scholarly journals RNA viral communities are structured by host plant phylogeny in oak and conifer leaves

2021 ◽  
Author(s):  
Anneliek M ter Horst ◽  
Jane D Fudyma ◽  
Aurelie Bak ◽  
Min Sook Hwang ◽  
Christian Santos-Medellin ◽  
...  
Keyword(s):  
Host Plant ◽  
De Novo ◽  
Wild Plants ◽  
Agricultural Crops ◽  
Persistent Infections ◽  
Plant Phylogeny ◽  
Viral Community ◽  
Viral Communities ◽  
Oak Tree ◽  
Conifer Trees

Wild plants can suffer devastating diseases, experience asymptomatic, persistent infections, and serve as reservoirs for viruses of agricultural crops, yet we have a limited understanding of the natural plant virosphere. To access representatives of locally and globally distinct wild plants and investigate their viral diversity, we extracted and sequenced dsRNA from leaves from 16 healthy oak and conifer trees in the UC Davis Arboretum (Davis, California). From de novo assemblies, we recovered 389 RNA-dependent RNA polymerase (RdRp) gene sequences from 384 putative viral species, and a further 580 putative viral contigs were identified with virus prediction software followed by manual confirmation of virus annotation. Based on similarity to known viruses, most recovered viruses were predicted to infect plants or fungi, with the highest diversity and abundance observed in the Totiviridae and Mitoviridae families. Phyllosphere viral community composition differed significantly by host plant phylogeny, suggesting the potential for host-specific viromes. The phyllosphere viral community of one oak tree differed substantially from other oak viral communities and contained a greater proportion of putative mycoviral sequences, potentially due to the tree's more advanced senescence at the time of sampling. These results suggest that oaks and conifers harbor a vast diversity of viruses with as-yet unknown roles in plant health and phyllosphere microbial ecology.

Assessment of viral assemblages in different types of wetland water in northeast China using RAPD-PCR

2020 ◽  
Vol 85 ◽  
pp. 183-196
Author(s):  
Y Sun ◽  
J Liu ◽  
Q Yao ◽  
J Jin ◽  
X Liu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Water Samples ◽  
Northeast China ◽  
Bacterial Community Composition ◽  
Freshwater Wetlands ◽  
Viral Community ◽  
Rapd Pcr ◽  
Wetland Water ◽  
Different Types ◽  
Viral Communities

Viruses are the most abundant and ubiquitous biological entities in various ecosystems, yet few investigations of viral communities in wetlands have been performed. To address this data gap, water samples from 6 wetlands were randomly collected across northeast China; viruses in the water were concentrated by sequential tangential flow filtration, and viral communities were assessed through randomly amplified polymorphic DNA-PCR (RAPD-PCR) with 4 decamer oligonucleotide primers. Principal coordinate analysis and hierarchical clustering analysis of the DNA fingerprints showed that viral community compositions differed among the water samples: communities in the 2 coastal wetlands were more similar to each other than to those in the 4 freshwater wetlands. The Shannon-Weaver index (H) and evenness index (E) of the RAPD-PCR fingerprint also differed among the 6 wetlands. Mantel test revealed that the changes in viral communities in wetland water were most closely related to the water NH4+-N and inorganic C content, followed by total K, P, C and NO3--N. DNA sequence analysis of the excised bands revealed that viruses accounted for ~40% of all sequences. Among the hit viral homologs, the majority belonged to the Microviridae. Moreover, variance partitioning analysis showed that the viral community contributed 24.58% while environmental factors explained 30.56% of the bacterial community variation, indicating that the bacterial community composition was strongly affected by both viral community and water variables. This work provides an initial outline of the viral communities from different types of wetlands in northeast China and improves our understanding of the viral diversity in these ecosystems.

scholarly journals Fecal Viral Community Responses to High-Fat Diet in Mice

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Anjelique Schulfer ◽  
Tasha M. Santiago-Rodriguez ◽  
Melissa Ly ◽  
Joshua M. Borin ◽  
Jessica Chopyk ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
High Fat Diet ◽  
Alpha Diversity ◽  
Diet Shift ◽  
Significant Shift ◽  
Diet Change ◽  
Gi Tract ◽  
High Fat ◽  
Viral Community ◽  
Viral Communities

ABSTRACT Alterations in diet can have significant impact on the host, with high-fat diet (HFD) leading to obesity, diabetes, and inflammation of the gut. Although membership and abundances in gut bacterial communities are strongly influenced by diet, substantially less is known about how viral communities respond to dietary changes. Examining fecal contents of mice as the mice were transitioned from normal chow to HFD, we found significant changes in the relative abundances and the diversity in the gut of bacteria and their viruses. Alpha diversity of the bacterial community was significantly diminished in response to the diet change but did not change significantly in the viral community. However, the diet shift significantly impacted the beta diversity in both the bacterial and viral communities. There was a significant shift away from the relatively abundant Siphoviridae accompanied by increases in bacteriophages from the Microviridae family. The proportion of identified bacteriophage structural genes significantly decreased after the transition to HFD, with a conserved loss of integrase genes in all four experimental groups. In total, this study provides evidence for substantial changes in the intestinal virome disproportionate to bacterial changes, and with alterations in putative viral lifestyles related to chromosomal integration as a result of shift to HFD. IMPORTANCE Prior studies have shown that high-fat diet (HFD) can have profound effects on the gastrointestinal (GI) tract microbiome and also demonstrate that bacteria in the GI tract can affect metabolism and lean/obese phenotypes. We investigated whether the composition of viral communities that also inhabit the GI tract are affected by shifts from normal to HFD. We found significant and reproducible shifts in the content of GI tract viromes after the transition to HFD. The differences observed in virome community membership and their associated gene content suggest that these altered viral communities are populated by viruses that are more virulent toward their host bacteria. Because HFD also are associated with significant shifts in GI tract bacterial communities, we believe that the shifts in the viral community may serve to drive the changes that occur in associated bacterial communities.

scholarly journals Viral metagenomes of Lake Soyang, the largest freshwater lake in South Korea

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Kira Moon ◽  
Suhyun Kim ◽  
Ilnam Kang ◽  
Jang-Cheon Cho
Keyword(s):  
South Korea ◽  
Illumina Miseq ◽  
Freshwater Lakes ◽  
Genome Sequences ◽  
Illumina Miseq Platform ◽  
Viral Community ◽  
Viral Communities ◽  
Miseq Platform ◽  
Metagenome Sequencing ◽  
Freshwater Reservoir

Abstract A high number of viral metagenomes have revealed countless genomes of putative bacteriophages that have not yet been identified due to limitations in bacteriophage cultures. However, most virome studies have been focused on marine or gut environments, thereby leaving the viral community structure of freshwater lakes unclear. Because the lakes located around the globe have independent ecosystems with unique characteristics, viral community structures are also distinctive but comparable. Here, we present data on viral metagenomes that were seasonally collected at a depth of 1 m from Lake Soyang, the largest freshwater reservoir in South Korea. Through shotgun metagenome sequencing using the Illumina MiSeq platform, 3.08 to 5.54-Gbps of reads per virome were obtained. To predict the viral genome sequences within Lake Soyang, contigs were constructed and 648 to 1,004 putative viral contigs were obtained per sample. We expect that both viral metagenome reads and viral contigs would contribute in comparing and understanding of viral communities among different freshwater lakes depending on seasonal changes.

scholarly journals Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica)

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 979 ◽  
Author(s):  
Ping Liu ◽  
Wu Chen ◽  
Jin-Ping Chen
Keyword(s):  
De Novo ◽  
Sendai Virus ◽  
Sequence Similarity ◽  
Viral Metagenomics ◽  
Manis Javanica ◽  
Pathogenic Viruses ◽  
Viral Communities ◽  
High Level ◽  
Viral Sequences ◽  
Insight Into

Pangolins are endangered animals in urgent need of protection. Identifying and cataloguing the viruses carried by pangolins is a logical approach to evaluate the range of potential pathogens and help with conservation. This study provides insight into viral communities of Malayan Pangolins (Manis javanica) as well as the molecular epidemiology of dominant pathogenic viruses between Malayan Pangolin and other hosts. A total of 62,508 de novo assembled contigs were constructed, and a BLAST search revealed 3600 ones (≥300 nt) were related to viral sequences, of which 68 contigs had a high level of sequence similarity to known viruses, while dominant viruses were the Sendai virus and Coronavirus. This is the first report on the viral diversity of pangolins, expanding our understanding of the virome in endangered species, and providing insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into other mammals.

scholarly journals Specific response to herbivore-induced de novo synthesized plant volatiles provides reliable information for host plant selection in a moth

2013 ◽  
Vol 216 (17) ◽  
pp. 3257-3263 ◽  
Author(s):  
A. Zakir ◽  
M. Bengtsson ◽  
M. M. Sadek ◽  
B. S. Hansson ◽  
P. Witzgall ◽  
...  
Keyword(s):  
Host Plant ◽  
Plant Volatiles ◽  
De Novo ◽  
Reliable Information ◽  
Host Plant Selection ◽  
Specific Response ◽  
Plant Selection

scholarly journals Soil viral communities are structured by pH at local and global scales

2021 ◽  
Author(s):  
Sungeun Lee ◽  
Jackson W Sorensen ◽  
Robin L Walker ◽  
Joanne B Emerson ◽  
Graeme W Nicol ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Soil Ph ◽  
Environmental Gradients ◽  
Abiotic Factors ◽  
Global Scale ◽  
Community Structures ◽  
Viral Community ◽  
Viral Communities ◽  
Virus Communities

Viruses shape microbial community structures, impacting metabolic pathways and influencing biogeochemical cycles. Despite their importance, the influence of biotic and abiotic factors on viral community structures across environmental gradients in soil is relatively unknown compared to their prokaryotic hosts. While soil pH strongly influences microbial community structure, it is unclear whether there is a similar influence on soil virus communities. In this study, prokaryotic and viral communities were characterized in soils sampled from the extremes of a long-term pH-manipulated soil gradient (pH 4.5 and 7.5), and viral populations were compared to those in a variety of soil ecosystems ranging in pH (4.0 - 7.5). Prokaryotic and viral community structure were significantly influenced by soil pH at the local scale. Of 1,910 viral operational taxonomic units (vOTUs), 99% were restricted to pH 4.5 or 7.5 soil only. These were compared in gene sharing networks of populations from six other European and North American soil systems. A selection of viral clusters from acidic and neutral pH soils were more associated with those from the local gradient pH 4.5 or 7.5 soils, respectively. Results indicate that as with prokaryotes, soil pH is a factor structuring viral communities at the local and global scale.

scholarly journals Wind Speed Affects Pollination Success in Blackberries

Sociobiology ◽  
2018 ◽  
Vol 65 (2) ◽  
pp. 225 ◽  
Author(s):  
Allison Young ◽  
Pilar Gomez-Ruiz ◽  
Janelle Pena ◽  
Hiromi Uno ◽  
Rodolfo Jaffé
Keyword(s):  
Wind Speed ◽  
Environmental Factors ◽  
Solar Radiation ◽  
Environmental Factor ◽  
Ecosystem Service ◽  
Natural Habitat ◽  
Wild Plants ◽  
Agricultural Crops ◽  
Pollination Success ◽  
General Consensus

Pollination of wild plants and agricultural crops is a vitally important ecosystem service. Many landscape and environmental factors influence the pollination success of crops, including distance from natural habitat, wind speed, and solar radiation. Although there is a general consensus that increasing distance from forest decreases pollination success, few studies have examined the influence of specific environmental factors. In this study, we examined which environmental factors influence the pollination success of blackberries (Rubus glaucus). We measured the number of fruitlets per berry, a proxy for pollination success, as well as the weight and sweetness of each berry. Our results indicate that number of fruitlets is positively correlated with wind speed, but number of unripe red berries per bush is negatively correlated with wind speed. In addition, sweetness increased with increasing numbers of red berries per bush but was lower when flowers and berries were present, though this result should be considered with caution due to methodological limitations. Our findings suggest that a little studied environmental factor, wind, has a large impact on the number of fruitlets in blackberries. Although our findings should be confirmed in other locations to draw broader conclusions, they suggest that producers should consider the effect of wind on blackberry yield to optimize blackberry production.

scholarly journals The human gut virome is highly diverse, stable and individual-specific

2019 ◽  
Author(s):  
Andrey N. Shkoporov ◽  
Adam G. Clooney ◽  
Thomas D.S. Sutton ◽  
Feargal J. Ryan ◽  
Karen M. Daly ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
De Novo ◽  
Temporal Stability ◽  
Human Gut ◽  
Vast Array ◽  
Bacterial Microbiome ◽  
Viral Communities ◽  
Metagenomic Study ◽  
Individual Specificity ◽  
Taxonomic Annotation

SummaryThe human gut contains a vast array of viruses, mostly bacteriophages. The majority remain uncharacterised and their roles in shaping the gut microbiome and in impacting on human health remain poorly understood. Here we performed a longitudinal focused metagenomic study of faecal bacteriophage populations in healthy adults. Our results reveal high temporal stability and individual specificity of bacteriophage consortia which correlates with the bacterial microbiome. We report the existence of a stable, numerically predominant individual-specific persistent personal virome. Clustering of bacteriophage genomes and de novo taxonomic annotation identified several groups of crAss-like and Microviridae bacteriophages as the most stable colonizers of the human gut. CRISPR-based host prediction highlighted connections between these stable viral communities and highly predominant gut bacterial taxa such as Bacteroides, Prevotella and Faecalibacterium. This study provides insights into the structure of the human gut virome and serves as an important baseline for hypothesis-driven research.

scholarly journals Initial virome characterization of the common cnidarian lab model Nematostella vectensis

2020 ◽  
Author(s):  
Magda Lewandowska ◽  
Yael Hazan ◽  
Yehu Moran
Keyword(s):  
Developmental Stages ◽  
De Novo ◽  
Artemia Salina ◽  
Model Organisms ◽  
Nematostella Vectensis ◽  
Virus Identification ◽  
Functional Studies ◽  
Powerful Approach ◽  
Viral Communities ◽  
Viral Sequences

AbstractThe role of viruses in forming a stable holobiont has been a subject of extensive research in the recent years. However, many emerging model organisms still lack any data on the composition of the associated viral communities. Here, we re-analyzed seven publicly available transcriptome datasets of the starlet sea anemone Nematostella vectensis, the most commonly used anthozoan lab model, and searched for viral sequences. We applied a straightforward, yet powerful approach of de novo assembly followed by homology-based virus identification and a multi-step, thorough taxonomic validation. The comparison of different lab populations of N. vectensis revealed the existence of the core virome composed of 21 viral sequences, present in all adult datasets. Unexpectedly, we observed almost complete lack of viruses in the samples from the early developmental stages which together with the identification of the viruses shared with the major source of the food in the lab, the brine shrimp Artemia salina, shed new light on the course of viral species acquisition in N. vectensis. Our study provides an initial, yet comprehensive insight into N. vectensis virome and sets the first foundation for functional studies of viruses and antiviral systems in this lab model cnidarian.

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