Nuclear rRNA Research Articles

Updated phylogeny of Vestimentifera (Siboglinidae, Polychaeta, Annelida) based on mitochondrial genomes, with a new species

Siboglinid tubeworms are found at chemosynthetic environments worldwide and the Vestimentifera clade is particularly well known for their reliance on chemoautotrophic bacterial symbionts for nutrition. The mitochondrial genomes have been published for nine vestimentiferan species to date. This study provides new complete mitochondrial genomes for ten further Vestimentifera, including the first mitochondrial genomes sequenced for Alaysia spiralis, Arcovestia ivanovi, Lamellibrachia barhami, Lamellibrachia columna, Lamellibrachia donwalshi, and unnamed species of Alaysia and Oasisia. Phylogenetic analyses combining fifteen mitochondrial genes and the nuclear 18S rRNA gene recovered Lamellibrachia as sister to the remaining Vestimentifera and Riftia pachyptila as separate from the other vent-endemic taxa. Implications and auxiliary analyses regarding differing phylogenetic tree topologies, substitution saturation, ancestral state reconstruction, and divergence estimates are also discussed. Additionally, a new species of Alaysia is described from the Manus Basin.

2D approach to reconstruct the evolutionary history of clevelandellids (Ciliophora, Armophorea) inhabiting the hindgut of the Panesthiinae cockroaches

AbstractThe ciliate order Clevelandellida unites endosymbionts of the digestive tract of a variety of invertebrates and vertebrates. In the present study, the primary and secondary structures of nuclear and hydrogenosomal rRNA molecules were employed to reconstruct the phylogenetic relationships and to estimate the divergence times of clevelandellids inhabiting the hindgut of the Panesthiinae cockroaches. The secondary structure information was incorporated in phylogenetic analyses using two different strategies, viz., indirectly through 2D‐guided alignments and directly through so‐called pseudo‐protein data. Nuclear and hydrogenosomal markers carried a consistent phylogenetic signal and robustly supported the monophyletic origin of the family Clevelandellidae as well as of its four genera. According to Bayesian relaxed molecular clock analyses, the last common ancestor (LCA) of the family Clevelandellidae very likely emerged during the Late Cretaceous in the Oriental region. Its descendants most likely expanded to Australia in concert with the Neogene colonization and radiation of their host Panesthiinae cockroaches. Taking into account the time‐calibrated phylogenies and the fact that early branching members of the order Clevelandellida inhabit the digestive tracts of amphibians, it is tempting to speculate that the LCA of the Clevelandellida evolved in ectothermic vertebrates. Amphibians could have brought clevelandellids to the land, where they may have been transmitted to the cockroach digestive tract upon feeding on amphibian faeces.

Taxonomic contributions to Hapalidiales (Corallinophycidae, Rhodophyta): Boreolithothamnion gen. nov., Lithothamnion redefined and with three new species and Roseolithon with new combinations.

Phylogenetic analyses of rbcL gene sequences and of concatenated rbcL, psbA, and nuclear SSU rRNA gene sequences resolved the generitype of Lithothamnion, L. muelleri, in a clade with three other southern Australian species, L. kraftii sp. nov., L. saundersii sp. nov., and L. woelkerlingii sp. nov. Cold water boreal species currently classified in Lithothamnion and whose type specimens have been sequenced are transferred to Boreolithothamnion gen. nov., with B. glaciale comb. nov. as the generitype. The other species are B. giganteum comb. nov., B. phymatodeum comb. nov., and B. sonderi comb. nov., whose type specimens are newly sequenced, and B. lemoineae comb. nov., B. soriferum comb. nov., and B. tophiforme comb. nov., whose type specimens were already sequenced. Based on rbcL sequences from the type specimens of Lithothamnion crispatum, L. indicum, and L. superpositum, each is recognized as a distinct species and transferred to the recently described Roseolithon as R. crispatum comb. nov., R. indicum comb. nov., and R. superpositum com. nov., respectively. To correctly assign species to these three genera based only on morpho-anatomy, specimens must have multiporate conceptacles and some epithallial cells with flared walls. The discussion provides examples demonstrating that only with phylogenetic analyses of DNA sequences can the evolution of morpho-anatomical characters of non-geniculate corallines be understood and applied at the correct taxonomic rank. Finally, phylogenetic analyses of DNA sequences support recognition of the Hapalidiales as a distinct order characterized by having multiporate tetra/bisporangial conceptacles, and not as a suborder of Corallinales whose tetra/bisporangial conceptacles are uniporate.

Pseudosperma pamukkalense (Inocybaceae: Agaricomycetes), a new species from Turkey

A new species, Pseudosperma pamukkalense, discovered in Pinus nigra subsp. pallasiana forests is described from the Mediterranean climate zone of south-western Turkey. The novel species is recognized by the presence of pale straw to brownish yellowish pileus, mingled with reddish-brownish streaks with age, smooth to finely innately fibrillose pileus surface, whitish stipe with mainly cylindrical to clavate caulocystidia, large subphaseoliform basidiospores, and mostly narrowly to broadly clavate cheilocystidia. The description of the new species is based on morphological characters, and illustrations, line drawings and comparisons with allied species are provided. A molecular phylogenetic analysis of the internal transcribed spacer (ITS) and the nuclear 28S rRNA gene (nrLSU) regions supported the taxonomic recognition of the new species which was on a separate branch within the genus Pseudosperma.

Integrative taxonomy provides evidence for a cryptic lineage in the velvet worm Peripatopsis birgeri species complex (Onychophora: Peripatopsidae) in KwaZulu-Natal, South Africa

During the present study, species boundaries in the velvet worm Peripatopsis birgeri species complex in KwaZulu-Natal, South Africa, were examined with the use of DNA sequence data, gross morphology, scanning electron microscopy (SEM) and ecological niche modelling. Mitochondrial CO1 and nuclear 18S rRNA sequence data were used to generate a phylogeny using both a Bayesian inference and maximum likelihood approaches. Both the CO1 sequence data and the combined DNA sequence topology (CO1 + 18S rRNA) revealed the presence of two geographically distinct clades within the P. birgeri species complex. Results from three species delimitation methods (GMYC, PTP and ASAP), were incongruent in determining the number of species within the species complex and generally overestimated the number of operational taxonomic units. The latter result can be attributed to the marked genetic structure within the species complex, a result corroborated by the CO1 haplotype network and statistically significant F ST values. Divergence time estimation suggests that the two clades diverged during the Plio/Pleistocene. Niche modelling revealed that the two clades were differentially impacted by bioclimatic variables and occupied different habitats. Gross morphological characteristics, such as leg pair numbers and colour revealed no fixed differences between the two clades, however, a creamy white headband/collar occurred exclusively in specimens of clade 1 (P. birgeri). In contrast, SEM revealed fixed dorsal and ventral scale rank differences between the two clades. The results corroborate the presence of a novel species within the P. birgeri s.s. species complex. Peripatopsis birgeri s.s. is revised and restricted to the southern Drakensberg and a new species, P. polychroma sp. nov. (clade 2), from the northern Drakensberg and adjacent Afrotemperate forests in the interior of KwaZulu-Natal is described. https://zoobank.org/urn:lsid:zoobank:org:pub:569557AB-8BC8-49B6-B8AA-96507371297B

Assessing the degradation of environmental DNA and RNA based on genomic origin in a metabarcoding context

AbstractMolecular tools of species identification based on eNAs (environmental nucleic acids; environmental DNA [eDNA] and environmental RNA [eRNA]) have the potential to greatly transform biodiversity science. However, the ability of eNAs to obtain “real‐time” biodiversity estimates may be complicated by the differential persistence and degradation dynamics of the molecular template (eDNA or eRNA) and the barcode marker used. Here, we collected water samples over a 28‐day period to comparatively assess species detection using eDNA and eRNA metabarcoding of two distinct barcode markers—a mitochondrial mRNA marker (COI) and a nuclear rRNA marker (18S)—following complete removal of Arthropoda taxa in a semi‐natural freshwater system. Our findings demonstrate that Arthropoda community composition was largely influenced by marker choice, rather than molecular template, individual microcosm, or sampling time point. Furthermore, although eRNA may capture similar species diversity as the established eDNA method, this finding may be marker‐dependent. Although we found little to no difference in decay rates observed among sample groups (COI eDNA, COI eRNA, 18S eDNA, 18S eRNA), this result is likely due to limitations in the ability of eNA‐based metabarcoding to provide a strong correlation between true eNA copy numbers present in the environment and final read counts obtained (following the metabarcoding workflow). Collectively, our findings provide further support for the use of multi‐marker assessments in metabarcoding surveys to unravel the broadest taxonomic diversity possible, highlight the limitations of eNA metabarcoding methods in providing accurate decay rate estimates, as well as establish the need for further comparative studies using both metabarcoding and single‐species detection methods to assess the persistence and degradation dynamics of eNAs for a diverse range of taxa.

Systematic position of the genus Metacanthocephalus Yamaguti, 1959 (Palaeacanthocephala: Echinorhynchida) inferred from molecular evidence, with a redescription of Metacanthocephalus ovicephalus (Zhukov, 1960).

The familial affiliation of the echinorhynchid palaeacanthocephalan genus Metacanthocephalus has been uncertain, with the three families Echinorhynchidae, Leptorhynchoididae, and Rhadinorhynchidae having been suggested as its parent taxon. In this study, adult individuals of Metacanthocephalus ovicephalus from the intestine of the cresthead flounder Pseudopleuronectes schrenki (new host) and the dark flounder Pseudopleuronectes obscurus in Hokkaido, Japan, were examined. Using three gene markers (mitochondrial cytochrome c oxidase subunit I; nuclear 18S and 28S rRNA genes) determined from two specimens of M. ovicephalus, a molecular phylogenetic analysis was performed along with relevant sequences available in public databases representing 26 species in eight families of the order Echinorhynchida, along with five species from Polymorphida and two from Eoacanthocephala. The resulting phylogram showed that M. ovicephalus was nested within a clade along with nine species in eight genera (Brentisentis yangtzensis, Dentitruncus truttae, Dollfusentis bravoae, Koronacantha mexicana, K. pectinaria, Leptorhynchoides thecatus, Neotegorhynchus cyprini, Pseudoleptorhynchoides lamothei, and Tegorhynchus [= Illiosentis] sp.). In this paper, we propose i) a set of morphological characters to circumscribe members represented by this clade as a Linnaean higher taxon, ii) to place this taxon at the rank of family, iii) to refer to it as Leptorhynchoididae, and iv) to regard Illiosentidae as a junior synonym of Leptorhynchoididae. Our morphological examination revealed a single vaginal sphincter in M. ovicephalus, a character that was not mentioned in any of the previous literature. By this character, along with geographical distribution and host fish, six congeners currently recognized in Metacanthocephalus can be divided into two groups.

First mitochondrial genomes of Anaspidacea (Malacostraca, Crustacea) and the phylogenetic relationships of mountain shrimps (AnaspidesThomson, 1894) and their relatives within Anaspidesidae

AbstractWe present the first complete mitochondrial genomes for Anaspidacea by sequencing 24 specimens from 12 different species in four genera (AnaspidesThomson, 1894; ParanaspidesSmith, 1908; AllanaspidesSwain, Wilson, Hickman & Ong, 1970; and MicraspidesNicholls, 1931). We recovered 20 complete (13 protein coding genes, two ribosomal RNA genes, 22 transfer RNAs), and four partial mitogenomes. The full mitogenomes range in length from 15,213 bp to 17,962 bp. We found five different gene orders and reconstruct the ground pattern of Anaspidacea, which differs from the hypothetical pancrustacean ground pattern by the translocation and reversal of tRNA-L1. The same translocation is also found in Euphausiacea and could represent a synapomorphy of these two taxa. Moreover, we reconstruct the phylogenetic relationships of the Anaspidesidae using a data set consisting of the mitochondrial protein coding genes, the two ribosomal RNAs as well as nuclear 18S and 28S rRNA. Our results strongly corroborate the monophyly of all three anaspidesiid genera, with Paranaspides as the sister group to Anaspides, which together, are sister to Allanaspides. Lastly, we resolve the main phylogenetic relationships within Anaspides.

Suspended phosphorus sustains algal blooms in a dissolved phosphorus-depleted lake

The expansion of algal bloom in surface waters is a global problem in the freshwater ecosystem. Differential reactivity of organic phosphorus (Po) compounds from organic debris, suspended particulate matter (SPM), and sediment towards hydrolysis can dictate the extent of supply often limited inorganic P (Pi) for algal growth, thereby controlling the extent of bloom. Here, we combined solution P-31 nuclear magnetic resonance (31P NMR), sequential extraction, enzymatic hydrolysis, and 16S rRNA measurements to characterize speciation and biogeochemical cycling of P in Lake Erhai, China. Lower ratios of diester-P/monoester-P in SPM in January (mean 0.09) and July (0.14) than that in April (0.29) reflected the higher degree of diester-P remineralization in cold and warm months. Both H2O-Pi and Po were significantly higher in SPM (mean 1580 mg ·kg−1 and 1618 mg ·kg−1) than those in sediment (mean 8 mg ·kg−1 and 387 mg ·kg−1). In addition, results from enzymatic hydrolysis experiments demonstrated that 61% Po in SPM and 58% in sediment in the H2O, NaHCO3, and NaOH extracts could be hydrolyzed. These results suggested that H2O-Pi and Po from SPM were the primarily bioavailable P sources for algae. Changes of Pi contents (particularly H2O-Pi) in algae and alkaline phosphatase activity (APA) during the observation periods were likely to be controlled by the strategies of P uptake and utilization of algae. P remobilization/remineralization from SPM likely resulted from algae and bacteria (e.g., Pseudomonas). Collectively, these results provide important insights that SPM P could sustain the algal blooms even if the dissolved P was depleted in the water column.

Occurrence of an unidentified harrimaniid acorn worm in the genus Stereobalanus (Hemichordata: Enteropneusta) from the Japan Trench hadal zone

A number of soft fragments of uncertain identity, mostly taking a form of a disk or button, were found among trawled material from the hadal zone (7426–7654 m in depth) in the Japan Trench during the cruise KH-22-8 of the R/V Hakuho-maru in October 2022. These enigmatic ‘disks’ subsequently turned out to be the proboscides of enteropneusts severed from the collar. A molecular phylogenetic analysis based on the mitochondrial 16S rRNA and nuclear 18S rRNA gene sequences determined from one of the fragments along with others available in public databases indicated that the species in question was sister to the harrimaniid enteropneust Stereobalanus canadensis (Spengel, 1893). Some morphological features of the fragments—the proboscis longitudinal musculature arranged in radial plates, the four tubular ovaries, and the absence of synapticula on the gill bars—support that the Japan Trench species would belong to Stereobalanus Spengel, 1902. This study represents the deepest record of Stereobalanus and the first report of enteropneusts from the Japan Trench hadal zone, albeit identified to the genus level. While the species is putatively undescribed, a formal taxonomic description should await intact specimens in future studies.

First record of molecular and pathological investigations of physalopterid larvae infection in northern palm squirrel Funambulus pennantii.

Around 100 reported species of Physaloptera commonly infect mammals, reptiles, birds, and amphibians. The identification of Physaloptera species solely on morphological characteristics is difficult, especially in the case of larval and congeneric infections. The present study is an attempt to identify molecularly and to perform phylogeny and pathology of natural Physaloptera larval infection in northern palm squirrels. The molecular confirmation of the recovered parasitic stages was performed by targeting the nuclear 18S rRNA gene sequence. Phylogenetic analysis and evolutionary divergence of the present study isolate with GenBank™ archived Physaloptera sequences were performed. The cysts (containing the larval stages) were subjected to histopathological examination. Morphological identification of the larval stages revealed the presence of pseudolabia, two spines, and a collar-like projection at the anterior end. Histopathology of the cysts revealed transverse sections of parasites in the lumen along with the thickened cystic wall, infiltration of mononuclear cells, fibrous tissue proliferation in the wall, and cellular debris in the cystic lumen. The molecularly confirmed and sequenced present study isolate was submitted to GenBank™ under the accession number LC706442. Blast analysis revealed 96.82-98.64% nucleotide homology of the present study isolate to the GenBank™ archived Physaloptera sequences. The isolate of the present study was monophyletic with Physaloptera sp. and P. praeputialis recovered from the cats of Haryana, India. Also, evolutionary divergence studies revealed no difference among these sequences. The present study evinced the most probable role of the northern palm squirrel Funambulus pennantii as an aberrant or second intermediate host for P. praeputialis.

Confirmation of Neoporphyra cf. dentata on Shikinejima, Izu Islands, southcentral Japan, and comparison with co‐occurring Neoporphyra haitanensis

SUMMARYThe Izu Islands of southcentral Japan are thought to fall within the distribution range of Neoporphyra dentata. However, the gametophytic blades of Bangiales collected from Shikinejima and Hachijojima, Izu Islands, were identified as Neoporphyra haitanensis in our previous study. Thus, it became uncertain whether N. dentata is distributed in the Izu Islands, including Shikinejima. To clarify whether N. dentata grows on Shikinejima, we conducted a further distribution survey of N. dentata on the island. The morphological features of the blade samples collected from an additional sampling site on Shikinejima were more similar to those of N. dentata than to those of N. haitanensis: the blade thickness and the division formula of spermatangia resembled those of the former species rather than the latter species. However, the division formula of zygotosporangia was different from those of either species. The phylogenetic analyses of the rbcL gene indicated that the samples were resolved in a clade including N. dentata collected from Shirahama, Chiba Prefecture, and Enoshima, Kanagawa Prefecture, Honshu, Japan. The p‐distances of the chloroplast rbcL gene and nuclear 18S rRNA also supported identification of the samples as N. dentata. The results demonstrated that N. dentata is also distributed on Shikinejima with co‐occurring N. haitanensis, and that the island materials of the two species are genetically different from other materials of the two species, respectively.

Cryptomonas pyrenoidifera organellar genomes and estimation of its ITS2 sequence diversity using lineage directed barcode primers

ABSTRACT Cryptomonas is a common metropolitan freshwater microalgal genus that is easily recognizable due to its distinctive asymmetric cellular morphology and swimming pattern. There are currently 71 recognized Cryptomonas species but these can be difficult to identify by cellular morphology alone. This makes estimation of Cryptomonas diversity from environmental samples challenging as it requires culturing of strains followed by sequencing of genetic markers for clear identifications. In this paper we describe the isolation and culture of Cryptomonas pyrenoidifera from a small ephemeral pool in Southwestern Virginia, USA, with an annual recurrent population of this genus. Genomic resources from this isolate, including complete chloroplast and mitochondrial genomes, and nuclear and nucleomorph rRNA regions, were completed and archived. Metabarcoding, using lineage-directed primers designed to amplify the ITS2 region of Cryptomonas, was used to estimate an intra-specific variation of 99.3% for the C. pyrenoidifera ITS2 barcode from this natural environment. Metabarcoding also revealed that at least twelve phylogenetic species were present in this body of water. Our results provide new genomic resources for C. pyrenoidifera and suggest that metabarcoding with the ITS2 marker is a feasible approach to estimating Cryptomonas diversity and identification.

Multigene phylogeny reveals a cryptic diversity in the genus Dinobryon (Chrysophyceae) with integrative description of five new species.

The genus Dinobryon is one of the most recognizable chrysophyte genera, characterized by dendroid colonies with a biflagellate inside each cellulosic lorica. The representative forms of lorica are cylindrical, conical, vase, or funnel shaped, with undulation on the lorica wall. Traditionally, the morphological characteristics of the lorica and the colony organization have been used for the delimitation of Dinobryon species. To understand the taxonomy and phylogeny of colonial Dinobryon species, we performed molecular and morphological studies using 39 unialgal cultures and 46 single colony isolations from environmental specimens collected in Korea. We used a nuclear internal transcript spacer (ITS1-5.8S-ITS2) to find the genetic diversity of Dinobryon from environmental samples and a combined dataset from six gene sequences (nuclear SSU and LSU rRNA, plastid LSU rRNA, rbcL and psaA, and mitochondrial CO1 genes) for phylogenetic analysis. We found 15 different lineages based on the genetic diversity of the nuclear ITS sequences. The phylogenetic tree of the colonial species based on the combined multigene dataset were divided into 18 subclades, including five new species, each with unique molecular signatures for the E23-5 helix of the V4 region in the nuclear SSU rRNA and the E11-1 helix of D7b, and the E20-1 helix of D8 regions in the nuclear LSU rRNA. Morphological studies were focused on lorica dimension and shape, and stomatocyst morphology. The Dinobryon species showed similarities or differences in lorica morphologies between and within species, and also differences in lorica size between culture and environmental samples. Five Dinobryon species formed distinctive stomatocysts, their stomatocyst morphologies, including collar structure, surface ornamentation, and cyst shape, showed unique characteristics in each species and were useful for identification. Here, we propose five new species based on morphological and molecular evidences: D. cylindricollarium, D. exstoundulatum, D. inclinatum, D. similis, and D. spinum.

Hymenolepis diminuta, phylogenetic analyses of nuclear rRNA + ITS and mitochondrial cox1 and its infections in non-human primates.

Hymenolepis diminuta is a tapeworm commonly found worldwide in small rodents such as rats with occasional reports in other definitive hosts such as primates including chimpanzees and humans. It has not been reported in African green monkey (AGM, Chlorocebus sabaeus), and the parasite's molecular phenotype and phylogeny remain primitively sketchy. The aims of the current study were to determine if H. diminuta infected AGMs, to molecularly characterize H. diminuta and to review its infection in non-human primates. Feces of AGMs were examined visually for adult helminths and microscopically for eggs using centrifugation flotation. Total DNA extracted from eggs was amplified by PCR followed by DNA sequencing of targeted sequences of nuclear rRNA + internal transcribed spacers (ITS) and mitochondrial cox1. Phylogenetic analyses were performed. The DNA sequences of both nuclear rRNA + ITS and mitochondrial cox1 showed more than 98% and 99% identity to the known sequences respectively. Hymenolepis diminuta has been reported in various non-human primates with the highest prevalence of 38.5% in the white-headed capuchin monkey. The study presented here confirms that this tapeworm is capable of infecting various species of non-human primates with the first report of infections in AGM. Phylogenetic analyses of rRNA + ITS and mitochondrial cox1 demonstrated three separated clades I, II and III with the newly described AGM1 isolate belonging to the clade I. Whether these differences are at species level remains to be confirmed.

Genome skimming elucidates the evolutionary history of Octopoda

Phylogenies for Octopoda have, until now, been based on morphological characters or a few genes. Here we provide the complete mitogenomes and the nuclear 18S and 28S ribosomal genes of twenty Octopoda specimens, comprising 18 species of Cirrata and Incirrata, representing 13 genera and all five putative families of Cirrata (Cirroctopodidae, Cirroteuthidae, Grimpoteuthidae, Opisthoteuthidae and Stauroteuthidae) and six families of Incirrata (Amphitretidae, Argonautidae, Bathypolypodidae, Eledonidae, Enteroctopodidae, and Megaleledonidae) which were assembled using genome skimming. Phylogenetic trees were built using Maximum Likelihood and Bayesian Inference with several alignment matrices. All mitochondrial genomes had the ‘typical’ genome composition and gene order previously reported for octopodiforms, except Bathypolypus ergasticus, which appears to lack ND5, two tRNA genes that flank ND5 and two other tRNA genes. Argonautoidea was revealed as sister to Octopodidae by the mitochondrial protein-coding gene dataset, however, it was recovered as sister to all other incirrate octopods with strong support in an analysis using nuclear rRNA genes. Within Cirrata, our study supports two existing classifications suggesting neither is likely in conflict with the true evolutionary history of the suborder. Genome skimming is useful in the analysis of phylogenetic relationships within Octopoda; inclusion of both mitochondrial and nuclear data may be key.

Infant Vitamin D Supplements, Fecal Microbiota and Their Metabolites at 3 Months of Age in the CHILD Study Cohort.

Infant vitamin D liquid formulations often contain non-medicinal excipients such as glycerin (ie. glycerol) and 1,2-propanediol (1,2-PD). We examined whether infant vitamin D supplementation is associated with fecal glycerol and 1,2-PD concentrations at 3 months of age and characterized associations between these two molecules, and gut microbiota and their metabolites. Fecal metabolites and microbiota were quantified using Nuclear Magnetic Resonance Spectroscopy and 16S rRNA sequencing, respectively, in 575 infants from the CHILD Study at 3 months of age. Vitamin D supplement use was determined using questionnaires. Vitamin D supplementation was associated with greater odds of high 1,2-PD (adjusted OR 1.65 95% CI: 1.06, 2.53) and with decreased odds of high fecal glycerol (adjusted OR: 0.62 95% CI: 0.42, 0.90) after adjustment for breastfeeding and other covariates. Our findings were confirmed in linear regression models; vitamin D supplementation was positively associated with fecal 1,2-PD and inversely associated with glycerol (aβ: 0.37, 95% CI 0.03, 0.71 & aβ: -0.23 95% CI -0.44, -0.03, respectively). Fecal 1,2-PD and glycerol concentrations were negatively correlated with each other. Positive correlations between fecal 1,2-PD, Bifidobacteriaceae, Lactobacillaceae, Enterobacteriaceae and acetate levels were observed. Our research demonstrates that infant vitamin D supplement administration may differentially and independently influence infant gut microbiota metabolites.

Genetic features of the marine polychaete Sirsoe methanicola from metagenomic data

The methane ice worm Sirsoe methanicola is the only marine polychaete species observed to colonize the methane hydrates of the Gulf of Mexico. Methane hydrates are ephemeral features of deep-sea cold seeps, and finding worm-colonized hydrates is rare; thus, little is known about these organisms. Recent metagenomic analysis predicted prokaryotic taxa and pathways from S. methanicola gut contents and worm fragments. Here, we increase the genetic information known about S. methanicola by assembling its nuclear rRNA genes (18S rRNA and 28S rRNA), mitochondrial genome (mitogenome), and other protein-coding genes from metagenomic data. Assembled 18S rRNA and 28S rRNA gene sequences of S. methanicola were near-identical to previously reported S. methanicola sequences. The 17,403-bp mitogenome of S. methanicola is the first mitogenome sequence of the family Hesionidae, consisting of 39.03% G+C content, 13 protein-coding genes, 24 tRNAs (including two split trnM genes), and 2 rRNA genes. Protein-coding genes in the S. methanicola metagenomes assigned to the phylum Annelida were involved in cell adhesion, signaling, ubiquitin system, metabolism, transport, and other processes. From the metagenomes, we also found 42 homologs of the cytochrome P450 (CYP) superfamily putatively involved in polycyclic aromatic hydrocarbon (PAH) metabolism. Our results encourage further studies into the genetic adaptations of S. methanicola to its methane hydrate habitat, especially in the context of deep-sea ecology and nutrient cycling.

Molecular phylogeny of the spiny-surfaced species of the dinoflagellate Prorocentrum with the description of P. thermophilum sp. nov. and P.criophilum sp. nov. (Prorocentrales, Dinophyceae).

Spiny-surfaced species of Prorocentrum form harmful algal blooms, and its taxonomic identity is obscure due to the size and shape variability. Molecular phylogenies reveal two major clades: one for P. cordatum with sequences mainly retrieved as P. minimum, and the other for P. shikokuense with sequences also retrieved as P. dentatum and P. donghaiense. Several closely related clades still need to be characterized. Here, we provide nuclear SSU and LSU rRNA genes, and nuclear ITS region (ITS1-5.8S gene-ITS2) sequences of the strain CCMP3122 isolated from Florida (initially named P. donghaiense) and strains Prorocentrum sp. RCC6871-2 from the Ross Sea, Antarctica. We describe Prorocentrum thermophilum sp. nov. based on the strain CCMP3122, a species also distributed in the open waters of the Gulf of Mexico, New Zealand, and the Arabian Gulf; and Prorocentrum criophilum sp. nov. based on the strain RCC6872, which is distributed in the Antarctic Ocean and Arctic Sea. Prorocentrum thermophilum is roundish (~14 μm long, ~12 μm wide), with an inconspicuous anterior spine-like prolongation under light microscopy, valves with tiny, short knobs (5-7 per μm2 ), and several (<7) large trichocyst pores (~0.3 μm) in the right valve, as well as smaller pores (~0.15 μm). Prorocentrum criophilum is round in valve view (~11 μm long, 10 μm wide) and asymmetrically roundish in lateral view, the periflagellar area was not discernible under light microscopy, valves with very tiny, short knobs (6-10 per μm2 ), and at least 12 large pores in the right valve. Other potentially undescribed species of spiny-surfaced Prorocentrum are discussed.

Description of a new thermal species of the genus Hyalella from Peru with molecular phylogeny of the family Hyalellidae (Crustacea, Amphipoda)

In recent years, the impact of rising water temperatures associated with global warming on cold-water freshwater organisms has become a major issue, and understanding the physiological and ecological elements that support temperature limits is essential for the conservation biology of freshwater organisms. We describe a new species of thermophilic hyalellid amphipod, Hyalella yashmara sp. nov. from the Peruvian hot spring Baños del Inca Cajamarca and this could potentially contribute to understanding the high temperature preference of these. We found that this new species can live in water temperatures ranging from 19.8 to 52.1°C, that, to our knowledge, is the highest recorded habitat temperature of amphipods. Hyalella yashmara sp. nov. is most similar to H. meinerti Stebbing, 1899 from Peru. However, this new species differs from the latter in features of gnathopods 1 and 2, sternal gills, uropod 3 and telson. A detailed morphological comparison between Hyalella yashmara sp. nov. and Peruvian species is also provided. Our molecular phylogenetic analyses based on the nuclear 28S rRNA and mitochondrial cytochrome c oxidase subunit I (COI) gene sequences strongly support the monophyly of Hyalellidae (=Hyalella). Since Hyalellidae was found to form a sister group with Chiltoniidae, these two families were expected to have originated from a common ancestor that invaded freshwater habitats from marine environments when the continents of South America, Africa and Australia were united as Gondwana. Our findings suggest that the South American species of Hyalella are not monophyletic and that the North American species are likely to share a most recent common ancestor with H. yashmara sp. nov. ZooBank: urn:lsid:zoobank.org:act:190CFB16-7BE4-4786-A97F-0AFD8CD72DEA