Microbial Ecology

12 Key excerpts on "Microbial Ecology"

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  Visualizing Microbiology

  • Rodney P. Anderson, Linda Young, Kim R. Finer(Authors)
  • 2020(Publication Date)
  • Wiley

    (Publisher)

  The complex interactions of microorganisms with their physical surroundings and with other organisms are the focus of Microbial Ecology. This discipline examines the abundance and distribution of microorganisms and the factors influencing these parameters. As you recall from Chapter 1, microbes have had an enormous impact on the evolution of life on Earth (see Remember This!). Although we often empha- size the pathogenic role of microbes, examining their actions within natural habitats reminds us that most microorganisms are beneficial and essential to personal (Figure 24.1) and global health. 24.1 Microbial Ecology FIGURE 24.1 Beneficial bacterium A patient’s inoperable tumor is injected with spores of Clostridium sporogenes. As the spores grow within the tumor, their secreted enzymes activate the separately injected pro-drug, unleashing a powerful treatment only at the tumor site and preventing damage of surrounding healthy tissue. Inoperable tumor RIGHT BSIP/Getty Images Think Critically Clostridium sporogenes is an anaerobic bacterium. How does this contribute to its survival within a solid tumor? 648 CHAPTER 24 Environmental and Industrial Microbiology FIGURE 24.2 Interactions between organisms in a prairie habitat Researchers examining a prairie soil habitat can use the ecological hierarchy to focus on the different processes and organismal interactions to better understand the relationships between living organisms and between the organisms and their environment. MICROBIOLOGY INSIGHT O O 2 CO 2 CO CO 2 2 N 2 CO CO 2 2 Bacteria Mycorrhizal fungus Protozoan Actinomycetes Nematode Arthropods Sand Sand Silt Silt Clay Clay Water Water Bacteria Mycorrhizal fungus Protozoan Actinomycetes Root Nematode Increasing ecological complexity O 2 CO 2 N 2 O 2 CO 2 N 2 O 2 CO 2 N 2 1. Individual Researchers studying individual organisms analyze nutritional needs, tolerance limits of physical conditions, and other unique features of an organism such as this soil bacterium.

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  Environmental Microbiology for Engineers

  • Volodymyr Ivanov(Author)
  • 2020(Publication Date)
  • CRC Press

    (Publisher)

  9

  Microbial Ecology

  Ecosystem

  Microbial Ecology is the science of the interactions of microorganisms with their environment, other organisms, and between themselves. The main objects of ecology are ecosystems. An ecosystem comprises biotic (biological) and abiotic (physical, chemical) components interacting with each other and isolated from the environment by a boundary (Figure 9.1 ). An interaction between two elements can also affect the interaction between two other elements.

  FIGURE 9.1 Example of the simplest ecosystem containing two biotic (B1 and B2 ) and two abiotic elements (A1 and A2 ).

  Levels of Ecosystem

  The hierarchy of microbial ecosystems can be shown as a sequence of increasing spatial and biological complexity of ecosystems:

  1. 1. suspended cells (unicellular organisms) of one species
  2. 2. suspended cells (unicellular organisms) of a microbial community
  3. 3. aggregated cells and multicellular microorganisms
  4. 4. ecosystems of a biotope
  5. 5. ecosystems of a whole biosphere

  Boundaries of Ecosystems

  Every ecosystem has a boundary between an ecosystem and its surrounding environment. The main function of the boundary is to maintain the integrity of an ecosystem by controlled isolation from the environment, and to protect an ecosystem from the destructive effects of the environment.

  A boundary is a steep gradient of physical and/or chemical properties. The physical boundary is formed by an interface between solid and liquid phases, solid and gas phases, or liquid and gas phases. For example, the microbial ecosystem of an aerobic tank for wastewater treatment is separated from the environment by the reactor walls and an air–water interface. The steep gradient of chemical substances, for example oxygen, ferrous ions, hydrogen sulfide, etc., forms a chemical barrier in natural ecosystems. Such barriers separate aerobic and anaerobic ecosystems in a lake. The steep gradient of conditions can also be created by cell aggregation in flocs, granules, or biofilms, which could be considered in this case separate ecosystems.

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  Microbe

  • Michele S. Swanson, Elizabeth A. Joyce, Rachel E. A. Horak(Authors)
  • 2022(Publication Date)
  • ASM Press

    (Publisher)

  Microbial Ecology PART III IN THIS CHAPTER Introduction What is the power of Microbial Ecology? How do we know who is there? How do we know what microbes are doing in the environment? Is everything everywhere? Conclusions Supplemental material Confocal micrograph of a three- species biofilm community of the human oral bacteria Streptococcus oralis (green), Veillonella sp. (blue), and Fusobacterium nucleatum (red) 473 19 Microbe, Third Edition • Michele S. Swanson, Elizabeth A. Joyce, and Rachel E. A. Horak • © 2022 American Society for Microbiology CHAPTER NINETEEN Microbial Communities 19 Introduction T his chapter starts a new section of the book that focuses on Microbial Ecology. Ecology is the study of interactions between organisms and their environment—how the chemical, physical, and biological environments affect particular kinds of organisms and how the organisms affect their environments. You might ask, haven’t we been KEY CONCEPTS This chapter covers the following topics in the ASM Fundamental Statements. EVOLUTION • The traditional concept of species is not readily applicable to microbes due to asexual reproduction and the frequent occurrence of horizontal gene transfer. METABOLIC PATHWAYS • Bacteria and Archaea exhibit extensive, and often unique, metabolic diversity. • The survival and growth of any microorganism in a given environment depend on its metabolic characteristics. MICROBIAL SYSTEMS • Microorganisms are ubiquitous and live in diverse and dynamic ecosystems. • Microorganisms and their environment interact and modify each other. IMPACT OF MICROORGANISMS • Microbes are essential for life as we know it and the processes that support life (e.g., biogeochemical cycles and plant and/or animal microbiota). 474 | PART III Microbial Ecology discussing this topic throughout the book? True enough, but the next three chapters will put greater emphasis on the grander scheme of the activities of groups of microbes rather than on those of individuals.

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  Microbial Limit and Bioburden Tests

  Validation Approaches and Global Requirements,Second Edition

  • Lucia Clontz(Author)
  • 2008(Publication Date)
  • CRC Press

    (Publisher)

  1 Microbial Life and Ecology The. control. of. microbial. contamination. requires. an. understanding. of. the. nature.and.ecology.of.microorganisms.that.might.come.into.contact.with.the. products. being. manufactured . . In. this. chapter,. an. overview. of. microbiology. with.an.emphasis.on.bacteriology.(the.study.of.bacteria),.mycology.(the.study. of.fungi),.and.the.compendial.test.organisms.will.be.presented . AN OVERVIEW OF MICROBIAL LIFE A.microorganism.or.microbe.can.be.defined.as.a.living.organism.so.small.that.it. can.only.be.observed.through.a.microscope . .Microorganisms.consist.of.single.cells. or.clusters.of.cells . .A.microbial.cell.is.the.fundamental.unit.of.life;.it.maintains.the. structure.of.the.microbe.by.taking.up.chemicals.and.energy.from.the.environment. and.by.responding.to.stimuli.from.its.surroundings . .Microbes.reproduce.and.pass. on.their.genetic.makeup.to.their.offspring,.and.evolve.and.adapt.to.the.environment . . Single-celled.microorganisms.were.the.first.life.form.to.appear.on.earth.approxi-mately.3 .5 .billion.years.ago.[1].and.over.the.past.1 .5 .billion.years.there.has.been.a. tremendous.diversification.of.life,.culminating.in.complex.multicellular.organisms. such.as.plants.and.animals . .In.many.cases,.microorganisms.have.evolved.to.live.in. intimate.symbiotic.relationships.with.other.organisms,.including.plants.and.animals . . Human.beings,.for.example,.have.mutualistic.relationships.with.many.bacteria.that. live.in.the.human.gut . .In.other.extreme.cases,.through.evolution,.microbes.have.been. assimilated.by.and.become.part.of.other.cells;.many.recent.studies.have.provided. hard.evidence.that.chloroplasts.and.mitochondria.were.once.free-living.bacteria.that. were.incorporated.into.eukaryotic.cells.to.become.energy-producing.organelles.[1] . Microorganisms.are.ubiquitous,.and.their.natural.habitats.are.extremely.diverse . . They.survive.within.a.wide.range.of.temperature,.pH,.salt.concentration,.nutrients,.

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  E-Z Microbiology

  • Barron's Educational Series, Rene Kratz(Authors)
  • 2011(Publication Date)
  • Barrons Educational Services

    (Publisher)

  14

  EnvironmentalMicrobiology

  WHAT YOU WILL LEARN

  This chapter presents the role of microorganisms in the environment. As you study this chapter, you will: • discover the role of microorganisms in ecosystems; • examine the importance of microbial diversity in the cycling of matter; • look at the role of gradients in the structuring of microbial communities; • explore microbial habitats; • learn how microbes are used in sewage treatment and the cleanup of pollution.

  SECTIONS IN THIS CHAPTER

  • Microbial Ecosystems

  • Biogeochemical Cycles

  • Microenvironments and Gradients

  • Microbial Habitats

  • Microorganisms and Water Quality

  • Sewage Treatment

  • Bioremediation

  Microbes are everywhere. They are inside our intestines, in the soil, in the sea, in the saltiest lake, and in boiling hot springs. Microbes live and grow, using nutrients and releasing wastes that change the environment around them. They were the first life on Earth, at a time when Earth was hot and had no oxygen in the atmosphere. Microbes transformed the Earth, inventing oxygenic photosynthesis and releasing oxygen gas to the atmosphere. They are still transforming the Earth, producing oxygen, fixing carbon and nitrogen, and recycling nutrients. Without microbes, life on Earth would not exist.

  Microbial Ecosystems

  METABOLIC DIVERSITY

  Microbes inhabit so many different types of environments because of their great metabolic diversity (Chapter 5 ). Photosynthetic microbes use light energy and carbon dioxide (CO2 ) to make sugar (C6 H12 O6

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  Microbial Ecology

  • Allen I. Laskin(Author)
  • 2018(Publication Date)
  • CRC Press

    (Publisher)

  III. Methods of Studying Microbial Ecology in Soil

  The variety of methods that have been used to study the activity, ecology, and population dynamics of microbes in soil reflects the complexity of this microbial habitat. Despite the multitude of methods, few, if any, have completely achieved their purpose, i.e., to study microbes in soil . Most methods either remove microbes from soil and study them in the laboratory or move soil to the laboratory and there study it for some function. No methods currently available begin to approach the level of the microhabitat, and, therefore, they only provide data which are some mathematical function of enumerable individual microhabitats. This is stated not to denigrate soil microbiologists but to emphasize the difficulties inherent in studying an environment as complex as soil and to underscore the ingenuity that soil microbiologists have demonstrated in their attempts to resolve these difficulties.

  Perhaps the greatest dereliction on the part of many investigators has been the tendency to extrapolate from relatively simple experiments – even though these may be well designed and employ extremely sophisticated instrumentation and techniques – to the in situ situation without verifying that the phenomena observed in vitro do occur, in essentially the same manner in vivo. Because the real purpose of Microbial Ecology is to determine what is occurring in the environment of interest – in this instance, soil – and not in the test tube, the investigator must shuttle continuously back and forth between model experimental designs and the in situ condition. Consequently, the soil microbial ecologist, perhaps more than any other microbial ecologist, must operate simultaneously on many levels of experimental complexity, ranging from natural field conditions to artificial pure culture systems and, where necessary, to the molecular level. In this multipronged approach, imagination, ingenuity, and the asking of critical questions are the key ingredients, and, although modern instrumentation can be an asset in many experiments, much can yet be learned by applying standard and relatively inexpensive methods to well-designed experiments.

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  Soils as a Key Component of the Critical Zone 1

  Functions and Services

  • Jacques Berthelin, Christian Valentin, Jean Charles Munch, Jacques Berthelin, Christian Valentin, Jean Charles Munch(Authors)
  • 2018(Publication Date)
  • Wiley-ISTE

    (Publisher)

  Chapter 1 of this volume), form a major compartment of continental ecosystems, and they are the key component of the Critical Zone of human activities. They are open, interactive, four-dimensional (space-time) biosystems with five types of constituents; namely organic matter, mineral matter, water (solutions), gas (soil atmosphere) and living organisms (microorganisms, animals, plants) [GOB 10, BER 11]. Soils are biosystems [MUN 17] whose functions and services are determined by the dynamics and activity of living organisms and environmental parameters, whether they are natural or of anthropic origins. The richness of energy substrates and the structures in porous systems and aggregates guarantee the diversity and activity of organisms [BRU 17, MUN 17]. In addition, the organisms shape habitats in soils, which are favorable to their activity and their survival [DOM 70, HAT 73, STO 86, LAV 01, GOB 10, MAR 10, DEC 10, COL 15, MUN 17].

  This chapter is not exhaustive, but it emphasizes the richness of the communities of soil living organisms and their functional diversity. It underlines:

  • – the potential of this biological wealth;
  • – the need to maintain and protect these soil properties and qualities;
  • – the need to know and understand the organisms better, as well as their ecology, the conditions of their activities and the interactions between “organisms and environments” to better define, model and manage the soil–plant systems, and also in view of using it intensively for improving plant production.

  5.2. Emergence and development of Microbial Ecology and soil biology

  5.2.1. Discovery of the microbial world, a turning point in the knowledge of the functioning of soil–plant systems

  In the 1870s, chemists thought that they could solve the questions of plant nutrition like the origin of nitrates in soils, while Pasteur had already suggested a bacterial explanation (cited by Berthelin et al. [BER 06]). It was the work of Schloesing and Muntz between 1877 and 1879 that proved the role of microorganisms, and then that of Winogradsky, who, in 1890, isolated nitrifying bacteria [WIN 49].

  It was Winogradsky, on the one hand, and Beijerinck, on the other hand, who, by discovering the richness of the microbial world, initiated soil microbiology at the end of the 19th Century [BER 06]. First, it was developed for agronomic purposes before becoming microbial soil ecology. This discipline had (and still has) a major role in the emergence and development of biogeochemistry, geomicrobiology, phytopathology, biotechnologies and environmental engineering (water treatment, mineral and organic raw materials, waste) and in the definition of parameters to control the quality of water, air, etc. [BER 06, BER 07].

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  Environmental Engineering

  Basic Principles

  • Vesna Tomašić, Bruno Zelić, Vesna Tomašić, Bruno Zelić(Authors)
  • 2018(Publication Date)
  • De Gruyter

    (Publisher)

  Felicita Briški and Marija Vuković Domanovac

  4 Environmental microbiology

  This article has previously been published in the journal Physical Sciences Reviews. Please cite as: Briški, F., Vuković Domanovac, M. Environmental Microbiology. Physical Sciences Reviews [Online]

  Abstract: For most people, microorganisms are out of sight and therefore out of mind but they are large, extremely diverse group of organisms, they are everywhere and are the dominant form of life on planet Earth. Almost every surface is colonized by microorganisms, including our skin; however most of them are harmless to humans. Some microorganisms can live in boiling hot springs, whereas others form microbial communities in frozen sea ice. Among their many roles, microorganisms are necessary for biogeochemical cycling, soil fertility, decomposition of dead plants and animals and biodegradation of many complex organic compounds present in the environment. Environmental microbiology is concerned with the study of microorganisms in the soil, water and air and their application in bioremediation to reduce environmental pollution through the biological degradation of pollutants into nontoxic or less toxic substances. Field of environmental microbiology also covers the topics such as microbially induced biocorrosion, biodeterioration of constructing materials and microbiological quality of outdoor and indoor air.

  Keywords: microorganisms, environment, indicator microorganisms, biodegradation, bioremediation

  Gentlemen, it is the microbes who will have the last word .

  (Louis Pasteur)

  4.1 Evolution of microorganisms

  Earth is about 4.5 billion years old and scientists estimate that life first emerged at least 3.8 billion years ago after the surface of crust had cooled enough to allow liquid water to form. Early Earth was inhospitable from time to time because space rocks crushed into the Earth’s surface. Some impacts were powerful enough to vaporize oceans and create clouds of steam which sterilized the Earth’s surface. Nonetheless, some microorganisms were able to survive this period deep underground while some may have had the capacity of modern microorganism to produce survival forms called endospores. Early in the planet’s history conditions were harsh. The Earth’s surface was exposed to strong ultraviolet (UV) radiation because the ozone layer was not yet formed in the atmosphere. Nevertheless, the prokaryotic microorganisms began to develop. The first prokaryotic microorganisms lived in anaerobic environment because atmosphere was a mixture of CO2 , N2 , and H2 O vapour and in traces H2 . O2 gas began to appear in significant amount in the Earth’s atmosphere between 2.5 and 2 billion years ago as a result of microbial metabolic process called oxygenic photosynthesis. Oxygenic photosynthesis which started around 3 billion years ago differed from earlier forms of photosynthesis and the bacteria responsible for this type of photosynthesis are called cyanobacteria . Cyanobacteria brought the O2 level of the Earth’s atmosphere up to 10% of today’s level and due to it the formation of ozone layer started. O2 level was high enough to enable evolution of oxygen-utilizing organisms [1 , 2 ]. An approximate timeline of the development of life on Earth is presented in Figure 4.1 . Since many eukaryotes are O2

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  Manual of Environmental Microbiology

  • Cindy H. Nakatsu, Robert V. Miller, Suresh D. Pillai(Authors)
  • 2016(Publication Date)
  • ASM Press

    (Publisher)

  Evolutionary Ecology of Microorganisms: From the Tamed to the Wild JAY T. LENNON AND VINCENT J. DENEF 4.1.2 OVERVIEW: INTERPLAY BETWEEN ECOLOGICAL AND EVOLUTIONARY PROCESSES

  An overarching goal of biology is to understand how evolutionary and ecological processes generate and maintain biodiversity. Despite this seemingly unified goal, historically the fields of evolutionary biology and ecology have largely advanced separately. Although evolutionary biologists interested in biodiversity tend to focus on the mechanisms controlling rates of evolution and how this influences the phylogenetic relationship among species, ecologists attempt to explain the distribution and abundance of taxa based on interactions among species and their environment. Recently, a more concerted effort has been made to integrate some of the theoretical and empirical approaches from the fields of ecology and evolutionary biology. This has been motivated in part by the growing evidence that evolution can happen on “rapid” or contemporary time scales (1 ). When this occurs, evolutionary changes can select for functional traits and behaviors of species in ways that influence ecological processes, such as population dynamics, the outcome of species interactions, and even ecosystem functioning (2 –5 ). Ultimately eco-evolutionary feedbacks can alter system dynamics in ways that cannot be predicted based on ecological principles alone (6 ) (Fig. 1 ). As such, it may be inappropriate to ignore evolutionary processes when attempting to understand ecological phenomena in natural and managed ecosystems.

  FIGURE 1 Conceptual diagram depicting feedbacks between ecological and evolutionary processes. Within the domain of ecological processes, there are interacting hierarchical levels of organization (individuals, populations, communities, and ecosystems), which can affect microevolutionary processes (i.e., anagenesis) and macroevolutionary processes (cladogenesis). Reciprocally, evolutionary processes can affect ecological processes. The strength of these feedbacks is influenced by the time scale at which ecological and evolutionary processes take place and by factors such as mutation rates, genetic drift, gene flow/disperal, and the diversity of a biological community. Adapted from (8

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  Soil Microbiology

  • Robert L. Tate, III(Authors)
  • 2020(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  Thus, situations are readily envisioned where minorities or newly imported members of the community may become more competitive due to the changing ecosystem properties and therefore become major players in community dynamics. The soil dynamic forces controlling these changing community dynamics are the same delimiters determining successful soil inoculation for bioremediation or purification of sewage effluent. Thus, to understand situations where insufficient die‐off of undesirable microbes occurs in soil or the contrasting inability to establish desirable microbial species in a soil site, a clear delineation of the interactions within the total soil community (i.e. viruses, bacteria, fungi, protozoa, nematodes, and higher animals) is required. Thus this chapter is presented with the objective of analyzing the general traits or types of microbial interactions in soil and determination of the impact of these interactions on community adaptation and resilience following ecological insult. This chapter plus Chapter 8 (The Rhizosphere?Mycorrhizosphere) provide a preview of the concepts of soil, plant, and microbial interactions supporting soil biological remediation processes such as those presented in Chapter 16 (Soil Microbes: Optimizers of System Sustainability and Reparation of Damaged Soils). 7.1 Common Concepts of Microbial Community Interaction To elucidate the basic principles of the interactive nature of the components of the soil biological community, the nature of the soil ecosystem must be appreciated. Thus, a consideration of the terms delimiting an ecosystem and the life contained therein is necessary. Foremost among these relationships is emergence of a common concept regarding the meaning of the statement “ecology of the organism.” The word “ecology” is commonly misused by both the general public and the scientific community. By definition, ecology is the study of the relationship of organisms to their environment

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  Science Needs for Microbial Forensics: Developing Initial International Research Priorities

  • (Author)
  • 2014(Publication Date)
  • The National Academies Press

    (Publisher)

  2 Microbial Science: Ecology, Diversity, and Characterizing the Microbial World One might think that the age of great discoveries in biology is past––that humans have been everywhere and seen everything on Earth. But in fact, biology still boasts some formidable unknowns, and many are now be- ing explored in the once invisible world of microbes. In the last 20 years, technological advances have made it possible to explore a microbial world that has proven vastly more extensive, important, and diverse than previously imagined. Analyses of microbial communities in the soil, in the ocean, and even in the human body have shown that previ- ous methods detected only a tiny percentage of the different microbes in these environments. It seems that each technological advance and every new environment sampled reveal even greater diversity in the microbial world. Is there a limit? How can the nature and extent of microbial di- versity be satisfactorily characterized? Source: AAM, 2011a. Although the world of living things is dominated by microbes, very little is known about the vast majority of them. According to the American Academy of Microbiology, “There are ten-million-fold more bacterial and archaeal cells on our small planet than there are stars in the visible uni- verse, and they may contain as much carbon as all plant and animal life put together” (AAM, 2011b). Much of what is known is based on the very few microorganisms that are culturable in laboratories. Prior to the advent of nucleic acid sequencing, only the phenotypes of culturable microor- ganisms could be readily studied using tools that had been available for the previous 150 years—growth on selective and differential media, 35 Science Needs for Microbial Forensics: Developing Initial International Research Priorities Copyright National Academy of Sciences. All rights reserved.

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  Microbial Ecology

  An Evolutionary Approach

  • J Vaun McArthur(Author)
  • 2006(Publication Date)
  • Academic Press

    (Publisher)

  Immigration and emigra-tion together constitute dispersal. Immigration is very important in colonization of new populations or where “new” habitat has formed or been exposed. The measure-ment of microbial movement out of a particular habitat is fraught with difficulties. It Chapter 7 Fundamentals of Microbial Population Ecology 132 is not known if the microbes that are being transported out are “native” or autochtho-nous to the habitat or whether the emigrating microbes are just passing through. Emigration assumes that an organism was established within a habitat and has subsequently “chosen” to leave because of degradation of the habitat, biological interactions (especially intraspecific and interspecific competition), or other factors assessed by the emigrating organism. Emigration may also occur as the excess repro-ductive output from a resident group of organisms that were unable to find or secure suitable habitat. One additional caveat in regard to populations is that populations are not restricted to individual organisms. We can have a population of aggregates or populations of colonies. The concept of what is an individual is very important in defining what a population is or is not. Microbial Population Ecology In this section, we discuss various aspects of populations especially as they relate to microbes. In our discussion, we sometimes discuss phenotypic traits that promote the survival of one population over another. We assume at times that all individuals within a population are equivalent, and we sometimes highlight their differences and the underlying variation found in natural populations. We discuss ways in which microbes communicate within groups and discuss the evolutionary consequences of such communication strategies. Fundamental to our discussion are estimates of population growth, expansion, and senescence. Let us first consider the growth of populations using simple but established population models.

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