Recent Advancements in Microbial Diversity

Microorganisms are a major part of the Earth’s biological diversity. Although a lot of research has been done on microbial diversity, most of it is fragmented. This book creates the need for a unified text to be published, full of information about microbial diversity from highly reputed and impactful sources. Recent Advancements in Microbial Diversity brings a comprehensive understanding of the recent advances in microbial diversity research focused on different bodily systems, such as the gut. Recent Advancements in Microbial Diversity also discusses how the application of advanced sequencing technologies is used to reveal previously unseen microbial diversity and show off its function.

• Gives insight into microbial diversity in different bodily systems
• Explains novel approaches to studying microbial diversity
• Highlights the use of omics to analyze the microbial community and its functional attributes
• Discusses the techniques used to examine microbial diversity, including their applications and respective strengths and weaknesses

• Language: English
• Publisher: Academic Press
• Release date: Jun 2, 2020
• ISBN: 9780128212660

Book preview

Recent Advancements in Microbial Diversity

Edited by

Surajit De Mandal

Pankaj Bhatt

Contents

Cover

Title page

Copyright

Contributors

Chapter 1: Biodiversity of microbial life: Indian Himalayan region

Abstract

1. Introduction

2. Microbial diversity of IHR region

3. Indian Himalayan region (IHR): psychrophilic microorganisms

4. Applications of psychrophilic microbes

5. Diversity of aquatic microorganisms in IHR

6. Challenges for micro-diversity conservation

7. Factors responsible for functioning of ecosystem of Indian Himalaya

8. Conclusion and future vision

Chapter 2: Microbial endophytes of plants: diversity, benefits, and their interaction with host

Abstract

1. Introduction

2. Isolation of endophytes

3. Biodiversity of endophytic microorganism

4. Plant-microbe interactions and benefits to the plant

5. Conclusion

Chapter 3: A spotlight on the recent advances in bacterial plant diseases and their footprint on crop production

Abstract

1. Introduction

2. Bacterial communities

3. Mechanisms of bacterial plant disease

4. Impact of bacterial disease in crop production

5. Bacterial disease detection methods

6. Bacterial disease management and resistance

7. Recent techniques to overcome plant diseases

8. Conclusion

Chapter 4: Bacterial diseases of banana: detection, characterization, and control management

Abstract

1. Background

2. Bacterial diseases of banana

3. Isolation and identification of the causal bacterial agents of the diseased banana

4. Control management

Chapter 5: Toward an enhanced understanding of plant growth promoting microbes for sustainable agriculture

Abstract

1. Introduction

2. Microbial communities

3. Mechanistic approach of various PGPMs

4. Applications of PGPMs

5. Conclusion

Chapter 6: Multifaceted beneficial effects of plant growth promoting bacteria and rhizobium on legume production in hill agriculture

Abstract

1. Introduction

2. Rhizobium- legume symbiotic relationship

3. Rhizobium-legume symbiosis: mechanism

4. Legume –rhizobium interaction: advantages to non-legumes

5. PGPR and its effect on rhizobial-legume interaction

6. Effect of PGPRs on rhizobial- legume interaction

7. Establishment of additional infection sites

8. Release of plant growth-promoting substances

9. Biological nitrogen fixation (BNF)

10. Decreasing ethylene level (ACC deaminase)

11. Nutrient solubilisation and its uptake by plants

12. Siderophore production

13. Biological control

14. Improved water-use efficiency

15. Conclusion

16. Future perspectives

Chapter 7: Role of rhizospheric microbial diversity in plant growth promotion in maintaining the sustainable agrosystem at high altitude regions

Abstract

1. Introduction

2. Microbial diversity at high altitude regions

3. Microbial adaptations in cold high altitude regions

4. Plant-microbes (PM) interaction

5. The role of rhizosphere microorganisms in hilly agricultural area

6. Enhancement of growth and yield of crops grown in hilly areas

7. Mechanisms involved in plant growth promotions

8. Biofertilizers as a tool for sustainable agriculture

9. Use of carriers for biofertilizers production

10. Liquid bio-inoculums as biofertilizers

11. The current status of effectiveness of bioinoculants developed from native PGPM

12. Conclusion

Chapter 8: Microbes adapted to cold and their use as biofertilizers for mountainous regions

Abstract

1. Introduction

2. Mechanism of plant growth promotion at low temperature

3. Conclusion

Chapter 9: Actinobacteria: diversity and biotechnological applications

Abstract

1. Introduction

2. Occurrence and habitats

3. Diversity of actinobacteria

4. Biotechnology and importance of actinobacteria

5. Actinobacteria as a source of natural products

6. Actinobacteria as a source of enzymes

7. Other aspects of actinomycetes having biotechnological applications

8. Conclusion

Chapter 10: Quorum sensing: the microbial linguistic

Abstract

1. The world of microbes

2. Overview of Quorum sensing: social engagement of microbes

3. Mechanism of Quorum sensing

4. Biofilm: a shield against the challenging environment

5. Applications of Quorum sensing

6. Conclusion

Chapter 11: Exploration of microbial communities of Indian hot springs and their potential biotechnological applications

Abstract

1. Introduction

2. Hot springs: formation and distribution

3. India: a hot spring hub

4. Microbial diversity of Indian hot springs

5. Biotechnological applications of thermophiles

6. Conclusion

Chapter 12: Microbial diversity and functional potential in wetland ecosystems

Abstract

1. Introduction

2. Microbial communities in wetland

3. Biogeochemical transformations driven by microbes in wetlands

4. Conclusion

Chapter 13: Effect of climate change on microbial diversity and its functional attributes

Abstract

1. Introduction

2. Climate change and its causes

3. Impacts of climate changes on microbial diversity

4. Conclusion

Chapter 14: Spatial variation of the microbial diversity in the mangrove dominated Sundarban Forest of India

Abstract

1. Indian Sundarbans at a glance

2. Physiography of the area

3. Microbial diversities in Sundarban Biosphere Reserve (SBR)

4. Study approach

5. Results

6. Discussion

7. Future prospective

Chapter 15: Microbe assisted plant stress management

Abstract

1. Introduction

2. Fungi for mitigation of plant abiotic stress

3. Microbes in mitigating biotic stresses

4. Mechanisms of plant stress management through microbes

5. Conclusion

Chapter 16: Insect gut microbiome and its applications

Abstract

1. Introduction

2. Structure of insect gut

3. The gut as a medium for microbial colonization

4. Insect gut symbionts

5. Role of insect symbiotic microbiota

6. Methods to investigate insect gut microbiome

7. The microbiome of common insects gut

8. Applications of insect gut microbiome

9. Conclusion

Chapter 17: Diversity and the antimicrobial activity of vaginal lactobacilli: current status and future prospective

Abstract

1. Introduction

2. Normal vaginal flora

3. Diversity in lactic acid bacteria (LAB)

4. Influence of age on vaginal microbiota

5. Defense mechanism by LAB

6. Current status and future prospective

Acknowledgments

Chapter 18: Gut microbiota and brain development: A review

Abstract

1. Introduction

2. Various pathways involved in a microbiota- gut communication

3. Immune system

4. Gut microbiome and microglia

5. Synthesis of microbial metabolites

6. Conclusion

Chapter 19: Role of microbial communities in traditionally fermented foods and beverages in North East India

Abstract

1. Introduction

2. Various traditionally fermented foods consumed in North East India

3. Health benefits and importance of different types of traditionally fermented foods

4. Health risks of fermented foods

5. Future aspects of microbes involved in fermentation

6. Conclusion

Chapter 20: Metagenomics: Applications of functional and structural approaches and meta-omics

Abstract

1. Introduction

2. Culture-dependent approaches

3. Culture-independent approaches ‘evolution of metagenomics’

4. Next-generation sequencing

5. Enrichment of metagenome

6. Taxonomic classification of metagenomes

7. Binning

8. Metagenomics approaches

9. Meta-omics approaches

10. Conclusion

Chapter 21: Metagenomics: a vital source of information for modeling interaction networks in bacterial communities

Abstract

1. Introduction

2. Community level dynamics

3. Mathematical modeling in bacterial systems

4. Complexities in building predictive models for bacterial ecologies

5. Metagenomics

6. Metagenomics and bacterial evolution

7. A metagenomics perspective on bacterial interaction

8. Biodiversity analysis

9. Experiments and metagenomics

Chapter 22: Metagenomics based approach to reveal the secrets of unculturable microbial diversity from aquatic environment

Abstract

1. Introduction

2. Cultivation- dependent methods in exploring bacterial diversity

3. Cultivation-independent detection methods

4. Need of metagenomics

5. Metagenomics

6. History of metagenomics

7. Types of metagenomic approaches

8. Metagenomics: aquatic ecosystem

9. Bacterial biodiversity

10. Fungal biodiversity

11. Viral biodiversity

12. Methodology

13. Conclusion

Chapter 23: Metagenomic-based approach to a comprehensive understanding of cave microbial diversity

Abstract

1. Introduction

2. Cave–a unique natural habitat for microorganisms

3. Taxonomic profiling analysis of microbial communities in the era of metagenomics and high-throughput sequencing

4. Taxonomic distribution of cave microbiomes based on targeted 16S rRNA metagenomic sequencing

5. Taxonomic distribution based on whole metagenome shotgun (WMS) sequencing

6. Metabolic potential of cave microbiomes based on whole metagenome shotgun (WMS) sequencing

7. The neglected world of fungi in cave microbiomes

8. Concluding remarks

Acknowledgments

Index

Copyright

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Contributors

Pooja Arya,     ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India

Yaacov Ben-David

State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou

The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, Guizhou, P.R. China

Geeta Bhandari,     Sardar Bhagwan Singh University, Balawala, Dehradun, Uttarakhand, India

Sneha Bhandari,     Department of Biotechnology, Kumaun University Nainital, Bhimtal Campus, Bhimtal, Uttarakhand, India

Mrinal K. Bhattacharya,     Department of Botany & Biotechnology, Karimganj College, Karimganj, Assam, India

Subhash Chandra,     Department of Botany, Kumaun University, SSJ Campus, Almora, Uttarakhand, India

Juan Chen,     XinQiao Hospital, Army Medical University, Chongqing, P.R. China

Arulvasu Chinnasamy,     Department of Zoology, University of Madras, Guindy Campus, Chennai, Tamil Nadu, India

Khushboo Dasauni,     Department of Biotechnology, Kumaun University Nainital, Bhimtal Campus, Bhimtal, Uttarakhand, India

Surajit De Mandal,     Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, P.R. China

Prasenjit Debbarma,     School of Agriculture, Graphic era Hill University, Dehradun, Uttarakhand, India

Purva Dubey,     Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidhyalaya, Raipur, Chhattisgarh, India

Babu Gajendran

State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou

The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, Guizhou, P.R. China

Saurabh Gangola,     School of Agriculture, Graphic era Hill University, Bhimtal, Uttarakhand, India

Anwesha Gohain,     Department of Botany, Arunachal University of Studies, Namsai, Arunachal Pradesh, India

Vinita Gouri,     Cell and Molecular Biology Laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora, Uttarakhand, India

Rasiravathanahalli Kaveriyappan Govindarajan,     Guangdong Province Key Laboratory of Microbial Signals and Disease Control and Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, Guangdong, P.R. China

Sathya Narayanan Govindarajulu,     Department of Physiology, Dr. ALM PGIBMS, University of Madras, Taramani Campus, Chennai, Tamil Nadu, India

Pankaj Kumar Jain,     Indira Gandhi Centre for Human Ecology, Environmental and Population Studies, University of Rajasthan, Jaipur, Rajasthan, India

Dheepthi Jayamurali,     Department of Physiology, Dr. ALM PGIBMS, University of Madras, Taramani Campus, Chennai, Tamil Nadu, India

Diksha Joshi,     Cell and Molecular Biology Laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora, Uttarakhand, India

Tanuja Joshi,     Department of Botany, Kumaun University, SSJ Campus, Almora, Uttarakhand, India

Tushar Joshi

Department of Biotechnology, Kumaun University, Bhimtal Campus, Bhimtal, Uttarakhand;

Department of Botany, Kumaun University, SSJ Campus, Almora, Uttarakhand, India

Arpita Karandikar,     Department of Medical Biochemistry, Dr. ALM PGIBMS, University of Madras, Taramani Campus, Chennai, Tamil Nadu, India

Vikas Kumar,     School of Engineering, The University of British Columbia Okanagan, Kelowna, BC, Canada

Vinay Kumar,     ICAR-National Institute of Biotic Stress Management, Baronda, Raipur, Chhattisgarh, India

Folguni Laskar,     Department of Botany and Biotechnology, Karimganj College, Karimganj, Assam, India

Yanmei Li

State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou;

The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, Guizhou, P.R. China

Boppa Linggi,     Faculty of Agriculture Sciences, Arunachal University of Studies, Namsai, Arunachal Pradesh, India

Wuling Liu

State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, Guizhou

The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, Guizhou, P.R. China

Priyanka Maiti,     Department of Botany, Kumaun University, SSJ Campus, Almora, Uttarakhand, India

Nivedita Manoharan,     Department of Physiology, Dr. ALM PGIBMS, University of Madras, Taramani Campus, Chennai, Tamil Nadu, India

Chowlani Manpoong,     Faculty of Agriculture Sciences, Arunachal University of Studies, Namsai, Arunachal Pradesh, India

Rojita Mishra,     Department of Botany, Polasara Science College, Polasara, Ganjam, Odisha, India

Abhijit Mitra,     Department of Marine Science, University of Calcutta, Kolkata, West Bengal, India

Tapan Kumar Nailwal,     Department of Biotechnology, Kumaun University Nainital, Bhimtal Campus, Bhimtal, Uttarakhand, India

Mahesha Nand,     G.B. Pant National Institute of Himalayan Environment & Sustainable Development, Kosi-Katarmal, Almora, Uttarakhand, India

Amrita Kumari Panda,     Department of Biotechnology, Sarguja University, Ambikapur, Chhattisgarh, India

Veena Pande,     Department of Biotechnology, Kumaun University Nainital, Bhimtal Campus, Bhimtal, Uttarakhand, India

Veni Pande,     Cell and Molecular Biology Laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora, Uttarakhand, India

Anupam Pandey

ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, Uttarakhand

Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, Uttarakhand, India

Satish Chandra Pandey

Cell and Molecular Biology Laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora;

Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, Uttarakhand, India

Ajit Kumar Passari,     Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Mexico City, Mexico

Karthika Ponnusamy,     Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidhyalaya, Raipur, Chhattisgarh, India

Kusol Pootanakit,,     Institute of Molecular Biosciences, Mahidol University, Nakhorn, Pathom, Thailand

Himanshu K. Prasad,     Department of Life Science & Bioinformatics, Assam University, Silchar, Assam, India

Thangjam Premabati,     Department of Biotechnology, Mizoram University, Aizawl, Mizoram, India

Sumi Das Purkayastha

Department of Botany & Biotechnology, Karimganj College, Karimganj, Assam

Department of Life Science & Bioinformatics, Assam University, Silchar, Assam, India

Ravindra,     ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India

Jyoti Rawat,     Department of Biotechnology, Kumaun University Nainital, Bhimtal Campus, Bhimtal, Uttarakhand, India

Ratul Saikia,     Biotechnology Group, Biotechnological Science & Technology Division, CSIR-North East Institute of Science & Technology, Jorhat, Assam, India

Lilly M. Saleena,     Department of Biotechnology, SRM Institute of Science & Technology, Kattankulathur, India

Mukesh Samant,     Cell and Molecular Biology Laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora, Uttarakhand, India

Diksha Sati,     Cell and Molecular Biology Laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora, Uttarakhand, India

Tapti Sengupta,     Department of Microbiology, West Bengal State University, Berunanpukuria, Malikapur, Kolkata, West Bengal, India

Indu Sharma,     Department of Microbiology, Assam University, Silchar, Assam, India

Priyanka Sharma,     Department of Botany, Kumaun University, DSB Campus, Nainital, Uttarakhand, India

Xiangchun Shen,     School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, P.R. China

Anup Kumar Singh,     Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidhyalaya, Raipur, Chhattisgarh, India

Ravindra Soni,     Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidhyalaya, Raipur, Chhattisgarh, India

Rajendra Sonwani,     Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidhyalaya, Raipur, Chhattisgarh, India

Jithin S. Sunny,     Department of Biotechnology, SRM Institute of Science & Technology, Kattankulathur, India

Deep Chandra Suyal,     Department of Microbiology, Eternal University, Baru Sahib, Sirmaur-Himachal Pradesh, India

Lokesh Kumar Tripathi,     Department of Biotechnology, Kumaun University Nainital, Bhimtal Campus, Bhimtal, Uttarakhand, India

Priyanka H. Tripathi

ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, Uttarakhand

Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, Uttarakhand, India

Shobha Upreti,     Cell and Molecular Biology Laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora, Uttarakhand, India

Krishnapriya M. Varier

Department of Medical Biochemistry, Dr. ALM PGIBMS, University of Madras, Taramani Campus, Chennai, Tamil Nadu

Department of Zoology, University of Madras, Guindy Campus, Chennai, Tamil Nadu, India

Apirak Wiseschart,     Institute of Molecular Biosciences, Mahidol University, Nakhorn, Pathom, Thailand

Nirmal Yadav,     Department of Biotechnology, Kumaun University Nainital, Bhimtal Campus, Bhimtal, Uttarakhand, India

Sagolsem Yaiphathoi,     Department of Microbiology, Assam University, Silchar, Assam, India

Chapter 1

Biodiversity of microbial life: Indian Himalayan region

Khushboo Dasauni

Tapan Kumar Nailwal    Department of Biotechnology, Kumaun University Nainital, Bhimtal Campus, Bhimtal, Uttarakhand, India

Abstract

Microbes are primitive organisms inhabiting the earth since origin of life on earth. Having versatile adaptability, they not only survived millions of years of evolution; they are also highly significant in maintaining ecological balance on earth. Intense cold environments are the hot spots of biodiversity of various groups of microbes. The cold habitats of Indian Himalayan region have a huge diversity of psychrophilic microbes. Cold-adapted microbes have applications in agriculture, medicine and industry as they can produce cold-adapted enzymes, anti-freezing compounds, antibiotics etc. Further, recent research studies are focused to understand their species richness, functional and phylogenetic diversity. Throughout the world majority of these microorganisms especially in extreme habitats still remain unseen and need to be explored and utilized for better use of mankind. Present chapter deals with particulars of microbial biodiversity of Indian Himalaya region and their probable use in industries.

Keywords

Indian Himalayan region

psychrophilic microbes

functional diversity

phylogenetic diversity

biodiversity

1. Introduction

Himalayas are major "hotspots’ of microbial biodiversity, with an enormous but mostly underexplored genetic and biological pool, which can be exploited for novel genes, their products and metabolic pathways. Microbial diversity is varied with living organisms due to evolution, which represents structural and functional diversity (Rampelotto, Ferreira, Barboza, & Roesch, 2013). It comprehends the spectrum of variability among all types of microorganisms in nature and as transformed by human intervention. The probable subsistence of hidden microbial life has been reported from ancient times, such as in Jain scriptures of sixth century BC in India and in first century book On Agriculture by Marcus Terentius Varro. Microbiology, the scientific research on microorganisms begins with their observation under the microscope in the 1670s by Antoine van Leeuwenhoek. In 1850s, Louis Pasteur isolated microorganisms in culture-dependent fashion. This culture dependent method helped in exploration of microorganisms for potential biotechnological practices moreover, it also opened a way for discovery of novel isolates for future studies (Kumar, Yadav, Tiwari, Prasanna, & Saxena, 2014; Piterina & Pembroke, 2010; Barea, Pozo, Azcon, & Aguilar, 2005). Microorganism is a microscopic organism, which survives as single-celled or as a colony of cells. Microorganisms are found in more or less every habitat present in nature, including hostile environments such as the North and South poles, deserts, geysers, rocks and Himalayas.

Himalayan mountain region in the subcontinent of India extends from 2500 Km from east to west (Altitudinal range (over 3000 m), rapid change in altitude (Chitale, Behera, & Roy, 2014) makes it an interesting and one of the richest sources of microflora predominantly fungi, algae, actinomycetes and bacteria (psychrophilic/psychrotolerant bacteria). The Himalayas are divided into (1) Greater Himalaya, (2) Inner Himalayas or Central or Lesser Himalayas and (3) the Sub-Himalayan foothills and nearby areas of Terai and Bhabhar plains. Mountains inhabit approximately 24% of the world's land area and support 12% of the world populations that are living within mountain areas and depend directly on Himalaya for their lives and livelihoods (Sharma, Chettri, & Oli, 2010).

Microbes Isolated from the Himalayas of India could be valuable in agriculture, food and pharmaceuticals industries and these microorganisms are also sensitive indicators of environmental quality, thus microbial diversity may be helpful in determining the environmental status of a given ecosystem habitat. These microorganisms also play an important role as a causative agent for various disease thus they could potentially serve as biological weapons, further this can also be used for removing unwanted materials from environment (Yadav, Sachan, Verma, Kaushik, & Saxena, 2016). In temperate, subtropical, tropical and cold environments, microbial diversity in the Indian Himalayas will give insight into various biological products and processes that may be developed in future.

2. Microbial diversity of IHR region

2.1. Distribution and types

Indian Himalayan Region (IHR) starts from foothills of Shiwaliks in the south and extends up to Tibetan Plateau in the north and spreads between latitudes 26° 20'N and 35° 40'N, and between longitudes 74° 50'E and 95° 40'E. IHR is blessed with affluent natural resources in the form of forest, water, climate, soil and beautiful landscapes. The Indian cold desert is suitable for selection of psychrophiles, fungi, archae with biotechnological application in diverse sectors (Sharma et al., 2010; Singh et al., 2016). Mountain ecosystems are most delicate in world and are susceptible to climate change, urbanization, invasive alien species and other anthropogenic changes (Yadav, Verma, Sachan, Kaushik, & Saxena, 2018).

Northwestern Himalayan region which passes through Jammu and Kashmir up to Ladakh consists of various climatic zones with changeable high-altitude peaks and diverse soil textures. These characteristic features like different altitudes with green meadow, valleys, alpine glaciers and string of different elevation zones harbor remarkable plethora of microorganisms. Microorganisms have been evolving for nearly four billion years and have ability to exploit a vast range of energy sources flourishing in almost every habitat. Alpine glaciers are a rich reservoir of extremophilic microorganisms, particularly psychrophilic/psychrotolerant bacteria and actinomycetes. Some of the major high-altitude areas of Kashmir Himalaya like Thajiwas glacier, Kolahoi, Haramukh, Amarnath glacier and the Apharwatare are a rich source of psychrophilic microorganisms. Its climatic conditions and topological characteristics have been home for thousands of psychrophiles or cold-adapted microbes. Glaciers and the ice cover is the largest freshwater reservoirs which embody about 10% of the surface of Earth. These topological and climatic conditions are vital components of the Earth's atmosphere, still global warming has led to increase in melting rate melting rate of these freshwater reservoirs (Cazenave & Le Cozanne, 2014).

High saline soils and dry elevated plains of Ladakh region of IHR are a massive resource of halophilic and radio resistant bacteria and fungi. These organisms have resistance to high levels of ionizing radiation, most commonly ultraviolet radiation. The greater part of the Himalayas, however, lies below the snow line where mostly mesophilic bacteria, fungi, actinomycetes and endophytes are found. These low elevation areas and slopes usually have a thick soil cover, supporting dense forests along with a diversity of medicinal plants and grasses. All these medicinal plants in different elevations of this zone are an incredible source of bioactive endophytic bacteria and fungi.

2.2. Conditions

Extreme environmental conditions of IHR generally considered unfavorable for growth and survival of plants and animals are usually colonized by microorganisms capable of growth and survivability under the prevailing severe climate. Due to the presence of extremophilic enzymes, proteins and biomolecules in these cold-adapted microorganisms are of great importance in industrial, agriculture and biotechnological applications. Bacteria associated with various phyla have been reported from Indian Himalayan trees such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Planctomycetes, Chlamydiae, Chlorobi, Chloroflexi, Dictyoglomi, Fibrobacteres, Nitrospirae and Verruco microbia. Temperature has a major impact on whether an organism can survive and/or reproduce, and the impact can be direct, indirect or both. Cold environments of Himalayas signify a foremost section of Earth's biosphere which has been occupied by cold-adapted microbes, usually term as psychrophiles. These microorganisms can be cultured at low temperature. In the present scenario, biodiversity across all the major systems like terrestrial or freshwater and levels (genetic, species, and ecosystem) is undergoing major changes and resulting in altered biodiversity, circulation of various ecosystem services downstream and affecting the welfare of people linked to them. Psychrophiles have evolved a complete set of complex morphological and physiological adaptations for their survival. As an outcome, there is evidence of varied metabolic activities in cold ecosystems (Pandit, Manish, & Koh, 2014; De Maayer, Anderson, Cary, & Cowan, 2014).

2.3. Importance

According to ZSI (Zoological survey of India) The Indian Himalaya, acquires 12% of countries landmass, and about 30.16% of its fauna (Pandey & Negi, 1995). Looking into the microbial biodiversity of entire IHR, the chance of finding novel enzyme producing microorganisms which could be exploited for their use in biotechnological applications is certain. IHR is blessed with abundant natural resources in form of forest, water, climate, soil and beautiful landscapes. One-fifth of mankind gets a wide array of ecosystem services from it. They also fulfill the freshwater needs of greater than half of humanity and are regarded as one of the most important water storage reservoirs. Their ecological, aesthetic and socio-economic significance is not only important and beneficial to the people living in them but also to those living downstream and beyond them. Besides this, the management and proper exploitation of microbial diversity of Himalayas which includes mainly bacteria, fungi and actinomycetes, mostly soil inhabiting, have a significant role in sustainable industrial and commercial applications. Further, study of dry mountains of Ladakh revealed the dominance of phototrophic microbial communities with wide diversity of soil cyanobacteria and microalga (Řeháková, Chlumská, & Doležal, 2011; Srinivas et al., 2011). Analysis of the bacterial diversity of the Kafni Glacier in Kumoan Himalayas (altitude of about 3853 m) based on the 16S rRNA gene clone libraries suggests that majority of bacterial genera belonged to the phylum Proteobacteria (Jain, Reza, & Pal, 2014).

Microorganisms living in soil ecosystem control carbon and nitrogen cycle and establish a link between plant diversity and soil ecosystem. Similarly, plant diversity also has an impact on microbial community structure of soil surrounding plant roots. Plant roots secrete root exudates which are used by microorganism for their growth and development. Rhizospheric effect is caused by 5–21% of carbon fixed by plant which is secreted mainly as root exudate (Lugtenberg & Kamilova, 2009; Pala et al., 2011; Sharma, Gosai, Dutta, Arunachalam, & Shukla, 2015). Ascomycota was the dominant phylum, followed by Zygomycota, Basidiomycota and Heterokontophyta. Other dominant group of microorganisms inhabiting Himalayan soil other than bacteria is fungi. Fungi are the most diverse group of organisms, which are the largest group of living organism in terms of species richness. Besides this fact, fungi also constitute more soil biomass compared to bacteria and maintain global carbon cycle by decomposing plant-derived polymeric substances like cellulose, soil organic content, soil texture, surface vegetation and other physiochemical properties of soil. Fungal diversity in soil at higher altitudes of Sikkim and Uttarakhand Himalaya has shown that Penicillium is most abundant and diverse genus present over there. P. raistrickii, P. janthinellum, P. pinophillum, P. javanicum, P. chrysogenum, P. oxalicum, P. purpurogenum and P. aurantiogriseum are some of the commonly occurring species of Penicillium. Aspergillus, Epicoccum, Fusarium, Myrothecium, Cladosporium, Paecilomyces, Gangronella and Trichoderma are other genera contributing to fungal flora of this Himalayan region (Rai & Kumar, 2015). Various Himalayan glaciers have been explored for microbial diversity, documentation and conservation of psychrophilic and psychrotolerant microorganisms (Řeháková et al., 2011; Shivaji et al., 2011). Studies of these Himalayan glaciers reported that Proteobacteria viz., Cytophaga–Flavobacterium–Bacteroides (CFB) and high G + C gram-positive bacteria are common inhabitant of such cold habitats (Srinivas et al., 2011).

3. Indian Himalayan region (IHR): psychrophilic microorganisms

Psychrophiles are extremophilic organisms that are capable of growth and reproduction in extreme low temperatures, ranging from −20 °C to +10 °C. They are found in places that are permanently cold, regions of poles and deep sea. Many such organisms are bacteria or archaea, but some eukaryotes such as lichens, snow algae, fungi, and wingless midges, are also classified as psychrophiles for their ability to grow at low temperature. Presence of more unsaturated fatty acids in phospholipids of cell membrane makes it more liquid, and the protein conformation functional at low temperature.

Psychrophiles grow and divide at freezing temperatures. This unique property of them means that they have successfully overcome two main challenges: viscosity at low temperatures. Significant adaptations of certain organisms have been observed such as Moritella profunda, thermophilic microorganisms suitable for cold and living in the deep ocean. Its optimal growth rate is exhibited at 2 °C with a maximum growth temperature of only 12 °C (Xu et al., 2003). This suggests that certain enzymes or supra-molecular structures have shown conformational changes at temperatures as low as 2 °C with a negative impact on metabolic flux. Psychrophilic microbes have successfully faced two main physical challenges: low heat and high viscosity, both of which slow down metabolic flux.

3.1. Habitat

The cold environments that psychrophiles live in are ubiquitous on Earth, as a large fraction of our planetary surface experiences temperatures lower than 15 °C. They are present in permafrost, polar ice, glaciers, snowfields and deep ocean waters. These organisms can also be found in pockets of sea ice with high salinity content. Microbial activity has been measured in soils frozen below −39 °C. In addition to their temperature limit, psychrophiles must also adapt to other extreme environmental constraints that may arise as a result of their habitat. These constraints include high pressure in the deep sea, and high salt concentration on some sea ice (Saikia et al., 2011).

3.2. Taxonomy of psychrophiles

Psychrophiles comprises bacteria, lichens, fungi, and insects. Among the bacteria that can tolerate extreme cold are Arthrobacter sp. Psychrobacter sp. and members of the genera Halomanas, Pseudomonas, Hyphomonas and Sphingomonas. Another example is Chryseobacterium greenlandensis, found in 120,000-year-old ice. Penicillium is a genus of fungi found in a wide range of environments including extreme cold. Many novel microbes have been sort out from cold environments worldwide including Sphingobacterium antarcticus, Psychromonas ingrahamii, Exiguobacterium soli, Cryobacterium roopkundense, Sphingomonas glacialis, Pedobacterarcticus Sphingobacterium psychroaquaticum Pedobacterarcticus, Sphingobacterium psychroaquaticum Lacinutrix jangbogonensis (Yadav et al., 2015; Chaturvedi et al., 2008; Reddy Pradhan, Manorama, & Shivaji, 2010; Shivaji et al., 2011; Zachariah, Kumari, & Das, 2017; Yadav et al., 2016). Along with novel species of psychrotrophic microbes, some microbial species including Arthrobacter nicotianae, Brevundimonas terrae, Paenibacillus tylopili and Pseudomonas cedrina have been reported first time from cold deserts of North Western Himalayas and exhibited multifunctional plant growth promoting (PGP) attributes at low temperatures (Yadav et al., 2015). The psychrotrophic microbial species Aurantimona saltamirensis, Bacillus baekryungensis, B. marisflavi, Paenibacillus xylanexedens, Pontibacillus sp., Providencia sp., Pseudomonas frederiksbergensis and Vibrio metschnikovii have been reported first time from high altitude and low temperature environments of Indian Himalayas.

Biodiversity of psychrotrophic microbes inhabiting cold habitats has been extensively investigated worldwide and has been reported from phylum, namely Actinobacteria, Gemmatimonadetes, Ascomycota, Acidobacteria, Bacteroidetes, Basidiomycota, Chlamydiae, Chloroflexi, Proteobacteria, Cyanobacteria, Firmicutes, Mucoromycota, Verrucomicrobia, Nitrospirae, Planctomycetes, Spirochaetes, Thaumarchaeota, and Euryarchaeota. Cold habitats of microbiomes includes subglacial lakes, Antarctic, Arctic glacier, permanently ice-covered sea, permafrost, and Himalayan and Mountain lakes and have diverse psychrotrophic, psychrophilic, and psychrotolerant microbes (Rai & Kumar, 2015).

Generally, the distribution of psychrotrophic microbes varied in all bacterial phyla, Proteobacteria were most dominant followed by firmicutes and actinobacteria. Least number of microbes was reported from phylum Chlamydiae followed by Chloroflexi. On review of different cold environments in IHR (permanently ice-covered lakes, ice caped rivers and glaciers), 8 different phylum were found viz., Proteobacteria (42.57%), Firmicutes (32.94%), Actinobacteria (17.78%), Bacteroidetes (2.62%), Basidiomycota (1.75%), Cyanobacteria (1.17%), Chlamydiae (0.58%) and Chloroflexi (0.58%). There are fifteen different extreme cold environments in the IHR including glacier (Roopkund glacier, Pindari glacier, Gangotri glacier, Lahaul and Spiti); Sub-glacial lakes (Chandratal Lake, Dal Lake, Dashair Lake, Gurudongmar lake, Pangong Lake); the Cold desert of Himalayas (Chumathang, Khardungla Pass, Rohtang Pass); Ice-coped revivers (Indus River, Zanskar River, Beas River) (Bhardwaj, Tiwari, & Bahuguna, 2010).

4. Applications of psychrophilic microbes

The Psychrophilic microbes from IHR have engrossed in scientific society due to having the potential valuable in industries, food and medical process and in PGP at low temperatures, additionally have use as biofertilizers, biocontrol agents, bioremediation as well as have various biotechnological applications in agriculture, medicine, industry, food, and allied sectors. (Verma, Yadav, Shukla, Saxena, & Suman, 2015) The psychrophilic/psychrotolerant/psychrotrophic microbes are important for many reasons, particularly because they contain antifreezing, antibiotics, and bioactive compounds (Yadav et al., 2015) and produce extracellular hydrolytic enzymes useful for various biotechnological applications for different processes in industry, pharmaceuticals, medicine, food and feed industry as shown in Table 1.1

Table 1.1

Enzymes from psychrophiles has been fascinating for industrial applications, These enzymes offer opportunities to study the adaptation of life at very low temperature and the potential for biotechnological exploitation (Robb & Maeder, 1998). Most of the work focused on cold-adapted enzymes (amylase, protease, lipase, pectinase, xylanase, cellulase, β-galactosidase and chitinase) produced by psychrophilic microbes, namely Acinetobacter, Aquaspirillum, Arthrobacter, Moraxella, Bacillus, Moritella, Carnobacterium, Planococcus, Clostridium, Cytophaga, Shewanella, Vibrio, Flavobacterium, Marinomonas, Paenibacillus, Pseudoalteromonas, Pseudomonas, Psychrobacter and Xanthomonas (Yadav, Verma, Kumar, Sachan, & Saxena, 2017).

Antifreezing compounds from psychrophilic microbes are helpful in cryosurgery, cryopreservation of whole organisms, isolated organs, cell lines, and tissues. In food industry, anti-freezing protein (AFPs) can be used to maintain the quality of frozen food. Enhanced cold tolerance in fishes has been achieved in some cases by direct injection of AFPs (Singh et al., 2016; Gerday et al., 2000; Groudieva et al., 2004). Cold-adapted microbes possess varied genes responsible for cold adaptation and genes for various molecules and alleles with possible applications in various fields.

The entire genome sequences of cold-adapted microbes helps us to understand the adaptation of microbes under the intense cold habitats and also potential genes for functional attributes, for example, A. agilis L77, is an important psychrophilic bacterium isolated from Pangong lake, Northwest (NW) Himalayas, India. The whole genome sequences of psychrophilic bacteria revealed different genes for adaptation and metabolic activities (Singh et al., 2016).

The PGP psychrotrophic bacilli were investigated from different sites in North-Western Himalayas of India and bacteria have been reported from different genera, namely Desemzia, Exiguobacterium, Lysinibacillus, Sporosarcina, Jeotgalicoccus, Planococcus, Paenibacillus, Sinobaca, Pontibacillus, Staphylococcus, and Virgibacillus (Verma et al., 2015).

Among all known bacterial strains, Bacillus muralis, Bacillus licheniformis, Sporosarcinaglobispora, P. tylopili, and Desemzia incerta, were found to be an important biofertilizers for Indian Himalayan agriculture (Yadav et al., 2016).

Psychrotrophic microbes exhibited multifarious PGP attributes such as ACC deaminase activity, potassium zinc and phosphate solubilization, biological N2 fixation, and production of different bioactive compounds such as gibberellic acids, ammonia, cytokinins, Fe-chelating compounds, hydrogen cyanide, and indole-3-acetic acid. PGP microbes improve plant growth by supplying plant nutrients, which can help maintain environmental health and soil productivity (Yadav et al., 2018) (Table 1.2).

Table 1.2

Psychrotrophic PGP microbes were found in several genera, including Arthrobacter, Bacillus, Burkholderia, Pseudomonas, Exiguobacterium, Janthinobacterium, Lysinibacillus, Methylobacterium, Microbacterium, Paenibacillus, Providencia, and Serratia (Yadav, Tiwari, Kumar, Prasanna, and Saxena, 2014). Microbes having ACC deaminase activity help plant to improve cold stress tolerance (Verma et al., 2015; Yadav et al., 2015; Yadav et al., 2017). Indian cold deserts are suitable for selection of psychrotrophic and psychrotolerant bacteria, archaea, and fungi with potential biotechnological application in diverse sectors. One report (Yadav et al., 2017) shows the presence of Pseudomonas cedrina, Brevundimonas terrae, Arthrobacter nicotianae, and Paenibacillus tylopili in cold habitats for the first time and exhibitions multifarious PGP attributes at low-temperature conditions. In another investigation by (Yadav et al., 2015) the culturable biodiversity of microbiomes in Leh Ladakh region included four phyla, namely Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria with different genera; Bacillus, Desemzia, Pseudomonas, Sporosarcina, Arthrobacter, Psychrobacter, Exiguobacterium, Flavobacterium, Alishewanella, Staphylococcus, Brachybacterium, Klebsiella, Providencia, Paracoccus, Planococcus, Sinobaca, Janthinobacterium, Sphingobacterium, Kocuria, Aurantimonas, Citricoccus, Cellulosimicrobium, Brevundimonas, Stenotrophomonas, Vibrio, and Sanguibacter. These microbes possess PGP attributes and may be applicable as bioinoculants. These microorganisms are known for their degrading activity in feed. Some are pathogenic or toxic to humans, animals or plants. However, in natural microbial ecosystem, during cold season, psychotrophic and psychrophilic microorganisms can play a huge role in biodegradation of organic matter. Psychotrophic microorganisms have been reported as plant growth promoters and biological control agents for sustainable agriculture, as cold-adapted hydrolase in industry, and as secondary metabolites in medicine. Persistent cold conditions in this habitat lead to reduced nutrient bioavailability, reduced enzyme activity, and changes in soil pH, water activity, and soil salinity. These microorganisms have cold shock proteins (CSPs) which provide protection against cold stress, and the presence of CSPs in these microorganisms has been confirmed by the previously done genomic and proteomic analysis of bacterial isolates from Western Indian Himalayas (Suyal, Yadav, Shouche, & Goel, 2014; Soni et al., 2015).

5. Diversity of aquatic microorganisms in IHR

Microbial diversity of Indian Himalayan hot springs was extensively studied using metagenomics and culture-dependent approaches (Sharma et al., 2015; Bhardwaj et al., 2010). Culturable diversity of aquatic microorganisms in soldhar and Ringigad hot springs in the chamoli area of Garhwal Himalaya were studied. Bacteria, filamentous organisms and yeast were the major groups observed. 16S rRNA gene cloning library, denaturing gradient gel electrophoresis (DGGE) and band sequencing of DGGE were used to study the bacterial diversity of Soldhar Hot Springs. Results showed that Proteus was the main population in this habitat, followed by Deinococcus, Thermos and Aquificae. The only archaea found in this hot spring was Pyrobaculum (Sharma et al., 2015). In addition, several cyanobacterial species have been reported from Soldhar and Ringigad hot springs like, Micrococcus, Chroococcus turgidus, Chroococcustenax, Synecococcus elongatus, Synecococcussallensis, Gloeocapsalivida, Myxosarcina sp. Animal Oscillatoria animalis and Oscillatoria limnosa (Kumar, Gupta, Bhatt, & Tiwari, 2011).

6. Challenges for micro-diversity conservation

•Increasing Temperature: Mountains are significant indicators of climate change (Singh, Singh, & Skutsch, 2010). Green house effect has carried increase in temperature and (Cook, Smerdon, Seager, & Coats, 2014) rise in temperature over last 100 years is larger than the overall average of 0.74°C (Joshi, Kumar, & Palni, 2015). Major problem is its least predictability and the effects are detrimental in the long run.

•Variation in precipitation pattern: The Himalayas form major natural water resource of the major river systems of India (Nandargi & Dhar, 2011). Variable rainfall trend has been prevalent across Asia during the last few decades. Both increasing and decreasing precipitation patterns were observed in the Himalayan region

•Retreating glaciers: Himalayan glaciers are receding at a very fast rate (Kulkarni, Rathore, Singh, & Bahuguna, 2011). It is generally a combination of precipitation decrease and temperature increase in the Himalayas. According to an estimate the decrease of glaciers will accelerate if global warming persist for extended period, and many glaciers will retreat even more in the coming years (Li et al., 2015), while smaller ones may completely vanish. It will be severe threat to microbiota native to these glaciers.

7. Factors responsible for functioning of ecosystem of Indian Himalaya

Species richness, functional and phylogenetic diversity and changing abiotic and biotic factors are responsible for normal functioning of ecosystem. Throughout the world, species richness of these micro-organisms needs to be explored and utilized for better use of humankind in particular, and for the environment. Microbial evolution has entered a new era with the use of molecular phylogenies to determine relatedness. Phylogenetic analysis has opened up possibility of comparing very diverse microbes. Therefore, microbial culture collections are encouraged worldwide to create novel and better techniques for bioprospecting of these novel microorganisms. Microbial diversity had addressed biological diversity at three levels: the genetic diversity within species, the species diversity in numerical terms, and the ecological diversity of the community Fig. 1.1.

Figure 1.1   Functional diversity of microorganisms for better use of humankind.

The Himalayas of Arunachal Pradesh, India have species and phylogenetic diversity which provides shift in tree community. In general, elevational declines in richness are due to factors similar to those driving the decline in richness observed along the latitudinal gradient, such as the reduced availability of resources, colder temperatures, and increased extinction rates at regional scales (Lomolino, 2001, McCain & Grytnes, 2010). A reduction of resources (lush soils and nutrients, for example) and colder temperatures at high raises can limit the number of individuals and select for species with specific niche attributes (McCain & Grytnes, 2010), and only those species possessing the appropriate traits and adaptations will be able to establish and flourish in these environments (Jin, Cadotte, & Fortin, 2015; Webb, Ackerly, McPeek, & Donoghue, 2002).

The presence of glacial relicts has roles in determining phylogenetic clustering at high elevations in strongly filtered communities and also contributes to the uniqueness or β diversity of those communities. There is no strong evidence for higher phylogenetic diversity within higher elevation plots in Arunachal Pradesh; it is shown that high elevation plots do indeed contribute disproportionately to regional β diversity, because highly contributing plots are those that contain communities with relatively greater species uniqueness (Legendre & De Cáceres, 2013), this would be consistent with the presence of narrow ranged and evolutionarily distinct endemics at higher elevations.

There is a relationship between elevation and its contribution to beta diversity. It was suggested that there may be a greater incidence of landscape modification and anthropogenic influence (Menon, Pontius, Rose, Khan, & Bawa, 2001; Bhuyan, Khan, & Tripathi, 2003; Roy & Behera, 2005), which may have reformed community structure (Puri et al., 2011; Saqib et al., 2013), which are endemic to the region. The regions with unique species, high endemicity, and distinct geography should become priorities for research and conservation.

Nearly 99% of the microbial group of certain environments cannot be cultivated by standard laboratory techniques and hence there is a necessity for culture-independent methods to know the genetic diversity, population structure and ecological roles of this microbiota. DNA is the most elemental level of biodiversity, drives the process of speciation, and reinforces other levels of biodiversity, comprises functional traits, species and ecosystems (Jobbágy & Jackson, 2000; Kraft, Cornwell, Webb, & Ackerly, 2007; Losos, 2011; Read, Moorhead, Swenson, Bailey, & Sanders, 2014) (Fig. 1.2).

Figure 1.2   Elemental levels of microbial and functional diversity.

Effect of abiotic factors; drought, heat and salinity on the growth and development of Gluconacetobacter diazotrophicus, and the impact of salt stress on some enzymes involved in carbon metabolism of these bacteria was observed. Enzymes glucose dehydrogenase, alcohol dehydrogenase, fumarase, isocitrate dehydrogenase, malate dehydrogenase and Gluconacetobacter diazotrophicus, regardless of its endophytic nature, tolerated heat treatments and salinity stress, while nitrogenase activity and carbon metabolism enzymes were affected by high NaCl dosage. Examination of the biological activity of G. diazotrophicus in response to different abiotic factors led to more knowledge of this endophyte and may help to elucidate pathways involved in its spread into the host plant (Verma et al., 2015; Yadav et al., 2016).

8. Conclusion and future vision

Psychrophilic microbes from IHR produced industrially significant cold-active extracellular hydrolytic enzymes which have diverse role in industrial, agricultural and medical processes. Diversity analyses of different genera by searching extreme cold environments assisted in the development of an enormous database including baseline information on the distribution of psychotropic microbes in different niches and identifying niche-specific microbes. This database also helped in identifying novel microbes with plant growth promoting attributes and biomolecules. The cultures tolerant to low temperatures signify an affluent bioresources for useful genes and alleles, which can aid in the generation of abiotic cold-tolerant transgenics. Microbial diversity of cold environments has attracted the scientific community for production of cold active enzymes production, anti-freezing compounds, secondary metabolites and bioactive compounds. Psychrophilic microbes with multifarious PGP attributes could be used as biofertilizers and biocontrol agents in hilly and low temperature condition for enhanced and sustainable agriculture. Psychrophilic microbes having biodegradation capacity could be used for bioremediation, and waste water treatments for sustainable environments. Psychrophilic microbiomes are widely distributed and have been reported to raise plant growth and alleviation of cold stress in plants. These cold-adapted microbes may be used for biofuels and biodiesel production for future energy systems.

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Chapter 2

Microbial endophytes of plants: diversity, benefits, and their interaction with host

Anwesha Gohaina

Chowlani Manpoongb

Boppa Linggib

Ratul Saikiac

Surajit De Mandald

a    Department of Botany, Arunachal University of Studies, Namsai, Arunachal Pradesh, India

b    Faculty of Agriculture Sciences, Arunachal University of Studies, Namsai, Arunachal Pradesh, India

c    Biotechnology Group, Biotechnological Science & Technology Division, CSIR-North East Institute of Science & Technology, Jorhat, Assam, India

d    Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, P. R. China

Abstract

Plant-microbe interaction has constantly been a fascinating field of research for taxonomists, ecologists, agronomists, chemists as well as evolutionary biologists. The endophytic microbial community has the ability to influence plant growth and yield, suppress plant associated pathogens, increase stress tolerance of plants, solubilise phosphate, contribute nitrogen to plants which is an essential nutrient for many important functions, such as proper growth and development of crops, and thus enhance their ability to withstand the environmental stresses. This community conjointly manufacture a massive array of bioactive compounds, such as antibiotics, antitumor and anti-infection agents, which opens up a new prospect for the drug analysis sector in the field of drug research. In this chapter, we have tried to emphasize the potential benefits of microbial endophytes, their significance and impact on plants.

Keywords

endophytes

plant-microbe interaction

bioactive compounds

1. Introduction

The term endophytes is derived from the Greek ‘endo’ >< ‘endon’ meaning within, and ‘phyte’>< ‘phyton’ meaning plant in the year 1866 and includes microorganisms (mostly bacteria and fungai) that colonizes in the inner tissues of plants and exhibits a symbiotic relationship during a variable period of time (De Bary, 1986). However pathogens and nodule-producing microbes are not included under endophytes. During their life cycle, they draw nutrition and protect the host against pathogen, pests, and insects by synthesizing bioactive metabolites (Strobel & Daisy, 2003). Vogl (1898) was the first person who had reported the presence of endophytes in the grass seed of Lolium temulentum. However, presence of endophytic fungus came into existence in annual grass in Germany (Freeman, 1904). However, the promising niche for isolation of endophytes is the inner tissues of higher plants. There is hardly any plant species where endophytes are not available. The probability of occurrence of endophytic bacteria increases at lower population densities than rhizospheric microorganisms or bacterial pathogens (Hallmann, Quadt-Hallmann, Mahaffee, & Kloepper, 1997; Rosenblueth and Martinez Romero, 2004). However, question may arise that whether endophytes are more beneficial to plants or rhizospheric microorganism. The question is not yet resolved, though, this chapter elucidate the benefits confer by endophytes.

2. Isolation of endophytes

Isolation of endophytes from different plant tissues has always been a challenge for the researchers since the studies on endophytes started. For isolation of endophytes extensively different methods have studied (Reinhold-Hurek & Hurek, 1998, Coombs & Franco, 2003, Taechowisan & Lumyong, 2003). Apart from root, stem, bark, leaf blade, petiole (Hata & Sone, 2008), isolation of endophytes has been also carried out from scale primordia, meristem and resin ducts, leaf segments with midrib (Hata & Sone, 2008). To avoid contamination by surface microbes, surface sterilization of plant tissues is the first and mandatory step for endophyte isolation. The common surface disinfectants used in the process is ethanol (70–95%), sodium hypochlorite (1–10%), hydrogen peroxide, Tween 20 and sometimes Tween 80 and Triton X-100 can also be used to improve the efficacy surface sterilization process (Hallmann, Gabriele, & Schulz, 2006). Coombs and Franco (2003) described a common three-step procedure protocol for surface sterilization; however, Qin et al. (2009) recommended a five-step surface sterilization procedure. Use of sodium hypochlorite as a plant surface disinfectant is beneficial, but sometimes residual sodium hypochlorite solution may kill or effect the growth of endophytes. That is why to improve cultivation efficiency on media plates, addition of sodium thiosulfate solution is necessary to minimize the effects of residual NaOCl on plant material surfaces. Since the sensitivity varies with plant species, age and organs, generally the sterilization procedure should be optimized for each plant tissue. Reinhold-Hurek and Hurek (1998) validated the key rules to recognize true endophytic bacteria. According to his report, to be a true endophytic bacterium microscopic evidence is also necessary. Growth of Endophytic bacteria had studied in the laboratory and revealed that it is dependent on the composition of the media and the cultivation conditions. Mishra et al. (2012) reported that mycological agar (MCA) medium was the most suitable medium for isolation of endophytes with the greatest species richness. Even so, instead of culturing, a new approach is emerging now days. In this context, Araujo et al. (2002) reported that endophytes isolated from citrus plant had not cultured, but were obtained by denaturing gradient gel electrophoresis profiles of 16S rRNA gene fragments amplified from total plant DNA. However, both cultured and culture-independent isolation methods gave similar type of bacteria from genera Pseudomonas and Rahnella in Norway spruce seeds (Cankar, Kreiger, Ravnikar, & Rupnik, 2005).

3. Biodiversity of endophytic microorganism

Among the varied types of ecosystems on Earth, the most diverse microorganisms may be isolated from the one having greatest biodiversity. The most biologically diverse and species rich ecosystems on earth is the tropical and temperate rainforests (Strobel et al., 2002). They reported that tropical and temperature regions are the most effective reservoir for the greatest diversity of endophytes. A total of 123 endophytic actinomycetes were isolated from tropical plants collected from a number of sites in Papua New Guinea and Mborokua Island, Solomon Islands (Janso & Carter, 2010). Though these sites cover only 1.44% of surface of land, yet they yield more than 60% of the world’s terrestrial biodiversity (Mittermeier, Meyers, Gil, & Mittermeier, 1999) such that variation within endophytic population can also be obtained. Yu et al. (2010) also reported that ethno-botanical medicinal plants are potential repertoire for the isolation of endophytic microbes. For example, Zhao et al. (2011) isolated 560 endophytic actinomycetes from Chinese medicinal plants and confirmed the broad-spectrum antimicrobial activities in them. Du, Su, Yu, & Zhang (2013) studied the endophytic diversity among 37 medicinal plants and consequently reported 600 actinobacteria which belong to 34 genera and 7 unknown taxa. Likewise, enormous evidences were obtained on endophytic fungi (Hasegawa, Meguro, Shimizu, Nishimura, & Kunoh, 2006; Gunatilaka, 2006; Ryan, Germaine, Franks, Ryan, & Dowling, 2008; Verma, Kharwar, & Strobel, 2009a; Verma et al., 2009b). Endophytic populations had already been studied from 2400 segments of Oryza sativa where nineteen different fungal taxa, a Streptomyces sp. and bacterial species were isolated. Interestingly, diversity of endophytes population varies depending on bacterial species and host genotypes; the host developmental stage as well as inoculum density also influences endophytic population (Pillay & Nowak, 1997; Tan, Hurek, & Reinhold-Hurek, 2003). However, the different environmental conditions may also affect the diversity and species distribution among the host plants (Hou et al., 2009).

It has been reported that only 1% of bacteria are presently identified (Davis, Joseph, & Janssen, 2005) which indicate that there are still millions of microbial species left to be discovered and identified. To find out the complex endophytic microbial community, applications of 16S rRNA gene-based culture independent molecular approaches, viz. polymerase chain reaction (PCR)-based 16S rRNA gene clone library, denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism (T-RFLP) analysis are convenient tools. But, to explore the endophytic community, both culturing methods and culture-independent methods are essential. A large diversity of actinobacteria was obtained from wheat root using the T-RFLP cultured independent method (Conn