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Eissler Y, Castillo-Reyes A, Dorador C, Cornejo-D'Ottone M, Celis-Plá PSM, Aguilar P, Molina V. Virus-to-prokaryote ratio in the Salar de Huasco and different ecosystems of the Southern hemisphere and its relationship with physicochemical and biological parameters. Front Microbiol 2022; 13:938066. [PMID: 36060762 PMCID: PMC9434117 DOI: 10.3389/fmicb.2022.938066] [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: 05/06/2022] [Accepted: 07/31/2022] [Indexed: 11/13/2022] Open
Abstract
The virus-to-prokaryote ratio (VPR) has been used in many ecosystems to study the relationship between viruses and their hosts. While high VPR values indicate a high rate of prokaryotes' cell lysis, low values are interpreted as a decrease in or absence of viral activity. Salar de Huasco is a high-altitude wetland characterized by a rich microbial diversity associated with aquatic sites like springs, ponds, streams and a lagoon with variable physicochemical conditions. Samples from two ponds, Poza Rosada (PR) and Poza Verde (PV), were analyzed by epifluorescence microscopy to determine variability of viral and prokaryotic abundance and to calculate the VPR in a dry season. In addition, to put Salar de Huasco results into perspective, a compilation of research articles on viral and prokaryotic abundance, VPR, and metadata from various Southern hemisphere ecosystems was revised. The ecosystems were grouped into six categories: high-altitude wetlands, Pacific, Atlantic, Indian, and Southern Oceans and Antarctic lakes. Salar de Huasco ponds recorded similar VPR values (an average of 7.4 and 1.7 at PR and PV, respectively), ranging from 3.22 to 15.99 in PR. The VPR variability was associated with VA and chlorophyll a, when considering all data available for this ecosystem. In general, high-altitude wetlands recorded the highest VPR average (53.22 ± 95.09), followed by the Oceans, Southern (21.91 ± 25.72), Atlantic (19.57 ± 15.77) and Indian (13.43 ± 16.12), then Antarctic lakes (11.37 ± 15.82) and the Pacific Ocean (6.34 ± 3.79). Physicochemical variables, i.e., temperature, conductivity, nutrients (nitrate, ammonium, and phosphate) and chlorophyll a as a biological variable, were found to drive the VPR in the ecosystems analyzed. Thus, the viral activity in the Wetland followed similar trends of previous reports based on larger sets of metadata analyses. In total, this study highlights the importance of including viruses as a biological variable to study microbial temporal dynamics in wetlands considering their crucial role in the carbon budgets of these understudied ecosystems in the southern hemisphere.
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Affiliation(s)
- Yoanna Eissler
- Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- *Correspondence: Yoanna Eissler
| | - Alonso Castillo-Reyes
- Escuela de Biología Marina, Facultad de Ciencias del Mar y de Recursos Naturales, Universidad de Valparaíso, Viña del Mar, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto de Antofagasta, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
| | - Marcela Cornejo-D'Ottone
- Escuela de Ciencias del Mar e Instituto Milenio de Oceanografía, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Paula S. M. Celis-Plá
- Laboratory of Aquatic Environmental Research, Centro de Estudios Avanzados, Universidad de Playa Ancha, Viña del Mar, Chile
- HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile
| | - Polette Aguilar
- HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile
| | - Verónica Molina
- HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile
- Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile
- Centro de Investigación Oceanográfica COPAS COASTAL, Universidad de Concepción, Concepción, Chile
- Verónica Molina
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2
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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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3
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Roy K, Ghosh D, DeBruyn JM, Dasgupta T, Wommack KE, Liang X, Wagner RE, Radosevich M. Temporal Dynamics of Soil Virus and Bacterial Populations in Agricultural and Early Plant Successional Soils. Front Microbiol 2020; 11:1494. [PMID: 32733413 PMCID: PMC7358527 DOI: 10.3389/fmicb.2020.01494] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
Abstract
As reported in many aquatic environments, recent studies in terrestrial ecosystems implicate a role for viruses in shaping the structure, function, and evolution of prokaryotic soil communities. However, given the heterogeneity of soil and the physical constraints (i.e., pore-scale hydrology and solid-phase adsorption of phage and host cells) on the mobility of viruses and bacteria, phage-host interactions likely differ from those in aquatic systems. In this study, temporal changes in the population dynamics of viruses and bacteria in soils under different land management practices were examined. The results showed that bacterial abundance was significantly and positively correlated to both virus and inducible prophage abundance. Bacterial and viral abundance were also correlated with soil organic carbon and nitrogen content as well as with C:N ratio. The seasonal variability in viral abundance increased with soil organic carbon content. The prokaryotic community structure was influenced more by land use than by seasonal variation though considerable variation was evident in the early plant successional and grassland sites. The free extracellular viral communities were also separated by land use, and the forest soil viral assemblage exhibiting the most seasonal variability was more distinct from the other sites. Viral assemblages from the agricultural soils exhibited the least seasonal variability. Similar patterns were observed for inducible prophage viral assemblages. Seasonal variability of viral assemblages was greater in mitomycin-C (mitC) induced prophages than in extracellular viruses irrespective of land use and management. Taken together, the data suggest that soil viral production and decay are likely balanced but there was clear evidence that the structure of viral assemblages is influenced by land use and by season.
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Affiliation(s)
- Krishnakali Roy
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Dhritiman Ghosh
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - K Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, United States
| | - Xiaolong Liang
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Regan E Wagner
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
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Ruiz-Perez CA, Tsementzi D, Hatt JK, Sullivan MB, Konstantinidis KT. Prevalence of viral photosynthesis genes along a freshwater to saltwater transect in Southeast USA. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:672-689. [PMID: 31265211 DOI: 10.1111/1758-2229.12780] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 06/29/2019] [Indexed: 05/28/2023]
Abstract
Bacteriophages encode host-acquired functional genes known as auxiliary metabolic genes (AMGs). Photosynthesis AMGs are commonly found in marine cyanobacteria-infecting Myoviridae and Podoviridae cyanophages, but their ecology remains understudied in freshwater environments. To advance knowledge of this issue, we analysed viral metagenomes collected in the summertime for four years from five lakes and two estuarine locations interconnected by the Chattahoochee River, Southeast USA. Sequences representing ten different AMGs were recovered and found to be prevalent in all sites. Most freshwater AMGs were 10-fold less abundant than estuarine and marine AMGs and were encoded by novel Myoviridae and Podoviridae cyanophage genera. Notably, several of the corresponding viral genomes showed endemism to a specific province along the river. This translated into psbA gene phylogenetic clustering patterns that matched a marine vs. freshwater origin indicating that psbA may serve as a robust classification and source-tracking biomarker. Genomes classified in a novel viral lineage represented by isolate S-EIVl contained psbA, which is unprecedented for this lineage. Collectively, our findings indicated that the acquisition of photosynthesis AMGs is a widespread strategy used by cyanophages in aquatic ecosystems, and further indicated the existence of viral provinces in which certain viral species and/or genotypes are locally abundant.
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Affiliation(s)
- Carlos A Ruiz-Perez
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Despina Tsementzi
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, USA
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5
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Zhong KX, Suttle CA, Baudoux AC, Derelle E, Colombet J, Cho A, Caleta J, Six C, Jacquet S. A New Freshwater Cyanosiphovirus Harboring Integrase. Front Microbiol 2018; 9:2204. [PMID: 30283423 PMCID: PMC6157547 DOI: 10.3389/fmicb.2018.02204] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 08/29/2018] [Indexed: 11/13/2022] Open
Abstract
Pelagic cyanobacteria are key players in the functioning of aquatic ecosystems, and their viruses (cyanophages) potentially affect the abundance and composition of cyanobacterial communities. Yet, there are few well-described freshwater cyanophages relative to their marine counterparts, and in general, few cyanosiphoviruses (family Siphoviridae) have been characterized, limiting our understanding of the biology and the ecology of this prominent group of viruses. Here, we characterize S-LBS1, a freshwater siphovirus lytic to a phycoerythrin-rich Synechococcus isolate (Strain TCC793). S-LBS1 has a narrow host range, a burst size of ∼400 and a relatively long infecting step before cell lysis occurs. It has a dsDNA 34,641 bp genome with putative genes for structure, DNA packing, lysis, replication, host interactions, DNA repair and metabolism. S-LBS1 is similar in genome size, genome architecture, and gene content, to previously described marine siphoviruses also infecting PE-rich Synechococcus, e.g., S-CBS1 and S-CBS3. However, unlike other Synechococcus phages, S-LBS1 encodes an integrase, suggesting its ability to establish lysogenic relationships with its host. Sequence recruitment from viral metagenomic data showed that S-LBS1-like viruses are diversely present in a wide range of aquatic environments, emphasizing their potential importance in controlling and structuring Synechococcus populations. A comparative analysis with 16 available sequenced cyanosiphoviruses reveals the absence of core genes within the genomes, suggesting high degree of genetic variability in siphoviruses infecting cyanobacteria. It is likely that cyanosiphoviruses have evolved as distinct evolutionary lineages and that adaptive co-evolution occurred between these viruses and their hosts (i.e., Synechococcus, Prochlorococcus, Nodularia, and Acaryochloris), constituting an important driving force for such phage diversification.
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Affiliation(s)
- Kevin Xu Zhong
- INRA, UMR 042 CARRTEL, Thonon-les-Bains, France.,Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Curtis A Suttle
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.,Department of Botany, Institute for Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada
| | - Anne-Claire Baudoux
- Sorbonne Universités UPMC Paris 06, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Evelyne Derelle
- Integrative Marine Biology Laboratory (BIOM), CNRS UMR7232, Sorbonne Universities, Banyuls-sur-Mer, France
| | - Jonathan Colombet
- CNRS, Université Blaise Pascal, UMR 6023, Laboratory of Microorganismes, Aubière, France
| | - Anna Cho
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Jessica Caleta
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Christophe Six
- Sorbonne Universités UPMC Paris 06, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
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Colombet J, Robin A, Sime-Ngando T. Genotypic, size and morphological diversity of virioplankton in a deep oligomesotrophic freshwater lake (Lac Pavin, France). J Environ Sci (China) 2017; 53:48-59. [PMID: 28372760 DOI: 10.1016/j.jes.2016.05.016] [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: 12/01/2015] [Revised: 05/02/2016] [Accepted: 05/05/2016] [Indexed: 06/07/2023]
Abstract
We examined changes in morphological and genomic diversities of viruses by means of transmission electronic microscopy and pulsed field gel electrophoresis (PFGE) over a nine-month period (April-December 2005) at four different depths in the oligomesotrophic Lac Pavin. We found that the majority of viruses in this lake belonged to the family of Siphoviridae or were untailed, with capsid sizes ranging from 30 to 60nm, and exhibited genome sizes ranging from 15 to 45kb. On average, 12 different genotypes dominated each of the PFGE fingerprints. The highest genomic viral richness was recorded in summer (mean=14 bands per PFGE fingerprint) and in the epilimnion (mean=13 bands per PFGE fingerprint). Among the physico-chemical and biological variables considered, the availability of the hosts appeared to be the main factor regulating the variations in the viral diversity.
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Affiliation(s)
- Jonathan Colombet
- Laboratory Microorganisms: Genome and Environment, Clermont University Blaise Pascal, UMR CNRS 6023, 24 avenue des Landais, BP 80026, F-63171 Aubière, France.
| | - Agnès Robin
- CIRAD, UMR Eco&Sols, 2 place Viala, 34060 Montpellier Cedex 1, France
| | - Télesphore Sime-Ngando
- Laboratory Microorganisms: Genome and Environment, Clermont University Blaise Pascal, UMR CNRS 6023, 24 avenue des Landais, BP 80026, F-63171 Aubière, France
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7
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Parikka KJ, Le Romancer M, Wauters N, Jacquet S. Deciphering the virus-to-prokaryote ratio (VPR): insights into virus-host relationships in a variety of ecosystems. Biol Rev Camb Philos Soc 2016; 92:1081-1100. [DOI: 10.1111/brv.12271] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 02/18/2016] [Accepted: 03/01/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Kaarle J. Parikka
- Laboratory of Microbiology of Extreme Environments; lnstitut Universitaire Européen de la Mer; Plouzané 29280 France
- LabMCT, Belgian Department of Defense; Queen Astrid Military Hospital; Brussels 1120 Belgium
| | - Marc Le Romancer
- Laboratory of Microbiology of Extreme Environments; lnstitut Universitaire Européen de la Mer; Plouzané 29280 France
| | - Nina Wauters
- Biological Evolution and Ecology; Université Libre de Bruxelles; Brussels 1050 Belgium
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8
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Pradeep Ram AS, Colombet J, Perriere F, Thouvenot A, Sime-Ngando T. Viral Regulation of Prokaryotic Carbon Metabolism in a Hypereutrophic Freshwater Reservoir Ecosystem (Villerest, France). Front Microbiol 2016; 7:81. [PMID: 26903963 PMCID: PMC4746248 DOI: 10.3389/fmicb.2016.00081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/18/2016] [Indexed: 01/27/2023] Open
Abstract
The current consensus concerning the viral regulation of prokaryotic carbon metabolism is less well-studied, compared to substrate availability. We explored the seasonal and vertical distribution of viruses and its relative influence on prokaryotic carbon metabolism in a hypereutrophic reservoir, Lake Villerest (France). Flow cytometry and transmission electron microscopy (TEM) analyses to determine viral abundance (VA; range = 6.1–63.5 × 107 ml-1) and viral infection rates of prokaryotes (range = 5.3–32%) respectively suggested that both the parameters varied more significantly with depths than with seasons. Prokaryotic growth efficiency (PGE, considered as a proxy of prokaryotic carbon metabolism) calculated from prokaryotic production and respiration measurements (PGE = prokaryotic production/[prokaryotic production + prokaryotic respiration] × 100) varied from 14 to 80% across seasons and depths. Viruses through selective lyses had antagonistic impacts on PGE by regulating key prokaryotic metabolic processes (i.e., production and respiration). Higher viral lysis accompanied by higher respiration rates and lower PGE in the summer (mean = 22.9 ± 10.3%) than other seasons (mean = 59.1 ± 18.6%), led to significant loss of carbon through bacterial-viral loop and shifted the reservoir system to net heterotrophy. Our data therefore suggests that the putative adverse impact of viruses on the growth efficiency of the prokaryotic community can have strong implications on nutrient flux patterns and on the overall ecosystem metabolism in anthropogenic dominated aquatic systems such as Lake Villerest.
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Affiliation(s)
- Angia Sriram Pradeep Ram
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal Aubière, France
| | - Jonathan Colombet
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal Aubière, France
| | - Fanny Perriere
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal Aubière, France
| | | | - Télesphore Sime-Ngando
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal Aubière, France
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9
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Mankiewicz-Boczek J, Jaskulska A, Pawełczyk J, Gągała I, Serwecińska L, Dziadek J. Cyanophages Infection of Microcystis Bloom in Lowland Dam Reservoir of Sulejów, Poland. MICROBIAL ECOLOGY 2016; 71:315-25. [PMID: 26403721 DOI: 10.1007/s00248-015-0677-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 09/10/2015] [Indexed: 05/28/2023]
Abstract
An increased incidence of cyanobacterial blooms, which are largely composed of toxigenic cyanobacteria from the Microcystis genus, leads to a disruption of aquatic ecosystems worldwide. Therefore, a better understanding of the impact of environmental parameters on the development and collapse of blooms is important. The objectives of the present study were as follows: (1) to investigate the presence and identity of Microcystis-specific cyanophages capable of cyanobacterial cell lysis in a lowland dam reservoir in Central Europe; (2) to investigate Microcystis sensitivity to phage infections with regard to toxic genotypes; and (3) to identify key abiotic parameters influencing phage infections during the summer seasons between 2009 and 2013. Sequencing analysis of selected g91 gene amplification products confirmed that the identified cyanophages belonged to the family Myoviridae (95 % homology). Cyanophages and Microcystis hosts, including toxic genotypes, were positively correlated in 4 of the 5 years analyzed (r = 0.67-0.82). The average percentage of infected Microcystis cells varied between 0.1 and 32 %, and no particular sensitivity of the phages to toxigenic genotypes was recorded. The highest number of cyanophages (>10(4) gene copy number per microliter) was observed in the period preceded by the following: an increase of the water retention time, growth of the water temperature, optimum nutrient concentrations, and the predomination of Microcystis bloom.
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Affiliation(s)
- J Mankiewicz-Boczek
- Department of Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Łódź, Poland.
- European Regional Centre for Ecohydrology, Polish Academy of Sciences, Tylna 3, 90-364, Łódź, Poland.
| | - A Jaskulska
- Department of Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Łódź, Poland
- European Regional Centre for Ecohydrology, Polish Academy of Sciences, Tylna 3, 90-364, Łódź, Poland
| | - J Pawełczyk
- Institute for Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - I Gągała
- European Regional Centre for Ecohydrology, Polish Academy of Sciences, Tylna 3, 90-364, Łódź, Poland
| | - L Serwecińska
- European Regional Centre for Ecohydrology, Polish Academy of Sciences, Tylna 3, 90-364, Łódź, Poland
| | - J Dziadek
- Institute for Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
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10
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Dann LM, Paterson JS, Newton K, Oliver R, Mitchell JG. Distributions of Virus-Like Particles and Prokaryotes within Microenvironments. PLoS One 2016; 11:e0146984. [PMID: 26785114 PMCID: PMC4718716 DOI: 10.1371/journal.pone.0146984] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/23/2015] [Indexed: 11/18/2022] Open
Abstract
Microbial interactions are important for ecosystem function, but occur at the microscale and so are difficult to observe. Previous studies in marine systems have shown significant shifts in microbial community abundance and composition over scales of micrometres to centimetres. This study investigates the microscale abundance distributions of virus-like particles (VLPs) and prokaryotes in the lower reaches of a river to determine the extent to which microscale microbial patchiness exists in freshwater systems. Here we report local hotspots surrounded by gradients that reach a maximum 80 and 107 fold change in abundance over 0.9 cm for prokaryotic and VLP subpopulations. Changes in prokaryotic and VLP hotspots were tightly coupled. There were no gradients at tens of centimetres across the boundary layers, which is consistent with strong mixing and turbulence-driven aggregation found in river systems. Quantification of the patchiness shows a marked asymmetry with patches 10 times greater than background common, but depletions being rare or absent in most samples. This consistent asymmetry suggests that coldspots depleted by grazing and lysis are rapidly mixed to background concentrations, while the prevalence of hotspots indicates persistence against disruption. The hotspot to coldspot relative abundance may be useful for understanding microbial river dynamics. The patchiness indicates that the mean- field approach of bulk phase sampling misses the microbially relevant community variation and may underestimate the concentrations of these important microbial groups.
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Affiliation(s)
- Lisa M. Dann
- School of Biological Sciences at Flinders University, Adelaide, South Australia
- * E-mail:
| | - James S. Paterson
- School of Biological Sciences at Flinders University, Adelaide, South Australia
| | - Kelly Newton
- School of Biological Sciences at Flinders University, Adelaide, South Australia
| | - Rod Oliver
- Land and Water Research Division at the Commonwealth Scientific and Industrial Research Organisation (CSIRO), Adelaide, South Australia
| | - James G. Mitchell
- School of Biological Sciences at Flinders University, Adelaide, South Australia
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11
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Meunier A, Jacquet S. Do phages impact microbial dynamics, prokaryotic community structure and nutrient dynamics in Lake Bourget? Biol Open 2015; 4:1528-37. [PMID: 26500223 PMCID: PMC4728344 DOI: 10.1242/bio.013003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phages are the most abundant and diversified biological entities in aquatic ecosystems. Understanding their functional role requires laboratory experiments on a short time-scale. Using samples of surface waters of Lake Bourget, we studied whether viruses impact (i) the abundance patterns of the bacterial and phytoplankton communities, (ii) a part of the prokaryotic community composition (both for Eubacteria and Archaea), and (iii) the recycling of nutrients and/or organic matter. Three experiments were performed (one each in February, March and April) at the transition between winter and spring in 2013. The experiment reduced or increased the abundance of virus-like particles in samples containing only the picoplanktonic fraction. Viral and cellular abundances, bacterial and archaeal community structures as well as nutrient concentrations were analysed every 24 h for 3 days. Some of the results reveal that increasing the phage abundance increased the diversity of the eubacterial community. Consistent with the ‘killing the winner’ concept, viruses are thus likely to significantly change the composition of the bacterial community. This suggests a positive association between viral abundance and bacterial diversity. In contrast, the composition of the archaeal community did not seem to be affected by phage abundance, suggesting the absence of viral control on this community or the inability to observe it at this period of year, either based on the time scale of the investigation or because the archaeal virus titre was too low to induce a significant and visible effect. Lastly, we were unable to demonstrate viruses driving the cycling of nutrients or the response of plankton to nutrient concentration changes in a significant way, suggesting that the role of viruses may be subtle or difficult to assess through the use of such experimental procedures. Summary: Phages can exert important control on the structure of the bacterial community. By contrast, neither the archaeal community nor the cycling of nutrients seems to be affected by phage abundance.
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Affiliation(s)
- Antony Meunier
- INRA, UMR CARRTEL, 75 avenue de Corzent, Thonon-les-Bains 74203, Cedex, France
| | - Stéphan Jacquet
- INRA, UMR CARRTEL, 75 avenue de Corzent, Thonon-les-Bains 74203, Cedex, France
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Zhong X, Guidoni B, Jacas L, Jacquet S. Structure and diversity of ssDNA Microviridae viruses in two peri-alpine lakes (Annecy and Bourget, France). Res Microbiol 2015; 166:644-54. [PMID: 26226335 DOI: 10.1016/j.resmic.2015.07.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/30/2015] [Accepted: 07/10/2015] [Indexed: 11/26/2022]
Abstract
Microviridae is a subset of single-stranded DNA (ssDNA) viruses infecting bacteria. This group of phages has been previously observed to be very abundant (representing >90% of the total known viral metagenomic sequences) in Lake Bourget. However, this observation was made only during one period (in summer) and from a single sample collected at a single depth (near surface). This result suggests the importance of these viruses, poorly examined thus far, especially in fresh waters. In this study, performed on the two largest natural lakes in France (e.g. Lakes Annecy and Bourget), Microviridae structure was determined each month throughout the year (2011) using PCR-DGGE, with primers that target the major-capsid-protein-encoding gene VP1; cloning/sequencing was used to investigate their diversity. Our results confirm that Microviridae are diverse in peri-alpine lakes and are mainly represented by gokushoviruses. We also found for the first time ssDNA viruses belonging to Alpavirinae, another subfamily within Microviridae recently proposed by Krupovic and Forterre (2011), generally prophages infecting members of the Phylum Bacteroidetes. Our data also support highly variable community composition and dynamics of individual components whose patterns were different between lakes, suggesting distinct host communities and/or abiotic influences between the two ecosystems. We point out that most of the major observed ssDNA Microviridae viruses display boom-bust patterns (with a sharp increase/decline) in their dynamics, with high relative abundances, suggesting brutal control of hosts and rapid regulation of the host community structure.
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Affiliation(s)
- Xu Zhong
- INRA, UMR CARRTEL, 75 Avenue de Corzent, 74203 Thonon-les-Bains, France
| | - Baptiste Guidoni
- INRA, UMR CARRTEL, 75 Avenue de Corzent, 74203 Thonon-les-Bains, France
| | - Louis Jacas
- INRA, UMR CARRTEL, 75 Avenue de Corzent, 74203 Thonon-les-Bains, France
| | - Stéphan Jacquet
- INRA, UMR CARRTEL, 75 Avenue de Corzent, 74203 Thonon-les-Bains, France.
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Using signature genes as tools to assess environmental viral ecology and diversity. Appl Environ Microbiol 2015; 80:4470-80. [PMID: 24837394 DOI: 10.1128/aem.00878-14] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viruses (including bacteriophages) are the most abundant biological entities on the planet. As such, they are thought to have a major impact on all aspects of microbial community structure and function. Despite this critical role in ecosystem processes, the study of virus/phage diversity has lagged far behind parallel studies of the bacterial and eukaryotic kingdoms, largely due to the absence of any universal phylogenetic marker. Here we review the development and use of signature genes to investigate viral diversity, as a viable strategy for data sets of specific virus groups. Genes that have been used include those encoding structural proteins, such as portal protein, major capsid protein, and tail sheath protein, auxiliary metabolism genes, such as psbA, psbB,and phoH, and several polymerase genes. These marker genes have been used in combination with PCR-based fingerprinting and/or sequencing strategies to investigate spatial, temporal, and seasonal variations and diversity in a wide range of habitats.
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