scholarly journals Ubiquity, Diversity, and Genomic Complexity of Cyanophages in Freshwater Environments

Proceedings ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 105
Author(s):  
Qi-Ya Zhang
Keyword(s):  
Morphological Diversity ◽  
Freshwater Ecosystems ◽  
Open Reading Frames ◽  
Morphological Observation ◽  
Filamentous Cyanobacterium ◽  
Putative Orfs ◽  
Virus Like Particles ◽  
Blue Green Algae ◽  
Short Tail ◽  
Freshwater Environments

Cyanophages are viruses that infect cyanobacteria (also known as blue-green algae) and are ubiquitious in marine and freshwater environments. In recent years, freshwater cyanophages have attracted more attention because they can affect global freshwater ecosystems. The spatial distribution and morphological diversity of cyanophage populations were examined in Lake Donghu with three trophic regions: hypertrophic, eutrophic, and mesotrophic regions. The surprisingly high viral abundance (ranging from 108 to 109 phage mL−1) and morphological diversity were detected. Most of them have tails and belong to the families Siphoviridae, Myoviridae, and Podoviridae. Various morphotypes were observed, such as prolate-headed virus-like particles and lemon-shaped virus-like particles. In addition, some cyanophages were studied by virological experiments and whole-genome analyses, combined with morphological observation. For example, three cyanophages were isolated and their whole genomes were sequenced. Contractile tail myonophage MaMV-DC infects bloom-forming cyanobacterium Microcystis aeruginosa. Tailless cyanophage Planktothrix agardhii virus isolated from Lake Donghu (PaV-LD) infects filamentous cyanobacterium. Short-tail podovirus A-4L can infect the model cyanobacterium Anabaena sp. strain PCC 7120. The MaMV-DC genome contains 169,223 bp encoding 170 putative open reading frames (ORFs). The PaV-LD genome posseses 95,299 bp encoding 142 putative ORFs. The genome of short-tail podovirus A-4L has 41,750 bp encoding 38 putative ORFs. There are significant differences in their genomic size and encoded tail proteins, but all three cyanophages contain genes that are not commonly found in phages. By studying the vast biodiversity of viruses in freshwater environments, these novel findings of cyanophages broaden our insights, and allow us to gain more useful knowledge about the global impact of these viruses in freshwater ecosystems.

scholarly journals Knowledge about Microplastic in Mediterranean Tributary River Ecosystems: Lack of Data and Research Needs on Such a Crucial Marine Pollution Source

2020 ◽  
Vol 8 (3) ◽  
pp. 216 ◽  
Author(s):  
Cristiana Guerranti ◽  
Guido Perra ◽  
Tania Martellini ◽  
Luisa Giari ◽  
Alessandra Cincinelli
Keyword(s):  
Marine Pollution ◽  
Distribution Patterns ◽  
Pollution Source ◽  
Freshwater Ecosystems ◽  
Abundance Distribution ◽  
Plastic Pollution ◽  
Marine Systems ◽  
Final Destination ◽  
Lack Of Information ◽  
Freshwater Environments

Plastic debris occurring in freshwater environments, which can either come from the surrounding terrestrial areas or transported from upstream, has been identified as one of the main sources and routes of plastic pollution in marine systems. The ocean is the final destination of land- based microplastic sources, but compared to marine environments, the occurrence and effects of microplastics in freshwater ecosystems remain largely unknown. A thorough examination of scientific literature on abundance, distribution patterns, and characteristics of microplastics in freshwater environments in Mediterranean tributary rivers has shown a substantial lack of information and the need to apply adequate and uniform measurement methods.

scholarly journals Odonata (Insecta) from Nova Xavantina, Mato Grosso, Central Brazil: Information on species distribution and new records

Check List ◽  
2014 ◽  
Vol 10 (2) ◽  
pp. 299 ◽  
Author(s):  
Lenize Batista Calvão ◽  
Paulo De Marco Júnior ◽  
Joana Darc Batista
Keyword(s):  
Species Distribution ◽  
New Records ◽  
Freshwater Ecosystems ◽  
Species List ◽  
Mato Grosso ◽  
Central Brazil ◽  
Fixed Area ◽  
Freshwater Environments ◽  
Tropical Freshwater

Odonates are found in all freshwater environments, and are specially species rich in tropical freshwater ecosystems. Currently about 800 odonate species are known to Brazil, but only 29% of the Brazil territory have been surveyed for this group. Here we provide a species list with information on distribution and new records for Odonata in nine streams in Nova Xavantina, Mato Grosso, Central Brazil. We used the scan procedure with a fixed area for three days in each stream between 10:00 and 14:00h. We collected 1038 dragonfly specimens belonging to 67 species, which represents 8% of the known Brazil odonate fauna. Additionally, five new records for the study area are presented.

scholarly journals Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostocsp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Caroline Chénard ◽  
Jennifer F. Wirth ◽  
Curtis A. Suttle
Keyword(s):  
Dna Polymerase ◽  
Evolutionary History ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Filamentous Cyanobacterium ◽  
Filamentous Cyanobacteria ◽  
Evolutionary Trajectory ◽  
Crispr Array ◽  
History Of ◽  
Pcc 7120

ABSTRACT  Here we present the first genomic characterization of viruses infectingNostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infectNostocsp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids ofCyanothecesp. strain PCC 7424,Nostocsp. strain PCC 7120, andAnabaena variabilisATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome ofNostocsp. strain PCC 7524. TheNostoccyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages.IMPORTANCEFilamentous cyanobacteria belonging to the genusNostocare widespread and ecologically important in freshwater, yet little is known about the genomic content of their viruses. Here we report the first genomic analysis of cyanophages infecting filamentous freshwater cyanobacteria, revealing that their gene content is unlike that of other cyanophages. In addition to sharing many gene homologues with freshwater cyanobacteria, cyanophage N-1 encodes a CRISPR array and expresses it upon infection. Also, both viruses contain a DNA polymerase B-encoding gene with high similarity to genes found in proteobacterial plasmids of filamentous cyanobacteria. The observation that phages can acquire CRISPRs from their hosts suggests that phages can also move them among hosts, thereby conferring resistance to competing phages. The presence in these cyanophages of CRISPR and DNA polymerase B sequences, as well as a suite of other host-related genes, illustrates the long and complex evolutionary history of these viruses and their hosts.

scholarly journals A Novel Type of Polyhedral Viruses Infecting Hyperthermophilic Archaea

2017 ◽  
Vol 91 (13) ◽  
Author(s):  
Ying Liu ◽  
Sonoko Ishino ◽  
Yoshizumi Ishino ◽  
Gérard Pehau-Arnaudet ◽  
Mart Krupovic ◽  
...  
Keyword(s):  
Genetic Material ◽  
Morphological Diversity ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Host Recognition ◽  
Hyperthermophilic Archaea ◽  
Virion Protein ◽  
Content Type ◽  
Polyhedral Particles ◽  
Isolation And Characterization

ABSTRACT Encapsidation of genetic material into polyhedral particles is one of the most common structural solutions employed by viruses infecting hosts in all three domains of life. Here, we describe a new virus of hyperthermophilic archaea, Sulfolobus polyhedral virus 1 (SPV1), which condenses its circular double-stranded DNA genome in a manner not previously observed for other known viruses. The genome complexed with virion proteins is wound up sinusoidally into a spherical coil which is surrounded by an envelope and further encased by an outer polyhedral capsid apparently composed of the 20-kDa virion protein. Lipids selectively acquired from the pool of host lipids are integral constituents of the virion. None of the major virion proteins of SPV1 show similarity to structural proteins of known viruses. However, minor structural proteins, which are predicted to mediate host recognition, are shared with other hyperthermophilic archaeal viruses infecting members of the order Sulfolobales. The SPV1 genome consists of 20,222 bp and contains 45 open reading frames, only one-fifth of which could be functionally annotated. IMPORTANCE Viruses infecting hyperthermophilic archaea display a remarkable morphological diversity, often presenting architectural solutions not employed by known viruses of bacteria and eukaryotes. Here we present the isolation and characterization of Sulfolobus polyhedral virus 1, which condenses its genome into a unique spherical coil. Due to the original genomic and architectural features of SPV1, the virus should be considered a representative of a new viral family, “Portogloboviridae.”

scholarly journals Clustered Genes Required for the Synthesis of Heterocyst Envelope Polysaccharide in Anabaena sp. Strain PCC 7120

2005 ◽  
Vol 187 (3) ◽  
pp. 1114-1123 ◽  
Author(s):  
Guocun Huang ◽  
Qing Fan ◽  
Sigal Lechno-Yossef ◽  
Elizabeth Wojciuch ◽  
C. Peter Wolk ◽  
...  
Keyword(s):  
Open Reading Frames ◽  
Filamentous Cyanobacterium ◽  
Anabaena Sp ◽  
Pcc 7120 ◽  
Polysaccharide Layer ◽  
Reading Frames

ABSTRACT As demonstrated with alr2835 (hepA) and alr2834 (hepC) mutants, heterocysts of Anabaena sp. strain PCC 7120, a filamentous cyanobacterium, must have an envelope polysaccharide layer (the Hep+ phenotype) to fix dinitrogen in an oxygen-containing milieu (the Fox+ phenotype). Transpositions presumptively responsible for a Fox− phenotype were localized in open reading frames (ORFs) near hepA and hepC. A mutation in each of nine of these ORFs was complemented by a clone bearing only that single, intact ORF. Heterocysts of the nine mutants were found to lack an envelope polysaccharide layer. Complementation of mutations in alr2832 and alr2840 may have resulted from recombination. However, alr2825, alr2827, alr2831, alr2833, alr2837, alr2839, and alr2841, like hepA and hepC, are required for a Hep+ Fox+ phenotype.

Remarkable morphological diversity of viruses and virus-like particles in hot terrestrial environments

2002 ◽  
Vol 147 (12) ◽  
pp. 2419-2429 ◽  
Author(s):  
R. Rachel ◽  
M. Bettstetter ◽  
B. P. Hedlund ◽  
M. Häring ◽  
A. Kessler ◽  
...  
Keyword(s):  
Morphological Diversity ◽  
Virus Like Particles ◽  
Terrestrial Environments

scholarly journals The zooplankton biodiversity of some freshwater environments in Parnaíba basin (Piauí, Northeastern Brazil)

2013 ◽  
Vol 73 (1) ◽  
pp. 125-134 ◽  
Author(s):  
JDN. Paranhos ◽  
VLS. Almeida ◽  
JP. Silva Filho ◽  
MN. Paranaguá ◽  
M. Melo Júnior ◽  
...  
Keyword(s):  
Grey Literature ◽  
Course Completion ◽  
Freshwater Ecosystems ◽  
The State ◽  
Northeastern Brazil ◽  
The Subject ◽  
Total Fauna ◽  
New Occurrences ◽  
Freshwater Environments ◽  
Parnaíba Basin

The plankton fauna of the state of Piauí, Northeastern Brazil, especially in the Parnaíba basin, is still poorly known; the results of most studies of the subject have not been published and can only be found in grey literature (unpublished scientific works), such as course completion work and consulting reports. Thus, this paper presents data from samples taken recently from different water bodies in Piauí and represents the second study to be published on the region's zooplankton since the pioneering work of Spandl (1926). A total of 38 species were recorded, including 23 new occurrences of rotifers, 10 of cladocerans and 2 of copepods for the state of Piauí. The greatest richness was observed for the rotifers, of which the genus Brachionus must be highlighted, especially at the Joana reservoir. Among the crustaceans, the greatest richness was observed at the Bezerra reservoir, where cladocerans of the genus Bosmina were prominent. The rotifers Brachionus havanaensis Rousselet, 1911 and Filinia longiseta (Ehrenberg, 1834); the cladocerans Diaphanosoma spinulosum Herbst, 1967 and Moina micrura Kurz, 1874; and the copepods Notodiaptomus cearensis Wright, 1936 and Thermocyclops decipiens Kiefer, 1927 occurred in all or in most environments in which the respective groups were studied. The results presented here expand the taxonomic list of zooplankton for the state of Piauí, including a total fauna of 30 species of rotifers, 15 of cladocerans and 3 of copepods. The zooplankton richness was considered low in the studied reservoirs compared to other freshwater ecosystems from Northeastern Brazil; however, the few studies developed in the Parnaíba basin suggest that the diversity for these organisms should be higher.

scholarly journals Analysis of transcripts from predicted open reading frames of Musca domestica salivary gland hypertrophy virus

2009 ◽  
Vol 90 (5) ◽  
pp. 1270-1280 ◽  
Author(s):  
Tamer Z. Salem ◽  
Alejandra Garcia-Maruniak ◽  
Verena-U. Lietze ◽  
James E. Maruniak ◽  
Drion G. Boucias
Keyword(s):  
Salivary Gland ◽  
Musca Domestica ◽  
Direct Sequencing ◽  
Open Reading Frames ◽  
Rt Pcr ◽  
Putative Orfs ◽  
Single Transcript ◽  
Rapid Amplification ◽  
Salivary Gland Hypertrophy ◽  
Salivary Gland Hypertrophy Virus

The Musca domestica salivary gland hypertrophy virus (MdSGHV) is a large dsDNA virus that infects and sterilizes adult houseflies. The transcriptome of this newly described virus was analysed by rapid amplification of cDNA 3′-ends (3′-RACE) and RT-PCR. Direct sequencing of 3′-RACE products revealed 78 poly(A) transcripts containing 95 of the 108 putative ORFs. An additional six ORFs not amplified by 3′-RACE were detected by RT-PCR. Only seven of the 108 putative ORFs were not amplified by either 3′-RACE or RT-PCR. A series of 5′-RACE reactions were conducted on selected ORFs that were identified by 3′-RACE to be transcribed in tandem (tandem transcripts). In the majority of cases, the downstream ORFs were detected as single transcripts as well as components of the tandem transcripts, whereas the upstream ORFs were found only in tandem transcripts. The only exception was the upstream ORF MdSGHV084, which was differentially transcribed as a single transcript at 1 and 2 days post-infection (days p.i.) and as a tandem transcript (MdSGHV084/085) at 2 days p.i. Transcriptome analysis of MdSGHV detected splicing in the 3′ untranslated region (3′-UTR) and extensive heterogeneity in the polyadenylation signals and cleavage sites. In addition, 23 overlapping antisense transcripts were found. In conclusion, sequencing the 3′-RACE products without cloning served as an alternative approach to detect both 3′-UTRs and transcript variants of this large DNA virus.

scholarly journals Global geographic variability in freshwater methane hydrogen isotope ratios and its implications for emissions source apportionment and microbial biogeochemistry

2020 ◽  
Author(s):  
Peter M. J. Douglas ◽  
Emerald Stratigopoulos ◽  
Jenny Park ◽  
Dawson Phan
Keyword(s):  
Hydrogen Isotope ◽  
Environmental Water ◽  
Freshwater Ecosystems ◽  
Rice Paddies ◽  
Source Attribution ◽  
Atmospheric Measurements ◽  
Ch4 Emissions ◽  
Spatially Resolved ◽  
Hydrogenotrophic Methanogenesis ◽  
Freshwater Environments

Abstract. There is growing interest in developing spatially resolved methane (CH4) isotopic source signatures to aid in geographic source attribution of CH4 emissions. CH4 hydrogen isotope measurements (δ2H-CH4) have the potential to be a powerful tool for spatial resolution of CH4 emissions from freshwater environments, as well as other microbial sources. This is because microbial δ2H-CH4 values are partially dependent on the δ2H of environmental water (δ2H-H2O), which exhibits large and well-characterized spatial variability globally. We compiled a comprehensive global dataset of paired CH4 δ2H and δ13C measurements from freshwater environments, including wetlands, inland waters, and rice paddies, comprising a total of 131 different ecosystems, and compared these with measurements and estimates of δ2H-H2O. We found that the estimated δ2H of annual precipitation (δ2Hp) explained approximately 35 % of the observed variation in δ2H-CH4, and that the relationship between δ2H-CH4 and δ2Hp led to significant differences in the distribution of freshwater δ2H-CH4 between the northern high latitudes (60–90º N) relative to other global regions. Residual variability in δ2H-CH4 is partially explained by differences in the dominant methanogenic pathway and CH4 oxidation, as inferred from carbon isotope fractionation between CH4 and carbon dioxide (αC). Our results imply that hydrogenotrophic methanogenesis is characterized by a steeper slope of δ2H-CH4 vs. δ2Hp than acetoclastic methanogenesis, a pattern that is consistent with previous predictions. Biogeochemical sources of variability in δ2H-CH4 are reflected in apparent differences between different freshwater ecosystems, with relatively high values in rivers and bogs, and low values in fens and rice paddies, although more data is needed to verify whether these differences are significant. To estimate how changes in the spatial distribution of freshwater emissions would influence global atmospheric CH4 isotopic measurements, we developed a bottom-up mixing model of global CH4 δ2H and δ13C sources, including spatially resolved signatures for freshwater CH4 sources. This model implies that changes in high-latitude freshwater CH4 emissions would have an especially strong influence on global source δ2H-CH4. We estimate that global CH4 emissions sources have a combined δ2H value of −277±8 ‰, which is consistent with top-down estimates based on atmospheric measurements. In contrast our estimated δ13C value of −56.4±1.4 ‰ is not consistent with atmospheric measurements, suggesting possible errors in either emissions inventories or estimates of sink fluxes and isotopic fractionations. Overall our results emphasize the value of δ2H-CH4 measurements to help constrain atmospheric CH4 budgets.

Sign in / Sign up

Export Citation Format

Share Document