scholarly journals Epilithic Microalgae Isolated from Biofilm on Borobudur Temple Stone

2020 ◽  
Vol 5 (3) ◽  
pp. 239
Author(s):  
Debora Christin Purbani ◽  
Ade Lia Putri ◽  
Moh. Habibi
Keyword(s):  
Building Materials ◽  
Monitoring And Evaluation ◽  
18S Rrna Gene ◽  
Culture Conditions ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Ankistrodesmus Falcatus ◽  
Stone Materials ◽  
Historical Heritage ◽  
Living Organisms

Borobudur Temple is a historical heritage building located in an open area and made of porous building materials (stone materials). This condition makes the Borobudur Temple susceptible to various problems related to degradation and weathering. Biodeterioration of Borobudur Temple may be caused by activities of living organisms present in the biofilm of stone. Continuous monitoring and evaluation need to be carried out by observing and isolating the growth of micro-organisms, including epilithic microalgae. Therefore, this study aims to isolate and identify epilithic microalgae from the biofilm on Borobudur Temple stones. Epilithic microalgae were isolated to obtain a uni-algae and maintained under culture conditions. The morphological of microalgae were observed using light microscopy, while the 18S rRNA gene sequence determined the molecular identification of microalgae for eukaryotic and 16S rRNA sequence for prokaryotic. A total of nine epilithic microalgae were successfully isolated from the biofilm of Borobudur Temple stones. The isolated were identified as Ankistrodesmus falcatus, Tetraselmis cordiformis, Pseudendoclonium arthropyreniae,  Anabaena cylindrica,  Nostoc gelatinosum, Oscillatoria limnetica, Messastrum gracile, Stigeoclonium aestivale, and Scenedesmus acuminatus. This is the first study for the identification of microalgae from Borobudur temple stones. The isolates will be collected and will be used as a source for further study.

scholarly journals Hylodesmus singaporensis gen. et sp. nov., a new autosporic subaerial green alga (Scenedesmaceae, Chlorophyta) from Singapore

2010 ◽  
Vol 60 (5) ◽  
pp. 1224-1235 ◽  
Author(s):  
Marek Eliáš ◽  
Yvonne Němcová ◽  
Pavel Škaloud ◽  
Jiří Neustupa ◽  
Veronika Kaufnerová ◽  
...  
Keyword(s):  
Cell Wall ◽  
Green Alga ◽  
Phylogenetic Analyses ◽  
18S Rrna Gene ◽  
Culture Conditions ◽  
Culture Collection ◽  
Its2 Region ◽  
Rrna Gene ◽  
Cell Periphery ◽  
Algal Flora

The algal flora of subaerial habitats in the tropics remains largely unexplored, despite the fact that it potentially encompasses a wealth of new evolutionary diversity. Here we present a detailed morphological and molecular characterization of an autosporic coccoid green alga isolated from decaying wood in a natural forest in Singapore. Depending on culture conditions, this alga formed globular to irregularly oval solitary cells. Autosporulation was the only mode of reproduction observed. The cell periphery was filled with numerous vacuoles, and a single parietal chloroplast contained a conspicuous pyrenoid surrounded by a bipartite starch envelope. The cell wall was composed of a thick inner layer and a thin trilaminar outer layer, and the cell surface was ornamented with a few delicate ribs. Phylogenetic analyses of 18S rRNA gene sequences placed our strain in the family Scenedesmaceae (Sphaeropleales, Chlorophyceae) as a strongly supported sister branch of the genus Desmodesmus. Analyses of an alternative phylogenetic marker widely used for the Scenedesmaceae, the ITS2 region, confirmed that the strain is distinct from any scenedesmacean alga sequenced to date, but is related to the genus Desmodesmus, despite lacking the defining phenotypic features of Desmodesmus (cell wall with four sporopolleninic layers ornamented with peculiar submicroscopic structures). Collectively, our results establish that we identified a novel, previously undocumented, evolutionary lineage of scenedesmacean algae necessitating its description as a new species in a new genus. We propose it be named Hylodesmus singaporensis gen. et sp. nov. A cryopreserved holotype specimen has been deposited into the Culture Collection of Algae of Charles University in Prague, Czech Republic (CAUP) as CAUP C-H8001.

Resistance of Binding Systems of Various Compositions to the Action of Molds

2020 ◽  
Vol 786 (11) ◽  
pp. 41-46
Author(s):  
V.V. STROKOVA ◽  
◽  
V.V. NELUBOVA ◽  
M.N. SIVALNEVA ◽  
M.D. RYKUNOVA ◽  
...  
Keyword(s):  
Aging Process ◽  
Building Materials ◽  
Environmental Safety ◽  
Fungal Resistance ◽  
Building Structures ◽  
Vital Activity ◽  
Regulatory Documents ◽  
Living Organisms ◽  
Biological Corrosion ◽  
Test Objects

The dynamic development of urbanization contributes to an increase in emissions of industrial waste, which is the cause dysfunction of the ecosystem balance and leads to the development of biological corrosion on building materials associated with the products of the vital activity of microorganisms. In this regard, it is necessary to assess the resistance of composites to predict the durability of building structures under conditions of biological influence of microorganisms. Binder systems of various compositions were studied: cementless nanostructured binders (NB) based on quartz sand and granodiorite, gypsum, Portland cement and alumina cement. The toxicity of binders was assessed by biotesting on living organisms – cladocerans Daphnia Magna – according to the criteria of the intensity of their growth and viability. As a result, the high environmental safety of NB is substantiated, and the ranking of the studied binders according to the degree of increase in their toxicity to test objects is presented. Fungal resistance was assessed by the ability of molds for growing and reproduction on the studied samples. It was found that the most active in terms of the development of binders were representatives of the genus Aspergillus, the intensity of growing of which in all variants did not decrease below 3 points. Gypsum and NB were especially vulnerable, where the degree of fouling repeatedly reached 5 points. Even the initially biostable cement, after the aging process, lost its stability at different extent. The obtained results indicate the need to increase the resistance of composites for various purposes under conditions of biocorrosion at the stage of design and updating of regulatory documents, including tests for fungal resistance in the list of mandatory.

scholarly journals An experimental intraradicular biofilm model in the pig for evaluating irrigation techniques

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Toshinori Tanaka ◽  
Yoshio Yahata ◽  
Keisuke Handa ◽  
Suresh V. Venkataiah ◽  
Mary M. Njuguna ◽  
...  
Keyword(s):  
16S Rrna ◽  
Root Canal ◽  
Apical Periodontitis ◽  
Exposure Model ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Bacterial Phyla ◽  
Biofilm Model ◽  
Biofilm Removal

Abstract Background We established an in vivo intraradicular biofilm model of apical periodontitis in pigs in which we compared the efficacy of different irrigant activation techniques for biofilm removal. Methods Twenty roots from the deciduous mandibular second premolar of 5 male pigs were used. After pulpectomy, canals were left open for 2 weeks and then sealed for 4 weeks to enable the development of an intracanal biofilm. The intraradicular biofilms was evaluated using SEM and bacterial 16S rRNA gene-sequencing. To investigate the efficacy of biofilm removal, root canal irrigations were performed using conventional needle, passive ultrasonic, subsonic, or laser-activated irrigation. Real-time PCR was conducted to quantitate the remaining biofilm components. Statistical analysis was performed using ANOVA followed by a Tukey kramer post-hoc test with α = 0.05. Results The pulp exposure model was effective in inducing apical periodontitis and SEM analysis revealed a multi-layer biofilm formation inside the root canal. 16S rRNA sequence analysis identified Firmicutes, Bacteroidetes, and Fusobacteria as the predominant bacterial phyla components, which is similar to the microbiome profile seen in humans. None of the tested irrigation techniques completely eradicated the biofilm components from the root canal, but the subsonic and laser-activated irrigation methods produced the lowest bacterial counts (p < 0.05). Conclusions An experimental intraradicular biofilm model has been successfully established in pigs. Within the limitations of the study, subsonic or laser-activated irrigation demonstrated the best biofilm removal results in the pig system.

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

scholarly journals Analytical validation of a real-time hydrolysis probe PCR assay for quantifying Plasmodium falciparum parasites in experimentally infected human adults

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Claire Y. T. Wang ◽  
Emma L. Ballard ◽  
Zuleima Pava ◽  
Louise Marquart ◽  
Jane Gaydon ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Plasmodium Falciparum ◽  
18S Rrna ◽  
Drug Efficacy ◽  
18S Rrna Gene ◽  
Molecular Techniques ◽  
Qpcr Assay ◽  
Rrna Gene ◽  
Analytical Sensitivity ◽  
Blood Samples

Abstract Background Volunteer infection studies have become a standard model for evaluating drug efficacy against Plasmodium infections. Molecular techniques such as qPCR are used in these studies due to their ability to provide robust and accurate estimates of parasitaemia at increased sensitivity compared to microscopy. The validity and reliability of assays need to be ensured when used to evaluate the efficacy of candidate drugs in clinical trials. Methods A previously described 18S rRNA gene qPCR assay for quantifying Plasmodium falciparum in blood samples was evaluated. Assay performance characteristics including analytical sensitivity, reportable range, precision, accuracy and specificity were assessed using experimental data and data compiled from phase 1 volunteer infection studies conducted between 2013 and 2019. Guidelines for validation of laboratory-developed molecular assays were followed. Results The reportable range was 1.50 to 6.50 log10 parasites/mL with a limit of detection of 2.045 log10 parasites/mL of whole blood based on a parasite diluted standard series over this range. The assay was highly reproducible with minimal intra-assay (SD = 0.456 quantification cycle (Cq) units [0.137 log10 parasites/mL] over 21 replicates) and inter-assay (SD = 0.604 Cq units [0.182 log10 parasites/mL] over 786 qPCR runs) variability. Through an external quality assurance program, the QIMR assay was shown to generate accurate results (quantitative bias + 0.019 log10 parasites/mL against nominal values). Specificity was 100% after assessing 164 parasite-free human blood samples. Conclusions The 18S rRNA gene qPCR assay is specific and highly reproducible and can provide reliable and accurate parasite quantification. The assay is considered fit for use in evaluating drug efficacy in malaria clinical trials.

scholarly journals 16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica

Polar Biology ◽  
2021 ◽  
Author(s):  
Eleanor E. Jackson ◽  
Ian Hawes ◽  
Anne D. Jungblut
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
High Throughput Sequencing ◽  
Microbial Mats ◽  
Gene Diversity ◽  
Salinity Gradient ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Ice Shelf ◽  
The Impact

AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.

scholarly journals 18S rRNA gene sequences of leptocephalus gut contents, particulate organic matter, and biological oceanographic conditions in the western North Pacific

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tsuyoshi Watanabe ◽  
Satoshi Nagai ◽  
Yoko Kawakami ◽  
Taiga Asakura ◽  
Jun Kikuchi ◽  
...  
Keyword(s):  
Organic Matter ◽  
Particulate Organic Matter ◽  
North Pacific ◽  
Western North Pacific ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Gut Contents ◽  
Rrna Gene ◽  
Marine Snow ◽  
Chlorophyll Maximum

AbstractEel larvae apparently feed on marine snow, but many aspects of their feeding ecology remain unknown. The eukaryotic 18S rRNA gene sequence compositions in the gut contents of four taxa of anguilliform eel larvae were compared with the sequence compositions of vertically sampled seawater particulate organic matter (POM) in the oligotrophic western North Pacific Ocean. Both gut contents and POM were mainly composed of dinoflagellates as well as other phytoplankton (cryptophytes and diatoms) and zooplankton (ciliophoran and copepod) sequences. Gut contents also contained cryptophyte and ciliophoran genera and a few other taxa. Dinoflagellates (family Gymnodiniaceae) may be an important food source and these phytoplankton were predominant in gut contents and POM as evidenced by DNA analysis and phytoplankton cell counting. The compositions of the gut contents were not specific to the species of eel larvae or the different sampling areas, and they were most similar to POM at the chlorophyll maximum in the upper part of the thermocline (mean depth: 112 m). Our results are consistent with eel larvae feeding on marine snow at a low trophic level, and feeding may frequently occur in the chlorophyll maximum in the western North Pacific.

scholarly journals Molecular Characterization of Ciliate Diversity in Stream Biofilms

2008 ◽  
Vol 74 (6) ◽  
pp. 1740-1747 ◽  
Author(s):  
Andrew Dopheide ◽  
Gavin Lear ◽  
Rebecca Stott ◽  
Gillian Lewis
Keyword(s):  
18S Rrna ◽  
Pcr Primers ◽  
18S Rrna Gene ◽  
Sequence Diversity ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Specific Pcr ◽  
Stream Biofilms

ABSTRACT Free-living protozoa are thought to be of fundamental importance in aquatic ecosystems, but there is limited understanding of their diversity and ecological role, particularly in surface-associated communities such as biofilms. Existing eukaryote-specific PCR primers were used to survey 18S rRNA gene sequence diversity in stream biofilms but poorly revealed protozoan diversity, demonstrating a need for protozoan-targeted primers. Group-specific PCR primers targeting 18S rRNA genes of the protozoan phylum Ciliophora were therefore designed and tested using DNA extracted from cultured protozoan isolates. The two most reliable primer combinations were applied to stream biofilm DNA, followed by cloning and sequencing analysis. Of 44 clones derived from primer set 384F/1147R, 86% were of probable ciliate origin, as were 25% of 44 clones detected by primer set 121F/1147R. A further 29% of 121F/1147R-detected clones matched sequences from the closely related phylum Apicomplexa. The highly ciliate-specific primer set 384F/1147R was subsequently used in PCRs on biofilm DNA from four streams exhibiting different levels of human impact, revealing differences in ciliate sequence diversity in samples from each site. Of a total of 240 clones, 73% were of probable ciliate origin; 54 different putative ciliate sequences were detected from throughout seven taxonomic ciliate classes. Sequences from Oligohymenophorea were most commonly detected in all samples, followed by either Spirotrichea or Phyllopharyngea. Restriction fragment length polymorphism profile-based analysis of clones suggested a potentially higher level of diversity than did sequencing. Nevertheless, newly designed PCR primers 384F/1147R were considered to provide an effective molecular basis for characterization of ciliate diversity in stream biofilms.

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