Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

Though biofilms were first described by Antonie van Leeuwenhoek, the theory describing the biofilm process was not developed until 1978. We now understand that biofilms are universal, occurring in aquatic and industrial water systems as well as a large number of environments and medical devices relevant for public health. Using tools such as the scanning electron microscope and, more recently, the confocal laser scanning microscope, biofilm researchers now understand that biofilms are not unstructured, homogeneous deposits of cells and accumulated slime, but complex communities of surface-associated cells enclosed in a polymer matrix containing open water channels. Further studies have shown that the biofilm phenotype can be described in terms of the genes expressed by biofilm-associated cells. Microorganisms growing in a biofilm are highly resistant to antimicrobial agents by one or more mechanisms. Biofilm-associated microorganisms have been shown to be associated with several human diseases, such as native valve endocarditis and cystic fibrosis, and to colonize a wide variety of medical devices. Though epidemiologic evidence points to biofilms as a source of several infectious diseases, the exact mechanisms by which biofilm-associated microorganisms elicit disease are poorly understood. Detachment of cells or cell aggregates, production of endotoxin, increased resistance to the host immune system, and provision of a niche for the generation of resistant organisms are all biofilm processes which could initiate the disease process. Effective strategies to prevent or control biofilms on medical devices must take into consideration the unique and tenacious nature of biofilms. Current intervention strategies are designed to prevent initial device colonization, minimize microbial cell attachment to the device, penetrate the biofilm matrix and kill the associated cells, or remove the device from the patient. In the future, treatments may be based on inhibition of genes involved in cell attachment and biofilm formation.

Biofilms: Survival Mechanisms of Clinically Relevant Microorganisms

Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial cellulose utilization, kinetics of microbial cellulose utilization, and contrasting features compared to soluble substrate kinetics. A biological perspective on processing cellulosic biomass is presented, including features of pretreated substrates and alternative process configurations. Organism development is considered for "consolidated bioprocessing" (CBP), in which the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars to desired products occur in one step. Two organism development strategies for CBP are examined: (i) improve product yield and tolerance in microorganisms able to utilize cellulose, or (ii) express a heterologous system for cellulose hydrolysis and utilization in microorganisms that exhibit high product yield and tolerance. A concluding discussion identifies unresolved issues pertaining to microbial cellulose utilization, suggests approaches by which such issues might be resolved, and contrasts a microbially oriented cellulose hydrolysis paradigm to the more conventional enzymatically oriented paradigm in both fundamental and applied contexts.

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Microbial cellulose utilization: fundamentals and biotechnology.

This paper contrasts the natural and anthropogenic controls on the conversion of unreactive N2 to more reactive forms of nitrogen (Nr). A variety of data sets are used to construct global N budgets for 1860 and the early 1990s and to make projections for the global N budget in 2050. Regional N budgets for Asia, North America, and other major regions for the early 1990s, as well as the marine N budget, are presented to highlight the dominant fluxes of nitrogen in each region. Important findings are that human activities increasingly dominate the N budget at the global and at most regional scales, the terrestrial and open ocean N budgets are essentially dis- connected, and the fixed forms of N are accumulating in most environmental reservoirs. The largest uncertainties in our understanding of the N budget at most scales are the rates of natural biological nitrogen fixation, the amount of Nr storage in most environmental reservoirs, and the production rates of N2 by denitrification.

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Nitrogen cycles: past, present, and future

The evolution of marine microbes over billions of years predicts that the composition of microbial communities should be much greater than the published estimates of a few thousand distinct kinds of microbes per liter of seawater. By adopting a massively parallel tag sequencing strategy, we show that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment. A relatively small number of different populations dominate all samples, but thousands of low-abundance populations account for most of the observed phylogenetic diversity. This "rare biosphere" is very ancient and may represent a nearly inexhaustible source of genomic innovation. Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes.

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Microbial diversity in the deep sea and the underexplored “rare biosphere”

Microbial degradation of petroleum hydrocarbons: an environmental perspective.

Chapter 1 contains a short historical introduction. Chapter 2, represents an updated review of microbial diversity and systematics. It also provides essential information required for the understanding of the form, function, and systematic relationship of microorganisms. Chapter 3 is devoted to the formation and structure of microbial communities, and deals with this subject both in the evolutionary and successional senses. Chapter 4 describes the interactions between microorganisms, and Chapters 5 and 6 explore the interactions of microorganisms with plants and with animals, respectively. Chapter 7 discusses the quantitative measurement of numbers, biomass, and activity of microorganisms; Chapter 8 examines the influence and the measurement of their environmental determinants. Chapter 9 presents air, water, and soil as microbial habitats and describes the typical composition of their communities. Chapters 10 and 11 contain an expanded discussion of the biogeochemical cycling activities performed by microbial communities. Chapters 12-15 deal with applied aspects of microbial ecology evident in biodeterioration control, sanitation, soil conservation, pollution control, resource recovery, and biological control.

Microbial Ecology: Fundamentals and Applications

Oil biodegradation and bioremediation: A tale of the two worst spills in U. S. history. Ronald M. Atlas, University of Louisville, Louisville KY 40292 Terry C. Hazen, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 Biography Ronald Atlas is Professor of Biology at the University of Louisville. He has over 40 years experience studying the role of microorganisms in oil biodegradation and helped pioneer the field of bioremediation. He has worked extensively on the bioremediation the Exxon Valdez spill. Terry Hazen is DOE BER distinguished scientist in the Earth Sciences Division at Lawrence Berkeley National Laboratory. He has studied oil, chlorinated solvent, and metal and radionuclide bioremediation for more then 30 years. He has been extensively studying the microbial degradation of the BP Deepwater Horizon Spill in the Gulf of Mexico. Abstract The devastating environmental impacts of the Exxon Valdez spill in 1989 and its media notoriety made it a frequent comparison to the BP Deepwater Horizon spill in the popular press in 2010, even though the nature of the two spills and the environments impacted were vastly different. Fortunately, unlike higher organisms that are adversely impacted by oil spills, microorganisms are able to consume petroleum hydrocarbons. These oil degrading indigenous microorganisms played a significant role in reducing the overall environmental impact of both the Exxon Valdez and BP Deepwater Horizon (MC252) oil spills. Introduction to Biodegradation of Petroleum Hydrocarbons Petroleum hydrocarbons in crude oils, such as those released into marine ecosystems by the Exxon Valdez and BP Deepwater Horizon spills, are natural products derived from aquatic algae laid down between 180 and 85 million years ago. Crude oils, composed mostly of diverse aliphatic and aromatic hydrocarbons, regularly escape into the environment from underground reservoirs. Because petroleum hydrocarbons occur naturally in all marine environments there has been time for numerous diverse microorganisms to evolve the capability of utilizing hydrocarbons as sources of carbon and energy for growth. Oil-degrading microorganisms are ubiquitous, but may only be a small proportion of the pre-spill microbial community. Bacteria, archaea, and fungi each have hundreds of species that can degrade petroleum. Most petroleum hydrocarbons are biodegradable under aerobic conditions; though a few compounds found in crude oils, e.g. resins, hopanes, polar molecules, and asphaltenes, have practically imperceptible biodegradation rates. Lighter crudes, such as the oil released from the BP Deepwater Horizon spill, contain a higher proportion of simpler lower molecular weight hydrocarbons that are more readily biodegraded than heavy crudes, such as the oil released from the Exxon Valdez. The polycyclic aromatic hydrocarbons (PAH) are a minor constituent of crude oils; however, they are among the most toxic to plants and animals. Bacteria can convert PAHs completely to biomass, CO 2 , and H 2 O, but they usually require the initial insertion of O 2 via dioxygenase enzymes. Anaerobic degradation of petroleum hydrocarbons can also occur albeit at a much slower rates. Petroleum hydrocarbons can be biodegraded at temperatures below freezing to more than 80°C. Microorganisms require elements other than carbon for

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Oil Biodegradation and Bioremediation: A Tale of the Two Worst Spills in U.S. History

The effectiveness of bioremediation for oil spills has been difficult to establish on dynamic, heterogeneous marine shorelines A new interpretative technique used following the 1989 Exxon Valdez spill in Alaska shows that fertilizer applications significantly increased rates of oil biodegradation Biodegradation rates depended mainly on the concentration of nitrogen within the shoreline, the oil loading, and the extent to which natural biodegradation had already taken place The results suggest ways to improve the effectiveness of bioremediation measures in the future

Effectiveness of bioremediation for the Exxon Valdez oil spill

Experiments were performed to evaluate the effectiveness of two different methodological approaches for recovering DNA from soil and sediment bacterial communities: cell extraction followed by lysis and DNA recovery (cell extraction method) versus direct cell lysis and alkaline extraction to recover DNA (direct lysis method). Efficiency of DNA recovery by each method was determined by spectrophotometric absorbance and using a tritiated thymidine tracer. With both procedures, the use of polyvinylpolypyrrolidone was important for the removal of humic compounds to improve the purity of the recovered DNA; without extensive purification, various restriction enzymes failed to cut added target DNA. Milligram quantities of high-purity DNA were recovered from 100-g samples of both soils and sediments by the direct lysis method, which was a greater than 1-order-of-magnitude-higher yield than by the cell extraction method. The ratio of labeled thymidine to total DNA, however, was higher in the DNA recovered by the cell extraction method. than by the direct lysis method, suggesting that the DNA recovered by the cell extraction method came primarily from active bacterial cells, whereas that recovered by the direct lysis method may have contained DNA from other sources.

Ronald M. Atlas

Papers

Microbial degradation of petroleum hydrocarbons: an environmental perspective.

Microbial Ecology: Fundamentals and Applications

Oil Biodegradation and Bioremediation: A Tale of the Two Worst Spills in U.S. History

Effectiveness of bioremediation for the Exxon Valdez oil spill

Recovery of DNA from soils and sediments.