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Tytuł:
Metagenomic 16s rRNA investigation of microbial communities in the Black Sea estuaries in South-West of Ukraine
Autorzy:
Bobrova, Oleksandra
Kristoffersen, Jon
Oulas, Anastasis
Ivanytsia, Volodymyr
Powiązania:
https://bibliotekanauki.pl/articles/1038820.pdf
Data publikacji:
2016
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
prokaryotic diversity
Black Sea estuaries
16S rDNA analysis
metagenomic analysis
Opis:
The Black Sea estuaries represent interfaces of the sea and river environments. Microorganisms that inhabit estuarine water play an integral role in all biochemical processes that occur there and form unique ecosystems. There are many estuaries located in the Southern-Western part of Ukraine and some of them are already separated from the sea. The aim of this research was to determine the composition of microbial communities in the Khadzhibey, Dniester and Sukhyi estuaries by metagenomic 16S rDNA analysis. This study is the first complex analysis of estuarine microbiota based on isolation of total DNA from a biome that was further subjected to sequencing. DNA was extracted from water samples and sequenced on the Illumina Miseq platform using primers to the V4 variable region of the 16S rRNA gene. Computer analysis of the obtained raw sequences was done with QIIME (Quantitative Insights Into Microbial Ecology) software. As the outcome, 57970 nucleotide sequences were retrieved. Bioinformatic analysis of bacterial community in the studied samples demonstrated a high taxonomic diversity of Prokaryotes at above genus level. It was shown that majority of 16S rDNA bacterial sequences detected in the estuarine samples belonged to phyla Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, Planctomycetes. The Khadhzibey estuary was dominated by the Proteobacteria phylum, while Dniester and Sukhyi estuaries were characterized by dominance of Cyanobacteria. The differences in bacterial populations between the Khadzhibey, Dniester and Sukhyi estuaries were demonstrated through the Beta-diversity analysis. It showed that the Khadzhibey estuary's microbial community significantly varies from the Sukhyi and Dniester estuaries. The majority of identified bacterial species is known as typical inhabitants of marine environments, however, for 2.5% of microbial population members in the studied estuaries no relatives were determined.
Źródło:
Acta Biochimica Polonica; 2016, 63, 2; 315-319
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Identification and phenotypic plasticity of Pseudanabaena catenata from the Svalbard archipelago
Autorzy:
Khan, Zoya
Smykla, Jerzy
Wan Omar, Wan Maznah
Merican Mohd Sidik Merican, Faradina
Asmawarnie Azizan, Asmimie
Pin Foong, Choon
Convey, Peter
Najimudin, Nazalan
Aisyah Alias, Siti
Powiązania:
https://bibliotekanauki.pl/articles/2042152.pdf
Data publikacji:
2017
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
16S rRNA
Arctic
Cyanobacteria
Polyphasic approach
Pseudanabaena
Źródło:
Polish Polar Research; 2017, 38, 4; 445-458
0138-0338
2081-8262
Pojawia się w:
Polish Polar Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Some corrosive bacteria isolated from the technogenic soil ecosystem in Chernihiv city (Ukraine)
Autorzy:
Tkachuk, Nataliia
Zelena, Liubov
Powiązania:
https://bibliotekanauki.pl/articles/2026000.pdf
Data publikacji:
2021
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
16S rRNA gene
microbial induced corrosion
phenotypic characteristics
Opis:
The soil microbiome is exposed to technogenic influence during the operation of metal structures. There are quantitative and qualitative changes in the microbiota of the technogenic ecosystem. During the study of the technogenic soil ecosystem (ferrosphere), samples of which were taken in the field (Chernihiv, Ukraine: 51°29’58”N, 31°16’09”E), the presence of corrosively active microbial cenosis was established: sulfate-reducing, denitrifying, iron-reducing (using acetate as the only electron donor, and Fe (III) as the only electron acceptor) and ammonifying bacteria. The predominant representatives of corrosively active groups of bacteria were isolated. They were identified as Bacillus simplex, Streptomyces gardneri, Streptomyces canus (ammonifying bacteria), Fictibacillus sp. (ammonifying bacteria with iron-reducing ability), Anaerotignum (Clostridium) propionicum (organic acid-producing bacteria), Desulfovibrio oryzae (sulfate-reducing bacteria) based on some microbiological, physiological and biochemical, genetic features. Strains of heterotrophic and hemolitotrophic bacteria (individual representatives and their associations) isolated from the technogenic ecosystem can be used in both industrial and technological spheres. The interaction of isolated bacteria in the process of microbial induced corrosion is a prospect for further research.
Źródło:
Studia Quaternaria; 2021, 38, 2; 101-108
1641-5558
2300-0384
Pojawia się w:
Studia Quaternaria
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular diversity of the bacterial community associated with Acropora digitifera (Dana, 1846) corals on Rancabuaya coastline, Garut District, Indonesia
Autorzy:
Rizal, Achmad
Akbarsyah, Nora
Kdyp, Pringgo
Permana, Rega
Andhikawati, Aulia
Powiązania:
https://bibliotekanauki.pl/articles/1030642.pdf
Data publikacji:
2020
Wydawca:
Przedsiębiorstwo Wydawnictw Naukowych Darwin / Scientific Publishing House DARWIN
Tematy:
Acropora digitifera
Bacteria
Culture
Gen 16S rRNA
Metagenome
Opis:
Bacteria are one of the prokaryotic microorganisms that are symbiotic with coral reefs. The purpose of this study was to determine the diversity of bacterial communities associated with Acropora digitifera corals in the rancabuaya coastline of Garut district, West Java through a metagenomic and cultural approach. Stages of research include tissue isolation using waterpics, isolation of bacterial genomic DNA, sequencing using the NGS (Next Generation Sequencing) method of Hiseq using 16S rRNA V3-V4 region 341F and 806R primers for the metagenomic approach. While the culture approach, carried out inoculation, bacterial cultivation, gram staining, then proceed with the identification of molecular characteristics of DNA with 16S rRNA gene sequences. Dominantly, the results of bacterial identification were obtained as many as 77 species from 10 genera 10 families 10 orders of 10 classes and 4 phylum and unidentified reads of 6%. The results of the identification of 16S rRNA showed that the isolate ACD.P4.PH7.P had a close relationship with the Bacillus flexus strain BF strain zb strain with a similarity of 85.44%. Isolate ACD.P4.PH9.P has a close relationship with Bacillus sp. c234 with a 98.50% similarity. Isolate ACD.P4.PH9.K has an approach with the species Bacillus sp. strain 6RM1 with a similarity of 94.78%.
Źródło:
World Scientific News; 2020, 144; 384-396
2392-2192
Pojawia się w:
World Scientific News
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Detection and identification of potentially toxic cyanobacteria in Polish water bodies
Autorzy:
Głowacka, Joanna
Szefel-Markowska, Magdalena
Waleron, Małgorzata
Łojkowska, Ewa
Waleron, Krzysztof
Powiązania:
https://bibliotekanauki.pl/articles/1039881.pdf
Data publikacji:
2011
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
mcyB
microcystins
toxins
16S rRNA
Cyanobacteria
mcyE
rpoC1
Opis:
The main goal of this study was to determine the distribution of potentially toxic cyanobacteria in 39 selected Polish water bodies. From the water bodies with blooms and also from those in which blooms were not visible 87 samples were investigated. For the first time samples from ponds localized in villages with high agricultural activities were included. Lakes for which microcystin concentrations had been determined before were included as a reference for the research. The detection of cyanobacteria was conducted by microscopic observation as well as by PCR amplification of the rpoC1 gene fragment. Cyanobacteria were present in 75 out of 87 samples. The presence of potentially toxic cyanobacteria was detected by amplification of the mcyB and mcyE genes, which are involved in the biosynthesis of microcystins. Both genes were detected in 7 out of 9 blooms investigated. In the case of samples collected from water bodies in which blooms were not observed, the mcyB and mcyE genes were detected in 20 out of 36. In order to identify the cyanobacteria occurring in selected reservoirs, 16S plus ITS clone libraries were constructed. The method allowed distinguishing 18 different genotypes. After sequence analysis, cyanobacteria belonging to genera Microcystis, Planktothrix, Anabaena, Pseudanabaena, Synechocystis, Synechococcus and Woronichinia were identified. Results confirmed the usefulness of the rpoC1 and mcy genes for monitoring water bodies and detection of potentially toxic cyanobacteria. Application of molecular markers allowed detecting potentially toxic cyanobacteria before the bloom was visible. This is the first comprehensive study concerning cyanobacteria present in different types of Polish water bodies performed using molecular markers.
Źródło:
Acta Biochimica Polonica; 2011, 58, 3; 321-333
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Metagenomic Analysis Reveals Microbial Communities in Lake Qarun – Egypt
Autorzy:
Yosef, Mahmoud Mohamed
Elrefy, Ali Mohamed
Elfeky, Fawzy Ali
Powiązania:
https://bibliotekanauki.pl/articles/2027812.pdf
Data publikacji:
2022
Wydawca:
Polskie Towarzystwo Inżynierii Ekologicznej
Tematy:
bacterial community
Ion Torrent
Qarun Lake
16S rRNA high throughput
Opis:
Characterization of water quality in Lake Qarun indicated that the water is very poor for irrigation and aquatic life. At the same time, the bacterial community was represented mainly by five bacterial phyla with different proportions: Firmicutes (53%), Proteobacteria (33%), Bacteroidetes (7%), Actinobacteria (5%) and Thermi (1%). Furthermore, metagenomes prediction of bacterial communities using PICRUSt indicated important functional gene families associated with metabolism, environmental information, genetic information processing, and cellular processes. It is worth noting that Benzoate degradation had the highest average relative abundance, followed by aminobenzoate degradation among 18 individual KEGG pathways from xenobiotics biodegradation and metabolism which showed higher relative abundance. The obtained data indicate that a different source of pollution in Qarun Lakes has an impact on the bacterial community’s structure, as well as the biota and is expected to cause health problems.
Źródło:
Journal of Ecological Engineering; 2022, 23, 2; 70-76
2299-8993
Pojawia się w:
Journal of Ecological Engineering
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Microbial biodiversity in arable soils is affected by agricultural practices
Autorzy:
Wolińska, Agnieszka
Górniak, Dorota
Zielenkiewicz, Urszula
Goryluk-Salmonowicz, Agata
Kuźniar, Agnieszka
Stępniewska, Zofia
Błaszczyk, Mieczysław
Powiązania:
https://bibliotekanauki.pl/articles/972735.pdf
Data publikacji:
2017
Wydawca:
Polska Akademia Nauk. Instytut Agrofizyki PAN
Tematy:
dgge
16s rrna gene
simpson diversity
bacterial communities
arable soils
Opis:
The aim of the study was to examine the differences in microbial community structure as a result of agricultural practices. Sixteen samples of cultivated and the same number of non-cultivated soils were selected. Gel bands were identified using the GelCompar software to create the presence-absence matrix, where each band represented a bacterial operational taxonomic unit. The data were used for principal-component analysis and additionally, the Shannon-Weaver index of general diversity, Simpson index of dominance and Simpson index of diversity were calculated. Denaturing gradient gel electrophoresis profiles clearly indicated differentiation of tested samples into two clusters: cultivated and non-cultivated soils. Greater numbers of dominant operational taxonomic units (65) in non-cultivated soils were noted compared to cultivated soils (47 operational taxonomic units). This implies that there was a reduction of dominant bacterial operational taxonomic units by nearly 30% in cultivated soils. Simpson dominance index expressing the number of species weighted by their abundance amounted to 1.22 in cultivated soils, whereas a 3-fold higher value (3.38) was observed in non-cultivated soils. Land-use practices seemed to be a important factors affected on biodiversity, because more than soil type determined the clustering into groups.
Źródło:
International Agrophysics; 2017, 31, 2; 259-271
0236-8722
Pojawia się w:
International Agrophysics
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Characteristics of selected molecular methods used in identification and assessment of genetic diversity of bacteria belonging to the genus Azotobacter
Autorzy:
Kozieł, Monika
Gałązka, Anna
Powiązania:
https://bibliotekanauki.pl/articles/2147979.pdf
Data publikacji:
2019-09-30
Wydawca:
Instytut Uprawy Nawożenia i Gleboznawstwa – Państwowy Instytut Badawczy
Tematy:
Azotobacter
ITS PCR
16S rRNA gen
PCR MP
RAPD
ARDRA
Opis:
Modern molecular techniques have greatly increased our knowledge concerning phylogenetic and functional diversity of microorganisms inhabiting the soil environment. Soil ecosys-tem is relatively complex with a high level of microbiologically diversity. The application of traditional culture-based techniques dose not reflect the total diversity of microbial community in-habiting in soil environment. On the other hand commonly used molecular methods allow for quick and accurate identification and evaluation of the genetic diversity of microorganisms in-habiting this environment. Free-living bacteria belonging to the genus Azotobacter commonly occurring in soil. Azotobacter spp. are the subject of many studies conducted both in Poland and in the world. The interest in these bacteria is largely related to their properties very useful for agriculture. Owing to their capability of fixing atmospheric nitrogen and making it available to plants and production of plant growth promotion and fungicidal substances, they are used in the production of soil bacterial inoculants. In addition, these bacteria are an excellent indicator of soil fertil-ity, which is why they are often used as test microorganisms in many studies. The paper presents an overview of molecular mi-crobiological techniques used to identify and evaluate the genetic diversity of Azotobacter spp. in studies conducted both in Poland and across the world. The ITS PCR, PCR-RFLP methods and 16S rRNA gene amplification are used to identify bacteria of the ge-nus Azotobacter, and PCR MP, RAPD PCR and ARDRA are used to assess the genetic diversity of these microorganisms.
Źródło:
Polish Journal of Agronomy; 2019, 38; 37-45
2081-2787
Pojawia się w:
Polish Journal of Agronomy
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Evidence of amorphous Ca-phosphate precipitate caused by bio mineralisation in 4-5th CE lime plasters of the previously submerged east coastal monument of Salvankuppam
Autorzy:
Singh, Manager R.
Kumar, S. Vinodh
Ganaraj, Kuntikana
Powiązania:
https://bibliotekanauki.pl/articles/2086560.pdf
Data publikacji:
2021
Wydawca:
Polskie Towarzystwo Mineralogiczne
Tematy:
Amorphous Ca-phosphate
16S rRNA
Bio-mineralization
calcite
lime plasters
Opis:
The lime plasters of the excavated monument of Salvankuppam, previously submerged and exposed by the Tsunami occurred in the Indian Ocean on 26th December 2004 was studied with different analytical techniques. The temple is dated 4-5th century CE. The XRF, XRD, FTIR, NMR, SEM-EDX analysis of the lime plasters evidenced particular occurrence of phosphatised bacterial remains in saline conditions. The formation of amorphous Ca-phosphate by bio mineralization was identified in the plasters by the analyses. The plasters are made of air-lime with coarse aggregates and seashells inclusion as confirmed by the thermal and chemical analysis. The microstructure and morphological investigations of mineralized microbial structures by SEM-EDX indicated the formation of amorphous Ca-phosphate. The unordered and fibrous spherulites have hardened and reduced porosity of the plaster by bio mineralization as observed through MIP analysis. The 16S rRNA sequencing has identified the Pseudomonas strains mainly responsible for the clustering of amorphous Ca-phosphate particles around the bacterial colony.
Źródło:
Mineralogia; 2021, 52, 1; 19--30
1899-8291
1899-8526
Pojawia się w:
Mineralogia
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Dynamika ilościowa AOB w procesie biologicznego oczyszczania odcieków składowiskowych w warunkach beztlenowych
Quantitative dynamics of AOB in the biological treatment of landfill leachate in anaerobic conditions
Autorzy:
Jurczyk, Ł.
Koc-Jurczyk, J.
Różalska, P.
Powiązania:
https://bibliotekanauki.pl/articles/296871.pdf
Data publikacji:
2011
Wydawca:
Politechnika Częstochowska. Wydawnictwo Politechniki Częstochowskiej
Tematy:
odcieki składowiskowe
SBR
AOB
16S rRNA
Q-PCR
landfill leachate
Opis:
Składowanie odpadów, nawet na obiektach prawidłowo zaprojektowanych i eksploatowanych może stwarzać wiele zagrożeń dla środowiska. Jednym z najpoważniejszych jest powstawanie w obrębie składowiska odcieków, charakteryzujących się między innymi dużymi stężeniami azotu amonowego oraz znaczną zawartością trudno rozkładalnych związków organicznych. Podstawową metodą unieszkodliwiania odcieków składowiskowych jest ich oczyszczanie w reaktorach biologicznych. U podstaw tego procesu leży biochemiczny rozkład azotu amonowego przez mikroorganizmy wykazujące ekspresję genu monooksygenazy amoniaku, a jednym ze sposobów zwiększenia jego efektywności jest stosowanie różnych typów nośników stwarzających tym mikroorganizmom optymalne warunki życia. Odcieki wykorzystane w badaniach pochodziły ze składowiska odpadów komunalnych w Kozodrzy (woj. podkarpackie). Badania prowadzono w trzech sekwencyjnych reaktorach biologicznych o pojemności 2 l (SBR 1-3), w warunkach beztlenowych, w temperaturze 42°C i przy stałym czasie zatrzymania wynoszącym 6 d. SBR 1 pracował tylko z osadem czynnym zawieszonym, natomiast SBR 2 i 3 zostały wyposażone w wypełnienia z PCV o różnej średnicy porów (odpowiednio 2 ÷ 3 oraz 4 ÷ 5 mm). W pobranych z reaktorów próbkach osadu badano, za pomocą techniki ilościowej łańcuchowej reakcji polimerazy (Q-PCR), zawartość kopii genu 16S rRNA o sekwencji charakterystycznej dla wszystkich znanych β-proteobakterii mających zdolność do utleniania amoniaku. Porównując w badanych próbkach dynamikę ilości badanego genu, stwierdzono, że wypełnienie zastosowane w SBR 2 powodowało najmniejsze wahania liczebności bakterii w procesie ich adaptacji do warunków technologicznych. Efektywność usuwania azotu amonowego we wszystkich reaktorach miała związek z ilością kopii badanego genu.
Waste disposal, even on properly designed and operated landfills may be environmentally hazardous. One of the most onerous aspects of landfilling is formation of the leachate, characterized by high concentrations of ammonia nitrogen and organic compounds. One of the most common method applied for nitrogen neutralization in landfill leachate is biological treatment based on biochemical decomposition of an ammonia by micro-organisms expressing gene of ammonia monooxygenase. The way to increasing efficiency of this process is the application of different types of fillings creating optimal conditions for microorganisms life. Leachate used in the study came from a large scale municipal waste landfill in Kozodrza (podkarpackie province, Poland). The research was conducted in three sequential batch reactors of 2 l (SBR 1-3), in anaerobic conditions, high temperature (42°C) and a constant HRT of 6 d. SBR 1 ran with suspended activated sludge, while the SBR 2 and 3 were equipped with PVC filling of different pore diameters (respectively 2 ÷ 3 and 4 ÷ 5 mm). The samples of sludge were examined for number of 16S rDNA copies characterized for ammonia oxidizing β-proteobacteria. Comparing the quantitative dynamics of 16S rRNA gene in samples it was found that fillings used in the SBR 2 resulted in slightest hesitation of the number of bacteria during the process of their adaptation to technological conditions. The ammonia nitrogen removal efficiency in all reactors was related to the number of 16S rRNA gene copies.
Źródło:
Inżynieria i Ochrona Środowiska; 2011, 14, 4; 309-322
1505-3695
2391-7253
Pojawia się w:
Inżynieria i Ochrona Środowiska
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
First insight into microbial community composition in a phosphogypsum waste heap soil
Autorzy:
Zielińska, Sylwia
Radkowski, Piotr
Ossowski, Tadeusz
Ludwig-Gałęzowska, Agnieszka
Łoś, Joanna
Łoś, Marcin
Powiązania:
https://bibliotekanauki.pl/articles/1038561.pdf
Data publikacji:
2017
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
microbial community
16S rRNA gene
soil sample
postproduction waste
phosphogypsum
reclamation
Opis:
The aim of this study was to investigate the soil microbial communities of a phosphogypsum waste heap. The soil microbial community structures can differ over time, as they are affected by the changing environmental conditions caused by a long-term exposure to different kinds of pollutions, like is the case of soil in the post-production waste area in Wiślinka (in the northern part of Poland) currently undergoing restoration. Our analyses indicated that the most abundant phyla were Proteobacteria, Acidobacteria, and Actinobacteria, and generally such an abundance is common for most of the studied soils. The most dominant class were Alphaproteobacteria, with their participation in 33.46% of the total reads. Among this class, the most numbered order was Sphingomonadales, whereas among this order the Sphingomonadaceae family was the most abundant one. The Sphingomonadaceae family is currently in the center of interest of many researchers, due to the ability of some of its members to utilize a wide range of naturally occurring organic compounds and many types of environmental contaminants. This kind of knowledge about microbial populations can support efforts in bioremediation and can improve monitoring changes in the contaminated environments.
Źródło:
Acta Biochimica Polonica; 2017, 64, 4; 693-698
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Comparison of PCR-DGGE and Nested-PCR-DGGE Approach for Ammonia Oxidizers Monitoring in Membrane Bioreactors’ Activated Sludge
zalety i wady wykorzystywania techniki nested-PCR w monitoringu bakterii utleniających amoniak w osadzie czynnym bioreaktora membranowego
Autorzy:
Ziembińska-Buczyńska, A.
Wiszniowski, J.
Ciesielski, S.
Powiązania:
https://bibliotekanauki.pl/articles/204755.pdf
Data publikacji:
2014
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
ammonia oxidizing bacteria
AOB
16S rRNA gene
Polymerase Chain Reaction – Denaturing Gradient Gel Electrophoresis
PCR-DGGE
nested-PCR
utlenianie amoniaku
bakteria utleniająca amoniak
gen kodujący 16S rRNA
Opis:
Nitritation, the first stage of ammonia removal process is known to be limiting for total process performance. Ammonia oxidizing bacteria (AOB) which perform this process are obligatory activated sludge habitants, a mixture consisting of Bacteria, Protozoa and Metazoa used for biological wastewater treatment. Due to this fact they are an interesting bacterial group, from both the technological and ecological point of view. AOB changeability and biodiversity analyses both in wastewater treatment plants and lab-scale reactors are performed on the basis of 16S rRNA gene sequences using PCR-DGGE (Polymerase Chain Reaction – Denaturing Gradient Gel Electrophoresis) as a molecular biology tool. AOB researches are usually led with nested PCR. Because the application of nested PCR is laborious and time consuming, we have attempted to check the possibility of using only first PCR round to obtain DGGE fingerprinting of microbial communities. In this work we are comparing the nested and non-nested PCR-DGGE monitoring of an AOB community and presenting advantages and disadvantages of both methods used. The experiment revealed that PCR technique is a very sensitive tool for the amplification of even a minute amount of DNA sample. But in the case of nested-PCR, the sensitivity is higher and the template amount could be even smaller. The nested PCR-DGGE seems to be a better tool for AOB community monitoring and complexity research in activated sludge, despite shorter fragments of DNA amplification which seems to be a disadvantage in the case of bacteria identification. It is recommended that the sort of analysis approach should be chosen according to the aim of the study: nested-PCR-DGGE for community complexity analysis, while PCR-DGGE for identification of the dominant bacteria.
Nitiritacja – pierwszy etap nitryfikacji, jest uznawany za krok limitujący przebieg całości procesu utleniania amoniaku. Bakterie utleniające amoniak (ang. ammonia oxidizing bacteria, AOB), które prowadzą ten proces są stałymi mieszkańcami osadu czynnego – mieszaniny bakterii, Protozoa i Metazoa, wykorzystywanych do biologicznego oczyszczania ścieków. Z tego powodu są one interesujące zarówno z punktu widzenia technologii, jak i ekologii mikroorganizmów. Analizy zmienności i bioróżnorodności bakterii utleniających amoniak, zarówno w oczyszczalni ścieków, jak i w reaktorach w skali laboratoryjnej, są prowadzone w oparciu o sekwencje genu kodującego 16S rRNA z użyciem metody biologii molekularnej, jaką jest PCR-DGGE (Polymerase Chain Reaction – Denaturing Gradient Gel Electrophoresis). Analizy te są zazwyczaj prowadzone techniką tzw. nested-PCR. Ze względu na fakt, że metoda ta wymaga większego nakładu pracy i czasu, niż tradycyjny jednoetapowy PCR (ang. non-nested PCR) podjęto próbę sprawdzenia możliwości zastosowania techniki jednoetapowego PCR do uzyskania wzorów prążkowych DGGE bakterii utleniających amoniak. W tej pracy zaprezentowano wyniki analizy PCR-DGGE z użyciem technik nested i non-nested PCR oraz podjęto próbę wykazania ich wad i zalet.
Źródło:
Archives of Environmental Protection; 2014, 40, 4; 31-38
2083-4772
2083-4810
Pojawia się w:
Archives of Environmental Protection
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Zastosowanie techniki PCR w badaniach bakteriologicznych
Applications of PCR in microbiology
Autorzy:
Adaszek, L.
Dziegiel, B.
Mazurek, L.
Winiarczyk, S.
Powiązania:
https://bibliotekanauki.pl/articles/859637.pdf
Data publikacji:
2018
Wydawca:
Krajowa Izba Lekarsko-Weterynaryjna
Tematy:
bakteriologia
diagnostyka bakteriologiczna
metody badan
lancuchowa reakcja polimerazy
16S rRNA
diagnostyka molekularna
Źródło:
Życie Weterynaryjne; 2018, 93, 04
0137-6810
Pojawia się w:
Życie Weterynaryjne
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Monitoring the occurrence of bacteria in stored cabbage heads
Autorzy:
Eichmeier, Aleš
Peňázová, Eliška
Pečenka, Jakub
Čechová, Jana
Pokluda, Robert
Tekielska, Dorota
Baránek, Miroslav
Powiązania:
https://bibliotekanauki.pl/articles/961651.pdf
Data publikacji:
2017
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
bacteria
cabbage
identifi cation
isolation
mpa medium
pseudomonas
sequencing
16s rrna
Bacillus
Opis:
Twenty-six cabbage heads stored under typical conditions in a storage hall in Moravia, Czech Republic, were tested for the presence of bacteria by the method of isolation from three different parts of the cabbage heads. Isolations were carried out from stalks, inner and superficial leaves. Two samplings were done; in November 2015 and February 2016. Bacterial cultures were sequenced in the part of 16S rRNA region; bacteria were identified according to the sequences obtained. The most prevalent bacteria were of the genus Pseudomonas. Genera: Klebsiella, Erwinia, Pantoea, Bacillus were also identified. The results provided an interesting insight into the bacterial spectrum in stored cabbage heads and their dynamics during storage. Th e nucleotide sequences which were found were saved in GenBank/NCBI under accession numbers KX160104-KX160145.
Źródło:
Journal of Plant Protection Research; 2017, 57, 1
1427-4345
Pojawia się w:
Journal of Plant Protection Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Genetic characterization of some rhizobial isolates from various legumes
Autorzy:
El-Ghany, E.M.A.
Eissa, R.A.
Fahmi, A.I.
Nagaty, H.H.
El-Zanaty, A.M.
Powiązania:
https://bibliotekanauki.pl/articles/2097126.pdf
Data publikacji:
2020
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
rhizobia
morphological
API 20E and API 20NE
16S rRNA
phylogenetic
Opis:
In the last few decades, there has been a growing interest in environmentally friendly sustainable agricultural practices, thus increasing the role of biofertilizers such as rhizobia, which can decrease the need for chemical fertilizers, reduce adverse environmental effects, and help to save money. Therefore, information on the distribution and genetic variation of native rhizobial isolates would aid in selecting novel rhizobial strains that could be developed and used as biofertilizers in legume production. This research was conducted to characterize 24 rhizobial isolates from five legumes on morphological, biochemical, and molecular aspects and determine the phylogenetic relationships among them. Rhizobial isolates were obtained from five Egyptian legumes: faba bean, lentil, pea, clover, and soybean. Morphological characterization classified the isolates into fast and slow growers. Biochemical characterization using API 20E and API 20NE systems showed a large diversity, which may reflect their adaptation in different environments. Moreover, molecular detection of the 16S rRNA gene enabled to characterize 19 of them to the species level. Rhizobial isolates from pea, faba bean, clover, and lentil were identified as Rhizobium leguminosarum and those from soybean were identified as Bradyrhizobium japonicum. These data reflected a narrow diversity of rhizobial species in Egypt. A phylogenetic analysis of the 19 isolates confirmed that B. japonicum isolates were divergent from all other isolates. Furthermore, the phylogram revealed that each group of isolates that originated from the root nodule of a certain legume formed a separate subcluster. The obtained data suggested a narrow range of interspecies variations, which is consistent with the idea of the presence of biovars among the species.
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2020, 101, 3; 179-191
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The Application of PCR Reaction for Identification of MHB Bacteria Species
Zastosowanie reakcji PCR do identyfikacji gatunkowej bakterii MHB
Autorzy:
Ząbkiewicz, A.
Myga-Nowak, M.
Bandurska, K.
Paczyńska, J.
Szybecka, A.
Krupa, P.
Powiązania:
https://bibliotekanauki.pl/articles/205412.pdf
Data publikacji:
2014
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
mycorrhiza
helper bacteria
MHB
16S rRNA gene
mikoryza
bakterie wspomagające
gen 16sRNA
Opis:
This study characterizes mycorrhiza helper bacteria (MHB) from selected unpolluted locations as well as subjected to industrial emissions. To determine the species of bacteria isolated from the roots of ectomycorrhizal pine and birch, a method based on the sequence analysis of a 16S rRNA gene was used. The isolated bacteria were initially characterized by available biochemical methods and phenotypic observation. On the selected bacteria representatives isolation of DNA was performed, on which the PCR reaction was carried out. In this way amplified samples were automatically sequenced and the obtained results were compared to public databases. Among the isolated bacteria Pseudomonas fluorescens SBW25 and Burkholderia xenovorans LB400 species were dominant.
W pracy scharakteryzowano bakterie wspomagające mikoryzę pochodzące z wybranych terenów ekologicznie czystych oraz z terenów poddanych emisji przemysłowej. Przedstawiono wykorzystanie metody opartej na analizie sekwencji genu 16S rRNA do określenia przynależności gatunkowej bakterii wyizolowanych z korzeni ektomikoryzowych sosny i brzozy. Wyizolowane bakterie zostały wstępnie scharakteryzowane przy pomocy dostępnych metod biochemicznych i obserwacji fenotypowej. Dla wybranych przedstawicieli dokonano izolacji DNA, względem którego przeprowadzono reakcję PCR. Powielone w ten sposób próbki automatycznie zsekwencjonowano, a uzyskane sekwencje porównywano w ogólnodostępnych bazach danych. Wśród wyizolowanych bakterii dominowały gatunki Pseudomonas fluorescens SBW25 oraz Burkholderia xenovorans LB400.
Źródło:
Archives of Environmental Protection; 2014, 40, 2; 115-122
2083-4772
2083-4810
Pojawia się w:
Archives of Environmental Protection
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Soil microbiomes of reclaimed and abandoned mines of the Yamal region
Autorzy:
Pershina, Elizaveta
Ivanova, Ekaterina
Kimeklis, Anastasia
Zverev, Alexey
Kichko, Arina
Aksenova, Tatiana
Andronov, Evgeny
Abakumov, Evgeny
Powiązania:
https://bibliotekanauki.pl/articles/2041836.pdf
Data publikacji:
2020
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
Arctic
Yamal Peninsula
microbiome
soil
high-throughput sequencing
16S rRNA
qPCR
mining
reclamation
Źródło:
Polish Polar Research; 2020, 41, 1; 95-114
0138-0338
2081-8262
Pojawia się w:
Polish Polar Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Characterization of phytoplasmas related to aster yellows group infecting annual plants in Iran, based on the studies of 16S rRNA and rp genes
Autorzy:
Sichani, F.V.
Bahar, M.
Zirak, L.
Powiązania:
https://bibliotekanauki.pl/articles/65352.pdf
Data publikacji:
2014
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Opis:
Several annual field crops, vegetables, ornamentals, oilseed crops, and weeds showing phytoplasma diseases symptoms were collected to detect phytoplasmas related to ‘Candidatus Phytoplasma asteris’. The collecting was done in the central regions of Iran. For general detection of phytoplasmas, 16S rRNA gene fragments were amplified using phytoplasma universal primer pair P1/P7 in polymerase chain reaction (PCR) followed by primer pair R16F2n/R16R2 in nested PCR. Then, for finer detection of phytoplasmas related to ‘Ca. P. asteris’, DNA samples were used to extend the rp and tuf gene fragments by PCR using aster yellows group specific primer pairs rp(I)F1A/rp(I)R1A and fTufAy/rTufAy, respectively. Restriction fragment lenght polymorphism (RFLP) analysis of rp gene fragments using digestion with AluI, MseI, and Tsp509I restriction enzymes indicated that aster yellows group related phytoplasmas in these Iranian regions, belong to rpI-B subgroups. Sequence analysis of partial 16S rRNA and rp genes from representative phytoplasma isolates confirmed the RFLP results. This research is the first report of annual plants infected with phytoplasmas related to subgroup rpI-B in Iran.
Źródło:
Journal of Plant Protection Research; 2014, 54, 1
1427-4345
Pojawia się w:
Journal of Plant Protection Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Prevalence of Anaplasma phagocytophilum in Ixodes ricinus ticks determined by polymerase chain reaction with two pairs of primers detecting 16S rRNA and ankA genes
Autorzy:
Chmielewska-Badora, J
Zwolinski, J.
Cisak, E.
Wojcik-Fatla, A.
Buczek, A.
Dutkiewicz, J.
Powiązania:
https://bibliotekanauki.pl/articles/51023.pdf
Data publikacji:
2007
Wydawca:
Instytut Medycyny Wsi
Tematy:
Lublin region
Polska
pathogen
Ixodes ricinus
Eastern Poland
tick
determination
animal pathogen
human pathogen
ankA gene
16S rRNA gene
granulocytic anaplasmosis
bacteria
Anaplasma phagocytophilum
polymerase chain reaction
Opis:
A total of 684 Ixodes ricinus ticks (321 nymphs, 184 males, and 179 females) were collected by fl agging lower vegetation in 6 forest districts located on the territory of Lublin province (eastern Poland). Ticks were examined by polymerase chain reaction (PCR) method for the presence of Anaplasma phagocytophilum DNA with two pairs of primers: EHR521/EHR747 for detecting 16S rRNA gene, and LA6/LA1 for detecting ankA gene. To study the relationship between infection in ticks and people occupationally exposed to tick bite, blood serum samples of 261 forestry workers employed in the same forest districts were examined by immunofl uorescence method for the presence of specifi c antibodies against A. phagocytophilum. A total of 70 ticks out of 684 examined (10.2%) showed the presence of A. phagocytophilum 16S rRNA gene. The prevalence of infection was signifi cantly dependent on tick’s stage (χ2=49.2, p<0.00001) and geographical locality (χ2=34.4, p<0.00001). The percentage of I. ricinus females infected with A. phagocytophilum (24.6%) was signifi cantly greater compared to males (6.5%) and nymphs (4.4%) (p<0.00001). Only 19 ticks out of 684 examined (2.8%) showed the presence of A. phagocytophilum ankA gene, signifi cantly less compared to 16S rRNA gene (p<0.00001). The prevalence of infection demonstrated by the presence of ankA gene was also signifi cantly dependent on tick’s stage (χ2=23.6, p<0.00001) but not on locality (χ2=9.8, p=0.082). A signifi cant correlation was found between the presence of A. phagocytophilum 16S rRNA gene in I. ricinus female ticks from the particular forest districts and the serologic response to A. phagocytophilum of forestry workers employed in the same districts (p<0.05). No signifi cant correlation was found between the presence of A. phagocytophilum ankA gene in I. ricinus ticks and serologic response of exposed workers. In conclusion, detection of A. phagocytophilum infection in ticks by PCR with the use of EHR521/EHR747 primers detecting 16S rRNA gene is signifi cantly more sensitive compared to LA6/LA1 primers detecting ankA gene.
Źródło:
Annals of Agricultural and Environmental Medicine; 2007, 14, 2
1232-1966
Pojawia się w:
Annals of Agricultural and Environmental Medicine
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Microbial community during the initial stage of biologically active carbon filters’ operation and its role in organic matter removal from water
Zbiorowisko drobnoustrojów w początkowej fazie pracy biologicznie aktywnych filtrów węglowych i ich rola w usuwaniu materii organicznej z wody
Autorzy:
Mądrecka-Witkowska, Beata
Komorowska-Kaufman, Małgorzata
Pruss, Alina
Holc, Dorota
Trzebny, Artur
Dabert, Mirosława
Powiązania:
https://bibliotekanauki.pl/articles/27311566.pdf
Data publikacji:
2023
Wydawca:
Polska Akademia Nauk. Czasopisma i Monografie PAN
Tematy:
biofilm formation
drinking water
biodegradation
biologically active carbon filters
PICRUSt analysis
16S rRNA-profiling
Opis:
Filtration through biologically active carbon (BAC) filters is an effective method of organic matter removal during drinking water treatment. In this study, the microbial community in the initial period of filters’ operation, as well as its role in the organic matter removal were investigated. Research was carried out in a pilot scale on two BAC filters (Filter 1 and Filter 2) which were distinguished by the type of inflowing water. It was observed that the number of heterotrophic plate count bacteria and total microbial activity were significantly higher in water samples collected from Filter 2, which received an additional load of organic matter and microorganisms. Despite the differences in the values of chemical and microbiological parameters of inflowing water, the composition of the microbiome in both filters was similar. The predominant taxon was a bacterium related to Spongiibacter sp. (Gammaproteobacteria) (>50% of relative abundance). In both filters, the efficiency of organic matter removal was at the same level, and the composition and relative frequency of predicted functional pathways related to metabolism determined using PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States Software) at level 3 of KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology – were also similar. The study demonstrated that a 40-day period of filter operation after filling with virgin granular activated carbon, was sufficient to initiate biofilm development. It was proved, that during the initial stage of filter operation, microorganisms capable of biodegradation of various organic compounds, including xenobiotics like nitrotoluene, colonized the filters.
Filtracja przez biologicznie aktywne filtry węglowe (BAF) jest skuteczną metodą usuwania materii organicznej podczas uzdatniania wody przeznaczonej do spożycia przez ludzi. W niniejszej pracy zbadano zbiorowisko drobnoustrojów w początkowym okresie eksploatacji filtrów oraz jego rolę w usuwaniu materii organicznej z wody. Badania przeprowadzono w skali pilotowej na dwóch filtrach BAF (Filtr 1 i Filtr 2) różniących się składem dopływającej wody. Stwierdzono, że liczba bakterii heterotroficznych i całkowita aktywność mikrobiologiczna były znacząco większe w próbkach wody pobranych z Filtra 2 – zasilanego wodą wzbogaconą o dodatkowy ładunek materii organicznej i mikroorganizmów. Pomimo różnic w wartościach parametrów chemicznych i mikrobiologicznych dopływającej wody, skład mikrobiomu w filtrach był podobny. W obu filtrach dominującym taksonem była bakteria spokrewniona z Spongiibacter sp. (Gammaproteobacteria) (>50% względnej liczebności). W obydwóch filtrach efektywność usuwania materii organicznej była na podobnym poziomie oraz skład i względna częstość występowania przewidywanych szlaków funkcjonalnych związanych z metabolizmem, oznaczone przy użyciu PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States Software) na poziomie 3 KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology były również zbliżone. Badania wykazały, że 40-dniowy okres pracy filtrów po napełnieniu świeżym granulowanym węglem aktywnym był wystarczający do rozwoju biofilmu. Udowodniono, że w początkowym okresie pracy złoża filtracyjne zasiedlane były przez mikroorganizmy zdolne do biodegradacji różnych związków organicznych, w tym ksenobiotyków, np. nitrotoluenu.
Źródło:
Archives of Environmental Protection; 2023, 49, 3; 67--77
2083-4772
2083-4810
Pojawia się w:
Archives of Environmental Protection
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Isolation and characterization of biosurfactants-producing bacteria isolated from palm oil industry and evaluation for biosurfactants production using low-cost substrates
Autorzy:
Saisa-Ard, K.
Manerrat, S.
Saimmai, A.
Powiązania:
https://bibliotekanauki.pl/articles/81283.pdf
Data publikacji:
2013
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
isolation
biosurfactant
phylogenetic analysis
palm oil
contaminated soil
surface tension
phylogenetic position
16S rRNA gene
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 3
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Biodiversity and antibiotic resistance of bacteria isolated from tap water in Wrocław, Poland
Autorzy:
Leginowicz, M.
Siedlecka, A.
Piekarska, K.
Powiązania:
https://bibliotekanauki.pl/articles/207741.pdf
Data publikacji:
2018
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
water supply
drinking water
biological diversity
16S rRNA gene
systemy zasilania
woda pitna
różnorodność biologiczna
Opis:
Microbial contamination and biodiversity were determined for the drinking water samples collected from selected points of the water supply system in Wroclaw, Poland. All tested samples met the requirements of Polish law, i.e., the Regulation of the Minister of Health. However, the antibiotic resistant bacteria were found. The correlation between the distance of sampling points from water treatment plants and their microbial contamination was not established. Nevertheless, the Na Grobli treatment plant seemed to produce water of higher microbial quality than the Mokry Dwor treatment plant at the moment of sampling. The identification of representative isolates was performed with 16S rRNA gene sequencing and MALDI-TOF mass spectrometry and the results of these two methods were compared, indicating some discrepancies. Nevertheless, bacteria dwelling in drinking water in Wroclaw belonged to the phyla Actinobacteria, Proteobacteria (alpha-, beta-, gamma-Proteobacteria) and Firmicutes . The determination of antibiotic resistance profiles showed that 12 from 17 tested isolates revealed resistance to at least one antibiotic and two strains were multi-drug-resistant.
Źródło:
Environment Protection Engineering; 2018, 44, 4; 85-98
0324-8828
Pojawia się w:
Environment Protection Engineering
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Bacterial species identification
Autorzy:
Kshikhundo, Ronald
Itumhelo, Shayalethu
Powiązania:
https://bibliotekanauki.pl/articles/1153736.pdf
Data publikacji:
2016
Wydawca:
Przedsiębiorstwo Wydawnictw Naukowych Darwin / Scientific Publishing House DARWIN
Tematy:
16S rRNA gene
Bacteria
Biolog
Gram staining
MALDI-TOF MS
RiboPrinter
computational tools
fatty acids
identification
metagenomics
morphology
Opis:
The traditional methods of bacterial identification are based on observation of either the morphology of single cells or colony characteristics. However, the adoption of newer and automated methods offers advantage in terms of rapid and reliable identification of bacterial species. The review provides a comprehensive appreciation of new and improved technologies such fatty acid profiling, sequence analysis of the 16S rRNA gene, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF), metabolic finger profiling using BIOLOG, ribotyping, together with the computational tools employed for querying the databases that are associated with these identification tools and high throughput genomic sequencing in bacterial identification. It is evident that with the increase in the adoption of new technologies, bacterial identification is becoming easier.
Źródło:
World News of Natural Sciences; 2016, 3; 26-38
2543-5426
Pojawia się w:
World News of Natural Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Anaplasma phagocytophilum infection of red foxes [Vulpes vulpes]
Autorzy:
Karbowiak, G
Vichova, B.
Majlathova, V.
Hapunik, J.
Pet'ko, B.
Powiązania:
https://bibliotekanauki.pl/articles/50073.pdf
Data publikacji:
2009
Wydawca:
Instytut Medycyny Wsi
Tematy:
Polska
Mazovia region
parasite
Anaplasma phagocytophilum
infection
animal disease
red fox
Vulpes vulpes
16S rRNA gene
msp4 gene
Źródło:
Annals of Agricultural and Environmental Medicine; 2009, 16, 2; 299-300
1232-1966
Pojawia się w:
Annals of Agricultural and Environmental Medicine
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
16S microbial phylogeny of multifunctional plant-growth-promoting rhizobacteria from the rhizosphere of maize (Zea mays L.) for agricultural soil fortification
Autorzy:
Reena, J.
Jubu, T.
Powiązania:
https://bibliotekanauki.pl/articles/79870.pdf
Data publikacji:
2019
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
maize
Zea mays
rhizosphere
agricultural soil
Fusarium moniliforme
16S rRNA sequence
indoloacetic acid
siderophore
biological control
plant growth promoting rhizobacteria
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2019, 100, 2
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
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