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Yu BS, Lee SY, Sim SJ. Effective contamination control strategies facilitating axenic cultivation of Haematococcus pluvialis: Risks and challenges. BIORESOURCE TECHNOLOGY 2022; 344:126289. [PMID: 34748979 DOI: 10.1016/j.biortech.2021.126289] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
With industrialization, anthropogenic mishandlings have resulted in the discharge of abundant amount of CO2 into the atmosphere. This has triggered an unnatural warming that has dramatically increased the Earth's temperature in a short duration. This problem can be addressed by the biological conversion of CO2; several studies have been conducted using H. pluvialis culture that produces high value-added materials, such as astaxanthin and omega-3 fatty acids. However, although H. pluvialis has a high market value, the market size is quite small. Because H. pluvialis cells are susceptible to contamination due to its slow growth rate, hence large-scale culture of H. pluvialis without reliable contamination control strategies poses significant risks. This review comprehensively discusses the contamination that occurs during the culturing of H. pluvialis in various culture systems under different culture conditions. The review also discusses the strategies in controlling the biotic contaminants, such as bacteria and fungi.
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Affiliation(s)
- Byung Sun Yu
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - So Young Lee
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.
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Van Etten JL, Agarkova IV, Dunigan DD. Chloroviruses. Viruses 2019; 12:E20. [PMID: 31878033 PMCID: PMC7019647 DOI: 10.3390/v12010020] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/20/2022] Open
Abstract
Chloroviruses are large dsDNA, plaque-forming viruses that infect certain chlorella-like green algae; the algae are normally mutualistic endosymbionts of protists and metazoans and are often referred to as zoochlorellae. The viruses are ubiquitous in inland aqueous environments throughout the world and occasionally single types reach titers of thousands of plaque-forming units per ml of native water. The viruses are icosahedral in shape with a spike structure located at one of the vertices. They contain an internal membrane that is required for infectivity. The viral genomes are 290 to 370 kb in size, which encode up to 16 tRNAs and 330 to ~415 proteins, including many not previously seen in viruses. Examples include genes encoding DNA restriction and modification enzymes, hyaluronan and chitin biosynthetic enzymes, polyamine biosynthetic enzymes, ion channel and transport proteins, and enzymes involved in the glycan synthesis of the virus major capsid glycoproteins. The proteins encoded by many of these viruses are often the smallest or among the smallest proteins of their class. Consequently, some of the viral proteins are the subject of intensive biochemical and structural investigation.
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Affiliation(s)
- James L. Van Etten
- Department of Plant Pathology, Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA; (I.V.A.); (D.D.D.)
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Lam TP, Lee TM, Chen CY, Chang JS. Strategies to control biological contaminants during microalgal cultivation in open ponds. BIORESOURCE TECHNOLOGY 2018; 252:180-187. [PMID: 29306613 DOI: 10.1016/j.biortech.2017.12.088] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/26/2017] [Accepted: 12/27/2017] [Indexed: 05/26/2023]
Abstract
Microalgal biomass is in great demand for many applications, including aquaculture feed. The most suitable system for microalgal culture is open pond cultivation, but it is also highly vulnerable to biological contamination. Contamination greatly reduces the biomass yield and depending on the contaminant, the quality of the biomass as a feed additive is compromised. Five groups of organisms that are the most common contaminants, including grazers, fungi, photosynthetic organisms, bacteria and viruses, are presented and the best possible ways to control these contaminants are indicated. Selection of a fast growing species along with selective technologies previously used for wastewater treatment can keep grazer population in control, while exploiting host-specific characteristic of fungal infection can protect from fungal attacks. Control of photosynthetic organisms and bacteria by good cultivation practices and the use of probiotics are critically important, as these organisms compete with the microalgal culture for sunlight and organic substrate.
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Affiliation(s)
- Tan Phat Lam
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Tse-Min Lee
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Chun-Yen Chen
- University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan; Research Center for Energy Technology and Strategy, National Cheng Kung University, Tainan 701, Taiwan.
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Quispe CF, Sonderman O, Khasin M, Riekhof WR, Van Etten JL, Nickerson KW. Comparative genomics, transcriptomics, and physiology distinguish symbiotic from free-living Chlorella strains. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Kim EJ, Ma X, Cerutti H. Gene silencing in microalgae: mechanisms and biological roles. BIORESOURCE TECHNOLOGY 2015; 184:23-32. [PMID: 25466994 DOI: 10.1016/j.biortech.2014.10.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/22/2014] [Accepted: 10/24/2014] [Indexed: 05/18/2023]
Abstract
Microalgae exhibit enormous diversity and can potentially contribute to the production of biofuels and high value compounds. However, for most species, our knowledge of their physiology, metabolism, and gene regulation is fairly limited. In eukaryotes, gene silencing mechanisms play important roles in both the reversible repression of genes that are required only in certain contexts and the suppression of genome invaders such at transposons. The recent sequencing of several algal genomes is providing insights into the complexity of these mechanisms in microalgae. Collectively, glaucophyte, red, and green microalgae contain the machineries involved in repressive histone H3 lysine methylation, DNA cytosine methylation, and RNA interference. However, individual species often only have subsets of these gene silencing mechanisms. Moreover, current evidence suggests that algal silencing systems function in transposon and transgene repression but their role(s) in gene regulation or other cellular processes remains virtually unexplored, hindering rational genetic engineering efforts.
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Affiliation(s)
- Eun-Jeong Kim
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Xinrong Ma
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Heriberto Cerutti
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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Rowe JM, Jeanniard A, Gurnon JR, Xia Y, Dunigan DD, Van Etten JL, Blanc G. Global analysis of Chlorella variabilis NC64A mRNA profiles during the early phase of Paramecium bursaria chlorella virus-1 infection. PLoS One 2014; 9:e90988. [PMID: 24608695 PMCID: PMC3946773 DOI: 10.1371/journal.pone.0090988] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 02/05/2014] [Indexed: 11/18/2022] Open
Abstract
The PBCV-1/Chlorella variabilis NC64A system is a model for studies on interactions between viruses and algae. Here we present the first global analyses of algal host transcripts during the early stages of infection, prior to virus replication. During the course of the experiment stretching over 1 hour, about a third of the host genes displayed significant changes in normalized mRNA abundance that either increased or decreased compared to uninfected levels. The population of genes with significant transcriptional changes gradually increased until stabilizing at 40 minutes post infection. Functional categories including cytoplasmic ribosomal proteins, jasmonic acid biosynthesis and anaphase promoting complex/cyclosomes had a significant excess in upregulated genes, whereas spliceosomal snRNP complexes and the shikimate pathway had significantly more down-regulated genes, suggesting that these pathways were activated or shut-down in response to the virus infection. Lastly, we examined the expression of C. varibilis RNA polymerase subunits, as PBCV-1 transcription depends on host RNA polymerases. Two subunits were up-regulated, RPB10 and RPC34, suggesting that they may function to support virus transcription. These results highlight genes and pathways, as well as overall trends, for further refinement of our understanding of the changes that take place during the early stages of viral infection.
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Affiliation(s)
- Janet M. Rowe
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Adrien Jeanniard
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
- Laboratoire Information Structurale and Génomique UMR7256 CNRS, Aix-Marseille Université, Marseille, France
| | - James R. Gurnon
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Yuannan Xia
- Center for Biotechnology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - David D. Dunigan
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - James L. Van Etten
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Guillaume Blanc
- Laboratoire Information Structurale and Génomique UMR7256 CNRS, Aix-Marseille Université, Marseille, France
- * E-mail:
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Blanc G, Mozar M, Agarkova IV, Gurnon JR, Yanai-Balser G, Rowe JM, Xia Y, Riethoven JJ, Dunigan DD, Van Etten JL. Deep RNA sequencing reveals hidden features and dynamics of early gene transcription in Paramecium bursaria chlorella virus 1. PLoS One 2014; 9:e90989. [PMID: 24608750 PMCID: PMC3946568 DOI: 10.1371/journal.pone.0090989] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 02/05/2014] [Indexed: 11/18/2022] Open
Abstract
Paramecium bursaria chlorella virus 1 (PBCV-1) is the prototype of the genus Chlorovirus (family Phycodnaviridae) that infects the unicellular, eukaryotic green alga Chlorella variabilis NC64A. The 331-kb PBCV-1 genome contains 416 major open reading frames. A mRNA-seq approach was used to analyze PBCV-1 transcriptomes at 6 progressive times during the first hour of infection. The alignment of 17 million reads to the PBCV-1 genome allowed the construction of single-base transcriptome maps. Significant transcription was detected for a subset of 50 viral genes as soon as 7 min after infection. By 20 min post infection (p.i.), transcripts were detected for most PBCV-1 genes and transcript levels continued to increase globally up to 60 min p.i., at which time 41% or the poly (A+)-containing RNAs in the infected cells mapped to the PBCV-1 genome. For some viral genes, the number of transcripts in the latter time points (20 to 60 min p.i.) was much higher than that of the most highly expressed host genes. RNA-seq data revealed putative polyadenylation signal sequences in PBCV-1 genes that were identical to the polyadenylation signal AAUAAA of green algae. Several transcripts have an RNA fragment excised. However, the frequency of excision and the resulting putative shortened protein products suggest that most of these excision events have no functional role but are probably the result of the activity of misled splicesomes.
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Affiliation(s)
- Guillaume Blanc
- Laboratoire Information Structurale and Génomique UMR7256 CNRS, Aix-Marseille Université, Marseille, France
- * E-mail:
| | - Michael Mozar
- Laboratoire Information Structurale and Génomique UMR7256 CNRS, Aix-Marseille Université, Marseille, France
| | - Irina V. Agarkova
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - James R. Gurnon
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Giane Yanai-Balser
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Janet M. Rowe
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Yuannan Xia
- Center for Biotechnology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Jean-Jack Riethoven
- Center for Biotechnology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - David D. Dunigan
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - James L. Van Etten
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
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Medina-Hernández D, Rivera-Bustamante RF, Tenllado F, Holguín-Peña RJ. Effects and effectiveness of two RNAi constructs for resistance to Pepper golden mosaic virus in Nicotiana benthamiana plants. Viruses 2013; 5:2931-45. [PMID: 24287597 PMCID: PMC3967154 DOI: 10.3390/v5122931] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 11/14/2013] [Accepted: 11/20/2013] [Indexed: 01/11/2023] Open
Abstract
ToChLPV and PepGMV are Begomoviruses that have adapted to a wide host range and are able to cause major diseases in agronomic crops. We analyzed the efficacy of induced resistance to PepGMV in Nicotiana benthamiana plants with two constructs: one construct with homologous sequences derived from PepGMV, and the other construct with heterologous sequences derived from ToChLPV. Plants protected with the heterologous construct showed an efficacy to decrease the severity of symptoms of 45%, while plants protected with the homologous construct showed an efficacy of 80%. Plants protected with the heterologous construct showed a reduction of incidence of 42.86%, while the reduction of incidence in plants protected with the homologous construct was 57.15%. The efficacy to decrease viral load was 95.6% in plants protected with the heterologous construct, and 99.56% in plants protected with the homologous construct. We found, in both constructs, up-regulated key components of the RNAi pathway. This demonstrates that the efficacy of the constructs was due to the activation of the gene silencing mechanism, and is reflected in the decrease of viral genome copies, as well as in recovery phenotype. We present evidence that both constructs are functional and can efficiently induce transient resistance against PepGMV infections. This observation guarantees a further exploration as a strategy to control complex Begomovirus diseases in the field.
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Affiliation(s)
- Diana Medina-Hernández
- Laboratorio de Fitopatología, Centro de Investigaciones Biológicas del Noroeste, Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur, 23096, Mexico; E-Mails: (R.J.H.P.); (D.M.H.)
| | - Rafael Francisco Rivera-Bustamante
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Km. 9.6 Libramiento Norte, Irapuato, Guanajuato, 36821, Mexico; E-Mail: (R.F.R.B.)
| | - Francisco Tenllado
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, Madrid, 28040, Spain; E-Mail: (F.T.)
| | - Ramón Jaime Holguín-Peña
- Laboratorio de Fitopatología, Centro de Investigaciones Biológicas del Noroeste, Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur, 23096, Mexico; E-Mails: (R.J.H.P.); (D.M.H.)
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