LRES 580 Introduction to Thermal Biology 1.

A Review of the Biology of Microorganisms

(adapted from Brock: Biology of Microorganisms Madigan et al., 2003. 10th ed., Prentice Hall) Microbiology is the study of microorganisms; a large and diverse group of microscopic organisms that exist as single cells or in cell clusters; it also includes viruses which are microscopic but not cellular. Microbial cells are thus distinct from cells of animals and plants, which are unable to live alone in nature, and can exist only as parts of multicellular organisms. Microorganisms are able to carryout the life processes of growth, energy generation, independently of other cells. The science of microbiology is about living cells and how they work, and revolves around two themes: basic and applied. 1. As a basic biological science, microbiology provides some of the most accessible research tools for understanding the nature of life processes. The most sophisticated understanding of the chemical and physical basis of life has arisen through studying microorganisms. Microbial cells can be grown in extremely high densities in laboratories making them easy to study genetically and biochemically. Microbial cells share many biochemical properties with cells of multicellular organisms so much information is transferable. 2. As an applied biological science, microbiology answers questions related to medicine, agriculture, and industry. Some important diseases of plants, animals, and humans are caused by microorganisms. Microorganisms also have an important role in soil fertility, and farm animal production. The emerging field of biotechnology is also rooted in microbial processes. No other life forms approach the importance of microorganisms in supporting and maintaining all life on earth. Oxygen we breathe is the result of microbial activity Microbes recycle key elements necessary for sustaining life Microbes break down organic matter Microorganisms existed on the earth for billions of years before plants and animals (microbes = ancestors) and have evolved in both very beneficial and extremely harmful relationships with these multicellular organisms.

A single cell is often considered the fundamental unit of life, which is composed of: 1. Cell membrane (or wall) 2. Nucleus or nucleoid; that contains genetic information in DNA 3. Cytoplasm; includes machinery for cell function and growth

All cells are made up of four primary macromolecules including proteins, nucleic acids, lipids, and polysaccharides. Furthermore, all cellular organisms require some form of metabolism and they all reproduce (conduct their own synthesis). Cells can differentiate, a process by which new substances or structures are formed, communicate by responding to chemical signals in the environment, or exhibit motility in response to external stimuli (e.g. toxins, light, substrate, surfaces). Importantly, the rapid regeneration times in many microorganisms can result in genetic adaptations that permanently change the organisms characteristics. As these changes are transmitted in reproduction, a given species may then evolve in response to changes in external environment. Cells can be considered both chemical machines and coding devices. 1. Cells carry out chemical processes that both are dependent on the external environment and that impact the external environment (e.g. the utilization of Fe(II) to form Fe(III) solid phases). 2. Cells act as coding devices through the cellular replication of genetic material.

Prokaryotic cells constitute the major portion of biomass on the earth. Estimates of total numbers of prokaryotes on Earth is 5 X 10 30. Total carbon present in this mass of cells is equal to that of all the plants on earth. The collective contents of nitrogen and phosphorous in prokaryotic cells is over 10 times that of all plant biomass. Most prokaryotic cells are not found on the Earths surface, but exist underground in oceanic and terrestrial subsurface environments, many yet to be explored!

The phylogenetic tree of life as defined by comparative ribosomal RNA sequencing. The tree consists of three domains (or lineages) of organisms: the Bacteria and Archaea, cells of which are prokaryotic and the Eukarya (eukaryotes). These domains are thought to have diverged from a common ancestral organism, the universal ancestor early in the history of life on earth. Only a few groups of organisms within each domain are shown. Hyperthermophiles are prokaryotes that grow best at temperatures of 80 oC or higher. The groups shaded in red are macroorganisms. All other organisms on the tree of life are microorganisms.

Nucleus vs. Nucleoid

The genetic makeup of prokaryotic and eukaryotic cells is organized differently. In prokaryotic cells, DNA is present in a large double-stranded molecule called the bacterial chromosome to form a visible mass called the nucleoid. In eukaryotes, DNA is present in linear modules within the nucleus packaged in highly organized chromosomes. Chromosomes in eukaryotes contain more than just DNA; they include proteins that assist in folding and packing DNA and other proteins that are required for gene expression. A key genetic difference between prokaryotes and eukaryotes typically contain two copies of each

gene and are considered genetically diploid. Eukaryotic cells divide through mitosis, prokaryotic cells do not. Besides clearly showing that all the prokaryotes are not phylogenetically closely related, the tree of life reveals another important evolutionary fact; species of Archaea are more closely related to eukaryotes than are species of the Bacterial domain!

Archaea were not discovered as distinctly different until the 1970s and were originally thought to be members of the Bacterial domain. Evolutionary diversification from the universal ancestor originally went in two directions; Bacteria versus other that eventually diverged to yield separate domains of Archaea and the Eukarya. Because the cells of higher animals and plants are eukaryotic, it follows that eukaryotic microorganisms were the ancestors of multicellular organisms. Eukaryotic cells contain genomes from cells of two domains of organisms; bacteria and Eukarya, through the process of endosymbiosis.

2. Physiological Diversity of Microorganisms

A. Energy Requirements: All cells require energy, which can be obtained via three primary routes: 1. Metabolism of organic chemicals such as glucose (Chemoorganotrophs). Glucose + O2 = CO2 + H20 (energy derived here can be used to generate ATP) 2. Metabolism of inorganic chemicals such as H2, H2S, Fe, NH4 (Chemolithotrophs). H2S + O2 = H2O + S (energy derived here can be used to generate ATP) In this example, 2 electrons are transferred from S(-II) to O2(0) forming and H2O and elemental S as a waste product. Chemolithotrophs have evolved strategies for exploiting reduced inorganic chemical species that other organisms find unusable This type of metabolism is found only in prokaryotes (Bacteria and Archaea)

3. Photosynthesis: the conversion of solar energy to chemical energy (Phototrophs). Phototropic microorganisms contain pigments that absorb light at particular wavelengths causing these cells to be highly colored (e.g. green plants contain chlorophyll). Phototrophs do not require inorganic or organic chemicals as a source of energy; ATP generation is coupled with the light harvesting photosynthetic apparatus. B. Carbon. All cells require carbon as a major nutrient for biosynthesis of cellular components. Cells obtain carbon in one of two ways.

1. Heterotrophic organisms use one or more organic compounds as a carbon source. 2. Autotrophic organisms utilize CO2 as a carbon source. Chemoorganotrophs are heterotrophic. Many chemolithotrophs and most phototrophs are autotrophic. Autotrophs are also called primary producers because they synthesize organic matter for there own growth, but then provide organic C compounds required by other heterotrophic organisms. Chemoorganotrophs are generally secondary producers, feeding on autotrophs or the products they excrete.

3. Geothermal Chemistry
A. Hydrothermal fluids Sources. Composition. Role of chemical signatures in identifying sources and mixing ratios with meteoric water. B. The Periodic Table Essential Elements for microbial life: C, H, O, P, K, N, S, Ca Fe, Mg. Examples of essential trace elements: Cu, Mn, Zn, Co, Cl, B, F, Cr Elements important in energy transfer: H2, O2, S, Fe, Mn, As, N C. Case Study: Acid-sulfate-chloride springs: Primary chemical constituents available to chemolithoautotrophs: H2, H2S, Fe(II), As(III), CO2 Metabolic activities will be based on energy available from chemical reactions involving electron transfer. What are those possibilities and how does it relate to chemical transformation and mineralization of solid phases observed in thermal features. Taking stock of Important Chemical Species and Transformation Reactions H2(g), H2S(g), So, SO42Fe2+, Fe3+, Fe(OH)3 (solid phases) H3AsO3o, H3AsO4o The importance of accurate measurements of oxidized and reduced species for understanding chemolithotrophic metabolism

Units of concentration and measurement scales. pH= -log (H+) pH + pOH = 14 Molarity = moles of a substance per liter of solution Parts per million = milligrams of a substance per liter of solution 1 mole = 6.023 x 1023 atoms (Avagadros Number) H2O = H+ + OHKw = 1 x 10-14

4. Ecology of Geothermal Habitats

The word ecology was originally coined in 1866 in General Morphology, a book on biology and philosophy by Professor Ernst Haeckel who based this new word on the classical Greek words oikos, meaning a household or homestead and logos, meaning study. Haeckel defined ecology (oecologia) as: The economy of naturethe investigation of the total relations of the animal both to its inorganic and its organic environment, above all its friendly and inimical relations with those animals and plants with which it comes directly and indirectly into contactin a word, ecology is the study of all those complex interrelations referred to by Darwin as the conditions of the struggle for existence. An ecosystem is a dynamic collection of plants, animals and their physical environment interacting through a variety of processes and operating as a unit. Energy flow, nutrient cycling, population dynamics, herbivory and predation, and geologic forces are some of the processes that make an ecosystem work. Three fundamental units of ecology: individuals, populations, and communities. Focus on the interrelationships among environment and evolution of biological species

Laboratory Exercises in Geomicrobiology

A. Examination of microbial mats using scanning electron microscopy (SEM) What is a scanning electron microscope? What information by way of different detectors is available using SEM? Examine microbial mats, and identify S, Fe and As rich solid phases that are linked with metabolic processes.

B. Analysis of solid phases using x-ray diffraction. What is x-ray diffraction? How is it used to identify crystalline minerals? What kinds of solid phases are considered amorphous?