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Wastewater microbiology
Published in Rumana Riffat, Taqsim Husnain, Fundamentals of Wastewater Treatment and Engineering, 2022
The three major domains of living organisms are the Bacteria, the Archaea, and the Eukarya. This is according to the Universal Phylogenetic (Evolutionary) Tree, which was derived from comparative sequencing of 16S or 18S ribosomal RNA (Madigan et al., 2021). Based on cell structure, all living organisms are divided into two types: Prokaryotic and eukaryotic. The major structural difference between prokaryotes and eukaryotes is their nuclear structure. The eukaryotic nucleus is surrounded by a nuclear membrane, contains deoxyribonucleic acid (DNA) molecules, and undergoes division by mitosis. On the other hand, the prokaryotic nuclear region is not surrounded by a membrane, contains a single DNA molecule whose division is non-mitotic. The prokaryotes include bacteria, blue-green algae (cyanobacter), and archaea. Figures 3.1(a) and (b) show typical cell structures of prokaryotes and eukaryotes, respectively. The archaea are separated from bacteria due to their DNA composition and unique cellular chemistry. Examples of archaea are the methane-producers, e.g. Methanococcus, Methanosarcina. The eukaryotes are much more complex and include plants and animals, as well as protozoa, fungi, and algae. Table 3.1 presents the classifications. Macroscopic animals include Rotifers, Crustaceans, etc. Rotifers act as polishers of effluent from wastewater treatment plants by consuming organic colloids, bacteria, and algae. The microorganisms are discussed in more detail in the following sections.
Contamination of fresh vegetables in municipal stores with pathogenic Acanthamoeba genotypes; a public health concern
Published in International Journal of Environmental Health Research, 2023
Marziye Fatemi, Maryam Niyyati, Soheila Rouhani, Seyed Ahmad Karamati, Hamed Mirjalali, Panagiotis Karanis
Acanthamoeba spp. identification is usually based on the morphological and molecular analyses. Based on the sequencing of the diagnostic fragment 3 (DF3) region of 18S ribosomal RNA (rRNA) gene, 22 genotypes (T1-T22) of Acanthamoeba spp. have been identified (Fuerst et al. 2015; Corsaro 2020, 2021). Several genotypes including T1, T2, T3, T4, T5, T6, T9, T11, T13, and T15 have been reported in environmental or clinical samples from different regions of Iran (Maghsood et al. 2005; Hajialilo et al. 2016; Karamati et al. 2016; Shokri et al. 2016; Javanmard et al. 2017; Latifi et al. 2020; Pazoki et al. 2020a; Mahmoudi et al. 2021). The genotypes T2, T3, T4, T5, T6, T11, and recently T9 have been identified in patients with AK in Iran (Maghsood et al. 2005; Hajialilo et al. 2016).
Effective kinetic modeling and phycoremediation of Cr(IV) ions from tannery effluent by using microalgae – Chlamydomonas moewusii, Auxenochlorella pyrenoidosa, Scenedesmus sp.
Published in Bioremediation Journal, 2023
Praveena Venkatesan, Mythili Sathiavelu
In the present work, the molecular or taxonomical characterization of microalgae species (SMA1, SMA2, and SMA3) were identified by base molecular marker “18S ribosomal RNA (rRNA)” gene sequencing. The phylogenetic analysis was represented the species classification through the molecular markers (Priyadashani et al., 2011). Isolated DNA was extracted from microalgae culture by using the DNeasy Mini Kit. The quantity was measured using NanoDrop Spectrophotometer and the determination of quality is done by using 2% agarose gel. The DNA observation was found to be a single band of high-molecular-weight. The microalgae 18S ribosomal RNA (18S rRNA gene) region was amplified using universal primers by PCR from the isolated DNA. A single discrete PCR amplicon band of 600 bp was observed when resolved on agarose gel (Kightlinger et al., 2014). The PCR product was purified to remove contaminants. The purified PCR amplicon was sequenced using the universal forward and reverse primers. Sequencing was done using BDT v3.1 Cycle sequencing kit on ABI 3500 Genetic Analyzer. The generated sequences were compared to the GenBank nucleotide database using the BLAST program further phylogenetic tree was constructed through evolutionary relationship and homologous sequencing was retrieved and searched from the GenBank BLAST tool (Chaidir et al., 2016). The achieved 18 s rRNA gene sequences were submitted to the GenBank accession numbers (SMA1, SMA2, and SMA3). The MEGA10 was used to determine the performance of Molecular Evolutionary Genetics Analysis (Berard et al., 2005).
Molecular biological tools in concrete biodeterioration – a mini review
Published in Environmental Technology, 2019
Vinita Vishwakarma, Balakrishnan Anandkumar
Molecular methods, such as 16S ribosomal RNA (16S rRNA) gene analysis, have been used to identify microbial communities from a variety of environments [35–38]. Vincke et al. initiated both conventional as well as molecular techniques to determine the microbial communities present on the concrete walls of sewer pipes [39]. Hernandez et al. had studied on an in-situ assessment of active Thiobacillus sp. in corroding sewers using fluorescent RNA probe [40]. To find the microbial components of the biofilms DGGE analysis was made and this identified the cyanobacteria, green microalgae, bacteria and fungi by targeting the 16S and 18S ribosomal RNA genes [41]. Sometimes, the DNA-based molecular biology techniques are used to identify the components of microbial biofilms. Isolation, molecular identification and phylogenetic analysis of dominant species of bacteria in the biofilm on the three types of concrete cube specimens (normal concrete, concrete with fly ash and superplasticizer and concrete with only superplasticizer) were carried out to understand the diversity of different types of bacteria [16]. Verdier et al. reviewed both sampling and analysis methods on building materials [2]. The author reported different microbial sampling methods such as in-situ and laboratory experiments and found that laboratory testing gave reliable information on microbial development on building materials.