scholarly journals Comparison of PCR Primers for Analyzing Denitrifying Microorganisms in the Hyporheic Zone

2020 ◽  
Vol 10 (12) ◽  
pp. 4172 ◽  
Author(s):  
Heejung Kim
Keyword(s):  
Hyporheic Zone ◽  
Stream Water ◽  
Pcr Primers ◽  
Polymerase Chain Reaction Primer ◽  
Aqueous Environments ◽  
Specific Amplification ◽  
Specific Band ◽  
Primer Sets ◽  
Denitrifying Microorganisms ◽  
Pcr Primer

In this study, the specific amplifications of six denitrification-associated genes using PCR(Polymerase Chain Reaction) primer sets were compared. Thereafter, the PCR primer sets that were determined to be suitable for each denitrification-associated gene were used to test samples from sixteen aqueous environments (three from groundwater, three from stream water, and ten from hyporheic zone water). The specific amplification was determined using PCR primer sets for denitrification-associated genes and nucleic acids from eleven types of strains. NosZ was the most frequently amplified gene from the nucleic acid of type, with a specific band seen in all eleven strains. The specific band amplification and PCR time of the strains were analyzed to select one PCR primer set for each gene. The selected PCR primer sets were used to analyze sixteen samples from the aqueous environments in which denitrifying microorganisms were expected to be present. Specific bands of narG, nirS, and nosZ were most frequently observed in the hyporheic water samples. The results showed that microorganisms containing nirG (involved in the reduction of nitrate to nitrite), nirS (involved in the reduction of nitrite to nitric oxide), and nosZ (involved in the reduction of nitrous oxide to nitrogen gas) were the most abundant in the hyporheic zone samples used in this study.

Development of a PCR-based allele-specific assay from an RFLP probe linked to resistance to cereal cyst nematode in wheat

Genome ◽  
1996 ◽  
Vol 39 (4) ◽  
pp. 798-801 ◽  
Author(s):  
Kevin J. Williams ◽  
John M. Fisher ◽  
Peter Langridge
Keyword(s):  
Wheat Chromosome ◽  
Pcr Primers ◽  
Cyst Nematode ◽  
Cereal Cyst Nematode ◽  
Wheat Line ◽  
Allele Specific ◽  
Specific Amplification ◽  
Rflp Probe ◽  
Primer Sets ◽  
Wheat Lines

The RFLP locus Xglk605 identified by the probe Tag605 maps to a proximal position on the long arm of wheat chromosome 2B about 7 cM away from a gene conditioning resistance to cereal cyst nematode in the wheat line AUS10894. The clone Tag605 was partially sequenced and the PCR primer set AWP1 was designed. The 292-bp product, which showed no polymorphism between varieties, was cloned and sequenced. A single base difference was found in the sequence of the AWP1 products amplified and cloned from the wheat lines AUS10894 and 'Spear'. PCR primers were designed with 3′ termini that corresponded to the two alleles. A dual-PCR system was developed in which the primer sets AWP2 and AWP3 produced allele-specific amplification. The concentration of the oligonucleotide primers and the sequence of the primer–template mismatches were critical to the success of discriminatory allele amplification. Key words : Triticum aestivum, STS, cereal cyst nematode, RFLP.

Effects of riffle–step restoration on hyporheic zone chemistry in N-rich lowland streams

2006 ◽  
Vol 63 (1) ◽  
pp. 120-133 ◽  
Author(s):  
Tamao Kasahara ◽  
Alan R Hill
Keyword(s):  
Urban Areas ◽  
Hyporheic Zone ◽  
Stream Water ◽  
Ion Concentration ◽  
Hyporheic Exchange ◽  
Ecosystem Functions ◽  
Exchange Flow ◽  
Nutrient Inputs ◽  
Lowland Streams ◽  
Hyporheic Zones

Stream restoration projects that aim to rehabilitate ecosystem health have not considered surface–subsurface linkages, although stream water and groundwater interaction has an important role in sustaining stream ecosystem functions. The present study examined the effect of constructed riffles and a step on hyporheic exchange flow and chemistry in restored reaches of several N-rich agricultural and urban streams in southern Ontario. Hydrometric data collected from a network of piezometers and conservative tracer releases indicated that the constructed riffles and steps were effective in inducing hyporheic exchange. However, despite the use of cobbles and boulders in the riffle construction, high stream dissolved oxygen (DO) concentrations were depleted rapidly with depth into the hyporheic zones. Differences between observed and predicted nitrate concentrations based on conservative ion concentration patterns indicated that these hyporheic zones were also nitrate sinks. Zones of low hydraulic conductivity and the occurrence of interstitial fines in the restored cobble-boulder layers suggest that siltation and clogging of the streambed may reduce the downwelling of oxygen- and nitrate-rich stream water. Increases in streambed DO levels and enhancement of habitat for hyporheic fauna that result from riffle–step construction projects may only be temporary in streams that receive increased sediment and nutrient inputs from urban areas and croplands.

Periodic alterations of the hydrological exchange in hyporheic sediments: colmation, hyporheic fauna and abiotic parameters in a second order stream during one year 

2021 ◽  
Author(s):  
Heide Stein ◽  
Hans Jürgen Hahn
Keyword(s):  
Hyporheic Zone ◽  
Stream Water ◽  
Anthropogenic Activities ◽  
Second Order ◽  
Critical Periods ◽  
Order Stream ◽  
Fine Sediments ◽  
Stream Discharge ◽  
One Year ◽  
Hydrological Exchange

<p>In this study, the temporal variability of the hydrological exchange between stream water (SW) and groundwater (GW), colmation, hyporheic invertebrate fauna, organic matter (OM) and physicochemical parameters were examined for the period of one year. Sampling and measuring were conducted monthly from May 2019 to April 2020 at the Guldenbach river, a second order stream in Rhineland-Palatinate, Germany. All hyporheic samples were extracted from a depth of 15 cm below stream bottom. Colmation was measured quantitatively in the same depth.</p><p>Following the biotic and abiotic patterns found, three temporal stages of different hydrological conditions can be described:</p><ul><li>1) Strong floods, in February and March 2020 caused hydromorphological alterations of the river bed, leading to a decolmation of the hyporheic zone, a wash out of OM and hyporheic fauna. Due to high GW tables the vertical hydrological gradient (VHG) was positive indicating upwelling GW.</li> <li>2) In the months of Mai to August 2019 and April 2020, precipitation and stream discharge were lowest. Predominantly exfiltrating conditions were observed, while the amount of fine sediments (clay and silt) increased as well as colmation. High densities of hyporheic fauna, dominated by fine sediment dwelling taxa, were assessed.</li> <li>3) From September 2019 to January 2020 stream discharge was low. The VHG became increasingly negative, indicating downwelling SW. In accordance, colmation increased continuously, while densities of hyporheic invertebrates decreased and sediment dwellers became more dominant.</li> </ul><p>Precipitation, discharge events and GW table were found to be the driving factors for the annual dynamics of the hydrological exchange as well as for colmation, fauna and hydrochemistry. Electric conductivity seems a suitable indicator for the origin of water with high values in months of low precipitation and lower values after extensive precipitation events, respectively. Hyporheic fauna displayed a significant seasonality and the community structure was correlated with colmation and changes in the VHG.</p><p>This pronounced seasonality seems to be typical of many streams and should be considered for the monitoring of sediments and hyporheic habitats: Seasons with lower stream discharge are probably the most critical periods for sediment conditions.</p><p>We assume that the basic patterns of the dynamics observed basically reflect the natural situation in the catchment. However, the strength of surface run-off and the amount of fine sediments are mainly the result of anthropogenic activities and land use in the catchment.</p><p>These findings underline the significance of dynamical processes for the assessment and implementation of the Water Framework Directive.</p>

scholarly journals Assessment of Hydrologic Transient Storage of Three Streams

2003 ◽  
Vol 27 ◽  
pp. 79-80
Author(s):  
Michael Gooseff
Keyword(s):  
Porous Media ◽  
Hyporheic Zone ◽  
Stream Water ◽  
Stream Sediments ◽  
Hyporheic Exchange ◽  
Ecosystem Functions ◽  
Main Stream ◽  
Stream Channel ◽  
Ample Opportunity ◽  
Biogeochemical Transformations

Stream sediments are important locations of biogeochemical transformations upon which many stream ecosystem functions depend. Stream water is often exchanged between the stream channel and surrounding subsurface locations - this process is known as hyporheic exchange. While stream water is moving through the hyporheic zone, solutes and nutrients may undergo important chemical reactions that are not possible in the main stream channel. Further, because the hyporheic zone is composed of porous media (sand, sediment, alluvium, etc.), flow inherently slows down and the exchanging water has ample opportunity to interact with mineral grain surfaces and biofilms.

scholarly journals New PCR Primer Pairs Specific for Cryptococcus neoformans Serotype A or B Prepared on the Basis of Random Amplified Polymorphic DNA Fingerprint Pattern Analyses

1999 ◽  
Vol 37 (2) ◽  
pp. 315-320 ◽  
Author(s):  
Francisco Hideo Aoki ◽  
Tamae Imai ◽  
Reiko Tanaka ◽  
Yuzuru Mikami ◽  
Hideaki Taguchi ◽  
...  
Keyword(s):  
Cryptococcus Neoformans ◽  
Dna Sequences ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Primers ◽  
Dna Fingerprint ◽  
Serotype A ◽  
Specific Pcr ◽  
Fingerprint Pattern ◽  
Serotype B ◽  
Pcr Primer

Thirty-three strains of Cryptococcus neoformans were isolated from clinical specimens, including specimens from AIDS patients in Brazil, and were classified into two serotypes; we detected 31 and 2 strains of serotypes A and B, respectively. Random amplified polymorphic DNA (RAPD) fingerprint pattern analyses of these strains of serotypes A and B showed that the patterns were similar for strains of each serotype when three 10-mer primers were used as the RAPD primers. Comparative studies of the fingerprint patterns of the study isolates with those of the reference strains also showed that the RAPD patterns for strains of each serotype were related and that most of the fingerprint bands existed commonly for all strains of each serotype tested. The common RAPD bands (an approximately 700-bp band for serotype A and an approximately 450-bp band for serotype B) were extracted and the DNA sequences were determined. Using this information, we prepared two and one PCR primer pairs which were expected to be specific for C. neoformans serotypes A and B, respectively. Use of each PCR primer combination thus prepared for serotype A or B was 100% successful in identifying the respectiveC. neoformans serotypes, including the 33 clinical isolates tested in the present study. Among these combinations, one for serotype A was found to amplify DNA from C. neoformans serotype B as well as serotype A. Serotype B-specific PCR primer pairs amplified DNA from not only serotype B strains but also from serotype C strains. The usefulness of other serotype-specific PCR primers for clinical C. neoformans isolates is discussed.

scholarly journals The influence of riparian-hyporheic zone on the hydrological responses in an intermittent stream

2002 ◽  
Vol 6 (3) ◽  
pp. 515-526 ◽  
Author(s):  
A. Butturini ◽  
S. Bernal ◽  
S. Sabater ◽  
F. Sabater
Keyword(s):  
Groundwater Level ◽  
Mediterranean Climate ◽  
Hyporheic Zone ◽  
Stream Water ◽  
Wide Spectrum ◽  
Groundwater Hydrology ◽  
Dry Period ◽  
Intermittent Stream ◽  
Hydrological Responses ◽  
Runoff Variability

Abstract. Stream and riparian groundwater hydrology has been studied in a small intermittent stream draining a forested catchment for a system representative of a Mediterranean climate. The relationship between precipitation and stream runoff and the interactions between stream water and the surrounding riparian groundwater have been analysed under a wide spectrum of meteorological conditions. The hypothesis that the hydrological condition of the near-stream groundwater compartment can regulate the runoff generation during precipitation events was tested. Stream runoff is characterised by a summer dry period, and precipitation input explained only 25% of runoff variability over the study period (r2 =0.25, d.f.=51, p<0.001). The variability of precipitation v. stream runoff is explained partly by the hydrogeological properties of the riparian near-stream zone. This zone is characterised by high hydrological conductivity values and abrupt changes in groundwater level in summer. The summer dry period begins with a rapid decrease in near-stream groundwater level, and ends just after the first autumnal rain when the original groundwater level recovers suddenly. Within this period, storms do not cause major stream runoff since water infiltrates rapidly into the riparian compartment until it is refilled during the subsequent winter and spring; then the precipitation explains the 80% of the stream runoff variability (r2=0.80, d.f.=34, p<0.001). These results suggest that the hydrological interaction between the riparian groundwater compartment and the stream channel is important in elucidating the hydrological responses during drought periods in small Mediterranean streams. Keywords: riparian zone, groundwater hydrology, runoff, intermittent stream, Mediterranean climate

scholarly journals Polymerase chain reaction primer sets for the detection of genetically diverse human sapoviruses

2020 ◽  
Vol 165 (10) ◽  
pp. 2335-2340
Author(s):  
Tomoichiro Oka ◽  
Seiji P. Yamamoto ◽  
Nobuhiro Iritani ◽  
Shigenori Sato ◽  
Chika Tatsumi ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Polymerase Chain Reaction Primer ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Primer Sets

scholarly journals Deep Sequencing of a Dimethylsulfoniopropionate-Degrading Gene (dmdA) by Using PCR Primer Pairs Designed on the Basis of Marine Metagenomic Data

2009 ◽  
Vol 76 (2) ◽  
pp. 609-617 ◽  
Author(s):  
Vanessa A. Varaljay ◽  
Erinn C. Howard ◽  
Shulei Sun ◽  
Mary Ann Moran
Keyword(s):  
Sequence Data ◽  
Gene Clusters ◽  
Amino Acid Identity ◽  
Metagenomic Data ◽  
Data Sets ◽  
Free Living ◽  
Metagenomic Sequence ◽  
Primer Sets ◽  
Design And Testing ◽  
Pcr Primer

ABSTRACT In silico design and testing of environmental primer pairs with metagenomic data are beneficial for capturing a greater proportion of the natural sequence heterogeneity in microbial functional genes, as well as for understanding limitations of existing primer sets that were designed from more restricted sequence data. PCR primer pairs targeting 10 environmental clades and subclades of the dimethylsulfoniopropionate (DMSP) demethylase protein, DmdA, were designed using an iterative bioinformatic approach that took advantage of thousands of dmdA sequences captured in marine metagenomic data sets. Using the bioinformatically optimized primers, dmdA genes were amplified from composite free-living coastal bacterioplankton DNA (from 38 samples over 5 years and two locations) and sequenced using 454 technology. An average of 6,400 amplicons per primer pair represented more than 700 clusters of environmental dmdA sequences across all primers, with clusters defined conservatively at >90% nucleotide sequence identity (∼95% amino acid identity). Degenerate and inosine-based primers did not perform better than specific primer pairs in determining dmdA richness and sometimes captured a lower degree of richness of sequences from the same DNA sample. A comparison of dmdA sequences in free-living versus particle-associated bacteria in southeastern U.S. coastal waters showed that sequence richness in some dmdA subgroups differed significantly between size fractions, though most gene clusters were shared (52 to 91%) and most sequences were affiliated with the shared clusters (∼90%). The availability of metagenomic sequence data has significantly enhanced the design of quantitative PCR primer pairs for this key functional gene, providing robust access to the capabilities and activities of DMSP demethylating bacteria in situ.

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