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Silva TP, Gamalier JP, Zarantonello V, Soares CR, Resende NS, Barros NO, Melo RCN. Enhanced ability of freshwater bacteria to secrete extracellular vesicles upon interaction with virus. Environ Microbiol 2022; 24:5882-5897. [PMID: 36054062 DOI: 10.1111/1462-2920.16166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 08/08/2022] [Indexed: 01/12/2023]
Abstract
The ability of freshwater bacteria to secrete extracellular vesicles (EVs) upon interaction with viruses remains to be established. Here, we investigated for the first time if freshwater virus-infected bacteria release EVs in both natural ecosystems and virus-like particles (VLPs)-enriched cultures. We performed a systematic study using transmission electron microscopy to visualize viruses and EVs at high resolution and single-cell imaging analyses to quantitate nascent EVs at the surface of gram-negative bacteria. First, by analysing freshwater samples from a tropical ecosystem (Negro River/Amazon Basin/Brazil), we captured bacteriophages-infected bacteria releasing EVs from their outer membrane. Next, VLPs isolated from these samples and inoculated in bacterial cultures not only impacted bacteria growth and viability but also led them to a significant release of EVs (~300% increase in numbers/cell section) compared to controls. The numbers of both budding and free EVs and EVs per linear micrometre of cell envelope were significantly higher in infected bacteria. Our findings identify a yet-not recognized capability of freshwater bacteria in generating EVs (overvesiculation) in response to viral infection. Since viruses are abundant members of aquatic ecosystems and bacteria are natural hosts for them, such interaction is an interesting event for microbial communities to be explored in freshwater ecosystems.
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Affiliation(s)
- Thiago P Silva
- Laboratory of Cellular Biology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora
| | - Juliana P Gamalier
- Laboratory of Cellular Biology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora
| | - Victor Zarantonello
- Laboratory of Cellular Biology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora
| | - Caique R Soares
- Laboratory of Cellular Biology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora
| | - Nathália S Resende
- Laboratory of Aquatic Ecology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Brazil
| | - Nathan O Barros
- Laboratory of Aquatic Ecology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Brazil
| | - Rossana C N Melo
- Laboratory of Cellular Biology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora
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2
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Roux S, Emerson JB. Diversity in the soil virosphere: to infinity and beyond? Trends Microbiol 2022; 30:1025-1035. [PMID: 35644779 DOI: 10.1016/j.tim.2022.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 01/13/2023]
Abstract
Viruses are key members of Earth's microbiomes, shaping microbial community composition and metabolism. Here, we describe recent advances in 'soil viromics', that is, virus-focused metagenome and metatranscriptome analyses that offer unprecedented windows into the soil virosphere. Given the emerging picture of high soil viral activity, diversity, and dynamics over short spatiotemporal scales, we then outline key eco-evolutionary processes that we hypothesize are the major diversity drivers for soil viruses. We argue that a community effort is needed to establish a 'global soil virosphere atlas' that can be used to address the roles of viruses in soil microbiomes and terrestrial biogeochemical cycles across spatiotemporal scales.
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Affiliation(s)
- Simon Roux
- DOE (Department of Energy) Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA; Genome Center, University of California, Davis, Davis, CA, USA.
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3
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Gao Y, Lu Y, Dungait JAJ, Liu J, Lin S, Jia J, Yu G. The "Regulator" Function of Viruses on Ecosystem Carbon Cycling in the Anthropocene. Front Public Health 2022; 10:858615. [PMID: 35425734 PMCID: PMC9001988 DOI: 10.3389/fpubh.2022.858615] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/07/2022] [Indexed: 01/18/2023] Open
Abstract
Viruses act as "regulators" of the global carbon cycle because they impact the material cycles and energy flows of food webs and the microbial loop. The average contribution of viruses to the Earth ecosystem carbon cycle is 8.6‰, of which its contribution to marine ecosystems (1.4‰) is less than its contribution to terrestrial (6.7‰) and freshwater (17.8‰) ecosystems. Over the past 2,000 years, anthropogenic activities and climate change have gradually altered the regulatory role of viruses in ecosystem carbon cycling processes. This has been particularly conspicuous over the past 200 years due to rapid industrialization and attendant population growth. The progressive acceleration of the spread and reproduction of viruses may subsequently accelerate the global C cycle.
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Affiliation(s)
- Yang Gao
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yao Lu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jennifer A J Dungait
- Geography, College of Life and Environmental Science, University of Exeter, Exeter, United Kingdom.,Carbon Management Centre, SRUC-Scotland's Rural College, Edinburgh, United Kingdom
| | - Jianbao Liu
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,Chinese Academy of Sciences (CAS) Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shunhe Lin
- Department of Obstetrics and Gynecology, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Junjie Jia
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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4
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Top-Down Controls of Bacterial Metabolism: A Case Study from a Temperate Freshwater Lake Ecosystem. Microorganisms 2022; 10:microorganisms10040715. [PMID: 35456766 PMCID: PMC9031129 DOI: 10.3390/microorganisms10040715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 12/10/2022] Open
Abstract
In freshwater environments, limited data exist on the impact of mortality forces (viruses and heterotrophic nanoflagellates) on bacterial growth efficiency (BGE, index of bacterial carbon metabolism) compared to resource availability. An investigation to determine the relative influence of viral lysis and flagellate predation (top-down forces) on BGE was conducted in a mesotrophic freshwater system (Lake Goule, France) with time and space. Viral abundance was significantly (p < 0.001) related to bacterial abundance by a power law function with an exponent less than 1, emphasizing that the increases in host population (bacteria) together with viruses were not proportionate. A lytic viral strategy was evident throughout the study period, with high lysis of the bacterial population (up to 60%) supported by viral production rates. Viral processes (lysis and production) that were influenced by bacterial production and heterotrophic nanoflagellate abundance had a positive impact on BGE. Estimates of BGE were variable (9.9−45.5%) due to uncoupling between two metabolic parameters—namely bacterial production and respiration. The existence of a synergistic relationship between viruses and flagellates with bacteria in Lake Goule highlighted the decisive impact of top-down agents in sustaining the bacterial carbon metabolism of non-infected population through the nature of vital resources released via mortality processes.
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Yang X, Zhang Y, Liu Q, Guo J, Zhou Q. Progress in the interaction of dissolved organic matter and microbes (1991-2020): a bibliometric review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:16817-16829. [PMID: 34997929 DOI: 10.1007/s11356-022-18540-4] [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: 07/28/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Dissolved organic matter (DOM) and microbes are key in the planetary carbon cycle, and research on them can lead to a better understanding of the global carbon cycle and an improved ability to cope with environmental challenges. Several papers have reviewed one or several aspects of the interaction of DOM and microbes, but no overall review has been performed. Here, we bibliometrically analyzed all publications from the Web of Science on DOM and microbes (1991-2020). The results showed that studies on DOM and microbes grew exponentially during this period; the USA contributed the most to the total publications, and China has had the fastest increasing rate since 2010. Moreover, we used the Latent Dirichlet Allocation model to identify topics and determine their (cold or hot) trends by analyzing the abstracts of 9851 publications related to DOM and microbes. A total of 96 topics were extracted, and these topics that are related to the source, composition, and removal path of DOM and the temporal-spatial patterns of DOM and microbes consistently rose from 1991 to 2020. Most studies have used accurate and rapid methods combined with microbiological genetic approaches to study the interaction of DOM and microbes in terrestrial and aquatic ecosystems. The results also showed that the impacts of climate change and land use on the interaction of DOM and microbes, and topics related to human health have received considerable attention. In the future, the interaction mechanism of DOM and microbes and its response to environmental change should be further elucidated.
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Affiliation(s)
- Xuan Yang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China
| | - Yun Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China
| | - Qi Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China
| | - Jishu Guo
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China
| | - Qichao Zhou
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China.
- Yunnan Key Laboratory of Pollution Process and Management of Plateau Lake-Watershed, Yunnan Research Academy of Eco-Environmental Sciences, Kunming, 650034, China.
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CO2 acidification and pandemic situation. CO2 ACIDIFICATION IN AQUATIC ECOSYSTEMS 2022. [PMCID: PMC9217738 DOI: 10.1016/b978-0-12-823552-2.00016-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This chapter reviews the situation of CO2 acidification and its effects in aquatic ecosystems related to the pandemic situation associated with COVID-19, but also includes the effects of other infections such as malaria, dengue, etc., and the relationship between human health, ecosystem health, and risk assessment. The interactions between these processes (infection and CO2 acidification) are compared and analyzed, and considerations about the role of these viruses and bacteria in the risk assessment will be commented on as part of the LoEs and WoEs discussed in the book. Some recent data about the influence of the pandemic on CO2 emissions and the acidification in the aquatic ecosystem will be presented and discussed too.
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Sorensen JW, Zinke LA, ter Horst AM, Santos-Medellín C, Schroeder A, Emerson JB. DNase Treatment Improves Viral Enrichment in Agricultural Soil Viromes. mSystems 2021; 6:e0061421. [PMID: 34491084 PMCID: PMC8547471 DOI: 10.1128/msystems.00614-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/11/2021] [Indexed: 11/20/2022] Open
Abstract
The small genomes of most viruses make it difficult to fully capture viral diversity in metagenomes dominated by DNA from cellular organisms. Viral size fraction metagenomics (viromics) protocols facilitate the enrichment of viral DNA from environmental samples, and these protocols typically include DNase treatment of the post-0.2-μm-filtered viromic fraction to remove contaminating free DNA prior to virion lysis. However, DNase may also remove desirable viral genomic DNA (e.g., contained in virions compromised due to frozen storage or laboratory processing), suggesting that DNase-untreated viromes might be useful in some cases. In order to understand how virome preparation with and without DNase treatment influences the resultant data, here, we compared 15 soil viromes (7 DNase treated and 8 untreated) from 8 samples collected from agricultural fields prior to tomato planting. DNase-treated viromes yielded significantly more assembled viral contigs, contained significantly less nonviral microbial DNA, and recovered more viral populations (viral operational taxonomic units [vOTUs]) through read mapping. However, DNase-treated and untreated viromes were statistically indistinguishable in terms of ecological patterns across viral communities. Although the results suggest that DNase treatment is preferable where possible, in comparison to previously reported total metagenomes from the same samples, both DNase-treated and untreated viromes were significantly enriched in viral signatures by all metrics compared, including a 225-times-higher proportion of viral reads in untreated viromes compared to total metagenomes. Thus, even without DNase treatment, viromics was preferable to total metagenomics for capturing viral diversity in these soils, suggesting that preparation of DNase-untreated viromes can be worthwhile when DNase treatment is not possible. IMPORTANCE Viromics is becoming an increasingly popular method for characterizing soil viral communities. DNase treatment of the viral size fraction prior to DNA extraction is meant to reduce contaminating free DNA and is a common step within viromics protocols to ensure that sequences are of viral origin. However, some samples may not be amenable to DNase treatment due to viral particles being compromised either in storage (i.e., frozen) or during other sample processing steps. To date, the effect of DNase treatment on the recovery of viruses and downstream ecological interpretations of soil viral communities is not thoroughly understood. This work sheds light on these questions and indicates that while DNase treatment of soil viromes improves the recovery of viral populations, this improvement is modest in comparison to the gains made by viromics over total soil metagenomics. Furthermore, DNase treatment may not be necessary to observe the ecological patterns structuring soil viral communities.
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Affiliation(s)
- Jackson W. Sorensen
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | - Laura A. Zinke
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | - Anneliek M. ter Horst
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | | | - Alena Schroeder
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | - Joanne B. Emerson
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
- Genome Center, University of California, Davis, Davis, California, USA
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Nelson DR, Hazzouri KM, Lauersen KJ, Jaiswal A, Chaiboonchoe A, Mystikou A, Fu W, Daakour S, Dohai B, Alzahmi A, Nobles D, Hurd M, Sexton J, Preston MJ, Blanchette J, Lomas MW, Amiri KMA, Salehi-Ashtiani K. Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution. Cell Host Microbe 2021; 29:250-266.e8. [PMID: 33434515 DOI: 10.1016/j.chom.2020.12.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/08/2020] [Accepted: 11/18/2020] [Indexed: 01/08/2023]
Abstract
Being integral primary producers in diverse ecosystems, microalgal genomes could be mined for ecological insights, but representative genome sequences are lacking for many phyla. We cultured and sequenced 107 microalgae species from 11 different phyla indigenous to varied geographies and climates. This collection was used to resolve genomic differences between saltwater and freshwater microalgae. Freshwater species showed domain-centric ontology enrichment for nuclear and nuclear membrane functions, while saltwater species were enriched in organellar and cellular membrane functions. Further, marine species contained significantly more viral families in their genomes (p = 8e-4). Sequences from Chlorovirus, Coccolithovirus, Pandoravirus, Marseillevirus, Tupanvirus, and other viruses were found integrated into the genomes of algal from marine environments. These viral-origin sequences were found to be expressed and code for a wide variety of functions. Together, this study comprehensively defines the expanse of protein-coding and viral elements in microalgal genomes and posits a unified adaptive strategy for algal halotolerance.
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Affiliation(s)
- David R Nelson
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.
| | - Khaled M Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), UAE University, Al Ain, Abu Dhabi, UAE; Biology Department, College of Science, UAE University, Al Ain, Abu Dhabi, UAE
| | - Kyle J Lauersen
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Ashish Jaiswal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | | | - Alexandra Mystikou
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Weiqi Fu
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sarah Daakour
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Bushra Dohai
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Amnah Alzahmi
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - David Nobles
- UTEX Culture Collection of Algae at the University of Texas at Austin, Austin, TX, USA
| | - Mark Hurd
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Julie Sexton
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Michael J Preston
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Joan Blanchette
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Michael W Lomas
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Khaled M A Amiri
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), UAE University, Al Ain, Abu Dhabi, UAE; Biology Department, College of Science, UAE University, Al Ain, Abu Dhabi, UAE
| | - Kourosh Salehi-Ashtiani
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE; Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.
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Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar de Huasco, Chile. Microorganisms 2020; 8:microorganisms8071077. [PMID: 32698305 PMCID: PMC7409041 DOI: 10.3390/microorganisms8071077] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 12/18/2022] Open
Abstract
Salar de Huasco is a wetland in the Andes mountains, located 3800 m above sea level at the Chilean Altiplano. Here we present a study aimed at characterizing the viral fraction and the microbial communities through metagenomic analysis. Two ponds (H0 and H3) were examined in November 2015. Water samples were processed using tangential flow filtration to obtain metagenomes from which the DNA fraction of the sample was amplified and sequenced (HiSeq system, Illumina). The ponds were characterized by freshwater and the viral-like particles to picoplankton ratio was 12.1 and 2.3 for H0 and H3, respectively. A great number of unassigned viral sequences were found in H0 (55.8%) and H3 (32.8%), followed by the family Fuselloviridae 20.8% (H0) and other less relatively abundant groups such as Microviridae (H0, 11.7% and H3, 3.3%) and Inoviridae (H3, 2.7%). The dominant viral sequences in both metagenomes belong to the order Caudovirales, with Siphoviridae being the most important family, especially in H3 (32.7%). The most important bacteria phyla were Proteobacteria, Bacteroidetes and Firmicutes in both sites, followed by Cyanobacteria (H0). Genes encoding lysogenic and lytic enzymes (i.e., recombinases and integrases) were found in H0 and H3, indicating a potential for active viral replication at the time of sampling; this was supported by the presence of viral metabolic auxiliary genes at both sites (e.g., cysteine hydrolase). In total, our study indicates a great novelty of viral groups, differences in taxonomic diversity and replication pathways between sites, which contribute to a better understanding of how viruses balance the cycling of energy and matter in this extreme environment.
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