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Journal articles on the topic 'Aquatic virology'

Author: Grafiati

Published: 4 June 2021

Last updated: 11 February 2022

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1

Nkili-Meyong, Andriniaina Andy, Laurent Bigarré, Ingrid Labouba, Tatiana Vallaeys, Jean-Christophe Avarre, and Nicolas Berthet. "Contribution of Next-Generation Sequencing to Aquatic and Fish Virology." Intervirology 59, no. 5-6 (2016): 285–300. http://dx.doi.org/10.1159/000477808.

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2

Yau, Sheree, and Mansha Seth-Pasricha. "Viruses of Polar Aquatic Environments." Viruses 11, no. 2 (February 22, 2019): 189. http://dx.doi.org/10.3390/v11020189.

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The poles constitute 14% of the Earth’s biosphere: The aquatic Arctic surrounded by land in the north, and the frozen Antarctic continent surrounded by the Southern Ocean. In spite of an extremely cold climate in addition to varied topographies, the polar aquatic regions are teeming with microbial life. Even in sub-glacial regions, cellular life has adapted to these extreme environments where perhaps there are traces of early microbes on Earth. As grazing by macrofauna is limited in most of these polar regions, viruses are being recognized for their role as important agents of mortality, thereby influencing the biogeochemical cycling of nutrients that, in turn, impact community dynamics at seasonal and spatial scales. Here, we review the viral diversity in aquatic polar regions that has been discovered in the last decade, most of which has been revealed by advances in genomics-enabled technologies, and we reflect on the vast extent of the still-to-be explored polar microbial diversity and its “enigmatic virosphere”.

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3

Lewis, G. D., M. W. Loutit, and F. J. Austin. "A method for detecting human enteroviruses in aquatic sediments." Journal of Virological Methods 10, no. 2 (February 1985): 153–62. http://dx.doi.org/10.1016/0166-0934(85)90101-6.

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4

Coy, Samantha, Eric Gann, Helena Pound, Steven Short, and Steven Wilhelm. "Viruses of Eukaryotic Algae: Diversity, Methods for Detection, and Future Directions." Viruses 10, no. 9 (September 11, 2018): 487. http://dx.doi.org/10.3390/v10090487.

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The scope for ecological studies of eukaryotic algal viruses has greatly improved with the development of molecular and bioinformatic approaches that do not require algal cultures. Here, we review the history and perceived future opportunities for research on eukaryotic algal viruses. We begin with a summary of the 65 eukaryotic algal viruses that are presently in culture collections, with emphasis on shared evolutionary traits (e.g., conserved core genes) of each known viral type. We then describe how core genes have been used to enable molecular detection of viruses in the environment, ranging from PCR-based amplification to community scale “-omics” approaches. Special attention is given to recent studies that have employed network-analyses of -omics data to predict virus-host relationships, from which a general bioinformatics pipeline is described for this type of approach. Finally, we conclude with acknowledgement of how the field of aquatic virology is adapting to these advances, and highlight the need to properly characterize new virus-host systems that may be isolated using preliminary molecular surveys. Researchers can approach this work using lessons learned from the Chlorella virus system, which is not only the best characterized algal-virus system, but is also responsible for much of the foundation in the field of aquatic virology.

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Sadeghi, Mohammadreza, Yuji Tomaru, and Tero Ahola. "RNA Viruses in Aquatic Unicellular Eukaryotes." Viruses 13, no. 3 (February 25, 2021): 362. http://dx.doi.org/10.3390/v13030362.

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Increasing sequence information indicates that RNA viruses constitute a major fraction of marine virus assemblages. However, only 12 RNA virus species have been described, infecting known host species of marine single-celled eukaryotes. Eight of these use diatoms as hosts, while four are resident in dinoflagellate, raphidophyte, thraustochytrid, or prasinophyte species. Most of these belong to the order Picornavirales, while two are divergent and fall into the families Alvernaviridae and Reoviridae. However, a very recent study has suggested that there is extraordinary diversity in aquatic RNA viromes, describing thousands of viruses, many of which likely use protist hosts. Thus, RNA viruses are expected to play a major ecological role for marine unicellular eukaryotic hosts. In this review, we describe in detail what has to date been discovered concerning viruses with RNA genomes that infect aquatic unicellular eukaryotes.

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6

Novoa, B., S. Nun˜ez, C. Fernández-Puentes, A. J. Figueras, and A. E. Toranzo. "Epizootic study in a turbot farm: bacteriology, virology, parasitology and histology." Aquaculture 107, no. 2-3 (October 1992): 253–58. http://dx.doi.org/10.1016/0044-8486(92)90074-u.

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7

Balmer, Bethany F., Rodman G. Getchell, Rachel L. Powers, Jihye Lee, Tinghu Zhang, Michael E. Jung, Maureen K. Purcell, Kevin Snekvik, and Hector C. Aguilar. "Broad-spectrum antiviral JL122 blocks infection and inhibits transmission of aquatic rhabdoviruses." Virology 525 (December 2018): 143–49. http://dx.doi.org/10.1016/j.virol.2018.09.009.

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8

Wartecki, Adrian, and Piotr Rzymski. "On the Coronaviruses and Their Associations with the Aquatic Environment and Wastewater." Water 12, no. 6 (June 4, 2020): 1598. http://dx.doi.org/10.3390/w12061598.

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The outbreak of Coronavirus Disease 2019 (COVID-19), a severe respiratory disease caused by betacoronavirus SARS-CoV-2, in 2019 that further developed into a pandemic has received an unprecedented response from the scientific community and sparked a general research interest into the biology and ecology of Coronaviridae, a family of positive-sense single-stranded RNA viruses. Aquatic environments, lakes, rivers and ponds, are important habitats for bats and birds, which are hosts for various coronavirus species and strains and which shed viral particles in their feces. It is therefore of high interest to fully explore the role that aquatic environments may play in coronavirus spread, including cross-species transmissions. Besides the respiratory tract, coronaviruses pathogenic to humans can also infect the digestive system and be subsequently defecated. Considering this, it is pivotal to understand whether wastewater can play a role in their dissemination, particularly in areas with poor sanitation. This review provides an overview of the taxonomy, molecular biology, natural reservoirs and pathogenicity of coronaviruses; outlines their potential to survive in aquatic environments and wastewater; and demonstrates their association with aquatic biota, mainly waterfowl. It also calls for further, interdisciplinary research in the field of aquatic virology to explore the potential hotspots of coronaviruses in the aquatic environment and the routes through which they may enter it.

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9

Rastrojo, Alberto, and Antonio Alcamí. "Aquatic viral metagenomics: Lights and shadows." Virus Research 239 (July 2017): 87–96. http://dx.doi.org/10.1016/j.virusres.2016.11.021.

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10

Chu, D. K. W., C. Y. H. Leung, M. Gilbert, P. H. Joyner, E. M. Ng, T. M. Tse, Y. Guan, J. S. M. Peiris, and L. L. M. Poon. "Avian Coronavirus in Wild Aquatic Birds." Journal of Virology 85, no. 23 (September 28, 2011): 12815–20. http://dx.doi.org/10.1128/jvi.05838-11.

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11

Nishizawa, Toyohiko, Shinichi Kinoshita, and Mamoru Yoshimizu. "An approach for genogrouping of Japanese isolates of aquabirnaviruses in a new genogroup, VII, based on the VP2/NS junction region." Journal of General Virology 86, no. 7 (July 1, 2005): 1973–78. http://dx.doi.org/10.1099/vir.0.80438-0.

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Aquabirnaviruses, represented by Infectious pancreatic necrosis virus (IPNV), have been isolated from epizootics in salmonids and a variety of aquatic animals in the world; six genogroups of aquabirnaviruses have been identified. In comparisons of nucleotide sequences of the VP2/NS junction region, maximum nucleotide diversities of 30·8 % were observed among 93 worldwide aquabirnavirus isolates. A phylogenetic tree revealed the existence of a new genogroup, VII, for Japanese aquabirnavirus isolates from marine fish and molluscan shellfish. Nucleotide diversities between genogroups VII and I–VI were 18·7 % or greater. At the nucleotide level, Japanese IPNV isolates from epizootics in salmonids were nearly identical to a genogroup I strain from the USA or Canada. It is suggested that Japanese IPNV isolates belonging to genogroup I were originally introduced from North American sources, whereas Japanese aquabirnavirus isolates of genogroup VII were from marine aquatic animals indigenous to Japan.

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12

S�ss, J., J. Sch�fer, H. Sinnecker, and R. G. Webster. "Influenza virus subtypes in aquatic birds of eastern Germany." Archives of Virology 135, no. 1-2 (March 1994): 101–14. http://dx.doi.org/10.1007/bf01309768.

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13

Moriette, Coralie, Monique LeBerre, Soasig Kerbart Boscher, Jeannette Castric, and Michel Brémont. "Characterization and mapping of monoclonal antibodies against the Sleeping disease virus, an aquatic alphavirus." Journal of General Virology 86, no. 11 (November 1, 2005): 3119–27. http://dx.doi.org/10.1099/vir.0.81030-0.

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Sleeping disease virus (SDV) is an emerging pathogen in salmonid aquacultures, the impact of which is underestimated to date due to the lack of efficient diagnostic tools. To better characterize this new aquatic alphavirus and to make molecular tools available, a panel of monoclonal antibodies (mAbs) directed against SDV non-structural and structural proteins has been generated by immunizing mice with SDV-specific recombinant proteins overexpressed in Escherichia coli as antigens. So far, mAbs against nsP1, nsP3, E2 and E1 SDV proteins have been produced and their reactivity has been characterized by Western blot, radioimmunoprecipitation and indirect immunofluorescence assays. In addition, protein domains recognized by each mAb have been determined by immunofluorescence assay on truncated expressed SDV-derived proteins. Finally, one mAb directed against the E1 glycoprotein has been evaluated as a potential tool to be used in immunohistochemistry assay on experimentally infected trout.

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14

Guixiang, Tong, Weili Yin, Xiangqing Wu, Yong Lin, Xiaohan Chen, Wanwen Liang, Quoqiu Huang, et al. "Establishment of pyrosequencing technology to detect White Spot Syndrome Virus (WSSV) in cultured aquatic animals." Journal of Virological Methods 273 (November 2019): 113683. http://dx.doi.org/10.1016/j.jviromet.2019.113683.

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15

Nakano, Hiroyuki, Toshiki Kameyama, Kasthuri Venkateswaran, Hideyuki Kawakami, and Hideo Hashimoto. "Distribution and Characterization of Hemolytic, and Enteropathogenic MotileAeromonasin Aquatic Environment." Microbiology and Immunology 34, no. 5 (May 1990): 447–58. http://dx.doi.org/10.1111/j.1348-0421.1990.tb01027.x.

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16

Alam, Munirul, Nur-A-Hasan, Sunjukta Ahsan, Gururaja Perumal Pazhani, Kazumichi Tamura, Thadavarayan Ramamurthy, Donald James Gomes, et al. "Phenotypic and Molecular Characteristics ofEscherichia coliIsolated from Aquatic Environment of Bangladesh." Microbiology and Immunology 50, no. 5 (May 2006): 359–70. http://dx.doi.org/10.1111/j.1348-0421.2006.tb03802.x.

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17

Hernández, A., C. F. Marina, J. Valle, and T. Williams. "Persistence of invertebrate iridescent virus 6 in tropical artificial aquatic environments." Archives of Virology 150, no. 11 (June 28, 2005): 2357–63. http://dx.doi.org/10.1007/s00705-005-0584-z.

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18

Feng, Junli, Yi Wang, Renyao Jin, and Guijie Hao. "A universal random DNA amplification and labeling strategy for microarray to detect multiple pathogens of aquatic animals." Journal of Virological Methods 275 (January 2020): 113761. http://dx.doi.org/10.1016/j.jviromet.2019.113761.

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19

Winton, J. R., C. N. Lannan, J. L. Fryer, R. P. Hedrick, T. R. Meyers, J. A. Plumb, and T. Yamamoto. "Morphological and Biochemical Properties of Four Members of a Novel Group of Reoviruses Isolated from Aquatic Animals." Journal of General Virology 68, no. 2 (February 1, 1987): 353–64. http://dx.doi.org/10.1099/0022-1317-68-2-353.

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20

Campitelli, Laura, Concetta Fabiani, Simona Puzelli, Alessandro Fioretti, Emanuela Foni, Alessandra De Marco, Scott Krauss, Robert G. Webster, and Isabella Donatelli. "H3N2 influenza viruses from domestic chickens in Italy: an increasing role for chickens in the ecology of influenza?" Journal of General Virology 83, no. 2 (February 1, 2002): 413–20. http://dx.doi.org/10.1099/0022-1317-83-2-413.

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In Italy, multiple H3N2 influenza viruses were isolated from chickens with mild respiratory disease and were shown to replicate in the respiratory tracts of experimentally infected chickens; this finding is the first to show that H3N2 influenza viruses can replicate and cause disease in chickens. H3N2 influenza viruses in pigs on nearby farms seemed a likely source of the virus; however, antigenic and molecular analyses revealed that the gene segments of the viruses in chickens were mainly of Eurasian avian origin and were distinguishable from those isolated from pigs and wild aquatic birds in Italy. Thus, several different H3 influenza viruses were circulating in Italy, but we failed to identify the source of the chicken H3N2 influenza viruses that have disappeared subsequently from Italian poultry. Until recently, the transmission of influenza viruses (other than the H5 and H7 subtypes) from their reservoir in aquatic birds to chickens was rarely detected and highly pathogenic and non-pathogenic viruses were considered to be restricted to poultry species. However, the recent reports of the transmission of H9N2 and H5N1 influenza viruses to chickens in Hong Kong and, subsequently, to humans and our findings of the transmission of H3N2 influenza viruses to domestic chickens in Italy suggest an increased role for chickens as an intermediate host in the ecology of influenza.

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21

Brunet, Camille D., Aurélie Hennebique, Julien Peyroux, Isabelle Pelloux, Yvan Caspar, and Max Maurin. "Presence of Francisella tularensis subsp. holarctica DNA in the Aquatic Environment in France." Microorganisms 9, no. 7 (June 28, 2021): 1398. http://dx.doi.org/10.3390/microorganisms9071398.

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In 2018, the incidence of tularemia increased twofold in the west of France, with many pneumonic forms, suggesting environmental sources of infection. We investigated the presence of Francisellatularensis subsp. holarctica and other Francisella species DNA in the natural aquatic environment of this geographic area. Two sampling campaigns, in July 2019 and January 2020, allowed the collection of 87 water samples. Using a combination of real-time PCR assays, we tested the presence of either Francisella sp., F. tularensis/F. novicida, and F. tularensis subsp. holarctica, the latter being the only tularemia agent in Europe. Among 57 water samples of the first campaign, 15 (26.3%) were positive for Francisella sp., nine (15.8%) for F. tularensis and/or F. novicida, and four (7.0%) for F. tularensis subsp. holarctica. Ratios were 25/30 (83.3%), 24/30 (80.0%), and 4/30 (13.3%) for the second campaign. Among the thirty sites sampled during the two campaigns, nine were positive both times for Francisella sp., seven for F. tularensis and/or F. novicida, and one for F. tularensis subsp. holarctica. Altogether, our study reveals a high prevalence of Francisella sp. DNA (including the tularemia agent) in the studied aquatic environment. This aquatic environment could therefore participate in the endemicity of tularemia in the west of France.

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22

Killeen, Gerry F., Steven W. Lindsay, Ulrike Fillinger, Martin S. Kalongolela, Marcel Tanner, Marcia Caldas de Castro, Khadija Kannady, and W. Richard Mukabana. "HABITAT TARGETING FOR CONTROLLING AQUATIC STAGES OF MALARIA VECTORS IN AFRICA." American Journal of Tropical Medicine and Hygiene 74, no. 4 (April 1, 2006): 517–18. http://dx.doi.org/10.4269/ajtmh.2006.74.517.

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23

Krauss, Scott, David Walker, S. Paul Pryor, Larry Niles, Li Chenghong, Virginia S. Hinshaw, and Robert G. Webster. "Influenza A Viruses of Migrating Wild Aquatic Birds in North America." Vector-Borne and Zoonotic Diseases 4, no. 3 (September 2004): 177–89. http://dx.doi.org/10.1089/vbz.2004.4.177.

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24

Canuti, Marta, Ashley N. K. Kroyer, Davor Ojkic, Hugh G. Whitney, Gregory J. Robertson, and Andrew S. Lang. "Discovery and Characterization of Novel RNA Viruses in Aquatic North American Wild Birds." Viruses 11, no. 9 (August 21, 2019): 768. http://dx.doi.org/10.3390/v11090768.

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Wild birds are recognized viral reservoirs but our understanding about avian viral diversity is limited. We describe here three novel RNA viruses that we identified in oropharyngeal/cloacal swabs collected from wild birds. The complete genome of a novel gull metapneumovirus (GuMPV B29) was determined. Phylogenetic analyses indicated that this virus could represent a novel avian metapneumovirus (AMPV) sub-group, intermediate between AMPV-C and the subgroup of the other AMPVs. This virus was detected in an American herring (1/24, 4.2%) and great black-backed (4/26, 15.4%) gulls. A novel gull coronavirus (GuCoV B29) was detected in great black-backed (3/26, 11.5%) and American herring (2/24, 8.3%) gulls. Phylogenetic analyses of GuCoV B29 suggested that this virus could represent a novel species within the genus Gammacoronavirus, close to other recently identified potential novel avian coronaviral species. One GuMPV–GuCoV co-infection was detected. A novel duck calicivirus (DuCV-2 B6) was identified in mallards (2/5, 40%) and American black ducks (7/26, 26.9%). This virus, of which we identified two different types, was fully sequenced and was genetically closest to other caliciviruses identified in Anatidae, but more distant to other caliciviruses from birds in the genus Anas. These discoveries increase our knowledge about avian virus diversity and host distributions.

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Doss, Janis, Kayla Culbertson, Delilah Hahn, Joanna Camacho, and Nazir Barekzi. "A Review of Phage Therapy against Bacterial Pathogens of Aquatic and Terrestrial Organisms." Viruses 9, no. 3 (March 18, 2017): 50. http://dx.doi.org/10.3390/v9030050.

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26

Reshi, Latif, Jen-Leih Wu, Hao-Ven Wang, and Jiann-Ruey Hong. "Aquatic viruses induce host cell death pathways and its application." Virus Research 211 (January 2016): 133–44. http://dx.doi.org/10.1016/j.virusres.2015.10.018.

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27

Chu, D. K. W., C. Y. H. Leung, H. K. K. Perera, E. M. Ng, M. Gilbert, P. H. Joyner, A. Grioni, et al. "A Novel Group of Avian Astroviruses in Wild Aquatic Birds." Journal of Virology 86, no. 24 (October 3, 2012): 13772–78. http://dx.doi.org/10.1128/jvi.02105-12.

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28

Isokpehi, Raphael D., Dominique S. McInnis, Antoinette M. Destefano, Gabrielle S. Johnson, Akimio D. Walker, Yessenia A. Hall, Baraka W. Mapp, Matilda O. Johnson, and Shaneka S. Simmons. "Bioinformatics Investigations of Universal Stress Proteins from Mercury-Methylating Desulfovibrionaceae." Microorganisms 9, no. 8 (August 21, 2021): 1780. http://dx.doi.org/10.3390/microorganisms9081780.

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The presence of methylmercury in aquatic environments and marine food sources is of global concern. The chemical reaction for the addition of a methyl group to inorganic mercury occurs in diverse bacterial taxonomic groups including the Gram-negative, sulfate-reducing Desulfovibrionaceae family that inhabit extreme aquatic environments. The availability of whole-genome sequence datasets for members of the Desulfovibrionaceae presents opportunities to understand the microbial mechanisms that contribute to methylmercury production in extreme aquatic environments. We have applied bioinformatics resources and developed visual analytics resources to categorize a collection of 719 putative universal stress protein (USP) sequences predicted from 93 genomes of Desulfovibrionaceae. We have focused our bioinformatics investigations on protein sequence analytics by developing interactive visualizations to categorize Desulfovibrionaceae universal stress proteins by protein domain composition and functionally important amino acids. We identified 651 Desulfovibrionaceae universal stress protein sequences, of which 488 sequences had only one USP domain and 163 had two USP domains. The 488 single USP domain sequences were further categorized into 340 sequences with ATP-binding motif and 148 sequences without ATP-binding motif. The 163 double USP domain sequences were categorized into (1) both USP domains with ATP-binding motif (3 sequences); (2) both USP domains without ATP-binding motif (138 sequences); and (3) one USP domain with ATP-binding motif (21 sequences). We developed visual analytics resources to facilitate the investigation of these categories of datasets in the presence or absence of the mercury-methylating gene pair (hgcAB). Future research could utilize these functional categories to investigate the participation of universal stress proteins in the bacterial cellular uptake of inorganic mercury and methylmercury production, especially in anaerobic aquatic environments.

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29

Sánchez-Jiménez, Miryan Margot, Paula Andrea Rincón-Ruiz, Sara Duque, María Adelaida Giraldo, Diber Marcela Ramírez-Monroy, Gloria Jaramillo, and Nora Cardona-Castro. "Salmonella enterica in semi-aquatic turtles in Colombia." Journal of Infection in Developing Countries 5, no. 05 (February 7, 2011): 361–64. http://dx.doi.org/10.3855/jidc.1126.

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Introduction: Turtles can be hosts of Salmonella enterica serovars which can cause disease both in the animals themselves and in people they come into contact with, especially when the turtles are kept as pets. To investigate the prevalence of Salmonella in turtles in Colombia, we studied animals at a wildlife protection centre. The turtles had either been confiscated or donated to the centre. Methodology: Detection of Salmonella spp. was conducted in feces samples using bacteriological cultures and polymerase chain reaction to identify genus and serovar. Results: By PCR and culture, 30/110 samples (27%) were positive while by PCR alone eight further samples were positive (total of 38/110 (35%) positive). The most common serovar was S. Enteritidis (26/38 (68%) with only one isolate being S. Typhimurium (3%). Four (11%) samples were positive for both serovars and seven (18%) could only be identified as Salmonella enterica spp. Conclusions: These results show that turtles in Colombia are commonly infected with Salmonella and are a risk for infection to people who come into contact with them.

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Blokesch, Melanie, and Gary K. Schoolnik. "Serogroup Conversion of Vibrio cholerae in Aquatic Reservoirs." PLoS Pathogens 3, no. 6 (June 8, 2007): e81. http://dx.doi.org/10.1371/journal.ppat.0030081.

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31

Merour, E., M. LeBerre, A. Lamoureux, J. Bernard, M. Bremont, and S. Biacchesi. "Completion of the full-length genome sequence of the infectious salmon anemia virus, an aquatic orthomyxovirus-like, and characterization of mAbs." Journal of General Virology 92, no. 3 (December 1, 2010): 528–33. http://dx.doi.org/10.1099/vir.0.027417-0.

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Islam, Mohammad Sirajul, Mohammad Iqbal Kabir Jahid, Mohammad Majibur Rahman, Mohammed Ziaur Rahman, Mohammad Shafiqul Islam, Mohammad Shahidul Kabir, David Allen Sack, and Gary K. Schoolnik. "Biofilm Acts as a Microenvironment for Plankton-AssociatedVibrio choleraein the Aquatic Environment of Bangladesh." Microbiology and Immunology 51, no. 4 (April 2007): 369–79. http://dx.doi.org/10.1111/j.1348-0421.2007.tb03924.x.

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Yoneda, Yasuko, Kyosuke Yamamoto, Ayaka Makino, Yasuhiro Tanaka, Xian-Ying Meng, Junko Hashimoto, Kazuo Shin-ya, et al. "Novel Plant-Associated Acidobacteria Promotes Growth of Common Floating Aquatic Plants, Duckweeds." Microorganisms 9, no. 6 (May 24, 2021): 1133. http://dx.doi.org/10.3390/microorganisms9061133.

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Duckweeds are small, fast growing, and starch- and protein-rich aquatic plants expected to be a next generation energy crop and an excellent biomaterial for phytoremediation. Despite such an importance, very little is known about duckweed–microbe interactions that would be a key biological factor for efficient industrial utilization of duckweeds. Here we first report the duckweed growth promoting ability of bacterial strains belonging to the phylum Acidobacteria, the members of which are known to inhabit soils and terrestrial plants, but their ecological roles and plant–microbe interactions remain largely unclear. Two novel Acidobacteria strains, F-183 and TBR-22, were successfully isolated from wild duckweeds and phylogenetically affiliated with subdivision 3 and 6 of the phylum, respectively, based on 16S rRNA gene sequence analysis. In the co-culture experiments with aseptic host plants, the F-183 and TBR-22 strains visibly enhanced growth (frond number) of six duckweed species (subfamily Lemnoideae) up to 1.8–5.1 times and 1.6–3.9 times, respectively, compared with uninoculated controls. Intriguingly, both strains also increased the chlorophyll content of the duckweed (Lemna aequinoctialis) up to 2.4–2.5 times. Under SEM observation, the F-183 and TBR-22 strains were epiphytic and attached to the surface of duckweed. Taken together, our findings suggest that indigenous plant associated Acidobacteria contribute to a healthy growth of their host aquatic plants.

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Horas, Elena, Loukas Theodosiou, and Lutz Becks. "Why Are Algal Viruses Not Always Successful?" Viruses 10, no. 9 (September 5, 2018): 474. http://dx.doi.org/10.3390/v10090474.

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Algal viruses are considered to be key players in structuring microbial communities and biogeochemical cycles due to their abundance and diversity within aquatic systems. Their high reproduction rates and short generation times make them extremely successful, often with immediate and strong effects for their hosts and thus in biological and abiotic environments. There are, however, conditions that decrease their reproduction rates and make them unsuccessful with no or little immediate effects. Here, we review the factors that lower viral success and divide them into intrinsic—when they are related to the life cycle traits of the virus—and extrinsic factors—when they are external to the virus and related to their environment. Identifying whether and how algal viruses adapt to disadvantageous conditions will allow us to better understand their role in aquatic systems. We propose important research directions such as experimental evolution or the resurrection of extinct viruses to disentangle the conditions that make them unsuccessful and the effects these have on their surroundings.

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35

Colombet, Jonathan, Maxime Fuster, Hermine Billard, and Télesphore Sime-Ngando. "Femtoplankton: What’s New?" Viruses 12, no. 8 (August 12, 2020): 881. http://dx.doi.org/10.3390/v12080881.

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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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Tang, Xiangming, Guijuan Xie, Keqiang Shao, Wei Tian, Guang Gao, and Boqiang Qin. "Aquatic Bacterial Diversity, Community Composition and Assembly in the Semi-Arid Inner Mongolia Plateau: Combined Effects of Salinity and Nutrient Levels." Microorganisms 9, no. 2 (January 20, 2021): 208. http://dx.doi.org/10.3390/microorganisms9020208.

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Due to the recent decades of climate change and intensive human activities, endorheic lakes are threatened by both salinization and eutrophication. However, knowledge of the aquatic bacterial community’s response to simultaneous increasing salinity and trophic status is still poor. To address this knowledge gap, we collected 40 surface water samples from five lakes and six rivers on the semi-arid Inner Mongolia Plateau, and investigated their bacterial communities using 16S rRNA gene-targeted amplicon sequencing. We found that bacterial species diversity significantly decreased from the mesotrophic freshwater river habitat to the eutrophic high-brackish lake habitat; salinity was more important than trophic status in explaining this decreased diversity. Salinity was the most important environmental factor in shaping community composition, while increased nitrogen loading was more important in structuring predicted functional composition. Within the lake habitats, the impact of environmental filtering on bacterial community assembly increased with the increasing salinity. The results suggested that the elevated salinity and nutrients have combined effects on the aquatic bacterial community, resulting in dramatic declines in species diversity, and promoted the importance of deterministic processes in community assembly. Our findings provide new insights into bacterial communities’ responses to the intensified climate-driven and anthropogenic environmental changes in aquatic ecosystems.

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Samal, S. K., C. P. Dopazo, K. Subramanian, B. Lupiani, S. B. Mohanty, and F. M. Hetrick. "Heterogeneity in the Genome RNAs and Polypeptides of Five Members of a Novel Group of Rotavirus-like Viruses Isolated from Aquatic Animals." Journal of General Virology 72, no. 1 (January 1, 1991): 181–84. http://dx.doi.org/10.1099/0022-1317-72-1-181.

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38

Shinya, Kyoko, Masato Hatta, Shinya Yamada, Ayato Takada, Shinji Watanabe, Peter Halfmann, Taisuke Horimoto, et al. "Characterization of a Human H5N1 Influenza A Virus Isolated in 2003." Journal of Virology 79, no. 15 (August 1, 2005): 9926–32. http://dx.doi.org/10.1128/jvi.79.15.9926-9932.2005.

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ABSTRACT In 2003, H5N1 avian influenza virus infections were diagnosed in two Hong Kong residents who had visited the Fujian province in mainland China, affording us the opportunity to characterize one of the viral isolates, A/Hong Kong/213/03 (HK213; H5N1). In contrast to H5N1 viruses isolated from humans during the 1997 outbreak in Hong Kong, HK213 retained several features of aquatic bird viruses, including the lack of a deletion in the neuraminidase stalk and the absence of additional oligosaccharide chains at the globular head of the hemagglutinin molecule. It demonstrated weak pathogenicity in mice and ferrets but caused lethal infection in chickens. The original isolate failed to produce disease in ducks but became more pathogenic after five passages. Taken together, these findings portray the HK213 isolate as an aquatic avian influenza A virus without the molecular changes associated with the replication of H5N1 avian viruses in land-based poultry such as chickens. This case challenges the view that adaptation to land-based poultry is a prerequisite for the replication of aquatic avian influenza A viruses in humans.

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Marti, Elisabet, Eleni Variatza, and Jose Luis Balcazar. "The role of aquatic ecosystems as reservoirs of antibiotic resistance." Trends in Microbiology 22, no. 1 (January 2014): 36–41. http://dx.doi.org/10.1016/j.tim.2013.11.001.

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Blanchette, Melanie L., and Mark A. Lund. "Aquatic Ecosystems of the Anthropocene: Limnology and Microbial Ecology of Mine Pit Lakes." Microorganisms 9, no. 6 (June 3, 2021): 1207. http://dx.doi.org/10.3390/microorganisms9061207.

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Mine pit lakes (‘pit lakes’) are new aquatic ecosystems of the Anthropocene. Potentially hundreds of meters deep, these lakes are prominent in the landscape and in the public consciousness. However, the ecology of pit lakes is underrepresented in the literature. The broad goal of this research was to determine the environmental drivers of pelagic microbe assemblages in Australian coal pit lakes. The overall experimental design was four lakes sampled three times, top and bottom, in 2019. Instrument chains were installed in lakes and measurements of in situ water quality and water samples for metals, metalloids, nutrients and microbe assemblage were collected. Lakes were monomictic and the timing of mixing was influenced by high rainfall events. Water quality and microbial assemblages varied significantly across space and time, and most taxa were rare. Lakes were moderately saline and circumneutral; Archeans were not prevalent. Richness also varied by catchment. Microbial assemblages correlated to environmental variables, and no one variable was consistently significant, spatially or temporally. Study lakes were dominated by ‘core’ taxa exhibiting temporal turnover likely driven by geography, water quality and interspecific competition, and the presence of water chemistry associated with an artificial aquifer likely influenced microbial community composition. Pit lakes are deceptively complex aquatic ecosystems that host equally complex pelagic microbial communities. This research established links between microbial assemblages and environmental variables in pit lakes and determined core communities; the first steps towards developing a monitoring program using microbes.

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Kadoya, Syun-suke, Osamu Nishimura, Hiroyuki Kato, and Daisuke Sano. "Predictive Water Virology: Hierarchical Bayesian Modeling for Estimating Virus Inactivation Curve." Water 11, no. 10 (October 21, 2019): 2187. http://dx.doi.org/10.3390/w11102187.

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Hazard analysis and critical control point (HACCP) are a series of actions to be taken to ensure product consumption safety. In food poisoning risk management, researchers in the field of predictive microbiology calculate the values that provide minimum stress (e.g., temperature and contact time in heating) for sufficient microbe inactivation based on mathematical models. HACCP has also been employed for health risk management in sanitation safety planning (SSP), but the application of predictive microbiology to water-related pathogens is difficult because the variety of pathogen types and the complex composition of the wastewater matrix does not allow us to make a simple mathematical model to predict inactivation efficiency. In this study, we performed a systematic review and meta-analysis to construct predictive inactivation curves using free chlorine for enteric viruses based on a hierarchical Bayesian model using parameters such as water quality. Our model considered uncertainty among virus disinfection tests and difference in genotype-dependent sensitivity of a virus to disinfectant. The proposed model makes it possible to identify critical disinfection stress capable of reducing virus concentration that is below the tolerable concentration to ensure human health.

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Zeng, Weiwei, Hanxu Dong, Xiaoyu Chen, Sven M. Bergmann, Ying Yang, Xinxian Wei, Guixiang Tong, Hua Li, Hui Yu, and Yanfeng Chen. "Establishment and characterization of a permanent heart cell line from largemouth bass Micropterus salmoides and its application to fish virology and immunology." Aquaculture 547 (January 2022): 737427. http://dx.doi.org/10.1016/j.aquaculture.2021.737427.

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Leacy, Alexander, Éva Nagy, Phuc H. Pham, and Leonardo Susta. "In Vitro and In Ovo Host Restriction of Aquatic Bird Bornavirus 1 in Different Avian Hosts." Viruses 12, no. 11 (November 7, 2020): 1272. http://dx.doi.org/10.3390/v12111272.

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Aquatic bird bornavirus 1 (ABBV-1) is associated with chronic meningoencephalitis and ganglioneuritis. Although waterfowl species act as the natural host of ABBV-1, the virus has been sporadically isolated from other avian species, showing the potential for a broad host range. To evaluate the host restriction of ABBV-1, and its potential to infect commercial poultry species, we assessed the ability of ABBV-1 to replicate in cells and embryos of different avian species. ABBV-1 replication was measured using multi- and single-step growth curves in primary embryo fibroblasts of chicken, duck, and goose. Embryonated chicken and duck eggs were infected through either the yolk sac or chorioallantoic cavity, and virus replication was assessed by immunohistochemistry and RT-qPCR in embryonic tissues harvested at two time points after infection. Multi-step growth curves showed that ABBV-1 replicated and spread in goose and duck embryo fibroblasts, establishing a population of persistently infected cells, while it was unable to do so in chicken fibroblasts. Single-step growth curves showed that cells from all three species could be infected; however, persistence was only established in goose and duck fibroblasts. In ovo inoculation yielded no detectable viral replication or lesion in tissues. Data indicate that although chicken, duck, and goose embryo fibroblasts can be infected with ABBV-1, a persistent infection is more easily established in duck and goose cells. Therefore, ABBV-1 may be able to infect chickens in vivo, albeit inefficiently. Additionally, our data indicate that an in ovo model is inadequate to investigating ABBV-1 host restriction and pathogenesis.

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Mishra, Charitra Kumar, Tae Jin Choi, and Sun Chul Kang. "Isolation and characterization of a bacteriophage F20 virulent to Enterobacter aerogenes." Journal of General Virology 93, no. 10 (October 1, 2012): 2310–14. http://dx.doi.org/10.1099/vir.0.043562-0.

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An aquatic phage, designated F20, was characterized and its physico-chemical characteristics studied. F20 was specifically virulent to only two strains of Enterobacter aerogenes (ATCC 13048 and the multi-drug-resistant strain K113) among other species tested (n = 15). It was classified in the family Siphoviridae of T1-like viruses and contained a linear dsDNA genome estimated to be 51.5 kbp enclosed by an isometric capsid of 50±2 nm in diameter and a tail of 150±3 nm in length. F20 was able to survive in a broad pH range between 4 and 11, showed potential for future animal trials using oral solution and resisted chloroform and ethanol. It exhibited remarkable stability between room temperature and 70 °C for up to 150 min, and even up to 6 months at room temperature. Knowledge of this phage belonging to the widespread T1-like viruses might be helpful for adopting therapeutic strategies against E. aerogenes.

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Gudenkauf, Brent M., James B. Eaglesham, William M. Aragundi, and Ian Hewson. "Discovery of urchin-associated densoviruses (family Parvoviridae) in coastal waters of the Big Island, Hawaii." Journal of General Virology 95, no. 3 (March 1, 2014): 652–58. http://dx.doi.org/10.1099/vir.0.060780-0.

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Echinoderms are important constituents of marine ecosystems, where they may influence the recruitment success of benthic flora and fauna, and are important consumers of detritus and plant materials. There are currently no described viruses of echinoderms. We used a viral metagenomic approach to examine viral consortia within three urchins – Colobocentrotus atratus, Tripneustes gratilla and Echinometra mathaei – which are common constituents of reef communities in the Hawaiian archipelago. Metagenomic libraries revealed the presence of bacteriophages and densoviruses (family Parvoviridae) in tissues of all three urchins. Densoviruses are known typically to infect terrestrial and aquatic arthropods. Urchin-associated densoviruses were detected by quantitative PCR in all tissues tested, and were also detected in filtered suspended matter (>0.2 µm) from plankton and in sediments at several locations near to where the urchins were collected for metagenomic analysis. To the best of our knowledge, this is the first report of echinoderm-associated viruses, which extends the known host range of parvoviruses.

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46

Hon, Chung-Chau, Tommy Tsan-Yuk Lam, Chi-Wai Yip, Raymond Tsz-Yeung Wong, Mang Shi, Jingwei Jiang, Fanya Zeng, and Frederick Chi-Ching Leung. "Phylogenetic evidence for homologous recombination within the family Birnaviridae." Journal of General Virology 89, no. 12 (December 1, 2008): 3156–64. http://dx.doi.org/10.1099/vir.0.2008/004101-0.

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Birnaviruses are bi-segmented double-stranded RNA (dsRNA) viruses infecting insects, avian species and a wide range of aquatic species. Although homologous recombination is a common phenomenon in positive-sense RNA viruses, recombination in dsRNA viruses is rarely reported. Here we performed a comprehensive survey on homologous recombination in all available sequences (>1800) of the family Birnaviridae based on phylogenetic incongruence. Although inter-species recombination was not evident, potential intra-species recombination events were detected in aquabirnaviruses and infectious bursal disease virus (IBDV). Eight potential recombination events were identified and the possibility that these events were non-naturally occurring was assessed case by case. Five of the eight events were identified in IBDVs and all of these five events involved live attenuated vaccine strains. This finding suggests that homologous recombination between vaccine and wild-type IBDV strains may have occurred; the potential risk of mass vaccination using live vaccines is discussed. This is the first report of evidence for homologous recombination within the family Birnaviridae.

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O’Brien, Caitlin A., Cassandra L. Pegg, Amanda S. Nouwens, Helle Bielefeldt-Ohmann, Bixing Huang, David Warrilow, Jessica J. Harrison, et al. "A Unique Relative of Rotifer Birnavirus Isolated from Australian Mosquitoes." Viruses 12, no. 9 (September 22, 2020): 1056. http://dx.doi.org/10.3390/v12091056.

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The family Birnaviridae are a group of non-enveloped double-stranded RNA viruses which infect poultry, aquatic animals and insects. This family includes agriculturally important pathogens of poultry and fish. Recently, next-generation sequencing technologies have identified closely related birnaviruses in Culex, Aedes and Anopheles mosquitoes. Using a broad-spectrum system based on detection of long double-stranded RNA, we have discovered and isolated a birnavirus from Aedes notoscriptus mosquitoes collected in northern New South Wales, Australia. Phylogenetic analysis of Aedes birnavirus (ABV) showed that it is related to Rotifer birnavirus, a pathogen of microscopic aquatic animals. In vitro cell infection assays revealed that while ABV can replicate in Aedes-derived cell lines, the virus does not replicate in vertebrate cells and displays only limited replication in Culex- and Anopheles-derived cells. A combination of SDS-PAGE and mass spectrometry analysis suggested that the ABV capsid precursor protein (pVP2) is larger than that of other birnaviruses and is partially resistant to trypsin digestion. Reactivity patterns of ABV-specific polyclonal and monoclonal antibodies indicate that the neutralizing epitopes of ABV are SDS sensitive. Our characterization shows that ABV displays a number of properties making it a unique member of the Birnaviridae and represents the first birnavirus to be isolated from Australian mosquitoes.

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Islam, Mohammad Sirajul, Kaisar Ali Talukder, Nurul Huda Khan, Zahid Hayat Mahmud, Mohammed Ziaur Rahman, Gopinath Balakrish Nair, Abul K. M. Siddique, et al. "Variation of ToxigenicVibrio choleraeO1 in the Aquatic Environment of Bangladesh and Its Correlation with the Clinical Strains." Microbiology and Immunology 48, no. 10 (October 2004): 773–77. http://dx.doi.org/10.1111/j.1348-0421.2004.tb03604.x.

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Paim, Francine C., Andrew S. Bowman, Lauren Miller, Brandi J. Feehan, Douglas Marthaler, Linda J. Saif, and Anastasia N. Vlasova. "Epidemiology of Deltacoronaviruses (δ-CoV) and Gammacoronaviruses (γ-CoV) in Wild Birds in the United States." Viruses 11, no. 10 (September 26, 2019): 897. http://dx.doi.org/10.3390/v11100897.

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Porcine deltacoronavirus (δ-CoV) is the object of extensive research in several countries including the United States. In contrast, the epidemiology of δ-CoVs in wild birds in the US is largely unknown. Our aim was to comparatively assess the prevalence of δ- and γ-CoVs in wild migratory terrestrial and aquatic birds in Arkansas, Illinois, Indiana, Maryland, Mississippi, Missouri, Ohio, Tennessee and Wisconsin. A total of 1236 cloacal/fecal swabs collected during the period 2015–2018 were tested for γ- and δ-CoVs using genus-specific reverse transcription-PCR assays. A total of 61 (4.99%) samples were γ-CoV positive, with up to 29 positive samples per state. In contrast, only 14 samples were positive for δ-CoV (1.14%) with only 1–4 originating from the same state. Thus, unlike previous reports from Asia, γ-CoVs are more prevalent than δ-CoVs in the US, suggesting that δ-CoVs may spread in birds with lower efficiency. This may indicate δ-CoV emerging status and incomplete adaptation to new host species limiting its spread. Phylogenetic analysis of the partial N gene revealed that the newly identified δ-CoV strains were most closely related to the HKU20 (wigeon) strain. Further studies are necessary to investigate the role of aquatic bird δ-CoVs in the epidemiology of δ-CoVs in swine and terrestrial birds.

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Karunasagar, Indrani. "Guest Editor’s Note on the Special Issue of Indian Journal of Virology: Viruses of Cultured Aquatic Animals in the Asia–Pacific Region." Indian Journal of Virology 23, no. 2 (September 2012): 87. http://dx.doi.org/10.1007/s13337-012-0107-y.

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