scholarly journals A new framework for the study of apicomplexan diversity across environments

2018 ◽  
Author(s):  
Javier del Campo ◽  
Thierry Heger ◽  
Raquel Rodríguez-Martínez ◽  
Alexandra Z. Worden ◽  
Thomas A. Richards ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Epidemiological Studies ◽  
Small Subunit ◽  
Reference Database ◽  
Rrna Gene ◽  
Natural Environments ◽  
Ssu Rrna ◽  
Free Living ◽  
Microbial Eukaryotes ◽  
Living Environments

Apicomplexans are a group of microbial eukaryotes that contain some of the most well-studied parasites, including widespread intracellular pathogens of mammals such as Toxoplasma and Plasmodium (the agent of malaria), and emergent pathogens like Cryptosporidium and Babesia. Decades of research have illuminated the pathogenic mechanisms, molecular biology, and genomics of model apicomplexans, but we know surprisingly little about their diversity and distribution in natural environments. In this study we analyze the distribution of apicomplexans across a range of both host-associated and free-living environments, covering animal hosts from cnidarians to mammals, and ecosystems from soils to fresh and marine waters. Using publicly available small subunit (SSU) rRNA gene databases, high-throughput environmental sequencing (HTES) surveys such as Tara Oceans and VAMPS, as well as our own generated HTES data, we developed an apicomplexan reference database, which includes the largest apicomplexan SSU rRNA tree available to date and encompasses comprehensive sampling of this group and their closest relatives. This tree allowed us to identify and correct incongruences in the molecular identification of sequences, particularly within the hematozoans and the gregarines. Analyzing the diversity and distribution of apicomplexans in HTES studies with this curated reference database also showed a widespread, and quantitatively important, presence of apicomplexans across a variety of free-living environments. These data allow us to describe a remarkable molecular diversity of this group compared with our current knowledge, especially when compared with that identified from described apicomplexan species. This revision is most striking in marine environments, where potentially the most diverse apicomplexans apparently exist, but have not yet been formally recognized. The new database will be useful for both microbial ecology and epidemiological studies, and provide valuable reference for medical and veterinary diagnosis especially in cases of emerging, zoonotic, and cryptic infections.

scholarly journals Molecular Subtyping of Blastocystis sp. Isolated from Farmed Animals in Southern Italy

2021 ◽  
Vol 9 (8) ◽  
pp. 1656
Author(s):  
Simona Gabrielli ◽  
Marialetizia Palomba ◽  
Federica Furzi ◽  
Emanuele Brianti ◽  
Gabriella Gaglio ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Pcr Amplification ◽  
Epidemiological Studies ◽  
Fallow Deer ◽  
Small Subunit ◽  
Zoonotic Transmission ◽  
Ssu Rrna ◽  
Molecular Approaches ◽  
Wide Range ◽  
Blastocystis Sp

Blastocystis is a common intestinal protist distributed worldwide, infecting humans and a wide range of domestic and wild animals. It exhibits an extensive genetic diversity and, so far, 25 distinct small subunit ribosomal RNA (SSU rRNA) lineages termed subtypes (STs)) have been characterized; among them, 12 have thus far been reported in humans. The aims of the present study were to detect and genetically characterize Blastocystis sp. in synantropic animals to improve our current knowledge on the distribution and zoonotic transmission of Blastocystis STs in Italy. Samples were collected from N = 193 farmed animals and submitted to DNA extraction and PCR amplification of the SSU rRNA. Blastocystis was detected in 60 samples (31.08%) and successfully subtyped. Phylogenetic analysis evidenced that the isolates from fallow deer, goats, and pigs (N = 9) clustered within the ST5; those from pheasants (N = 2) in the ST6; those from chickens (N = 8) in the ST7; those from sheep (N = 6) in the ST10; and those from water buffaloes (N = 9) in the ST14 clade. The comparison between the present isolates from animals and those previously detected in humans in Italy suggested the animal-to-human spillover for ST6 and ST7. The present study represents the widest Blastocystis survey performed thus far in farmed animals in Italy. Further epidemiological studies using molecular approaches are required to determine the occurrence and distribution of Blastocystis STs in other potential animal reservoirs in Italy and to define the pathways of zoonotic transmission.

scholarly journals phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Harald R. Gruber-Vodicka ◽  
Brandon K. B. Seah ◽  
Elmar Pruesse
Keyword(s):  
High Throughput ◽  
Small Subunit ◽  
General Purpose ◽  
Reference Database ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Small Subunit Rrna ◽  
Ssu Rrna Gene ◽  
Domains Of Life ◽  
Environmental Microbes

ABSTRACT The small-subunit rRNA (SSU rRNA) gene is the key marker in molecular ecology for all domains of life, but it is largely absent from metagenome-assembled genomes that often are the only resource available for environmental microbes. Here, we present phyloFlash, a pipeline to overcome this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based binning of full metagenomic assemblies. We show that a cleanup of artifacts is pivotal even with a curated reference database. With such a filtered database, the general-purpose mapper BBmap extracts SSU rRNA reads five times faster than the rRNA-specialized tool SortMeRNA with similar sensitivity and higher selectivity on simulated metagenomes. Reference-based targeted assemblers yielded either highly fragmented assemblies or high levels of chimerism, so we employ the general-purpose genomic assembler SPAdes. Our optimized implementation is independent of reference database composition and has satisfactory levels of chimera formation. phyloFlash quickly processes Illumina (meta)genomic data, is straightforward to use, even as part of high-throughput quality control, and has user-friendly output reports. The software is available at https://github.com/HRGV/phyloFlash (GPL3 license) and is documented with an online manual. IMPORTANCE To track organisms across all domains of life, the SSU rRNA gene is the gold standard. Many environmental microbes are known only from high-throughput sequence data, but the SSU rRNA gene, the key to visualization by molecular probes and link to existing literature, is often missing from metagenome-assembled genomes (MAGs). The easy-to-use phyloFlash software suite tackles this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based linking to MAGs. Starting from a cleaned reference database, phyloFlash profiles the taxonomic diversity and assembles the sorted SSU rRNA reads. The phyloFlash design is domain agnostic and covers eukaryotes, archaea, and bacteria alike. phyloFlash also provides utilities to visualize multisample comparisons and to integrate the recovered SSU rRNAs in a metagenomics workflow by linking them to MAGs using assembly graph parsing.

scholarly journals Phylogeny, evidence for a cryptic plastid, and distribution of Chytriodinium parasites (Dinophyceae) infecting copepods

2018 ◽  
Author(s):  
Jürgen F. H. Strassert ◽  
Elisabeth Hehenberger ◽  
Javier del Campo ◽  
Noriko Okamoto ◽  
Martin Kolisko ◽  
...  
Keyword(s):  
Phylogenetic Position ◽  
Rrna Gene ◽  
Ancestral State ◽  
Ssu Rrna ◽  
Gene Sequences ◽  
Free Living ◽  
Surface Ocean ◽  
Lsu Rrna Gene ◽  
Important Host ◽  
Copepod Eggs

ABSTRACTSpores of the dinoflagellate Chytriodinium are known to infest copepod eggs causing their lethality. Despite the potential to control the population of such an ecologically important host, knowledge about Chytriodinium parasites is limited: we know little about phylogeny, parasitism, abundance, or geographical distribution. We carried out genome sequence surveys on four manually isolated sporocytes from the same sporangium to analyse the phylogenetic position of Chytriodinium based on SSU and concatenated SSU/LSU rRNA gene sequences, and also characterize two genes related to the plastidial heme pathway, hemL and hemY. The results suggest the presence of a cryptic plastid in Chytriodinium and a photosynthetic ancestral state of the parasitic Chytriodinium/Dissodinium clade. Finally, by mapping Tara Oceans V9 SSU amplicon data to the recovered SSU rRNA gene sequences from the sporocytes, we show that globally, Chytriodinium parasites are most abundant within the pico/nano- and mesoplankton of the surface ocean and almost absent within microplankton, a distribution indicating that they generally exist either as free-living spores or host-associated sporangia.

scholarly journals Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria

2018 ◽  
Author(s):  
Jeffrey S. McLean ◽  
Batbileg Bor ◽  
Thao T. To ◽  
Quanhui Liu ◽  
Kristopher A. Kerns ◽  
...  
Keyword(s):  
Oral Cavity ◽  
De Novo ◽  
Gc Content ◽  
Single Copy ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
Human Oral Cavity

ABSTRACTRecently, we discovered that a member of the Saccharibacteria/TM7 phylum (strain TM7x) isolated from the human oral cavity, has an ultra-small cell size (200-300nm), a highly reduced genome (705 Kbp) with limited de novo biosynthetic capabilities, and a very novel lifestyle as an obligate epibiont on the surface of another bacterium 1. There has been considerable interest in uncultivated phyla, particularly those that are now classified as the proposed candidate phyla radiation (CPR) reported to include 35 or more phyla and are estimated to make up nearly 15% of the domain Bacteria. Most members of the larger CPR group share genomic properties with Saccharibacteria including reduced genomes (<1Mbp) and lack of biosynthetic capabilities, yet to date, strain TM7x represents the only member of the CPR that has been cultivated and is one of only three CPR routinely detected in the human body. Through small subunit ribosomal RNA (SSU rRNA) gene surveys, members of the Saccharibacteria phylum are reported in many environments as well as within a diversity of host species and have been shown to increase dramatically in human oral and gut diseases. With a single copy of the 16S rRNA gene resolved on a few limited genomes, their absolute abundance is most often underestimated and their potential role in disease pathogenesis is therefore underappreciated. Despite being an obligate parasite dependent on other bacteria, six groups (G1-G6) are recognized using SSU rRNA gene phylogeny in the oral cavity alone. At present, only genomes from the G1 group, which includes related and remarkably syntenic environmental and human oral associated representatives1, have been uncovered to date. In this study we systematically captured the spectrum of known diversity in this phylum by reconstructing completely novel Class level genomes belonging to groups G3, G6 and G5 through cultivation enrichment and/or metagenomic binning from humans and mammalian rumen. Additional genomes for representatives of G1 were also obtained from modern oral plaque and ancient dental calculus. Comparative analysis revealed remarkable divergence in the host-associated members across this phylum. Within the human oral cavity alone, variation in as much as 70% of the genes from nearest oral clade (AAI 50%) as well as wide GC content variation is evident in these newly captured divergent members (G3, G5 and G6) with no environmental relatives. Comparative analyses suggest independent episodes of transmission of these TM7 groups into humans and convergent evolution of several key functions during adaptation within hosts. In addition, we provide evidence from in vivo collected samples that each of these major groups are ultra-small in size and are found attached to larger cells.

Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea)

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Ran Li ◽  
Wenbao Zhuang ◽  
Congcong Wang ◽  
Hamed El-Serehy ◽  
Saleh A. Al-Farraj ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Gene Trees ◽  
Ssu Rrna Gene ◽  
Anaerobic Ciliate ◽  
Pr China

The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.

Ficophagus chaozhouensis n. sp. (Nematoda: Aphelenchoididae), an associate of Ficus hirta Vahl var. roxburghii (Miq.) King in China

Nematology ◽  
2020 ◽  
Vol 22 (3) ◽  
pp. 299-312
Author(s):  
Wensheng Zeng ◽  
Dayuan Zhang ◽  
Jianghua Huang ◽  
Yongsan Zeng ◽  
Weimin Ye ◽  
...  
Keyword(s):  
Large Subunit ◽  
Nematode Species ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Monophyletic Clade ◽  
Male Tail ◽  
Lsu Rrna Gene ◽  
Ficus Hirta ◽  
Tail Tip

Summary A new nematode species was recovered from the syconia of Ficus hirta var. roxburghii from Chaozhou, Guangdong, China. It is described herein as Ficophagus chaozhouensis n. sp. and is characterised by possessing the combined characters of a short post-uterine sac, excretory pore located near the head, amoeboid sperm, three pairs of subventral papillae on the male tail, rounded male tail tip with mucron (occasionally swollen), absence of gubernaculum (or apophysis), a blunt rosethorn-shaped spicule without a terminal cucullus, and a digitate rostrum with a broadly squared tip. Ficophagus chaozhouensis n. sp. was separated from other sequenced species by differences in the partial small subunit (SSU) rRNA gene and D2-D3 expansion segments of the large subunit (LSU) rRNA gene. Phylogenetic analysis with LSU D2-D3 expansion segment sequences suggested that F. chaozhouensis n. sp. is clustered in the same highly supported monophyletic clade with F. aculeata, F. maxima and F. yoponensis, and is sister to F. aculeata.

Free-living nematodes associated with pine cones of Pinus thunbergii and P. taeda at Japanese coastal and inland forest sites

Nematology ◽  
2019 ◽  
Vol 21 (4) ◽  
pp. 389-400 ◽  
Author(s):  
Yudai Kitagami ◽  
Natsumi Kanzaki ◽  
Toko Tanikawa ◽  
Yosuke Matsuda
Keyword(s):  
Gene Sequence ◽  
Small Subunit ◽  
Pinus Thunbergii ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Free Living ◽  
Small Subunit Rrna Gene ◽  
Forest Sites ◽  
High Bootstrap ◽  
Pine Cones

Summary We surveyed the distribution of nematodes in 56 cones of Pinus thunbergii collected from both live branches and on the forest floor in three coastal and inland habitats and in 11 cones of P. taeda collected at different heights. We identified 47 nematodes to family or genera by analysis of an 18S small subunit rRNA gene sequence. The frequencies of occurrence of free-living cone nematodes were 97% in coastal P. thunbergii, 92% in inland P. thunbergii, and 82% in P. taeda. Phylogenetic analysis assigned the nematodes to four clades with high bootstrap values. Nine sequences that were found only in cones on live branches were clustered with Panagrobelus stammeri and an unknown Panagrobelus sp. Our results imply that nematodes are commonly associated with cones in pine forest ecosystems and that a capacity for anhydrobiosis may be a key to surviving above-ground.

scholarly journals Telonema antarcticum sp. nov., a common marine phagotrophic flagellate

2005 ◽  
Vol 55 (6) ◽  
pp. 2595-2604 ◽  
Author(s):  
Dag Klaveness ◽  
Kamran Shalchian-Tabrizi ◽  
Helge Abildhauge Thomsen ◽  
Wenche Eikrem ◽  
Kjetill S. Jakobsen
Keyword(s):  
Molecular Phylogeny ◽  
Small Subunit ◽  
Food Vacuole ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Small Subunit Rrna ◽  
Ssu Rrna Gene ◽  
Structural Identity ◽  
Food Particles ◽  
Ssu Rrna Gene Sequence

Telonema is a widely distributed group of phagotrophic flagellates with two known members. In this study, the structural identity and molecular phylogeny of Telonema antarcticum was investigated and a valid description is proposed. Molecular phylogeny was studied using small-subunit rRNA (SSU rRNA) gene sequences. The pear-shaped cell had two subequal flagella that emerged laterally on the truncated antapical tail. One flagellum had tripartite hairs. The cell was naked, but had subsurface vesicles containing angular paracrystalline bodies of an unknown nature. A unique complex cytoskeletal structure, the subcortical lamina, was found to be an important functional and taxonomic feature of the genus. Telonema has an antero-ventral depression where food particles are ingested and then transferred to a conspicuous anterior food vacuole. The molecular phylogeny inferred from the SSU rRNA gene sequence suggested that Telonema represents an isolated and deep branch among the tubulocristate protists.

scholarly journals An ITS-based phylogenetic framework for the genus Vorticella : finding the molecular and morphological gaps in a taxonomically difficult group

2013 ◽  
Vol 280 (1771) ◽  
pp. 20131177 ◽  
Author(s):  
Ping Sun ◽  
John C. Clamp ◽  
Dapeng Xu ◽  
Bangqin Huang ◽  
Mann Kyoon Shin ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Branching Order ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

Vorticella includes more than 100 currently recognized species and represents one of the most taxonomically challenging genera of ciliates. Molecular phylogenetic analysis of Vorticella has been performed so far with only sequences coding for small subunit ribosomal RNA (SSU rRNA); only a few of its species have been investigated using other genetic markers owing to a lack of similar sequences for comparison. Consequently, phylogenetic relationships within the genus remain unclear, and molecular discrimination between morphospecies is often difficult because most regions of the SSU rRNA gene are too highly conserved to be helpful. In this paper, we move molecular systematics for this group of ciliates to the infrageneric level by sequencing additional molecular markers—fast-evolving internal transcribed spacer (ITS) regions—in a broad sample of 66 individual samples of 28 morphospecies of Vorticella collected from Asia, North America and Europe. Our phylogenies all featured two strongly supported, highly divergent, paraphyletic clades (I, II) comprising the morphologically defined genus Vorticella . Three major lineages made up clade I, with a relatively well-resolved branching order in each one. The marked divergence of clade II from clade I confirms that the former should be recognized as a separate taxonomic unit as indicated by SSU rRNA phylogenies. We made the first attempt to elucidate relationships between species in clade II using both morphological and multi-gene approaches, and our data supported a close relationship between some morphospecies of Vorticella and Opisthonecta , indicating that relationships between species in the clade are far more complex than would be expected from their morphology. Different patterns of helix III of ITS2 secondary structure were clearly specific to clades and subclades of Vorticella and, therefore, may prove useful for resolving phylogenetic relationships in other groups of ciliates.

scholarly journals Morphological and Genetic Evidence that the Cyanobacterium Lyngbya wollei (Farlow ex Gomont) Speziale and Dyck Encompasses at Least Two Species

2008 ◽  
Vol 74 (12) ◽  
pp. 3710-3717 ◽  
Author(s):  
Jennifer J. Joyner ◽  
R. Wayne Litaker ◽  
Hans W. Paerl
Keyword(s):  
Phylogenetic Analysis ◽  
Habitat Degradation ◽  
Sequence Similarity ◽  
Inorganic Nitrogen ◽  
Small Subunit ◽  
Morphological Data ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Lyngbya Wollei ◽  
Ssu Rrna Gene

ABSTRACT Dense blooms of the cyanobacterium Lyngbya wollei are increasingly responsible for declining water quality and habitat degradation in numerous springs, rivers, and reservoirs. This research represents the first molecular phylogenetic analysis of L. wollei in comparison with the traditional morphological characterization of this species. Specimens were collected from several springs in Florida and a reservoir in North Carolina. Segments of the small-subunit (SSU) rRNA and nifH genes were PCR amplified, cloned, and sequenced. The phylogenetic analysis of the SSU rRNA gene revealed sequences that fell into three distinct subclusters, each with >97% sequence similarity. These were designated operational taxonomic unit 1 (OTU1), OTU2, and OTU3. Similarly, the nifH sequences fell into three distinct subclusters named S1, S2, and S3. When either bulk samples or individual filaments were analyzed, we recovered OTU1 with S1, OTU2 with S2, and OTU3 with S3. The coherence between the three SSU rRNA gene and nifH subclusters was consistent with genetically distinct strains or species. Cells associated with subclusters OTU3 and S3 were significantly wider and longer than those associated with other subclusters. The combined molecular and morphological data indicate that the species commonly identified as L. wollei in the literature represents two or possibly more species. Springs containing OTU3 and S3 demonstrated lower ion concentrations than other collection sites. Geographical locations of Lyngbya subclusters did not correlate with residual dissolved inorganic nitrogen or phosphorus concentrations. This study emphasizes the need to complement traditional identification with molecular characterization to more definitively detect and characterize harmful cyanobacterial species or strains.

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