Freshwater Microbiology: Perspectives of Bacterial Dynamics in Lake Ecosystems

Freshwater Microbiology: Perspectives of Bacterial Dynamics in Lake Ecosystems provides a comprehensive and systematic analysis of microbial ecology in lakes. It offers basic information on how well the bacterial community composition varies along the spatio-temporal and trophic gradients along with the evaluation of the bioindicator species of bacteria so as to act as a key to predict the trophic status of lake ecosystems. The book helps to identify the factors of potential importance in structuring the bacterial communities in lakes as it delves into the dynamics and diversity of bacterial community composition in relation to various water quality parameters. It helps to identify the possibility of bioremediation plans and devising future policy decisions, with better conservation and management practices.

• Provides a comprehensive and systematic analysis of microbial ecology
• Helps to identify the factors of potential importance in structuring the bacterial community composition
• Gives insight into the bacterial diversity of freshwater lake ecosystems along with their industrial potential
• Caters to the needs and aspirations of students and professional researchers

• Language: English
• Publisher: Academic Press
• Release date: Aug 1, 2019
• ISBN: 9780128174968

Book preview

Freshwater Microbiology

Perspectives of Bacterial Dynamics in Lake Ecosystems

Editors

Suhaib A. Bandh

Sana Shafi

Nowsheen Shameem

P. G. Department of Environmental Science, Sri Pratap College Campus, Cluster University, Srinagar, India

Table of Contents

Cover image

Title page

Copyright

List of contributors

Preface

Acknowledgments

Chapter 1. Bacterial community composition in lakes

Introduction

Historical perspective of lake bacterial communities

Study of bacteria in lake environments; why is it so important?

Bacterial biogeography in lakes

Biodiversity and abundance of bacteria from freshwater lakes

Bacterial alpha diversity

Bacterial beta diversity

Bacterial abundances and spatial patterns

Bacterial population dynamics

Diversity-productivity relationship in freshwater bacterial communities

Microbial dormancy

Influence of habitat heterogeneity and submerged macrophytes on bacterial community composition in freshwater lakes

Top-down and bottom-up induced shifts in bacterial abundance production and community composition

Zooplankton and aquatic bacterial linkages in freshwater lakes

Bacterial community resistance and resilience in lakes

Novel bacteria from freshwater lake ecosystems

Case studies of bacterial community of lake ecosystems

Lake Baikal, Russia

Dianchi Lake, China

Lake Tanganyika, Africa

Yunnan Plateau, China

Chandra Tal and Dashair Lake, India

Manasbal Lake, India

Dal Lake, India

Gurudongmar Lake, India

Comparative study of some freshwater lakes in India

Conclusions

Chapter 2. Bacterial diversity of the rock-water interface in freshwater ecosystem

Introduction

Sessile bacteria

Attachment of freshwater bacteria to solid surfaces

Microbial epilithic and endolithic biofilms

Microbial dynamics of epilithic mat communities

Role of epilithic and endolithic microbes

Colonization pattern of bacterial communities in endolithic habitats

Epilithic bacteria and mineral formation

Chemolithotrophic microbial mats on subsurface rocks

Microbial life in deep granitic rocks

Identification of lithic bacteria

Effect of different factors on bacterial attachment to submerged rock surfaces

Case study

Conclusions

Chapter 3. Impact of environmental changes and human activities on bacterial diversity of lakes

Introduction

Sources of bacteria in lake water

Association of lake bacterial diversity with changing environmental features

Human activities and lake bacterial diversity

Climatic variables and lake bacterial diversity

Socioeconomic factors and lake bacterial diversity

Fecal contamination of surface waters

Advances in aquatic microbial detection and quantification

Conclusions

Chapter 4. Spatio-temporal patterns of bacterial diversity along environmental gradients and bacterial attachment to organic aggregates

Introduction

Spatio-temporal distribution of microbial communities

Drivers of microbial communities in lakes

Effect of grazers on bacterial community structure and production in trophic lakes

Diversity-functioning relationships in lake bacterial communities

Environmental heterogeneity and diversity-functioning relationship

Organic aggregates in surface water bodies

Structural composition of aggregate-associated bacterial communities

Diversity of organic aggregate–attached bacteria in lakes

Aggregate-associated organic matter and bacterial turnover

Ecological significance of organic aggregate–attached bacteria

Conclusions

Chapter 5. Metagenomic insights into the diversity and functions of microbial assemblages in lakes

Introduction

Metagenomics: historical perspectives

Sequencing technologies

Metagenomics of freshwater lakes—basic steps (Fig. 5.1)

Freshwater lakes metagenomic studies

Conclusions

Chapter 6. Depth distribution of microbial diversity in lakes

Introduction

The neuston layer

Planktonic freshwater prokaryotes

Phototrophic bacteria

Sediment layer

Vertical distribution of sulfate-reducing bacteria

Vertical distribution of iron-oxidizing bacteria

Vertical distribution of manganese-oxidizing bacteria

Vertical distribution of ammonia-oxidizing archaea in lakes

Case studies

Conclusions

Chapter 7. Exploring bacterial diversity: from cell to sequence

Introduction

Microbial diversity and its importance

Microbial cell structure

Bacillus

Coccus

Vibrio

Spirilla

Structural components of a bacterial cell

Plasma membrane

Cytoplasm

Surface appendages

Bacterial genome

Exploring microbial diversity

Phenotypic approach

Plate counting

Community level physiological profiling

Phospholipid fatty acid analysis

Fatty acid methyl ester analysis

Identification of microorganisms using fatty acid methyl ester analysis

Molecular approach

Barcodes/molecular markers of microbial world

16S rRNA gene

gyrB

23S rRNA gene

rpoB

dnaK

dsrAB

16S-23S rDNA ISR

Molecular tools for exploring microbial diversity

Polymerase chain reaction

Basic concept of PCR

Steps in PCR

Types of PCR

Denature gradient gel electrophoresis (DGGE)

Terminal restriction fragment length polymorphisms (T-RFLP)

Single-strand conformation polymorphism

Amplified ribosomal DNA restriction analysis (ARDRA)

Fluorescent in situ hybridization

Clone libraries

Gel electrophoresis

Polyacrylamide gel electrophoresis

Sequencing of DNA

Conclusions

Chapter 8. Bacterial biofilms: the remarkable heterogeneous biological communities and nitrogen fixing microorganisms in lakes

Introduction

Availability of biofilms in fresh water systems

Biofilm diversity

Biofilm structure

Biofilm formation

Biofilm maturation

Factors influencing bacterial biofilm formation

Quorum sensing and biofilm development

General stress response

Persisters

Culturing biofilms

Methods for characterization of biofilms

Techniques for studying biofilms

Role of biofilms in bioremediation

Types of pollutants remediated by biofilms

Nitrogen fixing microorganisms in lakes

Conclusions

Chapter 9. Microbial diversity in freshwater ecosystems and its industrial potential

Freshwater lake characteristics

Microbial diversity of cyanobacteria

Classification of microalgae and its significance

Biotechnological importance of Cyanobacteria and microalgae

Future industrial potentials of Cyanobacteria (blue-green algae) and microalgae

Industrial processes for microalgae and cyanobacteria

Conclusions

Chapter 10. Bacteria: the natural indicator of environmental pollution

Introduction

Air pollution

Water pollution

Fresh water pollution

Marine pollution

Fecal contamination of fresh and marine waters

Eutrophication

Soil and land pollution

Antibiotic-resistant bacteria as pollution indicators

Pollutant-specific bacterial indicators

Conclusions

Index

Copyright

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List of contributors

Insha Amin,     Department of Environmental Science, University of Kashmir, Srinagar, India

Uqab ali Baba,     Department of Environmental Science, University of Kashmir, Srinagar, India

Suhaib A. Bandh,     P.G. Department of Environmental Science, Sri Pratap College Campus, Cluster University, Srinagar, India

Deepali Bhagat,     School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India

Vinay Singh Chauhan,     Department of Biotechnology, Bundelkhand University, Jhansi, India

Rubiya Dar,     Center of Research for Development (CORD)/P.G. Department of Environmental Science, University of Kashmir, Srinagar, India

Bashir A. Ganai,     Center of Research for Development (CORD)/P.G. Department of Environmental Science, University of Kashmir, Srinagar, India

Qazi A. Hussain,     P. G. Department of Environmental Science, Sri Pratap College, Srinagar, Kashmir, India

M.M.M. Islam,     Ministry of Planning, Sher-e-Bangla Nagar, Dhaka, Bangladesh

Azra N. Kamili,     Center of Research for Development (CORD)/P.G. Department of Environmental Science, University of Kashmir, Srinagar, India

Divjot Kour,     Department of Biotechnology, Akal College of Agriculture, Eternal University, Baru Sahib, India

Akhilesh Kumar,     Department of Botany, Dayalbagh Educational Institute, Agra, India

Amit Kumar,     Department of Botany, Dayalbagh Educational Institute, Agra, India

Halil Kurt,     Department of Earth and Environmental Engineering, Columbia University, United States, New York City

Ruqeya Nazir,     Centre of Research for Development, University of Kashmir, Srinagar, India

Marofull Nisa,     Centre of Research for Development, University of Kashmir, Srinagar, India

Neelu Raina,     School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India

Ali A. Rastegari,     Department of Molecular and Cell Biochemistry, Falavarjan Branch, Islamic Azad University, Isfahan, Iran

Sabeehah Rehman,     Centre of Research for Development, University of Kashmir, Srinagar, India

Shashwati Ghosh Sachan,     Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, India

Lateef B. Salam,     Department of Biological Sciences, Microbiology Unit, Summit University, Offa, Kwara State, Nigeria

Anil Kumar Saxena,     ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India

Sana Shafi,     P.G. Department of Environmental Science, Sri Pratap College Campus, Cluster University, Srinagar, India

Nowsheen Shameem,     P.G. Department of Environmental Science, Sri Pratap College Campus, Cluster University, Srinagar, India

Preeti Sharma,     School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India

Bhanumati Singh,     Department of Biotechnology, Bundelkhand University, Jhansi, India

Parvez Singh Slathia,     School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India

Ajar Nath Yadav,     Department of Biotechnology, Akal College of Agriculture, Eternal University, Baru Sahib, India

Kritika Yadav,     Department of Botany, Dayalbagh Educational Institute, Agra, India

Neelam Yadav,     Gopi Nath P.G. College, Veer Bahadur Singh Purvanchal University, Ghazipur, India

Mir Riasa Zaffar,     Department of Environmental Science, University of Kashmir, Srinagar, India

Preface

Microbiology—the study of miniscule organisms is an exceptionally diverse discipline including many branches like food microbiology, industrial microbiology, soil microbiology, freshwater microbiology, environmental microbiology, and microbial ecology. Microbial ecology—the study of microorganisms in relation to their biotic and abiotic environments is a link between all the branches of microbiology. Although the study of freshwater microbiology involves all the major disciplines within biology including taxonomy, molecular biology, biochemistry, and structural biology, this book has been compiled as a systematic and comprehensive guide of microbial ecology in lakes with particular reference to the dynamics of bacteria in freshwater lakes. It is designed to cater to the needs of the students and researchers in the related fields, who otherwise find themselves in a chaotic situation due to lack of concentrated literature in this growing and all important field of science. It has been designed as an effective research tool, as it is easy for the researchers to use because of its enhanced readability due to the use of simple, organized, and direct outline formatting. The content of the book is arranged in a logical progression from the fundamental to the more advanced concepts. It provides a detailed overview of the bacterial diversity, its ecological interactions, spatiotemporal dynamics in relation to the various water quality parameters, and metagenomic insights into the diversity and functions of microbial assemblages in lakes. It provides the basic information on how well the bacterial community composition varies vis-à-vis the changing seasons and the anthropogenic activities taking place in the catchment of the lakes along with the evaluation of the bioindicator species of bacteria. It identifies the factors of potential importance in structuring the bacterial communities in the lakes. Although lots of books are available on the different microbiological themes, none of them gives a detailed compilation of the bacterial diversity of aquatic ecosystems, especially freshwater lakes. The book contains many illustrations in the form of tables, diagrams, and case studies to better understand the basic facts about microbes and factors affecting them without drowning the student in unexplained jargons and impenetrable details. The book provides a detailed description of the methods involved for exploring the bacterial diversity from freshwater ecosystems and the students and researchers will find it useful in further evaluating the diversity of bacteria in the lake ecosystems. We hope this book proves useful for researchers and students.

Suhaib A. Bandh

Acknowledgments

If every project has its secret inspiration or at least its one motivation, here that is the PEACE of my life

In the name of Allah, the most Gracious, the most Merciful. May the praise of Allah, in the highest of assemblies, and His peace, safety and security, both in this world and the next, be on Prophet Mohammad (peace be upon Him), the best of mankind, the most respectable personality for whom Allah created the whole universe and the seal of the Prophets and Messengers. We are highly thankful to Allah, Who in his great mercy and benevolence provided us the courage, the guidance, and the love to undertake and complete this project.

First and foremost, we would like to thank all our teachers who held our finger to tread the path of learning and enabled us to compile a book. We deeply thank them for the advice and encouragement which became the guiding light towards our personal and professional development. To be very honest, publication of a research article, review article, or for that matter a book requires the efforts of many people besides the authors. We wish to express our special appreciation to the editorial and production staff of Elsevier for their excellent and efficient work. In particular, we would like to thank Linda Versteeg-Buschman, our Acquisitions Editor, for her unwavering confidence in us and Sandra Harron, our editorial project manager, for her time, guidance, patience, and support. She was there whenever needed. Inevitably, a book of this type relies heavily on previously published work, and I would like to thank holders of copyright for granting permission to publish original diagrams and data. Special thanks are due to our copyright coordinator Indhumathi Mani who supervised all the copyright permissions for the material used in the form of images, etc., in the production of this book. Our production manager Sreejith Viswanathan supervised the production of this project with commendable attention to all the minute and vivid details. Our special thanks go to all the authors who have contributed chapters for this book, but we would fail in our duty if we fail to give the most special thanks to Dr. Lateef Salam one of the authors who wrote on the metagenomic insights into the microbial diversity for the timely and accurate completion of his assignment to help us to meet all the deadlines from the publisher. We would also like to thank those who first agreed to contribute chapter for the book but finally pulled out of the same that too at some crucial junctures. We wish to extend our appreciation to all the people who assisted us individually in the completion of this project. Suhaib Bandh is grateful to his friends particularly Dr. J. A. Parray and Dr. B. A. Lone for commenting on some sections of some chapters, and for the helpful and detailed comments of other reviewers on the rest of the work. Finally, our thanks are due to all those who have directly or indirectly worked for the successful completion of the project. Finally, but most importantly we wish to extend our appreciation to our families for their patience and encouragement during the compilation of the project. We owe a debt of gratitude to them for their patient forbearance and unwavering support.

We would also like to take the opportunity to thank our friends, colleagues, and students in the Department of Environmental Science, Sri Pratap College Campus at the Cluster University Srinagar and outside.

Suhaib A. Bandh

Sana Shafi

Nowsheen Shameem

Chapter 1

Bacterial community composition in lakes

Ajar Nath Yadav ¹ , Neelam Yadav ² , Divjot Kour ¹ , Akhilesh Kumar ³ , Kritika Yadav ³ , Amit Kumar ³ , Ali A. Rastegari ⁴ , Shashwati Ghosh Sachan ⁵ , Bhanumati Singh ⁶ , Vinay Singh Chauhan ⁶ , and Anil Kumar Saxena ⁷       ¹ Department of Biotechnology, Akal College of Agriculture, Eternal University, Baru Sahib, India      ² Gopi Nath P.G. College, Veer Bahadur Singh Purvanchal University, Ghazipur, India      ³ Department of Botany, Dayalbagh Educational Institute, Agra, India      ⁴ Department of Molecular and Cell Biochemistry, Falavarjan Branch, Islamic Azad University, Isfahan, Iran      ⁵ Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, India      ⁶ Department of Biotechnology, Bundelkhand University, Jhansi, India      ⁷ ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India

Abstract

Bacteria are ubiquitous organisms, inhabiting almost every part of earth including the extreme habitats, and in aquatic ecosystems they represent dense assemblages with varied morphological, physiological and ecological preferences. In these freshwater ecosystems bacterial community composition is determined by using various culture-dependent as well as culture-independent techniques (DNA isolation, PCR amplifications, amplified ribosomal DNA restriction analysis, sequencing, and phylogenetic profiling). The chapter deals with the bacterial community composition of lakes, their diversity, distribution, functional annotations, and their relationship with other organisms in aquatic ecosystem. Later in the chapter the bacterial community's responses to disturbance (natural as well as anthropogenic) are discussed. The chapter further reviews the bacterial community composition of various lakes, novel species obtained from these lakes, and the dominant phyla (Actinobacteria, Cyanobacteria, Acidobacteria, Caldeserica, Calditrichaeota, Verrucomicrobia, Chlorobi, Planctomycetes, Nitrospirae, Chloroflexi, Bacteriodetes, Firmicutes, and Proteobacteria) found in these freshwater ecosystems.

Keywords

Bacterial community composition; Biodiversity; Lake habitats; Novel bacterial species; Population dynamic

Introduction

During the course of evolution of life on earth, microbes evolved long before the origin of plants and animals, thus making them the oldest life forms on earth. They are more than 3.5–3.8   billion   years old, single-celled organisms, so small in size that millions of microbes fit in the eye of a needle. Microbes are omnipresent on earth, inhabiting almost every part of the earth including soil, water, air, and even other organisms (Canganella & Wiegel, 2011; Yadav, Kumar et al., 2017; Yadav, Verma, Kumar, Sachan, & Saxena, 2017). They also inhabit the extreme habitats including hot springs (Brock, 2012; Brook, 1980; Kumar, Yadav, Tiwari, Prasanna, & Saxena, 2014; Sahay et al., 2017; Suman, Verma, Yadav, & Saxena, 2015; Verma, Yadav, Suman, & Saxena, 2012; Yadav, Verma et al., 2015), deep sea hydrothermal vents (McCollom & Shock, 1997); saline environments (Antón, Rosselló-Mora, Rodríguez-Valera, & Amann, 2000; Saxena et al., 2016; Yadav, Sharma et al., 2015); cold environments—Permafrost soils, glaciers, ice sheets, and snow cover (Boyd et al., 2011; Singh et al., 2016; Yadav, 2015, p. 234; Yadav, Sachan, Verma, & Saxena, 2015; Yadav, Sachan, Verma, Tyagi et al., 2015); acid mine drainages (Baker & Banfield, 2003); and kilometers beneath earth’s surface (White, Phelps, & Onstot, 1998). The extremophilic microbes have also been reported as associated with plants growing in extreme environmental conditions (Kour et al., 2017; Rana, Kour, Yadav, Kumar, & Dhaliwal, 2016; Srivastava et al., 2013; Yadav, Verma, Sachan, Kaushik, & Saxena, 2013). Bacteria appear more abundantly than other creatures, like plants and animals, in these diverse habitats on the face of earth, with their numbers ranging from 4   ×   10³⁰ to 6   ×   10³⁰ on earth (Horner-Devine, Carney, & Bohannan, 2004). They are also abundantly found in oceanic and terrestrial environments, for example, in marine waters bacterial numbers range from 0.2 to 2.0   ×   10⁹ cells/L (Turley & Mackie, 1994). These extreme environments usually present hostile conditions to humans and the majority of life forms on earth, but the extremophilic bacteria found therein have evolved to tolerate or even thrive well within these environments (Canganella & Wiegel, 2011; Yadav, Verma, Sachan, Kaushik, & Saxena, 2018). Such environments contain relatively simplified microbial communities that have evolved specific life history strategies to survive in these environments (Oren, 2002). Thermophiles, for example, have amino acid substitutions in many of their most important proteins that decrease their flexibility and increase their resilience (Aguilar, Ingemansson, & Magnien, 1998). Psychrophiles, in contrast, have experienced mutations that increase protein flexibility to maintain stable active sites in very cold environments (Lonhienne, Baise, Feller, Bouriotis, & Gerday, 2001; Yadav, Verma, Sachan et al., 2018). In hot deserts the bacteria like Deinococcus radiodurans has evolved sets of polymerases capable of reassembling the entire genome after being fragmented by years of UV radiation and cellular desiccation, and reviving when water becomes available again (Zahradka et al., 2006). In order to combat the osmotic pressure of high-saline environments, halophile genomes encode multiple Na+/H+ antiporters, Na+ gradient-powered ATPases, cytoplasmic accumulation of K+, or even the synthesis of organic osmolytes to control osmotic pressure (Ciulla, Diaz, Taylor, & Roberts, 1997; Mesbah & Wiegel, 2011).

Freshwater bacteria are a very dense assemblage of prokaryotic organisms with varied morphology, physiology, and ecological preferences. Bacteria are widespread in freshwater environments, forming extensive pelagic and benthic populations in a wide range of habitats including mudflats, bogs, sulfur springs, lakes, and rivers. In lake environments, different species of pelagic bacteria position themselves in the water column in relation to local conditions like light intensity, oxygen level, and nutrient concentration. So, bacterial community composition (BCC) among lakes varies with different environmental variables (Van der Gucht et al., 2005; Yang, Jiang, Wu, Liu, & Zhang, 2016). Lake water and sediments of the different habitats with unique intrinsic environmental conditions result in their unique bacterial community composition (Yang et al., 2013) and such difference account for different microbial biogeographies in lake environments (Lindström & Langenheder, 2012; Yang et al., 2016).

Historical perspective of lake bacterial communities

Till recently the traditional culture-based cultivation techniques lead to the notion that the microorganisms inhabiting the terrestrial and aquatic habitats were quite similar (Rheinheimer, 1980). But the advent of modern tools and techniques like the molecular techniques provided unprecedented access to the diversity and composition of bacterial communities helping the scientists to note down a clear distinction between the bacteria found in these distinct habitats (Lozupone & Knight, 2007), thus revealing their unique physical and chemical characteristics (Rappé, Vergin, & Giovannoni, 2000; Zwart et al., 2003). The BCC not only varies along the larger gradient of oceans and continents but also within and between the aquatic habitats, as contrastingly distinct BCC was observed from oceans and freshwater lakes (Lozupone & Knight, 2007; Rappé et al., 2000). Zwart, Crump, Kamst-van Agterveld, Hagen, and Han (2002) gathered the reported 16S rRNA gene sequences from some 11 freshwater lakes and 2, as part of an independent study and resulted in the collection of 689 bacterial 16S rRNA gene sequences and enabled the identification of 10 freshwater phyla and 34 supposed bacterial freshwater clusters, defined as a monophyletic branch of a phylogenetic tree that contained at least two sequences with ≥95% gene identity from more than one freshwater environment. Many of the identified clusters were seen to be common in the freshwater, representing the unique bacterial taxa found only in the freshwater ecosystems. However over the past many years, the frequent use of molecular techniques have helped to fill the gap in the literature about the freshwater bacterial communities to a larger extent by retrieving innumerable bacterial groups from these freshwater ecosystems. Hence a large number of newly observed freshwater lake clusters have come to fore in the recent times. However, the lack of a cohesive collection of the known sequences and defined clusters from these habitats still leaves a huge scope to work in the direction of compiling a comprehensive data base of the sequences and gene clusters of the freshwater environments.

Study of bacteria in lake environments; why is it so important?

Prokaryotes are among the most important contributors to the transformation of complex organic compounds and minerals in freshwater sediments (Jurgens et al., 2000). Bacteria the main heterotrophic (using organic substances as a carbon and energy source) microorganisms in various aquatic ecosystems, play key roles in biogeochemical cycles and are the key components of the microbial food webs, especially of the microbial loop. They play a very critical role not only for the normal functioning of life on the planet earth but also for its maintenance and continuity. Being the pioneering colonizers, their ability to survive, propagate, and inhabit a wide variety of environs manifests their evolutionary success. Microbial biodiversity is gaining more importance not only to understand the evolution of the bacterial communities in lake ecosystems but also to determine the ecological impact of certain niches and changing climate on the distribution and diversity of the BCC (Joshi, Pande, & Joshi, 2016). In lake ecosystems these bacteria participate in the decomposition of organic material into nutrients taken as food by other organisms and controlling the water quality in lakes (Newton, Jones, Eiler, McMahon, & Bertilsson, 2011). These microorganisms also play a critical role in remineralizing and restoring the nutrients which influence the material circulation in aquatic ecosystems (Tong et al., 2005). Since the bacteria are present in the sediments of the lake ecosystems, they are responsible for biodegradation of contaminant compounds, such as polycyclic aromatic hydrocarbons (PAHs) (McNally, Mihelcic, & Lueking, 1998). Beside these, the microorganisms also act an important food and nutrient sources for other organisms such as protozoans present in the aquatic ecosystems. In absence of aquatic microorganisms, the food chain system may be disturbed greatly and ecosystem imbalance may occur, thereby affecting the existence of the biotic and abiotic system associated with it. The microbes play an important role on nutritional chains as well as maintaining the biological balance (Madsen, 2008). The anthropogenic activities like religious activities, tourism, bathing, washing, open defecation, surface drainage, irrigation runoff, industrial discharge, and domestic wastewaters adversely affect the water quality of the lakes, and lakes being sensitive ecosystems respond quickly to any natural or human-induced change in their watershed. By the nature of their biological activities, autotrophic and heterotrophic microorganisms are sensitive indicators of the ecological and water-quality status of aquatic environments. However, only by thoroughly understanding how microorganisms function in healthy aquatic ecosystems helps us to recognize or accurately predict their responses to water-quality changes or other environmental disturbances. Here comes the role of our tiny natural scavengers (microorganisms in general and bacteria in particular) which are widely distributed in nature for their ability to treat these wastes and maintain the ecological balance. As these microorganisms are well adapted and diversified in almost all lakes, they have been used as an indicator for the suitability of water quality (Okpokwasili & Akujobi, 1996).

Besides working as scavengers, nowadays microbes in these aquatic ecosystems are also gaining attention for their byproducts and are being extracted for production of useful chemicals. These aquatic bacteria as a rich source of hydrolytic enzymes such as amylases, lipases, proteases, phospholipase, catalases, and other important industrial enzymes (Mudryk & Podgorska, 2006). The extracted enzymes have industrial potential due to their wide biochemical applications in food industries, medicinal formulations, detergents, and waste treatment (Saurabh, 2007). Presently, the largest part of the enzyme market is occupied by the alkaline proteases (derived from Bacillus species) having varied applications. Similarly the enzyme phospholipase obtained from lake lipolytic bacteria plays a key role in bakery and is used in bread making, egg yolk industry, and refinement of vegetable oils. Another important enzyme α-amylase obtained from the bacteria, used in hydrolyzing of the starch molecules is important in many industrial processes and constitutes 25% of the worldwide enzyme market (Syed, Agasar, & Pandey, 2009). The microbes by virtue of their pivotal roles in organic matter production and decomposition, by dissolved to particulate organic matter conversions, nutrient uptake and regeneration, and biogeochemical transformations, are essential to the ecological functioning of aquatic systems.

Prokaryotes are responsible for biological, geological, and chemical processes in aquatic environments (Matcher, Dorrington, Henninger, & Froneman, 2011). All organisms in an ecosystem rely on the activities of microorganisms. In many aquatic environments, increased phytoplankton numbers like algae are followed by increase in heterotrophic bacterial activities and production. The function and metabolism of an ecosystem is highly influenced by bacterial activities because an important proportion of planktonic biomass is dominated by bacteria. The active bacterial community is involved in uptake of substrates, metabolic process, growth, and reproduction (Freese & Schink, 2011). In aquatic ecosystems 36% of the total bacterial populations were involved in respiration in freshwater samples, while in marine systems they represent only 12% (Zimmermann, Iturriaga, & Becker-Birck, 1978).

More than 50 phyla of bacteria and archaea are responsible for decomposition of dissolved organic matter (DOM) in natural aquatic environments (Kirchman, Cottrell, & Lovejoy, 2010). Determination of dominant bacterial groups of heterotrophic nature in freshwater ecosystems is very important because the bacterial groups take up and control dissolved organic matter and contribute to other processes like cycling of matter and energy in the environment (Kirchman, Dittel, Findlay, & Fischer, 2004). Study of bacterial community composition is also important to understand the active bacterial cells in the environment, for example, decomposition of organic matter, bacterial entity, and viability (Kenzaka, Yamaguchi, Prapagdee, Mikami, & Nasu, 2001; Verma, Yadav, Kumar, Singh, & Saxena, 2017; Yadav, Kumar, Prasad, Saxena, & Dhaliwal, 2018; Yadav, Verma, Kumar et al., 2018). The study of bacterial community in aquatic environment is important due to following reasons:

1. To acquire knowledge about the diversity of microbial genetic resources in aquatic environment.

2. To understand the distribution pattern of microorganisms in aquatic environment.

3. To understand the functional role of microbial diversity in aquatic environment, and.

4. To understand the regulation of microbial biodiversity in freshwater lake environments

.

Bacterial biogeography in lakes

Biogeography is the observation, recording, and explanation of the geographic ranges of organisms (Pielou, 1979). Although microbes do have biogeographies, this subject has received very little attention. Microbial biogeography is generally absent from recent books (Bull, 2004; Ogunsseitan, 2005) as are microbes from the discussions on biogeography (Lomolino & Heaney, 2004; Pielou, 1979) or ecological geography (Longhurst, 1998). To some extent this is probably because of the perception that there is no interesting microbial biogeography as all microbes exist potentially everywhere. The earlier application of new molecular tools and techniques to bacterial biogeography in freshwaters showed that the bacterial community composition (like phytoplanktons and zooplanktons) changes with the changing seasons and the nearby lakes differ in BCC (Konopka, Bercot, & Nakatsu, 1999; Lindström, 2000) indicating no clear relationship between lake location and BCC as, for example, Lindström (2000) compared communities of five small lakes in southern Sweden, all within a distance of 75   km from each other, using denaturing gradient gel electrophoresis (DGGE) and observed that the community composition differed with seasons as much as it varied between lakes. Statistical analysis suggested strongest relationships between the variability of BCC and variability in the biomass of microzooplankton, cryptophytes, and chrysophytes rather than between lake location or size. A spatial scale comparison of bacterioplankton communities in a set of lakes in different climatic zones of Sweden (northern and southern) and Norwegian Arctic showed little evidence that the neighboring lakes share bacterioplankton communities (Lindström & Leskinen, 2002) which can be an artifact of the spatiotemporal sampling scales. However, it clearly displayed the importance of biological interactions, and/or physiochemical conditions of the lakes to determine the bacterioplankton communities. Considering the spatial variability in the bacterioplankton communities, Yannarell and Triplett (2004) investigated some 13 northern temperate lakes (Wisconsin, USA) using automated ribosomal intergenic spacer analysis (ARISA) (a 16S rDNA community fingerprinting technique) to study the variability within and between the lakes and observed that the bacterial communities differed less within a lake than between the lakes. Within the lake, the average dissimilarity was 17%, while between lakes it was 75%. Further, the lake bacterial diversity positively related to lake productivity is determined through chlorophyll concentration range. In the next year Yannarell and Triplett, found that the bacterial community composition related to both location and lake type from a study carried out on a larger spatial scale in two sets of Wisconsin lakes separated by about 300   km, sampled during the spring, summer, and fall (Yannarell & Triplett, 2005). Studies carried out on northern temperate lakes (both Scandinavian and North American) showed that the overall composition and characteristics of bacterial communities and the lake geography are interrelated, suggesting that the lake location is a poor predictor of BCC, and taxonomic richness is not closely related to lake size. These findings are in conflict with basic predictions of Island Biogeography theory (MacArthur & Wilson, 1967): (1) neighboring lakes should resemble one another in taxonomic composition more than distant lakes; and (2) system size should be related to taxonomic richness. However, Dolan (2005) mentioned in his paper on Biogeography of aquatic microbes that a few recent studies (Bell, Ager, Song, Newman, Thompson, Lilley, & vander Gast, 2005; Reche, Pulido-Villena, Morales-Baquero, & Casamayor, 2005) carried out specifically to test predictions of Island Biogeography, concluded that freshwater bacterioplankton communities do conform to the theory of Island Biogeography. In contrast to the contradictory studies, Reche et al. (2005) reported that nearby lakes contained similar taxa. Overall there exist some support that the existence of biogeographic patterns in lake bacteria, in terms of "species" as ribotypes, seems to depend on the spatiotemporal scales.

Biodiversity and abundance of bacteria from freshwater lakes

In order to evaluate any community, it is essential to quantify the different aspects of the community by way of alpha diversity (number of taxa present in a single community or location), beta diversity (variation in the community composition), and gamma diversity (total diversity across a landscape) (Magurran, 2013; Solow & Polasky, 1994). However, in bacterial communities, alpha and beta diversity are the two important measures which are generally used to explain, evaluate, and scrutinize any changes in the community structure across the spatiotemporal environmental gradients. Further selection, drift, dispersal, and mutation are the four processes that structure the microbial communities (Hanson, Fuhrman, Horner-Devine, & Martiny, 2012). The BCC in the freshwater lake ecosystems have been investigated worldwide (Fig. 1.1)

Bacterial alpha diversity

Maintaining bacterial alpha diversity in natural and managed ecosystems is critical for both purpose and firmness of ecosystem processes (Bell, Newman, Silverman, Turner, & Lilley, 2005; Eisenhauer, Scheu, & Jousset, 2012) because reduction in bacterial alpha diversity possibly results in the loss of crucial ecosystem services. Bacterial alpha diversity has been revealed to modify across environmental gradients, including crossway gradients of primary productivity (Horner-Devine et al., 2004). The diversity-productivity relationship is not constant for all bacterial taxa, suggesting that patterns of alpha diversity may not be universal for all taxonomic groups of bacteria. The high diversity may be due to the complex and fine-scale chemical gradients established in saline sediments, which present exceptionally high numbers of ecological niches for higher bacterial diversity (Torsvik, Øvreås, & Thingstad, 2002). In comparison to the sediment habitats, aquatic habitats are characteristically considered to host less bacterial taxa, probably as a result of a smaller amount of heterogeneity (Chao, Chazdon, Colwell, & Shen, 2006; Curtis, Sloan, & Scannell, 2002; Hughes, Hellmann, Ricketts, & Bohannan, 2001; Torsvik et al., 2002). The processes generating and maintaining bacterial alpha diversity are budding as patterns of variety (Fierer & Lennon, 2011). Due to rapid mutation and lateral gene transfer, evolution of bacterial taxa having novel phenotypic and/or ecological functions are taking place rapidly thus increasing the bacterial biodiversity (Kassen & Rainey, 2004). Due to the significance of bacterial alpha diversity, microbial ecologists have got interested in unfolding the patterns of bacterial prosperity across space and time (Shaw et al., 2008).

Figure 1.1 Map of world depicting freshwater lakes for biodiversity of bacterial community.

Bacterial beta diversity

Beta diversity, variation of species composition along space or time, is a measure of difference in microbial community composition between pairwise sites. The pioneering investigations on beta diversity can be dated back to Whittaker (1972). Beta diversity has been explicitly and thoroughly examined for microbes in both terrestrial and aquatic ecosystems (Green & Bohannan, 2006; Green et al., 2004; Lozupone, Hamady, Kelley, & Knight, 2007; Shade, Jones, & McMahon, 2008), and has further been used in a framework of microbial biogeography to examine the relative importance of habitat (contemporary environmental factors) and province (historical legacies) (Martiny et al., 2006; Takacs-Vesbach, Mitchell, Jackson-Weaver, & Reysenbach, 2008). Microbial beta diversity is not less important than alpha diversity because information on beta diversity helps in understanding the processes shaping microbial distribution pattern (Martiny et al., 2006), in designing systems for preservation of biodiversity (Franklin & Mills, 2007; Green & Bohannan, 2006), in managing microbial communities for bioremediation, and even in developing ecological theories that can be applied to microorganisms ( Hubbell, 2001; Prosser et al., 2007; Ramette & Tiedje, 2007).

It was long thought that because bacteria are microscopic and easily dispersed, the geographic separation could not influence diversity but rather environmental filtering structured the bacterial community. However, patterns of BCC across space and time have emerged and made it evident that taxa are distributed nonrandomly across ecosystems (Horner-Devine et al., 2004). Characterizing BCC and drivers of change in beta diversity has provided insight into some process that leads to assembly and structure. The divergence of depositional environments affects the variation of beta diversity, because the subsurface sediment is strongly shaped by the vertical arrangement of geologic units and their weathering profiles (Lehman, 2007). Furthermore, consideration of the spatiotemporal scales in measuring and comparing beta diversity is crucial, as this scale is known to affect ecological studies in microorganisms (Levin, 1992; Martiny, Eisen, Penn, Allison, & Horner-Devine, 2011; Zinger et al., 2011).

Bacterial abundances and spatial patterns

Structure of bacterial communities is maintained by variable environmental conditions across space and time that represents habitat heterogeneity (Shade et al., 2008; Stocker & Seymour, 2012). Ecological niche separation of coexisting microbial taxa might be triggered by bottom-up (resource availability) and/or top-down control (mortality factors), leading to distinct spatial (longitudinal and vertical) and temporal patterns of distribution of different microbes (Salcher, 2014) within lakes. These spatial patterns range from microscale to larger-scale patchiness (e.g., Green & Bohannan, 2006; Pinel-Alloul & Ghadouani, 2007; Salcher, Pernthaler, Frater, & Posch, 2011; Van der Gucht et al., 2007). Advance in molecular techniques have resulted in significant knowledge of prokaryotic diversity, allowing the evaluation of patterns of spatiotemporal distribution of bacteria (Logue & Lindstrom, 2008). In freshwater ecosystems it has been found that there are different factors responsible for shaping the bacterial community structure (Barberan & Casamayor, 2010; Corno & Jurgens, 2008; Lindström, Kamst-Van Agterveld, & Zwart, 2005; Logue, Burgmann, & Robinson, 2008). The factors include both intrinsic (e.g., dispersal rate, trophic factors) as well as extrinsic (such as latitude, ecosystem size, habitat isolation) factors responsible for the turnover of community composition in space and time. The relevance of each factor varies across large geographical gradients (Schiaffino et al., 2011; Soininen, 2010). Among the factors that regulate prokaryotic assemblages, some of the most important are temperature, ultraviolet radiation, quality and quantity of dissolved organic matter, nutrient concentrations, and grazing pressure (Glaeser, Grossart, & Glaeser, 2010; Lindström et al., 2005; Logue et al., 2015; Newton & McMahon, 2011; Pernthaler, 2005), which can vary in relation to the geographic position, watershed, and surrounding landscape of the lakes. Recent reports based on high-frequency multiyear datasets of site-specific studies have shown that seasonal patterns in bacterial community structure recur in freshwater ecosystems, and these seasonal patterns indicate that some microbial communities change directionally according to environmental conditions (Kara, Hanson, Hen Hu, Winslow, & McMahon, 2013; Rosel, Allgair, & Grossart, 2012; Tammert, Tsertova, Kiprovskaja, Baty, Noges, & Kisand, 2015).

The spatial scale on which bacterial community is analyzed has the ability to influence the interpretation of the relative contribution of selection, mutation, drift, or migration to the community composition (Martiny et al., 2011; Saxena, Yadav, Kaushik, Tyagi, & Shukla, 2015). In terrestrial systems, spatial scale is easily quantified using geographic distance. However, in aquatic ecosystems hydrologic regimes quickly move water parcels thus transporting bacteria and other planktonic organisms with the water mass. A pyrosequencing study compared the composition of bacterial community at three different depths throughout the water column at multiple stations in the North Atlantic Ocean and reported that bacterial community composition was most similar within the same water mass, defined by depth, regardless of horizontal space (Agogué, Lamy, Neal, Sogin, & Herndl, 2011; Cram et al., 2015; Yadav, Sachan, Verma, Suman, & Saxena, 2014).

Long-term observation of marine ecosystems has provided the data mandatory for showing that, along with spatial scale, bacterial communities also vary over time (Gilbert et al., 2012), which also affects the interpretation of the relative contribution of the underlying processes of bacterial community composition. The transformations in beta diversity over time are typically accredited to environmental variation as a result of seasonal or annual changes within the water mass. Additionally, it is possible that on temporal scales different stochastic events further drive changes in beta diversity, for example, on short time scales, ecological drift arising from stochastic events such as births and deaths contribute to heterogeneity in diversity, while on longer time scales stochastic mutation genetic processes lead to evolutionary drift (Martiny et al., 2011).

Bacterial population dynamics

Today, lakes are ecologically regarded as a part of a larger unit, that is, the drainage basin. At a standstill, efforts in lake microbial ecology and diversity have basically focused on within-lake selective forces, rather than external influences on community structure and diversity. Although various studies have shown that lake as well as estuarine community compositions are mainly prejudiced by incoming bacteria (Crump, Adams, Hobbie, & Kling, 2007; Van der Gucht et al., 2005).

The degree of isolation a lake bacterial community experiences, and the degree of influence by inside flow in bacteria on structure of local community depends on the hydrological retention time of the lakes. Lakes with short hydrological retention time contain bacterial communities that are approximately similar to those of the incoming water in comparison to lakes having longer hydrological retention times. This difference is due to the larger amount of imported bacteria into the former type of lake. Thus external factors play an important role in determination of lake bacterial communities, similar to other microbial communities in general (Curtis, Koss, & Grier, 2002; Curtis & Sloan, 2004; Lindström, Forslund, Algesten, & Bergström, 2006). The possible method behind the external control of BCC in lakes is cell transport rate. It means the local community structure is controlled by regional processes like dispersal rates. This external control in large number of lakes may be due to the flow through systems rather than as microcosms with respect to bacterial community that comes to the lake with running water. The cells and growth media continuously reaching the lake from nearby drainage influence the composition of the bacterial community.

Diversity-productivity relationship in freshwater bacterial communities

Huge volume of ecological literature is witness to the fact that the numbers of morphospecies or functional types of macroorganisms in a given habitat are strongly influenced by the rate of conversion of energy and abiotic resources into biomass, that is, productivity (Waide et al., 1999) and as reported by Smith (2007) in his review on Microbial diversity-productivity relationships in aquatic ecosystems there are accumulating evidences from the microbial ecological literature about the obedience of key principles of macroecology by microorganisms. The species–area relationship, considered to be the oldest documented diversity pattern in macroecology (Rosenzweig, 1995), has now been confirmed for bacteria (Bell, Ager et al., 2005; Reche et al., 2005) as well. After a thorough investigation and deeper analysis of the published work (as in Waide et al., 1999) on the diversity-functioning relationships, Smith (2007) classified the relationships into six general categories: (1) flat or random; (2) humped; (3) negative; (4) positive; (5) U-shaped; or (6) variable. The reported shapes of diversity–productivity patterns were found to be dependent on various factors such as geographical region, ecosystem size, community assembly history, or food web structure. Critical analysis of 70 studies carried out on 43 natural systems and 27 experimental or engineered systems could find only one U-shaped relationship in the entire analytical research data set which experimentally obtained relationship for alphaproteobacteria richness (Horner-Devine, Carney, & Bohannan, 2003; Horner-Devine, Leibold, Smith, & Bohannon, 2003). Furthermore, roughly equal numbers of the remaining diversity–productivity patterns were found in the data sets. The diversity–productivity patterns from natural systems were predominantly either negative (35%), positive (28%), or humped (23%); and only a few (14%) showed flat, random, or variable relationships. As illustrated in the literature (Ogawa & Ichimura, 1984), humped diversity–productivity patterns have been reported in natural phytoplankton assemblages (Dodson, Arnott, & Cottingham, 2000; Leibold, 1999) as well as in experimental microbial communities (Horner-Devine, Carney et al., 2003; Horner-Devine, Leibold et al., 2003; Kassen, Buckling, Bell, & Rainey, 2000). (Fig. 1.2a) represent the phylogenetic tree showed the relationship among freshwater bacterial community worldwide. The major generalizations of the