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

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

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

Contrasting Life Strategies of Viruses That Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging (vol 3, e00373, 2012)

ABSTRACT Ocean viruses are ubiquitous and abundant and play important roles in global biogeochemical cycles by means of their mortality, horizontal gene transfer, and manipulation of host metabolism. However, the obstacles involved in linking viruses to their hosts in a high-throughput manner bottlenecks our ability to understand virus-host interactions in complex communities. We have developed a method called viral tagging (VT), which combines mixtures of host cells and fluorescent viruses with flow cytometry. We investigated multiple viruses which infect each of two model marine bacteria that represent the slow-growing, photoautotrophic genus Synechococcus (Cyanobacteria) and the fast-growing, heterotrophic genus Pseudoalteromonas (Gammaproteobacteria). Overall, viral tagging results for viral infection were consistent with plaque and liquid infection assays for cyanobacterial myo-, podo- and siphoviruses and some (myo- and podoviruses) but not all (four siphoviruses) heterotrophic bacterial viruses. Virus-tagged Pseudoalteromonas organisms were proportional to the added viruses under varied infection conditions (virus-bacterium ratios), while no more than 50% of the Synechococcus organisms were virus tagged even at viral abundances that exceeded (5 to 10×) that of their hosts. Further, we found that host growth phase minimally impacts the fraction of virus-tagged Synechococcus organisms while greatly affecting phage adsorption to Pseudoalteromonas. Together these findings suggest that at least two contrasting viral life strategies exist in the oceans and that they likely reflect adaptation to their host microbes. Looking forward to the point at which the virus-tagging signature is well understood (e.g., for Synechococcus), application to natural communities should begin to provide population genomic data at the proper scale for predictively modeling two of the most abundant biological entities on Earth. IMPORTANCE Viral study suffers from an inability to link viruses to hosts en masse, and yet delineating “who infects whom” is fundamental to viral ecology and predictive modeling. This article describes viral tagging—a high-throughput method to investigate virus-host interactions by combining the fluorescent labeling of viruses for “tagging” host cells that can be analyzed and sorted using flow cytometry. Two cultivated hosts (the cyanobacterium Synechococcus and the gammaproteobacterium Pseudoalteromonas) and their viruses (podo-, myo-, and siphoviruses) were investigated to validate the method. These lab-based experiments indicate that for most virus-host pairings, VT (viral tagging) adsorption is equivalent to traditional infection by liquid and plaque assays, with the exceptions being confined to promiscuous adsorption by Pseudoalteromonas siphoviruses. These experiments also reveal variability in life strategies across these oceanic virus-host systems with respect to infection conditions and host growth status, which highlights the need for further model system characterization to break open this virus-host interaction “black box.

ConsensusCGs

Assembly and gene predictions (CDS and aminoacid sequences) for the 26 candidatus genomes referred in the manuscript