16S rDNA Data Research Articles

Corynoneura Winnertz species from Hunan Province, Oriental China, delineated with morphological and 16S rDNA data (Diptera, Chironomidae).

The genus Corynoneura Winnertz, 1846 from Hunan Province in Oriental China is reviewed. Four new species, C.enormis Fu sp. nov., C.gibbera Fu sp. nov., C.incuria Fu sp. nov., and C.longshanensis Fu sp. nov. are described and illustrated based on adult males. Sequence data from the 16S rDNA gene were used to infer relationships between these species and complement morphological delineation. Sequences from the mitochondrial large ribosomal subunit (16S rDNA) from these species are uploaded to the National Center for Biotechnology Information (NCBI). Relationships were inferred using the Neighbor-Joining method based on 16S rDNA.

A New Species and New Record of Freshwater Turbellarians of the Genus Gieysztoria (Platyhelminthes: Rhabdocoela) from China.

A new species of Dalyelliidae, Gieysztoria pellucida Wang and You, is described based on material collected in southern China through an integrative approach combining morphological, histological, and molecular (18S and 28S rDNA) data. Gieysztoria pellucida sp. nov. is morphologically characterized by a fan-shaped (about 270° when pressed) stylet, consisting of 13 similar distal spines and a broad girdle without fenestrae region. This stylet is distinct from that of any other similar species in the Aequales group to which this species belongs. In addition, specimens identifiable as Gieysztoria garudae Van Steenkiste, Van Mulken, and Artois, 2012 were discovered from the same location as G. pellucida sp. nov. Gieysztoria garudae has previously been known only from India; the present study thus represents the first record of the species from China.

18S and ITS2 rDNA sequence-structure phylogeny of Prototheca (Chlorophyta, Trebouxiophyceae)

Protothecosis is an infectious disease caused by organisms currently classified within the green algal genus Prototheca. The disease can manifest as cutaneous lesions, olecranon bursitis or disseminated or systemic infections in both immunocompetent and immunosuppressed patients. Concerning diagnostics, taxonomic validity is important. Prototheca, closely related to the Chlorella species complex, is known to be polyphyletic, branching with Auxenochlorella and Helicosporidium. The phylogeny of Prototheca was discussed and revisited several times in the last decade; new species have been described. Phylogenetic analyses were performed using ribosomal DNA (rDNA) and partial mitochondrial cytochrome b (cytb) sequence data. In this work we use Internal Transcribed Spacer 2 (ITS2) as well as 18S rDNA data. However, for the first time, we reconstruct phylogenetic relationships of Prototheca using primary sequence and RNA secondary structure information simultaneously, a concept shown to increase robustness and accuracy of phylogenetic tree estimation. Using encoded sequence-structure data, Neighbor-Joining, Maximum-Parsimony and Maximum-Likelihood methods yielded well-supported trees in agreement with other trees calculated on rDNA; but differ in several aspects from trees using cytb as a phylogenetic marker. ITS2 secondary structures of Prototheca sequences are in agreement with the well-known common core structure of eukaryotes but show unusual differences in their helix lengths. An elongation of the fourth helix of some species seems to have occurred independently in the course of evolution.

Capsalids (Platyhelminthes: Monogenea) from marine fishes off Okinawa in Japan with the proposal of two new genera.

Molecular studies of the Capsalidae suggested that the genus Benedenia is polyphyletic, but a taxonomic organization of the genus that reflects molecular data has not yet been proposed. As a result of molecular analysis (28S rDNA, ITS1-5.8S-ITS2, and cox1 data) including specimens of Benedeniinae newly obtained from Okinawa-jima Island in Japan, two new genera and the revival of Tareenia independent to the genus Benedenia are proposed. Gracilobenedenia n. gen. is distinguished from the other genera of Benedeniinae based on morphological characteristics. This new genus comprises 6 species: G. lutjani n. comb. (type species), G. anticavaginata n. comb., G. rohdei n. comb., G. beverleyburtonae n. comb., G. kuremibai n. gen., n. sp., and G. hichi n. gen., n. sp. Armatobenedenia n. gen. is a monotypic genus for A. armata n. comb. The present molecular phylogenetic analysis showed the independence of Tareenia, and it can be morphologically separated from the other benedeniines. Four species including two new species obtained from Okinawa-jima Island are reported: G. kuremibai n. sp., G. hichi n. sp., G. lutjani n. comb., and Metabenedeniella parva. Furthermore, in the species identification and phylogenetic analysis of capsalids, the usefulness of not only the 28S rDNA but also ITS and the cox1 regions was suggested. These genes were evaluated the efficacy of those regions in DNA barcoding, and the ITS and cox1 regions shown to be useful for DNA barcoding in capsalids compared to the 28S rDNA sequence.

Comparison of Periodontal Bacteria of Edo and Modern Periods Using Novel Diagnostic Approach for Periodontitis With Micro-CT.

Ancient dental calculus, formed from dental plaque, is a rich source of ancient DNA and can provide information regarding the food and oral microbiology at that time. Genomic analysis of dental calculus from Neanderthals has revealed the difference in bacterial composition of oral microbiome between Neanderthals and modern humans. There are few reports investigating whether the pathogenic bacteria of periodontitis, a polymicrobial disease induced in response to the accumulation of dental plaque, were different between ancient and modern humans. This study aimed to compare the bacterial composition of the oral microbiome in ancient and modern human samples and to investigate whether lifestyle differences depending on the era have altered the bacterial composition of the oral microbiome and the causative bacteria of periodontitis. Additionally, we introduce a novel diagnostic approach for periodontitis in ancient skeletons using micro-computed tomography. Ancient 16S rDNA sequences were obtained from 12 samples at the Unko-in site (18th-19th century) of the Edo era (1603–1867), a characteristic period in Japan when immigrants were not accepted. Furthermore, modern 16S rDNA data from 53 samples were obtained from a database to compare the modern and ancient microbiome. The microbial co-occurrence network was analyzed based on 16S rDNA read abundance. Eubacterium species, Mollicutes species, and Treponema socranskii were the core species in the Edo co-occurrence network. The co-occurrence relationship between Actinomyces oricola and Eggerthella lenta appeared to have played a key role in causing periodontitis in the Edo era. However, Porphyromonas gingivalis, Fusobacterium nucleatum subsp. vincentii, and Prevotella pleuritidis were the core and highly abundant species in the co-occurrence network of modern samples. These results suggest the possibility of differences in the pathogens causing periodontitis during different eras in history.

Identification of the molecular mechanisms underlying brisket disease in Holstein heifers via microbiota and metabolome analyses

Brisket disease (BD) is common among Holstein heifers in high-altitude environments, and this disease may result in serious economic loss. At present, no effective treatment is available for brisket disease. In this study, liver and cecum samples were collected from five heifers with BD and five healthy heifers (HH) for analyses of the metabolome and microbiota. The mean pulmonary arterial pressure and systolic blood pressure were significantly higher in BD heifers, whereas the average breathing rate, blood oxygen saturation, and glucose level were significantly lower in BD group than in the HH group. Further, 16S rDNA data showed that the abundance of Firmicutes was significantly lower and that of Bacteroidetes was significantly higher in BD group than in the HH group. At the genus level, the BD group heifers harbored fewer Ruminococcaceae and Lachnospiraceae than the HH group. Several metabolites, including beta-d-fructose, d-ribose, 1,4-beta-d-glucan, sucrose, and glucose-6-phosphate were present at low levels in BD heifers. Moreover, the mean pulmonary arterial pressure was negatively correlated with beta-d-fructose (r = − 0.74; P = 0.013), d-ribose (r = − 0.72; P = 0.018), and acetyl-tyrosine-ethyl-ester (r = − 0.71; P = 0.022). We also found that mean pulmonary arterial pressure was negatively correlated with most of the genera, including those in the families of Lachnospiraceae and Ruminococcaceae. In summary, the decreased levels of metabolites and microbial genera might affect BD by limiting the energy supply. This study may help us better understand the role of the microbiota in BD and provide new insights into the management of feeding to decrease the rate of BD in Holstein dairy cows in the Qinghai-Tibetan plateau.

Molecular diagnostic based on 18S rDNA and supplemental taxonomic data of the cnidarian coelozoic Ceratomyxa (Cnidaria, Myxosporea) and comments on the intraspecific morphological variation

Ceratomyxa amazonensis is a cnidarian myxosporean originally described with strongly arcuate crescent-shaped myxospores, absence of vegetative stages and infecting Symphysodon discus, an important Amazonian ornamental fish in the aquarium industry. As part of a long-term investigation concerning myxosporeans that infect discus fish Symphysodon spp. from different rivers of the Amazon Basin, thirty specimens of S. discus collected from Unini River were examined. Plasmodial vegetative stages therefrom were found freely floating in the bile of gall bladders from eighteen fish. Mature myxospores were slightly crescent-shaped, measuring 4.72 ± 0.1 (4.52–4.81) μm in length, 24.2 ± 0.4 (23.9–25.3) μm in thickness with polar capsules 2.31 ± 0.1 (2.29–2.33) μm in length and 2.15 ± 0.1 (2.13–2.17) μm in width. Strong morphological differences were observed between the newly isolated myxospores obtained and the previously described C. amazonensis; however, molecular assessment, based on 18S rDNA, revealed a high similarity (99.91%), with only a single nucleotide base change. This study provides new data, expanding the original description of the species with a discussion on differences in myxospore-morphology in the context of intraspecific morphological plasticity.

First molecular assessment of two digenean parasites of the lancehead snake Bothrops moojeni Hoge, 1966 (Serpentes, Viperidae) in Brazil.

Two digenean species, Infidum infidum Faria, 1910 (Dicrocoeliidae) and Travtrema stenocotyle Cohn, 1902 (Plagiorchiidae), were collected in the large pit viper Bothrops moojeni Hoge, 1966 from Reserva Particular do Patrimônio Natural Cisalpina, municipality of Brasilândia, Mato Grosso do Sul State, Brazil. In this study, we provide the first molecular characterisation using the 28S rDNA and phylogenetic position data of these two common digeneans from B. moojeni. The molecular framework revealed topologies with strongly supported clades using maximum likelihood and Bayesian inference methods, positioned I. infidum among Plagiorchiidae and not among Dicrocoeliidae as expected and T. stenocotyle (Plagiorchiidae) surprisingly grouped as a sister group to Allassogonoporidae, Microphallidae, Pleurogenidae, and Prosthogonimidae, not related to plagiorchids. Our molecular phylogenetic data showed that these species may not correspond to their assigned families and encourage future studies on the systematic of these understudied groups.

Gut Microbiota Composition Associated With Clostridium difficile-Positive Diarrhea and C. difficile Type in ICU Patients

The gut microbiota composition of intensive care unit (ICU) patients suffering from Clostridium difficile-positive diarrhea (CDpD) is poorly understood. This prospective study aims to use 16S rDNA (and metagenome) sequencing to compare the microbiota composition of 58 (and 5) ICU patients with CDpD (CDpD group), 33 (and 4) ICU patients with C. difficile-negative diarrhea (CDnD group), and 21 (and 5) healthy control subjects (control group), as well as CDpD patients in the A+B+ (N = 34; A/B: C. difficile TcdA/B), A−B+ (N = 7), and A−B− (N = 17) subgroups. For 16S rDNA data, OTU clustering (tool: UPARSE), taxonomic assignment (tool: RDP classifier), α-diversity, and β-diversity analyses (tool: QIIME) were conducted. For metagenome data, metagenome assembly (tool: SOAPdenovo), gene calling (tools: MetaGeneMark, CD-HIT, and SoapAligner), unigene alignment (tool: DIAMOND), taxon difference analysis (tool: Metastats), and gene annotation (tool: DIAMOND) were performed. The microbial diversity of the CDpD group was lower than that of the CDnD and control groups. The abundances of 10 taxa (e.g., Deferribacteres, Cryptomycota, Acetothermia) were significantly higher in the CDpD group than in the CDnD group. The abundances of Saccharomycetes and Clostridia were significantly lower in CDpD in comparison with control. Some taxa were significantly different between the A+B+ and A−B− subgroups. CDpD might relate to a decrease in beneficial taxa (i.e., Saccharomycetes and Clostridia) and an increase in harmful taxa (e.g., Deferribacteres, Cryptomycota, Acetothermia) in gut microbiota of ICU patients. C. difficile toxin type might be slightly associated with gut microbiota composition.

RNA consensus structures for inferring green algal phylogeny: A three-taxon analysis for Golenkinia/Jenufa, Sphaeropleales and Volvocales (Chlorophyta, Chlorophyceae)

Background and Aims: Order please! was a recently published, very nice and apt title for a persistent problem in green algae phylogenetics. The green algal class Chlorophyceae comprises two clades (SV and OCC) made up of five orders (Sphaeropleales, Volvocales, Oedogoniales, Chaetopeltidales and Chaetophorales). A variety of data and methods have shown that one further group (Golenkinia+Jenufa) cannot be unambiguously placed among the five orders. In addition, concerning Sphaeropleaceae and/or Treubarinia the monophyly of Sphaeropleales and Volvocales remain unresolved. Methods: IUPAC (International Union of Pure and Applied Chemistry) encoded consensus sequences for different 18S rDNA data sets as well as corresponding 18S rDNA consensus structures were assembled for Sphaeropleales, Volvocales (with or without Treubarinia) and a Golenkinia+Jenufa assemblage to independently infer phylogenetic relationships in a three-taxon analysis. Using a known template structure, individual 18S rDNA secondary structures were predicted by homology modelling. Sequences and their individual secondary structures, automatically encoded by a 12-letter alphabet (each nucleotide with its three structural states, paired left, paired right, or unpaired), were simultaneously aligned; consensus structures and IUPAC encoded consensus sequences were read out from the different sequence-structure alignments. Key Results: In contrast to previous studies using 18S rDNA data, results of this study corroborate chloroplast data and strongly support a sister group relationship between Golenkinia+Jenufa and the Sphaeropleales. The Golenkinia+Jenufa assemblage shows 330 matches to the Sphaeropleales (sequence-structure consensus) but only 214 matches to the Volvocales (sequence-structure consensus). Phylogenetically informative nucleotides are highlighted and visualized in their structural context taking into account structural domains (I-IV) and hypervariable regions (V2-V9). Rooting the three-taxon scenario remains difficult because the extremely long branches of Golenkinia and Jenufa are attracted to a chosen outgroup, reducing bootstrap support in any conceivable four-taxon tree obtained by parsimony or profile-neighbor-joining analysis. Conclusions: This algal case study of 18S rDNA consensus data (IUPAC encoded sequences and consensus structures) coupled with profile distances between groups of sequences, demonstrated that a phylogenetic problem can be reduced to a three-taxon analysis.

Common dace (Leuciscus leuciscus) - A new host of the myxozoan fish parasite, Myxobolus elegans (Cnidaria: Myxozoa) - Short communication.

This paper reports the detection of the myxozoan species Myxobolus elegans Kashkovsky 1966 in common dace (Leuciscus leuciscus) that has not been previously listed as its host. The problem of differentiation of phenotypically similar Myxobolus species is addressed. During parasitological survey of common dace from the desalinated part of the Gulf of Finland at the city of Sestroretsk, Russia, numerous oval-shaped plasmodia, 0.2-0.4 mm in size, filled with Myxobolus spores were found on the gills. Pear-shaped myxospores were 15.4 (14.8-16.0) × 10.2 (9.6-10.9) µm in size with a rib on each valve. On the basis of spore morphology, the species appeared to be similar to M. elegans and Myxobolus hungaricus Jaczó, 1940. In order to identify the species, molecular genetic analysis was performed, and the species was identified on the basis of morphological characteristics and 18S rDNA data. The results obtained indicate that the Myxobolus species observed on the gills of dace is M. elegans. Thus, common dace is another valid host of M. elegans besides the type host, ide (Leuciscus idus).

Insights into the Tricholomatineae (Agaricales, Agaricomycetes): a new arrangement of Biannulariaceae and Callistosporium, Callistosporiaceae fam. nov., Xerophorus stat. nov., and Pleurocollybia incorporated into Callistosporium

A new classification of the taxa formerly ascribed to Biannulariaceae (≡ Catathelasmataceae), viz. Catathelasma (type), Callistosporium, Pleurocollybia, Macrocybe, Pseudolaccaria, Guyanagarika and Anupama is here proposed. Phylogenetic inference of the Tricholomatineae based on the analysis of a combined dataset of nuclear genes including ITS, 18S and 28S rDNA, tef1 and rpb2 data supports significantly a monophyletic origin of the aforementioned genera with the exception of Catathelasma, which is significantly related with Bonomyces and Cleistocybe. Biannulariaceae is therefore emended to include the clade formed by Catathelasma, Bonomyces and Cleistocybe. Consequently, the new family Callistosporiaceae is proposed to name the clade containing Callistosporium (= Pleurocollybia) and related genera. Species of Callistosporium with distant lamellae, long hygrophoroid basidia and large amygdaliform spores are accommodated in the new genus Xerophorus. Finally, the new species Callistosporium pseudofelleum and Macrocybe sardoa are described, Clitocybe hesleri and C. fellea are combined into Callistosporium and Pseudolaccaria, respectively, and Callistosporium olivascens var. donadinii is upgraded to species rank and combined into Xerophorus.

Morphological and molecular characterisation of one new and one known species of Makatinus Heyns, 1965 (Dorylaimida: Aporcelaimidae) from Ukraine, with new insights into its phylogeny

Summary Makatinus ukrainicus sp. n. and a population of M. aquaticus, both from Ukraine, are described and illustrated using morphological, morphometric and molecular (28S rDNA) data. The new species is characterised by its 2.17-2.70 mm long body, 20-23 μm broad lip region, odontostyle 20.5-25 μm long at its ventral side and 23-27 μm long at its dorsal side, 591-672 μm long neck, uterus simple and 163-174 μm long or 2.0-4.7 corresponding body diam. long, V = 49.5-52.8, tail convex-conoid (29-39 μm, c = 61-86, c′ = 0.6-0.9), spicules 86-93 μm long, two pairs of adcloacal supplements, and 17-21 closely and regularly spaced ventromedian supplements without an hiatus. In general, the Ukrainian population of M. aquaticus fits well those previously known from Spain and Hungary, and its study confirms the identity of this species. The morphological and molecular data of the Ukrainian populations reveal an interesting diversity within the genus, which might not be a monophyletic taxon.

Phylogenetic Affinity of Genolopa (Digenea: Monorchiidae) with Descriptions of Two New Species

The validity of Genolopa Linton, 1910 has been controversial because the observation of presently recognized critical diagnostic morphological features (spines in the genital atrium and a bipartite, anteriorly spined terminal organ) were omitted from the original diagnosis, and these features were not universally appreciated as important diagnostic features until 2008. Modern taxonomists have been further challenged by inappropriate fixation techniques that have resulted in various interpretations of morphological features. Consequently, named species in the genus have fluctuated among other monorchiid genera depending on various interpretations by taxonomists, and a modern consensus on classifying these species is lacking. This study combines a molecular approach with modern conventional morphological techniques to investigate the validity of Genolopa as a lineage within the Monorchiidae. New morphology and molecular sequence data from the type-species of Genolopa were studied, and two new species in the genus were described, Genolopa vesca n. sp. and Genolopa minuscula n. sp. Interrelationships among the Monorchiidae were explored using Bayesian inference analysis of the partial 28S rDNA fragment, incorporating three species of Genolopa for the first time. The phylogenetic analysis revealed that the genus represents a natural lineage, supporting the presence of spines in the genital atrium in conjunction with a bipartite and anteriorly spined terminal organ as key features of the generic diagnosis. This study also provides for the first time partial 28S rDNA data for Postmonorchis orthopristis, Lasiotocus trachinoti, Lasiotocus glebulentus, and an unidentified species of Lasiotocus.

OP22 Crohn’s disease exclusion diet reduces bacterial dysbiosis towards healthy controls in paediatric Crohn’s disease

Abstract Background Dietary therapy with the Crohn’s disease Exclusion Diet (CDED) or Exclusive Enteral Nutrition (EEN) induces remission, reduces inflammation and is associated with compositional changes in the microbiome. We performed metagenome analysis to elucidate whether diet induces remission via correction of dysbiosis and/or community structure. Methods Whole metagenome and 16S rDNA sequences were obtained in 178 samples from 70 participants at 3 time points (baseline, week 6, week 12) from the two study groups (CDED+PEN/EEN). For metagenome analysis, we divided the groups further into samples of patients achieving ITT-remission at week 6 (CDED+PEN: 31/38 and EEN: 23/32) and those who did not. Results Dietary therapy decreased the relative abundance of genera from Proteobacteria towards healthy controls. CDED+PEN remission is associated with a significant increase (p < .05) in Clostridiales, and a significant decrease (p < .05) in Proteobacteria (particularly Γproteobacteria). Microbiome comparison of all baseline CD samples with healthy controls showed significant (p < .05) increases in Proteobacteria in an active CD at baseline. Healthy controls had increased Firmicutes species notably Roseburia, Oscillibacter and Anaerostipes, as well as increased Bacteroides and Ascomycota (driven by Saccharomyces). Proteobacteria decreased when diet-induced remission was achieved (with either CDED+PEN or EEN) at week 6: relative abundance of Proteobacteria (including Α- and Γproteobacteria (e.g. Escherichia, Klebsiella and Citrobacter) were significantly lower compared with baseline but were still more abundant in CD patients, whereas Bacilli and Firmicutes remained more predominant in healthy samples. Continued dietary treatment with CDED+PEN between week 6 and week 12 was associated with a further decrease in Proteobacteria: although improving with dietary treatment, only Escherichia remained more abundant in CD. Faecalibacterium became more abundant in CD by week 12, as did Blautia and Sutterella. Anaerostipes, Ruminococcus, Bacilli, Porphyromonadaceae, Bifidobacteriales, Ascomycota and Caudovirales were more abundant in healthy samples compared with week 12 of CDED+PEN. Bayesian analysis of the 16S rDNA data training on patients in remission at week 6 compared with baseline (week 0) samples identified seven assemblages. Predominate taxa identified in these assemblages (Posterior Probability >.01) are shown as a connected network, with taxa (nodes) found in the same assemblage connected to each other by edges (Figures). Conclusion Dietary therapy corrected dysbiosis towards healthy controls. Sustained dietary therapy beyond 6 weeks with CDED+PEN avoids the ‘rebound’ in disease-associated species, notably Proteobacteria, when the oral diet is reintroduced.

Phylogeny and biogeography of the Cavernicola (Platyhelminthes: Tricladida): Relicts of an epigean group sheltering in caves?

The planarian suborder Cavernicola Sluys, 1990 was originally created to house five species of triclad flatworms with special morphological features and a surprisingly discontinuous and broad geographic distribution. These five species could not be accommodated with any degree of certainty in any of the three taxonomic groups existing at that moment, viz., Paludicola Hallez, 1892, Terricola Hallez, 1892, and Maricola Hallez, 1892. The scarce representation of the group and the peculiarities of the morphological features of the species, including several described more recently, have complicated new tests of the monophyly of the Cavernicola, the assessment of its taxonomic status, as well as the resolution of its internal relationships. Here we present the first molecular study including all genera currently known for the group, excepting one. We analysed newly generated 18S and 28S rDNA data for these species, together with a broad representation of other triclad flatworms. The resulting phylogenetic trees supported the monophyly of the Cavernicola, as well as its sister-group relationship to the Maricola. The sister-group relationship to the Maricola and affinities within the Cavernicola falsify the morphology-based phylogeny of the latter that was proposed previously. The relatively high diversity of some cavernicolan genera suggests that the presumed rarity of the group actually may in part be due to a collecting artefact. Ancestral state reconstruction analyses suggest that the ancestral habitat of the group concerned epigean freshwater conditions. Our results point to an evolutionary scenario in which the Cavernicola (a) originated in a freshwater habitat, (b) as the sister clade of the marine triclads, and (c) subsequently radiated and colonized both epigean and hypogean environments. Competition with other planarians, notably members of the Continenticola, or changes in epigean habitat conditions are two possible explanations -still to be tested- for the loss of most epigean diversity of the Cavernicola, which is currently reflected in their highly disjunct distributions.

California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals.

Around the world, scavenging birds such as vultures and condors have been experiencing drastic population declines. Scavenging birds have a distinct digestive process to deal with higher amounts of bacteria in their primary diet of carcasses in varying levels of decay. These observations motivate us to present an analysis of captive and healthy California condor (Gymnogyps californianus) microbiomes to characterize a population raised together under similar conditions. Shotgun metagenomic DNA sequences were analyzed from fecal and cloacal samples of captive birds. Classification of shotgun DNA sequence data with peptide signatures using the Sequedex package provided both phylogenetic and functional profiles, as well as individually annotated reads for targeted confirmatory analysis. We observed bacterial species previously associated with birds and gut microbiomes, including both virulent and opportunistic pathogens such as Clostridium perfringens, Propionibacterium acnes, Shigella flexneri, and Fusobacterium mortiferum, common flora such as Lactobacillus johnsonii, Lactobacillus ruminus, and Bacteroides vulgatus, and mucosal microbes such as Delftia acidovorans, Stenotrophomonas maltophilia, and Corynebacterium falsnii. Classification using shotgun metagenomic reads from phylogenetic marker genes was consistent with, and more specific than, analysis based on 16S rDNA data. Classification of samples based on either phylogenetic or functional profiles of genomic fragments differentiated three types of samples: fecal, mature cloacal and immature cloacal, with immature birds having approximately 40% higher diversity of microbes.

<p><strong><em>Neowollea manoromense</em> gen. & sp. nov. (Nostocales, Cyanobacteria), a novel geosmin producer isolated from Thailand</strong></p>

In the present study, two new filamentous cyanobacterial strains (NUACC12 and NUACC15) were described based on a comprehensive study of morphological characteristics and molecular analyses. The novel strains were isolated from a shallow freshwater pond in the central region of Thailand. The morphological features of both strains are similar to those of Wollea species, W. ambigua, but are different in the dimensions of heterocyte and akinete cells as well as the absence of a sheath around the trichome. Phylogenetic analyses based on 16S rDNA and 16S–23S rDNA internal transcribed spacer sequences (ITS) revealed that new strains formed a robust supported clade which does not belong to the same clade with the type species of other cyanobacterial genera. Moreover, 16S rDNA sequence similarity between new strains and other putatively related taxa such as Wollea, Amphiheterocytum, Sphaerospermopsis, and Raphidiopsis raciborskii ranged from 96.1–97.4%, a level of similarity low enough for separating species differences. The unique patterns of the ITS secondary structure also clearly support two new strains representing a distinct cyanobacterial species. Considering all the results obtained in the present study, we here name the new genus Neowollea gen. nov., with the type species N. manoromense sp. nov. Based on morphology, ecology, 16S rDNA data and D1–D1′ helix structure, we also propose N. salina comb. nov. (basionym Wollea salina) as an additional species in the novel genus. Furthermore, the results of PCR amplification and GC/MS/MS analysis confirmed that two N. manoromense strains could produce an odorous compound, geosmin.

Mitochondrial genomes and 28S rDNA contradict the proposed obsoletion of the order Tetraonchidea (Platyhelminthes: Monogenea)

Due to the incongruence of morphology-based hypotheses and scarcity of molecular data, validity of the order Tetraonchidea remains contentious. The only complete mitogenome currently available for the entire order is that of Paratetraonchoides inermis (Tetraonchoididae). To study the phylogeny of Tetraonchidea from mitogenomic perspective, we sequenced the first mitogenome for the family Tetraonchidae: Tetraonchus monenteron (Tetraonchidea). To get a nuclear-data perspective, we also sequenced nuclear 28S rDNA gene of both species. The mitogenome of T. monenteron does not have high A + T content, nor tRNA pseudo-genes, both of which were unique features reported in P. inermis. However, T. monenteron exhibits a unique gene order, with a large number of tRNA rearrangements in comparison to P. inermis and other monogeneans. Phylogenetic analyses conducted using Bayesian inference and maximum likelihood methods, complemented with partitioning, consistently support the sister-group relationship of T. monenteron (Tetraonchidae) and P. inermis (Tetraonchoididae). This is also partially supported by the 28S rDNA data and two morphologic apomorphies. This close relationship of Tetraonchidae and Tetraonchoididae challenges the latest major morphology-based classification, which proposed obsoletion of the Tetraonchidea order, and grouped Tetraonchoididae into the Gyrodactylidea clade. The validity of this order shall have to be further confirmed with more data.

Effects of Habitat Partitioning on the Distribution of Bacterioplankton in Deep Lakes.

In deep lakes, many investigations highlighted the existence of exclusive groups of bacteria adapted to deep oxygenated and hypoxic and anoxic hypolimnia. Nevertheless, the extent of bacterial strain diversity has been much less scrutinized. This aspect is essential for an unbiased estimation of genetic variation, biodiversity, and population structure, which are essential for studying important research questions such as biogeographical patterns, temporal and spatial variability and the environmental factors affecting this variability. This study investigated the bacterioplankton community in the epilimnetic layers and in the oxygenated and hypoxic/anoxic hypolimnia of five large and deep lakes located at the southern border of the Alps using high throughput sequencing (HTS) analyses (16S rDNA) and identification of amplicon sequence variants (ASVs) resolving reads differing by as little as one nucleotide. The study sites, which included two oligomictic (Garda and Como) and three meromictic lakes (Iseo, Lugano, and Idro) with maximum depths spanning from 124 to 410 m, were chosen among large lakes to represent an oxic-hypoxic gradient. The analyses showed the existence of several unique ASVs in the three layers of the five lakes. In the case of cyanobacteria, this confirmed previous analyses made at the level of strains or based on oligotyping methods. As expected, the communities in the hypoxic/anoxic monimolimnia showed a strong differentiation from the oxygenated layer, with the exclusive presence in single lakes of several unique ASVs. In the meromictic lakes, results supported the hypothesis that the formation of isolated monimolimnia sustained the development of highly diversified bacterial communities through ecological selection, leading to the establishment of distinctive biodiversity zones. The genera identified in these layers are well-known to activate a wide range of redox reactions at low O2 conditions. As inferred from 16S rDNA data, the highly diversified and coupled processes sustained by the monimolimnetic microbiota are essential ecosystem services that enhance mineralization of organic matter and formation of reduced compounds, and also abatement of undesirable greenhouse gasses.