scholarly journals Seasonal Dynamics of Algae-Infecting Viruses and Their Inferred Interactions with Protists

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1043 ◽  
Author(s):  
Sandra Gran-Stadniczeñko ◽  
Anders K. Krabberød ◽  
Ruth-Anne Sandaa ◽  
Sheree Yau ◽  
Elianne Egge ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Phylogenetic Analyses ◽  
Future Studies ◽  
Algal Virus ◽  
Operational Taxonomic Units ◽  
Virus Diversity ◽  
Environmental Reference ◽  
Algal Host ◽  
Dsdna Viruses ◽  
Planktonic Communities

Viruses are a highly abundant, dynamic, and diverse component of planktonic communities that have key roles in marine ecosystems. We aimed to reveal the diversity and dynamics of marine large dsDNA viruses infecting algae in the Northern Skagerrak, South Norway through the year by metabarcoding, targeting the major capsid protein (MCP) and its correlation to protist diversity and dynamics. Metabarcoding results demonstrated a high diversity of algal viruses compared to previous metabarcoding surveys in Norwegian coastal waters. We obtained 313 putative algal virus operational taxonomic units (vOTUs), all classified by phylogenetic analyses to either the Phycodnaviridae or Mimiviridae families, most of them in clades without any cultured or environmental reference sequences. The viral community showed a clear temporal variation, with some vOTUs persisting for several months. The results indicate co-occurrences between abundant viruses and potential hosts during long periods. This study gives new insights into the virus-algal host dynamics and provides a baseline for future studies of algal virus diversity and temporal dynamics.

Freshwater Perkinsea: diversity, ecology and genomic information

2019 ◽  
Vol 42 (1) ◽  
pp. 3-17 ◽  
Author(s):  
M Jobard ◽  
I Wawrzyniak ◽  
G Bronner ◽  
D Marie ◽  
A Vellet ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Meta Analysis ◽  
Freshwater Ecosystems ◽  
Protein Coding ◽  
Lake Ecosystems ◽  
Operational Taxonomic Units ◽  
Clade 1 ◽  
Almost All ◽  
Parasitic Association

Abstract Studies on freshwater Perkinsea are scarce compared to their marine counterparts; they are therefore not well ecologically characterized. In this study, we investigated the diversity, distribution and ecological role of Perkinsea in freshwater ecosystems. Our approach included (1) the phylogenetic analyses of near full-length SSU and LSU sequences of freshwater Perkinsea, (2) a meta-analysis of public Perkinsea 18S ribosomal RNA gene sequences available from the freshwater environments (25 lakes, 4 rivers), (3) microscopic observations of Perkinsea associated with planktonic communities and (4) single amplified genome analysis. Whereas Perkinsea appear to be rare in river ecosystems (85 reads), they are found in almost all of the lakes studied. However, their diversity does vary considerably between lakes (from 0 to 2 463 Operational Taxonomic Units (OTUs)). Phylogenetic analysis showed that the Parvilucifera/Dinovorax/Snorkelia and Perkinsus/Xcellia/Gadixcellia clades resulted from an initial speciation event. This second clade is further split into well-supported, monophyletic groups, including a clade dominated by freshwater representatives, which is further structured into three distinct subclades: freshwater clade 1, freshwater clade 2 and a freshwater and brackish clade. The Perkinsea Single Amplified Genome (SAG) as well as most of the abundant Operational Taxonomic Units (OTUs) fall into freshwater clade 2. The tyramide signal amplification-fluorescent in situ hybridization method showed an internal association between Perkinsea and the colonial phytoplankton Sphaerocystis. The Single Amplified Genome (SAG) annotation contained 698 genes and gene ontology terms could be assigned to 486 protein-coding genes. Although the number of genes appears to be low (10.6% of the entire gene set assessed by BUSCO), the analysis of the proteome revealed some putative secreted virulence factors. This study showed a large distribution of Perkinsea across lake ecosystems and potential parasitic association with phytoplankton. However, further investigations are needed for a better knowledge on the role of these microorganisms in freshwater ecosystems.

scholarly journals Acquisition of intact polar lipids from the prymnesiophyte <i>Phaeocystis globosa</i> by its lytic virus PgV-07T

2014 ◽  
Vol 11 (1) ◽  
pp. 185-194 ◽  
Author(s):  
D. S. Maat ◽  
N. J. Bale ◽  
E. C. Hopmans ◽  
A.-C. Baudoux ◽  
J. S. Sinninghe Damsté ◽  
...  
Keyword(s):  
Viral Infection ◽  
Lower Proportion ◽  
Specific Lipids ◽  
Phaeocystis Globosa ◽  
Host Interactions ◽  
Algal Virus ◽  
Host Interaction ◽  
Betaine Lipids ◽  
Algal Host ◽  
Intact Polar Lipids

Abstract. Recent studies showed changes in phytoplankton lipid composition during viral infection and have indicated roles for specific lipids in the mechanisms of algal virus-host interaction. To investigate the generality of these findings and obtain a better understanding of the allocation of specific lipids to viruses, we studied the intact polar lipid (IPL) composition of virally infected and non-infected cultures of the prymnesiophyte Phaeocystis globosa G(A) and its lytic virus PgV-07T. The P. globosa IPL composition was relatively stable over a diel cycle and not strongly affected by viral infection. Glycolipids, phospholipids and betaine lipids were present in both the host and virus, although specific groups such as the diacylglyceryl-hydroxymethyltrimethyl-β-alanines and the sulfoquinovosyldiacylglycerols, were present in a lower proportion or were not detected in the virus. Viral glycosphingolipids (vGSLs), which have been shown to play a role in the infection strategy of the virus EhV-86, infecting the prymnesiophyte Emiliania huxleyi CCMP374, were not encountered. Our results show that the involvement of lipids in virus–algal host interactions can be very different amongst virus–algal host systems.

scholarly journals Novel Cell-Virus-Virophage Tripartite Infection Systems Discovered in the Freshwater Lake Dishui Lake in Shanghai, China

2020 ◽  
Vol 94 (11) ◽  
Author(s):  
Shengzhong Xu ◽  
Liang Zhou ◽  
Xiaosha Liang ◽  
Yifan Zhou ◽  
Hao Chen ◽  
...  
Keyword(s):  
Green Algae ◽  
Green Alga ◽  
Phylogenetic Analyses ◽  
Freshwater Lake ◽  
Metagenomic Data ◽  
Data Sets ◽  
Data Set ◽  
Dna Viruses ◽  
Oligonucleotide Frequency ◽  
Dsdna Viruses

ABSTRACT Virophages are small parasitic double-stranded DNA (dsDNA) viruses of giant dsDNA viruses infecting unicellular eukaryotes. Except for a few isolated virophages characterized by parasitization mechanisms, features of virophages discovered in metagenomic data sets remain largely unknown. Here, the complete genomes of seven virophages (26.6 to 31.5 kbp) and four large DNA viruses (190.4 to 392.5 kbp) that coexist in the freshwater lake Dishui Lake, Shanghai, China, have been identified based on environmental metagenomic investigation. Both genomic and phylogenetic analyses indicate that Dishui Lake virophages (DSLVs) are closely related to each other and to other lake virophages, and Dishui Lake large DNA viruses are affiliated with the micro-green alga-infecting Prasinovirus of the Phycodnaviridae (named Dishui Lake phycodnaviruses [DSLPVs]) and protist (protozoan and alga)-infecting Mimiviridae (named Dishui Lake large alga virus [DSLLAV]). The DSLVs possess more genes with closer homology to that of large alga viruses than to that of giant protozoan viruses. Furthermore, the DSLVs are strongly associated with large green alga viruses, including DSLPV4 and DSLLAV1, based on codon usage as well as oligonucleotide frequency and correlation analyses. Surprisingly, a nonhomologous CRISPR-Cas like system is found in DSLLAV1, which appears to protect DSLLAV1 from the parasitization of DSLV5 and DSLV8. These results suggest that novel cell-virus-virophage (CVv) tripartite infection systems of green algae, large green alga virus (Phycodnaviridae- and Mimiviridae-related), and virophage exist in Dishui Lake, which will contribute to further deep investigations of the evolutionary interaction of virophages and large alga viruses as well as of the essential roles that the CVv plays in the ecology of algae. IMPORTANCE Virophages are small parasitizing viruses of large/giant viruses. To our knowledge, the few isolated virophages all parasitize giant protozoan viruses (Mimiviridae) for propagation and form a tripartite infection system with hosts, here named the cell-virus-virophage (CVv) system. However, the CVv system remains largely unknown in environmental metagenomic data sets. In this study, we systematically investigated the metagenomic data set from the freshwater lake Dishui Lake, Shanghai, China. Consequently, four novel large alga viruses and seven virophages were discovered to coexist in Dishui Lake. Surprisingly, a novel CVv tripartite infection system comprising green algae, large green alga viruses (Phycodnaviridae- and Mimiviridae-related), and virophages was identified based on genetic link, genomic signature, and CRISPR system analyses. Meanwhile, a nonhomologous CRISPR-like system was found in Dishui Lake large alga viruses, which appears to protect the virus host from the infection of Dishui Lake virophages (DSLVs). These findings are critical to give insight into the potential significance of CVv in global evolution and ecology.

Analysis of the genus Sunamphitoe Spence Bate, 1857 (Amphipoda: Ampithoidae) with descriptions of eight new species

Zootaxa ◽  
2017 ◽  
Vol 4269 (3) ◽  
pp. 301 ◽  
Author(s):  
RACHAEL A. PEART
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
New Zealand ◽  
Phylogenetic Analyses ◽  
Senior Synonym ◽  
The Status ◽  
Molecular Phylogenetic ◽  
Algal Host

Sunamphitoe Spence Bate, 1857 is one of several ampithoid amphipod genera to be reasonably specific to its algal host. Sunamphitoe was recently shown to be a senior synonym of Peramphithoe Conlan & Bousfield, 1982 by both morphological and molecular phylogenetic analyses that included selected exemplars of both putative genera. Phylogenetic analysis considering all species of Sunamphitoe herein corroborates the validity of this synonymy and also delineates several morphological groups within the genus. Eight new species are descibed herein, Sunamphitoe angrox sp. nov., S. batavia sp. nov., S. dampierensis sp. nov., S. jonathani sp. nov., S. lehae sp. nov., S. mixtura sp. nov., S. naturaliste sp. nov., and S. stevesmithi sp. nov., all from Australia and New Zealand; the status of the problematic New Zealand species, Sunamphitoe aorangi is resolved.

scholarly journals Quantitative phosphoproteomics unveils temporal dynamics of thrombin signaling in human endothelial cells

Blood ◽  
2014 ◽  
Vol 123 (12) ◽  
pp. e22-e36 ◽  
Author(s):  
Maartje van den Biggelaar ◽  
Juan Ramon Hernández-Fernaud ◽  
Bart L. van den Eshof ◽  
Lisa J. Neilson ◽  
Alexander B. Meijer ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Temporal Dynamics ◽  
Human Endothelial Cells ◽  
Time Resolved ◽  
Future Studies ◽  
Key Points ◽  
First Time ◽  
Quantitative Phosphoproteomics

Key Points This is the first time-resolved quantitative phosphoproteomic analysis of thrombin signaling in human endothelial cells. We provide 2224 phosphosites regulated by thrombin as a unique resource for future studies on thrombin and PAR signaling.

Phylogeny of the Parmeliaceae–DNA Data Versus Morphological Data

1998 ◽  
Vol 30 (4-5) ◽  
pp. 463-472 ◽  
Author(s):  
Jan-Eric Mattsson ◽  
Mats Wedin
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
Slight Variation ◽  
Hypogymnia Physodes ◽  
Nuclear Rdna ◽  
Future Studies ◽  
The Family ◽  
Rdna Sequence Data ◽  
Close Relationship

AbstractIn order to identify monophyletic groups within the family Parmeliaceae, eleven taxa (Bryoria capillaris, Cetraria islandica, Evernia pruniastri, Hypogymnia physodes, Parmelia saxatilis, Platismatia glauca, Pleurosticta acetabulum, Usneaflorida, Vulpicida juniperina, V. pinastri, and Xanthoparmelia conspersa) were studied using newly produced nuclear rDNA sequence data from the ITS and 5·8S regions. The resulting evolutionary hypothesis was compared with results from previous phylogenetic analyses based on anatomy, morphology, and chemistry. The outcome of this comparison does not support the earlier proposed phylogenies but is not stable enough for identifying monophyletic groups, with one exception. The results indicate a close relationship between Cetraria and Vulpicida, which is contradictory to previous published analyses. The variation in ascus structures in the Parmeliaceae is discussed and it is questioned whether the earlier distinguished ‘ forms ’ of ascus types represent synapomorphies, if they are based on poorly supported analyses, or if they are exaggerations of relatively slight variation in shape. Further interpretations of the results are discussed and areas of future studies based on DNA-data are suggested.

Zooplankton in Advective Environments: The Hudson River Community and a Comparative Analysis

1992 ◽  
Vol 49 (5) ◽  
pp. 1060-1069 ◽  
Author(s):  
Michael L. Pace ◽  
Stuart E. G. Findlay ◽  
David Lints
Keyword(s):  
Spatial Distribution ◽  
Dominant Species ◽  
Temporal Dynamics ◽  
Hudson River ◽  
Zooplankton Biomass ◽  
Spatial Distributions ◽  
Water Residence Time ◽  
Advective Transport ◽  
Lotic Environments ◽  
Planktonic Communities

The temporal dynamics and spatial distributions of zooplankton in the tidal freshwater portion of the Hudson River were studied over a 3-yr period. We tested the hypothesis that advective transport regulates zooplankton biomass in the Hudson and in lakes, estuaries, and rivers for which we have published values. In the Hudson, zooplankton biomass was negatively correlated with discharge over the entire season (P < 0.0001) as well as during the warmer period of the year (P = 0.007) when biomass was greatest. The spatial distribution of zooplankton over 160-km transects was heterogeneous. Downstream changes in the abundance of a dominant species, Bosmina longirostris, indicate that certain areas of the river support net population growth whereas other areas are population sinks. We infer that zooplankton biomass in the Hudson is a function of the balance between reproduction determined by resources and losses due to advection. Zooplankton biomass differs among lakes, estuaries, and rivers in a manner consistent with the differences in water residence time. Biomass is highest in lakes, lower in saline estuaries and tidal rivers, and lowest in rivers. Advective losses appear to be important in explaining differences between planktonic communities in lentic and lotic environments.

scholarly journals Acquisition of intact polar lipids from the Prymnesiophyte <i>Phaeocystis globosa</i> by its lytic virus PgV-07T

2013 ◽  
Vol 10 (7) ◽  
pp. 11705-11727 ◽  
Author(s):  
D. S. Maat ◽  
N. J. Bale ◽  
E. C. Hopmans ◽  
A.-C. Baudoux ◽  
J. S. Sinninghe Damsté ◽  
...  
Keyword(s):  
Viral Infection ◽  
Lower Proportion ◽  
Specific Lipids ◽  
Phaeocystis Globosa ◽  
Host Interactions ◽  
Algal Virus ◽  
Host Interaction ◽  
Betaine Lipids ◽  
Algal Host ◽  
Intact Polar Lipids

Abstract. Recent studies showed changes in phytoplankton lipid composition during viral infection and have indicated roles for specific lipids in the mechanisms of algal virus-host interaction. To investigate the generality of these findings and obtain a better understanding of the allocation of specific lipids to viruses, we studied the intact polar lipid (IPL) composition of virally infected and non-infected cultures of the Prymnesiophyte Phaeocystis globosa G(A) and its lytic virus PgV-07T. The P. globosa IPL composition was relatively stable over a diel cycle and not strongly affected by viral infection. Glycolipids, phospholipids and betaine lipids were present in both the host and virus, although specific groups such as the diacylglyceryl-hydroxymethyltrimethyl-β-alanines and the sulfoquinovosyldiacylglycerols, were present in a lower proportion or were not detected in the virus. Viral glycosphingolipids (vGSLs), which have been shown to play a role in the infection strategy of the virus EhV-86, infecting the Prymnesiophyte Emiliania huxleyi CCMP374, were not encountered. Our results show that the involvement of lipids in virus-algal host interactions can be very different amongst virus-algal host systems.

scholarly journals Evaluating species in Botryosphaeriales

2021 ◽  
Author(s):  
W. Zhang ◽  
J.Z. Groenewald ◽  
L. Lombard ◽  
R.K. Schumacher ◽  
A.J.L. Phillips ◽  
...  
Keyword(s):  
South Africa ◽  
Woody Plants ◽  
Phylogenetic Analyses ◽  
Culture Collection ◽  
Morphological Data ◽  
Culture Collections ◽  
Future Studies ◽  
The Past ◽  
Wide Range ◽  
Solid Foundation

The Botryosphaeriales (Dothideomycetes) includes numerous endophytic, saprobic, and plant pathogenic species associated with a wide range of symptoms, most commonly on woody plants. In a recent phylogenetic treatment of 499 isolates in the culture collection (CBS) of the Westerdijk Institute, we evaluated the families and genera accommodated in this order of important fungi. The present study presents multigene phylogenetic analyses for an additional 230 isolates, using ITS, tef1, tub2, LSU and rpb2 loci, in combination with morphological data. Based on these data, 58 species are reduced to synonymy, and eight novel species are described. They include Diplodia afrocarpi (Afrocarpus, South Africa), Dothiorella diospyricola (Diospyros, South Africa), Lasiodiplodia acaciae (Acacia, Indonesia), Neofusicoccum podocarpi (Podocarpus, South Africa), N. rapaneae (Rapanea, South Africa), Phaeobotryon ulmi (Ulmus, Germany), Saccharata grevilleae (Grevillea, Australia) and S. hakeiphila (Hakea, Australia). The results have clarified the identity of numerous isolates that lacked Latin binomials or had been deposited under incorrect names in the CBS collection in the past. They also provide a solid foundation for more in-depth future studies on taxa in the order. Sequences of the tef1, tub2 and rpb2 genes proved to be the most reliable markers. At the species level, results showed that the most informative genes were inconsistent, but that a combination of four candidate barcodes (ITS, tef1, tub2 and rpb2) provided reliable resolution. Furthermore, given the large number of additional isolates included in this study, and newly generated multigene DNA datasets, several species could also be reduced to synonymy. The study illustrates the value of reassessing the identity of older collections in culture collections utilising modern taxonomic frameworks and methods.

scholarly journals A completely resolved phylogenetic tree of British spiders (Arachnida: Araneae)

2021 ◽  
Vol 46 ◽  
pp. 1-51
Author(s):  
Rainer Breitling
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationships ◽  
British Isles ◽  
Future Studies ◽  
Starting Point ◽  
Geographical Scale ◽  
Phylogenetic Hypotheses

The recent accumulation of increasingly densely sampled phylogenetic analyses of spiders has greatly advanced our understanding of evolutionary relationships within this group. Here, this diverse literature is reviewed and combined with earlier morphological analyses in an attempt to reconstruct the first fully resolved phylogeny for the spider fauna of the British Isles. The resulting tree highlights parts of the group where data are still too limited for a confident assessment of relationships, proposes a number of deviations from previously suggested phylogenetic hypotheses, and can serve as a framework for evolutionary and ecological interpretations of the biology of British spiders, as well as a starting point for future studies on a larger geographical scale.

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