scholarly journals Safe-Site Effects on Rhizosphere Bacterial Communities in a High-Altitude Alpine Environment

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Sonia Ciccazzo ◽  
Alfonso Esposito ◽  
Eleonora Rolli ◽  
Stefan Zerbe ◽  
Daniele Daffonchio ◽  
...  
Keyword(s):  
High Altitude ◽  
Developmental Stage ◽  
Bacterial Communities ◽  
Developmental Stages ◽  
Gene Diversity ◽  
Intergenic Spacer ◽  
Intermediate Stage ◽  
Plant Colonization ◽  
Early Developmental Stage ◽  
Rrna Gene

The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites) which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS) site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P<0.05) on 16S rRNA gene diversity revealed significant differences (P<0.05) between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

scholarly journals Energetic constraints on an early developmental stage: a comparative view

2007 ◽  
Vol 4 (1) ◽  
pp. 123-126 ◽  
Author(s):  
James F Gillooly ◽  
Gustavo A Londoño ◽  
Andrew P Allen
Keyword(s):  
Metabolic Rate ◽  
Developmental Stage ◽  
Developmental Stages ◽  
The Body ◽  
Early Developmental Stage ◽  
Time Required ◽  
Taxonomic Groups ◽  
Relationship Of ◽  
The Relationship ◽  
Early Developmental

Biologists have long sought a means by which to quantify similarities and differences in embryonic development across species. Here we present a quantitative approach for predicting the timing of developmental events based on principles of allometry and biochemical kinetics. Data from diverse oviparous species support model predictions that most variation in the time required to reach one early developmental stage—the time to first heartbeat—is explained by the body size and temperature dependence of metabolic rate. Furthermore, comparisons of this stage with later developmental stages suggest that, after correcting for size and temperature, the relationship of metabolic rate to the rate of embryogenesis is approximately invariant across taxonomic groups and stages of ontogeny.

scholarly journals Automated Approach for Ribosomal Intergenic Spacer Analysis of Microbial Diversity and Its Application to Freshwater Bacterial Communities

1999 ◽  
Vol 65 (10) ◽  
pp. 4630-4636 ◽  
Author(s):  
Madeline M. Fisher ◽  
Eric W. Triplett
Keyword(s):  
Microbial Diversity ◽  
Bacterial Communities ◽  
Limit Of Detection ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Rrna Gene ◽  
Cycle Number ◽  
Intergenic Spacer Region ◽  
Automated Method ◽  
Ribosomal Intergenic Spacer

ABSTRACT An automated method of ribosomal intergenic spacer analysis (ARISA) was developed for the rapid estimation of microbial diversity and community composition in freshwater environments. Following isolation of total community DNA, PCR amplification of the 16S-23S intergenic spacer region in the rRNA operon was performed with a fluorescence-labeled forward primer. ARISA-PCR fragments ranging in size from 400 to 1,200 bp were next discriminated and measured by using an automated electrophoresis system. Database information on the 16S-23S intergenic spacer was also examined, to understand the potential biases in diversity estimates provided by ARISA. In the analysis of three natural freshwater bacterial communities, ARISA was rapid and sensitive and provided highly reproducible community-specific profiles at all levels of replication tested. The ARISA profiles of the freshwater communities were quantitatively compared in terms of both their relative diversity and similarity level. The three communities had distinctly different profiles but were similar in their total number of fragments (range, 34 to 41). In addition, the pattern of major amplification products in representative profiles was not significantly altered when the PCR cycle number was reduced from 30 to 15, but the number of minor products (near the limit of detection) was sensitive to changes in cycling parameters. Overall, the results suggest that ARISA is a rapid and effective community analysis technique that can be used in conjunction with more accurate but labor-intensive methods (e.g., 16S rRNA gene cloning and sequencing) when fine-scale spatial and temporal resolution is needed.

scholarly journals Benthic Bacterial Diversity in Submerged Sinkhole Ecosystems

2009 ◽  
Vol 76 (1) ◽  
pp. 347-351 ◽  
Author(s):  
Stephen C. Nold ◽  
Joseph B. Pangborn ◽  
Heidi A. Zajack ◽  
Scott T. Kendall ◽  
Richard R. Rediske ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Physicochemical Characterization ◽  
Intergenic Spacer ◽  
16S Rrna Gene Sequencing ◽  
Sediment Surface ◽  
Rrna Gene ◽  
Cyanobacterial Mats ◽  
Ribosomal Intergenic Spacer ◽  
Community Profiling ◽  
Rrna Gene Sequencing

ABSTRACT Physicochemical characterization, automated ribosomal intergenic spacer analysis (ARISA) community profiling, and 16S rRNA gene sequencing approaches were used to study bacterial communities inhabiting submerged Lake Huron sinkholes inundated with hypoxic, sulfate-rich groundwater. Photosynthetic cyanobacterial mats on the sediment surface were dominated by Phormidium autumnale, while deeper, organically rich sediments contained diverse and active bacterial communities.

scholarly journals Anaerobic Carbon Monoxide Uptake by Microbial Communities in Volcanic Deposits at Different Stages of Successional Development on O-yama Volcano, Miyake-jima, Japan

2020 ◽  
Vol 9 (1) ◽  
pp. 12
Author(s):  
Amber N. DePoy ◽  
Gary M. King ◽  
Hiroyuki Ohta
Keyword(s):  
Carbon Monoxide ◽  
Microbial Communities ◽  
Developmental Stages ◽  
Plant Colonization ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Microbial Succession ◽  
Wide Range ◽  
Volcanic Deposits ◽  
Successional Development

Research on Kilauea and O-yama Volcanoes has shown that microbial communities and their activities undergo major shifts in response to plant colonization and that molybdenum-dependent CO oxidizers (Mo-COX) and their activities vary with vegetation and deposit age. Results reported here reveal that anaerobic CO oxidation attributed to nickel-dependent CO oxidizers (Ni-COX) also occurs in volcanic deposits that encompass different developmental stages. Ni-COX at three distinct sites responded rapidly to anoxia and oxidized CO from initial concentrations of about 10 ppm to sub-atmospheric levels. CO was also actively consumed at initial 25% concentrations and 25 °C, and during incubations at 60 °C; however, uptake under the latter conditions was largely confined to an 800-year-old forested site. Analyses of microbial communities based on 16S rRNA gene sequences in treatments with and without 25% CO incubated at 25 °C or 60 °C revealed distinct responses to temperature and CO among the sites and evidence for enrichment of known and potentially novel Ni-COX. The results collectively show that CO uptake by volcanic deposits occurs under a wide range of conditions; that CO oxidizers in volcanic deposits may be more diverse than previously imagined; and that Ni-dependent CO oxidizers might play previously unsuspected roles in microbial succession.

scholarly journals Dietary and developmental shifts in butterfly-associated bacterial communities

2018 ◽  
Vol 5 (5) ◽  
pp. 171559 ◽  
Author(s):  
Kruttika Phalnikar ◽  
Krushnamegh Kunte ◽  
Deepa Agashe
Keyword(s):  
Bacterial Communities ◽  
Developmental Stages ◽  
Bacterial Community Composition ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Butterfly Species ◽  
Active Selection ◽  
Key Factor ◽  
Taxonomic Groups ◽  
The Impact

Bacterial communities associated with insects can substantially influence host ecology, evolution and behaviour. Host diet is a key factor that shapes bacterial communities, but the impact of dietary transitions across insect development is poorly understood. We analysed bacterial communities of 12 butterfly species across different developmental stages, using amplicon sequencing of the 16S rRNA gene. Butterfly larvae typically consume leaves of a single host plant, whereas adults are more generalist nectar feeders. Thus, we expected bacterial communities to vary substantially across butterfly development. Surprisingly, only few species showed significant dietary and developmental transitions in bacterial communities, suggesting weak impacts of dietary transitions across butterfly development. On the other hand, bacterial communities were strongly influenced by butterfly species and family identity, potentially due to dietary and physiological variation across the host phylogeny. Larvae of most butterfly species largely mirrored bacterial community composition of their diets, suggesting passive acquisition rather than active selection. Overall, our results suggest that although butterflies harbour distinct microbiomes across taxonomic groups and dietary guilds, the dramatic dietary shifts that occur during development do not impose strong selection to maintain distinct bacterial communities across all butterfly hosts.

Characteristics of calcium sparks in cardiomyocytes derived from embryonic stem cells

2001 ◽  
Vol 281 (1) ◽  
pp. H411-H421 ◽  
Author(s):  
Heinrich Sauer ◽  
Tobias Theben ◽  
Jürgen Hescheler ◽  
Michael Lindner ◽  
Mathias C. Brandt ◽  
...  
Keyword(s):  
Developmental Stage ◽  
Developmental Stages ◽  
Es Cells ◽  
Embryonic Stem ◽  
Early Developmental Stage ◽  
Es Cell ◽  
Intracellular Ca ◽  
Late Developmental Stage ◽  
Cardiac Precursor Cells ◽  
Early Developmental

In embryonic stem (ES) cell-derived cardiomyocytes, spontaneous Ca2+ sparks representing Ca2+ release through ryanodine receptor (RyR) channels were characterized and correlated to the expression of RyRs as well as the Ca2+ load of the sarcoplasmic reticulum (SR). In very early developmental stage (VEDS) cardiac precursor cells, global intracellular Ca2+ concentration ([Ca2+]i) fluctuations occurred, whereas Ca2+ sparks and contractions were absent. In early developmental stages (EDS), contractions as well as Ca2+sparks were obvious. During the further differentiation to late developmental stage (LDS) cardiomyocytes, a marked increase in the frequency of global [Ca2+]i transients, the amplitude and the frequency of Ca2+ sparks, as well as the expression of RyRs and the volume of RyR-positive SR, was observed. Furthermore, the caffeine-releasable SR Ca2+ load was elevated in LDS compared with EDS cardiomyocytes. A high-Ca2+ solution raised spark frequency as well as amplitude in EDS cardiomyocytes to the levels of LDS cardiomyocytes. The characteristics of Ca2+ sparks occurring in cardiomyocytes differentiated from ES cells may be governed by the Ca2+ load of the SR and/or the density of RyRs.

scholarly journals 16S rRNA Gene Diversity in the Salt Crust of Salar de Uyuni, Bolivia, the World’s Largest Salt Flat

2020 ◽  
Vol 9 (21) ◽  
Author(s):  
Wolf T. Pecher ◽  
Fabiana L. Martínez ◽  
Priya DasSarma ◽  
Daniel Guzmán ◽  
Shiladitya DasSarma
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Altitude ◽  
Gene Diversity ◽  
Halophilic Bacteria ◽  
Rrna Gene ◽  
Near Surface ◽  
Geochemical Properties ◽  
Salt Flat ◽  
Salt Crust

ABSTRACT Salar de Uyuni is a vast, high-altitude salt flat in Bolivia with extreme physico-geochemical properties approaching multiple limits of life. Evidence for diverse halophilic bacteria and archaea was found in its surface and near-surface salt crust using 16S amplicon analysis, providing a snapshot of prokaryotic life.

scholarly journals The capacity of wastewater treatment plants drives bacterial community structure and its assembly

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Young Kyung Kim ◽  
Keunje Yoo ◽  
Min Sung Kim ◽  
Il Han ◽  
Minjoo Lee ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Community Structure ◽  
Bacterial Community ◽  
Activated Sludge ◽  
Community Assembly ◽  
Bacterial Communities ◽  
Wastewater Treatment Plants ◽  
High Capacity ◽  
Operating Conditions ◽  
Rrna Gene

Abstract Bacterial communities in wastewater treatment plants (WWTPs) affect plant functionality through their role in the removal of pollutants from wastewater. Bacterial communities vary extensively based on plant operating conditions and influent characteristics. The capacity of WWTPs can also affect the bacterial community via variations in the organic or nutrient composition of the influent. Despite the importance considering capacity, the characteristics that control bacterial community assembly are largely unknown. In this study, we discovered that bacterial communities in WWTPs in Korea and Vietnam, which differ remarkably in capacity, exhibit unique structures and interactions that are governed mainly by the capacity of WWTPs. Bacterial communities were analysed using 16S rRNA gene sequencing and exhibited clear differences between the two regions, with these differences being most pronounced in activated sludge. We found that capacity contributed the most to bacterial interactions and community structure, whereas other factors had less impact. Co-occurrence network analysis showed that microorganisms from high-capacity WWTPs are more interrelated than those from low-capacity WWTPs, which corresponds to the tighter clustering of bacterial communities in Korea. These results will contribute to the understanding of bacterial community assembly in activated sludge processing.

scholarly journals A Grain-Based SARA Challenge Affects the Composition of Epimural and Mucosa-Associated Bacterial Communities throughout the Digestive Tract of Dairy Cows

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1658
Author(s):  
Jan C. Plaizier ◽  
Anne-Mette Danscher ◽  
Paula A. Azevedo ◽  
Hooman Derakhshani ◽  
Pia H. Andersen ◽  
...  
Keyword(s):  
Digestive Tract ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Dry Matter ◽  
Control Diet ◽  
Rrna Gene ◽  
Ruminal Acidosis ◽  
Clustering Patterns ◽  
The 16S Rrna Gene ◽  
Distal Jejunum

The effects of a subacute ruminal acidosis (SARA) challenge on the composition of epimural and mucosa-associated bacterial communities throughout the digestive tract were determined in eight non-lactating Holstein cows. Treatments included feeding a control diet containing 19.6% dry matter (DM) starch and a SARA-challenge diet containing 33.3% DM starch for two days after a 4-day grain step-up. Subsequently, epithelial samples from the rumen and mucosa samples from the duodenum, proximal, middle and distal jejunum, ileum, cecum and colon were collected. Extracted DNA from these samples were analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Distinct clustering patterns for each diet existed for all sites. The SARA challenge decreased microbial diversity at all sites, with the exception of the middle jejunum. The SARA challenge also affected the relative abundances of several major phyla and genera at all sites but the magnitude of these effects differed among sites. In the rumen and colon, the largest effects were an increase in the relative abundance of Firmicutes and a reduction of Bacteroidetes. In the small intestine, the largest effect was an increase in the relative abundance of Actinobacteria. The grain-based SARA challenge conducted in this study did not only affect the composition and cause dysbiosis of epimural microbiota in the rumen, it also affected the mucosa-associated microbiota in the intestines. To assess the extent of this dysbiosis, its effects on the functionality of these microbiota must be determined in future.

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