A protocol for online documentation of spider biodiversity inventories applied to a Mexican tropical wet forest (Araneae, Araneomorphae)

Zootaxa ◽  
2020 ◽  
Vol 4722 (3) ◽  
pp. 241-269 ◽  
Author(s):  
FERNANDO ÁLVAREZ-PADILLA ◽  
M. ANTONIO GALÁN-SÁNCHEZ ◽  
F. JAVIER SALGUEIRO-SEPÚLVEDA
Keyword(s):  
Taxonomic Status ◽  
Primary Forest ◽  
Phenotypic Data ◽  
Tropical Regions ◽  
Biodiversity Inventory ◽  
Species Lists ◽  
Biodiversity Inventories ◽  
Spider Community ◽  
Species Comparisons ◽  
Sampling Allocation

Spider community inventories have relatively well-established standardized collecting protocols. Such protocols set rules for the orderly acquisition of samples to estimate community parameters and to establish comparisons between areas. These methods have been tested worldwide, providing useful data for inventory planning and optimal sampling allocation efforts. The taxonomic counterpart of biodiversity inventories has received considerably less attention. Species lists and their relative abundances are the only link between the community parameters resulting from a biotic inventory and the biology of the species that live there. However, this connection is lost or speculative at best for species only partially identified (e. g., to genus but not to species). This link is particularly important for diverse tropical regions were many taxa are undescribed or little known such as spiders. One approach to this problem has been the development of biodiversity inventory websites that document the morphology of the species with digital images organized as standard views. Their main contributions are the dissemination of phenotypic data for species difficult to identify or new with the assignment of species codes, allowing species comparisons between areas regardless of their taxonomic status. The present paper describes a protocol to produce these websites almost automatically. This protocol was successfully applied to 237 species from a tropical primary forest in Mexico. The time and infrastructure required for the documentation of these species are discussed. Taxonomic information in terms of identification challenges, possible new species, and potential nomenclatural issues is described. In addition, the conventional community parameters (e. g., inventory completeness, species richness estimations, sampling intensity) are also calculated and compared through time and between methods. An optimized version for sampling allocation effort per season is presented and compared with protocols optimized for other tropical forests. 

scholarly journals Classification of Streptomyces griseus (Krainsky 1914) Waksman and Henrici 1948 and related species and the transfer of ‘Microstreptospora cinerea’ to the genus Streptomyces as Streptomyces yanii sp. nov.

2005 ◽  
Vol 55 (4) ◽  
pp. 1605-1610 ◽  
Author(s):  
Zhiheng Liu ◽  
Yanlin Shi ◽  
Yamei Zhang ◽  
Zhihong Zhou ◽  
Zhitang Lu ◽  
...  
Keyword(s):  
Streptomyces Griseus ◽  
Taxonomic Status ◽  
Morphological Data ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Genus Streptomyces ◽  
Actinomycete Strain ◽  
Soil Actinomycete

A soil actinomycete, strain 80-133T, with the non-validly published name ‘Microstreptospora cinerea’, was the subject of a polyphasic study designed to clarify its taxonomic status. Comparative 16S rRNA gene sequence studies indicated that the organism belonged to the genus Streptomyces, a result in line with previous chemotaxonomic and morphological data. The strain belonged to the Streptomyces griseus clade, but could be distinguished from representatives of species assigned to this taxon by using DNA–DNA relatedness and phenotypic data. In light of these findings, it is proposed that the organism should be recognized as a novel species of the genus Streptomyces. The name proposed for this taxon is Streptomyces yanii sp. nov., with isolate 80-133T (=AS 4.1146T=JCM 3331T) as the type strain. It was also shown that representative strains of Streptomyces argenteolus, Streptomyces caviscabies, S. griseus and Streptomyces setonii belong to the same genomic species and have key phenotypic properties in common. It is proposed that S. caviscabies and S. setonii should be considered as later heterotypic synonyms of S. griseus and that S. argenteolus AS 4.1693T should also be assigned to this taxon.

scholarly journals Reclassification of Deinococcus xibeiensis Wang et al. 2010 as a heterotypic synonym of Deinococcus wulumuqiensis Wang et al. 2010

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 1083-1085 ◽  
Author(s):  
Sunhee Hong ◽  
Christine E. Farrance ◽  
Anne Russell ◽  
Hana Yi
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Taxonomic Status ◽  
Single Species ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Genomic Relatedness

Two species of the genus Deinococcus , namely Deinococcus wulumuqiensis Wang et al. 2010 and Deinococcus xibeiensis Wang et al. 2010, were simultaneously proposed and described in the same publication. However, the identical 16S rRNA gene sequence of the two type strains strongly raised the probability of their relatedness at the species level. Thus, the genomic relatedness of the two species of the genus Deinococcus was investigated here to clarify their taxonomic status. The high (99.9 %) average nucleotide identity (ANI) between the genome sequences of the two type strains suggested that the two species are synonymous. Additional phenotypic data including enzymic activities and substrate-utilization profiles showed no pronounced differences between the type strains of the two species. Data from this study demonstrated that the two taxa constitute a single species. According to Rule 42 of the Bacteriological Code, we propose that D. xibeiensis Wang et al. 2010 should be reclassified as a subjective heterotypic synonym of D. wulumuqiensis Wang et al. 2010.

Cissus lombardiana a new name for Cissus ulmifolia (Vitaceae)

Phytotaxa ◽  
2020 ◽  
Vol 477 (1) ◽  
pp. 97-98
Author(s):  
RAMALINGAM KOTTAIMUTHU ◽  
MUTHURAMALINGAM JOTHI BASU ◽  
KULLAIYAN SATHIYADASH ◽  
VELUSWAMY KARTHIKEYAN
Keyword(s):  
South America ◽  
Taxonomic Status ◽  
Distinct Species ◽  
Tropical Regions ◽  
Fossil Taxon ◽  
New Name ◽  
Recent Estimate ◽  
The Family

Cissus Linnaeus (1753: 117) is the most speciose genus in the family Vitaceae and notable for its pantropical intercontinental disjunct pattern (Liu et al. 2013). According to the recent estimate, the genus is known to have 291 accepted species (POWO 2020) and it is widely distributed in tropical regions of Africa, Asia, Australia, Central and South America and Mexico (Wen 2007). The main characters delimiting Cissus from other Vitaceae genera are the well-developed, thick and undivided floral disks, tetramerous flowers, one-seeded berries, and seeds with a long and linear chalaza (Wen 2007). In South America, Cissus is represented by 64 species (Lombardi 2000, 2007, Rodrigues et al. 2014). Amongst C. ulmifolia (Baker 1871: 213) Planchon (1887: 552) that is a later homonym of an Italian fossil taxon Cissus ulmifolia Massalongo (1858: 80). While checking the literature and relevant websites for the availability of any synonyms, we found that C. allenii Croat (1977: 358) and C. serrulatifolia Williams (1962: 375) are listed as heterotypic synonyms of C. ulmifolia in Tropicos (2020) following Nelson (2010). However, C. allenii was synonymized under C. serrulatifolia by most of the workers (Govaerts 1999, Lombardi 2007, Morales 2015, POWO 2020, Raz & Zamora 2020) but C. ulmifolia was treated as a distinct species. So in order to ascertain the taxonomic status, we critically studied the protologues and digital specimens including types of these three species, we found that the characters of C. allenii are well within the range of C. serrulatifolia but C. ulmifolia differs from them by its 4-sided, distinctly winged stem (vs. stem terete, not winged or wingless in C. serrulatifolia) and the fruits ovoid or ovoid–subglobose, smooth (vs. obovoid or subpyriform, lenticellate in C. serrulatifolia). Since no other validly published legitimate name is available for this species (Lombardi 2007, Mota de Oliveira & Jansen-Jacobs 2016, POWO 2020), therefore, the authors propose Cissus lombardiana as a replacement name.

scholarly journals Williamsia marianensis sp. nov., a novel actinomycete isolated from the Mariana Trench

2006 ◽  
Vol 56 (5) ◽  
pp. 1123-1126 ◽  
Author(s):  
Wasu Pathom-aree ◽  
Yuichi Nogi ◽  
Iain C. Sutcliffe ◽  
Alan C. Ward ◽  
Koki Horikoshi ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Gene Tree ◽  
Taxonomic Status ◽  
Morphological Properties ◽  
Rrna Gene ◽  
Hexadecenoic Acid ◽  
Phenotypic Data ◽  
Mariana Trench ◽  
Phyletic Line

The taxonomic status of an actinomycete isolated from sediment collected from the Mariana Trench was established using a combination of genotypic and phenotypic data. Isolate MT8T had chemotaxonomic and morphological properties consistent with its classification in the genus Williamsia, and formed a distinct phyletic line in the 16S rRNA gene tree together with the type strain of Williamsia muralis. The isolate was readily distinguished from the latter, and from representatives of other Williamsia species, using DNA–DNA relatedness and phenotypic criteria. Predominant cellular fatty acids were oleic, palmitic and tuberculostearic acids and a hexadecenoic acid. The DNA G+C content was 65.2 mol%. It is apparent that the isolate belongs to a novel species of Williamsia. Strain MT8T (=DSM 44944T=NCIMB 14085T) was thus considered to be the type strain of a novel species in the genus Williamsia, for which the name Williamsia marianensis sp. nov. is proposed.

scholarly journals Neutrotolerant acidophilic Streptomyces species isolated from acidic soils in China: Streptomyces guanduensis sp. nov., Streptomyces paucisporeus sp. nov., Streptomyces rubidus sp. nov. and Streptomyces yanglinensis sp. nov.

2006 ◽  
Vol 56 (5) ◽  
pp. 1109-1115 ◽  
Author(s):  
Chunguang Xu ◽  
Liming Wang ◽  
Qingfeng Cui ◽  
Ying Huang ◽  
Zhiheng Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Phylogenetic Trees ◽  
Gene Tree ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Acidic Soils ◽  
Phenotypic Data ◽  
Streptomyces Species

The taxonomic status of six neutrotolerant acidophilic streptomycetes isolated from acidic soils in Yunnan Province, China, was established using a polyphasic approach. The morphological and chemotaxonomic characteristics revealed that the isolates belong to the genus Streptomyces. Almost complete 16S rRNA gene sequences of the isolates were determined and aligned with available corresponding sequences of representatives of the family Streptomycetaceae; phylogenetic trees were inferred using four tree-making algorithms. The isolates formed a distinct, albeit heterogeneous, subclade in the Streptomyces 16S rRNA gene tree together with the type strain of Streptomyces yeochonensis, but were readily distinguishable from the latter using DNA–DNA hybridization and phenotypic data. It was evident from the genotypic and phenotypic data that the isolates belonged to four novel Streptomyces species, for which the following names are proposed: Streptomyces guanduensis sp. nov. (type strain 701T=CGMCC 4.2022T=JCM 13274T), Streptomyces paucisporeus sp. nov. (type strain 1413T=CGMCC 4.2025T=JCM 13276T), Streptomyces rubidus sp. nov. (type strain 13c15T=CGMCC 4.2026T=JCM 13277T) and Streptomyces yanglinensis sp. nov. (type strain 1307T=CGMCC 4.2023T=JCM 13275T); isolates 317 and 913 belong to this latter species.

scholarly journals Amycolatopsis nigrescens sp. nov., an actinomycete isolated from a Roman catacomb

2007 ◽  
Vol 57 (3) ◽  
pp. 513-519 ◽  
Author(s):  
Ingrid Groth ◽  
Geok Yuan Annie Tan ◽  
Juan M. González ◽  
Leonila Laiz ◽  
Marc René Carlsohn ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Taxonomic Status ◽  
Maximum Parsimony Tree ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Parsimony Tree ◽  
High Bootstrap

The taxonomic status of two actinomycetes isolated from the wall of a hypogean Roman catacomb was established based on a polyphasic investigation. The organisms were found to have chemical and morphological markers typical of members of the genus Amycolatopsis. They also shared a range of chemical, molecular and phenotypic markers which served to separate them from representatives of recognized Amycolatopsis species. The new isolates formed a branch in the Amycolatopsis 16S rRNA gene sequence tree with Amycolatopsis minnesotensis NRRL B-24435T, but this association was not supported by a particularly high bootstrap value or by the product of the maximum-parsimony tree-making algorithm. The organisms were distinguished readily from closely related Amycolatopsis species based on a combination of phenotypic properties and from all Amycolatopsis strains by their characteristic menaquinone profiles, in which tetra-hydrogenated menaquinones with 11 isoprene units predominated. The combined genotypic and phenotypic data indicate that the isolates merit recognition as representing a novel species of the genus Amycolatopsis. The name proposed for this novel species is Amycolatopsis nigrescens sp. nov., with type strain CSC17Ta-90T (=HKI 0330T=DSM 44992T=NRRL B-24473T).

scholarly journals Micromonospora lupini sp. nov. and Micromonospora saelicesensis sp. nov., isolated from root nodules of Lupinus angustifolius

2007 ◽  
Vol 57 (12) ◽  
pp. 2799-2804 ◽  
Author(s):  
Martha E. Trujillo ◽  
Reiner M. Kroppenstedt ◽  
Carmen Fernández-Molinero ◽  
Peter Schumann ◽  
Eustoquio Martínez-Molina
Keyword(s):  
Type Strain ◽  
Sequence Data ◽  
Novel Species ◽  
Root Nodules ◽  
Taxonomic Status ◽  
Lupinus Angustifolius ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Data ◽  
Fatty Acid Patterns

A study was conducted to determine the taxonomic status of six actinomycete strains isolated from root nodules of Lupinus angustifolius. The strains were filamentous, Gram-positive and produced single spores at the tip of the hyphae. Phylogenetic, chemotaxonomic and morphological analyses demonstrated that all six strains belonged to the genus Micromonospora. According to the 16S rRNA gene sequence data, the strains were divided into two clusters that are moderately related to Micromonospora mirobrigensis, Micromonospora matsumotoense and Micromonospora purpureochromogenes. Fatty acid patterns also supported the division of the strains, and significant differences between the two groups were found in the amounts of iso-15 : 0, iso-16 : 0, iso-16 : 1 and iso-17 : 0. Furthermore, the two groups showed physiological differences which included utilization of arabinose, trehalose, alanine and sucrose and xylan hydrolysis. Finally, DNA–DNA hybridization and ribotyping studies confirmed that each group represents a novel species. Based on the genotypic and phenotypic data, the novel species Micromonospora lupini sp. nov. (type strain Lupac 14NT =DSM 44874T =LMG 24055T) and Micromonospora saelicesensis sp. nov. (type strain Lupac 09T =DSM 44871T =LMG 24056T) are proposed.

scholarly journals An inventory of Ichthyofauna of the Pindaré River drainage, Mearim River basin, Northeastern Brazil

2020 ◽  
Vol 20 (4) ◽  
Author(s):  
Erick C. Guimarães ◽  
Pâmella S. de Brito ◽  
Cléverson S. Gonçalves ◽  
Felipe P. Ottoni
Keyword(s):  
Freshwater Fish ◽  
River Basin ◽  
Native Species ◽  
Fish Fauna ◽  
Taxonomic Status ◽  
Northeastern Brazil ◽  
Neotropical Fish ◽  
River Drainage ◽  
Number Of Species ◽  
Species Lists

Abstract: In the present work, we conducted an extensive long-lasting inventory of the fishes, using different collection methodologies, covering almost the entire Pindaré River drainage, one of the principal tributaries of the Mearim River basin, an area included in the Amazônia Legal region, northeastern Brazil. We reported 101 species, just three of them being non-native, demonstrating that the composition of this studied fish community is majority composed of native species. We found a predominance of species of the orders Characiformes and Siluriformes, corroborating the pattern usually found for the Neotropical fish fauna. Similar to other studies, this inventory was mainly dominated by small characids, representing 21% of the species herein recorded. When comparing the present survey with other species lists published for this region (including the States of Maranhão and Piaui), we can conclude that the freshwater fish fauna of the State of Maranhão is probably still underestimated. We reported 41 more species, and one more species than Soares (2005, 2013) and Abreu et al. (2019) recorded for the entire Mearim River basin, respectively. We believe, however, that the number of species presented by Abreu et al. (2019) is overestimated. We compared our results with all other freshwater fish species inventories performed for the hydrological units Maranhão and Parnaíba sensu Hubbert & Renno (2006). With these comparisons, we concluded that our results evidenced that a high effort was put in the inventory here presented. The two works including more species recorded from coastal river basins of the hydrological units Maranhão and Parnaíba were the works published by Ramos et al. (2014) for the Parnaíba River basin, one of the main and larger river basin of Brazil, and the compiled data published by Castro & Dourado (2011) for the Mearim, Pindaré, Pericumã, and upper Turiaçu River drainages, including 146 and 109 species, respectively. Our survey recorded only 45 less species than Ramos et al. (2014), and eight less species than Castro & Dourado (2011). However, it is essential to emphasize that the number of species presented by Castro & Dourado (2011) is probably overestimated since they did not update and check the taxonomic status of the species of their compiled data. In several cases, they considered more than one name for the same species.

scholarly journals Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas with Stenotrophomonas and Pseudoxanthomonas as misclassified relatives

2021 ◽  
Author(s):  
Kanika Bansal ◽  
Sanjeet Kumar ◽  
Amandeep Kaur ◽  
Anu Singh ◽  
Prabhu B. Patil
Keyword(s):  
Comparative Studies ◽  
Gc Content ◽  
Taxonomic Status ◽  
Gene Clusters ◽  
Insect Vector ◽  
Phenotypic Data ◽  
Specific Host ◽  
Variant Lineage ◽  
A Minor

AbstractGenus Xanthomonas is a group of phytopathogens which is phylogenetically related to Xylella, Stenotrophomonas and Pseudoxanthomonas following diverse lifestyles. Xylella is a lethal plant pathogen with highly reduced genome, atypical GC content and is taxonomically related to these three genera. Deep phylo-taxono-genomics reveals that Xylella is a variant Xanthomonas lineage that is sandwiched between Xanthomonas species. Comparative studies suggest the role of unique pigment and exopolysaccharide gene clusters in the emergence of Xanthomonas and Xylella clades. Pan genome analysis identified set of unique genes associated with sub-lineages representing plant associated Xanthomonas clade and nosocomial origin Stenotrophomonas. Overall, our study reveals importance to reconcile classical phenotypic data and genomic findings in reconstituting taxonomic status of these four genera.Significance StatementXylella fastidiosa is a devastating pathogen of perennial dicots such as grapes, citrus, coffee, and olives. The pathogen is transmitted by an insect vector to its specific host wherein the infection leads to complete wilting of the plants. The genome of X. fastidiosa is extremely reduced both in terms of size (2Mb) and GC content (50%) when compared with its relatives such as Xanthomonas, Stenotrophomonas, and Pseudoxanthomonas that have higher GC content (65%) and larger genomes (5Mb). In this study, using systematic and in-depth genome-based taxonomic and phylogenetic criteria along with comparative studies, we assert the need of unification of Xanthomonas with its misclassified relatives (Xylella, Stenotrophomonas and Pseudoxanthomonas). Interestingly, Xylella revealed itself as a minor lineage embedded within two major Xanthomonas lineages comprising member species of different hosts.

scholarly journals Williamsia serinedens sp. nov., isolated from an oil-contaminated soil

2007 ◽  
Vol 57 (3) ◽  
pp. 558-561 ◽  
Author(s):  
A. F. Yassin ◽  
Chiu Chung Young ◽  
Wei-An Lai ◽  
H. Hupfer ◽  
A. B. Arun ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Contaminated Soil ◽  
Gene Sequence ◽  
Taxonomic Status ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data ◽  
Type Strains

The taxonomic status of a bacterium designated strain IMMIB SR-4T isolated from an oil-contaminated soil sample was characterized by using a polyphasic approach. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV, short-chain mycolic acids that co-migrated with those extracted from members of the genus Williamsia and that on pyrolysis GC produce C16 : 0 and C18 : 0 fatty acids, and dihydrogenated menaquinone with nine isoprene units as the predominant menaquinone. The generic assignment was confirmed by 16S rRNA gene sequence analysis. Comparative analysis of the 16S rRNA gene sequence showed that strain IMMIB SR-4T formed a distinct phyletic line within the genus Williamsia, displaying sequence similarities of 95.5–98.1 % with the type strains of recognized Williamsia species. Strain IMMIB SR-4T was distinguished from the type strains of recognized species of the genus Williamsia based on a set of phenotypic features. The genotypic and phenotypic data indicated that strain IMMIB SR-4T represents a novel species of the genus Williamsia, for which the name Williamsia serinedens sp. nov. is proposed. The type strain is IMMIB SR-4T (=DSM 45037T=CCUG 53151T).

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