16s rdna sequences
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2021 ◽  
Vol 19 (2) ◽  
pp. 359-369
Author(s):  
Le Phuong Chung ◽  
Nguyen Thi Hai ◽  
Nguyen Huynh Minh Quyen ◽  
Pham The Hai ◽  
Dinh Thuy Hang

Ammonium removal from wastewater is a crucial step in wastewater treatment. Presently employed technologies based on nitrification/denitrification and partial nitritation/anammox principles require oxygen for the nitrification step, and are therefore still not yet fully satisfied with the application practice. In recent years, biological ammonium oxidation coupled with ferric iron reduction (feammox) has been proposed to be responsible for the nitrogen loss in different ecological habitats. Related to the wastewater aspect, the feammox principle has been discussed as an alternative approach for ammonium removal without dependency on oxygen. From a laboratory-scaled feammox bioreactor operated under neutral pH, two bacterial strains FN7 and FN9 were isolated by using the anaerobic Hungate technique. Comparative analyses of 16S rDNA sequences showed that these strains were most closely related to the b-proteobacterium Aciclyphilus denitrificans and the g-proteobacterium Pseudomonas stutzeri, respectively. Although being phylogenetically apart, strains FN7 and FN9 shared several common physiological characteristics that are considered meaningful for the feammox process, i.e. (i) heteroptrophic ammonium oxidation, (ii) denitrification, and (iii) ferric iron reduction. These isolates are proposed to play certain roles in the studied feammox system, contributing to the ammonium removal under heterotrophic feammox condition. The 16S rDNA sequences of strains FN7 and FN9 were available in GenBank under the accession numbers LC474369 and MT568614, respectively.


Author(s):  
Sonja Lick ◽  
Daniel Wibberg ◽  
Annika Winkler ◽  
Jochen Blom ◽  
Christina Grimmler ◽  
...  

A polyphasic approach was applied to investigate the diversity of microbiota that evolved during cold storage beef ripening. Isolate V4/DAB/S4/2aT with a unique BOX-rep-PCR fingerprint profile revealed more than 99 % nucleotide identities upon pairwise comparisons of 16S rDNA sequences from the type strains Pseudomonas versuta DSM 101070T, Pseudomonas saxonica DSM 108989T, Pseudomonas deceptionensis DSM 26521T and Pseudomonas weihenstephanensis DSM 29166T, placing it within the Pseudomonas fragi / lundensis branch of the genus Pseudomonas . Additional rpoB based comparison revealed P. versuta DSM 101070T as the nearest relative, with 98.5 % nucleotide identity. Calculation of ANIb values of the V4/DAB/S4/2aT draft genome identified P. versuta DSM 101070T with 90.1 %, P. deceptionensis DSM 26521T with 85.1 %, P. fragi DSM 3456T with 84.4 %, Pseudomonas psychrophila DSM 17535T and Pseudomonas bubulae DSM 107389T with 84.2 % similarities each. Pairwise genome-to-genome distance calculations [digital DNA–DNA hybridization (dDDH)] resulted in values of 47.1, 35.1, 34.8, 34.2 and 34.1 %, respectively. A second isolate was detected years later in ground beef and showed ANIb values of 99.3 % and dDDH of 96.1 % relatedness to V4/DAB/S4/2aT. The DNA G+C content was 58.6 mol% for both isolates. The predominant cellular fatty acids of V4/DAB/S4/2aT were C16 : 0, C18 : 1ω7c, C17 : 0 cyclo and a summed feature containing C16 : 1ω7c and/or C15 : 0 iso 2-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol, the major respiratory quinone was Q9, with a small portion of Q8. The combined data on genotypic and phenotypic features support the proposal of a novel species, for which the name Pseudomonas paraversuta sp. nov. is proposed. The type strain is V4/DAB/S4/2aT (=DSM 111361T=LMG 31844T) and a second isolate is UBT376 (=DSM 111360=LMG 31845).


Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 355
Author(s):  
Sabrine Dhaouadi ◽  
Amira Mougou Hamdane ◽  
Ali Rhouma

The purpose of this study was to isolate and identify Rhodococcus spp. strains from almond and pistachio rootstocks and trees in Tunisia. Twenty-eight strains were identified through 16S rDNA and vicA genes amplification and sequencing. Pea bioassay was performed to determine the pathogenicity of the strains. Representative 16S rDNA and vicA sequences of eight strains from pistachio and seven strains from almond were closely related (>98% similarity) to Rhodococcus spp. accessions in GenBank. Phylogenetic analysis based on 16S rDNA sequences revealed that the yellow-colored strains clustered with phytopathogenic Rhodococcusfascians. The red and orange-colored strains were separated into a different group with R. kroppenstedtii and R. corynebacteiroides isolates. Eleven strains affected the pea seedlings’ growth and exhibited different levels of virulence. The number of shoots was significantly higher in seedlings inoculated with four Rhodococcus strains, whereas the other three strains caused up to 80% of plant height reduction and reduced root secondary growth compared to non-inoculated pea seedlings. These strains, most of which are epiphytes from asymptomatic hosts, showed strong pathogenicity during pea bioassay and were established endophytically in pea tissues. Ten att and five fas genes were detected in four strains and may represent a novel model of plant pathogenic Rhodococcus virulence. The results of our survey showed that Rhodococcus is present but not prevalent in all visited orchards of almond and pistachio rootstocks and trees. Our surveys complemented the investments being made on ornamental species in Tunisia and unveiled the presence of undocumented plant-associated Rhodococcus spp. on economically important crops.


2021 ◽  
Author(s):  
Sunguk Shin ◽  
Jihyun F. Kim

Abstract Competition or antagonism is common in microbial interactions. Therefore, computationally identifying those relationships in the microbial community is in demand. Here, we defined exclusive correlation value (ECV) to better detect mutually exclusive relationships during microbiota analysis. We present METATEA (https://sourceforge.net/projects/metatea/) as a handy toolbox for the calculation of ECV and the analysis of community members with identical 16S rDNA sequences to define intraspecies groups. We analyzed community data related to inflammatory bowel disease to validate the utility of our ECV and METATEA. ECV identified strains antagonistic to disease-associated bacteria, thus providing their potential as probiotics in precision medicine. Klebsiella pneumoniae showed exclusive relationships with various bacteria, and its proportion was associated with microbial diversity and Crohn’s disease. Further, many putative pathobionts were detected using METATEA, some of which were reported to be isolated from other body sites and cause illness to the host.


ZooKeys ◽  
2020 ◽  
Vol 1008 ◽  
pp. 1-15
Author(s):  
Chao Huang ◽  
Shane T. Ahyong ◽  
Hsi-Te Shih

A new genus and new species of blind freshwater cave crab are described from Chongzuo City, Guangxi Zhuang Autonomous Region, China based on morphology and mitochondrial 16S rDNA sequences. The new genus, Phasmongen. nov., is established for P. typhlopssp. nov., which is only the second blind cave crab known from China and East Asia. The combination of a very wide carapace, overall depigmentation, reduced orbits and vestigial unpigmented eyes of Phasmon immediately separates it from all known potamid genera. Molecular divergence estimates based on 16S rDNA suggest that the lineage to which the new genus belongs diverged from other potamids at the beginning of the Late Miocene (10.8 million years ago), much earlier than other Chinese cave crabs.


Author(s):  
Igor A Balashov ◽  
Marco T Neiber ◽  
Bernhard Hausdorf

Abstract We here study the steppe-inhabiting land snail genus Helicopsis (Gastropoda: Geomitridae: Helicellinae) across Eastern Europe using mitochondrial 16S rDNA sequences and nuclear AFLP markers and compare the biogeographical patterns with those of other steppe-inhabiting organisms. The subdivision of Central and Eastern European Helicopsis reflects the geographical subdivision of the European steppe belt in Pontic, Pannonian and Northern steppes. The subdivision within Helicopsis is deeper, at the species level, than in most other steppe-inhabiting groups. Helicopsis populations from the Pontic steppes can be classified into two sister-species. Helicopsis lunulata includes mainly populations with depressed conical shells previously identified as H. striata, but also populations with disc-like shells previously identified as H. instabilis, and it is distributed mainly west of the Dnieper River. Most Helicopsis populations from east of the Dnieper, especially from Crimea, belong to the variable H. filimargo that includes H. gasprensis, H. retowskii, H. arenosa, H. luganica, H. martynovi and H. subfilimargo. The species inhabiting the Pannonian Basin and the Northern steppes form a well-supported monophylum, including H. hungarica in the Pannonian Basin, H. austriaca at the fringe of the Eastern Alps and H. striata mainly in the Northern steppes.


Crustaceana ◽  
2020 ◽  
Vol 93 (11-12) ◽  
pp. 1295-1313
Author(s):  
Si-Ying Mao ◽  
Chao Huang

Abstract A new genus new species of freshwater crab and a new Minpotamon Dai & Türkay, 1997 species are described from eastern Guangdong, China, based on morphology and mitochondrial 16S rDNA sequences. The new genus, Teoswamon gen. nov., is established for T. scolasticum sp. nov., which resembles species from several other genera from Guangdong, but its unique combination of carapace, male gonopod and female vulvae characters set it apart from others. Minpotamon kityang sp. nov. is almost identical with Minpotamon nasicum (Dai, Chen, Song, Fan, Lin & Zeng, 1979) externally, but differs drastically in the male gonopod morphology. Molecular analysis supports the current taxonomic treatments. Teoswamon scolasticum sp. nov. forms its own lineage closely related to Huananpotamon Dai & Ng, 1994. Minpotamon kityang sp. nov. clusters with Minpotamon nasicum, but their genetic distance is of an interspecific level.


Plant Disease ◽  
2020 ◽  
Author(s):  
Zeng-Liang LIU ◽  
Shuangyun Zhou ◽  
Wenlong Zhang ◽  
Shengjin Wu ◽  
Xuefeng Chen ◽  
...  

Pleurotus pulmonarius is a popular edible fungus and widely cultivated in many areas of China. In June 2018, yellow rot (more than 10% incidence) was found on the first crop of P. pulmonarius fruiting bodies in a mushroom factory in Nanning, Guangxi Province, China. At first, yellow water-soaked lesions appeared in the infected fruiting bodies. Lesions then spread and purulent tissues were formed. Severe rot induced production of deformed fruiting bodies and offensive odor. Internal sections of the diseased tissue (approximately 0.5 × 0.5 cm) were sterilized in 75% alcohol for 30 s, rinsed three times with sterilized and deionized water, crushed and suspended in sterilized and deionized water. The suspension was spread on the Luria-Bertani (LB) medium. After incubation at 30°C for 2 days, dominant bacterial colonies were oyster white, smooth, convex, and circular. Individual colonies were transferred two times to LB medium using the conventional streak plate techniques to obtain the pure cultures. The cells were gram-negative, short rods, motile, and no capsules or endospores were observed. Using a BoJian Gram-negative bacteria biochemical analysis kit (5 CARDS, Hopebio, Qingdao, China), data were obtained and analyzed, showing that the isolated strain belongs to the Cedecea genus (positive for β-galactosidase, citric acid, arginine, sucrose, mannitol, sorbitol, D-glucose, gelatin hydrolysis and VP test but negative for H2S, urease, oxidase, indole, rhamnose, melibiose, amygdalin, lysine, ornithine, lactose, inositol and arabinose). Amplified 16S rDNA gene sequences (1,424 bp, GenBank accession No. MT925570) of the isolate using the universal primers 27f and 1492r (Lane 1991) exhibited 99.86% identity with Cedecea neteri M006 (CP009458.1). Based on its morphological characteristics, 16S rDNA sequences, and biochemical test results, the strain was identified as C. neteri. Pathogenicity tests for this strain were performed with bacterial suspensions (approximately 1 × 108 CFU/ml) after growing for 24 h in LB medium at 30°C. Mycelia of P. pulmonarius were cultivated for 60 days in plastic bags. Then young fruiting bodies were formed after induced with low temperature stimulation to serve as a host source. The prepared bacterial suspensions were directly sprayed onto the surface of three bags of fruiting bodies; another three bags were sprayed with sterilized and deionized water as negative control. All inoculated fruiting bodies were then incubated at 20°C with 90 to 95% relative humidity. All experiments were repeated three times. After 2 days, all the fruiting bodies inoculated with the bacterial suspensions showed yellow water-soaked lesions, and the normal growth of the fruiting bodies was inhibited. An offensive odor then developed along with a severe soft rot that was similar to the disease symptoms observed under natural conditions. The fruiting bodies of negative control were growing healthily with no symptoms. Koch's postulates were fulfilled by isolating bacteria from lesions on artificially inoculated fruiting bodies that were identical to the original isolates based on morphological characteristics, 16S rDNA sequences and biochemical test results. C. neteri was formally reported as a pathogen to humans that could cause bacteremia (Farmer et al. 1982). Recently, it has also been reported causing soft rot disease on mushrooms of Pholiota nameko (Yan et al. 2018) and yellow sticky disease on mushrooms of Flammulina velutipes (Yan et al. 2019). However, to the best of our knowledge, this is the first report of C. neteri-induced yellow rot disease of P. pulmonarius in China.


ZooKeys ◽  
2020 ◽  
Vol 980 ◽  
pp. 1-21
Author(s):  
Zewei Zhang ◽  
Da Pan ◽  
Xiyang Hao ◽  
Hongying Sun

Two new species of potamid crabs, Eosamon daiaesp. nov. and Indochinamon malipoensesp. nov. are described from the Sino-Burmese border, southwestern Yunnan and from the Sino-Vietnamese border, southeastern Yunnan, China. The two new species can be distinguished from their closest congeners by several characters, among which is the form of the first gonopod structures. Molecular analyses based on partial mitochondrial 16S rDNA sequences also support the systematic status of these new taxa.


3 Biotech ◽  
2020 ◽  
Vol 10 (9) ◽  
Author(s):  
Aido Taloh ◽  
D. V. S. Raju ◽  
Namita Banyal ◽  
Gunjeet Kumar ◽  
Priyam Panda ◽  
...  

Abstract Symptoms typical of phytoplasma infection such as phyllody, virescence, witches’ broom and yellowing were observed in 12 varieties of Chrysanthemum morifolium in floral nurseries and experimental fields at New Delhi, Karnataka, Maharashtra and Andhra Pradesh, India, during surveys made from 2015 to 2017. Disease incidence ranged from 15 to 30%. Phytoplasma presence was confirmed in all symptomatic chrysanthemum varieties by molecular identification assays. Sequence comparison, phylogenetic and in silico RFLP analyses of 16S rDNA sequences allowed the identification of the chrysanthemum infecting phytoplasma strains into different ribosomal groups and subgroups, namely 16SrI, 16SrII-D, 16SrVI-D and 16SrXIV. Detection of phytoplasma strains of 16SrII-D subgroup were also confirmed in symptomatic Chenopodium album and Parthenium hysterophorus plants grown in and around the surveyed chrysanthemum fields at New Delhi, whereas 16SrVI-D phytoplasma strains were detected in symptomatic Cannabis sativa weed and leafhopper Hishimonus phycitis individuals collected from the symptomatic chrysanthemum fields at New Delhi. This is the first report on the presence of 16SrVI and 16SrXIV groups of phytoplasmas in chrysanthemum plants. Studies on genetic diversity of phytoplasmas infecting the major chrysanthemum varieties in India and their epidemiological aspects had previously not been reported. The detection and identification of phytoplasmas in different chrysanthemum varieties could contribute to increase the awareness among farmers in the management of these diseases.


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