scholarly journals Dynamics in coastal RNA viruses and bacteriophages are driven by shifts in the community phylogenetic structure

2019 ◽  
Author(s):  
Julia A. Gustavsen ◽  
Curtis A. Suttle
Keyword(s):  
High Throughput Sequencing ◽  
Temporal Dynamics ◽  
Rna Viruses ◽  
Phylogenetic Signal ◽  
Marine Ecosystem ◽  
Marker Genes ◽  
Phylogenetic Groups ◽  
Eukaryotic Phytoplankton ◽  
Viral Marker ◽  
Viral Communities

AbstractMarine microbes including viruses are an essential part of the marine ecosystem that forms the base of the foodweb, and drives biogeochemical cycles. Marine viral communities display repeatable changes in abundance and community composition throughout time; however, whether these changes reflect shifts in dominance within evolutionarily related groups of viruses and their hosts is unexplored. To examine these dynamics, changes in the composition and phylogenetic makeup of two ecologically important groups of viruses, and their potential hosts, were sampled every two weeks for 13 months at a coastal site in British Columbia, Canada. Changes in the taxonomic composition within DNA bacteriophages related to T4-like viruses and marnavirus-like RNA viruses infecting eukaryotic phytoplankton, as well as bacteria and eukaryotes, were examined using amplicon sequencing of gene fragments encoding the major capsid protein (gp23), the RNA-dependent RNA polymerase (RdRp) and the 16S and 18S ribosomes, respectively. The results showed that for both viral marker genes, the dominant groups of phylogenetically-related viruses shifted over time and contained many transient taxa and few persistent taxa; yet, different community structures were observed in these different viral communities. Additionally, with strong lagged correlations between viral richness and community similarity of putative hosts, the results imply that viruses influence the composition of the host communities.ImportanceUsing high-throughput sequencing of coastal seawater collected every two weeks for one year, the dynamics of two groups of ecologically important groups of viruses were described in the context of their putative hosts and the environment. There was a large diversity of viruses and putative hosts in this study, and groups of phylogenetically-related viruses showed temporal dynamics in dominance. Examining the richness of viruses by phylogenetic groups showed different dynamics of either boom-bust or continued persistence. At the OTU-level, some members of these related groups persisted throughout time, while others were more ephemeral. These findings were put in context of potential quasispecies behaviour, and the dynamics of putative hosts. These results showed that temporal dynamics of viral communities have a phylogenetic signal which is important for understanding the ecology of these viruses since it elucidated one of the drivers of the community structure.

scholarly journals Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

2019 ◽  
Vol 116 (51) ◽  
pp. 25900-25908 ◽  
Author(s):  
Evan P. Starr ◽  
Erin E. Nuccio ◽  
Jennifer Pett-Ridge ◽  
Jillian F. Banfield ◽  
Mary K. Firestone
Keyword(s):  
Carbon Cycling ◽  
Temporal Dynamics ◽  
Rna Viruses ◽  
Marker Genes ◽  
Experimental Conditions ◽  
Time Resolved ◽  
Host Cell Death ◽  
Root Litter ◽  
Viral Communities ◽  
Microbial Systems

Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity wasNarnaviridaethat may parasitize fungi orLeviviridae, which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics byLeviviridaeand their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.

scholarly journals Role of phylogenetic structure in the dynamics of coastal viral assemblages

2021 ◽  
Author(s):  
Julia A. Gustavsen ◽  
Curtis A. Suttle
Keyword(s):  
High Throughput Sequencing ◽  
Environmental Changes ◽  
Marine Ecosystem ◽  
Marker Genes ◽  
Marine Microbes ◽  
Phylogenetic Structure ◽  
Genes Encoding ◽  
One Year ◽  
Rna And Dna

Marine microbes, including viruses, are an essential part of the marine ecosystem, forming the base of the foodweb and driving biogeochemical cycles. Within this system, the composition of viral assemblages changes markedly with time, with some of these changes being repeatable through time; however, the extent to which these dynamics are reflected within versus among evolutionarily-related groups of viruses is largely unexplored. To examine these dynamics, changes in the composition of two groups of ecologically important viruses and communities of their potential hosts were sampled every two weeks for 13 months at a coastal site in British Columbia, Canada. We sequenced two marker genes for viruses, the major capsid protein (gp23) of T4-like phages and their relatives, and the RNA-dependent RNA polymerase (RdRp) of marnavirus-like RNA viruses, as well as their bacterial and eukaryotic host communities, the genes encoding 16S and 18S ribosomal RNA (rRNA). There were strong lagged correlations between viral diversity and community similarity of putative hosts implying that the viruses influenced the composition of the host communities. The results showed that for both viral assemblages, the dominant clusters of phylogenetically-related viruses shifted over time and this was correlated with environmental changes. Viral clusters contained many ephemeral taxa and few persistent taxa, but within a viral assemblage the ephemeral and persistent taxa were closely related implying ecological dynamics within these clusters. Furthermore, these dynamics occurred in both the RNA and DNA viral assemblages surveyed, implying that this structure is common in natural viral assemblages. Importance Viruses are major agents of microbial mortality in marine systems; yet, little is known about changes in the composition of viral assemblages in relation to that of the microbial communities that they infect. Here, we sampled coastal seawater every two weeks for one year and used high-throughput sequencing of marker genes to follow changes in the composition of two groups of ecologically important viruses, as well as the communities of bacteria and protists that serve as their respective hosts. Different subsets of genetically related viruses dominated at different times. These results demonstrate that although the genetic composition of viral genotypes is highly dynamic temporally, for the most part the shuffling of genotypes occurs within a few clusters of phylogenetically related viruses. Thus, it appears that even in temperate coastal waters with large seasonal changes the highly dynamic shuffling of viral genotypes largely occurs within a few subsets of related individuals.

Spatial and temporal dynamics of Pacific capelin Mallotus catervarius in the Gulf of Alaska: implications for ecosystem-based fisheries management

2020 ◽  
Vol 637 ◽  
pp. 117-140 ◽  
Author(s):  
DW McGowan ◽  
ED Goldstein ◽  
ML Arimitsu ◽  
AL Deary ◽  
O Ormseth ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Marine Ecosystem ◽  
Gulf Of Alaska ◽  
Data Series ◽  
Limited Information ◽  
Important Species ◽  
Multiple Data ◽  
Spatial And Temporal Dynamics ◽  
Spawning Areas ◽  
Spatio Temporal

Pacific capelin Mallotus catervarius are planktivorous small pelagic fish that serve an intermediate trophic role in marine food webs. Due to the lack of a directed fishery or monitoring of capelin in the Northeast Pacific, limited information is available on their distribution and abundance, and how spatio-temporal fluctuations in capelin density affect their availability as prey. To provide information on life history, spatial patterns, and population dynamics of capelin in the Gulf of Alaska (GOA), we modeled distributions of spawning habitat and larval dispersal, and synthesized spatially indexed data from multiple independent sources from 1996 to 2016. Potential capelin spawning areas were broadly distributed across the GOA. Models of larval drift show the GOA’s advective circulation patterns disperse capelin larvae over the continental shelf and upper slope, indicating potential connections between spawning areas and observed offshore distributions that are influenced by the location and timing of spawning. Spatial overlap in composite distributions of larval and age-1+ fish was used to identify core areas where capelin consistently occur and concentrate. Capelin primarily occupy shelf waters near the Kodiak Archipelago, and are patchily distributed across the GOA shelf and inshore waters. Interannual variations in abundance along with spatio-temporal differences in density indicate that the availability of capelin to predators and monitoring surveys is highly variable in the GOA. We demonstrate that the limitations of individual data series can be compensated for by integrating multiple data sources to monitor fluctuations in distributions and abundance trends of an ecologically important species across a large marine ecosystem.

scholarly journals TASPERT: Target-Specific Reverse Transcript Pools to Improve HTS Plant Virus Diagnostics

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1223
Author(s):  
Andres S. Espindola ◽  
Daniela Sempertegui-Bayas ◽  
Danny F. Bravo-Padilla ◽  
Viviana Freire-Zapata ◽  
Francisco Ochoa-Corona ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Rna Viruses ◽  
Limit Of Detection ◽  
Cost Effective ◽  
Bioinformatic Analysis ◽  
Metagenomic Sample ◽  
Rrna Depletion ◽  
Virus Diagnostics ◽  
Management Preparation ◽  
Reverse Transcript

High-throughput sequencing (HTS) is becoming the new norm of diagnostics in plant quarantine settings. HTS can be used to detect, in theory, all pathogens present in any given sample. The technique’s success depends on various factors, including methods for sample management/preparation and suitable bioinformatic analysis. The Limit of Detection (LoD) of HTS for plant diagnostic tests can be higher than that of PCR, increasing the risk of false negatives in the case of low titer of the target pathogen. Several solutions have been suggested, particularly for RNA viruses, including rRNA depletion of the host, dsRNA, and siRNA extractions, which increase the relative pathogen titer in a metagenomic sample. However, these solutions are costly and time-consuming. Here we present a faster and cost-effective alternative method with lower HTS-LoD similar to or lower than PCR. The technique is called TArget-SPecific Reverse Transcript (TASPERT) pool. It relies on pathogen-specific reverse primers, targeting all RNA viruses of interest, pooled and used in double-stranded cDNA synthesis. These reverse primers enrich the sample for only pathogens of interest. Evidence on how TASPERT is significantly superior to oligodT, random 6-mer, and 20-mer in generating metagenomic libraries containing the pathogen of interest is presented in this proof of concept.

scholarly journals A three-dimensional view on biodiversity changes: spatial, temporal, and functional perspectives on fish communities in the Baltic Sea

2018 ◽  
Vol 75 (7) ◽  
pp. 2463-2475 ◽  
Author(s):  
Romain Frelat ◽  
Alessandro Orio ◽  
Michele Casini ◽  
Andreas Lehmann ◽  
Bastien Mérigot ◽  
...  
Keyword(s):  
Baltic Sea ◽  
Environmental Conditions ◽  
Environmental Changes ◽  
Temporal Dynamics ◽  
Marine Ecosystem ◽  
Fish Communities ◽  
The Baltic Sea ◽  
Functional Richness ◽  
Holistic Understanding ◽  
The Baltic

Abstract Fisheries and marine ecosystem-based management requires a holistic understanding of the dynamics of fish communities and their responses to changes in environmental conditions. Environmental conditions can simultaneously shape the spatial distribution and the temporal dynamics of a population, which together can trigger changes in the functional structure of communities. Here, we developed a comprehensive framework based on complementary multivariate statistical methodologies to simultaneously investigate the effects of environmental conditions on the spatial, temporal and functional dynamics of species assemblages. The framework is tested using survey data collected during more than 4000 fisheries hauls over the Baltic Sea between 2001 and 2016. The approach revealed the Baltic fish community to be structured into three sub-assemblages along a strong and temporally stable salinity gradient decreasing from West to the East. Additionally, we highlight a mismatch between species and functional richness associated with a lower functional redundancy in the Baltic Proper compared with other sub-areas, suggesting an ecosystem more susceptible to external pressures. Based on a large dataset of community data analysed in an innovative and comprehensive way, we could disentangle the effects of environmental changes on the structure of biotic communities—key information for the management and conservation of ecosystems.

scholarly journals Global diversity and biogeography of the Zostera marina mycobiome

2021 ◽  
Author(s):  
Cassandra L. Ettinger ◽  
Laura E. Vann ◽  
Jonathan A. Eisen
Keyword(s):  
Fungal Community ◽  
Community Assembly ◽  
Zostera Marina ◽  
High Throughput Sequencing ◽  
Marine Fungi ◽  
Marine Ecosystem ◽  
Fungal Community Composition ◽  
Functional Roles ◽  
Functional Guilds ◽  
The Many

Seagrasses are marine flowering plants that provide critical ecosystem services in coastal environments worldwide. Marine fungi are often overlooked in microbiome and seagrass studies, despite terrestrial fungi having critical functional roles as decomposers, pathogens or endophytes in global ecosystems. Here we characterize the distribution of fungi associated with the seagrass, Zostera marina, using leaves, roots, and rhizosphere sediment from 16 locations across its full biogeographic range. Using high throughput sequencing of the ribosomal internal transcribed spacer (ITS) region and 18S ribosomal RNA gene, we first measured fungal community composition and diversity. We then tested hypotheses of neutral community assembly theory and the degree to which deviations suggested amplicon sequence variants (ASVs) were plant-selected or dispersal-limited. Finally, we identified a core mycobiome and investigated the global distribution of differentially abundant ASVs. We found that the fungal community is significantly different between sites and that the leaf mycobiome follows a weak, but significant pattern of distance decay in the Pacific Ocean. Generally, there was evidence for both deterministic and stochastic factors contributing to community assembly of the mycobiome, with most taxa assembling through stochastic processes. The Z. marina core leaf and root mycobiomes were dominated by unclassified Sordariomycetes spp., unclassified Chytridiomycota lineages (including Lobulomycetaceae spp.), unclassified Capnodiales spp. and Saccharomyces sp. It is clear from the many unclassified fungal ASVs and fungal functional guilds, that knowledge of marine fungi is still rudimentary. Further studies characterizing seagrass-associated fungi are needed to understand the roles of these microorganisms generally and when associated with seagrasses. Importance Fungi have important functional roles when associated with land plants, yet very little is known about the roles of fungi associated with marine plants, like seagrasses. In this study, we report the results of a global effort to characterize the fungi associated with the seagrass, Zostera marina, across its full biogeographic range. Although we defined a putative global core fungal community, it is apparent from the many fungal sequences and predicted functional guilds that had no matches to existing databases, that general knowledge of seagrass-associated fungi and marine fungi generally is lacking. This work serves as an important foundational step towards future work investigating the functional ramifications of fungi in the marine ecosystem.

scholarly journals Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life

2017 ◽  
Author(s):  
Ross Mounce
Keyword(s):  
Large Scale ◽  
Phylogenetic Signal ◽  
Scientific Progress ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Phylogenetic Groups ◽  
Use Of Data ◽  
Wide Range ◽  
Cladistic Analyses

In this thesis I attempt to gather together a wide range of cladistic analyses of fossil and extant taxa representing a diverse array of phylogenetic groups. I use this data to quantitatively compare the effect of fossil taxa relative to extant taxa in terms of support for relationships, number of most parsimonious trees (MPTs) and leaf stability. In line with previous studies I find that the effects of fossil taxa are seldom different to extant taxa – although I highlight some interesting exceptions. I also use this data to compare the phylogenetic signal within vertebrate morphological data sets, by choosing to compare cranial data to postcranial data. Comparisons between molecular data and morphological data have been previously well explored, as have signals between different molecular loci. But comparative signal within morphological data sets is much less commonly characterized and certainly not across a wide array of clades. With this analysis I show that there are many studies in which the evidence provided by cranial data appears to be be significantly incongruent with the postcranial data – more than one would expect to see just by the effect of chance and noise alone. I devise and implement a modification to a rarely used measure of homoplasy that will hopefully encourage its wider usage. Previously it had some undesirable bias associated with the distribution of missing data in a dataset, but my modification controls for this. I also take an in-depth and extensive review of the ILD test, noting it is often misused or reported poorly, even in recent studies. Finally, in attempting to collect data and metadata on a large scale, I uncovered inefficiencies in the research publication system that obstruct re-use of data and scientific progress. I highlight the importance of replication and reproducibility – even simple reanalysis of high profile papers can turn up some very different results. Data is highly valuable and thus it must be retained and made available for further re-use to maximize the overall return on research investment.

scholarly journals Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Marius Welzel ◽  
Anja Lange ◽  
Dominik Heider ◽  
Michael Schwarz ◽  
Bernd Freisleben ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Workflow Management ◽  
Amplicon Sequencing ◽  
Version Control ◽  
Marker Genes ◽  
Sequencing Data ◽  
Taxonomic Assignment ◽  
Ecological Processes ◽  
Link Type ◽  
User Friendly

Abstract Background Sequencing of marker genes amplified from environmental samples, known as amplicon sequencing, allows us to resolve some of the hidden diversity and elucidate evolutionary relationships and ecological processes among complex microbial communities. The analysis of large numbers of samples at high sequencing depths generated by high throughput sequencing technologies requires efficient, flexible, and reproducible bioinformatics pipelines. Only a few existing workflows can be run in a user-friendly, scalable, and reproducible manner on different computing devices using an efficient workflow management system. Results We present Natrix, an open-source bioinformatics workflow for preprocessing raw amplicon sequencing data. The workflow contains all analysis steps from quality assessment, read assembly, dereplication, chimera detection, split-sample merging, sequence representative assignment (OTUs or ASVs) to the taxonomic assignment of sequence representatives. The workflow is written using Snakemake, a workflow management engine for developing data analysis workflows. In addition, Conda is used for version control. Thus, Snakemake ensures reproducibility and Conda offers version control of the utilized programs. The encapsulation of rules and their dependencies support hassle-free sharing of rules between workflows and easy adaptation and extension of existing workflows. Natrix is freely available on GitHub (https://github.com/MW55/Natrix) or as a Docker container on DockerHub (https://hub.docker.com/r/mw55/natrix). Conclusion Natrix is a user-friendly and highly extensible workflow for processing Illumina amplicon data.

scholarly journals Bacterial and Fungal Diversity Inside the Medieval Building Constructed with Sandstone Plates and Lime Mortar as an Example of the Microbial Colonization of a Nutrient-Limited Extreme Environment (Wawel Royal Castle, Krakow, Poland)

2019 ◽  
Vol 7 (10) ◽  
pp. 416 ◽  
Author(s):  
Dyda ◽  
Pyzik ◽  
Wilkojc ◽  
Kwiatkowska-Kopka ◽  
Sklodowska
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
High Throughput Sequencing ◽  
Extreme Environment ◽  
Microbial Colonization ◽  
Marker Genes ◽  
Lime Mortar ◽  
Preventive Actions ◽  
Important Challenge ◽  
Cultural Heritage Objects

Biodeterioration is a serious threat to cultural heritage objects and buildings. The deterioration of a given material often incurs irreparable losses in terms of uniqueness and historical value. Hence preventive actions should be taken. One important challenge is to identify microbes involved in the biodeterioration process. In this study, we analyzed the microbial diversity of an ancient architectonical structure of the Rotunda of Sts. Felix and Adauctus, which is a part of the Wawel Royal Castle located in Krakow, Poland. The Rotunda is unavailable to tourists and could be treated as an extreme habitat due to the low content of nutrients coming either from sandstone plates bound with lime mortar or air movement. Microbial diversity was analyzed with the use of the high-throughput sequencing of marker genes corresponding to fragments of 16S rDNA (for Bacteria) and ITS2 (internal transcribed spacer 2) (for Fungi). The results showed that the microbial community adhered to wall surfaces is, to a large extent, endemic. Furthermore, alongside many microorganisms that could be destructive to masonry and mortar (e. g., Pseudomonas, Aspergillus), there were also bacteria, such as species of genera Bacillus, Paenisporosarcina, and Amycolatopsis, that can positively affect wall surface properties by reducing the damage caused by the presence of other microorganisms. We also showed that airborne microorganisms probably have little impact on the biodeterioration process as their abundance in the microbial community adhered to the ancient walls was very low.

scholarly journals High-Throughput Sequencing Facilitates Discovery of New Plant Viruses in Poland

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 820
Author(s):  
Julia Minicka ◽  
Aleksandra Zarzyńska-Nowak ◽  
Daria Budzyńska ◽  
Natasza Borodynko-Filas ◽  
Beata Hasiów-Jaroszewska
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Plant Viruses ◽  
Yellow Mosaic Virus ◽  
Virus Species ◽  
Phylogenetic Groups ◽  
Accurate Identification ◽  
Detection And Identification ◽  
New Finding ◽  
Recent Occurrence

Viruses cause epidemics on all major crops of agronomic importance, and a timely and accurate identification is essential for control. High throughput sequencing (HTS) is a technology that allows the identification of all viruses without prior knowledge on the targeted pathogens. In this paper, we used HTS technique for the detection and identification of different viral species occurring in single and mixed infections in plants in Poland. We analysed various host plants representing different families. Within the 20 tested samples, we identified a total of 13 different virus species, including those whose presence has not been reported in Poland before: clover yellow mosaic virus (ClYMV) and melandrium yellow fleck virus (MYFV). Due to this new finding, the obtained sequences were compared with others retrieved from GenBank. In addition, cucurbit aphid-borne yellows virus (CABYV) was also detected, and due to the recent occurrence of this virus in Poland, a phylogenetic analysis of these new isolates was performed. The analysis revealed that CABYV population is highly diverse and the Polish isolates of CABYV belong to two different phylogenetic groups. Our results showed that HTS-based technology is a valuable diagnostic tool for the identification of different virus species originating from variable hosts, and can provide rapid information about the spectrum of plant viruses previously not detected in a region.

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