SSU rRNA Sequences Research Articles

Barcodes Reveal 48 New Species of Tetrahymena, Dexiostoma, and Glaucoma: Phylogeny, Ecology, and Biogeography of New and Established Species.

Tetrahymena mitochondrial cox1 barcodes and nuclear SSUrRNA sequences are particularly effective at distinguishing among its many cryptic species. In a project to learn more about Tetrahymena natural history, the majority of >1,000 Tetrahymena-like fresh water isolates were assigned to established Tetrahymena species with the remaining assigned to 37 new species of Tetrahymena, nine new species of Dexiostoma and 12 new species of Glaucoma. Phylogenetically, all but three Tetrahymena species belong to the well-established "australis" or "borealis" clades; the minority forms a divergent "paravorax" clade. Most Tetrahymena species are micronucleate, but others are exclusively amicronucleate. The self-splicing intron of the LSUrRNA precursor is absent in Dexiostoma and Glaucoma and was likely acquired subsequent to the "australis/borealis" split; in some instances, its sequence is diagnostic of species. Tetrahymena americanis, T.elliotti, T.gruchyi n. sp., and T.borealis, together accounted for >50% of isolates, consistent with previous findings for established species. The biogeographic range of species found previously in Austria, China, and Pakistan was extended to the Nearctic; some species show evidence of population structure consistent with endemism. Most species were most frequently collected from ponds or lakes, while others, particularly Dexiostoma species, were collected most often from streams or rivers. The results suggest that perhaps hundreds of species remain to be discovered, particularly if collecting is global and includes hosts of parasitic forms.

Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias.

Small subunit ribosomal RNA (SSU rRNA) genes, 16S in bacteria and 18S in eukaryotes, have been the standard phylogenetic markers used to characterize microbial diversity and evolution for decades. However, the reference databases of full-length SSU rRNA gene sequences are skewed to well-studied ecosystems and subject to primer bias and chimerism, which results in an incomplete view of the diversity present in a sample. We combine poly(A)-tailing and reverse transcription of SSU rRNA molecules with synthetic long-read sequencing to generate high-quality, full-length SSU rRNA sequences, without primer bias, at high throughput. We apply our approach to samples from seven different ecosystems and obtain more than a million SSU rRNA sequences from all domains of life, with an estimated raw error rate of 0.17%. We observe a large proportion of novel diversity, including several deeply branching phylum-level lineages putatively related to the Asgard Archaea. Our approach will enable expansion of the SSU rRNA reference databases by orders of magnitude, and contribute to a comprehensive census of the tree of life.

A Modified Low-quantity RNA-Seq Method for Microbial Community and Diversity Analysis Using Small Subunit Ribosomal RNA.

We propose a modified RNA-Seq method for small subunit ribosomal RNA (SSU rRNA)-based microbial community analysis that depends on the direct ligation of a 5' adaptor to RNA before reverse-transcription. The method requires only a low-input quantity of RNA (10-100 ng) and does not require a DNA removal step. Using this method, we could obtain more 16S rRNA sequences of the same regions (variable regions V1-V2) without the interference of DNA in order to analyze OTU (operational taxonomic unit)-based microbial communities and diversity. The generated SSU rRNA sequences are also suitable for the coverage evaluation for bacterial universal primer 8F (Escherichia coli position 8 to 27), which is commonly used for bacterial 16S rRNA gene amplification. The modified RNA-Seq method will be useful to determine potentially active microbial community structures and diversity for various environmental samples, and will also be useful for identifying novel microbial taxa.

A new microsporidium, Vairimorpha subcoccinellae n. sp. (Microsporidia: Burenellidae), isolated from Subcoccinella vigintiquatuorpunctata L. (Coleoptera: Coccinellidae).

A new microsporidium was isolated from Subcoccinella vigintiquatuorpunctata L. (Coleoptera: Coccinellidae), a pest of Galega officinalis L. in Turkey. Infection in larval and adult stages was systemic with mature spores produced in the midgut, gonads, Malpighian tubules and, most extensively, fat body tissues. The microsporidium was polymorphic with two sporulation sequences producing two types of spores, binucleate spores with 13-15 coils of the polar tube, and uninucleate spores with 7 coils of the polar tube that developed within a sporophorous vesicle (SPV) to form meiospores. The 16S small subunit rRNA (SSU rRNA) gene of the microsporidium was sequenced and compared with twenty-seven microsporidian sequences from GenBank. Based on the phylogenetic analysis of the SSU rRNA sequence, this microsporidium is unique within the Vairimorpha group. Morphological and genetic characters indicate that the described microsporidium is dissimilar to all known Vairimorpha species, and so is named here as Vairimorpha subcoccinellae n. sp.

Phylogenetic analysis of simian Plasmodium spp. infecting Anopheles balabacensis Baisas in Sabah, Malaysia.

BackgroundAnopheles balabacensis of the Leucospyrus group has been confirmed as the primary knowlesi malaria vector in Sabah, Malaysian Borneo for some time now. Presently, knowlesi malaria is the only zoonotic simian malaria in Malaysia with a high prevalence recorded in the states of Sabah and Sarawak.Methodology/Principal findingsAnopheles spp. were sampled using human landing catch (HLC) method at Paradason village in Kudat district of Sabah. The collected Anopheles were identified morphologically and then subjected to total DNA extraction and polymerase chain reaction (PCR) to detect Plasmodium parasites in the mosquitoes. Identification of Plasmodium spp. was confirmed by sequencing the SSU rRNA gene with species specific primers. MEGA4 software was then used to analyse the SSU rRNA sequences and bulid the phylogenetic tree for inferring the relationship between simian malaria parasites in Sabah.PCR results showed that only 1.61% (23/1,425) of the screened An. balabacensis were infected with one or two of the five simian Plasmodium spp. found in Sabah, viz. Plasmodium coatneyi, P. inui, P. fieldi, P. cynomolgi and P. knowlesi. Sequence analysis of SSU rRNA of Plasmodium isolates showed high percentage of identity within the same Plasmodium sp. group. The phylogenetic tree based on the consensus sequences of P. knowlesi showed 99.7%–100.0% nucleotide identity among the isolates from An. balabacensis, human patients and a long-tailed macaque from the same locality.Conclusions/SignificanceThis is the first study showing high molecular identity between the P. knowlesi isolates from An. balabacensis, human patients and a long-tailed macaque in Sabah. The other common simian Plasmodium spp. found in long-tailed macaques and also detected in An. balabacensis were P. coatneyi, P. inui, P. fieldi and P. cynomolgi. The high percentage identity of nucleotide sequences between the P. knowlesi isolates from the long-tailed macaque, An. balabacensis and human patients suggests a close genetic relationship between the parasites from these hosts.

Phylogenetic taxonomy of Dematiopleospora fusiformis sp. nov. (Phaeosphaeriaceae) from Russia

Dematiopleospora fusiformis sp. nov., isolated from a decaying upright stem of Achillea millefolium (Asteraceae) in the Rostov Region of Russia is described herein based on morphology and ITS, LSU and SSU rRNA sequence based analyses. The new taxon is similar to D. mariae, the type species of Dematiopleospora, and shares similar features such as unilocular ascomata with brown setae in the ostiole, cylindrical asci and fusiform, muriform ascospores. However, D. fusiformis differs from the type and other species in Dematiopleospora in having light brown and larger ascospores. Maximum likelihood and Bayesian inference analyses reveal that our new taxon belongs to the family Phaeosphaeriaceae and is nested in between Dematiopleospora mariae and D. cirsii with high support. A comparison with other similar species also points out to other morphological differences that segregates D. fusiformis. Phylogenies also indicate that the affinities of two other Dematiopleospora species (viz. D. luzulae and D. alliariae) are rather ambiguous. Although the latter clearly fits within the Phaeosphaeriaceae, they are phylogenetically distant from all other Dematiopleospora strains that belong to this genus and in addition their relationships to other taxa are not supported. Further taxonomic studies are warranted to clarify their morpho-phylo taxonomy. Dematiopleospora mariae, D. cirsii and D. fusiformis could be treated as Dematiopleospora sensu stricto.

Molecular analysis of Giardia duodenalis isolates from symptomatic and asymptomatic children from La Habana, Cuba

Giardiasis is considered the most common intestinal parasitic disease in humans worldwide. In Cuba, this infection has particularly a strong clinical impact on the child population. Giardia duodenalis is a highly diverse protozoan, which comprises a complex of eight morphologically identical genetic assemblages, further divided into sub-assemblages. The present study used triose phosphate isomerase (tpi) and small-subunit ribosomal RNA (SSU rRNA) genes as genetic markers for the identification of G. duodenalis assemblages and sub-assemblages in correlation with clinical and epidemiological data in children attended at the Paediatric Hospital “William Soler” and at Pedro Kouri Institute, between 2015 and 2016. A prevalence of 8% of G. duodenalis infection was recorded in stool samples after concentration techniques from 68 children out of 847 analysed. A 100% detection of Giardia DNA was achieved by a SSU-rRNA PCR, whereas DNA from 63 of 68 (92.6%) was successfully amplified by tpi-PCR. By this assemblage-specific tpi-PCR 32 (50.8%) assemblage B, 17 (27.0%) assemblage A and 14 (22.2%) mixed infection (A+B) were identified. Assemblage B was significantly (P<0.02) more frequently found in children with diarrhoea. Sequence analysis of the tpi gene of Giardia isolates from symptomatic children showed that assemblage A belonged to the sub-assemblage AII, and 4 sub assemblages BIV and 1 sub assemblage BIII were also recorded. Only 2 discordant genotyping results were observed by phylogenetic comparison of SSU-rRNA and tpi sequences. Further studies with novel molecular tools for a better discrimination at the sub-assemblage level are needed to identify the dynamics of spread of giardiasis and to verify possible correlations between Giardia genetic diversity and clinical manifestation.

High genetic diversities between isolates of the fish parasite Cryptocaryon irritans (Ciliophora) suggest multiple cryptic species

The ciliate protozoan Cryptocaryon irritans parasitizes marine fish and causes lethal white spot disease. Sporadic infections as well as large-scale outbreaks have been reported globally and the parasite’s broad host range poses particular threat to the aquaculture and ornamental fish markets. In order to better understand C. irritans’ population structure, we sequenced and compared mitochondrial cox-1, SSU rRNA, and ITS-1 sequences from 8 new isolates of C. irritans collected in China, Japan, and Taiwan. We detected two SSU rRNA haplotypes, which differ at three positions, separating the isolates into two main groups (I and II). Cox-1 sequences also support the division into two groups, and the cox-1 divergence between these two groups is unexpectedly high (9.28% for 1582 nucleotide positions). The divergence is much greater than that detected in Ichthyophthirius multifiliis, the ciliate protozoan causing freshwater white spot disease in fish, where intraspecies divergence on cox-1 sequence is only 1.95%. ITS-1 sequences derived from these eight isolates and from all other C. irritans isolates (deposited in the GenBank) not only support the two groups, but further suggest the presence of a third group with even greater sequence divergence. Finally, a small Ka/Ks ratio estimated from cox-1 sequences suggests that this gene in C. irritans remains under strong purifying selection. Taken together, the C. irritans species may consists of many subspecies and/or syngens. Further work is needed to determine if there is reproductive isolation between the groups we have defined.

Molecular epidemiology of Cryptosporidium infection in infants with diarrhea in Wuhan City

To understand the prevalence of Cryptosporidium infection in diarrhea infants under 2 years old in Wuhan City, so as to provide the epidemiological evidence for the prevention and treatment of cryptosporidiosis. The fecal samples from infants under 2 years old with diarrhea were collected in Hubei General Hospital and Central South Hospital in Wuhan City, Hubei Province from August 2014 to July 2015. The fecal samples were stored in 2.5% potassium dichromate at 4 ℃ after filtered. The DNA was extracted from the fecal pellets with the phenol-chloroform method. The Cryptosporidium species were detected by a nested PCR assay targeting the SSU rRNA gene of the parasite. All the positive PCR products were sequenced on ABI 3100 automated sequencer, and the amplified sequences were compared to homologous sequences in the NCBI database by using the Basic Local Alignment Search Tool (BLAST). Phylogenetic analyses were performed by using the software MEGA (version 4.0) based on the Neighbour-Joining method. The human stool specimens (n = 298) were screened for the presence of Cryptosporidium by nested PCR. The infection rate of Cryptosporidium was 3.02% (9/298). The infection rate of Cryptosporidium was 5.93% (7/118) in the infants between 1-2 years old, and the infection rate was 1.11% (2/180) in the infants under 1 year old, and there was a significant difference between the two groups (χ2 = 4.13, P < 0.05). The nine samples which were positive by nested PCR were successfully sequenced and compared with the reference sequences in GenBank. The results revealed the nine positive specimens were all infected with C. parvum, and two of them were co-infected with C. hominis. Neighbor-joining trees were constructed from the aligned partial SSU rRNA sequences of these nine isolates, and in the SSU rRNA locus, the nine isolates were grouped with C. parvum. There exists Cryptosporidium infection in the infants under 2 years old with diarrhea in Wuhan City, and the main species of Cryptosporidium is C. parvum.

English

Two microsporidian isolates extracted from infected tasar silkworms (Antheraea mylitta)&nbsp; collected from forest area in Deoghar district, Jharkhand, India were subjected to PCR amplification using intergenic spacer (IGS) region and small subunit rRNA (SSU-rRNA) gene specific primers followed by cloning and sequencing. The IGS and SSU-rRNA gene sequences were analysed to derive the identity of the microspoidian isolates and establish their phylogenetic relationships. The phylogenetic analysis of test isolates included assessment of variation in sequences and length of IGS and SSU-rRNA genes with reference to 16 different microsporidian sequences. The results proved that IGS sequences have more variation than SSU-rRNA gene sequences. Analysis of phylogenetic trees reveal that both test isolates have very close relationship with each other as well as with three Nosema reference species viz., N. philosamia and N. antheraea isolated from Philosamia cynthia ricini and Antheraea pernyi in China respectively, and N. disstriae isolated from Malacosma disstriae in Canada. The test microsporidian isolates revealed closer relationship with other Nosema reference strains compared to Nosema sp. (NIK-1s_mys) from India. The study results indicate that the IGS or/and SSU rRNA sequence based analysis is suitable and valuable to ascertain phylogenetic relationships between various microsporidian strains/species. Key words: Microsporidia, Antheraea mylitta, small subunit rRNA, intergenic spacer, phylogenetic relationship.

A Novel Colonial Ciliate Zoothamnium ignavum sp. nov. (Ciliophora, Oligohymenophorea) and Its Ectosymbiont Candidatus Navis piranensis gen. nov., sp. nov. from Shallow-Water Wood Falls.

Symbioses between ciliate hosts and prokaryote or unicellular eukaryote symbionts are widespread. Here, we report on a novel ciliate species within the genus Zoothamnium Bory de St. Vincent, 1824, isolated from shallow-water sunken wood in the North Adriatic Sea (Mediterranean Sea), proposed as Zoothamnium ignavum sp. nov. We found this ciliate species to be associated with a novel genus of bacteria, here proposed as “Candidatus Navis piranensis” gen. nov., sp. nov. The descriptions of host and symbiont species are based on morphological and ultrastructural studies, the SSU rRNA sequences, and in situ hybridization with symbiont-specific probes. The host is characterized by alternate microzooids on alternate branches arising from a long, common stalk with an adhesive disc. Three different types of zooids are present: microzooids with a bulgy oral side, roundish to ellipsoid macrozooids, and terminal zooids ellipsoid when dividing or bulgy when undividing. The oral ciliature of the microzooids runs 1¼ turns in a clockwise direction around the peristomial disc when viewed from inside the cell and runs into the infundibulum, where it makes another ¾ turn. The ciliature consists of a paroral membrane (haplokinety), three adoral membranelles (polykineties), and one stomatogenic kinety (germinal kinety). One circular row of barren kinetosomes is present aborally (trochal band). Phylogenetic analyses placed Z. ignavum sp. nov. within the clade II of the polyphyletic family Zoothamniidae (Oligohymenophorea). The ectosymbiont was found to occur in two different morphotypes, as rods with pointed ends and coccoid rods. It forms a monophyletic group with two uncultured Gammaproteobacteria within an unclassified group of Gammaproteobacteria, and is only distantly related to the ectosymbiont of the closely related peritrich Z. niveum (Hemprich and Ehrenberg, 1831) Ehrenberg, 1838.

Gambierdiscus balechii sp. nov (Dinophyceae), a new benthic toxic dinoflagellate from the Celebes Sea (SW Pacific Ocean)

A new benthic toxic dinoflagellate is described from the Celebes Sea. Gambierdiscus balechii sp. nov. was isolated from seaweeds growing in tidal ponds. Its morphology was studied by means of LM and SEM; G. balechii has a very ornamented theca, a hatchet shaped second apical plate, a narrow second antapical plate and an asymmetrical third precigular plate, a unique combination of characters among Gambierdiscus species. It has a very wide size range with widths from 36 to 88μm. Phylogenetic analyses of two G. balechii strains, based on LSU rRNA (D8–D10) and partial SSUrRNA sequences confirmed that these clustererd in its’ own group, separated from the rest of Gambierdiscus species and with G. pacificus, G. belizeanus and G. scabrosus as its closest relatives. Thecate cysts are described from culture as non motile vegetative-like cells which germinated after being isolated and transferred to fresh medium. Mouse tests showed that this species is toxic and hence it is a potential cause of ciguatera in the Celebes Sea.

Molecular Phylogeny and Evolutionary Relationships between the Ciliate Genera Peniculistoma and Mytilophilus (Peniculistomatidae, Pleuronematida).

Peniculistoma mytili and Mytilophilus pacificae are placed in the pleuronematid scuticociliate family Peniculistomatidae based on morphology and ecological preference for the mantle cavity of mytiloid bivalves. We tested this placement with sequences of the small subunit rRNA (SSUrRNA) and cytochrome c oxidase subunit 1 (cox1) genes. These species are very closely related sister taxa with no distinct genetic difference in the SSUrRNA sequence but about 21% genetic difference for cox1, supporting their placement together but separation as distinct taxa. Using infection frequencies, M.pacificae, like its sister species P.mytili, does not interact with Ancistrum spp., co-inhabitants of the mantle cavity. On the basis of these ecological similarities, the fossil record of host mussels, and features of morphology and stomatogenesis of these two ciliates, we argue that M.pacificae derived from a Peniculistoma-like ancestor after divergence of the two host mussels. Our phylogenetic analyses of pleuronematid ciliates includes the SSUrRNA gene sequence of Sulcigera comosa, a Histiobalantium-like ciliate from Lake Baikal. We conclude: (i) that the pleuronematids are a monophyletic group; (ii) that the genus Pleuronema is paraphyletic; and (iii) that S.comosa is a Histiobalantium species. We transfer S.comosa to Histiobalantium and propose a new combination Histiobalantium comosa n. comb.

New considerations on the phylogeny of cyrtophorian ciliates (Protozoa, Ciliophora): expanded sampling to understand their evolutionary relationships

To rationalize the confusing relationships among the cyrtophorian ciliates, we expanded the taxon sampling by sequencing the small subunit ribosomal RNA (SSU rRNA) gene of representatives of 12 genera (20 species, 23 new sequences). The SSU rRNA sequences of Spirodysteria, Agnathodysteria, Brooklynella and Odontochlamys are reported for the first time. Phylogenetic trees were constructed, and secondary structures of variable region 4 (V4) of all genera for which SSU rRNA gene sequence data are available were predicted. The results indicate that (i) Brooklynella is likely an intermediate taxon between Dysteriidae and Hartmannulidae; (ii) the genus Dysteria is paraphyletic with Spirodysteria and Mirodysteria nested within it; (iii) the genus Agnathodysteria is well separated from Dysteria based on both molecular and morphological data; and (iv) Trithigmostoma is a basal genus of Chilodonellidae, based on both the morphological and molecular data.

Phylogenetic and morphological characterization of trypanosomes from Brazilian armoured catfishes and leeches reveal high species diversity, mixed infections and a new fish trypanosome species.

BackgroundSeveral Trypanosoma species transmitted by leeches infect marine and freshwater fish worldwide. To date, all South American fish trypanosome species identified have been based on unreliable morphological parameters. We recently isolated and cultured trypanosomes from the Brazilian armoured catfishes Hypostomus luetkeni and H. affinis. Here, we report the first phylogenetic analyses of South American (Brazilian) trypanosomes isolated from fish, and from leeches removed from these fish. We also analysed morphologically and morphometrically the different forms of fish, leech and cultured trypanosomes.MethodsV7V8 SSU rRNA and gGAPDH sequences were used for phylogenetic analysis of Brazilian fish and leech trypanosomes. Trypanosomes from cultures, fish blood and leech samples were also characterized morphologically and morphometrically by light and electron microscopy.ResultsIn blood smears from fish high trypanosome prevalence (90–100 %) and parasitemia (0.9-1.0x102) were observed. Phylogenetic relationships using SSU rRNA and gGAPDH showed that, despite relevant sequence divergence, all Brazilian fish (and derived cultures) and leech trypanosomes clustered together into a single clade. The Brazilian clade clustered with European, North American and African fish trypanosomes. Based on sequence analysis, we uncovered a new species of Brazilian fish trypanosome, Trypanosoma abeli n. sp. Trypanosoma abeli cultures contained pleomorphic epimastigotes, small trypomastigotes and rare sphaeromastigotes. Ultrastructural features of T. abeli included a cytostome-cytopharynx complex in epi- and trypomastigotes, a compact rod-like kinetoplast, lysosome-related organelles (LROs) and multivesicular bodies. Trypanosomes found in fish blood smears and leech samples were highly pleomorphic, in agreement with sequence data suggesting that catfishes and leeches often have mixed trypanosome infections.ConclusionsTrypanosoma abeli n. sp. is the first trypanosome from South American fishes isolated in culture, positioned in phylogenetic trees and characterized at the ultrastructural level. Trypanosoma abeli n. sp. is highly prevalent in H. luetkeni and H. affinis armoured catfish from the Atlantic Forest biome, and in other catfish species from the Amazon and the Pantanal. Sequencing data suggested that Brazilian catfish often have mixed trypanosome infections, highlighting the importance of molecular characterization to identify trypanosome species in fishes and leeches.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-015-1193-7) contains supplementary material, which is available to authorized users.

Genetic identification of Entamoeba polecki subtype 3 from pigs in Japan and characterisation of its pathogenic role in ulcerative colitis

To date, three Entamoeba spp. (E. suis, zoonotic E. polecki and E. histolytica) have been identified in pigs, but their pathogenicity and molecular classification have not been fully determined. Examination and pathological analysis of pigs (n=3) with diarrhoea was conducted and revealed the presence of Entamoeba organisms. We performed a genetic analysis of the isolate using the small-subunit ribosomal RNA (SSU rRNA) gene region to identify the species. A severe ulcerative colitis was observed histopathologically with inflammatory cells, including macrophages and neutrophils, infiltrating the mucous membranes of the cecum and colon. Many Entamoeba trophozoites were found at the erosion site or at ulcerative lesions. Pathogenic viruses or bacteria were not detected. The SSU rRNA sequence of the Entamoeba isolate was found to be completely homologous to that of E. polecki subtype 3.

Extending the conserved phylogenetic core of archaea disentangles the evolution of the third domain of life.

Initial studies of the archaeal phylogeny relied mainly on the analysis of the RNA component of the small subunit of the ribosome (SSU rRNA). The resulting phylogenies have provided interesting but partial information on the evolutionary history of the third domain of life because SSU rRNA sequences do not contain enough phylogenetic signal to resolve all nodes of the archaeal tree. Thus, many relationships, and especially the most ancient ones, remained elusive. Moreover, SSU rRNA phylogenies can be heavily biased by tree reconstruction artifacts. The sequencing of complete genomes allows using a variety of protein markers as an alternative to SSU rRNA. Taking advantage of the recent burst of archaeal complete genome sequences, we have carried out an in-depth phylogenomic analysis of this domain. We have identified 200 new protein families that, in addition to the ribosomal proteins and the subunits of the RNA polymerase, form a conserved phylogenetic core of archaeal genes. The accurate analysis of these markers combined with desaturation approaches shed new light on the evolutionary history of Archaea and reveals that several relationships recovered in recent analyses are likely the consequence of tree reconstruction artifacts. Among others, we resolve a number of important relationships, such as those among methanogens Class I, and we propose the definition of two new superclasses within the Euryarchaeota: Methanomada and Diaforarchaea.

Further resolving the phylogeny of Myxogastria (slime molds) based on COI and SSU rRNA genes.

To date, molecular systematics of Myxogastria has been based primarily on small subunit ribosomal RNA (SSU rRNA) and elongation factor 1-alpha (EF-1α) genes. To establish a natural classification system for the organisms, we examined phylogenetic relationships among myxogastrian species using cytochrome c oxidase subunit I (COL) and SSU rRNA genes. Twenty new sequences were obtained, including 10 COI and 10 SSU rRNA sequences, were compared with sequences of related species from GenBank in order to construct phylogenic trees. The analysis of the two data sets supported the modern phylogeny of myxogastria: orders Liceida and Trichiida formed a sister group at the most basal clade, while orders Stemonitida and Physarida formed a close group, and order Echinostelida was a sister group to Stemonitida and Physarida. However, the partial COI sequences were too conserved to resolve of the branches in Stemonitida and Physarida. In addition, we also deemed the specific edited mRNA events of COI sequences in myxogastrian species.

Andersenia, a genus of filamentous, sand-dwelling Pelagophyceae from southeastern Australia

:A new marine pelagophyte genus, Andersenia, was described from clonal cultures established from sand samples collected in coastal tide pools from southeastern Australia. Thin, uniseriate, unbranched filaments were variable in length up to 1.0 mm, 7–12 μm in width and surrounded by a gelatinous envelope. Cells contained one or two golden brown, lobed chloroplasts. Growing filaments often segmented into fragments of varying length that were continuous within the filament envelope and eventually produced multicellular knots, giving mature filaments a gnarled appearance. Most vegetative cells generated asexual motile zoospores that were heterokont with two unequal, heterodynamic flagella that arose together approximately one-third the length of the cell from the anterior surface; one or two lobed chloroplasts were located towards the posterior of the cells, while numerous granules of uniform size were typically obvious at the cell periphery. During segmentation, zoospore formation and release, the unusual cross walls shaped like biconcave discs were revealed and were characteristic of the genus. Zoospores adhered and secreted an adhesive pad within minutes of attachment and initiated new filaments. Phylogenetic analysis based on the nuclear-encoded small subunit ribosomal RNA (SSU rRNA) as well as morphological differences placed the new genus Andersenia in the class Pelagophyceae, and the three strains studied formed two species, A. nodulosa sp. nov. and A. australica sp. nov. Andersenia nodulosa filaments were longer and the cells smaller than in A. australica, and they differed by 16 nucleotides (99.2% identity) at the SSU rRNA sequence level.

DNA typing of ancient parasite eggs from environmental samples identifies human and animal worm infections in Viking-age settlement.

Ancient parasite eggs were recovered from environmental samples collected at a Viking-age settlement in Viborg, Denmark, dated 1018-1030 A.D. Morphological examination identified Ascaris sp., Trichuris sp., and Fasciola sp. eggs, but size and shape did not allow species identification. By carefully selecting genetic markers, PCR amplification and sequencing of ancient DNA (aDNA) isolates resulted in identification of: the human whipworm, Trichuris trichiura , using SSUrRNA sequence homology; Ascaris sp. with 100% homology to cox1 haplotype 07; and Fasciola hepatica using ITS1 sequence homology. The identification of T. trichiura eggs indicates that human fecal material is present and, hence, that the Ascaris sp. haplotype 07 was most likely a human variant in Viking-age Denmark. The location of the F. hepatica finding suggests that sheep or cattle are the most likely hosts. Further, we sequenced the Ascaris sp. 18S rRNA gene in recent isolates from humans and pigs of global distribution and show that this is not a suited marker for species-specific identification. Finally, we discuss ancient parasitism in Denmark and the implementation of aDNA analysis methods in paleoparasitological studies. We argue that when employing species-specific identification, soil samples offer excellent opportunities for studies of human parasite infections and of human and animal interactions of the past.