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Advances in PGPR Research

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Rhizosphere biology is approaching a century of investigations wherein growth-promoting rhizomicroorganisms (PGPR) have attracted special attention for their ability to enhance productivity, profitability and sustainability at a time when food security and rural livelihood are a key priority. Bio-inputs - either directly in the form of microbes or their by-products - are gaining tremendous momentum and harnessing the potential of agriculturally important microorganisms could help in providing low-cost and environmentally safe technologies to farmers. One approach to such biologically-based strategies is the use of naturally occurring products such as PGPR. Written by an international team of experts, this book considers new concepts and global issues in biopesticide research and evaluates the implications for sustainable productivity. It is an invaluable resource for researchers in applied agricultural biotechnology, microbiology and soil science, and also for industry personnel in these areas.

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1 Mechanisms of Growth Promotion by Members of the Rhizosphere Fungal Genus Trichoderma

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Mechanisms of Growth Promotion by Members of the Rhizosphere

Fungal Genus Trichoderma

Artemio Mendoza-Mendoza,1,* Guillermo Nogueira-López,1

Fabiola Padilla Arizmendi,1 Natalia Cripps-Guazzone,1

María Fernanda Nieto-Jacobo,1 Robert Lawry,1 Diwakar Kandula,1

Fatima Berenice Salazar-Badillo,2 Silvia Salas-Muñoz,3

Jorge Armando Mauricio-Castillo,2 Robert Hill,1 Alison Stewart4 and Johanna Steyaert1

1

Bio-Protection Research Centre, Lincoln University, Canterbury, New Zealand;

2

Unidad Académica de Agronomía, Universidad Autónoma de Zacatecas,

Zacatecas, México; 3CONACYT- Campo Experimental Zacatecas, Instituto de Investigaciones Forestales, Agrícolas y Pecuarias, Calera de V. R. Zacatecas,

México; 4SCION, Rotorua, New Zealand

1.1 Introduction

Trichoderma species are cosmopolitan filamentous fungi found in agricultural, native prairie, forest, salt marsh, and desert soils of all biomes (rainforests, savannas, deserts, grasslands, temperate deciduous forest, temperate, conifer forest, Mediterranean scrub, taiga and tundra), as well as in lake water, dead plant material, living roots of virtually any plant species, seeds and air

 

2 Physiological and Molecular Mechanisms of Bacterial Phytostimulation

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Physiological and Molecular Mechanisms of Bacterial Phytostimulation

Randy Ortiz-Castro,1 Jesús Salvador López-Bucio2 and José López-Bucio3*

Red de estudios moleculares avanzados, Instituto de Ecología A.C., Carretera

Antigua a Coatepec 351, Veracruz, México; 2Instituto de Biotecnología,

Universidad Nacional Autónoma de México, Morelos, México; 3Instituto de

Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Michoacán, México

1

2.1 Introduction

Plants and bacteria have coexisted for millions of years. As a result, sophisticated signalling mechanisms allow cross-kingdom communication, which benefits plant health, growth and productivity (Singh et al., 2014).

Rhizobacteria sense roots via chemotaxis systems and chemoreceptors, which have been identified in the genomes of several plant-associated species (Scharf et al., 2016).

Chemotaxis provides a competitive advantage to motile flagellated bacteria in colonization of root epidermis, as it enables cells to sense and respond to gradients of chemical compounds released by plants (Scharf et al., 2016).

 

3 Real-time PCR as a Tool towards Understanding Microbial Community Dynamics in Rhizosphere

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Real-time PCR as a Tool towards

Understanding Microbial Community

Dynamics in Rhizosphere

Gautam Anand, Upma Singh, Abhineet Sain, Virendra S. Bisaria and Shilpi Sharma*

Department of Biochemical Engineering and Biotechnology, Indian

Institute of Technology Delhi, New Delhi, India

3.1 Introduction

Soil is a complex amalgam of minerals,

­organic phase, porous phase and diverse life forms. Soil processes, such as nutrient cycling, are of prime importance for the maintenance of our ecosystem (Keswani et al., 2013;

2016; Bisen et al., 2015; Mishra et al., 2015).

Microorganisms play a pivotal role in these soil processes. Changes in the soil microbial community have been linked with varying soil functional capabilities (Torsvik and Øvreås,

2002; Nannipieri et al., 2003; Singh et al.,

2014) that are still poorly understood. Despite the meticulous efforts of scientists to unravel the vast expanse of the microbial community in soil, till now only 1–2% of the total microorganisms present in the soil have been cultured in the laboratory (Amann et al., 1995).

 

4 Biosafety Evaluation: A Necessary Process Ensuring the Equitable Beneficial Effects of PGPR

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Biosafety Evaluation: A Necessary

Process Ensuring the Equitable

Beneficial Effects of PGPR

Juan Ignacio Vílchez,1* Richard Daniel Lally2 and Rafael Jorge León Morcillo1

1

Department of Plant Growth Promotion Rhizobacteria, Plant Stress

Centre for Biology (PSC), Chinese Academy of Sciences (CAS), Shanghai, China;

2

EnviroCORE, The Dargan Centre, Department of Science and Health, Institute of Technology Carlow, County Carlow, Ireland and Alltech, Dunboyne,

County Meath, Ireland

4.1  Biosafety of PGPR in Soil

Today bio-inoculants capable of stimulating plant growth and providing plant protection against environmental stresses are sought with the aim to isolate efficient commercial products for field effective application

(Niranjan Raj et al., 2006; Turan et al., 2010;

Keswani et al., 2014; Singh et al., 2016).

Plant growth-promoting rhizobacteria (PGPR) applied as biofertilizers and biocontrol agents have been used broadly both in natural and agricultural soils. To date, PGPR products have only been perceived to contribute positive effects as a result of their use in plant growth promotion (Niranjan Raj et al., 2006; Gupta et al., 2015; Bisen et al., 2016; Keswani et al.,

 

5 Role of Plant Growth-Promoting Microorganisms in Sustainable Agriculture and Environmental Remediation

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Role of Plant Growth-Promoting

Microorganisms in Sustainable Agriculture and Environmental Remediation

Rama Kant Dubey,1 Vishal Tripathi,1 Sheikh Adil Edrisi,1 Mansi Bakshi,1 Pradeep

Kumar Dubey,1 Ajeet Singh,1 Jay Prakash Verma,1 Akanksha Singh,2 B.K. Sarma,3

Amitava Rakshit,4 D.P. Singh,5 H.B. Singh3 and P.C. Abhilash1*

1

Institute of Environment and Sustainable Development, Banaras Hindu University,

Varanasi, India; 2Microbial Technology and Nematology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India; 3Department. of Mycology and

Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi,

India; 4Department of Soil Science and Agricultural Chemistry, Institute of Agricultural

Sciences, Banaras Hindu University, Varanasi, India; 5ICAR-National Bureau of

­Agriculturally Important Microorganisms, Kushmaur, Mau Nath Bhanjan, Mau, India

5.1  Introduction: Plant GrowthPromoting Rhizobacteria (PGPR)

 

6 Pseudomonas Communities in Soil Agroecosystems

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Pseudomonas Communities in Soil

Agroecosystems

Betina Cecilia Agaras,* Luis Gabriel Wall and Claudio Valverde

Laboratorio de Bioquímica, Microbiología e Interacciones Biológicas en el Suelo,

Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes,

Buenos Aires, Argentina

6.1 Introduction

Among all soil bacterial genera having a representative described as a plant-growth promoter, Pseudomonas comprise a wide variety of PGPR species, with different mechanisms of action (Lugtenberg and Kamilova,

2009). Several pseudomonads have demonstrated high rhizosphere competence, production of different kinds of secondary

­metabolites involved in antagonism, phytostimulation or fertilization, and an ability to degrade complex organic compounds, hence being able to contribute not only to plant health but also to bioremediation of soils

(Lugtenberg and Dekkers, 1999; Haas and

Défago, 2005; Tapadar and Jha, 2013; Agaras et al., 2015; Mishra et  al., 2015; Kumar,

 

7 Management of Soilborne Plant Pathogens with Beneficial Root-Colonizing Pseudomonas

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Management of Soilborne Plant Pathogens with Beneficial Root-Colonizing Pseudomonas

Dmitri V. Mavrodi,1 Mingming Yang,2* Olga V. Mavrodi1 and Shanshan Wen2

Department of Biological Sciences, University of Southern Mississippi, Hattiesburg,

Mississippi, USA; 2Department of Agronomy, Northwest A&F University, Yangling,

Shaanxi, China

1

7.1 Introduction

Soilborne plant pathogens are a significant constraint to crop production worldwide.

There are no adequate seed treatments against many soilborne diseases, no resistant cultivars, and current trends towards reduced tillage and longer crop rotations favour the disease. Soilborne diseases reduce the quantity and quality of marketable yields, and their control adds considerably to the cost of production. Economic losses due to soilborne diseases in the United States alone are estimated at >$4 billion per year (Lumsden et al., 1995). It has been estimated that from

2001 to 2003 an average of 7–15% of crop loss occurred on the main world crops due to soilborne fungi and oomycetes (Gaeumannomyces graminis var. tritici, Fusarium

 

8 Rhizosphere, Mycorrhizosphere and Hyphosphere as Unique Niches for Soil-Inhabiting Bacteria and Micromycetes

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Rhizosphere, Mycorrhizosphere and

Hyphosphere as Unique Niches for SoilInhabiting Bacteria and Micromycetes

Elena Voronina* and Irina Sidorova

Lomonosov Moscow State University, Moscow, Russia

8.1 Introduction

Soil is a natural body abounding in diverse life forms which belong to all domains of life and to a range of functional groups. Soil heterogeneity at a fine scale provides numerous microhabitats and hosts a number of microbial communities different in size and composition, influenced by soil properties (Haq et al., 2014). Vice versa, fungi, especially, symbiotic in mycorrhizas and bacteria, act as soil engineers, and it was revealed that more than 50% of the humus in boreal forest soil originated from roots and their microbe associates (Clemmensen et al.,

2013).

Soil microbial communities since the

20th century were known to play a key role in plant growth, health and productivity both at individual and ecosystem levels. Root microorganisms interfere with plant nutrition, attack the plant or protect it from attackers, and carry out multiple functions in plant life often based on intense interactions within the microbial community (Keswani et al., 2013; Bisen et al., 2015; Mishra et al., 2015;

 

9 The Rhizospheres of Arid and Semi-arid Ecosystems are a Source of Microorganisms with Growth-Promoting Potential

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The Rhizospheres of Arid and Semi-arid

Ecosystems are a Source of Microorganisms with Growth-Promoting Potential

Fatima Berenice Salazar-Badillo,1* Silvia Salas-Muñoz,2 Jorge Armando

Mauricio-­Castillo,1 Jorge Sáenz-Mata,3 Artemio Mendoza-Mendoza,4 Maria Fernanda

Nieto-Jacobo4 and Johanna Steyaert4

1

Unidad Académica de Agronomía, Universidad Autónoma de Zacatecas, Cieneguillas,

Zacatecas, México; 2CONACYT-Campo ­Experimental Zacatecas, Instituto de

Investigaciónes Forestales, Agrícolas y Pecuarias, Calera de V. R. Zacatecas,

México; 3Laboratorio de Ecología Microbiana, Facultad de Ciencias Biológicas,

Universidad Juárez del Estado de ­Durango, Durango, México; 4Bio-Protection

Research Centre, Lincoln University, Canterbury, New Zealand

9.1 Introduction

Approximately 47% of the earth’s surface has been classified as arid lands (Fig. 9.1)

(United Nations Environment Programme,

1992). In general terms an arid land is a region where the water supply and the values of precipitation and atmospheric moisture are lower than the annual global average

 

10 Rhizosphere Colonization by Plant-Beneficial Pseudomonas spp.: Thriving in a Heterogeneous and Challenging Environment

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Rhizosphere Colonization by

Plant-Beneficial Pseudomonas spp.: Thriving in a Heterogeneous and Challenging

Environment

Antoine Zboralski, Adrien Biessy and Martin Filion*

Université de Moncton, Département de biologie, Moncton, Canada

10.1 Introduction

Soils are the richest ecosystems on Earth in terms of biodiversity, as well as major components of agricultural systems (Hinsinger et  al., 2009). They are deeply involved in food webs, providing essential functions for sustaining life both below- and aboveground.

However, soils are relatively poor in nutrients, except for some hotspots under the influence of living plant roots, a concept known as the rhizosphere. The rhizosphere is usually defined as the first 1–5 mm of soil surrounding plant roots (Bertin et al., 2003;

Angus and Hirsch, 2013; Prashar et  al.,

2014). It is supplied in nutrients by plant roots through the release of 5% to 30% of the net carbon fixed by photosynthesis

 

11 Endophytomicrobiont: A Multifaceted Beneficial Interaction

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11  Endophytomicrobiont: A Multifaceted

Beneficial Interaction

Shatrupa Ray,1 Vivek Singh,1 Kartikay Bisen,2 Chetan Keswani,3

Surendra Singh1 and H.B. Singh2*

1

Department of Botany, Institute of Science, Banaras Hindu University,

Varanasi, India; 2Department of Mycology and Plant Pathology, Institute of

Agricultural Sciences, Banaras Hindu University, Varanasi, India; 3Department of

Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India

11.1 Introduction

Successful interaction between plants and beneficial microbes lays a foundation for improving plant growth and soil structure.

However, several attempts to introduce beneficial bacteria into the rhizospheric region of agricultural plants have met with varying degrees of failure, particularly because of the huge competition posed by the pre-existing established rhizomicrobiota (Keswani et al.,

2013, 2014; Bisen et  al., 2015, 2016; Keswani, 2015; Keswani et al., 2016a, b). Moreover, several reports claim loss of microbial bioactivity owing to long-term storage (Nautiyal, 1997). Considering the biodiversity and population density of indigenous soil microbiota, causing permanent structural changes to the rhizospheric microbiota may become quite hectic and cumbersome, or to be more succinct, impossible (Singh et al.,

 

12 Contribution of Plant Growth-Promoting Bacteria to the Maize Yield

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Contribution of Plant Growth-Promoting

Bacteria to the Maize Yield

Vivian Jaskiw Szilagyi Zecchin,1* Angela Cristina Ikeda2 and Átila Francisco Mógor1

1

Federal University of Parana Department of Plant Science and

Crop Protection, Curitiba, Brazil; 2Federal University of Parana,

Department of Forest Science, Curitiba, Brazil

12.1 Introduction

Maize (Zea mays L.) is one of the most important cereal crops, revered widely for its high nutritional value and as a resource for animal feed and bioenergy. Responding to the increasing demands of society, modest initiatives, such as the development of plant production technologies promoting maize yield as well as reduction of synthetic inputs thereby improving farmers’ profits, however, remain an unresolved issue. Fortunately, natural reservoirs, particularly rhizospheric and/or endophytic bacteria, can act as plausible alternative sources for plant nutrition or growth promotion (Barretti et al., 2008).

 

13 The Potential of Mycorrhiza Helper Bacteria as PGPR

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The Potential of Mycorrhiza Helper

Bacteria as PGPR

Marieta Marin Bruzos

Belowground Ecosystem Group, Department of Forest and Conservation Sciences,

University of British Columbia, Vancouver, British Columbia, Canada

13.1 Introduction

The belowground environment is an active space where living organisms and plant roots interact among themselves and with the soil components. As a consequence, the root system of many crops in different ecosystems lives in a mutualistic interaction with mycorrhiza-forming fungi. The resulting association benefits the plants by improving their nutrients uptake and increasing the resistance against soilborne pathogens and abiotic stresses (Finlay, 2008). While this symbiosis is generally considered a dual plant– fungus interaction, other microorganisms like bacteria and yeasts are also closely related

(Frey-Klett and Garbaye, 2005).

Foster and Marks (1967) introduced the definition of “mycorrhizosphere” as the soil area influenced by the mycorrhizal roots and peripheral fungal mycelium. Some of the bacterial groups living within the mycorrhizosphere are able to stimulate the mycorrhiza development. Bacterial strains showing this property were named mycorrhiza helper bacteria (MHB) by Garbaye (1994). Since then, different studies have been performed to evaluate the combined effect of MHB and their associated fungi on the plant growth,

 

14 Methods for Evaluating Plant Growth-Promoting Rhizobacteria Traits

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Methods for Evaluating Plant

Growth-Promoting Rhizobacteria Traits

Antonio Castellano-Hinojosa*1,2 and E.J. Bedmar2

Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín-CSIC. E-419, Granada, Spain; 2Department of Microbiology, Faculty of

Pharmacy, Campus of Cartuja, University of Granada, Granada, Spain

1

14.1 Introduction

14.1.1  Plant growth-promoting rhizobacteria

The presence of microorganisms, bacteria, fungi, actinomycetes, protozoa and algae is critical to the maintenance and health of soil function, in both natural and managed agricultural soils. This is due to their involvement in key processes such as soil structure formation, decomposition of organic matter, toxin removal, suppression of plant disease and, overall, the cycling of carbon, nitrogen, phosphorus and sulphur (Doran et al., 1996; van Elsas et  al., 1997; Mishra et  al., 2015;

Keswani et al., 2016). Bacteria are the most common of those microorganisms reaching

 

15 The Rhizosphere Microbial Community and Methods of its Analysis

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The Rhizosphere Microbial Community and Methods of its Analysis

Mukesh Meena,* Manish Kumar Dubey, Prashant Swapnil, Andleeb Zehra,

Shalini Singh, Punam Kumari and R.S. Upadhyay

Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India

15.1 Introduction

The rhizosphere is the narrow zone of soil surrounding a root wherein the biological, chemical and physical parameters of soil are influenced by the living plant root. The rhizosphere supports a favourable environment for the multiplication of diverse, microbial population, which has a significant role in the organic matter transformation and biogeochemical cycles of the essential nutrients of plant (Bisen et al., 2015; Lagos et al., 2015;

Keswani et al., 2016a, b). The components of root exudates act as chemotactic attractants for microbes, where they flourish in a carbon-rich environment (Lugtenberg and

Kamilova, 2009; Philippot et al., 2013).

The rhizosphere of actively growing plants and their root exudates play an important role in plant–microbe interaction (Badri and Vivanco, 2009). Various compounds of root exudation are sugars, organic acid anions and amino acids which are released within proximity of the roots, provide nutrients and support to numerous microorganisms for their robust growth and activity (Mendes et al., 2013). The rhizosphere microbiota includes bacteria, fungi, nematodes, viruses, protozoa, and algae inhabiting the rhizosphere

 

16 Improving Crop Performance under Heat Stress using Thermotolerant Agriculturally Important Microorganisms

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Improving Crop Performance under Heat

Stress using Thermotolerant Agriculturally

Important Microorganisms

M.K. Chitara,1 Chetan Keswani,2* Kartikay Bisen,1 Vivek Singh,3 S.P. Singh,2

B.K. Sarma1 and H.B. Singh1

1

Department of Mycology and Plant Pathology, Institute of Agricultural Sciences,

Banaras Hindu University, Varanasi, India; 2Department of Biochemistry, Institute of

Science, Banaras Hindu University, Varanasi, India; 3Department of Botany, Institute of

Science, Banaras Hindu University, Varanasi, India

16.1 Introduction

(Hasanuzzaman et al., 2012, 2013) (Fig. 16.1).

One of the major effects of high temperature

Agriculture, particularly in tropical regions, (HT) stress is the excess generation of reactis considered as a sector highly prone to ive oxygen species (ROS), which leads to oxi­climate-change and crop production, due to dative stress (Hasanuzzaman et  al., 2012, incessant stresses caused by natural and an- 2013). Effects of high temperature can be seen thropogenic factors. Increasing incidences at different levels of plant behaviour, i.e. morof biotic and abiotic stresses have become a phological, physiological (photosynthesis, major cause for decline in productivity of ­ respiration), and biochemical/molecular crops. Global climate change, with a predicted changes, in growth as well as in developmen1.5–5.8°C rise in temperatures by 2100, is tal changes resulting in altered life cycle durimposing a great risk to agricultural produc- ation. The basic properties of cellular organtion (Rosenzweig et al., 2001). elles, such as strength of cell membrane,

 

17 Phytoremediation and the Key Role of PGPR

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1

Phytoremediation and the Key Role of PGPR

Elisabetta Franchi1* and Gianniantonio Petruzzelli2

Eni S.p.A, Renewable Energy & Environmental R&D, S. Donato Milanese, Italy;

2

Institute of Ecosystem Study, National Council of Research, Pisa, Italy

17.1 Phytoremediation

The original concept of phytoremediation is derived from studies on plants which can uptake and tolerate extremely high levels of heavy metals. These plants were defined hyperaccumulators (Brooks et al., 1977) and these studies originated from an article

(Minguzzi and Vergnano, 1948), describing the ability of Alyssum bertolonii to accumulate very high amounts of nickel. Brooks

(1998) underlined the seminal importance of this article for the development of phytoremediation: ‘a small perennial shrub in

Tuscany, Italy, was destined to lead the way to a whole range of new technologies and discoveries’. Nowadays, phytoremediation identifies a series of plant-based technologies that can be applied to a wide range of organic and inorganic contaminants for remediating polluted soil, water and sediments, by exploiting the multiple properties of plants, which can be used in different specific processes.

 

18 Role of Plant Growth-Promoting Rhizobacteria (PGPR) in Degradation of Xenobiotic Compounds and Allelochemicals

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Role of Plant Growth-Promoting

Rhizobacteria (PGPR) in Degradation of

Xenobiotic Compounds and Allelochemicals

Deepika Goyal,1 Janmejay Pandey1* and Om Prakash2#

Department of Biotechnology, School of Life Sciences, Central University of Rajasthan,

Bandarsindri, NH-8, Kishangarh, Ajmer-305817, Rajasthan, India; 2Microbial Culture

Collection, National Centre for Cell Sciences, Pune-411007, Maharashtra, India

1

they are characterized by extreme chemical and thermodynamic stability. While this property makes them ideally suited for industrial application and enhances their commercial value, it also makes them extremely

18.1.1  Xenobiotic compounds as priority persistent in the environment. Furthermore, environmental pollutants many of the xenobiotic compounds, e.g. hexachlorocyclohexane (HCH), pentachloropheContamination of Earth’s environment with nol (PCP), polychlorinated biphenols (PCB), toxic xenobiotic pollutants has been a major etc., also exhibit a strong tendency to biocause of concern for several decades. This accumulation. Therefore, organisms posisituation has emerged largely due to non-­ tioned at higher levels in food chains and judicious production, usage and disposal of food webs (including human beings) will xenobiotic pollutants during urbanization tend to have greater accumulation of these and activities related to industrialization toxic compounds compared to those organand agriculture. Xenobiotic compounds are isms present at the lower levels. Noticeably, man-made chemicals (such as explosives, these bioaccumulating xenobiotic compounds pesticides, fungicides, synthesized azo dyes, can be passed from mothers to their children industrial solvents, alkanes, polycyclic aro- during embryonic development as well as matic hydrocarbons, dioxins and furans, through post-­natal breastfeeding. Apart from polychlorinated biphenyls, chlorinated the tendency to bioaccumulate, a large numaromatic compounds and nitro-aromatic ber of xenobiotic compounds can also impart compounds, petroleum products, and bromi- toxic effects to human beings, ranging from nated flame retardants, etc.) that are synthe- acute toxicity, mutagenicity, carcinogenicity, sized for industrial and agricultural application. teratogenicity, etc. In addition, they are harmA majority of the xenobiotic compounds ful due to their ability to poison animals and do not have any known natural source and plants and alter ecosystem functions.

 

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