Variations In Marine Microbiomes

Microorganisms are the dominant life form on Earth and inextricably tied to the ecology and evolution of all multicellular life, including marine animals. As the importance of microorganisms to our conception of life gains prominence, animals (and other macroorganisms) are increasingly viewed as “holobionts”, an assemblage of the host plus all its symbiotic microbes. This dissertation examines holobiont biology from the perspective of the microbial communities that live in and around marine hosts. Using both amplicon and metagenomic sequencing, I study the microbiomes of reef-associated seawater and Atlantic killifish to better understand habitat and host effects on microbiome structure. In two Caribbean reef systems, I used examined the biogeography of reef water microbes. I found that the microbiome of reef seawater varies with reef system and individual reefs but that microbiomes within individual reefs were similar to each other and did not vary with benthic composition. The regionalism of reef seawater microbiomes was further assessed upon incorporation of global scale data from five additional studies, which revealed that microbial communities were more distinct with increasing geographic distance. These results contribute to our understanding of the coral holobiont’s microbial environment and can inform monitoring efforts for reef health. Atlantic killifish populations can be categorized as sensitive or tolerant to industrial pollutants based on history of pollutant exposure. Thus, they are an excellent “natural laboratory” for understanding the combined effect of environment and host on microbiome composition. I examined the gut microbiomes of two populations of wild fish as well as captive fish originating from each of these wild populations. I found that living in and adapting to polluted waters can impact microbiome composition and structure, resulting in a microbiome that appears more disordered. Additionally, captivity resulted in a complete turnover of dominant microbial taxa, indicating the environment plays a large role in shaping killifish gut microbiomes. This dissertation demonstrates that diverse systems, from coral reefs to killifish, can benefit from a better understanding of its associated microorganisms. For holobiont studies, these results highlight the importance of considering the context of microbial communities, from environment to host population.

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.

This book covers the contemporary environmental issues faced by life on the planet and the role planetary microbiomes play in such issues. Providing insights on the net favorable and adverse effect of microbial processes, this volume covers both the spontaneous and anthropocentric events that impact climate change and life on the planet. The book describes the ecological significance of microbiomes associated with the kingdoms Plantae and Animalia with respect to climate change, natural and anthropogenic causes of climate change, microbial interactions in nature, planetary microbiomes and food security, climate change in relation to disease epidemiology and human health and engineering microorganisms to mitigate the consequences of climate change. The individual chapters in the intended book provide both theoretical and practical exposure to the current issues and future challenges of climate change in relation to the microbiomes. This collection should serve as ready reference to the researchers working in the area to reshape their future research in addressing the challenges of global climate change.

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.