Marine Microbiology: Ecology & Applications

Cover
Half Title
Title Page
Copyright Page
Contents
List of Research Focus Boxes
Preface
Acknowledgments
Chapter 1: Microbes in the Marine Environment
	Marine microbiology has developed into one of the most important areas of modern science
		Microbes include microscopic cellular organisms and non-cellular viruses
		Marine microorganisms are found in all three domains of cellular life
		Horizontal gene transfer confounds our understanding of evolution
		Viruses are non-cellular entities with great importance in marine ecosystems
		Microbial processes shape the living world
		Marine microbes show great variation in size
	Ocean Habitats
		The world’s oceans and seas form an interconnected water system
		The upper surface of the ocean is in constant motion owing to winds
		Deep-water circulation systems transport water between the ocean basins
		Light and temperature have important effects on microbial processes
		Microbes occur in all the varied habitats found in the oceans
		Seawater is a complex mixture of inorganic and organic compounds, colloids, and gels
		The sea surface is covered by a gelatinous biofilm
	Sediments and Surfaces
		Microbes play a major role in marine sediments
		Deep marine sediments contain a vast reservoir of ancient microbes
		Microbes colonize surfaces through formation of biofilms and mats
		Microbial activity at hydrothermal vents fuels an oasis of life in the deep sea
		Cold seeps also support diverse life based on chemosynthesis
		Microbes inhabit the interface of brine pools in the deep sea
		Microbes in sea ice form an important part of the food web in polar regions
		Microbial activity underpins productive food webs in coral reefs
		Living organisms are the habitats of many microbes
		Conclusions
		References and further reading
Chapter 2: Methods in Marine Microbiology
	Key Concepts
		Sampling the marine environment requires special techniques
		Light and electron microscopy are used to study morphology and structure of microbes
		Confocal laser scanning microscopy enables recognition of living microbes within their habitat
		Flow cytometry measures the number and size of particles
		Fluorescent in situ hybridization (FISH) allows visualization and quantification of specific microbes
		Different microorganisms require specific culture media and conditions for growth
		Enrichment culture selects for microbes with specific growth requirements
		Analysis of microbial cell components can be used for bacterial classification and identification
		Nucleic acid-based methods have transformed understanding of marine microbial diversity and ecology
		Amplification and sequencing of ribosomal RNA genes is widely used in microbial systematics and diversity studies
		Isolation of genomic DNA or RNA is the first step in all nucleic acid-based investigations
		The polymerase chain reaction (PCR) forms the basis of many techniques
		Genomic fingerprinting can be used to assess diversity of cultured isolates
		Determination of DNA properties is used in bacterial and archaeal taxonomy
		DNA sequence data are used for identification and phylogenetic analysis
		DGGE and TRFLP can be used to assess composition of microbial communities
		Advances in DNA sequencing enable improved microbial community analysis
		Elucidating the full genome sequence of microbes provides insights into their functional roles
		Metabarcoding and metagenomics have led to major advances in microbial community analysis
		Omics technologies provide information about the functional gene composition of a microbial community
		Genomes can now be obtained from single cells in environmental samples
		Microelectrodes and biosensors measure microbial processes at the microhabitat scale
		Radioisotopes can be used to detect metabolic activity in a community
		Stable-isotope probing (SIP) tracks fluxes of nutrients in communities
		NanoSIMS allows metabolic transfers to be measured at subcellular levels
		Microarrays enable assessment of gene activity in the environment
		Metatranscriptomics, metaproteomics, and metabolomics reveal microbial activities in the environment
		Microfluidics enables study of microscale processes
		Mesocosm experiments attempt to simulate natural conditions
		Remote sensing permits global analysis of microbial activities
	Conclusions
	References and further reading
Chapter 3: Metabolic Diversity and Ecophysiology
	A Brief Overview of Cell Structure and Function
		Bacteria and archaea show a variety of cell forms and structural features
		The cytoplasmic membrane controls cell processes via transport of ions and molecules
		Cells may contain organelles, microcompartments, and inclusion bodies
		The nature of the cell envelope has a major effect on physiology
		Genome size and organization determines bacterial and archaeal lifestyles
		Microbes use a variety of mechanisms to regulate cellular activities
	Sources of Energy and Carbon
		Microbes obtain energy from light or oxidation of compounds
		Microbes differ in their source of carbon to make cellular material
	Phototrophy and Chemotrophy
		Phototrophy involves conversion of light energy to chemical energy
		Oxygenic photosynthesis involves two distinct but coupled photosystems
		Anaerobic anoxygenic photosynthesis uses only one type of reaction center
		Aerobic anoxygenic phototrophy is widespread in planktonic bacteria
		Some phototrophs use rhodopsins as light-harvesting pigments
		Chemolithotrophs use inorganic electron donors as a source of energy and reducing power
		Many bacteria oxidize sulfur compounds
		Many chemolithotrophs use hydrogen as an electron donor
		Bacterial and archaeal nitrification is a major process in the marine nitrogen cycle
		Ammonia can also support anaerobic chemolithoautotrophy
	Carbon and Nitrogen Fixation
		The Calvin–Benson–Bassham (CBB) cycle is the main method of carbon fixation in autotrophs
		Some Archaea and Bacteria use alternative pathways to fix CO2
		Fixation of nitrogen makes this essential element available for building cellular material in all life
	Heterotrophic Metabolism
		Many marine microbes obtain energy by the fermentation of organic compounds
		Anaerobic respiration has major importance in marine processes
		Nitrate reduction and denitrification release nitrogen and other gases
		Sulfate reduction is a major process in marine sediments
	Microbial Production and Oxidation Of Methane
		Methanogenesis is unique to the Archaea
		Methane is produced in the surface ocean by bacterial cleavage of phosphonates
		Anaerobic oxidation of methane (AOM) in sediments is coupled to sulfate reduction
		Many marine microbes oxidize methane and other C1 compounds
	Nutrient Acquisition and Microbial Growth
		Microbial metabolism depends on nutrient uptake
		Acquisition of iron is a major challenge for marine microbes
		Marine bacterioplankton use two trophic strategies
		Growth rate and turnover of organic material depend on nutrient concentrations
		Copiotrophic marine bacteria may show rapid growth in culture
		Bacteria adapt to starvation by coordinated changes to cell metabolism
		Some bacteria enter a “viable but nonculturable” state in the environment
		Many bacteria use motility to search for nutrients and optimal conditions
		Flagella also have a mechanosensory function
		Microbes also respond to light, magnetic fields, and other stimuli
		Gliding and twitching motility occur on surfaces
		Microbes colonize surfaces via formation of biofilms
		Pili are important for bacterial attachment to surfaces and genetic exchange
		Antagonistic interactions between microbes occur on particles or surfaces
		Quorum sensing is an intercellular communication system for regulation of gene expression
	Physical Effects on Microbial Growth and Survival
		Most marine microbes grow at low temperatures
		Microbes growing in hydrothermal systems are adapted to very high temperatures
		Microbes that inhabit the deep ocean must withstand a very high hydrostatic pressure
		Ultraviolet irradiation has lethal and mutagenic effects
		Bacterial bioluminescence may protect bacteria from ROS and UV damage
		Microbes use various mechanisms to prevent osmotic damage
		Conclusions
		References and further reading
Chapter 4: Diversity of Marine Bacteria
	Overview of Bacterial Diversity
		Understanding of diversity has been revolutionized by phylogenetic and genomic techniques
		Bacterial systematics is in transition due to application of genomic methods
		OTUs and ASVs are used to represent diversity in community analyses
		Marine microbial communities show high alpha diversity
	A Tour of the Bacterial Aquarium
		The Proteobacteria account for about half of all bacterial ocean diversity
		Members of the class Alphaproteobacteria are the most abundant marine bacteria
		The order Caulobacterales contains prosthecate bacteria
		Several alphaproteobacterial genera show magnetotaxis
		Magnetotaxis is also found in other classes and phyla
		The order Betaproteobacteriales includes many rare OTUs
		The Gammaproteobacteria is a very large and diverse class
		The Gammaproteobacteria includes many uncultivated species of sulfide-oxidizing bacteria (SOB)
		The family Vibrionaceae includes many important pathogens and symbionts
		Members of the order Oceanospirillales break down complex organic compounds
		The family Thiotrichaceae includes some important SOB
		The proposed phylum Desulfobacterota contains anaerobic sulfate- or sulfur-reducing bacteria (SRB)
		The proposed phylum Epsilonbactereota contains major contributors to productivity at hydrothermal vents
		Myxobacteria have a complex life cycle
		The Bdellovibrionales contains predatory bacteria
		Members of the Zetaproteobacteria are microaerophilic iron-oxidizers
		Members of the Cyanobacteria carry out oxygenic photosynthesis
		A genome-based classification of the Cyanobacteria is under development
		Prochlorococcus is the most abundant photosynthetic organism
		Synechococcus spp. dominate the upper photic zone
		Some free-living and symbiotic cyanobacteria fix nitrogen
		Filamentous cyanobacteria are important in the formation of microbial mats
		Members of the Planctomycetes have atypical cell structure
		The phylum Bacteroidetes has a major role in nutrient cycling via degradation of polymers
		Members of the phylum Chloroflexi are widespread but poorly characterized
		The phyla Aquificae and Thermotogae are deeply branching primitive thermophiles
		The Firmicutes are a major branch of Gram-positive Bacteria
		Members of the Actinobacteria are a rich source of secondary metabolites, including antibiotics
		Conclusions
		References and further reading
Chapter 5: Marine Archaea
	Several aspects of cell structure and function distinguish the Archaea and Bacteria
	New phylogenomic methods have led to recognition of multiple phyla of the Archaea
	Phylum Euryarchaeota
		Many members of the Euryarchaeota produce methane
		Anaerobic oxidation of methane (AOM) in sediments is carried out by syntrophic archaea
		The class Thermococci contains hyperthermophiles found at hydrothermal vents
		Archaeoglobus and Ferroglobus are hyperthermophilic sulfate-reducers and iron-oxidizers
		The Euryarchaeota contains extreme halophiles
		Uncultivated members of the Euryarchaeota are abundant in the plankton
	Phylum Crenarchaeota
		Members of the Crenarchaeota are thermophiles occurring in hydrothermal vents
	Phylum Thaumarchaeota
		A single clade of ammonia-oxidizing archaea comprises 20% of the picoplankton
	Phylum Nanoarchaeota
		Nanoarchaeum is an obligate parasite of another archaeon
		Conclusions
		References and further reading
Chapter 6: Marine Eukaryotic Microbes
	Marine Protists
		Protists are a highly diverse collection of unicellular eukaryotic microbes
		Protists show enormous diversity and classification systems are regularly revised
		The -omics approaches have some limitations for understanding protist diversity
		Picoeukaryotes play a major role in ocean food webs
		Heterotrophic flagellated protists play a major role in grazing of other microbes
		Heterotrophic flagellated protists have different feeding mechanisms
		Many protists are mixotrophic
		The choanoflagellates have a unique morphology and feeding mechanism
		Dinoflagellates have several critical roles in marine systems
		Dinoflagellates and other protists undertake diel vertical migration
		Some dinoflagellates exhibit bioluminescence
		The ciliates are voracious grazers of other protists and bacteria
		The haptophytes (prymnesiophytes) are some of the most abundant components of ocean phytoplankton
		Diatoms are extremely diverse and abundant primary producers in the oceans
		Other stramenopiles may cause harmful blooms
		Thraustochytrids and labyrinthulids are active degraders of organic matter
		Photosynthetic prasinophytes are abundant members of the picoplankton
		Amoebozoa are important grazers of particle-associated bacteria
		Radiolarians and foraminifera have highly diverse morphologies with mineral shells
	Marine Fungi
		The Fungi form a distinct monophyletic group on a branch within the Nucletmycea
		Fungi are increasingly recognized to be major components of the marine microbiome
		Conclusions
		References and further reading
Chapter 7: Marine Viruses
	Phages are viruses that infect bacterial and archaeal cells
	The life cycle of phages shows a number of distinct stages
	Lysogeny occurs when the phage genome is integrated into the host genome
	Loss of viral infectivity arises from damage to the nucleic acid or capsid
	Measurement of virus production rates is important for quantifying virus-induced mortality
	Viral mortality “lubricates” the biological pump
	Nucleocytoplasmic large DNA viruses (NCLDVs) are important pathogens of microalgae and other protists
	Other giant viruses are abundant pathogens of heterotrophic protists
	RNA viruses also infect protists
	Viral mortality plays a major role in structuring diversity of microbial communities
	Marine viruses show enormous genetic diversity
	Viromes are creators of genetic diversity and exchange
	Conclusions
	References and further reading
Chapter 8: Microbes in Ocean Processes—Carbon Cycling
	Physical factors and biotic processes determine the fate of carbon in the oceans
	Marine phytoplankton are responsible for about half of the global primary production
	There are wide geographical and seasonal variations in primary production
	Dark ocean carbon fixation makes a major contribution to primary production
	Classic food chain and microbial loop processes occur in the epipelagic
	The microbial loop results in retention of dissolved nutrients
	The biological pump transports fixed carbon to the deep ocean and sediments
	Carbon export of primary production may change due to ocean warming and acidification
	Ingestion of bacteria by protists plays a key role in the microbial loop
	The viral shunt catalyzes nutrient regeneration in the upper ocean
	Microbial processes alter the composition of DOM
	Eutrophication of coastal waters stimulates microbial activity
	Conclusions
	References and further reading
Chapter 9: Microbes in Ocean Processes—Nitrogen, Sulfur, Iron, Phosphorus, and Silicon Cycling
	Nutrient Limitation
		Key elements act as limiting nutrients for phytoplankton
		Productivity of surface waters shows marked geographical variations
		Ocean microbes require iron
		Terrestrial runoff, dust, and volcanic ash are major sources of iron input
		Hydrothermal vents and glacial melting also supply iron to the oceans
		Whales and seabirds play a major role in supply of iron to phytoplankton
	The Nitrogen Cycle
		There have been major shifts in our understanding of the marine nitrogen cycle
		Diazotrophs incorporate atmospheric nitrogen into organic material
		Fixed nitrogen is returned to the inorganic pool by ammonification and nitrification
		Assimilation of ammonium and nitrate fuels growth of phytoplankton and other microbes
		Nitrate reduction, denitrification, and anammox reactions return nitrogen to its elemental form and other gases
		Diverse microbial metabolic processes occur in oxygen minimum zones (OMZs)
		Microbial processes in sediments are a major contributor to nitrogen cycling
	The Sulfur Cycle
		The oceans and sediments contain large quantities of sulfur compounds
		Metabolism of organic sulfur compounds is especially important in surface waters
		DMSP production leads to release of the climate-active gas dimethyl sulfide (DMS)
	The Phosphorus Cycle
		Phosphorus is often a limiting or co-limiting nutrient
		Marine microbes are adapted to low and variable levels of phosphorus
	The Silicon Cycle
		Silicification of diatoms is an economic process for construction of a cell wall
		Diatom blooms depend on the availability of silica in the environment
		Eutrophication alters the silicon balance in coastal zones
		Conclusions
		References and further reading
Chapter 10: Microbial Symbioses of Marine Animals
	Symbioses occur in many forms
	Chemosynthetic bacterial endosymbionts of animals were discovered at hydrothermal vents
	A wide range of other chemosynthetic endosymbioses occurs in the deep sea
	Chemosynthetic symbioses are also widespread in shallow-water sediments
	Animals colonizing whale falls depend on autotrophic and heterotrophic symbionts
	Sea squirts harbor photosynthetic bacteria
	Endosymbionts of bryozoans produce compounds that protect the host from predation
	Sponges contain dense communities of specific microbes
	Many marine invertebrates depend on photosynthetic endosymbionts
	Zooxanthellae (Symbiodiniaceae) show extensive genetic diversity and host specificity
	Many corals are dependent on zooxanthellae for nutrition
	Coral bleaching occurs when the host–symbiont interactions are uncoupled
	The coral holobiont contains multiple microbial partners
	Zooxanthellae boost the growth of giant clams
	Some fish and invertebrates employ symbiotic bacteria to make light
	The bobtail squid uses bacterial bioluminescence for camouflage
	Conclusions
	References and further reading
Chapter 11: Microbial Diseases of Marine Organisms
	Diseases of marine organisms have major ecological and economic impact
	Diseases of Corals, Sponges, and Echinoderms
		Infectious diseases threaten the survival of corals
		Vibrios are associated with many coral diseases
		The fungus Aspergillus sydowii caused mass mortality of sea fans in the Caribbean Sea
		Black band disease of corals is a disease of corals worldwide
		White plague and white pox are major diseases affecting Caribbean reefs
		Protistan parasites may cause tissue necrosis and skeletal erosion
		Viruses have a pivotal role in coral health
		Sponge disease is a poorly investigated global phenomenon
		Mass mortalities of echinoderms have caused major shifts in reef and coastal ecology
	Diseases of Molluscs
		Bacteria are a major cause of disease in molluscs
		Several protistan diseases affect culture of oysters and mussels
		Virus infections are a major problem in oyster culture
	Diseases of Crustaceans
		Bacteria cause epizootics with high mortalities in crustaceans
		Expansion of crustacean aquaculture is threatened by viral diseases
		Parasitic dinoflagellates also cause disease in crustaceans
	Diseases of Fish
		Microbial diseases of fish cause major losses in aquaculture and natural populations
		Microbial infections of fish cause a variety of disease signs
		Fish-pathogenic bacteria possess a range of virulence mechanisms
		Vibrios are responsible for some of the main infections of marine fish
		Pasteurellosis affects warm-water marine fish
		Aeromonas salmonicida has a broad geographic range affecting fish in fresh and marine waters
		Marine flexibacteriosis is caused by a weakly virulent opportunist pathogen
		Piscirickettsia and Francisella are intracellular proteobacteria infecting salmon and cod
		Intracellular Gram-positive bacteria cause chronic infections of fish
		Some Gram-positive cocci affect the central nervous system of fish
		Viruses cause numerous diseases of marine fish
		Infectious salmon anemia (ISA) is one of the most serious diseases in salmon culture
		Viral hemorrhagic septicemia (VHS) virus infects many species of wild fish
		Lymphocystis virus causes chronic skin infection of fish
		Birnaviruses appear to be widespread in marine fish and invertebrates
		Viral nervous necrosis (VNN) is an emerging disease with major impact
		Protists cause disease in fish via infections, toxins, and direct physical effects
	Diseases of Mammals
		Dinoflagellate and diatom toxins affect marine mammals
		Virus diseases cause mass mortalities in cetaceans and pinnipeds
		Viruses from nine different families have been linked to diseases of marine mammals
		Several species of bacteria and fungi infect marine mammals
	Diseases of Sea Turtles
		Sea turtles are affected by a virus promoting growth of tumors
	Diseases of Seagrasses and Seaweeds
		Heterokont protists cause ecologically important mortality of seagrasses
		Bacteria, fungi, and viruses infect marine macroalgae
		Conclusions
		References and further reading
Chapter 12: Marine Microbes as Agents of Human Disease
	Microbial Infections
		Pathogenic vibrios are common in marine and estuarine environments
		Vibrio cholerae is an autochthonous aquatic bacterium
		Complex regulatory networks control human colonization and virulence of V. cholerae
		Mobile genetic elements play a major role in the biology of Vibrio spp.
		Non-O1 and non-O139 serotypes of Vibrio cholerae are widely distributed in coastal and estuarine waters
		Vibrio vulnificus is a deadly opportunistic pathogen
		Pathogenicity of V. vulnificus is due to the interaction of multiple gene products
		Environmental factors affect the pathogenicity of V. vulnificus
		Vibrio parahaemolyticus is the leading cause of seafood-associated gastroenteritis
		Microbes associated with fish and marine mammals can be transmitted to humans
	Diseases Caused by Marine Microbial Toxins
		Scombroid fish poisoning results from bacterial enzyme activity
		Botulism is a rare lethal intoxication from seafood
		Fugu poisoning is caused by a neurotoxin of bacterial origin
		TTX is widespread amongst marine animals
		Some dinoflagellates and diatoms produce harmful toxins
		Paralytic shellfish poisoning is caused by saxitoxins produced by dinoflagellates
		Brevetoxin causes illness via ingestion or inhalation during red tides
		Dinophysiotoxins and azaspiracid toxins from shellfish result in gastrointestinal symptoms
		Amnesic shellfish poisoning is caused by toxic diatoms
		Ciguatera fish poisoning has a major impact on the health of tropical islanders
		Bacteria influence the production of HAB toxins
		Dinoflagellate and diatom toxins may be antipredator defense mechanisms
		Complex factors affect the incidence of HABs and toxin-associated diseases
		Coastal waters must be regularly monitored to assess the development of HABs
		Conclusions
		References and further reading
Chapter 13: Microbial Aspects of Marine Biofouling, Biodeterioration, and Pollution
	Biofouling and Biodeterioration
		Microbial biofilms initiate the process of biofouling
		Microbes induce corrosion of metals, alloys, and composite materials
		Microbes cause biodeterioration of timber and marine wooden structures
		Microbial growth and metabolism cause spoilage of seafood products
		Processing, packaging, and inhibitors of spoilage are used to extend shelf-life
		Some seafood products are made by deliberate manipulation of microbial activities
	Marine Pollution by Sewage and Wastewater
		Coastal pollution by wastewater is a source of human disease
		Human viral pathogens occur in sewage-polluted seawater
		Fecal indicator organisms (FIOs) are used to assess public health risks
		Coliforms and E. coli are unreliable FIOs for seawater monitoring
		Enterococci are more reliable FIOs for seawater monitoring
		Molecular-based methods permit quicker analysis of indicator organisms and microbial source tracking
		Various alternative indicator species have been investigated
		Countries have different quality standards for bathing waters
		Shellfish from sewage-polluted waters can cause human infection
		Microbiological standards are used for classification of shellfish production areas
		Direct testing for pathogens in shellfish is possible with molecular methods
	Oil and Other Chemical Pollution
		Oil pollution of the marine environment is a major problem
		Microbes naturally degrade oil in the sea
		Physical and biological processes affect the fate of oil spills
		Bioremediation of oil spills may be enhanced by emulsifiers and nutrients
		Microbes can detoxify heavy metals from contaminated sediments
		Microbial systems can be used for ecotoxicological testing
		Microbial adsorption and metabolism affect accumulation of mercury
		Microbial cycling is important in the distribution of persistent organic pollutants
		Plastic pollution of the oceans is a major global problem
		Conclusions
		References and further reading
Chapter 14: Marine Microbial Biotechnology
	Enzymes From Marine Microbes Have Many Applications
		DNA polymerases from hydrothermal vent organisms are widely used in molecular biology
		Metagenomics and bioinformatics lead to new biotechnological developments
		Polymers from marine bacteria have many applications
		Microalgae can produce biofuels and edible oils
		Marine microbes are a rich source of biomedical products
		Many bioactive compounds from marine invertebrates are produced by microbes
		With so much potential from the sea, why are there so few new drugs?
		Study of complex microbial communities may lead to new antibiotics
		Marine microbes provide various health-promoting products
		Marine microbes have applications in biomimetics, nanotechnology, and bioelectronics
		Microbial biotechnology has many applications in aquaculture
		Antimicrobial agents are widely used in aquaculture
		Antimicrobial resistance (AMR) is a major problem in aquaculture
		Vaccination of finfish is widely used in aquaculture
		Recombinant DNA technology is used to produce vaccines for diseases caused by viruses and some bacteria
		Live attenuated vaccines are effective but not widely used
		DNA vaccination depends on fish cells expressing a protective antigen
		Probiotics, prebiotics, and immunostimulants are widely used in aquaculture
		Conclusions
		References and further reading
Chapter 15: Concluding Remarks
Index