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Handbook of Aquatic
Microbiology
This comprehensive handbook covers the different aspects of the aquatic environment, micro-
biology, and microbial applications. The world’s aquatic environment is facing a serious threat
due to inappropriate planning, implementation, and management. This book compiles effective
strategies for managing the aquatic environment. It highlights the role of microorganisms as
pollution indicators, in bioremediation, and as bio-control agents. The book also covers the im-
pact of pollution on microorganisms, biolms, cyanobacterial blooms, and the metagenomics
approach to isolate microbes. This book is essential for students and researchers of microbiol-
ogy, environmental sciences, and biotechnology.
Pramod Kumar Pandey is the director of ICAR-Directorate of Coldwater Fisheries Research,
Anusandhan Bhavan, Bhimtal, Uttarakhand, India.
Sumanta Kumar Mallik is a scientist (SS) at the ICAR-Directorate of Coldwater Fisheries
Research, Anusandhan Bhavan, Industrial Area, Bhimtal, Uttarakhand, India.
Rameshori Yumnam is an assistant professor in the Department of Zoology at the Manipur
University, Imphal, India.
Handbook of Aquatic
Microbiology
Edited by
Pramod Kumar Pandey, Sumanta Kumar Mallik, and
Rameshori Yumnam
Designed cover image: Shutterstock
First edition published 2025
by CRC Press
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and by CRC Press
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CRC Press is an imprint of Taylor & Francis Group, LLC
© 2025 selection and editorial matter, Pramod Kumar Pandey, Sumanta Kumar Mallik, and Rameshori Yumnam; individual chapters,
the contributors
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ISBN: 9781032526805 (hbk)
ISBN: 9781032528205 (pbk)
ISBN: 9781003408543 (ebk)
DOI: 10.1201/9781003408543
Typeset in Times
by Deanta Global Publishing Services, Chennai, India
v
Dedicated
to
Dr. Panjab Singh
in recognition of his unwavering service to the pursuit of
knowledge and his remarkable impact on Indian agriculture
vii
Contents Contents
Contents
Foreword ............................................................................................................................................x
Preface...............................................................................................................................................xi
Contributors .....................................................................................................................................xii
Chapter 1 Microbiomes of the Aquatic Environment ................................................................... 1
Pragyan Dash, Ritesh Shantilal Tandel, and Raja Aadil Hussain Bhat
Chapter 2 Microbial Planktonic Communities ........................................................................... 12
Garima, Kishor Kunal, and Parvaiz Ahmad Ganie
Chapter 3 Climate Change: A Strong Driving Force for Cyanobacterial Bloom ....................... 28
Snatashree Mohanty, Anirban Paul, and Pramoda Kumar Sahoo
Chapter 4 Benthic Microbial Community in the Aquatic Environment ..................................... 40
Pramod Kumar Pandey, Richa Pathak,
Rameshori Yumnam, and Sumanta Kumar Mallik
Chapter 5 Sediment Microbiology in the Aquatic Environment ................................................ 56
Sumanta Kumar Mallik, Richa Pathak, and Neetu Shahi
Chapter 6 Biogeochemical Cycles and Their Signicance in Nutrient Recycling ..................... 77
Abhay Kumar Giri, Sumanta Kumar Mallik, Parvaiz Ahmad Ganie, and
Suresh Chandra
Chapter 7 Probiotics in Aquaculture ........................................................................................... 90
Suresh Chandra and Nupur Joshi
Chapter 8 Microbiome in Aquaponics: Emergent Roles and Potential Applications ............... 100
Rameshori Yumnam and Maibam Birla Singh
Chapter 9 Microbial Community of Biooc ............................................................................. 135
M. Rajkumar
Chapter 10 Extremophiles in Aquatic Environments and Their Ecological Signicance.......... 141
Sumanta Kumar Mallik, Richa Pathak, Satya Narayan Sahoo, and Neetu Shahi
viii Contents
Chapter 11 Algicidal Microbes in the Aquatic Environment ..................................................... 161
Kapil S. Sukhdhane and Pramod Kumar Pandey
Chapter 12 Microbial Indicators of Aquatic Pollution ................................................................ 171
Kundan Kumar, Saurav Kumar, Satya Prakash Shukla,
and Rajive Kumar Bhramchari
Chapter 13 Impact of Emerging Pollutants on Freshwater Microbes ......................................... 183
Saurav Kumar, Pritam Sarkar, Tapas Paul, and Kundan Kumar
Chapter 14 Eutrophication in Freshwater and Its Microbial Implications .................................. 194
Debajit Sarma and Deepak Kumar
Chapter 15 Bacterial Biolm in the Aquatic Environment and Its Impact ................................ 210
Pramod Kumar Pandey
Chapter 16 Microbial Remediation in an Aquatic Environment ................................................ 228
Ritesh Shantilal Tandel, Sanjay Rathod,
Raja Aadil Hussain Bhat, and Pragyan Dash
Chapter 17 Environmental DNA and Its Application in Microbial Biodiversity Assessment ...239
Neetu Shahi, Bhupendra Singh, Aslah Mohamad,
and Sumanta Kumar Mallik
Chapter 18 Metagenomic Approach to Unculturable Microbes of the Aquatic Environment .......251
Mamta Singh
Chapter 19 Microalgal Remediation in the Aquatic Environment ............................................. 260
V. Santhana Kumar, Dhruba Jyoti Sarkar,
Soma Das Sarkar, and Basanta Kumar Das
Chapter 20 Role of Microorganisms as Biocontrol Agents in Aquatic Environments ............... 271
Sumanta Kumar Mallik, Richa Pathak, Neetu Shahi,
and Mohan Singh
Chapter 21 Thermophilic Microbial Enzymes from Hot Springs and Their Role in
Bioprocessing ........................................................................................................... 293
Amit Seth
Chapter 22 Overview of Microbial Toxins in the Aquatic Environment ....................................303
Pramod Kumar Pandey, M. Junaid Sidiq, and Rameshori Yumnam
ixContents
Chapter 23 Applications of Geospatial Technology in the Mapping of Aquatic Microbes
and Risk Assessment ................................................................................................ 323
Ganesan Kantharajan, R. Bharathi Rathinam, Arur Anand,
Ayyathurai Kathirvelpandian, Ajey Kumar Pathak, and Uttam Kumar Sarkar
Chapter 24 Statistical Aspects of Aquatic Microbiology............................................................ 333
V. Ramasubramanian and H. Sanath Kumar
Index .............................................................................................................................................. 351
x
Foreword
The world’s aquatic ecosystems are vital to the health of our planet,
sustaining a myriad of life forms and serving as a critical compo-
nent of the Earth’s biogeochemical cycles. As our understanding of
these intricate environments deepens, so does our appreciation for
the pivotal role played by microorganisms in shaping the dynamics of
aquatic ecosystems. It is with great pleasure that I would like to intro-
duce the Handbook of Aquatic Microbiology edited by Dr. Pramod
Kumar Pandey and others. This comprehensive volume will serve as
an indispensable guide to the multifaceted world of aquatic microbiol-
ogy, offering a profound exploration of the microbial life that thrives
beneath the surface of our oceans, lakes, rivers, and other water bodies. The importance of this eld
cannot be overstated, as the microbial inhabitants of aquatic environments inuence fundamental
ecological processes, drive nutrient cycling, and impact water quality.
In this handbook, the editors and authors have come together to provide a treasure trove of
knowledge, encompassing a wide range of topics related to aquatic microbiology. From pristine
freshwater systems to the most extreme aquatic habitats, the diversity and adaptability of aquatic
microorganisms are showcased in intricate detail. Readers will have knowledge of the latest
advancements in research, gaining insights into the vital roles played by aquatic microorganisms in
nutrient cycling, bioremediation, and the maintenance of ecosystem health. It serves as an essential
reference not only for researchers and professionals in the eld but also for academicians, students,
and anyone with a passion for understanding and protecting our planet’s aquatic treasures. As we
confront the challenges posed by climate change, pollution, and the ever-increasing demands on our
water resources, a deep understanding of aquatic microbiology has never been more critical. The
Handbook of Aquatic Microbiology is a beacon of knowledge in this endeavour, providing a com-
pass to navigate the intricate and awe-inspiring world of microorganisms that inhabit our waters.
I commend and congratulate the authors and editors for their dedication to advancing our under-
standing of aquatic microbiology, and I am condent that this volume will be a source of inspiration
and guidance for all who seek to explore and safeguard our planet’s aquatic ecosystems.
Anupam Mishra
28 October 2023
xi
Preface
The aquatic realm, comprising the vast expanses of oceans, rivers, lakes, and wetlands, is an intri-
cate and dynamic ecosystem teeming with life, much of which is hidden from the naked eye. Within
these watery realms, an invisible world of microorganisms plays a pivotal role in shaping the very
fabric of our planet. From the blue depths of the open ocean to the serene tranquillity of freshwater
ponds, microbial life forms the foundation of aquatic ecosystems, impacting not only the health of
these environments but also the global biogeochemical cycles that sustain life on Earth.
The Handbook of Aquatic Microbiology is a culmination of the tireless efforts of numerous
scientists, researchers, and experts in the eld, each driven by an insatiable curiosity to unravel the
mysteries of aquatic microbiology. In this comprehensive volume, we delve into the microscopic
wonders that inhabit our waters, examining their ecological signicance, their contributions to bio-
geochemical processes, their role in shaping aquatic food webs, and their interactions with human
activities.
This book is intended as a compendium of knowledge, a guide for both seasoned researchers and
newcomers to the eld. It presents a synthesis of the current state of aquatic microbiology, offering
a multidisciplinary perspective that bridges the gap between the fundamental principles of micro-
biology and the complex, dynamic aquatic environments in which these microorganisms thrive.
Throughout these pages, readers will nd a wealth of information ranging from microbial physiol-
ogy to the ecological consequences of microbial activities in aquatic ecosystems.
Our aim is to provide a valuable resource for scientists, educators, policymakers, and anyone
with an interest in the intricate web of life that ourishes beneath the water’s surface. By exploring
the world of aquatic microbiology, we hope to inspire curiosity and foster a deeper appreciation
for the crucial role that these tiny organisms play in sustaining life on Earth. As editors, we are
indebted to the dedicated contributors who have shared their expertise and insights, making this
handbook a reality. Their commitment to advancing our understanding of aquatic microbiology is
evident in the wealth of knowledge presented within these pages. We also extend our gratitude to the
reviewers whose meticulous scrutiny ensured the quality and accuracy of the content.
In closing, we invite you to embark on a journey into the unseen world of aquatic microbiology.
We hope that this handbook will serve as a valuable reference and a source of inspiration for all
those who seek to explore the fascinating realm of aquatic microorganisms.
Pramod Kumar Pandey
Sumanta Kumar Mallik
Rameshori Yumnam
xii
Contributors
Arur Anand
Regional Remote Sensing Centre
National Remote Sensing Centre
Indian Space Research Organisation
Department of Space
Nagpur, Maharashtra, India
Raja Aadil Hussain Bhat
Indian Council of Agricultural Research
Directorate of Coldwater Fisheries
Research
Bhimtal
Nainital, Uttarakhand, India
Rajive Kumar Bhramchari
College of Fisheries
Dholi
Dr. Rajendra Prasad Central Agricultural
University
Bihar, India
Suresh Chandra
Indian Council of Agricultural Research
Directorate of Coldwater Fisheries Research
Bhimtal
Nainital, Uttarakhand, India
Basanta Kumar Das
Aquatic Environmental Biotechnology and
Nanotechnology Division
Indian Council of Agricultural Research
Central Inland Fisheries Research Institute
Barrackpore
Kolkata, West Bengal, India
Pragyan Dash
Indian Council of Agricultural Research
Directorate of Coldwater Fisheries Research
Bhimtal
Nainital, Uttarakhand, India
Parvaiz Ahmad Ganie
Indian Council of Agricultural Research
Directorate of Coldwater Fisheries Research
Bhimtal
Nainital, Uttarakhand, India
Garima
Indian Council of Agricultural Research
Directorate of Coldwater Fisheries Research
Bhimtal
Nainital, Uttarakhand, India
Abhay Kumar Giri
Indian Council of Agricultural Research
Indian Agricultural Research Institute
Gauria Karma
Hazaribagh, Jharkhand, India
Nupur Joshi
Himalayan School of Biosciences
Swami Rama Himalayan University
Jollygrant
Dehradun, Uttarakhand, India
Ganesan Kantharajan
Indian Council of Agricultural Research
National Bureau of Fish Genetic Resources
Lucknow, Uttar Pradesh, India
Ayyathurai Kathirvelpandian
Centre for Peninsular Aquatic Genetic
Resources
Indian Council of Agricultural Research
National Bureau of Fish Genetic Resources,
Kochi, Kerala, India
Deepak Kumar
Indian Council of Agricultural Research
Directorate of Coldwater Fisheries Research
Bhimtal
Nainital, Uttarakhand, India
H. Sanath Kumar
Indian Council of Agricultural Research
Central Institute of Fisheries Education
Mumbai, India
Kundan Kumar
Aquatic Environment & Health Management
Division
Indian Council of Agricultural Research
Central Institute of Fisheries Education
Mumbai, India
Contributors Contributors
xiiiContributors
Contributors
Saurav Kumar
Aquatic Environment & Health Management
Division
Indian Council of Agricultural Research
Central Institute of Fisheries Education
Mumbai, India
and
National Bureau of Fish Genetic Resources
Kochi
Kerala, India
V. Santhana Kumar
Aquatic Environmental Biotechnology and
Nanotechnology Division
Indian Council of Agricultural Research
Central Inland Fisheries Research Institute
Barrackpore
Kolkata, West Bengal, India
Kishor Kunal
Indian Council of Agricultural Research
Directorate of Coldwater Fisheries Research
Bhimtal
Nainital, Uttarakhand, India
Sumanta Kumar Mallik
Indian Council of Agricultural Research
Directorate of Coldwater Fisheries Research
Bhimtal
Uttarakhand, India
Aslah Mohamad
Laboratory of Aquatic Animal Health and
Therapeutics
Institute of Bioscience
University of Putra Malaysia
Serdang
Selangor, Malaysia
Snatashree Mohanty
Indian Council of Agricultural Research
Central Institute of Freshwater Aquaculture
Bhubaneswar
Odisha, India
Pramod Kumar Pandey
Indian Council of Agricultural Research
Directorate of Coldwater Fisheries Research
Bhimtal
Uttarakhand, India
Ajey Kumar Pathak
Indian Council of Agricultural Research
National Bureau of Fish Genetic
Resources
Luck now
Uttar Pradesh, India
Richa Pathak
Indian Council of Agricultural Research
Directorate of Coldwater Fisheries
Research
Bhimtal
Uttarakhand, India
Anirban Paul
Indian Council of Agricultural Research
Central Institute of Freshwater Aquaculture
Bhubaneswar
Odisha, India
Tapas Paul
Department of Aquatic Environment
Management
College of Fisheries
Bihar Animal Sciences University
Patna
Bihar, India
M. Rajkumar
Indian Council of Agricultural Research
Central Marine Fisheries Research Institute
Kochi
Kerala, India
V. Ramasubramanian
Indian Council of Agricultural Research
National Academy of Agricultural Research
Management
Hyderabad, India
R. Bharathi Rathinam
Indian Council of Agricultural Research
Indian Agricultural Research Institute
Hazaribagh
Jharkhand, India
Sanjay Rathod
Indian Council of Agricultural Research
Central Institute of Fisheries Education
Mumbai, India
xiv Contributors
Pramoda Kumar Sahoo
Indian Council of Agricultural Research
Central Institute of Freshwater Aquaculture
Bhubaneswar
Odisha, India
Satya Narayan Sahoo
Fish Health Management Division
Indian Council of Agricultural Research
Central Institute of Freshwater Aquaculture
Kausalyaganga
Bhubaneswar
Odisha, India
Dhruba Jyoti Sarkar
Aquatic Environmental Biotechnology and
Nanotechnology Division
Indian Council of Agricultural Research
Central Inland Fisheries Research Institute
Barrackpore
Kolkata
West Bengal, India
Pritam Sarkar
Aquatic Environment & Health Management
Division
Indian Council of Agricultural Research
Central Institute of Fisheries Education
Mumbai, India
Soma Das Sarkar
Fisheries Resource Assessment and Informatics
Division
Indian Council of Agricultural Research
Central Inland Fisheries Research Institute
Barrackpore
Kolkata
West Bengal, India
Uttam Kumar Sarkar
Indian Council of Agricultural Research
National Bureau of Fish Genetic Resources
Luck now
Uttar Pradesh, India
Debajit Sarma
Indian Council of Agricultural Research
Central Institute of Fisheries Education
Mumbai
Maharashtra, India
Amit Seth
Department of Life Sciences (Botany)
Manipur University
Canchipur
Imphal, India
Neetu Shahi
Indian Council of Agricultural Research
Directorate of Coldwater Fisheries
Research
Bhimtal
Uttarakhand, India
Satya Prakash Shukla
Aquatic Environment & Health Management
Division
Indian Council of Agricultural Research
Central Institute of Fisheries Education
Mumbai, India
M. Junaid Sidiq
Department of Aquaculture
Indian Council of Agricultural Research
Central Institute of Fisheries Education
Mumbai, India
Bhupendra Singh
Indian Council of Agricultural Research
Directorate of Coldwater Fisheries Research
Bhimtal
Uttarakhand, India
Maibam Birla Singh
Blue-Green Agro-tech
KhabamLamkhai
Imphal, Manipur, India
Mamta Singh
College of Fisheries
Bihar Animal Sciences University
DKAC Campus
Arrabari
Kishanganj
Bihar, India
Mohan Singh
Indian Council of Agricultural Research
Directorate of Coldwater Fisheries Research
Bhimtal
Uttarakhand, India
xvContributors
Kapil S. Sukhdhane
Aquaculture Division
Indian Council of Agricultural Research
Central Institute of Fisheries Education
Mumbai, India
Ritesh Shantilal Tandel
Indian Council of Agricultural Research
Directorate of Coldwater Fisheries Research
Bhimtal
Nainital, Uttarakhand, India
Rameshori Yumnam
Department of Zoology
Canchipur
Manipur University
Manipur, India
1
1Microbiomes of the
Aquatic Environment
Pragyan Dash, Ritesh Shantilal Tandel,
and Raja Aadil Hussain Bhat
1.1 INTRODUCTION
Freshwater and marine ecosystems are home to a complex and diverse array of microorganisms,
including viruses, bacteria, fungi, and algae. These microorganisms play an important role in
aquatic ecosystem by acting as decomposers, as producers, and in nutrient cycles. Microorganisms
interact with one another and their surroundings to inuence the health and function of aquatic eco-
systems. The community of microorganisms and combined genetic material, inhabiting a particular
environment is summarized in the term ‘microbiome.’ For a million years, the aquatic microbiome
has shaped the microbiome of each aquatic plant and animal; however, the host-associated micro-
biome is not a direct reection of the water’s microbial community. Aquatic animals are subjected
to multiple environmental, nutritional, and genetical selection forces, which impact the coevolved
alliances between microbiome and organism (Song et al., 2017).
The functions of aquatic ecosystems depend on interaction between microorganisms and aquatic
animals. Bacterial strains competing for nutrients can form more diverse and stable communities
(Ghoul and Mitri, 2016). Symbiotic associations between bacteria and algae can improve photosyn-
thesis and primary production efciency in aquatic environments (Zhou et al., 2018).
The distribution and abundance at higher trophic levels, such as sh and other aquatic creatures,
can be affected by changes in the composition of the microbial community. This can also have
signicant effects on nutrient cycling and ecosystem function. Therefore, for efcient ecosystem
management and conservation, a deeper comprehension of the function of microbial communities
in aquatic ecosystems is necessary. Aquatic habitats are projected to see considerable changes in
microbial community structure and function as global temperatures rise. These changes will have
a signicant impact on ecosystem services and human well-being. Monitoring these changes and
developing targeted management strategies can mitigate the impacts of climate change on aquatic
ecosystems. This chapter emphasizes the diversity of microbiomes in aquatic algae, vertebrates, and
macrophytes, and their interaction in the aquatic environment (Figure 1.1).
1.2 ALGAE-ASSOCIATED MICROBIOME
Algae, the phytoplankton, are a diverse group of aquatic organisms that play signicant roles in
maintaining the ecological balance of aquatic ecosystems. Interactions between phytoplankton,
microalgae, and their associated microorganisms can be inuenced by the production and release of
various chemical mediators (Cirri and Pohnert, 2019).
The chemical signals exchanged between algae and microorganisms are associated with their
survival, functioning, and health. There are several compounds, such as orfamide A, oxylipins,
amino acids, vibrioferrin, methylamine, s-containing osmolytes, auxin, and vitamins, which play
a role as defense metabolites, nutrients, growth promoters, antibiotics, signaling molecules, in the
binding and uptake of iron, demobilization and killing, as osmolytes, etc. (Cirri and Pohnert, 2019).
Handbook of Aquatic Microbiology Microbiomes of the Aquatic Environment
DOI: 10.1201/97810034 085 43-1
10.1201/9781003408543-1
2Handbook of Aquatic Microbiology
For example, nitrogen-xing bacteria and methylamine-degrading bacteria release ammonia (NH3),
which increases nitrogen availability for microalgae. Tryptophan produced by microalgae serves as
a precursor for the biosynthesis of auxins in bacteria and promotes mutualism (Amin et al., 2015).
Bacteria from the Roseobacter clade (such as Phaeobacter inhibens and Dinoroseobacter shibae)
can trade vitamins or vitamin precursors with algae that cannot synthesize them de novo (Croft
et al., 2005; Wienhausen et al., 2017). In exchange for the amino acid tryptophan, P. inhibens and
Sultobacter supply auxins and ammonium to diatoms and coccolithophores (Amin et al., 2015;
Segev et al., 2016). Ruegeria pomeroyi can sense various sulfuric compounds released by micro-
algae and respond by producing auxins that support algal growth as well as quorum-sensing mol-
ecules that promote bacterial proliferation (Johnson et al., 2016; Durham et al., 2015).
Algicidal bacteria can even control the algal bloom by inducing the lysis of algal cells. A typical
example is the bacterium Pseudomonas protegens, which surrounds the microalga Chlamydomonas
reinhardtii. P. protegens deagellates the alga and disrupts its Ca2+ homeostasis (Aiyar et al., 2017).
Further, P. inhibens initially increases the coccolithophore’s growth by releasing the growth-pro-
moting indole-3-acetic acid (IAA), but later on, it triggers algal cell death by activation of pathways
of oxidative stress.
Diatoms and most microalgae require inorganic nitrogen such as nitrate or ammonium, provided
by cyanobacteria and nitrogen-xing bacteria (Foster et al., 2011). Accordingly, the association
of algae with nitrogen-xing bacteria is seen in an ecosystem. Further, other bacteria, like the
α-proteobacterium Donghicola, can convert the organic nitrogen source methylamine to ammonia.
The ammonia is readily taken up by the diatom Phaeodactylum tricornutum, and in return, bacteria
proliferate with the exudates of the diatom (Suleiman et al., 2016).
FIGURE 1.1 Interactions of microbiome in an aquatic ecosystem.
3Microbiomes of the Aquatic Environment
Microbiome composition and diversity can be inuenced by factors such as water quality, nutri-
ent availability, and habitat. Algae living in polluted water have a less diverse microbiome, domi-
nated by potentially pathogenic bacteria, than algae living in clean water. Some algae, like Navicula
accomoda and Stigeoclonium tenue, can comfortably live in the most heavily polluted zones, while
some, like Cocconeis and Chamaesiphon, are reported to occur only in unpolluted parts of streams
(Sen et al., 2013).
Algal-associated microbial populations can control an ecosystem’s primary production, carbon
sequestration, and nutrient cycling. Additionally, algae are a crucial part of aquaculture, and the
microbiomes linked to algae can have a direct impact on the species used for aquaculture in terms
of nutrient availability, water quality, and disease resistance.
1.3 AQUATIC ORGANISMS–ASSOCIATED MICROBIOME
Aquatic organisms, including sh, crustaceans, and other fauna, rely on their associated microbi-
omes for their physiology and health (Colston and Jackson, 2016; Sehnal et al., 2021). Microbiomes
related to aquatic organisms are found in various organs, including the skin, gills, gut, and mucus.
Skin and gill of sh are the critical site for microbial colonization and play a signicant role in
protecting sh from pathogenic microbes (Ross et al., 2019), while the gut microbiome contributes
signicantly to the digestion and nutrient utilization, immune function, health, and overall behavior
and ecology of aquatic organisms.
The gut microbial community is broadly divided into allochthonous and autochthonous micro-
biota based on their interaction with the host. The allochthonous microbiota comprises microorgan-
isms that passes through the lumen along with the food, while the autochthonous microbiota resides
permanently in the sh gut without causing any harm to it (Rajeev et al., 2021).
Microorganisms found in the gut of sh and other aquatic organisms can break down complex car-
bohydrates, proteins, and lipids that are otherwise indigestible by the host (Ringø et al., 2016; Givens
et al., 2015). For example, a study on Atlantic salmon (Salmo salar) indicated that the gut microbiome
produced enzymes that facilitated the digestion of complex carbohydrates, such as cellulose and chitin
(Ringø et al., 2016). Similarly, in zebrash (Danio rerio), the microbiota stimulated fatty acid uptake
and lipid droplet formation in the intestinal epithelium and liver (Carmody and Turnbaugh, 2012;
Semova et al., 2012). The gut microbiome is also known to modulate the host’s immune response
by producing antimicrobial compounds and promoting the development of immune cells (Gómez
and Balcáza r, 2008). In Nile tilapia (Oreochromis niloticus), certain bacteria in the gut microbiome
were reported to be associated with increased resistance to bacterial infections (Tan et al., 2019). Li
et al. (2018) and Yao et al. (2021) also reported that the gut microbiome of shrimp (Litopenaeus van-
namei) played a crucial role in regulating the expression of immune-related genes and protecting the
host against viral infections. In addition to digestion and immune function, the microbiome can also
inuence the behavior and ecology of aquatic organisms (Sullam et al., 2012). In killish (Fundulus
heteroclitus), the gut microbiome inuenced their reproductive success, with certain microbial com-
munities associated with higher reproductive output (Lombardo et al., 2011; Scott et al., 2020).
Interaction between host physiology, gut architecture, and ecological and environmental factors
determines the diversity of the gut microbiome (Ghanbari et al., 2015). Also, the gut microbiome
shows a direct relationship when feeding habit changes from herbivore to omnivore to carnivore in
nsh species (Givens, 2012; Larsen et al., 2014). As reported in many studies, the early coloni-
zation of gut microbiota starts from the egg stage, based on the binding glycoproteins on the egg
surface (Larsen et al., 2014). Upon hatching, a bacterium linked with egg chorions rst emerges
as a colony in the gastrointestinal system. Following that, different kinds of gut microbiota begin
to colonize when sh drink water and consume food from the environment (Hansen and Olafsen,
1999). A healthy sh has a more varied alpha gut microbiota than a sick sh, and this variation can
be used as a diagnosis to manage sh health (Clarke et al., 2014). Moreover, varied and abundant
populations of gut microbes improve sh defense and protection mechanisms (Johnson et al., 2008).
4Handbook of Aquatic Microbiology
The microbiome composition and diversity of these organs can be inuenced by various factors
such as water quality, diet, and habitat. Larsen et al. (2014) found that sh living in polluted water
had a less diverse microbiome than sh living in clean water. The study also found that poten-
tially pathogenic bacteria dominated the microbiome of sh living in polluted water. Similarly,
Ingerslev et al. (2014) found that the gut microbiome of rainbow trout (Oncorhynchus mykiss) fed on
a plant-based diet was composed of Leuconostoc, Weissella, Streptococcus, etc. The gut microbi-
ome composition of sh fed on an animal-based diet consisted of Bacteroidetes, Proteobacteria, and
Actinobacteria, which was different from the sh fed with a plant-based diet. Also, the microbiome
of sh from freshwater habitats differs from that of sh from marine habitat (Fan et al., 2019). Among
freshwater sh microbiome species, Acinetobacter, Aeromonas, Flavobacterium, Lactococcus,
and Pseudomonas, obligate anaerobes Bacteroides, Clostridium, and Fusobacterium, and mem-
bers of the family Enterobacteriaceae persist, whereas in marine sh, Aeromonas, Alcaligenes,
Alteromonas, Carnobacterium, Flavobacterium, Micrococcus, Moraxella, Pseudomonas, and
Vibrio dominate (Gomez and Balcáza r, 2008).
1.4 AQUATIC MACROPHYTES–ASSOCIATED MICROBIOME
Aquatic macrophytes are dominant primary producers in many freshwater and marine environ-
ments, providing essential ecosystem services such as nutrient cycling, sediment stabilization, and
habitat provision. Aquatic macrophytes interact with the environmental microbiome through vari-
ous pathways, including the provision of organic matter, changes in water quality, and creation of
microhabitats. Aquatic macrophytes release organic matter, which acts as a food source for the
microbial community, increasing their abundance and diversity. The composition of the microbi-
ome can be altered due to the water quality, which includes increased nutrient availability and light
penetration, with some taxa ourishing in nutrient-rich habitats and others in nutrient-poor environ-
ments (Bárta et al., 2021). Moreover, the creation of microhabitats by aquatic macrophytes, such
as roots and leaves, can provide a physical structure for the attachment and growth of microbes,
leading to the formation of specialized microbial communities.
Furthermore, the microbiome is shown to signicantly impact the growth and health of aquatic
macrophytes. Some bacteria can form a symbiotic relationship with aquatic macrophytes, providing
essential nutrients and improving their growth and survival (Zhu et al., 2021). On the other hand,
pathogenic microorganisms can cause diseases in aquatic macrophytes, leading to declines in their
populations and altering the structure and function of the ecosystem (Saha and Weinberger, 2019).
1.5 MICROPLASTIC-ASSOCIATED MICROBIOME
The makeup of microbial communities on the surface of microplastics or nanoplastics in an aquatic
environment, referred to as the ‘plastisphere,’ has been an interest of research for several decades
(Amaral-Zettler et al., 2020). The ability of bacteria and fungi to digest plastic particles, as well as
the interaction between the microbial community and microplastics, has piqued scientists’ interest
in environmental biotechnology (Barros et al., 2021).
Microplastics provide a surface for microbial attachment, leading to the formation of biolms.
The microbial communities associated with microplastics in aquatic ecosystems are diverse and
depend upon the attachment on different types of plastics and water bodies (Table 1.1). Biolms
of microplastic in ponds had higher relative abundances of the phyla Proteobacteria, Firmicutes,
and Chloroexi, while river biolms of microplastic had higher relative abundances of the phylum
Acidobacteria and family Nitrospiraceae, Nitrosomonadaceae, and lower relative abundances of
Proteobacteria (Hoellein et al., 2014).
Microbiomes belonging to bacterial genera such as Klebsiella, Pseudomonas, and Sphingomonas
can degrade plastic (Kelly et al., 2021). Rhodococcus ruber C208 can degrade polyethylene lm by
up to 8% within 30 days of incubation, which increases with mineral oil up to 50% (Hadar and Sivan
5Microbiomes of the Aquatic Environment
2004). Changes in microbial communities in microplastics can inuence the biomass of plastics, as
reported in polyethylene terephthalate (PET) and polyvinyl chloride (PVC), and hence, can affect
the buoyancy and dispersion of plastics in water (Miao et al., 2021).
Due to their small size, microplastics are ingested by a wide range of aquatic organisms, includ-
ing bacteria, zooplankton, and sh. Plastic debris has been found in shes, shellsh, and mussels,
which after consumption, can enter the human body through trophic transfer, biomagnication, and
bioaccumulation (Giani et al., 2019; Hermabessiere et al., 2019). Microplastic intake can adversely
affect the health of aquatic organisms, as microplastics are potential carriers for pathogenic bacte-
ria, antimicrobials, and toxic compounds (Campanale et al., 2020).
1.6 IMPACT OF ENVIRONMENTAL FACTORS ON THE STRUCTURE
AND FUNCTION OF THE AQUATIC MICROBIOME
The aquatic microbiome is particularly vulnerable to environmental stressors, i.e., pollutants and
changes in water quality. In recent years, researchers have explored the impact of various environ-
mental stressors on the microbiome in aquatic environments, including pollution, temperature, and
nutrient availability.
1.6.1 TemperaTure
Temperature is a key factor that shapes the diversity and composition of aquatic microbial com-
munities, and it has been shown to impact the metabolic rates of these organisms signicantly.
TABLE 1.1
Microorganisms Associated with Microplastics in an Aquatic Environment
Microorganism Type of Microplastic Source of Isolation Reference
Vibrio alginolyticus Polyethylene Mangrove Tan et al. (2022)
Vibrio harveyi, Enterococcus faecalis Polyethylene Seawater Hchaichi et al. (2020)
Vibrio parahaemolyticus Polyethylene, polystyrene,
polypropylene
North/Baltic Sea Kirstein et al. (2016)
Pseudomonas monteilii, P.
mendocina, P. syringae
Polyvinyl chloride (PVC) River water in
controlled
conditions
Wu et al. (2019)
Bacillus cereus and Bacillus gottheilii Polystyrene Mangrove
ecosystems
Auta et al. (2017)
Acinetobacter Polypropylene River Mughini-Gras et al.
(2021)
Flavobacterium Polyethylene terephthalate
(PET)
River Mughini-Gras et al.
(2021)
Aspergillus, Cladosporium, Wallemia Polyethylene (PE), Polyamide
(PA), polyurethane (PU),
polypropylene (PP),
polystyrene (PS), and
cellulose acetate (CA)
Western South
Atlantic and
Antarctic
Peninsula
Lacerda et al. (2020)
Aspergillus niger, Penicillium spp.,
Rhizopus spp., Mucor spp.,
Aspergillus nidulans, Fusarium spp.,
Microsporum canis, and Aspergillus
fumigatus
Polypropylene, polyester,
polyvinyl chloride
Estuary Williams et al. (2021)
6Handbook of Aquatic Microbiology
As temperature increases, the microbial community structure shifts, with thermophilic bacteria
becoming dominant (Chiriac et al., 2017). In a study on a eutrophic lake, temperature increase was
associated with a decrease in the abundance of cyanobacteria and an increase in the abundance of
other phytoplankton taxa (Paerl and Paul, 2012; O’Neil et al., 2012).
Temperature can also inuence the diversity of the microbial community, affecting the com-
petitive dynamics between various species. In research on a freshwater reservoir, warming was
linked to increased dominance of a single bacterial taxon, which displaced other taxa and reduced
total diversity (Wang et al., 2021). On the contrary, another report on the freshwater lake shows an
increase in microbial diversity and a more signicant number of rare and low-abundance species
with increasing temperatures (Islam et al., 2019).
Temperature profoundly impacts how the microbial community functions by affecting microbial
metabolic rates. Changes in community composition, such as a decrease in the abundance of cyano-
bacteria and a rise in the quantity of other phytoplankton species, were linked to changes in nutrient
cycling rates, such as enhanced rates of nitrogen xation and denitrication at higher temperatures
(Paerl and Paul, 2012).
Temperature can also inuence microbial community function by affecting interactions between
various microbial populations. In one freshwater lake, warming was linked to a decrease in the
population of bacteria that consume methane, resulting in higher methane emissions from the
lake (Schulz and Conrad, 1996). Similarly, higher temperature in a coastal marine ecosystem was
linked to a decrease in the abundance of microbial populations engaged in the breakdown of petro-
leum hydrocarbons, implying that rising temperature may limit the ability of these communities to
respond to oil spills (Chong et al., 2018).
1.6.2 SaliniTy
Many aquatic habitats, including estuaries, salt marshes, and hypersaline lakes, experience changes
in salinity due to uctuations in water ow, evaporation, and precipitation, which can signicantly
change the composition and diversity of the aquatic microbiome. In the Great Salt Lake in Utah,
it was found that extreme halophilic bacteria prevail in the north arm, which has a salinity range
from 20 to 30ppt, whereas moderate halophiles prevail in the south arm at around 15–17ppt
(Baxter et al., 2005). A similar nding was also observed in the lakes of China; Bacteroidetes,
Cyanobacteria, and Alpha proteobacteria were the dominant bacterial phyla in low saline lakes,
whereas Gamma proteobacteria and Euryarchaeota were abundant in moderately saline lakes
(50–250ppt). The hypersaline lakes (>250ppt) were dominated by extreme halophiles such as
Halorubrum, Halohasta, and Natronomonas from Euryarchaeota (Banda et al., 2021). Changes in
salinity are shown to be connected with changes in the abundance of pathogenic Vibrio bacteria in
the Baltic Sea and shrimp farms in Vietnam (Baker-Austin et al., 2013).
1.6.3 polluTion
Pollution, due to anthropogenic activities such as agriculture, industry, and urbanization, can intro-
duce a wide range of pollutants into aquatic environments. These include nutrients, heavy metals,
and organic chemicals. Several reports have shown that pollution can seriously affect the composi-
tion and performance of the aquatic microbiome. For example, a study conducted in a polluted river
in Northeastern China revealed that the pollution decreased the overall bacterial diversity. However,
the community was dominated by opportunistic and pathogenic bacteria such as Acinetobacter
johnsonii, Clostridium cellulovorans, and Trichococcus pasteurii (Zhao et al., 2014). This shift in
microbial composition can signicantly impact ecosystem functioning, including nutrient cycling
and water quality. In addition to changes in microbial composition, pollution can also lead to changes
in microbial metabolism. In an estuary of China polluted with polycyclic aromatic hydrocarbons
(PAHs), the microbial community was dominated by proteobacteria containing genes encoding for
7Microbiomes of the Aquatic Environment
dehydrogenases, which are the key enzymes for pyrene degradation (Zhang et al., 2019). However,
these adaptations can also negatively impact ecosystem functioning, such as releasing greenhouse
gases.
Pollution in the form of eutrophication is also a threat to aquatic microbiomes, leading to algal
blooms and oxygen depletion. Eutrophication can lead to changes in the composition of microbial
communities, most notably a shift from an autotrophic to a heterotrophic population (Meyer-Reil
and Köster, 2000; Andersson et al., 2006). Furthermore, increased nutrient availability can lead to
increased abundance of harmful bacteria, such as Vibrio (Baker-Austin et al., 2013).
1.7 CONSERVATION AND MANAGEMENT
IMPLICATIONS FOR THE ECOSYSTEM
Understanding the interactions between the aquatic microbiome and its environment has important
implications for conserving and managing aquatic ecosystems. Management of water quality, such
as temperature, pH, and salinity, including controlling the levels of pollutants, can help to protect
the diversity and stability of the aquatic microbiome.
One of the critical challenges in managing aquatic ecosystems in a changing climate scenario
is predicting how microbial communities will respond to temperature changes. Many factors can
inuence the sensitivity of microbial communities to temperature, including the specic micro-
bial taxa present, the availability of nutrients and other resources, and the presence of other
stressors, such as pollution or invasive species. As a result, it can be challenging to predict the
exact nature and magnitude of the impacts of temperature on microbial community structure and
function.
However, several strategies can be employed to manage and conserve aquatic ecosystems in a
changing climate scenario. One approach is to monitor microbial community structure and function
over time, using high-throughput sequencing and other molecular techniques to track changes in
community composition and metabolic activity. These facts can be used to identify critical micro-
bial taxa and processes that may be particularly sensitive to temperature changes and to develop
targeted management strategies to mitigate the impacts of climate change on ecosystem function.
Developing bioremediation strategies, which utilize microorganisms to remove pollutants from
aquatic environments, is another important consideration for conserving and managing aquatic
ecosystems (Gao et al., 2018). Another approach is to manage other stressors that can exacerbate
temperature impacts on aquatic microbial communities. For example, reducing nutrient pollution
can help maintain the resilience of microbial communities to temperature changes by reducing the
risk of harmful algal blooms and other negative impacts on ecosystem function. Similarly, reducing
the impact of invasive species can help maintain the diversity and function of native microbial com-
munities, which may be more resilient to temperature changes than introduced species.
1.8 CONCLUSION
Microbiomes can have benecial and detrimental effects on aquatic organisms, and host genetics,
environmental conditions, and the surrounding microbiome community can inuence their compo-
sition and function. However, there are still many knowledge gaps and future research directions
in aquatic microbiome research, including understanding the mechanisms underlying microbiome–
host interactions, identifying key microbial taxa and functional genes involved in these interactions,
and investigating the effects of anthropogenic activities on aquatic microbiomes.
The microbiome plays a crucial role in maintaining the health of aquatic ecosystems and is
shaped by a complex interplay of physical, chemical, and biological factors. Despite this, the aquatic
microbiome is vulnerable to disturbance from eutrophication and global warming. Further research
is needed for proper understanding of the impact of these disturbances on the overall ecosystem
8Handbook of Aquatic Microbiology
health. Ultimately, this type of study will help chart out the management and conservation strategies
for protecting aquatic ecosystems and the microorganisms that inhabit them.
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