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.

Genetic diversity of N2-fixing bacteria associated with rice roots by molecular evolutionary analysis of a nifD library

1995 ◽  
Vol 41 (3) ◽  
pp. 235-240 ◽  
Author(s):  
T. Ueda ◽  
Y. Suga ◽  
N. Yahiro ◽  
T. Matsuguchi
Keyword(s):  
Heterotrophic Bacteria ◽  
Root Zone ◽  
Rice Root ◽  
Evolutionary Analysis ◽  
Chain Reaction ◽  
Rice Roots ◽  
Rice Rhizosphere ◽  
Polymerase Chain ◽  
Molecular Evolutionary Analysis ◽  
Diazotrophic Community

The rhizosphere of wetland rice has significant N2-fixing activity. It has been suggested that N2 fixation in the rice root zone is associated with the activity of various N2-fixing heterotrophic bacteria that inhabit the rice rhizosphere. Because of the generic diversity, many different isolation media and conditions are required to count and isolate these bacteria. In an attempt to overcome any bias from culture-dependent methods we amplified nifD segments from crude rice root DNA by the polymerase chain reaction. The nifD fragments were then cloned into a pT7 BlueT-vector to construct a nifD library. Sixteen cloned nifD genes chosen at random from the library were sequenced. A comparison with published sequences indicated the presence of seven novel groups of NifD proteins, which implies the existence of at least seven components in the diazotrophic community of rice roots, dominated mainly by proteobacteria. We also observed genetic variability within the clusters, which suggests the coexistence of many closely related bacterial lineages. However, we did not find Azospirillum-like nifD clones, although many reports indicated the widespread presence of Azospirillum spp. Therefore, it remains to be clarified whether Azospirillum species are the widespread N2-fixing bacteria in rice roots.Key words: N2 fixation, molecular evolution, nifD, rice rhizosphere.

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...

scholarly journals Adaptation Mechanism of Roots to Low and High Nitrogen Revealed by Proteomic Analysis

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Wei Xin ◽  
Lina Zhang ◽  
Jiping Gao ◽  
Wenzhong Zhang ◽  
Jun Yi ◽  
...  
Keyword(s):  
Root Growth ◽  
Nitrogen Use Efficiency ◽  
Root Morphology ◽  
Nitrogen Availability ◽  
Rice Root ◽  
Global Changes ◽  
High Nitrogen ◽  
Nitrogen Use ◽  
Rice Roots ◽  
Use Efficiency

Abstract Background Nitrogen-based nutrients are the main factors affecting rice growth and development. Root systems play an important role in helping plants to obtain nutrients from the soil. Root morphology and physiology are often closely related to above-ground plant organs performance. Therefore, it is important to understand the regulatory effects of nitrogen (N) on rice root growth to improve nitrogen use efficiency. Results In this study, changes in the rice root traits under low N (13.33 ppm), normal N (40 ppm) and high N (120 ppm) conditions were performed through root morphology analysis. These results show that, compared with normal N conditions, root growth is promoted under low N conditions, and inhibited under high N conditions. To understand the molecular mechanism underlying the rice root response to low and high N conditions, comparative proteomics analysis was performed using a tandem mass tag (TMT)-based approach, and differentially abundant proteins (DAPs) were further characterized. Compared with normal N conditions, a total of 291 and 211 DAPs were identified under low and high N conditions, respectively. The abundance of proteins involved in cell differentiation, cell wall modification, phenylpropanoid biosynthesis, and protein synthesis was differentially altered, which was an important reason for changes in root morphology. Furthermore, although both low and high N can cause nitrogen stress, rice roots revealed obvious differences in adaptation to low and high N. Conclusions These results provide insights into global changes in the response of rice roots to nitrogen availability and may facilitate the development of rice cultivars with high nitrogen use efficiency through root-based genetic improvements.

Isolation and identification of N2-fixing Pseudomonas associated with wetland rice

1983 ◽  
Vol 29 (8) ◽  
pp. 867-873 ◽  
Author(s):  
W. L. Barraquio ◽  
J. K. Ladha ◽  
I. Watanabe
Keyword(s):  
New Species ◽  
Yeast Extract ◽  
Heterotrophic Bacteria ◽  
Fluorescent Antibody ◽  
Wetland Rice ◽  
Isolation And Identification ◽  
Biochemical Characteristics ◽  
Yeast Extract Medium ◽  
Extract Medium ◽  
A New Species

Semisolid yeast extract medium amended with glucose and tryptic soy agar were used to isolate aerobically N2-fixing (C2H2-reducing) heterotrophic bacteria from the root of wetland rice. The isolates were identified as Pseudomonas by gel immunodiffusion and fluorescent antibody techniques in combination with their morphological, cultural, and biochemical characteristics. The N2-fixing H2-utilizing Pseudomonas described in this paper is a new species.

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 An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Root Growth Regulation Mechanisms in Response to Nitrogen Availability

2019 ◽  
Vol 20 (23) ◽  
pp. 5893 ◽  
Author(s):  
Wei Xin ◽  
Lina Zhang ◽  
Wenzhong Zhang ◽  
Jiping Gao ◽  
Jun Yi ◽  
...  
Keyword(s):  
Root Growth ◽  
Differentially Expressed Genes ◽  
Nitrogen Availability ◽  
Rice Root ◽  
Integrated Analysis ◽  
High Nitrogen ◽  
Rice Roots ◽  
Regulation Mechanisms ◽  
Low Nitrogen ◽  
Nitrogen Conditions

Nitrogen is an essential nutrient for plant growth and basic metabolic processes. Root systems play an important role in the ability of plants to obtain nutrients from the soil, and are closely related to the growth and development of above-ground plants. Root morphology analysis showed that root growth was induced under low-nitrogen conditions and inhibited under high-nitrogen conditions. To better understand the molecular mechanisms and metabolic basis underlying the rice root response to nitrogen availability, an integrated analysis of the rice root transcriptome and metabolome under three environmental conditions (low-, control, and high-nitrogen conditions) was conducted. A total of 262 and 262 differentially level metabolites were identified under low- and high-nitrogen conditions, respectively. A total of 696 and 808 differentially expressed genes were identified under low- and high-nitrogen conditions, respectively. For both the differentially expressed genes and metabolites, KEGG pathway analysis indicated that amino acid metabolism, carbon and nitrogen metabolism, phenylpropanoid metabolism, and phytohormones’ signal transduction were significantly affected by nitrogen availability. Additionally, variable levels of 65 transcription factors (TFs) were identified in rice leaves exposed to high and low nitrogen, covering 22 TF families. These results also indicate that there is a significant difference in the transcriptional regulation mechanisms of rice roots between low and high nitrogen. In summary, our study provides new information for a further understanding of the response of rice roots to low-nitrogen and high-nitrogen conditions.

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

scholarly journals Converting the NiFeS Carbon Monoxide Dehydrogenase to a Hydrogenase and a Hydroxylamine Reductase

2002 ◽  
Vol 184 (21) ◽  
pp. 5894-5897 ◽  
Author(s):  
Jongyun Heo ◽  
Marcus T. Wolfe ◽  
Christopher R. Staples ◽  
Paul W. Ludden
Keyword(s):  
Carbon Monoxide ◽  
Amino Acid ◽  
Active Site ◽  
Reductase Activity ◽  
Carbon Monoxide Dehydrogenase ◽  
Hydrogenase Activity ◽  
Uptake Hydrogenase ◽  
Site Cluster ◽  
Metal Ligand

ABSTRACT Substitution of one amino acid for another at the active site of an enzyme usually diminishes or eliminates the activity of the enzyme. In some cases, however, the specificity of the enzyme is changed. In this study, we report that the changing of a metal ligand at the active site of the NiFeS-containing carbon monoxide dehydrogenase (CODH) converts the enzyme to a hydrogenase or a hydroxylamine reductase. CODH with alanine substituted for Cys531 exhibits substantial uptake hydrogenase activity, and this activity is enhanced by treatment with CO. CODH with valine substituted for His265 exhibits hydroxylamine reductase activity. Both Cys531 and His265 are ligands to the active-site cluster of CODH. Further, CODH with Fe substituted for Ni at the active site acquires hydroxylamine reductase activity.

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.

Use of 13C Isotope Discrimination Analysis to Quantify Distribution of Barnyardgrass and Rice Roots in a Four-Year Study of Weed-Suppressive Rice

Weed Science ◽  
2012 ◽  
Vol 60 (1) ◽  
pp. 133-142 ◽  
Author(s):  
David R. Gealy ◽  
Karen A. K. Moldenhauer
Keyword(s):  
Yield Loss ◽  
Rice Yield ◽  
Weed Suppression ◽  
Rice Root ◽  
Japonica Rice ◽  
Root Mass ◽  
Rice Cultivars ◽  
Tropical Japonica ◽  
Rice Roots ◽  
13C Isotope

In a 4-yr field study, “weed suppressive” rice cultivars provided 30% greater control of barnyardgrass and sustained 44% less yield loss (relative to weed-free) compared to “nonsuppressive” tropical japonica rice cultivars. 13C analysis revealed that rice root mass predominated vertically and laterally within the soil profile of plots infested with barnyardgrass. Among all cultivars, rice roots accounted for 75 to 90% of the total root mass in samples, and this was most concentrated in the surface 5 cm of soil in the row. Barnyardgrass roots were most prevalent in the surface 5 cm between rows where they accounted for 30% of total root mass. Overall, barnyardgrass root mass was about twice as high in nonsuppressive rice compared to suppressive rice. Weed suppression by indica/tropical japonica rice crosses generally was intermediate between that of the other two rice groups. At the 0- to 5-cm depth, between-rows, barnyardgrass root mass was correlated negatively with rice height (r = −0.424), yield (r = −0.306), and weed control ratings (r = −0.524) in weedy plots. Control ratings in weedy plots also were negatively correlated with rice percent height reduction (r = −0.415) and % yield loss (r = −0.747) relative to weed-free plots, and with barnyardgrass root mass as a percent of total root mass (r = −0.612). Control ratings were positively correlated with rice yield under weed pressure (r = 0.429) but were correlated with rice root mass in-rows only (r = −0.322). Clearly, rice root mass could not have been the major cause of the differences in barnyardgrass control between cultivars.

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