Publication date and author spelling for the hidden angelshark Squatina occulta.

Two dates of publication have been associated with the hidden angelshark Squatina occulta. Additionally, the name of the second author of this species has been cited with different spellings in different publications. Both inconsistencies are addressed in this study. It is suggested that the hidden angelshark be consistently cited as Squatina occulta Vooren & da Silva 1991.

Novel database for accA gene revealed a vertical variability pattern of autotrophic carbon fixation potential of ammonia oxidizing archaea in a permeable subterranean estuary.

The autotrophic carbon fixation pathway of ammonia-oxidizing archaea (AOA) was the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle, of which the acetyl-CoA carboxylase α-submit (accA) gene is widely recognized as the indicator. To date, there is no reference database or suitable cut-off value for operational taxonomic unit (OTU) clustering to analyze the diversity of AOA based on the accA gene. In this study, a reference database with 489 sequences was constructed, all the accA gene sequences was obtained from the AOA enrichment culture, pure culture and environmental samples. Additionally, the 79% was determined as the cut-off value for OTU clustering by comparing the similarity between the accA gene and the 16S rRNA gene. The developed method was verified by analyzing samples from the subterranean estuary and a vertical variation pattern of autotrophic carbon fixation potential of AOA was revealed. This study provided an effective method to analyze the diversity and autotrophic carbon fixation potential of AOA based on accA gene.

Novel database and cut-off value for bacterial amoA gene revealed a spatial variability pattern of the ammonia-oxidizing bacteria community from river to sea.

Ammonia-oxidizing bacteria (AOB) catalyze the first step of nitrification, oxidizing ammonia to nitrite, and are characterized by amoA gene encoding ammonia monooxygenase. To analyze the AOB community effectively, an integral taxonomy database containing 14,058 amoA sequences and the optimal cut-off value at 95 % for OTU clustering were determined. This method was evaluated to be efficient by the analysis of environmental samples from the river, estuary, and sea. Using this method, a significant spatial variance of the AOB community was found. The diversity of AOB was highest in the estuary and lowest in the ocean. Nitrosomonas were the predominant AOB in the sediments of the freshwater river and estuary. Nearly all the AOB-amoA sequences belonged to uncultured bacterium in the sediments of deep sea. In general, an integral AOB taxonomic database and a suitable cut-off value were constructed for the comprehensive exploration of the diversity of AOB from river to sea.

New primers, taxonomic database and cut-off value for processing nxrB gene high-throughput sequencing data by MOTHUR.

To analyse the diversity of Nitrospira with functional nxrB genes, we designed and optimized a new primer set, Nxr-f27/Nxr-r617, and constructed a database for taxonomic classification. We also propose a cut-off value for processing the high-throughput sequencing data with MOTHUR.

Optimization of a method for diversity analysis of anammox bacteria using high-throughput sequencing of 16S rRNA gene amplicon.

High-throughput sequencing of 16S rRNA amplicons is an effective method for diversity analysis of anammox bacteria. However, the corresponding taxonomic database and suitable cut-off value are unavailable for processing high-throughput sequencing data. This study is the first to construct a taxonomic database, comprising 17 sequences of enriched anammox strains (regarded as seed sequences) and 2925 uncultured sequences from environmental samples. Moreover, a suitable cut-off value was determined based on pairwise evolutionary distances between the 16S rRNA gene sequences of the 17 identified species and diversity indexes of community in the taxonomic database. Furthermore, the proposed method was validated with multiple environmental samples. In summary, the taxonomic database and proposed cut-off value targeting the 16S rRNA gene presented in this study can be effectively employed to explore the diversity of anammox bacteria.

An online taxonomic database of the stick insect (Phasmida) egg-parasitising subfamilies Amiseginae and Loboscelidiinae (Hymenoptera: Chrysididae).

BACKGROUND: The wasp subfamilies Amiseginae and Loboscelidiinae (Hymenoptera: Chrysididae) were last catalogued in Kimsey and Bohart (1991). The subfamilies are considered to be obligate egg parasitoids of the Phasmida (stick insects), which are known to be pests in many areas of the world (Baker 2015). Our lack of knowledge of these wasps, in particular their host associations and host specificity, prevents studies into using them as potential control agents for pest phasmids. Phasmids are popular throughout the world with people from a wide range of backgrounds, from pet keepers to professional entomologists. NEW INFORMATION: A taxonomic database of the subfamilies Amiseginae and Loboscelidiinae has been created as the Chrysididae SpeciesFile, summarising the current state of scientific knowledge about these groups. In addition, a bibliography of works on these subfamilies has been created. In total information is provided for 187 valid species.

Taxonomic database and cut-off value for processing mcrA gene 454 pyrosequencing data by MOTHUR.

The functional mcrA gene of methanogens can generate phylogeny as congruent as the 16S rRNA gene phylogeny. For the mcrA sequences amplified by mlas/mcrA-rev primers, we created a database for taxonomical classification and propose cut-off values for OTU clustering and further analysis of α- and ß-diversity with the MOTHUR software.

Avibase - a database system for managing and organizing taxonomic concepts.

Scientific names of biological entities offer an imperfect resolution of the concepts that they are intended to represent. Often they are labels applied to entities ranging from entire populations to individual specimens representing those populations, even though such names only unambiguously identify the type specimen to which they were originally attached. Thus the real-life referents of names are constantly changing as biological circumscriptions are redefined and thereby alter the sets of individuals bearing those names. This problem is compounded by other characteristics of names that make them ambiguous identifiers of biological concepts, including emendations, homonymy and synonymy. Taxonomic concepts have been proposed as a way to address issues related to scientific names, but they have yet to receive broad recognition or implementation. Some efforts have been made towards building systems that address these issues by cataloguing and organizing taxonomic concepts, but most are still in conceptual or proof-of-concept stage. We present the on-line database Avibase as one possible approach to organizing taxonomic concepts. Avibase has been successfully used to describe and organize 844,000 species-level and 705,000 subspecies-level taxonomic concepts across every major bird taxonomic checklist of the last 125 years. The use of taxonomic concepts in place of scientific names, coupled with efficient resolution services, is a major step toward addressing some of the main deficiencies in the current practices of scientific name dissemination and use.