1
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Galvez NMS, Sheehan ML, Lin AZ, Cao Y, Lam EC, Jackson AM, Balazs AB. QuickFit: A High-Throughput RT-qPCR-Based Assay to Quantify Viral Growth and Fitness In Vitro. Viruses 2024; 16:1320. [PMID: 39205294 PMCID: PMC11360610 DOI: 10.3390/v16081320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 08/14/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
Quantifying viral growth rates is key to understanding evolutionary dynamics and the potential for mutants to escape antiviral drugs. Defining evolutionary escape paths and their impact on viral fitness allows for the development of drugs that are resistant to escape. In the case of HIV, combination antiretroviral therapy can successfully prevent or treat infection, but it relies on strict adherence to prevent escape. Here, we present a method termed QuickFit that enables the quantification of viral fitness by employing large numbers of parallel viral cultures to measure growth rates accurately. QuickFit consistently recapitulated HIV growth measurements obtained by traditional approaches, but with significantly higher throughput and lower rates of error. This method represents a promising tool for rapid and consistent evaluation of viral fitness.
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Affiliation(s)
| | | | | | | | | | | | - Alejandro B. Balazs
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Cambridge, MA 02139, USA
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2
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Kiørboe T. Organismal trade-offs and the pace of planktonic life. Biol Rev Camb Philos Soc 2024. [PMID: 38855937 DOI: 10.1111/brv.13108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/11/2024]
Abstract
No one is perfect, and organisms that perform well in some habitat or with respect to some tasks, do so at the cost of performance in others: there are inescapable trade-offs. Organismal trade-offs govern the structure and function of ecosystems and attempts to demonstrate and quantify trade-offs have therefore been an important goal for ecologists. In addition, trade-offs are a key component in trait-based ecosystem models. Here, I synthesise evidence of trade-offs in plankton organisms, from bacteria to zooplankton, and show how a slow-fast gradient in life histories emerges. I focus on trade-offs related to the main components of an organism's Darwinian fitness, that is resource acquisition, survival, and propagation. All consumers need to balance the need to eat without being eaten, and diurnal vertical migration, where zooplankton hide at depth during the day to avoid visual predators but at the cost of missed feeding opportunities in the productive surface layer, is probably the best documented result of this trade-off. However, there are many other more subtle but equally important behaviours that similarly are the result of an optimisation of these trade-offs. Most plankton groups have also developed more explicit defence mechanisms, such as toxin production or evasive behaviours that are harnessed in the presence of their predators; the costs of these have often proved difficult to quantify or even demonstrate, partly because they only materialise under natural conditions. Finally, all multicellular organisms must allocate time and resources among growth, reproduction, and maintenance (e.g. protein turnover and DNA repair), and mate finding may compromise both survival and feeding. The combined effects of all these trade-offs is the emergence of a slow-fast gradient in the pace-of-life, likely the most fundamental principle for the organisation of organismal life histories. This crystallisation of trade-offs may offer a path to further simplification of trait-based models of marine ecosystems.
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Affiliation(s)
- Thomas Kiørboe
- Centre for Ocean Life, DTU Aqua, Technical University of Denmark, 2800 Kgs, Kemitorvet, Kgs. Lyngby, Denmark
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3
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Gilman RT, Muldoon MR, Megremis S, Robertson DL, Chanishvili N, Papadopoulos NG. Lysogeny destabilizes computationally simulated microbiomes. Ecol Lett 2024; 27:e14464. [PMID: 38923281 DOI: 10.1111/ele.14464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/06/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Microbiomes are ecosystems, and their stability can impact the health of their hosts. Theory predicts that predators influence ecosystem stability. Phages are key predators of bacteria in microbiomes, but phages are unusual predators because many have lysogenic life cycles. It has been hypothesized that lysogeny can destabilize microbiomes, but lysogeny has no direct analog in classical ecological theory, and no formal theory exists. We studied the stability of computationally simulated microbiomes with different numbers of temperate (lysogenic) and virulent (obligate lytic) phage species. Bacterial populations were more likely to fluctuate over time when there were more temperate phages species. After disturbances, bacterial populations returned to their pre-disturbance densities more slowly when there were more temperate phage species, but cycles engendered by disturbances dampened more slowly when there were more virulent phage species. Our work offers the first formal theory linking lysogeny to microbiome stability.
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Affiliation(s)
- R Tucker Gilman
- Department of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Mark R Muldoon
- Department of Mathematics, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Spyridon Megremis
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Department of Genetics and Genome Biology, Centre for Phage Research, Institute for Precision Health, University of Leicester, Leicester, UK
| | | | - Nina Chanishvili
- George Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, Georgia
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
- NewVision University, Tbilisi, Georgia
| | - Nikolaos G Papadopoulos
- Allergy Department, 2nd Pediatric Clinic, University of Athens, Athens, Greece
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK
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4
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Brüwer JD, Sidhu C, Zhao Y, Eich A, Rößler L, Orellana LH, Fuchs BM. Globally occurring pelagiphage infections create ribosome-deprived cells. Nat Commun 2024; 15:3715. [PMID: 38698041 PMCID: PMC11066056 DOI: 10.1038/s41467-024-48172-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024] Open
Abstract
Phages play an essential role in controlling bacterial populations. Those infecting Pelagibacterales (SAR11), the dominant bacteria in surface oceans, have been studied in silico and by cultivation attempts. However, little is known about the quantity of phage-infected cells in the environment. Using fluorescence in situ hybridization techniques, we here show pelagiphage-infected SAR11 cells across multiple global ecosystems and present evidence for tight community control of pelagiphages on the SAR11 hosts in a case study. Up to 19% of SAR11 cells were phage-infected during a phytoplankton bloom, coinciding with a ~90% reduction in SAR11 cell abundance within 5 days. Frequently, a fraction of the infected SAR11 cells were devoid of detectable ribosomes, which appear to be a yet undescribed possible stage during pelagiphage infection. We dubbed such cells zombies and propose, among other possible explanations, a mechanism in which ribosomal RNA is used as a resource for the synthesis of new phage genomes. On a global scale, we detected phage-infected SAR11 and zombie cells in the Atlantic, Pacific, and Southern Oceans. Our findings illuminate the important impact of pelagiphages on SAR11 populations and unveil the presence of ribosome-deprived zombie cells as part of the infection cycle.
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Affiliation(s)
- Jan D Brüwer
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.
| | - Chandni Sidhu
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Yanlin Zhao
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Andreas Eich
- PSL Research University: EPHE-UPVD-CNRS,UAR 3278 CRIOBE, Moorea, French Polynesia
| | - Leonard Rößler
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Luis H Orellana
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.
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5
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Bharali P, Gogoi B, Sorhie V, Acharjee SA, Walling B, Alemtoshi, Vishwakarma V, Shah MP. Autochthonous psychrophilic hydrocarbonoclastic bacteria and its ecological function in contaminated cold environments. Biodegradation 2024; 35:1-46. [PMID: 37436665 DOI: 10.1007/s10532-023-10042-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/30/2023] [Indexed: 07/13/2023]
Abstract
Petroleum hydrocarbon (PH) pollution has mostly been caused by oil exploration, extraction, and transportation activities in colder regions, particularly in the Arctic and Antarctic regions, where it serves as a primary source of energy. Due to the resilience feature of nature, such polluted environments become the realized ecological niches for a wide community of psychrophilic hydrocarbonoclastic bacteria (PHcB). In contrast, to other psychrophilic species, PHcB is extremely cold-adapted and has unique characteristics that allow them to thrive in greater parts of the cold environment burdened with PHs. The stated group of bacteria in its ecological niche aids in the breakdown of litter, turnover of nutrients, cycling of carbon and nutrients, and bioremediation. Although such bacteria are the pioneers of harsh colder environments, their growth and distribution remain under the influence of various biotic and abiotic factors of the environment. The review discusses the prevalence of PHcB community in colder habitats, the metabolic processes involved in the biodegradation of PH, and the influence of biotic and abiotic stress factors. The existing understanding of the PH metabolism by PHcB offers confirmation of excellent enzymatic proficiency with high cold stability. The discovery of more flexible PH degrading strategies used by PHcB in colder environments could have a significant beneficial outcome on existing bioremediation technologies. Still, PHcB is least explored for other industrial and biotechnological applications as compared to non-PHcB psychrophiles. The present review highlights the pros and cons of the existing bioremediation technologies as well as the potential of different bioaugmentation processes for the effective removal of PH from the contaminated cold environment. Such research will not only serve to investigate the effects of pollution on the basic functional relationships that form the cold ecosystem but also to assess the efficacy of various remediation solutions for diverse settings and climatic conditions.
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Affiliation(s)
- Pranjal Bharali
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India.
| | - Bhagyudoy Gogoi
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Viphrezolie Sorhie
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Shiva Aley Acharjee
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Bendangtula Walling
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Alemtoshi
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Vinita Vishwakarma
- Centre for Nanoscience and Nanotechnology, Galgotias University, Greater Noida, NCR Delhi, India
| | - Maulin Pramod Shah
- Industrial Waste Water Research Lab, Division of Applied and Environmental Microbiology Lab at Enviro Technology Ltd., Ankleshwar, Gujarat, India
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6
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Liu L, Zhong KX, Chen Q, Wang Y, Zhang T, Jiao N, Zheng Q. Selective cell lysis pressure on rare and abundant prokaryotic taxa across a shelf-to-slope continuum in the Northern South China Sea. Appl Environ Microbiol 2023; 89:e0139323. [PMID: 38014961 PMCID: PMC10734510 DOI: 10.1128/aem.01393-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Virus-induced host lysis contributes up to 40% of total prokaryotic mortality and plays crucial roles in shaping microbial composition and diversity in the ocean. Nonetheless, what taxon-specific cell lysis is caused by viruses remains to be studied. The present study, therefore, examined the taxon-specific cell lysis and estimated its contribution to the variations in the rare and abundant microbial taxa. The results demonstrate that taxon-specific mortality differed in surface and bottom of the coastal environment. In addition, active rare taxa are more susceptible to heightened lytic pressure and suggested the importance of viral lysis in regulating the microbial community composition. These results improve our understanding of bottom-up (abiotic environmental variables) and top-down (viral lysis) controls contributing to microbial community assembly in the ocean.
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Affiliation(s)
- Lu Liu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Qi Chen
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Ting Zhang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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7
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Yadav P, Quattrone A, Yang Y, Owens J, Kiat R, Kuppusamy T, Russo SE, Weber KA. Zea mays genotype influences microbial and viral rhizobiome community structure. ISME COMMUNICATIONS 2023; 3:129. [PMID: 38057501 DOI: 10.1038/s43705-023-00335-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/08/2023]
Abstract
Plant genotype is recognized to contribute to variations in microbial community structure in the rhizosphere, soil adherent to roots. However, the extent to which the viral community varies has remained poorly understood and has the potential to contribute to variation in soil microbial communities. Here we cultivated replicates of two Zea mays genotypes, parviglumis and B73, in a greenhouse and harvested the rhizobiome (rhizoplane and rhizosphere) to identify the abundance of cells and viruses as well as rhizobiome microbial and viral community using 16S rRNA gene amplicon sequencing and genome resolved metagenomics. Our results demonstrated that viruses exceeded microbial abundance in the rhizobiome of parviglumis and B73 with a significant variation in both the microbial and viral community between the two genotypes. Of the viral contigs identified only 4.5% (n = 7) of total viral contigs were shared between the two genotypes, demonstrating that plants even at the level of genotype can significantly alter the surrounding soil viral community. An auxiliary metabolic gene associated with glycoside hydrolase (GH5) degradation was identified in one viral metagenome-assembled genome (vOTU) identified in the B73 rhizobiome infecting Propionibacteriaceae (Actinobacteriota) further demonstrating the viral contribution in metabolic potential for carbohydrate degradation and carbon cycling in the rhizosphere. This variation demonstrates the potential of plant genotype to contribute to microbial and viral heterogeneity in soil systems and harbors genes capable of contributing to carbon cycling in the rhizosphere.
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Affiliation(s)
- Pooja Yadav
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Amanda Quattrone
- Complex Biosystems, University of Nebraska-Lincoln, Lincoln, NE, USA
- Texas A&M University, College Station, TX, USA
| | - Yuguo Yang
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jacob Owens
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
- University of Nebraska-Medical Center, Omaha, NE, USA
| | - Rebecca Kiat
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Sabrina E Russo
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Karrie A Weber
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
- Department of Earth and Atmospheric Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
- Daugherty Water for Food Global Institute, University of Nebraska, Lincoln, NE, USA.
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8
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Cissell EC, McCoy SJ. Top-heavy trophic structure within benthic viral dark matter. Environ Microbiol 2023; 25:2303-2320. [PMID: 37381050 DOI: 10.1111/1462-2920.16457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 06/16/2023] [Indexed: 06/30/2023]
Abstract
A better understanding of system-specific viral ecology in diverse environments is needed to predict patterns of virus-host trophic structure in the Anthropocene. This study characterised viral-host trophic structure within coral reef benthic cyanobacterial mats-a globally proliferating cause and consequence of coral reef degradation. We employed deep longitudinal multi-omic sequencing to characterise the viral assemblage (ssDNA, dsDNA, and dsRNA viruses) and profile lineage-specific host-virus interactions within benthic cyanobacterial mats sampled from Bonaire, Caribbean Netherlands. We recovered 11,012 unique viral populations spanning at least 10 viral families across the orders Caudovirales, Petitvirales, and Mindivirales. Gene-sharing network analyses provided evidence for extensive genomic novelty of mat viruses from reference and environmental viral sequences. Analysis of coverage ratios of viral sequences and computationally predicted hosts spanning 15 phyla and 21 classes revealed virus-host abundance (from DNA) and activity (from RNA) ratios consistently exceeding 1:1, suggesting a top-heavy intra-mat trophic structure with respect to virus-host interactions. Overall, our article contributes a curated database of viral sequences found in Caribbean coral reef benthic cyanobacterial mats (vMAT database) and provides multiple lines of field-based evidence demonstrating that viruses are active members of mat communities, with broader implications for mat functional ecology and demography.
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Affiliation(s)
- Ethan C Cissell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sophie J McCoy
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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9
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Burian A, Gruber-Dorninger M, Schweichart J, Yasindi A, Bulling M, Jirsa F, Winter C, Muia AW, Schagerl M. Drivers of microbial food-web structure along productivity gradients. Proc Biol Sci 2023; 290:20231531. [PMID: 37876193 PMCID: PMC10598424 DOI: 10.1098/rspb.2023.1531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
Ratios between viruses, heterotrophic prokaryotes and chlorophyll a are key indicators of microbial food structure and both virus-prokaryote and prokaryote-chlorophyll ratios have been proposed to decrease with system productivity. However, the mechanisms underlying these responses are still insufficiently resolved and their consistency across aquatic ecosystem types requires critical evaluation. We assessed microbial community ratios in highly productive African soda-lakes and used our data from naturally hypereutrophic systems which are largely underrepresented in literature, to complement earlier across-system meta-analyses. In contrast to marine and freshwater systems, prokaryote-chlorophyll ratios in African soda-lakes did not decrease along productivity gradients. High-resolution time series from two soda-lakes indicated that this lack of response could be driven by a weakened top-down control of heterotrophic prokaryotes. Our analysis of virus-prokaryote relationships, revealed a reduction of virus-prokaryote ratios by high suspended particle concentrations in soda-lakes. This effect, likely driven by the adsorption of free-living viruses, was also found in three out of four additionally analysed marine datasets. However, the decrease of virus-prokaryote ratios previously reported in highly productive marine systems, was neither detectable in soda-lakes nor freshwaters. Hence, our study demonstrates that system-specific analyses can reveal the diversity of mechanisms that structure microbial food-webs and shape their response to productivity increases.
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Affiliation(s)
- Alfred Burian
- Department of Computational Landscape Ecology, UFZ– Helmholtz Centre for Environmental Research, Leipzig, Germany
- Marine Ecology Department, Lurio University, Nampula, Mozambique
| | | | - Johannes Schweichart
- Biology Centre, University of South Bohemia in České, České Budějovice, Czech Republic
| | - Andrew Yasindi
- Department of Biological Sciences, Egerton University, Njoro, Kenya
| | - Mark Bulling
- Environmental Sustainability Research Centre, University of Derby, Derby, UK
| | - Franz Jirsa
- Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria
- Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Christian Winter
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | | | - Michael Schagerl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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10
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Sabbagh EI, Calleja ML, Daffonchio D, Morán XAG. Seasonality of top-down control of bacterioplankton at two central Red Sea sites with different trophic status. Environ Microbiol 2023; 25:2002-2019. [PMID: 37286523 DOI: 10.1111/1462-2920.16439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 05/22/2023] [Indexed: 06/09/2023]
Abstract
The role of bottom-up (nutrient availability) and top-down (grazers and viruses mortality) controls on tropical bacterioplankton have been rarely investigated simultaneously from a seasonal perspective. We have assessed them through monthly samplings over 2 years in inshore and offshore waters of the central Red Sea differing in trophic status. Flow cytometric analysis allowed us to distinguish five groups of heterotrophic bacteria based on physiological properties (nucleic acid content, membrane integrity and active respiration), three groups of cyanobacteria (two populations of Synechococcus and Prochlorococcus), heterotrophic nanoflagellates (HNFs) and three groups of viruses based on nucleic acid content. The dynamics of bacterioplankton and their top-down controls varied with season and location, being more pronounced in inshore waters. HNFs abundances showed a strong preference for larger prey inshore (r = -0.62 to -0.59, p = 0.001-0.002). Positive relationships between viruses and heterotrophic bacterioplankton abundances were more marked inshore (r = 0.67, p < 0.001) than offshore (r = 0.44, p = 0.03). The negative correlation between HNFs and viruses abundances (r = -0.47, p = 0.02) in shallow waters indicates a persistent seasonal switch between protistan grazing and viral lysis that maintains the low bacterioplankton stocks in the central Red Sea area.
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Affiliation(s)
- Eman I Sabbagh
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maria Ll Calleja
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Climate Geochemistry, Max Plank Institute for Chemistry (MPIC), Mainz, Germany
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xosé Anxelu G Morán
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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11
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Chen X, Hu C, Wei W, Yang Y, Weinbauer MG, Li H, Ren S, Ma R, Huang Y, Luo T, Jiao N, Zhang R. Virus-Host Interactions Drive Contrasting Bacterial Diel Dynamics in the Ocean. RESEARCH (WASHINGTON, D.C.) 2023; 6:0213. [PMID: 37614364 PMCID: PMC10443526 DOI: 10.34133/research.0213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/05/2023] [Indexed: 08/25/2023]
Abstract
Marine organisms perform a sea of diel rhythmicity. Planktonic diel dynamics have been shown to be driven by light, energy resources, circadian rhythms, and the coordinated coupling of photoautotrophs and heterotrophic bacterioplankton. Here, we explore the diel fluctuation of viral production and decay and their impact on the total and active bacterial community in the coastal and open seawaters of the South China Sea. The results showed that the night-production diel pattern of lytic viral production was concurrent with the lower viral decay at night, contributing to the accumulation of the viral population size during the night for surface waters. The diel variations in bacterial activity, community composition, and diversity were found highly affected by viral dynamics. This was revealed by the finding that bacterial community diversity was positively correlated to lytic viral production in the euphotic zone of the open ocean but was negatively related to lysogenic viral production in the coastal ocean. Such distinct but contrasting correlations suggest that viral life strategies can not only contribute to diversifying bacterial community but also potentially piggyback their host to dominate bacterial community, suggesting the tightly synchronized depth-dependent and habitat-specific diel patterns of virus-host interactions. It further implies that viruses serve as an ecologically important driver of bacterial diel dynamics across the ocean, highlighting the viral roles in bacterial ecological and biogeochemical processes in the ocean.
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Affiliation(s)
- Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
| | - Chen Hu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, PR China
| | - Wei Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, PR China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, PR China
| | - Markus G Weinbauer
- Sorbonne Universités, UPMC, Université Paris 06, CNRS, Laboratoire d'Océanographie de Villefranche (LOV), Villefranche-sur-Mer 06230, France
| | - Hongbo Li
- National Marine Environmental Monitoring Center, Ministry of Ecological Environment, Dalian 116023, PR China
| | - Shiying Ren
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
| | - Ruijie Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
| | - Yibin Huang
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
- NOAA/OAR Pacific Marine Environmental Laboratory, Seattle, WA, USA
| | - Tingwei Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
- Institute for Advanced Study, Shenzhen University, Shenzhen 518055, PR China
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12
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Fan L, Peng W, Duan H, Lü F, Zhang H, He P. Presence and role of viruses in anaerobic digestion of food waste under environmental variability. MICROBIOME 2023; 11:170. [PMID: 37537690 PMCID: PMC10401857 DOI: 10.1186/s40168-023-01585-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 05/28/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND The interaction among microorganisms in the anaerobic digestion of food waste (ADFW) reactors lead to the degradation of organics and the recycling of energy. Viruses are an important component of the microorganisms involved in ADFW, but are rarely investigated. Furthermore, little is known about how viruses affect methanogenesis. RESULTS Thousands of viral sequences were recovered from five full-scale ADFW reactors. Gene-sharing networks indicated that the ADFW samples contained substantial numbers of unexplored anaerobic-specific viruses. Moreover, the viral communities in five full-scale reactors exhibited both commonalities and heterogeneities. The lab-scale dynamic analysis of typical ADFW scenarios suggested that the viruses had similar kinetic characteristics to their prokaryotic hosts. By associating with putative hosts, a majority of the bacteria and archaea phyla were found to be infected by viruses. Viruses may influence prokaryotic ecological niches, and thus methanogenesis, by infecting key functional microorganisms, such as sulfate-reducing bacteria (SRB), syntrophic acetate-oxidizing bacteria (SAOB), and methanogens. Metabolic predictions for the viruses suggested that they may collaborate with hosts at key steps of sulfur and long-chain fatty acid (LCFA) metabolism and could be involved in typical methanogenesis pathways to participate in methane production. CONCLUSIONS Our results expanded the diversity of viruses in ADFW systems and suggested two ways that viral manipulated ADFW biochemical processes. Video Abstract.
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Affiliation(s)
- Lu Fan
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, 200092, China
| | - Wei Peng
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, 200092, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
- Shanghai Engineering Research Center of Multi-Source Solid Wastes Co-processing and Energy Utilization, Shanghai, 200092, China.
| | - Haowen Duan
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, 200092, China
| | - Fan Lü
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
- Shanghai Engineering Research Center of Multi-Source Solid Wastes Co-processing and Energy Utilization, Shanghai, 200092, China
| | - Hua Zhang
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
- Shanghai Engineering Research Center of Multi-Source Solid Wastes Co-processing and Energy Utilization, Shanghai, 200092, China
| | - Pinjing He
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, 200092, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
- Shanghai Engineering Research Center of Multi-Source Solid Wastes Co-processing and Energy Utilization, Shanghai, 200092, China.
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13
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Silveira CB, Luque A, Haas AF, Roach TNF, George EE, Knowles B, Little M, Sullivan CJ, Varona NS, Wegley Kelly L, Brainard R, Rohwer F, Bailey B. Viral predation pressure on coral reefs. BMC Biol 2023; 21:77. [PMID: 37038111 PMCID: PMC10088212 DOI: 10.1186/s12915-023-01571-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 03/17/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Predation pressure and herbivory exert cascading effects on coral reef health and stability. However, the extent of these cascading effects can vary considerably across space and time. This variability is likely a result of the complex interactions between coral reefs' biotic and abiotic dimensions. A major biological component that has been poorly integrated into the reefs' trophic studies is the microbial community, despite its role in coral death and bleaching susceptibility. Viruses that infect bacteria can control microbial densities and may positively affect coral health by controlling microbialization. We hypothesize that viral predation of bacteria has analogous effects to the top-down pressure of macroorganisms on the trophic structure and reef health. RESULTS Here, we investigated the relationships between live coral cover and viruses, bacteria, benthic algae, fish biomass, and water chemistry in 110 reefs spanning inhabited and uninhabited islands and atolls across the Pacific Ocean. Statistical learning showed that the abundance of turf algae, viruses, and bacteria, in that order, were the variables best predicting the variance in coral cover. While fish biomass was not a strong predictor of coral cover, the relationship between fish and corals became apparent when analyzed in the context of viral predation: high coral cover (> 50%) occurred on reefs with a combination of high predator fish biomass (sum of sharks and piscivores > 200 g m-2) and high virus-to-bacteria ratios (> 10), an indicator of viral predation pressure. However, these relationships were non-linear, with reefs at the higher and lower ends of the coral cover continuum displaying a narrow combination of abiotic and biotic variables, while reefs at intermediate coral cover showed a wider range of parameter combinations. CONCLUSIONS The results presented here support the hypothesis that viral predation of bacteria is associated with high coral cover and, thus, coral health and stability. We propose that combined predation pressures from fishes and viruses control energy fluxes, inhibiting the detrimental accumulation of ecosystem energy in the microbial food web.
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Affiliation(s)
- Cynthia B Silveira
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, 33149, USA.
| | - Antoni Luque
- Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
- Computational Science Research Center, San Diego State University, San Diego, CA, 92182, USA
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, 92182, USA
| | - Andreas F Haas
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Ty N F Roach
- Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Emma E George
- Botany Department, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ben Knowles
- Department of Ecology and Evolutionary Biology, UC Los Angeles, Los Angeles, CA, 90095, USA
| | - Mark Little
- Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | | | - Natascha S Varona
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Linda Wegley Kelly
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92037, USA
| | - Russel Brainard
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
- Pacific Islands Fisheries Science Center, National Oceanic & Atmospheric Administration, Honolulu, HI, 96818, USA
| | - Forest Rohwer
- Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Barbara Bailey
- Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA.
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, 92182, USA.
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14
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Fan X, Ji M, Sun K, Li Q. Microbial and phage communities as well as their interaction in PO saponification wastewater treatment systems. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2023; 87:354-365. [PMID: 36706286 DOI: 10.2166/wst.2022.422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Viruses or phages were considered affecting microbial community composition, metabolic process, and biogeochemical cycles. However, phage communities and their potential associations with microbial community are not well understood in the activated sludge (AS) of wastewater treatment plants (WWTPs). In this study, we explored the interactions between phages and microbial community by using propylene oxide (PO) saponification WWTPs as an example. Bacterial, eukaryal and archaeal communities were investigated and 34 phage contigs (>10 kb) were recovered from PO saponification WWTPs. At least 3 complete phage genomes were assembled. In all 34 phages, 21 of them have been predicted to their host. The association network analysis showed that abundant phages were associated with abundant microorganisms. This result conformed to Kill-the-Winner model. Notably, 45 auxiliary metabolic genes (AMGs) were identified from phage genomes (including small contig fragments). They influenced bacterial metabolism through facilitating phages replication and avoiding host death. Collectively, our results suggested that phage community affect microbial community and metabolic pathways by killing their hosts and AMGs transfer in AS of PO saponification WWTPs.
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Affiliation(s)
- Xiangyu Fan
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China E-mail:
| | - Mengzhi Ji
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China E-mail:
| | - Kaili Sun
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China E-mail:
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China E-mail:
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15
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Effects of phytoplankton, viral communities, and warming on free-living and particle-associated marine prokaryotic community structure. Nat Commun 2022; 13:7905. [PMID: 36550140 PMCID: PMC9780322 DOI: 10.1038/s41467-022-35551-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Free-living and particle-associated marine prokaryotes have physiological, genomic, and phylogenetic differences, yet factors influencing their temporal dynamics remain poorly constrained. In this study, we quantify the entire microbial community composition monthly over several years, including viruses, prokaryotes, phytoplankton, and total protists, from the San-Pedro Ocean Time-series using ribosomal RNA sequencing and viral metagenomics. Canonical analyses show that in addition to physicochemical factors, the double-stranded DNA viral community is the strongest factor predicting free-living prokaryotes, explaining 28% of variability, whereas the phytoplankton (via chloroplast 16S rRNA) community is strongest with particle-associated prokaryotes, explaining 31% of variability. Unexpectedly, protist community explains little variability. Our findings suggest that biotic interactions are significant determinants of the temporal dynamics of prokaryotes, and the relative importance of specific interactions varies depending on lifestyles. Also, warming influenced the prokaryotic community, which largely remained oligotrophic summer-like throughout 2014-15, with cyanobacterial populations shifting from cold-water ecotypes to warm-water ecotypes.
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16
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Munson-McGee JH, Lindsay MR, Sintes E, Brown JM, D'Angelo T, Brown J, Lubelczyk LC, Tomko P, Emerson D, Orcutt BN, Poulton NJ, Herndl GJ, Stepanauskas R. Decoupling of respiration rates and abundance in marine prokaryoplankton. Nature 2022; 612:764-770. [PMID: 36477536 PMCID: PMC9771814 DOI: 10.1038/s41586-022-05505-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
The ocean-atmosphere exchange of CO2 largely depends on the balance between marine microbial photosynthesis and respiration. Despite vast taxonomic and metabolic diversity among marine planktonic bacteria and archaea (prokaryoplankton)1-3, their respiration usually is measured in bulk and treated as a 'black box' in global biogeochemical models4; this limits the mechanistic understanding of the global carbon cycle. Here, using a technology for integrated phenotype analyses and genomic sequencing of individual microbial cells, we show that cell-specific respiration rates differ by more than 1,000× among prokaryoplankton genera. The majority of respiration was found to be performed by minority members of prokaryoplankton (including the Roseobacter cluster), whereas cells of the most prevalent lineages (including Pelagibacter and SAR86) had extremely low respiration rates. The decoupling of respiration rates from abundance among lineages, elevated counts of proteorhodopsin transcripts in Pelagibacter and SAR86 cells and elevated respiration of SAR86 at night indicate that proteorhodopsin-based phototrophy3,5-7 probably constitutes an important source of energy to prokaryoplankton and may increase growth efficiency. These findings suggest that the dependence of prokaryoplankton on respiration and remineralization of phytoplankton-derived organic carbon into CO2 for its energy demands and growth may be lower than commonly assumed and variable among lineages.
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Affiliation(s)
| | | | - Eva Sintes
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Instituto Español de Oceanografía-CSIC, Centro Oceanográfico de Baleares, Palma, Spain
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | - Joe Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | | | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, The Netherlands
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17
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Tang X, Fan C, Zeng G, Zhong L, Li C, Ren X, Song B, Liu X. Phage-host interactions: The neglected part of biological wastewater treatment. WATER RESEARCH 2022; 226:119183. [PMID: 36244146 DOI: 10.1016/j.watres.2022.119183] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/29/2022] [Accepted: 09/29/2022] [Indexed: 05/25/2023]
Abstract
In wastewater treatment plants (WWTPs), the stable operation of biological wastewater treatment is strongly dependent on the stability of associated microbiota. Bacteriophages (phages), viruses that specifically infect bacteria and archaea, are highly abundant and diverse in WWTPs. Although phages do not have known metabolic functions for themselves, they can shape functional microbiota via various phage-host interactions to impact biological wastewater treatment. However, the developments of phage-host interaction in WWTPs and their impact on biological wastewater treatment are overlooked. Here, we review the current knowledge regarding the phage-host interactions in biological wastewater treatment, mainly focusing on the characteristics of different phage populations, the phage-driven changes in functional microbiota, and the potential driving factors of phage-host interactions. We also discuss the efforts required further to understand and manipulate the phage-host interactions in biological wastewater treatment. Overall, this review advocates more attention to the phage dynamics in WWTPs.
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Affiliation(s)
- Xiang Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Changzheng Fan
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China.
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Linrui Zhong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Chao Li
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China; Nova Skantek (Hunan) Environ Energy Co., Ltd., Changsha 410100, P.R. China
| | - Xiaoya Ren
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Biao Song
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Xigui Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
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18
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Debroas D, Hochart C, Galand PE. Seasonal microbial dynamics in the ocean inferred from assembled and unassembled data: a view on the unknown biosphere. ISME COMMUNICATIONS 2022; 2:87. [PMID: 37938749 PMCID: PMC9723795 DOI: 10.1038/s43705-022-00167-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 11/09/2023]
Abstract
In environmental metagenomic experiments, a very high proportion of the microbial sequencing data (> 70%) remains largely unexploited because rare and closely related genomes are missed in short-read assemblies. The identity and the potential metabolisms of a large fraction of natural microbial communities thus remain inaccessible to researchers. The purpose of this study was to explore the genomic content of unassembled metagenomic data and test their level of novelty. We used data from a three-year microbial metagenomic time series of the NW Mediterranean Sea, and conducted reference-free and database-guided analysis. The results revealed a significant genomic difference between the assembled and unassembled reads. The unassembled reads had a lower mean identity against public databases, and fewer metabolic pathways could be reconstructed. In addition, the unassembled fraction presented a clear temporal pattern, unlike the assembled ones, and a specific community composition that was similar to the rare communities defined by metabarcoding using the 16S rRNA gene. The rare gene pool was characterised by keystone bacterial taxa, and the presence of viruses, suggesting that viral lysis could maintain some taxa in a state of rarity. Our study demonstrates that unassembled metagenomic data can provide important information on the structure and functioning of microbial communities.
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Affiliation(s)
- Didier Debroas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, 63000, Clermont-Ferrand, France.
| | - Corentin Hochart
- Sorbonne Universités, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Pierre E Galand
- Sorbonne Universités, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
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19
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Marantos A, Mitarai N, Sneppen K. From kill the winner to eliminate the winner in open phage-bacteria systems. PLoS Comput Biol 2022; 18:e1010400. [PMID: 35939510 PMCID: PMC9387927 DOI: 10.1371/journal.pcbi.1010400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/18/2022] [Accepted: 07/17/2022] [Indexed: 11/23/2022] Open
Abstract
Phages and bacteria manage to coexist and sustain ecosystems with a high diversity of strains, despite limited resources and heavy predation. This diversity can be explained by the “kill the winner” model where virulent phages predominantly prey on fast-growing bacteria and thereby suppress the competitive exclusion of slower-growing bacteria. Here we computationally investigate the robustness of these systems against invasions, where new phages or bacteria may interact with more than one of the resident strains. The resulting interaction networks were found to self-organize into a network with strongly interacting specialized predator-prey pairs, resembling that of the “kill the winner” model. Furthermore, the “kill the winner” dynamics is enforced with the occasional elimination of even the fastest-growing bacteria strains due to a phage infecting the fast and slow growers. The frequency of slower-growing strains was increased with the introduction of even a few non-diagonal interactions. Hence, phages capable of infecting multiple hosts play significant roles both in the evolution of the ecosystem by eliminating the winner and in supporting diversity by allowing slow growers to coexist with faster growers. We demonstrate that in an open system of phages and bacteria with very limited resources, a bacterial strain that has a high growth rate can still be outcompeted by a slower-growing strain if they have a common phage. The impact of this on ecosystem structure is significant as soon as there is a small probability to have a common phage among bacterial strains. Furthermore, by analysing the structure of the interaction network we show that it self-organizes into a network with strongly interacting specialized predator-prey pairs, in order to reduce phages competition. Nevertheless, the presence of the remaining links is very important for the network dynamics since even a few of them significantly enhance the frequency of slower-growing strains.
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Affiliation(s)
- Anastasios Marantos
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Namiko Mitarai
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kim Sneppen
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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20
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Han M, Luo G, He J, Liang Y, Chen X, Liu G, Su Y, Ge F, Yu H, Zhao J, Hao Q, Shao H, Sung YY, Mok WJ, Wong LL, McMinn A, Wang M. Distributions and relationships of virio- and picoplankton in the epi-, meso- and bathypelagic zones of the Amundsen Sea, West Antarctica during the austral summer. Front Microbiol 2022; 13:941323. [PMID: 35966700 PMCID: PMC9363919 DOI: 10.3389/fmicb.2022.941323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Virioplankton and picoplankton are the most abundant marine biological entities on earth and mediate biogeochemical cycles in the Southern Ocean. However, understanding of their distribution and relationships with environmental factors is lacking. Here, we report on their distribution and relationships with environmental factors at 48 stations from 112.5° to 150°W and 67° to 75.5°S in the Amundsen Sea of West Antarctica. The epipelagic stations were grouped into four clusters based on the virio- and picoplankton composition and abundance. Clusters three and four, which were associated with the ice-edge blooms in the coastal and Amundsen Sea Polynya (ASP) areas, had high abundances of autotrophic picoeukaryotes; this resulted in subsequent high abundances of heterotrophic prokaryotes and viruses. Cluster two stations were in open oceanic areas, where the abundances of autotrophic and heterotrophic picoplankton were low. Cluster one stations were located between the areas of blooms and the oceanic areas, which had a low abundance of heterotrophic prokaryotes and picoeukaryotes and a high abundance of virioplankton. The abundance of viruses was significantly correlated with the abundances of autotrophic picoeukaryotes and Chl-a concentration in oceanic areas, although this reflected a time-lag with autotrophic picoeukaryote and heterotrophic prokaryotes abundances in ice-edge bloom areas. The upwelling of Circumpolar Deep Water (CDW) might have induced the high abundance of autotrophic picoeukaryotes in the epipelagic zone, and the sinking particulate organic carbon (POC) might have induced the high abundance of heterotrophic prokaryotes and virioplankton in the meso- and bathypelagic zones. This study shows that the summer distribution of virio- and picoplankton in the Amundsen Sea of West Antarctica was mainly controlled by upwelling of the CDW and the timing of ice-edge blooms.
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Affiliation(s)
- Meiaoxue Han
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Guangfu Luo
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Shanghai, China
- MNR Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
- College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Jianfeng He
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Shanghai, China
- MNR Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
- College of Environmental Science and Engineering, Tongji University, Shanghai, China
- *Correspondence: Jianfeng He,
| | - Yantao Liang
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Yantao Liang,
| | - Xuechao Chen
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Gang Liu
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yue Su
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Fuyue Ge
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Hao Yu
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jun Zhao
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Qiang Hao
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Hongbing Shao
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, University of Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, University of Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, University of Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Andrew McMinn
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Min Wang
- College of Marine Life Sciences, Key Lab of Polar Oceanography and Global Ocean Change, Institute of Evolution and Marine Biodiversity, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Department of Critical Care Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
- Min Wang,
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Grupstra CGB, Howe-Kerr LI, Veglia AJ, Bryant RL, Coy SR, Blackwelder PL, Correa AMS. Thermal stress triggers productive viral infection of a key coral reef symbiont. THE ISME JOURNAL 2022; 16:1430-1441. [PMID: 35046559 PMCID: PMC9038915 DOI: 10.1038/s41396-022-01194-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 01/03/2022] [Accepted: 01/07/2022] [Indexed: 04/27/2023]
Abstract
Climate change-driven ocean warming is increasing the frequency and severity of bleaching events, in which corals appear whitened after losing their dinoflagellate endosymbionts (family Symbiodiniaceae). Viral infections of Symbiodiniaceae may contribute to some bleaching signs, but little empirical evidence exists to support this hypothesis. We present the first temporal analysis of a lineage of Symbiodiniaceae-infecting positive-sense single-stranded RNA viruses ("dinoRNAVs") in coral colonies, which were exposed to a 5-day heat treatment (+2.1 °C). A total of 124 dinoRNAV major capsid protein gene "aminotypes" (unique amino acid sequences) were detected from five colonies of two closely related Pocillopora-Cladocopium (coral-symbiont) combinations in the experiment; most dinoRNAV aminotypes were shared between the two coral-symbiont combinations (64%) and among multiple colonies (82%). Throughout the experiment, seventeen dinoRNAV aminotypes were found only in heat-treated fragments, and 22 aminotypes were detected at higher relative abundances in heat-treated fragments. DinoRNAVs in fragments of some colonies exhibited higher alpha diversity and dispersion under heat stress. Together, these findings provide the first empirical evidence that exposure to high temperatures triggers some dinoRNAVs to switch from a persistent to a productive infection mode within heat-stressed corals. Over extended time frames, we hypothesize that cumulative dinoRNAV production in the Pocillopora-Cladocopium system could affect colony symbiotic status, for example, by decreasing Symbiodiniaceae densities within corals. This study sets the stage for reef-scale investigations of dinoRNAV dynamics during bleaching events.
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Affiliation(s)
| | | | - Alex J Veglia
- BioSciences at Rice, Rice University, Houston, TX, USA
| | - Reb L Bryant
- BioSciences at Rice, Rice University, Houston, TX, USA
- Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS, USA
| | | | - Patricia L Blackwelder
- Department of Chemistry, University of Miami Center for Advanced Microscopy (UMCAM), 1301 Memorial Dr, Coral Gables, FL, 33146-0630, USA
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22
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Landa KJ, Mossman LM, Whitaker RJ, Rapti Z, Clifton SM. Phage-Antibiotic Synergy Inhibited by Temperate and Chronic Virus Competition. Bull Math Biol 2022; 84:54. [PMID: 35316421 DOI: 10.1007/s11538-022-01006-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 02/10/2022] [Indexed: 12/12/2022]
Abstract
As antibiotic resistance grows more frequent for common bacterial infections, alternative treatment strategies such as phage therapy have become more widely studied in the medical field. While many studies have explored the efficacy of antibiotics, phage therapy, or synergistic combinations of phages and antibiotics, the impact of virus competition on the efficacy of antibiotic treatment has not yet been considered. Here, we model the synergy between antibiotics and two viral types, temperate and chronic, in controlling bacterial infections. We demonstrate that while combinations of antibiotic and temperate viruses exhibit synergy, competition between temperate and chronic viruses inhibits bacterial control with antibiotics. In fact, our model reveals that antibiotic treatment may counterintuitively increase the bacterial load when a large fraction of the bacteria are antibiotic resistant, and both chronic and temperate phages are present.
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Affiliation(s)
- Kylie J Landa
- Department of Mathematics, Statistics, and Computer Science, St. Olaf College, Northfield, MN, 55057, USA
| | - Lauren M Mossman
- Department of Mathematics, Statistics, and Computer Science, St. Olaf College, Northfield, MN, 55057, USA
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Zoi Rapti
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Mathematics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sara M Clifton
- Department of Mathematics, Statistics, and Computer Science, St. Olaf College, Northfield, MN, 55057, USA.
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23
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Mechanisms Generating Dichotomies in the Life Strategies of Heterotrophic Marine Prokaryotes. DIVERSITY 2022. [DOI: 10.3390/d14030217] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Understanding the mechanisms that generate and maintain diversity in marine prokaryotic communities is one of the main challenges for contemporary marine microbiology. We here review how observational, experimental, and theoretical evidence converge on the conclusion that the marine pelagic community of heterotrophic prokaryotes consists of organisms with two main types of life strategies. We illustrate this dichotomy by SAR11 and Vibrio spp. as typical representatives of the two strategies. A theory for life strategy dichotomy exists in classical r/K-selection. We here discuss an additional dichotomy introduced by what we term S/L-selection (for Small and Large, respectively). While r/K-selection focuses on the role of environmental disturbances, steady-state models suggest that high abundance at species level should be closely related to a low trade-off between competition and defense. We summarize literature indicating that the high availability of organic C is an essential environmental factor favoring Vibrio spp. and suggest that the essence of the generalized L-strategy is to reduce the competition-predator defense trade-off by using non-limiting organic C to increase size. The “streamlining” theory that has been suggested for the S-strategist SAR11 proposes the opposite: that low trade-off is achieved by a reduction in size. We show how this apparent contradiction disappears when the basic assumptions of diffusion-limited uptake are considered. We propose a classification scheme that combines S/L and r/K-selection using the two dimensions of organic C availability and environmental disturbance. As organic C in terrestrial runoff and size of the oligotrophic oceanic gyres are both changing, habitat size for both S- and L-strategists are affected by global change. A theory capturing the main aspects of prokaryote life strategies is therefore crucial for predicting responses of the marine microbial food web to climate change and other anthropogenic influences.
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24
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Han LL, Yu DT, Bi L, Du S, Silveira C, Cobián Güemes AG, Zhang LM, He JZ, Rohwer F. Distribution of soil viruses across China and their potential role in phosphorous metabolism. ENVIRONMENTAL MICROBIOME 2022; 17:6. [PMID: 35130971 PMCID: PMC8822697 DOI: 10.1186/s40793-022-00401-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Viruses are the most abundant biological entities on the planet and drive biogeochemical cycling on a global scale. Our understanding of biogeography of soil viruses and their ecological functions lags significantly behind that of Bacteria and Fungi. Here, a viromic approach was used to investigate the distribution and ecological functions of viruses from 19 soils across China. RESULTS Soil viral community were clustered more significantly by geographical location than type of soil (agricultural and natural). Three clusters of viral communities were identified from North, Southeast and Southwest regions; these clusters differentiated using taxonomic composition and were mainly driven by geographic location and climate factors. A total of 972 viral populations (vOTUs) were detected spanning 23 viral families from the 19 viromes. Phylogenetic analyses of the phoH gene showed a remarkable diversity and the distribution of viral phoH genes was more dependent on the environment. Notably, five proteins involved in phosphorus (P) metabolism-related nucleotide synthesis functions, including dUTPase, MazG, PhoH, Thymidylate synthase complementing protein (Thy1), and Ribonucleoside reductase (RNR), were mainly identified in agricultural soils. CONCLUSIONS The present work revealed that soil viral communities were distributed across China according to geographical location and climate factors. In addition, P metabolism genes encoded by these viruses probably drive the synthesis of nucleotides for their own genomes inside bacterial hosts, thereby affecting P cycling in the soil ecosystems.
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Affiliation(s)
- Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA.
| | - Dan-Ting Yu
- Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, Fujian, China.
| | - Li Bi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuai Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cynthia Silveira
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
- Viral Information Institute at San Diego State University, San Diego, CA, 92182, USA
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Ana Georgina Cobián Güemes
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
- Viral Information Institute at San Diego State University, San Diego, CA, 92182, USA
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Zheng He
- Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, Fujian, China
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
- Viral Information Institute at San Diego State University, San Diego, CA, 92182, USA
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25
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Sandaa RA, Saltvedt MR, Dahle H, Wang H, Våge S, Blanc-Mathieu R, Steen IH, Grimsley N, Edvardsen B, Ogata H, Lawrence J. Adaptive evolution of viruses infecting marine microalgae (haptophytes), from acute infections to stable coexistence. Biol Rev Camb Philos Soc 2021; 97:179-194. [PMID: 34514703 DOI: 10.1111/brv.12795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 08/27/2021] [Accepted: 09/01/2021] [Indexed: 12/13/2022]
Abstract
Collectively known as phytoplankton, photosynthetic microbes form the base of the marine food web, and account for up to half of the primary production on Earth. Haptophytes are key components of this phytoplankton community, playing important roles both as primary producers and as mixotrophs that graze on bacteria and protists. Viruses influence the ecology and diversity of phytoplankton in the ocean, with the majority of microalgae-virus interactions described as 'boom and bust' dynamics, which are characteristic of acute virus-host systems. Most haptophytes are, however, part of highly diverse communities and occur at low densities, decreasing their chance of being infected by viruses with high host specificity. Viruses infecting these microalgae have been isolated in the laboratory, and there are several characteristics that distinguish them from acute viruses infecting bloom-forming haptophytes. Herein we synthesise what is known of viruses infecting haptophyte hosts in the ocean, discuss the adaptive evolution of haptophyte-infecting viruses -from those that cause acute infections to those that stably coexist with their host - and identify traits of importance for successful survival in the ocean.
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Affiliation(s)
- Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Marius R Saltvedt
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Håkon Dahle
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Haina Wang
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Selina Våge
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Romain Blanc-Mathieu
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Université Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
| | - Ida H Steen
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Nigel Grimsley
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Bente Edvardsen
- Department of Biosciences, University of Oslo, Postbox 1066, N-0316, Oslo, Norway
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Janice Lawrence
- Biology Department, University of New Brunswick, PO Box 4400, Fredericton, NB, E3B 5A3, Canada
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26
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Wisnoski NI, Lennon JT. Stabilising role of seed banks and the maintenance of bacterial diversity. Ecol Lett 2021; 24:2328-2338. [PMID: 34322982 DOI: 10.1111/ele.13853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/19/2021] [Accepted: 07/07/2021] [Indexed: 01/09/2023]
Abstract
Coexisting species often exhibit negative frequency dependence due to mechanisms that promote population growth and persistence when rare. These stabilising mechanisms can maintain diversity through interspecific niche differences, but also through life-history strategies like dormancy that buffer populations in fluctuating environments. However, there are few tests demonstrating how seed banks contribute to long-term community dynamics and the maintenance of diversity. Using a multi-year, high-frequency time series of bacterial community data from a north temperate lake, we documented patterns consistent with stabilising coexistence. Bacterial taxa exhibited differential responses to seasonal environmental conditions, while seed bank dynamics helped maintain diversity over less-favourable winter periods. Strong negative frequency dependence in rare, but metabolically active, taxa suggested a role for biotic interactions in promoting coexistence. Together, our results provide field-based evidence that niche differences and seed banks contribute to recurring community dynamics and the long-term maintenance of diversity in nature.
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Affiliation(s)
- Nathan I Wisnoski
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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27
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Jahn MT, Lachnit T, Markert SM, Stigloher C, Pita L, Ribes M, Dutilh BE, Hentschel U. Lifestyle of sponge symbiont phages by host prediction and correlative microscopy. THE ISME JOURNAL 2021; 15:2001-2011. [PMID: 33603147 PMCID: PMC8245591 DOI: 10.1038/s41396-021-00900-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/22/2020] [Accepted: 01/18/2021] [Indexed: 01/31/2023]
Abstract
Bacteriophages (phages) are ubiquitous elements in nature, but their ecology and role in animals remains little understood. Sponges represent the oldest known extant animal-microbe symbiosis and are associated with dense and diverse microbial consortia. Here we investigate the tripartite interaction between phages, bacterial symbionts, and the sponge host. We combined imaging and bioinformatics to tackle important questions on who the phage hosts are and what the replication mode and spatial distribution within the animal is. This approach led to the discovery of distinct phage-microbe infection networks in sponge versus seawater microbiomes. A new correlative in situ imaging approach ('PhageFISH-CLEM') localised phages within bacterial symbiont cells, but also within phagocytotically active sponge cells. We postulate that the phagocytosis of free virions by sponge cells modulates phage-bacteria ratios and ultimately controls infection dynamics. Prediction of phage replication strategies indicated a distinct pattern, where lysogeny dominates the sponge microbiome, likely fostered by sponge host-mediated virion clearance, while lysis dominates in seawater. Collectively, this work provides new insights into phage ecology within sponges, highlighting the importance of tripartite animal-phage-bacterium interplay in holobiont functioning. We anticipate that our imaging approach will be instrumental to further understanding of viral distribution and cellular association in animal hosts.
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Affiliation(s)
- M T Jahn
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
- Department of Zoology and Department of Biochemistry, University of Oxford, Oxford, UK.
| | - T Lachnit
- Christian-Albrechts-University of Kiel, Kiel, Germany
| | - S M Markert
- Imaging Core Facility, Biocenter, University of Würzburg, Würzburg, Germany
| | - C Stigloher
- Imaging Core Facility, Biocenter, University of Würzburg, Würzburg, Germany
| | - L Pita
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - M Ribes
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - B E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - U Hentschel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Christian-Albrechts-University of Kiel, Kiel, Germany
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28
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Bacteriophage ecology in biological wastewater treatment systems. Appl Microbiol Biotechnol 2021; 105:5299-5307. [PMID: 34181033 DOI: 10.1007/s00253-021-11414-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/12/2022]
Abstract
Biological wastewater treatment (BWT) is currently the most widely applied approach for treating wastewater. The performance of BWT systems depends on the complex microbial communities they support. Although bacteriophages (phages), which are the viruses that infect prokaryotes, are recognized as the most abundant life entities, understanding of their ecological roles in BWT systems remains limited. Here, we review recent progress in phage-associated researches in BWT systems, including the interactions between phage and host, polyvalent phages, the influence of phage activity on BWT performance, and the potential applications of phage-based control for sludge bulking/foaming and pathogens. The challenges and perspectives of phage ecology are also outlined, which are expected to provide implications for future research and applications.Key points• Phage-host interactions in BWT systems are summarized• Impacts of phage activities on BWT performance• Potential applications of phages in BWT systems.
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29
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Demory D, Weitz JS, Baudoux AC, Touzeau S, Simon N, Rabouille S, Sciandra A, Bernard O. A thermal trade-off between viral production and degradation drives virus-phytoplankton population dynamics. Ecol Lett 2021; 24:1133-1144. [PMID: 33877734 DOI: 10.1111/ele.13722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/24/2020] [Accepted: 02/11/2021] [Indexed: 12/13/2022]
Abstract
Marine viruses interact with microbial hosts in dynamic environments shaped by variation in abiotic factors, including temperature. However, the impacts of temperature on viral infection of phytoplankton are not well understood. Here we coupled mathematical modelling with experiments to explore the effect of temperature on virus-phytoplankton interactions. Our model shows the negative consequences of high temperatures on infection and suggests a temperature-dependent threshold between viral production and degradation. Modelling long-term dynamics in environments with different average temperatures revealed the potential for long-term host-virus coexistence, epidemic free or habitat loss states. We generalised our model to variation in global sea surface temperatures corresponding to present and future seas and show that climate change may differentially influence virus-host dynamics depending on the virus-host pair. Temperature-dependent changes in the infectivity of virus particles may lead to shifts in virus-host habitats in warmer oceans, analogous to projected changes in the habitats of macro-, microorganisms and pathogens.
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Affiliation(s)
- David Demory
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anne-Claire Baudoux
- Sorbonne Université, CNRS, UMR 7144 - Ecology of Marine Plankton, Station Biologique de Roscoff, Roscoff, 29860, France
| | - Suzanne Touzeau
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORE, Sophia Antipolis, 06902, France.,Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Natalie Simon
- Sorbonne Université, CNRS, UMR 7144 - Ecology of Marine Plankton, Station Biologique de Roscoff, Roscoff, 29860, France
| | - Sophie Rabouille
- Sorbonne Université, CNRS, UMR 7621 - Laboratoire d'Océanographie Microbienne, Banyuls-sur-Mer, 66650, France
| | - Antoine Sciandra
- Sorbonne Université, CNRS, UMR 7093 - Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, 06230, France
| | - Olivier Bernard
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORE, Sophia Antipolis, 06902, France
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30
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Pascoal F, Costa R, Magalhães C. The microbial rare biosphere: current concepts, methods and ecological principles. FEMS Microbiol Ecol 2021; 97:5974270. [PMID: 33175111 DOI: 10.1093/femsec/fiaa227] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/06/2020] [Indexed: 01/04/2023] Open
Abstract
Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.
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Affiliation(s)
- Francisco Pascoal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Rodrigo Costa
- Department of Bioengineering, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais 1049-001, Lisbon, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.,U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, CA 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, CA 94720 Berkeley, USA
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,School of Science, University of Waikato, Gate 1, Knighton Road 3240, Hamilton, New Zealand.,Ocean Frontier Institute, Dalhousie University, Steele Ocean Sciences Building, Dalhousie University 1355 Oxford St., B3H4R2 Halifax, NS, Canada
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31
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Carreira C, Lønborg C, Kühl M, Lillebø AI, Sandaa RA, Villanueva L, Cruz S. Fungi and viruses as important players in microbial mats. FEMS Microbiol Ecol 2021; 96:5910486. [PMID: 32966583 DOI: 10.1093/femsec/fiaa187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/18/2020] [Indexed: 11/14/2022] Open
Abstract
Microbial mats are compacted, surface-associated microbial ecosystems reminiscent of the first living communities on early Earth. While often considered predominantly prokaryotic, recent findings show that both fungi and viruses are ubiquitous in microbial mats, albeit their functional roles remain unknown. Fungal research has mostly focused on terrestrial and freshwater ecosystems where fungi are known as important recyclers of organic matter, whereas viruses are exceptionally abundant and important in aquatic ecosystems. Here, viruses have shown to affect organic matter cycling and the diversity of microbial communities by facilitating horizontal gene transfer and cell lysis. We hypothesise fungi and viruses to have similar roles in microbial mats. Based on the analysis of previous research in terrestrial and aquatic ecosystems, we outline novel hypotheses proposing strong impacts of fungi and viruses on element cycling, food web structure and function in microbial mats, and outline experimental approaches for studies needed to understand these interactions.
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Affiliation(s)
- Cátia Carreira
- ECOMARE, CESAM-Centre for Environmental and Marine Studies, Departament of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Christian Lønborg
- Section for Applied Marine Ecology and Modelling, Department of Bioscience, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark
| | - Ana I Lillebø
- ECOMARE, CESAM-Centre for Environmental and Marine Studies, Departament of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Texel, The Netherlands
| | - Sónia Cruz
- ECOMARE, CESAM-Centre for Environmental and Marine Studies, Departament of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
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32
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Temperate and chronic virus competition leads to low lysogen frequency. J Theor Biol 2021; 523:110710. [PMID: 33839160 DOI: 10.1016/j.jtbi.2021.110710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 04/04/2021] [Accepted: 04/05/2021] [Indexed: 11/23/2022]
Abstract
The canonical bacteriophage is obligately lytic: the virus infects a bacterium and hijacks cell functions to produce large numbers of new viruses which burst from the cell. These viruses are well-studied, but there exist a wide range of coexisting virus lifestyles that are less understood. Temperate viruses exhibit both a lytic cycle and a latent (lysogenic) cycle, in which viral genomes are integrated into the bacterial host. Meanwhile, chronic (persistent) viruses use cell functions to produce more viruses without killing the cell; chronic viruses may also exhibit a latent stage in addition to the productive stage. Here, we study the ecology of these competing viral strategies. We demonstrate the conditions under which each strategy is dominant, which aids in control of human bacterial infections using viruses. We find that low lysogen frequencies provide competitive advantages for both virus types; however, chronic viruses maximize steady state density by eliminating lysogeny entirely, while temperate viruses exhibit a non-zero 'sweet spot' lysogen frequency. Viral steady state density maximization leads to coexistence of temperate and chronic viruses, explaining the presence of multiple viral strategies in natural environments.
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Yang M, Xia Q, Du S, Zhang Z, Qin F, Zhao Y. Genomic Characterization and Distribution Pattern of a Novel Marine OM43 Phage. Front Microbiol 2021; 12:651326. [PMID: 33841378 PMCID: PMC8024684 DOI: 10.3389/fmicb.2021.651326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/04/2021] [Indexed: 11/21/2022] Open
Abstract
Bacteriophages have a significant impact on the structure and function of marine microbial communities. Phages of some major bacterial lineages have recently been shown to dominate the marine viral communities. However, phages that infect many important bacterial clades still remained unexplored. Members of the marine OM43 clade are methylotrophs that play important roles in C1 metabolism. OM43 phages (phages that infect the OM43 bacteria) represent an understudied viral group with only one known isolate. In this study, we describe the genomic characterization and biogeography of an OM43 phage that infects the strain HTCC2181, designated MEP301. MEP301 has a genome size of 34,774 bp. We found that MEP301 is genetically distinct from other known phage isolates and only displays significant sequence similarity with some metagenomic viral genomes (MVGs). A total of 12 MEP301-type MVGs were identified from metagenomic datasets. Comparative genomic and phylogenetic analyses revealed that MEP301-type phages can be separated into two subgroups (subgroup I and subgroup II). We also performed a metagenomic recruitment analysis to determine the relative abundance of reads mapped to these MEP301-type phages, which suggested that subgroup I MEP301-type phages are present predominantly in the cold upper waters with lower salinity. Notably, subgroup II phages have an inverse different distribution pattern, implying that they may infect hosts from a distinct OM43 subcluster. Our study has expanded the knowledge about the genomic diversity of marine OM43 phages and identified a new phage group that is widespread in the ocean.
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Affiliation(s)
- Mingyu Yang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qian Xia
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sen Du
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zefeng Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fang Qin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Evans C, Brandsma J, Meredith MP, Thomas DN, Venables HJ, Pond DW, Brussaard CPD. Shift from Carbon Flow through the Microbial Loop to the Viral Shunt in Coastal Antarctic Waters during Austral Summer. Microorganisms 2021; 9:460. [PMID: 33672195 PMCID: PMC7927135 DOI: 10.3390/microorganisms9020460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/30/2022] Open
Abstract
The relative flow of carbon through the viral shunt and the microbial loop is a pivotal factor controlling the contribution of secondary production to the food web and to rates of nutrient remineralization and respiration. The current study examines the significance of these processes in the coastal waters of the Antarctic during the productive austral summer months. Throughout the study a general trend towards lower bacterioplankton and heterotrophic nanoflagellate (HNF) abundances was observed, whereas virioplankton concentration increased. A corresponding decline of HNF grazing rates and shift towards viral production, indicative of viral infection, was measured. Carbon flow mediated by HNF grazing decreased by more than half from 5.7 µg C L-1 day-1 on average in December and January to 2.4 µg C L-1 day-1 in February. Conversely, carbon flow through the viral shunt increased substantially over the study from on average 0.9 µg C L-1 day-1 in December to 7.6 µg C L-1 day-1 in February. This study shows that functioning of the coastal Antarctic microbial community varied considerably over the productive summer months. In early summer, the system favors transfer of matter and energy to higher trophic levels via the microbial loop, however towards the end of summer carbon flow is redirected towards the viral shunt, causing a switch towards more recycling and therefore increased respiration and regeneration.
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Affiliation(s)
- Claire Evans
- Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg, 1790 AB Texel, The Netherlands; (J.B.); (C.P.D.B.)
- Ocean BioGeosciences, National Oceanography Centre, Southampton, European Way, Southampton SO14 3ZH, UK
| | - Joost Brandsma
- Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg, 1790 AB Texel, The Netherlands; (J.B.); (C.P.D.B.)
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Michael P. Meredith
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; (M.P.M.); (H.J.V.); (D.W.P.)
| | - David N. Thomas
- Ecosystems & Environment, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland;
| | - Hugh J. Venables
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; (M.P.M.); (H.J.V.); (D.W.P.)
| | - David W. Pond
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; (M.P.M.); (H.J.V.); (D.W.P.)
- Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Corina P. D. Brussaard
- Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg, 1790 AB Texel, The Netherlands; (J.B.); (C.P.D.B.)
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Foraging trade-offs, flagellar arrangements, and flow architecture of planktonic protists. Proc Natl Acad Sci U S A 2021; 118:2009930118. [PMID: 33431666 DOI: 10.1073/pnas.2009930118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unicellular flagellated protists are a key element in aquatic microbial food webs. They all use flagella to swim and to generate feeding currents to encounter prey and enhance nutrient uptake. At the same time, the beating flagella create flow disturbances that attract flow-sensing predators. Protists have highly diverse flagellar arrangements in terms of number of flagella and their position, beat pattern, and kinematics, but it is unclear how the various arrangements optimize the fundamental trade-off between resource acquisition and predation risk. Here we describe the near-cell flow fields produced by 15 species and demonstrate consistent relationships between flagellar arrangement and swimming speed and between flagellar arrangement and flow architecture, and a trade-off between resource acquisition and predation risk. The flow fields fall in categories that are qualitatively described by simple point force models that include the drag force of the moving cell body and the propulsive forces of the flagella. The trade-off between resource acquisition and predation risk varies characteristically between flow architectures: Flagellates with multiple flagella have higher predation risk relative to their clearance rate compared to species with only one active flagellum, with the exception of the highly successful dinoflagellates that have simultaneously achieved high clearance rates and stealth behavior due to a unique flagellar arrangement. Microbial communities are shaped by trade-offs and environmental constraints, and a mechanistic explanation of foraging trade-offs is a vital part of understanding the eukaryotic communities that form the basis of pelagic food webs.
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Heinrichs ME, De Corte D, Engelen B, Pan D. An Advanced Protocol for the Quantification of Marine Sediment Viruses via Flow Cytometry. Viruses 2021; 13:v13010102. [PMID: 33451082 PMCID: PMC7828538 DOI: 10.3390/v13010102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 11/16/2022] Open
Abstract
Viruses are highly abundant, diverse, and active components of marine environments. Flow cytometry has helped to increase the understanding of their impact on shaping microbial communities and biogeochemical cycles in the pelagic zone. However, to date, flow cytometric quantification of sediment viruses is still hindered by interference from the sediment matrix. Here, we developed a protocol for the enumeration of marine sediment viruses by flow cytometry based on separation of viruses from sediment particles using a Nycodenz density gradient. Results indicated that there was sufficient removal of background interference to allow for flow cytometric quantification. Applying this new protocol to deep-sea and tidal-flat samples, viral abundances enumerated by flow cytometry correlated well (R2 = 0.899) with counts assessed by epifluorescence microscopy over several orders of magnitude from marine sediments of various compositions. Further optimization may be needed for sediments with low biomass or high organic content. Overall, the new protocol enables fast and accurate quantification of marine sediment viruses, and opens up the options for virus sorting, targeted viromics, and single-virus sequencing.
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Affiliation(s)
- Mara Elena Heinrichs
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, 26129 Oldenburg, Germany; (M.E.H.); (D.D.C.); (B.E.)
| | - Daniele De Corte
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, 26129 Oldenburg, Germany; (M.E.H.); (D.D.C.); (B.E.)
| | - Bert Engelen
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, 26129 Oldenburg, Germany; (M.E.H.); (D.D.C.); (B.E.)
| | - Donald Pan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka 237-0061, Japan
- Department of Ecology and Environmental Studies, The Water School, Florida Gulf Coast University, Fort Myers, FL 33913, USA
- Correspondence:
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Sabbagh EI, Huete-Stauffer TM, Calleja MLL, Silva L, Viegas M, Morán XAG. Weekly variations of viruses and heterotrophic nanoflagellates and their potential impact on bacterioplankton in shallow waters of the central Red Sea. FEMS Microbiol Ecol 2020; 96:5800985. [PMID: 32149360 PMCID: PMC7104677 DOI: 10.1093/femsec/fiaa033] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 03/08/2020] [Indexed: 11/14/2022] Open
Abstract
Bacterioplankton play a pivotal role in marine ecosystems. However, their temporal dynamics and underlying control mechanisms are poorly understood in tropical regions such as the Red Sea. Here, we assessed the impact of bottom-up (resource availability) and top-down (viruses and heterotrophic nanoflagellates) controls on bacterioplankton abundances by weekly sampling a coastal central Red Sea site in 2017. We monitored microbial abundances by flow cytometry together with a set of environmental variables including temperature, salinity, dissolved organic and inorganic nutrients and chlorophyll a. We distinguished five groups of heterotrophic bacteria depending on their physiological properties relative nucleic acid content, membrane integrity and cell-specific respiratory activity, two groups of Synechococcus cyanobacteria and three groups of viruses. Viruses controlled heterotrophic bacteria for most of the year, as supported by a negative correlation between their respective abundances and a positive one between bacterial mortality rates and mean viral abundances. On the contrary, heterotrophic nanoflagellates abundance covaried with that of heterotrophic bacteria. Heterotrophic nanoflagellates showed preference for larger bacteria from both the high and low nucleic acid content groups. Our results demonstrate that top-down control is fundamental in keeping heterotrophic bacterioplankton abundances low (< 5 × 10 5 cells mL−1) in Red Sea coastal waters.
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Affiliation(s)
- Eman I Sabbagh
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, Thuwal, Kingdom of Saudi Arabia
| | - Tamara M Huete-Stauffer
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, Thuwal, Kingdom of Saudi Arabia
| | - Maria L L Calleja
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, Thuwal, Kingdom of Saudi Arabia.,Max Planck Institute for Chemistry, Hahn-Meitner Weg 1, 55128 Mainz, Germany
| | - Luis Silva
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, Thuwal, Kingdom of Saudi Arabia
| | - Miguel Viegas
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, Thuwal, Kingdom of Saudi Arabia
| | - Xosé Anxelu G Morán
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, Thuwal, Kingdom of Saudi Arabia
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Zakem EJ, Polz MF, Follows MJ. Redox-informed models of global biogeochemical cycles. Nat Commun 2020; 11:5680. [PMID: 33173062 PMCID: PMC7656242 DOI: 10.1038/s41467-020-19454-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/15/2020] [Indexed: 12/13/2022] Open
Abstract
Microbial activity mediates the fluxes of greenhouse gases. However, in the global models of the marine and terrestrial biospheres used for climate change projections, typically only photosynthetic microbial activity is resolved mechanistically. To move forward, we argue that global biogeochemical models need a theoretically grounded framework with which to constrain parameterizations of diverse microbial metabolisms. Here, we explain how the key redox chemistry underlying metabolisms provides a path towards this goal. Using this first-principles approach, the presence or absence of metabolic functional types emerges dynamically from ecological interactions, expanding model applicability to unobserved environments. “Nothing is less real than realism. It is only by selection, by elimination, by emphasis, that we get at the real meaning of things.” –Georgia O’Keefe Marine microbial activities fuel biogeochemical cycles that impact the climate, but global models do not account for the myriad physiological processes that microbes perform. Here the authors argue for a model framework that reinterprets the ocean as physics coupled to biologically-driven redox chemistry.
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Affiliation(s)
- Emily J Zakem
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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Morimoto D, Šulčius S, Yoshida T. Viruses of freshwater bloom-forming cyanobacteria: genomic features, infection strategies and coexistence with the host. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:486-502. [PMID: 32754956 DOI: 10.1111/1758-2229.12872] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Freshwater bloom-forming cyanobacteria densely grow in the aquatic environments, leading to an increase in the viral-contact rate. They possess numerous antiviral genes, as well as cell differentiation- and physiological performance-related genes, owing to genome expansion. Their genomic features and unique lifestyles suggest that they coexist with cyanoviruses in ways different from marine cyanobacteria. Furthermore, genome contents of isolated freshwater bloom-forming cyanobacterial viruses have little in common with those of marine cyanoviruses studied to date. They lack the marine cyanoviral hallmark genes that sustain photosynthetic activity and redirect host metabolism to viral reproduction; therefore, they are predicted to share metabolisms and precursor pools with host cyanobacteria to ensure efficient viral reproduction and avoid nutrient deficiencies and antiviral response. Additionally, cyanovirus-cyanobacteria coexistence strategies may change as bloom density increases. Diverse genotypic populations of cyanoviruses and hosts coexist and fluctuate under high viral-contact rate conditions, leading to their rapid coevolution through antiviral responses. The ancestral and newly evolved genotypes coexist, thereby expanding the diversity levels of host and viral populations. Bottleneck events occurring due to season-related decreases in bloom-forming species abundance provide each genotype within cyanobacterial population an equal chance to increase in prevalence during the next bloom and enhance further diversification.
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Affiliation(s)
- Daichi Morimoto
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Sigitas Šulčius
- Laboratory of Algology and Microbial Ecology, Nature Research Centre, Akademijos 2, Vilnius, 08412, Lithuania
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan
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Temperate infection in a virus-host system previously known for virulent dynamics. Nat Commun 2020; 11:4626. [PMID: 32934228 PMCID: PMC7493887 DOI: 10.1038/s41467-020-18078-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
The blooming cosmopolitan coccolithophore Emiliania huxleyi and its viruses (EhVs) are a model for density-dependent virulent dynamics. EhVs commonly exhibit rapid viral reproduction and drive host death in high-density laboratory cultures and mesocosms that simulate blooms. Here we show that this system exhibits physiology-dependent temperate dynamics at environmentally relevant E. huxleyi host densities rather than virulent dynamics, with viruses switching from a long-term non-lethal temperate phase in healthy hosts to a lethal lytic stage as host cells become physiologically stressed. Using this system as a model for temperate infection dynamics, we present a template to diagnose temperate infection in other virus-host systems by integrating experimental, theoretical, and environmental approaches. Finding temperate dynamics in such an established virulent host-virus model system indicates that temperateness may be more pervasive than previously considered, and that the role of viruses in bloom formation and decline may be governed by host physiology rather than by host-virus densities.
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Impact of Viral Lysis on the Composition of Bacterial Communities and Dissolved Organic Matter in Deep-Sea Sediments. Viruses 2020; 12:v12090922. [PMID: 32842650 PMCID: PMC7552059 DOI: 10.3390/v12090922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 12/17/2022] Open
Abstract
Viral lysis is a main mortality factor for bacteria in deep-sea sediments, leading to changing microbial community structures and the release of cellular components to the environment. Nature and fate of these compounds and the role of viruses for microbial diversity is largely unknown. We investigated the effect of viruses on the composition of bacterial communities and the pool of dissolved organic matter (DOM) by setting up virus-induction experiments using mitomycin C with sediments from the seafloor of the Bering Sea. At the sediment surface, no substantial prophage induction was detected, while incubations from 20 cm below seafloor showed a doubling of the virus-to-cell ratio. Ultra-high resolution mass spectrometry revealed an imprint of cell lysis on the molecular composition of DOM, showing an increase of molecular formulas typical for common biomolecules. More than 50% of these compounds were removed or transformed during incubation. The remaining material potentially contributed to the pool of refractory DOM. Next generation sequencing of the bacterial communities from the induction experiment showed a stable composition over time. In contrast, in the non-treated controls the abundance of dominant taxa (e.g., Gammaproteobacteria) increased at the expense of less abundant phyla. Thus, we conclude that viral lysis was an important driver in sustaining bacterial diversity, consistent with the "killing the winner" model.
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Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation. Appl Environ Microbiol 2020; 86:AEM.00943-20. [PMID: 32561583 PMCID: PMC7440811 DOI: 10.1128/aem.00943-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/13/2020] [Indexed: 12/13/2022] Open
Abstract
Even before the coining of the term “great plate count anomaly” in the 1980s, scientists had noted the discrepancy between the number of microorganisms observed under the microscope and the number of colonies that grew on traditional agar media. New cultivation approaches have reduced this disparity, resulting in the isolation of some of the “most wanted” bacterial lineages. Nevertheless, the vast majority of microorganisms remain uncultured, hampering progress toward answering fundamental biological questions about many important microorganisms. Furthermore, few studies have evaluated the underlying factors influencing cultivation success, limiting our ability to improve cultivation efficacy. Our work details the use of dilution-to-extinction (DTE) cultivation to expand the phylogenetic and geographic diversity of available axenic cultures. We also provide a new model of the DTE approach that uses cultivation results and natural abundance information to predict taxon-specific viability and iteratively constrain DTE experimental design to improve cultivation success. Cultivated bacterioplankton representatives from diverse lineages and locations are essential for microbiology, but the large majority of taxa either remain uncultivated or lack isolates from diverse geographic locales. We paired large-scale dilution-to-extinction (DTE) cultivation with microbial community analysis and modeling to expand the phylogenetic and geographic diversity of cultivated bacterioplankton and to evaluate DTE cultivation success. Here, we report results from 17 DTE experiments totaling 7,820 individual incubations over 3 years, yielding 328 repeatably transferable isolates. Comparison of isolates to microbial community data for source waters indicated that we successfully isolated 5% of the observed bacterioplankton community throughout the study; 43% and 26% of our isolates matched operational taxonomic units and amplicon single-nucleotide variants, respectively, within the top 50 most abundant taxa. Isolates included those from previously uncultivated clades such as SAR11 LD12 and Actinobacteria acIV, as well as geographically novel members from other ecologically important groups like SAR11 subclade IIIa, SAR116, and others, providing isolates in eight putatively new genera and seven putatively new species. Using a newly developed DTE cultivation model, we evaluated taxon viability by comparing relative abundance with cultivation success. The model (i) revealed the minimum attempts required for successful isolation of taxa amenable to growth on our media and (ii) identified possible subpopulation viability variation in abundant taxa such as SAR11 that likely impacts cultivation success. By incorporating viability in experimental design, we can now statistically constrain the effort necessary for successful cultivation of specific taxa on a defined medium. IMPORTANCE Even before the coining of the term “great plate count anomaly” in the 1980s, scientists had noted the discrepancy between the number of microorganisms observed under the microscope and the number of colonies that grew on traditional agar media. New cultivation approaches have reduced this disparity, resulting in the isolation of some of the “most wanted” bacterial lineages. Nevertheless, the vast majority of microorganisms remain uncultured, hampering progress toward answering fundamental biological questions about many important microorganisms. Furthermore, few studies have evaluated the underlying factors influencing cultivation success, limiting our ability to improve cultivation efficacy. Our work details the use of dilution-to-extinction (DTE) cultivation to expand the phylogenetic and geographic diversity of available axenic cultures. We also provide a new model of the DTE approach that uses cultivation results and natural abundance information to predict taxon-specific viability and iteratively constrain DTE experimental design to improve cultivation success.
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Colombet J, Fuster M, Billard H, Sime-Ngando T. Femtoplankton: What's New? Viruses 2020; 12:E881. [PMID: 32806713 PMCID: PMC7472349 DOI: 10.3390/v12080881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/10/2020] [Accepted: 08/10/2020] [Indexed: 01/01/2023] Open
Abstract
Since the discovery of high abundances of virus-like particles in aquatic environment, emergence of new analytical methods in microscopy and molecular biology has allowed significant advances in the characterization of the femtoplankton, i.e., floating entities filterable on a 0.2 µm pore size filter. The successive evidences in the last decade (2010-2020) of high abundances of biomimetic mineral-organic particles, extracellular vesicles, CPR/DPANN (Candidate phyla radiation/Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota), and very recently of aster-like nanoparticles (ALNs), show that aquatic ecosystems form a huge reservoir of unidentified and overlooked femtoplankton entities. The purpose of this review is to highlight this unsuspected diversity. Herein, we focus on the origin, composition and the ecological potentials of organic femtoplankton entities. Particular emphasis is given to the most recently discovered ALNs. All the entities described are displayed in an evolutionary context along a continuum of complexity, from minerals to cell-like living entities.
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Affiliation(s)
- Jonathan Colombet
- Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France; (M.F.); (H.B.); (T.S.-N.)
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Stabilization of extensive fine-scale diversity by ecologically driven spatiotemporal chaos. Proc Natl Acad Sci U S A 2020; 117:14572-14583. [PMID: 32518107 DOI: 10.1073/pnas.1915313117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
It has recently become apparent that the diversity of microbial life extends far below the species level to the finest scales of genetic differences. Remarkably, extensive fine-scale diversity can coexist spatially. How is this diversity stable on long timescales, despite selective or ecological differences and other evolutionary processes? Most work has focused on stable coexistence or assumed ecological neutrality. We present an alternative: extensive diversity maintained by ecologically driven spatiotemporal chaos, with no assumptions about niches or other specialist differences between strains. We study generalized Lotka-Volterra models with antisymmetric correlations in the interactions inspired by multiple pathogen strains infecting multiple host strains. Generally, these exhibit chaos with increasingly wild population fluctuations driving extinctions. But the simplest spatial structure, many identical islands with migration between them, stabilizes a diverse chaotic state. Some strains (subspecies) go globally extinct, but many persist for times exponentially long in the number of islands. All persistent strains have episodic local blooms to high abundance, crucial for their persistence as, for many, their average population growth rate is negative. Snapshots of the abundance distribution show a power law at intermediate abundances that is essentially indistinguishable from the neutral theory of ecology. But the dynamics of the large populations are much faster than birth-death fluctuations. We argue that this spatiotemporally chaotic "phase" should exist in a wide range of models, and that even in rapidly mixed systems, longer-lived spores could similarly stabilize a diverse chaotic phase.
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Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems. mSystems 2020; 5:5/2/e00098-20. [PMID: 32184367 PMCID: PMC7380583 DOI: 10.1128/msystems.00098-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Interactions between viral communities and their microbial hosts have been the subject of many recent studies in a wide range of ecosystems. The degree of coordination between ecological assembly processes influencing viral and microbial communities, however, has been explored to a much lesser degree. By using a combined null modeling approach, this study investigated the ecological assembly processes influencing both viral and microbial community structure within hydraulically fractured shale environments. Among other results, significant relationships between the structuring processes affecting both the viral and microbial community were observed, indicating that ecological assembly might be coordinated between these communities despite differing selective pressures. Within this deep subsurface ecosystem, these results reveal a potentially important balance of ecological dynamics that must be maintained to enable long-term microbial community persistence. More broadly, this relationship begins to provide insight into the development of communities across trophic levels. The ecological drivers that concurrently act upon both a virus and its host and that drive community assembly are poorly understood despite known interactions between viral populations and their microbial hosts. Hydraulically fractured shale environments provide access to a closed ecosystem in the deep subsurface where constrained microbial and viral community assembly processes can be examined. Here, we used metagenomic analyses of time-resolved-produced fluid samples from two wells in the Appalachian Basin to track viral and host dynamics and to investigate community assembly processes. Hypersaline conditions within these ecosystems should drive microbial community structure to a similar configuration through time in response to common osmotic stress. However, viral predation appears to counterbalance this potentially strong homogeneous selection and pushes the microbial community toward undominated assembly. In comparison, while the viral community was also influenced by substantial undominated processes, it assembled, in part, due to homogeneous selection. When the overall assembly processes acting upon both these communities were directly compared with each other, a significant relationship was revealed, suggesting an association between microbial and viral community development despite differing selective pressures. These results reveal a potentially important balance of ecological dynamics that must be in maintained within this deep subsurface ecosystem in order for the microbial community to persist over extended time periods. More broadly, this relationship begins to provide knowledge underlying metacommunity development across trophic levels. IMPORTANCE Interactions between viral communities and their microbial hosts have been the subject of many recent studies in a wide range of ecosystems. The degree of coordination between ecological assembly processes influencing viral and microbial communities, however, has been explored to a much lesser degree. By using a combined null modeling approach, this study investigated the ecological assembly processes influencing both viral and microbial community structure within hydraulically fractured shale environments. Among other results, significant relationships between the structuring processes affecting both the viral and microbial community were observed, indicating that ecological assembly might be coordinated between these communities despite differing selective pressures. Within this deep subsurface ecosystem, these results reveal a potentially important balance of ecological dynamics that must be maintained to enable long-term microbial community persistence. More broadly, this relationship begins to provide insight into the development of communities across trophic levels.
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Dion MB, Oechslin F, Moineau S. Phage diversity, genomics and phylogeny. Nat Rev Microbiol 2020; 18:125-138. [PMID: 32015529 DOI: 10.1038/s41579-019-0311-5] [Citation(s) in RCA: 388] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2019] [Indexed: 12/23/2022]
Abstract
Recent advances in viral metagenomics have enabled the rapid discovery of an unprecedented catalogue of phages in numerous environments, from the human gut to the deep ocean. Although these advances have expanded our understanding of phage genomic diversity, they also revealed that we have only scratched the surface in the discovery of novel viruses. Yet, despite the remarkable diversity of phages at the nucleotide sequence level, the structural proteins that form viral particles show strong similarities and conservation. Phages are uniquely interconnected from an evolutionary perspective and undergo multiple events of genetic exchange in response to the selective pressure of their hosts, which drives their diversity. In this Review, we explore phage diversity at the structural, genomic and community levels as well as the complex evolutionary relationships between phages, moulded by the mosaicity of their genomes.
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Affiliation(s)
- Moïra B Dion
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Frank Oechslin
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada. .,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada. .,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Québec, Canada.
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Thingstad TF, Våge S. Host-virus-predator coexistence in a grey-box model with dynamic optimization of host fitness. THE ISME JOURNAL 2019; 13:3102-3111. [PMID: 31527663 PMCID: PMC6864060 DOI: 10.1038/s41396-019-0496-7] [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: 12/06/2018] [Revised: 08/01/2019] [Accepted: 08/15/2019] [Indexed: 11/09/2022]
Abstract
Lytic viruses are believed to affect both flow patterns and host diversity in microbial food webs. Models resolving host and virus communities into subgroups can represent both aspects. However, when flow pattern is the prime interest, such models may seem unnecessary complex. This has led to proposals of black-box models using only total community sizes as state variables. This simplification creates a coexistence problem, however, since predator and virus communities then compete for the same, shared, prey = host community. Mathematically, this problem can be solved by introducing feedbacks allowing community-level properties to adapt. The different mathematical alternatives for such feedback represent different ecological assumptions and thus different hypotheses for how the balance between predators and viruses is controlled in nature. We here explore a model where the feedback works through an increase in host community resistance in response to high virus abundances, thereby reducing virus production. We use a dynamic "strategy" index S to describe the balance between defensive and competitive abilities in the host community, and assume the rate of change in S to be proportional to the local slope of the per capita fitness gradient for the host. We explore how such a "grey-box" model can allow stable coexistence of viruses and predators, and how equilibrium food web structure, virus-to-host ratio, and partitioning of host production varies; both as functions of host community traits, and as functions of external bottom-up and top-down drivers.
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Affiliation(s)
| | - Selina Våge
- Department of Biological Sciences, University of Bergen, 5020, Bergen, Norway
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Chen X, Ma R, Yang Y, Jiao N, Zhang R. Viral Regulation on Bacterial Community Impacted by Lysis-Lysogeny Switch: A Microcosm Experiment in Eutrophic Coastal Waters. Front Microbiol 2019; 10:1763. [PMID: 31417537 PMCID: PMC6685395 DOI: 10.3389/fmicb.2019.01763] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/16/2019] [Indexed: 11/13/2022] Open
Abstract
Marine viruses are major drivers of global biogeochemical cycles and energy fluxes, yet the importance of viral impacts on the succession and diversity of the bacterial community remains largely unexplored. Here, we explored viral life strategy and its potential effect on the bacterial community by experimental incubations of eutrophic coastal waters under lysogen-induced and non-induced treatments. The lysogen-induced treatment showed relatively constant viral and bacterial abundances, lytic and lysogenic viral production throughout the experimental period, together with the progressive declines in not only the relative abundances for SAR11, Rhodobacteraceae, Alteromonadaceae, and SAR86 but the bacterial community diversity. Conversely, the non-induced treatment observed the marked variation in the abundances of viruses, bacteria and cells with high nucleic acid content over the time course of incubation, which was congruent with the drastic shift in lytic and lysogenic viral production as well as the succession of bacterial community. Our results supported the hypotheses that a high level of lysogeny would occur with the increasing density of bacteria with rapid growth rate, which may contribute to a relatively lower host community diversity, whereas the lysogeny to lysis switching would fuel growth opportunities for less-active or initially rare bacterial taxa and generate a more diverse bacterial community. Altogether, the present study underscored the crucial regulatory role of the viral lysis-lysogeny pattern in bacterial community dynamics, composition and diversity, highlighting the viral impact on the microbial food web and biogeochemical processes.
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Affiliation(s)
- Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Ruijie Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.,College of the Environment and Ecology, Xiamen University, Xiamen, 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, 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, China
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García-López R, Pérez-Brocal V, Moya A. Beyond cells - The virome in the human holobiont. MICROBIAL CELL (GRAZ, AUSTRIA) 2019; 6:373-396. [PMID: 31528630 PMCID: PMC6717880 DOI: 10.15698/mic2019.09.689] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/14/2019] [Accepted: 04/03/2019] [Indexed: 01/01/2023]
Abstract
Viromics, or viral metagenomics, is a relatively new and burgeoning field of research that studies the complete collection of viruses forming part of the microbiota in any given niche. It has strong foundations rooted in over a century of discoveries in the field of virology and recent advances in molecular biology and sequencing technologies. Historically, most studies have deconstructed the concept of viruses into a simplified perception of viral agents as mere pathogens, which demerits the scope of large-scale viromic analyses. Viruses are, in fact, much more than regular parasites. They are by far the most dynamic and abundant entity and the greatest killers on the planet, as well as the most effective geo-transforming genetic engineers and resource recyclers, acting on all life strata in any habitat. Yet, most of this uncanny viral world remains vastly unexplored to date, greatly hindered by the bewildering complexity inherent to such studies and the methodological and conceptual limitations. Viromic studies are just starting to address some of these issues but they still lag behind microbial metagenomics. In recent years, however, higher-throughput analysis and resequencing have rekindled interest in a field that is just starting to show its true potential. In this review, we take a look at the scientific and technological developments that led to the advent of viral and bacterial metagenomics with a particular, but not exclusive, focus on human viromics from an ecological perspective. We also address some of the most relevant challenges that current viral studies face and ponder on the future directions of the field.
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Affiliation(s)
- Rodrigo García-López
- Institute of Evolutionary Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), València, Spain
| | - Vicente Pérez-Brocal
- Institute of Evolutionary Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), València, Spain
| | - Andrés Moya
- Institute of Evolutionary Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), València, Spain
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Zimmerman AE, Bachy C, Ma X, Roux S, Jang HB, Sullivan MB, Waldbauer JR, Worden AZ. Closely related viruses of the marine picoeukaryotic alga Ostreococcus lucimarinus exhibit different ecological strategies. Environ Microbiol 2019; 21:2148-2170. [PMID: 30924271 PMCID: PMC6851583 DOI: 10.1111/1462-2920.14608] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/16/2019] [Accepted: 03/23/2019] [Indexed: 01/01/2023]
Abstract
In marine ecosystems, viruses are major disrupters of the direct flow of carbon and nutrients to higher trophic levels. Although the genetic diversity of several eukaryotic phytoplankton virus groups has been characterized, their infection dynamics are less understood, such that the physiological and ecological implications of their diversity remain unclear. We compared genomes and infection phenotypes of the two most closely related cultured phycodnaviruses infecting the widespread picoprasinophyte Ostreococcus lucimarinus under standard- (1.3 divisions per day) and limited-light (0.41 divisions per day) nutrient replete conditions. OlV7 infection caused early arrest of the host cell cycle, coinciding with a significantly higher proportion of infected cells than OlV1-amended treatments, regardless of host growth rate. OlV7 treatments showed a near-50-fold increase of progeny virions at the higher host growth rate, contrasting with OlV1's 16-fold increase. However, production of OlV7 virions was more sensitive than OlV1 production to reduced host growth rate, suggesting fitness trade-offs between infection efficiency and resilience to host physiology. Moreover, although organic matter released from OlV1- and OlV7-infected hosts had broadly similar chemical composition, some distinct molecular signatures were observed. Collectively, these results suggest that current views on viral relatedness through marker and core gene analyses underplay operational divergence and consequences for host ecology.
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Affiliation(s)
| | - Charles Bachy
- Monterey Bay Aquarium Research InstituteMoss LandingCAUSA
| | - Xiufeng Ma
- Department of the Geophysical SciencesUniversity of ChicagoChicagoILUSA
| | - Simon Roux
- Department of MicrobiologyEnvironmental and Geodetic Engineering, The Ohio State UniversityColumbusOHUSA
| | - Ho Bin Jang
- Department of MicrobiologyEnvironmental and Geodetic Engineering, The Ohio State UniversityColumbusOHUSA
- Department of CivilEnvironmental and Geodetic Engineering, The Ohio State UniversityColumbusOHUSA
| | - Matthew B. Sullivan
- Department of MicrobiologyEnvironmental and Geodetic Engineering, The Ohio State UniversityColumbusOHUSA
- Department of CivilEnvironmental and Geodetic Engineering, The Ohio State UniversityColumbusOHUSA
| | | | - Alexandra Z. Worden
- Monterey Bay Aquarium Research InstituteMoss LandingCAUSA
- Ocean EcoSystems Biology Unit, Marine Ecology DivisionGEOMAR Helmholtz Centre for Ocean Research KielKielDE
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