Diverse viruses of marine archaea discovered using metagenomics

During the past decade, metagenomics became a method of choice for the discovery of novel viruses. However, host assignment for uncultured viruses remains challenging, especially for archaeal viruses, which are grossly undersampled compared to viruses of bacteria and eukaryotes. Here, we assessed the utility of CRISPR spacer targeting, tRNA gene matching and homology searches for viral signature proteins, such as major capsid proteins, for the assignment of archaeal hosts and validated these approaches on metaviromes from Yangshan Harbor (YSH). We report 35 new genomes of viruses which could be confidently assigned to hosts representing diverse lineages of marine archaea. We show that the archaeal YSH virome is highly diverse, with some viruses enriching the previously described virus groups, such as magroviruses of Marine Group II Archaea (Poseidoniales), and others representing novel groups of marine archaeal viruses. Metagenomic recruitment of Tara Oceans datasets on the YSH viral genomes demonstrated the presence of YSH Poseidoniales and Nitrososphaeria viruses in the global oceans, but also revealed the endemic YSH-specific viral lineages. Furthermore, our results highlight the relationship between the soil and marine thaumarchaeal viruses. We propose three new families within the class Caudoviricetes for the classification of the five complete viral genomes predicted to replicate in marine Poseidoniales and Nitrososphaeria, two ecologically important and widespread archaeal groups. This study illustrates the utility of viral metagenomics in exploring the archaeal virome and provides new insights into the diversity, distribution and evolution of marine archaeal viruses.     

Exploring the diversity of plant proteome

The tremendous functional, spatial, and temporal diversity of the plant proteome is regulated by multiple factors that continuously modify protein abundance, modifications, interactions, localization, and activity to meet the dynamic needs of plants. Dissecting the proteome complexity and its underlying genetic variation is attracting increasing research attention. Mass spectrometry (MS)-based proteomics has become a powerful approach in the global study of protein functions and their relationships on a systems level. Here, we review recent breakthroughs and strategies adopted to unravel the diversity of the proteome, with a specific focus on the methods used to analyze posttranslational modifications (PTMs), protein localization, and the organization of proteins into functional modules. We also consider PTM crosstalk and multiple PTMs temporally regulating the life cycle of proteins. Finally, we discuss recent quantitative studies using MS to measure protein turnover rates and examine future directions in the study of the plant proteome.     

Ecdysteroids and juvenile hormones of whiteflies, important insect vectors for plant viruses

Ecdysteroids and juvenile hormones (JHs) regulate many physiological events throughout the insect life cycle, including molting, metamorphosis, ecdysis, diapause, reproduction, and behavior. Fluctuation of whitefly ecdysteroid levels and the identity of the whitefly molting hormone (20-hydroxyecdysone) have only been reported within the last few years. An ecdysteroid commitment peak that is associated with the reprogramming of tissues for a metamorphic molt in many holometabolous and some hemimetabolous insect species was not observed in last nymphal instars of either the sweet potato whitefly, Bemisia tabaci (Biotype B), or the greenhouse whitefly, Trialeurodes vaporariorum. Ecdysteroids reach peak levels 1-2 days prior to the initiation of the nymphal-adult metamorphic molt. Adult eye and wing differentiation which signal the onset of this molt begin earlier in 4th instar T. vaporariorum (Stages 4 and 5, respectively) than in B. tabaci (Stage 6), and the premolt peak is 3-4 times greater in B. tabaci ( approximately 400 fg/microg protein) than in T. vaporariorum ( approximately 120 fg/microg protein). The JH of B. tabaci nymphs and eggs was found to be JH III, supporting the view that JHs I and II are, with rare exception, only present in lepidopteran insects. In B. tabaci eggs, JH levels were approximately 10 times greater on day 2/3 (0.44 fg/egg or 0.54 ng/g) than on day 5 (0.04 fg/egg or 0.054 ng/g) post-oviposition. Approximately, 1.4 fg/2nd-3rd instar nymph (0.36 ng/g) was detected. It is probable that the relatively high level of JH in day 2/3 eggs is associated with the differentiation of various whitefly tissues during embryonic development.     

Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses

Recent metagenomic studies have provided an unprecedented wealth of data, which are revolutionizing our understanding of virus diversity. A redrawn landscape highlights viruses as active players in the phytobiome, and surveys have uncovered their positive roles in environmental stress tolerance of plants. Viral infectious clones are key tools for functional characterization of known and newly identified viruses. Knowledge of viruses and their components has been instrumental for the development of modern plant molecular biology and biotechnology. In this review, we provide extensive guidelines built on current synthetic biology advances that streamline infectious clone assembly, thus lessening a major technical constraint of plant virology. The focus is on generation of infectious clones in binary T‐DNA vectors, which are delivered efficiently to plants by Agrobacterium. We then summarize recent applications of plant viruses and explore emerging trends in microbiology, bacterial and human virology that, once translated to plant virology, could lead to the development of virus‐based gene therapies for ad hoc engineering of plant traits. The systematic characterization of plant virus roles in the phytobiome and next‐generation virus‐based tools will be indispensable landmarks in the synthetic biology roadmap to better crops.     

Exploring the molecular diversity of Eleotridae (Gobiiformes) using mitochondrial DNA

Species with wide geographic distributions can consist of different lineages or even of different species. The present study evaluated the molecular diversity of the family Eleotridae by analyzing sequences of the COI gene from species collected in different locations in a Neotropical region as well as sequences from BOLD and GenBank. The analysis revealed the distinction and differentiation of a variety of species with high statistical support, including Gobiomorus dormitor (two lineages), Dormitator maculatus (three lineages) and Eleotris fusca (three lineages), and a number of different lineages of Microphilypnus. This indicates the existence of a number of unknown cryptic species that have not been reported previously, increasing the potential diversity of eleotrid species in the Neotropics.     

Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing

Background

Influenza viruses exist as a large group of closely related viral genomes, also called quasispecies. The composition of this influenza viral quasispecies can be determined by an accurate and sensitive sequencing technique and data analysis pipeline. We compared the suitability of two benchtop next-generation sequencers for whole genome influenza A quasispecies analysis: the Illumina MiSeq sequencing-by-synthesis and the Ion Torrent PGM semiconductor sequencing technique.

Results

We first compared the accuracy and sensitivity of both sequencers using plasmid DNA and different ratios of wild type and mutant plasmid. Illumina MiSeq sequencing reads were one and a half times more accurate than those of the Ion Torrent PGM. The majority of sequencing errors were substitutions on the Illumina MiSeq and insertions and deletions, mostly in homopolymer regions, on the Ion Torrent PGM. To evaluate the suitability of the two techniques for determining the genome diversity of influenza A virus, we generated plasmid-derived PR8 virus and grew this virus in vitro. We also optimized an RT-PCR protocol to obtain uniform coverage of all eight genomic RNA segments. The sequencing reads obtained with both sequencers could successfully be assembled de novo into the segmented influenza virus genome. After mapping of the reads to the reference genome, we found that the detection limit for reliable recognition of variants in the viral genome required a frequency of 0.5% or higher. This threshold exceeds the background error rate resulting from the RT-PCR reaction and the sequencing method. Most of the variants in the PR8 virus genome were present in hemagglutinin, and these mutations were detected by both sequencers.

Conclusions

Our approach underlines the power and limitations of two commonly used next-generation sequencers for the analysis of influenza virus gene diversity. We conclude that the Illumina MiSeq platform is better suited for detecting variant sequences whereas the Ion Torrent PGM platform has a shorter turnaround time. The data analysis pipeline that we propose here will also help to standardize variant calling in small RNA genomes based on next-generation sequencing data.     

Harnessing plant viruses in the metagenomics era: from the development of infectious clones to applications

Recent metagenomic studies which focused on virus characterization in the entire plant environment have revealed a remarkable viral diversity in plants. The exponential discovery of viruses also requires the concomitant implementation of high-throughput methods to perform their functional characterization. Despite several limitations, the development of viral infectious clones remains a method of choice to understand virus biology, their role in the phytobiome, and plant resilience. Here, we review the latest approaches for efficient characterization of plant viruses and technical advances built on high-throughput sequencing and synthetic biology to streamline assembly of viral infectious clones. We then discuss the applications of plant viral vectors in fundamental and applied plant research as well as their technical and regulatory limitations, and we propose strategies for their safer field applications.     

Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes

Viruses are the most abundant and diverse genetic entities on Earth; however, broad surveys of viral diversity are hindered by the lack of a universal assay for viruses and the inability to sample a sufficient number of individual hosts. This study utilized vector-enabled metagenomics (VEM) to provide a snapshot of the diversity of DNA viruses present in three mosquito samples from San Diego, California. The majority of the sequences were novel, suggesting that the viral community in mosquitoes, as well as the animal and plant hosts they feed on, is highly diverse and largely uncharacterized. Each mosquito sample contained a distinct viral community. The mosquito viromes contained sequences related to a broad range of animal, plant, insect and bacterial viruses. Animal viruses identified included anelloviruses, circoviruses, herpesviruses, poxviruses, and papillomaviruses, which mosquitoes may have obtained from vertebrate hosts during blood feeding. Notably, sequences related to human papillomaviruses were identified in one of the mosquito samples. Sequences similar to plant viruses were identified in all mosquito viromes, which were potentially acquired through feeding on plant nectar. Numerous bacteriophages and insect viruses were also detected, including a novel densovirus likely infecting Culex erythrothorax. Through sampling insect vectors, VEM enables broad survey of viral diversity and has significantly increased our knowledge of the DNA viruses present in mosquitoes.     

Rapid identification of adult whiteflies in plant consignments using monoclonal antibodies

A rapid and simple method for the identification of adult whiteflies (Homoptera: Aleyrodidae) would be valuable, both to facilitate pest management decision making and, more importantly, to prevent the introduction of new pests into non-infested areas. Considering the enormous economic losses that have resulted in the recent past from the accidental introduction of harmful species, there is a clear and urgent need for a reliable antibody-based test kit that would allow non-specialist growers, extension workers and customs authorities to identify whiteflies. As a first step in this process, this paper describes the development and characterisation of monoclonal antibodies capable of distinguishing between major pest species of whitefly, and application of these antibodies in an enzyme-linked immunosorbent assay (ELISA). A monoclonal antibody is described that reacts strongly with both male and female Trialeurodes vaporariorum (Westwood) but not with either Bemisia tabaci (Gennadius) or B. argentifolii Bellows & Perring. A second antibody is reported that gives a strong response to female Bemisia sp. that does not react with T. vaporariorum of either sex. The two antibodies used in combination provide a powerful means of distinguishing between adult whitefly, particularly at low levels of infestation in plant consignments, when pupae cannot easily be found.     

Extraordinary diversity of viruses in deep-sea sediments as revealed by metagenomics without prior virion separation

Our current knowledge of the virosphere in deep-sea sediments remains rudimentary. Here we investigated viral diversity at both gene and genomic levels in deep-sea sediments of Southwest Indian Ocean. Analysis of 19 676 106 non-redundant genes from the metagenomic DNA sequences revealed a large number of unclassified viral groups in these samples. A total of 1106 high-confidence viral contigs were obtained after two runs of assemblies, and 217 of these contigs with sizes up to ~120 kb were shown to represent complete viral genomes. These contigs are clustered with no known viral genomes, and over 2/3 of the ORFs on the viral contigs encode no known functions. Furthermore, most of the complete viral contigs show limited similarity to known viral genomes in genome organization. Most of the classified viral contigs are derived from dsDNA viruses belonging to the order Caudovirales, including primarily members of the families Myoviridae, Podoviridae and Siphoviridae. Most of these viruses infect Proteobacteria and, less frequently, Planctomycetes, Firmicutes, Chloroflexi, etc. Auxiliary metabolic genes (AMGs), present in abundance on the viral contigs, appear to function in modulating the host ability to sense environmental gradients and community changes, and to uptake and metabolize nutrients.     

Exploring the relationship between canopy height and terrestrial plant diversity

A relatively small number of broad-scale patterns describe the distribution of biodiversity across the earth. All of them explore biodiversity focusing on a mono or bi-dimensional space. Conversely, the volume of the forests is rarely considered. In the present work, we tested a global correlation between vascular plant species richness (S) and average forest canopy height (H), the latter regarded as a proxy of volume, using the NASA product of Global Forest Canopy Height map and the global map of plant species diversity. We found a significant correlation between H and S both at global and macro-climate scales, with strongest confidence in the tropics. Hence, two different regression models were compared and discussed to provide a possible pattern of the H–S relation. We suggested that the volume of forest ecosystems should be considered in ecological studies as well as in planning and managing natural sites, although in this first attempt, we cannot definitively prove our hypothesis. Again, high-resolution spatial data could be highly important to confirm the H–S relation, even at different scales.     

Ancient saltern metagenomics: tracking changes in microbes and their viruses from the underground to the surface

Microbial communities in hypersaline underground waters derive from ancient organisms trapped within the evaporitic salt crystals and are part of the poorly known subterranean biosphere. Here, we characterized the viral and prokaryotic assemblages present in the hypersaline springs that dissolve Triassic-Keuper evaporite rocks and feed the Añana Salt Valley (Araba/Alava, Basque Country, Spain). Four underground water samples (around 23% total salinity) with different levels of exposure to the open air were analysed by means of microscopy and metagenomics. Cells and viruses in the spring water had lower concentrations than what are normally found in hypersaline environments and seemed to be mostly inactive. Upon exposure to the open air, there was an increase in activity of both cells and viruses as well as a selection of phylotypes. The underground water was inhabited by a rich community harbouring a diverse set of genes coding for retinal binding proteins. A total of 35 viral contigs from 15 to 104 kb, representing partial or total viral genomes, were assembled and their evolutionary changes through the spring system were followed by SNP analysis and metagenomic island tracking. Overall, both the viral and the prokaryotic assemblages changed quickly upon exposure to the open air conditions.     

Identification of plant chemicals attracting and repelling whiteflies

The harmful side effects of chemical pest control have focused increasing attention on the potential for environmentally friendly, sustainable and efficient methods to control the sweet potato whitefly, Bemisia tabaci (Gennadius). One control method employs a volatile repellent (push), and an alluring volatile trap (pull) to manipulate the distribution and control the whitefly. Here, a Y-tube olfactometer was used to investigate the orientation responses of the whitefly toward the volatile components of six plants: tomato, tobacco, cabbage, cotton, cucumber and celery. Gas chromatography coupled with mass spectrometry was used to identify and quantify extracts from the six plants. Six treatments were conducted to demonstrate the “push–pull” method’s effects on the host selection behaviors of B. tabaci in a greenhouse. Four of the plant extracts tested had exceedingly attractive effects on the adult insects, but not those from celery. B. tabaci exhibited a prominent attraction response to (E)-2-hexenal, 3-hexen-1-ol and mixtures of these compounds, with the response rates exceeding 80 % for all tested proportions. Limonene diluted 500 times had a 62 % greater deterrent effect on adults than was observed in its absence, and it repelled egg-laying by more than 80 % in the greenhouse experiment. These data show that (E)-2-hexenal, 3-hexen-1-ol and limonene can be expected to be used for the “push–pull” method to control B. tabaci.     

探索中国山地植物多样性的分布规律

目前地球上的生物物种每年以0．1％-1．1％的速率在急剧减少(World Conservation Monitoring Centre,1992),人类社会开始进入保护生物多样性的时代。大规模开垦土地导致的自然生境快速丧失是生物多样性急剧减少的根本原因。山地由于具有浓缩的环境梯度和高度异质化的生境、相对较低的人类干扰强度,以及在地质历史上常成为大量物种     

Assembly of flexuous plant viruses and their proteins.

Recent experiments on the disassembly and assembly of some flexuous plant viruses and their proteins are described. The properties of reconstituted potato virus X and those of assembled potato virus Y protein are considered as well as the suitability of other flexuous viruses for reconstitution studies.     

Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA

DNA sequencing technology has proven very valuable for analysing the microbiota of poorly accessible ecosystems such as hydrothermal vents. Using a combination of amplicon and shotgun sequencing of small-subunit rRNA and its gene, we examined the composition and diversity of microbial communities from the recently discovered Jan Mayen vent field, located on Mohn's Ridge in the Norwegian-Greenland Sea. The communities were dominated by the epsilonproteobacterial genera Sulfurimonas and Sulfurovum. These are mesophiles involved in sulphur metabolism and typically found in vent fluid mixing zones. Composition and diversity predictions differed systematically between extracted DNA and RNA samples as well as between amplicon and shotgun sequencing. These differences were more substantial than those between two biological replicates. Amplicon vs. shotgun sequencing differences could be explained to a large extent by bias introduced during PCR, caused by preferential primer-template annealing, while DNA vs. RNA differences were thought to be caused by differences between the activity levels of taxa. Further, predicted diversity from RNA samples was consistently lower than that from DNA. In summary, this study illustrates how different methods can provide complementary ecological insights.     

Phylogenetic diversity and metagenomics of candidate division OP3

Except for environmental 16S rRNA gene sequences, no information is available for members of the candidate division OP3. These bacteria appear to thrive in anoxic environments, such as marine sediments, hypersaline deep sea, freshwater lakes, aquifers, flooded paddy soils and methanogenic bioreactors. The 16S rRNA phylogeny suggests that OP3 belongs to the Planctomycetes/Verrucomicrobia/Chlamydiae (PVC) superphylum. Metagenomic fosmid libraries were constructed from flooded paddy soil and screened for 16S rRNA gene‐containing fragments affiliated with the PVC superphylum. The screening of 63 000 clones resulted in 23 assay‐positive fosmids, of which three clones were affiliated with OP3. The 16S rRNA gene sequence divergence between the fragments OP3/1, OP3/2 and OP3/3 ranges from 18% to 25%, indicating that they belong to different OP3 subdivisions. The 23S rRNA phylogeny confirmed the membership of OP3 in the PVC superphylum. Sequencing the OP3 fragments resulted in a total of 105 kb of genomic information and 90 ORFs, of which 47 could be assigned a putative function and 11 were conserved hypothetical. Using BLASTP searches, a high proportion of ORFs had best matches to homologues from Deltaproteobacteria, rather than to those of members of the PVC superphylum. On the fragment OP3/3, a cluster of nine ORFs was predicted to encode the bacterial NADH dehydrogenase I. Given the high proportion of homologues present in deltaproteobacteria and anoxic conditions in the natural environment of OP3 bacteria, the detection of NADH dehydrogenase I may suggest an anaerobic respiration mode. Oligonucleotide frequencies calculated for OP3/1, OP3/2 and OP/3 show high intraphylum correlations. This novel sequence information could therefore be used to identify OP3‐related fragments in large metagenomic data sets using marker gene‐independent procedures in the future. In addition to the OP3 fragments, a single metagenomic fragment affiliated with the candidate division BRC1 was obtained and analysed.