Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mara, P., Vik, D., Pachiadaki, M. G., Suter, E. A., Poulos, B., Taylor, G. T., Sullivan, M. B., & Edgcomb, V. P. Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline. ISME Journal, (2020), doi:10.1038/s41396-020-00739-3.Little is known about viruses in oxygen-deficient water columns (ODWCs). In surface ocean waters, viruses are known to act as gene vectors among susceptible hosts. Some of these genes may have metabolic functions and are thus termed auxiliary metabolic genes (AMGs). AMGs introduced to new hosts by viruses can enhance viral replication and/or potentially affect biogeochemical cycles by modulating key microbial pathways. Here we identify 748 viral populations that cluster into 94 genera along a vertical geochemical gradient in the Cariaco Basin, a permanently stratified and euxinic ocean basin. The viral communities in this ODWC appear to be relatively novel as 80 of these viral genera contained no reference viral sequences, likely due to the isolation and unique features of this system. We identify viral elements that encode AMGs implicated in distinctive processes, such as sulfur cycling, acetate fermentation, signal transduction, [Fe–S] formation, and N-glycosylation. These AMG-encoding viruses include two putative Mu-like viruses, and viral-like regions that may constitute degraded prophages that have been modified by transposable elements. Our results provide an insight into the ecological and biogeochemical impact of viruses oxygen-depleted and euxinic habitats.This work was supported by the National Science Foundation grant OCE-1336082 to VPE, OCE-1335436 to GTT, OCE-1536989, a Moore Foundation Award (#3790) to MBS, and WHOI subaward A101259 to MP. The sequencing conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231

Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods

While the collective impact of marine viruses has become more apparent over the last decade, a deeper understanding of virus-host dynamics and the role of viruses in nutrient cycling would benefit from direct observations at the single-virus level. We describe two new complementary approaches - stable isotope probing coupled with nanoscale secondary ion mass spectrometry (nanoSIMS) and fluorescence-based biorthogonal non-canonical amino acid tagging (BONCAT) - for studying the activity and biogeochemical influence of marine viruses. These tools were developed and tested using several ecologically relevant model systems (Emiliania huxleyi/EhV207, Synechococcus sp. WH8101/Syn1, and Escherichia coli/T7). By resolving carbon and nitrogen enrichment in viral particles, we demonstrate the power of nanoSIMS tracer experiments in obtaining quantitative estimates for the total number of viruses produced directly from a particular production pathway (by isotopically labeling host substrates). Additionally, we show through laboratory experiments and a pilot field study that BONCAT can be used to directly quantify viral production (via epifluorescence microscopy) with minor sample manipulation and no dependency on conversion factors. This technique can also be used to detect newly synthesized viral proteins. Together these tools will help fill critical gaps in our understanding of the biogeochemical impact of viruses in the ocean

Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods

While the collective impact of marine viruses has become more apparent over the last decade, a deeper understanding of virus-host dynamics and the role of viruses in nutrient cycling would benefit from direct observations at the single-virus level. We describe two new complementary approaches - stable isotope probing coupled with nanoscale secondary ion mass spectrometry (nanoSIMS) and fluorescence-based biorthogonal non-canonical amino acid tagging (BONCAT) - for studying the activity and biogeochemical influence of marine viruses. These tools were developed and tested using several ecologically relevant model systems (Emiliania huxleyi/EhV207, Synechococcus sp. WH8101/Syn1, and Escherichia coli/T7). By resolving carbon and nitrogen enrichment in viral particles, we demonstrate the power of nanoSIMS tracer experiments in obtaining quantitative estimates for the total number of viruses produced directly from a particular production pathway (by isotopically labeling host substrates). Additionally, we show through laboratory experiments and a pilot field study that BONCAT can be used to directly quantify viral production (via epifluorescence microscopy) with minor sample manipulation and no dependency on conversion factors. This technique can also be used to detect newly synthesized viral proteins. Together these tools will help fill critical gaps in our understanding of the biogeochemical impact of viruses in the ocean

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world’s planktonic ecosystems

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems

Effect of secretory immunoglobulin A on group B streptococci

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Detection of Lettuce Infectious Yellow Virus (LIYV) in Greenhouse and Field Inoculated Plots Using an Indirect Enzyme-linked Immunosorbent Assay (Indirect ELISA)

Lettuce infectious yellows virus (LIYV), a recently recognized plant virus, causes dramatic yellowing symptoms and severe diseases in a wide range of vegetable crops in Arizona, adjacent southwestern states and Mexico. Until now, the only available diagnostic method was a time-consuming bioassay that used the insect vector to transmit the virus, with subsequent manipulation of indicator plants. A rapid, sensitive diagnostic technique (termed an indirect enzyme-linked immunoassay, called indirect ELISA) system was developed to detect lettuce infectious yellows virus (LIYV) in infected plant material. A virus specific antibody was made to viral capsid protein which was purified by polyacrylamide gel electrophoresis. The indirect ELISA system was optimized and used to detect viral antigen in greenhouse-inoculated melons. The system was subsequently adapted to detect LIYV in symptomatic and asymptomatic weed and cultivated plant species collected from infected fields near Yuma and in central Arizona. The indirect ELISA system described here allows for the detection of approximately 100 ng of virus per well. The LIYV was detectable in symptomatic (but not in asymptomatic) leaves of melon plants infected with the virus. In contrast, the virus could be detected in both symptomatic and symptomless cheeseweed plants collected in the field. The optical density readings for infected weed species were generally lower than those for cultivated species, such as melons, lettuce, and spinach, suggesting that there is less virus in the weed hosts tested than in infected, cultivated hosts

Assessment of Virus Disease Incidence and Whitefly Population in an Isolated Agroecosystem in Central Arizona

A survey study was undertaken to identify the plant viruses, to document the occurrence of virus diseases, and to document the seasonal population dynamics of insect vectors in a semi-isolated agricultural site in Central Arizona. A typical year-round cropping history at the site consists of cotton and seasonal sequences of vegetables. The most abundant insects caught using 24-hr exposures of yellow sticky traps were whiteflies (Trialeurodes abutilonea Haldeman and Bemisia tabaci Genn.) and the cotton (or melon) aphid (Aphis gossypii Glover). Of the three, only B. tabaci and A. gossvpii are recognized as virus vectors in Arizona. The most prevalent plant virus identified in vegetable crops and/or weeds was lettuce infectious yellows virus (LIYV), a whitefly-transmitted virus. The virus was detected in lettuce, (greenleaf, romaine, iceberg, red leaf) watermelon, cantaloupe, spinach, and cilantro. In addition, the watermelon curly mottle/squash leaf curl virus complex (WCMoV-SLCV), watermelon mosaic virus 2 (WMV-2) zucchini yellow mosaic virus (ZYMV), cucumber mosaic virus (CMV), and squash mosaic virus (SqMV) were identified in cucurbits at various times and locations throughout the season