoviruses, and thus can be used to describe environmental cyanomyovirus communities; (2) spatial and seasonal patterns in cyanomyovirus communities were related to environmental variables; (3) salinity and temperature, combined with nutrient concentration were predictors of cyanomyovirus richness, diversity and community composition. This study shows that environmental variables shape viral communities by drawing on a diverse seed bank of viral genotypes. From these results it is evident that that viral ecotypes with their corresponding genetic repertoires underlie selection pressures. However, the mechanisms involved in selecting for specific viral genotypes remain to be fully understood.
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Affiliation(s)
- Jan F. Finke
- Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Curtis A. Suttle
- Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
- Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, BC, Canada
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120
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Harrison AO, Moore RM, Polson SW, Wommack KE. Reannotation of the Ribonucleotide Reductase in a Cyanophage Reveals Life History Strategies Within the Virioplankton. Front Microbiol 2019; 10:134. [PMID: 30804913 PMCID: PMC6370689 DOI: 10.3389/fmicb.2019.00134] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 01/21/2019] [Indexed: 01/16/2023] Open
Abstract
Ribonucleotide reductases (RNRs) are ancient enzymes that catalyze the reduction of ribonucleotides to deoxyribonucleotides. They are required for virtually all cellular life and are prominent within viral genomes. RNRs share a common ancestor and must generate a protein radical for direct ribonucleotide reduction. The mechanisms by which RNRs produce radicals are diverse and divide RNRs into three major classes and several subclasses. The diversity of radical generation methods means that cellular organisms and viruses typically contain the RNR best-suited to the environmental conditions surrounding DNA replication. However, such diversity has also fostered high rates of RNR misannotation within subject sequence databases. These misannotations have resulted in incorrect translative presumptions of RNR biochemistry and have diminished the utility of this marker gene for ecological studies of viruses. We discovered a misannotation of the RNR gene within the Prochlorococcus phage P-SSP7 genome, which caused a chain of misannotations within commonly observed RNR genes from marine virioplankton communities. These RNRs are found in marine cyanopodo- and cyanosiphoviruses and are currently misannotated as Class II RNRs, which are O2-independent and require cofactor B12. In fact, these cyanoviral RNRs are Class I enzymes that are O2-dependent and may require a di-metal cofactor made of Fe, Mn, or a combination of the two metals. The discovery of an overlooked Class I β subunit in the P-SSP7 genome, together with phylogenetic analysis of the α and β subunits confirms that the RNR from P-SSP7 is a Class I RNR. Phylogenetic and conserved residue analyses also suggest that the P-SSP7 RNR may constitute a novel Class I subclass. The reannotation of the RNR clade represented by P-SSP7 means that most lytic cyanophage contain Class I RNRs, while their hosts, B12-producing Synechococcus and Prochlorococcus, contain Class II RNRs. By using a Class I RNR, cyanophage avoid a dependence on host-produced B12, a more effective strategy for a lytic virus. The discovery of a novel RNR β subunit within cyanopodoviruses also implies that some unknown viral genes may be familiar cellular genes that are too divergent for homology-based annotation methods to identify.
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Affiliation(s)
- Amelia O. Harrison
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
| | - Ryan M. Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States
| | - Shawn W. Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States
| | - K. Eric Wommack
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
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121
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Yang Y, Gu X, Te SH, Goh SG, Mani K, He Y, Gin KYH. Occurrence and distribution of viruses and picoplankton in tropical freshwater bodies determined by flow cytometry. WATER RESEARCH 2019; 149:342-350. [PMID: 30469020 DOI: 10.1016/j.watres.2018.11.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 10/11/2018] [Accepted: 11/11/2018] [Indexed: 06/09/2023]
Abstract
This study aimed to examine the drivers in shaping the occurrence and distribution of total viruses and picoplankton in tropical freshwater ecosystems. Flow cytometry was used to quantify the concentrations of total viruses, picoheterotrophs, picophytoplankton, and picocyanobacteria. Three land use patterns (urban-, agriculture- and parkland-dominated) were evaluated using ArcGIS. Significant correlations were observed between water-borne microbial targets and water quality parameters (0.175 ≤ |r| ≤ 0.441), nutrients (0.250 ≤ r ≤ 0.570) and land use factors (0.200 ≤ |r| ≤ 0.460). In particular, the concentrations of total viruses and picoheterotrophic cells were higher in catchments whereas the abundances of picophytoplankton and picocyanobacteria were higher in reservoirs. Total viruses and picoplankton had higher concentrations in urban- and agriculture-dominated areas, probably due to anthropogenic inputs and agricultural inputs, respectively. Although surface water is a complex matrix influenced by niche-based (i.e., physicochemical properties, nutrients, land use impact etc.) and neutral-based factors (i.e., ecological drift, dispersal and species), land use patterns could help to elucidate the occurrence and distribution of the total microbial community at the macroscopic level. Meanwhile, inter-correlations among viruses, picoplankton and picoheterotrophs (0.715 ≤ r ≤ 0.990) also substantiates their mutual interactions in influencing the microbial community. Furthermore, the relationships between total microbial cells and bacterial and viral indicators were also investigated. Concentrations of total viruses, picoplankton and picoheterotrophs were positively correlated with bacterial indicators (0.427 ≤ r ≤ 0.590) and viral indicators (0.201 ≤ r ≤ 0.563). These results indicated that faecal and viral contamination could contribute to the numbers of total viruses and bacteria.
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Affiliation(s)
- Yi Yang
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
| | - Xiaoqiong Gu
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
| | - Shu Harn Te
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
| | - Shin Giek Goh
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
| | - Kalaivani Mani
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore; Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore.
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122
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Yang Q, Gao C, Jiang Y, Wang M, Zhou X, Shao H, Gong Z, McMinn A. Metagenomic Characterization of the Viral Community of the South Scotia Ridge. Viruses 2019; 11:E95. [PMID: 30678352 PMCID: PMC6410227 DOI: 10.3390/v11020095] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/28/2018] [Accepted: 01/22/2019] [Indexed: 12/16/2022] Open
Abstract
Viruses are the most abundant biological entities in aquatic ecosystems and harbor an enormous amount of genetic diversity. Whereas their influence on marine ecosystems is widely acknowledged, current information about their diversity remains limited. We conducted a viral metagenomic analysis of water samples collected during the austral summer of 2016 from the South Scotia Ridge (SSR), near the Antarctic Peninsula. The taxonomic composition and diversity of the viral communities were investigated, and a functional assessment of the sequences was performed. Phylotypic analysis showed that most viruses belonged to the order Caudovirales, especially the family Podoviridae (41.92⁻48.7%), which is similar to the situation in the Pacific Ocean. Functional analysis revealed a relatively high frequency of phage-associated and metabolism genes. Phylogenetic analyses of phage TerL and Capsid_NCLDV (nucleocytoplasmic large DNA viruses) marker genes indicated that many sequences associated with Caudovirales and NCLDV were novel and distinct from known phage genomes. High Phaeocystis globosa virus virophage (Pgvv) signatures were found and complete and partial Pgvv-like were obtained, which influence host⁻virus interactions. Our study expands existing knowledge of viral communities and their diversities from the Antarctic region and provides basic data for further exploring polar microbiomes.
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Affiliation(s)
- Qingwei Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Chen Gao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Xinhao Zhou
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Zheng Gong
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Andrew McMinn
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia.
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123
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Jacquiod S, Nunes I, Brejnrod A, Hansen MA, Holm PE, Johansen A, Brandt KK, Priemé A, Sørensen SJ. Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages. MICROBIOME 2018; 6:223. [PMID: 30545417 PMCID: PMC6292020 DOI: 10.1186/s40168-018-0606-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/25/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND It remains unclear whether adaptation and changes in diversity associated to a long-term perturbation are sufficient to ensure functional resilience of soil microbial communities. We used RNA-based approaches (16S rRNA gene transcript amplicon coupled to shotgun mRNA sequencing) to study the legacy effects of a century-long soil copper (Cu) pollution on microbial activity and composition, as well as its effect on the capacity of the microbial community to react to temporal fluctuations. RESULTS Despite evidence of microbial adaptation (e.g., iron homeostasis and avoidance/resistance strategies), increased heterogeneity and richness loss in transcribed gene pools were observed with increasing soil Cu, together with an unexpected predominance of phage mRNA signatures. Apparently, phage activation was either triggered directly by Cu, or indirectly via enhanced expression of DNA repair/SOS response systems in Cu-exposed bacteria. Even though total soil carbon and nitrogen had accumulated with increasing Cu, a reduction in temporally induced mRNA functions was observed. Microbial temporal response groups (TRGs, groups of microbes with a specific temporal response) were heavily affected by Cu, both in abundance and phylogenetic composition. CONCLUSION Altogether, results point toward a Cu-mediated "decoupling" between environmental fluctuations and microbial activity, where Cu-exposed microbes stopped fulfilling their expected contributions to soil functioning relative to the control. Nevertheless, some functions remained active in February despite Cu, concomitant with an increase in phage mRNA signatures, highlighting that somehow, microbial activity is still happening under these adverse conditions.
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Affiliation(s)
- Samuel Jacquiod
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Agroécologie, AgroSup Dijon, INRA, Univ Bourgogne Franche-Comté, 17 rue Sully, 21000, Dijon, France
| | - Inês Nunes
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Present address: Microbe Technology Department, Novozymes A/S, Krogshoejvej 36, 2880, Bagsværd, Denmark
| | - Asker Brejnrod
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Present address: Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3A, 2200, Copenhagen, Denmark
| | - Martin A Hansen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Peter E Holm
- Present address: Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Anders Johansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Kristian K Brandt
- Present address: Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Anders Priemé
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.
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124
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Diversity of Active Viral Infections within the Sphagnum Microbiome. Appl Environ Microbiol 2018; 84:AEM.01124-18. [PMID: 30217851 DOI: 10.1128/aem.01124-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/10/2018] [Indexed: 11/20/2022] Open
Abstract
Sphagnum-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the Sphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnum peat bog. The vegetative portions of six Sphagnum plants were obtained from a peatland in northern Minnesota, and the total RNA was extracted and sequenced. Metatranscriptomes were assembled and contigs were screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein gp23 as a marker for phage diversity, we identified 33 contigs representing undocumented phages that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the nucleocytoplasmic large DNA virus (NCLDV) major capsid protein were used as markers for single-stranded RNA (ssRNA) viruses and NCLDV, respectively. In total, 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent nearly complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinton-like viruses. We developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene rpb1 to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades and suggests that viruses may play a considerable role in the ecology of the Sphagnum microbiome.IMPORTANCE Sphagnum-dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor the growth of Sphagnum over that of other plant species. This lowers the rate of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by Sphagnum enriches for the growth of a diverse microbial consortia that benefit from and support the moss's growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize Sphagnum, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. This study provides insight into the significant viral influence on the Sphagnum microbiome and identifies new potential model systems to study virus-host interactions in the peatland ecosystem.
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125
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Zhang QY, Gui JF. Diversity, evolutionary contribution and ecological roles of aquatic viruses. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1486-1502. [DOI: 10.1007/s11427-018-9414-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/26/2018] [Indexed: 01/21/2023]
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126
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Coloma S, Gaedke U, Sivonen K, Hiltunen T. Frequency of virus-resistant hosts determines experimental community dynamics. Ecology 2018; 100:e02554. [PMID: 30411791 DOI: 10.1002/ecy.2554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 09/19/2018] [Accepted: 10/01/2018] [Indexed: 11/11/2022]
Abstract
Parasites, such as bacterial viruses (phages), can have large effects on host populations both at the ecological and evolutionary levels. In the case of cyanobacteria, phages can reduce primary production and infected hosts release intracellular nutrients influencing planktonic food web structure, community dynamics, and biogeochemical cycles. Cyanophages may be of great importance in aquatic food webs during large cyanobacterial blooms unless the host population becomes resistant to phage infection. The consequences on plankton community dynamics of the evolution of phage resistance in bloom forming cyanobacterial populations are still poorly studied. Here, we examined the effect of different frequencies of a phage-resistant genotype within a filamentous nitrogen-fixing Nodularia spumigena population on an experimental plankton community. Three Nodularia populations with different initial frequencies (0%, 5%, and 50%) of phage-resistant genotypes were inoculated in separate treatments with the phage 2AV2, the green alga Chlorella vulgaris, and the rotifer Brachionus plicatilis, which formed the experimental plankton community subjected to either nitrogen-limited or nitrogen-rich conditions. We found that the frequency of the phage-resistant Nodularia genotype determined experimental community dynamics. Cyanobacterial populations with a high frequency (50%) of the phage-resistant genotype dominated the cultures despite the presence of phages, retaining most of the intracellular nitrogen in the plankton community. In contrast, populations with low frequencies (0% and 5%) of the phage-resistant genotype were lysed and reduced to extinction by the phage, transferring the intracellular nitrogen held by Nodularia to Chlorella and rotifers, and allowing Chlorella to dominate the communities and rotifers to survive. This study shows that even though phages represent minuscule biomass, they can have key effects on community composition and eco-evolutionary feedbacks in plankton communities.
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Affiliation(s)
- Sebastián Coloma
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - Ursula Gaedke
- Department of Ecology and Ecosystem Modelling, Institute for Biochemistry and Biology, University of Potsdam, Am Neuen Palais 10, 14469, Potsdam, Germany
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - Teppo Hiltunen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland.,Department of Biology, University of Turku, 20014, Turku, Finland
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127
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Zhang X, Xu W, Liu Y, Cai M, Luo Z, Li M. Metagenomics Reveals Microbial Diversity and Metabolic Potentials of Seawater and Surface Sediment From a Hadal Biosphere at the Yap Trench. Front Microbiol 2018; 9:2402. [PMID: 30369913 PMCID: PMC6194347 DOI: 10.3389/fmicb.2018.02402] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/19/2018] [Indexed: 11/13/2022] Open
Abstract
Hadal biosphere represents the deepest part of the ocean with water depth >6,000 m. Accumulating evidence suggests the existence of unique microbial communities dominated by heterotrophic processes in this environment. However, investigations of the microbial diversity and their metabolic potentials are limited because of technical constraints for sample collection. Here, we provide a detailed metagenomic analysis of three seawater samples at water depths 5,000-6,000 m below sea level (mbsl) and three surface sediment samples at water depths 4,435-6,578 mbsl at the Yap Trench of the western Pacific. Distinct microbial community compositions were observed with the dominance of Gammaproteobacteria in seawater and Thaumarchaeota in surface sediment. Comparative analysis of the genes involved in carbon, nitrogen and sulfur metabolisms revealed that heterotrophic processes (i.e., degradation of carbohydrates, hydrocarbons, and aromatics) are the most common microbial metabolisms in the seawater, while chemolithoautotrophic metabolisms such as ammonia oxidation with the HP/HB cycle for CO2 fixation probably dominated the surface sediment communities of the Yap Trench. Furthermore, abundant genes involved in stress response and metal resistance were both detected in the seawater and sediments, thus the enrichment of metal resistance genes is further hypothesized to be characteristic of the hadal microbial communities. Overall, this study sheds light on the metabolic versatility of microorganisms in the Yap Trench, their roles in carbon, nitrogen, and sulfur biogeochemical cycles, and how they have adapted to this unique hadal environment.
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Affiliation(s)
- Xinxu Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Mingwei Cai
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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128
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Bachy C, Charlesworth CJ, Chan AM, Finke JF, Wong CH, Wei CL, Sudek S, Coleman ML, Suttle CA, Worden AZ. Transcriptional responses of the marine green alga Micromonas pusilla and an infecting prasinovirus under different phosphate conditions. Environ Microbiol 2018; 20:2898-2912. [PMID: 29749714 DOI: 10.1111/1462-2920.14273] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/06/2018] [Accepted: 05/07/2018] [Indexed: 12/12/2022]
Abstract
Prasinophytes are widespread marine algae for which responses to nutrient limitation and viral infection are not well understood. We studied the picoprasinophyte, Micromonas pusilla, grown under phosphate-replete (0.65 ± 0.07 d-1 ) and 10-fold lower (low)-phosphate (0.11 ± 0.04 d-1 ) conditions, and infected by the phycodnavirus MpV-SP1. Expression of 17% of Micromonas genes in uninfected cells differed by >1.5-fold (q < 0.01) between nutrient conditions, with genes for P-metabolism and the uniquely-enriched Sel1-like repeat (SLR) family having higher relative transcript abundances, while phospholipid-synthesis genes were lower in low-P than P-replete. Approximately 70% (P-replete) and 30% (low-P) of cells were lysed 24 h post-infection, and expression of ≤5.8% of host genes changed relative to uninfected treatments. Host genes for CAZymes and glycolysis were activated by infection, supporting importance in viral production, which was significantly lower in slower growing (low-P) hosts. All MpV-SP1 genes were expressed, and our analyses suggest responses to differing host-phosphate backgrounds involve few viral genes, while the temporal program of infection involves many more, and is largely independent of host-phosphate background. Our study (i) identifies genes previously unassociated with nutrient acclimation or viral infection, (ii) provides insights into the temporal program of prasinovirus gene expression by hosts and (iii) establishes cell biological aspects of an ecologically important host-prasinovirus system that differ from other marine algal-virus systems.
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Affiliation(s)
- Charles Bachy
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Christina J Charlesworth
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Amy M Chan
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jan F Finke
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Chee-Hong Wong
- Lawrence Berkeley National Laboratory, Sequencing Technology Group, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Chia-Lin Wei
- Lawrence Berkeley National Laboratory, Sequencing Technology Group, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada.,Departments of Botany, and Microbiology & Immunology, and Institute of Oceans & Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada
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129
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Horas EL, Theodosiou L, Becks L. Why Are Algal Viruses Not Always Successful? Viruses 2018; 10:v10090474. [PMID: 30189587 PMCID: PMC6165140 DOI: 10.3390/v10090474] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/31/2018] [Accepted: 09/02/2018] [Indexed: 12/14/2022] Open
Abstract
Algal viruses are considered to be key players in structuring microbial communities and biogeochemical cycles due to their abundance and diversity within aquatic systems. Their high reproduction rates and short generation times make them extremely successful, often with immediate and strong effects for their hosts and thus in biological and abiotic environments. There are, however, conditions that decrease their reproduction rates and make them unsuccessful with no or little immediate effects. Here, we review the factors that lower viral success and divide them into intrinsic—when they are related to the life cycle traits of the virus—and extrinsic factors—when they are external to the virus and related to their environment. Identifying whether and how algal viruses adapt to disadvantageous conditions will allow us to better understand their role in aquatic systems. We propose important research directions such as experimental evolution or the resurrection of extinct viruses to disentangle the conditions that make them unsuccessful and the effects these have on their surroundings.
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Affiliation(s)
- Elena L Horas
- Community Dynamics Group, Max-Planck for Evolutionary Biology, 24306 Plön, Germany.
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, 78464 Konstanz, Germany.
| | - Loukas Theodosiou
- Community Dynamics Group, Max-Planck for Evolutionary Biology, 24306 Plön, Germany.
- Department of Microbial Population Biology, Max-Planck for Evolutionary Biology, 24306 Plön, Germany.
| | - Lutz Becks
- Community Dynamics Group, Max-Planck for Evolutionary Biology, 24306 Plön, Germany.
- Limnology-Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, 78464 Konstanz, Germany.
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130
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Quantitative Infection Dynamics of Cafeteria Roenbergensis Virus. Viruses 2018; 10:v10090468. [PMID: 30200276 PMCID: PMC6163432 DOI: 10.3390/v10090468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 08/24/2018] [Accepted: 08/26/2018] [Indexed: 01/29/2023] Open
Abstract
The discovery of giant viruses in unicellular eukaryotic hosts has raised new questions on the nature of viral life. Although many steps in the infection cycle of giant viruses have been identified, the quantitative life history traits associated with giant virus infection remain unknown or poorly constrained. In this study, we provide the first estimates of quantitative infection traits of a giant virus by tracking the infection dynamics of the bacterivorous protist Cafeteria roenbergensis and its lytic virus CroV. Leveraging mathematical models of infection, we quantitatively estimate the adsorption rate, onset of DNA replication, latency time, and burst size from time-series data. Additionally, by modulating the initial ratio of viruses to hosts, we also provide evidence of a potential MOI-dependence on adsorption and burst size. Our work provides a baseline characterization of giant virus infection dynamics relevant to ongoing efforts to understand the ecological role of giant viruses.
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131
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Sanders AJ, Taylor BW. Using ecological stoichiometry to understand and predict infectious diseases. OIKOS 2018. [DOI: 10.1111/oik.05418] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Andrew J. Sanders
- Dept of Applied Ecology; North Carolina State Univ.; Raleigh NC 27695 USA
- Rocky Mountain Biological Laboratory; Crested Butte CO 81224 USA
| | - Brad W. Taylor
- Dept of Applied Ecology; North Carolina State Univ.; Raleigh NC 27695 USA
- Rocky Mountain Biological Laboratory; Crested Butte CO 81224 USA
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132
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White Iii RA, Wong HL, Ruvindy R, Neilan BA, Burns BP. Viral Communities of Shark Bay Modern Stromatolites. Front Microbiol 2018; 9:1223. [PMID: 29951046 PMCID: PMC6008428 DOI: 10.3389/fmicb.2018.01223] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/22/2018] [Indexed: 01/21/2023] Open
Abstract
Single stranded DNA viruses have been previously shown to populate the oceans on a global scale, and are endemic in microbialites of both marine and freshwater systems. We undertook for the first time direct viral metagenomic shotgun sequencing to explore the diversity of viruses in the modern stromatolites of Shark Bay Australia. The data indicate that Shark Bay marine stromatolites have similar diversity of ssDNA viruses to that of Highbourne Cay, Bahamas. ssDNA viruses in cluster uniquely in Shark Bay and Highbourne Cay, potentially due to enrichment by phi29-mediated amplification bias. Further, pyrosequencing data was assembled from the Shark Bay systems into two putative viral genomes that are related to Genomoviridae family of ssDNA viruses. In addition, the cellular fraction was shown to be enriched for antiviral defense genes including CRISPR-Cas, BREX (bacteriophage exclusion), and DISARM (defense island system associated with restriction-modification), a potentially novel finding for these systems. This is the first evidence for viruses in the Shark Bay stromatolites, and these viruses may play key roles in modulating microbial diversity as well as potentially impacting ecosystem function through infection and the recycling of key nutrients.
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Affiliation(s)
- Richard Allen White Iii
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States.,Crop and Soil Sciences, Washington State University, Pullman, WA, United States.,Plant Pathology, Washington State University, Pullman, WA, United States.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,RAW Molecular Systems (RMS) LLC, Spokane, WA, United States
| | - Hon L Wong
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW, Australia
| | - Rendy Ruvindy
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW, Australia
| | - Brett A Neilan
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW, Australia
| | - Brendan P Burns
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW, Australia
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133
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Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol 2018; 3:754-766. [PMID: 29867096 DOI: 10.1038/s41564-018-0166-y] [Citation(s) in RCA: 313] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 04/20/2018] [Indexed: 11/09/2022]
Abstract
Viruses numerically dominate our oceans; however, we have only just begun to document the diversity, host range and infection dynamics of marine viruses, as well as the subsequent effects of infection on both host cell metabolism and oceanic biogeochemistry. Bacteriophages (that is, phages: viruses that infect bacteria) are highly abundant and are known to play critical roles in bacterial mortality, biogeochemical cycling and horizontal gene transfer. This Review Article summarizes current knowledge of marine viral ecology and highlights the importance of phage particles to the dissolved organic matter pool, as well as the complex interactions between phages and their bacterial hosts. We emphasize the newly recognized roles of phages as puppet masters of their bacterial hosts, where phages are capable of altering the metabolism of infected bacteria through the expression of auxiliary metabolic genes and the redirection of host gene expression patterns. Finally, we propose the 'royal family model' as a hypothesis to describe successional patterns of bacteria and phages over time in marine systems, where despite high richness and significant seasonal differences, only a small number of phages appear to continually dominate a given marine ecosystem. Although further testing is required, this model provides a framework for assessing the specificity and ecological consequences of phage-host dynamics.
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Affiliation(s)
- Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA.
| | - Chelsea Bonnain
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Kema Malki
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Natalie A Sawaya
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
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134
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Abstract
The composition of the biosphere is a fundamental question in biology, yet a global quantitative account of the biomass of each taxon is still lacking. We assemble a census of the biomass of all kingdoms of life. This analysis provides a holistic view of the composition of the biosphere and allows us to observe broad patterns over taxonomic categories, geographic locations, and trophic modes. A census of the biomass on Earth is key for understanding the structure and dynamics of the biosphere. However, a global, quantitative view of how the biomass of different taxa compare with one another is still lacking. Here, we assemble the overall biomass composition of the biosphere, establishing a census of the ≈550 gigatons of carbon (Gt C) of biomass distributed among all of the kingdoms of life. We find that the kingdoms of life concentrate at different locations on the planet; plants (≈450 Gt C, the dominant kingdom) are primarily terrestrial, whereas animals (≈2 Gt C) are mainly marine, and bacteria (≈70 Gt C) and archaea (≈7 Gt C) are predominantly located in deep subsurface environments. We show that terrestrial biomass is about two orders of magnitude higher than marine biomass and estimate a total of ≈6 Gt C of marine biota, doubling the previous estimated quantity. Our analysis reveals that the global marine biomass pyramid contains more consumers than producers, thus increasing the scope of previous observations on inverse food pyramids. Finally, we highlight that the mass of humans is an order of magnitude higher than that of all wild mammals combined and report the historical impact of humanity on the global biomass of prominent taxa, including mammals, fish, and plants.
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135
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Hannigan GD, Duhaime MB, Koutra D, Schloss PD. Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome. PLoS Comput Biol 2018; 14:e1006099. [PMID: 29668682 PMCID: PMC5927471 DOI: 10.1371/journal.pcbi.1006099] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 04/30/2018] [Accepted: 03/21/2018] [Indexed: 01/17/2023] Open
Abstract
Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks. The human microbiome, the collection of microbial communities that colonize the human body, is a crucial component to health and disease. Two major components of the human microbiome are the bacterial and viral communities. These communities have primarily been studied separately using metrics of community composition and diversity. These approaches have failed to capture the complex dynamics of interacting bacteria and phage communities, which frequently share genetic information and work together to maintain ecosystem homestatsis (e.g. kill-the-winner dynamics). Removal of bacteria or phage can disrupt or even collapse those ecosystems. Relationship-based network approaches allow us to capture this interaction information. Using this network-based approach with three independent human cohorts, we were able to present an initial understanding of how phage-bacteria networks differ throughout the human body, so as to provide a baseline for future studies of how and why microbiome networks differ in disease states.
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Affiliation(s)
- Geoffrey D. Hannigan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Melissa B. Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Danai Koutra
- Department of Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Patrick D. Schloss
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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136
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Sarkar S, Das M, Bhowmick TS, Koley H, Atterbury R, Chakrabarti AK, Sarkar BL. Isolation and Characterization of Novel Broad Host Range Bacteriophages of Vibrio cholerae O1 from Bengal. J Glob Infect Dis 2018; 10:84-88. [PMID: 29910569 PMCID: PMC5987377 DOI: 10.4103/jgid.jgid_37_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVES We have isolated a total of five newer cholera phages which are novel broad host range to incorporate with the existing phage typing schemes for an extended typing scheme. MATERIALS AND METHODS These newly isolated phages were well characterized including the electron micrograph. A total of 300 Vibrio cholerae strains were isolated from the different endemic region in India were included in phage typing study. RESULTS These phages were found different from the existing phages. Electron microscopic results showed that the phages belonged to myophage and podophage group. Characterization of the phages based on pH, temperature, and organic solvent sensitivity showed differences among the phages used in this study. All the strains of Vibrio O1 were typeable (100%) with the five set of cholera phages. Of these, 40% strains were clustered under Type-1. CONCLUSION The newer Vibrio phages are novel and broad host range and will be useful to incorporate with the existing phage typing system for more precisely discriminate the strains of Vibrio cholerae.
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Affiliation(s)
- Sounak Sarkar
- Division of Bacteriology, Vibrio Phage Reference Laboratory, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Mayukh Das
- Department of Plant Pathology and Microbiology, Texas Aandm University, Texas, USA
| | | | - Hemanta Koley
- Division of Bacteriology, Vibrio Phage Reference Laboratory, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Robert Atterbury
- Department of Veterinary infectioua Diseases, School of Veterinary Medicine and Science, The University of Nottingham, Leicestershire, UK
| | - Alok K Chakrabarti
- Division of Bacteriology, Vibrio Phage Reference Laboratory, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Banwarilal L Sarkar
- Division of Bacteriology, Vibrio Phage Reference Laboratory, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
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137
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Winter C, Köstner N, Kruspe C, Urban D, Muck S, Reinthaler T, Herndl GJ. Mixing alters the lytic activity of viruses in the dark ocean. Ecology 2018; 99:700-713. [PMID: 29315529 PMCID: PMC5905300 DOI: 10.1002/ecy.2135] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/17/2017] [Accepted: 12/18/2017] [Indexed: 11/11/2022]
Abstract
In aquatic habitats, viral lysis of prokaryotic cells lowers the overall efficiency of the microbial loop, by which dissolved organic carbon is transfered to higher trophic levels. Mixing of water masses in the dark ocean occurs on a global scale and may have far reaching consequences for the different prokaryotic and virus communities found in these waters by altering the environmental conditions these communities experience. We hypothesize that mixing of deep ocean water masses enhances the lytic activity of viruses infecting prokaryotes. To address this hypothesis, major deep-sea water masses of the Atlantic Ocean such as North Atlantic Deep Water, Mediterranean Sea Overflow Water, Antarctic Intermediate Water, and Antarctic Bottom Water were sampled at five locations. Prokaryotic cells from these samples were collected by filtration and subsequently incubated in virus-reduced water from either the same (control) or a different water mass (transplantation treatment). Additionally, mixtures of prokaryotes obtained from two different water masses were incubated in a mixture of virus-reduced water from the same water masses (control) or in virus-reduced water from the source water masses separately (mixing treatments). Pronounced differences in productivity-related parameters (prokaryotic leucine incorporation, prokaryotic and viral abundance) between water masses caused strong changes in viral lysis of prokaryotes. Often, mixing of water masses increased viral lysis of prokaryotes, indicating that lysogenic viruses were induced into the lytic cycle. Mixing-induced changes in viral lysis had a strong effect on the community composition of prokaryotes and viruses. Our data show that mixing of deep-sea water masses alters levels of viral lysis of prokaryotes and in many cases weakens the efficiency of the microbial loop by enhancing the recycling of organic carbon in the deep ocean.
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Affiliation(s)
- Christian Winter
- Department of Limnology and Bio‐OceanographyCenter of EcologyUniversity of ViennaAlthanstrasse 14Vienna1090Austria
| | - Nicole Köstner
- Department of Limnology and Bio‐OceanographyCenter of EcologyUniversity of ViennaAlthanstrasse 14Vienna1090Austria
| | - Carl‐Philip Kruspe
- Department of Limnology and Bio‐OceanographyCenter of EcologyUniversity of ViennaAlthanstrasse 14Vienna1090Austria
| | - Damaris Urban
- Department of Limnology and Bio‐OceanographyCenter of EcologyUniversity of ViennaAlthanstrasse 14Vienna1090Austria
| | - Simone Muck
- Department of Limnology and Bio‐OceanographyCenter of EcologyUniversity of ViennaAlthanstrasse 14Vienna1090Austria
| | - Thomas Reinthaler
- Department of Limnology and Bio‐OceanographyCenter of EcologyUniversity of ViennaAlthanstrasse 14Vienna1090Austria
| | - Gerhard J. Herndl
- Department of Limnology and Bio‐OceanographyCenter of EcologyUniversity of ViennaAlthanstrasse 14Vienna1090Austria
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138
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Schatz D, Vardi A. Extracellular vesicles - new players in cell-cell communication in aquatic environments. Curr Opin Microbiol 2018; 43:148-154. [PMID: 29448174 DOI: 10.1016/j.mib.2018.01.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 01/28/2018] [Accepted: 01/29/2018] [Indexed: 02/07/2023]
Abstract
Communication between microorganisms in aquatic environments can influence ecosystem function and determine the structure and composition of microbial populations. This microbial cross talk can be mediated by excretion of specialized metabolites or extracellular vesicles (EVs). Recently it has become apparent that cells across all domains of life produce EVs that may convey specific targeted signals that can modulate cell fate, morphology and susceptibility to viruses. The vast majority of knowledge about EVs is derived from studies of mammalian tissues, parasitic host-pathogen interactions and model bacterial systems. Very little is known about the role of EVs in aquatic environments, although they have potential to influence community structure and trophic-level interactions. We propose functions and ecological implications of communication via EVs in aquatic microbial ecosystems.
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Affiliation(s)
- Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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139
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Wei W, Zhang R, Peng L, Liang Y, Jiao N. Effects of temperature and photosynthetically active radiation on virioplankton decay in the western Pacific Ocean. Sci Rep 2018; 8:1525. [PMID: 29367730 PMCID: PMC5784127 DOI: 10.1038/s41598-018-19678-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/08/2018] [Indexed: 12/04/2022] Open
Abstract
In this study, we investigated virioplankton decay rates and their responses to changes in temperature and photosynthetically active radiation (PAR) in the western Pacific Ocean. The mean decay rates for total, high-fluorescence, and low-fluorescence viruses were 1.64 ± 0.21, 2.46 ± 0.43, and 1.57 ± 0.26% h−1, respectively. Higher temperatures and PAR increased viral decay rates, and the increases in the decay rates of low-fluorescence viruses were greater than those of high-fluorescence viruses. Our results revealed that low-fluorescence viruses are more sensitive to warming and increasing PAR than are high-fluorescence viruses, which may be related to differences in their biological characteristics, such as the density of packaged nucleic acid materials. Our study provided experimental evidence for the responses of natural viral communities to changes in global environmental factors (e.g., temperature and solar radiation).
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Affiliation(s)
- Wei Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China.
| | - Lulu Peng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China
| | - Yantao Liang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China.,Research Center for Marine Biology and Carbon Sequestration, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and BioProcess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, PR China.
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140
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Lacroix C, Seabloom EW, Borer ET. Environmental Nutrient Supply Directly Alters Plant Traits but Indirectly Determines Virus Growth Rate. Front Microbiol 2017; 8:2116. [PMID: 29163408 PMCID: PMC5681519 DOI: 10.3389/fmicb.2017.02116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 10/17/2017] [Indexed: 11/13/2022] Open
Abstract
Ecological stoichiometry and resource competition theory both predict that nutrient rates and ratios can alter infectious disease dynamics. Pathogens such as viruses hijack nutrient rich host metabolites to complete multiple steps of their epidemiological cycle. As the synthesis of these molecules requires nitrogen (N) and phosphorus (P), environmental supply rates, and ratios of N and P to hosts can directly limit disease dynamics. Environmental nutrient supplies also may alter virus epidemiology indirectly by changing host phenotype or the dynamics of coinfecting pathogens. We tested whether host nutrient supplies and coinfection control pathogen growth within hosts and transmission to new hosts, either directly or through modifications of plant tissue chemistry (i.e., content and stoichiometric ratios of nutrients), host phenotypic traits, or among-pathogen interactions. We examined two widespread plant viruses (BYDV-PAV and CYDV-RPV) in cultivated oats (Avena sativa) grown along a range of N and of P supply rates. N and P supply rates altered plant tissue chemistry and phenotypic traits; however, environmental nutrient supplies and plant tissue content and ratios of nutrients did not directly alter virus titer. Infection with CYDV-RPV altered plant traits and resulted in thicker plant leaves (i.e., higher leaf mass per area) and there was a positive correlation between CYDV-RPV titer and leaf mass per area. CYDV-RPV titer was reduced by the presence of a competitor, BYDV-PAV, and higher CYDV-RPV titer led to more severe chlorotic symptoms. In our experimental conditions, virus transmission was unaffected by nutrient supply rates, co-infection, plant stoichiometry, or plant traits, although nutrient supply rates have been shown to increase infection and coinfection rates. This work provides a robust test of the role of plant nutrient content and ratios in the dynamics of globally important pathogens and reveals a more complex relationship between within-host virus growth and alterations of plant traits. A deeper understanding of the differential effects of environmental nutrient supplies on virus epidemiology and ecology is particularly relevant given the rapid increase of nutrients flowing into Earth's ecosystems as a result of human activities.
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141
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Communication via extracellular vesicles enhances viral infection of a cosmopolitan alga. Nat Microbiol 2017; 2:1485-1492. [PMID: 28924189 DOI: 10.1038/s41564-017-0024-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 08/14/2017] [Indexed: 01/26/2023]
Abstract
Communication between microorganisms in the marine environment has immense ecological impact by mediating trophic-level interactions and thus determining community structure 1 . Extracellular vesicles (EVs) are produced by bacteria 2,3 , archaea 4 , protists 5 and metazoans, and can mediate pathogenicity 6 or act as vectors for intercellular communication. However, little is known about the involvement of EVs in microbial interactions in the marine environment 7 . Here we investigated the signalling role of EVs produced during interactions between the cosmopolitan alga Emiliania huxleyi and its specific virus (EhV, Phycodnaviridae) 8 , which leads to the demise of these large-scale oceanic blooms 9,10 . We found that EVs are highly produced during viral infection or when bystander cells are exposed to infochemicals derived from infected cells. These vesicles have a unique lipid composition that differs from that of viruses and their infected host cells, and their cargo is composed of specific small RNAs that are predicted to target sphingolipid metabolism and cell-cycle pathways. EVs can be internalized by E. huxleyi cells, which consequently leads to a faster viral infection dynamic. EVs can also prolong EhV half-life in the extracellular milieu. We propose that EVs are exploited by viruses to sustain efficient infectivity and propagation across E. huxleyi blooms. As these algal blooms have an immense impact on the cycling of carbon and other nutrients 11,12 , this mode of cell-cell communication may influence the fate of the blooms and, consequently, the composition and flow of nutrients in marine microbial food webs.
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142
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Gainer PJ, Pound HL, Larkin AA, LeCleir GR, DeBruyn JM, Zinser ER, Johnson ZI, Wilhelm SW. Contrasting seasonal drivers of virus abundance and production in the North Pacific Ocean. PLoS One 2017; 12:e0184371. [PMID: 28880951 PMCID: PMC5589214 DOI: 10.1371/journal.pone.0184371] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/22/2017] [Indexed: 11/23/2022] Open
Abstract
The North Pacific Ocean (between approximately 0°N and 50°N) contains the largest continuous ecosystem on Earth. This region plays a vital role in the cycling of globally important nutrients as well as carbon. Although the microbial communities in this region have been assessed, the dynamics of viruses (abundances and production rates) remains understudied. To address this gap, scientific cruises during the winter and summer seasons (2013) covered the North Pacific basin to determine factors that may drive virus abundances and production rates. Along with information on virus particle abundance and production, we collected a spectrum of oceanographic metrics as well as information on microbial diversity. The data suggest that both biotic and abiotic factors affect the distribution of virus particles. Factors influencing virus dynamics did not vary greatly between seasons, although the abundance of viruses was almost an order of magnitude greater in the summer. When considered in the context of microbial community structure, our observations suggest that members of the bacterial phyla Proteobacteria, Planctomycetes, and Bacteroidetes were correlated to both virus abundances and virus production rates: these phyla have been shown to be enriched in particle associated communities. The findings suggest that environmental factors influence virus community functions (e.g., virion particle degradation) and that particle-associated communities may be important drivers of virus activity.
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Affiliation(s)
- P. Jackson Gainer
- Department of Microbiology, The University of Tennessee, Knoxville, TN, United States of America
| | - Helena L. Pound
- Department of Microbiology, The University of Tennessee, Knoxville, TN, United States of America
| | - Alyse A. Larkin
- Nicholas School of the Environment and Biology Department, Duke University Marine Laboratory, Beaufort, NC, United States of America
| | - Gary R. LeCleir
- Department of Microbiology, The University of Tennessee, Knoxville, TN, United States of America
| | - Jennifer M. DeBruyn
- Biosystems Engineering & Soil Sciences, The University of Tennessee, Knoxville, TN, United States of America
| | - Erik R. Zinser
- Department of Microbiology, The University of Tennessee, Knoxville, TN, United States of America
| | - Zackary I. Johnson
- Nicholas School of the Environment and Biology Department, Duke University Marine Laboratory, Beaufort, NC, United States of America
| | - Steven W. Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, TN, United States of America
- * E-mail:
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143
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Lara E, Vaqué D, Sà EL, Boras JA, Gomes A, Borrull E, Díez-Vives C, Teira E, Pernice MC, Garcia FC, Forn I, Castillo YM, Peiró A, Salazar G, Morán XAG, Massana R, Catalá TS, Luna GM, Agustí S, Estrada M, Gasol JM, Duarte CM. Unveiling the role and life strategies of viruses from the surface to the dark ocean. SCIENCE ADVANCES 2017; 3:e1602565. [PMID: 28913418 PMCID: PMC5587022 DOI: 10.1126/sciadv.1602565] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 08/09/2017] [Indexed: 05/31/2023]
Abstract
Viruses are a key component of marine ecosystems, but the assessment of their global role in regulating microbial communities and the flux of carbon is precluded by a paucity of data, particularly in the deep ocean. We assessed patterns in viral abundance and production and the role of viral lysis as a driver of prokaryote mortality, from surface to bathypelagic layers, across the tropical and subtropical oceans. Viral abundance showed significant differences between oceans in the epipelagic and mesopelagic, but not in the bathypelagic, and decreased with depth, with an average power-law scaling exponent of -1.03 km-1 from an average of 7.76 × 106 viruses ml-1 in the epipelagic to 0.62 × 106 viruses ml-1 in the bathypelagic layer with an average integrated (0 to 4000 m) viral stock of about 0.004 to 0.044 g C m-2, half of which is found below 775 m. Lysogenic viral production was higher than lytic viral production in surface waters, whereas the opposite was found in the bathypelagic, where prokaryotic mortality due to viruses was estimated to be 60 times higher than grazing. Free viruses had turnover times of 0.1 days in the bathypelagic, revealing that viruses in the bathypelagic are highly dynamic. On the basis of the rates of lysed prokaryotic cells, we estimated that viruses release 145 Gt C year-1 in the global tropical and subtropical oceans. The active viral processes reported here demonstrate the importance of viruses in the production of dissolved organic carbon in the dark ocean, a major pathway in carbon cycling.
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Affiliation(s)
- Elena Lara
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
- Institute of Marine Sciences, National Research Council (CNR-ISMAR), Castello 2737/F Arsenale-Tesa 104, 30122 Venezia, Italy
| | - Dolors Vaqué
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Elisabet Laia Sà
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Julia A. Boras
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Ana Gomes
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Encarna Borrull
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Cristina Díez-Vives
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Eva Teira
- Departamento de Ecología y Biología Animal, Universidad de Vigo, University of Vigo, 36310 Vigo, Spain
| | - Massimo C. Pernice
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Francisca C. Garcia
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Avenida Príncipe de Asturias, 70, 33212 Gijón/Xixón, Spain
| | - Irene Forn
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Yaiza M. Castillo
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Aida Peiró
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Guillem Salazar
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Xosé Anxelu G. Morán
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ramon Massana
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Teresa S. Catalá
- Instituto de Investigaciones Marinas, CSIC, Eduardo Cabello, 6, 36208 Vigo, Spain
- Departamento de Ecología and Instituto del Agua, Universidad de Granada, Avenida del Hospicio, S/N, 18010 Granada, Spain
| | | | - Susana Agustí
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Marta Estrada
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Josep M. Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Carlos M. Duarte
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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144
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Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton. Proc Natl Acad Sci U S A 2017; 114:E7489-E7498. [PMID: 28827361 DOI: 10.1073/pnas.1708097114] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytoplankton community structure is shaped by both bottom-up factors, such as nutrient availability, and top-down processes, such as predation. Here we show that marine viruses can blur these distinctions, being able to amend how host cells acquire nutrients from their environment while also predating and lysing their algal hosts. Viral genomes often encode genes derived from their host. These genes may allow the virus to manipulate host metabolism to improve viral fitness. We identify in the genome of a phytoplankton virus, which infects the small green alga Ostreococcus tauri, a host-derived ammonium transporter. This gene is transcribed during infection and when expressed in yeast mutants the viral protein is located to the plasma membrane and rescues growth when cultured with ammonium as the sole nitrogen source. We also show that viral infection alters the nature of nitrogen compound uptake of host cells, by both increasing substrate affinity and allowing the host to access diverse nitrogen sources. This is important because the availability of nitrogen often limits phytoplankton growth. Collectively, these data show that a virus can acquire genes encoding nutrient transporters from a host genome and that expression of the viral gene can alter the nutrient uptake behavior of host cells. These results have implications for understanding how viruses manipulate the physiology and ecology of phytoplankton, influence marine nutrient cycles, and act as vectors for horizontal gene transfer.
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145
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Duhaime MB, Solonenko N, Roux S, Verberkmoes NC, Wichels A, Sullivan MB. Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept. Front Microbiol 2017; 8:1241. [PMID: 28729861 PMCID: PMC5498523 DOI: 10.3389/fmicb.2017.01241] [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: 02/24/2017] [Accepted: 06/20/2017] [Indexed: 11/25/2022] Open
Abstract
Viruses influence the ecology and evolutionary trajectory of microbial communities. Yet our understanding of their roles in ecosystems is limited by the paucity of model systems available for hypothesis generation and testing. Further, virology is limited by the lack of a broadly accepted conceptual framework to classify viral diversity into evolutionary and ecologically cohesive units. Here, we introduce genomes, structural proteomes, and quantitative host range data for eight Pseudoalteromonas phages isolated from Helgoland (North Sea, Germany) and use these data to advance a genome-based viral operational taxonomic unit (OTU) definition. These viruses represent five new genera and inform 498 unaffiliated or unannotated protein clusters (PCs) from global virus metagenomes. In a comparison of previously sequenced Pseudoalteromonas phage isolates (n = 7) and predicted prophages (n = 31), the eight phages are unique. They share a genus with only one other isolate, Pseudoalteromonas podophage RIO-1 (East Sea, South Korea) and two Pseudoalteromonas prophages. Mass-spectrometry of purified viral particles identified 12–20 structural proteins per phage. When combined with 3-D structural predictions, these data led to the functional characterization of five previously unidentified major capsid proteins. Protein functional predictions revealed mechanisms for hijacking host metabolism and resources. Further, they uncovered a hybrid sipho-myovirus that encodes genes for Mu-like infection rarely described in ocean systems. Finally, we used these data to evaluate a recently introduced definition for virus populations that requires members of the same population to have >95% average nucleotide identity across at least 80% of their genes. Using physiological traits and genomics, we proposed a conceptual model for a viral OTU definition that captures evolutionarily cohesive and ecologically distinct units. In this trait-based framework, sensitive hosts are considered viral niches, while host ranges and infection efficiencies are tracked as viral traits. Quantitative host range assays revealed conserved traits within virus OTUs that break down between OTUs, suggesting the defined units capture niche and fitness differentiation. Together these analyses provide a foundation for model system-based hypothesis testing that will improve our understanding of marine copiotrophs, as well as phage–host interactions on the ocean particles and aggregates where Pseudoalteromonas thrive.
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Affiliation(s)
- Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann ArborMI, United States
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, ColumbusOH, United States
| | - Simon Roux
- Department of Microbiology, The Ohio State University, ColumbusOH, United States
| | - Nathan C Verberkmoes
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso, El PasoTX, United States
| | - Antje Wichels
- Biologische Anstalt Helgoland, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine ResearchHelgoland, Germany
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, ColumbusOH, United States.,Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, ColumbusOH, United States
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146
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Finke JF, Hunt BPV, Winter C, Carmack EC, Suttle CA. Nutrients and Other Environmental Factors Influence Virus Abundances across Oxic and Hypoxic Marine Environments. Viruses 2017. [PMID: 28629143 PMCID: PMC5490827 DOI: 10.3390/v9060152] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Virus particles are highly abundant in seawater and, on average, outnumber microbial cells approximately 10-fold at the surface and 16-fold in deeper waters; yet, this relationship varies across environments. Here, we examine the influence of a suite of environmental variables, including nutrient concentrations, salinity and temperature, on the relationship between the abundances of viruses and prokaryotes over a broad range of spatial and temporal scales, including along a track from the Northwest Atlantic to the Northeast Pacific via the Arctic Ocean, and in the coastal waters of British Columbia, Canada. Models of varying complexity were tested and compared for best fit with the Akaike Information Criterion, and revealed that nitrogen and phosphorus concentrations, as well as prokaryote abundances, either individually or combined, had significant effects on viral abundances in all but hypoxic environments, which were only explained by a combination of physical and chemical factors. Nonetheless, multivariate models of environmental variables showed high explanatory power, matching or surpassing that of prokaryote abundance alone. Incorporating both environmental variables and prokaryote abundances into multivariate models significantly improved the explanatory power of the models, except in hypoxic environments. These findings demonstrate that environmental factors could be as important as, or even more important than, prokaryote abundance in describing viral abundance across wide-ranging marine environments.
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Affiliation(s)
- Jan F Finke
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
- Institute of Oceans and Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Brian P V Hunt
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
- Institute of Oceans and Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
- Hakai Institute, P.O. Box 309, Heriot Bay, BC, Canada.
| | - Christian Winter
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Eddy C Carmack
- Fisheries and Oceans Canada, Institute of Ocean Sciences, Sidney, BC V8L 4B2, Canada.
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
- Institute of Oceans and Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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147
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Cheng K, Van de Waal DB, Niu XY, Zhao YJ. Combined Effects of Elevated pCO 2 and Warming Facilitate Cyanophage Infections. Front Microbiol 2017; 8:1096. [PMID: 28659906 PMCID: PMC5468398 DOI: 10.3389/fmicb.2017.01096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 05/30/2017] [Indexed: 11/25/2022] Open
Abstract
Elevated pCO2 and warming are generally expected to influence cyanobacterial growth, and may promote the formation of blooms. Yet, both climate change factors may also influence cyanobacterial mortality by favoring pathogens, such as viruses, which will depend on the ability of the host to adapt. To test this hypothesis, we grew Plectonema boryanum IU597 under two temperature (25 and 29°C) and two pCO2 (400 and 800 μatm) conditions for 1 year, after which all treatments were re-exposed to control conditions for a period of 3 weeks. At several time points during the 1 year period, and upon re-exposure, we measured various infection characteristics of it associated cyanophage PP, including the burst size, latent period, lytic cycle and the efficiency of plaquing (EOP). As expected, elevated pCO2 promoted growth of P. boryanum equally over the 1 year period, but warming did not. Burst size increased in the warm treatment, but decreased in both the elevated pCO2 and combined treatment. The latent period and lytic cycle both became shorter in the elevated pCO2 and higher temperature treatment, and were further reduced by the combined effect of both factors. Efficiency of plaquing (EOP) decreased in the elevated pCO2 treatment, increased in the warm treatment, and increased even stronger in the combined treatment. These findings indicate that elevated pCO2 enhanced the effect of warming, thereby further promoting the virus infection rate. The re-exposure experiments demonstrate adaptation of the host leading to higher biomass build-up with elevated pCO2 over the experimental period, and lower performance upon re-exposure to control conditions. Similarly, virus burst size and EOP increased when given warm adapted host, but were lower as compared to the control when the host was re-exposed to control conditions. Our results demonstrate that adaptation but particularly physiological acclimation to climate change conditions favored viral infections, while limited host plasticity and slow adaptation after re-exposure to control conditions impeded host biomass build-up and viral infections.
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Affiliation(s)
- Kai Cheng
- Hubei Key Laboratory of Ecological Restoration for River-Lakes and Algal Utilization, College of Resources and Environmental Engineering, Hubei University of TechnologyWuhan, China
- College of Life Science, Central China Normal UniversityWuhan, China
| | - Dedmer B. Van de Waal
- Department of Aquatic Ecology, Netherlands Institute of EcologyWageningen, Netherlands
| | - Xiao Ying Niu
- College of Life Science, Central China Normal UniversityWuhan, China
| | - Yi Jun Zhao
- Hubei Key Laboratory of Ecological Restoration for River-Lakes and Algal Utilization, College of Resources and Environmental Engineering, Hubei University of TechnologyWuhan, China
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148
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Abstract
Viruses are incapable of autonomous energy production. Although many experimental studies make it clear that viruses are parasitic entities that hijack the molecular resources of the host, a detailed estimate for the energetic cost of viral synthesis is largely lacking. To quantify the energetic cost of viruses to their hosts, we enumerated the costs associated with two very distinct but representative DNA and RNA viruses, namely, T4 and influenza. We found that, for these viruses, translation of viral proteins is the most energetically expensive process. Interestingly, the costs of building a T4 phage and a single influenza virus are nearly the same. Due to influenza's higher burst size, however, the overall cost of a T4 phage infection is only 2-3% of the cost of an influenza infection. The costs of these infections relative to their host's estimated energy budget during the infection reveal that a T4 infection consumes about a third of its host's energy budget, whereas an influenza infection consumes only ≈ 1%. Building on our estimates for T4, we show how the energetic costs of double-stranded DNA phages scale with the capsid size, revealing that the dominant cost of building a virus can switch from translation to genome replication above a critical size. Last, using our predictions for the energetic cost of viruses, we provide estimates for the strengths of selection and genetic drift acting on newly incorporated genetic elements in viral genomes, under conditions of energy limitation.
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Affiliation(s)
- Gita Mahmoudabadi
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rob Phillips
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125;
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125
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149
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Hulo C, Masson P, Toussaint A, Osumi-Sutherland D, de Castro E, Auchincloss AH, Poux S, Bougueleret L, Xenarios I, Le Mercier P. Bacterial Virus Ontology; Coordinating across Databases. Viruses 2017; 9:E126. [PMID: 28545254 PMCID: PMC5490803 DOI: 10.3390/v9060126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 12/29/2022] Open
Abstract
Bacterial viruses, also called bacteriophages, display a great genetic diversity and utilize unique processes for infecting and reproducing within a host cell. All these processes were investigated and indexed in the ViralZone knowledge base. To facilitate standardizing data, a simple ontology of viral life-cycle terms was developed to provide a common vocabulary for annotating data sets. New terminology was developed to address unique viral replication cycle processes, and existing terminology was modified and adapted. Classically, the viral life-cycle is described by schematic pictures. Using this ontology, it can be represented by a combination of successive events: entry, latency, transcription/replication, host-virus interactions and virus release. Each of these parts is broken down into discrete steps. For example enterobacteria phage lambda entry is broken down in: viral attachment to host adhesion receptor, viral attachment to host entry receptor, viral genome ejection and viral genome circularization. To demonstrate the utility of a standard ontology for virus biology, this work was completed by annotating virus data in the ViralZone, UniProtKB and Gene Ontology databases.
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Affiliation(s)
- Chantal Hulo
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland.
| | - Patrick Masson
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland.
| | - Ariane Toussaint
- University Libre de Bruxelles, Génétique et Physiologie Bactérienne (LGPB), 12 rue des Professeurs Jeener et Brachet, 6041 Charleroi, Belgium.
| | - David Osumi-Sutherland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.
| | - Edouard de Castro
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland.
| | - Andrea H Auchincloss
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland.
| | - Sylvain Poux
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland.
| | - Lydie Bougueleret
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland.
| | - Ioannis Xenarios
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland.
| | - Philippe Le Mercier
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, 1211 Geneva, Switzerland.
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150
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Louca S, Doebeli M. Taxonomic variability and functional stability in microbial communities infected by phages. Environ Microbiol 2017; 19:3863-3878. [PMID: 28371143 DOI: 10.1111/1462-2920.13743] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 03/16/2017] [Accepted: 03/24/2017] [Indexed: 11/28/2022]
Abstract
Microbial communities can display large variation in taxonomic composition, yet this variation can coincide with stable metabolic functional structure and performance. The mechanisms driving the taxonomic variation within functional groups remain largely unknown. Biotic interactions, such as predation by phages, have been suggested as potential cause of taxonomic turnover, but the conditions for this scenario have not been rigorously examined. Further, it is unknown how predation by phages affects community function, and how these effects are modulated by functional redundancy in the communities. Here, we address these questions using a model for a methanogenic microbial community that includes several interacting metabolic functional groups. Each functional group comprises multiple competing clades, and each clade is attacked by a specialist lytic phage. Our model predicts that phages induce intense taxonomic turnover, resembling the variability observed in previous experiments. The functional structure and performance of the community are also disturbed by phage predation, but they become more stable as the functional redundancy in the community increases. The extent of this stabilization depends on the particular functions considered. Our model suggests mechanisms by which functional redundancy stabilizes community function and supports the interpretation that biotic interactions promote taxonomic turnover within microbial functional groups.
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Affiliation(s)
- Stilianos Louca
- Biodiversity Research Centre, University of British Columbia, Canada.,Department of Zoology, University of British Columbia, Canada
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Canada.,Department of Zoology, University of British Columbia, Canada.,Department of Mathematics, University of British Columbia, Canada
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