This book describes the state-of-the-art concerning the ‘marine microbiome’ and its uses in biotechnology. The first part discusses the diversity and ecology of marine microorganisms and viruses, including all three domains of life: Bacteria, Archaea, and Eukarya. It discusses whether marine microorganisms exist and, if so, why they might be unique. The second part presents selected marine habitats, their inhabitants and how they influence biogeochemical cycles, while the third discusses the utilization of marine microbial resources, including legal aspects, dissemination, and public awareness. The marine microbiome is the total of microorganisms and viruses in the ocean and seas and in any connected environment, including the seafloor and marine animals and plants. The diversity of microbial life remains unquantified and largely unknown, and could represent a hidden treasure for human society. Accordingly, this book is also intended to connect academics and industry, providing essential information for microbiologists from both fields.

This updated and expanded second edition reviews numerous aspects of the marine microbiome and its possible industrial applications. The marine microbiome is the total of microorganisms and viruses in the ocean and seas and in any connected environment, including the seafloor and marine animals and plants. In the first part of the book, diversity, origin and evolution of the marine microorganisms and viruses are discussed. The microbes presented originate from all three domains of life: Bacteria, Archaea, and Eukarya. The second part sheds some light on the different communities: it describes marine habitats and how their inhabitants control biogeochemical cycles. The third part finally examines the microbial ocean as a global system and evaluates methods of utilizing marine microbial resources. Adopting a translational approach, the book connects academic research with industrial applications, making it a fascinating read and valuable resource for microbiologists from both domains.

In the pelagic environment, microbes act as the base of the food web (photosynthetic autotrophs), recycle nutrients (microbial loop), and perform other crucial ecosystem processes and services (such as carbon sequestration). The relative scale of these different process is driven by changes in marine microbiome community structure, diversity, and function. Over the last two decades, meta-omic sampling has provided a pathway forward with which to observe the community structure and function of the marine microbiome at a previously inaccessible resolution. However, with this increase in data complexity (large numbers of identified species and genes), it can be challenging to synthesize results across the multitude of observed taxonomic and functional groups. The goal of this thesis is to provide a general framework for understanding marine microbiome community responses (structure, diversity, and function) to environmental perturbations at previously unresolvable scales. The first study (Chapter 2) identifies the mechanisms that shape patterns in marine microbiome community structure and diversity across space and time within a coastal upwelling region. While traditional methods (such as microscopy and flow cytometry) have highlighted general patterns for broad taxonomic groups and or conspicuous taxa, this study represents a comprehensive examination of the mechanisms that shape all types of marine microbial groups, and in particular, highlights cryptic groups that could not be identified through more traditional means. The second study (Chapter 3) takes a more species-centric approach and asks, what is the rate of habitat specificity within marine microbes. Terrestrial systems often contain many species that are endemic to habitats or locales. Within the marine environment, habitats are constantly in motion, moving dynamically across space in time. The dynamic marine environment, coupled with the fast generation times of most microbes is thought by many to lead to less habitat specificity and more cosmopolitan (universally distributed) species. By identifying water mases (with internally consistent physical and chemical environments) we present a view of habitat specificity within the marine microbiome in a way that is comparable to terrestrial studies. The third study (Chapter 4) shifts to look at regional metatranscriptomic data and asks what are the mechanisms that shape the function and distribution of active marine microbes. Metatranscriptomics provides a framework to identify which taxa and their associated functions are active within a community in response to changing environmental conditions. In targeting the active community, we identify how environmental conditions can lead to in-situ functional traits within the microbial community--a crucial next step to better understanding the links between environmental conditions and the local to global magnitude of key ecological functions such as primary productivity, nutrient recycling, and carbon sequestration in the pelagic ocean.

Marine Microbiology brings together microbial biology and ecology to create an integrated approach that addresses environmental management, human health, and economic concerns. The Second Edition takes into account many new discoveries in the field including the role of microbes in ocean processes and nutrient cycles, the importance of viruses, the beneficial role of marine microbes in biotechnology, biofuels, metagenomics and synthetic biology, and new research on the impact of climate change and ocean acidification. The first three sections review the main features of the marine environment and key aspects of marine microbial life; the second section examines the role of marine microorganisms in ecology; and the final section considers some of the applications of this knowledge in areas such as disease and biodegradation. Marine Microbiology is ideally suited for upper level undergraduate and graduate students, and researchers.

A decade of technological advances and research on the human microbiome has re-defined our understanding of biological systems, and now offers diagnostic tools and new approaches to human health. Likewise, marine ecosystems are driven by their microbiome, the ensemble of microscopic organisms that inhabit the water column, sediments and aquatic organisms, and regulate most fluxes of energy and matter. While the human microbiome is composed principally of bacteria, the marine microbiome has a much broader ensemble of microscopic organisms with sizes spanning from viruses of a few tens of nanometres to metazoans of several centimetres. Advances in high throughput imaging and sequencing are emerging in aquatic science, providing important insights into ecosystem structure and functions, and contributing to develop new indicators of ecosystem health and potential hazards to living resources and humans. A number of research exploration and monitoring programs such as the Tara Oceans global expedition and the Marine Biological Observing Network (MBON), and the rising popularity of environmental DNA (eDNA) already led to a wealth of data. However, the wide range of methodologies used in this early exploration phase poses a challenge to integrative studies, prompting community responses such as the Genomic Standards Consortium. This Research Topic will foster cross-community exchange of standards and best practices. It is an opportunity for the different communities working on marine microbiomes to discuss the advantages and the limitations of their sampling and analysis methods. The collection of papers will constitute a knowledge base aimed at (1) addressing the integration of existing observations from heterogenous methods and data types, and (2) working towards cross-communities standards and best practices for future observations and experiments. This Research Topic will publish comprehensive methodological papers that review a sufficiently large body of field or experimental work. Supporting (meta)data, such as environmental context, sampling materials, sample treatments, extraction and imaging yields, must be provided and should preferably be uploaded to an online sample registry such as BioSamples. Protocols and analytical methods should preferably be uploaded to an online repository such as Protocols.io. We welcome contributions from communities working in different environments: · focus on marine systems, but also interested in estuarine and freshwater systems · coastal, open ocean and deep-sea regions · benthic, pelagic and aerosol environments We strongly encourage contributions from communities involved in: · networks of local observatories and long-term monitoring programs · regional & basin-scale surveys, and global expeditions · biodiscovery linked to economic sectors such as pharmaceutics and bioengineering · environmental and health assessments linked to economic sectors such as aquaculture, fisheries, seabed mining, wind-farms, and oil and gas

The third edition of this bestselling text has been rigorously updated to reflect major new discoveries and concepts since 2011, especially progress due to extensive application of high-throughput sequencing, single cell genomics and analysis of large datasets. Significant advances in understanding the diversity and evolution of bacteria, archaea, fungi, protists, and viruses are discussed and their importance in marine processes is explored in detail. Now in full colour throughout, all chapters have been significantly expanded, with many new diagrams, illustrations and boxes to aid students’ interest and understanding. Novel pedagogy is designed to encourage students to explore current high-profile research topics. Examples include the impacts of rising CO2 levels on microbial community structure and ocean processes, interactions of microbes with plastic pollution, symbiotic interactions, and emerging diseases of marine life. This is the only textbook addressing such a broad range of topics in the specific area of marine microbiology, now a core topic within broader Marine Science degrees. A Companion Website provides additional online resources for instructors and students, including a summary of key concepts and terminology for each chapter, links to further resources, and flashcards to aid self-assessment.

"Marine Microbiome and Microbial Bioprospecting" comprehensively discusses the diversity of microbes present in various marine ecosystems, the bioprospecting potential, and how they can be utilized to derive bioproducts that benefit different fields and industries. The book leads off the discussion with an overview of marine microbes, their ex situ conservation, and the tools and techniques used to study marine microbial diversity and taxonomy. It also explores and details microorganisms in different marine ecosystems and considers how bioactive metabolites from diverse marine microorganisms can be harnessed to combat pathogens, be employed in industrial products, used in environmental remediation and degradation, and enhanced for agricultural and aquaculture applications. With contributions from experts in the field, "Marine Microbiome and Microbial Bioprospecting" aims to be a valuable resource for researchers and industry professionals in microbiology and biotechnology involved in finding lead molecules from marine microbial resources for wide-ranging application.• Discusses existing and novel metabolites from marine microbes• Offers tools and techniques to exploit marine microbial resources• Explores the applications of marine microbial bioproducts

The newly revised and updated third edition of the bestselling book on microbial ecology in the oceans The third edition of Microbial Ecology of the Oceans features new topics, as well as different approaches to subjects dealt with in previous editions. The book starts out with a general introduction to the changes in the field, as well as looking at the prospects for the coming years. Chapters cover ecology, diversity, and function of microbes, and of microbial genes in the ocean. The biology and ecology of some model organisms, and how we can model the whole of the marine microbes, are dealt with, and some of the trophic roles that have changed in the last years are discussed. Finally, the role of microbes in the oceanic P cycle are presented. Microbial Ecology of the Oceans, Third Edition offers chapters on The Evolution of Microbial Ecology of the Ocean; Marine Microbial Diversity as Seen by High Throughput Sequencing; Ecological Significance of Microbial Trophic Mixing in the Oligotrophic Ocean; Metatranscritomics and Metaproteomics; Advances in Microbial Ecology from Model Marine Bacteria; Marine Microbes and Nonliving Organic Matter; Microbial Ecology and Biogeochemistry of Oxygen-Deficient Water Columns; The Ocean’s Microscale; Ecological Genomics of Marine Viruses; Microbial Physiological Ecology of The Marine Phosphorus Cycle; Phytoplankton Functional Types; and more. A new and updated edition of a key book in aquatic microbial ecology Includes widely used methodological approaches Fully describes the structure of the microbial ecosystem, discussing in particular the sources of carbon for microbial growth Offers theoretical interpretations of subtropical plankton biogeography Microbial Ecology of the Oceans is an ideal text for advanced undergraduates, beginning graduate students, and colleagues from other fields wishing to learn about microbes and the processes they mediate in marine systems.

A keystone reference that presents both up-to-date research and the far-reaching applications of marine biotechnology Featuring contributions from 100 international experts in the field, this five-volume encyclopedia provides comprehensive coverage of topics in marine biotechnology. It starts with the history of the field and delivers a complete overview of marine biotechnology. It then offers information on marine organisms, bioprocess techniques, marine natural products, biomaterials, bioenergy, and algal biotechnology. The encyclopedia also covers marine food and biotechnology applications in areas such as pharmaceuticals, cosmeceuticals, and nutraceuticals. Each topic in Encyclopedia of Marine Biotechnology is followed by 10-30 subtopics. The reference looks at algae cosmetics, drugs, and fertilizers; biodiversity; chitins and chitosans; aeroplysinin-1, toluquinol, astaxanthin, and fucoxanthin; and algal and fish genomics. It examines neuro-protective compounds from marine microorganisms; potential uses and medical management of neurotoxic phycotoxins; and the role of metagenomics in exploring marine microbiomes. Other sections fully explore marine microbiology, pharmaceutical development, seafood science, and the new biotechnology tools that are being used in the field today. One of the first encyclopedic books to cater to experts in marine biotechnology Brings together a diverse range of research on marine biotechnology to bridge the gap between scientific research and the industrial arena Offers clear explanations accompanied by color illustrations of the techniques and applications discussed Contains studies of the applications of marine biotechnology in the field of biomedical sciences Edited by an experienced author with contributions from internationally recognized experts from around the globe Encyclopedia of Marine Biotechnology is a must-have resource for researchers, scientists, and marine biologists in the industry, as well as for students at the postgraduate and graduate level. It will also benefit companies focusing on marine biotechnology, pharmaceutical and biotechnology, and bioenergy.