Publications by authors named "Madhu Choudhary"

14 Publications

  • Page 1 of 1

Climate-smart agriculture practices influence weed density and diversity in cereal-based agri-food systems of western Indo-Gangetic plains.

Sci Rep 2021 08 5;11(1):15901. Epub 2021 Aug 5.

ICAR-Central Soil Salinity Research Institute (CSSRI), Karnal, India.

Climate-smart agriculture (CSA)-based management practices are getting popular across South-Asia as an alternative to the conventional system for particular weed suppression, resources conservation and environmental quality. An 8-year study (2012-2013 to 2019-2020) was conducted to understand the shift in weed density and diversity under different CSA-based management practices called scenarios (Sc). These Sc involved: Sc1, conventional tillage (CT)-based rice-wheat system with flood irrigation (farmers' practice); Sc2, CT-rice, zero tillage (ZT)-wheat-mungbean with flood irrigation (partial CA-based); Sc3, ZT rice-wheat-mungbean with flood irrigation (partial CSA-based rice); Sc4, ZT maize-wheat-mungbean with flood irrigation (partial CSA-based maize); Sc5, ZT rice-wheat-mungbean with subsurface drip irrigation (full CSA-based rice); and Sc6, ZT maize-wheat-mungbean with subsurface drip irrigation (full CSA-based maize). The most abundant weed species were P. minor > A. arvensis > M. indicus > C. album and were favored by farmers' practice. However, CSA-based management practices suppressed these species and favored S. nigrum and R. dentatus and the effect of CSAPs was more evident in the long-term. Maximum total weed density was observed for Sc1, while minimum value was recorded under full CSA-based maize systems, where seven weed-species vanished, and P. minor density declined to 0.33 instead of 25.93 plant m after 8-years of continuous cultivation. Full CSA-based maize-wheat system could be a promising alternative for the conveniently managed rice-wheat system in weed suppression in north-west India.
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http://dx.doi.org/10.1038/s41598-021-95445-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8342518PMC
August 2021

Isolation and characterization of salt-tolerant bacteria with plant growth-promoting activities from saline agricultural fields of Haryana, India.

J Genet Eng Biotechnol 2021 Jun 28;19(1):99. Epub 2021 Jun 28.

ICAR-Central Soil Salinity Research Institute (CSSRI), Karnal, 132001, India.

Background: Soil salinity has been one of the biggest hurdles in achieving better crop yield and quality. Plant growth-promoting rhizobacteria (PGPR) are the symbiotic heterogeneous bacteria that play an important role in the recycling of plant nutrients through phytostimulation and phytoremediation. In this study, bacterial isolates were isolated from salt-polluted soil of Jhajjar and Panipat districts of Haryana, India. The potential salt-tolerant bacteria were screened for their PGPR activities such as phosphate solubilization, hydrogen cyanide (HCN), indole acetic acid (IAA) and ammonia production. The molecular characterization of potent isolates with salt tolerance and PGPR activity was done by 16S rDNA sequencing.

Results: Eighteen soil samples from saline soils of Haryana state were screened for salt-tolerant bacteria. The bacterial isolates were analyzed for salt tolerance ranging from 2 to 10%. Thirteen isolates were found salt tolerant at varied salt concentrations. Isolates HB6P2 and HB6J2 showed maximum tolerance to salts at 10% followed by HB4A1, HB4N3 and HB8P1. All the salt-tolerant bacterial isolates showed HCN production with maximum production by HB6J2. Phosphate solubilization was demonstrated by three isolates viz., HB4N3, HB6P2 and HB6J2. IAA production was maximum in HB4A1 (15.89) and HB6P2 (14.01) and least in HB4N3 (8.91). Ammonia production was maximum in HB6P2 (12.3) and least in HB8P1 (6.2). Three isolates HB6J2, HB8P1 and HB4N3 with significant salt tolerance, and PGPR ability were identified through sequencing of amplified 16SrRNA gene and were found to be Bacillus paramycoides, Bacillus amyloliquefaciens and Bacillus pumilus, respectively.

Conclusions: The salt-tolerant plant growth-promoting rhizobacteria (PGPR) isolated from saline soil can be used to overcome the detrimental effects of salt stress on plants, with beneficial effects of physiological functions of plants such as growth and yield, and overcome disease resistance. Therefore, application of microbial inoculants to alleviate stresses and enhance yield in plants could be a low cost and environmental friendly option for the management of saline soil for better crop productivity.
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http://dx.doi.org/10.1186/s43141-021-00186-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8239113PMC
June 2021

Soil enzymes activity: Effect of climate smart agriculture on rhizosphere and bulk soil under cereal based systems of north-west India.

Eur J Soil Biol 2021 Mar-Apr;103:103292

International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India.

In agriculture production system, soil enzymes are important indicators of soil quality. Measurements of soil quality parameter changes are essential for assessing the impact of soil and crop management practices. Keeping this in view, an experiment was conducted to evaluate the enzyme activities namely dehydrogenase (DHA), β-glucosidase, acid and alkaline phosphatase ( & ), fluorescein diacetate hydrolases (FDH), cellulase, urease and aryl sulphatase in rhizosphere and bulk soil after 8 years of different management regimes. Soil organic carbon (SOC), moisture content and few enzyme indices such as enzymatic pH indicator (), alteration index three () and geometric mean () were also measured. The treatments were conventional rice-wheat system (termed as scenario (Sc1), CT system), partial conservation agriculture (CA)-based rice-wheat-mungbean system (Sc2, PCA-RW), partial climate smart agriculture (CSA)-based rice-wheat-mungbean system (Sc3), partial CSA-based maize-wheat-mungbean system (Sc4), full CSA-based rice-wheat-mungbean system (Sc5), and full CSA-based maize-wheat-mungbean system (Sc6). Soil samples were collected from rhizosphere and away from roots (bulk soil) at 0-15 cm soil depth before sowing (from rhizosphere of previous crops), at maximum tillering, flowering, and after harvesting of wheat crop. Results showed that DHA activity was higher before sowing (59.8%), at maximum tillering (48.4%), flowering (8.6%) and after harvesting (19.1%) in rice based CSA systems (mean of Sc3 and Sc5) over maize based CSA systems (mean of Sc4 and Sc6) in rhizospheric soil. On average, β-glucosidase activity was significantly higher in rhizospheric soils of rice based system over maize based CSA system. Before sowing of wheat, significantly higher (21.4%) acid phosphatase activity was observed in rhizosphere over bulk soils of maize based CSA system. Significantly higher alkaline phosphatase activity was observed before sowing of wheat in bulk soils of rice (25.3%) and maize (38.5%) based CSA systems over rhizospheric soils. Rice based CSA systems showed 27% higher FDH activity than maize based systems. Significant interaction effect was observed between the managements and enzymes. SOC played an important role in regulating the enzymes activity both in rhizosphere and bulk soil. Significant variation in , and was observed among the managements. Therefore, CSA managements are beneficial in improving enzyme activities not only in rhizosphere but also in bulk soil where residues are retained thereby may help in improving nutrient cycling.
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http://dx.doi.org/10.1016/j.ejsobi.2021.103292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7977442PMC
March 2021

In situ decomposition of crop residues using lignocellulolytic microbial consortia: a viable alternative to residue burning.

Environ Sci Pollut Res Int 2021 Feb 24. Epub 2021 Feb 24.

ICAR-Indian Institute of Soil Science, Bhopal, 462038, India.

Open field burning of crop residue causes severe air pollution and greenhouse gas emission contributing to global warming. In order to seek an alternative, the current study was initiated to explore the prospective of lignocellulolytic microbes to expedite in situ decomposition of crop residues. Field trials on farmers' field were conducted in the state of Haryana and Maharashtra, to target the burning of rice and wheat residue and sugarcane trash, respectively. A comparative study among crop residue removal (CRR), crop residue burning (CRB) and in situ decomposition of crop residues (IND) revealed that IND of rice and wheat residues took 30 days whereas IND of sugarcane trash took 45 days. The decomposition status was assessed by determining the initial and final lignin to cellulose ratio which increased significantly from 0.23 to 0.25, 0.21 to 0.23 and 0.24 to 0.27 for rice, wheat residues and sugarcane trash, respectively. No yield loss was noticed in IND for both rice-wheat system and sugarcane-based system; rather IND showed relatively better crop yield as well as soil health parameters than CRB and CRR. Furthermore, the environmental impact assessment of residue burning indicated a substantial loss of nutrients (28-31, 23-25 and 51-77 kg ha of N+PO+KO for rice, wheat and sugarcane residue) as well as the emission of pollutants to the atmosphere. However, more field trials, as well as refinement of the technology, are warranted to validate and establish the positive potential of in situ decomposition of crop residue to make it a successful solution against the crop residue burning.
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http://dx.doi.org/10.1007/s11356-021-12611-8DOI Listing
February 2021

Designing profitable, resource use efficient and environmentally sound cereal based systems for the Western Indo-Gangetic plains.

Sci Rep 2020 11 6;10(1):19267. Epub 2020 Nov 6.

ICAR-Central Soil Salinity Research Institute (CSSRI), Karnal, India.

In the western Indo-Gangetic plains, issues of deterioration in soil, water, and environment quality coupled with low profitability jeopardize the sustainability of the dominant rice-wheat (RW) system. To address these issues, crop diversification and conservation agriculture (CA)-based management hold considerable promise but the adoption of both approaches has been low, and additional evidence generation from a multi-criteria productivity and sustainability perspective is likely required to help drive the change. Compared to prevailing farmers' practice (FP), results suggest that CA-based rice management increased profitability by 13% and energy use efficiency (EUE) by 21% while reducing irrigation by 19% and global warming potential (GWP) by 28%. By substituting CA-based maize for rice, similar mean profitability gains were realized (16%) but transformative improvements in irrigation (- 84%), EUE (+ 231%), and GWP (- 95%) were observed compared to FP. Inclusion of mungbean in the rotation (i.e. maize-wheat-mungbean) with CA-based management increased the system productivity, profitability, and EUE by 11, 25 and 103%, respectively while decreasing irrigation water use by 64% and GWP by 106% compared to FP. Despite considerable benefits from the CA-based maize-wheat system, adoption of maize is not widespread due to uneven market demand and assured price guarantees for rice.
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http://dx.doi.org/10.1038/s41598-020-76035-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7648623PMC
November 2020

Topsoil Bacterial Community Changes and Nutrient Dynamics Under Cereal Based Climate-Smart Agri-Food Systems.

Front Microbiol 2020 28;11:1812. Epub 2020 Jul 28.

International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India.

Soil microorganisms play a critical role in soil biogeochemical processes, nutrient cycling, and resilience of agri-food systems and are immensely influenced by agronomic management practices. Understanding soil bacterial community and nutrient dynamics under contrasting management practices is of utmost importance for building climate-smart agri-food systems. Soil samples were collected at 0-15 cm soil depth from six management scenarios in long-term conservation agriculture (CA) and climate-smart agriculture (CSA) practices. These scenarios (Sc) involved; ScI-conventional tillage based rice-wheat rotation, ScII- partial CA based rice-wheat-mungbean, ScIII- partial CSA based rice-wheat-mungbean, ScIV is partial CSA based maize-wheat-mungbean, ScV and ScVI are CSA based scenarios, were similar to ScIII and ScIV respectively, layered with precision water & nutrient management. The sequencing of soil DNA results revealed that across the six scenarios, a total of forty bacterial phyla were observed, with as dominant in all scenarios, followed by and . The relative abundance of was 29% higher in rice-based CSA scenarios (ScIII and ScV) and 16% higher in maize-based CSA scenarios (ScIV and ScVI) compared to conventional-till practice (ScI). The relative abundance of and was respectively 29% and 91% higher in CT than CSA based rice and 27% and 110% higher than maize-based scenarios. Some taxa are present relatively in very low abundance or exclusively in some scenarios, but these might play important roles there. Three phyla are exclusively present in ScI and ScII i.e., , , and . Shannon diversity index was 11% higher in CT compared to CSA scenarios. Maize based CSA scenarios recorded higher diversity indices than rice-based CSA scenarios. Similar to changes in soil bacterial community, the nutrient dynamics among the different scenarios also varied significantly. After nine years of continuous cropping, the soil organic carbon was improved by 111% and 31% in CSA and CA scenarios over the CT scenario. Similarly, the available nitrogen, phosphorus, and potassium were improved by, respectively, 38, 70, and 59% in CSA scenarios compared to the CT scenario. These results indicate that CSA based management has a positive influence on soil resilience in terms of relative abundances of bacterial groups, soil organic carbon & available plant nutrients and hence may play a critical role in the sustainability of the intensive cereal based agri-food systems.
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http://dx.doi.org/10.3389/fmicb.2020.01812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7399647PMC
July 2020

Temporal changes in soil microbial properties and nutrient dynamics under climate smart agriculture practices.

Soil Tillage Res 2020 May;199:104595

ICAR-Central Soil Salinity Research Institute (CSSRI), Karnal, 132001, Haryana, India.

Climate smart agriculture (CSA) practices are emerging as sustainable alternative to conventional rice-wheat system to pull up natural resources degradation across south Asia. After five years of continuous CSA based experiment, a two years study was conducted to evaluate changes in microbial biomasses (microbial biomass carbon and nitrogen), enzyme activities (alkaline phosphatase, dehydrogenase and -glucosidase), nutrient release and uptake (N, P and K) at different wheat crop growth stages. Effect of CSA practices was also studied for carbon mineralization in an incubation experiment. Four scenarios (Sc) were included in this study- conventional tillage (CT) based rice-wheat system (Sc1), partial CSA based rice-wheat-mungbean system (Sc2), full CSA based rice-wheat-mungbean system (Sc3), and full CSA based maize-wheat-mungbean system (Sc4). Soil samples were collected from scenarios at 0-15 and 15-30 cm depth at different growth stages of wheat crop namely sowing, crown root initiation (CRI), active tillering, panicle initiation, and harvesting. Analysis of soil was done for chemical properties . pH, electrical conductivity, available N, P, K, NPK uptake and mineralizable carbon and biological properties ., microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), dehydrogenase activity (DHA), alkaline phosphatase activity (APA) and β-glucosidase. Significantly higher microbial biomass carbon (42 %) and nitrogen (79 %) were found in surface soil (0-15 cm depth) under CSA based scenarios (Sc2, Sc3 and Sc4) at harvest stage of wheat over CT based/ conventional scenario (Sc1). At surface soil, alkaline phosphatase, dehydrogenase and -glucosidase activity was 58, 14 and 13 % higher in CSA based scenarios, respectively than CT based scenario. CSA based scenarios showed significantly higher C mineralization after 3 days of the incubation experiment at harvest. An increase of respectively 15, 48 and 17 % of N, P and K uptake was observed with CSA based scenarios than CT based scenario. At harvest stage, 7 % higher amount of dry matter was reported with full CSA based scenarios (mean of Sc2 to Sc4) compared to Sc1. Higher wheat grain yield of ∼10 % was recorded with CSA based scenarios over CT based scenario. Therefore, CSA based scenarios with improved biological properties and nutrient availability and uptake at different wheat growth stages resulted in higher yields and hence need to be popularized among the farmers.
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http://dx.doi.org/10.1016/j.still.2020.104595DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7074002PMC
May 2020

Re-designing irrigated intensive cereal systems through bundling precision agronomic innovations for transitioning towards agricultural sustainability in North-West India.

Sci Rep 2019 11 29;9(1):17929. Epub 2019 Nov 29.

International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India.

A study was conducted to design productive, profitable, irrigation water¸ nitrogen and energy use efficient intensive cereal systems (rice-wheat; RW and maize-wheat; MW) in North-West India. Bundling of conservation agriculture (CA) with sub-surface drip irrigation termed as CA were compared with CA alone and conventional tillage based and flood irrigated RW rotation (farmer's practice; ScI). In contrast to conventional till RW rotation which consumed 1889 mm ha irrigation water (2-yr mean), CA system saved 58.4 and 95.5% irrigation water in RW and MW rotations, respectively. CA practices saved 45.8 and 22.7% of irrigation water in rice and maize, respectively compared to CA with flood irrigation. On a system basis, CA practices saved 46.7 and 44.7% irrigation water under RW (ScV) and MW (ScVI) systems compared to their respective CA-based systems with flood irrigation (ScIII and ScIV). CA in RW system recorded 11.2% higher crop productivity and improved irrigation water productivity by 145% and profitability by 29.2% compared to farmers' practice. Substitution of rice with maize (MW system; ScVI) recorded 19.7% higher productivity, saved 84.5% of irrigation water and increased net returns by 48.9% compared to farmer's practice. CA RW and MW system improved energy productivity by 75 and 169% and partial factor productivity of N by 44.6 and 49.6%, respectively compared to ScI. The sub-surface drip irrigation system saved the fertilizer N by 20% under CA systems. CA in RW and MW systems recorded ~13 and 5% (2-yr mean) higher profitability with 80% subsidy on installing sub-surface drip irrigation system and similar profitability without subsidy scenario compared with their respective flood irrigated CA-based systems.
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http://dx.doi.org/10.1038/s41598-019-54086-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884493PMC
November 2019

Carbon mineralization in soil as influenced by crop residue type and placement in an of Northwest India.

Carbon Manag 2019 1;10(1):37-50. Epub 2019 Feb 1.

International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India.

Carbon (C) mineralization of crop residues is an important process occurring in soil which is helpful in predicting CO emission to the atmosphere and nutrient availability to plants. A laboratory experiment was conducted in which C mineralization of residues of rice (), wheat (), maize (), mungbean () and their mixtures was applied to the soil surface or incorporated into an Alfisols from Northwest India. C mineralization was significantly affected by residue placement and type and their interactions. Rice residue had a higher decomposition rate (k = 0.121 and 0.076 day) than wheat (0.073 and 0.042 day) and maize residues (0.041 day) irrespective of placements. Higher decomposition rates of rice and wheat were observed when placed on soil surface than incorporated in the soils. Additive effects of the contribution of each residue type to C mineralization of the residue mixture were observed. When mungbean residue was added to the rice/wheat or maize/wheat mixture, decomposition of the residue mixture was enhanced. Crop residues with low N and high C/N ratio such as maize, wheat, rice and their mixtures can be applied on the soil surface for faster C and N mineralization, thereby helping to manage high volumes of residues under conservation agriculture-based practices in northwest India.
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http://dx.doi.org/10.1080/17583004.2018.1544830DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7077384PMC
February 2019

Soil bacterial diversity under conservation agriculture-based cereal systems in Indo-Gangetic Plains.

3 Biotech 2018 Jul 4;8(7):304. Epub 2018 Jul 4.

International Maize and Wheat Improvement Centre (CIMMYT), New Delhi, India.

In Indo-Gangetic plains (IGP) of India, natural resources (soil, water, and environment) are degrading under the conventional-till (CT)-based management practices in rice-wheat cropping system. A long-term field experiment was conducted to understand the soil bacterial diversity and abundance under different sets of management scenarios (Sc). The study comprised of four scenarios, namely, -Sc.I CT-based rice-wheat system (farmers' practice); Sc.II, partial conservation agriculture (CA) based in which rice is under CT-wheat and mungbean under zero-tillage (ZT); Sc.III, full CA-based in which rice-wheat-mungbean are under ZT and Sc.IV, where maize-wheat-mungbean are under ZT. These scenarios varied in cropping system, tillage, and crop residue management practices. Using Illumina MiSeq sequencing technology, the variable regions V3-V4 of 16S rRNA were sequenced and the obtained reads were analyzed to study the diversity patterns in the scenarios. Results showed the presence of 53 bacterial phyla across scenarios. The predominant phyla in all scenarios were , and which accounted for more than 70% of the identified phyla. However, the rice-based systems (Sc.I, Sc.II, and Sc.III) were dominated by phylum however, maize-based system (Sc.IV) was dominated by . The class and of and of were exceptionally higher in Sc.IV. Shannon diversity index was 8.8% higher in Sc.I, 7.5% in Sc.II, and 2.7% in Sc.III compared to Sc.IV. The findings revealed that soil bacterial diversity and abundance are influenced by agricultural management practices as bacterial diversity under full CA-based management systems (Sc.III and Sc.IV) was lower when compared to farmer's practice (Sc.I) and partial CA (Sc.II) scenarios.
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http://dx.doi.org/10.1007/s13205-018-1317-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031527PMC
July 2018

Assessing soil properties and nutrient availability under conservation agriculture practices in a reclaimed sodic soil in cereal-based systems of North-West India.

Arch Acker Pflanzenbau Bodenkd 2018 23;64(4):531-545. Epub 2017 Aug 23.

Sustainable Intensification Programme, International Maize and Wheat Improvement Center (CIMMYT), Kathmandu, Nepal.

Soil quality degradation associated with resources scarcity is the major concern for the sustainability of conventional rice-wheat system in South Asia. Replacement of conventional management practices with conservation agriculture (CA) is required to improve soil quality. A field experiment was conducted to assess the effect of CA on soil physical (bulk density, penetration resistance, infiltration) and chemical (N, P, K, S, micronutrients) properties after 4 years in North-West India. There were four scenarios (Sc) namely conventional rice-wheat cropping system (Sc1); partial CA-based rice-wheat-mungbean system (RWMS) (Sc2); CA-based RWMS (Sc3); and CA-based maize-wheat-mungbean (Sc4) system. Sc2 (1.52 Mg m) showed significantly lower soil bulk density (BD). In Sc3 and Sc4, soil penetration resistance (SPR) was reduced and infiltration was improved compared to Sc1. Soil organic C was significantly higher in Sc4 than Sc1. Available N was 33% and 68% higher at 0-15 cm depth in Sc3 and Sc4, respectively, than Sc1. DTPA extractable Zn and Mn were significantly higher under Sc3 and Sc4 compared to Sc1. Omission study showed 30% saving in N and 50% in K in wheat after four years. Therefore, CA improved soil properties and nutrient availability and have potential to reduce external fertilizer inputs in long run.
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http://dx.doi.org/10.1080/03650340.2017.1359415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6183874PMC
August 2017

Evaluation of Brevibacillus brevis as a potential plant growth promoting rhizobacteria for cotton (Gossypium hirsutum) crop.

Springerplus 2016 30;5(1):948. Epub 2016 Jun 30.

Division of Soil and Crop Management, Central Soil Salinity Research Institute, Karnal, Haryana 132 001 India.

The present investigation was undertaken to isolate, screen and evaluate a selected promising PGPR Brevibacillus brevis on cotton crop. Out of 156 bacterial isolates one of the most promising isolate was analyzed for the various PGP traits. A seed germination analysis was conducted with cotton seeds to evaluate the potential of the isolate to promote plant growth. The bacterial isolate was checked for its growth and survival at high temperatures. The isolate was also analyzed for the PGP traits exhibited after the heat treatment. To identify the isolate morphological, biochemical and molecular characterization was performed. The isolate was found positive for many of the PGP attributes like IAA, ARA, anti-fungal activity and ammonia production. Effect of seed bacterization on various plant growth parameters was used as an indicator. The isolate showed significant growth and exhibited various PGP traits at high temperature making it suitable as an inoculant for cotton crop. Isolate was identified as Brevibacillus brevis [SVC(II)14] based on phenotypic as well as genotypic attributes and after conducting this research we propose that the B. brevis which is reported for the first time for its PGP potential in cotton, exerts its beneficial effects on cotton crop through combined modes of actions.
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http://dx.doi.org/10.1186/s40064-016-2584-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4929095PMC
July 2016

A reanalysis of protein polymorphism in Drosophila melanogaster, D. simulans, D. sechellia and D. mauritiana: effects of population size and selection.

Genetica 2004 Mar;120(1-3):101-14

Department of Biology, McMaster University, 1280 Main Street West Hamilton, Ont., Canada L8S 4K1.

Comparison of synonymous and nonsynonymous variation/substitution within and between species at individual genes has become a widely used general approach to detect the effect of selection versus drift. The sibling species group comprised of two cosmopolitan (Drosophila melanogaster and Drosophila simulans) and two island (Drosophila mauritiana and Drosophila sechellia) species has become a model system for such studies. In the present study we reanalyzed the pattern of protein variation in these species, and the results were compared against the patterns of nucleotide variation obtained from the literature, mostly available for melanogaster and simulans. We have mainly focused on the contrasting patterns of variation between the cosmopolitan pair. The results can be summarized as follows: (1) As expected the island species D. mauritiana and D. sechellia showed much less variation than the cosmopolitan species D. melanogaster and D. simulans. (2) The chromosome 2 showed significantly less variation than chromosome 3 and X in all four species which may indicate effects of past selective sweeps. (3) In contrast to its overall low variation, D. mauritiana showed highest variation for X-linked loci which may indicate introgression from its sibling, D. simulans. (4) An average population of D. simulans was as heterozygous as that of D. melanogaster (14.4% v.s. 13.9%) but the difference was large and significant when considering only polymorphic loci (37.2% v.s. 26.1%). (5) The species-wise pooled populations of these two species showed similar results (all loci = 18.3% v.s. 20.0%, polymorphic loci = 47.2% v.s. 37.6%). (6) An average population of D. simulans had more low-frequency alleles than D. melanogaster, and the D. simulans alleles were found widely distributed in all populations whereas the D. melanogaster alleles were limited to local populations. As a results of this, pooled populations of D. melanogaster showed more polymorphic loci than those of D. simulans (48.0% v.s. 32.0%) but the difference was reduced when the comparison was made on the basis of an average population (29.1% v.s. 21.4%). (7) While the allele frequency distributions within populations were nonsignificant in both D. melanogaster and D. simulans, melanogaster had fewer than simulans, but more than expected from the neutral theory, low frequency alleles. (8) Diallelic loci with the second allele with a frequency less than 20% had similar frequencies in all four species but those with the second allele with a frequency higher than 20% were limited to only melanogaster the latter group of loci have clinal (latitudinal) patterns of variation indicative of balancing selection. (9) The comparison of D. simulans/D. melanogaster protein variation gave a ratio of 1.04 for all loci and 1.42 for polymorphic loci, against a ratio of approximately 2-fold difference for silent nucleotide sites. This suggests that the species ratios of protein and silent nucleotide polymorphism are too close to call for selective difference between silent and allozyme variation in D. simulans. In conclusion, the contrasting levels of allozyme polymorphism, distribution of rare alleles, number of diallelic loci and the patterns of geographic differentiation between the two species suggest the role of natural selection in D. melanogaster, and of possibly ancient population structure and recent worldwide migration in D. simulans. Population size differences alone are insufficient as an explanation for the patterns of variation between these two species.
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http://dx.doi.org/10.1023/b:gene.0000017634.17098.aaDOI Listing
March 2004

A second and unusual pucBA operon of Rhodobacter sphaeroides 2.4.1: genetics and function of the encoded polypeptides.

J Bacteriol 2003 Oct;185(20):6171-84

Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, Houston, Texas 77030, USA.

A new operon (designated the puc2BA operon) displaying a high degree of similarity to the original pucBA genes of Rhodobacter sphaeroides 2.4.1 (designated puc1) was identified and studied genetically and biochemically. The puc2B-encoded polypeptide is predicted to exhibit 94% identity with the original beta-apoprotein. The puc2A-encoded polypeptide is predicted to be much larger (263 amino acids) than the 54-amino-acid puc1A-encoded polypeptide. In the first 48 amino acids of the puc2A-encoded polypeptide there is 58% amino acid sequence identity to the original puc1A-encoded polypeptide. We found that puc2BA is expressed, and DNA sequence data suggested that puc2BA is regulated by the PpsR/AppA repressor-antirepressor and FnrL. Employing genetic and biochemical approaches, we obtained evidence that the puc2B-encoded polypeptide is able to enter into LH2 complex formation, but neither the full-length puc2A-encoded polypeptide nor its N-terminal 48-amino-acid derivative is able to enter into LH2 complex formation. Thus, the sole source of alpha-polypeptides for the LH2 complex is puc1A. The role of the puc1C-encoded polypeptide was also determined. We found that the presence of this polypeptide is essential for normal levels of transcription and translation of the puc1 operon but not for transcription and translation of the puc2 operon. Thus, the puc1C gene product appears to have both transcriptional and posttranscriptional roles in LH2 formation. Finally, the absence of any LH2 complex when puc1B was deleted in frame was surprising since we know that in the presence of functional puc2BA, approximately 30% of the LH2 complexes normally observed contain a puc2B-encoded beta-polypeptide.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC225038PMC
http://dx.doi.org/10.1128/JB.185.20.6171-6184.2003DOI Listing
October 2003
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