scholarly journals Cellulose Degradation by Micromonosporas Recovered from Freshwater Lakes and Classification of These Actinomycetes by DNA Gyrase B Gene Sequencing

2008 ◽  
Vol 74 (22) ◽  
pp. 7080-7084 ◽  
Author(s):  
Alexandre B. de Menezes ◽  
Robert J. Lockhart ◽  
Michael J. Cox ◽  
Heather E. Allison ◽  
Alan J. McCarthy

ABSTRACT A number of Micromonospora strains isolated from the water column, sediment, and cellulose baits placed in freshwater lakes were shown to be able to degrade cellulose in lake water without any addition of nutrients. A selective isolation method was also developed to demonstrate that CFU arose from both spores and hyphae that inhabit the lake environment. Gyrase B gene sequencing performed on the isolates identified a number of new centers of variation within Micromonospora, but the most actively cellulolytic strains were recovered in a single cluster that equated with the type species of the genus, M. chalcea.

2011 ◽  
Vol 20 (1) ◽  
pp. 161-173
Author(s):  
A.P. Kassatkina

Resuming published and own data, a revision of classification of Chaetognatha is presented. The family Sagittidae Claus & Grobben, 1905 is given a rank of subclass, Sagittiones, characterised, in particular, by the presence of two pairs of sac-like gelatinous structures or two pairs of fins. Besides the order Aphragmophora Tokioka, 1965, it contains the new order Biphragmosagittiformes ord. nov., which is a unique group of Chaetognatha with an unusual combination of morphological characters: the transverse muscles present in both the trunk and the tail sections of the body; the seminal vesicles simple, without internal complex compartments; the presence of two pairs of lateral fins. The only family assigned to the new order, Biphragmosagittidae fam. nov., contains two genera. Diagnoses of the two new genera, Biphragmosagitta gen. nov. (type species B. tarasovi sp. nov. and B. angusticephala sp. nov.) and Biphragmofastigata gen. nov. (type species B. fastigata sp. nov.), detailed descriptions and pictures of the three new species are presented.


2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Sebastian Racedo ◽  
Ivan Portnoy ◽  
Jorge I. Vélez ◽  
Homero San-Juan-Vergara ◽  
Marco Sanjuan ◽  
...  

Abstract Background High-throughput sequencing enables the analysis of the composition of numerous biological systems, such as microbial communities. The identification of dependencies within these systems requires the analysis and assimilation of the underlying interaction patterns between all the variables that make up that system. However, this task poses a challenge when considering the compositional nature of the data coming from DNA-sequencing experiments because traditional interaction metrics (e.g., correlation) produce unreliable results when analyzing relative fractions instead of absolute abundances. The compositionality-associated challenges extend to the classification task, as it usually involves the characterization of the interactions between the principal descriptive variables of the datasets. The classification of new samples/patients into binary categories corresponding to dissimilar biological settings or phenotypes (e.g., control and cases) could help researchers in the development of treatments/drugs. Results Here, we develop and exemplify a new approach, applicable to compositional data, for the classification of new samples into two groups with different biological settings. We propose a new metric to characterize and quantify the overall correlation structure deviation between these groups and a technique for dimensionality reduction to facilitate graphical representation. We conduct simulation experiments with synthetic data to assess the proposed method’s classification accuracy. Moreover, we illustrate the performance of the proposed approach using Operational Taxonomic Unit (OTU) count tables obtained through 16S rRNA gene sequencing data from two microbiota experiments. Also, compare our method’s performance with that of two state-of-the-art methods. Conclusions Simulation experiments show that our method achieves a classification accuracy equal to or greater than 98% when using synthetic data. Finally, our method outperforms the other classification methods with real datasets from gene sequencing experiments.


Author(s):  
Xue Zhang ◽  
Lida Zhang ◽  
XiaoYan Yu ◽  
Jing Zhang ◽  
Yanjie Jiao ◽  
...  

A novel actinobacterium, designated strain NEAU-351T, was isolated from cow dung collected from Shangzhi, Heilongjiang Province, northeast PR China and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-351T belonged to the genus Nocardia , with the highest similarity (98.96 %) to Nocardia takedensis DSM 44801T and less than 98.0 % identity with other type strains of the genus Nocardia . The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major menaquinone was observed to contain MK-8(H4, ω-cycl) (78.2 %). The fatty acid profile mainly consisted of C16 : 0, C18 : 1  ω9c and 10-methyl C18 : 0. Mycolic acids were present. The genomic DNA G+C content of strain NEAU-351T was 68.1 mol%. In addition, the average nucleotide identity values between strain NEAU-351T and its reference strains, Nocardia takedensis DSM 44801T and Nocardia arizonensis NBRC 108935T, were found to be 81.4 and 82.9 %, respectively, and the level of digital DNA–DNA hybridization between them were 24.8 % (22.5–27.3 %) and 26.3 % (24–28.8 %), respectively. Here we report on the taxonomic characterization and classification of the isolate and propose that strain NEAU-351T represents a new species of the genus Nocardia , for which the name Nocardia bovistercoris is proposed. The type strain is NEAU-351T (=CCTCC AA 2019090T=DSM 110681T).


Zootaxa ◽  
2018 ◽  
Vol 4540 (1) ◽  
pp. 7
Author(s):  
BEVERLY S. GERDEMAN ◽  
RUFINO C. GARCIA ◽  
ANDREW HERCZAK ◽  
HANS KLOMPEN

The generic classification of millipede associated Heterozerconidae in the Oriental region is revised. The genus Allozercon Vitzthum is re-diagnosed and Asioheterozercon Fain is designated as an subjective junior synonym of Allozercon. Philippinozercon gen. nov., with the type species P. makilingensis sp. nov., is described for all instars. This genus may be endemic for the Philippines, but is quite widespread in that country. All immature instars are described, making this the second species of Heterozerconidae known for all instars. The morphology of the immatures is compared with that of immatures of the temperate species Narceoheterozercon ohioensis and unnamed species from Brazil and Thailand. All immatures were collected from millipede frass and litter, never from millipedes. Adults are associated with millipedes in the family Trigoniulidae (Spirobolida). 


Koedoe ◽  
1995 ◽  
Vol 38 (1) ◽  
Author(s):  
G.J. Bredenkamp ◽  
H. Bezuidenhout

A procedure for the effective classification of large phytosociological data sets, and the combination of many data sets from various parts of the South African grasslands is demonstrated. The procedure suggests a region by region or project by project treatment of the data. The analyses are performed step by step to effectively bring together all releves of similar or related plant communities. The first step involves a separate numerical classification of each subset (region), and subsequent refinement by Braun- Blanquet procedures. The resulting plant communities are summarised in a single synoptic table, by calculating a synoptic value for each species in each community. In the second step all communities in the synoptic table are classified by numerical analysis, to bring related communities from different regions or studies together in a single cluster. After refinement of these clusters by Braun-Blanquet procedures, broad vegetation types are identified. As a third step phytosociological tables are compiled for each iden- tified broad vegetation type, and a comprehensive abstract hierarchy constructed.


2020 ◽  
Vol 5 (1) ◽  
pp. 17-38 ◽  
Author(s):  
K. Seto ◽  
S. Van Den Wyngaert ◽  
Y. Degawa ◽  
M. Kagami

During the last decade, the classification system of chytrids has dramatically changed based on zoospore ultrastructure and molecular phylogeny. In contrast to well-studied saprotrophic chytrids, most parasitic chytrids have thus far been only morphologically described by light microscopy, hence they hold great potential for filling some of the existing gaps in the current classification of chytrids. The genus Zygorhizidium is characterized by an operculate zoosporangium and a resting spore formed as a result of sexual reproduction in which a male thallus and female thallus fuse via a conjugation tube. All described species of Zygorhizidium are parasites of algae and their taxonomic positions remain to be resolved. Here, we examined morphology, zoospore ultrastructure, host specificity, and molecular phylogeny of seven cultures of Zygorhizidium spp. Based on thallus morphology and host specificity, one culture was identified as Z. willei parasitic on zygnematophycean green algae, whereas the others were identified as parasites of diatoms, Z. asterionellae on Asterionella, Z. melosirae on Aulacoseira, and Z. planktonicum on Ulnaria (formerly Synedra). According to phylogenetic analysis, Zygorhizidium was separated into two distinct order-level novel lineages; one lineage was composed singly of Z. willei, which is the type species of the genus, and the other included the three species of diatom parasites. Zoospore ultrastructural observation revealed that the two lineages can be distinguished from each other and both possess unique characters among the known orders within the Chytridiomycetes. Based on these results, we accommodate the three diatom parasites, Z. asterionellae, Z. melosirae, and Z. planktonicum in the distinct genus Zygophlyctis, and propose two new orders: Zygorhizidiales and Zygophlyctidales.


2016 ◽  
Vol 11 (10) ◽  
pp. 1934578X1601101 ◽  
Author(s):  
Rita Könye ◽  
Ágnes Evelin Ress ◽  
Anna Sólyomváry ◽  
Gergő Tóth ◽  
András Darcsi ◽  
...  

In Jurinea mollis fruit, the dibenzylbutyrolactone-type lignan glycoside arctiin and its aglycone arctigenin were determined for the first time using a combination of optimized enzymatic treatment and complementary spectrometric (HPLC-MS, GC-MS) and spectroscopic (CD and NMR) methods. Analysis of separated fruit parts, i.e., the fruit wall and embryo, demonstrated the specific accumulation of arctiin, since it was exclusively found in the embryo. Arctiin in the embryo samples (71.5 mg/g) was found to be quantitatively converted into arctigenin (50.7 mg/g) by endogenous enzymatic hydrolysis, resulting in one of the highest arctigenin-containing plant tissues reported to date and allowing the selective isolation of arctigenin by our recently reported three-step isolation method. The absolute configuration of the isolated arctigenin was determined to be (-)-(8 R,8′ R). Conformational analysis of arctigenin was also performed, resulting in three major low energy conformations.


2019 ◽  
Vol 11 (23) ◽  
pp. 2883 ◽  
Author(s):  
Soomets ◽  
Uudeberg ◽  
Jakovels ◽  
Zagars ◽  
Reinart ◽  
...  

Inland waters play a critical role in our drinking water supply. Additionally, they areimportant providers of food and recreation possibilities. Inland waters are known to be opticallycomplex and more diverse than marine or ocean waters. The optical properties of natural waters areinfluenced by three different and independent sources: phytoplankton, suspended matter, andcolored dissolved organic matter. Thus, the remote sensing of these waters is more challenging.Different types of waters need different approaches to obtain correct water quality products;therefore, the first step in remote sensing of lakes should be the classification of the water types. Theclassification of optical water types (OWTs) is based on the differences in the reflectance spectra ofthe lake water. This classification groups lake and coastal waters into five optical classes: Clear,Moderate, Turbid, Very Turbid, and Brown. We studied the OWTs in three different Latvian lakes:Burtnieks, Lubans, and Razna, and in a large Estonian lake, Lake Võrtsjärv. The primary goal of thisstudy was a comparison of two different Copernicus optical instrument data for opticalclassification in lakes: Ocean and Land Color Instrument (OLCI) on Sentinel-3 and MultispectralInstrument (MSI) on Sentinel-2. We found that both satellite OWT classifications in lakes werecomparable (R2 = 0.74). We were also able to study the spatial and temporal changes in the OWTs ofthe study lakes during 2017. The comparison between two satellites was carried out to understandif the classification of the OWTs with both satellites is compatible. Our results could give us not onlya better overview of the changes in the lake water by studying the temporal and spatial variabilityof the OWTs, but also possibly better retrieval of Level 2 satellite products when using OWT guidedapproach.


2017 ◽  
Vol 15 (1) ◽  
Author(s):  
Alice Hirschmann ◽  
Nelson J. R. Fagundes ◽  
Luiz R. Malabarba

ABSTRACT Bryconamericus lethostigmus is the type-species of the monotypic genus Odontostoechus, diagnosed in part based on the presence of a unique tooth series in the premaxilla. Recently a new proposal of classification of the Stevardiinae placed Odontostoechus as a junior synonym of a monophyletic genus Bryconamericus sensu stricto, a genus characterized by the presence of two tooth series. Bryconamericus lethostigmus is redescribed herein and the single tooth series in the premaxilla is demonstrated to originate from merging of the external tooth row with the inner row during ontogeny refuting primary hypothesis of homology between the mouth morphology of B. lethostigmus and the genera Bryconacidnus, Ceratobranchia, Monotocheirodon, Othonocheirodus, Rhinopetitia and Rhinobrycon. A phylogeographic analysis indicated that the pattern described for the sympatric species Diapoma itaimbe is not mirrored by B. lethostigmus. The results also do not support the hypothesis of a new species in the rio Araranguá drainage.


Zootaxa ◽  
2005 ◽  
Vol 1032 (1) ◽  
pp. 29 ◽  
Author(s):  
ANDREW B.T. SMITH ◽  
ARTHUR V. EVANS

The checklist of the New World Melolonthinae published in 2003 by Evans is updated to 30 June 2005. Corrections and omissions to the previous checklist are also noted and necessary taxonomic changes are made. Melolontha elongata Fabricius, 1792 is designated as the type species of Philochloenia Dejean, 1833, syn. nov. thereby placing this genus as a junior synonym of Dichelonyx Harris, 1827. Phyllophaga guatemalica (Moser, 1918), syn. nov. and Phyllophaga longiclava (Moser, 1918), syn. nov. are placed in synonymy with Phyllophaga ravida (Blanchard, 1851). The Australian genus Deuterocaulobius Dalla Torre, 1912, stat. nov. is brought out of synonymy and considered the valid name for “Phyllochlaenia Blanchard, 1846.” Warwickia, nom. nov. is proposed as a replacement name for the junior homonym Benedictia Sanderson, 1939 (non Dybowski, 1875) and consequently, Warwickia pilosa (Sanderson, 1939), comb. nov. is a new combination for the single species in this genus. A brief overview of the tribal classification of Melolonthinae is presented.


Sign in / Sign up

Export Citation Format

Share Document