ORCID Profile
0000-0002-3957-0807
Current Organisations
Western Sydney University
,
University of Western Australia
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Publisher: University of Latvia
Date: 11-01-2023
DOI: 10.22364/EEB.20.19
Abstract: Root endophytes are considered to be one of the potent environment-friendly substitutes for chemical fertilizers, as they possess an ability to induce crosstalk inside the hosts for growth promotion, nitrogen fixation, phosphate solubilization and iron sequestration. This study aimed to explore and evaluate the key root endophytic bacterial consortia of two widely cultivated varieties of rice (Oryza sativa L.), cv. ‘Saraswati’ (OS01) and cv. ‘Kunti’ (OS04). Detailed comparative metagenome data were generated for endophytes of OS01 and OS04 and the species richness was calculated. OS01 showed higher endophyte species richness than OS04, with alpha ersity values of 3.10 and 2.40, respectively. Bacillus, Magnetospirillum, Methanocystis, Desulfomicrobium and Pantoea were identified as common endophyte members for both cultivars. Solibacillus, Paenibacillus, Candidatus, and Melospira were unique members of OS01, and Herbaspirillum, Pandoraea, Anabaenopsis for OS04. Considerable occurrence of nitrogen fixing bacteria and methanogenic bacteria in the cultivars confirmed biological nitrogen fixation, which can contribute to plant development. Core homeotic pathways of amino acid biosynthesis and carbon metabolism were also reflected in endophytes from both cultivars, indicating a supportive environment for microorganisms. Sulfur metabolism pathways were likewise predicted to be active in the niche under study, which may be attributed as a response to arsenic stress. Furthermore, the most abundant genera identified may potentially serve as crucial consortium candidates for host plant development and contribute to better yield in a sustainable manner.
Publisher: Biomedical Informatics
Date: 31-10-2017
Publisher: Elsevier BV
Date: 06-2017
Publisher: Cold Spring Harbor Laboratory
Date: 02-03-2023
DOI: 10.1101/2023.03.02.530479
Abstract: Plant microbiome contribute directly to plant health and productivity but mechanisms that underpin plant microbiome assembly in different compartments (e.g. root, leaf) are not fully understood. Identifying environmental and management factors that affect plant microbiome assembly is important to advance understanding of fundamental ecological processes and harnessing microbiome for improved primary productivity and environmental sustainability. Irrigation and fertilization are two common management practices in Australian tree plantations, but little is known about the effects of these treatments on soil, plant host, and their microbiome. Here, we investigated the impact of a decade long irrigation, fertilization, and their combined application, on soil, plant traits and microbiome of a Eucalyptus saligna plantation at the Hawkesbury Forest Experiment, Western Sydney University, Richmond, NSW. Microbial profiling of bulk soil, rhizosphere, root, and leaves was performed using licon sequencing 16S rDNA and ITS markers for bacteria and fungi, respectively, along with measurements of soil properties and plant traits. The results indicated that both management practices affected soil properties and soil and root microbiome significantly. Irrigation increased but fertilizer treatment reduced microbial alpha ersity. However, neither irrigation nor fertilizer treatment significantly impacted the leaf microbiome. Our findings imply that management practices impact soil edaphic factors, which in turn influence the below ground microbiome (soil and root). In addition, the leaf microbiome was distinct from soil and root microbiome, and a source tracker analysis suggested root and bulk soils only contributed to 53% and 10% OTUs of the leaf bacterial community, suggesting strong and sequential host selection of the leaf microbiome. In addition, management practices had limited impact on leaf traits and, consequently, the leaf microbiome maintained its distinct composition. These findings provide mechanistic evidence for ecological processes that drive plant microbiome assembly and indicate that host selection plays a more important role than management practices on leaf microbiome assembly.
Publisher: Elsevier
Date: 2020
Publisher: Springer Science and Business Media LLC
Date: 20-06-2019
DOI: 10.1038/S41598-019-45383-W
Abstract: Mungbean Yellow Mosaic India Virus (MYMIV)-infection creates major hindrance in V . mungo cultivation and poses significant threat to other grain legume production. Symptoms associated include severe patho-physiological alterations characterized by chlorotic foliar lesion accompanied by reduced growth. However, dissection of the host’s defense machinery remains a tough challenge due to limited of host’s genomic resources. A comparative RNA-Seq transcriptomes of resistant (VM84) and susceptible (T9) plants was carried out to identify genes potentially involved in V . mungo resistance against MYMIV. Distinct gene expression landscapes were observed in VM84 and T9 with 2158 and 1679 differentially expressed genes (DEGs), respectively. Transcriptomic responses in VM84 reflect a prompt and intense immune reaction demonstrating an efficient pathogen surveillance leading to activation of basal and induced immune responses. Functional analysis of the altered DEGs identified multiple regulatory pathways to be activated or repressed over time. Up-regulation of DEGs including NB-LRR, WRKY33, ankyrin, argonaute and NAC transcription factor revealed an insight on their potential roles in MYMIV-resistance and qPCR validation shows a propensity of their accumulation in VM84. Analyses of the current RNA-Seq dataset contribute immensely to decipher molecular responses that underlie MYMIV-resistance and will aid in the improvement strategy of V . mungo and other legumes through comparative functional genomics.
Publisher: Springer Science and Business Media LLC
Date: 13-10-2018
Publisher: Wiley
Date: 06-05-2023
DOI: 10.1002/SAE2.12043
Abstract: Plant microbiomes contribute directly to plant health and productivity, but mechanisms that underpin plant microbiome assembly in different compartments (e.g., root, leaf) are not fully understood. Identifying environmental and management factors that affect plant microbiome assembly is important to advance understanding of fundamental ecological processes, and to harness microbiome for improved primary productivity and environmental sustainability. Irrigation and fertilization are two common management practices in Australian tree plantations, but little is known about the effects of these treatments on soil, plant host and their microbiome. Here, we investigated the impact of decade‐long irrigation, fertilization and their combined application on soil, plant traits and microbiome of a Eucalyptus saligna plantation. Microbial profiling of bulk soil, rhizosphere, root and leaves was performed using licon sequencing 16S ribosomal DNA and internal transcribed spacer (ITS) markers for bacteria and fungi, respectively, along with measurements of soil properties and plant traits. The results indicated that both management practices significantly affected soil properties and soil and root microbiomes. Irrigation increased but fertilizer treatment reduced microbial alpha ersity. However, neither irrigation nor fertilizer treatment impacted the leaf microbiome. Our findings suggest that management practices impact soil edaphic factors, which in turn influence the below‐ground microbiome (soil and root), but the leaf microbiome remains unaffected. In addition, the leaf microbiome was distinct from soil and root microbiomes, and a source tracker analysis suggested that root and bulk soils only contributed to 53% and 10% operational taxonomic units of the leaf bacterial community, suggesting strong and sequential host selection of the leaf microbiome. In addition, management practices had a limited impact on leaf traits and, consequently, the leaf microbiome maintained its distinct composition. These findings provide mechanistic evidence for ecological processes that drive plant microbiome assembly and indicate that host selection plays a more important role than management practices in the leaf microbiome assembly.
Publisher: AOA Academic Open Access Ltd.
Date: 12-2013
DOI: 10.18052/WWW.SCIPRESS.COM/ILNS.7.23
Abstract: HIV-1 or Human Immuno Deficiency Virus-1 is the main causative agent of Acquired Immuno Deficiency Syndrome (AIDS). Human host infected with HIV - 1 extensively harbours many viral variants but very little is known about the difference in pattern [17] of evolution of phylogenetic lineages of HIV-1 non recombinant, normal inter subtype recombinant and main two specific recombinant forms of HIV-1 i.e., Circulating Recombinant Forms (CRFs) and Unique Recombinant Forms (URFs). This study is mainly concerned with study of the difference in evolutionary lineages of non-recombinant and recombinant sequences of HIV-1 genome sequences and identification of geographically rich areas which has reported high degree of HIV-1 occurrence and variety. Total 1550 HIV-1 genome sequences were obtained from HIV Los Alamos Database. The sequences were aligned using MAFFT (Multiple Alignment using Fast Fourier Transform) web server tool. Alignment was carried out using 10 different set of alignment parameter values. After alignment the aligned file was used for constructing N-J phylogenetic tree using Clustal X2 tool. Phylogenetic analysis was performed keeping in mind the category to which the sequence belongs. Upon analysis it was observed that the clade containing the probable ancestor belongs remained constant in all cases of different alignment values. Non recombinant isolates, inter subtype recombinants, CRFs, URFs all followed different patterns of evolution. Non recombinant sequences were found geographically specific and subtype specific to some extent whereas, normal recombinants were subtype specific and less geographically specific. CRFs showed variation among the pattern of their evolution. At some instances the sequences occurred as sister taxa of non-recombinant or normal inter subtype recombinant sequences, while at some instances as sister taxa of other CRFs where they were geographically specific. Three CRFs existed as completely erged sequences. URFs were four in number two of them were Indian isolates of while other two were Japanese isolates. URFs were found to be totally geographically specific. Geography wise high rate of variation was observed in India and Japan as these two countries had sequences belonging to all of the above categories. Cameroon and South Africa have very large number isolates and a considerable amount of genetic variation among isolates but they lack URFs.
Publisher: Elsevier BV
Date: 04-2018
Publisher: IEEE
Date: 03-2016
Publisher: Elsevier BV
Date: 12-2017
No related grants have been discovered for PANKAJ KUMAR SINGH.