Annotated Species Research Articles

BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis.

The bacterial metadatabase BacDive (http://bacdive.dsmz.de) has become a comprehensive resource for structured data on the taxonomy, morphology, physiology, cultivation, isolation and molecular data of prokaryotes. With its current release (7/2018) the database offers information for 63 669 bacterial and archaeal strains including 12 715 type strains. During recent developments of BacDive, the enrichment of information on existing strains was prioritized. This has resulted in a 146% increase of database content over the past three years. Especially rich datasets were integrated from 4782 manual annotated species descriptions in the International Journal of Systematic and Evolutionary Microbiology which yielded standardized phenotypic data for 5468 type strains. Another important improvement of content was achieved through the mobilization of 8977 Analytical Profile Index (API®) test results that constitute physiological data for the identification of 5237 strains. BacDive offers a unique API® data collection with respect to size and diversity. In addition, data on fatty acid profiles and antibiotic susceptibility tests were integrated. A revised graphical user interface and new search tools such as the API® test finder, the TAXplorer, or the Microbial Isolation Source Search significantly improve the user experience.

Propionate-producing bacteria in the intestine may associate with skewed responses of IL10-producing regulatory T cells in patients with relapsing polychondritis.

Relapsing polychondritis (RP) is an inflammatory disease of unknown causes, characterized by recurrent inflammation in cartilaginous tissues of the whole body. Recently, researchers have reported that, in mouse experiments, altered gut microbe-dependent T cell differentiation occurred in gut associated lymphoid tissues. Here, we investigated whether gut microbe alteration existed, and if so, the alteration affected peripheral T cell differentiation in patients with RP. In an analysis of gut microbiota, we found increased annotated species numbers in RP patients compared with normal individuals. In the RP gut microbiota, we observed several predominant species, namely Veillonella parvula, Bacteroides eggerthii, Bacteroides fragilis, Ruminococcus bromii, and Eubacterium dolichum, all species of which were reported to associate with propionate production in human intestine. Propionate is a short-chain fatty acid and is suggested to associate with interleukin (IL)10-producing regulatory T (Treg) cell differentiation in gut associated lymphoid tissues. IL10 gene expressions were moderately higher in freshly isolated peripheral blood mononuclear cells (PBMC) of RP patients than those of normal individuals. Six hours after the initiation of the cell culture, regardless of the presence and absence of mitogen stimulation, IL10 gene expressions were significantly lower in RP patients than those in normal individuals. It is well known that PBMC of patients with autoimmune and inflammatory diseases show hyporesponsiveness to mitogen stimulation. We suggest that, in RP patients, continuous stimulation of intestinal T cells by excessive propionate leads to the spontaneous IL10 production and a subsequent refractory period of T cells in patients with RP. The hyporesponsiveness of Treg cells upon activation may associate with inflammatory cytokine production of PBMC and subsequently relate to chondritis in RP patients.

Fish, Coral, and Sponge Assemblages Associated With Altiphotic and Mesophotic Reefs Along the Guánica Biosphere Reserve Continental Shelf Edge, Southwest Puerto Rico

The benthic and fish communities of the central portion of the Guanica, Puerto Rico shelf edge were studied to determine species abundance, distributions and species overlap between two depth stratifications, 20 and 45 m, at eight sites. A total of 67 fish species belonging to 21 families were identified. Similar species richness estimates were observed between depths, though fish assemblage composition differed significantly, with observable changes in feeding guild contributions of herbivore and omnivore (20 m) to a deeper assemblage composed of piscivores and planktivores (45 m). Coral assemblages consisted of 31 species at 20 m and 11 species at 45 m, accounting for 17.0% (±1.76 SE) and 2.6% (±0.89 SE) benthic cover for the altiphotic and mesophotic surveys, respectively. The altiphotic and mesophotic coral reef communities support different scleractinian coral assemblages with minimal species overlap. Altiphotic surveys of sponges yielded a higher species richness than mesophotic, with 60 and 54 species respectively, and an overall total of 71 species identified from both depths, with 45 species overlapping (63.0%). The percent cover of sponges surveyed at altiphotic reefs accounted for 9.0% (±1.04 SE), while the percent cover of sponges surveyed at mesophotic reefs was 14.0% (±1.96 SE). Our data show fish, coral, and sponge assemblages are differentiated between 20 and 45 m along thes provides an annotated species list of the local sponge fauna. Combined, these results highlight the need for con Guanica shelf edge offshore of the Guanica Biosphere Reserve. This study represents the first observations for species distributions of adjacent altiphotic and mesophotic coral reef habitats along the Guanica shelf edge, as well atinued environmental stewardship and conservation in the area.

TORTONIAN CLYPEASTER FAUNA (ECHINOIDEA: CLYPEASTEROIDA) FROM GAVDOS ISLAND (GREECE

The Tortonian sediments of Gavdos Island (Greece) contain a rich and diverse echinoidfauna. Clypeasteroid (sand dollars) echinoids are an important component of this fauna and sixteen taxa are recognized. Of these, eleven species are new records for Gavdos Island. The present paper is an annotated species list along with notes on certain aspects of the ecology of the determined echinoderms.

<b>An annotated checklist of the herpetofauna of the Rashtrapati Bhawan Estates, New Delhi, India</b>

Rashtrapati Bhavan Estates is a large semi-natural area comprising significant patches of secondary forest, cultivation, wetlands and parks in the heart of Delhi, the capital city of India. An inventory of herpetofauna was undertaken from May 15 to July 31, 2015, which revealed four species of amphibians and eight of reptiles. One reptilian species—Striped Keelback—was a new record for the Delhi region. In addition, secondary records of the presence of five snake species were obtained. Given the paucity of published data on natural history of the national capital, this annotated species checklist assumes importance and will be of use for urban planning and conservation.

<b>An annotated checklist of the herpetofauna of the Rashtrapati Bhawan Estates, New Delhi, India</b>

Rashtrapati Bhavan Estates is a large semi-natural area comprising significant patches of secondary forest, cultivation, wetlands and parks in the heart of Delhi, the capital city of India. An inventory of herpetofauna was undertaken from May 15 to July 31, 2015, which revealed four species of amphibians and eight of reptiles. One reptilian species—Striped Keelback—was a new record for the Delhi region. In addition, secondary records of the presence of five snake species were obtained. Given the paucity of published data on natural history of the national capital, this annotated species checklist assumes importance and will be of use for urban planning and conservation.

The Global Invasion of the Suckermouth Armored Catfish Genus Pterygoplichthys (Siluriformes: Loricariidae): Annotated List of Species, Distributional Summary, and Assessment of Impacts.

Alexander Benjamin Orfinger and Daniel Douglas Goodding (2018) The suckermouth armored catfish genus Pterygoplichthys (Siluriformes: Loricariidae) includes popular aquarium fishes and constitutes one of the most successful freshwater invasive taxa, having achieved global distribution. To date, however, no comprehensive distributional record nor impact assessment exist for the spread of the genus, precluding informed management strategies. To provide these tools, our study aims to (1) provide an annotated checklist of species for this taxonomically confusing genus, (2) survey all available literature on the spread of the genus and summarize and map its invasive distribution, and (3) assess the overall socioeconomic and environmental impact of the genus on a global scale using the Generic Impact Scoring System (GISS). First, we provide an updated annotated species list. We then summarize seventy-one unique invasion records along with twenty-one instances of demonstrated impacts. Species of the genus Pterygoplichthys have now invaded five continents and twenty-one countries, and show an extended range in their native South America. Impact analysis yielded a GISS score of 18 to 19, indicating low to moderate levels of socioeconomic and environmental threats. However, to bolster the confidence in this analysis in future iterations, more research should aim to move beyond just "first records" and instead empirically evaluate species' effects on native ecosystems.

Semi-targeted Lipidomics of Plant Acyl Lipids Using UPLC-HR-MS in Combination with a Data-Independent Acquisition Mode.

In recent years, multiple mass-spectrometric methods have been developed to tackle fundamental analytical questions in the field of biology and biochemistry. One essential approach relies on the use of liquid chromatography (LC), for efficient compound separation, coupled to high-resolution mass spectrometry (HR-MS). Even though these techniques are highly sensitive allowing for the reliable measurement of several thousand mass features, the major bottleneck is to convert the measured masses into annotated lipid species. To overcome this problem, we present a simple, example-based workflow, which provides an introduction to basic strategies for the manual validation of LC-MS-based lipidomic data. The whole strategy makes use of a data-independent acquisition (DIA) method, where alternating MS measurement cycles using high and low-energy scans are used. This measurement strategy allows to reliably annotate lipids, based on the exact mass measurements of intact, but also fragmented lipids from continuously recorded spectra.

The history of mycological studies in Khanty-Mansi autonomous okrug: 2) studies of Macromycetes, Lichens and Myxomycetes, state of mycological collections and fungal records database

В предыдущей части работы мы затронули вопросы актуальности развития микологических исследований на территории севера Западной Сибири (конкретно – ХМАО) и необходимость проведения ревизии уже выполненных за 100 лет работ. Был сделан обзор первых разрозненных работ, проведенных в начале 20 века, описание истории изучения дереворазрушающих базидиомицетов и фитопатологических исследований. Во второй части мы продолжаем анализ других направлений и подводим некоторые итоги.
 Большое внимание на территории ХМАО уделено также изучению наземных макромицетов (в узком смысле – агарикоидных базидиомицетов), однако исследования носят локальный характер. Хорошо изучены две территории – в окр. г. Ханты-Мансийска и Юганский заповедник. Изучается как видовой состав, так и количественная структура сообществ макромицетов лесных и болотных экосистем, а также особенности биологии и экологии отдельных редких видов. Ввиду высокой заболоченности территории округа особое внимание в исследованиях было уделено сообществам грибов верховых болот (макро- и микромицеты, дрожжи, ксилотрофные базидиомицеты, миксомицеты). Выявление видового состава лихенобиоты проходило лишь в отдельных районах ХМАО, однако суммарный список видов достаточно велик. Выявлено видовое разнообразие миксомицетов на территориях некоторых ООПТ. В контексте таксономических исследований всего за период микологической истории ХМАО было описано четыре новых вида и одна комбинация, в работах сообщаются сведения о новых, еще не описанных видах. Охрана грибов в ХМАО началась с выпуска Красной книги региона в 2003 г. (второе издание вышло в 2013 году). За это время вышел ряд публикаций, посвященных микологическим природоохранным мероприятиям. Коллекции грибов являются неотъемлемой частью развития микологических исследований: на территории мы насчитываем около 5 фунгариев. Кроме того, большое число коллекций грибов, собранных в ХМАО, хранятся в исследовательских институтах других регионов. На основе опубликованных работ нами была составлена база данных находок грибов и грибоподобных организмов ХМАО (Fungal Records Database of Yugra). В настоящее время база включает около 14 тыс. записей находок грибов. Ссылка на базу данных размещена на странице сайта Фунгария ЮГУ и база данных доступна для скачивания. Анализ базы данных показал, что для территории ХМАО опубликовано около 2600 видов и подвидовых таксонов грибов и грибоподобных организмов. Из них большая часть приходится на агарикоидные базидиомицеты (30%), лишайники (37%), а также афиллофоровые базидиомицеты (19%).

Hyphodontia (Hymenochaetales, Basidiomycota) and similar taxa from Central Asia

Wood-inhabiting fungi are noteworthy components of woody ecosystems that are responsible for the decomposition and turnover of wood nutrients. While the diversity and ecology of these fungi in the temperate forests has been relatively well explored, little is known on diversity of these fungi in the arid and semi-arid forest ecosystems. This is the first study on diversity, distribution, and ecology of the fungal genus Hyphodontia s.l. in the five countries of Central Asia, viz., Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan, and Uzbekistan. Altogether, 11 species are confirmed for the region, among which the following six species are reported for the first time from Central Asia: Hyphodontia alutaria, H. pallidula, Kneiffiella alutacea, Lyomyces crustosus, L. erastii, and L. sambuci. In addition to the morphological evidence, the identity of three species is confirmed with phylogenetic analysis based on ITS nuclear ribosomal DNA region. The spectra of known hosts for many of the studied species were expanded. An annotated species list and geo-referenced distribution maps are provided as well as notes on taxonomy, ecology, and local, regional, and global distribution. An identification key to the species of Hyphodontia s.l. recorded in arid and semi-arid regions of Central Asia is also provided.

A plasma lipidomics strategy reveals perturbed lipid metabolic pathways and potential lipid biomarkers of human colorectal cancer.

To explore underlying molecular mechanisms and identify novel lipid biomarkers promising for colorectal cancer (CRC) diagnosis, a continuous-flow two dimensional liquid chromatography-quadrupole time-of-flight mass spectrometry (2D LC-QToF/MS) method was employed to comprehensively measure lipid species in human plasma of CRC patients and healthy controls. With a total of 427 annotated lipid species, we identified 64 lipid species with corrected p value less than 0.05 and fold change more than 1.5. These significantly altered lipid species were mainly involved in glycerolipids and glycerophospholipids metabolism and sphingolipids metabolism. After the diagnosis ability evaluation based on the receiver operating characteristic (ROC) curve, phosphatidylglycerol (34:0), sphingomyelin (42:2), ceramide (44:5), lysophosphatidylcholine (18:3), lysophosphatidylcholine (18:2), phosphatidylethanolamine (O-36:3), phosphatidylethanolamine (O-38:3) and sphingomyelin (38:8) were finally proposed as the potential biomarkers with the area under the curve (AUC) more than 0.900. These results suggest that this 2D LC-QToF/MS-based lipidomics profiling has great potential as a noninvasive diagnostic method in detecting CRC and hopefully provide new clues to understand its underlying mechanism.

Further new or interesting lichens and lichenicolous fungi from La Palma (Canary Islands, Spain)

Forty-five taxa of lichens and lichenicolous fungi are recorded from La Palma for the first time. Twelve are new to the Canary Islands archipelago. One further species, Didymocyrtis canarienis, is described as new for science. The total number of known taxa from the island La Palma has raised to 874. An alphabetical annotated species list of all taxa with collection localities, substrate and occasional further annotations is presented.

REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes.

Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated methods depend heavily on sequence composition and often underestimate the complexity of the proteome. We developed RibosomeE Profiling Assisted (re-)AnnotaTION (REPARATION), a de novo machine learning algorithm that takes advantage of experimental protein synthesis evidence from ribosome profiling (Ribo-seq) to delineate translated open reading frames (ORFs) in bacteria, independent of genome annotation (https://github.com/Biobix/REPARATION). REPARATION evaluates all possible ORFs in the genome and estimates minimum thresholds based on a growth curve model to screen for spurious ORFs. We applied REPARATION to three annotated bacterial species to obtain a more comprehensive mapping of their translation landscape in support of experimental data. In all cases, we identified hundreds of novel (small) ORFs including variants of previously annotated ORFs and >70% of all (variants of) annotated protein coding ORFs were predicted by REPARATION to be translated. Our predictions are supported by matching mass spectrometry proteomics data, sequence composition and conservation analysis. REPARATION is unique in that it makes use of experimental translation evidence to intrinsically perform a de novo ORF delineation in bacterial genomes irrespective of the sequence features linked to open reading frames.

Using non-negative matrix factorisation to facilitate efficient bird species richness surveys

This paper considers computer-assisted learning of sound spectra in environmental recordings to facilitate manual bird species identification. Today, a variety of automated methods have been successfully applied for acoustic recognition of specific bird species. These methods are more effective for single targeted species detection. For in-field recordings, however, simultaneous vocalisations and unknown species usually make such methods less effective.In this study, we propose a non-negative matrix factorisation based method to facilitate manual bird species identification from environmental recordings. First, distinct sound spectra are extracted from each audio clip by applying non-negative matrix factorisation and clustering techniques. Based on these distinct sound spectra, a greedy algorithm is then designed to sample audio clips. Each sampled audio clip maximises the number of new spectra. People who follow this sampled sequence of audio clips should be able to identify the most species given a fixed number of audio clips. The efficiency is validated with annotated bird species per minute provided by experienced ornithologists.

Research on bats (Chiroptera) from the state of São Paulo, southeastern Brazil: annotated species list and bibliographic review

The state of São Paulo has a high number of mammal species, a great part of those is represented by bats. In this study I conducted historical review about the research on bats from the state of São Paulo and provide the first annotated species list and bibliographic review for the state. A total of 79 extant species belonging to eight families of bats occur in São Paulo. At least seven species are represented by fossils, two of these are extinct. I also present new records of rarely sampled species in the state such as Diaemus youngii, Diphylla ecaudata, Saccopteryx leptura, Thyroptera tricolor and Micronycteris microtis. Three species, Micronycteris brosseti, Mimon crenulatum and Uroderma bilobatum were removed from the list. Also is confirmed the occurrence of Histiotus montanus and Molossus aztecus in the state.

New occurrences of aphyllophoroid fungi (Agaricomycetes, Basidiomycota) in the Central Forest State Biosphere Nature Reserve, Tver Region, Russia

New data on non-agaricoid wood-inhabiting basidiomycetes collected from dead wood in the Central Forest Nature Reserve are provided. In total, 228 species were recorded during short-term visits in 2009–2015, of which 37 are reported as new to the reserve. An annotated species list is presented including details of associated substrata and, when available, personal fungarium specimen numbers. The paper increases the total number of species reported for the reserve and provides notes on specimens belonging to the genus Phlebiella, which is probably an undescribed species. Records of some rare, or rarely collected species, such as Antrodiella foliaceodentata, Basidiodendron radians, Phlebiella fibrillosa and Tulasnella eichleriana are discussed.

The making of a pest: Insights from the evolution of chemosensory receptor families in a pestiferous and invasive fly, Drosophila suzukii.

BackgroundDrosophila suzukii differs from other melanogaster group members in their proclivity for laying eggs in fresh fruit rather than in fermenting fruits. Olfaction and gustation play a critical role during insect niche formation, and these senses are largely mediated by two important receptor families: olfactory and gustatory receptors (Ors and Grs). Earlier work from our laboratory has revealed how the olfactory landscape of D. suzukii is dominated by volatiles derived from its unique niche. Signaling and reception evolve in synchrony, since the interaction of ligands and receptors together mediate the chemosensory behavior. Here, we manually annotated the Ors and Grs in D. suzukii and two close relatives, D. biarmipes and D. takahashii, and compared these repertoires to those in other melanogaster group drosophilids to identify candidate chemoreceptors associated with D. suzukii’s unusual niche utilization.ResultsOur comprehensive annotations of the chemosensory genomes in three species, and comparative analysis with other melanogaster group members provide insights into the evolution of chemosensation in the pestiferous D. suzukii. We annotated a total of 71 Or genes in D. suzukii, with nine of those being pseudogenes (12.7 %). Alternative splicing of two genes brings the total to 62 genes encoding 66 Ors. Duplications of Or23a and Or67a expanded D. suzukii’s Or repertoire, while pseudogenization of Or74a, Or85a, and Or98b reduced the number of functional Ors to roughly the same as other annotated species in the melanogaster group. Seventy-one intact Gr genes and three pseudogenes were annotated in D. suzukii. Alternative splicing in three genes brings the total number of Grs to 81. We identified signatures of positive selection in two Ors and three Grs at nodes leading to D. suzukii, while three copies in the largest expanded Or lineage, Or67a, also showed signs of positive selection at the external nodes.ConclusionOur analysis of D. suzukii’s chemoreceptor repertoires in the context of nine melanogaster group drosophilids, including two of its closest relatives (D. biarmipes and D. takahashii), revealed several candidate receptors associated with the adaptation of D. suzukii to its unique ecological niche.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2983-9) contains supplementary material, which is available to authorized users.

Analysis of small non-coding RNAs of poorly annotated species in Galaxy with the help of ortholog information of well annotated species

Analysis of small non-coding RNAs of poorly annotated species in Galaxy with the help of ortholog information of well annotated species

Bolivian Mimosa (Leguminosae, Mimosoideae): three new species and a species checklist

Three new species of Mimosa (Leguminosae, Mimosoideae) M. chiquitaniensis, M. chochisensis and M. rastrera, two of them endemic to Bolivia, and the third also occurring in Brazil, are described and an annotated species checklist for the genus in Bolivia is presented. This brings the tally of species of Mimosa recorded from Bolivia to 55 (plus five doubtful species to be confirmed), an increase of ca. 50% since the monographic account of the genus published just over 25 years ago.

A contribution to the knowledge of Orthoptera diversity from Peninsular Malaysia: Bukit Larut, Perak.

Bukit Larut is a hill station at the southern tip of the Bintang Range, Perak of Peninsular Malaysia. While the biodiversity of Bukit Larut has been previously documented, its entomofauna, including the Orthoptera, remains relatively unknown. A faunistic survey was conducted in 2015 as part of the continuous exploration of the highlands in Malay Peninsula. An annotated species list of 71 (24 Caelifera and 47 Ensifera) species of Orthoptera from ten families (five from each order) is presented here. While the coverage of lineages in the orthopteran phylogeny is well-represented, the diversity in Bukit Larut is dominated by the three main families: Acrididae, Gryllidae and Tettigoniidae. Eight new locality records for Bukit Larut and/or Peninsular Malaysia and potential new species awaiting description highlight that the orthopteran diversity in Bukit Larut is not exhaustive.