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 Gastrointestinal Segments Influenced Fermentation End-Products, Microbiota and Microbial Abundances in Goats

2021 ◽  
Author(s):  
Tsegay Gebremariam ◽  
Zhiliang Tan
Keyword(s):  
Fatty Acids ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Gene Copies ◽  
End Products ◽  
The Impact

Abstract Purpose: Carbohydrate diets altered fermentation end-products and microbial community in the gastrointestinal tracts (GIT) of goats. Gastrointestinal contents used to determine the impact of carbohydrate feeds on fermentation end-products and microbial community in goats.Methodology: in the study goats were assigned to one of the two treatments corn meal (CM) or Corn gluten (CG) in a randomized block design (400 g/kg DM each). Goats were slaughtered, GIT liquids were used to determine dissolved gasses, fatty acids and microbial community.Results: Goats fed CG increased molar acetate (P < 0.05), lowered butyrate and propionate in the fore and hindgut comparing to those goats received CM. Goats received CM had higher (P < 0.05) dH2 while lowered dH2S in the fore and hindgut than those goats fed with CG treatment. The fore and hindgut had higher (P < 0.01) 16S rRNA gene copies of bacteria, protozoa, methanogens and 18S rRNA gene copies fungi than in the ileum and cecum. Goats fed CG diet had higher (P < 0.05)16S rRNA gene copies of bacteria, protozoa, methanogens, and 18S rRNA gene copies of fungi than those goats fed with CM diet. Conclusion fore and hindguts improved dissolved gasses, fatty acids and microbial community comparing with in the ileum and cecum. Goats fed CM had improved the Methanobacterials order and Methanobrevibacter genus as compared with those goats fed CG. The study suggested that hindgut segments have a reasonable contribution as foregut to methane emissions from goats.

scholarly journals Feasibility of Transferring Fluorescent In Situ Hybridization Probes to an 18S rRNA Gene Phylochip and Mapping of Signal Intensities

2008 ◽  
Vol 74 (9) ◽  
pp. 2814-2821 ◽  
Author(s):  
Katja Metfies ◽  
Linda K. Medlin
Keyword(s):  
In Situ Hybridization ◽  
Secondary Structure ◽  
16S Rrna ◽  
Fluorescent In Situ Hybridization ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Rrna Molecule ◽  
The 16S Rrna Gene

ABSTRACT DNA microarray technology offers the possibility to analyze microbial communities without cultivation, thus benefiting biodiversity studies. We developed a DNA phylochip to assess phytoplankton diversity and transferred 18S rRNA probes from dot blot or fluorescent in situ hybridization (FISH) analyses to a microarray format. Similar studies with 16S rRNA probes have been done determined that in order to achieve a signal on the microarray, the 16S rRNA molecule had to be fragmented, or PCR amplicons had to be <150 bp in length to minimize the formation of a secondary structure in the molecule so that the probe could bind to the target site. We found different results with the 18S rRNA molecule. Four out of 12 FISH probes exhibited false-negative signals on the microarray; eight exhibited strong but variable signals using full-length 18S RNA molecules. A systematic investigation of the probe's accessibility to the 18S rRNA gene was made using Prymenisum parvum as the target. Fourteen additional probes identical to this target covered the regions not tested with existing FISH probes. Probes with a binding site in the first 900 bp of the gene generated positive signals. Six out of nine probes binding in the last 900 bp of the gene produced no signal. Our results suggest that although secondary structure affected probe binding, the effect is not the same for the 18S rRNA gene and the 16S rRNA gene. For the 16S rRNA gene, the secondary structure is stronger in the first half of the molecule, whereas in the 18S rRNA gene, the last half of the molecule is critical. Probe-binding sites within 18S rRNA gene molecules are important for the probe design for DNA phylochips because signal intensity appears to be correlated with the secondary structure at the binding site in this molecule. If probes are designed from the first half of the 18S rRNA molecule, then full-length 18S rRNA molecules can be used in the hybridization on the chip, avoiding the fragmentation and the necessity for the short PCR amplicons that are associated with using the 16S rRNA molecule. Thus, the 18S rRNA molecule is a more attractive molecule for use in environmental studies where some level of quantification is desired. Target size was a minor problem, whereas for 16S rRNA molecules target size rather than probe site was important.

scholarly journals Karakterisasi Mikrobia Rizosfer asal Tanaman Ginseng Jawa (Talinum triangulare) berdasarkan Gen Ribosomal 16S rRNA dan 18S rRNA

2018 ◽  
Vol 3 (2) ◽  
pp. 74-81
Author(s):  
Alimuddin Ali ◽  
Herlina Rante
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
Rhizosphere Soil ◽  
18S Rrna Gene ◽  
Biologically Active ◽  
Plate Count ◽  
Rrna Gene ◽  
Plate Count Method ◽  
Bacteria And Fungi ◽  
Talinum Triangulare

The rhizosphere is a biologically active zone of the soil around plant roots that contains soil-borne microbes including bacteria and fungi.  The microbes were isolated from rhizosphere soil roots of Java ginseng. The population of microbes was estimated by plate count method. The isolates were identified based on a great variety of morphological, and cultural characteristics. The total of rhizosphere soil microbe population were  20.91(106 cfu.g−1soils) and showed that 12 isolates of bacteria, 15 isolates of actinomycetes, and 10 isolates of fungi which were found in all of soil samples. The molecular analysis of the ribosomal genes showed that the bacterial isolate, actinomycetes and fungi were closely related to of Staphylococcus sp. DGM  (JF923460), Streptomyces avidinii (EU593640) and fungi Aspergillus niger (HQ379853), respectively. Key words: rhizosphere, Java ginseng, 16S rRNA gene, 18S rRNA gene

scholarly journals A DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0245936
Author(s):  
Takuhei Shiozaki ◽  
Fumihiro Itoh ◽  
Yuu Hirose ◽  
Jonaotaro Onodera ◽  
Akira Kuwata ◽  
...  
Keyword(s):  
Community Structure ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Formalin Fixation ◽  
Plankton Sample ◽  
Rrna Gene ◽  
Dna Metabarcoding ◽  
Plankton Diversity ◽  
The Impact ◽  
Formalin Fixed

Plankton samples have been routinely collected and preserved in formalin in many laboratories and museums for more than 100 years. Recently, attention has turned to use DNA information from formalin-fixed samples to examine changes in plankton diversity over time. However, no molecular ecological studies have evaluated the impact of formalin fixation on the genetic composition of the plankton community structure. Here, we developed a method for extracting DNA from archived formalin-preserved plankton samples to determine their community structure by a DNA metabarcoding approach. We found that a lysis solution consisting of borate-NaOH buffer (pH 11) with SDS and proteinase K effectively cleaved the cross-link formed by formalin fixation. DNA was extracted from samples preserved for decades in formalin, and the diatom community of the extracted DNA was in good agreement with the microscopy analysis. Furthermore, we stored a plankton sample for 1.5 years and demonstrated that 18S rRNA gene community structures did not change significantly from non-formalin-fixed, time-zero samples. These results indicate that our method can be used to describe the original community structure of plankton archived in formalin for years. Our approach will be useful for examining the long-term variation of plankton diversity by metabarcoding analysis of 18S rRNA gene community structure.

Bacterial, archaeal and eukaryotic diversity in Arctic sediment as revealed by 16S rRNA and 18S rRNA gene clone libraries analysis

Polar Biology ◽  
2008 ◽  
Vol 32 (1) ◽  
pp. 93-103 ◽  
Author(s):  
Fei Tian ◽  
Yong Yu ◽  
Bo Chen ◽  
Huirong Li ◽  
Yu-Feng Yao ◽  
...  
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Gene Clone ◽  
Rrna Gene ◽  
Clone Libraries ◽  
Eukaryotic Diversity ◽  
Arctic Sediment

Life in Hot Spring Microbial Mats Located in the Trans-Mexican Volcanic Belt: A 16S/18S rRNA Gene and Metagenomic Analysis

2018 ◽  
Vol 35 (8) ◽  
pp. 704-712 ◽  
Author(s):  
Cristina M. Prieto-Barajas ◽  
Luis D. Alcaraz ◽  
Eduardo Valencia-Cantero ◽  
Gustavo Santoyo
Keyword(s):  
18S Rrna ◽  
Microbial Mats ◽  
Hot Spring ◽  
Volcanic Belt ◽  
18S Rrna Gene ◽  
Metagenomic Analysis ◽  
Rrna Gene ◽  
Mexican Volcanic Belt ◽  
Trans Mexican Volcanic Belt

scholarly journals Depthwise microbiome and isotopic profiling of a moderately saline microbial mat in a solar saltern

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Varun Paul ◽  
Yogaraj Banerjee ◽  
Prosenjit Ghosh ◽  
Susheel Bhanu Busi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Mats ◽  
Salinity Gradient ◽  
Microbial Mat ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Eukaryotic Algae ◽  
Culture Independent ◽  
Isotopic Characterization

AbstractThe solar salterns in Tuticorin, India, are man-made, saline to hypersaline systems hosting some uniquely adapted populations of microorganisms and eukaryotic algae that have not been fully characterized. Two visually different microbial mats (termed ‘white’ and ‘green’) developing on the reservoir ponds (53 PSU) were isolated from the salterns. Firstly, archaeal and bacterial diversity in different vertical layers of the mats were analyzed. Culture-independent 16S rRNA gene analysis revealed that both bacteria and archaea were rich in their diversity. The top layers had a higher representation of halophilic archaea Halobacteriaceae, phylum Chloroflexi, and classes Anaerolineae, Delta- and Gamma- Proteobacteria than the deeper sections, indicating that a salinity gradient exists within the mats. Limited presence of Cyanobacteria and detection of algae-associated bacteria, such as Phycisphaerae, Phaeodactylibacter and Oceanicaulis likely implied that eukaryotic algae and other phototrophs could be the primary producers within the mat ecosystem. Secondly, predictive metabolic pathway analysis using the 16S rRNA gene data revealed that in addition to the regulatory microbial functions, methane and nitrogen metabolisms were prevalent. Finally, stable carbon and nitrogen isotopic compositions determined from both mat samples showed that the δ13Corg and δ15Norg values increased slightly with depth, ranging from − 16.42 to − 14.73‰, and 11.17 to 13.55‰, respectively. The isotopic signature along the microbial mat profile followed a pattern that is distinctive to the community composition and net metabolic activities, and comparable to saline mats in other salterns. The results and discussions presented here by merging culture-independent studies, predictive metabolic analyses and isotopic characterization, provide a collective strategy to understand the compositional and functional characteristics of microbial mats in saline environments.

scholarly journals Effects of Transgenic Hybrid Aspen Overexpressing Polyphenol Oxidase on Rhizosphere Diversity

2008 ◽  
Vol 74 (17) ◽  
pp. 5340-5348 ◽  
Author(s):  
Kathryn L. Oliver ◽  
Richard C. Hamelin ◽  
William E. Hintz
Keyword(s):  
16S Rrna ◽  
Polyphenol Oxidase ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Oxidase Gene ◽  
Bacterial Gene ◽  
Gene Libraries ◽  
Cpn 60

ABSTRACT This study assessed the potential effects of transgenic aspen overexpressing a polyphenol oxidase gene on diversity in rhizosphere communities. Cultivation-independent methods were used to better delineate bacterial and fungal populations associated with transgenic and nontransgenic trees. Gene libraries for the bacterial component of the rhizosphere were established using 16S rRNA and chaperonin-60 (CPN-60) gene sequences, while the fungal community was characterized using 18S rRNA gene sequences. The 16S rRNA gene libraries were dominated by alphaproteobacterial sequences, while the CPN-60 gene libraries were dominated by members of the Bacteroidetes/Chlorobi group. In both the CPN-60 and 16S rRNA libraries, there were differences in only minor components of the bacterial community between transgenic and unmodified trees, and no significant differences in species diversity were observed. Compared to the bacterial gene libraries, greater coverage of the underlying population was achieved with the fungal 18S rRNA libraries. Members of the Zygomycota, Chytridiomycota, Ascomycota, and Basidiomycota were recovered from both libraries. The dominant groups of fungi associated with each tree type were very similar, although there were some qualitative differences in the recovery of less-abundant fungi, likely as a result of the underlying heterogeneity of the fungal population. The methods employed revealed only minor differences between the bacterial and fungal communities associated with transgenic and unmodified trees.

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