Shilpi Sharma

• Trinity Western University

Purpose In soil, several factors, like environment and pathogens, can modulate the rhizospheric microbial communities, thereby impacting the overall fitness of host. A pathobiome includes members of the microbiome that interact with the host and pathogen to favor the infection process. Methods and results In this study, the microbial diversity was...

Due to extensive anthropogenic activities, soil fertility may degrade severely, threatening the food security. Traditional soil sampling from fields, and their subsequent chemical analysis, is invasive, time-consuming, and not economical at the regional or global level. Remote sensing techniques, specifically the hyperspectral imaging due to their...

Soil salinization adversely impacts plant and soil health. While amendment with chemicals is not sustainable, the application of bioinoculants suffers from competition with indigenous microbes. Hence, microbiome‐based rhizosphere engineering, focussing on acclimatization of rhizosphere microbiome under selection pressure to facilitate plant growth,...

Application of bacterial consortia exhibiting plant growth promotion abilities has emerged as an effective tool for enhancing the productivity of crops. However, tracking their persistence has been difficult in the soil microenvironment. In our previous study, spontaneous mutants of three plant growth-promoting bacteria, viz. Azotobacter chroococcu...

The colonization of textiles by axillary skin bacteria produces an unpleasant odour due to the rapid growth of a selective community of bacteria. Such colonized textiles subsequently act as vectors for transmitting nosocomial infections among healthcare workers and patients. An in-depth understanding of bacterial behaviour on soft surfaces like fab...

The study explores the potential of next-generation satellite hyperspectral imaging systems for screening and predicting surface‐soil contamination and degradation by exploiting various spectral indices and signature‐matching techniques at a heavily industrialized area in India. The soil moisture content, desertification and salinity status, clay o...

Aim Bacterial exopolysaccharides (EPS) possess numerous properties beneficial for the growth of microbes and plants under hostile conditions. The study aimed to develop a bioformulation with bacterial EPS to enhance the bioinoculant’s shelf life and functional efficacy under salinity stress. Methods and results High EPS-producing and salt-tolerant...

Organic agriculture is a sustainable method of farming, and confers disease-suppressing abilities to disease-conducive soils via specialized soil microbiomes. This study aimed at transforming a disease-conducive soil from a conventional field into disease-suppressive soil by inoculating soil from an organic field previously established as “disease-...

Indiscriminate use of chemicals in agriculture impacts soil properties, significantly compromising microbial diversity. Therefore, integrating eco-friendly strategies with minimal adverse impact on soil microflora and increasing crop productivity are essential for sustainable agriculture. The study was designed to understand the impact of different...

Large-scale mass gatherings, such as religious pilgrimages, and sports events, attract multitudes of participants from diverse geographic and cultural backgrounds [[1], [2], [3], [4], [5]]. Despite fostering communal bonds and celebrations, the WHO highlights that such mass gathering events are associated with serious health risks due to disease tr...

Fabrics act as fomites for microorganisms, thereby playing a significant role in infection transmission, especially in the healthcare and hospitality sectors. This study aimed to examine the biofilm formation ability of four nosocomial infection–causing bacteria (Acinetobacter calcoaceticus, Escherichia coli, Pseudomonas aeruginosa, and Staphylococ...

Chemicals are used extensively in agriculture to increase crop production to meet the nutritional needs of an expanding world population. However, their injudicious application adversely affects the soil's physical, chemical and biological properties, subsequently posing a substantial threat to human health and global food security. Beneficial micr...

The top-down approach of microbiome-mediated rhizosphere engineering has emerged as an eco-friendly approach for mitigating stress and enhancing crop productivity. It has been established to mitigate salinity stress in Vigna radiata using multi-passaging approach. During the process of acclimatization under increasing levels of salinity stress, the...

The female spikes (fruits) of Piper longum are widely used in Ayurvedic, Siddha and Unani medicine systems to treat respiratory and digestive disorders. The spikes are rich in piperine, a pharmacologically active amide alkaloid and a potent bioavailability enhancer, which accumulates to the highest level during the dark-green stage of spike develop...

Excessive use of chemicals to enhance soil nutrient status and crop yield has resulted in a decline in soil health. Organic farming promotes organic amendments, which help to balance the ecosystem. Understanding the dynamic patterns of belowground microbial populations is essential for developing sustainable agricultural systems. Therefore, the stu...

Nosocomial infections or healthcare-associated infections (HAIs) are acquired under medical care in healthcare facilities. In hospital environments, the transmission of infectious diseases through textiles such as white coats, bed linen, curtains, and towels are well documented. Textile hygiene and infection control measures have become more import...

The use of fertilizers and pesticides has resulted in enhanced crop productivity and disease management over the years. However, the prevalence of several abiotic and biotic stress factors has also enormously increased across diverse agroecosystems. This necessitates employing eco-friendly approaches like the application of plant growth promoting m...

Antimicrobial resistance (AMR) in cattle is widespread because of the increased use of antibiotics to combat microbial diseases and enhance milk production. The cattle excreta released into the environment can be a potent source of contamination in spreading antibiotic resistance, especially upon its application in agriculture. However, the correla...

Soil microbial communities are key players responsible for imparting suppressive potential to the soil against soil-bornephytopathogens. Fungi have an immense potential to inhibit soil-borne phytopathogens, but the fungal counterpart hasbeen less explored in this context. We assessed the composition of fungal communities in soil under long-term org...

The global food crisis has triggered a rapid evolution of the agricultural sector to meet requisite demand. Deciphering interactions in the soil microbiome would lead to sustainable agricultural development. 1-ami-nocyclopropane-1-carboxylic acid (ACC) deaminase producing bacteria help plants to counter stress. The study's primary aim was to demons...

Purpose Soil management exerts profound impact on the structure and function of the microbiome. Organic practice is believed to positively affect disease suppressiveness compared to conventional systems. While Pseudomonas has been established as a major player in conferring suppressiveness, the impact of farming practices on its diversity at specie...

Bacterial consortia, comprising plant growth promoting (PGP) rhizobacteria, are known to outcompete their impacts on plant attributes compared with individual application. However, tracking of individual bacterial strains post application as consortium remains challenging. The primary goal of this study was to develop an efficient method of trackin...

Presently, agriculture worldwide is facing the major challenge of feeding the increasing population sustainably. The conventional practices have not only failed to meet the projected needs, but also led to tremendous environmental consequences. Hence, to ensure a food‐secure and environmentally sound future, the major thrust is on sustainable alter...

Microbes regulate soil health by negating ecological disturbances, and improve plant productivity in a sustainable manner. Indiscriminate application of pesticides creates a detrimental impact on the rhizospheric microbiota, thereby affecting soil health. Azadirachtin, earlier believed to be an environment-friendly alternative to chemical pesticide...

The administration of antibiotics for the treatment and prevention of microbial diseases in livestock farming ends up in the accumulation of antibiotic residues and their metabolites in animal waste. In agro-ecosystems, the application of animal waste as a source of nutrition is associated with the risk of the development of antibiotic resistance i...

Microbiome-based rhizospheric engineering has emerged as a promising approach towards attaining agricultural sustainability. While the top-down approach of acclimatizing the rhizospheric microbiome to stressors is relatively easy to perform, the mechanisms involved in plant growth promotion by directed evolution are yet to be understood. The presen...

The rhizosphere is a dynamic and complex interface between plant roots and microorganisms. Owing to exudates, a web of interactions establishes among the microbial members of this micro-environment. The present study explored the impact of a bacterial consortium (Azotobacter chroococcum, Bacillus megaterium and Pseudomonas fluorescens, ABP), on the...

Salinity stress is one of the major abiotic stresses that hampers the growth and productivity of plants. One of the sustainable approaches offering advantages over traditional bioinoculants is microbiome-based rhizospheric engineering for improving agricultural productivity and stress mitigation. Native members of the rhizospheric microbiome under...

Fabrics serve as fomites in spreading nosocomial infections. As a patient is in close contact with bedsheets, it is important to assess the seasonal variation in bacterial diversity on these in healthcare units. The study was conducted to characterise the bacterial diversity on patients’ bedsheets across 7 months in a primary healthcare unit. Polye...

Soil fertility is disrupted by diverse anthropogenic activities, including intensive agricultural practices (viz., conventional agriculture (CT)), affecting environmental sustainability. Hence, for sustainability, alternative agricultural practices, such as conservation agriculture (CA) and organic agriculture (OA) that can preserve the native soil...

Abiotic stresses detrimentally affect both plant and soil health, threatening food security in an ever-increasing world population. Sustainable agriculture is necessary to augment crop yield with simultaneous management of stresses. Limitations of conventional bioinoculants has shifted the focus on more effective alternatives. With the realisation...

Among the various plant-associated microbiota, endophytes (the microbial communities inhabiting plant endosphere without causing disease symptoms) exhibit the most intimate and specific association with host plants. Endophytic microbes influence various aspects of plant responses (such as increasing availability of nutrients, tolerance against biot...

In agriculture, soil health is disturbed by various anthropogenic activities, including applications of chemicals, and highly mechanized cropping methods, leading to a gradual loss in soil fertility and microbial diversity. Therefore, it is the need of the hour to shift towards eco-friendly and sustainable agri-management practices. The practice of...

Soil microbiome is a dynamic micro-ecosystem driving and fine-tuning several biological processes in the global macro-ecosystems. Its tremendous potential towards mediating sustainability in the ecosystem necessitates the urgent need to store it optimally and efficiently as “next-generation biologicals” for future applications via soil transplantat...

The increasing concern over the survival and efficacy of bioinoculants in fields has emphasized the need to develop a more robust strategy for the enhancement of plant growth. Microbiome-based approaches hold immense potential in offering a sustainable strategy for improvement of soil and plant health by mimicking the soil’s natural microbial commu...

Biocontrol agents serve as a sustainable means of controlling wilt caused by the widespread plant pathogen, Fusarium oxysporum f. sp. lycopersici. The present study aimed to develop water dispersible granules (WDG) using response surface methodology (RSM) for Bacillus subtilis MTCC 2274 and Trichoderma harzianum MTCC 3928, and to compare their anti...

Antimicrobial resistance (AMR) in cattle is widespread because of the increased use of antibiotics to combat microbial diseases and enhance milk production. The cattle excreta released into the environment can be a potent source of contamination in spreading antibiotic resistance, especially upon its application in agriculture. However, the correla...

Background Contaminated textiles serve as fomites in healthcare settings. The extent of transfer of pathogens from fabrics depends on the surface properties of the two contact surfaces. Methods In the current study, the effect of surface energy and surface roughness of fabrics on the transfer of Escherichia coli and Staphylococcus aureus to and fr...

In this article, we report on a new class of biodegradable piperazine-based aliphatic pH-responsive polyesters with tunable hydrophilicity. The aliphatic polyesters PC1-PC4 with high thermal stability up to 340 ℃ were synthesized by polycondensation of dimethyl 2,2’-(piperazin-1,4-diyl)diacetate with a series of alkane diols (C4 to C10). The result...

In an attempt to attain sustainability in agriculture, microbiome-based approaches have been investigated as "next-generation biologicals". The top-down strategy of plant-mediated indirect selection of rhizospheric microbiome holds potential in generating a robust and efficient microbiome for enhancement of desired plant phenotype and its overall f...

Salinity is a major abiotic stress that negatively impacts plant health and soil microbiota. ACC (1-aminocyclopropane carboxylic acid) deaminase producing microorganisms act as natural stress busters that protect plants from different kinds of stresses. The study focused on the isolation of potent, indigenous, multi-trait ACC deaminase producers. T...

A patient is in close proximity to different types of textiles in hospital environment, which contribute to the transfer of drug-resistant bacteria in healthcare settings. This study was undertaken to estimate the temporal variations in bacterial load on bedsheets in a primary healthcare unit in Delhi. Data were collected for a period of 7 months....

Disease suppressive soils are instrumental in combating phytopathogens, which cause severe diseases in plants. They provide an eco-friendly way to mitigate biotic stresses in agricultural systems worldwide. Efforts have been made to understand the mechanisms of disease suppressiveness in soil using culture-dependent and culture-independent methods....

Intensive agricultural practices have led to a decline in soil health, thereby affecting environmental sustainability. To feed the ever-increasing global population in a sustainable manner, shifting to eco-friendly agricultural practices is of paramount importance. In this respect organic farming, which excludes chemicals, has been widely popularis...

Pigeonpea is an important legume cultivated in India, owing to its high nutritive and protein value. Various eco-friendly and green strategies have been proposed by researchers for enhancing the productivity of this pulse crop. In the present study, different bioformulations were prepared from plant growth promoting (PGP) bacterial strains and coat...

Under natural conditions plants are not individual entities; they are associated with diverse microbiota to form the plant holobiont. The concept of plant holobiont is being actively explored to address the issues related to plant's health. Endophytes are a class of plant-associated microbes, which reside within the internal tissues of plants. They...

Improper nutrient management is one of the major limitations linked with cultivation of Cajanus cajan. This calls for an urgent need for a promising alternative, employing both bioinoculants and chemical fertilizer. Present study attempted to understand the impact of bioinoculants {Azotobacter chroococcum, Bacillus megaterium, and Pseudomonas fluor...

Sustainable management practices are the need of the hour to counter the ever-deteriorating environmental conditions in agro-ecosystems. While bioinoculants have served as eco-friendly means to mitigate stresses, their survivability and competitiveness in field conditions have been a major challenge. The present study aimed to adopt a multi-generat...

A rapid increase in waste generation has quickly become one of the key challenges of today’s world. However, the wastes originating from a range of sources, including industries and residences, can be used as a potential resource—if managed properly. This management includes developing technologies to safely reuse waste, and the conversion of waste...

BACKGROUND Modern agricultural management approaches are often dependent on the application of chemicals, resulting in adverse impacts on human and environmental health. Therefore, for sustainable agriculture, there is a need to implement integrated agriculture practices that can maintain natural soil microbiome and enhance crop production. Various...

In sectors like healthcare and hospitality, it has been realized that fabrics play a pivotal role in transfer of nosocomial infections. However, there is a major gap in drawing correlation between different fibre types and their interaction with microorganisms. Such information is important to formulate guidelines for textile materials for use in t...

The antagonistic efficacy of a biocontrol agent in combination with oilseed cake against fungal phytopathogens has been sparsely explored. The present study aimed to evaluate the antifungal activity of a biocontrol agent (Trichoderma harzianum MTCC 3928) formulated with oilseed cake (OSC) against Fusarium oxysporum f. sp. lycopersici responsible fo...

The intensification of agriculture to meet the ever-increasing demand for food has exerted a negative impact on the ecosystem. Conservation agriculture has been highlighted as a comprehensive approach to sustainability. The present study aimed to assess the performance of conservation agriculture (CA) on plant growth, and its impact on bacterial co...

Here, we report the annotated whole-genome sequence of Pseudomonas sp. strain SK, isolated in India from organic wheat rhizosphere. This strain has proved to be a species with potential biocontrol activity against soilborne plant pathogens based on antiSMASH analysis.

Soil microbiome plays a primary role in soil ecosystem functioning by being involved in necessary biochemical processes. Any changes to soil microbiome lead to differences in physiochemical properties of soil such as salinity, pH, and organic content, which eventually leads to soil infertility. Indiscriminate use of pesticides to meet global food r...

Due to rhizodeposits and various microbial interactions, the rhizosphere is an extremely dynamic system, which provides a conductive niche not only for bacteria beneficial to plants but also for those that might pose a potential threat to humans. The importance of bioinoculants as biocontrol agents to combat phytopathogens has been widely recognize...

The present study is an attempt to understand the impact of bioinoculants, Azotobacter chroococcum (A), Bacillus megaterium (B), Pseudomonas fluorescens (P), on (a) soil and plant nutrient status, (b) total resident and active bacterial communities, and (c) genes and transcripts involved in nitrogen cycle, during cultivation of Cajanus cajan. In te...

The importance of studying microbial load on fabrics has been recently realized with reports on fabrics being a source of spread of infection in medical and hospitality sectors. However, methodological limitations have restricted the analysis of microbial diversity on fabrics. Hence, the study aimed to develop a robust method for extraction of DNA...

The significance of microbial diversity in soil has been demonstrated since decades. Assorted variety of microorganisms in soil is fundamental to support soil health, as an extensive diversity of microorganisms is associated with essential soil functions. Several abiotic and biotic factors have been reported to affect the structural and functional...

Rhizosphere is the zone where the microbe-mediated processes are influenced by root exudates. Owing to its high nutrient content due to root exudates, and ability to provide a safe home, it acts as a natural reservoir to not only beneficial bacteria but also to those which can be potential threat for humans, and hence acts as a ‘microbial hot spot’...

Salinity and drought are the major abiotic stresses limiting agricultural productivity. Application of plant growth promoting rhizobacteria (PGPR) is an attractive technology but with the bottlenecks of reduced efficacy and survivability in the environment. For increased efficiency of PGPR strains, the impact of stresses on the native bacterial com...

Rhizosphere is considered to be supportive of a high microbial diversity because of rich exudation from plant roots. Roots recruit a specific microbial community in this zone, which is beneficial to the plant. Potential of plant growth promoting rhizobacteria (PGPR) has been harnessed since years to serve as bioinoculants. Despite being an eco-frie...

Biocontrol agents are currently considered as promising alternative to chemical fungicides because of the latter’s negative impacts on consumer health, plant health, and the environment. In the current biopesticide world, Trichoderma spp. has been globally accepted to prevent the invasion of pathogens, viz., Fusarium oxysporum, Verticillium dahliae...

Bacillus subtilis and Trichoderma harzianum are known for their antagonistic potential against several fungal phytopathogens. However, limited studies have assessed the non-target effects of these biocontrol agents. The present study aimed to investigate the antagonistic efficacy of B. subtilis (MTCC 2274) and T. harzianum (MTCC 3928) in mitigation...

With increasing reports of textiles serving as vectors for the transmission of infections, it is crucial to study the factors influencing such transfers. This is of concern in various sectors, including healthcare and hospitality, where fabrics constitute an integral part. A better understanding of the fabric types that discourage microbial transfe...

Total nucleic extraction from fabrics

Microbial endophytes represent an endosymbiotic group that colonizes internal plant tissues. Endophytes are one of the least studied and unexplored groups of microbes that need attention, so as to provide comprehensive knowledge regarding beneficial plant-microbe interactions. One of the emerging issues in the area of agriculture is a gradual decre...

In the present study, three strains each of Bacillus subtilis and Trichoderma harzianum were compared for their antagonism against Fusarium oxysporum f. sp. lycopersici (FOL), responsible for causing wilt disease in tomato plant. In vitro antifungal volatile assay revealed that B. subtilis 2274 caused significantly (p < 0.05) higher inhibition of r...

This book includes 25 contributions from vastly experienced, global experts in PGPR research in a comprehensive and influential manner, with the most recent facts and extended case studies. Also, the chapters address the current global issues in biopesticide research.

Studies on diversity of microbial community in the field of rhizosphere ecology vastly rely on nucleic acid markers for analysis. The extraction can be a tedious and complicated task owing to the vast heterogeneity present in soil in terms of organic and inorganic constituents, texture and moisture content, and also the huge repertoire of life form...

As bioinoculants are considered to be free from adverse effects on environment, the knowledge of their survival in field and their effect on resident microflora is of great interest. Plant symbionts belonging to the order Rhizobiales fix atmospheric nitrogen and hence hold economic importance by providing an eco-friendly alternative to chemical fer...

India is one of the leading countries in production and indiscriminate consumption of pesticides. Owing to their xenobiotic nature, pesticides affect soil microorganisms that serve as mediators in plant growth promotion. Our study aimed to deliver a comprehensive picture, by comparing the effects of synthetic pesticides (chlorpyriphos, cypermethrin...

During the anaerobic digestion (AD) of waste and production of methane as an alternative fuel, unpredictability and instability of bioreactors are a challenge. Leading cause of such failure is the lack of knowledge about the microbial consortia involved in AD under different process conditions or perturbations during field applications. Over the la...

Despite the long history of application of bioinoculants for improving crop productivity, very little information is available on their impact on native microbial communities in crops' rhizosphere. The present study compares the effects of a microbial consortium comprising of Bacillus megaterium, Pseudomonas fluorescens and Trichoderma harzianum, w...

Bioinoculants have been known to promote plant growth and grain yield by more than one mechanism, though it has been difficult to pinpoint them. The contribution of the impact exerted by these live microorganisms on the resident rhizospheric microbial community functioning in enhancing plant growth cannot be ruled out. The chapter aims to criticall...

Inoculation of leguminous seeds with bioinoculants has been practiced in agriculture for decades to ameliorate grain yield by enhanced growth parameters and soil fertility. However , effective enhancement of plant growth parameters results not only from the direct effects these bioinoculants impose on them but also from their non-target effects. Th...

Intensive agriculture has resulted in an indiscriminate use of pesticides, which demands in-depth analysis of their impact on indigenous rhizospheric microbial community structure and function. Hence, the objective of the present work was to study the impact of two chemical pesticides (chlorpyrifos and cypermethrin) and one biological pesticide (az...

With increasing application of pesticides in agriculture, their non-target effects on soil microbial communities are critical to soil health maintenance. The present study aimed to evaluate the effects of chemical pesticides (chlorpyrifos and cypermethrin) and a biological pesticide (azadirachtin) on growth parameters and the rhizospheric bacterial...

The study aimed at assessing the biotechnological potential of Bacillus sp. PU1T (JCM-16712, NBRC-106750, KCTC-13722), a halotolerant bacterium of the family Bacillaceae isolated from saline rhizosphere of Sesbania grandiflora from Mahabubnagar (16.4600° N, 77.5600° E), India, with respect to its plant growth promoting (PGP) properties, and as a so...

To compare the target and non-target effects of two chemical-pesticides (chlorpyrifos and endosulfan) with that of a bio-pesticide (azadirachtin), Vigna radiata (mung bean) was grown in a randomized pot experiment with recommended and higher application rates of pesticides. Colony counts enumerating specific microbial populations, viz. fungi, Pseud...

“Bioinoculants” have become a useful, environment-friendly tool in agriculture to increase crop yield. Previous work has shown that Cajanus cajan, India's most important pulse, can profit considerably from applications of the three bioinoculants, viz. Bacillus megaterium MTCC 453, Pseudomonas fluorescens LPK2 and Trichoderma harzianum MTCC 801. For...

A series of chain-coupled polyesters based on tartaric acid was synthesized and characterized following a two-step procedure. In the first step, tartaric acid based hydroxyl terminated polyesters with various alkane diols were prepared and then, in a second step, a chain-coupling approach using hexamethylene diisocyanate was employed on the synthes...

BACKGROUND Hydrodynamic shear plays a major role in the formation, maintenance, structure, and metabolism of self-immobilized microbial communities in reactors. The study attempts to correlate the performance and microbial community structure of granular sludge in a mesophilic hybrid anaerobic reactor under different upflow velocities to fluidize t...

To study the effects of two chemical pesticides (chlorpyrifos and endosulfan), and a bio-pesticide (azadirachtin) on bacterial diversity in rhizospheric soil, a randomized pot experiment was conducted on mung bean (Vigna radiata) with recommended and higher doses of pesticides. Denaturing gradient gel electrophoresis was used to analyze such effect...

Analysis of diversity of phosphate solubilizers in agricultural soil is essential to understand their ecological role and their utilization in sustainable agriculture. One of the factors contributing to the success of weeds, even in nutrient limiting conditions, is the microbial community they select in their vicinity. Phosphate solubilizers from t...

Artemisinin is an alternate anti-malarial drug which is widely used in the cure of multi-drug resistant Plasmodium falciparum malaria. In this study, enhancement of artemisinin content by using several elicitors and precursors was attempted initially by using one at a time (OVAT) approach. The most potent elicitor(s) & precursor were thereafter ide...

Poor understanding of the response of microbial communities to sudden changes in organic and hydraulic loads is one of the major reasons for the inability to prevent operational instabilities in anaerobic reactors. Effect of changes in hydraulic retention time (HRT) and organic loading rate (OLR) on reactor performance and its anaerobic microbial c...

Background and aims Bioinoculants are commonly used for enhancing crop productivity but little information is available on their effect on key microbial communities such as those involved in the cycling of nitrogen, a major plant nutrient. Here we developed a formulation combining different bioinoculants (Bacillus megaterium, Pseudomonas fluorescen...

An improved protocol for extraction of prokaryotic mRNA from soil samples was developed by modifying the extraction procedure to obtain higher yields of mRNA and to reduce co-extraction of humic acids. The modified protocol was found to be more robust and efficient compared to the original protocol by Griffiths et al. (2000) without compromising wi...