Single Taxon Research Articles

Comparative micro-morphological and phylogenetic analysis between Rhinoestrus purpureus and Rhinoestrus usbekistanicus (Diptera: Oestridae) larvae and its adults

Rhinoestrus purpureus and Rhinoestrus usbekistanicus (Diptera: Oestridae) cause specific nasal myiases of family equidae and are of importance in the horse medicine since it causes severe respiratory diseases. During an epidemiological survey in donkeys from Beni Suef government, Egypt; some morphological and taxonomical doubts arose concerning the identification of Rhinoestrus spp. 1st, 2nd and 3rd stage larvae based on the features of the posterior spiracles and the distribution of dorsal spines on the third segment. Four different morphotypes were retrieved: R. usbekistanicus, R. purpureus and two morphotypes with shared features. The genes encoding for the mitochondrial cytochrome oxidase I (COI) and for the ribosomal subunits 16S and 28S of the four morphotypes of Rhinoestrus were investigated to determine whether they belonged to a single taxon or they displayed genetic differences indicative of more than one species. The genes showed a very low level of sequence variation (COI 0–0.43%, 16S 0–1.45%, 28S 0–0.23%) falling within the intraspecific ranges. Finally, the peritreme features and the spinulation of the third segment of the two morphotypes examined could not be used to differentiate the Rhinoestrus spp.

Concise review of green algal genus Ulva Linnaeus

The green algal genus Ulva is widely distributed around all continents. Plants with both distromatic or monostromatic thalli now form a single taxon based on ITS rDNA and rbcL gene sequencing. Ulva is known to occupy several ecological niches including freshwater and marine (intertidal and subtidal) habitats, attributed to its tolerance to key determinants such as light, temperature, and salinity. The genus is perceived as model system to study life cycle, morphogenesis and development from simple to complex multicellularity. The life cycle is isomorphic and biphasic type, knowledge of which is important in developing viable cultivation techniques. The culture of Ulva is by photo-bioreactor, land-based, and open-sea farming producing about 1500 t dry annum−1 biomass. The understanding of scientific basis for eutrophication-driven green tide events is of paramount importance for coastal ecosystem management. Studies related to cross-kingdom cross-talk between Ulva and surrounding microbes have been recently undertaken through high-throughput techniques to understand their role in growth, development, and morphogenesis. Several regional species are rich in vital nutrients and thus qualify in the functional food sector, and recent research is poised to develop a bio-refinery model for complete utilization of feedstock. Ulva spp. are also used as a feed source in aquaculture and for environmental bioremediation.

A review of the challenges and opportunities for restoring animal-mediated pollination of native plants.

Ecological restoration is increasingly implemented to reverse habitat loss and concomitant declines in biological diversity. Typically, restoration success is evaluated by measuring the abundance and/or diversity of a single taxon. However, for a restoration to be successful and persistent, critical ecosystem functions such as animal-mediated pollination must be maintained. In this review, we focus on three aspects of pollination within ecological restorations. First, we address the need to measure pollination directly in restored habitats. Proxies such as pollinator abundance and richness do not always accurately assess pollination function. Pollen supplementation experiments, pollen deposition studies, and pollen transport networks are more robust methods for assessing pollination function within restorations. Second, we highlight how local-scale management and landscape-level factors may influence pollination within restorations. Local-scale management actions such as prescribed fire and removal of non-native species can have large impacts on pollinator communities and ultimately on pollination services. In addition, landscape context including proximity and connectivity to natural habitats may be an important factor for land managers and conservation practitioners to consider to maximize restoration success. Third, as climate change is predicted to be a primary driver of future loss in biodiversity, we discuss the potential effects climate change may have on animal-mediated pollination within restorations. An increased mechanistic understanding of how climate change affects pollination and incorporation of climate change predictions will help practitioners design stable, functioning restorations into the future.

Molecular Species Delimitation of the Genus Reishia (Mollusca: Gastropoda) along the Coasts of China and Korea.

Species of the predatory gastropod genus Reishia Kuroda and Habe, 1971 (Muricidae) inhabit intertidal rocky shores in East Asia. Due to their highly variable external shell morphology, the taxonomy of this genus at species-level is still in need of re-evaluation. Using DNA-based delimitation methods, we aimed to ascertain the number of species of Reishia along the coasts of China and adjacent Asian areas. Also, we looked for diagnostic traits using morphology-based statistical approaches. Our genetic data suggest that the studied individuals comprised two separate species of a Reishia complex in this region, in contrast to the previously proposed four or more taxa. This conclusion is further supported by statistical analyses of shell morphological characteristics. The morphospecies R. bronni (Dunker, 1860), R. jubilaea (Tan and Sigurdsson, 1990), and R. luteostoma (Holten, 1803) were assigned to a single taxon, indicating that they might be synonyms of the same species. The morphospecies R. clavigera (Küster, 1860) singly formed one group, suggesting that it is likely a valid name. The estimated divergence time of the two identified taxa indicates that speciation might have been associated with the sea level and temperature fluctuations during the Plio-Pleistocene period. Our study on Reishia species provides crucial information for further research on the ecology, evolutionary biology, and conservation of this genus.

Culicidae-centric metabarcoding through targeted use of D2 ribosomal DNA primers.

A practical limitation to many metabarcoding initiatives is that sampling methods tend to collect many non-target taxa, which become “amplicon noise” that can saturate Next Generation Sequencing results and lead to both financial and resource inefficiencies. An available molecular tool that can significantly decrease these non-target amplicons and decrease the need for pre-DNA-extraction sorting of bycatch is the design of PCR primers tailored to the taxa under investigation. We assessed whether the D2 extension segment of the 28S ribosomal operon can limit this shortcoming within the context of mosquito (Culicidae) monitoring. We designed PCR primers that are fully conserved across mosquitos and exclude from amplification most other taxa likely to be collected with current sampling apparatuses. We show that, given enough sequencing depth, D2 is an effective marker for the detection of mosquito sequences within mock genomic DNA pools. As few as 3,050 quality-filtered Illumina reads were able to recover all 17 species in a bulk pool containing as little as 0.2% of constituent DNA from single taxa. We also mixed these mosquito DNA pools with high concentrations of non-Culicidae bycatch DNA and show that the component mosquito species are generally still recoverable and faithful to their original relative frequencies. Finally, we show that there is little loss of fidelity in abundance parameters when pools from degraded DNA samples were sequenced using the D2 primers.

New taxa among a remarkably diverse assemblage of fossil squamates from the Aguja Formation (lower Campanian) of West Texas

A diverse microfauna from the lower shale of the Aguja Formation of West Texas records a rare, early Campanian assemblage of fossil squamates from North America. This assemblage is comprised of scincomorph, anguimorph, and ophidian taxa and is the most inclusive of its kind thus far described from the southern faunal province of Laramidia. Among numerous taxa described herein, three (Hypostylos lehmani gen. et sp. nov., Bothriagenys flectomendax sp. nov., and Hydrargysaurus gladius gen. et sp. nov) pertain to new scincomorphs which dominate the assemblage; however, subordinate anguimorphs are also well-represented. Snakes are represented by a single taxon, aff. Coniophis; a species seemingly ubiquitous throughout most Campanian strata in the southern Western Interior. Comparison among squamate assemblages from similar coastal facies in the upper shale of the Aguja Formation as well as the paracontemporaneous Wahweap and Kaiparowits formations of southern Utah reveals patterns of biogeographic segregation among some lizard species and the presence of two distinct communities. These two ‘southern’ squamate faunas are likely the result of variables involving climate and eustacy which facilitated diversity as well as the development of sub-provincial quarters of endemism during early-middle Campanian time.

Sigilmassasaurus is Spinosaurus: A reappraisal of African spinosaurines

Remains of enigmatic spinosaurs from mid-Cretaceous North African strata have, for over a century, been the subject of taxonomic deliberations. The gigantic Spinosaurus aegyptiacus Stromer, 1915 has gained iconic status in the vertebrate palaeontological community and amongst the general public. Perhaps the largest predatory dinosaur to have lived, this animal exhibits a bizarre range of adaptations consistent with a piscivorous diet and semiaquatic mode of life. Despite its popularity, the systematics of this taxon remains a matter of considerable debate. African spinosaur taxonomy is complex, with up to three separate species proposed for the Cretaceous Kem Kem Group of Morocco: Spinosaurus aegyptiacus, Spinosaurus maroccanus Russell, 1996 and Sigilmassasaurus brevicollis Russell, 1996.Here, the taxonomic status of spinosaurs in the Kem Kem Group is examined, and the morphology of the cervical and dorsal vertebrae re-evaluated in the light of this taxonomic reappraisal.The validity of Spinosaurus maroccanus and Sigilmassasaurus brevicollis are not supported, as all autapomorphies of these taxa are proposed here to be the result of intraspecific variation, or morphological changes through the axial column of a single taxon. Both taxa are junior synonyms of Spinosaurus aegyptiacus.This reanalysis has implications for the taxonomy of spinosaurs from other deposits. Based on the currently available material, the Brazilian spinosaurid Oxalaia quilombensis is determined to fall within the Spinosaurus aegyptiacus hypodigm. The prevalence of spinosaurid heterodonty and limited diagnostic potential of spinosaur teeth necessitates that two spinosaurid tooth taxa: Ostafrikasaurus crassiserratus and Siamosaurus suteethorni, be regarded nomina dubia.

The evolution of conspecific acceptance threshold models.

How do organisms balance different types of recognition errors when cues associated with desirable and undesirable individuals or resources overlap? This is a fundamental question of signal detection theory (SDT). As applied in sociobiology, SDT is not limited to a single context or animal taxon, therefore its application can span what may be considered dissimilar systems. One of the applications of SDT is the suite of acceptance threshold models proposed by Reeve (1989), which analysed how individuals should balance acceptance and rejection errors in social discrimination decisions across a variety of recognition contexts, distinguished by how these costs and benefits relatively combine. We conducted a literature review to evaluate whether these models' specific predictions have been upheld. By examining over 350 research papers, we quantify how Reeve's models (Reeve 1989 Am. Nat.133, 407-435 (doi:10.1086/284926)) have influenced the field of ecological and behavioural recognition systems research. We found overall empirical support for the predictions of the specific models proposed by Reeve, and argue for further expansion of their applications into more diverse taxonomic and additional recognition contexts. This article is part of the theme issue 'Signal detection theory in recognition systems: from evolving models to experimental tests'.

High Resolution Melting (HRM) Genotyping in the Genus Origanum: Molecular Identification and Discrimination for Authentication Purposes.

Origanum L. (Lamiaceae) is an important genus of medicinal and aromatic plants used since ancient times as culinary herbs and remedies in traditional medicine. Although it is a relatively small genus, intra-generic species delineation, as well as its inter-generic relationships within tribe Mentheae, are still poorly understood. High resolution melting (HRM) analysis, coupled with microsatellite markers (SSRs), could facilitate the molecular identification and characterization of certain genotypes more efficiently and relatively faster when compared to other analytical methods. In this study, 38 Origanum samples corresponding to six Origanum taxa (O. dictamnus, O. majorana, O. onites, O. scabrum, O. sipyleum, and O. vulgare subsp. hirtum) were analyzed, using six microsatellite loci. Our goal was to molecularly identify and discriminate among the selected samples and to evaluate the ability of the HRM technique as an analytical tool for the discrimination of Origanum species from Greece. The temperature-shifted melting curves produced by the HRM analysis, resulted in 98 unique HRM profiles, which enabled the discrimination of the Origanum genotypes studied. According to the similarity dendrogram based on the HRM profiles, six unique clusters were formed, each one corresponding to a single taxon. In conclusion, HRM genotyping provided a fast, cost-effective method, well suited for the molecular characterization and identification of Origanum taxa and for the authentication of the original genetic material.

Corynebacterium godavarianum Jani et al. 2018 and Corynebacterium hadale Wei et al. 2018 are both later heterotypic synonyms of Corynebacterium gottingense Atasayar et al. 2017, proposal of an emended description of Corynebacterium gottingense Atasayar et al. 2017.

Seven strains of an unidentifiable Corynebacterium species recovered from blood cultures, urine or cerebrospinal fluid over 26 years, closest to but differentiated from Corynebacterium imitans by 16S rRNA gene and partial rpoB gene sequencing, were studied. In November 2017, Atasayar et al. described a blood culture isolate as Corynebacterium gottingense sp. nov., which had >99 % similarity by 16S rRNA gene sequencing to the Canadian strains. In January 2018, Jani et al. described Corynebacterium godavarianum sp. nov., recovered from the Godavari River, India, which also had >99 % similarity by 16S/rpoB sequencing to the Canadian strains and C. gottingense. In May 2018, Wei et al. described Corynebacterium hadale recovered from hadopelagic water; this too had >99 % similarity by 16S rRNA gene sequencing to C. gottingense, C. godavarianum and the Canadian strains. C. gottingense DSM 103494T and C. godavarianum LMG 29598T were acquired and whole genome sequencing was performed (not previously done). Results were compared with genomes from C. hadale (GenBank accession NQMQ01) and the Canadian isolates. We found that these ten genomes formed a single taxon when compared using digital DNA-DNAhybridization, average nucleotide identity using blastn and average amino acid identity criteria but exhibited some subtle biochemical and chemotaxonomic differences. Heuristically, we propose that C. godavarianum and C. hadale are later heterotypic synonyms of, and the Canadian isolates are identifiable as, C. gottingense. We provide an emended description of Corynebacterium gottingense Atasayar et al. 2017; genomes ranged from 2.48 to 2.69 Mb (C. gottingense DSM 103494T, 2.62 Mb) with G+C content of 65.1-65.6 mol% (WGS), recovered from clinical and environmental sites.

Abstract IA22: The role of the intestinal microbiome in allogeneic hematopoietic cell transplantation

Abstract Relationships between microbiota composition and clinical outcomes of patients following allogeneic hematopoietic cell transplantation (allo-HCT) have been described in single-center studies. Geographic variations in the composition of human microbial communities and differences in clinical practices across institutions raise the question of whether these associations are generalizable. Therefore, we studied 8,767 fecal samples from 1,362 allo-HCT patients at four centers on three continents by 16S ribosomal sequencing. In an observational study, we examined associations between microbiota diversity and overall survival during two years of follow-up after allo-HCT with proportional-hazards analysis. We observed reproducible patterns of microbiota disruption characterized by loss of diversity and domination by single taxa. Low diversity in the peri-neutrophil engraftment period was reproducibly associated with increased risk of death (multivariate-adjusted HR 0.48, 95% CI 0.30-0.77, p = 0.002 in the largest cohort). Subset analysis suggested that these reductions in overall survival were in part due to an increased risk of transplant-related mortality and graft-versus-host disease. Baseline pre-HCT samples already bore evidence of microbiome disruption, and low diversity prior to transplantation was associated with poor survival. In addition, we found that Enterococcus faecium dominates the intestinal microbiota of up to 65% allo-HCT patients early after transplant at all four transplant centers. Enterococcus domination was associated with an increased incidence of acute graft-versus-host disease (GVHD), increased GVHD-related mortality, and reduced overall survival. Post-transplant expansion of Enterococci was also observed in mouse models of GVHD in the absence of antibiotic treatment. Spiking a minimal flora with Enterococci in gnotobiotic mice exacerbated lethal GVHD. Metagenomic sequencing of human and murine Enterococcus-dominated fecal samples revealed an enrichment of lactose and galactose degradation genes, a pathway necessary for Enterococcus growth in vitro. A lactose-free chow attenuated the intestinal outgrowth of Enterococcus and reduced the severity of lethal GVHD in mice. In patients, a lactose-nonabsorber genotype was associated with an increased Enterococcus abundance after cessation of antibiotic treatment after allo-HCT. In conclusion, the concordance of microbiota disruption patterns and their associations with clinical outcomes suggest that approaches to manipulate the intestinal microbiota with the aim of improving allo-HCT clinical outcomes may be generalizable. Citation Format: Marcel van den Brink. The role of the intestinal microbiome in allogeneic hematopoietic cell transplantation [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr IA22.

Abstract IA03: Control over colorectal tumor growth via bacteria-specific T-cell activation of the local immune response

Abstract Colorectal cancer (CRC) is a leading cause of cancer-related death and its incidence is on the rise, particularly in young people. Therapy for late-stage CRC is often ineffective, and colorectal tumors are most often detected at stage 3 or 4. Immunotherapy is revolutionizing the treatment of many types of cancer but is only effective for a very small subset of CRC patients. Thus, there is a tremendous need for improved therapies for CRC. Colorectal tumors grow from the intestinal epithelium and are therefore subject to interaction with the dense and diverse colonic microbiota. Indeed, CRC has been associated with shifts in the composition of the microbiota that effect inflammation and tumor growth. How the microbiota shapes the CRC immune microenvironment is not fully understood. In general, the microbiota can directly shape T-cell responses, directing the differentiation of CD4 T cells to develop into either regulatory (Treg) or effector (Th1, Th17, etc.) T cells. This is particularly true of those T cells local to the intestine that are often specific to antigens derived from intestinal bacteria. We became interested in how colonization with different bacterial taxa might affect the T-cell immune response and control over colorectal cancer. Using a mouse model of CRC, we show that colonization with a single bacterial taxon, after tumors have already developed, leads to a reduction in tumor burden and size. Bacteria-dependent tumor reduction depended upon CD4 T cells but not CD8 T cells as antibody depletion of CD4 T cells completely abrogated the effect. Accordingly, de novo bacterial colonization was associated with a colorectal tumor environment that possessed fewer Tregs, increased CD4 IFNgamma-producing T cells, and increased CD103+ dendritic cells. We also observed that colonized mice develop increased numbers of organized tertiary lymphoid structures that were adjacent to colonic tumor. Importantly, bacteria-specific CD4 T cells were commonly found in these tertiary lymphoid structures, as were bacteria. Our hypothesis is that microbiota-driven and T cell-dependent development of TLS structures leads to enhanced tumor antigen presentation and augmented antitumor immune responses. This work has the potential to inform CRC therapies via the rational modification of the local microbiota to support TLS formation and antitumor immunity. Citation Format: Abigail Overacre-Delgoffe, Hannah Bumgarner, Tim Hand. Control over colorectal tumor growth via bacteria-specific T-cell activation of the local immune response [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr IA03.

True Size Matters for Conservation: A Robust Method to Determine the Size of Deep-Sea Coral Reefs Shows They Are Typically Small on Seamounts in the Southwest Pacific Ocean

Protection of vulnerable marine ecosystems (VME) is a critical goal for marine conservation. Yet, in many deep-sea settings, where quantitative data are typically sparse, it is challenging to correctly identify the location and size of VMEs. Here we assess the sensitivity of a method to identify coral reef VMEs based on bottom cover and abundance of the stony coral Solenosmilia variabilis on deep seamounts, using image data from a 2018 large survey off Tasmania, Australia. Whilst there was some detectable influence of varying coral cover and the abundance of live coral heads, the distribution of coral reef VMEs was not substantially shifted by changing these criteria or altering the attributes of a moving window used to spatially aggregate coral patches. Whilst applying stricter criteria for classifying VMEs predictably produced smaller areas of coral reef VME, these differences are not sizeable and were often negligible. A model prediction of the area of suitable habitat for coral reef in the Tasmanian area was much greater than that estimated in this study. Coral reef VMEs formed large contiguous ‘blankets’, mainly on the peaks and flanks of seamounts, but were absent from the continental slope where S. variabilis occurred at low abundance (cover) and/or had no living colonies. The true size of the Tasmanian coral reef VMEs ranged from 0.02 to 1.16 km2; this was relatively large compared to reefs of S. variabilis mapped on New Zealand seamounts, but is small compared to the scales used for regional model predictions of suitable habitat (typically 1 km2 grid cell), much smaller than the smallest units of management interest (100s – 1000s km²). That the method is not overly sensitive to the choice of criteria is highly encouraging in the context of designing spatial conservation measures that are robust, although its broader application, including to other VME indicator taxa, needs to be substantiated by scenario testing in different environments. Importantly, it should encourage uptake by the broader community (e.g. fishing and mining sectors) and forms the basis for better predictive VME models at larger spatial scales and beyond single taxa.

Fascinorbis gen. nov., a new genus of Stephanodiscaceae (Bacillariophyta) from a Late Miocene lacustrine diatomite

We used light and electron microscopy to characterize a Late Miocene freshwater diatomite deposit in the Chalk Hills Formation, near Payette, Idaho, USA. The diatom assemblage from this sample was nearly monotypic, dominated by a single taxon with similarities to Lindavia bodanica (Thalassiosirales) but with several features uncharacteristic of the genus Lindavia, such as a rimoportula(e) on the valve mantle located on a costa, simple alveolar structure, and spines at the external valve face-mantle junction. A combination of other characters for this species complicate its placement into existing genera, including a lack of central fultoportulae, central area with loculate areolae with domed cribra, and a single ring of mantle fultoportulae with three satellite pores with well-developed cowlings and broad satellite pore covers. Based on this unique set of features, we have established a new genus, Fascinorbis, which appears to represent an important transitional form in the evolution of the Lindavia lineage.

Taboo on spiritual incest: justification of the anthropic principle

This article makes an attempt to demonstrate that the evolution of culture is isomorphic to the evolution of life, and thus, such isomorphism can be considered a basic metaphor for studying the evolution of culture. Such research allows explicating the key cultural processes, which are imperceptible to other methods, and suggest algorithms for adjusting these processes. Leaning on fact that life due to the impact of isolating mechanisms of nature constantly forms different taxa, in which the evolution rapidly fades, it is proven that isolation of cultural memes leads to their degeneration. The emergence of certain taboos, such as the taboo on incest, cause fusion of taxa, which accelerates the evolution and results in structural revolutions. Such evolutionary pattern can be described with Freud’s metaphor from the eponymous book “Totem and Taboo». Totemism explicates teleologicity of evolution as the need for uniting all taxa into one. The work displays that culture has already formed the plurality of “semantic taxa”, which require unification, or at least, interaction with each other; such interaction should stimulate the taboo on “spiritual incest, which means limitation of evolution within a single semantic taxon.

Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation

BackgroundRelationships between microbiota composition and clinical outcomes after allogeneic hematopoietic-cell transplantation have been described in single-center studies. Geographic variations in the composition of human microbial communities and differences in clinical practices across institutions raise the question of whether these associations are generalizable.MethodsThe microbiota composition of fecal samples obtained from patients who were undergoing allogeneic hematopoietic-cell transplantation at four centers was profiled by means of 16S ribosomal RNA gene sequencing. In an observational study, we examined associations between microbiota diversity and mortality using Cox proportional-hazards analysis. For stratification of the cohorts into higher- and lower-diversity groups, the median diversity value that was observed at the study center in New York was used. In the analysis of independent cohorts, the New York center was cohort 1, and three centers in Germany, Japan, and North Carolina composed cohort 2. Cohort 1 and subgroups within it were analyzed for additional outcomes, including transplantation-related death.ResultsWe profiled 8767 fecal samples obtained from 1362 patients undergoing allogeneic hematopoietic-cell transplantation at the four centers. We observed patterns of microbiota disruption characterized by loss of diversity and domination by single taxa. Higher diversity of intestinal microbiota was associated with a lower risk of death in independent cohorts (cohort 1: 104 deaths among 354 patients in the higher-diversity group vs. 136 deaths among 350 patients in the lower-diversity group; adjusted hazard ratio, 0.71; 95% confidence interval [CI], 0.55 to 0.92; cohort 2: 18 deaths among 87 patients in the higher-diversity group vs. 35 deaths among 92 patients in the lower-diversity group; adjusted hazard ratio, 0.49; 95% CI, 0.27 to 0.90). Subgroup analyses identified an association between lower intestinal diversity and higher risks of transplantation-related death and death attributable to graft-versus-host disease. Baseline samples obtained before transplantation already showed evidence of microbiome disruption, and lower diversity before transplantation was associated with poor survival.ConclusionsPatterns of microbiota disruption during allogeneic hematopoietic-cell transplantation were similar across transplantation centers and geographic locations; patterns were characterized by loss of diversity and domination by single taxa. Higher diversity of intestinal microbiota at the time of neutrophil engraftment was associated with lower mortality. (Funded by the National Cancer Institute and others.)

The Cytochrome P450 Monooxygenase Inventory of Grapevine (Vitis vinifera L.): Genome-Wide Identification, Evolutionary Characterization and Expression Analysis.

The cytochrome P450 (CYP) monooxygenase superfamily, belonging to heme-thiolate protein products, plays a vital role in metabolizing physiologically valuable compounds in plants. To date, CYP superfamily genes have not yet been characterized in grapevine (V. vinifera L.), and their functions remain unclear. In this study, a sum of 236 VvCYPs, divided into 46 families and clustered into nine clans, have been identified based on bioinformatics analyses in grapevine genome. The characteristics of both exon–intron organizations and motif structures further supported the close evolutionary relationships of VvCYP superfamily as well as the reliability of phylogenetic analysis. The gene number-based hierarchical cluster of CYP subfamilies of different plants demonstrated that the loss of CYP families seems to be limited to single species or single taxa. Promoter analysis elucidated various cis-regulatory elements related to phytohormone signaling, plant growth and development, as well as abiotic/biotic stress responses. The tandem duplication mainly contributed to the expansion of the VvCYP superfamily, followed by singleton duplication in grapevine. Global RNA-sequencing data of grapevine showed functional divergence of VvCYPs as diverse expression patterns of VvCYPs in various organs, tissues, and developmental phases, which were confirmed by quantitative real-time reverse transcription PCR (qRT-PCR). Taken together, our results provided valuable inventory for understanding the classification and biological functions of the VvCYPs and paved the way for further functional verification of these VvCYPs and are helpful to grapevine molecular breeding.

Pseudomonas kirkiae sp. nov., a novel species isolated from oak in the United Kingdom, and phylogenetic considerations of the genera Pseudomonas, Azotobacter and Azomonas.

As the current episode of Acute Oak Decline (AOD) continues to affect native British oak in the United Kingdom, ongoing isolations from symptomatic and healthy oak have yielded a large Pseudomonas species population. These strains could be divided into taxa representing three potential novel species. Recently, two of these taxa were described as novel Pseudomonas species in the Pseudomonas fluorescens lineage. Here, we demonstrate using a polyphasic approach that the third taxon represents another novel Pseudomonas species. The 16S rRNA gene sequencing assigned the strains to the Pseudomonas aeruginosa lineage, while multilocus sequence analysis (based on partial gyrB, rpoB and rpoD sequences) placed the 13 strains in a single cluster on the border of the Pseudomonas stutzeri group. Whole genome intra-species comparisons (based on average nucleotide identity and in silico DNA-DNA hybridization) confirmed that the strains belong to a single taxon, while the inter-species comparisons with closest phylogenetic relatives yielded similarity values below the accepted species threshold. Therefore, we propose these strains as a novel species, namely Pseudomonas kirkiae sp. nov., with the type strain FRB 229T (P4CT=LMG 31089T=NCPPB 4674T). The phylogenetic analyses performed in this study highlighted the difficulties in assigning novel species to the genus Pseudomonas due to its polyphyletic nature and close relationship to the genus Azotobacter. We further propose that a thorough taxonomic re-evaluation of the genus Pseudomonas is essential and should be performed in the near future.

The role of freshwater bioacoustics in ecological research

AbstractConventional methodologies used to estimate biodiversity in freshwater ecosystems can be nonselective and invasive, sometimes leading to capture and potential injury of vulnerable species. Therefore, interest in noninvasive surveying techniques is growing among freshwater ecologists. Passive acoustic monitoring, the noninvasive recording of environmental sounds, has been shown to effectively survey biota in terrestrial and marine ecosystems. However, knowledge of the sounds produced by freshwater species is relatively scarce. Furthermore, little is known about the representation of different freshwater taxonomic groups and habitat types within the literature. Here we present results of a systematic review of research literature on freshwater bioacoustics and identify promising areas of future research. The review showed that fish are the focal taxonomic group in 44% of published studies and were studied primarily in laboratory aquaria and lotic habitats. By contrast, lentic habitats and other taxonomic groups have received relatively little research interest. It is particularly striking that arthropods are only represented by 26% of studies, despite their significant contributions to freshwater soundscapes. This indicates a mismatch between the representation of taxonomic groups within the freshwater bioacoustic literature and their relative acoustic contribution to natural freshwater soundscapes. In addition, the review indicates an ongoing shift from behavioral studies, often with focus on a single taxonomic group, towards field‐based studies using ecoacoustic approaches. On the basis of this review we suggest that future freshwater bioacoustics research should focus on passive acoustic monitoring and arthropod sound, which would likely yield novel insights into freshwater ecosystem function and condition.This article is categorized under: Water and Life > Nature of Freshwater Ecosystems Water and Life > Conservation, Management, and Awareness Water and Life > Methods

Contrasting Patterns of Movement across Life Stages in an Insular Iguana Population

West Indian rock iguanas (genus Cyclura) represent the most endangered group of lizards in the world, with most taxa restricted to few or single islands. In addition to distribution and availability of resources, factors influencing optimal use of insular space in these large vertebrates may include a combination of social, ontogenetic, and long-term demographic factors. Life stage-specific dispersal and habitat use patterns have previously been characterized in Cyclura, but assessments across the lifespan are lacking. This study evaluates shifting patterns of movement in a single taxon, Cyclura nubila caymanensis. We used mark–recapture and radio tracking simultaneously to assess age- and sex-dependent variation in spatial ecology. Evidence for prolonged site fidelity among adults was consistent with territoriality-modulating space use in this long-lived taxon. Over 5–10 yr, some females were never resighted or recaptured outside of an 80-m perimeter. A notable exception was that gravid females migrated 1.17 ± 0.91 km to utilize coastal areas during the nesting season. In contrast, neonates dispersed farther (2.32 ± 2.26 km) and their trajectories were often nonlinear. Radio-tracked brother–sister pairs exhibited no tendency to disperse together during their first 4 wk, settling into final known locations at pairwise distances of 2.16 ± 1.74 km. Annual net displacement remained high over the first 1–3 yr of life. Our data are consistent with studies of related taxa wherein individual spatial requirements vary with population density and island size. Notably, panmixis of small island iguana populations appears largely driven by pre-reproductive movements.