Newly identified HMO-2011-type phages reveal genomic diversity and biogeographic distributions of this marine viral group

AbstractViruses play critical roles in influencing biogeochemical cycles and adjusting host mortality, population structure, physiology, and evolution in the ocean. Marine viral communities are composed of numerous genetically distinct subfamily/genus-level viral groups. Among currently identified viral groups, the HMO-2011-type group is known to be dominant and broadly distributed. However, only four HMO-2011-type cultivated representatives that infect marine SAR116 and Roseobacter strains have been reported to date, and the genetic diversity, potential hosts, and ecology of this group remain poorly elucidated. Here, we present the genomes of seven HMO-2011-type phages that were isolated using four Roseobacter strains and one SAR11 strain, as well as additional 207 HMO-2011-type metagenomic viral genomes (MVGs) identified from various marine viromes. Phylogenomic and shared-gene analyses revealed that the HMO-2011-type group is a subfamily-level group comprising at least 10 discernible genus-level subgroups. Moreover, >2000 HMO-2011-type DNA polymerase sequences were identified, and the DNA polymerase phylogeny also revealed that the HMO-2011-type group contains diverse subgroups and is globally distributed. Metagenomic read-mapping results further showed that most HMO-2011-type phages are prevalent in global oceans and display distinct geographic distributions, with the distribution of most HMO-2011-type phages being associated with temperature. Lastly, we found that members in subgroup IX, represented by pelagiphage HTVC033P, were among the most abundant HMO-2011-type phages, which implies that SAR11 bacteria are crucial hosts for this viral group. In summary, our findings substantially expand current knowledge regarding the phylogenetic diversity, evolution, and distribution of HMO-2011-type phages, highlighting HMO-2011-type phages as major ecological agents that can infect certain key bacterial groups.

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Novel pelagiphages prevail in the ocean

10.1101/2019.12.14.876532 ◽

2019 ◽

Cited By ~ 1

Author(s):

Zefeng Zhang ◽

Fang Qin ◽

Feng Chen ◽

Xiao Chu ◽

Haiwei Luo ◽

...

Keyword(s):

Genetic Diversity ◽

Ecological Strategies ◽

Genome Sequences ◽

Host Interactions ◽

Type Group ◽

Host Mortality ◽

Marine Phage ◽

Global Oceans ◽

Globally Distributed ◽

Geographical Locations

AbstractViruses play a key role in biogeochemical cycling and host mortality, metabolism, physiology and evolution in the ocean. Viruses that infect the globally abundant marine SAR11 bacteria (pelagiphages) were reported to be an important component of the marine viral community. In this study, ten pelagiphages that infect three different Pelagibacter strains were isolated from various geographical locations and were genomically characterized. All ten pelagiphages are novel, representing four new lineages of the Podoviridae family. Although they share limited homology with cultured phage isolates, they are all closely related to some environmental viral fragments. Two HTVC023P-type pelagiphages are shown to be related to the abundant VC_6 and VC_8 viral populations of the Global Oceans Viromes (GOV) datasets. Interestingly, HTVC103P-type pelagiphages contain a structural module similar to that in SAR116 phage HMO-2011. Three HTVC111P-type pelagiphages and HTVC106P are also novel and related to GOV VC_41 and VC_67 viral populations, respectively. Remarkably, these pelagiphage represented phage groups are all globally distributed and predominant. Half of the top ten most abundant known marine phage groups are represented by pelagiphages. The HTVC023P-type group is the most abundant known viral group, exceeding the abundance of HTVC010P-type and HMO-2011-type groups. Furthermore, the HTVC023P-type group is also abundant throughout the water column. Altogether, this study has greatly broadened our understanding of pelagiphages regarding their genetic diversity, phage-host interactions and the distribution pattern. Availability of these newly isolated pelagiphages and their genome sequences will allow us to further explore their phage-host interactions and ecological strategies.

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Unique viruses that infect Archaea related to eukaryotes

10.1101/2021.07.29.454249 ◽

2021 ◽

Author(s):

Ian M Rambo ◽

Valerie De Anda ◽

Marguerite V Langwig ◽

Brett J Baker

Keyword(s):

Transcriptional Regulation ◽

Deep Sea ◽

Structural Proteins ◽

Genome Replication ◽

Dna Viruses ◽

Viral Genomes ◽

Archaeal Viruses ◽

Hydrothermal Sediments ◽

Nucleocytoplasmic Large Dna Viruses ◽

Globally Distributed

Asgard archaea are newly described microbes that are related to eukaryotes. Asgards are diverse and globally distributed, however, their viruses have not been described. Here we characterize seven viral genomes that infected Lokiarchaeota, Helarchaeota, and Thorarchaeota in deep-sea hydrothermal sediments. These viruses code for structural proteins similar to those in Caudovirales, as well as proteins distinct from those described in archaeal viruses. They also have genes common in eukaryotic nucleocytoplasmic large DNA viruses (NCLDVs), and are predicted to be capable of semi-autonomous genome replication, repair, epigenetic modifications, and transcriptional regulation. Moreover, Helarchaeota viruses may hijack host ubiquitin systems similar to eukaryotic viruses. This first glimpse of Asgard viruses reveals they have features of both prokaryotic and eukaryotic viruses, and provides insights into their roles in the ecology and evolution of these globally distributed microbes.

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Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

The ISME Journal ◽

10.1038/s41396-020-0705-4 ◽

2020 ◽

Vol 14 (10) ◽

pp. 2527-2541 ◽

Cited By ~ 5

Author(s):

Jessica K. Jarett ◽

Mária Džunková ◽

Frederik Schulz ◽

Simon Roux ◽

David Paez-Espino ◽

...

Keyword(s):

Single Cell ◽

Hot Spring ◽

Current Knowledge ◽

Single Cells ◽

Metagenomic Data ◽

Viral Genomes ◽

Active Viral Replication ◽

High Layer ◽

Host Virus Interactions ◽

Virus Interactions

Abstract Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus–host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host–virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed “Piggyback-the-Winner” theory.

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Revision of the status of some genus-level water mite taxa in the families Pionidae Thor, 1900, Aturidae Thor, 1900, and Nudomideopsidae Smith, 1990 (Acari: Hydrachnidiae)

Zootaxa ◽

10.11646/zootaxa.3919.1.6 ◽

2015 ◽

Vol 3919 (1) ◽

pp. 111 ◽

Cited By ~ 3

Author(s):

IAN M. SMITH ◽

DAVID R. COOK ◽

REINHARD GERECKE

Keyword(s):

Species Diversity ◽

Current Knowledge ◽

Family Group ◽

Water Mites ◽

Water Mite ◽

Genus Level ◽

The Family ◽

The Status ◽

Apparent Age

A number of changes to the status of genus group names in water mites are proposed to foster a more consistent and phylogenetically defensible approach to the ranking of taxa at this level of the classification. The water mite taxa Acercopsis Viets, 1926 (Pionidae: Tiphyinae), Madawaska Habeeb, 1954 (Pionidae: Foreliinae), Brachypodopsis Piersig, 1903, Cubanaxonopsis Orghidan & Gruia, 1981, Hexaxonopsis Viets, 1926, Paraxonopsis Motaş & Tanasachi, 1947, Vicinaxonopsis Cook, 1974, Parabrachypoda Viets, 1929, and Ocybrachypoda Cook, 1974 (Aturidae: Axonopsinae), Ameribrachypoda Smith, 1991 (Aturidae: Aturinae), and Allomideopsis Smith, 1990 (Nudomideopsidae) are elevated in rank from subgenera to full genera to reflect current knowledge of their species diversity, morphological distinctness, relationships and apparent age. In light of the above changes in the subfamily Axonopsinae, the subgenera Kalobrachypoda Viets, 1929 and Navinaxonopsis Cook, 1967 are transferred from the genus Axonopsis to the genus Brachypodopsis, the subgenus Plesiobrachypoda Viets, 1942 is transferred from the genus Axonopsis to the genus Hexaxonopsis, and the species formerly placed in the subgenus Hemibrachypoda Viets, 1937 are transferred from the genus Brachypoda to the genus Parabrachypoda Viets, 1929, and Hemibrachypoda is placed in synonymy with Parabrachypoda. The family group taxa to which all of these genera belong are reviewed to provide context for the proposed changes.

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Metagenomic Analysis of the Viral Communities in Fermented Foods

Applied and Environmental Microbiology ◽

10.1128/aem.01859-10 ◽

2010 ◽

Vol 77 (4) ◽

pp. 1284-1291 ◽

Cited By ~ 57

Author(s):

Eun-Jin Park ◽

Kyoung-Ho Kim ◽

Guy C. J. Abell ◽

Min-Soo Kim ◽

Seong Woon Roh ◽

...

Keyword(s):

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Fermented Foods ◽

Human Feces ◽

Viral Genomes ◽

Double Stranded Dna ◽

Viral Communities ◽

Rrna Gene Sequencing ◽

Viral Sequences ◽

Homology Comparison

ABSTRACTViruses are recognized as the most abundant biological components on Earth, and they regulate the structure of microbial communities in many environments. In soil and marine environments, microorganism-infecting phages are the most common type of virus. Although several types of bacteriophage have been isolated from fermented foods, little is known about the overall viral assemblages (viromes) of these environments. In this study, metagenomic analyses were performed on the uncultivated viral communities from three fermented foods, fermented shrimp, kimchi, and sauerkraut. Using a high-throughput pyrosequencing technique, a total of 81,831, 70,591 and 69,464 viral sequences were obtained from fermented shrimp, kimchi and sauerkraut, respectively. Moreover, 37 to 50% of these sequences showed no significant hit against sequences in public databases. There were some discrepancies between the prediction of bacteriophages hosts via homology comparison and bacterial distribution, as determined from 16S rRNA gene sequencing. These discrepancies likely reflect the fact that the viral genomes of fermented foods are poorly represented in public databases. Double-stranded DNA viral communities were amplified from fermented foods by using a linker-amplified shotgun library. These communities were dominated by bacteriophages belonging to the viral orderCaudovirales(i.e.,Myoviridae,Podoviridae, andSiphoviridae). This study indicates that fermented foods contain less complex viral communities than many other environmental habitats, such as seawater, human feces, marine sediment, and soil.

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Discovery of divided RdRp sequences and a hitherto unknown genomic complexity in fungal viruses

10.1101/2020.09.08.288829 ◽

2020 ◽

Author(s):

Yuto Chiba ◽

Takashi Yaguchi ◽

Syun-ichi Urayama ◽

Daisuke Hagiwara

Keyword(s):

Rna Polymerase ◽

Rna Viruses ◽

Current Knowledge ◽

Single Gene ◽

Rna Seq ◽

Rna Dependent Rna Polymerase ◽

Independent Manner ◽

Viral Genomes ◽

True Diversity ◽

Fungal Viruses

AbstractBy identifying variations in viral RNA genomes, cutting-edge metagenome technology has potential to reshape current concepts about the evolution of RNA viruses. This technology, however, cannot process low-homology genomic regions properly, leaving the true diversity of RNA viruses unappreciated. To overcome this technological limitation we applied an advanced method, Fragmented and Primer-Ligated Double-stranded (ds) RNA Sequencing (FLDS), to screen RNA viruses from 155 fungal isolates, which allowed us to obtain complete viral genomes in a homology-independent manner. We created a high-quality catalog of 19 RNA viruses (12 viral species) that infect Aspergillus isolates. Among them, nine viruses were not detectable by the conventional methodology involving agarose gel electrophoresis of dsRNA, a hallmark of RNA virus infections. Segmented genome structures were determined in 42% of the viruses. Some RNA viruses had novel genome architectures; one contained a dual methyltransferase domain and another had a separated RNA-dependent RNA polymerase (RdRp) gene. A virus from a different fungal taxon (Pyricularia) had an RdRp sequence that was separated on different segments, suggesting that a divided RdRp is widely present among fungal viruses, despite the belief that all RNA viruses encode RdRp as a single gene. These findings illustrate the previously hidden diversity and evolution of RNA viruses, and prompt reconsideration of the structural plasticity of RdRp. By highlighting the limitations of conventional surveillance methods for RNA viruses, we showcase the potential of FLDS technology to broaden current knowledge about these viruses.Author SummaryThe development of RNA-seq technology has facilitated the discovery of RNA viruses in all types of biological samples. However, it is technically difficult to detect highly novel viruses using RNA-seq. We successfully reconstructed the genomes of multiple novel fungal RNA viruses by screening host fungi using a new technology, FLDS. Surprisingly, we identified two viral species whose RNA-dependent RNA polymerase (RdRp) proteins were separately encoded on different genome segments, overturning the commonly accepted view of the positional unity of RdRp proteins in viral genomes. This new perspective on divided RdRp proteins should hasten the discovery of viruses with unique RdRp structures that have been overlooked, and further advance current knowledge and understanding of the diversity and evolution of RNA viruses.

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Climate change prompts monitoring and systematic utilization of honey bee diversity in Turkey

10.32942/osf.io/92n68 ◽

2020 ◽

Author(s):

Mert Kükrer ◽

C. Can Bilgin

Keyword(s):

Climate Change ◽

Honey Bee ◽

Current Knowledge ◽

Genomic Diversity ◽

Local Adaptations ◽

Species Response ◽

Genomic Tools ◽

The Face ◽

Bee Diversity ◽

The Impact

Quantitative studies concerning the impact of climate change on pollinators are generally lacking. Relationship between honey bee diversity, present local adaptations and adaptive capacity of subspecies and ecotypes in the face of climate change is an urgent but rather poorly studied topic worldwide. Actually, such an effort lies at the crossroads of various fields of inquiry. Those include conservation of local honey bee diversity, breeding various local stocks for desirable traits, and enabling resilient ecosystem services. With the ever-increasing availability of genomic tools, now it is more probable than ever to simultaneously fill such gaps. Current knowledge and growing awareness on honey bee diversity in Turkey let us progress into a more systematic utilization of this resource through development of climate-conscious models. Here we provide a framework that takes genomic diversity into account for assessing and monitoring various aspects of species’ response to climate change which can potentially lead to drastic impacts.

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Cryptosporidium spp. infections in livestock and wild animals in Azerbaijan territory

Journal of Water and Health ◽

10.2166/wh.2021.050 ◽

2021 ◽

Author(s):

S. Mamedova ◽

P. Karanis

Keyword(s):

Current Knowledge ◽

Protozoan Parasite ◽

Wild Animals ◽

Vertebrate Species ◽

Cryptosporidium Spp ◽

Globally Distributed ◽

Intracellular Protozoan Parasite

Abstract Cryptosporidium is an intracellular protozoan parasite, globally distributed and capable of infecting various vertebrate species, including humans as well as domestic and wild animals. Cryptosporidium is increasingly gaining attention as a human and an animal pathogen mainly due to its dominant involvement in worldwide waterborne outbreaks. The present paper reviews the current knowledge and understanding of Cryptosporidium spp. in terrestrial and water animals in Azerbaijan.

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Undocumented potential for primary productivity in a globally-distributed bacterial photoautotroph

10.1101/140715 ◽

2017 ◽

Cited By ~ 4

Author(s):

E.D. Graham ◽

J.F. Heidelberg ◽

B.J. Tully

Keyword(s):

Microbial Communities ◽

Mediterranean Sea ◽

East Africa ◽

Primary Productivity ◽

North Pacific ◽

Carbon Fixation ◽

The North ◽

Global Oceans ◽

Globally Distributed ◽

The North Pacific

AbstractAerobic anoxygenic phototrophs (AAnPs) are common in the global oceans and are associated with photoheterotrophic activity. To date, AAnPs have not been identified in the surface ocean that possess the potential for carbon fixation. Using the Tara Oceans metagenomic dataset, we have reconstructed draft genomes of four bacteria that possess the genomic potential for anoxygenic phototrophy, carbon fixation via the Calvin-Benson-Bassham cycle, and the oxidation of sulfite and thiosulfate. Forming a monophyletic clade within the Alphaproteobacteria and lacking cultured representatives, the organisms compose minor constituents of local microbial communities (0.1-1.0%), but are globally distributed, present in multiple samples from the North Pacific, Mediterranean Sea, the East Africa Coastal Province, and the South Atlantic. These organisms represent a shift in our understanding of microbially-mediated photoautotrophy in the global oceans and provide a previously undiscovered route of primary productivity.Significance StatementIn examining the genomic content of organisms collected during the Tara Oceans expedition, we have identified a novel clade within the Alphaproteobacteria that has the potential for photoautotrophy. Based on genome observations, these organisms have the potential to couple inorganic sulfur compounds as electron donors to fix carbon into biomass. They are globally distributed, present in samples from the North Pacific, Mediterranean Sea, East Africa Coastal Current, and the South Atlantic. This discovery may require re-examination of the microbial communities in the global ocean to understand and constrain the impacts of this group of organisms on the global carbon cycle.

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A Global Review and Network Analysis of Phytophagous Insect Interactions With Ferns and Lycophytes

10.21203/rs.3.rs-301036/v1 ◽

2021 ◽

Author(s):

Luis Javier Fuentes-Jacques ◽

Paul Hanson-Snortum ◽

Vicente Hernández-Ortiz ◽

Cecilia Díaz-Castelazo ◽

Klaus Mehltreter

Keyword(s):

Vascular Plants ◽

Current Knowledge ◽

Geographic Location ◽

Feeding Habit ◽

Future Research ◽

Phytophagous Insects ◽

Genus Level ◽

Fern Species ◽

Low Levels ◽

Insect Interactions

Abstract Ferns are the second largest lineage of vascular plants, yet our understanding of their interactions with phytophagous insects is very limited. Which insects feed on ferns? Do insects prefer specific fern taxa? Which feeding habit is the most common on ferns? Is there any evidence for coevolution between insects and ferns? Is our current knowledge on fern-insect interactions biased? To answer these questions, we analyzed 2,318 records of fern-insect interactions from 122 literature sources, based on the feeding habit of insects, fern taxa, and geographic location. We found evidence for interactions comprising 809 insect species (mainly Hemiptera, Lepidoptera, and Coleoptera) and 382 fern species (mainly Dennstaedtiaceae, Dryopteridaceae, and Pteridaceae). Leaf chewers contributed over 50% of the species, followed by sap-sucking insects (29.1%) and spore feeders (6.5%). The overall interaction analyses revealed that the entire fern-insect network had medium levels of nestedness (NODF = 43.37) and relatively low levels of specialization (H2’ = 0.24). The interaction networks of fern-feeding Coleoptera were the most specialized at family (H2’ = 0.40) and genus level (H2’ = 0.65), whereas 6 out of 10 most specialized insect families were Lepidoptera (d’ ≥ 0.44). At the genus level, all networks had a fern-biased asymmetry. Although fern-feeding generalists were common, few cases of coevolutionary radiation have been documented. We discuss the possible biases of our dataset, which also highlight gaps to perform future research, and suggest that many more phytophagous insects on ferns remain to be discovered, especially sap-sucking, gall-forming, and spore-feeding insects on modern fern groups.

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