Quantitative assessment of the bacterial rhizosphere flora of Pinus contorta var. latifolia

1975 ◽  
Vol 21 (12) ◽  
pp. 2034-2038 ◽  
Author(s):  
J. A. Dangerfield ◽  
D. W. S. Westlake ◽  
F. D. Cook
Keyword(s):  
Pinus Contorta ◽  
Quantitative Assessment ◽  
Rhizosphere Soil ◽  
Bacterial Flora ◽  
Root Systems ◽  
Control Soil ◽  
Root Radius ◽  
Area Basis ◽  
Soil Rhizosphere ◽  
Surface Area Basis

The bacterial flora associated with root systems of young and mature lodgepole pine was investigated by sampling forest-grown trees. Counts were performed and expressed on a surface-area basis to give a more realistic comparison of organism density or activity within the control soil, rhizosphere soil, and rhizoplane. On this basis, densities increased by an order of 104- to 106-fold from control soil to rhizoplane, with the degree of stimulation being inversely related to root radius.

Characterization of the bacterial flora associated with root systems of Pinus contorta var. latifolia

1978 ◽  
Vol 24 (12) ◽  
pp. 1520-1525 ◽  
Author(s):  
J. A. Dangerfield ◽  
D. W. S. Westlake ◽  
F. D. Cook
Keyword(s):  
Amino Acid ◽  
Pinus Contorta ◽  
Bacterial Flora ◽  
Root Systems ◽  
Growth Media ◽  
Agricultural Crops ◽  
Control Soil ◽  
Mature Tree ◽  
And Control

Root systems of young and mature lodgepole pine (Pinus contorta Dougl. var. latifolia Englem.) were removed from forest stands and the associated aerobic bacterial flora isolated. Characterization of rhizoplane and control soil isolates from these tree root systems demonstrated differences from that reported for agricultural crops. Ammonifying, proteolytic, and amylolytic organisms were proportionately reduced within the rhizoplane. The rhizoplane organisms grew more slowly than the control soil isolates, although they responded in greater numbers to the addition of an amino acid supplement to the growth media. The rhizoplane organisms also showed an increased ability to solubilize phosphate. The chitinolytic organisms were suppressed within the rhizoplane of the mature tree but were stimulated by the young trees. With this exception, the rhizoplane microflora of older and younger trees were similar.

Divergent response of heavy metal bioavailability in soil rhizosphere to agricultural land use change from paddy field to various drylands

2021 ◽  
Author(s):  
Yujuan Gao ◽  
Jianli Jia ◽  
Beidou Xi ◽  
Dongyu Cui ◽  
Wenbing Tan
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Land Use ◽  
Land Use Change ◽  
Agricultural Land ◽  
Rhizosphere Soil ◽  
Agricultural Land Use ◽  
Metal Bioavailability ◽  
Soil Rhizosphere ◽  
Divergent Response

The heavy metal pollution induced by agricultural land use change has attracted great attention. In this study, the divergent response of bioavailability of heavy metals in rhizosphere soil to different...

The disposition of benzo(a)pyrene in the periphyton communities of two South Carolina streams: uptake and biotransformation

1982 ◽  
Vol 60 (10) ◽  
pp. 2084-2091 ◽  
Author(s):  
Mary G. Bruno ◽  
Timothy E. Fannin ◽  
Gordon J. Leversee
Keyword(s):  
South Carolina ◽  
Slide Surface ◽  
Uptake Rates ◽  
Area Basis ◽  
Autoradiographic Analysis ◽  
Colonization Time ◽  
Microscope Slides ◽  
Surface Area Basis ◽  
Glass Microscope ◽  
Sheath Material

The effect of periphyton community composition and colonization time on the uptake and biotransformation of benzo(a)pyrene (BaP) was determined in laboratory studies. Naturally colonized glass microscope slides were collected after 3 and 6 weeks from Castor Creek, which has a predominantly desmid flora, and after 3 and 5 weeks from diatom-dominated Upper Three Runs Creek. When expressed on a slide surface-area basis, the Castor Creek periphyton showed significantly greater BaP uptake rates at both colonization periods. Within streams, uptake rates increased significantly with colonization time. Autoradiographic analysis suggests that BaP was accumulated by surface sorption, especially to gelatinous sheath material. Active biotransformation as measured by the percentage extractable non-BaP 14C was not detected in either community.

scholarly journals Evaluating the accuracy of variant calling methods using the frequency of parent-offspring genotype mismatch

2021 ◽  
Author(s):  
Russ Jasper ◽  
Tegan Krista McDonald ◽  
Pooja Singh ◽  
Mengmeng Lu ◽  
Clément Rougeux ◽  
...  
Keyword(s):  
Pinus Contorta ◽  
Quantitative Assessment ◽  
Variant Calling ◽  
Error Rates ◽  
Snp Genotyping ◽  
Genotyping Error ◽  
Snp Calling ◽  
Full Sibling ◽  
Model Study ◽  
Offspring Genotype

The use of NGS datasets has increased dramatically over the last decade, however, there have been few systematic analyses quantifying the accuracy of the commonly used variant caller programs. Here we used a familial design consisting of diploid tissue from a single Pinus contorta parent and the maternally derived haploid tissue from 106 full-sibling offspring, where mismatches could only arise due to mutation or bioinformatic error. Given the rarity of mutation, we used the rate of mismatches between parent and offspring genotype calls to infer the SNP genotyping error rates of FreeBayes, HaplotypeCaller, SAMtools, UnifiedGenotyper, and VarScan. With baseline filtering HaplotypeCaller and UnifiedGenotyper yielded one to two orders of magnitude larger numbers of SNPs and error rates, whereas FreeBayes, SAMtools and VarScan yielded lower numbers of SNPs and more modest error rates. To facilitate comparison between variant callers we standardized each SNP set to the same number of SNPs using additional filtering, where UnifiedGenotyper consistently produced the smallest proportion of genotype errors, followed by HaplotypeCaller, VarScan, SAMtools, and FreeBayes. Additionally, we found that error rates were minimized for SNPs called by more than one variant caller. Finally, we evaluated the performance of various commonly used filtering metrics on SNP calling. Our analysis provides a quantitative assessment of the accuracy of five widely used variant calling programs and offers valuable insights into both the choice of variant caller program and the choice of filtering metrics, especially for researchers using non-model study systems.

scholarly journals Digitaria insularis Management and Nematode Dynamics in Off-season Maize

2020 ◽  
Vol 8 (2) ◽  
pp. 729
Author(s):  
Marcos Massuo Kashiwaqui ◽  
Claudia Regina Dias-Arieira ◽  
João Paulo Matias ◽  
André A. Pazinato da Silva ◽  
José Cristimiano dos Santos Neto ◽  
...  
Keyword(s):  
Weed Management ◽  
Management System ◽  
Rhizosphere Soil ◽  
Control Level ◽  
Management Systems ◽  
Acetyl Coa Carboxylase ◽  
Continuous Increase ◽  
Maize Roots ◽  
Excellent Control ◽  
Soil Rhizosphere

Maize stands out as one of the most important crops in succession to soybean in tropic countries. However, the susceptibility of both crops to nematodes, can cause a continuous increase in the nematode population, especially in areas where there is the occurrence of weeds susceptible to the parasites. Thus, the objective was to evaluate the nematodes dynamics in a growing area with off-season maize under chemical weed management. The experiment was installed at Tuneiras do Oeste County, Brazil, designed in randomized blocks, with seven treatments and five replications, constituted by sourgrass (Digitaria insularis) management systems with glyphosate associated to herbicides inhibitors of the enzyme acetyl-CoA carboxylase (ACCase) and auxin-mimetic, and complement with glyphosate + atrazine + tembotrione in post-emergence. The effect of treatments on Pratylenchus spp. population was observed in roots and soil rhizosphere soil of D. insularis and in maize roots. Glyphosate application followed by glyphosate + atrazine was inefficient in controlling sourgrass. Management system with glyphosate + clethodim + 2.4-D followed by glyphosate + atrazine + tembotrione reduced the Pratylenchus spp. population in sourgrass, but any management system repeated this effect in maize. Management systems of D. insularis with associations of glyphosate + clethodim; glyphosate + clethodim + 2.4-D and glyphosate + fenoxaprop-p-ethyl, all followed by glyphosate + atrazine + tembotrione, showed excellent control level of sourgrass without affecting plant height, grain and rank numbers and grain yield. It is concluded that the management system using herbicides association controlled sourgrass and may interferer on Pratylenchus spp. population.

scholarly journals Effect of Some Environmental Factors on the Growth of Azospirillum Species Isolated from Saline Soils of Satkhira District, Bangladesh

1970 ◽  
Vol 23 (2) ◽  
pp. 145-148 ◽  
Author(s):  
M Motiur Rahman ◽  
S Mubassara ◽  
Sirajul Hoque ◽  
Zahed UM Khan
Keyword(s):  
Rhizosphere Soil ◽  
Cynodon Dactylon ◽  
Optimal Growth ◽  
Maximum Growth ◽  
Alkaline Condition ◽  
Saline Soils ◽  
Azospirillum Lipoferum ◽  
Nacl Concentration ◽  
Saline Area ◽  
Soil Rhizosphere

Twelve isolates of Azospirillum, recovered and identified from non-rhizosphere soil, rhizosphere soil of Cynodon dactylon and the roots of the same plant, were collected from five different locations of saline area in the district Satkhira, Bangladesh. The isolates were belonged to Azospirillum lipoferum, A. brasilense, A. halopraeferans and A. amazonense. All isolates, except MR-5, preferred neutral to alkaline condition for their optimal growth. Three isolates (MR-3, MR-4 and MR-8) showed maximum growth at 41°C, while the others grew best at temperature between 35° and 37°C. The optimal NaCl concentration for the growth was found to be 3% for 5 isolates (MR-1, MR-3, MR-4, MR-8 and MR-11) and 5% for the rest 7 isolates (MR-5, MR-6, MR-7, MR-13, MR-14, MR-15 and MR-16). All isolates were true halophilic since they did not show grow in absence of salinity, and all of them were also fungicide (Perfeckthion and Indofil M-45) tolerants to some extent. Keywords: Azospirillum, Growth characteristics, Halophilic, Tolerance to fungicideDOI: http://dx.doi.org/10.3329/bjm.v23i2.881 Bangladesh J Microbiol, Volume 23, Number 2, December 2006, pp 145-148

Populations of the spinach wilt pathogen, Fusarium oxysporum f. sp. spinaciae, in the root tissues, rhizosphere, and soil in the field

1979 ◽  
Vol 25 (2) ◽  
pp. 227-229 ◽  
Author(s):  
Andres A. Reyes
Keyword(s):  
Fusarium Oxysporum ◽  
Chinese Cabbage ◽  
Rhizosphere Soil ◽  
Infested Field ◽  
Soil Rhizosphere ◽  
Root Tissues

Populations of Fusarium oxysporum f. sp. spinaciae in root tissues and rhizosphere soil of diseased spinach plants were higher than in the root tissues and rhizosphere soil of healthy plants. Populations in soil rhizosphere were higher than in nonrhizosphere soil. The fungus populations were very low in the root tissues of the nonsusceptible strawberry, broccoli, Chinese cabbage, and mustard grown in the infested field. The populations were low at the beginning of the season, increased, and remained high during the summer, then dropped in the fall. The fungus populations ranged from 1600 to 2600 propagules/g in the top 10 cm of soil, declined sharply between 11 and 20 cm, and were nondetectable between 41 and 60 cm.

scholarly journals Evaluating the accuracy of variant calling methods using the frequency of parent-offspring genotype mismatch

2021 ◽  
Author(s):  
Russ Jasper ◽  
Tegan Krista McDonald ◽  
Pooja Singh ◽  
Menhmeng Lu ◽  
Clément Rougeux ◽  
...  
Keyword(s):  
Pinus Contorta ◽  
Quantitative Assessment ◽  
Variant Calling ◽  
Error Rates ◽  
Snp Genotyping ◽  
Genotyping Error ◽  
Snp Calling ◽  
Full Sibling ◽  
Model Study ◽  
Offspring Genotype

The use of NGS datasets has increased dramatically over the last decade, however, there have been few systematic analyses quantifying the accuracy of the commonly used variant caller programs. Here we used a familial design consisting of diploid tissue from a single Pinus contorta parent and the maternally derived haploid tissue from 106 full-sibling offspring, where mismatches could only arise due to mutation or bioinformatic error. Given the rarity of mutation, we used the rate of mismatches between parent and offspring genotype calls to infer the SNP genotyping error rates of FreeBayes, HaplotypeCaller, SAMtools, UnifiedGenotyper, and VarScan. With baseline filtering HaplotypeCaller and UnifiedGenotyper yielded one to two orders of magnitude larger numbers of SNPs and error rates, whereas FreeBayes, SAMtools and VarScan yielded lower numbers of SNPs and more modest error rates. To facilitate comparison between variant callers we standardized each SNP set to the same number of SNPs using additional filtering, where UnifiedGenotyper consistently produced the smallest proportion of genotype errors, followed by HaplotypeCaller, VarScan, SAMtools, and FreeBayes. Additionally, we found that error rates were minimized for SNPs called by more than one variant caller. Finally, we evaluated the performance of various commonly used filtering metrics on SNP calling. Our analysis provides a quantitative assessment of the accuracy of five widely used variant calling programs and offers valuable insights into both the choice of variant caller program and the choice of filtering metrics, especially for researchers using non-model study systems.

Catalytic Activity and Surface Characterization Study of Pd Supported on Nanocrystalline and Polycrystalline CeO2

1999 ◽  
Vol 581 ◽  
Author(s):  
Gar B. Hoflund ◽  
Zhenhua Li ◽  
Timothy J. Campbell ◽  
William S. Epling ◽  
Horst W. Hahn
Keyword(s):  
Catalytic Activity ◽  
Surface Area ◽  
Photoelectron Spectroscopy ◽  
Surface Characterization ◽  
Surface Concentration ◽  
Slow Step ◽  
Activity Increase ◽  
Area Basis ◽  
Surface Area Basis ◽  
Supported Pd

ABSTRACTThe catalytic activity of polycrystalline and nanocrystalline CeO2-supported Pd (Pd/pCeO2 and Pd/nCeO2) has been determined as a function of temperature and Pd loading. While the untreated nCeO2 support gives 50% methane conversion at 420°C, the untreated pCeO2 support exhibits little activity under the conditions examined due to its low surface area. A Pd loading of 5 wt% increases the activity of pCeO2 to 50% conversion at 260°C, while a 40 wt% Pd loading on nCeO2 exhibits a relatively smaller activity increase, yielding 50% conversion at 240°C. On a mass basis the 40 wt% Pd/nCeO2 catalyst is the most active tested in this study, but it is less active than the 5 wt% Pd/pCeO2 catalyst on a surface-area basis. Furthermore, the activity of the 40 wt% Pd/nCeO2 catalyst does not decrease during 100 hrs of exposure to CH4 and O2 at 250°C.X-ray photoelectron spectroscopy (XPS) and ion scattering spectroscopy (ISS) have been used to characterize the surfaces of both bare supports and Pd-containing catalysts before and after exposure to reactor conditions. The XPS results reveal that the Pd surface concentration is more than an order of magnitude higher for 5 wt% Pd/pCeO2 than for 5 wt% Pd/nCeO2 due to the larger surface area of nCeO2 and that the 40 wt% Pd/nCeO2 catalyst has a lower Pd loading on a surface-area basis than the 5 wt% Pd/pCeO2 catalyst. Most of the supported Pd is in the form of PdO, but higher PdO2/PdO ratios are observed for both CeO2 supports compared to Pd supported on ZrO2 or CO3O4. Furthermore, a significant amount of metallic Pd forms on Pd/nCeO2 but not on Pd/pCeO2 during reaction. The nanocrystalline and polycrystalline CeO2 behave differently chemically which is consistent with the fact that the nanocrystalline catalysts are less active on a surface-area basis. Accumulation of H20 on the Pd/pCeO2 surface during reaction is significant but not on the Pd/nCeO2 surface. This suggests that the rate limiting step may be H2O desorption on Pd/pCeO2 while for Pd on nCeO2 adsorption of methane appears to be the slow step. The ISS data indicate that the outermost atomic layer of Pd/nCeO2 consists mostly of O and C, which is not the case for Pd/pCeO2. Site blockage by these species may also contribute to the lower activity on a surface-area basis of Pd/nCeO2 compared to Pd/pCeO2.

Predominance of hydrogen-utilizing bacteria among N2-fixing bacteria in wetland rice roots

1982 ◽  
Vol 28 (9) ◽  
pp. 1051-1054 ◽  
Author(s):  
I. Watanabe ◽  
W. L. Barraquio ◽  
Maria Luisa Daroy
Keyword(s):  
Rhizosphere Soil ◽  
Heterotrophic Bacteria ◽  
Rice Root ◽  
Wetland Rice ◽  
Hydrogenase Activity ◽  
Wetland Soil ◽  
Uptake Hydrogenase ◽  
Autotrophic Growth ◽  
Rice Roots ◽  
Soil Rhizosphere

Heterotrophic bacteria were isolated from wetland soil, rhizosphere soil, root and basal shoot of wetland rice, dryland soil, and root of dryland rice. The isolates were tested for N2-fixing activity and the ability to grow autotrophically under H2 + CO2 + O2. N2-fixing bacteria capable of autotrophic growth were found almost exclusively from the rhizosphere and the root of wetland rice. In another experiment, all N2-fixing bacteria isolated from wetland rice root had uptake hydrogenase activity. These findings indicate the predominance of hydrogen-utilizing bacteria among N2-fixing bacteria from wetland rice roots.

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